diff --git a/404.html b/404.html
index 37b931b..6be7897 100644
--- a/404.html
+++ b/404.html
@@ -8,67 +8,54 @@
 <title>Page not found (404) • dracarys</title>
 <script src="https://umccr.github.io/dracarys/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="https://umccr.github.io/dracarys/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="https://umccr.github.io/dracarys/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://umccr.github.io/dracarys/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<script src="https://umccr.github.io/dracarys/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://umccr.github.io/dracarys/deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="https://umccr.github.io/dracarys/deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="https://umccr.github.io/dracarys/deps/headroom-0.11.0/headroom.min.js"></script><script src="https://umccr.github.io/dracarys/deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="https://umccr.github.io/dracarys/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="https://umccr.github.io/dracarys/deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="https://umccr.github.io/dracarys/deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="https://umccr.github.io/dracarys/deps/search-1.0.0/fuse.min.js"></script><script src="https://umccr.github.io/dracarys/deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="https://umccr.github.io/dracarys/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 </head>
 <body>
     <a href="https://umccr.github.io/dracarys/#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="https://umccr.github.io/dracarys/index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="https://umccr.github.io/dracarys/index.html">Intro</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="https://umccr.github.io/dracarys/index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="https://umccr.github.io/dracarys/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/files.html">Files</a>
-  </div>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="https://umccr.github.io/dracarys/articles/files.html">Files</a></li>
+  </ul>
 </li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="nav-link" href="https://umccr.github.io/dracarys/reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="https://umccr.github.io/dracarys/reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="https://umccr.github.io/dracarys/" class="logo" alt=""><h1>Page not found (404)</h1>
-      
+
+      <h1>Page not found (404)</h1>
+
     </div>
 
 Content not found. Please use links in the navbar.
@@ -82,15 +69,15 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index eb70fa1..66d557c 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contributor Covenant Code of Conduct • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contributor Covenant Code of Conduct • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Contributor Covenant Code of Conduct</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/CODE_OF_CONDUCT.md" class="external-link"><code>CODE_OF_CONDUCT.md</code></a></small>
+
+      <h1>Contributor Covenant Code of Conduct</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/CODE_OF_CONDUCT.md" class="external-link"><code>CODE_OF_CONDUCT.md</code></a></small>
     </div>
 
 <div id="contributor-covenant-code-of-conduct" class="section level1">
@@ -120,7 +106,7 @@ <h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#att
 </div>
 </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -129,14 +115,14 @@ <h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#att
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 78d7c6f..3eb647b 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>License</h1>
-      
+
+      <h1>License</h1>
+
     </div>
 
 <pre>YEAR: 2024
@@ -64,14 +50,14 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/LICENSE.html b/LICENSE.html
index 7d580bc..8ee9611 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MIT License • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="MIT License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MIT License • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="MIT License"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MIT License</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/LICENSE.md" class="external-link"><code>LICENSE.md</code></a></small>
+
+      <h1>MIT License</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/LICENSE.md" class="external-link"><code>LICENSE.md</code></a></small>
     </div>
 
 <div id="mit-license" class="section level1">
@@ -68,14 +54,14 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/articles/developers.html b/articles/developers.html
index 8010e1d..4097a68 100644
--- a/articles/developers.html
+++ b/articles/developers.html
@@ -5,66 +5,50 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="dracarys">
 <title>Developers • dracarys</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Developers">
-<meta property="og:description" content="dracarys">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Developers">
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul>
 </li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -73,10 +57,11 @@
 
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Developers</h1>
+
+      <h1>Developers</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/vignettes/developers.Rmd" class="external-link"><code>vignettes/developers.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/vignettes/developers.Rmd" class="external-link"><code>vignettes/developers.Rmd</code></a></small>
       <div class="d-none name"><code>developers.Rmd</code></div>
     </div>
 
@@ -93,26 +78,26 @@ <h3 id="r-package-dev">R package dev<a class="anchor" aria-label="anchor" href="
 <col width="50%">
 <col width="50%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th>Command</th>
 <th>Comment</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td><code><a href="https://devtools.r-lib.org/reference/check.html" class="external-link">devtools::check()</a></code></td>
 <td>build and check the pkg</td>
 </tr>
-<tr class="even">
+<tr>
 <td><code><a href="https://devtools.r-lib.org/reference/load_all.html" class="external-link">devtools::load_all()</a></code></td>
 <td>load the pkg</td>
 </tr>
-<tr class="odd">
+<tr>
 <td><code>R CMD INSTALL --no-multiarch --with-keep.source pcgr.git/pcgrr</code></td>
 <td>install the pkg into the first library of
 <code><a href="https://rdrr.io/r/base/libPaths.html" class="external-link">.libPaths()</a></code>
 </td>
 </tr>
-<tr class="even">
+<tr>
 <td><code>options(lifecycle_verbosity = "warning")</code></td>
 <td>ensure lifecycle deprecated messages are shown</td>
 </tr>
@@ -127,11 +112,11 @@ <h3 id="python-package-dev">Python package dev<a class="anchor" aria-label="anch
 <col width="50%">
 <col width="50%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th>Command</th>
 <th>Comment</th>
 </tr></thead>
-<tbody><tr class="odd">
+<tbody><tr>
 <td><code>pip install -e .</code></td>
 <td>install Python pkg in <a href="https://stackoverflow.com/a/35064498/2169986" class="external-link">editable mode</a>
 (think of it like loading the dev version)</td>
@@ -146,31 +131,31 @@ <h3 id="conda">conda<a class="anchor" aria-label="anchor" href="#conda"></a>
 <col width="50%">
 <col width="50%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th>Command</th>
 <th>Comment</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td><code>mamba install foo -c bar</code></td>
 <td>install pkg <code>foo</code> from channel <code>bar</code>
 </td>
 </tr>
-<tr class="even">
+<tr>
 <td><code>mamba create --file env.yml --prefix ./pcgr</code></td>
 <td>install conda pkgs listed in <code>env.yml</code> into the
 <code>./pcgr</code> directory</td>
 </tr>
-<tr class="odd">
+<tr>
 <td><code>conda info -e</code></td>
 <td>list conda environments installed on this machine</td>
 </tr>
-<tr class="even">
+<tr>
 <td><code>conda-lock --mamba -f env.yml -p osx-64 -p linux-64</code></td>
 <td>build conda lock files from given <code>env.yml</code> for both osx
 and linux</td>
 </tr>
-<tr class="odd">
+<tr>
 <td><code>conda mambabuild recipe_folder/ -c conda-forge -c bioconda</code></td>
 <td>build conda pkg from given recipe (folder with
 <code>meta.yaml</code>, <code>build.sh</code>)</td>
@@ -182,16 +167,16 @@ <h3 id="conda">conda<a class="anchor" aria-label="anchor" href="#conda"></a>
 <h3 id="pkgdown">pkgdown<a class="anchor" aria-label="anchor" href="#pkgdown"></a>
 </h3>
 <table class="table">
-<thead><tr class="header">
+<thead><tr>
 <th>Command</th>
 <th>Comment</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td><code><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">pkgdown::build_site()</a></code></td>
 <td>builds entire site</td>
 </tr>
-<tr class="even">
+<tr>
 <td><code><a href="https://pkgdown.r-lib.org/reference/build_articles.html" class="external-link">pkgdown::build_articles()</a></code></td>
 <td>builds vignettes only</td>
 </tr>
@@ -199,7 +184,7 @@ <h3 id="pkgdown">pkgdown<a class="anchor" aria-label="anchor" href="#pkgdown"></
 </table>
 </div>
 </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -210,15 +195,15 @@ <h3 id="pkgdown">pkgdown<a class="anchor" aria-label="anchor" href="#pkgdown"></
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/articles/files.html b/articles/files.html
index edef3eb..9d40039 100644
--- a/articles/files.html
+++ b/articles/files.html
@@ -5,66 +5,50 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="dracarys">
 <title>Files Supported • dracarys</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Files Supported">
-<meta property="og:description" content="dracarys">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Files Supported">
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul>
 </li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -73,10 +57,11 @@
 
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Files Supported</h1>
+
+      <h1>Files Supported</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/vignettes/files.Rmd" class="external-link"><code>vignettes/files.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/vignettes/files.Rmd" class="external-link"><code>vignettes/files.Rmd</code></a></small>
       <div class="d-none name"><code>files.Rmd</code></div>
     </div>
 
@@ -113,63 +98,63 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <div class="active  tab-pane" id="wgs_alignment_qc" role="tabpanel" aria-labelledby="wgs_alignment_qc-tab">
 
 <table class="table">
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">replay.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">fastqc_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">fragment_length_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">mapping_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">ploidy_estimation_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">time_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">trimmer_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">wgs_contig_mean_cov.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">wgs_coverage_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">wgs_fine_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">wgs_hist.csv</td>
 <td align="left">NA</td>
@@ -185,94 +170,94 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="33%">
 <col width="64%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">replay.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">fastqc_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">fragment_length_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">mapping_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">ploidy_estimation_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">time_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">trimmer_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">wgs_contig_mean_cov.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">wgs_coverage_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">wgs_fine_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">wgs_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">fusion_metrics.csv</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">quant_metrics.csv</td>
 <td align="left">
 <strong>TODO</strong>: QC for RNA txs and
 quantification</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">quant.transcript_fragment_lengths.txt</td>
 <td align="left">
 <strong>TODO</strong>: Full fragment length
 distribution of reads mapped to txs</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">quant.transcript_coverage.txt</td>
 <td align="left">
 <strong>TODO</strong>: Coverage uniformity with avg of
 5’ to 3’ cvg pattern along txs</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">16</td>
 <td align="left">saturation.txt</td>
 <td align="left">
@@ -290,94 +275,94 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="33%">
 <col width="64%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">replay.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">fastqc_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">fragment_length_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">mapping_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">ploidy_estimation_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">time_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">trimmer_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">wgs_contig_mean_cov.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">wgs_coverage_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">wgs_fine_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">wgs_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">fusion_metrics.csv</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">quant_metrics.csv</td>
 <td align="left">
 <strong>TODO</strong>: QC for RNA txs and
 quantification</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">quant.transcript_fragment_lengths.txt</td>
 <td align="left">
 <strong>TODO</strong>: Full fragment length
 distribution of reads mapped to txs</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">quant.transcript_coverage.txt</td>
 <td align="left">
 <strong>TODO</strong>: Coverage uniformity with avg of
 5’ to 3’ cvg pattern along txs</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">16</td>
 <td align="left">saturation.txt</td>
 <td align="left">
@@ -390,78 +375,78 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <div class="tab-pane" id="wgs_tumor_normal-germ" role="tabpanel" aria-labelledby="wgs_tumor_normal-germ-tab">
 
 <table class="table">
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">replay.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">fastqc_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">fragment_length_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">mapping_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">ploidy_estimation_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">roh.bed</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">roh_metrics.csv</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">time_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">trimmer_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">wgs_contig_mean_cov.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">wgs_coverage_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">wgs_fine_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">wgs_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">vc_metrics.csv</td>
 <td align="left">NA</td>
@@ -472,83 +457,83 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <div class="tab-pane" id="wgs_tumor_normal-som" role="tabpanel" aria-labelledby="wgs_tumor_normal-som-tab">
 
 <table class="table">
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">replay.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">cnv_metrics.csv</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">fastqc_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">fragment_length_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">hrdscore.csv</td>
 <td align="left"><strong>TODO</strong></td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">mapping_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">ploidy_estimation_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">sv_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">time_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">trimmer_metrics.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">wgs_contig_mean_cov_(tumor/normal).csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">wgs_coverage_metrics_(tumor/normal).csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">wgs_fine_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">wgs_hist.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">vc_metrics.csv</td>
 <td align="left">NA</td>
@@ -564,103 +549,103 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="53%">
 <col width="43%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">cancer_report_tables/qc_summary.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">cancer_report_tables/hrd/chord.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">cancer_report_tables/hrd/hrdetect.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">cancer_report_tables/sigs/snv_2015.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">cancer_report_tables/sigs/snv_2020.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">coverage/(tumor/normal).mosdepth.summary.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">coverage/(tumor/normal).samtools_stats.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">oncoviruses/oncoviral_breakpoints.vcf</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">oncoviruses/prioritized_oncoviruses.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">purple/purple.cnv.gene.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">purple/purple.cnv.somatic.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">purple/purple.purity.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">purple/purple.qc</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">small_variants/stats/bcftools_stats.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">small_variants/stats/pass_bcftools_stats_germline.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">16</td>
 <td align="left">small_variants/stats/pass_predispose_bcftools_stats_germline.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">17</td>
 <td align="left">small_variants/somatic.pcgr.snvs_indels.tiers.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">18</td>
 <td align="left">small_variants/somatic.pcgr.json.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">19</td>
 <td align="left">multiqc_report_data/multiqc_conpair.txt</td>
 <td align="left">Needed since conpair is not copied over to final
@@ -677,118 +662,118 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="46%">
 <col width="50%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">pipeline_info/execution_trace.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">pipeline_info/software_versions.yml</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">amber/amber.homozygousregion.tsv</td>
 <td align="left">For BAF gaps</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">amber/amber.qc</td>
 <td align="left">Includes ConsanguinityProportion, Contamination</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">bamtools/wgsmetrics</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">chord/chord_prediction.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">cuppa/cup.data.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">cuppa/cuppa.conclusion.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">flagstats/flagstat</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">lilac/lilac.candidates.coverage.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">lilac/lilac.qc.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">lilac/lilac.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">orange/orange.json</td>
 <td align="left">Has majority of columns from WGS results.</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">purple/purple.cnv.gene.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">purple/purple.cnv.somatic.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">16</td>
 <td align="left">purple/purple.purity.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">17</td>
 <td align="left">purple/purple.qc</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">18</td>
 <td align="left">sigs/sig.allocation.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">19</td>
 <td align="left">sigs/sig.snv_counts.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">20</td>
 <td align="left">virusbreakend/virusbreakend.vcf</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">21</td>
 <td align="left">virusbreakend/virusbreakend.vcf.summary.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">22</td>
 <td align="left">virusinterpreter/virus.annotated.tsv</td>
 <td align="left">NA</td>
@@ -799,28 +784,28 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <div class="tab-pane" id="oncoanalyser_wts" role="tabpanel" aria-labelledby="oncoanalyser_wts-tab">
 
 <table class="table">
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">pipeline_info/execution_trace.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">pipeline_info/software_versions.yml</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">cuppa/cup.data.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">isofox/isf.summary.csv</td>
 <td align="left">NA</td>
@@ -836,38 +821,38 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="40%">
 <col width="56%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">lilac/lilac.candidates.coverage.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">lilac/lilac.qc.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">lilac/lilac.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">orange/orange.json</td>
 <td align="left">Has majority of columns from WGS and WTS results.</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">cuppa/cup.data.csv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">cuppa/cuppa.conclusion.txt</td>
 <td align="left">NA</td>
@@ -883,103 +868,103 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 <col width="81%">
 <col width="15%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th align="right">N</th>
 <th align="left">file</th>
 <th align="left">description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td align="right">1</td>
 <td align="left">pipeline_info/execution_trace.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">2</td>
 <td align="left">pipeline_info/software_versions.yml</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">3</td>
 <td align="left">cancer_report_tables/qc_summary.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">4</td>
 <td align="left">cancer_report_tables/hrd/chord.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">5</td>
 <td align="left">cancer_report_tables/hrd/hrdetect.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">6</td>
 <td align="left">cancer_report_tables/hrd/dragen.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">7</td>
 <td align="left">cancer_report_tables/sigs/snv_2015.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">8</td>
 <td align="left">cancer_report_tables/sigs/snv_2020.tsv.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">9</td>
 <td align="left">purple/purple.cnv.gene.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">10</td>
 <td align="left">purple/purple.cnv.somatic.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">11</td>
 <td align="left">purple/purple.purity.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">12</td>
 <td align="left">purple/purple.qc</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">13</td>
 <td align="left">smlv_somatic/report/pcgr/pcgr_acmg.grch38.snvs_indels.tiers.tsv</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">14</td>
 <td align="left">smlv_somatic/report/pcgr/pcgr_acmg.grch38.json.gz</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">15</td>
 <td align="left">smlv_somatic/report/somatic.bcftools_stats.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">16</td>
 <td align="left">smlv_somatic/report/somatic.variant_counts_process.json</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">17</td>
 <td align="left">smlv_somatic/report/somatic.variant_counts_type.yaml</td>
 <td align="left">NA</td>
 </tr>
-<tr class="even">
+<tr>
 <td align="right">18</td>
 <td align="left">smlv_germline/report/germline.bcftools_stats.txt</td>
 <td align="left">NA</td>
 </tr>
-<tr class="odd">
+<tr>
 <td align="right">19</td>
 <td align="left">smlv_germline/report/germline.variant_counts_type.yaml</td>
 <td align="left">NA</td>
@@ -999,15 +984,15 @@ <h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-l
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/articles/flames.html b/articles/flames.html
index 11be1aa..30d09e7 100644
--- a/articles/flames.html
+++ b/articles/flames.html
@@ -5,66 +5,50 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="dracarys">
 <title>Flames • dracarys</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Flames">
-<meta property="og:description" content="dracarys">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Flames">
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul>
 </li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -73,10 +57,11 @@
 
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Flames</h1>
+
+      <h1>Flames</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/vignettes/flames.Rmd" class="external-link"><code>vignettes/flames.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/vignettes/flames.Rmd" class="external-link"><code>vignettes/flames.Rmd</code></a></small>
       <div class="d-none name"><code>flames.Rmd</code></div>
     </div>
 
@@ -131,7 +116,7 @@ <h3 id="germline-duplication-rate">Germline duplication rate<a class="anchor" ar
 </ul>
 </div>
 </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -142,15 +127,15 @@ <h3 id="germline-duplication-rate">Germline duplication rate<a class="anchor" ar
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/articles/index.html b/articles/index.html
index 6bd9039..5ad4d70 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,54 +1,40 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • dracarys</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"></head><body>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="index.html">Intro</a></li>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
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 </nav><div class="container template-citation-authors">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Authors and Citation</h1>
+
+      <h1>Authors and Citation</h1>
     </div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2>Authors</h2>
-      
+
       <ul class="list-unstyled"><li>
           <p><strong><a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a></strong>. Author, maintainer. <a href="https://orcid.org/0000-0002-7502-7545" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
@@ -64,22 +50,24 @@ <h2>Authors</h2>
         </li>
       </ul></div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2 id="citation">Citation</h2>
-      <p><small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
       <p>Diakumis P, Lin V (2024).
 <em>dracarys: Post-processing DRAGEN workflows</em>.
-https://github.com/umccr/dracarys, https://umccr.github.io/dracarys/. 
+R package version 0.15.0, https://umccr.github.io/dracarys/, <a href="https://github.com/umccr/dracarys" class="external-link">https://github.com/umccr/dracarys</a>.
 </p>
       <pre>@Manual{,
   title = {dracarys: Post-processing DRAGEN workflows},
   author = {Peter Diakumis and Victor San Kho Lin},
   year = {2024},
-  note = {https://github.com/umccr/dracarys, https://umccr.github.io/dracarys/},
+  note = {R package version 0.15.0, https://umccr.github.io/dracarys/},
+  url = {https://github.com/umccr/dracarys},
 }</pre>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+
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@@ -88,14 +76,14 @@ <h2 id="citation">Citation</h2>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
index 7204d3a..1b7fc5e 100644
--- a/deps/bootstrap-5.3.1/bootstrap.min.css
+++ b/deps/bootstrap-5.3.1/bootstrap.min.css
@@ -2,4 +2,4 @@
    * Bootstrap  v5.3.1 (https://getbootstrap.com/)
    * Copyright 2011-2023 The Bootstrap Authors
    * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
-   */:root,[data-bs-theme="light"]{--bs-blue: #007bff;--bs-indigo: #6610f2;--bs-purple: #9b479f;--bs-pink: #e83e8c;--bs-red: #d9230f;--bs-orange: #d9831f;--bs-yellow: #ffc107;--bs-green: #469408;--bs-teal: #20c997;--bs-cyan: #029acf;--bs-black: #000;--bs-white: #fff;--bs-gray: #777;--bs-gray-dark: #373a3c;--bs-gray-100: #f8f9fa;--bs-gray-200: #ddd;--bs-gray-300: #ccc;--bs-gray-400: #bbb;--bs-gray-500: #adb5bd;--bs-gray-600: #777;--bs-gray-700: #444;--bs-gray-800: #373a3c;--bs-gray-900: #212529;--bs-default: #fff;--bs-primary: #d9230f;--bs-secondary: #fff;--bs-success: #469408;--bs-info: #029acf;--bs-warning: #d9831f;--bs-danger: #9b479f;--bs-light: #fff;--bs-dark: #373a3c;--bs-default-rgb: 255,255,255;--bs-primary-rgb: 217,35,15;--bs-secondary-rgb: 255,255,255;--bs-success-rgb: 70,148,8;--bs-info-rgb: 2,154,207;--bs-warning-rgb: 217,131,31;--bs-danger-rgb: 155,71,159;--bs-light-rgb: 255,255,255;--bs-dark-rgb: 55,58,60;--bs-primary-text-emphasis: #570e06;--bs-secondary-text-emphasis: 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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #ccc;--bs-dropdown-bg: #373a3c;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #ccc;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #d9230f;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group.show .dropdown-toggle{box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)}.btn-group.show .dropdown-toggle.btn-link{box-shadow:none}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .9rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: #bbb;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(217,35,15,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: #eee;--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) #eee;--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #d9230f}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(0,0,0,0.65);--bs-navbar-hover-color: rgba(0,0,0,0.8);--bs-navbar-disabled-color: rgba(0,0,0,0.3);--bs-navbar-active-color: #000;--bs-navbar-brand-padding-y: .7125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: #000;--bs-navbar-brand-hover-color: #000;--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%280,0,0,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(0,0,0,0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;box-shadow:none;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg 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viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: #eee;--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23570e06'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #ec9187;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23e87b6f'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23e87b6f'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: .75rem;--bs-breadcrumb-padding-y: .375rem;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: .25rem;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: #eee;--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: #fff;--bs-pagination-hover-bg: #d9230f;--bs-pagination-hover-border-color: #d9230f;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #d9230f;--bs-pagination-active-border-color: #d9230f;--bs-pagination-disabled-color: #bbb;--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: #eee;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #d9230f;--bs-progress-bar-bg: #d9230f;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius);box-shadow:var(--bs-progress-box-shadow)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: #eee;--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: #eee;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #d9230f;--bs-list-group-active-border-color: #d9230f;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: #eee;--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #eee;--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #eee;--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);box-shadow:var(--bs-modal-box-shadow);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y) * .5) calc(var(--bs-modal-header-padding-x) * .5);margin:calc(-.5 * var(--bs-modal-header-padding-y)) calc(-.5 * var(--bs-modal-header-padding-x)) calc(-.5 * var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap) * .5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap) * .5)}@media (min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media (min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media (min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media (max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media (max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media (max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media (max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: .5rem;--bs-tooltip-padding-y: .25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: .9;--bs-tooltip-arrow-width: .8rem;--bs-tooltip-arrow-height: .4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow{left:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow{top:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: #eee;--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: .5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: .5rem;--bs-popover-arrow-border: 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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #ccc;--bs-dropdown-bg: #373a3c;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #ccc;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #d9230f;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group.show .dropdown-toggle{box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)}.btn-group.show .dropdown-toggle.btn-link{box-shadow:none}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .9rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: #bbb;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(217,35,15,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: #eee;--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) #eee;--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #d9230f}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(0,0,0,0.65);--bs-navbar-hover-color: rgba(0,0,0,0.8);--bs-navbar-disabled-color: rgba(0,0,0,0.3);--bs-navbar-active-color: #000;--bs-navbar-brand-padding-y: .7125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: #000;--bs-navbar-brand-hover-color: #000;--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%280,0,0,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(0,0,0,0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;box-shadow:none;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg 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viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: #eee;--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23570e06'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #ec9187;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23e87b6f'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23e87b6f'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: .75rem;--bs-breadcrumb-padding-y: .375rem;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: .25rem;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: #eee;--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: #fff;--bs-pagination-hover-bg: #d9230f;--bs-pagination-hover-border-color: #d9230f;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #d9230f;--bs-pagination-active-border-color: #d9230f;--bs-pagination-disabled-color: #bbb;--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: #eee;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #d9230f;--bs-progress-bar-bg: #d9230f;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius);box-shadow:var(--bs-progress-box-shadow)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: #eee;--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: #eee;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #d9230f;--bs-list-group-active-border-color: #d9230f;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(217,35,15,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: #eee;--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #eee;--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #eee;--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);box-shadow:var(--bs-modal-box-shadow);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y) * .5) calc(var(--bs-modal-header-padding-x) * .5);margin:calc(-.5 * var(--bs-modal-header-padding-y)) calc(-.5 * var(--bs-modal-header-padding-x)) calc(-.5 * var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap) * .5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap) * .5)}@media (min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media (min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media (min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media (max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media (max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media (max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media (max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: .5rem;--bs-tooltip-padding-y: .25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: .9;--bs-tooltip-arrow-width: .8rem;--bs-tooltip-arrow-height: .4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow{left:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow{top:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: #eee;--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: .5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: .5rem;--bs-popover-arrow-border: 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diff --git a/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js b/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
new file mode 100644
index 0000000..c628326
--- /dev/null
+++ b/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap Table of Contents v1.0.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+!function(a){"use strict";window.Toc={helpers:{findOrFilter:function(e,t){var n=e.find(t);return e.filter(t).add(n).filter(":not([data-toc-skip])")},generateUniqueIdBase:function(e){return a(e).text().trim().replace(/\'/gi,"").replace(/[& +$,:;=?@"#{}|^~[`%!'<>\]\.\/\(\)\*\\\n\t\b\v]/g,"-").replace(/-{2,}/g,"-").substring(0,64).replace(/^-+|-+$/gm,"").toLowerCase()||e.tagName.toLowerCase()},generateUniqueId:function(e){for(var t=this.generateUniqueIdBase(e),n=0;;n++){var r=t;if(0<n&&(r+="-"+n),!document.getElementById(r))return r}},generateAnchor:function(e){if(e.id)return e.id;var t=this.generateUniqueId(e);return e.id=t},createNavList:function(){return a('<ul class="nav navbar-nav"></ul>')},createChildNavList:function(e){var t=this.createNavList();return e.append(t),t},generateNavEl:function(e,t){var n=a('<a class="nav-link"></a>');n.attr("href","#"+e),n.text(t);var r=a("<li></li>");return r.append(n),r},generateNavItem:function(e){var t=this.generateAnchor(e),n=a(e),r=n.data("toc-text")||n.text();return this.generateNavEl(t,r)},getTopLevel:function(e){for(var t=1;t<=6;t++){if(1<this.findOrFilter(e,"h"+t).length)return t}return 1},getHeadings:function(e,t){var n="h"+t,r="h"+(t+1);return this.findOrFilter(e,n+","+r)},getNavLevel:function(e){return parseInt(e.tagName.charAt(1),10)},populateNav:function(r,a,e){var i,s=r,c=this;e.each(function(e,t){var n=c.generateNavItem(t);c.getNavLevel(t)===a?s=r:i&&s===r&&(s=c.createChildNavList(i)),s.append(n),i=n})},parseOps:function(e){var t;return(t=e.jquery?{$nav:e}:e).$scope=t.$scope||a(document.body),t}},init:function(e){(e=this.helpers.parseOps(e)).$nav.attr("data-toggle","toc");var t=this.helpers.createChildNavList(e.$nav),n=this.helpers.getTopLevel(e.$scope),r=this.helpers.getHeadings(e.$scope,n);this.helpers.populateNav(t,n,r)}},a(function(){a('nav[data-toggle="toc"]').each(function(e,t){var n=a(t);Toc.init(n)})})}(jQuery);
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new file mode 100644
index 0000000..1103f81
--- /dev/null
+++ b/deps/clipboard.js-2.0.11/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.11
+ * https://clipboardjs.com/
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body},n="";return"string"==typeof t?n=o(t,e):t instanceof HTMLInputElement&&!["text","search","url","tel","password"].includes(null==t?void 0:t.type)?n=o(t.value,e):(n=r()(t),c("copy")),n};function l(t){return(l="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var s=function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{},e=t.action,n=void 0===e?"copy":e,o=t.container,e=t.target,t=t.text;if("copy"!==n&&"cut"!==n)throw new Error('Invalid "action" value, use either "copy" or "cut"');if(void 0!==e){if(!e||"object"!==l(e)||1!==e.nodeType)throw new Error('Invalid "target" value, use a valid Element');if("copy"===n&&e.hasAttribute("disabled"))throw new Error('Invalid "target" attribute. 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diff --git a/deps/data-deps.txt b/deps/data-deps.txt
index 693b82d..8aa49e2 100644
--- a/deps/data-deps.txt
+++ b/deps/data-deps.txt
@@ -2,3 +2,12 @@
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet" />
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script>
+<link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
+<script src="deps/headroom-0.11.0/headroom.min.js"></script>
+<script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script>
+<script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script>
+<script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script>
+<script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script>
+<script src="deps/search-1.0.0/fuse.min.js"></script>
+<script src="deps/search-1.0.0/mark.min.js"></script>
diff --git a/deps/font-awesome-6.4.2/css/all.css b/deps/font-awesome-6.4.2/css/all.css
new file mode 100644
index 0000000..bdb6e3a
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/all.css
@@ -0,0 +1,7968 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa {
+  font-family: var(--fa-style-family, "Font Awesome 6 Free");
+  font-weight: var(--fa-style, 900); }
+
+.fa,
+.fa-classic,
+.fa-sharp,
+.fas,
+.fa-solid,
+.far,
+.fa-regular,
+.fab,
+.fa-brands {
+  -moz-osx-font-smoothing: grayscale;
+  -webkit-font-smoothing: antialiased;
+  display: var(--fa-display, inline-block);
+  font-style: normal;
+  font-variant: normal;
+  line-height: 1;
+  text-rendering: auto; }
+
+.fas,
+.fa-classic,
+.fa-solid,
+.far,
+.fa-regular {
+  font-family: 'Font Awesome 6 Free'; }
+
+.fab,
+.fa-brands {
+  font-family: 'Font Awesome 6 Brands'; }
+
+.fa-1x {
+  font-size: 1em; }
+
+.fa-2x {
+  font-size: 2em; }
+
+.fa-3x {
+  font-size: 3em; }
+
+.fa-4x {
+  font-size: 4em; }
+
+.fa-5x {
+  font-size: 5em; }
+
+.fa-6x {
+  font-size: 6em; }
+
+.fa-7x {
+  font-size: 7em; }
+
+.fa-8x {
+  font-size: 8em; }
+
+.fa-9x {
+  font-size: 9em; }
+
+.fa-10x {
+  font-size: 10em; }
+
+.fa-2xs {
+  font-size: 0.625em;
+  line-height: 0.1em;
+  vertical-align: 0.225em; }
+
+.fa-xs {
+  font-size: 0.75em;
+  line-height: 0.08333em;
+  vertical-align: 0.125em; }
+
+.fa-sm {
+  font-size: 0.875em;
+  line-height: 0.07143em;
+  vertical-align: 0.05357em; }
+
+.fa-lg {
+  font-size: 1.25em;
+  line-height: 0.05em;
+  vertical-align: -0.075em; }
+
+.fa-xl {
+  font-size: 1.5em;
+  line-height: 0.04167em;
+  vertical-align: -0.125em; }
+
+.fa-2xl {
+  font-size: 2em;
+  line-height: 0.03125em;
+  vertical-align: -0.1875em; }
+
+.fa-fw {
+  text-align: center;
+  width: 1.25em; }
+
+.fa-ul {
+  list-style-type: none;
+  margin-left: var(--fa-li-margin, 2.5em);
+  padding-left: 0; }
+  .fa-ul > li {
+    position: relative; }
+
+.fa-li {
+  left: calc(var(--fa-li-width, 2em) * -1);
+  position: absolute;
+  text-align: center;
+  width: var(--fa-li-width, 2em);
+  line-height: inherit; }
+
+.fa-border {
+  border-color: var(--fa-border-color, #eee);
+  border-radius: var(--fa-border-radius, 0.1em);
+  border-style: var(--fa-border-style, solid);
+  border-width: var(--fa-border-width, 0.08em);
+  padding: var(--fa-border-padding, 0.2em 0.25em 0.15em); }
+
+.fa-pull-left {
+  float: left;
+  margin-right: var(--fa-pull-margin, 0.3em); }
+
+.fa-pull-right {
+  float: right;
+  margin-left: var(--fa-pull-margin, 0.3em); }
+
+.fa-beat {
+  -webkit-animation-name: fa-beat;
+          animation-name: fa-beat;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-bounce {
+  -webkit-animation-name: fa-bounce;
+          animation-name: fa-bounce;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1)); }
+
+.fa-fade {
+  -webkit-animation-name: fa-fade;
+          animation-name: fa-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-beat-fade {
+  -webkit-animation-name: fa-beat-fade;
+          animation-name: fa-beat-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-flip {
+  -webkit-animation-name: fa-flip;
+          animation-name: fa-flip;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-shake {
+  -webkit-animation-name: fa-shake;
+          animation-name: fa-shake;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 2s);
+          animation-duration: var(--fa-animation-duration, 2s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin-reverse {
+  --fa-animation-direction: reverse; }
+
+.fa-pulse,
+.fa-spin-pulse {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, steps(8));
+          animation-timing-function: var(--fa-animation-timing, steps(8)); }
+
+@media (prefers-reduced-motion: reduce) {
+  .fa-beat,
+  .fa-bounce,
+  .fa-fade,
+  .fa-beat-fade,
+  .fa-flip,
+  .fa-pulse,
+  .fa-shake,
+  .fa-spin,
+  .fa-spin-pulse {
+    -webkit-animation-delay: -1ms;
+            animation-delay: -1ms;
+    -webkit-animation-duration: 1ms;
+            animation-duration: 1ms;
+    -webkit-animation-iteration-count: 1;
+            animation-iteration-count: 1;
+    -webkit-transition-delay: 0s;
+            transition-delay: 0s;
+    -webkit-transition-duration: 0s;
+            transition-duration: 0s; } }
+
+@-webkit-keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@-webkit-keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@-webkit-keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@-webkit-keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@-webkit-keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@-webkit-keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@-webkit-keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+@keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+.fa-rotate-90 {
+  -webkit-transform: rotate(90deg);
+          transform: rotate(90deg); }
+
+.fa-rotate-180 {
+  -webkit-transform: rotate(180deg);
+          transform: rotate(180deg); }
+
+.fa-rotate-270 {
+  -webkit-transform: rotate(270deg);
+          transform: rotate(270deg); }
+
+.fa-flip-horizontal {
+  -webkit-transform: scale(-1, 1);
+          transform: scale(-1, 1); }
+
+.fa-flip-vertical {
+  -webkit-transform: scale(1, -1);
+          transform: scale(1, -1); }
+
+.fa-flip-both,
+.fa-flip-horizontal.fa-flip-vertical {
+  -webkit-transform: scale(-1, -1);
+          transform: scale(-1, -1); }
+
+.fa-rotate-by {
+  -webkit-transform: rotate(var(--fa-rotate-angle, none));
+          transform: rotate(var(--fa-rotate-angle, none)); }
+
+.fa-stack {
+  display: inline-block;
+  height: 2em;
+  line-height: 2em;
+  position: relative;
+  vertical-align: middle;
+  width: 2.5em; }
+
+.fa-stack-1x,
+.fa-stack-2x {
+  left: 0;
+  position: absolute;
+  text-align: center;
+  width: 100%;
+  z-index: var(--fa-stack-z-index, auto); }
+
+.fa-stack-1x {
+  line-height: inherit; }
+
+.fa-stack-2x {
+  font-size: 2em; }
+
+.fa-inverse {
+  color: var(--fa-inverse, #fff); }
+
+/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen
+readers do not read off random characters that represent icons */
+
+.fa-0::before {
+  content: "\30"; }
+
+.fa-1::before {
+  content: "\31"; }
+
+.fa-2::before {
+  content: "\32"; }
+
+.fa-3::before {
+  content: "\33"; }
+
+.fa-4::before {
+  content: "\34"; }
+
+.fa-5::before {
+  content: "\35"; }
+
+.fa-6::before {
+  content: "\36"; }
+
+.fa-7::before {
+  content: "\37"; }
+
+.fa-8::before {
+  content: "\38"; }
+
+.fa-9::before {
+  content: "\39"; }
+
+.fa-fill-drip::before {
+  content: "\f576"; }
+
+.fa-arrows-to-circle::before {
+  content: "\e4bd"; }
+
+.fa-circle-chevron-right::before {
+  content: "\f138"; }
+
+.fa-chevron-circle-right::before {
+  content: "\f138"; }
+
+.fa-at::before {
+  content: "\40"; }
+
+.fa-trash-can::before {
+  content: "\f2ed"; }
+
+.fa-trash-alt::before {
+  content: "\f2ed"; }
+
+.fa-text-height::before {
+  content: "\f034"; }
+
+.fa-user-xmark::before {
+  content: "\f235"; }
+
+.fa-user-times::before {
+  content: "\f235"; }
+
+.fa-stethoscope::before {
+  content: "\f0f1"; }
+
+.fa-message::before {
+  content: "\f27a"; }
+
+.fa-comment-alt::before {
+  content: "\f27a"; }
+
+.fa-info::before {
+  content: "\f129"; }
+
+.fa-down-left-and-up-right-to-center::before {
+  content: "\f422"; }
+
+.fa-compress-alt::before {
+  content: "\f422"; }
+
+.fa-explosion::before {
+  content: "\e4e9"; }
+
+.fa-file-lines::before {
+  content: "\f15c"; }
+
+.fa-file-alt::before {
+  content: "\f15c"; }
+
+.fa-file-text::before {
+  content: "\f15c"; }
+
+.fa-wave-square::before {
+  content: "\f83e"; }
+
+.fa-ring::before {
+  content: "\f70b"; }
+
+.fa-building-un::before {
+  content: "\e4d9"; }
+
+.fa-dice-three::before {
+  content: "\f527"; }
+
+.fa-calendar-days::before {
+  content: "\f073"; }
+
+.fa-calendar-alt::before {
+  content: "\f073"; }
+
+.fa-anchor-circle-check::before {
+  content: "\e4aa"; }
+
+.fa-building-circle-arrow-right::before {
+  content: "\e4d1"; }
+
+.fa-volleyball::before {
+  content: "\f45f"; }
+
+.fa-volleyball-ball::before {
+  content: "\f45f"; }
+
+.fa-arrows-up-to-line::before {
+  content: "\e4c2"; }
+
+.fa-sort-down::before {
+  content: "\f0dd"; }
+
+.fa-sort-desc::before {
+  content: "\f0dd"; }
+
+.fa-circle-minus::before {
+  content: "\f056"; }
+
+.fa-minus-circle::before {
+  content: "\f056"; }
+
+.fa-door-open::before {
+  content: "\f52b"; }
+
+.fa-right-from-bracket::before {
+  content: "\f2f5"; }
+
+.fa-sign-out-alt::before {
+  content: "\f2f5"; }
+
+.fa-atom::before {
+  content: "\f5d2"; }
+
+.fa-soap::before {
+  content: "\e06e"; }
+
+.fa-icons::before {
+  content: "\f86d"; }
+
+.fa-heart-music-camera-bolt::before {
+  content: "\f86d"; }
+
+.fa-microphone-lines-slash::before {
+  content: "\f539"; }
+
+.fa-microphone-alt-slash::before {
+  content: "\f539"; }
+
+.fa-bridge-circle-check::before {
+  content: "\e4c9"; }
+
+.fa-pump-medical::before {
+  content: "\e06a"; }
+
+.fa-fingerprint::before {
+  content: "\f577"; }
+
+.fa-hand-point-right::before {
+  content: "\f0a4"; }
+
+.fa-magnifying-glass-location::before {
+  content: "\f689"; }
+
+.fa-search-location::before {
+  content: "\f689"; }
+
+.fa-forward-step::before {
+  content: "\f051"; }
+
+.fa-step-forward::before {
+  content: "\f051"; }
+
+.fa-face-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-flag-checkered::before {
+  content: "\f11e"; }
+
+.fa-football::before {
+  content: "\f44e"; }
+
+.fa-football-ball::before {
+  content: "\f44e"; }
+
+.fa-school-circle-exclamation::before {
+  content: "\e56c"; }
+
+.fa-crop::before {
+  content: "\f125"; }
+
+.fa-angles-down::before {
+  content: "\f103"; }
+
+.fa-angle-double-down::before {
+  content: "\f103"; }
+
+.fa-users-rectangle::before {
+  content: "\e594"; }
+
+.fa-people-roof::before {
+  content: "\e537"; }
+
+.fa-people-line::before {
+  content: "\e534"; }
+
+.fa-beer-mug-empty::before {
+  content: "\f0fc"; }
+
+.fa-beer::before {
+  content: "\f0fc"; }
+
+.fa-diagram-predecessor::before {
+  content: "\e477"; }
+
+.fa-arrow-up-long::before {
+  content: "\f176"; }
+
+.fa-long-arrow-up::before {
+  content: "\f176"; }
+
+.fa-fire-flame-simple::before {
+  content: "\f46a"; }
+
+.fa-burn::before {
+  content: "\f46a"; }
+
+.fa-person::before {
+  content: "\f183"; }
+
+.fa-male::before {
+  content: "\f183"; }
+
+.fa-laptop::before {
+  content: "\f109"; }
+
+.fa-file-csv::before {
+  content: "\f6dd"; }
+
+.fa-menorah::before {
+  content: "\f676"; }
+
+.fa-truck-plane::before {
+  content: "\e58f"; }
+
+.fa-record-vinyl::before {
+  content: "\f8d9"; }
+
+.fa-face-grin-stars::before {
+  content: "\f587"; }
+
+.fa-grin-stars::before {
+  content: "\f587"; }
+
+.fa-bong::before {
+  content: "\f55c"; }
+
+.fa-spaghetti-monster-flying::before {
+  content: "\f67b"; }
+
+.fa-pastafarianism::before {
+  content: "\f67b"; }
+
+.fa-arrow-down-up-across-line::before {
+  content: "\e4af"; }
+
+.fa-spoon::before {
+  content: "\f2e5"; }
+
+.fa-utensil-spoon::before {
+  content: "\f2e5"; }
+
+.fa-jar-wheat::before {
+  content: "\e517"; }
+
+.fa-envelopes-bulk::before {
+  content: "\f674"; }
+
+.fa-mail-bulk::before {
+  content: "\f674"; }
+
+.fa-file-circle-exclamation::before {
+  content: "\e4eb"; }
+
+.fa-circle-h::before {
+  content: "\f47e"; }
+
+.fa-hospital-symbol::before {
+  content: "\f47e"; }
+
+.fa-pager::before {
+  content: "\f815"; }
+
+.fa-address-book::before {
+  content: "\f2b9"; }
+
+.fa-contact-book::before {
+  content: "\f2b9"; }
+
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+  content: "\f0cc"; }
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+  content: "\4b"; }
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+  content: "\e51c"; }
+
+.fa-pencil::before {
+  content: "\f303"; }
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+.fa-pencil-alt::before {
+  content: "\f303"; }
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+.fa-backward::before {
+  content: "\f04a"; }
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+.fa-caret-right::before {
+  content: "\f0da"; }
+
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+  content: "\f086"; }
+
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+  content: "\f0ea"; }
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+  content: "\f0ea"; }
+
+.fa-code-pull-request::before {
+  content: "\e13c"; }
+
+.fa-clipboard-list::before {
+  content: "\f46d"; }
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+  content: "\f4de"; }
+
+.fa-truck-loading::before {
+  content: "\f4de"; }
+
+.fa-user-check::before {
+  content: "\f4fc"; }
+
+.fa-vial-virus::before {
+  content: "\e597"; }
+
+.fa-sheet-plastic::before {
+  content: "\e571"; }
+
+.fa-blog::before {
+  content: "\f781"; }
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+  content: "\f504"; }
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+  content: "\e539"; }
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+  content: "\f6a0"; }
+
+.fa-torah::before {
+  content: "\f6a0"; }
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+.fa-broom-ball::before {
+  content: "\f458"; }
+
+.fa-quidditch::before {
+  content: "\f458"; }
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+  content: "\f458"; }
+
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+  content: "\f204"; }
+
+.fa-box-archive::before {
+  content: "\f187"; }
+
+.fa-archive::before {
+  content: "\f187"; }
+
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+  content: "\e545"; }
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+  content: "\f886"; }
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+  content: "\f886"; }
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+  content: "\f886"; }
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+  content: "\f58a"; }
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+  content: "\f58a"; }
+
+.fa-spray-can::before {
+  content: "\f5bd"; }
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+.fa-truck-monster::before {
+  content: "\f63b"; }
+
+.fa-w::before {
+  content: "\57"; }
+
+.fa-earth-africa::before {
+  content: "\f57c"; }
+
+.fa-globe-africa::before {
+  content: "\f57c"; }
+
+.fa-rainbow::before {
+  content: "\f75b"; }
+
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+  content: "\f1ce"; }
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+.fa-tablet-screen-button::before {
+  content: "\f3fa"; }
+
+.fa-tablet-alt::before {
+  content: "\f3fa"; }
+
+.fa-paw::before {
+  content: "\f1b0"; }
+
+.fa-cloud::before {
+  content: "\f0c2"; }
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+.fa-trowel-bricks::before {
+  content: "\e58a"; }
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+.fa-face-flushed::before {
+  content: "\f579"; }
+
+.fa-flushed::before {
+  content: "\f579"; }
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+  content: "\f80d"; }
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+  content: "\e57f"; }
+
+.fa-gavel::before {
+  content: "\f0e3"; }
+
+.fa-legal::before {
+  content: "\f0e3"; }
+
+.fa-binoculars::before {
+  content: "\f1e5"; }
+
+.fa-microphone-slash::before {
+  content: "\f131"; }
+
+.fa-box-tissue::before {
+  content: "\e05b"; }
+
+.fa-motorcycle::before {
+  content: "\f21c"; }
+
+.fa-bell-concierge::before {
+  content: "\f562"; }
+
+.fa-concierge-bell::before {
+  content: "\f562"; }
+
+.fa-pen-ruler::before {
+  content: "\f5ae"; }
+
+.fa-pencil-ruler::before {
+  content: "\f5ae"; }
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+.fa-people-arrows::before {
+  content: "\e068"; }
+
+.fa-people-arrows-left-right::before {
+  content: "\e068"; }
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+.fa-mars-and-venus-burst::before {
+  content: "\e523"; }
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+.fa-square-caret-right::before {
+  content: "\f152"; }
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+.fa-caret-square-right::before {
+  content: "\f152"; }
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+.fa-scissors::before {
+  content: "\f0c4"; }
+
+.fa-cut::before {
+  content: "\f0c4"; }
+
+.fa-sun-plant-wilt::before {
+  content: "\e57a"; }
+
+.fa-toilets-portable::before {
+  content: "\e584"; }
+
+.fa-hockey-puck::before {
+  content: "\f453"; }
+
+.fa-table::before {
+  content: "\f0ce"; }
+
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+  content: "\e521"; }
+
+.fa-tachograph-digital::before {
+  content: "\f566"; }
+
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+  content: "\f566"; }
+
+.fa-users-slash::before {
+  content: "\e073"; }
+
+.fa-clover::before {
+  content: "\e139"; }
+
+.fa-reply::before {
+  content: "\f3e5"; }
+
+.fa-mail-reply::before {
+  content: "\f3e5"; }
+
+.fa-star-and-crescent::before {
+  content: "\f699"; }
+
+.fa-house-fire::before {
+  content: "\e50c"; }
+
+.fa-square-minus::before {
+  content: "\f146"; }
+
+.fa-minus-square::before {
+  content: "\f146"; }
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+.fa-helicopter::before {
+  content: "\f533"; }
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+.fa-compass::before {
+  content: "\f14e"; }
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+  content: "\f150"; }
+
+.fa-caret-square-down::before {
+  content: "\f150"; }
+
+.fa-file-circle-question::before {
+  content: "\e4ef"; }
+
+.fa-laptop-code::before {
+  content: "\f5fc"; }
+
+.fa-swatchbook::before {
+  content: "\f5c3"; }
+
+.fa-prescription-bottle::before {
+  content: "\f485"; }
+
+.fa-bars::before {
+  content: "\f0c9"; }
+
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+  content: "\f0c9"; }
+
+.fa-people-group::before {
+  content: "\e533"; }
+
+.fa-hourglass-end::before {
+  content: "\f253"; }
+
+.fa-hourglass-3::before {
+  content: "\f253"; }
+
+.fa-heart-crack::before {
+  content: "\f7a9"; }
+
+.fa-heart-broken::before {
+  content: "\f7a9"; }
+
+.fa-square-up-right::before {
+  content: "\f360"; }
+
+.fa-external-link-square-alt::before {
+  content: "\f360"; }
+
+.fa-face-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-film::before {
+  content: "\f008"; }
+
+.fa-ruler-horizontal::before {
+  content: "\f547"; }
+
+.fa-people-robbery::before {
+  content: "\e536"; }
+
+.fa-lightbulb::before {
+  content: "\f0eb"; }
+
+.fa-caret-left::before {
+  content: "\f0d9"; }
+
+.fa-circle-exclamation::before {
+  content: "\f06a"; }
+
+.fa-exclamation-circle::before {
+  content: "\f06a"; }
+
+.fa-school-circle-xmark::before {
+  content: "\e56d"; }
+
+.fa-arrow-right-from-bracket::before {
+  content: "\f08b"; }
+
+.fa-sign-out::before {
+  content: "\f08b"; }
+
+.fa-circle-chevron-down::before {
+  content: "\f13a"; }
+
+.fa-chevron-circle-down::before {
+  content: "\f13a"; }
+
+.fa-unlock-keyhole::before {
+  content: "\f13e"; }
+
+.fa-unlock-alt::before {
+  content: "\f13e"; }
+
+.fa-cloud-showers-heavy::before {
+  content: "\f740"; }
+
+.fa-headphones-simple::before {
+  content: "\f58f"; }
+
+.fa-headphones-alt::before {
+  content: "\f58f"; }
+
+.fa-sitemap::before {
+  content: "\f0e8"; }
+
+.fa-circle-dollar-to-slot::before {
+  content: "\f4b9"; }
+
+.fa-donate::before {
+  content: "\f4b9"; }
+
+.fa-memory::before {
+  content: "\f538"; }
+
+.fa-road-spikes::before {
+  content: "\e568"; }
+
+.fa-fire-burner::before {
+  content: "\e4f1"; }
+
+.fa-flag::before {
+  content: "\f024"; }
+
+.fa-hanukiah::before {
+  content: "\f6e6"; }
+
+.fa-feather::before {
+  content: "\f52d"; }
+
+.fa-volume-low::before {
+  content: "\f027"; }
+
+.fa-volume-down::before {
+  content: "\f027"; }
+
+.fa-comment-slash::before {
+  content: "\f4b3"; }
+
+.fa-cloud-sun-rain::before {
+  content: "\f743"; }
+
+.fa-compress::before {
+  content: "\f066"; }
+
+.fa-wheat-awn::before {
+  content: "\e2cd"; }
+
+.fa-wheat-alt::before {
+  content: "\e2cd"; }
+
+.fa-ankh::before {
+  content: "\f644"; }
+
+.fa-hands-holding-child::before {
+  content: "\e4fa"; }
+
+.fa-asterisk::before {
+  content: "\2a"; }
+
+.fa-square-check::before {
+  content: "\f14a"; }
+
+.fa-check-square::before {
+  content: "\f14a"; }
+
+.fa-peseta-sign::before {
+  content: "\e221"; }
+
+.fa-heading::before {
+  content: "\f1dc"; }
+
+.fa-header::before {
+  content: "\f1dc"; }
+
+.fa-ghost::before {
+  content: "\f6e2"; }
+
+.fa-list::before {
+  content: "\f03a"; }
+
+.fa-list-squares::before {
+  content: "\f03a"; }
+
+.fa-square-phone-flip::before {
+  content: "\f87b"; }
+
+.fa-phone-square-alt::before {
+  content: "\f87b"; }
+
+.fa-cart-plus::before {
+  content: "\f217"; }
+
+.fa-gamepad::before {
+  content: "\f11b"; }
+
+.fa-circle-dot::before {
+  content: "\f192"; }
+
+.fa-dot-circle::before {
+  content: "\f192"; }
+
+.fa-face-dizzy::before {
+  content: "\f567"; }
+
+.fa-dizzy::before {
+  content: "\f567"; }
+
+.fa-egg::before {
+  content: "\f7fb"; }
+
+.fa-house-medical-circle-xmark::before {
+  content: "\e513"; }
+
+.fa-campground::before {
+  content: "\f6bb"; }
+
+.fa-folder-plus::before {
+  content: "\f65e"; }
+
+.fa-futbol::before {
+  content: "\f1e3"; }
+
+.fa-futbol-ball::before {
+  content: "\f1e3"; }
+
+.fa-soccer-ball::before {
+  content: "\f1e3"; }
+
+.fa-paintbrush::before {
+  content: "\f1fc"; }
+
+.fa-paint-brush::before {
+  content: "\f1fc"; }
+
+.fa-lock::before {
+  content: "\f023"; }
+
+.fa-gas-pump::before {
+  content: "\f52f"; }
+
+.fa-hot-tub-person::before {
+  content: "\f593"; }
+
+.fa-hot-tub::before {
+  content: "\f593"; }
+
+.fa-map-location::before {
+  content: "\f59f"; }
+
+.fa-map-marked::before {
+  content: "\f59f"; }
+
+.fa-house-flood-water::before {
+  content: "\e50e"; }
+
+.fa-tree::before {
+  content: "\f1bb"; }
+
+.fa-bridge-lock::before {
+  content: "\e4cc"; }
+
+.fa-sack-dollar::before {
+  content: "\f81d"; }
+
+.fa-pen-to-square::before {
+  content: "\f044"; }
+
+.fa-edit::before {
+  content: "\f044"; }
+
+.fa-car-side::before {
+  content: "\f5e4"; }
+
+.fa-share-nodes::before {
+  content: "\f1e0"; }
+
+.fa-share-alt::before {
+  content: "\f1e0"; }
+
+.fa-heart-circle-minus::before {
+  content: "\e4ff"; }
+
+.fa-hourglass-half::before {
+  content: "\f252"; }
+
+.fa-hourglass-2::before {
+  content: "\f252"; }
+
+.fa-microscope::before {
+  content: "\f610"; }
+
+.fa-sink::before {
+  content: "\e06d"; }
+
+.fa-bag-shopping::before {
+  content: "\f290"; }
+
+.fa-shopping-bag::before {
+  content: "\f290"; }
+
+.fa-arrow-down-z-a::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-desc::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-down-alt::before {
+  content: "\f881"; }
+
+.fa-mitten::before {
+  content: "\f7b5"; }
+
+.fa-person-rays::before {
+  content: "\e54d"; }
+
+.fa-users::before {
+  content: "\f0c0"; }
+
+.fa-eye-slash::before {
+  content: "\f070"; }
+
+.fa-flask-vial::before {
+  content: "\e4f3"; }
+
+.fa-hand::before {
+  content: "\f256"; }
+
+.fa-hand-paper::before {
+  content: "\f256"; }
+
+.fa-om::before {
+  content: "\f679"; }
+
+.fa-worm::before {
+  content: "\e599"; }
+
+.fa-house-circle-xmark::before {
+  content: "\e50b"; }
+
+.fa-plug::before {
+  content: "\f1e6"; }
+
+.fa-chevron-up::before {
+  content: "\f077"; }
+
+.fa-hand-spock::before {
+  content: "\f259"; }
+
+.fa-stopwatch::before {
+  content: "\f2f2"; }
+
+.fa-face-kiss::before {
+  content: "\f596"; }
+
+.fa-kiss::before {
+  content: "\f596"; }
+
+.fa-bridge-circle-xmark::before {
+  content: "\e4cb"; }
+
+.fa-face-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-chess-bishop::before {
+  content: "\f43a"; }
+
+.fa-face-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-ear-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deafness::before {
+  content: "\f2a4"; }
+
+.fa-hard-of-hearing::before {
+  content: "\f2a4"; }
+
+.fa-road-circle-check::before {
+  content: "\e564"; }
+
+.fa-dice-five::before {
+  content: "\f523"; }
+
+.fa-square-rss::before {
+  content: "\f143"; }
+
+.fa-rss-square::before {
+  content: "\f143"; }
+
+.fa-land-mine-on::before {
+  content: "\e51b"; }
+
+.fa-i-cursor::before {
+  content: "\f246"; }
+
+.fa-stamp::before {
+  content: "\f5bf"; }
+
+.fa-stairs::before {
+  content: "\e289"; }
+
+.fa-i::before {
+  content: "\49"; }
+
+.fa-hryvnia-sign::before {
+  content: "\f6f2"; }
+
+.fa-hryvnia::before {
+  content: "\f6f2"; }
+
+.fa-pills::before {
+  content: "\f484"; }
+
+.fa-face-grin-wide::before {
+  content: "\f581"; }
+
+.fa-grin-alt::before {
+  content: "\f581"; }
+
+.fa-tooth::before {
+  content: "\f5c9"; }
+
+.fa-v::before {
+  content: "\56"; }
+
+.fa-bangladeshi-taka-sign::before {
+  content: "\e2e6"; }
+
+.fa-bicycle::before {
+  content: "\f206"; }
+
+.fa-staff-snake::before {
+  content: "\e579"; }
+
+.fa-rod-asclepius::before {
+  content: "\e579"; }
+
+.fa-rod-snake::before {
+  content: "\e579"; }
+
+.fa-staff-aesculapius::before {
+  content: "\e579"; }
+
+.fa-head-side-cough-slash::before {
+  content: "\e062"; }
+
+.fa-truck-medical::before {
+  content: "\f0f9"; }
+
+.fa-ambulance::before {
+  content: "\f0f9"; }
+
+.fa-wheat-awn-circle-exclamation::before {
+  content: "\e598"; }
+
+.fa-snowman::before {
+  content: "\f7d0"; }
+
+.fa-mortar-pestle::before {
+  content: "\f5a7"; }
+
+.fa-road-barrier::before {
+  content: "\e562"; }
+
+.fa-school::before {
+  content: "\f549"; }
+
+.fa-igloo::before {
+  content: "\f7ae"; }
+
+.fa-joint::before {
+  content: "\f595"; }
+
+.fa-angle-right::before {
+  content: "\f105"; }
+
+.fa-horse::before {
+  content: "\f6f0"; }
+
+.fa-q::before {
+  content: "\51"; }
+
+.fa-g::before {
+  content: "\47"; }
+
+.fa-notes-medical::before {
+  content: "\f481"; }
+
+.fa-temperature-half::before {
+  content: "\f2c9"; }
+
+.fa-temperature-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-half::before {
+  content: "\f2c9"; }
+
+.fa-dong-sign::before {
+  content: "\e169"; }
+
+.fa-capsules::before {
+  content: "\f46b"; }
+
+.fa-poo-storm::before {
+  content: "\f75a"; }
+
+.fa-poo-bolt::before {
+  content: "\f75a"; }
+
+.fa-face-frown-open::before {
+  content: "\f57a"; }
+
+.fa-frown-open::before {
+  content: "\f57a"; }
+
+.fa-hand-point-up::before {
+  content: "\f0a6"; }
+
+.fa-money-bill::before {
+  content: "\f0d6"; }
+
+.fa-bookmark::before {
+  content: "\f02e"; }
+
+.fa-align-justify::before {
+  content: "\f039"; }
+
+.fa-umbrella-beach::before {
+  content: "\f5ca"; }
+
+.fa-helmet-un::before {
+  content: "\e503"; }
+
+.fa-bullseye::before {
+  content: "\f140"; }
+
+.fa-bacon::before {
+  content: "\f7e5"; }
+
+.fa-hand-point-down::before {
+  content: "\f0a7"; }
+
+.fa-arrow-up-from-bracket::before {
+  content: "\e09a"; }
+
+.fa-folder::before {
+  content: "\f07b"; }
+
+.fa-folder-blank::before {
+  content: "\f07b"; }
+
+.fa-file-waveform::before {
+  content: "\f478"; }
+
+.fa-file-medical-alt::before {
+  content: "\f478"; }
+
+.fa-radiation::before {
+  content: "\f7b9"; }
+
+.fa-chart-simple::before {
+  content: "\e473"; }
+
+.fa-mars-stroke::before {
+  content: "\f229"; }
+
+.fa-vial::before {
+  content: "\f492"; }
+
+.fa-gauge::before {
+  content: "\f624"; }
+
+.fa-dashboard::before {
+  content: "\f624"; }
+
+.fa-gauge-med::before {
+  content: "\f624"; }
+
+.fa-tachometer-alt-average::before {
+  content: "\f624"; }
+
+.fa-wand-magic-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-magic-wand-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-e::before {
+  content: "\45"; }
+
+.fa-pen-clip::before {
+  content: "\f305"; }
+
+.fa-pen-alt::before {
+  content: "\f305"; }
+
+.fa-bridge-circle-exclamation::before {
+  content: "\e4ca"; }
+
+.fa-user::before {
+  content: "\f007"; }
+
+.fa-school-circle-check::before {
+  content: "\e56b"; }
+
+.fa-dumpster::before {
+  content: "\f793"; }
+
+.fa-van-shuttle::before {
+  content: "\f5b6"; }
+
+.fa-shuttle-van::before {
+  content: "\f5b6"; }
+
+.fa-building-user::before {
+  content: "\e4da"; }
+
+.fa-square-caret-left::before {
+  content: "\f191"; }
+
+.fa-caret-square-left::before {
+  content: "\f191"; }
+
+.fa-highlighter::before {
+  content: "\f591"; }
+
+.fa-key::before {
+  content: "\f084"; }
+
+.fa-bullhorn::before {
+  content: "\f0a1"; }
+
+.fa-globe::before {
+  content: "\f0ac"; }
+
+.fa-synagogue::before {
+  content: "\f69b"; }
+
+.fa-person-half-dress::before {
+  content: "\e548"; }
+
+.fa-road-bridge::before {
+  content: "\e563"; }
+
+.fa-location-arrow::before {
+  content: "\f124"; }
+
+.fa-c::before {
+  content: "\43"; }
+
+.fa-tablet-button::before {
+  content: "\f10a"; }
+
+.fa-building-lock::before {
+  content: "\e4d6"; }
+
+.fa-pizza-slice::before {
+  content: "\f818"; }
+
+.fa-money-bill-wave::before {
+  content: "\f53a"; }
+
+.fa-chart-area::before {
+  content: "\f1fe"; }
+
+.fa-area-chart::before {
+  content: "\f1fe"; }
+
+.fa-house-flag::before {
+  content: "\e50d"; }
+
+.fa-person-circle-minus::before {
+  content: "\e540"; }
+
+.fa-ban::before {
+  content: "\f05e"; }
+
+.fa-cancel::before {
+  content: "\f05e"; }
+
+.fa-camera-rotate::before {
+  content: "\e0d8"; }
+
+.fa-spray-can-sparkles::before {
+  content: "\f5d0"; }
+
+.fa-air-freshener::before {
+  content: "\f5d0"; }
+
+.fa-star::before {
+  content: "\f005"; }
+
+.fa-repeat::before {
+  content: "\f363"; }
+
+.fa-cross::before {
+  content: "\f654"; }
+
+.fa-box::before {
+  content: "\f466"; }
+
+.fa-venus-mars::before {
+  content: "\f228"; }
+
+.fa-arrow-pointer::before {
+  content: "\f245"; }
+
+.fa-mouse-pointer::before {
+  content: "\f245"; }
+
+.fa-maximize::before {
+  content: "\f31e"; }
+
+.fa-expand-arrows-alt::before {
+  content: "\f31e"; }
+
+.fa-charging-station::before {
+  content: "\f5e7"; }
+
+.fa-shapes::before {
+  content: "\f61f"; }
+
+.fa-triangle-circle-square::before {
+  content: "\f61f"; }
+
+.fa-shuffle::before {
+  content: "\f074"; }
+
+.fa-random::before {
+  content: "\f074"; }
+
+.fa-person-running::before {
+  content: "\f70c"; }
+
+.fa-running::before {
+  content: "\f70c"; }
+
+.fa-mobile-retro::before {
+  content: "\e527"; }
+
+.fa-grip-lines-vertical::before {
+  content: "\f7a5"; }
+
+.fa-spider::before {
+  content: "\f717"; }
+
+.fa-hands-bound::before {
+  content: "\e4f9"; }
+
+.fa-file-invoice-dollar::before {
+  content: "\f571"; }
+
+.fa-plane-circle-exclamation::before {
+  content: "\e556"; }
+
+.fa-x-ray::before {
+  content: "\f497"; }
+
+.fa-spell-check::before {
+  content: "\f891"; }
+
+.fa-slash::before {
+  content: "\f715"; }
+
+.fa-computer-mouse::before {
+  content: "\f8cc"; }
+
+.fa-mouse::before {
+  content: "\f8cc"; }
+
+.fa-arrow-right-to-bracket::before {
+  content: "\f090"; }
+
+.fa-sign-in::before {
+  content: "\f090"; }
+
+.fa-shop-slash::before {
+  content: "\e070"; }
+
+.fa-store-alt-slash::before {
+  content: "\e070"; }
+
+.fa-server::before {
+  content: "\f233"; }
+
+.fa-virus-covid-slash::before {
+  content: "\e4a9"; }
+
+.fa-shop-lock::before {
+  content: "\e4a5"; }
+
+.fa-hourglass-start::before {
+  content: "\f251"; }
+
+.fa-hourglass-1::before {
+  content: "\f251"; }
+
+.fa-blender-phone::before {
+  content: "\f6b6"; }
+
+.fa-building-wheat::before {
+  content: "\e4db"; }
+
+.fa-person-breastfeeding::before {
+  content: "\e53a"; }
+
+.fa-right-to-bracket::before {
+  content: "\f2f6"; }
+
+.fa-sign-in-alt::before {
+  content: "\f2f6"; }
+
+.fa-venus::before {
+  content: "\f221"; }
+
+.fa-passport::before {
+  content: "\f5ab"; }
+
+.fa-heart-pulse::before {
+  content: "\f21e"; }
+
+.fa-heartbeat::before {
+  content: "\f21e"; }
+
+.fa-people-carry-box::before {
+  content: "\f4ce"; }
+
+.fa-people-carry::before {
+  content: "\f4ce"; }
+
+.fa-temperature-high::before {
+  content: "\f769"; }
+
+.fa-microchip::before {
+  content: "\f2db"; }
+
+.fa-crown::before {
+  content: "\f521"; }
+
+.fa-weight-hanging::before {
+  content: "\f5cd"; }
+
+.fa-xmarks-lines::before {
+  content: "\e59a"; }
+
+.fa-file-prescription::before {
+  content: "\f572"; }
+
+.fa-weight-scale::before {
+  content: "\f496"; }
+
+.fa-weight::before {
+  content: "\f496"; }
+
+.fa-user-group::before {
+  content: "\f500"; }
+
+.fa-user-friends::before {
+  content: "\f500"; }
+
+.fa-arrow-up-a-z::before {
+  content: "\f15e"; }
+
+.fa-sort-alpha-up::before {
+  content: "\f15e"; }
+
+.fa-chess-knight::before {
+  content: "\f441"; }
+
+.fa-face-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-wheelchair::before {
+  content: "\f193"; }
+
+.fa-circle-arrow-up::before {
+  content: "\f0aa"; }
+
+.fa-arrow-circle-up::before {
+  content: "\f0aa"; }
+
+.fa-toggle-on::before {
+  content: "\f205"; }
+
+.fa-person-walking::before {
+  content: "\f554"; }
+
+.fa-walking::before {
+  content: "\f554"; }
+
+.fa-l::before {
+  content: "\4c"; }
+
+.fa-fire::before {
+  content: "\f06d"; }
+
+.fa-bed-pulse::before {
+  content: "\f487"; }
+
+.fa-procedures::before {
+  content: "\f487"; }
+
+.fa-shuttle-space::before {
+  content: "\f197"; }
+
+.fa-space-shuttle::before {
+  content: "\f197"; }
+
+.fa-face-laugh::before {
+  content: "\f599"; }
+
+.fa-laugh::before {
+  content: "\f599"; }
+
+.fa-folder-open::before {
+  content: "\f07c"; }
+
+.fa-heart-circle-plus::before {
+  content: "\e500"; }
+
+.fa-code-fork::before {
+  content: "\e13b"; }
+
+.fa-city::before {
+  content: "\f64f"; }
+
+.fa-microphone-lines::before {
+  content: "\f3c9"; }
+
+.fa-microphone-alt::before {
+  content: "\f3c9"; }
+
+.fa-pepper-hot::before {
+  content: "\f816"; }
+
+.fa-unlock::before {
+  content: "\f09c"; }
+
+.fa-colon-sign::before {
+  content: "\e140"; }
+
+.fa-headset::before {
+  content: "\f590"; }
+
+.fa-store-slash::before {
+  content: "\e071"; }
+
+.fa-road-circle-xmark::before {
+  content: "\e566"; }
+
+.fa-user-minus::before {
+  content: "\f503"; }
+
+.fa-mars-stroke-up::before {
+  content: "\f22a"; }
+
+.fa-mars-stroke-v::before {
+  content: "\f22a"; }
+
+.fa-champagne-glasses::before {
+  content: "\f79f"; }
+
+.fa-glass-cheers::before {
+  content: "\f79f"; }
+
+.fa-clipboard::before {
+  content: "\f328"; }
+
+.fa-house-circle-exclamation::before {
+  content: "\e50a"; }
+
+.fa-file-arrow-up::before {
+  content: "\f574"; }
+
+.fa-file-upload::before {
+  content: "\f574"; }
+
+.fa-wifi::before {
+  content: "\f1eb"; }
+
+.fa-wifi-3::before {
+  content: "\f1eb"; }
+
+.fa-wifi-strong::before {
+  content: "\f1eb"; }
+
+.fa-bath::before {
+  content: "\f2cd"; }
+
+.fa-bathtub::before {
+  content: "\f2cd"; }
+
+.fa-underline::before {
+  content: "\f0cd"; }
+
+.fa-user-pen::before {
+  content: "\f4ff"; }
+
+.fa-user-edit::before {
+  content: "\f4ff"; }
+
+.fa-signature::before {
+  content: "\f5b7"; }
+
+.fa-stroopwafel::before {
+  content: "\f551"; }
+
+.fa-bold::before {
+  content: "\f032"; }
+
+.fa-anchor-lock::before {
+  content: "\e4ad"; }
+
+.fa-building-ngo::before {
+  content: "\e4d7"; }
+
+.fa-manat-sign::before {
+  content: "\e1d5"; }
+
+.fa-not-equal::before {
+  content: "\f53e"; }
+
+.fa-border-top-left::before {
+  content: "\f853"; }
+
+.fa-border-style::before {
+  content: "\f853"; }
+
+.fa-map-location-dot::before {
+  content: "\f5a0"; }
+
+.fa-map-marked-alt::before {
+  content: "\f5a0"; }
+
+.fa-jedi::before {
+  content: "\f669"; }
+
+.fa-square-poll-vertical::before {
+  content: "\f681"; }
+
+.fa-poll::before {
+  content: "\f681"; }
+
+.fa-mug-hot::before {
+  content: "\f7b6"; }
+
+.fa-car-battery::before {
+  content: "\f5df"; }
+
+.fa-battery-car::before {
+  content: "\f5df"; }
+
+.fa-gift::before {
+  content: "\f06b"; }
+
+.fa-dice-two::before {
+  content: "\f528"; }
+
+.fa-chess-queen::before {
+  content: "\f445"; }
+
+.fa-glasses::before {
+  content: "\f530"; }
+
+.fa-chess-board::before {
+  content: "\f43c"; }
+
+.fa-building-circle-check::before {
+  content: "\e4d2"; }
+
+.fa-person-chalkboard::before {
+  content: "\e53d"; }
+
+.fa-mars-stroke-right::before {
+  content: "\f22b"; }
+
+.fa-mars-stroke-h::before {
+  content: "\f22b"; }
+
+.fa-hand-back-fist::before {
+  content: "\f255"; }
+
+.fa-hand-rock::before {
+  content: "\f255"; }
+
+.fa-square-caret-up::before {
+  content: "\f151"; }
+
+.fa-caret-square-up::before {
+  content: "\f151"; }
+
+.fa-cloud-showers-water::before {
+  content: "\e4e4"; }
+
+.fa-chart-bar::before {
+  content: "\f080"; }
+
+.fa-bar-chart::before {
+  content: "\f080"; }
+
+.fa-hands-bubbles::before {
+  content: "\e05e"; }
+
+.fa-hands-wash::before {
+  content: "\e05e"; }
+
+.fa-less-than-equal::before {
+  content: "\f537"; }
+
+.fa-train::before {
+  content: "\f238"; }
+
+.fa-eye-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-crow::before {
+  content: "\f520"; }
+
+.fa-sailboat::before {
+  content: "\e445"; }
+
+.fa-window-restore::before {
+  content: "\f2d2"; }
+
+.fa-square-plus::before {
+  content: "\f0fe"; }
+
+.fa-plus-square::before {
+  content: "\f0fe"; }
+
+.fa-torii-gate::before {
+  content: "\f6a1"; }
+
+.fa-frog::before {
+  content: "\f52e"; }
+
+.fa-bucket::before {
+  content: "\e4cf"; }
+
+.fa-image::before {
+  content: "\f03e"; }
+
+.fa-microphone::before {
+  content: "\f130"; }
+
+.fa-cow::before {
+  content: "\f6c8"; }
+
+.fa-caret-up::before {
+  content: "\f0d8"; }
+
+.fa-screwdriver::before {
+  content: "\f54a"; }
+
+.fa-folder-closed::before {
+  content: "\e185"; }
+
+.fa-house-tsunami::before {
+  content: "\e515"; }
+
+.fa-square-nfi::before {
+  content: "\e576"; }
+
+.fa-arrow-up-from-ground-water::before {
+  content: "\e4b5"; }
+
+.fa-martini-glass::before {
+  content: "\f57b"; }
+
+.fa-glass-martini-alt::before {
+  content: "\f57b"; }
+
+.fa-rotate-left::before {
+  content: "\f2ea"; }
+
+.fa-rotate-back::before {
+  content: "\f2ea"; }
+
+.fa-rotate-backward::before {
+  content: "\f2ea"; }
+
+.fa-undo-alt::before {
+  content: "\f2ea"; }
+
+.fa-table-columns::before {
+  content: "\f0db"; }
+
+.fa-columns::before {
+  content: "\f0db"; }
+
+.fa-lemon::before {
+  content: "\f094"; }
+
+.fa-head-side-mask::before {
+  content: "\e063"; }
+
+.fa-handshake::before {
+  content: "\f2b5"; }
+
+.fa-gem::before {
+  content: "\f3a5"; }
+
+.fa-dolly::before {
+  content: "\f472"; }
+
+.fa-dolly-box::before {
+  content: "\f472"; }
+
+.fa-smoking::before {
+  content: "\f48d"; }
+
+.fa-minimize::before {
+  content: "\f78c"; }
+
+.fa-compress-arrows-alt::before {
+  content: "\f78c"; }
+
+.fa-monument::before {
+  content: "\f5a6"; }
+
+.fa-snowplow::before {
+  content: "\f7d2"; }
+
+.fa-angles-right::before {
+  content: "\f101"; }
+
+.fa-angle-double-right::before {
+  content: "\f101"; }
+
+.fa-cannabis::before {
+  content: "\f55f"; }
+
+.fa-circle-play::before {
+  content: "\f144"; }
+
+.fa-play-circle::before {
+  content: "\f144"; }
+
+.fa-tablets::before {
+  content: "\f490"; }
+
+.fa-ethernet::before {
+  content: "\f796"; }
+
+.fa-euro-sign::before {
+  content: "\f153"; }
+
+.fa-eur::before {
+  content: "\f153"; }
+
+.fa-euro::before {
+  content: "\f153"; }
+
+.fa-chair::before {
+  content: "\f6c0"; }
+
+.fa-circle-check::before {
+  content: "\f058"; }
+
+.fa-check-circle::before {
+  content: "\f058"; }
+
+.fa-circle-stop::before {
+  content: "\f28d"; }
+
+.fa-stop-circle::before {
+  content: "\f28d"; }
+
+.fa-compass-drafting::before {
+  content: "\f568"; }
+
+.fa-drafting-compass::before {
+  content: "\f568"; }
+
+.fa-plate-wheat::before {
+  content: "\e55a"; }
+
+.fa-icicles::before {
+  content: "\f7ad"; }
+
+.fa-person-shelter::before {
+  content: "\e54f"; }
+
+.fa-neuter::before {
+  content: "\f22c"; }
+
+.fa-id-badge::before {
+  content: "\f2c1"; }
+
+.fa-marker::before {
+  content: "\f5a1"; }
+
+.fa-face-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-helicopter-symbol::before {
+  content: "\e502"; }
+
+.fa-universal-access::before {
+  content: "\f29a"; }
+
+.fa-circle-chevron-up::before {
+  content: "\f139"; }
+
+.fa-chevron-circle-up::before {
+  content: "\f139"; }
+
+.fa-lari-sign::before {
+  content: "\e1c8"; }
+
+.fa-volcano::before {
+  content: "\f770"; }
+
+.fa-person-walking-dashed-line-arrow-right::before {
+  content: "\e553"; }
+
+.fa-sterling-sign::before {
+  content: "\f154"; }
+
+.fa-gbp::before {
+  content: "\f154"; }
+
+.fa-pound-sign::before {
+  content: "\f154"; }
+
+.fa-viruses::before {
+  content: "\e076"; }
+
+.fa-square-person-confined::before {
+  content: "\e577"; }
+
+.fa-user-tie::before {
+  content: "\f508"; }
+
+.fa-arrow-down-long::before {
+  content: "\f175"; }
+
+.fa-long-arrow-down::before {
+  content: "\f175"; }
+
+.fa-tent-arrow-down-to-line::before {
+  content: "\e57e"; }
+
+.fa-certificate::before {
+  content: "\f0a3"; }
+
+.fa-reply-all::before {
+  content: "\f122"; }
+
+.fa-mail-reply-all::before {
+  content: "\f122"; }
+
+.fa-suitcase::before {
+  content: "\f0f2"; }
+
+.fa-person-skating::before {
+  content: "\f7c5"; }
+
+.fa-skating::before {
+  content: "\f7c5"; }
+
+.fa-filter-circle-dollar::before {
+  content: "\f662"; }
+
+.fa-funnel-dollar::before {
+  content: "\f662"; }
+
+.fa-camera-retro::before {
+  content: "\f083"; }
+
+.fa-circle-arrow-down::before {
+  content: "\f0ab"; }
+
+.fa-arrow-circle-down::before {
+  content: "\f0ab"; }
+
+.fa-file-import::before {
+  content: "\f56f"; }
+
+.fa-arrow-right-to-file::before {
+  content: "\f56f"; }
+
+.fa-square-arrow-up-right::before {
+  content: "\f14c"; }
+
+.fa-external-link-square::before {
+  content: "\f14c"; }
+
+.fa-box-open::before {
+  content: "\f49e"; }
+
+.fa-scroll::before {
+  content: "\f70e"; }
+
+.fa-spa::before {
+  content: "\f5bb"; }
+
+.fa-location-pin-lock::before {
+  content: "\e51f"; }
+
+.fa-pause::before {
+  content: "\f04c"; }
+
+.fa-hill-avalanche::before {
+  content: "\e507"; }
+
+.fa-temperature-empty::before {
+  content: "\f2cb"; }
+
+.fa-temperature-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-empty::before {
+  content: "\f2cb"; }
+
+.fa-bomb::before {
+  content: "\f1e2"; }
+
+.fa-registered::before {
+  content: "\f25d"; }
+
+.fa-address-card::before {
+  content: "\f2bb"; }
+
+.fa-contact-card::before {
+  content: "\f2bb"; }
+
+.fa-vcard::before {
+  content: "\f2bb"; }
+
+.fa-scale-unbalanced-flip::before {
+  content: "\f516"; }
+
+.fa-balance-scale-right::before {
+  content: "\f516"; }
+
+.fa-subscript::before {
+  content: "\f12c"; }
+
+.fa-diamond-turn-right::before {
+  content: "\f5eb"; }
+
+.fa-directions::before {
+  content: "\f5eb"; }
+
+.fa-burst::before {
+  content: "\e4dc"; }
+
+.fa-house-laptop::before {
+  content: "\e066"; }
+
+.fa-laptop-house::before {
+  content: "\e066"; }
+
+.fa-face-tired::before {
+  content: "\f5c8"; }
+
+.fa-tired::before {
+  content: "\f5c8"; }
+
+.fa-money-bills::before {
+  content: "\e1f3"; }
+
+.fa-smog::before {
+  content: "\f75f"; }
+
+.fa-crutch::before {
+  content: "\f7f7"; }
+
+.fa-cloud-arrow-up::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload-alt::before {
+  content: "\f0ee"; }
+
+.fa-palette::before {
+  content: "\f53f"; }
+
+.fa-arrows-turn-right::before {
+  content: "\e4c0"; }
+
+.fa-vest::before {
+  content: "\e085"; }
+
+.fa-ferry::before {
+  content: "\e4ea"; }
+
+.fa-arrows-down-to-people::before {
+  content: "\e4b9"; }
+
+.fa-seedling::before {
+  content: "\f4d8"; }
+
+.fa-sprout::before {
+  content: "\f4d8"; }
+
+.fa-left-right::before {
+  content: "\f337"; }
+
+.fa-arrows-alt-h::before {
+  content: "\f337"; }
+
+.fa-boxes-packing::before {
+  content: "\e4c7"; }
+
+.fa-circle-arrow-left::before {
+  content: "\f0a8"; }
+
+.fa-arrow-circle-left::before {
+  content: "\f0a8"; }
+
+.fa-group-arrows-rotate::before {
+  content: "\e4f6"; }
+
+.fa-bowl-food::before {
+  content: "\e4c6"; }
+
+.fa-candy-cane::before {
+  content: "\f786"; }
+
+.fa-arrow-down-wide-short::before {
+  content: "\f160"; }
+
+.fa-sort-amount-asc::before {
+  content: "\f160"; }
+
+.fa-sort-amount-down::before {
+  content: "\f160"; }
+
+.fa-cloud-bolt::before {
+  content: "\f76c"; }
+
+.fa-thunderstorm::before {
+  content: "\f76c"; }
+
+.fa-text-slash::before {
+  content: "\f87d"; }
+
+.fa-remove-format::before {
+  content: "\f87d"; }
+
+.fa-face-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-file-word::before {
+  content: "\f1c2"; }
+
+.fa-file-powerpoint::before {
+  content: "\f1c4"; }
+
+.fa-arrows-left-right::before {
+  content: "\f07e"; }
+
+.fa-arrows-h::before {
+  content: "\f07e"; }
+
+.fa-house-lock::before {
+  content: "\e510"; }
+
+.fa-cloud-arrow-down::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download-alt::before {
+  content: "\f0ed"; }
+
+.fa-children::before {
+  content: "\e4e1"; }
+
+.fa-chalkboard::before {
+  content: "\f51b"; }
+
+.fa-blackboard::before {
+  content: "\f51b"; }
+
+.fa-user-large-slash::before {
+  content: "\f4fa"; }
+
+.fa-user-alt-slash::before {
+  content: "\f4fa"; }
+
+.fa-envelope-open::before {
+  content: "\f2b6"; }
+
+.fa-handshake-simple-slash::before {
+  content: "\e05f"; }
+
+.fa-handshake-alt-slash::before {
+  content: "\e05f"; }
+
+.fa-mattress-pillow::before {
+  content: "\e525"; }
+
+.fa-guarani-sign::before {
+  content: "\e19a"; }
+
+.fa-arrows-rotate::before {
+  content: "\f021"; }
+
+.fa-refresh::before {
+  content: "\f021"; }
+
+.fa-sync::before {
+  content: "\f021"; }
+
+.fa-fire-extinguisher::before {
+  content: "\f134"; }
+
+.fa-cruzeiro-sign::before {
+  content: "\e152"; }
+
+.fa-greater-than-equal::before {
+  content: "\f532"; }
+
+.fa-shield-halved::before {
+  content: "\f3ed"; }
+
+.fa-shield-alt::before {
+  content: "\f3ed"; }
+
+.fa-book-atlas::before {
+  content: "\f558"; }
+
+.fa-atlas::before {
+  content: "\f558"; }
+
+.fa-virus::before {
+  content: "\e074"; }
+
+.fa-envelope-circle-check::before {
+  content: "\e4e8"; }
+
+.fa-layer-group::before {
+  content: "\f5fd"; }
+
+.fa-arrows-to-dot::before {
+  content: "\e4be"; }
+
+.fa-archway::before {
+  content: "\f557"; }
+
+.fa-heart-circle-check::before {
+  content: "\e4fd"; }
+
+.fa-house-chimney-crack::before {
+  content: "\f6f1"; }
+
+.fa-house-damage::before {
+  content: "\f6f1"; }
+
+.fa-file-zipper::before {
+  content: "\f1c6"; }
+
+.fa-file-archive::before {
+  content: "\f1c6"; }
+
+.fa-square::before {
+  content: "\f0c8"; }
+
+.fa-martini-glass-empty::before {
+  content: "\f000"; }
+
+.fa-glass-martini::before {
+  content: "\f000"; }
+
+.fa-couch::before {
+  content: "\f4b8"; }
+
+.fa-cedi-sign::before {
+  content: "\e0df"; }
+
+.fa-italic::before {
+  content: "\f033"; }
+
+.fa-church::before {
+  content: "\f51d"; }
+
+.fa-comments-dollar::before {
+  content: "\f653"; }
+
+.fa-democrat::before {
+  content: "\f747"; }
+
+.fa-z::before {
+  content: "\5a"; }
+
+.fa-person-skiing::before {
+  content: "\f7c9"; }
+
+.fa-skiing::before {
+  content: "\f7c9"; }
+
+.fa-road-lock::before {
+  content: "\e567"; }
+
+.fa-a::before {
+  content: "\41"; }
+
+.fa-temperature-arrow-down::before {
+  content: "\e03f"; }
+
+.fa-temperature-down::before {
+  content: "\e03f"; }
+
+.fa-feather-pointed::before {
+  content: "\f56b"; }
+
+.fa-feather-alt::before {
+  content: "\f56b"; }
+
+.fa-p::before {
+  content: "\50"; }
+
+.fa-snowflake::before {
+  content: "\f2dc"; }
+
+.fa-newspaper::before {
+  content: "\f1ea"; }
+
+.fa-rectangle-ad::before {
+  content: "\f641"; }
+
+.fa-ad::before {
+  content: "\f641"; }
+
+.fa-circle-arrow-right::before {
+  content: "\f0a9"; }
+
+.fa-arrow-circle-right::before {
+  content: "\f0a9"; }
+
+.fa-filter-circle-xmark::before {
+  content: "\e17b"; }
+
+.fa-locust::before {
+  content: "\e520"; }
+
+.fa-sort::before {
+  content: "\f0dc"; }
+
+.fa-unsorted::before {
+  content: "\f0dc"; }
+
+.fa-list-ol::before {
+  content: "\f0cb"; }
+
+.fa-list-1-2::before {
+  content: "\f0cb"; }
+
+.fa-list-numeric::before {
+  content: "\f0cb"; }
+
+.fa-person-dress-burst::before {
+  content: "\e544"; }
+
+.fa-money-check-dollar::before {
+  content: "\f53d"; }
+
+.fa-money-check-alt::before {
+  content: "\f53d"; }
+
+.fa-vector-square::before {
+  content: "\f5cb"; }
+
+.fa-bread-slice::before {
+  content: "\f7ec"; }
+
+.fa-language::before {
+  content: "\f1ab"; }
+
+.fa-face-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-filter::before {
+  content: "\f0b0"; }
+
+.fa-question::before {
+  content: "\3f"; }
+
+.fa-file-signature::before {
+  content: "\f573"; }
+
+.fa-up-down-left-right::before {
+  content: "\f0b2"; }
+
+.fa-arrows-alt::before {
+  content: "\f0b2"; }
+
+.fa-house-chimney-user::before {
+  content: "\e065"; }
+
+.fa-hand-holding-heart::before {
+  content: "\f4be"; }
+
+.fa-puzzle-piece::before {
+  content: "\f12e"; }
+
+.fa-money-check::before {
+  content: "\f53c"; }
+
+.fa-star-half-stroke::before {
+  content: "\f5c0"; }
+
+.fa-star-half-alt::before {
+  content: "\f5c0"; }
+
+.fa-code::before {
+  content: "\f121"; }
+
+.fa-whiskey-glass::before {
+  content: "\f7a0"; }
+
+.fa-glass-whiskey::before {
+  content: "\f7a0"; }
+
+.fa-building-circle-exclamation::before {
+  content: "\e4d3"; }
+
+.fa-magnifying-glass-chart::before {
+  content: "\e522"; }
+
+.fa-arrow-up-right-from-square::before {
+  content: "\f08e"; }
+
+.fa-external-link::before {
+  content: "\f08e"; }
+
+.fa-cubes-stacked::before {
+  content: "\e4e6"; }
+
+.fa-won-sign::before {
+  content: "\f159"; }
+
+.fa-krw::before {
+  content: "\f159"; }
+
+.fa-won::before {
+  content: "\f159"; }
+
+.fa-virus-covid::before {
+  content: "\e4a8"; }
+
+.fa-austral-sign::before {
+  content: "\e0a9"; }
+
+.fa-f::before {
+  content: "\46"; }
+
+.fa-leaf::before {
+  content: "\f06c"; }
+
+.fa-road::before {
+  content: "\f018"; }
+
+.fa-taxi::before {
+  content: "\f1ba"; }
+
+.fa-cab::before {
+  content: "\f1ba"; }
+
+.fa-person-circle-plus::before {
+  content: "\e541"; }
+
+.fa-chart-pie::before {
+  content: "\f200"; }
+
+.fa-pie-chart::before {
+  content: "\f200"; }
+
+.fa-bolt-lightning::before {
+  content: "\e0b7"; }
+
+.fa-sack-xmark::before {
+  content: "\e56a"; }
+
+.fa-file-excel::before {
+  content: "\f1c3"; }
+
+.fa-file-contract::before {
+  content: "\f56c"; }
+
+.fa-fish-fins::before {
+  content: "\e4f2"; }
+
+.fa-building-flag::before {
+  content: "\e4d5"; }
+
+.fa-face-grin-beam::before {
+  content: "\f582"; }
+
+.fa-grin-beam::before {
+  content: "\f582"; }
+
+.fa-object-ungroup::before {
+  content: "\f248"; }
+
+.fa-poop::before {
+  content: "\f619"; }
+
+.fa-location-pin::before {
+  content: "\f041"; }
+
+.fa-map-marker::before {
+  content: "\f041"; }
+
+.fa-kaaba::before {
+  content: "\f66b"; }
+
+.fa-toilet-paper::before {
+  content: "\f71e"; }
+
+.fa-helmet-safety::before {
+  content: "\f807"; }
+
+.fa-hard-hat::before {
+  content: "\f807"; }
+
+.fa-hat-hard::before {
+  content: "\f807"; }
+
+.fa-eject::before {
+  content: "\f052"; }
+
+.fa-circle-right::before {
+  content: "\f35a"; }
+
+.fa-arrow-alt-circle-right::before {
+  content: "\f35a"; }
+
+.fa-plane-circle-check::before {
+  content: "\e555"; }
+
+.fa-face-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-meh-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-object-group::before {
+  content: "\f247"; }
+
+.fa-chart-line::before {
+  content: "\f201"; }
+
+.fa-line-chart::before {
+  content: "\f201"; }
+
+.fa-mask-ventilator::before {
+  content: "\e524"; }
+
+.fa-arrow-right::before {
+  content: "\f061"; }
+
+.fa-signs-post::before {
+  content: "\f277"; }
+
+.fa-map-signs::before {
+  content: "\f277"; }
+
+.fa-cash-register::before {
+  content: "\f788"; }
+
+.fa-person-circle-question::before {
+  content: "\e542"; }
+
+.fa-h::before {
+  content: "\48"; }
+
+.fa-tarp::before {
+  content: "\e57b"; }
+
+.fa-screwdriver-wrench::before {
+  content: "\f7d9"; }
+
+.fa-tools::before {
+  content: "\f7d9"; }
+
+.fa-arrows-to-eye::before {
+  content: "\e4bf"; }
+
+.fa-plug-circle-bolt::before {
+  content: "\e55b"; }
+
+.fa-heart::before {
+  content: "\f004"; }
+
+.fa-mars-and-venus::before {
+  content: "\f224"; }
+
+.fa-house-user::before {
+  content: "\e1b0"; }
+
+.fa-home-user::before {
+  content: "\e1b0"; }
+
+.fa-dumpster-fire::before {
+  content: "\f794"; }
+
+.fa-house-crack::before {
+  content: "\e3b1"; }
+
+.fa-martini-glass-citrus::before {
+  content: "\f561"; }
+
+.fa-cocktail::before {
+  content: "\f561"; }
+
+.fa-face-surprise::before {
+  content: "\f5c2"; }
+
+.fa-surprise::before {
+  content: "\f5c2"; }
+
+.fa-bottle-water::before {
+  content: "\e4c5"; }
+
+.fa-circle-pause::before {
+  content: "\f28b"; }
+
+.fa-pause-circle::before {
+  content: "\f28b"; }
+
+.fa-toilet-paper-slash::before {
+  content: "\e072"; }
+
+.fa-apple-whole::before {
+  content: "\f5d1"; }
+
+.fa-apple-alt::before {
+  content: "\f5d1"; }
+
+.fa-kitchen-set::before {
+  content: "\e51a"; }
+
+.fa-r::before {
+  content: "\52"; }
+
+.fa-temperature-quarter::before {
+  content: "\f2ca"; }
+
+.fa-temperature-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-quarter::before {
+  content: "\f2ca"; }
+
+.fa-cube::before {
+  content: "\f1b2"; }
+
+.fa-bitcoin-sign::before {
+  content: "\e0b4"; }
+
+.fa-shield-dog::before {
+  content: "\e573"; }
+
+.fa-solar-panel::before {
+  content: "\f5ba"; }
+
+.fa-lock-open::before {
+  content: "\f3c1"; }
+
+.fa-elevator::before {
+  content: "\e16d"; }
+
+.fa-money-bill-transfer::before {
+  content: "\e528"; }
+
+.fa-money-bill-trend-up::before {
+  content: "\e529"; }
+
+.fa-house-flood-water-circle-arrow-right::before {
+  content: "\e50f"; }
+
+.fa-square-poll-horizontal::before {
+  content: "\f682"; }
+
+.fa-poll-h::before {
+  content: "\f682"; }
+
+.fa-circle::before {
+  content: "\f111"; }
+
+.fa-backward-fast::before {
+  content: "\f049"; }
+
+.fa-fast-backward::before {
+  content: "\f049"; }
+
+.fa-recycle::before {
+  content: "\f1b8"; }
+
+.fa-user-astronaut::before {
+  content: "\f4fb"; }
+
+.fa-plane-slash::before {
+  content: "\e069"; }
+
+.fa-trademark::before {
+  content: "\f25c"; }
+
+.fa-basketball::before {
+  content: "\f434"; }
+
+.fa-basketball-ball::before {
+  content: "\f434"; }
+
+.fa-satellite-dish::before {
+  content: "\f7c0"; }
+
+.fa-circle-up::before {
+  content: "\f35b"; }
+
+.fa-arrow-alt-circle-up::before {
+  content: "\f35b"; }
+
+.fa-mobile-screen-button::before {
+  content: "\f3cd"; }
+
+.fa-mobile-alt::before {
+  content: "\f3cd"; }
+
+.fa-volume-high::before {
+  content: "\f028"; }
+
+.fa-volume-up::before {
+  content: "\f028"; }
+
+.fa-users-rays::before {
+  content: "\e593"; }
+
+.fa-wallet::before {
+  content: "\f555"; }
+
+.fa-clipboard-check::before {
+  content: "\f46c"; }
+
+.fa-file-audio::before {
+  content: "\f1c7"; }
+
+.fa-burger::before {
+  content: "\f805"; }
+
+.fa-hamburger::before {
+  content: "\f805"; }
+
+.fa-wrench::before {
+  content: "\f0ad"; }
+
+.fa-bugs::before {
+  content: "\e4d0"; }
+
+.fa-rupee-sign::before {
+  content: "\f156"; }
+
+.fa-rupee::before {
+  content: "\f156"; }
+
+.fa-file-image::before {
+  content: "\f1c5"; }
+
+.fa-circle-question::before {
+  content: "\f059"; }
+
+.fa-question-circle::before {
+  content: "\f059"; }
+
+.fa-plane-departure::before {
+  content: "\f5b0"; }
+
+.fa-handshake-slash::before {
+  content: "\e060"; }
+
+.fa-book-bookmark::before {
+  content: "\e0bb"; }
+
+.fa-code-branch::before {
+  content: "\f126"; }
+
+.fa-hat-cowboy::before {
+  content: "\f8c0"; }
+
+.fa-bridge::before {
+  content: "\e4c8"; }
+
+.fa-phone-flip::before {
+  content: "\f879"; }
+
+.fa-phone-alt::before {
+  content: "\f879"; }
+
+.fa-truck-front::before {
+  content: "\e2b7"; }
+
+.fa-cat::before {
+  content: "\f6be"; }
+
+.fa-anchor-circle-exclamation::before {
+  content: "\e4ab"; }
+
+.fa-truck-field::before {
+  content: "\e58d"; }
+
+.fa-route::before {
+  content: "\f4d7"; }
+
+.fa-clipboard-question::before {
+  content: "\e4e3"; }
+
+.fa-panorama::before {
+  content: "\e209"; }
+
+.fa-comment-medical::before {
+  content: "\f7f5"; }
+
+.fa-teeth-open::before {
+  content: "\f62f"; }
+
+.fa-file-circle-minus::before {
+  content: "\e4ed"; }
+
+.fa-tags::before {
+  content: "\f02c"; }
+
+.fa-wine-glass::before {
+  content: "\f4e3"; }
+
+.fa-forward-fast::before {
+  content: "\f050"; }
+
+.fa-fast-forward::before {
+  content: "\f050"; }
+
+.fa-face-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-square-parking::before {
+  content: "\f540"; }
+
+.fa-parking::before {
+  content: "\f540"; }
+
+.fa-house-signal::before {
+  content: "\e012"; }
+
+.fa-bars-progress::before {
+  content: "\f828"; }
+
+.fa-tasks-alt::before {
+  content: "\f828"; }
+
+.fa-faucet-drip::before {
+  content: "\e006"; }
+
+.fa-cart-flatbed::before {
+  content: "\f474"; }
+
+.fa-dolly-flatbed::before {
+  content: "\f474"; }
+
+.fa-ban-smoking::before {
+  content: "\f54d"; }
+
+.fa-smoking-ban::before {
+  content: "\f54d"; }
+
+.fa-terminal::before {
+  content: "\f120"; }
+
+.fa-mobile-button::before {
+  content: "\f10b"; }
+
+.fa-house-medical-flag::before {
+  content: "\e514"; }
+
+.fa-basket-shopping::before {
+  content: "\f291"; }
+
+.fa-shopping-basket::before {
+  content: "\f291"; }
+
+.fa-tape::before {
+  content: "\f4db"; }
+
+.fa-bus-simple::before {
+  content: "\f55e"; }
+
+.fa-bus-alt::before {
+  content: "\f55e"; }
+
+.fa-eye::before {
+  content: "\f06e"; }
+
+.fa-face-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-audio-description::before {
+  content: "\f29e"; }
+
+.fa-person-military-to-person::before {
+  content: "\e54c"; }
+
+.fa-file-shield::before {
+  content: "\e4f0"; }
+
+.fa-user-slash::before {
+  content: "\f506"; }
+
+.fa-pen::before {
+  content: "\f304"; }
+
+.fa-tower-observation::before {
+  content: "\e586"; }
+
+.fa-file-code::before {
+  content: "\f1c9"; }
+
+.fa-signal::before {
+  content: "\f012"; }
+
+.fa-signal-5::before {
+  content: "\f012"; }
+
+.fa-signal-perfect::before {
+  content: "\f012"; }
+
+.fa-bus::before {
+  content: "\f207"; }
+
+.fa-heart-circle-xmark::before {
+  content: "\e501"; }
+
+.fa-house-chimney::before {
+  content: "\e3af"; }
+
+.fa-home-lg::before {
+  content: "\e3af"; }
+
+.fa-window-maximize::before {
+  content: "\f2d0"; }
+
+.fa-face-frown::before {
+  content: "\f119"; }
+
+.fa-frown::before {
+  content: "\f119"; }
+
+.fa-prescription::before {
+  content: "\f5b1"; }
+
+.fa-shop::before {
+  content: "\f54f"; }
+
+.fa-store-alt::before {
+  content: "\f54f"; }
+
+.fa-floppy-disk::before {
+  content: "\f0c7"; }
+
+.fa-save::before {
+  content: "\f0c7"; }
+
+.fa-vihara::before {
+  content: "\f6a7"; }
+
+.fa-scale-unbalanced::before {
+  content: "\f515"; }
+
+.fa-balance-scale-left::before {
+  content: "\f515"; }
+
+.fa-sort-up::before {
+  content: "\f0de"; }
+
+.fa-sort-asc::before {
+  content: "\f0de"; }
+
+.fa-comment-dots::before {
+  content: "\f4ad"; }
+
+.fa-commenting::before {
+  content: "\f4ad"; }
+
+.fa-plant-wilt::before {
+  content: "\e5aa"; }
+
+.fa-diamond::before {
+  content: "\f219"; }
+
+.fa-face-grin-squint::before {
+  content: "\f585"; }
+
+.fa-grin-squint::before {
+  content: "\f585"; }
+
+.fa-hand-holding-dollar::before {
+  content: "\f4c0"; }
+
+.fa-hand-holding-usd::before {
+  content: "\f4c0"; }
+
+.fa-bacterium::before {
+  content: "\e05a"; }
+
+.fa-hand-pointer::before {
+  content: "\f25a"; }
+
+.fa-drum-steelpan::before {
+  content: "\f56a"; }
+
+.fa-hand-scissors::before {
+  content: "\f257"; }
+
+.fa-hands-praying::before {
+  content: "\f684"; }
+
+.fa-praying-hands::before {
+  content: "\f684"; }
+
+.fa-arrow-rotate-right::before {
+  content: "\f01e"; }
+
+.fa-arrow-right-rotate::before {
+  content: "\f01e"; }
+
+.fa-arrow-rotate-forward::before {
+  content: "\f01e"; }
+
+.fa-redo::before {
+  content: "\f01e"; }
+
+.fa-biohazard::before {
+  content: "\f780"; }
+
+.fa-location-crosshairs::before {
+  content: "\f601"; }
+
+.fa-location::before {
+  content: "\f601"; }
+
+.fa-mars-double::before {
+  content: "\f227"; }
+
+.fa-child-dress::before {
+  content: "\e59c"; }
+
+.fa-users-between-lines::before {
+  content: "\e591"; }
+
+.fa-lungs-virus::before {
+  content: "\e067"; }
+
+.fa-face-grin-tears::before {
+  content: "\f588"; }
+
+.fa-grin-tears::before {
+  content: "\f588"; }
+
+.fa-phone::before {
+  content: "\f095"; }
+
+.fa-calendar-xmark::before {
+  content: "\f273"; }
+
+.fa-calendar-times::before {
+  content: "\f273"; }
+
+.fa-child-reaching::before {
+  content: "\e59d"; }
+
+.fa-head-side-virus::before {
+  content: "\e064"; }
+
+.fa-user-gear::before {
+  content: "\f4fe"; }
+
+.fa-user-cog::before {
+  content: "\f4fe"; }
+
+.fa-arrow-up-1-9::before {
+  content: "\f163"; }
+
+.fa-sort-numeric-up::before {
+  content: "\f163"; }
+
+.fa-door-closed::before {
+  content: "\f52a"; }
+
+.fa-shield-virus::before {
+  content: "\e06c"; }
+
+.fa-dice-six::before {
+  content: "\f526"; }
+
+.fa-mosquito-net::before {
+  content: "\e52c"; }
+
+.fa-bridge-water::before {
+  content: "\e4ce"; }
+
+.fa-person-booth::before {
+  content: "\f756"; }
+
+.fa-text-width::before {
+  content: "\f035"; }
+
+.fa-hat-wizard::before {
+  content: "\f6e8"; }
+
+.fa-pen-fancy::before {
+  content: "\f5ac"; }
+
+.fa-person-digging::before {
+  content: "\f85e"; }
+
+.fa-digging::before {
+  content: "\f85e"; }
+
+.fa-trash::before {
+  content: "\f1f8"; }
+
+.fa-gauge-simple::before {
+  content: "\f629"; }
+
+.fa-gauge-simple-med::before {
+  content: "\f629"; }
+
+.fa-tachometer-average::before {
+  content: "\f629"; }
+
+.fa-book-medical::before {
+  content: "\f7e6"; }
+
+.fa-poo::before {
+  content: "\f2fe"; }
+
+.fa-quote-right::before {
+  content: "\f10e"; }
+
+.fa-quote-right-alt::before {
+  content: "\f10e"; }
+
+.fa-shirt::before {
+  content: "\f553"; }
+
+.fa-t-shirt::before {
+  content: "\f553"; }
+
+.fa-tshirt::before {
+  content: "\f553"; }
+
+.fa-cubes::before {
+  content: "\f1b3"; }
+
+.fa-divide::before {
+  content: "\f529"; }
+
+.fa-tenge-sign::before {
+  content: "\f7d7"; }
+
+.fa-tenge::before {
+  content: "\f7d7"; }
+
+.fa-headphones::before {
+  content: "\f025"; }
+
+.fa-hands-holding::before {
+  content: "\f4c2"; }
+
+.fa-hands-clapping::before {
+  content: "\e1a8"; }
+
+.fa-republican::before {
+  content: "\f75e"; }
+
+.fa-arrow-left::before {
+  content: "\f060"; }
+
+.fa-person-circle-xmark::before {
+  content: "\e543"; }
+
+.fa-ruler::before {
+  content: "\f545"; }
+
+.fa-align-left::before {
+  content: "\f036"; }
+
+.fa-dice-d6::before {
+  content: "\f6d1"; }
+
+.fa-restroom::before {
+  content: "\f7bd"; }
+
+.fa-j::before {
+  content: "\4a"; }
+
+.fa-users-viewfinder::before {
+  content: "\e595"; }
+
+.fa-file-video::before {
+  content: "\f1c8"; }
+
+.fa-up-right-from-square::before {
+  content: "\f35d"; }
+
+.fa-external-link-alt::before {
+  content: "\f35d"; }
+
+.fa-table-cells::before {
+  content: "\f00a"; }
+
+.fa-th::before {
+  content: "\f00a"; }
+
+.fa-file-pdf::before {
+  content: "\f1c1"; }
+
+.fa-book-bible::before {
+  content: "\f647"; }
+
+.fa-bible::before {
+  content: "\f647"; }
+
+.fa-o::before {
+  content: "\4f"; }
+
+.fa-suitcase-medical::before {
+  content: "\f0fa"; }
+
+.fa-medkit::before {
+  content: "\f0fa"; }
+
+.fa-user-secret::before {
+  content: "\f21b"; }
+
+.fa-otter::before {
+  content: "\f700"; }
+
+.fa-person-dress::before {
+  content: "\f182"; }
+
+.fa-female::before {
+  content: "\f182"; }
+
+.fa-comment-dollar::before {
+  content: "\f651"; }
+
+.fa-business-time::before {
+  content: "\f64a"; }
+
+.fa-briefcase-clock::before {
+  content: "\f64a"; }
+
+.fa-table-cells-large::before {
+  content: "\f009"; }
+
+.fa-th-large::before {
+  content: "\f009"; }
+
+.fa-book-tanakh::before {
+  content: "\f827"; }
+
+.fa-tanakh::before {
+  content: "\f827"; }
+
+.fa-phone-volume::before {
+  content: "\f2a0"; }
+
+.fa-volume-control-phone::before {
+  content: "\f2a0"; }
+
+.fa-hat-cowboy-side::before {
+  content: "\f8c1"; }
+
+.fa-clipboard-user::before {
+  content: "\f7f3"; }
+
+.fa-child::before {
+  content: "\f1ae"; }
+
+.fa-lira-sign::before {
+  content: "\f195"; }
+
+.fa-satellite::before {
+  content: "\f7bf"; }
+
+.fa-plane-lock::before {
+  content: "\e558"; }
+
+.fa-tag::before {
+  content: "\f02b"; }
+
+.fa-comment::before {
+  content: "\f075"; }
+
+.fa-cake-candles::before {
+  content: "\f1fd"; }
+
+.fa-birthday-cake::before {
+  content: "\f1fd"; }
+
+.fa-cake::before {
+  content: "\f1fd"; }
+
+.fa-envelope::before {
+  content: "\f0e0"; }
+
+.fa-angles-up::before {
+  content: "\f102"; }
+
+.fa-angle-double-up::before {
+  content: "\f102"; }
+
+.fa-paperclip::before {
+  content: "\f0c6"; }
+
+.fa-arrow-right-to-city::before {
+  content: "\e4b3"; }
+
+.fa-ribbon::before {
+  content: "\f4d6"; }
+
+.fa-lungs::before {
+  content: "\f604"; }
+
+.fa-arrow-up-9-1::before {
+  content: "\f887"; }
+
+.fa-sort-numeric-up-alt::before {
+  content: "\f887"; }
+
+.fa-litecoin-sign::before {
+  content: "\e1d3"; }
+
+.fa-border-none::before {
+  content: "\f850"; }
+
+.fa-circle-nodes::before {
+  content: "\e4e2"; }
+
+.fa-parachute-box::before {
+  content: "\f4cd"; }
+
+.fa-indent::before {
+  content: "\f03c"; }
+
+.fa-truck-field-un::before {
+  content: "\e58e"; }
+
+.fa-hourglass::before {
+  content: "\f254"; }
+
+.fa-hourglass-empty::before {
+  content: "\f254"; }
+
+.fa-mountain::before {
+  content: "\f6fc"; }
+
+.fa-user-doctor::before {
+  content: "\f0f0"; }
+
+.fa-user-md::before {
+  content: "\f0f0"; }
+
+.fa-circle-info::before {
+  content: "\f05a"; }
+
+.fa-info-circle::before {
+  content: "\f05a"; }
+
+.fa-cloud-meatball::before {
+  content: "\f73b"; }
+
+.fa-camera::before {
+  content: "\f030"; }
+
+.fa-camera-alt::before {
+  content: "\f030"; }
+
+.fa-square-virus::before {
+  content: "\e578"; }
+
+.fa-meteor::before {
+  content: "\f753"; }
+
+.fa-car-on::before {
+  content: "\e4dd"; }
+
+.fa-sleigh::before {
+  content: "\f7cc"; }
+
+.fa-arrow-down-1-9::before {
+  content: "\f162"; }
+
+.fa-sort-numeric-asc::before {
+  content: "\f162"; }
+
+.fa-sort-numeric-down::before {
+  content: "\f162"; }
+
+.fa-hand-holding-droplet::before {
+  content: "\f4c1"; }
+
+.fa-hand-holding-water::before {
+  content: "\f4c1"; }
+
+.fa-water::before {
+  content: "\f773"; }
+
+.fa-calendar-check::before {
+  content: "\f274"; }
+
+.fa-braille::before {
+  content: "\f2a1"; }
+
+.fa-prescription-bottle-medical::before {
+  content: "\f486"; }
+
+.fa-prescription-bottle-alt::before {
+  content: "\f486"; }
+
+.fa-landmark::before {
+  content: "\f66f"; }
+
+.fa-truck::before {
+  content: "\f0d1"; }
+
+.fa-crosshairs::before {
+  content: "\f05b"; }
+
+.fa-person-cane::before {
+  content: "\e53c"; }
+
+.fa-tent::before {
+  content: "\e57d"; }
+
+.fa-vest-patches::before {
+  content: "\e086"; }
+
+.fa-check-double::before {
+  content: "\f560"; }
+
+.fa-arrow-down-a-z::before {
+  content: "\f15d"; }
+
+.fa-sort-alpha-asc::before {
+  content: "\f15d"; }
+
+.fa-sort-alpha-down::before {
+  content: "\f15d"; }
+
+.fa-money-bill-wheat::before {
+  content: "\e52a"; }
+
+.fa-cookie::before {
+  content: "\f563"; }
+
+.fa-arrow-rotate-left::before {
+  content: "\f0e2"; }
+
+.fa-arrow-left-rotate::before {
+  content: "\f0e2"; }
+
+.fa-arrow-rotate-back::before {
+  content: "\f0e2"; }
+
+.fa-arrow-rotate-backward::before {
+  content: "\f0e2"; }
+
+.fa-undo::before {
+  content: "\f0e2"; }
+
+.fa-hard-drive::before {
+  content: "\f0a0"; }
+
+.fa-hdd::before {
+  content: "\f0a0"; }
+
+.fa-face-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-dumbbell::before {
+  content: "\f44b"; }
+
+.fa-rectangle-list::before {
+  content: "\f022"; }
+
+.fa-list-alt::before {
+  content: "\f022"; }
+
+.fa-tarp-droplet::before {
+  content: "\e57c"; }
+
+.fa-house-medical-circle-check::before {
+  content: "\e511"; }
+
+.fa-person-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-calendar-plus::before {
+  content: "\f271"; }
+
+.fa-plane-arrival::before {
+  content: "\f5af"; }
+
+.fa-circle-left::before {
+  content: "\f359"; }
+
+.fa-arrow-alt-circle-left::before {
+  content: "\f359"; }
+
+.fa-train-subway::before {
+  content: "\f239"; }
+
+.fa-subway::before {
+  content: "\f239"; }
+
+.fa-chart-gantt::before {
+  content: "\e0e4"; }
+
+.fa-indian-rupee-sign::before {
+  content: "\e1bc"; }
+
+.fa-indian-rupee::before {
+  content: "\e1bc"; }
+
+.fa-inr::before {
+  content: "\e1bc"; }
+
+.fa-crop-simple::before {
+  content: "\f565"; }
+
+.fa-crop-alt::before {
+  content: "\f565"; }
+
+.fa-money-bill-1::before {
+  content: "\f3d1"; }
+
+.fa-money-bill-alt::before {
+  content: "\f3d1"; }
+
+.fa-left-long::before {
+  content: "\f30a"; }
+
+.fa-long-arrow-alt-left::before {
+  content: "\f30a"; }
+
+.fa-dna::before {
+  content: "\f471"; }
+
+.fa-virus-slash::before {
+  content: "\e075"; }
+
+.fa-minus::before {
+  content: "\f068"; }
+
+.fa-subtract::before {
+  content: "\f068"; }
+
+.fa-chess::before {
+  content: "\f439"; }
+
+.fa-arrow-left-long::before {
+  content: "\f177"; }
+
+.fa-long-arrow-left::before {
+  content: "\f177"; }
+
+.fa-plug-circle-check::before {
+  content: "\e55c"; }
+
+.fa-street-view::before {
+  content: "\f21d"; }
+
+.fa-franc-sign::before {
+  content: "\e18f"; }
+
+.fa-volume-off::before {
+  content: "\f026"; }
+
+.fa-hands-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-hands-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-gear::before {
+  content: "\f013"; }
+
+.fa-cog::before {
+  content: "\f013"; }
+
+.fa-droplet-slash::before {
+  content: "\f5c7"; }
+
+.fa-tint-slash::before {
+  content: "\f5c7"; }
+
+.fa-mosque::before {
+  content: "\f678"; }
+
+.fa-mosquito::before {
+  content: "\e52b"; }
+
+.fa-star-of-david::before {
+  content: "\f69a"; }
+
+.fa-person-military-rifle::before {
+  content: "\e54b"; }
+
+.fa-cart-shopping::before {
+  content: "\f07a"; }
+
+.fa-shopping-cart::before {
+  content: "\f07a"; }
+
+.fa-vials::before {
+  content: "\f493"; }
+
+.fa-plug-circle-plus::before {
+  content: "\e55f"; }
+
+.fa-place-of-worship::before {
+  content: "\f67f"; }
+
+.fa-grip-vertical::before {
+  content: "\f58e"; }
+
+.fa-arrow-turn-up::before {
+  content: "\f148"; }
+
+.fa-level-up::before {
+  content: "\f148"; }
+
+.fa-u::before {
+  content: "\55"; }
+
+.fa-square-root-variable::before {
+  content: "\f698"; }
+
+.fa-square-root-alt::before {
+  content: "\f698"; }
+
+.fa-clock::before {
+  content: "\f017"; }
+
+.fa-clock-four::before {
+  content: "\f017"; }
+
+.fa-backward-step::before {
+  content: "\f048"; }
+
+.fa-step-backward::before {
+  content: "\f048"; }
+
+.fa-pallet::before {
+  content: "\f482"; }
+
+.fa-faucet::before {
+  content: "\e005"; }
+
+.fa-baseball-bat-ball::before {
+  content: "\f432"; }
+
+.fa-s::before {
+  content: "\53"; }
+
+.fa-timeline::before {
+  content: "\e29c"; }
+
+.fa-keyboard::before {
+  content: "\f11c"; }
+
+.fa-caret-down::before {
+  content: "\f0d7"; }
+
+.fa-house-chimney-medical::before {
+  content: "\f7f2"; }
+
+.fa-clinic-medical::before {
+  content: "\f7f2"; }
+
+.fa-temperature-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-temperature-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-mobile-screen::before {
+  content: "\f3cf"; }
+
+.fa-mobile-android-alt::before {
+  content: "\f3cf"; }
+
+.fa-plane-up::before {
+  content: "\e22d"; }
+
+.fa-piggy-bank::before {
+  content: "\f4d3"; }
+
+.fa-battery-half::before {
+  content: "\f242"; }
+
+.fa-battery-3::before {
+  content: "\f242"; }
+
+.fa-mountain-city::before {
+  content: "\e52e"; }
+
+.fa-coins::before {
+  content: "\f51e"; }
+
+.fa-khanda::before {
+  content: "\f66d"; }
+
+.fa-sliders::before {
+  content: "\f1de"; }
+
+.fa-sliders-h::before {
+  content: "\f1de"; }
+
+.fa-folder-tree::before {
+  content: "\f802"; }
+
+.fa-network-wired::before {
+  content: "\f6ff"; }
+
+.fa-map-pin::before {
+  content: "\f276"; }
+
+.fa-hamsa::before {
+  content: "\f665"; }
+
+.fa-cent-sign::before {
+  content: "\e3f5"; }
+
+.fa-flask::before {
+  content: "\f0c3"; }
+
+.fa-person-pregnant::before {
+  content: "\e31e"; }
+
+.fa-wand-sparkles::before {
+  content: "\f72b"; }
+
+.fa-ellipsis-vertical::before {
+  content: "\f142"; }
+
+.fa-ellipsis-v::before {
+  content: "\f142"; }
+
+.fa-ticket::before {
+  content: "\f145"; }
+
+.fa-power-off::before {
+  content: "\f011"; }
+
+.fa-right-long::before {
+  content: "\f30b"; }
+
+.fa-long-arrow-alt-right::before {
+  content: "\f30b"; }
+
+.fa-flag-usa::before {
+  content: "\f74d"; }
+
+.fa-laptop-file::before {
+  content: "\e51d"; }
+
+.fa-tty::before {
+  content: "\f1e4"; }
+
+.fa-teletype::before {
+  content: "\f1e4"; }
+
+.fa-diagram-next::before {
+  content: "\e476"; }
+
+.fa-person-rifle::before {
+  content: "\e54e"; }
+
+.fa-house-medical-circle-exclamation::before {
+  content: "\e512"; }
+
+.fa-closed-captioning::before {
+  content: "\f20a"; }
+
+.fa-person-hiking::before {
+  content: "\f6ec"; }
+
+.fa-hiking::before {
+  content: "\f6ec"; }
+
+.fa-venus-double::before {
+  content: "\f226"; }
+
+.fa-images::before {
+  content: "\f302"; }
+
+.fa-calculator::before {
+  content: "\f1ec"; }
+
+.fa-people-pulling::before {
+  content: "\e535"; }
+
+.fa-n::before {
+  content: "\4e"; }
+
+.fa-cable-car::before {
+  content: "\f7da"; }
+
+.fa-tram::before {
+  content: "\f7da"; }
+
+.fa-cloud-rain::before {
+  content: "\f73d"; }
+
+.fa-building-circle-xmark::before {
+  content: "\e4d4"; }
+
+.fa-ship::before {
+  content: "\f21a"; }
+
+.fa-arrows-down-to-line::before {
+  content: "\e4b8"; }
+
+.fa-download::before {
+  content: "\f019"; }
+
+.fa-face-grin::before {
+  content: "\f580"; }
+
+.fa-grin::before {
+  content: "\f580"; }
+
+.fa-delete-left::before {
+  content: "\f55a"; }
+
+.fa-backspace::before {
+  content: "\f55a"; }
+
+.fa-eye-dropper::before {
+  content: "\f1fb"; }
+
+.fa-eye-dropper-empty::before {
+  content: "\f1fb"; }
+
+.fa-eyedropper::before {
+  content: "\f1fb"; }
+
+.fa-file-circle-check::before {
+  content: "\e5a0"; }
+
+.fa-forward::before {
+  content: "\f04e"; }
+
+.fa-mobile::before {
+  content: "\f3ce"; }
+
+.fa-mobile-android::before {
+  content: "\f3ce"; }
+
+.fa-mobile-phone::before {
+  content: "\f3ce"; }
+
+.fa-face-meh::before {
+  content: "\f11a"; }
+
+.fa-meh::before {
+  content: "\f11a"; }
+
+.fa-align-center::before {
+  content: "\f037"; }
+
+.fa-book-skull::before {
+  content: "\f6b7"; }
+
+.fa-book-dead::before {
+  content: "\f6b7"; }
+
+.fa-id-card::before {
+  content: "\f2c2"; }
+
+.fa-drivers-license::before {
+  content: "\f2c2"; }
+
+.fa-outdent::before {
+  content: "\f03b"; }
+
+.fa-dedent::before {
+  content: "\f03b"; }
+
+.fa-heart-circle-exclamation::before {
+  content: "\e4fe"; }
+
+.fa-house::before {
+  content: "\f015"; }
+
+.fa-home::before {
+  content: "\f015"; }
+
+.fa-home-alt::before {
+  content: "\f015"; }
+
+.fa-home-lg-alt::before {
+  content: "\f015"; }
+
+.fa-calendar-week::before {
+  content: "\f784"; }
+
+.fa-laptop-medical::before {
+  content: "\f812"; }
+
+.fa-b::before {
+  content: "\42"; }
+
+.fa-file-medical::before {
+  content: "\f477"; }
+
+.fa-dice-one::before {
+  content: "\f525"; }
+
+.fa-kiwi-bird::before {
+  content: "\f535"; }
+
+.fa-arrow-right-arrow-left::before {
+  content: "\f0ec"; }
+
+.fa-exchange::before {
+  content: "\f0ec"; }
+
+.fa-rotate-right::before {
+  content: "\f2f9"; }
+
+.fa-redo-alt::before {
+  content: "\f2f9"; }
+
+.fa-rotate-forward::before {
+  content: "\f2f9"; }
+
+.fa-utensils::before {
+  content: "\f2e7"; }
+
+.fa-cutlery::before {
+  content: "\f2e7"; }
+
+.fa-arrow-up-wide-short::before {
+  content: "\f161"; }
+
+.fa-sort-amount-up::before {
+  content: "\f161"; }
+
+.fa-mill-sign::before {
+  content: "\e1ed"; }
+
+.fa-bowl-rice::before {
+  content: "\e2eb"; }
+
+.fa-skull::before {
+  content: "\f54c"; }
+
+.fa-tower-broadcast::before {
+  content: "\f519"; }
+
+.fa-broadcast-tower::before {
+  content: "\f519"; }
+
+.fa-truck-pickup::before {
+  content: "\f63c"; }
+
+.fa-up-long::before {
+  content: "\f30c"; }
+
+.fa-long-arrow-alt-up::before {
+  content: "\f30c"; }
+
+.fa-stop::before {
+  content: "\f04d"; }
+
+.fa-code-merge::before {
+  content: "\f387"; }
+
+.fa-upload::before {
+  content: "\f093"; }
+
+.fa-hurricane::before {
+  content: "\f751"; }
+
+.fa-mound::before {
+  content: "\e52d"; }
+
+.fa-toilet-portable::before {
+  content: "\e583"; }
+
+.fa-compact-disc::before {
+  content: "\f51f"; }
+
+.fa-file-arrow-down::before {
+  content: "\f56d"; }
+
+.fa-file-download::before {
+  content: "\f56d"; }
+
+.fa-caravan::before {
+  content: "\f8ff"; }
+
+.fa-shield-cat::before {
+  content: "\e572"; }
+
+.fa-bolt::before {
+  content: "\f0e7"; }
+
+.fa-zap::before {
+  content: "\f0e7"; }
+
+.fa-glass-water::before {
+  content: "\e4f4"; }
+
+.fa-oil-well::before {
+  content: "\e532"; }
+
+.fa-vault::before {
+  content: "\e2c5"; }
+
+.fa-mars::before {
+  content: "\f222"; }
+
+.fa-toilet::before {
+  content: "\f7d8"; }
+
+.fa-plane-circle-xmark::before {
+  content: "\e557"; }
+
+.fa-yen-sign::before {
+  content: "\f157"; }
+
+.fa-cny::before {
+  content: "\f157"; }
+
+.fa-jpy::before {
+  content: "\f157"; }
+
+.fa-rmb::before {
+  content: "\f157"; }
+
+.fa-yen::before {
+  content: "\f157"; }
+
+.fa-ruble-sign::before {
+  content: "\f158"; }
+
+.fa-rouble::before {
+  content: "\f158"; }
+
+.fa-rub::before {
+  content: "\f158"; }
+
+.fa-ruble::before {
+  content: "\f158"; }
+
+.fa-sun::before {
+  content: "\f185"; }
+
+.fa-guitar::before {
+  content: "\f7a6"; }
+
+.fa-face-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-horse-head::before {
+  content: "\f7ab"; }
+
+.fa-bore-hole::before {
+  content: "\e4c3"; }
+
+.fa-industry::before {
+  content: "\f275"; }
+
+.fa-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrow-alt-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrows-turn-to-dots::before {
+  content: "\e4c1"; }
+
+.fa-florin-sign::before {
+  content: "\e184"; }
+
+.fa-arrow-down-short-wide::before {
+  content: "\f884"; }
+
+.fa-sort-amount-desc::before {
+  content: "\f884"; }
+
+.fa-sort-amount-down-alt::before {
+  content: "\f884"; }
+
+.fa-less-than::before {
+  content: "\3c"; }
+
+.fa-angle-down::before {
+  content: "\f107"; }
+
+.fa-car-tunnel::before {
+  content: "\e4de"; }
+
+.fa-head-side-cough::before {
+  content: "\e061"; }
+
+.fa-grip-lines::before {
+  content: "\f7a4"; }
+
+.fa-thumbs-down::before {
+  content: "\f165"; }
+
+.fa-user-lock::before {
+  content: "\f502"; }
+
+.fa-arrow-right-long::before {
+  content: "\f178"; }
+
+.fa-long-arrow-right::before {
+  content: "\f178"; }
+
+.fa-anchor-circle-xmark::before {
+  content: "\e4ac"; }
+
+.fa-ellipsis::before {
+  content: "\f141"; }
+
+.fa-ellipsis-h::before {
+  content: "\f141"; }
+
+.fa-chess-pawn::before {
+  content: "\f443"; }
+
+.fa-kit-medical::before {
+  content: "\f479"; }
+
+.fa-first-aid::before {
+  content: "\f479"; }
+
+.fa-person-through-window::before {
+  content: "\e5a9"; }
+
+.fa-toolbox::before {
+  content: "\f552"; }
+
+.fa-hands-holding-circle::before {
+  content: "\e4fb"; }
+
+.fa-bug::before {
+  content: "\f188"; }
+
+.fa-credit-card::before {
+  content: "\f09d"; }
+
+.fa-credit-card-alt::before {
+  content: "\f09d"; }
+
+.fa-car::before {
+  content: "\f1b9"; }
+
+.fa-automobile::before {
+  content: "\f1b9"; }
+
+.fa-hand-holding-hand::before {
+  content: "\e4f7"; }
+
+.fa-book-open-reader::before {
+  content: "\f5da"; }
+
+.fa-book-reader::before {
+  content: "\f5da"; }
+
+.fa-mountain-sun::before {
+  content: "\e52f"; }
+
+.fa-arrows-left-right-to-line::before {
+  content: "\e4ba"; }
+
+.fa-dice-d20::before {
+  content: "\f6cf"; }
+
+.fa-truck-droplet::before {
+  content: "\e58c"; }
+
+.fa-file-circle-xmark::before {
+  content: "\e5a1"; }
+
+.fa-temperature-arrow-up::before {
+  content: "\e040"; }
+
+.fa-temperature-up::before {
+  content: "\e040"; }
+
+.fa-medal::before {
+  content: "\f5a2"; }
+
+.fa-bed::before {
+  content: "\f236"; }
+
+.fa-square-h::before {
+  content: "\f0fd"; }
+
+.fa-h-square::before {
+  content: "\f0fd"; }
+
+.fa-podcast::before {
+  content: "\f2ce"; }
+
+.fa-temperature-full::before {
+  content: "\f2c7"; }
+
+.fa-temperature-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-full::before {
+  content: "\f2c7"; }
+
+.fa-bell::before {
+  content: "\f0f3"; }
+
+.fa-superscript::before {
+  content: "\f12b"; }
+
+.fa-plug-circle-xmark::before {
+  content: "\e560"; }
+
+.fa-star-of-life::before {
+  content: "\f621"; }
+
+.fa-phone-slash::before {
+  content: "\f3dd"; }
+
+.fa-paint-roller::before {
+  content: "\f5aa"; }
+
+.fa-handshake-angle::before {
+  content: "\f4c4"; }
+
+.fa-hands-helping::before {
+  content: "\f4c4"; }
+
+.fa-location-dot::before {
+  content: "\f3c5"; }
+
+.fa-map-marker-alt::before {
+  content: "\f3c5"; }
+
+.fa-file::before {
+  content: "\f15b"; }
+
+.fa-greater-than::before {
+  content: "\3e"; }
+
+.fa-person-swimming::before {
+  content: "\f5c4"; }
+
+.fa-swimmer::before {
+  content: "\f5c4"; }
+
+.fa-arrow-down::before {
+  content: "\f063"; }
+
+.fa-droplet::before {
+  content: "\f043"; }
+
+.fa-tint::before {
+  content: "\f043"; }
+
+.fa-eraser::before {
+  content: "\f12d"; }
+
+.fa-earth-americas::before {
+  content: "\f57d"; }
+
+.fa-earth::before {
+  content: "\f57d"; }
+
+.fa-earth-america::before {
+  content: "\f57d"; }
+
+.fa-globe-americas::before {
+  content: "\f57d"; }
+
+.fa-person-burst::before {
+  content: "\e53b"; }
+
+.fa-dove::before {
+  content: "\f4ba"; }
+
+.fa-battery-empty::before {
+  content: "\f244"; }
+
+.fa-battery-0::before {
+  content: "\f244"; }
+
+.fa-socks::before {
+  content: "\f696"; }
+
+.fa-inbox::before {
+  content: "\f01c"; }
+
+.fa-section::before {
+  content: "\e447"; }
+
+.fa-gauge-high::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt-fast::before {
+  content: "\f625"; }
+
+.fa-envelope-open-text::before {
+  content: "\f658"; }
+
+.fa-hospital::before {
+  content: "\f0f8"; }
+
+.fa-hospital-alt::before {
+  content: "\f0f8"; }
+
+.fa-hospital-wide::before {
+  content: "\f0f8"; }
+
+.fa-wine-bottle::before {
+  content: "\f72f"; }
+
+.fa-chess-rook::before {
+  content: "\f447"; }
+
+.fa-bars-staggered::before {
+  content: "\f550"; }
+
+.fa-reorder::before {
+  content: "\f550"; }
+
+.fa-stream::before {
+  content: "\f550"; }
+
+.fa-dharmachakra::before {
+  content: "\f655"; }
+
+.fa-hotdog::before {
+  content: "\f80f"; }
+
+.fa-person-walking-with-cane::before {
+  content: "\f29d"; }
+
+.fa-blind::before {
+  content: "\f29d"; }
+
+.fa-drum::before {
+  content: "\f569"; }
+
+.fa-ice-cream::before {
+  content: "\f810"; }
+
+.fa-heart-circle-bolt::before {
+  content: "\e4fc"; }
+
+.fa-fax::before {
+  content: "\f1ac"; }
+
+.fa-paragraph::before {
+  content: "\f1dd"; }
+
+.fa-check-to-slot::before {
+  content: "\f772"; }
+
+.fa-vote-yea::before {
+  content: "\f772"; }
+
+.fa-star-half::before {
+  content: "\f089"; }
+
+.fa-boxes-stacked::before {
+  content: "\f468"; }
+
+.fa-boxes::before {
+  content: "\f468"; }
+
+.fa-boxes-alt::before {
+  content: "\f468"; }
+
+.fa-link::before {
+  content: "\f0c1"; }
+
+.fa-chain::before {
+  content: "\f0c1"; }
+
+.fa-ear-listen::before {
+  content: "\f2a2"; }
+
+.fa-assistive-listening-systems::before {
+  content: "\f2a2"; }
+
+.fa-tree-city::before {
+  content: "\e587"; }
+
+.fa-play::before {
+  content: "\f04b"; }
+
+.fa-font::before {
+  content: "\f031"; }
+
+.fa-rupiah-sign::before {
+  content: "\e23d"; }
+
+.fa-magnifying-glass::before {
+  content: "\f002"; }
+
+.fa-search::before {
+  content: "\f002"; }
+
+.fa-table-tennis-paddle-ball::before {
+  content: "\f45d"; }
+
+.fa-ping-pong-paddle-ball::before {
+  content: "\f45d"; }
+
+.fa-table-tennis::before {
+  content: "\f45d"; }
+
+.fa-person-dots-from-line::before {
+  content: "\f470"; }
+
+.fa-diagnoses::before {
+  content: "\f470"; }
+
+.fa-trash-can-arrow-up::before {
+  content: "\f82a"; }
+
+.fa-trash-restore-alt::before {
+  content: "\f82a"; }
+
+.fa-naira-sign::before {
+  content: "\e1f6"; }
+
+.fa-cart-arrow-down::before {
+  content: "\f218"; }
+
+.fa-walkie-talkie::before {
+  content: "\f8ef"; }
+
+.fa-file-pen::before {
+  content: "\f31c"; }
+
+.fa-file-edit::before {
+  content: "\f31c"; }
+
+.fa-receipt::before {
+  content: "\f543"; }
+
+.fa-square-pen::before {
+  content: "\f14b"; }
+
+.fa-pen-square::before {
+  content: "\f14b"; }
+
+.fa-pencil-square::before {
+  content: "\f14b"; }
+
+.fa-suitcase-rolling::before {
+  content: "\f5c1"; }
+
+.fa-person-circle-exclamation::before {
+  content: "\e53f"; }
+
+.fa-chevron-down::before {
+  content: "\f078"; }
+
+.fa-battery-full::before {
+  content: "\f240"; }
+
+.fa-battery::before {
+  content: "\f240"; }
+
+.fa-battery-5::before {
+  content: "\f240"; }
+
+.fa-skull-crossbones::before {
+  content: "\f714"; }
+
+.fa-code-compare::before {
+  content: "\e13a"; }
+
+.fa-list-ul::before {
+  content: "\f0ca"; }
+
+.fa-list-dots::before {
+  content: "\f0ca"; }
+
+.fa-school-lock::before {
+  content: "\e56f"; }
+
+.fa-tower-cell::before {
+  content: "\e585"; }
+
+.fa-down-long::before {
+  content: "\f309"; }
+
+.fa-long-arrow-alt-down::before {
+  content: "\f309"; }
+
+.fa-ranking-star::before {
+  content: "\e561"; }
+
+.fa-chess-king::before {
+  content: "\f43f"; }
+
+.fa-person-harassing::before {
+  content: "\e549"; }
+
+.fa-brazilian-real-sign::before {
+  content: "\e46c"; }
+
+.fa-landmark-dome::before {
+  content: "\f752"; }
+
+.fa-landmark-alt::before {
+  content: "\f752"; }
+
+.fa-arrow-up::before {
+  content: "\f062"; }
+
+.fa-tv::before {
+  content: "\f26c"; }
+
+.fa-television::before {
+  content: "\f26c"; }
+
+.fa-tv-alt::before {
+  content: "\f26c"; }
+
+.fa-shrimp::before {
+  content: "\e448"; }
+
+.fa-list-check::before {
+  content: "\f0ae"; }
+
+.fa-tasks::before {
+  content: "\f0ae"; }
+
+.fa-jug-detergent::before {
+  content: "\e519"; }
+
+.fa-circle-user::before {
+  content: "\f2bd"; }
+
+.fa-user-circle::before {
+  content: "\f2bd"; }
+
+.fa-user-shield::before {
+  content: "\f505"; }
+
+.fa-wind::before {
+  content: "\f72e"; }
+
+.fa-car-burst::before {
+  content: "\f5e1"; }
+
+.fa-car-crash::before {
+  content: "\f5e1"; }
+
+.fa-y::before {
+  content: "\59"; }
+
+.fa-person-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-truck-fast::before {
+  content: "\f48b"; }
+
+.fa-shipping-fast::before {
+  content: "\f48b"; }
+
+.fa-fish::before {
+  content: "\f578"; }
+
+.fa-user-graduate::before {
+  content: "\f501"; }
+
+.fa-circle-half-stroke::before {
+  content: "\f042"; }
+
+.fa-adjust::before {
+  content: "\f042"; }
+
+.fa-clapperboard::before {
+  content: "\e131"; }
+
+.fa-circle-radiation::before {
+  content: "\f7ba"; }
+
+.fa-radiation-alt::before {
+  content: "\f7ba"; }
+
+.fa-baseball::before {
+  content: "\f433"; }
+
+.fa-baseball-ball::before {
+  content: "\f433"; }
+
+.fa-jet-fighter-up::before {
+  content: "\e518"; }
+
+.fa-diagram-project::before {
+  content: "\f542"; }
+
+.fa-project-diagram::before {
+  content: "\f542"; }
+
+.fa-copy::before {
+  content: "\f0c5"; }
+
+.fa-volume-xmark::before {
+  content: "\f6a9"; }
+
+.fa-volume-mute::before {
+  content: "\f6a9"; }
+
+.fa-volume-times::before {
+  content: "\f6a9"; }
+
+.fa-hand-sparkles::before {
+  content: "\e05d"; }
+
+.fa-grip::before {
+  content: "\f58d"; }
+
+.fa-grip-horizontal::before {
+  content: "\f58d"; }
+
+.fa-share-from-square::before {
+  content: "\f14d"; }
+
+.fa-share-square::before {
+  content: "\f14d"; }
+
+.fa-child-combatant::before {
+  content: "\e4e0"; }
+
+.fa-child-rifle::before {
+  content: "\e4e0"; }
+
+.fa-gun::before {
+  content: "\e19b"; }
+
+.fa-square-phone::before {
+  content: "\f098"; }
+
+.fa-phone-square::before {
+  content: "\f098"; }
+
+.fa-plus::before {
+  content: "\2b"; }
+
+.fa-add::before {
+  content: "\2b"; }
+
+.fa-expand::before {
+  content: "\f065"; }
+
+.fa-computer::before {
+  content: "\e4e5"; }
+
+.fa-xmark::before {
+  content: "\f00d"; }
+
+.fa-close::before {
+  content: "\f00d"; }
+
+.fa-multiply::before {
+  content: "\f00d"; }
+
+.fa-remove::before {
+  content: "\f00d"; }
+
+.fa-times::before {
+  content: "\f00d"; }
+
+.fa-arrows-up-down-left-right::before {
+  content: "\f047"; }
+
+.fa-arrows::before {
+  content: "\f047"; }
+
+.fa-chalkboard-user::before {
+  content: "\f51c"; }
+
+.fa-chalkboard-teacher::before {
+  content: "\f51c"; }
+
+.fa-peso-sign::before {
+  content: "\e222"; }
+
+.fa-building-shield::before {
+  content: "\e4d8"; }
+
+.fa-baby::before {
+  content: "\f77c"; }
+
+.fa-users-line::before {
+  content: "\e592"; }
+
+.fa-quote-left::before {
+  content: "\f10d"; }
+
+.fa-quote-left-alt::before {
+  content: "\f10d"; }
+
+.fa-tractor::before {
+  content: "\f722"; }
+
+.fa-trash-arrow-up::before {
+  content: "\f829"; }
+
+.fa-trash-restore::before {
+  content: "\f829"; }
+
+.fa-arrow-down-up-lock::before {
+  content: "\e4b0"; }
+
+.fa-lines-leaning::before {
+  content: "\e51e"; }
+
+.fa-ruler-combined::before {
+  content: "\f546"; }
+
+.fa-copyright::before {
+  content: "\f1f9"; }
+
+.fa-equals::before {
+  content: "\3d"; }
+
+.fa-blender::before {
+  content: "\f517"; }
+
+.fa-teeth::before {
+  content: "\f62e"; }
+
+.fa-shekel-sign::before {
+  content: "\f20b"; }
+
+.fa-ils::before {
+  content: "\f20b"; }
+
+.fa-shekel::before {
+  content: "\f20b"; }
+
+.fa-sheqel::before {
+  content: "\f20b"; }
+
+.fa-sheqel-sign::before {
+  content: "\f20b"; }
+
+.fa-map::before {
+  content: "\f279"; }
+
+.fa-rocket::before {
+  content: "\f135"; }
+
+.fa-photo-film::before {
+  content: "\f87c"; }
+
+.fa-photo-video::before {
+  content: "\f87c"; }
+
+.fa-folder-minus::before {
+  content: "\f65d"; }
+
+.fa-store::before {
+  content: "\f54e"; }
+
+.fa-arrow-trend-up::before {
+  content: "\e098"; }
+
+.fa-plug-circle-minus::before {
+  content: "\e55e"; }
+
+.fa-sign-hanging::before {
+  content: "\f4d9"; }
+
+.fa-sign::before {
+  content: "\f4d9"; }
+
+.fa-bezier-curve::before {
+  content: "\f55b"; }
+
+.fa-bell-slash::before {
+  content: "\f1f6"; }
+
+.fa-tablet::before {
+  content: "\f3fb"; }
+
+.fa-tablet-android::before {
+  content: "\f3fb"; }
+
+.fa-school-flag::before {
+  content: "\e56e"; }
+
+.fa-fill::before {
+  content: "\f575"; }
+
+.fa-angle-up::before {
+  content: "\f106"; }
+
+.fa-drumstick-bite::before {
+  content: "\f6d7"; }
+
+.fa-holly-berry::before {
+  content: "\f7aa"; }
+
+.fa-chevron-left::before {
+  content: "\f053"; }
+
+.fa-bacteria::before {
+  content: "\e059"; }
+
+.fa-hand-lizard::before {
+  content: "\f258"; }
+
+.fa-notdef::before {
+  content: "\e1fe"; }
+
+.fa-disease::before {
+  content: "\f7fa"; }
+
+.fa-briefcase-medical::before {
+  content: "\f469"; }
+
+.fa-genderless::before {
+  content: "\f22d"; }
+
+.fa-chevron-right::before {
+  content: "\f054"; }
+
+.fa-retweet::before {
+  content: "\f079"; }
+
+.fa-car-rear::before {
+  content: "\f5de"; }
+
+.fa-car-alt::before {
+  content: "\f5de"; }
+
+.fa-pump-soap::before {
+  content: "\e06b"; }
+
+.fa-video-slash::before {
+  content: "\f4e2"; }
+
+.fa-battery-quarter::before {
+  content: "\f243"; }
+
+.fa-battery-2::before {
+  content: "\f243"; }
+
+.fa-radio::before {
+  content: "\f8d7"; }
+
+.fa-baby-carriage::before {
+  content: "\f77d"; }
+
+.fa-carriage-baby::before {
+  content: "\f77d"; }
+
+.fa-traffic-light::before {
+  content: "\f637"; }
+
+.fa-thermometer::before {
+  content: "\f491"; }
+
+.fa-vr-cardboard::before {
+  content: "\f729"; }
+
+.fa-hand-middle-finger::before {
+  content: "\f806"; }
+
+.fa-percent::before {
+  content: "\25"; }
+
+.fa-percentage::before {
+  content: "\25"; }
+
+.fa-truck-moving::before {
+  content: "\f4df"; }
+
+.fa-glass-water-droplet::before {
+  content: "\e4f5"; }
+
+.fa-display::before {
+  content: "\e163"; }
+
+.fa-face-smile::before {
+  content: "\f118"; }
+
+.fa-smile::before {
+  content: "\f118"; }
+
+.fa-thumbtack::before {
+  content: "\f08d"; }
+
+.fa-thumb-tack::before {
+  content: "\f08d"; }
+
+.fa-trophy::before {
+  content: "\f091"; }
+
+.fa-person-praying::before {
+  content: "\f683"; }
+
+.fa-pray::before {
+  content: "\f683"; }
+
+.fa-hammer::before {
+  content: "\f6e3"; }
+
+.fa-hand-peace::before {
+  content: "\f25b"; }
+
+.fa-rotate::before {
+  content: "\f2f1"; }
+
+.fa-sync-alt::before {
+  content: "\f2f1"; }
+
+.fa-spinner::before {
+  content: "\f110"; }
+
+.fa-robot::before {
+  content: "\f544"; }
+
+.fa-peace::before {
+  content: "\f67c"; }
+
+.fa-gears::before {
+  content: "\f085"; }
+
+.fa-cogs::before {
+  content: "\f085"; }
+
+.fa-warehouse::before {
+  content: "\f494"; }
+
+.fa-arrow-up-right-dots::before {
+  content: "\e4b7"; }
+
+.fa-splotch::before {
+  content: "\f5bc"; }
+
+.fa-face-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-dice-four::before {
+  content: "\f524"; }
+
+.fa-sim-card::before {
+  content: "\f7c4"; }
+
+.fa-transgender::before {
+  content: "\f225"; }
+
+.fa-transgender-alt::before {
+  content: "\f225"; }
+
+.fa-mercury::before {
+  content: "\f223"; }
+
+.fa-arrow-turn-down::before {
+  content: "\f149"; }
+
+.fa-level-down::before {
+  content: "\f149"; }
+
+.fa-person-falling-burst::before {
+  content: "\e547"; }
+
+.fa-award::before {
+  content: "\f559"; }
+
+.fa-ticket-simple::before {
+  content: "\f3ff"; }
+
+.fa-ticket-alt::before {
+  content: "\f3ff"; }
+
+.fa-building::before {
+  content: "\f1ad"; }
+
+.fa-angles-left::before {
+  content: "\f100"; }
+
+.fa-angle-double-left::before {
+  content: "\f100"; }
+
+.fa-qrcode::before {
+  content: "\f029"; }
+
+.fa-clock-rotate-left::before {
+  content: "\f1da"; }
+
+.fa-history::before {
+  content: "\f1da"; }
+
+.fa-face-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-file-export::before {
+  content: "\f56e"; }
+
+.fa-arrow-right-from-file::before {
+  content: "\f56e"; }
+
+.fa-shield::before {
+  content: "\f132"; }
+
+.fa-shield-blank::before {
+  content: "\f132"; }
+
+.fa-arrow-up-short-wide::before {
+  content: "\f885"; }
+
+.fa-sort-amount-up-alt::before {
+  content: "\f885"; }
+
+.fa-house-medical::before {
+  content: "\e3b2"; }
+
+.fa-golf-ball-tee::before {
+  content: "\f450"; }
+
+.fa-golf-ball::before {
+  content: "\f450"; }
+
+.fa-circle-chevron-left::before {
+  content: "\f137"; }
+
+.fa-chevron-circle-left::before {
+  content: "\f137"; }
+
+.fa-house-chimney-window::before {
+  content: "\e00d"; }
+
+.fa-pen-nib::before {
+  content: "\f5ad"; }
+
+.fa-tent-arrow-turn-left::before {
+  content: "\e580"; }
+
+.fa-tents::before {
+  content: "\e582"; }
+
+.fa-wand-magic::before {
+  content: "\f0d0"; }
+
+.fa-magic::before {
+  content: "\f0d0"; }
+
+.fa-dog::before {
+  content: "\f6d3"; }
+
+.fa-carrot::before {
+  content: "\f787"; }
+
+.fa-moon::before {
+  content: "\f186"; }
+
+.fa-wine-glass-empty::before {
+  content: "\f5ce"; }
+
+.fa-wine-glass-alt::before {
+  content: "\f5ce"; }
+
+.fa-cheese::before {
+  content: "\f7ef"; }
+
+.fa-yin-yang::before {
+  content: "\f6ad"; }
+
+.fa-music::before {
+  content: "\f001"; }
+
+.fa-code-commit::before {
+  content: "\f386"; }
+
+.fa-temperature-low::before {
+  content: "\f76b"; }
+
+.fa-person-biking::before {
+  content: "\f84a"; }
+
+.fa-biking::before {
+  content: "\f84a"; }
+
+.fa-broom::before {
+  content: "\f51a"; }
+
+.fa-shield-heart::before {
+  content: "\e574"; }
+
+.fa-gopuram::before {
+  content: "\f664"; }
+
+.fa-earth-oceania::before {
+  content: "\e47b"; }
+
+.fa-globe-oceania::before {
+  content: "\e47b"; }
+
+.fa-square-xmark::before {
+  content: "\f2d3"; }
+
+.fa-times-square::before {
+  content: "\f2d3"; }
+
+.fa-xmark-square::before {
+  content: "\f2d3"; }
+
+.fa-hashtag::before {
+  content: "\23"; }
+
+.fa-up-right-and-down-left-from-center::before {
+  content: "\f424"; }
+
+.fa-expand-alt::before {
+  content: "\f424"; }
+
+.fa-oil-can::before {
+  content: "\f613"; }
+
+.fa-t::before {
+  content: "\54"; }
+
+.fa-hippo::before {
+  content: "\f6ed"; }
+
+.fa-chart-column::before {
+  content: "\e0e3"; }
+
+.fa-infinity::before {
+  content: "\f534"; }
+
+.fa-vial-circle-check::before {
+  content: "\e596"; }
+
+.fa-person-arrow-down-to-line::before {
+  content: "\e538"; }
+
+.fa-voicemail::before {
+  content: "\f897"; }
+
+.fa-fan::before {
+  content: "\f863"; }
+
+.fa-person-walking-luggage::before {
+  content: "\e554"; }
+
+.fa-up-down::before {
+  content: "\f338"; }
+
+.fa-arrows-alt-v::before {
+  content: "\f338"; }
+
+.fa-cloud-moon-rain::before {
+  content: "\f73c"; }
+
+.fa-calendar::before {
+  content: "\f133"; }
+
+.fa-trailer::before {
+  content: "\e041"; }
+
+.fa-bahai::before {
+  content: "\f666"; }
+
+.fa-haykal::before {
+  content: "\f666"; }
+
+.fa-sd-card::before {
+  content: "\f7c2"; }
+
+.fa-dragon::before {
+  content: "\f6d5"; }
+
+.fa-shoe-prints::before {
+  content: "\f54b"; }
+
+.fa-circle-plus::before {
+  content: "\f055"; }
+
+.fa-plus-circle::before {
+  content: "\f055"; }
+
+.fa-face-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-hand-holding::before {
+  content: "\f4bd"; }
+
+.fa-plug-circle-exclamation::before {
+  content: "\e55d"; }
+
+.fa-link-slash::before {
+  content: "\f127"; }
+
+.fa-chain-broken::before {
+  content: "\f127"; }
+
+.fa-chain-slash::before {
+  content: "\f127"; }
+
+.fa-unlink::before {
+  content: "\f127"; }
+
+.fa-clone::before {
+  content: "\f24d"; }
+
+.fa-person-walking-arrow-loop-left::before {
+  content: "\e551"; }
+
+.fa-arrow-up-z-a::before {
+  content: "\f882"; }
+
+.fa-sort-alpha-up-alt::before {
+  content: "\f882"; }
+
+.fa-fire-flame-curved::before {
+  content: "\f7e4"; }
+
+.fa-fire-alt::before {
+  content: "\f7e4"; }
+
+.fa-tornado::before {
+  content: "\f76f"; }
+
+.fa-file-circle-plus::before {
+  content: "\e494"; }
+
+.fa-book-quran::before {
+  content: "\f687"; }
+
+.fa-quran::before {
+  content: "\f687"; }
+
+.fa-anchor::before {
+  content: "\f13d"; }
+
+.fa-border-all::before {
+  content: "\f84c"; }
+
+.fa-face-angry::before {
+  content: "\f556"; }
+
+.fa-angry::before {
+  content: "\f556"; }
+
+.fa-cookie-bite::before {
+  content: "\f564"; }
+
+.fa-arrow-trend-down::before {
+  content: "\e097"; }
+
+.fa-rss::before {
+  content: "\f09e"; }
+
+.fa-feed::before {
+  content: "\f09e"; }
+
+.fa-draw-polygon::before {
+  content: "\f5ee"; }
+
+.fa-scale-balanced::before {
+  content: "\f24e"; }
+
+.fa-balance-scale::before {
+  content: "\f24e"; }
+
+.fa-gauge-simple-high::before {
+  content: "\f62a"; }
+
+.fa-tachometer::before {
+  content: "\f62a"; }
+
+.fa-tachometer-fast::before {
+  content: "\f62a"; }
+
+.fa-shower::before {
+  content: "\f2cc"; }
+
+.fa-desktop::before {
+  content: "\f390"; }
+
+.fa-desktop-alt::before {
+  content: "\f390"; }
+
+.fa-m::before {
+  content: "\4d"; }
+
+.fa-table-list::before {
+  content: "\f00b"; }
+
+.fa-th-list::before {
+  content: "\f00b"; }
+
+.fa-comment-sms::before {
+  content: "\f7cd"; }
+
+.fa-sms::before {
+  content: "\f7cd"; }
+
+.fa-book::before {
+  content: "\f02d"; }
+
+.fa-user-plus::before {
+  content: "\f234"; }
+
+.fa-check::before {
+  content: "\f00c"; }
+
+.fa-battery-three-quarters::before {
+  content: "\f241"; }
+
+.fa-battery-4::before {
+  content: "\f241"; }
+
+.fa-house-circle-check::before {
+  content: "\e509"; }
+
+.fa-angle-left::before {
+  content: "\f104"; }
+
+.fa-diagram-successor::before {
+  content: "\e47a"; }
+
+.fa-truck-arrow-right::before {
+  content: "\e58b"; }
+
+.fa-arrows-split-up-and-left::before {
+  content: "\e4bc"; }
+
+.fa-hand-fist::before {
+  content: "\f6de"; }
+
+.fa-fist-raised::before {
+  content: "\f6de"; }
+
+.fa-cloud-moon::before {
+  content: "\f6c3"; }
+
+.fa-briefcase::before {
+  content: "\f0b1"; }
+
+.fa-person-falling::before {
+  content: "\e546"; }
+
+.fa-image-portrait::before {
+  content: "\f3e0"; }
+
+.fa-portrait::before {
+  content: "\f3e0"; }
+
+.fa-user-tag::before {
+  content: "\f507"; }
+
+.fa-rug::before {
+  content: "\e569"; }
+
+.fa-earth-europe::before {
+  content: "\f7a2"; }
+
+.fa-globe-europe::before {
+  content: "\f7a2"; }
+
+.fa-cart-flatbed-suitcase::before {
+  content: "\f59d"; }
+
+.fa-luggage-cart::before {
+  content: "\f59d"; }
+
+.fa-rectangle-xmark::before {
+  content: "\f410"; }
+
+.fa-rectangle-times::before {
+  content: "\f410"; }
+
+.fa-times-rectangle::before {
+  content: "\f410"; }
+
+.fa-window-close::before {
+  content: "\f410"; }
+
+.fa-baht-sign::before {
+  content: "\e0ac"; }
+
+.fa-book-open::before {
+  content: "\f518"; }
+
+.fa-book-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-handcuffs::before {
+  content: "\e4f8"; }
+
+.fa-triangle-exclamation::before {
+  content: "\f071"; }
+
+.fa-exclamation-triangle::before {
+  content: "\f071"; }
+
+.fa-warning::before {
+  content: "\f071"; }
+
+.fa-database::before {
+  content: "\f1c0"; }
+
+.fa-share::before {
+  content: "\f064"; }
+
+.fa-arrow-turn-right::before {
+  content: "\f064"; }
+
+.fa-mail-forward::before {
+  content: "\f064"; }
+
+.fa-bottle-droplet::before {
+  content: "\e4c4"; }
+
+.fa-mask-face::before {
+  content: "\e1d7"; }
+
+.fa-hill-rockslide::before {
+  content: "\e508"; }
+
+.fa-right-left::before {
+  content: "\f362"; }
+
+.fa-exchange-alt::before {
+  content: "\f362"; }
+
+.fa-paper-plane::before {
+  content: "\f1d8"; }
+
+.fa-road-circle-exclamation::before {
+  content: "\e565"; }
+
+.fa-dungeon::before {
+  content: "\f6d9"; }
+
+.fa-align-right::before {
+  content: "\f038"; }
+
+.fa-money-bill-1-wave::before {
+  content: "\f53b"; }
+
+.fa-money-bill-wave-alt::before {
+  content: "\f53b"; }
+
+.fa-life-ring::before {
+  content: "\f1cd"; }
+
+.fa-hands::before {
+  content: "\f2a7"; }
+
+.fa-sign-language::before {
+  content: "\f2a7"; }
+
+.fa-signing::before {
+  content: "\f2a7"; }
+
+.fa-calendar-day::before {
+  content: "\f783"; }
+
+.fa-water-ladder::before {
+  content: "\f5c5"; }
+
+.fa-ladder-water::before {
+  content: "\f5c5"; }
+
+.fa-swimming-pool::before {
+  content: "\f5c5"; }
+
+.fa-arrows-up-down::before {
+  content: "\f07d"; }
+
+.fa-arrows-v::before {
+  content: "\f07d"; }
+
+.fa-face-grimace::before {
+  content: "\f57f"; }
+
+.fa-grimace::before {
+  content: "\f57f"; }
+
+.fa-wheelchair-move::before {
+  content: "\e2ce"; }
+
+.fa-wheelchair-alt::before {
+  content: "\e2ce"; }
+
+.fa-turn-down::before {
+  content: "\f3be"; }
+
+.fa-level-down-alt::before {
+  content: "\f3be"; }
+
+.fa-person-walking-arrow-right::before {
+  content: "\e552"; }
+
+.fa-square-envelope::before {
+  content: "\f199"; }
+
+.fa-envelope-square::before {
+  content: "\f199"; }
+
+.fa-dice::before {
+  content: "\f522"; }
+
+.fa-bowling-ball::before {
+  content: "\f436"; }
+
+.fa-brain::before {
+  content: "\f5dc"; }
+
+.fa-bandage::before {
+  content: "\f462"; }
+
+.fa-band-aid::before {
+  content: "\f462"; }
+
+.fa-calendar-minus::before {
+  content: "\f272"; }
+
+.fa-circle-xmark::before {
+  content: "\f057"; }
+
+.fa-times-circle::before {
+  content: "\f057"; }
+
+.fa-xmark-circle::before {
+  content: "\f057"; }
+
+.fa-gifts::before {
+  content: "\f79c"; }
+
+.fa-hotel::before {
+  content: "\f594"; }
+
+.fa-earth-asia::before {
+  content: "\f57e"; }
+
+.fa-globe-asia::before {
+  content: "\f57e"; }
+
+.fa-id-card-clip::before {
+  content: "\f47f"; }
+
+.fa-id-card-alt::before {
+  content: "\f47f"; }
+
+.fa-magnifying-glass-plus::before {
+  content: "\f00e"; }
+
+.fa-search-plus::before {
+  content: "\f00e"; }
+
+.fa-thumbs-up::before {
+  content: "\f164"; }
+
+.fa-user-clock::before {
+  content: "\f4fd"; }
+
+.fa-hand-dots::before {
+  content: "\f461"; }
+
+.fa-allergies::before {
+  content: "\f461"; }
+
+.fa-file-invoice::before {
+  content: "\f570"; }
+
+.fa-window-minimize::before {
+  content: "\f2d1"; }
+
+.fa-mug-saucer::before {
+  content: "\f0f4"; }
+
+.fa-coffee::before {
+  content: "\f0f4"; }
+
+.fa-brush::before {
+  content: "\f55d"; }
+
+.fa-mask::before {
+  content: "\f6fa"; }
+
+.fa-magnifying-glass-minus::before {
+  content: "\f010"; }
+
+.fa-search-minus::before {
+  content: "\f010"; }
+
+.fa-ruler-vertical::before {
+  content: "\f548"; }
+
+.fa-user-large::before {
+  content: "\f406"; }
+
+.fa-user-alt::before {
+  content: "\f406"; }
+
+.fa-train-tram::before {
+  content: "\e5b4"; }
+
+.fa-user-nurse::before {
+  content: "\f82f"; }
+
+.fa-syringe::before {
+  content: "\f48e"; }
+
+.fa-cloud-sun::before {
+  content: "\f6c4"; }
+
+.fa-stopwatch-20::before {
+  content: "\e06f"; }
+
+.fa-square-full::before {
+  content: "\f45c"; }
+
+.fa-magnet::before {
+  content: "\f076"; }
+
+.fa-jar::before {
+  content: "\e516"; }
+
+.fa-note-sticky::before {
+  content: "\f249"; }
+
+.fa-sticky-note::before {
+  content: "\f249"; }
+
+.fa-bug-slash::before {
+  content: "\e490"; }
+
+.fa-arrow-up-from-water-pump::before {
+  content: "\e4b6"; }
+
+.fa-bone::before {
+  content: "\f5d7"; }
+
+.fa-user-injured::before {
+  content: "\f728"; }
+
+.fa-face-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-plane::before {
+  content: "\f072"; }
+
+.fa-tent-arrows-down::before {
+  content: "\e581"; }
+
+.fa-exclamation::before {
+  content: "\21"; }
+
+.fa-arrows-spin::before {
+  content: "\e4bb"; }
+
+.fa-print::before {
+  content: "\f02f"; }
+
+.fa-turkish-lira-sign::before {
+  content: "\e2bb"; }
+
+.fa-try::before {
+  content: "\e2bb"; }
+
+.fa-turkish-lira::before {
+  content: "\e2bb"; }
+
+.fa-dollar-sign::before {
+  content: "\24"; }
+
+.fa-dollar::before {
+  content: "\24"; }
+
+.fa-usd::before {
+  content: "\24"; }
+
+.fa-x::before {
+  content: "\58"; }
+
+.fa-magnifying-glass-dollar::before {
+  content: "\f688"; }
+
+.fa-search-dollar::before {
+  content: "\f688"; }
+
+.fa-users-gear::before {
+  content: "\f509"; }
+
+.fa-users-cog::before {
+  content: "\f509"; }
+
+.fa-person-military-pointing::before {
+  content: "\e54a"; }
+
+.fa-building-columns::before {
+  content: "\f19c"; }
+
+.fa-bank::before {
+  content: "\f19c"; }
+
+.fa-institution::before {
+  content: "\f19c"; }
+
+.fa-museum::before {
+  content: "\f19c"; }
+
+.fa-university::before {
+  content: "\f19c"; }
+
+.fa-umbrella::before {
+  content: "\f0e9"; }
+
+.fa-trowel::before {
+  content: "\e589"; }
+
+.fa-d::before {
+  content: "\44"; }
+
+.fa-stapler::before {
+  content: "\e5af"; }
+
+.fa-masks-theater::before {
+  content: "\f630"; }
+
+.fa-theater-masks::before {
+  content: "\f630"; }
+
+.fa-kip-sign::before {
+  content: "\e1c4"; }
+
+.fa-hand-point-left::before {
+  content: "\f0a5"; }
+
+.fa-handshake-simple::before {
+  content: "\f4c6"; }
+
+.fa-handshake-alt::before {
+  content: "\f4c6"; }
+
+.fa-jet-fighter::before {
+  content: "\f0fb"; }
+
+.fa-fighter-jet::before {
+  content: "\f0fb"; }
+
+.fa-square-share-nodes::before {
+  content: "\f1e1"; }
+
+.fa-share-alt-square::before {
+  content: "\f1e1"; }
+
+.fa-barcode::before {
+  content: "\f02a"; }
+
+.fa-plus-minus::before {
+  content: "\e43c"; }
+
+.fa-video::before {
+  content: "\f03d"; }
+
+.fa-video-camera::before {
+  content: "\f03d"; }
+
+.fa-graduation-cap::before {
+  content: "\f19d"; }
+
+.fa-mortar-board::before {
+  content: "\f19d"; }
+
+.fa-hand-holding-medical::before {
+  content: "\e05c"; }
+
+.fa-person-circle-check::before {
+  content: "\e53e"; }
+
+.fa-turn-up::before {
+  content: "\f3bf"; }
+
+.fa-level-up-alt::before {
+  content: "\f3bf"; }
+
+.sr-only,
+.fa-sr-only {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+
+.sr-only-focusable:not(:focus),
+.fa-sr-only-focusable:not(:focus) {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+:root, :host {
+  --fa-style-family-brands: 'Font Awesome 6 Brands';
+  --fa-font-brands: normal 400 1em/1 'Font Awesome 6 Brands'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Brands';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+.fab,
+.fa-brands {
+  font-weight: 400; }
+
+.fa-monero:before {
+  content: "\f3d0"; }
+
+.fa-hooli:before {
+  content: "\f427"; }
+
+.fa-yelp:before {
+  content: "\f1e9"; }
+
+.fa-cc-visa:before {
+  content: "\f1f0"; }
+
+.fa-lastfm:before {
+  content: "\f202"; }
+
+.fa-shopware:before {
+  content: "\f5b5"; }
+
+.fa-creative-commons-nc:before {
+  content: "\f4e8"; }
+
+.fa-aws:before {
+  content: "\f375"; }
+
+.fa-redhat:before {
+  content: "\f7bc"; }
+
+.fa-yoast:before {
+  content: "\f2b1"; }
+
+.fa-cloudflare:before {
+  content: "\e07d"; }
+
+.fa-ups:before {
+  content: "\f7e0"; }
+
+.fa-wpexplorer:before {
+  content: "\f2de"; }
+
+.fa-dyalog:before {
+  content: "\f399"; }
+
+.fa-bity:before {
+  content: "\f37a"; }
+
+.fa-stackpath:before {
+  content: "\f842"; }
+
+.fa-buysellads:before {
+  content: "\f20d"; }
+
+.fa-first-order:before {
+  content: "\f2b0"; }
+
+.fa-modx:before {
+  content: "\f285"; }
+
+.fa-guilded:before {
+  content: "\e07e"; }
+
+.fa-vnv:before {
+  content: "\f40b"; }
+
+.fa-square-js:before {
+  content: "\f3b9"; }
+
+.fa-js-square:before {
+  content: "\f3b9"; }
+
+.fa-microsoft:before {
+  content: "\f3ca"; }
+
+.fa-qq:before {
+  content: "\f1d6"; }
+
+.fa-orcid:before {
+  content: "\f8d2"; }
+
+.fa-java:before {
+  content: "\f4e4"; }
+
+.fa-invision:before {
+  content: "\f7b0"; }
+
+.fa-creative-commons-pd-alt:before {
+  content: "\f4ed"; }
+
+.fa-centercode:before {
+  content: "\f380"; }
+
+.fa-glide-g:before {
+  content: "\f2a6"; }
+
+.fa-drupal:before {
+  content: "\f1a9"; }
+
+.fa-hire-a-helper:before {
+  content: "\f3b0"; }
+
+.fa-creative-commons-by:before {
+  content: "\f4e7"; }
+
+.fa-unity:before {
+  content: "\e049"; }
+
+.fa-whmcs:before {
+  content: "\f40d"; }
+
+.fa-rocketchat:before {
+  content: "\f3e8"; }
+
+.fa-vk:before {
+  content: "\f189"; }
+
+.fa-untappd:before {
+  content: "\f405"; }
+
+.fa-mailchimp:before {
+  content: "\f59e"; }
+
+.fa-css3-alt:before {
+  content: "\f38b"; }
+
+.fa-square-reddit:before {
+  content: "\f1a2"; }
+
+.fa-reddit-square:before {
+  content: "\f1a2"; }
+
+.fa-vimeo-v:before {
+  content: "\f27d"; }
+
+.fa-contao:before {
+  content: "\f26d"; }
+
+.fa-square-font-awesome:before {
+  content: "\e5ad"; }
+
+.fa-deskpro:before {
+  content: "\f38f"; }
+
+.fa-sistrix:before {
+  content: "\f3ee"; }
+
+.fa-square-instagram:before {
+  content: "\e055"; }
+
+.fa-instagram-square:before {
+  content: "\e055"; }
+
+.fa-battle-net:before {
+  content: "\f835"; }
+
+.fa-the-red-yeti:before {
+  content: "\f69d"; }
+
+.fa-square-hacker-news:before {
+  content: "\f3af"; }
+
+.fa-hacker-news-square:before {
+  content: "\f3af"; }
+
+.fa-edge:before {
+  content: "\f282"; }
+
+.fa-threads:before {
+  content: "\e618"; }
+
+.fa-napster:before {
+  content: "\f3d2"; }
+
+.fa-square-snapchat:before {
+  content: "\f2ad"; }
+
+.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa-google-plus-g:before {
+  content: "\f0d5"; }
+
+.fa-artstation:before {
+  content: "\f77a"; }
+
+.fa-markdown:before {
+  content: "\f60f"; }
+
+.fa-sourcetree:before {
+  content: "\f7d3"; }
+
+.fa-google-plus:before {
+  content: "\f2b3"; }
+
+.fa-diaspora:before {
+  content: "\f791"; }
+
+.fa-foursquare:before {
+  content: "\f180"; }
+
+.fa-stack-overflow:before {
+  content: "\f16c"; }
+
+.fa-github-alt:before {
+  content: "\f113"; }
+
+.fa-phoenix-squadron:before {
+  content: "\f511"; }
+
+.fa-pagelines:before {
+  content: "\f18c"; }
+
+.fa-algolia:before {
+  content: "\f36c"; }
+
+.fa-red-river:before {
+  content: "\f3e3"; }
+
+.fa-creative-commons-sa:before {
+  content: "\f4ef"; }
+
+.fa-safari:before {
+  content: "\f267"; }
+
+.fa-google:before {
+  content: "\f1a0"; }
+
+.fa-square-font-awesome-stroke:before {
+  content: "\f35c"; }
+
+.fa-font-awesome-alt:before {
+  content: "\f35c"; }
+
+.fa-atlassian:before {
+  content: "\f77b"; }
+
+.fa-linkedin-in:before {
+  content: "\f0e1"; }
+
+.fa-digital-ocean:before {
+  content: "\f391"; }
+
+.fa-nimblr:before {
+  content: "\f5a8"; }
+
+.fa-chromecast:before {
+  content: "\f838"; }
+
+.fa-evernote:before {
+  content: "\f839"; }
+
+.fa-hacker-news:before {
+  content: "\f1d4"; }
+
+.fa-creative-commons-sampling:before {
+  content: "\f4f0"; }
+
+.fa-adversal:before {
+  content: "\f36a"; }
+
+.fa-creative-commons:before {
+  content: "\f25e"; }
+
+.fa-watchman-monitoring:before {
+  content: "\e087"; }
+
+.fa-fonticons:before {
+  content: "\f280"; }
+
+.fa-weixin:before {
+  content: "\f1d7"; }
+
+.fa-shirtsinbulk:before {
+  content: "\f214"; }
+
+.fa-codepen:before {
+  content: "\f1cb"; }
+
+.fa-git-alt:before {
+  content: "\f841"; }
+
+.fa-lyft:before {
+  content: "\f3c3"; }
+
+.fa-rev:before {
+  content: "\f5b2"; }
+
+.fa-windows:before {
+  content: "\f17a"; }
+
+.fa-wizards-of-the-coast:before {
+  content: "\f730"; }
+
+.fa-square-viadeo:before {
+  content: "\f2aa"; }
+
+.fa-viadeo-square:before {
+  content: "\f2aa"; }
+
+.fa-meetup:before {
+  content: "\f2e0"; }
+
+.fa-centos:before {
+  content: "\f789"; }
+
+.fa-adn:before {
+  content: "\f170"; }
+
+.fa-cloudsmith:before {
+  content: "\f384"; }
+
+.fa-pied-piper-alt:before {
+  content: "\f1a8"; }
+
+.fa-square-dribbble:before {
+  content: "\f397"; }
+
+.fa-dribbble-square:before {
+  content: "\f397"; }
+
+.fa-codiepie:before {
+  content: "\f284"; }
+
+.fa-node:before {
+  content: "\f419"; }
+
+.fa-mix:before {
+  content: "\f3cb"; }
+
+.fa-steam:before {
+  content: "\f1b6"; }
+
+.fa-cc-apple-pay:before {
+  content: "\f416"; }
+
+.fa-scribd:before {
+  content: "\f28a"; }
+
+.fa-debian:before {
+  content: "\e60b"; }
+
+.fa-openid:before {
+  content: "\f19b"; }
+
+.fa-instalod:before {
+  content: "\e081"; }
+
+.fa-expeditedssl:before {
+  content: "\f23e"; }
+
+.fa-sellcast:before {
+  content: "\f2da"; }
+
+.fa-square-twitter:before {
+  content: "\f081"; }
+
+.fa-twitter-square:before {
+  content: "\f081"; }
+
+.fa-r-project:before {
+  content: "\f4f7"; }
+
+.fa-delicious:before {
+  content: "\f1a5"; }
+
+.fa-freebsd:before {
+  content: "\f3a4"; }
+
+.fa-vuejs:before {
+  content: "\f41f"; }
+
+.fa-accusoft:before {
+  content: "\f369"; }
+
+.fa-ioxhost:before {
+  content: "\f208"; }
+
+.fa-fonticons-fi:before {
+  content: "\f3a2"; }
+
+.fa-app-store:before {
+  content: "\f36f"; }
+
+.fa-cc-mastercard:before {
+  content: "\f1f1"; }
+
+.fa-itunes-note:before {
+  content: "\f3b5"; }
+
+.fa-golang:before {
+  content: "\e40f"; }
+
+.fa-kickstarter:before {
+  content: "\f3bb"; }
+
+.fa-grav:before {
+  content: "\f2d6"; }
+
+.fa-weibo:before {
+  content: "\f18a"; }
+
+.fa-uncharted:before {
+  content: "\e084"; }
+
+.fa-firstdraft:before {
+  content: "\f3a1"; }
+
+.fa-square-youtube:before {
+  content: "\f431"; }
+
+.fa-youtube-square:before {
+  content: "\f431"; }
+
+.fa-wikipedia-w:before {
+  content: "\f266"; }
+
+.fa-wpressr:before {
+  content: "\f3e4"; }
+
+.fa-rendact:before {
+  content: "\f3e4"; }
+
+.fa-angellist:before {
+  content: "\f209"; }
+
+.fa-galactic-republic:before {
+  content: "\f50c"; }
+
+.fa-nfc-directional:before {
+  content: "\e530"; }
+
+.fa-skype:before {
+  content: "\f17e"; }
+
+.fa-joget:before {
+  content: "\f3b7"; }
+
+.fa-fedora:before {
+  content: "\f798"; }
+
+.fa-stripe-s:before {
+  content: "\f42a"; }
+
+.fa-meta:before {
+  content: "\e49b"; }
+
+.fa-laravel:before {
+  content: "\f3bd"; }
+
+.fa-hotjar:before {
+  content: "\f3b1"; }
+
+.fa-bluetooth-b:before {
+  content: "\f294"; }
+
+.fa-sticker-mule:before {
+  content: "\f3f7"; }
+
+.fa-creative-commons-zero:before {
+  content: "\f4f3"; }
+
+.fa-hips:before {
+  content: "\f452"; }
+
+.fa-behance:before {
+  content: "\f1b4"; }
+
+.fa-reddit:before {
+  content: "\f1a1"; }
+
+.fa-discord:before {
+  content: "\f392"; }
+
+.fa-chrome:before {
+  content: "\f268"; }
+
+.fa-app-store-ios:before {
+  content: "\f370"; }
+
+.fa-cc-discover:before {
+  content: "\f1f2"; }
+
+.fa-wpbeginner:before {
+  content: "\f297"; }
+
+.fa-confluence:before {
+  content: "\f78d"; }
+
+.fa-mdb:before {
+  content: "\f8ca"; }
+
+.fa-dochub:before {
+  content: "\f394"; }
+
+.fa-accessible-icon:before {
+  content: "\f368"; }
+
+.fa-ebay:before {
+  content: "\f4f4"; }
+
+.fa-amazon:before {
+  content: "\f270"; }
+
+.fa-unsplash:before {
+  content: "\e07c"; }
+
+.fa-yarn:before {
+  content: "\f7e3"; }
+
+.fa-square-steam:before {
+  content: "\f1b7"; }
+
+.fa-steam-square:before {
+  content: "\f1b7"; }
+
+.fa-500px:before {
+  content: "\f26e"; }
+
+.fa-square-vimeo:before {
+  content: "\f194"; }
+
+.fa-vimeo-square:before {
+  content: "\f194"; }
+
+.fa-asymmetrik:before {
+  content: "\f372"; }
+
+.fa-font-awesome:before {
+  content: "\f2b4"; }
+
+.fa-font-awesome-flag:before {
+  content: "\f2b4"; }
+
+.fa-font-awesome-logo-full:before {
+  content: "\f2b4"; }
+
+.fa-gratipay:before {
+  content: "\f184"; }
+
+.fa-apple:before {
+  content: "\f179"; }
+
+.fa-hive:before {
+  content: "\e07f"; }
+
+.fa-gitkraken:before {
+  content: "\f3a6"; }
+
+.fa-keybase:before {
+  content: "\f4f5"; }
+
+.fa-apple-pay:before {
+  content: "\f415"; }
+
+.fa-padlet:before {
+  content: "\e4a0"; }
+
+.fa-amazon-pay:before {
+  content: "\f42c"; }
+
+.fa-square-github:before {
+  content: "\f092"; }
+
+.fa-github-square:before {
+  content: "\f092"; }
+
+.fa-stumbleupon:before {
+  content: "\f1a4"; }
+
+.fa-fedex:before {
+  content: "\f797"; }
+
+.fa-phoenix-framework:before {
+  content: "\f3dc"; }
+
+.fa-shopify:before {
+  content: "\e057"; }
+
+.fa-neos:before {
+  content: "\f612"; }
+
+.fa-square-threads:before {
+  content: "\e619"; }
+
+.fa-hackerrank:before {
+  content: "\f5f7"; }
+
+.fa-researchgate:before {
+  content: "\f4f8"; }
+
+.fa-swift:before {
+  content: "\f8e1"; }
+
+.fa-angular:before {
+  content: "\f420"; }
+
+.fa-speakap:before {
+  content: "\f3f3"; }
+
+.fa-angrycreative:before {
+  content: "\f36e"; }
+
+.fa-y-combinator:before {
+  content: "\f23b"; }
+
+.fa-empire:before {
+  content: "\f1d1"; }
+
+.fa-envira:before {
+  content: "\f299"; }
+
+.fa-square-gitlab:before {
+  content: "\e5ae"; }
+
+.fa-gitlab-square:before {
+  content: "\e5ae"; }
+
+.fa-studiovinari:before {
+  content: "\f3f8"; }
+
+.fa-pied-piper:before {
+  content: "\f2ae"; }
+
+.fa-wordpress:before {
+  content: "\f19a"; }
+
+.fa-product-hunt:before {
+  content: "\f288"; }
+
+.fa-firefox:before {
+  content: "\f269"; }
+
+.fa-linode:before {
+  content: "\f2b8"; }
+
+.fa-goodreads:before {
+  content: "\f3a8"; }
+
+.fa-square-odnoklassniki:before {
+  content: "\f264"; }
+
+.fa-odnoklassniki-square:before {
+  content: "\f264"; }
+
+.fa-jsfiddle:before {
+  content: "\f1cc"; }
+
+.fa-sith:before {
+  content: "\f512"; }
+
+.fa-themeisle:before {
+  content: "\f2b2"; }
+
+.fa-page4:before {
+  content: "\f3d7"; }
+
+.fa-hashnode:before {
+  content: "\e499"; }
+
+.fa-react:before {
+  content: "\f41b"; }
+
+.fa-cc-paypal:before {
+  content: "\f1f4"; }
+
+.fa-squarespace:before {
+  content: "\f5be"; }
+
+.fa-cc-stripe:before {
+  content: "\f1f5"; }
+
+.fa-creative-commons-share:before {
+  content: "\f4f2"; }
+
+.fa-bitcoin:before {
+  content: "\f379"; }
+
+.fa-keycdn:before {
+  content: "\f3ba"; }
+
+.fa-opera:before {
+  content: "\f26a"; }
+
+.fa-itch-io:before {
+  content: "\f83a"; }
+
+.fa-umbraco:before {
+  content: "\f8e8"; }
+
+.fa-galactic-senate:before {
+  content: "\f50d"; }
+
+.fa-ubuntu:before {
+  content: "\f7df"; }
+
+.fa-draft2digital:before {
+  content: "\f396"; }
+
+.fa-stripe:before {
+  content: "\f429"; }
+
+.fa-houzz:before {
+  content: "\f27c"; }
+
+.fa-gg:before {
+  content: "\f260"; }
+
+.fa-dhl:before {
+  content: "\f790"; }
+
+.fa-square-pinterest:before {
+  content: "\f0d3"; }
+
+.fa-pinterest-square:before {
+  content: "\f0d3"; }
+
+.fa-xing:before {
+  content: "\f168"; }
+
+.fa-blackberry:before {
+  content: "\f37b"; }
+
+.fa-creative-commons-pd:before {
+  content: "\f4ec"; }
+
+.fa-playstation:before {
+  content: "\f3df"; }
+
+.fa-quinscape:before {
+  content: "\f459"; }
+
+.fa-less:before {
+  content: "\f41d"; }
+
+.fa-blogger-b:before {
+  content: "\f37d"; }
+
+.fa-opencart:before {
+  content: "\f23d"; }
+
+.fa-vine:before {
+  content: "\f1ca"; }
+
+.fa-paypal:before {
+  content: "\f1ed"; }
+
+.fa-gitlab:before {
+  content: "\f296"; }
+
+.fa-typo3:before {
+  content: "\f42b"; }
+
+.fa-reddit-alien:before {
+  content: "\f281"; }
+
+.fa-yahoo:before {
+  content: "\f19e"; }
+
+.fa-dailymotion:before {
+  content: "\e052"; }
+
+.fa-affiliatetheme:before {
+  content: "\f36b"; }
+
+.fa-pied-piper-pp:before {
+  content: "\f1a7"; }
+
+.fa-bootstrap:before {
+  content: "\f836"; }
+
+.fa-odnoklassniki:before {
+  content: "\f263"; }
+
+.fa-nfc-symbol:before {
+  content: "\e531"; }
+
+.fa-ethereum:before {
+  content: "\f42e"; }
+
+.fa-speaker-deck:before {
+  content: "\f83c"; }
+
+.fa-creative-commons-nc-eu:before {
+  content: "\f4e9"; }
+
+.fa-patreon:before {
+  content: "\f3d9"; }
+
+.fa-avianex:before {
+  content: "\f374"; }
+
+.fa-ello:before {
+  content: "\f5f1"; }
+
+.fa-gofore:before {
+  content: "\f3a7"; }
+
+.fa-bimobject:before {
+  content: "\f378"; }
+
+.fa-facebook-f:before {
+  content: "\f39e"; }
+
+.fa-square-google-plus:before {
+  content: "\f0d4"; }
+
+.fa-google-plus-square:before {
+  content: "\f0d4"; }
+
+.fa-mandalorian:before {
+  content: "\f50f"; }
+
+.fa-first-order-alt:before {
+  content: "\f50a"; }
+
+.fa-osi:before {
+  content: "\f41a"; }
+
+.fa-google-wallet:before {
+  content: "\f1ee"; }
+
+.fa-d-and-d-beyond:before {
+  content: "\f6ca"; }
+
+.fa-periscope:before {
+  content: "\f3da"; }
+
+.fa-fulcrum:before {
+  content: "\f50b"; }
+
+.fa-cloudscale:before {
+  content: "\f383"; }
+
+.fa-forumbee:before {
+  content: "\f211"; }
+
+.fa-mizuni:before {
+  content: "\f3cc"; }
+
+.fa-schlix:before {
+  content: "\f3ea"; }
+
+.fa-square-xing:before {
+  content: "\f169"; }
+
+.fa-xing-square:before {
+  content: "\f169"; }
+
+.fa-bandcamp:before {
+  content: "\f2d5"; }
+
+.fa-wpforms:before {
+  content: "\f298"; }
+
+.fa-cloudversify:before {
+  content: "\f385"; }
+
+.fa-usps:before {
+  content: "\f7e1"; }
+
+.fa-megaport:before {
+  content: "\f5a3"; }
+
+.fa-magento:before {
+  content: "\f3c4"; }
+
+.fa-spotify:before {
+  content: "\f1bc"; }
+
+.fa-optin-monster:before {
+  content: "\f23c"; }
+
+.fa-fly:before {
+  content: "\f417"; }
+
+.fa-aviato:before {
+  content: "\f421"; }
+
+.fa-itunes:before {
+  content: "\f3b4"; }
+
+.fa-cuttlefish:before {
+  content: "\f38c"; }
+
+.fa-blogger:before {
+  content: "\f37c"; }
+
+.fa-flickr:before {
+  content: "\f16e"; }
+
+.fa-viber:before {
+  content: "\f409"; }
+
+.fa-soundcloud:before {
+  content: "\f1be"; }
+
+.fa-digg:before {
+  content: "\f1a6"; }
+
+.fa-tencent-weibo:before {
+  content: "\f1d5"; }
+
+.fa-symfony:before {
+  content: "\f83d"; }
+
+.fa-maxcdn:before {
+  content: "\f136"; }
+
+.fa-etsy:before {
+  content: "\f2d7"; }
+
+.fa-facebook-messenger:before {
+  content: "\f39f"; }
+
+.fa-audible:before {
+  content: "\f373"; }
+
+.fa-think-peaks:before {
+  content: "\f731"; }
+
+.fa-bilibili:before {
+  content: "\e3d9"; }
+
+.fa-erlang:before {
+  content: "\f39d"; }
+
+.fa-x-twitter:before {
+  content: "\e61b"; }
+
+.fa-cotton-bureau:before {
+  content: "\f89e"; }
+
+.fa-dashcube:before {
+  content: "\f210"; }
+
+.fa-42-group:before {
+  content: "\e080"; }
+
+.fa-innosoft:before {
+  content: "\e080"; }
+
+.fa-stack-exchange:before {
+  content: "\f18d"; }
+
+.fa-elementor:before {
+  content: "\f430"; }
+
+.fa-square-pied-piper:before {
+  content: "\e01e"; }
+
+.fa-pied-piper-square:before {
+  content: "\e01e"; }
+
+.fa-creative-commons-nd:before {
+  content: "\f4eb"; }
+
+.fa-palfed:before {
+  content: "\f3d8"; }
+
+.fa-superpowers:before {
+  content: "\f2dd"; }
+
+.fa-resolving:before {
+  content: "\f3e7"; }
+
+.fa-xbox:before {
+  content: "\f412"; }
+
+.fa-searchengin:before {
+  content: "\f3eb"; }
+
+.fa-tiktok:before {
+  content: "\e07b"; }
+
+.fa-square-facebook:before {
+  content: "\f082"; }
+
+.fa-facebook-square:before {
+  content: "\f082"; }
+
+.fa-renren:before {
+  content: "\f18b"; }
+
+.fa-linux:before {
+  content: "\f17c"; }
+
+.fa-glide:before {
+  content: "\f2a5"; }
+
+.fa-linkedin:before {
+  content: "\f08c"; }
+
+.fa-hubspot:before {
+  content: "\f3b2"; }
+
+.fa-deploydog:before {
+  content: "\f38e"; }
+
+.fa-twitch:before {
+  content: "\f1e8"; }
+
+.fa-ravelry:before {
+  content: "\f2d9"; }
+
+.fa-mixer:before {
+  content: "\e056"; }
+
+.fa-square-lastfm:before {
+  content: "\f203"; }
+
+.fa-lastfm-square:before {
+  content: "\f203"; }
+
+.fa-vimeo:before {
+  content: "\f40a"; }
+
+.fa-mendeley:before {
+  content: "\f7b3"; }
+
+.fa-uniregistry:before {
+  content: "\f404"; }
+
+.fa-figma:before {
+  content: "\f799"; }
+
+.fa-creative-commons-remix:before {
+  content: "\f4ee"; }
+
+.fa-cc-amazon-pay:before {
+  content: "\f42d"; }
+
+.fa-dropbox:before {
+  content: "\f16b"; }
+
+.fa-instagram:before {
+  content: "\f16d"; }
+
+.fa-cmplid:before {
+  content: "\e360"; }
+
+.fa-facebook:before {
+  content: "\f09a"; }
+
+.fa-gripfire:before {
+  content: "\f3ac"; }
+
+.fa-jedi-order:before {
+  content: "\f50e"; }
+
+.fa-uikit:before {
+  content: "\f403"; }
+
+.fa-fort-awesome-alt:before {
+  content: "\f3a3"; }
+
+.fa-phabricator:before {
+  content: "\f3db"; }
+
+.fa-ussunnah:before {
+  content: "\f407"; }
+
+.fa-earlybirds:before {
+  content: "\f39a"; }
+
+.fa-trade-federation:before {
+  content: "\f513"; }
+
+.fa-autoprefixer:before {
+  content: "\f41c"; }
+
+.fa-whatsapp:before {
+  content: "\f232"; }
+
+.fa-slideshare:before {
+  content: "\f1e7"; }
+
+.fa-google-play:before {
+  content: "\f3ab"; }
+
+.fa-viadeo:before {
+  content: "\f2a9"; }
+
+.fa-line:before {
+  content: "\f3c0"; }
+
+.fa-google-drive:before {
+  content: "\f3aa"; }
+
+.fa-servicestack:before {
+  content: "\f3ec"; }
+
+.fa-simplybuilt:before {
+  content: "\f215"; }
+
+.fa-bitbucket:before {
+  content: "\f171"; }
+
+.fa-imdb:before {
+  content: "\f2d8"; }
+
+.fa-deezer:before {
+  content: "\e077"; }
+
+.fa-raspberry-pi:before {
+  content: "\f7bb"; }
+
+.fa-jira:before {
+  content: "\f7b1"; }
+
+.fa-docker:before {
+  content: "\f395"; }
+
+.fa-screenpal:before {
+  content: "\e570"; }
+
+.fa-bluetooth:before {
+  content: "\f293"; }
+
+.fa-gitter:before {
+  content: "\f426"; }
+
+.fa-d-and-d:before {
+  content: "\f38d"; }
+
+.fa-microblog:before {
+  content: "\e01a"; }
+
+.fa-cc-diners-club:before {
+  content: "\f24c"; }
+
+.fa-gg-circle:before {
+  content: "\f261"; }
+
+.fa-pied-piper-hat:before {
+  content: "\f4e5"; }
+
+.fa-kickstarter-k:before {
+  content: "\f3bc"; }
+
+.fa-yandex:before {
+  content: "\f413"; }
+
+.fa-readme:before {
+  content: "\f4d5"; }
+
+.fa-html5:before {
+  content: "\f13b"; }
+
+.fa-sellsy:before {
+  content: "\f213"; }
+
+.fa-sass:before {
+  content: "\f41e"; }
+
+.fa-wirsindhandwerk:before {
+  content: "\e2d0"; }
+
+.fa-wsh:before {
+  content: "\e2d0"; }
+
+.fa-buromobelexperte:before {
+  content: "\f37f"; }
+
+.fa-salesforce:before {
+  content: "\f83b"; }
+
+.fa-octopus-deploy:before {
+  content: "\e082"; }
+
+.fa-medapps:before {
+  content: "\f3c6"; }
+
+.fa-ns8:before {
+  content: "\f3d5"; }
+
+.fa-pinterest-p:before {
+  content: "\f231"; }
+
+.fa-apper:before {
+  content: "\f371"; }
+
+.fa-fort-awesome:before {
+  content: "\f286"; }
+
+.fa-waze:before {
+  content: "\f83f"; }
+
+.fa-cc-jcb:before {
+  content: "\f24b"; }
+
+.fa-snapchat:before {
+  content: "\f2ab"; }
+
+.fa-snapchat-ghost:before {
+  content: "\f2ab"; }
+
+.fa-fantasy-flight-games:before {
+  content: "\f6dc"; }
+
+.fa-rust:before {
+  content: "\e07a"; }
+
+.fa-wix:before {
+  content: "\f5cf"; }
+
+.fa-square-behance:before {
+  content: "\f1b5"; }
+
+.fa-behance-square:before {
+  content: "\f1b5"; }
+
+.fa-supple:before {
+  content: "\f3f9"; }
+
+.fa-rebel:before {
+  content: "\f1d0"; }
+
+.fa-css3:before {
+  content: "\f13c"; }
+
+.fa-staylinked:before {
+  content: "\f3f5"; }
+
+.fa-kaggle:before {
+  content: "\f5fa"; }
+
+.fa-space-awesome:before {
+  content: "\e5ac"; }
+
+.fa-deviantart:before {
+  content: "\f1bd"; }
+
+.fa-cpanel:before {
+  content: "\f388"; }
+
+.fa-goodreads-g:before {
+  content: "\f3a9"; }
+
+.fa-square-git:before {
+  content: "\f1d2"; }
+
+.fa-git-square:before {
+  content: "\f1d2"; }
+
+.fa-square-tumblr:before {
+  content: "\f174"; }
+
+.fa-tumblr-square:before {
+  content: "\f174"; }
+
+.fa-trello:before {
+  content: "\f181"; }
+
+.fa-creative-commons-nc-jp:before {
+  content: "\f4ea"; }
+
+.fa-get-pocket:before {
+  content: "\f265"; }
+
+.fa-perbyte:before {
+  content: "\e083"; }
+
+.fa-grunt:before {
+  content: "\f3ad"; }
+
+.fa-weebly:before {
+  content: "\f5cc"; }
+
+.fa-connectdevelop:before {
+  content: "\f20e"; }
+
+.fa-leanpub:before {
+  content: "\f212"; }
+
+.fa-black-tie:before {
+  content: "\f27e"; }
+
+.fa-themeco:before {
+  content: "\f5c6"; }
+
+.fa-python:before {
+  content: "\f3e2"; }
+
+.fa-android:before {
+  content: "\f17b"; }
+
+.fa-bots:before {
+  content: "\e340"; }
+
+.fa-free-code-camp:before {
+  content: "\f2c5"; }
+
+.fa-hornbill:before {
+  content: "\f592"; }
+
+.fa-js:before {
+  content: "\f3b8"; }
+
+.fa-ideal:before {
+  content: "\e013"; }
+
+.fa-git:before {
+  content: "\f1d3"; }
+
+.fa-dev:before {
+  content: "\f6cc"; }
+
+.fa-sketch:before {
+  content: "\f7c6"; }
+
+.fa-yandex-international:before {
+  content: "\f414"; }
+
+.fa-cc-amex:before {
+  content: "\f1f3"; }
+
+.fa-uber:before {
+  content: "\f402"; }
+
+.fa-github:before {
+  content: "\f09b"; }
+
+.fa-php:before {
+  content: "\f457"; }
+
+.fa-alipay:before {
+  content: "\f642"; }
+
+.fa-youtube:before {
+  content: "\f167"; }
+
+.fa-skyatlas:before {
+  content: "\f216"; }
+
+.fa-firefox-browser:before {
+  content: "\e007"; }
+
+.fa-replyd:before {
+  content: "\f3e6"; }
+
+.fa-suse:before {
+  content: "\f7d6"; }
+
+.fa-jenkins:before {
+  content: "\f3b6"; }
+
+.fa-twitter:before {
+  content: "\f099"; }
+
+.fa-rockrms:before {
+  content: "\f3e9"; }
+
+.fa-pinterest:before {
+  content: "\f0d2"; }
+
+.fa-buffer:before {
+  content: "\f837"; }
+
+.fa-npm:before {
+  content: "\f3d4"; }
+
+.fa-yammer:before {
+  content: "\f840"; }
+
+.fa-btc:before {
+  content: "\f15a"; }
+
+.fa-dribbble:before {
+  content: "\f17d"; }
+
+.fa-stumbleupon-circle:before {
+  content: "\f1a3"; }
+
+.fa-internet-explorer:before {
+  content: "\f26b"; }
+
+.fa-stubber:before {
+  content: "\e5c7"; }
+
+.fa-telegram:before {
+  content: "\f2c6"; }
+
+.fa-telegram-plane:before {
+  content: "\f2c6"; }
+
+.fa-old-republic:before {
+  content: "\f510"; }
+
+.fa-odysee:before {
+  content: "\e5c6"; }
+
+.fa-square-whatsapp:before {
+  content: "\f40c"; }
+
+.fa-whatsapp-square:before {
+  content: "\f40c"; }
+
+.fa-node-js:before {
+  content: "\f3d3"; }
+
+.fa-edge-legacy:before {
+  content: "\e078"; }
+
+.fa-slack:before {
+  content: "\f198"; }
+
+.fa-slack-hash:before {
+  content: "\f198"; }
+
+.fa-medrt:before {
+  content: "\f3c8"; }
+
+.fa-usb:before {
+  content: "\f287"; }
+
+.fa-tumblr:before {
+  content: "\f173"; }
+
+.fa-vaadin:before {
+  content: "\f408"; }
+
+.fa-quora:before {
+  content: "\f2c4"; }
+
+.fa-square-x-twitter:before {
+  content: "\e61a"; }
+
+.fa-reacteurope:before {
+  content: "\f75d"; }
+
+.fa-medium:before {
+  content: "\f23a"; }
+
+.fa-medium-m:before {
+  content: "\f23a"; }
+
+.fa-amilia:before {
+  content: "\f36d"; }
+
+.fa-mixcloud:before {
+  content: "\f289"; }
+
+.fa-flipboard:before {
+  content: "\f44d"; }
+
+.fa-viacoin:before {
+  content: "\f237"; }
+
+.fa-critical-role:before {
+  content: "\f6c9"; }
+
+.fa-sitrox:before {
+  content: "\e44a"; }
+
+.fa-discourse:before {
+  content: "\f393"; }
+
+.fa-joomla:before {
+  content: "\f1aa"; }
+
+.fa-mastodon:before {
+  content: "\f4f6"; }
+
+.fa-airbnb:before {
+  content: "\f834"; }
+
+.fa-wolf-pack-battalion:before {
+  content: "\f514"; }
+
+.fa-buy-n-large:before {
+  content: "\f8a6"; }
+
+.fa-gulp:before {
+  content: "\f3ae"; }
+
+.fa-creative-commons-sampling-plus:before {
+  content: "\f4f1"; }
+
+.fa-strava:before {
+  content: "\f428"; }
+
+.fa-ember:before {
+  content: "\f423"; }
+
+.fa-canadian-maple-leaf:before {
+  content: "\f785"; }
+
+.fa-teamspeak:before {
+  content: "\f4f9"; }
+
+.fa-pushed:before {
+  content: "\f3e1"; }
+
+.fa-wordpress-simple:before {
+  content: "\f411"; }
+
+.fa-nutritionix:before {
+  content: "\f3d6"; }
+
+.fa-wodu:before {
+  content: "\e088"; }
+
+.fa-google-pay:before {
+  content: "\e079"; }
+
+.fa-intercom:before {
+  content: "\f7af"; }
+
+.fa-zhihu:before {
+  content: "\f63f"; }
+
+.fa-korvue:before {
+  content: "\f42f"; }
+
+.fa-pix:before {
+  content: "\e43a"; }
+
+.fa-steam-symbol:before {
+  content: "\f3f6"; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-regular: normal 400 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+.far,
+.fa-regular {
+  font-weight: 400; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-solid: normal 900 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 900;
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+.fas,
+.fa-solid {
+  font-weight: 900; }
+@font-face {
+  font-family: 'Font Awesome 5 Brands';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 900;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-v4compatibility.woff2") format("woff2"), url("../webfonts/fa-v4compatibility.ttf") format("truetype"); }
diff --git a/deps/font-awesome-6.4.2/css/all.min.css b/deps/font-awesome-6.4.2/css/all.min.css
new file mode 100644
index 0000000..6604a06
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/all.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa{font-family:var(--fa-style-family,"Font Awesome 6 Free");font-weight:var(--fa-style,900)}.fa,.fa-brands,.fa-classic,.fa-regular,.fa-sharp,.fa-solid,.fab,.far,.fas{-moz-osx-font-smoothing:grayscale;-webkit-font-smoothing:antialiased;display:var(--fa-display,inline-block);font-style:normal;font-variant:normal;line-height:1;text-rendering:auto}.fa-classic,.fa-regular,.fa-solid,.far,.fas{font-family:"Font Awesome 6 Free"}.fa-brands,.fab{font-family:"Font Awesome 6 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diff --git a/deps/font-awesome-6.4.2/css/v4-shims.css b/deps/font-awesome-6.4.2/css/v4-shims.css
new file mode 100644
index 0000000..a85953d
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/v4-shims.css
@@ -0,0 +1,2194 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa.fa-glass:before {
+  content: "\f000"; }
+
+.fa.fa-envelope-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-o:before {
+  content: "\f0e0"; }
+
+.fa.fa-star-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-o:before {
+  content: "\f005"; }
+
+.fa.fa-remove:before {
+  content: "\f00d"; }
+
+.fa.fa-close:before {
+  content: "\f00d"; }
+
+.fa.fa-gear:before {
+  content: "\f013"; }
+
+.fa.fa-trash-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-trash-o:before {
+  content: "\f2ed"; }
+
+.fa.fa-home:before {
+  content: "\f015"; }
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+.fa.fa-file-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-file-o:before {
+  content: "\f15b"; }
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+.fa.fa-clock-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-clock-o:before {
+  content: "\f017"; }
+
+.fa.fa-arrow-circle-o-down {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-arrow-circle-o-down:before {
+  content: "\f358"; }
+
+.fa.fa-arrow-circle-o-up {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-arrow-circle-o-up:before {
+  content: "\f35b"; }
+
+.fa.fa-play-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-play-circle-o:before {
+  content: "\f144"; }
+
+.fa.fa-repeat:before {
+  content: "\f01e"; }
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+.fa.fa-rotate-right:before {
+  content: "\f01e"; }
+
+.fa.fa-refresh:before {
+  content: "\f021"; }
+
+.fa.fa-list-alt {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-list-alt:before {
+  content: "\f022"; }
+
+.fa.fa-dedent:before {
+  content: "\f03b"; }
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+.fa.fa-video-camera:before {
+  content: "\f03d"; }
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+.fa.fa-picture-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+  content: "\f03e"; }
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+.fa.fa-photo {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-photo:before {
+  content: "\f03e"; }
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+.fa.fa-image {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-image:before {
+  content: "\f03e"; }
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+.fa.fa-map-marker:before {
+  content: "\f3c5"; }
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+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-pencil-square-o:before {
+  content: "\f044"; }
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+.fa.fa-edit {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-edit:before {
+  content: "\f044"; }
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+.fa.fa-share-square-o:before {
+  content: "\f14d"; }
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+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-check-square-o:before {
+  content: "\f14a"; }
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+.fa.fa-arrows:before {
+  content: "\f0b2"; }
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+.fa.fa-times-circle-o {
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+  font-weight: 400; }
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+.fa.fa-times-circle-o:before {
+  content: "\f057"; }
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+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-check-circle-o:before {
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+.fa.fa-compress:before {
+  content: "\f422"; }
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+.fa.fa-eye {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-eye-slash {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
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+.fa.fa-warning:before {
+  content: "\f071"; }
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+.fa.fa-calendar:before {
+  content: "\f073"; }
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+  content: "\f338"; }
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+  content: "\f337"; }
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+.fa.fa-bar-chart:before {
+  content: "\e0e3"; }
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+.fa.fa-bar-chart-o:before {
+  content: "\e0e3"; }
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+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
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+  font-weight: 400; }
+
+.fa.fa-pause-circle-o:before {
+  content: "\f28b"; }
+
+.fa.fa-stop-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-stop-circle-o:before {
+  content: "\f28d"; }
+
+.fa.fa-bluetooth {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-bluetooth-b {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-gitlab {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpbeginner {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpforms {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-envira {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt:before {
+  content: "\f368"; }
+
+.fa.fa-question-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-question-circle-o:before {
+  content: "\f059"; }
+
+.fa.fa-volume-control-phone:before {
+  content: "\f2a0"; }
+
+.fa.fa-asl-interpreting:before {
+  content: "\f2a3"; }
+
+.fa.fa-deafness:before {
+  content: "\f2a4"; }
+
+.fa.fa-hard-of-hearing:before {
+  content: "\f2a4"; }
+
+.fa.fa-glide {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-glide-g {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-signing:before {
+  content: "\f2a7"; }
+
+.fa.fa-viadeo {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square:before {
+  content: "\f2aa"; }
+
+.fa.fa-snapchat {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost:before {
+  content: "\f2ab"; }
+
+.fa.fa-snapchat-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa.fa-pied-piper {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-first-order {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-yoast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-themeisle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official:before {
+  content: "\f2b3"; }
+
+.fa.fa-google-plus-circle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-circle:before {
+  content: "\f2b3"; }
+
+.fa.fa-font-awesome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa:before {
+  content: "\f2b4"; }
+
+.fa.fa-handshake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-handshake-o:before {
+  content: "\f2b5"; }
+
+.fa.fa-envelope-open-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-open-o:before {
+  content: "\f2b6"; }
+
+.fa.fa-linode {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-address-book-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-book-o:before {
+  content: "\f2b9"; }
+
+.fa.fa-vcard:before {
+  content: "\f2bb"; }
+
+.fa.fa-address-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-card-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-vcard-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-vcard-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-user-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-circle-o:before {
+  content: "\f2bd"; }
+
+.fa.fa-user-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-o:before {
+  content: "\f007"; }
+
+.fa.fa-id-badge {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license:before {
+  content: "\f2c2"; }
+
+.fa.fa-id-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-id-card-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-drivers-license-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-quora {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-free-code-camp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-telegram {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-thermometer-4:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer-3:before {
+  content: "\f2c8"; }
+
+.fa.fa-thermometer-2:before {
+  content: "\f2c9"; }
+
+.fa.fa-thermometer-1:before {
+  content: "\f2ca"; }
+
+.fa.fa-thermometer-0:before {
+  content: "\f2cb"; }
+
+.fa.fa-bathtub:before {
+  content: "\f2cd"; }
+
+.fa.fa-s15:before {
+  content: "\f2cd"; }
+
+.fa.fa-window-maximize {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-restore {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle:before {
+  content: "\f410"; }
+
+.fa.fa-window-close-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-close-o:before {
+  content: "\f410"; }
+
+.fa.fa-times-rectangle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle-o:before {
+  content: "\f410"; }
+
+.fa.fa-bandcamp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-grav {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-etsy {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-imdb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-ravelry {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast:before {
+  content: "\f2da"; }
+
+.fa.fa-snowflake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-snowflake-o:before {
+  content: "\f2dc"; }
+
+.fa.fa-superpowers {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpexplorer {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-meetup {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
diff --git a/deps/font-awesome-6.4.2/css/v4-shims.min.css b/deps/font-awesome-6.4.2/css/v4-shims.min.css
new file mode 100644
index 0000000..64e4e8d
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/v4-shims.min.css
@@ -0,0 +1,6 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa.fa-glass:before{content:"\f000"}.fa.fa-envelope-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-envelope-o:before{content:"\f0e0"}.fa.fa-star-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-star-o:before{content:"\f005"}.fa.fa-close:before,.fa.fa-remove:before{content:"\f00d"}.fa.fa-gear:before{content:"\f013"}.fa.fa-trash-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-trash-o:before{content:"\f2ed"}.fa.fa-home:before{content:"\f015"}.fa.fa-file-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-file-o:before{content:"\f15b"}.fa.fa-clock-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-clock-o:before{content:"\f017"}.fa.fa-arrow-circle-o-down{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-arrow-circle-o-down:before{content:"\f358"}.fa.fa-arrow-circle-o-up{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-arrow-circle-o-up:before{content:"\f35b"}.fa.fa-play-circle-o{font-family:"Font Awesome 6 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+/*!
+ * headroom.js v0.11.0 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(n):(t=t||self).Headroom=n()}(this,function(){"use strict";function t(){return"undefined"!=typeof window}function d(t){return function(t){return t&&t.document&&function(t){return 9===t.nodeType}(t.document)}(t)?function(t){var n=t.document,o=n.body,s=n.documentElement;return{scrollHeight:function(){return Math.max(o.scrollHeight,s.scrollHeight,o.offsetHeight,s.offsetHeight,o.clientHeight,s.clientHeight)},height:function(){return t.innerHeight||s.clientHeight||o.clientHeight},scrollY:function(){return void 0!==t.pageYOffset?t.pageYOffset:(s||o.parentNode||o).scrollTop}}}(t):function(t){return{scrollHeight:function(){return Math.max(t.scrollHeight,t.offsetHeight,t.clientHeight)},height:function(){return Math.max(t.offsetHeight,t.clientHeight)},scrollY:function(){return t.scrollTop}}}(t)}function n(t,s,e){var n,o=function(){var n=!1;try{var t={get passive(){n=!0}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){n=!1}return n}(),i=!1,r=d(t),l=r.scrollY(),a={};function c(){var t=Math.round(r.scrollY()),n=r.height(),o=r.scrollHeight();a.scrollY=t,a.lastScrollY=l,a.direction=l<t?"down":"up",a.distance=Math.abs(t-l),a.isOutOfBounds=t<0||o<t+n,a.top=t<=s.offset,a.bottom=o<=t+n,a.toleranceExceeded=a.distance>s.tolerance[a.direction],e(a),l=t,i=!1}function h(){i||(i=!0,n=requestAnimationFrame(c))}var u=!!o&&{passive:!0,capture:!1};return t.addEventListener("scroll",h,u),c(),{destroy:function(){cancelAnimationFrame(n),t.removeEventListener("scroll",h,u)}}}function o(t,n){n=n||{},Object.assign(this,o.options,n),this.classes=Object.assign({},o.options.classes,n.classes),this.elem=t,this.tolerance=function(t){return t===Object(t)?t:{down:t,up:t}}(this.tolerance),this.initialised=!1,this.frozen=!1}return o.prototype={constructor:o,init:function(){return o.cutsTheMustard&&!this.initialised&&(this.addClass("initial"),this.initialised=!0,setTimeout(function(t){t.scrollTracker=n(t.scroller,{offset:t.offset,tolerance:t.tolerance},t.update.bind(t))},100,this)),this},destroy:function(){this.initialised=!1,Object.keys(this.classes).forEach(this.removeClass,this),this.scrollTracker.destroy()},unpin:function(){!this.hasClass("pinned")&&this.hasClass("unpinned")||(this.addClass("unpinned"),this.removeClass("pinned"),this.onUnpin&&this.onUnpin.call(this))},pin:function(){this.hasClass("unpinned")&&(this.addClass("pinned"),this.removeClass("unpinned"),this.onPin&&this.onPin.call(this))},freeze:function(){this.frozen=!0,this.addClass("frozen")},unfreeze:function(){this.frozen=!1,this.removeClass("frozen")},top:function(){this.hasClass("top")||(this.addClass("top"),this.removeClass("notTop"),this.onTop&&this.onTop.call(this))},notTop:function(){this.hasClass("notTop")||(this.addClass("notTop"),this.removeClass("top"),this.onNotTop&&this.onNotTop.call(this))},bottom:function(){this.hasClass("bottom")||(this.addClass("bottom"),this.removeClass("notBottom"),this.onBottom&&this.onBottom.call(this))},notBottom:function(){this.hasClass("notBottom")||(this.addClass("notBottom"),this.removeClass("bottom"),this.onNotBottom&&this.onNotBottom.call(this))},shouldUnpin:function(t){return"down"===t.direction&&!t.top&&t.toleranceExceeded},shouldPin:function(t){return"up"===t.direction&&t.toleranceExceeded||t.top},addClass:function(t){this.elem.classList.add.apply(this.elem.classList,this.classes[t].split(" "))},removeClass:function(t){this.elem.classList.remove.apply(this.elem.classList,this.classes[t].split(" "))},hasClass:function(t){return this.classes[t].split(" ").every(function(t){return this.classList.contains(t)},this.elem)},update:function(t){t.isOutOfBounds||!0!==this.frozen&&(t.top?this.top():this.notTop(),t.bottom?this.bottom():this.notBottom(),this.shouldUnpin(t)?this.unpin():this.shouldPin(t)&&this.pin())}},o.options={tolerance:{up:0,down:0},offset:0,scroller:t()?window:null,classes:{frozen:"headroom--frozen",pinned:"headroom--pinned",unpinned:"headroom--unpinned",top:"headroom--top",notTop:"headroom--not-top",bottom:"headroom--bottom",notBottom:"headroom--not-bottom",initial:"headroom"}},o.cutsTheMustard=!!(t()&&function(){}.bind&&"classList"in document.documentElement&&Object.assign&&Object.keys&&requestAnimationFrame),o});
\ No newline at end of file
diff --git a/deps/headroom-0.11.0/jQuery.headroom.min.js b/deps/headroom-0.11.0/jQuery.headroom.min.js
new file mode 100644
index 0000000..17f70c9
--- /dev/null
+++ b/deps/headroom-0.11.0/jQuery.headroom.min.js
@@ -0,0 +1,7 @@
+/*!
+ * headroom.js v0.9.4 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery);
\ No newline at end of file
diff --git a/deps/search-1.0.0/autocomplete.jquery.min.js b/deps/search-1.0.0/autocomplete.jquery.min.js
new file mode 100644
index 0000000..fb63a6a
--- /dev/null
+++ b/deps/search-1.0.0/autocomplete.jquery.min.js
@@ -0,0 +1,7 @@
+/*!
+ * autocomplete.js 0.38.0
+ * https://github.com/algolia/autocomplete.js
+ * Copyright 2020 Algolia, Inc. and other contributors; Licensed MIT
+ */
+!function(a){function b(d){if(c[d])return c[d].exports;var e=c[d]={exports:{},id:d,loaded:!1};return a[d].call(e.exports,e,e.exports,b),e.loaded=!0,e.exports}var c={};b.m=a,b.c=c,b.p="",b(0)}([function(a,b,c){"use strict";a.exports=c(1)},function(a,b,c){"use strict";var d=c(2),e=c(3);d.element=e;var f=c(4);f.isArray=e.isArray,f.isFunction=e.isFunction,f.isObject=e.isPlainObject,f.bind=e.proxy,f.each=function(a,b){function c(a,c){return b(c,a)}e.each(a,c)},f.map=e.map,f.mixin=e.extend,f.Event=e.Event;var g,h,i,j=c(5),k=c(6);g=e.fn.autocomplete,h="aaAutocomplete",i={initialize:function(a,b){function c(){var c,d=e(this),f=new k({el:d});c=new j({input:d,eventBus:f,dropdownMenuContainer:a.dropdownMenuContainer,hint:void 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i[a]&&"initialize"!==a?(b=this.filter(function(){return!!e(this).data(h)}),i[a].apply(b,[].slice.call(arguments,1))):i.initialize.apply(this,arguments)},e.fn.autocomplete.noConflict=function(){return e.fn.autocomplete=g,this},e.fn.autocomplete.sources=j.sources,e.fn.autocomplete.escapeHighlightedString=f.escapeHighlightedString,a.exports=e.fn.autocomplete},function(a,b){"use strict";a.exports={element:null}},function(a,b){a.exports=jQuery},function(a,b,c){"use strict";function d(a){return a.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g,"\\$&")}var e=c(2);a.exports={isArray:null,isFunction:null,isObject:null,bind:null,each:null,map:null,mixin:null,isMsie:function(a){if(void 0===a&&(a=navigator.userAgent),/(msie|trident)/i.test(a)){var b=a.match(/(msie |rv:)(\d+(.\d+)?)/i);if(b)return b[2]}return!1},escapeRegExChars:function(a){return a.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g,"\\$&")},isNumber:function(a){return"number"==typeof a},toStr:function(a){return void 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f=document.createElement("div");f.appendChild(document.createTextNode(c));var g=document.createElement("div");return g.appendChild(document.createTextNode(a)),g.innerHTML.replace(RegExp(d(e.innerHTML),"g"),b).replace(RegExp(d(f.innerHTML),"g"),c)}}},function(a,b,c){"use strict";function d(a){var b,c;if(a=a||{},a.input||i.error("missing input"),this.isActivated=!1,this.debug=!!a.debug,this.autoselect=!!a.autoselect,this.autoselectOnBlur=!!a.autoselectOnBlur,this.openOnFocus=!!a.openOnFocus,this.minLength=i.isNumber(a.minLength)?a.minLength:1,this.autoWidth=void 0===a.autoWidth||!!a.autoWidth,this.clearOnSelected=!!a.clearOnSelected,this.tabAutocomplete=void 0===a.tabAutocomplete||!!a.tabAutocomplete,a.hint=!!a.hint,a.hint&&a.appendTo)throw new Error("[autocomplete.js] hint and appendTo options can't be used at the same 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d.Dropdown({appendTo:a.appendTo,wrapper:this.$node,menu:b,datasets:a.datasets,templates:a.templates,cssClasses:a.cssClasses,minLength:this.minLength}).onSync("suggestionClicked",this._onSuggestionClicked,this).onSync("cursorMoved",this._onCursorMoved,this).onSync("cursorRemoved",this._onCursorRemoved,this).onSync("opened",this._onOpened,this).onSync("closed",this._onClosed,this).onSync("shown",this._onShown,this).onSync("empty",this._onEmpty,this).onSync("redrawn",this._onRedrawn,this).onAsync("datasetRendered",this._onDatasetRendered,this),this.input=new 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g=n.dropdown.replace("%PREFIX%",a.cssClasses.prefix).replace("%DROPDOWN_MENU%",a.cssClasses.dropdownMenu);d=j.element(g).css(a.css.dropdown).attr({role:"listbox",id:a.listboxId}),a.templates&&a.templates.dropdownMenu&&d.html(i.templatify(a.templates.dropdownMenu)()),e=b.clone().css(a.css.hint).css(f(b)),e.val("").addClass(i.className(a.cssClasses.prefix,a.cssClasses.hint,!0)).removeAttr("id name placeholder required").prop("readonly",!0).attr({"aria-hidden":"true",autocomplete:"off",spellcheck:"false",tabindex:-1}),e.removeData&&e.removeData(),b.data(h,{"aria-autocomplete":b.attr("aria-autocomplete"),"aria-expanded":b.attr("aria-expanded"),"aria-owns":b.attr("aria-owns"),autocomplete:b.attr("autocomplete"),dir:b.attr("dir"),role:b.attr("role"),spellcheck:b.attr("spellcheck"),style:b.attr("style"),type:b.attr("type")}),b.addClass(i.className(a.cssClasses.prefix,a.cssClasses.input,!0)).attr({autocomplete:"off",spellcheck:!1,role:"combobox","aria-autocomplete":a.datasets&&a.datasets[0]&&a.datasets[0].displayKey?"both":"list","aria-expanded":"false","aria-label":a.ariaLabel,"aria-owns":a.listboxId}).css(a.hint?a.css.input:a.css.inputWithNoHint);try{b.attr("dir")||b.attr("dir","auto")}catch(a){}return c=a.appendTo?c.appendTo(j.element(a.appendTo).eq(0)).eq(0):b.wrap(c).parent(),c.prepend(a.hint?e:null).append(d),{wrapper:c,input:b,hint:e,menu:d}}function f(a){return{backgroundAttachment:a.css("background-attachment"),backgroundClip:a.css("background-clip"),backgroundColor:a.css("background-color"),backgroundImage:a.css("background-image"),backgroundOrigin:a.css("background-origin"),backgroundPosition:a.css("background-position"),backgroundRepeat:a.css("background-repeat"),backgroundSize:a.css("background-size")}}function g(a,b){var c=a.find(i.className(b.prefix,b.input));i.each(c.data(h),function(a,b){void 0===a?c.removeAttr(b):c.attr(b,a)}),c.detach().removeClass(i.className(b.prefix,b.input,!0)).insertAfter(a),c.removeData&&c.removeData(h),a.remove()}var h="aaAttrs",i=c(4),j=c(2),k=c(6),l=c(7),m=c(16),n=c(18),o=c(19);i.mixin(d.prototype,{_bindKeyboardShortcuts:function(a){if(a.keyboardShortcuts){var b=this.$input,c=[];i.each(a.keyboardShortcuts,function(a){"string"==typeof a&&(a=a.toUpperCase().charCodeAt(0)),c.push(a)}),j.element(document).keydown(function(a){var 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c=this.dropdown.getDatumForCursor(),d=this.dropdown.getCurrentCursor().attr("id");this.input.setActiveDescendant(d),c&&(b&&this.input.setInputValue(c.value,!0),this.eventBus.trigger("cursorchanged",c.raw,c.datasetName))},_onCursorRemoved:function(){this.input.resetInputValue(),this._updateHint(),this.eventBus.trigger("cursorremoved")},_onDatasetRendered:function(){this._updateHint(),this.eventBus.trigger("updated")},_onOpened:function(){this._updateHint(),this.input.expand(),this.eventBus.trigger("opened")},_onEmpty:function(){this.eventBus.trigger("empty")},_onRedrawn:function(){this.$node.css("top","0px"),this.$node.css("left","0px");var a=this.$input[0].getBoundingClientRect();this.autoWidth&&this.$node.css("width",a.width+"px");var b=this.$node[0].getBoundingClientRect(),c=a.bottom-b.top;this.$node.css("top",c+"px");var d=a.left-b.left;this.$node.css("left",d+"px"),this.eventBus.trigger("redrawn")},_onShown:function(){this.eventBus.trigger("shown"),this.autoselect&&this.dropdown.cursorTopSuggestion()},_onClosed:function(){this.input.clearHint(),this.input.removeActiveDescendant(),this.input.collapse(),this.eventBus.trigger("closed")},_onFocused:function(){if(this.isActivated=!0,this.openOnFocus){var a=this.input.getQuery();a.length>=this.minLength?this.dropdown.update(a):this.dropdown.empty(),this.dropdown.open()}},_onBlurred:function(){var a,b;a=this.dropdown.getDatumForCursor(),b=this.dropdown.getDatumForTopSuggestion();var c={selectionMethod:"blur"};this.debug||(this.autoselectOnBlur&&a?this._select(a,c):this.autoselectOnBlur&&b?this._select(b,c):(this.isActivated=!1,this.dropdown.empty(),this.dropdown.close()))},_onEnterKeyed:function(a,b){var c,d;c=this.dropdown.getDatumForCursor(),d=this.dropdown.getDatumForTopSuggestion();var 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a=this.input.getInputValue();a.length>=this.minLength?this.dropdown.update(a):this.dropdown.empty()}this.dropdown.open()},close:function(){this.dropdown.close()},setVal:function(a){a=i.toStr(a),this.isActivated?this.input.setInputValue(a):(this.input.setQuery(a),this.input.setInputValue(a,!0)),this._setLanguageDirection()},getVal:function(){return this.input.getQuery()},destroy:function(){this.input.destroy(),this.dropdown.destroy(),g(this.$node,this.cssClasses),this.$node=null},getWrapper:function(){return this.dropdown.$container[0]}}),d.Dropdown=m,d.Input=l,d.sources=c(20),a.exports=d},function(a,b,c){"use strict";function d(a){a&&a.el||e.error("EventBus initialized without el"),this.$el=f.element(a.el)}var e=c(4),f=c(2);e.mixin(d.prototype,{trigger:function(a,b,c,d){var f=e.Event("autocomplete:"+a);return this.$el.trigger(f,[b,c,d]),f}}),a.exports=d},function(a,b,c){"use strict";function d(a){var b,c,d,f,g=this;a=a||{},a.input||i.error("input is 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+var c=[].slice.call(arguments,1);this.cacheSuggestions(a,b,c),this._render.apply(this,[a,b].concat(c))}}if(this.query=a,this.canceled=!1,this.shouldFetchFromCache(a))b.apply(this,[this.cachedSuggestions].concat(this.cachedRenderExtraArgs));else{var c=this,d=function(){c.canceled||c.source(a,b.bind(c))};if(this.debounce){var e=function(){c.debounceTimeout=null,d()};clearTimeout(this.debounceTimeout),this.debounceTimeout=setTimeout(e,this.debounce)}else d()}},cacheSuggestions:function(a,b,c){this.cachedQuery=a,this.cachedSuggestions=b,this.cachedRenderExtraArgs=c},shouldFetchFromCache:function(a){return this.cache&&this.cachedQuery===a&&this.cachedSuggestions&&this.cachedSuggestions.length},clearCachedSuggestions:function(){delete this.cachedQuery,delete this.cachedSuggestions,delete this.cachedRenderExtraArgs},cancel:function(){this.canceled=!0},clear:function(){this.$el&&(this.cancel(),this.$el.empty(),this.trigger("rendered",""))},isEmpty:function(){return this._isEmpty},destroy:function(){this.clearCachedSuggestions(),this.$el=null}}),a.exports=d},function(a,b){"use strict";a.exports={wrapper:'<span class="%ROOT%"></span>',dropdown:'<span class="%PREFIX%%DROPDOWN_MENU%"></span>',dataset:'<div class="%PREFIX%%DATASET%-%CLASS%"></div>',suggestions:'<span class="%PREFIX%%SUGGESTIONS%"></span>',suggestion:'<div class="%PREFIX%%SUGGESTION%"></div>'}},function(a,b,c){"use strict";var d=c(4),e={wrapper:{position:"relative",display:"inline-block"},hint:{position:"absolute",top:"0",left:"0",borderColor:"transparent",boxShadow:"none",opacity:"1"},input:{position:"relative",verticalAlign:"top",backgroundColor:"transparent"},inputWithNoHint:{position:"relative",verticalAlign:"top"},dropdown:{position:"absolute",top:"100%",left:"0",zIndex:"100",display:"none"},suggestions:{display:"block"},suggestion:{whiteSpace:"nowrap",cursor:"pointer"},suggestionChild:{whiteSpace:"normal"},ltr:{left:"0",right:"auto"},rtl:{left:"auto",right:"0"},defaultClasses:{root:"algolia-autocomplete",prefix:"aa",noPrefix:!1,dropdownMenu:"dropdown-menu",input:"input",hint:"hint",suggestions:"suggestions",suggestion:"suggestion",cursor:"cursor",dataset:"dataset",empty:"empty"},appendTo:{wrapper:{position:"absolute",zIndex:"100",display:"none"},input:{},inputWithNoHint:{},dropdown:{display:"block"}}};d.isMsie()&&d.mixin(e.input,{backgroundImage:"url(data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)"}),d.isMsie()&&d.isMsie()<=7&&d.mixin(e.input,{marginTop:"-1px"}),a.exports=e},function(a,b,c){"use strict";a.exports={hits:c(21),popularIn:c(24)}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23),g=function(){function a(a,d){return window.Promise.resolve().then(function(){return b.length&&(e=a.search(b),b=[]),e}).then(function(a){if(a)return c=a.results,c[d]})}var b=[],c=[],e=window.Promise.resolve();return function(c,e){return function(f,g){a(c.as,b.push({indexName:c.indexName,query:f,params:e})-1).then(function(a){a&&g(a.hits,a)}).catch(function(a){d.error(a.message)})}}}();a.exports=function(a,b){var c=f(a.as._ua);if(c&&c[0]>=3&&c[1]>20){var d="autocomplete.js "+e;a.as._ua.indexOf(d)===-1&&(a.as._ua+="; "+d)}return g(a,b)}},function(a,b){a.exports="0.38.0"},function(a,b){"use strict";a.exports=function(a){var b=a.match(/Algolia for JavaScript \((\d+\.)(\d+\.)(\d+)\)/)||a.match(/Algolia for vanilla JavaScript (\d+\.)(\d+\.)(\d+)/);if(b)return[b[1],b[2],b[3]]}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23);a.exports=function(a,b,c,g){function h(h,i){a.search(h,b,function(a,h){if(a)return void d.error(a.message);if(h.hits.length>0){var l=h.hits[0],m=d.mixin({hitsPerPage:0},c);delete m.source,delete m.index;var n=f(k.as._ua);return n&&n[0]>=3&&n[1]>20&&(b.additionalUA="autocomplete.js "+e),void k.search(j(l),m,function(a,b){if(a)return void d.error(a.message);var c=[];if(g.includeAll){var e=g.allTitle||"All departments";c.push(d.mixin({facet:{value:e,count:b.nbHits}},d.cloneDeep(l)))}d.each(b.facets,function(a,b){d.each(a,function(a,e){c.push(d.mixin({facet:{facet:b,value:e,count:a}},d.cloneDeep(l)))})});for(var f=1;f<h.hits.length;++f)c.push(h.hits[f]);i(c,h)})}i([])})}var i=f(a.as._ua);if(i&&i[0]>=3&&i[1]>20&&(b=b||{},b.additionalUA="autocomplete.js "+e),!c.source)return d.error("Missing 'source' key");var j=d.isFunction(c.source)?c.source:function(a){return a[c.source]};if(!c.index)return d.error("Missing 'index' key");var k=c.index;return g=g||{},h}}]);
\ No newline at end of file
diff --git a/deps/search-1.0.0/fuse.min.js b/deps/search-1.0.0/fuse.min.js
new file mode 100644
index 0000000..7def598
--- /dev/null
+++ b/deps/search-1.0.0/fuse.min.js
@@ -0,0 +1,9 @@
+/**
+ * Fuse.js v6.4.6 - Lightweight fuzzy-search (http://fusejs.io)
+ *
+ * Copyright (c) 2021 Kiro Risk (http://kiro.me)
+ * All Rights Reserved. Apache Software License 2.0
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ */
+var e,t;e=this,t=function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(t)}function t(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function n(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}function r(e,t,r){return t&&n(e.prototype,t),r&&n(e,r),e}function i(e,t,n){return t in e?Object.defineProperty(e,t,{value:n,enumerable:!0,configurable:!0,writable:!0}):e[t]=n,e}function o(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),n.push.apply(n,r)}return n}function c(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?o(Object(n),!0).forEach((function(t){i(e,t,n[t])})):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):o(Object(n)).forEach((function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))}))}return e}function a(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&u(e,t)}function s(e){return(s=Object.setPrototypeOf?Object.getPrototypeOf:function(e){return e.__proto__||Object.getPrototypeOf(e)})(e)}function u(e,t){return(u=Object.setPrototypeOf||function(e,t){return e.__proto__=t,e})(e,t)}function h(e,t){return!t||"object"!=typeof t&&"function"!=typeof t?function(e){if(void 0===e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return e}(e):t}function f(e){var t=function(){if("undefined"==typeof 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\ No newline at end of file
diff --git a/deps/search-1.0.0/mark.min.js b/deps/search-1.0.0/mark.min.js
new file mode 100644
index 0000000..1eea053
--- /dev/null
+++ b/deps/search-1.0.0/mark.min.js
@@ -0,0 +1,7 @@
+/*!***************************************************
+* mark.js v8.11.1
+* https://markjs.io/
+* Copyright (c) 2014–2018, Julian Kühnel
+* Released under the MIT license https://git.io/vwTVl
+*****************************************************/
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):e.Mark=t()}(this,function(){"use strict";var e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e},t=function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")},n=function(){function e(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(t,n,r){return n&&e(t.prototype,n),r&&e(t,r),t}}(),r=Object.assign||function(e){for(var t=1;t<arguments.length;t++){var n=arguments[t];for(var r in n)Object.prototype.hasOwnProperty.call(n,r)&&(e[r]=n[r])}return e},i=function(){function e(n){var r=!(arguments.length>1&&void 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diff --git a/index.html b/index.html
index 8b5778f..a489260 100644
--- a/index.html
+++ b/index.html
@@ -5,66 +5,52 @@
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-home">
 <div class="row">
@@ -81,7 +67,7 @@
 </li>
 </ul>
 <!-- README.md is generated from README.Rmd. Please edit that file --><div class="section level1">
-<div class="page-header"><h1 id="id_-dracarys---umccr-workflow-tidying">🔥 dracarys - UMCCR Workflow Tidying<a class="anchor" aria-label="anchor" href="#id_-dracarys---umccr-workflow-tidying"></a>
+<div class="page-header"><h1 id="fire-dracarys---umccr-workflow-tidying">🔥 dracarys - UMCCR Workflow Tidying<a class="anchor" aria-label="anchor" href="#fire-dracarys---umccr-workflow-tidying"></a>
 </h1></div>
 <p><img src="https://emojis.slackmojis.com/emojis/images/1643515659/16823/flying_dragon.gif?1643515659" title="Dragon Flying"></p>
 <ul>
@@ -90,12 +76,12 @@
 </ul>
 <p><a href="https://anaconda.org/umccr/r-dracarys" class="external-link"><img src="https://anaconda.org/umccr/r-dracarys/badges/version.svg" alt="Conda install"></a> <a href="https://anaconda.org/umccr/r-dracarys" class="external-link"><img src="https://anaconda.org/umccr/r-dracarys/badges/latest_release_date.svg" alt="Conda install"></a></p>
 <div class="section level2">
-<h2 id="id_-aim">🏆 Aim<a class="anchor" aria-label="anchor" href="#id_-aim"></a>
+<h2 id="trophy-aim">🏆 Aim<a class="anchor" aria-label="anchor" href="#trophy-aim"></a>
 </h2>
 <p>Given a <a href="https://developer.illumina.com/illumina-connected-analytics" class="external-link">ICA GDS</a>, AWS S3 or local directory with results from a UMCCR workflow, {dracarys} will grab files of interest and transform them into ‘tidier’ structures for output into TSV/Parquet/RDS format for downstream ingestion into a database/data lake. See supported <a href="#supported-workflows">workflows</a>, <a href="#running">running</a> examples, and <a href="#cli">CLI</a> options in the sections below.</p>
 </div>
 <div class="section level2">
-<h2 id="id_-installation">🍕 Installation<a class="anchor" aria-label="anchor" href="#id_-installation"></a>
+<h2 id="pizza-installation">🍕 Installation<a class="anchor" aria-label="anchor" href="#pizza-installation"></a>
 </h2>
 <details><summary>
 R
@@ -128,7 +114,7 @@ <h2 id="id_-installation">🍕 Installation<a class="anchor" aria-label="anchor"
 </details><p><a name="supported-workflows"></a></p>
 </div>
 <div class="section level2">
-<h2 id="id_-supported-workflows">✨ Supported Workflows<a class="anchor" aria-label="anchor" href="#id_-supported-workflows"></a>
+<h2 id="sparkles-supported-workflows">✨ Supported Workflows<a class="anchor" aria-label="anchor" href="#sparkles-supported-workflows"></a>
 </h2>
 <p>{dracarys} supports most outputs from the following UMCCR workflows:</p>
 <table class="table">
@@ -136,57 +122,57 @@ <h2 id="id_-supported-workflows">✨ Supported Workflows<a class="anchor" aria-l
 <col width="13%">
 <col width="86%">
 </colgroup>
-<thead><tr class="header">
+<thead><tr>
 <th>Workflow</th>
 <th>Description</th>
 </tr></thead>
 <tbody>
-<tr class="odd">
+<tr>
 <td>bcl_convert</td>
 <td>
 <a href="https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html" class="external-link">BCLConvert</a> workflow</td>
 </tr>
-<tr class="even">
+<tr>
 <td>tso_ctdna_tumor_only</td>
 <td>
 <a href="https://support-docs.illumina.com/SW/DRAGEN_TSO500_ctDNA_v2.1/Content/SW/TSO500/WorkflowDiagram_appT500ctDNAlocal.htm" class="external-link">ctDNA TSO500</a> workflow</td>
 </tr>
-<tr class="odd">
+<tr>
 <td>wgs_alignment_qc</td>
 <td>
 <a href="https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm" class="external-link">DRAGEN DNA</a> (alignment) workflow</td>
 </tr>
-<tr class="even">
+<tr>
 <td>wts_alignment_qc</td>
 <td>
 <a href="https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm" class="external-link">DRAGEN RNA</a> (alignment) workflow</td>
 </tr>
-<tr class="odd">
+<tr>
 <td>wts_tumor_only</td>
 <td>
 <a href="https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm" class="external-link">DRAGEN RNA</a> workflow</td>
 </tr>
-<tr class="even">
+<tr>
 <td>wgs_tumor_normal</td>
 <td>
 <a href="https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm" class="external-link">DRAGEN Tumor/Normal</a> workflow</td>
 </tr>
-<tr class="odd">
+<tr>
 <td>umccrise</td>
 <td>
 <a href="https://github.com/umccr/umccrise" class="external-link">umccrise</a> workflow</td>
 </tr>
-<tr class="even">
+<tr>
 <td>rnasum</td>
 <td>
 <a href="https://github.com/umccr/RNAsum" class="external-link">RNAsum</a> workflow</td>
 </tr>
-<tr class="odd">
+<tr>
 <td>sash</td>
 <td>
 <a href="https://github.com/scwatts/sash" class="external-link">sash</a> workflow</td>
 </tr>
-<tr class="even">
+<tr>
 <td>oncoanalyser</td>
 <td>
 <a href="https://github.com/nf-core/oncoanalyser" class="external-link">oncoanalyser</a> workflow</td>
@@ -197,7 +183,7 @@ <h2 id="id_-supported-workflows">✨ Supported Workflows<a class="anchor" aria-l
 <p><a name="cli"></a></p>
 </div>
 <div class="section level2">
-<h2 id="id_-cli">🌀 CLI<a class="anchor" aria-label="anchor" href="#id_-cli"></a>
+<h2 id="cyclone-cli">🌀 CLI<a class="anchor" aria-label="anchor" href="#cyclone-cli"></a>
 </h2>
 <p>A <code>dracarys.R</code> command line interface is available for convenience.</p>
 <ul>
@@ -251,7 +237,7 @@ <h2 id="id_-cli">🌀 CLI<a class="anchor" aria-label="anchor" href="#id_-cli"><
 <p><a name="running"></a></p>
 </div>
 <div class="section level2">
-<h2 id="id_-running">🚕 Running<a class="anchor" aria-label="anchor" href="#id_-running"></a>
+<h2 id="taxi-running">🚕 Running<a class="anchor" aria-label="anchor" href="#taxi-running"></a>
 </h2>
 <p>{dracarys} takes as input (<code>--in_dir</code>) a directory with results from one of the UMCCR <a href="#supported-workflows">workflows</a>. It will recursively scan that directory for <a href="https://umccr.github.io/dracarys/articles/files.html">supported files</a>, download those into a local directory (<code>--gds_local_dir</code>), and then it will parse, transform and write the tidied versions into the specified output directory (<code>--out_dir</code>). A prefix (<code>--prefix</code>) is prepended to each of the tidied files. The output file format (<code>--format</code>) can be tsv, parquet, or both. To get just a list of supported files within the specified input directory, use the <code>-n (--dryrun)</code> option.</p>
 <details><summary>
@@ -336,15 +322,15 @@ <h2 data-toc-skip>Developers</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/katex-auto.js b/katex-auto.js
new file mode 100644
index 0000000..20651d9
--- /dev/null
+++ b/katex-auto.js
@@ -0,0 +1,14 @@
+// https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345
+document.addEventListener("DOMContentLoaded", function () {
+  var mathElements = document.getElementsByClassName("math");
+  var macros = [];
+  for (var i = 0; i < mathElements.length; i++) {
+    var texText = mathElements[i].firstChild;
+    if (mathElements[i].tagName == "SPAN") {
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+        throwOnError: false,
+        macros: macros,
+        fleqn: false
+      });
+    }}});
diff --git a/lightswitch.js b/lightswitch.js
new file mode 100644
index 0000000..9467125
--- /dev/null
+++ b/lightswitch.js
@@ -0,0 +1,85 @@
+
+/*!
+ * Color mode toggler for Bootstrap's docs (https://getbootstrap.com/)
+ * Copyright 2011-2023 The Bootstrap Authors
+ * Licensed under the Creative Commons Attribution 3.0 Unported License.
+ * Updates for {pkgdown} by the {bslib} authors, also licensed under CC-BY-3.0.
+ */
+
+const getStoredTheme = () => localStorage.getItem('theme')
+const setStoredTheme = theme => localStorage.setItem('theme', theme)
+
+const getPreferredTheme = () => {
+  const storedTheme = getStoredTheme()
+  if (storedTheme) {
+    return storedTheme
+  }
+
+  return window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light'
+}
+
+const setTheme = theme => {
+  if (theme === 'auto') {
+    document.documentElement.setAttribute('data-bs-theme', (window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light'))
+  } else {
+    document.documentElement.setAttribute('data-bs-theme', theme)
+  }
+}
+
+function bsSetupThemeToggle () {
+  'use strict'
+
+  const showActiveTheme = (theme, focus = false) => {
+    var activeLabel, activeIcon;
+
+    document.querySelectorAll('[data-bs-theme-value]').forEach(element => {
+      const buttonTheme = element.getAttribute('data-bs-theme-value')
+      const isActive = buttonTheme == theme
+      
+      element.classList.toggle('active', isActive)
+      element.setAttribute('aria-pressed', isActive)
+
+      if (isActive) {
+        activeLabel = element.textContent;
+        activeIcon = element.querySelector('span').classList.value;
+      }
+    })
+
+    const themeSwitcher = document.querySelector('#dropdown-lightswitch')
+    if (!themeSwitcher) {
+      return
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+
+    themeSwitcher.setAttribute('aria-label', activeLabel)
+    themeSwitcher.querySelector('span').classList.value = activeIcon;
+
+    if (focus) {
+      themeSwitcher.focus()
+    }
+  }
+
+  window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', () => {
+    const storedTheme = getStoredTheme()
+    if (storedTheme !== 'light' && storedTheme !== 'dark') {
+      setTheme(getPreferredTheme())
+    }
+  })
+
+  window.addEventListener('DOMContentLoaded', () => {
+    showActiveTheme(getPreferredTheme())
+
+    document
+      .querySelectorAll('[data-bs-theme-value]')
+      .forEach(toggle => {
+        toggle.addEventListener('click', () => {
+          const theme = toggle.getAttribute('data-bs-theme-value')
+          setTheme(theme)
+          setStoredTheme(theme)
+          showActiveTheme(theme, true)
+        })
+      })
+  })
+}
+
+setTheme(getPreferredTheme());
+bsSetupThemeToggle();
diff --git a/news/index.html b/news/index.html
index 518dbcb..4d78990 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-news">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Changelog</h1>
-      <small>Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
+
+      <h1>Changelog</h1>
+      <small>Source: <a href="https://github.com/umccr/dracarys/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
     <div class="section level2">
@@ -203,7 +189,7 @@ <h2 class="pkg-version" data-toc-text="0.1.0" id="dracarys-010-2022-07-11">draca
 <ul><li>Initially supporting just MultiQC json input (from dragen-alignment, dragen-transcriptome, dragen-tumor-normal, dragen-umccrise, and bcbio-umccrise).</li>
 </ul></li>
 </ul></div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -212,14 +198,14 @@ <h2 class="pkg-version" data-toc-text="0.1.0" id="dracarys-010-2022-07-11">draca
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/pkgdown.js b/pkgdown.js
index 9bd6621..9757bf9 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -152,5 +152,3 @@ async function searchFuse(query, callback) {
   });
   });
 })(window.jQuery || window.$)
-
-
diff --git a/pkgdown.yml b/pkgdown.yml
index bfd5597..4119d65 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,12 +1,11 @@
-pandoc: '3.2'
-pkgdown: 2.0.9
+pandoc: '3.3'
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   developers: developers.html
   files: files.html
   flames: flames.html
-last_built: 2024-05-13T13:16Z
+last_built: 2024-08-14T13:43Z
 urls:
   reference: https://umccr.github.io/dracarys/reference
   article: https://umccr.github.io/dracarys/articles
-
diff --git a/reference/BcftoolsStatsFile.html b/reference/BcftoolsStatsFile.html
index 8737394..eee0eca 100644
--- a/reference/BcftoolsStatsFile.html
+++ b/reference/BcftoolsStatsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-bcftools_stats.txt file (QUAL section) output from running bcftools stats."><title>BcftoolsStatsFile R6 Class — BcftoolsStatsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="BcftoolsStatsFile R6 Class — BcftoolsStatsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-bcftools_stats.txt file (QUAL section) output from running bcftools stats."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>BcftoolsStatsFile R6 Class — BcftoolsStatsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="BcftoolsStatsFile R6 Class — BcftoolsStatsFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+bcftools_stats.txt file (QUAL section) output from running bcftools stats."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+bcftools_stats.txt file (QUAL section) output from running bcftools stats."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>BcftoolsStatsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bcftools_stats.R" class="external-link"><code>R/bcftools_stats.R</code></a></small>
+
+      <h1>BcftoolsStatsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/bcftools_stats.R" class="external-link"><code>R/bcftools_stats.R</code></a></small>
       <div class="d-none name"><code>BcftoolsStatsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -151,15 +137,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/bcftools_stats.txt"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">BcftoolsStatsFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample123"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -168,14 +154,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/BclconvertReports.html b/reference/BclconvertReports.html
index 16a54fb..ef83544 100644
--- a/reference/BclconvertReports.html
+++ b/reference/BclconvertReports.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Reads and writes tidy versions of files within the Reports directory output
-from BCLConvert."><title>BclconvertReports R6 Class — BclconvertReports • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="BclconvertReports R6 Class — BclconvertReports"><meta property="og:description" content="Reads and writes tidy versions of files within the Reports directory output
-from BCLConvert."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>BclconvertReports R6 Class — BclconvertReports • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="BclconvertReports R6 Class — BclconvertReports"><meta name="description" content="Reads and writes tidy versions of files within the Reports directory output
+from BCLConvert."><meta property="og:description" content="Reads and writes tidy versions of files within the Reports directory output
+from BCLConvert."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>BclconvertReports R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
+
+      <h1>BclconvertReports R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
       <div class="d-none name"><code>BclconvertReports.Rd</code></div>
     </div>
 
@@ -75,7 +61,7 @@ <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -188,17 +174,17 @@ <h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="va">BclconvertReports</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/WGS_TsqNano/Reports"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">b</span><span class="op">$</span><span class="va">path</span></span></span>
 <span class="r-in"><span><span class="va">b</span><span class="op">$</span><span class="va">contents</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">b</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">b</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sampleA"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -207,14 +193,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/FastqcMetricsFile.html b/reference/FastqcMetricsFile.html
index 086db75..d0ca22c 100644
--- a/reference/FastqcMetricsFile.html
+++ b/reference/FastqcMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
-the fastqc_metrics.csv file output from DRAGEN."><title>FastqcMetrics R6 Class — FastqcMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="FastqcMetrics R6 Class — FastqcMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
-the fastqc_metrics.csv file output from DRAGEN."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>FastqcMetrics R6 Class — FastqcMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="FastqcMetrics R6 Class — FastqcMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
+the fastqc_metrics.csv file output from DRAGEN."><meta property="og:description" content="Contains methods for reading and displaying contents of
+the fastqc_metrics.csv file output from DRAGEN."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>FastqcMetrics R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen_fastqc.R" class="external-link"><code>R/dragen_fastqc.R</code></a></small>
+
+      <h1>FastqcMetrics R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen_fastqc.R" class="external-link"><code>R/dragen_fastqc.R</code></a></small>
       <div class="d-none name"><code>FastqcMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -159,7 +145,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -168,14 +154,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/File.html b/reference/File.html
index 3f002fc..4e33e56 100644
--- a/reference/File.html
+++ b/reference/File.html
@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="File is a base R6 class representing a TSV/CSV/JSON output from
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>File R6 Class — File • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="File R6 Class — File"><meta name="description" content="File is a base R6 class representing a TSV/CSV/JSON output from
 a UMCCR workflow.
-A File has a path, a basename, a type, and can be a presigned URL."><title>File R6 Class — File • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="File R6 Class — File"><meta property="og:description" content="File is a base R6 class representing a TSV/CSV/JSON output from
+A File has a path, a basename, a type, and can be a presigned URL."><meta property="og:description" content="File is a base R6 class representing a TSV/CSV/JSON output from
 a UMCCR workflow.
-A File has a path, a basename, a type, and can be a presigned URL."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+A File has a path, a basename, a type, and can be a presigned URL."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>File R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/File.R" class="external-link"><code>R/File.R</code></a></small>
+
+      <h1>File R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/File.R" class="external-link"><code>R/File.R</code></a></small>
       <div class="d-none name"><code>File.Rd</code></div>
     </div>
 
@@ -78,7 +64,7 @@ <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -181,7 +167,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -190,14 +176,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/FragmentLengthHistFile.html b/reference/FragmentLengthHistFile.html
index b6fc4ed..8fc6450 100644
--- a/reference/FragmentLengthHistFile.html
+++ b/reference/FragmentLengthHistFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and plotting contents of
-the fragment_length_hist.csv file output from DRAGEN."><title>FragmentLengthHistFile R6 Class — FragmentLengthHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="FragmentLengthHistFile R6 Class — FragmentLengthHistFile"><meta property="og:description" content="Contains methods for reading and plotting contents of
-the fragment_length_hist.csv file output from DRAGEN."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>FragmentLengthHistFile R6 Class — FragmentLengthHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="FragmentLengthHistFile R6 Class — FragmentLengthHistFile"><meta name="description" content="Contains methods for reading and plotting contents of
+the fragment_length_hist.csv file output from DRAGEN."><meta property="og:description" content="Contains methods for reading and plotting contents of
+the fragment_length_hist.csv file output from DRAGEN."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>FragmentLengthHistFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>FragmentLengthHistFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>FragmentLengthHistFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -189,7 +175,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">fl</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d</span> <span class="op">|&gt;</span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">count</span> <span class="op">&gt;</span> <span class="fl">10</span><span class="op">)</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"seqc_fl"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -198,14 +184,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/MappingMetricsFile.html b/reference/MappingMetricsFile.html
index 04991db..7415828 100644
--- a/reference/MappingMetricsFile.html
+++ b/reference/MappingMetricsFile.html
@@ -1,69 +1,55 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MappingMetricsFile R6 Class — MappingMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MappingMetricsFile R6 Class — MappingMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
 the mapping_metrics.csv file output from DRAGEN.
 This file contains mapping and aligning metrics, like the metrics computed by
 the Samtools Flagstat command. These metrics are available on an aggregate
 level (over all input data), and on a per read group level. NOTE: we are
 keeping only the read group level metrics (i.e. removing the aggregate data).
 Unless explicitly stated, the metrics units are in reads (i.e., not in
-terms of pairs or alignments)."><title>MappingMetricsFile R6 Class — MappingMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MappingMetricsFile R6 Class — MappingMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
+terms of pairs or alignments)."><meta property="og:description" content="Contains methods for reading and displaying contents of
 the mapping_metrics.csv file output from DRAGEN.
 This file contains mapping and aligning metrics, like the metrics computed by
 the Samtools Flagstat command. These metrics are available on an aggregate
 level (over all input data), and on a per read group level. NOTE: we are
 keeping only the read group level metrics (i.e. removing the aggregate data).
 Unless explicitly stated, the metrics units are in reads (i.e., not in
-terms of pairs or alignments)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+terms of pairs or alignments)."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MappingMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>MappingMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>MappingMetricsFile.Rd</code></div>
     </div>
 
@@ -85,7 +71,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -176,7 +162,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -185,14 +171,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/MultiqcFile.html b/reference/MultiqcFile.html
index 13e510a..8472705 100644
--- a/reference/MultiqcFile.html
+++ b/reference/MultiqcFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-multiqc_data.json file output from MultiQC."><title>MultiqcFile R6 Class — MultiqcFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiqcFile R6 Class — MultiqcFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-multiqc_data.json file output from MultiQC."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MultiqcFile R6 Class — MultiqcFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiqcFile R6 Class — MultiqcFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+multiqc_data.json file output from MultiQC."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+multiqc_data.json file output from MultiQC."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MultiqcFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>MultiqcFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>MultiqcFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -158,17 +144,17 @@ <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/multiqc_data.json"</span></span></span>
 <span class="r-in"><span><span class="va">mqc</span> <span class="op">&lt;-</span> <span class="va">MultiqcFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mqc_parsed</span> <span class="op">&lt;-</span> <span class="va">mqc</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(mqc)</span></span></span>
 <span class="r-in"><span><span class="va">mqc</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">mqc_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mqc_plots_parsed</span> <span class="op">&lt;-</span> <span class="va">mqc</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span>plot <span class="op">=</span> <span class="cn">TRUE</span>, plot_names <span class="op">=</span> <span class="st">"everything"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mqc</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">mqc_plots_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"rds"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -177,14 +163,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/PcgrJsonFile.html b/reference/PcgrJsonFile.html
index 989fc31..27cbebe 100644
--- a/reference/PcgrJsonFile.html
+++ b/reference/PcgrJsonFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-pcgr.json.gz file output from PCGR."><title>PcgrJson R6 Class — PcgrJsonFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PcgrJson R6 Class — PcgrJsonFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-pcgr.json.gz file output from PCGR."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>PcgrJson R6 Class — PcgrJsonFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PcgrJson R6 Class — PcgrJsonFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+pcgr.json.gz file output from PCGR."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+pcgr.json.gz file output from PCGR."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>PcgrJson R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/pcgr.R" class="external-link"><code>R/pcgr.R</code></a></small>
+
+      <h1>PcgrJson R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/pcgr.R" class="external-link"><code>R/pcgr.R</code></a></small>
       <div class="d-none name"><code>PcgrJsonFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -141,15 +127,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/pcgr.json.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">PcgrJsonFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"both"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -158,14 +144,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/PcgrTiersFile.html b/reference/PcgrTiersFile.html
index 3b3ca6b..cb2e5b5 100644
--- a/reference/PcgrTiersFile.html
+++ b/reference/PcgrTiersFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-pcgr.snvs_indels.tiers.tsv file output from PCGR."><title>PcgrTiersFile R6 Class — PcgrTiersFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PcgrTiersFile R6 Class — PcgrTiersFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-pcgr.snvs_indels.tiers.tsv file output from PCGR."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>PcgrTiersFile R6 Class — PcgrTiersFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PcgrTiersFile R6 Class — PcgrTiersFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+pcgr.snvs_indels.tiers.tsv file output from PCGR."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+pcgr.snvs_indels.tiers.tsv file output from PCGR."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>PcgrTiersFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/pcgr.R" class="external-link"><code>R/pcgr.R</code></a></small>
+
+      <h1>PcgrTiersFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/pcgr.R" class="external-link"><code>R/pcgr.R</code></a></small>
       <div class="d-none name"><code>PcgrTiersFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -141,15 +127,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/pcgr.snvs_indels.tiers.tsv"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">PcgrTiersFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"both"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -158,14 +144,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/PloidyEstimationMetricsFile.html b/reference/PloidyEstimationMetricsFile.html
index f5ed74d..7b2b8d1 100644
--- a/reference/PloidyEstimationMetricsFile.html
+++ b/reference/PloidyEstimationMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading contents of
-the ploidy_estimation_metrics.csv file output from DRAGEN."><title>PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile"><meta property="og:description" content="Contains methods for reading contents of
-the ploidy_estimation_metrics.csv file output from DRAGEN."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile"><meta name="description" content="Contains methods for reading contents of
+the ploidy_estimation_metrics.csv file output from DRAGEN."><meta property="og:description" content="Contains methods for reading contents of
+the ploidy_estimation_metrics.csv file output from DRAGEN."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>PloidyEstimationMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>PloidyEstimationMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>PloidyEstimationMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -158,7 +144,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -167,14 +153,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/ReplayFile.html b/reference/ReplayFile.html
index 1c9203b..171a0c7 100644
--- a/reference/ReplayFile.html
+++ b/reference/ReplayFile.html
@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>ReplayFile R6 Class — ReplayFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="ReplayFile R6 Class — ReplayFile"><meta name="description" content="Contains methods for reading contents of
 the replay.json file output from DRAGEN, which contains the DRAGEN command
-line, parameters and version for the specific run."><title>ReplayFile R6 Class — ReplayFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="ReplayFile R6 Class — ReplayFile"><meta property="og:description" content="Contains methods for reading contents of
+line, parameters and version for the specific run."><meta property="og:description" content="Contains methods for reading contents of
 the replay.json file output from DRAGEN, which contains the DRAGEN command
-line, parameters and version for the specific run."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+line, parameters and version for the specific run."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>ReplayFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>ReplayFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>ReplayFile.Rd</code></div>
     </div>
 
@@ -70,7 +56,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -154,7 +140,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">r</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"seqc_replay"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -163,14 +149,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/SvMetricsFile.html b/reference/SvMetricsFile.html
index 441eefd..a450980 100644
--- a/reference/SvMetricsFile.html
+++ b/reference/SvMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
-the sv_metrics.csv file output from DRAGEN"><title>SvMetricsFile R6 Class — SvMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SvMetricsFile R6 Class — SvMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
-the sv_metrics.csv file output from DRAGEN"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>SvMetricsFile R6 Class — SvMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="SvMetricsFile R6 Class — SvMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
+the sv_metrics.csv file output from DRAGEN"><meta property="og:description" content="Contains methods for reading and displaying contents of
+the sv_metrics.csv file output from DRAGEN"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>SvMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>SvMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>SvMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -152,7 +138,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -161,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TimeMetricsFile.html b/reference/TimeMetricsFile.html
index b90a9b2..ab7e4e3 100644
--- a/reference/TimeMetricsFile.html
+++ b/reference/TimeMetricsFile.html
@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TimeMetricsFile R6 Class — TimeMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TimeMetricsFile R6 Class — TimeMetricsFile"><meta name="description" content="Contains methods for reading contents of
 the time_metrics.csv file output from DRAGEN, which contains
-a breakdown of the run duration for each DRAGEN process."><title>TimeMetricsFile R6 Class — TimeMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TimeMetricsFile R6 Class — TimeMetricsFile"><meta property="og:description" content="Contains methods for reading contents of
+a breakdown of the run duration for each DRAGEN process."><meta property="og:description" content="Contains methods for reading contents of
 the time_metrics.csv file output from DRAGEN, which contains
-a breakdown of the run duration for each DRAGEN process."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+a breakdown of the run duration for each DRAGEN process."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TimeMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>TimeMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>TimeMetricsFile.Rd</code></div>
     </div>
 
@@ -70,7 +56,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -160,7 +146,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">tm</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"seqc_time"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -169,14 +155,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TrimmerMetricsFile.html b/reference/TrimmerMetricsFile.html
index 8aa7b93..f0e36fd 100644
--- a/reference/TrimmerMetricsFile.html
+++ b/reference/TrimmerMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
-the trimmer_metrics.csv file output from DRAGEN"><title>TrimmerMetricsFile R6 Class — TrimmerMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TrimmerMetricsFile R6 Class — TrimmerMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
-the trimmer_metrics.csv file output from DRAGEN"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TrimmerMetricsFile R6 Class — TrimmerMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TrimmerMetricsFile R6 Class — TrimmerMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
+the trimmer_metrics.csv file output from DRAGEN"><meta property="og:description" content="Contains methods for reading and displaying contents of
+the trimmer_metrics.csv file output from DRAGEN"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TrimmerMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>TrimmerMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>TrimmerMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -158,7 +144,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -167,14 +153,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoAlignCollapseFusionCallerMetricsFile.html b/reference/TsoAlignCollapseFusionCallerMetricsFile.html
index 9fe0def..7f9e9df 100644
--- a/reference/TsoAlignCollapseFusionCallerMetricsFile.html
+++ b/reference/TsoAlignCollapseFusionCallerMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-AlignCollapseFusionCaller_metrics.json.gz file output from TSO."><title>TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-AlignCollapseFusionCaller_metrics.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+AlignCollapseFusionCaller_metrics.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+AlignCollapseFusionCaller_metrics.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoAlignCollapseFusionCallerMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso_acfc.R" class="external-link"><code>R/tso_acfc.R</code></a></small>
+
+      <h1>TsoAlignCollapseFusionCallerMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso_acfc.R" class="external-link"><code>R/tso_acfc.R</code></a></small>
       <div class="d-none name"><code>TsoAlignCollapseFusionCallerMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -195,7 +181,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">m</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tsv"</span>, <span class="st">"rds"</span><span class="op">)</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -204,14 +190,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoCombinedVariantOutputFile.html b/reference/TsoCombinedVariantOutputFile.html
index 4edd037..63be13c 100644
--- a/reference/TsoCombinedVariantOutputFile.html
+++ b/reference/TsoCombinedVariantOutputFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-CombinedVariantOutput.tsv file output from TSO."><title>TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-CombinedVariantOutput.tsv file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+CombinedVariantOutput.tsv file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+CombinedVariantOutput.tsv file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoCombinedVariantOutputFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoCombinedVariantOutputFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoCombinedVariantOutputFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -152,14 +138,14 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/CombinedVariantOutput.tsv"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">TsoCombinedVariantOutputFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -168,14 +154,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoCopyNumberVariantsVcfFile.html b/reference/TsoCopyNumberVariantsVcfFile.html
index c93e8df..067605c 100644
--- a/reference/TsoCopyNumberVariantsVcfFile.html
+++ b/reference/TsoCopyNumberVariantsVcfFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-CopyNumberVariants.vcf.gz file output from TSO."><title>TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-CopyNumberVariants.vcf.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+CopyNumberVariants.vcf.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+CopyNumberVariants.vcf.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoCopyNumberVariantsVcfFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoCopyNumberVariantsVcfFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoCopyNumberVariantsVcfFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -162,16 +148,16 @@ <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/normalizePath.html" class="external-link">normalizePath</a></span><span class="op">(</span><span class="st">"CopyNumberVariants.vcf.gz"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">TsoCopyNumberVariantsVcfFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, prefix <span class="op">=</span> <span class="st">"FOO"</span>, out_format <span class="op">=</span> <span class="st">"delta"</span>, drid <span class="op">=</span> <span class="st">"wfr.123"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -180,14 +166,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoFragmentLengthHistFile.html b/reference/TsoFragmentLengthHistFile.html
index 2f92ccd..6c2d28c 100644
--- a/reference/TsoFragmentLengthHistFile.html
+++ b/reference/TsoFragmentLengthHistFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-fragment_length_hist.json.gz file output from TSO."><title>TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-fragment_length_hist.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+fragment_length_hist.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+fragment_length_hist.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoFragmentLengthHistFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoFragmentLengthHistFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoFragmentLengthHistFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -187,7 +173,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">fl</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -196,14 +182,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoFusionsCsvFile.html b/reference/TsoFusionsCsvFile.html
index 633936e..0e1c2a4 100644
--- a/reference/TsoFusionsCsvFile.html
+++ b/reference/TsoFusionsCsvFile.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile"><meta name="description" content="Contains methods for reading and displaying contents of the
 Fusions.csv file output from TSO.
 Returns a tibble where the columns are (based on the input file header metadata):
 Sample: input sample ID.
@@ -16,7 +16,7 @@
 Filter: Indicates whether the fusion has passed all of the fusion filters.
 Is_Cosmic_GenePair: Indicates whether the gene pair has been reported by Cosmic(True/False).
 
-"><title>TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
+"><meta property="og:description" content="Contains methods for reading and displaying contents of the
 Fusions.csv file output from TSO.
 Returns a tibble where the columns are (based on the input file header metadata):
 Sample: input sample ID.
@@ -33,57 +33,43 @@
 Filter: Indicates whether the fusion has passed all of the fusion filters.
 Is_Cosmic_GenePair: Indicates whether the gene pair has been reported by Cosmic(True/False).
 
-"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoFusionsCsvFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoFusionsCsvFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoFusionsCsvFile.Rd</code></div>
     </div>
 
@@ -112,7 +98,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -201,7 +187,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">fus</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -210,14 +196,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoMergedSmallVariantsGenomeVcfFile.html b/reference/TsoMergedSmallVariantsGenomeVcfFile.html
index 940d89b..8cadfa4 100644
--- a/reference/TsoMergedSmallVariantsGenomeVcfFile.html
+++ b/reference/TsoMergedSmallVariantsGenomeVcfFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-MergedSmallVariants.genome.vcf.gz file output from TSO."><title>TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-MergedSmallVariants.genome.vcf.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+MergedSmallVariants.genome.vcf.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+MergedSmallVariants.genome.vcf.gz file output from TSO."></head><body>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoMergedSmallVariantsGenomeVcfFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoMergedSmallVariantsGenomeVcfFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoMergedSmallVariantsGenomeVcfFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -162,15 +148,15 @@ <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"MergedSmallVariants.genome.vcf.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">TsoMergedSmallVariantsGenomeVcfFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -179,14 +165,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoMergedSmallVariantsVcfFile.html b/reference/TsoMergedSmallVariantsVcfFile.html
index e396a78..0cf6d9a 100644
--- a/reference/TsoMergedSmallVariantsVcfFile.html
+++ b/reference/TsoMergedSmallVariantsVcfFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-MergedSmallVariants.vcf.gz file output from TSO."><title>TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-MergedSmallVariants.vcf.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+MergedSmallVariants.vcf.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+MergedSmallVariants.vcf.gz file output from TSO."></head><body>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
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+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoMergedSmallVariantsVcfFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoMergedSmallVariantsVcfFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoMergedSmallVariantsVcfFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -162,16 +148,16 @@ <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"MergedSmallVariants.vcf.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">TsoMergedSmallVariantsVcfFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, prefix <span class="op">=</span> <span class="st">"FOO"</span>, out_format <span class="op">=</span> <span class="st">"delta"</span>, drid <span class="op">=</span> <span class="st">"wfr.123"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -180,14 +166,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoMsiFile.html b/reference/TsoMsiFile.html
index 340a4f6..bae2e9e 100644
--- a/reference/TsoMsiFile.html
+++ b/reference/TsoMsiFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-msi.json.gz file output from TSO."><title>TsoMsiFile R6 Class — TsoMsiFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoMsiFile R6 Class — TsoMsiFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-msi.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoMsiFile R6 Class — TsoMsiFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoMsiFile R6 Class — TsoMsiFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+msi.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+msi.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoMsiFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoMsiFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoMsiFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -150,7 +136,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">msi</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -159,14 +145,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoSampleAnalysisResultsFile.html b/reference/TsoSampleAnalysisResultsFile.html
index d354543..36e7779 100644
--- a/reference/TsoSampleAnalysisResultsFile.html
+++ b/reference/TsoSampleAnalysisResultsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-SampleAnalysisResults.json.gz file output from TSO."><title>TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-SampleAnalysisResults.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+SampleAnalysisResults.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+SampleAnalysisResults.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoSampleAnalysisResultsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso_sar.R" class="external-link"><code>R/tso_sar.R</code></a></small>
+
+      <h1>TsoSampleAnalysisResultsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso_sar.R" class="external-link"><code>R/tso_sar.R</code></a></small>
       <div class="d-none name"><code>TsoSampleAnalysisResultsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -157,7 +143,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">res</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempfile</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -166,14 +152,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoTargetRegionCoverageFile.html b/reference/TsoTargetRegionCoverageFile.html
index 75e335e..6b67bde 100644
--- a/reference/TsoTargetRegionCoverageFile.html
+++ b/reference/TsoTargetRegionCoverageFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-TargetRegionCoverage.json.gz file output from TSO."><title>TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-TargetRegionCoverage.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+TargetRegionCoverage.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+TargetRegionCoverage.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoTargetRegionCoverageFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoTargetRegionCoverageFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoTargetRegionCoverageFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -187,7 +173,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">trc</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -196,14 +182,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoTmbFile.html b/reference/TsoTmbFile.html
index 872ed72..c909beb 100644
--- a/reference/TsoTmbFile.html
+++ b/reference/TsoTmbFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-tmb.json.gz file output from TSO."><title>TsoTmbFile R6 Class — TsoTmbFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTmbFile R6 Class — TsoTmbFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-tmb.json.gz file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoTmbFile R6 Class — TsoTmbFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTmbFile R6 Class — TsoTmbFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+tmb.json.gz file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+tmb.json.gz file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoTmbFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoTmbFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoTmbFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -157,7 +143,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">tmb</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -166,14 +152,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/TsoTmbTraceTsvFile.html b/reference/TsoTmbTraceTsvFile.html
index cef7008..8610845 100644
--- a/reference/TsoTmbTraceTsvFile.html
+++ b/reference/TsoTmbTraceTsvFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-TMB_Trace.tsv file output from TSO."><title>TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-TMB_Trace.tsv file output from TSO."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+TMB_Trace.tsv file output from TSO."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+TMB_Trace.tsv file output from TSO."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>TsoTmbTraceTsvFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+
+      <h1>TsoTmbTraceTsvFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
       <div class="d-none name"><code>TsoTmbTraceTsvFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -156,7 +142,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -165,14 +151,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/UmChordTsvFile.html b/reference/UmChordTsvFile.html
index 9fa3500..79a083d 100644
--- a/reference/UmChordTsvFile.html
+++ b/reference/UmChordTsvFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-chord.tsv.gz file output from umccrise."><title>UmChordTsvFile R6 Class — UmChordTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmChordTsvFile R6 Class — UmChordTsvFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-chord.tsv.gz file output from umccrise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UmChordTsvFile R6 Class — UmChordTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmChordTsvFile R6 Class — UmChordTsvFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+chord.tsv.gz file output from umccrise."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+chord.tsv.gz file output from umccrise."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>UmChordTsvFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
+
+      <h1>UmChordTsvFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
       <div class="d-none name"><code>UmChordTsvFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -150,15 +136,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/chord.tsv.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">UmChordTsvFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -167,14 +153,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/UmHrdetectTsvFile.html b/reference/UmHrdetectTsvFile.html
index 0581878..e2da67d 100644
--- a/reference/UmHrdetectTsvFile.html
+++ b/reference/UmHrdetectTsvFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-hrdetect.tsv.gz file output from umccrise."><title>UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-hrdetect.tsv.gz file output from umccrise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+hrdetect.tsv.gz file output from umccrise."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+hrdetect.tsv.gz file output from umccrise."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>UmHrdetectTsvFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
+
+      <h1>UmHrdetectTsvFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
       <div class="d-none name"><code>UmHrdetectTsvFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -144,15 +130,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/hrdetect.tsv.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">UmHrdetectTsvFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -161,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/UmQcSumFile.html b/reference/UmQcSumFile.html
index 7f80ec2..a2dc143 100644
--- a/reference/UmQcSumFile.html
+++ b/reference/UmQcSumFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-qc_summary.tsv.gz file with QC summary metrics output from umccrise."><title>UmQcSumFile R6 Class — UmQcSumFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmQcSumFile R6 Class — UmQcSumFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-qc_summary.tsv.gz file with QC summary metrics output from umccrise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UmQcSumFile R6 Class — UmQcSumFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmQcSumFile R6 Class — UmQcSumFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+qc_summary.tsv.gz file with QC summary metrics output from umccrise."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+qc_summary.tsv.gz file with QC summary metrics output from umccrise."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>UmQcSumFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
+
+      <h1>UmQcSumFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
       <div class="d-none name"><code>UmQcSumFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -145,15 +131,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/snv_2015.tsv.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">UmQcSumFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -162,14 +148,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/UmSigsSnvFile.html b/reference/UmSigsSnvFile.html
index 1191577..24dd652 100644
--- a/reference/UmSigsSnvFile.html
+++ b/reference/UmSigsSnvFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of the
-snv_20XX.tsv.gz file with SNV signatures output from umccrise."><title>UmSigsSnvFile R6 Class — UmSigsSnvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmSigsSnvFile R6 Class — UmSigsSnvFile"><meta property="og:description" content="Contains methods for reading and displaying contents of the
-snv_20XX.tsv.gz file with SNV signatures output from umccrise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>UmSigsSnvFile R6 Class — UmSigsSnvFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="UmSigsSnvFile R6 Class — UmSigsSnvFile"><meta name="description" content="Contains methods for reading and displaying contents of the
+snv_20XX.tsv.gz file with SNV signatures output from umccrise."><meta property="og:description" content="Contains methods for reading and displaying contents of the
+snv_20XX.tsv.gz file with SNV signatures output from umccrise."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
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-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>UmSigsSnvFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
+
+      <h1>UmSigsSnvFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/umccrise.R" class="external-link"><code>R/umccrise.R</code></a></small>
       <div class="d-none name"><code>UmSigsSnvFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -144,15 +130,15 @@ <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#argum
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="st">"/path/to/snv_2015.tsv.gz"</span></span></span>
 <span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va">UmSigsSnvFile</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">d_parsed</span> <span class="op">&lt;-</span> <span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span> <span class="co"># or read(d)</span></span></span>
 <span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d_parsed</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"sample705"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -161,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/VCMetricsFile.html b/reference/VCMetricsFile.html
index 6cf5875..94d1b9c 100644
--- a/reference/VCMetricsFile.html
+++ b/reference/VCMetricsFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
-the vc_metrics.csv file output from DRAGEN, which contains variant calling metrics."><title>VCMetricsFile R6 Class — VCMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VCMetricsFile R6 Class — VCMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
-the vc_metrics.csv file output from DRAGEN, which contains variant calling metrics."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>VCMetricsFile R6 Class — VCMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="VCMetricsFile R6 Class — VCMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
+the vc_metrics.csv file output from DRAGEN, which contains variant calling metrics."><meta property="og:description" content="Contains methods for reading and displaying contents of
+the vc_metrics.csv file output from DRAGEN, which contains variant calling metrics."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/files.html">Files</a>
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-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>VCMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>VCMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>VCMetricsFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -152,7 +138,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -161,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/Wf.html b/reference/Wf.html
new file mode 100644
index 0000000..7253fcb
--- /dev/null
+++ b/reference/Wf.html
@@ -0,0 +1,211 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Workflow R6 Class — Wf • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Workflow R6 Class — Wf"><meta name="description" content="Workflow is a base R6 class representing a bioinformatic
+workflow run from a UMCCR workflow manager."><meta property="og:description" content="Workflow is a base R6 class representing a bioinformatic
+workflow run from a UMCCR workflow manager."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">dracarys</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Workflow R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/Wf.R" class="external-link"><code>R/Wf.R</code></a></small>
+      <div class="d-none name"><code>Wf.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Workflow is a base R6 class representing a bioinformatic
+workflow run from a UMCCR workflow manager.</p>
+    </div>
+
+
+    <div class="section level2">
+    <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
+    <p></p><div class="r6-fields"><dl><dt><code>prid</code></dt>
+<dd><p>Portal run ID.</p></dd>
+
+
+<dt><code>type</code></dt>
+<dd><p>Workflow type.</p></dd>
+
+
+<dt><code>start</code></dt>
+<dd><p>Workflow start datetime.</p></dd>
+
+
+<dt><code>end</code></dt>
+<dd><p>Workflow end datetime.</p></dd>
+
+
+<dt><code>status</code></dt>
+<dd><p>Workflow end status.</p></dd>
+
+
+<dt><code>input</code></dt>
+<dd><p>Workflow input JSON string.</p></dd>
+
+
+<dt><code>output</code></dt>
+<dd><p>Workflow output JSON string.</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div class="section level2">
+    <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
+
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-Wf-new"><code>Wf$new()</code></a></p></li>
+<li><p><a href="#method-Wf-print"><code>Wf$print()</code></a></p></li>
+<li><p><a href="#method-Wf-clone"><code>Wf$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-Wf-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+<p>Create a new Workflow object.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/Wf.html">Wf</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  prid <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  type <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  start <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  end <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  status <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  input <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  output <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>prid</code></dt>
+<dd><p>Portal run ID.</p></dd>
+
+
+<dt><code>type</code></dt>
+<dd><p>Workflow type.</p></dd>
+
+
+<dt><code>start</code></dt>
+<dd><p>Workflow start datetime.</p></dd>
+
+
+<dt><code>end</code></dt>
+<dd><p>Workflow end datetime.</p></dd>
+
+
+<dt><code>status</code></dt>
+<dd><p>Workflow end status.</p></dd>
+
+
+<dt><code>input</code></dt>
+<dd><p>Workflow input JSON string.</p></dd>
+
+
+<dt><code>output</code></dt>
+<dd><p>Workflow output JSON string.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-Wf-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
+<p>Print details about the Workflow.</p><div class="section">
+<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">Wf</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>...</code></dt>
+<dd><p>(ignored).</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-Wf-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">Wf</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">p1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/portaldb_workflow_top4.rds"</span>, package <span class="op">=</span> <span class="st">"rportal"</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">type_name</span> <span class="op">==</span> <span class="st">"umccrise"</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/slice.html" class="external-link">slice</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>cannot open compressed file '', probable reason 'No such file or directory'</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in gzfile(file, "rb"):</span> cannot open the connection</span>
+<span class="r-in"><span><span class="va">w</span> <span class="op">&lt;-</span> <span class="va">Wf</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span></span>
+<span class="r-in"><span>  prid <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">portal_run_id</span>, type <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">type_name</span>, start <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">start</span>, end <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">end</span>,</span></span>
+<span class="r-in"><span>  status <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">end_status</span>, input <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">input</span>, output <span class="op">=</span> <span class="va">p1</span><span class="op">$</span><span class="va">output</span></span></span>
+<span class="r-in"><span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'p1' not found</span>
+<span class="r-in"><span><span class="va">w</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'w' not found</span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/Wf_bcl_convert.html b/reference/Wf_bcl_convert.html
new file mode 100644
index 0000000..bda0e7e
--- /dev/null
+++ b/reference/Wf_bcl_convert.html
@@ -0,0 +1,150 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>bcl_convert Wf R6 Class — Wf_bcl_convert • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="bcl_convert Wf R6 Class — Wf_bcl_convert"><meta name="description" content="Contains methods for reading and processing files output from the UMCCR
+bcl_convert workflow."><meta property="og:description" content="Contains methods for reading and processing files output from the UMCCR
+bcl_convert workflow."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">dracarys</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>bcl_convert Wf R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
+      <div class="d-none name"><code>Wf_bcl_convert.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Contains methods for reading and processing files output from the UMCCR
+<code>bcl_convert</code> workflow.</p>
+    </div>
+
+
+    <div class="section level2">
+    <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
+    <p></p><div class="r6-fields"><dl><dt><code>indir</code></dt>
+<dd><p>Input directory containing Reports per assay type
+(e.g. /primary_data/240607_A01052_0209_BHLHFTDSXC/2024061140802544/).</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div class="section level2">
+    <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
+
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-Wf_bcl_convert-new"><code>Wf_bcl_convert$new()</code></a></p></li>
+<li><p><a href="#method-Wf_bcl_convert-print"><code>Wf_bcl_convert$print()</code></a></p></li>
+<li><p><a href="#method-Wf_bcl_convert-clone"><code>Wf_bcl_convert$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-Wf_bcl_convert-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+<p>Create a new Wf_bcl_convert object.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/Wf_bcl_convert.html">Wf_bcl_convert</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">indir</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>indir</code></dt>
+<dd><p>Input directory containing Reports per assay type.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-Wf_bcl_convert-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
+<p>Print details about the Workflow</p><div class="section">
+<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">Wf_bcl_convert</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>...</code></dt>
+<dd><p>(ignored).</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-Wf_bcl_convert-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">Wf_bcl_convert</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">indir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">sample_id</span> <span class="op">&lt;-</span> <span class="st">"PTC_ctTSO240429"</span></span></span>
+<span class="r-in"><span><span class="va">library_id</span> <span class="op">&lt;-</span> <span class="st">"L2400482"</span></span></span>
+<span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va"><a href="TsoCombinedVariantOutputFile.html">TsoCombinedVariantOutputFile</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/Wf_tso_ctdna_tumor_only.html b/reference/Wf_tso_ctdna_tumor_only.html
new file mode 100644
index 0000000..072fbd8
--- /dev/null
+++ b/reference/Wf_tso_ctdna_tumor_only.html
@@ -0,0 +1,122 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only"><meta name="description" content="Contains methods for reading and processing files output from the UMCCR
+tso_ctdna_tumor_only workflow."><meta property="og:description" content="Contains methods for reading and processing files output from the UMCCR
+tso_ctdna_tumor_only workflow."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">dracarys</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>tso_ctdna_tumor_only Wf R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tso.R" class="external-link"><code>R/tso.R</code></a></small>
+      <div class="d-none name"><code>Wf_tso_ctdna_tumor_only.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Contains methods for reading and processing files output from the UMCCR
+<code>tso_ctdna_tumor_only</code> workflow.</p>
+    </div>
+
+
+    <div class="section level2">
+    <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
+    <p></p><div class="r6-fields"><dl><dt><code>sid</code></dt>
+<dd><p>SampleID.</p></dd>
+
+
+<dt><code>lid</code></dt>
+<dd><p>LibraryID.</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div class="section level2">
+    <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
+
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-Wf_tso_ctdna_tumor_only-clone"><code>Wf_tso_ctdna_tumor_only$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-Wf_tso_ctdna_tumor_only-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">Wf_tso_ctdna_tumor_only</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="st">"~/icav1/g/production/analysis_data/SBJ00596/tso_ctdna_tumor_only"</span>,</span></span>
+<span class="r-in"><span>  <span class="st">"2024050555972acf/L2400482/Results/PTC_ctTSO240429_L2400482/dracarys_gds_sync"</span></span></span>
+<span class="r-in"><span>  <span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">sample_id</span> <span class="op">&lt;-</span> <span class="st">"PTC_ctTSO240429"</span></span></span>
+<span class="r-in"><span><span class="va">library_id</span> <span class="op">&lt;-</span> <span class="st">"L2400482"</span></span></span>
+<span class="r-in"><span><span class="va">d</span> <span class="op">&lt;-</span> <span class="va"><a href="TsoCombinedVariantOutputFile.html">TsoCombinedVariantOutputFile</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">d</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/WgsContigMeanCovFile.html b/reference/WgsContigMeanCovFile.html
index afd230a..c23c534 100644
--- a/reference/WgsContigMeanCovFile.html
+++ b/reference/WgsContigMeanCovFile.html
@@ -1,61 +1,47 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile"><meta name="description" content="Contains methods for reading and displaying contents of
 the wgs_contig_mean_cov_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
 This file contains the estimated coverage for all contigs, and an autosomal
-estimated coverage."><title>WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
+estimated coverage."><meta property="og:description" content="Contains methods for reading and displaying contents of
 the wgs_contig_mean_cov_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
 This file contains the estimated coverage for all contigs, and an autosomal
-estimated coverage."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+estimated coverage."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>WgsContigMeanCovFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>WgsContigMeanCovFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>WgsContigMeanCovFile.Rd</code></div>
     </div>
 
@@ -73,7 +59,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -210,7 +196,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -219,14 +205,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/WgsCoverageMetricsFile.html b/reference/WgsCoverageMetricsFile.html
index bb5b5b0..674b481 100644
--- a/reference/WgsCoverageMetricsFile.html
+++ b/reference/WgsCoverageMetricsFile.html
@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile"><meta name="description" content="Contains methods for reading and displaying contents of
 the wgs_coverage_metrics_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
-This file contains read depth of coverage metrics."><title>WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
+This file contains read depth of coverage metrics."><meta property="og:description" content="Contains methods for reading and displaying contents of
 the wgs_coverage_metrics_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
-This file contains read depth of coverage metrics."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+This file contains read depth of coverage metrics."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>WgsCoverageMetricsFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>WgsCoverageMetricsFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>WgsCoverageMetricsFile.Rd</code></div>
     </div>
 
@@ -70,7 +56,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -165,7 +151,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -174,14 +160,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/WgsFineHistFile.html b/reference/WgsFineHistFile.html
index 85210fd..8515933 100644
--- a/reference/WgsFineHistFile.html
+++ b/reference/WgsFineHistFile.html
@@ -1,63 +1,49 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>WgsFineHistFile R6 Class — WgsFineHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsFineHistFile R6 Class — WgsFineHistFile"><meta name="description" content="Contains methods for reading and displaying contents of
 the wgs_fine_hist_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
 This file contains two columns: Depth and Overall.
 The value in the Depth column ranges from 0 to 1000+ and the Overall
-column indicates the number of loci covered at the corresponding depth."><title>WgsFineHistFile R6 Class — WgsFineHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsFineHistFile R6 Class — WgsFineHistFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
+column indicates the number of loci covered at the corresponding depth."><meta property="og:description" content="Contains methods for reading and displaying contents of
 the wgs_fine_hist_&amp;lt;phenotype&amp;gt;.csv file output from DRAGEN.
 This file contains two columns: Depth and Overall.
 The value in the Depth column ranges from 0 to 1000+ and the Overall
-column indicates the number of loci covered at the corresponding depth."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+column indicates the number of loci covered at the corresponding depth."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>WgsFineHistFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>WgsFineHistFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>WgsFineHistFile.Rd</code></div>
     </div>
 
@@ -76,7 +62,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -201,7 +187,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">ch2</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span><span class="va">d2</span>, out_dir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span>, prefix <span class="op">=</span> <span class="st">"seqc_t"</span>, out_format <span class="op">=</span> <span class="st">"tsv"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -210,14 +196,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/WgsHistFile.html b/reference/WgsHistFile.html
index 2139bea..c49042f 100644
--- a/reference/WgsHistFile.html
+++ b/reference/WgsHistFile.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains methods for reading and displaying contents of
-the wgs_hist.csv file output from DRAGEN"><title>WgsHistFile R6 Class — WgsHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsHistFile R6 Class — WgsHistFile"><meta property="og:description" content="Contains methods for reading and displaying contents of
-the wgs_hist.csv file output from DRAGEN"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>WgsHistFile R6 Class — WgsHistFile • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="WgsHistFile R6 Class — WgsHistFile"><meta name="description" content="Contains methods for reading and displaying contents of
+the wgs_hist.csv file output from DRAGEN"><meta property="og:description" content="Contains methods for reading and displaying contents of
+the wgs_hist.csv file output from DRAGEN"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>WgsHistFile R6 Class</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>WgsHistFile R6 Class</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>WgsHistFile.Rd</code></div>
     </div>
 
@@ -67,7 +53,7 @@ <h2 id="super-class">Super class<a class="anchor" aria-label="anchor" href="#sup
     </div>
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -152,7 +138,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -161,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/bcftools_parse_vcf.html b/reference/bcftools_parse_vcf.html
index 412d7f0..165ed8a 100644
--- a/reference/bcftools_parse_vcf.html
+++ b/reference/bcftools_parse_vcf.html
@@ -1,59 +1,45 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Parse VCF with bcftools.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Parse VCF with bcftools — bcftools_parse_vcf • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse VCF with bcftools — bcftools_parse_vcf"><meta name="description" content="Parse VCF with bcftools.
 Uses bcftools under the hood to do the heavy lifting with field splitting,
-then converts the parsed character vector to a tibble."><title>Parse VCF with bcftools — bcftools_parse_vcf • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse VCF with bcftools — bcftools_parse_vcf"><meta property="og:description" content="Parse VCF with bcftools.
+then converts the parsed character vector to a tibble."><meta property="og:description" content="Parse VCF with bcftools.
 Uses bcftools under the hood to do the heavy lifting with field splitting,
-then converts the parsed character vector to a tibble."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+then converts the parsed character vector to a tibble."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse VCF with bcftools</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/vcf.R" class="external-link"><code>R/vcf.R</code></a></small>
+
+      <h1>Parse VCF with bcftools</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/vcf.R" class="external-link"><code>R/vcf.R</code></a></small>
       <div class="d-none name"><code>bcftools_parse_vcf.Rd</code></div>
     </div>
 
@@ -70,23 +56,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>vcf</dt>
+
+
+<dl><dt id="arg-vcf">vcf<a class="anchor" aria-label="anchor" href="#arg-vcf"></a></dt>
 <dd><p>VCF with one or more samples.</p></dd>
 
 
-<dt>only_pass</dt>
+<dt id="arg-only-pass">only_pass<a class="anchor" aria-label="anchor" href="#arg-only-pass"></a></dt>
 <dd><p>Keep PASS variants only (def: TRUE).</p></dd>
 
 
-<dt>alias</dt>
+<dt id="arg-alias">alias<a class="anchor" aria-label="anchor" href="#arg-alias"></a></dt>
 <dd><p>Substitute sample names with S1/S2/... alias (def: TRUE).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with all the main, FORMAT, and INFO fields detected in
+    <p>A tibble with all the main, FORMAT, and INFO fields detected in
 the VCF header as columns.</p>
     </div>
     <div class="section level2">
@@ -95,7 +81,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 columns.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -104,14 +90,14 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/bcftools_parse_vcf_regions.html b/reference/bcftools_parse_vcf_regions.html
index ea1785b..5fd70b0 100644
--- a/reference/bcftools_parse_vcf_regions.html
+++ b/reference/bcftools_parse_vcf_regions.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Parses VCF regions with bcftools. The VCF subset is written to a temporary
-file in the local filesystem, then parsed into a tibble object."><title>Parse VCF regions with bcftools — bcftools_parse_vcf_regions • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse VCF regions with bcftools — bcftools_parse_vcf_regions"><meta property="og:description" content="Parses VCF regions with bcftools. The VCF subset is written to a temporary
-file in the local filesystem, then parsed into a tibble object."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Parse VCF regions with bcftools — bcftools_parse_vcf_regions • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse VCF regions with bcftools — bcftools_parse_vcf_regions"><meta name="description" content="Parses VCF regions with bcftools. The VCF subset is written to a temporary
+file in the local filesystem, then parsed into a tibble object."><meta property="og:description" content="Parses VCF regions with bcftools. The VCF subset is written to a temporary
+file in the local filesystem, then parsed into a tibble object."></head><body>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse VCF regions with bcftools</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/vcf.R" class="external-link"><code>R/vcf.R</code></a></small>
+
+      <h1>Parse VCF regions with bcftools</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/vcf.R" class="external-link"><code>R/vcf.R</code></a></small>
       <div class="d-none name"><code>bcftools_parse_vcf_regions.Rd</code></div>
     </div>
 
@@ -67,37 +53,37 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>vcf</dt>
+
+
+<dl><dt id="arg-vcf">vcf<a class="anchor" aria-label="anchor" href="#arg-vcf"></a></dt>
 <dd><p>Path to VCF. Can be S3, http or local. If presigned URL, need to
 also concatenate the VCF index as in 'vcf_url##idx##vcfi_url'.</p></dd>
 
 
-<dt>r</dt>
+<dt id="arg-r">r<a class="anchor" aria-label="anchor" href="#arg-r"></a></dt>
 <dd><p>Character vector of regions to subset (e.g. c('chr1:123-456', 'chr2:789-1000'))</p></dd>
 
 
-<dt>only_pass</dt>
+<dt id="arg-only-pass">only_pass<a class="anchor" aria-label="anchor" href="#arg-only-pass"></a></dt>
 <dd><p>Keep PASS variants only (def: TRUE).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with all the main, FORMAT, and INFO fields detected in
+    <p>A tibble with all the main, FORMAT, and INFO fields detected in
 the VCF header as columns, for the regions specified in <code>r</code> (if any).</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">vcf_local</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"MergedSmallVariants.vcf.gz"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">r</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"chr1:115256529-115256529"</span>, <span class="st">"chr2:29443613-29443613"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">bcftools_parse_vcf_regions</span><span class="op">(</span><span class="va">vcf_local</span>, <span class="va">r</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -106,14 +92,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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   </body></html>
 
diff --git a/reference/bclconvert_read_adaptermetrics.html b/reference/bclconvert_read_adaptermetrics.html
deleted file mode 100644
index 9164cae..0000000
--- a/reference/bclconvert_read_adaptermetrics.html
+++ /dev/null
@@ -1,108 +0,0 @@
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-      <img src="" class="logo" alt=""><h1>BCLConvert Adapter Metrics</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
-      <div class="d-none name"><code>bclconvert_read_adaptermetrics.Rd</code></div>
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-output by BCLConvert.</p>
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-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>Path to <code>Adapter_Metrics.csv</code> file.</p></dd>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/WGS_TsqNano/Reports/Adapter_Metrics.csv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">bclconvert_read_adaptermetrics</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
-</code></pre></div>
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diff --git a/reference/bclconvert_read_demultiplexstats.html b/reference/bclconvert_read_demultiplexstats.html
deleted file mode 100644
index d828528..0000000
--- a/reference/bclconvert_read_demultiplexstats.html
+++ /dev/null
@@ -1,108 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Reads the Demultiplex_Stats.csv file in the Reports directory
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-      <img src="" class="logo" alt=""><h1>BCLConvert Demultiplex Stats</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
-      <div class="d-none name"><code>bclconvert_read_demultiplexstats.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads the <code>Demultiplex_Stats.csv</code> file in the <code>Reports</code> directory
-output by BCLConvert.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bclconvert_read_demultiplexstats</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>Path to <code>Demultiplex_Stats.csv</code> file.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/WGS_TsqNano/Reports/Demultiplex_Stats.csv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">bclconvert_read_demultiplexstats</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
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diff --git a/reference/bclconvert_read_indexhoppingcounts.html b/reference/bclconvert_read_indexhoppingcounts.html
deleted file mode 100644
index a8c62fb..0000000
--- a/reference/bclconvert_read_indexhoppingcounts.html
+++ /dev/null
@@ -1,108 +0,0 @@
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-      <img src="" class="logo" alt=""><h1>BCLConvert Index Hopping Counts</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
-      <div class="d-none name"><code>bclconvert_read_indexhoppingcounts.Rd</code></div>
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-    <p>Reads the <code>Index_Hopping_Counts.csv</code> file in the <code>Reports</code> directory
-output by BCLConvert.</p>
-    </div>
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-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bclconvert_read_indexhoppingcounts</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
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-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>Path to <code>Index_Hopping_Counts.csv</code> file.</p></dd>
-
-</dl></div>
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-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/WGS_TsqNano/Reports/Index_Hopping_Counts.csv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">bclconvert_read_indexhoppingcounts</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
-</code></pre></div>
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diff --git a/reference/bclconvert_read_topunknownbarcodes.html b/reference/bclconvert_read_topunknownbarcodes.html
deleted file mode 100644
index 3f8c067..0000000
--- a/reference/bclconvert_read_topunknownbarcodes.html
+++ /dev/null
@@ -1,108 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Reads the Top_Unknown_Barcodes.csv file in the Reports directory
-output by BCLConvert."><title>BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes"><meta property="og:description" content="Reads the Top_Unknown_Barcodes.csv file in the Reports directory
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-      <img src="" class="logo" alt=""><h1>BCLConvert Top Unknown Barcodes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/bclconvert.R" class="external-link"><code>R/bclconvert.R</code></a></small>
-      <div class="d-none name"><code>bclconvert_read_topunknownbarcodes.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads the <code>Top_Unknown_Barcodes.csv</code> file in the <code>Reports</code> directory
-output by BCLConvert.</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bclconvert_read_topunknownbarcodes</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p>Path to <code>Top_Unknown_Barcodes.csv</code> file.</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/WGS_TsqNano/Reports/Top_Unknown_Barcodes.csv"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">bclconvert_read_topunknownbarcodes</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
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-    <footer><div class="pkgdown-footer-left">
-  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
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diff --git a/reference/date_log.html b/reference/date_log.html
index d8d8851..23425d2 100644
--- a/reference/date_log.html
+++ b/reference/date_log.html
@@ -1,55 +1,41 @@
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Print current timestamp for logging — date_log • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Print current timestamp for logging — date_log"><meta name="description" content="Print current timestamp for logging"><meta property="og:description" content="Print current timestamp for logging"></head><body>
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Print current timestamp for logging</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+
+      <h1>Print current timestamp for logging</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>date_log.Rd</code></div>
     </div>
 
@@ -64,12 +50,10 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Current timestamp as character.</p>
+    <p>Current timestamp as character.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -78,14 +62,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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diff --git a/reference/dr_func_eval.html b/reference/dr_func_eval.html
index 0b6ad45..243f9a9 100644
--- a/reference/dr_func_eval.html
+++ b/reference/dr_func_eval.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This is somewhat a hack for getting a function to evaluate based on a lookup
-vector. If the function is not found, it returns NULL."><title>Evaluate dracarys Function — dr_func_eval • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Evaluate dracarys Function — dr_func_eval"><meta property="og:description" content="This is somewhat a hack for getting a function to evaluate based on a lookup
-vector. If the function is not found, it returns NULL."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Evaluate dracarys Function — dr_func_eval • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Evaluate dracarys Function — dr_func_eval"><meta name="description" content="This is somewhat a hack for getting a function to evaluate based on a lookup
+vector. If the function is not found, it returns NULL."><meta property="og:description" content="This is somewhat a hack for getting a function to evaluate based on a lookup
+vector. If the function is not found, it returns NULL."></head><body>
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-    
 
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Evaluate dracarys Function</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
+
+      <h1>Evaluate dracarys Function</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
       <div class="d-none name"><code>dr_func_eval.Rd</code></div>
     </div>
 
@@ -67,20 +53,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>f</dt>
+
+
+<dl><dt id="arg-f">f<a class="anchor" aria-label="anchor" href="#arg-f"></a></dt>
 <dd><p>Name of function to evaluate.</p></dd>
 
 
-<dt>v</dt>
+<dt id="arg-v">v<a class="anchor" aria-label="anchor" href="#arg-v"></a></dt>
 <dd><p>Character vector of strings evaluating to functions. By default,
 this points to the functions in the DR_FILE_REGEX dracarys tibble.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Evaluated function.</p>
+    <p>Evaluated function.</p>
     </div>
 
     <div class="section level2">
@@ -90,7 +76,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">obj</span> <span class="op">&lt;-</span> <span class="fu">dr_func_eval</span><span class="op">(</span><span class="st">"TsoFragmentLengthHistFile"</span><span class="op">)</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -99,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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diff --git a/reference/dr_gds_download.html b/reference/dr_gds_download.html
index d64112b..1755997 100644
--- a/reference/dr_gds_download.html
+++ b/reference/dr_gds_download.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Download only GDS files that can be processed by dracarys."><title>dracarys GDS Download — dr_gds_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys GDS Download — dr_gds_download"><meta property="og:description" content="Download only GDS files that can be processed by dracarys."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>dracarys GDS Download — dr_gds_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys GDS Download — dr_gds_download"><meta name="description" content="Download only GDS files that can be processed by dracarys."><meta property="og:description" content="Download only GDS files that can be processed by dracarys."></head><body>
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-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>dracarys GDS Download</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>dracarys GDS Download</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>dr_gds_download.Rd</code></div>
     </div>
 
@@ -73,42 +59,44 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gdsdir</dt>
+
+
+<dl><dt id="arg-gdsdir">gdsdir<a class="anchor" aria-label="anchor" href="#arg-gdsdir"></a></dt>
 <dd><p>Full path to GDS directory.</p></dd>
 
 
-<dt>outdir</dt>
+<dt id="arg-outdir">outdir<a class="anchor" aria-label="anchor" href="#arg-outdir"></a></dt>
 <dd><p>Path to output directory.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>Page size (def: 100).</p></dd>
 
 
-<dt>pattern</dt>
+<dt id="arg-pattern">pattern<a class="anchor" aria-label="anchor" href="#arg-pattern"></a></dt>
 <dd><p>Pattern to further filter the returned file type tibble.</p></dd>
 
 
-<dt>dryrun</dt>
+<dt id="arg-dryrun">dryrun<a class="anchor" aria-label="anchor" href="#arg-dryrun"></a></dt>
 <dd><p>If TRUE, just list the files that will be downloaded (don't
 download them).</p></dd>
 
 
-<dt>regexes</dt>
+<dt id="arg-regexes">regexes<a class="anchor" aria-label="anchor" href="#arg-regexes"></a></dt>
 <dd><p>Tibble with regex and function name.</p></dd>
 
 
-<dt>recursive</dt>
+<dt id="arg-recursive">recursive<a class="anchor" aria-label="anchor" href="#arg-recursive"></a></dt>
 <dd><p>Should files be returned recursively <em>in and under</em> the specified
 GDS directory (TRUE), or <em>only directly in</em> the specified GDS directory (FALSE) (def: TRUE).</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -117,14 +105,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
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-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/dr_output_format_valid.html b/reference/dr_output_format_valid.html
index 7f32ad2..f963bc7 100644
--- a/reference/dr_output_format_valid.html
+++ b/reference/dr_output_format_valid.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Checks that the specified output format is valid."><title>Output Format is Valid — dr_output_format_valid • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Output Format is Valid — dr_output_format_valid"><meta property="og:description" content="Checks that the specified output format is valid."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Output Format is Valid — dr_output_format_valid • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Output Format is Valid — dr_output_format_valid"><meta name="description" content="Checks that the specified output format is valid."><meta property="og:description" content="Checks that the specified output format is valid."></head><body>
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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-      <img src="" class="logo" alt=""><h1>Output Format is Valid</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+
+      <h1>Output Format is Valid</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>dr_output_format_valid.Rd</code></div>
     </div>
 
@@ -64,12 +50,14 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>Output format.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -78,14 +66,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/dr_s3_download.html b/reference/dr_s3_download.html
index 96e8253..7237498 100644
--- a/reference/dr_s3_download.html
+++ b/reference/dr_s3_download.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Download only S3 files that can be processed by dracarys."><title>dracarys S3 Download — dr_s3_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys S3 Download — dr_s3_download"><meta property="og:description" content="Download only S3 files that can be processed by dracarys."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>dracarys S3 Download — dr_s3_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys S3 Download — dr_s3_download"><meta name="description" content="Download only S3 files that can be processed by dracarys."><meta property="og:description" content="Download only S3 files that can be processed by dracarys."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
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-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>dracarys S3 Download</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
+
+      <h1>dracarys S3 Download</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
       <div class="d-none name"><code>dr_s3_download.Rd</code></div>
     </div>
 
@@ -71,27 +57,29 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>s3dir</dt>
+
+
+<dl><dt id="arg-s-dir">s3dir<a class="anchor" aria-label="anchor" href="#arg-s-dir"></a></dt>
 <dd><p>Full path to S3 directory.</p></dd>
 
 
-<dt>outdir</dt>
+<dt id="arg-outdir">outdir<a class="anchor" aria-label="anchor" href="#arg-outdir"></a></dt>
 <dd><p>Path to output directory.</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>Page size (def: 100).</p></dd>
 
 
-<dt>pattern</dt>
+<dt id="arg-pattern">pattern<a class="anchor" aria-label="anchor" href="#arg-pattern"></a></dt>
 <dd><p>Pattern to further filter the returned file type tibble.</p></dd>
 
 
-<dt>regexes</dt>
+<dt id="arg-regexes">regexes<a class="anchor" aria-label="anchor" href="#arg-regexes"></a></dt>
 <dd><p>Tibble with regex and function name.</p></dd>
 
 
-<dt>dryrun</dt>
+<dt id="arg-dryrun">dryrun<a class="anchor" aria-label="anchor" href="#arg-dryrun"></a></dt>
 <dd><p>If TRUE, just list the files that will be downloaded (don't
 download them).</p></dd>
 
@@ -107,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -116,14 +104,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/dracarys-package.html b/reference/dracarys-package.html
index 1529a7a..9954229 100644
--- a/reference/dracarys-package.html
+++ b/reference/dracarys-package.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Post-processing DRAGEN workflows."><title>dracarys: Post-processing DRAGEN workflows — dracarys-package • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys: Post-processing DRAGEN workflows — dracarys-package"><meta property="og:description" content="Post-processing DRAGEN workflows."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>dracarys: Post-processing DRAGEN workflows — dracarys-package • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="dracarys: Post-processing DRAGEN workflows — dracarys-package"><meta name="description" content="Post-processing DRAGEN workflows."><meta property="og:description" content="Post-processing DRAGEN workflows."></head><body>
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>dracarys: Post-processing DRAGEN workflows</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dracarys-package.R" class="external-link"><code>R/dracarys-package.R</code></a></small>
+
+      <h1>dracarys: Post-processing DRAGEN workflows</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dracarys-package.R" class="external-link"><code>R/dracarys-package.R</code></a></small>
       <div class="d-none name"><code>dracarys-package.Rd</code></div>
     </div>
 
@@ -71,7 +57,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 <p>Authors:</p><ul><li><p>Victor San Kho Lin (<a href="https://orcid.org/0000-0002-3940-4729" class="external-link">ORCID</a>) [contributor]</p></li>
 </ul></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -80,14 +66,14 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/dracarys.html b/reference/dracarys.html
new file mode 100644
index 0000000..29386ea
--- /dev/null
+++ b/reference/dracarys.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://umccr.github.io/dracarys/reference/dracarys-package.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://umccr.github.io/dracarys/reference/dracarys-package.html">
+  </head>
+</html>
+
diff --git a/reference/empty_tbl.html b/reference/empty_tbl.html
index 07b0156..21b687a 100644
--- a/reference/empty_tbl.html
+++ b/reference/empty_tbl.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="From https://stackoverflow.com/a/62535671/2169986. Useful for handling
-edge cases with empty data."><title>Create Empty Tibble Given Column Names — empty_tbl • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create Empty Tibble Given Column Names — empty_tbl"><meta property="og:description" content="From https://stackoverflow.com/a/62535671/2169986. Useful for handling
-edge cases with empty data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create Empty Tibble Given Column Names — empty_tbl • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create Empty Tibble Given Column Names — empty_tbl"><meta name="description" content="From https://stackoverflow.com/a/62535671/2169986. Useful for handling
+edge cases with empty data."><meta property="og:description" content="From https://stackoverflow.com/a/62535671/2169986. Useful for handling
+edge cases with empty data."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Create Empty Tibble Given Column Names</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+
+      <h1>Create Empty Tibble Given Column Names</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>empty_tbl.Rd</code></div>
     </div>
 
@@ -67,22 +53,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cnames</dt>
+
+
+<dl><dt id="arg-cnames">cnames<a class="anchor" aria-label="anchor" href="#arg-cnames"></a></dt>
 <dd><p>Character vector of column names to use.</p></dd>
 
 
-<dt>ctypes</dt>
+<dt id="arg-ctypes">ctypes<a class="anchor" aria-label="anchor" href="#arg-ctypes"></a></dt>
 <dd><p>Character vector of column types corresponding to <code>cnames</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with 0 rows and the given column names.</p>
+    <p>A tibble with 0 rows and the given column names.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -91,14 +77,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/file_regex_getter.html b/reference/file_regex_getter.html
index 0e184cd..6c30ee6 100644
--- a/reference/file_regex_getter.html
+++ b/reference/file_regex_getter.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get dracarys DR_FILE_REGEX"><title>Get dracarys DR_FILE_REGEX — file_regex_getter • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get dracarys DR_FILE_REGEX — file_regex_getter"><meta property="og:description" content="Get dracarys DR_FILE_REGEX"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get dracarys DR_FILE_REGEX — file_regex_getter • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get dracarys DR_FILE_REGEX — file_regex_getter"><meta name="description" content="Get dracarys DR_FILE_REGEX"><meta property="og:description" content="Get dracarys DR_FILE_REGEX"></head><body>
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Get dracarys <code>DR_FILE_REGEX</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
+
+      <h1>Get dracarys <code>DR_FILE_REGEX</code></h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
       <div class="d-none name"><code>file_regex_getter.Rd</code></div>
     </div>
 
@@ -64,12 +50,10 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>DR_FILE_REGEX</code> R tibble object.</p>
+    <p><code>DR_FILE_REGEX</code> R tibble object.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -78,14 +62,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_file_download.html b/reference/gds_file_download.html
index db5ce0b..ff412ec 100644
--- a/reference/gds_file_download.html
+++ b/reference/gds_file_download.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="GDS File Download via CLI"><title>GDS File Download via CLI — gds_file_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Download via CLI — gds_file_download"><meta property="og:description" content="GDS File Download via CLI"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GDS File Download via CLI — gds_file_download • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Download via CLI — gds_file_download"><meta name="description" content="GDS File Download via CLI"><meta property="og:description" content="GDS File Download via CLI"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>GDS File Download via CLI</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>GDS File Download via CLI</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_file_download.Rd</code></div>
     </div>
 
@@ -64,20 +50,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gds</dt>
+
+
+<dl><dt id="arg-gds">gds<a class="anchor" aria-label="anchor" href="#arg-gds"></a></dt>
 <dd><p>Full path to GDS file.</p></dd>
 
 
-<dt>out</dt>
+<dt id="arg-out">out<a class="anchor" aria-label="anchor" href="#arg-out"></a></dt>
 <dd><p>Path to output file.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -86,14 +74,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_file_download_api.html b/reference/gds_file_download_api.html
index 64415e0..99cdfd5 100644
--- a/reference/gds_file_download_api.html
+++ b/reference/gds_file_download_api.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="GDS File Download via API"><title>GDS File Download via API — gds_file_download_api • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Download via API — gds_file_download_api"><meta property="og:description" content="GDS File Download via API"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GDS File Download via API — gds_file_download_api • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Download via API — gds_file_download_api"><meta name="description" content="GDS File Download via API"><meta property="og:description" content="GDS File Download via API"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>GDS File Download via API</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>GDS File Download via API</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_file_download_api.Rd</code></div>
     </div>
 
@@ -64,29 +50,31 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gds_fileid</dt>
+
+
+<dl><dt id="arg-gds-fileid">gds_fileid<a class="anchor" aria-label="anchor" href="#arg-gds-fileid"></a></dt>
 <dd><p>GDS file ID.</p></dd>
 
 
-<dt>out_file</dt>
+<dt id="arg-out-file">out_file<a class="anchor" aria-label="anchor" href="#arg-out-file"></a></dt>
 <dd><p>Path to output file.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 </dl></div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">gds_fileid</span> <span class="op">&lt;-</span> <span class="st">"fil.f9aa2ba7af0c4330095d08dadd2e16b0"</span></span></span>
 <span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempfile</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">token</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"ICA_ACCESS_TOKEN"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -95,14 +83,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_file_presignedurl.html b/reference/gds_file_presignedurl.html
index 095da59..90f4a44 100644
--- a/reference/gds_file_presignedurl.html
+++ b/reference/gds_file_presignedurl.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns presigned URL of given GDS file."><title>GDS File Presigned URL — gds_file_presignedurl • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Presigned URL — gds_file_presignedurl"><meta property="og:description" content="Returns presigned URL of given GDS file."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GDS File Presigned URL — gds_file_presignedurl • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS File Presigned URL — gds_file_presignedurl"><meta name="description" content="Returns presigned URL of given GDS file."><meta property="og:description" content="Returns presigned URL of given GDS file."></head><body>
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>GDS File Presigned URL</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>GDS File Presigned URL</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_file_presignedurl.Rd</code></div>
     </div>
 
@@ -64,22 +50,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gds_fileid</dt>
+
+
+<dl><dt id="arg-gds-fileid">gds_fileid<a class="anchor" aria-label="anchor" href="#arg-gds-fileid"></a></dt>
 <dd><p>GDS file ID.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Presigned URL if valid.</p>
+    <p>Presigned URL if valid.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -88,14 +74,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_files_list.html b/reference/gds_files_list.html
index 4b3a283..b07fa46 100644
--- a/reference/gds_files_list.html
+++ b/reference/gds_files_list.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="List files on ICA GDS filesystem."><title>GDS Files List — gds_files_list • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS Files List — gds_files_list"><meta property="og:description" content="List files on ICA GDS filesystem."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GDS Files List — gds_files_list • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GDS Files List — gds_files_list"><meta name="description" content="List files on ICA GDS filesystem."><meta property="og:description" content="List files on ICA GDS filesystem."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>GDS Files List</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>GDS Files List</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_files_list.Rd</code></div>
     </div>
 
@@ -72,46 +58,46 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gdsdir</dt>
+
+
+<dl><dt id="arg-gdsdir">gdsdir<a class="anchor" aria-label="anchor" href="#arg-gdsdir"></a></dt>
 <dd><p>Full path to GDS directory.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>Page size (def: 10).</p></dd>
 
 
-<dt>include_url</dt>
+<dt id="arg-include-url">include_url<a class="anchor" aria-label="anchor" href="#arg-include-url"></a></dt>
 <dd><p>Include presigned URLs to all files within the GDS directory (def: FALSE).</p></dd>
 
 
-<dt>no_recurse</dt>
+<dt id="arg-no-recurse">no_recurse<a class="anchor" aria-label="anchor" href="#arg-no-recurse"></a></dt>
 <dd><p>Do not recurse through the file list i.e. just give the first &lt;page_size&gt; items
 without recursing further down the list using &lt;page_token&gt;.</p></dd>
 
 
-<dt>page_token</dt>
+<dt id="arg-page-token">page_token<a class="anchor" aria-label="anchor" href="#arg-page-token"></a></dt>
 <dd><p>Page token (def: NULL). Used internally for recursion.</p></dd>
 
 
-<dt>recursive</dt>
+<dt id="arg-recursive">recursive<a class="anchor" aria-label="anchor" href="#arg-recursive"></a></dt>
 <dd><p>Should files be returned recursively <em>in and under</em> the specified
 GDS directory, or <em>only directly in</em> the specified GDS directory (def: TRUE).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with file basename, file size, file full data path, file dir name.</p>
+    <p>Tibble with file basename, file size, file full data path, file dir name.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">gdsdir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="st">"gds://production/primary_data"</span>,</span></span>
 <span class="r-in"><span>  <span class="st">"240322_A00130_0290_BH5HLLDSXC/20240323f56ec5a5/WGS_TsqNano"</span></span></span>
@@ -131,10 +117,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">no_recurse</span> <span class="op">&lt;-</span> <span class="cn">TRUE</span></span></span>
 <span class="r-in"><span><span class="va">recursive</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span></span>
 <span class="r-in"><span><span class="fu">gds_files_list</span><span class="op">(</span><span class="va">gdsdir</span>, <span class="va">token</span>, <span class="va">page_size</span>, <span class="va">include_url</span>, <span class="va">no_recurse</span>, <span class="va">page_token</span>, <span class="va">recursive</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -143,14 +129,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_files_list_fastq.html b/reference/gds_files_list_fastq.html
new file mode 100644
index 0000000..24b0169
--- /dev/null
+++ b/reference/gds_files_list_fastq.html
@@ -0,0 +1,108 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>List FASTQs In GDS Directory — gds_files_list_fastq • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List FASTQs In GDS Directory — gds_files_list_fastq"><meta name="description" content="List FASTQs In GDS Directory"><meta property="og:description" content="List FASTQs In GDS Directory"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">dracarys</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>List FASTQs In GDS Directory</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+      <div class="d-none name"><code>gds_files_list_fastq.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>List FASTQs In GDS Directory</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">gds_files_list_fastq</span><span class="op">(</span><span class="va">gdsdir</span>, <span class="va">token</span>, include_url <span class="op">=</span> <span class="cn">FALSE</span>, page_size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-gdsdir">gdsdir<a class="anchor" aria-label="anchor" href="#arg-gdsdir"></a></dt>
+<dd><p>GDS directory.</p></dd>
+
+
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
+<dd><p>ICA access token.</p></dd>
+
+
+<dt id="arg-include-url">include_url<a class="anchor" aria-label="anchor" href="#arg-include-url"></a></dt>
+<dd><p>Include presigned URLs to all files within the GDS directory.</p></dd>
+
+
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
+<dd><p>Page size.</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>A tibble with type, bname, size, file_id, path, and presigned URL.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">prim</span> <span class="op">&lt;-</span> <span class="st">"gds://production/primary_data"</span></span></span>
+<span class="r-in"><span><span class="va">run</span> <span class="op">&lt;-</span> <span class="st">"240719_A00130_0323_BHMCYHDSXC/202407205bad380d/BiModal_BM-5L"</span></span></span>
+<span class="r-in"><span><span class="va">gdsdir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="va">prim</span>, <span class="va">run</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">token</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"ICA_ACCESS_TOKEN"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">include_url</span> <span class="op">&lt;-</span> <span class="cn">F</span></span></span>
+<span class="r-in"><span><span class="va">page_size</span> <span class="op">&lt;-</span> <span class="fl">100</span></span></span>
+<span class="r-in"><span><span class="fu">gds_files_list_fastq</span><span class="op">(</span><span class="va">gdsdir</span>, <span class="va">token</span>, <span class="va">include_url</span>, <span class="va">page_size</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://github.com/pdiakumis" class="external-link">Peter Diakumis</a>, <a href="https://github.com/victorskl" class="external-link">Victor San Kho Lin</a>.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/gds_files_list_filter_relevant.html b/reference/gds_files_list_filter_relevant.html
index 197fad4..67d7bd6 100644
--- a/reference/gds_files_list_filter_relevant.html
+++ b/reference/gds_files_list_filter_relevant.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Lists relevant files in a GDS directory."><title>List Relevant Files In GDS Directory — gds_files_list_filter_relevant • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List Relevant Files In GDS Directory — gds_files_list_filter_relevant"><meta property="og:description" content="Lists relevant files in a GDS directory."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>List Relevant Files In GDS Directory — gds_files_list_filter_relevant • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List Relevant Files In GDS Directory — gds_files_list_filter_relevant"><meta name="description" content="Lists relevant files in a GDS directory."><meta property="og:description" content="Lists relevant files in a GDS directory."></head><body>
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>List Relevant Files In GDS Directory</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>List Relevant Files In GDS Directory</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_files_list_filter_relevant.Rd</code></div>
     </div>
 
@@ -71,38 +57,38 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gdsdir</dt>
+
+
+<dl><dt id="arg-gdsdir">gdsdir<a class="anchor" aria-label="anchor" href="#arg-gdsdir"></a></dt>
 <dd><p>GDS directory.</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token.</p></dd>
 
 
-<dt>pattern</dt>
+<dt id="arg-pattern">pattern<a class="anchor" aria-label="anchor" href="#arg-pattern"></a></dt>
 <dd><p>Pattern to further filter the returned file type tibble.</p></dd>
 
 
-<dt>include_url</dt>
+<dt id="arg-include-url">include_url<a class="anchor" aria-label="anchor" href="#arg-include-url"></a></dt>
 <dd><p>Include presigned URLs to all files within the GDS directory (def: FALSE).</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>Page size (def: 100).</p></dd>
 
 
-<dt>regexes</dt>
+<dt id="arg-regexes">regexes<a class="anchor" aria-label="anchor" href="#arg-regexes"></a></dt>
 <dd><p>Tibble with regex and function name.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with type, bname, size, file_id, path, and presigned URL.</p>
+    <p>A tibble with type, bname, size, file_id, path, and presigned URL.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -111,14 +97,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gds_volumes_list.html b/reference/gds_volumes_list.html
index b918196..0253db4 100644
--- a/reference/gds_volumes_list.html
+++ b/reference/gds_volumes_list.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Lists GDS volumes accessible by the provided ICA token."><title>List GDS Volumes — gds_volumes_list • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List GDS Volumes — gds_volumes_list"><meta property="og:description" content="Lists GDS volumes accessible by the provided ICA token."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>List GDS Volumes — gds_volumes_list • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List GDS Volumes — gds_volumes_list"><meta name="description" content="Lists GDS volumes accessible by the provided ICA token."><meta property="og:description" content="Lists GDS volumes accessible by the provided ICA token."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
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     <div id="navbar" class="collapse navbar-collapse ms-3">
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>List GDS Volumes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>List GDS Volumes</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>gds_volumes_list.Rd</code></div>
     </div>
 
@@ -64,22 +50,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>token</dt>
+
+
+<dl><dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>Page size (def: 10).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with vol name and vol id.</p>
+    <p>A tibble with vol name and vol id.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -88,14 +74,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/ica_token_validate.html b/reference/ica_token_validate.html
index 79c2cbf..e05a455 100644
--- a/reference/ica_token_validate.html
+++ b/reference/ica_token_validate.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Validates ICA access token by parsing it and checking its expiration date."><title>Validate ICA access token — ica_token_validate • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Validate ICA access token — ica_token_validate"><meta property="og:description" content="Validates ICA access token by parsing it and checking its expiration date."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Validate ICA access token — ica_token_validate • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Validate ICA access token — ica_token_validate"><meta name="description" content="Validates ICA access token by parsing it and checking its expiration date."><meta property="og:description" content="Validates ICA access token by parsing it and checking its expiration date."></head><body>
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-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Validate ICA access token</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
+
+      <h1>Validate ICA access token</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/ica.R" class="external-link"><code>R/ica.R</code></a></small>
       <div class="d-none name"><code>ica_token_validate.Rd</code></div>
     </div>
 
@@ -64,18 +50,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>token</dt>
+
+
+<dl><dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (def: $ICA_ACCESS_TOKEN env var).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Returns the token if valid, or else errors out.</p>
+    <p>Returns the token if valid, or else errors out.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -84,14 +70,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/index.html b/reference/index.html
index 12f4923..c8560d0 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,435 +1,495 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body>
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+
 
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+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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+
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         <dd>BcftoolsStatsFile R6 Class</dd>
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-          <code><a href="BclconvertReports.html">BclconvertReports</a></code> 
+
+          <code><a href="BclconvertReports.html">BclconvertReports</a></code>
+
         </dt>
         <dd>BclconvertReports R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="FastqcMetricsFile.html">FastqcMetricsFile</a></code> 
+
+          <code><a href="FastqcMetricsFile.html">FastqcMetricsFile</a></code>
+
         </dt>
         <dd>FastqcMetrics R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="File.html">File</a></code> 
+
+          <code><a href="File.html">File</a></code>
+
         </dt>
         <dd>File R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="FragmentLengthHistFile.html">FragmentLengthHistFile</a></code> 
+
+          <code><a href="FragmentLengthHistFile.html">FragmentLengthHistFile</a></code>
+
         </dt>
         <dd>FragmentLengthHistFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="MappingMetricsFile.html">MappingMetricsFile</a></code> 
+
+          <code><a href="MappingMetricsFile.html">MappingMetricsFile</a></code>
+
         </dt>
         <dd>MappingMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="MultiqcFile.html">MultiqcFile</a></code> 
+
+          <code><a href="MultiqcFile.html">MultiqcFile</a></code>
+
         </dt>
         <dd>MultiqcFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="PcgrJsonFile.html">PcgrJsonFile</a></code> 
+
+          <code><a href="PcgrJsonFile.html">PcgrJsonFile</a></code>
+
         </dt>
         <dd>PcgrJson R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="PcgrTiersFile.html">PcgrTiersFile</a></code> 
+
+          <code><a href="PcgrTiersFile.html">PcgrTiersFile</a></code>
+
         </dt>
         <dd>PcgrTiersFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="PloidyEstimationMetricsFile.html">PloidyEstimationMetricsFile</a></code> 
+
+          <code><a href="PloidyEstimationMetricsFile.html">PloidyEstimationMetricsFile</a></code>
+
         </dt>
         <dd>PloidyEstimationMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="ReplayFile.html">ReplayFile</a></code> 
+
+          <code><a href="ReplayFile.html">ReplayFile</a></code>
+
         </dt>
         <dd>ReplayFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="SvMetricsFile.html">SvMetricsFile</a></code> 
+
+          <code><a href="SvMetricsFile.html">SvMetricsFile</a></code>
+
         </dt>
         <dd>SvMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TimeMetricsFile.html">TimeMetricsFile</a></code> 
+
+          <code><a href="TimeMetricsFile.html">TimeMetricsFile</a></code>
+
         </dt>
         <dd>TimeMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TrimmerMetricsFile.html">TrimmerMetricsFile</a></code> 
+
+          <code><a href="TrimmerMetricsFile.html">TrimmerMetricsFile</a></code>
+
         </dt>
         <dd>TrimmerMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoAlignCollapseFusionCallerMetricsFile.html">TsoAlignCollapseFusionCallerMetricsFile</a></code> 
+
+          <code><a href="TsoAlignCollapseFusionCallerMetricsFile.html">TsoAlignCollapseFusionCallerMetricsFile</a></code>
+
         </dt>
         <dd>TsoAlignCollapseFusionCallerMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoCombinedVariantOutputFile.html">TsoCombinedVariantOutputFile</a></code> 
+
+          <code><a href="TsoCombinedVariantOutputFile.html">TsoCombinedVariantOutputFile</a></code>
+
         </dt>
         <dd>TsoCombinedVariantOutputFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoCopyNumberVariantsVcfFile.html">TsoCopyNumberVariantsVcfFile</a></code> 
+
+          <code><a href="TsoCopyNumberVariantsVcfFile.html">TsoCopyNumberVariantsVcfFile</a></code>
+
         </dt>
         <dd>TsoCopyNumberVariantsVcfFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoFragmentLengthHistFile.html">TsoFragmentLengthHistFile</a></code> 
+
+          <code><a href="TsoFragmentLengthHistFile.html">TsoFragmentLengthHistFile</a></code>
+
         </dt>
         <dd>TsoFragmentLengthHistFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoFusionsCsvFile.html">TsoFusionsCsvFile</a></code> 
+
+          <code><a href="TsoFusionsCsvFile.html">TsoFusionsCsvFile</a></code>
+
         </dt>
         <dd>TsoFusionsCsvFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoMergedSmallVariantsGenomeVcfFile.html">TsoMergedSmallVariantsGenomeVcfFile</a></code> 
+
+          <code><a href="TsoMergedSmallVariantsGenomeVcfFile.html">TsoMergedSmallVariantsGenomeVcfFile</a></code>
+
         </dt>
         <dd>TsoMergedSmallVariantsGenomeVcfFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoMergedSmallVariantsVcfFile.html">TsoMergedSmallVariantsVcfFile</a></code> 
+
+          <code><a href="TsoMergedSmallVariantsVcfFile.html">TsoMergedSmallVariantsVcfFile</a></code>
+
         </dt>
         <dd>TsoMergedSmallVariantsVcfFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoMsiFile.html">TsoMsiFile</a></code> 
+
+          <code><a href="TsoMsiFile.html">TsoMsiFile</a></code>
+
         </dt>
         <dd>TsoMsiFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoSampleAnalysisResultsFile.html">TsoSampleAnalysisResultsFile</a></code> 
+
+          <code><a href="TsoSampleAnalysisResultsFile.html">TsoSampleAnalysisResultsFile</a></code>
+
         </dt>
         <dd>TsoSampleAnalysisResultsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoTargetRegionCoverageFile.html">TsoTargetRegionCoverageFile</a></code> 
+
+          <code><a href="TsoTargetRegionCoverageFile.html">TsoTargetRegionCoverageFile</a></code>
+
         </dt>
         <dd>TsoTargetRegionCoverageFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoTmbFile.html">TsoTmbFile</a></code> 
+
+          <code><a href="TsoTmbFile.html">TsoTmbFile</a></code>
+
         </dt>
         <dd>TsoTmbFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="TsoTmbTraceTsvFile.html">TsoTmbTraceTsvFile</a></code> 
+
+          <code><a href="TsoTmbTraceTsvFile.html">TsoTmbTraceTsvFile</a></code>
+
         </dt>
         <dd>TsoTmbTraceTsvFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="UmChordTsvFile.html">UmChordTsvFile</a></code> 
+
+          <code><a href="UmChordTsvFile.html">UmChordTsvFile</a></code>
+
         </dt>
         <dd>UmChordTsvFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="UmHrdetectTsvFile.html">UmHrdetectTsvFile</a></code> 
+
+          <code><a href="UmHrdetectTsvFile.html">UmHrdetectTsvFile</a></code>
+
         </dt>
         <dd>UmHrdetectTsvFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="UmQcSumFile.html">UmQcSumFile</a></code> 
+
+          <code><a href="UmQcSumFile.html">UmQcSumFile</a></code>
+
         </dt>
         <dd>UmQcSumFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="UmSigsSnvFile.html">UmSigsSnvFile</a></code> 
+
+          <code><a href="UmSigsSnvFile.html">UmSigsSnvFile</a></code>
+
         </dt>
         <dd>UmSigsSnvFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="VCMetricsFile.html">VCMetricsFile</a></code> 
+
+          <code><a href="VCMetricsFile.html">VCMetricsFile</a></code>
+
         </dt>
         <dd>VCMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="WgsContigMeanCovFile.html">WgsContigMeanCovFile</a></code> 
-        </dt>
-        <dd>WgsContigMeanCovFile R6 Class</dd>
-      </dl><dl><dt>
-          
-          <code><a href="WgsCoverageMetricsFile.html">WgsCoverageMetricsFile</a></code> 
+
+          <code><a href="Wf.html">Wf</a></code>
+
         </dt>
-        <dd>WgsCoverageMetricsFile R6 Class</dd>
+        <dd>Workflow R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="WgsFineHistFile.html">WgsFineHistFile</a></code> 
+
+          <code><a href="Wf_bcl_convert.html">Wf_bcl_convert</a></code>
+
         </dt>
-        <dd>WgsFineHistFile R6 Class</dd>
+        <dd>bcl_convert Wf R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="WgsHistFile.html">WgsHistFile</a></code> 
+
+          <code><a href="Wf_tso_ctdna_tumor_only.html">Wf_tso_ctdna_tumor_only</a></code>
+
         </dt>
-        <dd>WgsHistFile R6 Class</dd>
+        <dd>tso_ctdna_tumor_only Wf R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="bcftools_parse_vcf.html">bcftools_parse_vcf()</a></code> 
+
+          <code><a href="WgsContigMeanCovFile.html">WgsContigMeanCovFile</a></code>
+
         </dt>
-        <dd>Parse VCF with bcftools</dd>
+        <dd>WgsContigMeanCovFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="bcftools_parse_vcf_regions.html">bcftools_parse_vcf_regions()</a></code> 
+
+          <code><a href="WgsCoverageMetricsFile.html">WgsCoverageMetricsFile</a></code>
+
         </dt>
-        <dd>Parse VCF regions with bcftools</dd>
+        <dd>WgsCoverageMetricsFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="bclconvert_read_adaptermetrics.html">bclconvert_read_adaptermetrics()</a></code> 
+
+          <code><a href="WgsFineHistFile.html">WgsFineHistFile</a></code>
+
         </dt>
-        <dd>BCLConvert Adapter Metrics</dd>
+        <dd>WgsFineHistFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="bclconvert_read_demultiplexstats.html">bclconvert_read_demultiplexstats()</a></code> 
+
+          <code><a href="WgsHistFile.html">WgsHistFile</a></code>
+
         </dt>
-        <dd>BCLConvert Demultiplex Stats</dd>
+        <dd>WgsHistFile R6 Class</dd>
       </dl><dl><dt>
-          
-          <code><a href="bclconvert_read_indexhoppingcounts.html">bclconvert_read_indexhoppingcounts()</a></code> 
+
+          <code><a href="bcftools_parse_vcf.html">bcftools_parse_vcf()</a></code>
+
         </dt>
-        <dd>BCLConvert Index Hopping Counts</dd>
+        <dd>Parse VCF with bcftools</dd>
       </dl><dl><dt>
-          
-          <code><a href="bclconvert_read_topunknownbarcodes.html">bclconvert_read_topunknownbarcodes()</a></code> 
+
+          <code><a href="bcftools_parse_vcf_regions.html">bcftools_parse_vcf_regions()</a></code>
+
         </dt>
-        <dd>BCLConvert Top Unknown Barcodes</dd>
+        <dd>Parse VCF regions with bcftools</dd>
       </dl><dl><dt>
-          
-          <code><a href="date_log.html">date_log()</a></code> 
+
+          <code><a href="date_log.html">date_log()</a></code>
+
         </dt>
         <dd>Print current timestamp for logging</dd>
       </dl><dl><dt>
-          
-          <code><a href="dr_func_eval.html">dr_func_eval()</a></code> 
+
+          <code><a href="dr_func_eval.html">dr_func_eval()</a></code>
+
         </dt>
         <dd>Evaluate dracarys Function</dd>
       </dl><dl><dt>
-          
-          <code><a href="dr_gds_download.html">dr_gds_download()</a></code> 
+
+          <code><a href="dr_gds_download.html">dr_gds_download()</a></code>
+
         </dt>
         <dd>dracarys GDS Download</dd>
       </dl><dl><dt>
-          
-          <code><a href="dr_output_format_valid.html">dr_output_format_valid()</a></code> 
+
+          <code><a href="dr_output_format_valid.html">dr_output_format_valid()</a></code>
+
         </dt>
         <dd>Output Format is Valid</dd>
       </dl><dl><dt>
-          
-          <code><a href="dr_s3_download.html">dr_s3_download()</a></code> 
+
+          <code><a href="dr_s3_download.html">dr_s3_download()</a></code>
+
         </dt>
         <dd>dracarys S3 Download</dd>
       </dl><dl><dt>
-          
-          <code><a href="empty_tbl.html">empty_tbl()</a></code> 
+
+          <code><a href="empty_tbl.html">empty_tbl()</a></code>
+
         </dt>
         <dd>Create Empty Tibble Given Column Names</dd>
       </dl><dl><dt>
-          
-          <code><a href="file_regex_getter.html">file_regex_getter()</a></code> 
+
+          <code><a href="file_regex_getter.html">file_regex_getter()</a></code>
+
         </dt>
         <dd>Get dracarys <code>DR_FILE_REGEX</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_file_download.html">gds_file_download()</a></code> 
+
+          <code><a href="gds_file_download.html">gds_file_download()</a></code>
+
         </dt>
         <dd>GDS File Download via CLI</dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_file_download_api.html">gds_file_download_api()</a></code> 
+
+          <code><a href="gds_file_download_api.html">gds_file_download_api()</a></code>
+
         </dt>
         <dd>GDS File Download via API</dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_file_presignedurl.html">gds_file_presignedurl()</a></code> 
+
+          <code><a href="gds_file_presignedurl.html">gds_file_presignedurl()</a></code>
+
         </dt>
         <dd>GDS File Presigned URL</dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_files_list.html">gds_files_list()</a></code> 
+
+          <code><a href="gds_files_list.html">gds_files_list()</a></code>
+
         </dt>
         <dd>GDS Files List</dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_files_list_filter_relevant.html">gds_files_list_filter_relevant()</a></code> 
+
+          <code><a href="gds_files_list_fastq.html">gds_files_list_fastq()</a></code>
+
+        </dt>
+        <dd>List FASTQs In GDS Directory</dd>
+      </dl><dl><dt>
+
+          <code><a href="gds_files_list_filter_relevant.html">gds_files_list_filter_relevant()</a></code>
+
         </dt>
         <dd>List Relevant Files In GDS Directory</dd>
       </dl><dl><dt>
-          
-          <code><a href="gds_volumes_list.html">gds_volumes_list()</a></code> 
+
+          <code><a href="gds_volumes_list.html">gds_volumes_list()</a></code>
+
         </dt>
         <dd>List GDS Volumes</dd>
       </dl><dl><dt>
-          
-          <code><a href="ica_token_validate.html">ica_token_validate()</a></code> 
+
+          <code><a href="ica_token_validate.html">ica_token_validate()</a></code>
+
         </dt>
         <dd>Validate ICA access token</dd>
       </dl><dl><dt>
-          
-          <code><a href="match_regex.html">match_regex()</a></code> 
+
+          <code><a href="match_regex.html">match_regex()</a></code>
+
         </dt>
         <dd>Match File to Regex</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_column_map_append.html">multiqc_column_map_append()</a></code> 
+
+          <code><a href="multiqc_column_map_append.html">multiqc_column_map_append()</a></code>
+
         </dt>
         <dd>Append New MultiQC Workflow Columns</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_date_fmt.html">multiqc_date_fmt()</a></code> 
+
+          <code><a href="multiqc_date_fmt.html">multiqc_date_fmt()</a></code>
+
         </dt>
         <dd>Format MultiQC Config Date</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_bargraph_plot.html">multiqc_parse_bargraph_plot()</a></code> 
+
+          <code><a href="multiqc_parse_bargraph_plot.html">multiqc_parse_bargraph_plot()</a></code>
+
         </dt>
         <dd>MultiQC Extract Bar Graph Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_gen.html">multiqc_parse_gen()</a></code> 
+
+          <code><a href="multiqc_parse_gen.html">multiqc_parse_gen()</a></code>
+
         </dt>
         <dd>Parse MultiQC 'report_general_stats_data' JSON Element</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_plots.html">multiqc_parse_plots()</a></code> 
+
+          <code><a href="multiqc_parse_plots.html">multiqc_parse_plots()</a></code>
+
         </dt>
         <dd>Parse Plot Data from MultiQC JSON</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_raw.html">multiqc_parse_raw()</a></code> 
+
+          <code><a href="multiqc_parse_raw.html">multiqc_parse_raw()</a></code>
+
         </dt>
         <dd>Parse MultiQC 'report_saved_raw_data' JSON Element</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_raw_interop.html">multiqc_parse_raw_interop()</a></code> 
+
+          <code><a href="multiqc_parse_raw_interop.html">multiqc_parse_raw_interop()</a></code>
+
         </dt>
         <dd>Parse Interop MultiQC 'report_saved_raw_data' JSON Element</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_xyline_plot.html">multiqc_parse_xyline_plot()</a></code> 
+
+          <code><a href="multiqc_parse_xyline_plot.html">multiqc_parse_xyline_plot()</a></code>
+
         </dt>
         <dd>MultiQC Extract XY Line Plot Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_parse_xyline_plot_contig_cvg.html">multiqc_parse_xyline_plot_contig_cvg()</a></code> 
+
+          <code><a href="multiqc_parse_xyline_plot_contig_cvg.html">multiqc_parse_xyline_plot_contig_cvg()</a></code>
+
         </dt>
         <dd>MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage</dd>
       </dl><dl><dt>
-          
-          <code><a href="multiqc_tidy_json.html">multiqc_tidy_json()</a></code> 
+
+          <code><a href="multiqc_tidy_json.html">multiqc_tidy_json()</a></code>
+
         </dt>
         <dd>Tidy MultiQC JSON</dd>
       </dl><dl><dt>
-          
-          <code><a href="rdf2tab.html">rdf2tab()</a></code> 
+
+          <code><a href="rdf2tab.html">rdf2tab()</a></code>
+
         </dt>
         <dd>Write Local R Dataframe to Spark-backed Table</dd>
       </dl><dl><dt>
-          
-          <code><a href="read.File.html">read(<i>&lt;File&gt;</i>)</a></code> 
+
+          <code><a href="read.File.html">read(<i>&lt;File&gt;</i>)</a></code>
+
         </dt>
         <dd>Read File object</dd>
       </dl><dl><dt>
-          
-          <code><a href="read.html">read()</a></code> 
+
+          <code><a href="read.html">read()</a></code>
+
         </dt>
         <dd>Generic Reading</dd>
       </dl><dl><dt>
-          
-          <code><a href="s3_files_list_filter_relevant.html">s3_files_list_filter_relevant()</a></code> 
+
+          <code><a href="s3_files_list_filter_relevant.html">s3_files_list_filter_relevant()</a></code>
+
         </dt>
         <dd>List Relevant Files In AWS S3 Directory</dd>
       </dl><dl><dt>
-          
-          <code><a href="s3_search.html">s3_search()</a></code> 
+
+          <code><a href="s3_search.html">s3_search()</a></code>
+
         </dt>
         <dd>Search AWS S3 Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="session_info_kable.html">session_info_kable()</a></code> 
+
+          <code><a href="session_info_kable.html">session_info_kable()</a></code>
+
         </dt>
         <dd>Session Information Kable</dd>
       </dl><dl><dt>
-          
-          <code><a href="time_metrics_process.html">time_metrics_process()</a></code> 
+
+          <code><a href="time_metrics_process.html">time_metrics_process()</a></code>
+
         </dt>
         <dd>Process Multiple TimeMetricsFile Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="umccr_tidy.html">umccr_tidy()</a></code> 
+
+          <code><a href="umccr_tidy.html">umccr_tidy()</a></code>
+
         </dt>
         <dd>Tidy UMCCR Results</dd>
       </dl></div>
@@ -441,14 +501,14 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/match_regex.html b/reference/match_regex.html
index 0db7c4a..e2fc1a1 100644
--- a/reference/match_regex.html
+++ b/reference/match_regex.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Matches a given file with the regexes found in DR_FILE_REGEX and if there is
-a match, it returns the 'name' of that match."><title>Match File to Regex — match_regex • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Match File to Regex — match_regex"><meta property="og:description" content="Matches a given file with the regexes found in DR_FILE_REGEX and if there is
-a match, it returns the 'name' of that match."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Match File to Regex — match_regex • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Match File to Regex — match_regex"><meta name="description" content="Matches a given file with the regexes found in DR_FILE_REGEX and if there is
+a match, it returns the 'name' of that match."><meta property="og:description" content="Matches a given file with the regexes found in DR_FILE_REGEX and if there is
+a match, it returns the 'name' of that match."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
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-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Match File to Regex</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
+
+      <h1>Match File to Regex</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/regex.R" class="external-link"><code>R/regex.R</code></a></small>
       <div class="d-none name"><code>match_regex.Rd</code></div>
     </div>
 
@@ -67,19 +53,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>File to match.</p></dd>
 
 
-<dt>regexes</dt>
-<dd><p>Tibble with regex and function name.</p></dd>
+<dt id="arg-regexes">regexes<a class="anchor" aria-label="anchor" href="#arg-regexes"></a></dt>
+<dd><p>Tibble with <code>regex</code> and <code>fun</code>ction name.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The function corresponding to the matching regex from <code>DR_FILE_REGEX</code>, or
+    <p>The function corresponding to the matching regex from <code>DR_FILE_REGEX</code>, or
 NA if there is no match made.</p>
     </div>
 
@@ -92,7 +78,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -101,14 +87,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/multiqc_column_map_append.html b/reference/multiqc_column_map_append.html
index bd27d87..f1cfd3c 100644
--- a/reference/multiqc_column_map_append.html
+++ b/reference/multiqc_column_map_append.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Append New MultiQC Workflow Columns"><title>Append New MultiQC Workflow Columns — multiqc_column_map_append • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Append New MultiQC Workflow Columns — multiqc_column_map_append"><meta property="og:description" content="Append New MultiQC Workflow Columns"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Append New MultiQC Workflow Columns — multiqc_column_map_append • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Append New MultiQC Workflow Columns — multiqc_column_map_append"><meta name="description" content="Append New MultiQC Workflow Columns"><meta property="og:description" content="Append New MultiQC Workflow Columns"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Append New MultiQC Workflow Columns</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Append New MultiQC Workflow Columns</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_column_map_append.Rd</code></div>
     </div>
 
@@ -64,20 +50,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>d</dt>
+
+
+<dl><dt id="arg-d">d<a class="anchor" aria-label="anchor" href="#arg-d"></a></dt>
 <dd><p>Tidy MultiQC tibble with raw names (i.e. pre-rename).</p></dd>
 
 
-<dt>w</dt>
+<dt id="arg-w">w<a class="anchor" aria-label="anchor" href="#arg-w"></a></dt>
 <dd><p>New workflow name.</p></dd>
 
 
-<dt>m</dt>
+<dt id="arg-m">m<a class="anchor" aria-label="anchor" href="#arg-m"></a></dt>
 <dd><p>Path to the 'inst/extdata/multiqc_column_map.tsv' dracarys file.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -86,14 +74,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
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diff --git a/reference/multiqc_date_fmt.html b/reference/multiqc_date_fmt.html
index a9cdbfc..91a8f74 100644
--- a/reference/multiqc_date_fmt.html
+++ b/reference/multiqc_date_fmt.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Format MultiQC Config Date"><title>Format MultiQC Config Date — multiqc_date_fmt • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format MultiQC Config Date — multiqc_date_fmt"><meta property="og:description" content="Format MultiQC Config Date"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format MultiQC Config Date — multiqc_date_fmt • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Format MultiQC Config Date — multiqc_date_fmt"><meta name="description" content="Format MultiQC Config Date"><meta property="og:description" content="Format MultiQC Config Date"></head><body>
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+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-  <a class="nav-link" href="../index.html">Intro</a>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Format MultiQC Config Date</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Format MultiQC Config Date</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_date_fmt.Rd</code></div>
     </div>
 
@@ -64,15 +50,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cdate</dt>
+
+
+<dl><dt id="arg-cdate">cdate<a class="anchor" aria-label="anchor" href="#arg-cdate"></a></dt>
 <dd><p>String with config date in "YYYY-MM-DD, HH:MM UTC" format.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Properly formatted datetime string in "YYYY-MM-DDTHH:MM:SS" format.
+    <p>Properly formatted datetime string in "YYYY-MM-DDTHH:MM:SS" format.
 If the input string was formatted differently, it will return NA.</p>
     </div>
 
@@ -87,7 +73,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -96,14 +82,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/multiqc_parse_bargraph_plot.html b/reference/multiqc_parse_bargraph_plot.html
index 9490b8a..f5b7329 100644
--- a/reference/multiqc_parse_bargraph_plot.html
+++ b/reference/multiqc_parse_bargraph_plot.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extracts bar_graph data for the given plot name from a MultiQC JSON.
-Each bar_graph element in the JSON object contains:"><title>MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot"><meta property="og:description" content="Extracts bar_graph data for the given plot name from a MultiQC JSON.
-Each bar_graph element in the JSON object contains:"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot"><meta name="description" content="Extracts bar_graph data for the given plot name from a MultiQC JSON.
+Each bar_graph element in the JSON object contains:"><meta property="og:description" content="Extracts bar_graph data for the given plot name from a MultiQC JSON.
+Each bar_graph element in the JSON object contains:"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-  <a class="nav-link" href="../index.html">Intro</a>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MultiQC Extract Bar Graph Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>MultiQC Extract Bar Graph Data</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_bargraph_plot.Rd</code></div>
     </div>
 
@@ -67,19 +53,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>dat</dt>
+
+
+<dl><dt id="arg-dat">dat<a class="anchor" aria-label="anchor" href="#arg-dat"></a></dt>
 <dd><p>Parsed JSON list element with specific plot data to extract.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with name and data list-column.</p>
+    <p>Tibble with name and data list-column.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>a <code>samples</code> array of N subarrays (of strings) of length A.</p></li>
 <li><p>a <code>datasets</code> array of N subarrays (of objects) of length B.
 Each of the subarrays contains name (single string) and data (array of length
@@ -88,7 +74,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">j1</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/bcl_convert/multiqc_data.json"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">j2</span> <span class="op">&lt;-</span> <span class="fu">here</span><span class="fu">::</span><span class="fu"><a href="https://here.r-lib.org//reference/here.html" class="external-link">here</a></span><span class="op">(</span><span class="st">"nogit/dracarys_gds_sync/multiqc_data.json"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">j</span> <span class="op">&lt;-</span> <span class="va">j1</span></span></span>
@@ -100,10 +86,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">dat</span> <span class="op">&lt;-</span> <span class="va">parsed</span><span class="op">$</span><span class="va">report_plot_data</span><span class="op">$</span><span class="va">bclconvert_lane_counts</span></span></span>
 <span class="r-in"><span><span class="va">dat</span> <span class="op">&lt;-</span> <span class="va">parsed</span><span class="op">$</span><span class="va">report_plot_data</span><span class="op">$</span><span class="va">bclconvert_sample_counts</span></span></span>
 <span class="r-in"><span><span class="fu">multiqc_parse_bargraph_plot</span><span class="op">(</span><span class="va">dat</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +98,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/multiqc_parse_gen.html b/reference/multiqc_parse_gen.html
index 4838f0a..3d68fd3 100644
--- a/reference/multiqc_parse_gen.html
+++ b/reference/multiqc_parse_gen.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Parses MultiQC 'report_general_stats_data' JSON Element. Modified from the
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen"><meta name="description" content="Parses MultiQC 'report_general_stats_data' JSON Element. Modified from the
+awesome https://github.com/multimeric/TidyMultiqc."><meta property="og:description" content="Parses MultiQC 'report_general_stats_data' JSON Element. Modified from the
+awesome https://github.com/multimeric/TidyMultiqc."></head><body>
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse MultiQC 'report_general_stats_data' JSON Element</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Parse MultiQC 'report_general_stats_data' JSON Element</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_gen.Rd</code></div>
     </div>
 
@@ -67,18 +53,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>p</dt>
+
+
+<dl><dt id="arg-p">p<a class="anchor" aria-label="anchor" href="#arg-p"></a></dt>
 <dd><p>Parsed MultiQC JSON.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list.</p>
+    <p>A list.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -87,14 +73,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/reference/multiqc_parse_plots.html b/reference/multiqc_parse_plots.html
index 1b0e0d1..bd3ebe5 100644
--- a/reference/multiqc_parse_plots.html
+++ b/reference/multiqc_parse_plots.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Parse Plot Data from MultiQC JSON"><title>Parse Plot Data from MultiQC JSON — multiqc_parse_plots • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse Plot Data from MultiQC JSON — multiqc_parse_plots"><meta property="og:description" content="Parse Plot Data from MultiQC JSON"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Parse Plot Data from MultiQC JSON — multiqc_parse_plots • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parse Plot Data from MultiQC JSON — multiqc_parse_plots"><meta name="description" content="Parse Plot Data from MultiQC JSON"><meta property="og:description" content="Parse Plot Data from MultiQC JSON"></head><body>
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse Plot Data from MultiQC JSON</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Parse Plot Data from MultiQC JSON</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_plots.Rd</code></div>
     </div>
 
@@ -64,33 +50,33 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>j</dt>
+
+
+<dl><dt id="arg-j">j<a class="anchor" aria-label="anchor" href="#arg-j"></a></dt>
 <dd><p>Path to <code>multiqc_data.json</code> file.</p></dd>
 
 
-<dt>plot_names</dt>
+<dt id="arg-plot-names">plot_names<a class="anchor" aria-label="anchor" href="#arg-plot-names"></a></dt>
 <dd><p>Names of plots to parse. Use "everything" if you wantz all
 the plotz.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Nested tibble with plot name and result as list column (use <code><a href="https://tidyr.tidyverse.org/reference/unnest.html" class="external-link">tidyr::unnest</a></code> to access).</p>
+    <p>Nested tibble with plot name and result as list column (use <code><a href="https://tidyr.tidyverse.org/reference/unnest.html" class="external-link">tidyr::unnest</a></code> to access).</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">j</span> <span class="op">&lt;-</span> <span class="st">"dracarys_gds_sync/multiqc_data.json"</span></span></span>
 <span class="r-in"><span><span class="fu">multiqc_parse_plots</span><span class="op">(</span><span class="va">j</span>, plot_names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"dragen_coverage_per_contig"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">multiqc_parse_plots</span><span class="op">(</span><span class="va">j</span>, plot_names <span class="op">=</span> <span class="st">"everything"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">multiqc_parse_plots</span><span class="op">(</span><span class="va">j</span>, plot_names <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -99,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/multiqc_parse_raw.html b/reference/multiqc_parse_raw.html
index c108405..073c0cd 100644
--- a/reference/multiqc_parse_raw.html
+++ b/reference/multiqc_parse_raw.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse MultiQC 'report_saved_raw_data' JSON Element</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Parse MultiQC 'report_saved_raw_data' JSON Element</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_raw.Rd</code></div>
     </div>
 
@@ -64,19 +50,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>p</dt>
+
+
+<dl><dt id="arg-p">p<a class="anchor" aria-label="anchor" href="#arg-p"></a></dt>
 <dd><p>Parsed MultiQC JSON.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list of tibbles for each tool, where each tibble contains
+    <p>A list of tibbles for each tool, where each tibble contains
 metrics per sample.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -85,14 +71,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
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-  
 
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+
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diff --git a/reference/multiqc_parse_raw_interop.html b/reference/multiqc_parse_raw_interop.html
index d17f8b5..ea25df3 100644
--- a/reference/multiqc_parse_raw_interop.html
+++ b/reference/multiqc_parse_raw_interop.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
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+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Parse Interop MultiQC 'report_saved_raw_data' JSON Element</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Parse Interop MultiQC 'report_saved_raw_data' JSON Element</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_raw_interop.Rd</code></div>
     </div>
 
@@ -64,18 +50,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>p</dt>
+
+
+<dl><dt id="arg-p">p<a class="anchor" aria-label="anchor" href="#arg-p"></a></dt>
 <dd><p>Parsed Interop MultiQC JSON.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list with summary and per-lane tibbles.</p>
+    <p>A list with summary and per-lane tibbles.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -84,14 +70,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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-  
 
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   </body></html>
 
diff --git a/reference/multiqc_parse_xyline_plot.html b/reference/multiqc_parse_xyline_plot.html
index a1ffd12..4c3ab74 100644
--- a/reference/multiqc_parse_xyline_plot.html
+++ b/reference/multiqc_parse_xyline_plot.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extracts xy_line data for the given plot name from a MultiQC JSON."><title>MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot"><meta property="og:description" content="Extracts xy_line data for the given plot name from a MultiQC JSON."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot"><meta name="description" content="Extracts xy_line data for the given plot name from a MultiQC JSON."><meta property="og:description" content="Extracts xy_line data for the given plot name from a MultiQC JSON."></head><body>
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     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MultiQC Extract XY Line Plot Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>MultiQC Extract XY Line Plot Data</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_xyline_plot.Rd</code></div>
     </div>
 
@@ -64,15 +50,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>dat</dt>
+
+
+<dl><dt id="arg-dat">dat<a class="anchor" aria-label="anchor" href="#arg-dat"></a></dt>
 <dd><p>Parsed JSON list element with specific plot data to extract.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with name and data list-column.</p>
+    <p>Tibble with name and data list-column.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -80,7 +66,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 to the normal structure of <code>xy_line</code> plots, so we handle those separately.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -89,14 +75,14 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/reference/multiqc_parse_xyline_plot_contig_cvg.html b/reference/multiqc_parse_xyline_plot_contig_cvg.html
index 5d77959..3bf7bdd 100644
--- a/reference/multiqc_parse_xyline_plot_contig_cvg.html
+++ b/reference/multiqc_parse_xyline_plot_contig_cvg.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage"><title>MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg"><meta property="og:description" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg"><meta name="description" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage"><meta property="og:description" content="MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage"></head><body>
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-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_parse_xyline_plot_contig_cvg.Rd</code></div>
     </div>
 
@@ -64,18 +50,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>dat</dt>
+
+
+<dl><dt id="arg-dat">dat<a class="anchor" aria-label="anchor" href="#arg-dat"></a></dt>
 <dd><p>Parsed JSON list element with specific plot data to extract.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with name and data list-column.</p>
+    <p>Tibble with name and data list-column.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -84,14 +70,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/multiqc_tidy_json.html b/reference/multiqc_tidy_json.html
index 6c8f25b..47ee900 100644
--- a/reference/multiqc_tidy_json.html
+++ b/reference/multiqc_tidy_json.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Tidies 'multiqc_data.json' output from MultiQC.
-Modified from the awesome https://github.com/multimeric/TidyMultiqc."><title>Tidy MultiQC JSON — multiqc_tidy_json • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tidy MultiQC JSON — multiqc_tidy_json"><meta property="og:description" content="Tidies 'multiqc_data.json' output from MultiQC.
-Modified from the awesome https://github.com/multimeric/TidyMultiqc."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tidy MultiQC JSON — multiqc_tidy_json • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tidy MultiQC JSON — multiqc_tidy_json"><meta name="description" content="Tidies 'multiqc_data.json' output from MultiQC.
+Modified from the awesome https://github.com/multimeric/TidyMultiqc."><meta property="og:description" content="Tidies 'multiqc_data.json' output from MultiQC.
+Modified from the awesome https://github.com/multimeric/TidyMultiqc."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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 </nav><div class="container template-reference-topic">
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   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Tidy MultiQC JSON</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
+
+      <h1>Tidy MultiQC JSON</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/multiqc.R" class="external-link"><code>R/multiqc.R</code></a></small>
       <div class="d-none name"><code>multiqc_tidy_json.Rd</code></div>
     </div>
 
@@ -67,19 +53,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>j</dt>
+
+
+<dl><dt id="arg-j">j<a class="anchor" aria-label="anchor" href="#arg-j"></a></dt>
 <dd><p>Path to <code>multiqc_data.json</code> file.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tidy tibble where each column corresponds to a single metric,
+    <p>A tidy tibble where each column corresponds to a single metric,
 and each row corresponds to a single sample.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -88,14 +74,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/rdf2tab.html b/reference/rdf2tab.html
index 1110dc5..0440892 100644
--- a/reference/rdf2tab.html
+++ b/reference/rdf2tab.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="First converts local R dataframe to Spark DataFrame using SparkR,
-then appends it to the specified table."><title>Write Local R Dataframe to Spark-backed Table — rdf2tab • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Write Local R Dataframe to Spark-backed Table — rdf2tab"><meta property="og:description" content="First converts local R dataframe to Spark DataFrame using SparkR,
-then appends it to the specified table."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Write Local R Dataframe to Spark-backed Table — rdf2tab • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Write Local R Dataframe to Spark-backed Table — rdf2tab"><meta name="description" content="First converts local R dataframe to Spark DataFrame using SparkR,
+then appends it to the specified table."><meta property="og:description" content="First converts local R dataframe to Spark DataFrame using SparkR,
+then appends it to the specified table."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
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+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
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       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Write Local R Dataframe to Spark-backed Table</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+
+      <h1>Write Local R Dataframe to Spark-backed Table</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>rdf2tab.Rd</code></div>
     </div>
 
@@ -67,32 +53,34 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>rdf</dt>
+
+
+<dl><dt id="arg-rdf">rdf<a class="anchor" aria-label="anchor" href="#arg-rdf"></a></dt>
 <dd><p>Local R dataframe</p></dd>
 
 
-<dt>outpath</dt>
+<dt id="arg-outpath">outpath<a class="anchor" aria-label="anchor" href="#arg-outpath"></a></dt>
 <dd><p>Path to output table.</p></dd>
 
 
-<dt>drid</dt>
+<dt id="arg-drid">drid<a class="anchor" aria-label="anchor" href="#arg-drid"></a></dt>
 <dd><p>dracarys ID to use for the dataset (e.g. <code>wfrid.123</code>, <code>prid.456</code>)</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>Additional arguments for <code>SparkR::write.df</code>.</p></dd>
 
 </dl></div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">rdf</span> <span class="op">&lt;-</span> <span class="va">mtcars</span></span></span>
 <span class="r-in"><span><span class="fu">rdf2tab</span><span class="op">(</span><span class="va">rdf</span>, <span class="st">"dev.wf1.mtcars"</span>, drid <span class="op">=</span> <span class="st">"wfr.123"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -101,14 +89,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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diff --git a/reference/read.File.html b/reference/read.File.html
index 2363137..69bdf13 100644
--- a/reference/read.File.html
+++ b/reference/read.File.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Read the file based on its type."><title>Read File object — read.File • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Read File object — read.File"><meta property="og:description" content="Read the file based on its type."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Read File object — read.File • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Read File object — read.File"><meta name="description" content="Read the file based on its type."><meta property="og:description" content="Read the file based on its type."></head><body>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Read File object</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/File.R" class="external-link"><code>R/File.R</code></a></small>
+
+      <h1>Read File object</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/File.R" class="external-link"><code>R/File.R</code></a></small>
       <div class="d-none name"><code>read.File.Rd</code></div>
     </div>
 
@@ -59,22 +45,24 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for File</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'File'</span></span>
 <span><span class="fu"><a href="read.html">read</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>Object of class <code>File</code>.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>Arguments passed on to appropriate read_* function.</p></dd>
 
 </dl></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -83,14 +71,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/read.html b/reference/read.html
index 96efcc1..21c8878 100644
--- a/reference/read.html
+++ b/reference/read.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Generic function for reading dracarys objects."><title>Generic Reading — read • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generic Reading — read"><meta property="og:description" content="Generic function for reading dracarys objects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Generic Reading — read • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generic Reading — read"><meta name="description" content="Generic function for reading dracarys objects."><meta property="og:description" content="Generic function for reading dracarys objects."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
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-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Generic Reading</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/read.R" class="external-link"><code>R/read.R</code></a></small>
+
+      <h1>Generic Reading</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/read.R" class="external-link"><code>R/read.R</code></a></small>
       <div class="d-none name"><code>read.Rd</code></div>
     </div>
 
@@ -64,22 +50,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>Object of the respective class.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>Additional arguments.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Possibly a tibble or a list, depending on the object.</p>
+    <p>Possibly a tibble or a list, depending on the object.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -88,14 +74,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/s3_files_list_filter_relevant.html b/reference/s3_files_list_filter_relevant.html
index 82a8bd3..d1dac4b 100644
--- a/reference/s3_files_list_filter_relevant.html
+++ b/reference/s3_files_list_filter_relevant.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Lists relevant files in an AWS S3 directory."><title>List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant"><meta property="og:description" content="Lists relevant files in an AWS S3 directory."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant"><meta name="description" content="Lists relevant files in an AWS S3 directory."><meta property="og:description" content="Lists relevant files in an AWS S3 directory."></head><body>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
-  </div>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>List Relevant Files In AWS S3 Directory</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
+
+      <h1>List Relevant Files In AWS S3 Directory</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
       <div class="d-none name"><code>s3_files_list_filter_relevant.Rd</code></div>
     </div>
 
@@ -71,46 +57,46 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>s3dir</dt>
+
+
+<dl><dt id="arg-s-dir">s3dir<a class="anchor" aria-label="anchor" href="#arg-s-dir"></a></dt>
 <dd><p>S3 directory.</p></dd>
 
 
-<dt>pattern</dt>
+<dt id="arg-pattern">pattern<a class="anchor" aria-label="anchor" href="#arg-pattern"></a></dt>
 <dd><p>Pattern to further filter the returned file type tibble.</p></dd>
 
 
-<dt>page_size</dt>
+<dt id="arg-page-size">page_size<a class="anchor" aria-label="anchor" href="#arg-page-size"></a></dt>
 <dd><p>The size of each page to get in the AWS service call (def: 1000).</p></dd>
 
 
-<dt>max_items</dt>
+<dt id="arg-max-items">max_items<a class="anchor" aria-label="anchor" href="#arg-max-items"></a></dt>
 <dd><p>The total number of items to return in the command’s output (def: 1000).</p></dd>
 
 
-<dt>presign</dt>
+<dt id="arg-presign">presign<a class="anchor" aria-label="anchor" href="#arg-presign"></a></dt>
 <dd><p>Include presigned URLs (def: FALSE).</p></dd>
 
 
-<dt>expiry_sec</dt>
+<dt id="arg-expiry-sec">expiry_sec<a class="anchor" aria-label="anchor" href="#arg-expiry-sec"></a></dt>
 <dd><p>Number of seconds the presigned URL will be valid for (if generated) (def: 43200 (12hrs)).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A tibble with path, date, file size, file type, and presigned URL if requested.</p>
+    <p>A tibble with path, date, file size, file type, and presigned URL if requested.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">s3dir</span> <span class="op">&lt;-</span> <span class="st">"s3://umccr-primary-data-prod/cancer_report_tables"</span></span></span>
 <span class="r-in"><span><span class="fu">s3_files_list_filter_relevant</span><span class="op">(</span>s3dir <span class="op">=</span> <span class="va">s3dir</span>, presign <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -119,14 +105,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/s3_search.html b/reference/s3_search.html
index 9c41fc7..5145356 100644
--- a/reference/s3_search.html
+++ b/reference/s3_search.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Searches for the given pattern in the UMCCR umccr-primary-data-prod AWS S3
-bucket."><title>Search AWS S3 Objects — s3_search • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Search AWS S3 Objects — s3_search"><meta property="og:description" content="Searches for the given pattern in the UMCCR umccr-primary-data-prod AWS S3
-bucket."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Search AWS S3 Objects — s3_search • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Search AWS S3 Objects — s3_search"><meta name="description" content="Searches for the given pattern in the UMCCR umccr-primary-data-prod AWS S3
+bucket."><meta property="og:description" content="Searches for the given pattern in the UMCCR umccr-primary-data-prod AWS S3
+bucket."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
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-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <ul class="navbar-nav"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Search AWS S3 Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
+
+      <h1>Search AWS S3 Objects</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/s3.R" class="external-link"><code>R/s3.R</code></a></small>
       <div class="d-none name"><code>s3_search.Rd</code></div>
     </div>
 
@@ -67,30 +53,30 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>pat</dt>
+
+
+<dl><dt id="arg-pat">pat<a class="anchor" aria-label="anchor" href="#arg-pat"></a></dt>
 <dd><p>Pattern to search for (e.g. 'multiqc_data.json').</p></dd>
 
 
-<dt>rows</dt>
+<dt id="arg-rows">rows<a class="anchor" aria-label="anchor" href="#arg-rows"></a></dt>
 <dd><p>Max number of rows to return.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with S3 path, object size, date modified, id, unique hash.</p>
+    <p>Tibble with S3 path, object size, date modified, id, unique hash.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">pat</span> <span class="op">&lt;-</span> <span class="st">"qc_summary.tsv.gz"</span></span></span>
 <span class="r-in"><span><span class="fu">s3_search</span><span class="op">(</span><span class="va">pat</span>, <span class="fl">10</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -99,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/session_info_kable.html b/reference/session_info_kable.html
index be0b0a5..35167db 100644
--- a/reference/session_info_kable.html
+++ b/reference/session_info_kable.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Session Information Kable — session_info_kable • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Session Information Kable — session_info_kable"><meta name="description" content="Session information kables for vignettes."><meta property="og:description" content="Session information kables for vignettes."></head><body>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Session Information Kable</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+
+      <h1>Session Information Kable</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>session_info_kable.Rd</code></div>
     </div>
 
@@ -64,19 +50,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>pkgs</dt>
+
+
+<dl><dt id="arg-pkgs">pkgs<a class="anchor" aria-label="anchor" href="#arg-pkgs"></a></dt>
 <dd><p>Vector of R packages to display in the vignette. By default returns all.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list with two kables containing information about the platform and
+    <p>A list with two kables containing information about the platform and
 the specified packages.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -85,14 +71,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/time_metrics_process.html b/reference/time_metrics_process.html
index a989e71..5674036 100644
--- a/reference/time_metrics_process.html
+++ b/reference/time_metrics_process.html
@@ -1,55 +1,41 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Processes multiple TimeMetricsFile objects."><title>Process Multiple TimeMetricsFile Objects — time_metrics_process • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Process Multiple TimeMetricsFile Objects — time_metrics_process"><meta property="og:description" content="Processes multiple TimeMetricsFile objects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Process Multiple TimeMetricsFile Objects — time_metrics_process • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Process Multiple TimeMetricsFile Objects — time_metrics_process"><meta name="description" content="Processes multiple TimeMetricsFile objects."><meta property="og:description" content="Processes multiple TimeMetricsFile objects."></head><body>
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-    
 
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+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
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+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Process Multiple TimeMetricsFile Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
+
+      <h1>Process Multiple TimeMetricsFile Objects</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/dragen.R" class="external-link"><code>R/dragen.R</code></a></small>
       <div class="d-none name"><code>time_metrics_process.Rd</code></div>
     </div>
 
@@ -64,20 +50,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>Atomic vector with one or more TimeMetricsFile objects.</p></dd>
 
 
-<dt>id</dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
 <dd><p>ID for each input, which is used to disambiguate files
 generated from same samples. Default: index from 1 to length of <code>x</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>tibble with the following columns:</p><ul><li><p>Step: DRAGEN step</p></li>
+    <p>tibble with the following columns:</p><ul><li><p>Step: DRAGEN step</p></li>
 <li><p>Time: time in HH:MM</p></li>
 </ul></div>
 
@@ -101,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -110,14 +96,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/umccr_tidy.html b/reference/umccr_tidy.html
index 2a385ba..7834a38 100644
--- a/reference/umccr_tidy.html
+++ b/reference/umccr_tidy.html
@@ -1,57 +1,43 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Tidies UMCCR workflow results into a list of tibbles and writes individual
-tibbles to TSV, Parquet, SparkDF, or RDS format."><title>Tidy UMCCR Results — umccr_tidy • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tidy UMCCR Results — umccr_tidy"><meta property="og:description" content="Tidies UMCCR workflow results into a list of tibbles and writes individual
-tibbles to TSV, Parquet, SparkDF, or RDS format."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Tidy UMCCR Results — umccr_tidy • dracarys</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tidy UMCCR Results — umccr_tidy"><meta name="description" content="Tidies UMCCR workflow results into a list of tibbles and writes individual
+tibbles to TSV, Parquet, SparkDF, or RDS format."><meta property="og:description" content="Tidies UMCCR workflow results into a list of tibbles and writes individual
+tibbles to TSV, Parquet, SparkDF, or RDS format."></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.15.0</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../index.html">Intro</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/flames.html">FlameStories</a>
-    <a class="dropdown-item" href="../articles/developers.html">DevNotes</a>
-    <a class="dropdown-item" href="../articles/files.html">Files</a>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/flames.html">FlameStories</a></li>
+    <li><a class="dropdown-item" href="../articles/developers.html">DevNotes</a></li>
+    <li><a class="dropdown-item" href="../articles/files.html">Files</a></li>
+  </ul></li>
+      </ul><ul class="navbar-nav"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Tidy UMCCR Results</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/tidy.R" class="external-link"><code>R/tidy.R</code></a></small>
+
+      <h1>Tidy UMCCR Results</h1>
+      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/main/R/tidy.R" class="external-link"><code>R/tidy.R</code></a></small>
       <div class="d-none name"><code>umccr_tidy.Rd</code></div>
     </div>
 
@@ -70,56 +56,61 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  out_format <span class="op">=</span> <span class="st">"tsv"</span>,</span>
 <span>  dryrun <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  token <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"ICA_ACCESS_TOKEN"</span><span class="op">)</span>,</span>
-<span>  pattern <span class="op">=</span> <span class="cn">NULL</span></span>
+<span>  pattern <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  regexes <span class="op">=</span> <span class="va">DR_FILE_REGEX</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>in_dir</dt>
+
+
+<dl><dt id="arg-in-dir">in_dir<a class="anchor" aria-label="anchor" href="#arg-in-dir"></a></dt>
 <dd><p>Directory path to UMCCR workflow results (can be GDS, S3 or local).</p></dd>
 
 
-<dt>out_dir</dt>
+<dt id="arg-out-dir">out_dir<a class="anchor" aria-label="anchor" href="#arg-out-dir"></a></dt>
 <dd><p>Output directory.</p></dd>
 
 
-<dt>prefix</dt>
+<dt id="arg-prefix">prefix<a class="anchor" aria-label="anchor" href="#arg-prefix"></a></dt>
 <dd><p>Prefix of output file(s).</p></dd>
 
 
-<dt>local_dir</dt>
+<dt id="arg-local-dir">local_dir<a class="anchor" aria-label="anchor" href="#arg-local-dir"></a></dt>
 <dd><p>If <code>indir</code> is a GDS or S3 directory, 'recognisable' files
-will be first downloaded to this directory.</p></dd>
+will be first downloaded to this directory (def: &lt;out_dir&gt;/dracarys_&lt;s3_or_gds&gt;_sync).</p></dd>
 
 
-<dt>out_format</dt>
+<dt id="arg-out-format">out_format<a class="anchor" aria-label="anchor" href="#arg-out-format"></a></dt>
 <dd><p>Format of output (tsv, parquet, both) (def: tsv).</p></dd>
 
 
-<dt>dryrun</dt>
+<dt id="arg-dryrun">dryrun<a class="anchor" aria-label="anchor" href="#arg-dryrun"></a></dt>
 <dd><p>Just list the files that will be downloaded (def: FALSE).</p></dd>
 
 
-<dt>token</dt>
+<dt id="arg-token">token<a class="anchor" aria-label="anchor" href="#arg-token"></a></dt>
 <dd><p>ICA access token (by default uses $ICA_ACCESS_TOKEN env var).</p></dd>
 
 
-<dt>pattern</dt>
+<dt id="arg-pattern">pattern<a class="anchor" aria-label="anchor" href="#arg-pattern"></a></dt>
 <dd><p>Pattern to further filter the returned file type tibble (see
 <code>name</code> column in the <code>DR_FILE_REGEX</code> tibble).</p></dd>
 
+
+<dt id="arg-regexes">regexes<a class="anchor" aria-label="anchor" href="#arg-regexes"></a></dt>
+<dd><p>Tibble with <code>regex</code> and <code>fun</code>ction name.</p></dd>
+
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with path to input file and the resultant tidy object.</p>
+    <p>Tibble with path to input file and the resultant tidy object.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span><span class="va">in_dir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="st">"s3://umccr-primary-data-prod/UMCCR-Validation/SBJ00596"</span>,</span></span>
 <span class="r-in"><span>  <span class="st">"ctTSO/2021-03-17/PTC_SSqCMM05pc_L2100067"</span></span></span>
@@ -144,10 +135,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">prefix</span> <span class="op">&lt;-</span> <span class="st">"SBJ02858"</span></span></span>
 <span class="r-in"><span><span class="va">dryrun</span> <span class="op">&lt;-</span> <span class="cn">F</span></span></span>
 <span class="r-in"><span><span class="fu">umccr_tidy</span><span class="op">(</span>in_dir <span class="op">=</span> <span class="va">in_dir</span>, out_dir <span class="op">=</span> <span class="va">out_dir</span>, prefix <span class="op">=</span> <span class="va">prefix</span>, dryrun <span class="op">=</span> <span class="cn">F</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -156,14 +147,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/search.json b/search.json
index 7d88495..e4c98ce 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement peterdiakumis@gmail.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://umccr.github.io/dracarys/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 University Melbourne Centre Cancer Research - Genomics Platform Group Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://umccr.github.io/dracarys/articles/files.html","id":"workflows","dir":"Articles","previous_headings":"","what":"Workflows","title":"Files Supported","text":"wgs_alignment_qc wts_alignment_qc wts_tumor_only wgs_tumor_normal-germ wgs_tumor_normal-som umccrise oncoanalyser_wgs oncoanalyser_wts oncoanalyser_wgts sash","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"flames","dir":"Articles","previous_headings":"","what":"Flames","title":"Flames","text":"Flames dracarys user stories. D’oh.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"cttso-summary","dir":"Articles","previous_headings":"Flames","what":"ctTSO Summary","title":"Flames","text":"Slack link","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"ffpe-vs--fresh-frozen","dir":"Articles","previous_headings":"Flames","what":"FFPE vs. Fresh Frozen","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"coverage-depth-exploration","dir":"Articles","previous_headings":"Flames","what":"Coverage depth exploration","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"sv-runtime","dir":"Articles","previous_headings":"Flames","what":"SV runtime","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"msi-and-tmb","dir":"Articles","previous_headings":"Flames","what":"MSI and TMB","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"germline-duplication-rate","dir":"Articles","previous_headings":"Flames","what":"Germline duplication rate","title":"Flames","text":"Slack link1. Slack link2.","code":""},{"path":"https://umccr.github.io/dracarys/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Peter Diakumis. Author, maintainer. Victor San Kho Lin. Author, contributor.","code":""},{"path":"https://umccr.github.io/dracarys/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Diakumis P, Lin V (2024). dracarys: Post-processing DRAGEN workflows. https://github.com/umccr/dracarys, https://umccr.github.io/dracarys/.","code":"@Manual{,   title = {dracarys: Post-processing DRAGEN workflows},   author = {Peter Diakumis and Victor San Kho Lin},   year = {2024},   note = {https://github.com/umccr/dracarys, https://umccr.github.io/dracarys/}, }"},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-dracarys---umccr-workflow-tidying","dir":"","previous_headings":"","what":"Post-processing DRAGEN workflows","title":"Post-processing DRAGEN workflows","text":"Docs: https://umccr.github.io/dracarys/","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-aim","dir":"","previous_headings":"","what":"🏆 Aim","title":"Post-processing DRAGEN workflows","text":"Given ICA GDS, AWS S3 local directory results UMCCR workflow, {dracarys} grab files interest transform ‘tidier’ structures output TSV/Parquet/RDS format downstream ingestion database/data lake. See supported workflows, running examples, CLI options sections .","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-installation","dir":"","previous_headings":"","what":"🍕 Installation","title":"Post-processing DRAGEN workflows","text":"Linux & MacOS (non-M1) MacOS M1","code":"remotes::install_github(\"umccr/dracarys@vX.X.X\") # for vX.X.X Release/Tag mamba create \\   -n dracarys_env \\   -c umccr -c bioconda -c conda-forge \\   r-dracarys==X.X.X  conda activate dracarys_env CONDA_SUBDIR=osx-64 \\   mamba create \\   -n dracarys_env \\   -c umccr -c bioconda -c conda-forge \\   r-dracarys==X.X.X  conda activate dracarys_env docker pull --platform linux/amd64 ghcr.io/umccr/dracarys:X.X.X"},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-supported-workflows","dir":"","previous_headings":"","what":"✨ Supported Workflows","title":"Post-processing DRAGEN workflows","text":"{dracarys} supports outputs following UMCCR workflows: See output files workflows supported Supported Files.","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-cli","dir":"","previous_headings":"","what":"🌀 CLI","title":"Post-processing DRAGEN workflows","text":"dracarys.R command line interface available convenience. ’re using conda package, dracarys.R command already available inside activated conda environment. ’re using conda package, need export dracarys/inst/cli/ directory PATH order use dracarys.R.","code":"dracarys_cli=$(Rscript -e 'x = system.file(\"cli\", package = \"dracarys\"); cat(x, \"\\n\")' | xargs) export PATH=\"${dracarys_cli}:${PATH}\" dracarys.R --version dracarys.R 0.14.0  #-----------------------------------# dracarys.R --help usage: dracarys.R [-h] [-v] {tidy} ...  🐉 DRAGEN Output Post-Processing 🔥  positional arguments:   {tidy}         sub-command help     tidy         Tidy UMCCR Workflow Outputs  options:   -h, --help     show this help message and exit   -v, --version  show program's version number and exit  #-----------------------------------# #------- Tidy ----------------------# dracarys.R tidy --help usage: dracarys.R tidy [-h] -i IN_DIR -o OUT_DIR -p PREFIX [-t TOKEN]                        [-l LOCAL_DIR] [-f FORMAT] [-n] [-q]  options:   -h, --help            show this help message and exit   -i IN_DIR, --in_dir IN_DIR                         ⛄️ Directory with untidy UMCCR workflow results. Can                         be GDS, S3 or local.   -o OUT_DIR, --out_dir OUT_DIR                         🔥 Directory to output tidy results.   -p PREFIX, --prefix PREFIX                         🎻 Prefix string used for all results.   -t TOKEN, --token TOKEN                         🙈 ICA access token. Default: ICA_ACCESS_TOKEN env var.   -l LOCAL_DIR, --local_dir LOCAL_DIR                         📥 If input is a GDS/S3 directory, download the                         recognisable files to this directory. Default:                         '<out_dir>/dracarys_<gds|s3>_sync'.   -f FORMAT, --format FORMAT                         🎨 Format of output. Default: tsv.   -n, --dryrun          🐫 Dry run - just show files to be tidied.   -q, --quiet           😴 Shush all the logs."},{"path":"https://umccr.github.io/dracarys/index.html","id":"id_-running","dir":"","previous_headings":"","what":"🚕 Running","title":"Post-processing DRAGEN workflows","text":"{dracarys} takes input (--in_dir) directory results one UMCCR workflows. recursively scan directory supported files, download local directory (--gds_local_dir), parse, transform write tidied versions specified output directory (--out_dir). prefix (--prefix) prepended tidied files. output file format (--format) can tsv, parquet, . get just list supported files within specified input directory, use -n (--dryrun) option. within activated conda environment shell dracarys.R CLI available:","code":"# help(umccr_tidy) in_dir <- \"gds://path/to/subjectX_multiqc_data/\" out_dir <- tempdir() prefix <- \"subjectX\" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix) dracarys.R tidy \\       -i gds://path/to/subjectX_multiqc_data/ \\       -o local_output_dir \\       -p subjectX_prefix docker container run \\   -v $(PWD):/mount1 \\   --platform=linux/amd64 \\   --env \"ICA_ACCESS_TOKEN\" \\   --rm -it \\   ghcr.io/umccr/dracarys:X.X.X \\     dracarys.R tidy \\       -i gds://path/to/subjectX_multiqc_data/ \\       -o /mount1/output_dir \\       -p subjectX_prefix"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Contains methods reading displaying contents bcftools_stats.txt file (QUAL section) output running bcftools stats.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"dracarys::File -> BcftoolsStatsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"BcftoolsStatsFile$read() BcftoolsStatsFile$write() BcftoolsStatsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Reads QUAL section bcftools_stats.txt file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Writes tidy version bcftools_stats.txt (QUAL section) file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"if (FALSE) { x <- \"/path/to/bcftools_stats.txt\" d <- BcftoolsStatsFile$new(x) d_parsed <- d$read() d$write(d_parsed, out_dir = tempdir(), prefix = \"sample123\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":null,"dir":"Reference","previous_headings":"","what":"BclconvertReports R6 Class — BclconvertReports","title":"BclconvertReports R6 Class — BclconvertReports","text":"Reads writes tidy versions files within Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"BclconvertReports R6 Class — BclconvertReports","text":"path Path Reports directory. contents Tibble file path, basename, size.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"BclconvertReports R6 Class — BclconvertReports","text":"BclconvertReports$new() BclconvertReports$print() BclconvertReports$read() BclconvertReports$write() BclconvertReports$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Create new BclconvertReports object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$new(path = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"path Path Reports directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Print details BclconvertReports directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Reads contents Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$read()"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"BclconvertReports R6 Class — BclconvertReports","text":"list tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Writes tidied contents Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"BclconvertReports R6 Class — BclconvertReports","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"if (FALSE) { b <- BclconvertReports$new(here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports\")) b$path b$contents d <- b$read() b$write(d, out_dir = tempdir(), prefix = \"sampleA\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"FastqcMetrics R6 Class — FastqcMetricsFile","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Contains methods reading displaying contents fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File -> FastqcMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"FastqcMetricsFile$read() FastqcMetricsFile$write() FastqcMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Reads fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"tibble. TODO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Writes tidy version fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.fastqc_metrics.csv.gz\", package = \"dracarys\") fq <- FastqcMetricsFile$new(x) d <- fq$read() fq$write(d, out_dir = tempdir(), prefix = \"seqc_fq\", out_format = \"tsv\") # fq$plot(d)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":null,"dir":"Reference","previous_headings":"","what":"File R6 Class — File","title":"File R6 Class — File","text":"File base R6 class representing TSV/CSV/JSON output UMCCR workflow. File path, basename, type, can presigned URL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"File R6 Class — File","text":"path Name full path file. is_url file presigned URL?","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"File R6 Class — File","text":"File$new() File$bname() File$type() File$print() File$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"File R6 Class — File","text":"Create new File object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$new(path = NULL, is_url = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"path Name full path file. is_url file presigned URL?","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-bname-","dir":"Reference","previous_headings":"","what":"Method bname()","title":"File R6 Class — File","text":"Basename file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$bname()"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"File R6 Class — File","text":"Basename file character vector.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-type-","dir":"Reference","previous_headings":"","what":"Method type()","title":"File R6 Class — File","text":"Get type file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$type()"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"File R6 Class — File","text":"String describing specific type dracarys file (NA dracarys-recognised file).","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"File R6 Class — File","text":"Print details File.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"File R6 Class — File","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"File R6 Class — File","text":"","code":"F1 <- File$new(readr::readr_example(\"mtcars.csv\")) (bname_f1 <- F1$bname()) #> [1] \"mtcars.csv\" (F2 <- File$new(\"https://stratus-gds-aps2/foo/bar/baz.csv?bla\")) #> #--- File ---# #> Path: https://stratus-gds-aps2/foo/bar/baz.csv?bla  #> Basename: baz.csv  #> Type: NA  #> isURL: TRUE"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Contains methods reading plotting contents fragment_length_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"dracarys::File -> FragmentLengthHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"FragmentLengthHistFile$read() FragmentLengthHistFile$write() FragmentLengthHistFile$plot() FragmentLengthHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Reads fragment_length_hist.csv file, contains fragment length distribution sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"tibble following columns: sample: name sample fragmentLength: estimated fragment length count: number reads estimated fragment length","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Writes tidy version fragment_length_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Plots fragment length distributions given fragment_length_hist.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$plot(d, min_count = 10)"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"d Parsed object self$read(). min_count Minimum read count plotted (Default: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"ggplot2 plot containing fragment lengths X axis read counts Y axis sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.fragment_length_hist.csv.gz\", package = \"dracarys\") fl <- FragmentLengthHistFile$new(x) d <- fl$read() # or read(fl) fl$plot(d) # or plot(fl)  fl$write(d |> dplyr::filter(count > 10), out_dir = tempdir(), prefix = \"seqc_fl\")"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"MappingMetricsFile R6 Class — MappingMetricsFile","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Contains methods reading displaying contents mapping_metrics.csv file output DRAGEN. file contains mapping aligning metrics, like metrics computed Samtools Flagstat command. metrics available aggregate level (input data), per read group level. NOTE: keeping read group level metrics (.e. removing aggregate data). Unless explicitly stated, metrics units reads (.e., terms pairs alignments).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"dracarys::File -> MappingMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"MappingMetricsFile$read() MappingMetricsFile$write() MappingMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Reads mapping_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"tibble one row X metrics per read group.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Writes tidy version mapping_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.mapping_metrics.csv.gz\", package = \"dracarys\") mm <- MappingMetricsFile$new(x) d <- mm$read() # or read(mm) mm$write(d, out_dir = tempdir(), prefix = \"seqc_mm\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiqcFile R6 Class — MultiqcFile","title":"MultiqcFile R6 Class — MultiqcFile","text":"Contains methods reading displaying contents multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"MultiqcFile R6 Class — MultiqcFile","text":"dracarys::File -> MultiqcFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"MultiqcFile R6 Class — MultiqcFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"MultiqcFile R6 Class — MultiqcFile","text":"MultiqcFile$read() MultiqcFile$write() MultiqcFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"MultiqcFile R6 Class — MultiqcFile","text":"Reads multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$read(plot = FALSE, plot_names = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"plot Return tibble data plots (def: FALSE). plot_names Names plots parse. Use \"everything\" wantz plotz.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"MultiqcFile R6 Class — MultiqcFile","text":"tidy tibble. label:","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"MultiqcFile R6 Class — MultiqcFile","text":"Writes tidy version multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', ''). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"MultiqcFile R6 Class — MultiqcFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"if (FALSE) { x <- \"/path/to/multiqc_data.json\" mqc <- MultiqcFile$new(x) mqc_parsed <- mqc$read() # or read(mqc) mqc$write(mqc_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") mqc_plots_parsed <- mqc$read(plot = TRUE, plot_names = \"everything\") mqc$write(mqc_plots_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"rds\") }"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PcgrJson R6 Class — PcgrJsonFile","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Contains methods reading displaying contents pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PcgrJson R6 Class — PcgrJsonFile","text":"dracarys::File -> PcgrJsonFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PcgrJson R6 Class — PcgrJsonFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PcgrJson R6 Class — PcgrJsonFile","text":"PcgrJsonFile$read() PcgrJsonFile$write() PcgrJsonFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Reads pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PcgrJson R6 Class — PcgrJsonFile","text":"List tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Writes tidy version pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrJson R6 Class — PcgrJsonFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', '').","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrJson R6 Class — PcgrJsonFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"if (FALSE) { x <- \"/path/to/pcgr.json.gz\" d <- PcgrJsonFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"both\") }"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PcgrTiersFile R6 Class — PcgrTiersFile","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Contains methods reading displaying contents pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"dracarys::File -> PcgrTiersFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"PcgrTiersFile$read() PcgrTiersFile$write() PcgrTiersFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Reads pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"List tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Writes tidy version pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', '').","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"if (FALSE) { x <- \"/path/to/pcgr.snvs_indels.tiers.tsv\" d <- PcgrTiersFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"both\") }"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Contains methods reading contents ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"dracarys::File -> PloidyEstimationMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"PloidyEstimationMetricsFile$read() PloidyEstimationMetricsFile$write() PloidyEstimationMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Reads ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Writes tidy version ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.ploidy_estimation_metrics.csv.gz\", package = \"dracarys\") pem <- PloidyEstimationMetricsFile$new(x) d <- pem$read() # or read(pem) pem$write(d, out_dir = tempdir(), prefix = \"seqc_ploidy\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":null,"dir":"Reference","previous_headings":"","what":"ReplayFile R6 Class — ReplayFile","title":"ReplayFile R6 Class — ReplayFile","text":"Contains methods reading contents replay.json file output DRAGEN, contains DRAGEN command line, parameters version specific run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"ReplayFile R6 Class — ReplayFile","text":"dracarys::File -> ReplayFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"ReplayFile R6 Class — ReplayFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"ReplayFile R6 Class — ReplayFile","text":"ReplayFile$read() ReplayFile$write() ReplayFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"ReplayFile R6 Class — ReplayFile","text":"Reads replay.json file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"ReplayFile R6 Class — ReplayFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"ReplayFile R6 Class — ReplayFile","text":"Writes tidy version replay.json file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ReplayFile R6 Class — ReplayFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"ReplayFile R6 Class — ReplayFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"ReplayFile R6 Class — ReplayFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II-replay.json.gz\", package = \"dracarys\") r <- ReplayFile$new(x) d <- r$read() # or read(r) r$write(d, out_dir = tempdir(), prefix = \"seqc_replay\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"SvMetricsFile R6 Class — SvMetricsFile","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Contains methods reading displaying contents sv_metrics.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"dracarys::File -> SvMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"SvMetricsFile$read() SvMetricsFile$write() SvMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Reads sv_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Writes tidy version sv_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.sv_metrics.csv.gz\", package = \"dracarys\") sv <- SvMetricsFile$new(x) d <- sv$read() sv$write(d, out_dir = tempdir(), prefix = \"seqc_sv\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TimeMetricsFile R6 Class — TimeMetricsFile","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Contains methods reading contents time_metrics.csv file output DRAGEN, contains breakdown run duration DRAGEN process.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"dracarys::File -> TimeMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"TimeMetricsFile$read() TimeMetricsFile$write() TimeMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Reads time_metrics.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Writes tidy version time_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.time_metrics.csv.gz\", package = \"dracarys\") tm <- TimeMetricsFile$new(x) d <- tm$read() # or read(tm) tm$write(d, out_dir = tempdir(), prefix = \"seqc_time\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Contains methods reading displaying contents trimmer_metrics.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"dracarys::File -> TrimmerMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"TrimmerMetricsFile$read() TrimmerMetricsFile$write() TrimmerMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Reads trimmer_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Writes tidy version trimmer_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.trimmer_metrics.csv.gz\", package = \"dracarys\") tm <- TrimmerMetricsFile$new(x) d <- tm$read() tm$write(d, out_dir = tempdir(), prefix = \"seqc_tm\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Contains methods reading displaying contents AlignCollapseFusionCaller_metrics.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"dracarys::File -> TsoAlignCollapseFusionCallerMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"TsoAlignCollapseFusionCallerMetricsFile$read() TsoAlignCollapseFusionCallerMetricsFile$write() TsoAlignCollapseFusionCallerMetricsFile$plot() TsoAlignCollapseFusionCallerMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Reads AlignCollapseFusionCaller_metrics.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"tibble following columns: section: name original JSON element name: name metric value: value metric percent: percentage","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Writes tidy version AlignCollapseFusionCaller_metrics.json.gz file output TSO. Histo majority UmiStatistics section, write separately. Histo num supporting fragments: Num families 0/1/2/3... raw reads. Histo unique UMIs per fragment pos: Num pos 0/1/2/3... UMI seqs.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', ''). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Generates UmiStatistics Histogram plots AlignCollapseFusionCaller_metrics.json.gz file output TSO. Histo majority UmiStatistics section, deal separately. Histo num supporting fragments: Num families 0/1/2/3... raw reads. Histo unique UMIs per fragment pos: Num pos 0/1/2/3... UMI seqs.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$plot(d, max_num = 15)"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"d Parsed object self$read(). max_num Maximum number display plots.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"histogram plot objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz\",   package = \"dracarys\" ) m <- TsoAlignCollapseFusionCallerMetricsFile$new(x) d_parsed <- m$read() # or read(m) m$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = c(\"tsv\", \"rds\"))"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Contains methods reading displaying contents CombinedVariantOutput.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"dracarys::File -> TsoCombinedVariantOutputFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"TsoCombinedVariantOutputFile$read() TsoCombinedVariantOutputFile$write() TsoCombinedVariantOutputFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Reads CombinedVariantOutput.tsv file output TSO extracts Small Variants section (due inconsistencies sections).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Writes tidy version CombinedVariantOutput.tsv (Small Variants) file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"if (FALSE) { x <- \"/path/to/CombinedVariantOutput.tsv\" d <- TsoCombinedVariantOutputFile$new(x) d$read() }"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Contains methods reading displaying contents CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"dracarys::File -> TsoCopyNumberVariantsVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"TsoCopyNumberVariantsVcfFile$read() TsoCopyNumberVariantsVcfFile$write() TsoCopyNumberVariantsVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Reads CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Writes tidy version CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"if (FALSE) { x <- normalizePath(\"CopyNumberVariants.vcf.gz\") d <- TsoCopyNumberVariantsVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") d$write(d_parsed, prefix = \"FOO\", out_format = \"delta\", drid = \"wfr.123\") }"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Contains methods reading displaying contents fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"dracarys::File -> TsoFragmentLengthHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"TsoFragmentLengthHistFile$read() TsoFragmentLengthHistFile$write() TsoFragmentLengthHistFile$plot() TsoFragmentLengthHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Reads fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"tibble following columns: FragmentLength Count","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Writes tidy version fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Plots fragment length distributions given fragment_length_hist.json.gz file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$plot(d, min_count = 10)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"d Parsed object self$read(). min_count Minimum read count plotted (def: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"ggplot2 plot containing fragment lengths X axis read counts Y axis sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.fragment_length_hist.json.gz\", package = \"dracarys\") fl <- TsoFragmentLengthHistFile$new(x) d_parsed <- fl$read() # or read(fl) fl$plot(d_parsed, 5)  fl$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Contains methods reading displaying contents Fusions.csv file output TSO. Returns tibble columns (based input file header metadata): Sample: input sample ID. Name: Fusion name reported manta. Chr1/Chr2: chromosome 1st/2nd breakend. Pos1/Pos2: position 1st/2nd breakend. Direction: direction breakends joined together. Alt_Depth: number read-pairs supporting fusion call. BP1_Depth/BP2_Depth: Number read-pairs aligned 1st/2nd breakend. Total_Depth: Max number read-pairs aligned fusion breakend. VAF: Variant allele frequency. Gene1/Gene2: Genes overlap 1st/2nd breakend. Contig: fusion contig. Filter: Indicates whether fusion passed fusion filters. Is_Cosmic_GenePair: Indicates whether gene pair reported Cosmic(True/False).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"dracarys::File -> TsoFusionsCsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"TsoFusionsCsvFile$read() TsoFusionsCsvFile$write() TsoFusionsCsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Reads Fusions.csv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"tibble several columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Writes tidy version Fusions.csv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_Fusions.csv\", package = \"dracarys\") fus <- TsoFusionsCsvFile$new(x) d_parsed <- fus$read() # or read(fus) fus$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Contains methods reading displaying contents MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"dracarys::File -> TsoMergedSmallVariantsGenomeVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"TsoMergedSmallVariantsGenomeVcfFile$read() TsoMergedSmallVariantsGenomeVcfFile$write() TsoMergedSmallVariantsGenomeVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Reads MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Writes tidy version MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"if (FALSE) { x <- \"MergedSmallVariants.genome.vcf.gz\" d <- TsoMergedSmallVariantsGenomeVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Contains methods reading displaying contents MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"dracarys::File -> TsoMergedSmallVariantsVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"TsoMergedSmallVariantsVcfFile$read() TsoMergedSmallVariantsVcfFile$write() TsoMergedSmallVariantsVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Reads MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Writes tidy version MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"if (FALSE) { x <- \"MergedSmallVariants.vcf.gz\" d <- TsoMergedSmallVariantsVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") d$write(d_parsed, prefix = \"FOO\", out_format = \"delta\", drid = \"wfr.123\") }"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMsiFile R6 Class — TsoMsiFile","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Contains methods reading displaying contents msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"dracarys::File -> TsoMsiFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"TsoMsiFile$read() TsoMsiFile$write() TsoMsiFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Reads msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"tibble following columns: label:","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Writes tidy version msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.msi.json.gz\", package = \"dracarys\") msi <- TsoMsiFile$new(x) d_parsed <- msi$read() # or read(msi) msi$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Contains methods reading displaying contents SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"dracarys::File -> TsoSampleAnalysisResultsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"TsoSampleAnalysisResultsFile$read() TsoSampleAnalysisResultsFile$write() TsoSampleAnalysisResultsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Reads SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"list tibbles","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Writes tidy version SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_SampleAnalysisResults.json.gz\", package = \"dracarys\") res <- TsoSampleAnalysisResultsFile$new(x) d_parsed <- res$read() # or read(res) res$write(d_parsed, tempfile(), \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Contains methods reading displaying contents TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"dracarys::File -> TsoTargetRegionCoverageFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"TsoTargetRegionCoverageFile$read() TsoTargetRegionCoverageFile$write() TsoTargetRegionCoverageFile$plot() TsoTargetRegionCoverageFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Reads TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"tibble following columns: ConsensusReadDepth BasePair Percentage","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Writes tidy version TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Plots TargetRegionCoverage.json.gz file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$plot(d, min_pct = 2)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"d Parsed object self$read(). min_pct Minimum percentage plotted (def: 2).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"ggplot2 plot containing read depth X axis percentage covered Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.TargetRegionCoverage.json.gz\", package = \"dracarys\") trc <- TsoTargetRegionCoverageFile$new(x) d_parsed <- trc$read() # or read(trc) trc$plot(d_parsed, 0) # or plot(trc, d_parsed, 90)  trc$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTmbFile R6 Class — TsoTmbFile","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Contains methods reading displaying contents tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"dracarys::File -> TsoTmbFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"TsoTmbFile$read() TsoTmbFile$write() TsoTmbFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Reads tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"tibble following columns: TmbPerMb AdjustedTmbPerMb NonsynonymousTmbPerMb AdjustedNonsynonymousTmbPerMb SomaticCodingVariantsCount NonsynonymousSomaticCodingVariantsCount TotalRegionSizeMb CodingRegionSizeMb","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Writes tidy version tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.tmb.json.gz\", package = \"dracarys\") tmb <- TsoTmbFile$new(x) d_parsed <- tmb$read() # or read(tmb) tmb$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Contains methods reading displaying contents TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"dracarys::File -> TsoTmbTraceTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"TsoTmbTraceTsvFile$read() TsoTmbTraceTsvFile$write() TsoTmbTraceTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Reads TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Writes tidy version TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_TMB_Trace.tsv\", package = \"dracarys\") d <- TsoTmbTraceTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmChordTsvFile R6 Class — UmChordTsvFile","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Contains methods reading displaying contents chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"dracarys::File -> UmChordTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"UmChordTsvFile$read() UmChordTsvFile$write() UmChordTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Reads chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Writes tidy version chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"if (FALSE) { x <- \"/path/to/chord.tsv.gz\" d <- UmChordTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Contains methods reading displaying contents hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"dracarys::File -> UmHrdetectTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"UmHrdetectTsvFile$read() UmHrdetectTsvFile$write() UmHrdetectTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Reads hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Writes tidy version hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$write(d, out_dir, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"if (FALSE) { x <- \"/path/to/hrdetect.tsv.gz\" d <- UmHrdetectTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmQcSumFile R6 Class — UmQcSumFile","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Contains methods reading displaying contents qc_summary.tsv.gz file QC summary metrics output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"dracarys::File -> UmQcSumFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"UmQcSumFile$read() UmQcSumFile$write() UmQcSumFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Reads qc_summary.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Writes tidy version qc_summary.tsv.gz QC summary file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$write(d, out_dir, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"if (FALSE) { x <- \"/path/to/snv_2015.tsv.gz\" d <- UmQcSumFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmSigsSnvFile R6 Class — UmSigsSnvFile","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Contains methods reading displaying contents snv_20XX.tsv.gz file SNV signatures output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"dracarys::File -> UmSigsSnvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"UmSigsSnvFile$read() UmSigsSnvFile$write() UmSigsSnvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Reads snv.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Writes tidy version snv_20XX.tsv.gz signature file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"if (FALSE) { x <- \"/path/to/snv_2015.tsv.gz\" d <- UmSigsSnvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"VCMetricsFile R6 Class — VCMetricsFile","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Contains methods reading displaying contents vc_metrics.csv file output DRAGEN, contains variant calling metrics.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"dracarys::File -> VCMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"VCMetricsFile$read() VCMetricsFile$write() VCMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Reads vc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Writes tidy version vc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.vc_metrics.csv.gz\", package = \"dracarys\") vm <- VCMetricsFile$new(x) d <- vm$read() # or read(vm) vm$write(d, out_dir = tempdir(), prefix = \"seqc_vc\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Contains methods reading displaying contents wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN. file contains estimated coverage contigs, autosomal estimated coverage.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"dracarys::File -> WgsContigMeanCovFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"WgsContigMeanCovFile$read() WgsContigMeanCovFile$write() WgsContigMeanCovFile$plot() WgsContigMeanCovFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Reads wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$read(keep_alt = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"keep_alt Keep ALT + Mito chromosomes?","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"tibble following columns: label: file label. chrom: contig name. n_bases: number bases aligned contig (excludes bases duplicate marked reads, reads MAPQ=0, clipped bases). coverage: col2 / contig length","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Writes tidy version wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Plots wgs_contig_mean_cov_<phenotype>.csv files.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$plot(d, top_alt_n = 15)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"d Parsed object self$read(). top_alt_n Number top covered alt contigs plot per phenotype.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"ggplot2 object chromosomes X axis, coverage Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_contig_mean_cov_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_contig_mean_cov_tumor.csv.gz\", package = \"dracarys\") cc1 <- WgsContigMeanCovFile$new(x1) cc2 <- WgsContigMeanCovFile$new(x2) d1 <- cc1$read() d2 <- cc2$read() cc1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") cc2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")  cc1$plot(d1)  cc2$plot(d2)"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Contains methods reading displaying contents wgs_coverage_metrics_<phenotype>.csv file output DRAGEN. file contains read depth coverage metrics.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"dracarys::File -> WgsCoverageMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"WgsCoverageMetricsFile$read() WgsCoverageMetricsFile$write() WgsCoverageMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Reads wgs_coverage_metrics_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Writes tidy version wgs_coverage_metrics_<phenotype>.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_coverage_metrics_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_coverage_metrics_tumor.csv.gz\", package = \"dracarys\") cm1 <- WgsCoverageMetricsFile$new(x1) cm2 <- WgsCoverageMetricsFile$new(x2) d1 <- read(cm1) d2 <- read(cm2) cm1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") cm2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsFineHistFile R6 Class — WgsFineHistFile","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Contains methods reading displaying contents wgs_fine_hist_<phenotype>.csv file output DRAGEN. file contains two columns: Depth Overall. value Depth column ranges 0 1000+ Overall column indicates number loci covered corresponding depth.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"dracarys::File -> WgsFineHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"WgsFineHistFile$read() WgsFineHistFile$write() WgsFineHistFile$plot() WgsFineHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Reads wgs_fine_hist_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"tibble following columns: depth number loci given depth","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Writes tidy version wgs_fine_hist_<phenotype>.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Plots wgs_fine_hist_<phenotype>.csv files.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$plot(d, x_lim = c(0, 300))"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"d Parsed object self$read(). x_lim X axis range plot.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"ggplot2 object depth coverage X axis, number loci depth Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_fine_hist_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_fine_hist_tumor.csv.gz\", package = \"dracarys\") ch1 <- WgsFineHistFile$new(x1) ch2 <- WgsFineHistFile$new(x2) d1 <- read(ch1) d2 <- read(ch2) ch1$plot(d1)  ch2$plot(d2)  ch1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") ch2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsHistFile R6 Class — WgsHistFile","title":"WgsHistFile R6 Class — WgsHistFile","text":"Contains methods reading displaying contents wgs_hist.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsHistFile R6 Class — WgsHistFile","text":"dracarys::File -> WgsHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsHistFile R6 Class — WgsHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsHistFile R6 Class — WgsHistFile","text":"WgsHistFile$read() WgsHistFile$write() WgsHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsHistFile R6 Class — WgsHistFile","text":"Reads wgs_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsHistFile R6 Class — WgsHistFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsHistFile R6 Class — WgsHistFile","text":"Writes tidy version wgs_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsHistFile R6 Class — WgsHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsHistFile R6 Class — WgsHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsHistFile R6 Class — WgsHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.wgs_hist.csv.gz\", package = \"dracarys\") h <- WgsHistFile$new(x) d <- h$read() h$write(d, out_dir = tempdir(), prefix = \"seqc_sv\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse VCF with bcftools — bcftools_parse_vcf","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"Parse VCF bcftools. Uses bcftools hood heavy lifting field splitting, converts parsed character vector tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"","code":"bcftools_parse_vcf(vcf, only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"vcf VCF one samples. only_pass Keep PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"tibble main, FORMAT, INFO fields detected VCF header columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"VCFs 0 variants, returns tibble 0 rows proper number columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"Parses VCF regions bcftools. VCF subset written temporary file local filesystem, parsed tibble object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"","code":"bcftools_parse_vcf_regions(vcf, r, only_pass = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"vcf Path VCF. Can S3, http local. presigned URL, need also concatenate VCF index 'vcf_url##idx##vcfi_url'. r Character vector regions subset (e.g. c('chr1:123-456', 'chr2:789-1000')) only_pass Keep PASS variants (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"tibble main, FORMAT, INFO fields detected VCF header columns, regions specified r ().","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"","code":"if (FALSE) { vcf_local <- here::here(\"MergedSmallVariants.vcf.gz\") r <- c(\"chr1:115256529-115256529\", \"chr2:29443613-29443613\") bcftools_parse_vcf_regions(vcf_local, r) }"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html","id":null,"dir":"Reference","previous_headings":"","what":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","title":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","text":"Reads Adapter_Metrics.csv file Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","text":"","code":"bclconvert_read_adaptermetrics(x)"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","text":"x Path Adapter_Metrics.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","text":"Tibble","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics","text":"","code":"if (FALSE) { x <- here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports/Adapter_Metrics.csv\") bclconvert_read_adaptermetrics(x) }"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html","id":null,"dir":"Reference","previous_headings":"","what":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","title":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","text":"Reads Demultiplex_Stats.csv file Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","text":"","code":"bclconvert_read_demultiplexstats(x)"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","text":"x Path Demultiplex_Stats.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","text":"Tibble","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats","text":"","code":"if (FALSE) { x <- here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports/Demultiplex_Stats.csv\") bclconvert_read_demultiplexstats(x) }"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html","id":null,"dir":"Reference","previous_headings":"","what":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","title":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","text":"Reads Index_Hopping_Counts.csv file Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","text":"","code":"bclconvert_read_indexhoppingcounts(x)"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","text":"x Path Index_Hopping_Counts.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","text":"Tibble","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts","text":"","code":"if (FALSE) { x <- here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports/Index_Hopping_Counts.csv\") bclconvert_read_indexhoppingcounts(x) }"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html","id":null,"dir":"Reference","previous_headings":"","what":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","title":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","text":"Reads Top_Unknown_Barcodes.csv file Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","text":"","code":"bclconvert_read_topunknownbarcodes(x)"},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","text":"x Path Top_Unknown_Barcodes.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","text":"Tibble","code":""},{"path":"https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BCLConvert Top Unknown Barcodes — bclconvert_read_topunknownbarcodes","text":"","code":"if (FALSE) { x <- here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports/Top_Unknown_Barcodes.csv\") bclconvert_read_topunknownbarcodes(x) }"},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":null,"dir":"Reference","previous_headings":"","what":"Print current timestamp for logging — date_log","title":"Print current timestamp for logging — date_log","text":"Print current timestamp logging","code":""},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print current timestamp for logging — date_log","text":"","code":"date_log()"},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print current timestamp for logging — date_log","text":"Current timestamp character.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate dracarys Function — dr_func_eval","title":"Evaluate dracarys Function — dr_func_eval","text":"somewhat hack getting function evaluate based lookup vector. function found, returns NULL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate dracarys Function — dr_func_eval","text":"","code":"dr_func_eval(f, v = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate dracarys Function — dr_func_eval","text":"f Name function evaluate. v Character vector strings evaluating functions. default, points functions DR_FILE_REGEX dracarys tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate dracarys Function — dr_func_eval","text":"Evaluated function.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate dracarys Function — dr_func_eval","text":"","code":"mean_1_to_10 <- dr_func_eval(\"mean\", v = c(\"mean\", \"sd\"))(1:10) x <- system.file(\"extdata/tso/sample705.fragment_length_hist.json.gz\", package = \"dracarys\") obj <- dr_func_eval(\"TsoFragmentLengthHistFile\")$new(x)"},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys GDS Download — dr_gds_download","title":"dracarys GDS Download — dr_gds_download","text":"Download GDS files can processed dracarys.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dracarys GDS Download — dr_gds_download","text":"","code":"dr_gds_download(   gdsdir,   outdir,   token,   page_size = 100,   pattern = NULL,   dryrun = FALSE,   regexes = DR_FILE_REGEX,   recursive = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dracarys GDS Download — dr_gds_download","text":"gdsdir Full path GDS directory. outdir Path output directory. token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 100). pattern Pattern filter returned file type tibble. dryrun TRUE, just list files downloaded (download ). regexes Tibble regex function name. recursive files returned recursively specified GDS directory (TRUE), directly specified GDS directory (FALSE) (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"Output Format is Valid — dr_output_format_valid","title":"Output Format is Valid — dr_output_format_valid","text":"Checks specified output format valid.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Output Format is Valid — dr_output_format_valid","text":"","code":"dr_output_format_valid(x)"},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Output Format is Valid — dr_output_format_valid","text":"x Output format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys S3 Download — dr_s3_download","title":"dracarys S3 Download — dr_s3_download","text":"Download S3 files can processed dracarys.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dracarys S3 Download — dr_s3_download","text":"","code":"dr_s3_download(   s3dir,   outdir,   page_size = 100,   pattern = NULL,   regexes = DR_FILE_REGEX,   dryrun = FALSE )"},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dracarys S3 Download — dr_s3_download","text":"s3dir Full path S3 directory. outdir Path output directory. page_size Page size (def: 100). pattern Pattern filter returned file type tibble. regexes Tibble regex function name. dryrun TRUE, just list files downloaded (download ).","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"dracarys S3 Download — dr_s3_download","text":"","code":"s3dir <- file.path(   \"s3://umccr-primary-data-prod/UMCCR-Validation/SBJ00596\",   \"ctTSO/2021-03-17/PTC_SSqCMM05pc_L2100067\" ) outdir <- sub(\"s3:/\", \"~/s3\", s3dir)"},{"path":"https://umccr.github.io/dracarys/reference/dracarys-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys: Post-processing DRAGEN workflows — dracarys-package","title":"dracarys: Post-processing DRAGEN workflows — dracarys-package","text":"Post-processing DRAGEN workflows.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/dracarys-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dracarys: Post-processing DRAGEN workflows — dracarys-package","text":"Maintainer: Peter Diakumis peterdiakumis@gmail.com (ORCID) Authors: Victor San Kho Lin (ORCID) [contributor]","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Empty Tibble Given Column Names — empty_tbl","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"https://stackoverflow.com//62535671/2169986. Useful handling edge cases empty data.","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"","code":"empty_tbl(cnames, ctypes = readr::cols(.default = \"c\"))"},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"cnames Character vector column names use. ctypes Character vector column types corresponding cnames.","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"tibble 0 rows given column names.","code":""},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dracarys DR_FILE_REGEX — file_regex_getter","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"Get dracarys DR_FILE_REGEX","code":""},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"","code":"file_regex_getter()"},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"DR_FILE_REGEX R tibble object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Download via CLI — gds_file_download","title":"GDS File Download via CLI — gds_file_download","text":"GDS File Download via CLI","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Download via CLI — gds_file_download","text":"","code":"gds_file_download(gds, out, token = Sys.getenv(\"ICA_ACCESS_TOKEN\"))"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Download via CLI — gds_file_download","text":"gds Full path GDS file. Path output file. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Download via API — gds_file_download_api","title":"GDS File Download via API — gds_file_download_api","text":"GDS File Download via API","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Download via API — gds_file_download_api","text":"","code":"gds_file_download_api(gds_fileid, out_file, token)"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Download via API — gds_file_download_api","text":"gds_fileid GDS file ID. out_file Path output file. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GDS File Download via API — gds_file_download_api","text":"","code":"if (FALSE) { gds_fileid <- \"fil.f9aa2ba7af0c4330095d08dadd2e16b0\" out <- tempfile() token <- Sys.getenv(\"ICA_ACCESS_TOKEN\") }"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Presigned URL — gds_file_presignedurl","title":"GDS File Presigned URL — gds_file_presignedurl","text":"Returns presigned URL given GDS file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Presigned URL — gds_file_presignedurl","text":"","code":"gds_file_presignedurl(gds_fileid, token)"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Presigned URL — gds_file_presignedurl","text":"gds_fileid GDS file ID. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GDS File Presigned URL — gds_file_presignedurl","text":"Presigned URL valid.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS Files List — gds_files_list","title":"GDS Files List — gds_files_list","text":"List files ICA GDS filesystem.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS Files List — gds_files_list","text":"","code":"gds_files_list(   gdsdir,   token,   page_size = NULL,   include_url = FALSE,   no_recurse = TRUE,   page_token = NULL,   recursive = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS Files List — gds_files_list","text":"gdsdir Full path GDS directory. token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 10). include_url Include presigned URLs files within GDS directory (def: FALSE). no_recurse recurse file list .e. just give first <page_size> items without recursing list using <page_token>. page_token Page token (def: NULL). Used internally recursion. recursive files returned recursively specified GDS directory, directly specified GDS directory (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GDS Files List — gds_files_list","text":"Tibble file basename, file size, file full data path, file dir name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GDS Files List — gds_files_list","text":"","code":"if (FALSE) { gdsdir <- file.path(   \"gds://production/primary_data\",   \"240322_A00130_0290_BH5HLLDSXC/20240323f56ec5a5/WGS_TsqNano\" ) gdsdir <- file.path(   \"gds://bssh.acddbfda498038ed99fa94fe79523959/Runs\",   \"240322_A00130_0290_BH5HLLDSXC_r.3TbcOsEKZUyetygkqIOXcg/InterOp\" ) gdsdir <- file.path(   \"gds://production/analysis_data/SBJ00699/umccrise\",   \"202203277dcf8562/L2200352__L2100146/SBJ00699__MDX220105/coverage\" ) token <- ica_token_validate() page_size <- 11 include_url <- TRUE page_token <- NULL no_recurse <- TRUE recursive <- NULL gds_files_list(gdsdir, token, page_size, include_url, no_recurse, page_token, recursive) }"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":null,"dir":"Reference","previous_headings":"","what":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"Lists relevant files GDS directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"","code":"gds_files_list_filter_relevant(   gdsdir,   token,   pattern = NULL,   include_url = FALSE,   page_size = 100,   regexes = DR_FILE_REGEX )"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"gdsdir GDS directory. token ICA access token. pattern Pattern filter returned file type tibble. include_url Include presigned URLs files within GDS directory (def: FALSE). page_size Page size (def: 100). regexes Tibble regex function name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"tibble type, bname, size, file_id, path, presigned URL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List GDS Volumes — gds_volumes_list","title":"List GDS Volumes — gds_volumes_list","text":"Lists GDS volumes accessible provided ICA token.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List GDS Volumes — gds_volumes_list","text":"","code":"gds_volumes_list(token, page_size = 10)"},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List GDS Volumes — gds_volumes_list","text":"token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List GDS Volumes — gds_volumes_list","text":"tibble vol name vol id.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate ICA access token — ica_token_validate","title":"Validate ICA access token — ica_token_validate","text":"Validates ICA access token parsing checking expiration date.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate ICA access token — ica_token_validate","text":"","code":"ica_token_validate(token = Sys.getenv(\"ICA_ACCESS_TOKEN\"))"},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate ICA access token — ica_token_validate","text":"token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate ICA access token — ica_token_validate","text":"Returns token valid, else errors .","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":null,"dir":"Reference","previous_headings":"","what":"Match File to Regex — match_regex","title":"Match File to Regex — match_regex","text":"Matches given file regexes found DR_FILE_REGEX match, returns 'name' match.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match File to Regex — match_regex","text":"","code":"match_regex(x, regexes = DR_FILE_REGEX)"},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match File to Regex — match_regex","text":"x File match. regexes Tibble regex function name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match File to Regex — match_regex","text":"function corresponding matching regex DR_FILE_REGEX, NA match made.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match File to Regex — match_regex","text":"","code":"match_regex(\"foo.msi.json.gz\") #> [1] \"TsoMsiFile\" match_regex(\"foo.fake.tsv\") #> [1] NA"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":null,"dir":"Reference","previous_headings":"","what":"Append New MultiQC Workflow Columns — multiqc_column_map_append","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"Append New MultiQC Workflow Columns","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"","code":"multiqc_column_map_append(d, w, m)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"d Tidy MultiQC tibble raw names (.e. pre-rename). w New workflow name. m Path 'inst/extdata/multiqc_column_map.tsv' dracarys file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":null,"dir":"Reference","previous_headings":"","what":"Format MultiQC Config Date — multiqc_date_fmt","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"Format MultiQC Config Date","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"","code":"multiqc_date_fmt(cdate)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"cdate String config date \"YYYY-MM-DD, HH:MM UTC\" format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"Properly formatted datetime string \"YYYY-MM-DDTHH:MM:SS\" format. input string formatted differently, return NA.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"","code":"cdate <- \"2023-04-07, 09:09 UTC\" (res1 <- multiqc_date_fmt(cdate)) #> [1] \"2023-04-07T09:09:00\" (res2 <- multiqc_date_fmt(\"2023-04-07\")) #> [1] NA (res3 <- multiqc_date_fmt(\"UNKNOWN\")) #> [1] NA"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"Extracts bar_graph data given plot name MultiQC JSON. bar_graph element JSON object contains:","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"","code":"multiqc_parse_bargraph_plot(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"samples array N subarrays (strings) length . datasets array N subarrays (objects) length B. subarrays contains name (single string) data (array length equal length index-corresponding samples subarray).","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"","code":"if (FALSE) { j1 <- here::here(\"nogit/bcl_convert/multiqc_data.json\") j2 <- here::here(\"nogit/dracarys_gds_sync/multiqc_data.json\") j <- j1 j <- j2 multiqc_list_plots(j) parsed <- RJSONIO::fromJSON(j) dat <- parsed$report_plot_data$mapping_dup_percentage_plot dat <- parsed$report_plot_data$time_metrics_plot dat <- parsed$report_plot_data$bclconvert_lane_counts dat <- parsed$report_plot_data$bclconvert_sample_counts multiqc_parse_bargraph_plot(dat) }"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"Parses MultiQC 'report_general_stats_data' JSON Element. Modified awesome https://github.com/multimeric/TidyMultiqc.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"","code":"multiqc_parse_gen(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"p Parsed MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"list.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"Parse Plot Data MultiQC JSON","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"","code":"multiqc_parse_plots(j, plot_names = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"j Path multiqc_data.json file. plot_names Names plots parse. Use \"everything\" wantz plotz.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"Nested tibble plot name result list column (use tidyr::unnest access).","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"","code":"if (FALSE) { j <- \"dracarys_gds_sync/multiqc_data.json\" multiqc_parse_plots(j, plot_names = c(\"dragen_coverage_per_contig\")) multiqc_parse_plots(j, plot_names = \"everything\") multiqc_parse_plots(j, plot_names = NULL) }"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"Parses MultiQC 'report_saved_raw_data' JSON Element.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"","code":"multiqc_parse_raw(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"p Parsed MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"list tibbles tool, tibble contains metrics per sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"Parses Interop MultiQC 'report_saved_raw_data' JSON Element.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"","code":"multiqc_parse_raw_interop(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"p Parsed Interop MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"list summary per-lane tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Extracts xy_line data given plot name MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"","code":"multiqc_parse_xyline_plot(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Note dragen_coverage_per_contig/non_main_contig plots conform normal structure xy_line plots, handle separately.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"MultiQC Extract XY Line Plot Data DRAGEN Contig Coverage","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"","code":"multiqc_parse_xyline_plot_contig_cvg(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy MultiQC JSON — multiqc_tidy_json","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"Tidies 'multiqc_data.json' output MultiQC. Modified awesome https://github.com/multimeric/TidyMultiqc.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"","code":"multiqc_tidy_json(j)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"j Path multiqc_data.json file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"tidy tibble column corresponds single metric, row corresponds single sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Local R Dataframe to Spark-backed Table — rdf2tab","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"First converts local R dataframe Spark DataFrame using SparkR, appends specified table.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"","code":"rdf2tab(rdf, outpath, drid = NULL, ...)"},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"rdf Local R dataframe outpath Path output table. drid dracarys ID use dataset (e.g. wfrid.123, prid.456) ... Additional arguments SparkR::write.df.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"","code":"if (FALSE) { rdf <- mtcars rdf2tab(rdf, \"dev.wf1.mtcars\", drid = \"wfr.123\") }"},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":null,"dir":"Reference","previous_headings":"","what":"Read File object — read.File","title":"Read File object — read.File","text":"Read file based type.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read File object — read.File","text":"","code":"# S3 method for File read(x, ...)"},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read File object — read.File","text":"x Object class File. ... Arguments passed appropriate read_* function.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic Reading — read","title":"Generic Reading — read","text":"Generic function reading dracarys objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic Reading — read","text":"","code":"read(x, ...)"},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic Reading — read","text":"x Object respective class. ... Additional arguments.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic Reading — read","text":"Possibly tibble list, depending object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":null,"dir":"Reference","previous_headings":"","what":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"Lists relevant files AWS S3 directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"","code":"s3_files_list_filter_relevant(   s3dir,   pattern = NULL,   page_size = 1000,   max_items = 1000,   presign = FALSE,   expiry_sec = 43200 )"},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"s3dir S3 directory. pattern Pattern filter returned file type tibble. page_size size page get AWS service call (def: 1000). max_items total number items return command’s output (def: 1000). presign Include presigned URLs (def: FALSE). expiry_sec Number seconds presigned URL valid (generated) (def: 43200 (12hrs)).","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"tibble path, date, file size, file type, presigned URL requested.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"","code":"if (FALSE) { s3dir <- \"s3://umccr-primary-data-prod/cancer_report_tables\" s3_files_list_filter_relevant(s3dir = s3dir, presign = TRUE) }"},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search AWS S3 Objects — s3_search","title":"Search AWS S3 Objects — s3_search","text":"Searches given pattern UMCCR umccr-primary-data-prod AWS S3 bucket.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search AWS S3 Objects — s3_search","text":"","code":"s3_search(pat, rows)"},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search AWS S3 Objects — s3_search","text":"pat Pattern search (e.g. 'multiqc_data.json'). rows Max number rows return.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search AWS S3 Objects — s3_search","text":"Tibble S3 path, object size, date modified, id, unique hash.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search AWS S3 Objects — s3_search","text":"","code":"if (FALSE) { pat <- \"qc_summary.tsv.gz\" s3_search(pat, 10) }"},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Kable — session_info_kable","title":"Session Information Kable — session_info_kable","text":"Session information kables vignettes.","code":""},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Kable — session_info_kable","text":"","code":"session_info_kable(pkgs = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Kable — session_info_kable","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Kable — session_info_kable","text":"list two kables containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Multiple TimeMetricsFile Objects — time_metrics_process","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"Processes multiple TimeMetricsFile objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"","code":"time_metrics_process(x, id = seq_len(length(x)))"},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"x Atomic vector one TimeMetricsFile objects. id ID input, used disambiguate files generated samples. Default: index 1 length x.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"tibble following columns: Step: DRAGEN step Time: time HH:MM","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"","code":"p <- system.file(\"extdata/wgs/SEQC-II.time_metrics.csv.gz\", package = \"dracarys\") x <- TimeMetricsFile$new(p) (tm <- time_metrics_process(c(x, x), id = c(\"run1\", \"run2\"))) #> # A tibble: 2 × 20 #>   ID    `Total Runtime` `Loading Reference` `Aligning Reads` `Duplicate Marking` #>   <chr> <chr>           <chr>               <chr>            <chr>               #> 1 run1  04:10           00:01               00:35            00:01               #> 2 run2  04:10           00:01               00:35            00:01               #> # ℹ 15 more variables: `Sorting and Marking Duplicates` <chr>, #> #   `DRAGStr Calibration` <chr>, `Saving Map/Align Output` <chr>, #> #   `Partial Reconfiguration` <chr>, `Variant Calling` <chr>, #> #   `Calculating Target Counts` <chr>, `Correcting GC Bias` <chr>, #> #   `Normalizing Case Sample` <chr>, `Performing Segmentation` <chr>, #> #   `Generating Somatic Model Input` <chr>, `Fitting Somatic Model` <chr>, #> #   `Generating CNV Calls` <chr>, `Generating CNV Track Files` <chr>, …"},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy UMCCR Results — umccr_tidy","title":"Tidy UMCCR Results — umccr_tidy","text":"Tidies UMCCR workflow results list tibbles writes individual tibbles TSV, Parquet, SparkDF, RDS format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tidy UMCCR Results — umccr_tidy","text":"","code":"umccr_tidy(   in_dir = NULL,   out_dir = NULL,   prefix = NULL,   local_dir = NULL,   out_format = \"tsv\",   dryrun = FALSE,   token = Sys.getenv(\"ICA_ACCESS_TOKEN\"),   pattern = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tidy UMCCR Results — umccr_tidy","text":"in_dir Directory path UMCCR workflow results (can GDS, S3 local). out_dir Output directory. prefix Prefix output file(s). local_dir indir GDS S3 directory, 'recognisable' files first downloaded directory. out_format Format output (tsv, parquet, ) (def: tsv). dryrun Just list files downloaded (def: FALSE). token ICA access token (default uses $ICA_ACCESS_TOKEN env var). pattern Pattern filter returned file type tibble (see name column DR_FILE_REGEX tibble).","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tidy UMCCR Results — umccr_tidy","text":"Tibble path input file resultant tidy object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tidy UMCCR Results — umccr_tidy","text":"","code":"if (FALSE) { in_dir <- file.path(   \"s3://umccr-primary-data-prod/UMCCR-Validation/SBJ00596\",   \"ctTSO/2021-03-17/PTC_SSqCMM05pc_L2100067\" ) in_dir <- paste0(   \"gds://production/analysis_data/SBJ01639/tso_ctdna_tumor_only/\",   \"202204045ad5743c/L2200214/Results/PRJ220425_L2200214\" ) o1 <- sub(\"^gds://\", \"\", in_dir) o1 <- sub(\"s3:/\", \"~/s3\", in_dir) out_dir <- o1 out_dir <- file.path(fs::path_home(), \"icav1/g\", o1) # in_dir <- file.path(out_dir, \"dracarys_gds_sync\") prefix <- \"SBJ01639\" prefix <- \"PTC_SSqCMM05pc_L2100067\" out_format <- \"rds\" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, out_format = out_format, dryrun = F)  in_dir <- here::here(glue(\"nogit/tso/2022-12-13/SBJ02858/dracarys_gds_sync\")) out_dir <- file.path(in_dir, \"../out\") gds_local_dir <- NULL prefix <- \"SBJ02858\" dryrun <- F umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, dryrun = F) }"},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0140-2024-05-13","dir":"Changelog","previous_headings":"","what":"dracarys 0.14.0 (2024-05-13)","title":"dracarys 0.14.0 (2024-05-13)","text":"0.13.0 - 0.14.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0130-2024-03-15","dir":"Changelog","previous_headings":"","what":"dracarys 0.13.0 (2024-03-15)","title":"dracarys 0.13.0 (2024-03-15)","text":"0.12.0 - 0.13.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0120-2023-12-12","dir":"Changelog","previous_headings":"","what":"dracarys 0.12.0 (2023-12-12)","title":"dracarys 0.12.0 (2023-12-12)","text":"0.11.0 - 0.12.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0110-2023-08-22","dir":"Changelog","previous_headings":"","what":"dracarys 0.11.0 (2023-08-22)","title":"dracarys 0.11.0 (2023-08-22)","text":"0.10.0 - 0.11.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0100-2023-06-22","dir":"Changelog","previous_headings":"","what":"dracarys 0.10.0 (2023-06-22)","title":"dracarys 0.10.0 (2023-06-22)","text":"0.9.0 - 0.10.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-090-2023-05-10","dir":"Changelog","previous_headings":"","what":"dracarys 0.9.0 (2023-05-10)","title":"dracarys 0.9.0 (2023-05-10)","text":"0.8.0 - 0.9.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-080-2023-02-24","dir":"Changelog","previous_headings":"","what":"dracarys 0.8.0 (2023-02-24)","title":"dracarys 0.8.0 (2023-02-24)","text":"0.7.0 - 0.8.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-070-2023-02-15","dir":"Changelog","previous_headings":"","what":"dracarys 0.7.0 (2023-02-15)","title":"dracarys 0.7.0 (2023-02-15)","text":"0.6.0 - 0.7.0 diff Mostly added use cases based requests curation team related umccrise (CHORD, HRDetect, QC summary), PCGR, MultiQC. umccr_tidy: workhorse handles tidying method dispatch. gds_file_presignedurl PcgrJsonFile PcgrTiersFile UmChordTsvFile UmHrdetectTsvFile UmQcSumFile UmSigsSnvFile MultiqcFile Updated README unified dracarys tidy CLI. Added fun column FILE_REGEX handling method dispatch. GH Actions: Remove linux/arm64 docker since conda pkgs don’t generally ARM64 equivalents. GH Actions: use “miniforge-variant: Mambaforge” (see issue).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-060-2023-01-09","dir":"Changelog","previous_headings":"","what":"dracarys 0.6.0 (2023-01-09)","title":"dracarys 0.6.0 (2023-01-09)","text":"0.5.0 - 0.6.0 diff replace ::set-output. add linux/arm64 support. replace select .data quotes. bump Roxygen 7.2.1 -> 7.2.2 add {fs}, {httr}, {jose}, {sessioninfo} dependencies. import %||% {rlang} specify fallback values NULL cases. ✨ pkgdown: change theme simplex. bump mambaforge: 4.12.0-2 -> 22.9.0-2 bump conda-lock: 1.0.5 -> 1.3.0 add support tidying outputs UMCCR TSO500 ctDNA workflow, generating HTML file tidy results workflow. tso_tidy tidying outputs UMCCR TSO500 ctDNA workflow. tso_rmd generating HTML file tidy results workflow. dr_gds_download downloading dracarys-related files GDS. gds_files_list listing files GDS via API. gds_file_download gds_file_download_api downloading files GDS via ica binary API (via presigned URLs), respectively. ica_token_validate validating ICA access token valid expired. TsoCombinedVariantOutputFile: files deemed less info compared output files. dracarys_tidy_multiqc: renamed dracarys_multiqc. mkdir: use fs::create_dir instead. Remove {tibble}, {readr} {ggplot} multi-imports R6, since can get away just importing single function one R6 classes.","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-050-2022-09-28","dir":"Changelog","previous_headings":"","what":"dracarys 0.5.0 (2022-09-28)","title":"dracarys 0.5.0 (2022-09-28)","text":"0.4.0 - 0.5.0 diff move map separate TSV CLI: add option output format (tsv, parquet, ) (pr18). new contributors: @victorskl","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-040-2022-09-12","dir":"Changelog","previous_headings":"","what":"dracarys 0.4.0 (2022-09-12)","title":"dracarys 0.4.0 (2022-09-12)","text":"0.3.0 - 0.4.0 diff also add Quarto HTML report template","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-030-2022-08-28","dir":"Changelog","previous_headings":"","what":"dracarys 0.3.0 (2022-08-28)","title":"dracarys 0.3.0 (2022-08-28)","text":"0.2.0 - 0.3.0 diff ⭐ MultiQC: support DRAGEN ctdna output (pr13).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-020-2022-07-23","dir":"Changelog","previous_headings":"","what":"dracarys 0.2.0 (2022-07-23)","title":"dracarys 0.2.0 (2022-07-23)","text":"0.1.0 - 0.2.0 diff Add MULTIQC_COLUMNS tibble maps raw metric name cleaner name (pr12). Support MultiQC JSONs (bcbio-wts bcbio-wgs).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-010-2022-07-11","dir":"Changelog","previous_headings":"","what":"dracarys 0.1.0 (2022-07-11)","title":"dracarys 0.1.0 (2022-07-11)","text":"Initial release dracarys. Support MultiQC JSON tidying. Add conda, conda-lock, Docker support (pr11). Initially supporting just MultiQC json input (dragen-alignment, dragen-transcriptome, dragen-tumor-normal, dragen-umccrise, bcbio-umccrise).","code":""}]
+[{"path":[]},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement peterdiakumis@gmail.com. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://umccr.github.io/dracarys/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 University Melbourne Centre Cancer Research - Genomics Platform Group Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://umccr.github.io/dracarys/articles/files.html","id":"workflows","dir":"Articles","previous_headings":"","what":"Workflows","title":"Files Supported","text":"wgs_alignment_qc wts_alignment_qc wts_tumor_only wgs_tumor_normal-germ wgs_tumor_normal-som umccrise oncoanalyser_wgs oncoanalyser_wts oncoanalyser_wgts sash","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"flames","dir":"Articles","previous_headings":"","what":"Flames","title":"Flames","text":"Flames dracarys user stories. D’oh.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"cttso-summary","dir":"Articles","previous_headings":"Flames","what":"ctTSO Summary","title":"Flames","text":"Slack link","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"ffpe-vs--fresh-frozen","dir":"Articles","previous_headings":"Flames","what":"FFPE vs. Fresh Frozen","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"coverage-depth-exploration","dir":"Articles","previous_headings":"Flames","what":"Coverage depth exploration","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"sv-runtime","dir":"Articles","previous_headings":"Flames","what":"SV runtime","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"msi-and-tmb","dir":"Articles","previous_headings":"Flames","what":"MSI and TMB","title":"Flames","text":"Slack link.","code":""},{"path":"https://umccr.github.io/dracarys/articles/flames.html","id":"germline-duplication-rate","dir":"Articles","previous_headings":"Flames","what":"Germline duplication rate","title":"Flames","text":"Slack link1. Slack link2.","code":""},{"path":"https://umccr.github.io/dracarys/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Peter Diakumis. Author, maintainer. Victor San Kho Lin. Author, contributor.","code":""},{"path":"https://umccr.github.io/dracarys/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Diakumis P, Lin V (2024). dracarys: Post-processing DRAGEN workflows. R package version 0.15.0, https://umccr.github.io/dracarys/, https://github.com/umccr/dracarys.","code":"@Manual{,   title = {dracarys: Post-processing DRAGEN workflows},   author = {Peter Diakumis and Victor San Kho Lin},   year = {2024},   note = {R package version 0.15.0, https://umccr.github.io/dracarys/},   url = {https://github.com/umccr/dracarys}, }"},{"path":"https://umccr.github.io/dracarys/index.html","id":"fire-dracarys---umccr-workflow-tidying","dir":"","previous_headings":"","what":"Post-processing DRAGEN workflows","title":"Post-processing DRAGEN workflows","text":"Docs: https://umccr.github.io/dracarys/","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"trophy-aim","dir":"","previous_headings":"","what":"🏆 Aim","title":"Post-processing DRAGEN workflows","text":"Given ICA GDS, AWS S3 local directory results UMCCR workflow, {dracarys} grab files interest transform ‘tidier’ structures output TSV/Parquet/RDS format downstream ingestion database/data lake. See supported workflows, running examples, CLI options sections .","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"pizza-installation","dir":"","previous_headings":"","what":"🍕 Installation","title":"Post-processing DRAGEN workflows","text":"Linux & MacOS (non-M1) MacOS M1","code":"remotes::install_github(\"umccr/dracarys@vX.X.X\") # for vX.X.X Release/Tag mamba create \\   -n dracarys_env \\   -c umccr -c bioconda -c conda-forge \\   r-dracarys==X.X.X  conda activate dracarys_env CONDA_SUBDIR=osx-64 \\   mamba create \\   -n dracarys_env \\   -c umccr -c bioconda -c conda-forge \\   r-dracarys==X.X.X  conda activate dracarys_env docker pull --platform linux/amd64 ghcr.io/umccr/dracarys:X.X.X"},{"path":"https://umccr.github.io/dracarys/index.html","id":"sparkles-supported-workflows","dir":"","previous_headings":"","what":"✨ Supported Workflows","title":"Post-processing DRAGEN workflows","text":"{dracarys} supports outputs following UMCCR workflows: See output files workflows supported Supported Files.","code":""},{"path":"https://umccr.github.io/dracarys/index.html","id":"cyclone-cli","dir":"","previous_headings":"","what":"🌀 CLI","title":"Post-processing DRAGEN workflows","text":"dracarys.R command line interface available convenience. ’re using conda package, dracarys.R command already available inside activated conda environment. ’re using conda package, need export dracarys/inst/cli/ directory PATH order use dracarys.R.","code":"dracarys_cli=$(Rscript -e 'x = system.file(\"cli\", package = \"dracarys\"); cat(x, \"\\n\")' | xargs) export PATH=\"${dracarys_cli}:${PATH}\" dracarys.R --version dracarys.R 0.14.0  #-----------------------------------# dracarys.R --help usage: dracarys.R [-h] [-v] {tidy} ...  🐉 DRAGEN Output Post-Processing 🔥  positional arguments:   {tidy}         sub-command help     tidy         Tidy UMCCR Workflow Outputs  options:   -h, --help     show this help message and exit   -v, --version  show program's version number and exit  #-----------------------------------# #------- Tidy ----------------------# dracarys.R tidy --help usage: dracarys.R tidy [-h] -i IN_DIR -o OUT_DIR -p PREFIX [-t TOKEN]                        [-l LOCAL_DIR] [-f FORMAT] [-n] [-q]  options:   -h, --help            show this help message and exit   -i IN_DIR, --in_dir IN_DIR                         ⛄️ Directory with untidy UMCCR workflow results. Can                         be GDS, S3 or local.   -o OUT_DIR, --out_dir OUT_DIR                         🔥 Directory to output tidy results.   -p PREFIX, --prefix PREFIX                         🎻 Prefix string used for all results.   -t TOKEN, --token TOKEN                         🙈 ICA access token. Default: ICA_ACCESS_TOKEN env var.   -l LOCAL_DIR, --local_dir LOCAL_DIR                         📥 If input is a GDS/S3 directory, download the                         recognisable files to this directory. Default:                         '<out_dir>/dracarys_<gds|s3>_sync'.   -f FORMAT, --format FORMAT                         🎨 Format of output. Default: tsv.   -n, --dryrun          🐫 Dry run - just show files to be tidied.   -q, --quiet           😴 Shush all the logs."},{"path":"https://umccr.github.io/dracarys/index.html","id":"taxi-running","dir":"","previous_headings":"","what":"🚕 Running","title":"Post-processing DRAGEN workflows","text":"{dracarys} takes input (--in_dir) directory results one UMCCR workflows. recursively scan directory supported files, download local directory (--gds_local_dir), parse, transform write tidied versions specified output directory (--out_dir). prefix (--prefix) prepended tidied files. output file format (--format) can tsv, parquet, . get just list supported files within specified input directory, use -n (--dryrun) option. within activated conda environment shell dracarys.R CLI available:","code":"# help(umccr_tidy) in_dir <- \"gds://path/to/subjectX_multiqc_data/\" out_dir <- tempdir() prefix <- \"subjectX\" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix) dracarys.R tidy \\       -i gds://path/to/subjectX_multiqc_data/ \\       -o local_output_dir \\       -p subjectX_prefix docker container run \\   -v $(PWD):/mount1 \\   --platform=linux/amd64 \\   --env \"ICA_ACCESS_TOKEN\" \\   --rm -it \\   ghcr.io/umccr/dracarys:X.X.X \\     dracarys.R tidy \\       -i gds://path/to/subjectX_multiqc_data/ \\       -o /mount1/output_dir \\       -p subjectX_prefix"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Contains methods reading displaying contents bcftools_stats.txt file (QUAL section) output running bcftools stats.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"dracarys::File -> BcftoolsStatsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"BcftoolsStatsFile$read() BcftoolsStatsFile$write() BcftoolsStatsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Reads QUAL section bcftools_stats.txt file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"Writes tidy version bcftools_stats.txt (QUAL section) file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"BcftoolsStatsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BcftoolsStatsFile R6 Class — BcftoolsStatsFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/bcftools_stats.txt\" d <- BcftoolsStatsFile$new(x) d_parsed <- d$read() d$write(d_parsed, out_dir = tempdir(), prefix = \"sample123\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":null,"dir":"Reference","previous_headings":"","what":"BclconvertReports R6 Class — BclconvertReports","title":"BclconvertReports R6 Class — BclconvertReports","text":"Reads writes tidy versions files within Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"BclconvertReports R6 Class — BclconvertReports","text":"path Path Reports directory. contents Tibble file path, basename, size.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"BclconvertReports R6 Class — BclconvertReports","text":"BclconvertReports$new() BclconvertReports$print() BclconvertReports$read() BclconvertReports$write() BclconvertReports$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Create new BclconvertReports object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$new(path = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"path Path Reports directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Print details BclconvertReports directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Reads contents Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$read()"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"BclconvertReports R6 Class — BclconvertReports","text":"list tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"BclconvertReports R6 Class — BclconvertReports","text":"Writes tidied contents Reports directory output BCLConvert.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"BclconvertReports R6 Class — BclconvertReports","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"BclconvertReports$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"BclconvertReports R6 Class — BclconvertReports","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/BclconvertReports.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"BclconvertReports R6 Class — BclconvertReports","text":"","code":"if (FALSE) { # \\dontrun{ b <- BclconvertReports$new(here::here(\"nogit/bcl_convert/WGS_TsqNano/Reports\")) b$path b$contents d <- b$read() b$write(d, out_dir = tempdir(), prefix = \"sampleA\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"FastqcMetrics R6 Class — FastqcMetricsFile","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Contains methods reading displaying contents fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File -> FastqcMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"FastqcMetricsFile$read() FastqcMetricsFile$write() FastqcMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Reads fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"tibble. TODO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Writes tidy version fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"FastqcMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.fastqc_metrics.csv.gz\", package = \"dracarys\") fq <- FastqcMetricsFile$new(x) d <- fq$read() fq$write(d, out_dir = tempdir(), prefix = \"seqc_fq\", out_format = \"tsv\") # fq$plot(d)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":null,"dir":"Reference","previous_headings":"","what":"File R6 Class — File","title":"File R6 Class — File","text":"File base R6 class representing TSV/CSV/JSON output UMCCR workflow. File path, basename, type, can presigned URL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"File R6 Class — File","text":"path Name full path file. is_url file presigned URL?","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"File R6 Class — File","text":"File$new() File$bname() File$type() File$print() File$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"File R6 Class — File","text":"Create new File object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$new(path = NULL, is_url = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"path Name full path file. is_url file presigned URL?","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-bname-","dir":"Reference","previous_headings":"","what":"Method bname()","title":"File R6 Class — File","text":"Basename file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$bname()"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"File R6 Class — File","text":"Basename file character vector.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-type-","dir":"Reference","previous_headings":"","what":"Method type()","title":"File R6 Class — File","text":"Get type file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$type()"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"File R6 Class — File","text":"String describing specific type dracarys file (NA dracarys-recognised file).","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"File R6 Class — File","text":"Print details File.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"File R6 Class — File","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"File R6 Class — File","text":"","code":"File$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"File R6 Class — File","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/File.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"File R6 Class — File","text":"","code":"F1 <- File$new(readr::readr_example(\"mtcars.csv\")) (bname_f1 <- F1$bname()) #> [1] \"mtcars.csv\" (F2 <- File$new(\"https://stratus-gds-aps2/foo/bar/baz.csv?bla\")) #> #--- File ---# #> Path: https://stratus-gds-aps2/foo/bar/baz.csv?bla  #> Basename: baz.csv  #> Type: NA  #> isURL: TRUE"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Contains methods reading plotting contents fragment_length_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"dracarys::File -> FragmentLengthHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"FragmentLengthHistFile$read() FragmentLengthHistFile$write() FragmentLengthHistFile$plot() FragmentLengthHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Reads fragment_length_hist.csv file, contains fragment length distribution sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"tibble following columns: sample: name sample fragmentLength: estimated fragment length count: number reads estimated fragment length","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Writes tidy version fragment_length_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"Plots fragment length distributions given fragment_length_hist.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$plot(d, min_count = 10)"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"d Parsed object self$read(). min_count Minimum read count plotted (Default: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"ggplot2 plot containing fragment lengths X axis read counts Y axis sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"FragmentLengthHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FragmentLengthHistFile R6 Class — FragmentLengthHistFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.fragment_length_hist.csv.gz\", package = \"dracarys\") fl <- FragmentLengthHistFile$new(x) d <- fl$read() # or read(fl) fl$plot(d) # or plot(fl)  fl$write(d |> dplyr::filter(count > 10), out_dir = tempdir(), prefix = \"seqc_fl\")"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"MappingMetricsFile R6 Class — MappingMetricsFile","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Contains methods reading displaying contents mapping_metrics.csv file output DRAGEN. file contains mapping aligning metrics, like metrics computed Samtools Flagstat command. metrics available aggregate level (input data), per read group level. NOTE: keeping read group level metrics (.e. removing aggregate data). Unless explicitly stated, metrics units reads (.e., terms pairs alignments).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"dracarys::File -> MappingMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"MappingMetricsFile$read() MappingMetricsFile$write() MappingMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Reads mapping_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"tibble one row X metrics per read group.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"Writes tidy version mapping_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"MappingMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MappingMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MappingMetricsFile R6 Class — MappingMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.mapping_metrics.csv.gz\", package = \"dracarys\") mm <- MappingMetricsFile$new(x) d <- mm$read() # or read(mm) mm$write(d, out_dir = tempdir(), prefix = \"seqc_mm\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiqcFile R6 Class — MultiqcFile","title":"MultiqcFile R6 Class — MultiqcFile","text":"Contains methods reading displaying contents multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"MultiqcFile R6 Class — MultiqcFile","text":"dracarys::File -> MultiqcFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"MultiqcFile R6 Class — MultiqcFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"MultiqcFile R6 Class — MultiqcFile","text":"MultiqcFile$read() MultiqcFile$write() MultiqcFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"MultiqcFile R6 Class — MultiqcFile","text":"Reads multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$read(plot = FALSE, plot_names = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"plot Return tibble data plots (def: FALSE). plot_names Names plots parse. Use \"everything\" wantz plotz.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"MultiqcFile R6 Class — MultiqcFile","text":"tidy tibble. label:","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"MultiqcFile R6 Class — MultiqcFile","text":"Writes tidy version multiqc_data.json file output MultiQC.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', ''). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"MultiqcFile R6 Class — MultiqcFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"MultiqcFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiqcFile R6 Class — MultiqcFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/MultiqcFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MultiqcFile R6 Class — MultiqcFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/multiqc_data.json\" mqc <- MultiqcFile$new(x) mqc_parsed <- mqc$read() # or read(mqc) mqc$write(mqc_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") mqc_plots_parsed <- mqc$read(plot = TRUE, plot_names = \"everything\") mqc$write(mqc_plots_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"rds\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PcgrJson R6 Class — PcgrJsonFile","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Contains methods reading displaying contents pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PcgrJson R6 Class — PcgrJsonFile","text":"dracarys::File -> PcgrJsonFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PcgrJson R6 Class — PcgrJsonFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PcgrJson R6 Class — PcgrJsonFile","text":"PcgrJsonFile$read() PcgrJsonFile$write() PcgrJsonFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Reads pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PcgrJson R6 Class — PcgrJsonFile","text":"List tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"Writes tidy version pcgr.json.gz file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrJson R6 Class — PcgrJsonFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', '').","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PcgrJson R6 Class — PcgrJsonFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"PcgrJsonFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrJson R6 Class — PcgrJsonFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrJsonFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PcgrJson R6 Class — PcgrJsonFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/pcgr.json.gz\" d <- PcgrJsonFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"both\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PcgrTiersFile R6 Class — PcgrTiersFile","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Contains methods reading displaying contents pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"dracarys::File -> PcgrTiersFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"PcgrTiersFile$read() PcgrTiersFile$write() PcgrTiersFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Reads pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"List tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"Writes tidy version pcgr.snvs_indels.tiers.tsv file output PCGR.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', '').","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"PcgrTiersFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PcgrTiersFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PcgrTiersFile R6 Class — PcgrTiersFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/pcgr.snvs_indels.tiers.tsv\" d <- PcgrTiersFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"both\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Contains methods reading contents ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"dracarys::File -> PloidyEstimationMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"PloidyEstimationMetricsFile$read() PloidyEstimationMetricsFile$write() PloidyEstimationMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Reads ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"Writes tidy version ploidy_estimation_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"PloidyEstimationMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PloidyEstimationMetricsFile R6 Class — PloidyEstimationMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.ploidy_estimation_metrics.csv.gz\", package = \"dracarys\") pem <- PloidyEstimationMetricsFile$new(x) d <- pem$read() # or read(pem) pem$write(d, out_dir = tempdir(), prefix = \"seqc_ploidy\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":null,"dir":"Reference","previous_headings":"","what":"ReplayFile R6 Class — ReplayFile","title":"ReplayFile R6 Class — ReplayFile","text":"Contains methods reading contents replay.json file output DRAGEN, contains DRAGEN command line, parameters version specific run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"ReplayFile R6 Class — ReplayFile","text":"dracarys::File -> ReplayFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"ReplayFile R6 Class — ReplayFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"ReplayFile R6 Class — ReplayFile","text":"ReplayFile$read() ReplayFile$write() ReplayFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"ReplayFile R6 Class — ReplayFile","text":"Reads replay.json file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"ReplayFile R6 Class — ReplayFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"ReplayFile R6 Class — ReplayFile","text":"Writes tidy version replay.json file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ReplayFile R6 Class — ReplayFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"ReplayFile R6 Class — ReplayFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"ReplayFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"ReplayFile R6 Class — ReplayFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ReplayFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ReplayFile R6 Class — ReplayFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II-replay.json.gz\", package = \"dracarys\") r <- ReplayFile$new(x) d <- r$read() # or read(r) r$write(d, out_dir = tempdir(), prefix = \"seqc_replay\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"SvMetricsFile R6 Class — SvMetricsFile","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Contains methods reading displaying contents sv_metrics.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"dracarys::File -> SvMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"SvMetricsFile$read() SvMetricsFile$write() SvMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Reads sv_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"Writes tidy version sv_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"SvMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/SvMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"SvMetricsFile R6 Class — SvMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.sv_metrics.csv.gz\", package = \"dracarys\") sv <- SvMetricsFile$new(x) d <- sv$read() sv$write(d, out_dir = tempdir(), prefix = \"seqc_sv\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TimeMetricsFile R6 Class — TimeMetricsFile","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Contains methods reading contents time_metrics.csv file output DRAGEN, contains breakdown run duration DRAGEN process.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"dracarys::File -> TimeMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"TimeMetricsFile$read() TimeMetricsFile$write() TimeMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Reads time_metrics.csv file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"Writes tidy version time_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"TimeMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TimeMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TimeMetricsFile R6 Class — TimeMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.time_metrics.csv.gz\", package = \"dracarys\") tm <- TimeMetricsFile$new(x) d <- tm$read() # or read(tm) tm$write(d, out_dir = tempdir(), prefix = \"seqc_time\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Contains methods reading displaying contents trimmer_metrics.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"dracarys::File -> TrimmerMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"TrimmerMetricsFile$read() TrimmerMetricsFile$write() TrimmerMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Reads trimmer_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"Writes tidy version trimmer_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"TrimmerMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TrimmerMetricsFile R6 Class — TrimmerMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.trimmer_metrics.csv.gz\", package = \"dracarys\") tm <- TrimmerMetricsFile$new(x) d <- tm$read() tm$write(d, out_dir = tempdir(), prefix = \"seqc_tm\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Contains methods reading displaying contents AlignCollapseFusionCaller_metrics.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"dracarys::File -> TsoAlignCollapseFusionCallerMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"TsoAlignCollapseFusionCallerMetricsFile$read() TsoAlignCollapseFusionCallerMetricsFile$write() TsoAlignCollapseFusionCallerMetricsFile$plot() TsoAlignCollapseFusionCallerMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Reads AlignCollapseFusionCaller_metrics.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"tibble following columns: section: name original JSON element name: name metric value: value metric percent: percentage","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Writes tidy version AlignCollapseFusionCaller_metrics.json.gz file output TSO. Histo majority UmiStatistics section, write separately. Histo num supporting fragments: Num families 0/1/2/3... raw reads. Histo unique UMIs per fragment pos: Num pos 0/1/2/3... UMI seqs.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s) (one 'tsv' (def.), 'parquet', ''). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"Generates UmiStatistics Histogram plots AlignCollapseFusionCaller_metrics.json.gz file output TSO. Histo majority UmiStatistics section, deal separately. Histo num supporting fragments: Num families 0/1/2/3... raw reads. Histo unique UMIs per fragment pos: Num pos 0/1/2/3... UMI seqs.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$plot(d, max_num = 15)"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"d Parsed object self$read(). max_num Maximum number display plots.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"histogram plot objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"TsoAlignCollapseFusionCallerMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoAlignCollapseFusionCallerMetricsFile R6 Class — TsoAlignCollapseFusionCallerMetricsFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz\",   package = \"dracarys\" ) m <- TsoAlignCollapseFusionCallerMetricsFile$new(x) d_parsed <- m$read() # or read(m) m$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = c(\"tsv\", \"rds\"))"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Contains methods reading displaying contents CombinedVariantOutput.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"dracarys::File -> TsoCombinedVariantOutputFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"TsoCombinedVariantOutputFile$read() TsoCombinedVariantOutputFile$write() TsoCombinedVariantOutputFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Reads CombinedVariantOutput.tsv file output TSO extracts Small Variants section (due inconsistencies sections).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"Writes tidy version CombinedVariantOutput.tsv (Small Variants) file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"TsoCombinedVariantOutputFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoCombinedVariantOutputFile R6 Class — TsoCombinedVariantOutputFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/CombinedVariantOutput.tsv\" d <- TsoCombinedVariantOutputFile$new(x) d$read() } # }"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Contains methods reading displaying contents CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"dracarys::File -> TsoCopyNumberVariantsVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"TsoCopyNumberVariantsVcfFile$read() TsoCopyNumberVariantsVcfFile$write() TsoCopyNumberVariantsVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Reads CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"Writes tidy version CopyNumberVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"TsoCopyNumberVariantsVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoCopyNumberVariantsVcfFile R6 Class — TsoCopyNumberVariantsVcfFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- normalizePath(\"CopyNumberVariants.vcf.gz\") d <- TsoCopyNumberVariantsVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") d$write(d_parsed, prefix = \"FOO\", out_format = \"delta\", drid = \"wfr.123\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Contains methods reading displaying contents fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"dracarys::File -> TsoFragmentLengthHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"TsoFragmentLengthHistFile$read() TsoFragmentLengthHistFile$write() TsoFragmentLengthHistFile$plot() TsoFragmentLengthHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Reads fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"tibble following columns: FragmentLength Count","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Writes tidy version fragment_length_hist.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"Plots fragment length distributions given fragment_length_hist.json.gz file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$plot(d, min_count = 10)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"d Parsed object self$read(). min_count Minimum read count plotted (def: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"ggplot2 plot containing fragment lengths X axis read counts Y axis sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"TsoFragmentLengthHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoFragmentLengthHistFile R6 Class — TsoFragmentLengthHistFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.fragment_length_hist.json.gz\", package = \"dracarys\") fl <- TsoFragmentLengthHistFile$new(x) d_parsed <- fl$read() # or read(fl) fl$plot(d_parsed, 5)  fl$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Contains methods reading displaying contents Fusions.csv file output TSO. Returns tibble columns (based input file header metadata): Sample: input sample ID. Name: Fusion name reported manta. Chr1/Chr2: chromosome 1st/2nd breakend. Pos1/Pos2: position 1st/2nd breakend. Direction: direction breakends joined together. Alt_Depth: number read-pairs supporting fusion call. BP1_Depth/BP2_Depth: Number read-pairs aligned 1st/2nd breakend. Total_Depth: Max number read-pairs aligned fusion breakend. VAF: Variant allele frequency. Gene1/Gene2: Genes overlap 1st/2nd breakend. Contig: fusion contig. Filter: Indicates whether fusion passed fusion filters. Is_Cosmic_GenePair: Indicates whether gene pair reported Cosmic(True/False).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"dracarys::File -> TsoFusionsCsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"TsoFusionsCsvFile$read() TsoFusionsCsvFile$write() TsoFusionsCsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Reads Fusions.csv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"tibble several columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"Writes tidy version Fusions.csv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"TsoFusionsCsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoFusionsCsvFile R6 Class — TsoFusionsCsvFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_Fusions.csv\", package = \"dracarys\") fus <- TsoFusionsCsvFile$new(x) d_parsed <- fus$read() # or read(fus) fus$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Contains methods reading displaying contents MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"dracarys::File -> TsoMergedSmallVariantsGenomeVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"TsoMergedSmallVariantsGenomeVcfFile$read() TsoMergedSmallVariantsGenomeVcfFile$write() TsoMergedSmallVariantsGenomeVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Reads MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"Writes tidy version MergedSmallVariants.genome.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"TsoMergedSmallVariantsGenomeVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMergedSmallVariantsGenomeVcfFile R6 Class — TsoMergedSmallVariantsGenomeVcfFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"MergedSmallVariants.genome.vcf.gz\" d <- TsoMergedSmallVariantsGenomeVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Contains methods reading displaying contents MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"dracarys::File -> TsoMergedSmallVariantsVcfFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"TsoMergedSmallVariantsVcfFile$read() TsoMergedSmallVariantsVcfFile$write() TsoMergedSmallVariantsVcfFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Reads MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$read(only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"only_pass include PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"Writes tidy version MergedSmallVariants.vcf.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"TsoMergedSmallVariantsVcfFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMergedSmallVariantsVcfFile R6 Class — TsoMergedSmallVariantsVcfFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"MergedSmallVariants.vcf.gz\" d <- TsoMergedSmallVariantsVcfFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") d$write(d_parsed, prefix = \"FOO\", out_format = \"delta\", drid = \"wfr.123\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoMsiFile R6 Class — TsoMsiFile","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Contains methods reading displaying contents msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"dracarys::File -> TsoMsiFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"TsoMsiFile$read() TsoMsiFile$write() TsoMsiFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Reads msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"tibble following columns: label:","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"Writes tidy version msi.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"TsoMsiFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoMsiFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoMsiFile R6 Class — TsoMsiFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.msi.json.gz\", package = \"dracarys\") msi <- TsoMsiFile$new(x) d_parsed <- msi$read() # or read(msi) msi$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Contains methods reading displaying contents SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"dracarys::File -> TsoSampleAnalysisResultsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"TsoSampleAnalysisResultsFile$read() TsoSampleAnalysisResultsFile$write() TsoSampleAnalysisResultsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Reads SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"list tibbles","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"Writes tidy version SampleAnalysisResults.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"TsoSampleAnalysisResultsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoSampleAnalysisResultsFile R6 Class — TsoSampleAnalysisResultsFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_SampleAnalysisResults.json.gz\", package = \"dracarys\") res <- TsoSampleAnalysisResultsFile$new(x) d_parsed <- res$read() # or read(res) res$write(d_parsed, tempfile(), \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Contains methods reading displaying contents TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"dracarys::File -> TsoTargetRegionCoverageFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"TsoTargetRegionCoverageFile$read() TsoTargetRegionCoverageFile$write() TsoTargetRegionCoverageFile$plot() TsoTargetRegionCoverageFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Reads TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"tibble following columns: ConsensusReadDepth BasePair Percentage","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Writes tidy version TargetRegionCoverage.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"Plots TargetRegionCoverage.json.gz file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$plot(d, min_pct = 2)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"d Parsed object self$read(). min_pct Minimum percentage plotted (def: 2).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"ggplot2 plot containing read depth X axis percentage covered Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"TsoTargetRegionCoverageFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTargetRegionCoverageFile R6 Class — TsoTargetRegionCoverageFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.TargetRegionCoverage.json.gz\", package = \"dracarys\") trc <- TsoTargetRegionCoverageFile$new(x) d_parsed <- trc$read() # or read(trc) trc$plot(d_parsed, 0) # or plot(trc, d_parsed, 90)  trc$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTmbFile R6 Class — TsoTmbFile","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Contains methods reading displaying contents tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"dracarys::File -> TsoTmbFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"TsoTmbFile$read() TsoTmbFile$write() TsoTmbFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Reads tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"tibble following columns: TmbPerMb AdjustedTmbPerMb NonsynonymousTmbPerMb AdjustedNonsynonymousTmbPerMb SomaticCodingVariantsCount NonsynonymousSomaticCodingVariantsCount TotalRegionSizeMb CodingRegionSizeMb","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"Writes tidy version tmb.json.gz file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"TsoTmbFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTmbFile R6 Class — TsoTmbFile","text":"","code":"x <- system.file(\"extdata/tso/sample705.tmb.json.gz\", package = \"dracarys\") tmb <- TsoTmbFile$new(x) d_parsed <- tmb$read() # or read(tmb) tmb$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Contains methods reading displaying contents TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"dracarys::File -> TsoTmbTraceTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"TsoTmbTraceTsvFile$read() TsoTmbTraceTsvFile$write() TsoTmbTraceTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Reads TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"tibble variants.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"Writes tidy version TMB_Trace.tsv file output TSO.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"TsoTmbTraceTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"TsoTmbTraceTsvFile R6 Class — TsoTmbTraceTsvFile","text":"","code":"x <- system.file(\"extdata/tso/sample705_TMB_Trace.tsv\", package = \"dracarys\") d <- TsoTmbTraceTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmChordTsvFile R6 Class — UmChordTsvFile","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Contains methods reading displaying contents chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"dracarys::File -> UmChordTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"UmChordTsvFile$read() UmChordTsvFile$write() UmChordTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Reads chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"Writes tidy version chord.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"UmChordTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmChordTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmChordTsvFile R6 Class — UmChordTsvFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/chord.tsv.gz\" d <- UmChordTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Contains methods reading displaying contents hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"dracarys::File -> UmHrdetectTsvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"UmHrdetectTsvFile$read() UmHrdetectTsvFile$write() UmHrdetectTsvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Reads hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"Writes tidy version hrdetect.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$write(d, out_dir, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"UmHrdetectTsvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmHrdetectTsvFile R6 Class — UmHrdetectTsvFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/hrdetect.tsv.gz\" d <- UmHrdetectTsvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmQcSumFile R6 Class — UmQcSumFile","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Contains methods reading displaying contents qc_summary.tsv.gz file QC summary metrics output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"dracarys::File -> UmQcSumFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"UmQcSumFile$read() UmQcSumFile$write() UmQcSumFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Reads qc_summary.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"Writes tidy version qc_summary.tsv.gz QC summary file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$write(d, out_dir, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"UmQcSumFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmQcSumFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmQcSumFile R6 Class — UmQcSumFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/snv_2015.tsv.gz\" d <- UmQcSumFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":null,"dir":"Reference","previous_headings":"","what":"UmSigsSnvFile R6 Class — UmSigsSnvFile","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Contains methods reading displaying contents snv_20XX.tsv.gz file SNV signatures output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"dracarys::File -> UmSigsSnvFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"UmSigsSnvFile$read() UmSigsSnvFile$write() UmSigsSnvFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Reads snv.tsv.gz file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"Writes tidy version snv_20XX.tsv.gz signature file output umccrise.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$write(d, out_dir, prefix, out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"UmSigsSnvFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UmSigsSnvFile R6 Class — UmSigsSnvFile","text":"","code":"if (FALSE) { # \\dontrun{ x <- \"/path/to/snv_2015.tsv.gz\" d <- UmSigsSnvFile$new(x) d_parsed <- d$read() # or read(d) d$write(d_parsed, out_dir = tempdir(), prefix = \"sample705\", out_format = \"tsv\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"VCMetricsFile R6 Class — VCMetricsFile","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Contains methods reading displaying contents vc_metrics.csv file output DRAGEN, contains variant calling metrics.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"dracarys::File -> VCMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"VCMetricsFile$read() VCMetricsFile$write() VCMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Reads vc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"Writes tidy version vc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"VCMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/VCMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"VCMetricsFile R6 Class — VCMetricsFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.vc_metrics.csv.gz\", package = \"dracarys\") vm <- VCMetricsFile$new(x) d <- vm$read() # or read(vm) vm$write(d, out_dir = tempdir(), prefix = \"seqc_vc\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":null,"dir":"Reference","previous_headings":"","what":"Workflow R6 Class — Wf","title":"Workflow R6 Class — Wf","text":"Workflow base R6 class representing bioinformatic workflow run UMCCR workflow manager.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Workflow R6 Class — Wf","text":"prid Portal run ID. type Workflow type. start Workflow start datetime. end Workflow end datetime. status Workflow end status. input Workflow input JSON string. output Workflow output JSON string.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Workflow R6 Class — Wf","text":"Wf$new() Wf$print() Wf$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Workflow R6 Class — Wf","text":"Create new Workflow object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Workflow R6 Class — Wf","text":"","code":"Wf$new(   prid = NULL,   type = NULL,   start = NULL,   end = NULL,   status = NULL,   input = NULL,   output = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Workflow R6 Class — Wf","text":"prid Portal run ID. type Workflow type. start Workflow start datetime. end Workflow end datetime. status Workflow end status. input Workflow input JSON string. output Workflow output JSON string.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"Workflow R6 Class — Wf","text":"Print details Workflow.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Workflow R6 Class — Wf","text":"","code":"Wf$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Workflow R6 Class — Wf","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Workflow R6 Class — Wf","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Workflow R6 Class — Wf","text":"","code":"Wf$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Workflow R6 Class — Wf","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Workflow R6 Class — Wf","text":"","code":"p1 <- system.file(\"extdata/portaldb_workflow_top4.rds\", package = \"rportal\") |>   readRDS() |>   dplyr::filter(type_name == \"umccrise\") |>   dplyr::slice(1) #> Warning: cannot open compressed file '', probable reason 'No such file or directory' #> Error in gzfile(file, \"rb\"): cannot open the connection w <- Wf$new(   prid = p1$portal_run_id, type = p1$type_name, start = p1$start, end = p1$end,   status = p1$end_status, input = p1$input, output = p1$output ) #> Error in eval(expr, envir, enclos): object 'p1' not found w #> Error in eval(expr, envir, enclos): object 'w' not found"},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":null,"dir":"Reference","previous_headings":"","what":"bcl_convert Wf R6 Class — Wf_bcl_convert","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"Contains methods reading processing files output UMCCR bcl_convert workflow.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"indir Input directory containing Reports per assay type (e.g. /primary_data/240607_A01052_0209_BHLHFTDSXC/2024061140802544/).","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"Wf_bcl_convert$new() Wf_bcl_convert$print() Wf_bcl_convert$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"Create new Wf_bcl_convert object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"","code":"Wf_bcl_convert$new(indir)"},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"indir Input directory containing Reports per assay type.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"Print details Workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"","code":"Wf_bcl_convert$print(...)"},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"... (ignored).","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"","code":"Wf_bcl_convert$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_bcl_convert.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"bcl_convert Wf R6 Class — Wf_bcl_convert","text":"","code":"if (FALSE) { # \\dontrun{ indir <- file.path() sample_id <- \"PTC_ctTSO240429\" library_id <- \"L2400482\" d <- TsoCombinedVariantOutputFile$new(x) d$read() } # }"},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":null,"dir":"Reference","previous_headings":"","what":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"Contains methods reading processing files output UMCCR tso_ctdna_tumor_only workflow.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"sid SampleID. lid LibraryID.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"Wf_tso_ctdna_tumor_only$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"","code":"Wf_tso_ctdna_tumor_only$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/Wf_tso_ctdna_tumor_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"tso_ctdna_tumor_only Wf R6 Class — Wf_tso_ctdna_tumor_only","text":"","code":"if (FALSE) { # \\dontrun{ x <- file.path(   \"~/icav1/g/production/analysis_data/SBJ00596/tso_ctdna_tumor_only\",   \"2024050555972acf/L2400482/Results/PTC_ctTSO240429_L2400482/dracarys_gds_sync\"   ) sample_id <- \"PTC_ctTSO240429\" library_id <- \"L2400482\" d <- TsoCombinedVariantOutputFile$new(x) d$read() } # }"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Contains methods reading displaying contents wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN. file contains estimated coverage contigs, autosomal estimated coverage.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"dracarys::File -> WgsContigMeanCovFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"WgsContigMeanCovFile$read() WgsContigMeanCovFile$write() WgsContigMeanCovFile$plot() WgsContigMeanCovFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Reads wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$read(keep_alt = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"keep_alt Keep ALT + Mito chromosomes?","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"tibble following columns: label: file label. chrom: contig name. n_bases: number bases aligned contig (excludes bases duplicate marked reads, reads MAPQ=0, clipped bases). coverage: col2 / contig length","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Writes tidy version wgs_contig_mean_cov_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"Plots wgs_contig_mean_cov_<phenotype>.csv files.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$plot(d, top_alt_n = 15)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"d Parsed object self$read(). top_alt_n Number top covered alt contigs plot per phenotype.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"ggplot2 object chromosomes X axis, coverage Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"WgsContigMeanCovFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsContigMeanCovFile R6 Class — WgsContigMeanCovFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_contig_mean_cov_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_contig_mean_cov_tumor.csv.gz\", package = \"dracarys\") cc1 <- WgsContigMeanCovFile$new(x1) cc2 <- WgsContigMeanCovFile$new(x2) d1 <- cc1$read() d2 <- cc2$read() cc1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") cc2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")  cc1$plot(d1)  cc2$plot(d2)"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Contains methods reading displaying contents wgs_coverage_metrics_<phenotype>.csv file output DRAGEN. file contains read depth coverage metrics.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"dracarys::File -> WgsCoverageMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"WgsCoverageMetricsFile$read() WgsCoverageMetricsFile$write() WgsCoverageMetricsFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Reads wgs_coverage_metrics_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"Writes tidy version wgs_coverage_metrics_<phenotype>.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"WgsCoverageMetricsFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsCoverageMetricsFile R6 Class — WgsCoverageMetricsFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_coverage_metrics_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_coverage_metrics_tumor.csv.gz\", package = \"dracarys\") cm1 <- WgsCoverageMetricsFile$new(x1) cm2 <- WgsCoverageMetricsFile$new(x2) d1 <- read(cm1) d2 <- read(cm2) cm1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") cm2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsFineHistFile R6 Class — WgsFineHistFile","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Contains methods reading displaying contents wgs_fine_hist_<phenotype>.csv file output DRAGEN. file contains two columns: Depth Overall. value Depth column ranges 0 1000+ Overall column indicates number loci covered corresponding depth.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"dracarys::File -> WgsFineHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"WgsFineHistFile$read() WgsFineHistFile$write() WgsFineHistFile$plot() WgsFineHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Reads wgs_fine_hist_<phenotype>.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"tibble following columns: depth number loci given depth","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Writes tidy version wgs_fine_hist_<phenotype>.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$write(   d,   out_dir = NULL,   prefix,   out_format = \"tsv\",   drid = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-plot-","dir":"Reference","previous_headings":"","what":"Method plot()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"Plots wgs_fine_hist_<phenotype>.csv files.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$plot(d, x_lim = c(0, 300))"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"d Parsed object self$read(). x_lim X axis range plot.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"ggplot2 object depth coverage X axis, number loci depth Y axis.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"WgsFineHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsFineHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsFineHistFile R6 Class — WgsFineHistFile","text":"","code":"x1 <- system.file(\"extdata/wgs/SEQC-II.wgs_fine_hist_normal.csv.gz\", package = \"dracarys\") x2 <- system.file(\"extdata/wgs/SEQC-II.wgs_fine_hist_tumor.csv.gz\", package = \"dracarys\") ch1 <- WgsFineHistFile$new(x1) ch2 <- WgsFineHistFile$new(x2) d1 <- read(ch1) d2 <- read(ch2) ch1$plot(d1)  ch2$plot(d2)  ch1$write(d1, out_dir = tempdir(), prefix = \"seqc_n\", out_format = \"tsv\") ch2$write(d2, out_dir = tempdir(), prefix = \"seqc_t\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":null,"dir":"Reference","previous_headings":"","what":"WgsHistFile R6 Class — WgsHistFile","title":"WgsHistFile R6 Class — WgsHistFile","text":"Contains methods reading displaying contents wgs_hist.csv file output DRAGEN","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"WgsHistFile R6 Class — WgsHistFile","text":"dracarys::File -> WgsHistFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"WgsHistFile R6 Class — WgsHistFile","text":"dracarys::File$bname() dracarys::File$initialize() dracarys::File$print() dracarys::File$type()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"WgsHistFile R6 Class — WgsHistFile","text":"WgsHistFile$read() WgsHistFile$write() WgsHistFile$clone()","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-read-","dir":"Reference","previous_headings":"","what":"Method read()","title":"WgsHistFile R6 Class — WgsHistFile","text":"Reads wgs_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$read()"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"WgsHistFile R6 Class — WgsHistFile","text":"tibble one row metrics spread across individual columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-write-","dir":"Reference","previous_headings":"","what":"Method write()","title":"WgsHistFile R6 Class — WgsHistFile","text":"Writes tidy version wgs_hist.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$write(d, out_dir = NULL, prefix, out_format = \"tsv\", drid = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsHistFile R6 Class — WgsHistFile","text":"d Parsed object self$read(). out_dir Output directory. prefix Prefix output file(s). out_format Format output file(s). drid dracarys ID use dataset (e.g. wfrid.123, prid.456).","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"WgsHistFile R6 Class — WgsHistFile","text":"objects class cloneable method.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"WgsHistFile$clone(deep = FALSE)"},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"WgsHistFile R6 Class — WgsHistFile","text":"deep Whether make deep clone.","code":""},{"path":"https://umccr.github.io/dracarys/reference/WgsHistFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WgsHistFile R6 Class — WgsHistFile","text":"","code":"x <- system.file(\"extdata/wgs/SEQC-II.wgs_hist.csv.gz\", package = \"dracarys\") h <- WgsHistFile$new(x) d <- h$read() h$write(d, out_dir = tempdir(), prefix = \"seqc_sv\", out_format = \"tsv\")"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse VCF with bcftools — bcftools_parse_vcf","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"Parse VCF bcftools. Uses bcftools hood heavy lifting field splitting, converts parsed character vector tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"","code":"bcftools_parse_vcf(vcf, only_pass = TRUE, alias = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"vcf VCF one samples. only_pass Keep PASS variants (def: TRUE). alias Substitute sample names S1/S2/... alias (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"tibble main, FORMAT, INFO fields detected VCF header columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse VCF with bcftools — bcftools_parse_vcf","text":"VCFs 0 variants, returns tibble 0 rows proper number columns.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"Parses VCF regions bcftools. VCF subset written temporary file local filesystem, parsed tibble object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"","code":"bcftools_parse_vcf_regions(vcf, r, only_pass = TRUE)"},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"vcf Path VCF. Can S3, http local. presigned URL, need also concatenate VCF index 'vcf_url##idx##vcfi_url'. r Character vector regions subset (e.g. c('chr1:123-456', 'chr2:789-1000')) only_pass Keep PASS variants (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"tibble main, FORMAT, INFO fields detected VCF header columns, regions specified r ().","code":""},{"path":"https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse VCF regions with bcftools — bcftools_parse_vcf_regions","text":"","code":"if (FALSE) { # \\dontrun{ vcf_local <- here::here(\"MergedSmallVariants.vcf.gz\") r <- c(\"chr1:115256529-115256529\", \"chr2:29443613-29443613\") bcftools_parse_vcf_regions(vcf_local, r) } # }"},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":null,"dir":"Reference","previous_headings":"","what":"Print current timestamp for logging — date_log","title":"Print current timestamp for logging — date_log","text":"Print current timestamp logging","code":""},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print current timestamp for logging — date_log","text":"","code":"date_log()"},{"path":"https://umccr.github.io/dracarys/reference/date_log.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print current timestamp for logging — date_log","text":"Current timestamp character.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate dracarys Function — dr_func_eval","title":"Evaluate dracarys Function — dr_func_eval","text":"somewhat hack getting function evaluate based lookup vector. function found, returns NULL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate dracarys Function — dr_func_eval","text":"","code":"dr_func_eval(f, v = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate dracarys Function — dr_func_eval","text":"f Name function evaluate. v Character vector strings evaluating functions. default, points functions DR_FILE_REGEX dracarys tibble.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate dracarys Function — dr_func_eval","text":"Evaluated function.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_func_eval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate dracarys Function — dr_func_eval","text":"","code":"mean_1_to_10 <- dr_func_eval(\"mean\", v = c(\"mean\", \"sd\"))(1:10) x <- system.file(\"extdata/tso/sample705.fragment_length_hist.json.gz\", package = \"dracarys\") obj <- dr_func_eval(\"TsoFragmentLengthHistFile\")$new(x)"},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys GDS Download — dr_gds_download","title":"dracarys GDS Download — dr_gds_download","text":"Download GDS files can processed dracarys.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dracarys GDS Download — dr_gds_download","text":"","code":"dr_gds_download(   gdsdir,   outdir,   token,   page_size = 100,   pattern = NULL,   dryrun = FALSE,   regexes = DR_FILE_REGEX,   recursive = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/dr_gds_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dracarys GDS Download — dr_gds_download","text":"gdsdir Full path GDS directory. outdir Path output directory. token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 100). pattern Pattern filter returned file type tibble. dryrun TRUE, just list files downloaded (download ). regexes Tibble regex function name. recursive files returned recursively specified GDS directory (TRUE), directly specified GDS directory (FALSE) (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"Output Format is Valid — dr_output_format_valid","title":"Output Format is Valid — dr_output_format_valid","text":"Checks specified output format valid.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Output Format is Valid — dr_output_format_valid","text":"","code":"dr_output_format_valid(x)"},{"path":"https://umccr.github.io/dracarys/reference/dr_output_format_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Output Format is Valid — dr_output_format_valid","text":"x Output format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys S3 Download — dr_s3_download","title":"dracarys S3 Download — dr_s3_download","text":"Download S3 files can processed dracarys.","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dracarys S3 Download — dr_s3_download","text":"","code":"dr_s3_download(   s3dir,   outdir,   page_size = 100,   pattern = NULL,   regexes = DR_FILE_REGEX,   dryrun = FALSE )"},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dracarys S3 Download — dr_s3_download","text":"s3dir Full path S3 directory. outdir Path output directory. page_size Page size (def: 100). pattern Pattern filter returned file type tibble. regexes Tibble regex function name. dryrun TRUE, just list files downloaded (download ).","code":""},{"path":"https://umccr.github.io/dracarys/reference/dr_s3_download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"dracarys S3 Download — dr_s3_download","text":"","code":"s3dir <- file.path(   \"s3://umccr-primary-data-prod/UMCCR-Validation/SBJ00596\",   \"ctTSO/2021-03-17/PTC_SSqCMM05pc_L2100067\" ) outdir <- sub(\"s3:/\", \"~/s3\", s3dir)"},{"path":"https://umccr.github.io/dracarys/reference/dracarys-package.html","id":null,"dir":"Reference","previous_headings":"","what":"dracarys: Post-processing DRAGEN workflows — dracarys-package","title":"dracarys: Post-processing DRAGEN workflows — dracarys-package","text":"Post-processing DRAGEN workflows.","code":""},{"path":[]},{"path":"https://umccr.github.io/dracarys/reference/dracarys-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"dracarys: Post-processing DRAGEN workflows — dracarys-package","text":"Maintainer: Peter Diakumis peterdiakumis@gmail.com (ORCID) Authors: Victor San Kho Lin (ORCID) [contributor]","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Empty Tibble Given Column Names — empty_tbl","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"https://stackoverflow.com//62535671/2169986. Useful handling edge cases empty data.","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"","code":"empty_tbl(cnames, ctypes = readr::cols(.default = \"c\"))"},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"cnames Character vector column names use. ctypes Character vector column types corresponding cnames.","code":""},{"path":"https://umccr.github.io/dracarys/reference/empty_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Empty Tibble Given Column Names — empty_tbl","text":"tibble 0 rows given column names.","code":""},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dracarys DR_FILE_REGEX — file_regex_getter","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"Get dracarys DR_FILE_REGEX","code":""},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"","code":"file_regex_getter()"},{"path":"https://umccr.github.io/dracarys/reference/file_regex_getter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dracarys DR_FILE_REGEX — file_regex_getter","text":"DR_FILE_REGEX R tibble object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Download via CLI — gds_file_download","title":"GDS File Download via CLI — gds_file_download","text":"GDS File Download via CLI","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Download via CLI — gds_file_download","text":"","code":"gds_file_download(gds, out, token = Sys.getenv(\"ICA_ACCESS_TOKEN\"))"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Download via CLI — gds_file_download","text":"gds Full path GDS file. Path output file. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Download via API — gds_file_download_api","title":"GDS File Download via API — gds_file_download_api","text":"GDS File Download via API","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Download via API — gds_file_download_api","text":"","code":"gds_file_download_api(gds_fileid, out_file, token)"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Download via API — gds_file_download_api","text":"gds_fileid GDS file ID. out_file Path output file. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_download_api.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GDS File Download via API — gds_file_download_api","text":"","code":"if (FALSE) { # \\dontrun{ gds_fileid <- \"fil.f9aa2ba7af0c4330095d08dadd2e16b0\" out <- tempfile() token <- Sys.getenv(\"ICA_ACCESS_TOKEN\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS File Presigned URL — gds_file_presignedurl","title":"GDS File Presigned URL — gds_file_presignedurl","text":"Returns presigned URL given GDS file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS File Presigned URL — gds_file_presignedurl","text":"","code":"gds_file_presignedurl(gds_fileid, token)"},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS File Presigned URL — gds_file_presignedurl","text":"gds_fileid GDS file ID. token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GDS File Presigned URL — gds_file_presignedurl","text":"Presigned URL valid.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":null,"dir":"Reference","previous_headings":"","what":"GDS Files List — gds_files_list","title":"GDS Files List — gds_files_list","text":"List files ICA GDS filesystem.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GDS Files List — gds_files_list","text":"","code":"gds_files_list(   gdsdir,   token,   page_size = NULL,   include_url = FALSE,   no_recurse = TRUE,   page_token = NULL,   recursive = NULL )"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GDS Files List — gds_files_list","text":"gdsdir Full path GDS directory. token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 10). include_url Include presigned URLs files within GDS directory (def: FALSE). no_recurse recurse file list .e. just give first <page_size> items without recursing list using <page_token>. page_token Page token (def: NULL). Used internally recursion. recursive files returned recursively specified GDS directory, directly specified GDS directory (def: TRUE).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GDS Files List — gds_files_list","text":"Tibble file basename, file size, file full data path, file dir name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GDS Files List — gds_files_list","text":"","code":"if (FALSE) { # \\dontrun{ gdsdir <- file.path(   \"gds://production/primary_data\",   \"240322_A00130_0290_BH5HLLDSXC/20240323f56ec5a5/WGS_TsqNano\" ) gdsdir <- file.path(   \"gds://bssh.acddbfda498038ed99fa94fe79523959/Runs\",   \"240322_A00130_0290_BH5HLLDSXC_r.3TbcOsEKZUyetygkqIOXcg/InterOp\" ) gdsdir <- file.path(   \"gds://production/analysis_data/SBJ00699/umccrise\",   \"202203277dcf8562/L2200352__L2100146/SBJ00699__MDX220105/coverage\" ) token <- ica_token_validate() page_size <- 11 include_url <- TRUE page_token <- NULL no_recurse <- TRUE recursive <- NULL gds_files_list(gdsdir, token, page_size, include_url, no_recurse, page_token, recursive) } # }"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_fastq.html","id":null,"dir":"Reference","previous_headings":"","what":"List FASTQs In GDS Directory — gds_files_list_fastq","title":"List FASTQs In GDS Directory — gds_files_list_fastq","text":"List FASTQs GDS Directory","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_fastq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List FASTQs In GDS Directory — gds_files_list_fastq","text":"","code":"gds_files_list_fastq(gdsdir, token, include_url = FALSE, page_size = 100)"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_fastq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List FASTQs In GDS Directory — gds_files_list_fastq","text":"gdsdir GDS directory. token ICA access token. include_url Include presigned URLs files within GDS directory. page_size Page size.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_fastq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List FASTQs In GDS Directory — gds_files_list_fastq","text":"tibble type, bname, size, file_id, path, presigned URL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_fastq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List FASTQs In GDS Directory — gds_files_list_fastq","text":"","code":"if (FALSE) { # \\dontrun{ prim <- \"gds://production/primary_data\" run <- \"240719_A00130_0323_BHMCYHDSXC/202407205bad380d/BiModal_BM-5L\" gdsdir <- file.path(prim, run) token <- Sys.getenv(\"ICA_ACCESS_TOKEN\") include_url <- F page_size <- 100 gds_files_list_fastq(gdsdir, token, include_url, page_size) } # }"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":null,"dir":"Reference","previous_headings":"","what":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"Lists relevant files GDS directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"","code":"gds_files_list_filter_relevant(   gdsdir,   token,   pattern = NULL,   include_url = FALSE,   page_size = 100,   regexes = DR_FILE_REGEX )"},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"gdsdir GDS directory. token ICA access token. pattern Pattern filter returned file type tibble. include_url Include presigned URLs files within GDS directory (def: FALSE). page_size Page size (def: 100). regexes Tibble regex function name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Relevant Files In GDS Directory — gds_files_list_filter_relevant","text":"tibble type, bname, size, file_id, path, presigned URL.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List GDS Volumes — gds_volumes_list","title":"List GDS Volumes — gds_volumes_list","text":"Lists GDS volumes accessible provided ICA token.","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List GDS Volumes — gds_volumes_list","text":"","code":"gds_volumes_list(token, page_size = 10)"},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List GDS Volumes — gds_volumes_list","text":"token ICA access token (def: $ICA_ACCESS_TOKEN env var). page_size Page size (def: 10).","code":""},{"path":"https://umccr.github.io/dracarys/reference/gds_volumes_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List GDS Volumes — gds_volumes_list","text":"tibble vol name vol id.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate ICA access token — ica_token_validate","title":"Validate ICA access token — ica_token_validate","text":"Validates ICA access token parsing checking expiration date.","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate ICA access token — ica_token_validate","text":"","code":"ica_token_validate(token = Sys.getenv(\"ICA_ACCESS_TOKEN\"))"},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate ICA access token — ica_token_validate","text":"token ICA access token (def: $ICA_ACCESS_TOKEN env var).","code":""},{"path":"https://umccr.github.io/dracarys/reference/ica_token_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate ICA access token — ica_token_validate","text":"Returns token valid, else errors .","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":null,"dir":"Reference","previous_headings":"","what":"Match File to Regex — match_regex","title":"Match File to Regex — match_regex","text":"Matches given file regexes found DR_FILE_REGEX match, returns 'name' match.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match File to Regex — match_regex","text":"","code":"match_regex(x, regexes = DR_FILE_REGEX)"},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match File to Regex — match_regex","text":"x File match. regexes Tibble regex function name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match File to Regex — match_regex","text":"function corresponding matching regex DR_FILE_REGEX, NA match made.","code":""},{"path":"https://umccr.github.io/dracarys/reference/match_regex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match File to Regex — match_regex","text":"","code":"match_regex(\"foo.msi.json.gz\") #> [1] \"TsoMsiFile\" match_regex(\"foo.fake.tsv\") #> [1] NA"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":null,"dir":"Reference","previous_headings":"","what":"Append New MultiQC Workflow Columns — multiqc_column_map_append","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"Append New MultiQC Workflow Columns","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"","code":"multiqc_column_map_append(d, w, m)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append New MultiQC Workflow Columns — multiqc_column_map_append","text":"d Tidy MultiQC tibble raw names (.e. pre-rename). w New workflow name. m Path 'inst/extdata/multiqc_column_map.tsv' dracarys file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":null,"dir":"Reference","previous_headings":"","what":"Format MultiQC Config Date — multiqc_date_fmt","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"Format MultiQC Config Date","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"","code":"multiqc_date_fmt(cdate)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"cdate String config date \"YYYY-MM-DD, HH:MM UTC\" format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"Properly formatted datetime string \"YYYY-MM-DDTHH:MM:SS\" format. input string formatted differently, return NA.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format MultiQC Config Date — multiqc_date_fmt","text":"","code":"cdate <- \"2023-04-07, 09:09 UTC\" (res1 <- multiqc_date_fmt(cdate)) #> [1] \"2023-04-07T09:09:00\" (res2 <- multiqc_date_fmt(\"2023-04-07\")) #> [1] NA (res3 <- multiqc_date_fmt(\"UNKNOWN\")) #> [1] NA"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"Extracts bar_graph data given plot name MultiQC JSON. bar_graph element JSON object contains:","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"","code":"multiqc_parse_bargraph_plot(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"samples array N subarrays (strings) length . datasets array N subarrays (objects) length B. subarrays contains name (single string) data (array length equal length index-corresponding samples subarray).","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MultiQC Extract Bar Graph Data — multiqc_parse_bargraph_plot","text":"","code":"if (FALSE) { # \\dontrun{ j1 <- here::here(\"nogit/bcl_convert/multiqc_data.json\") j2 <- here::here(\"nogit/dracarys_gds_sync/multiqc_data.json\") j <- j1 j <- j2 multiqc_list_plots(j) parsed <- RJSONIO::fromJSON(j) dat <- parsed$report_plot_data$mapping_dup_percentage_plot dat <- parsed$report_plot_data$time_metrics_plot dat <- parsed$report_plot_data$bclconvert_lane_counts dat <- parsed$report_plot_data$bclconvert_sample_counts multiqc_parse_bargraph_plot(dat) } # }"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"Parses MultiQC 'report_general_stats_data' JSON Element. Modified awesome https://github.com/multimeric/TidyMultiqc.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"","code":"multiqc_parse_gen(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"p Parsed MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse MultiQC 'report_general_stats_data' JSON Element — multiqc_parse_gen","text":"list.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"Parse Plot Data MultiQC JSON","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"","code":"multiqc_parse_plots(j, plot_names = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"j Path multiqc_data.json file. plot_names Names plots parse. Use \"everything\" wantz plotz.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"Nested tibble plot name result list column (use tidyr::unnest access).","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse Plot Data from MultiQC JSON — multiqc_parse_plots","text":"","code":"if (FALSE) { # \\dontrun{ j <- \"dracarys_gds_sync/multiqc_data.json\" multiqc_parse_plots(j, plot_names = c(\"dragen_coverage_per_contig\")) multiqc_parse_plots(j, plot_names = \"everything\") multiqc_parse_plots(j, plot_names = NULL) } # }"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"Parses MultiQC 'report_saved_raw_data' JSON Element.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"","code":"multiqc_parse_raw(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"p Parsed MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw","text":"list tibbles tool, tibble contains metrics per sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"Parses Interop MultiQC 'report_saved_raw_data' JSON Element.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"","code":"multiqc_parse_raw_interop(p)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"p Parsed Interop MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop","text":"list summary per-lane tibbles.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Extracts xy_line data given plot name MultiQC JSON.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"","code":"multiqc_parse_xyline_plot(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiQC Extract XY Line Plot Data — multiqc_parse_xyline_plot","text":"Note dragen_coverage_per_contig/non_main_contig plots conform normal structure xy_line plots, handle separately.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"MultiQC Extract XY Line Plot Data DRAGEN Contig Coverage","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"","code":"multiqc_parse_xyline_plot_contig_cvg(dat)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"dat Parsed JSON list element specific plot data extract.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot_contig_cvg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage — multiqc_parse_xyline_plot_contig_cvg","text":"Tibble name data list-column.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy MultiQC JSON — multiqc_tidy_json","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"Tidies 'multiqc_data.json' output MultiQC. Modified awesome https://github.com/multimeric/TidyMultiqc.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"","code":"multiqc_tidy_json(j)"},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"j Path multiqc_data.json file.","code":""},{"path":"https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tidy MultiQC JSON — multiqc_tidy_json","text":"tidy tibble column corresponds single metric, row corresponds single sample.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Local R Dataframe to Spark-backed Table — rdf2tab","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"First converts local R dataframe Spark DataFrame using SparkR, appends specified table.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"","code":"rdf2tab(rdf, outpath, drid = NULL, ...)"},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"rdf Local R dataframe outpath Path output table. drid dracarys ID use dataset (e.g. wfrid.123, prid.456) ... Additional arguments SparkR::write.df.","code":""},{"path":"https://umccr.github.io/dracarys/reference/rdf2tab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Write Local R Dataframe to Spark-backed Table — rdf2tab","text":"","code":"if (FALSE) { # \\dontrun{ rdf <- mtcars rdf2tab(rdf, \"dev.wf1.mtcars\", drid = \"wfr.123\") } # }"},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":null,"dir":"Reference","previous_headings":"","what":"Read File object — read.File","title":"Read File object — read.File","text":"Read file based type.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read File object — read.File","text":"","code":"# S3 method for class 'File' read(x, ...)"},{"path":"https://umccr.github.io/dracarys/reference/read.File.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read File object — read.File","text":"x Object class File. ... Arguments passed appropriate read_* function.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic Reading — read","title":"Generic Reading — read","text":"Generic function reading dracarys objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic Reading — read","text":"","code":"read(x, ...)"},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic Reading — read","text":"x Object respective class. ... Additional arguments.","code":""},{"path":"https://umccr.github.io/dracarys/reference/read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic Reading — read","text":"Possibly tibble list, depending object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":null,"dir":"Reference","previous_headings":"","what":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"Lists relevant files AWS S3 directory.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"","code":"s3_files_list_filter_relevant(   s3dir,   pattern = NULL,   page_size = 1000,   max_items = 1000,   presign = FALSE,   expiry_sec = 43200 )"},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"s3dir S3 directory. pattern Pattern filter returned file type tibble. page_size size page get AWS service call (def: 1000). max_items total number items return command’s output (def: 1000). presign Include presigned URLs (def: FALSE). expiry_sec Number seconds presigned URL valid (generated) (def: 43200 (12hrs)).","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"tibble path, date, file size, file type, presigned URL requested.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_files_list_filter_relevant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List Relevant Files In AWS S3 Directory — s3_files_list_filter_relevant","text":"","code":"if (FALSE) { # \\dontrun{ s3dir <- \"s3://umccr-primary-data-prod/cancer_report_tables\" s3_files_list_filter_relevant(s3dir = s3dir, presign = TRUE) } # }"},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search AWS S3 Objects — s3_search","title":"Search AWS S3 Objects — s3_search","text":"Searches given pattern UMCCR umccr-primary-data-prod AWS S3 bucket.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search AWS S3 Objects — s3_search","text":"","code":"s3_search(pat, rows)"},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search AWS S3 Objects — s3_search","text":"pat Pattern search (e.g. 'multiqc_data.json'). rows Max number rows return.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search AWS S3 Objects — s3_search","text":"Tibble S3 path, object size, date modified, id, unique hash.","code":""},{"path":"https://umccr.github.io/dracarys/reference/s3_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search AWS S3 Objects — s3_search","text":"","code":"if (FALSE) { # \\dontrun{ pat <- \"qc_summary.tsv.gz\" s3_search(pat, 10) } # }"},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":null,"dir":"Reference","previous_headings":"","what":"Session Information Kable — session_info_kable","title":"Session Information Kable — session_info_kable","text":"Session information kables vignettes.","code":""},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Session Information Kable — session_info_kable","text":"","code":"session_info_kable(pkgs = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Session Information Kable — session_info_kable","text":"pkgs Vector R packages display vignette. default returns .","code":""},{"path":"https://umccr.github.io/dracarys/reference/session_info_kable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Session Information Kable — session_info_kable","text":"list two kables containing information platform specified packages.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":null,"dir":"Reference","previous_headings":"","what":"Process Multiple TimeMetricsFile Objects — time_metrics_process","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"Processes multiple TimeMetricsFile objects.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"","code":"time_metrics_process(x, id = seq_len(length(x)))"},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"x Atomic vector one TimeMetricsFile objects. id ID input, used disambiguate files generated samples. Default: index 1 length x.","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"tibble following columns: Step: DRAGEN step Time: time HH:MM","code":""},{"path":"https://umccr.github.io/dracarys/reference/time_metrics_process.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Process Multiple TimeMetricsFile Objects — time_metrics_process","text":"","code":"p <- system.file(\"extdata/wgs/SEQC-II.time_metrics.csv.gz\", package = \"dracarys\") x <- TimeMetricsFile$new(p) (tm <- time_metrics_process(c(x, x), id = c(\"run1\", \"run2\"))) #> # A tibble: 2 × 20 #>   ID    `Total Runtime` `Loading Reference` `Aligning Reads` `Duplicate Marking` #>   <chr> <chr>           <chr>               <chr>            <chr>               #> 1 run1  04:10           00:01               00:35            00:01               #> 2 run2  04:10           00:01               00:35            00:01               #> # ℹ 15 more variables: `Sorting and Marking Duplicates` <chr>, #> #   `DRAGStr Calibration` <chr>, `Saving Map/Align Output` <chr>, #> #   `Partial Reconfiguration` <chr>, `Variant Calling` <chr>, #> #   `Calculating Target Counts` <chr>, `Correcting GC Bias` <chr>, #> #   `Normalizing Case Sample` <chr>, `Performing Segmentation` <chr>, #> #   `Generating Somatic Model Input` <chr>, `Fitting Somatic Model` <chr>, #> #   `Generating CNV Calls` <chr>, `Generating CNV Track Files` <chr>, …"},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy UMCCR Results — umccr_tidy","title":"Tidy UMCCR Results — umccr_tidy","text":"Tidies UMCCR workflow results list tibbles writes individual tibbles TSV, Parquet, SparkDF, RDS format.","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tidy UMCCR Results — umccr_tidy","text":"","code":"umccr_tidy(   in_dir = NULL,   out_dir = NULL,   prefix = NULL,   local_dir = NULL,   out_format = \"tsv\",   dryrun = FALSE,   token = Sys.getenv(\"ICA_ACCESS_TOKEN\"),   pattern = NULL,   regexes = DR_FILE_REGEX )"},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tidy UMCCR Results — umccr_tidy","text":"in_dir Directory path UMCCR workflow results (can GDS, S3 local). out_dir Output directory. prefix Prefix output file(s). local_dir indir GDS S3 directory, 'recognisable' files first downloaded directory (def: <out_dir>/dracarys_<s3_or_gds>_sync). out_format Format output (tsv, parquet, ) (def: tsv). dryrun Just list files downloaded (def: FALSE). token ICA access token (default uses $ICA_ACCESS_TOKEN env var). pattern Pattern filter returned file type tibble (see name column DR_FILE_REGEX tibble). regexes Tibble regex function name.","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tidy UMCCR Results — umccr_tidy","text":"Tibble path input file resultant tidy object.","code":""},{"path":"https://umccr.github.io/dracarys/reference/umccr_tidy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tidy UMCCR Results — umccr_tidy","text":"","code":"if (FALSE) { # \\dontrun{ in_dir <- file.path(   \"s3://umccr-primary-data-prod/UMCCR-Validation/SBJ00596\",   \"ctTSO/2021-03-17/PTC_SSqCMM05pc_L2100067\" ) in_dir <- paste0(   \"gds://production/analysis_data/SBJ01639/tso_ctdna_tumor_only/\",   \"202204045ad5743c/L2200214/Results/PRJ220425_L2200214\" ) o1 <- sub(\"^gds://\", \"\", in_dir) o1 <- sub(\"s3:/\", \"~/s3\", in_dir) out_dir <- o1 out_dir <- file.path(fs::path_home(), \"icav1/g\", o1) # in_dir <- file.path(out_dir, \"dracarys_gds_sync\") prefix <- \"SBJ01639\" prefix <- \"PTC_SSqCMM05pc_L2100067\" out_format <- \"rds\" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, out_format = out_format, dryrun = F)  in_dir <- here::here(glue(\"nogit/tso/2022-12-13/SBJ02858/dracarys_gds_sync\")) out_dir <- file.path(in_dir, \"../out\") gds_local_dir <- NULL prefix <- \"SBJ02858\" dryrun <- F umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, dryrun = F) } # }"},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0140-2024-05-13","dir":"Changelog","previous_headings":"","what":"dracarys 0.14.0 (2024-05-13)","title":"dracarys 0.14.0 (2024-05-13)","text":"0.13.0 - 0.14.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0130-2024-03-15","dir":"Changelog","previous_headings":"","what":"dracarys 0.13.0 (2024-03-15)","title":"dracarys 0.13.0 (2024-03-15)","text":"0.12.0 - 0.13.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0120-2023-12-12","dir":"Changelog","previous_headings":"","what":"dracarys 0.12.0 (2023-12-12)","title":"dracarys 0.12.0 (2023-12-12)","text":"0.11.0 - 0.12.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0110-2023-08-22","dir":"Changelog","previous_headings":"","what":"dracarys 0.11.0 (2023-08-22)","title":"dracarys 0.11.0 (2023-08-22)","text":"0.10.0 - 0.11.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-0100-2023-06-22","dir":"Changelog","previous_headings":"","what":"dracarys 0.10.0 (2023-06-22)","title":"dracarys 0.10.0 (2023-06-22)","text":"0.9.0 - 0.10.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-090-2023-05-10","dir":"Changelog","previous_headings":"","what":"dracarys 0.9.0 (2023-05-10)","title":"dracarys 0.9.0 (2023-05-10)","text":"0.8.0 - 0.9.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-080-2023-02-24","dir":"Changelog","previous_headings":"","what":"dracarys 0.8.0 (2023-02-24)","title":"dracarys 0.8.0 (2023-02-24)","text":"0.7.0 - 0.8.0 diff","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-070-2023-02-15","dir":"Changelog","previous_headings":"","what":"dracarys 0.7.0 (2023-02-15)","title":"dracarys 0.7.0 (2023-02-15)","text":"0.6.0 - 0.7.0 diff Mostly added use cases based requests curation team related umccrise (CHORD, HRDetect, QC summary), PCGR, MultiQC. umccr_tidy: workhorse handles tidying method dispatch. gds_file_presignedurl PcgrJsonFile PcgrTiersFile UmChordTsvFile UmHrdetectTsvFile UmQcSumFile UmSigsSnvFile MultiqcFile Updated README unified dracarys tidy CLI. Added fun column FILE_REGEX handling method dispatch. GH Actions: Remove linux/arm64 docker since conda pkgs don’t generally ARM64 equivalents. GH Actions: use “miniforge-variant: Mambaforge” (see issue).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-060-2023-01-09","dir":"Changelog","previous_headings":"","what":"dracarys 0.6.0 (2023-01-09)","title":"dracarys 0.6.0 (2023-01-09)","text":"0.5.0 - 0.6.0 diff replace ::set-output. add linux/arm64 support. replace select .data quotes. bump Roxygen 7.2.1 -> 7.2.2 add {fs}, {httr}, {jose}, {sessioninfo} dependencies. import %||% {rlang} specify fallback values NULL cases. ✨ pkgdown: change theme simplex. bump mambaforge: 4.12.0-2 -> 22.9.0-2 bump conda-lock: 1.0.5 -> 1.3.0 add support tidying outputs UMCCR TSO500 ctDNA workflow, generating HTML file tidy results workflow. tso_tidy tidying outputs UMCCR TSO500 ctDNA workflow. tso_rmd generating HTML file tidy results workflow. dr_gds_download downloading dracarys-related files GDS. gds_files_list listing files GDS via API. gds_file_download gds_file_download_api downloading files GDS via ica binary API (via presigned URLs), respectively. ica_token_validate validating ICA access token valid expired. TsoCombinedVariantOutputFile: files deemed less info compared output files. dracarys_tidy_multiqc: renamed dracarys_multiqc. mkdir: use fs::create_dir instead. Remove {tibble}, {readr} {ggplot} multi-imports R6, since can get away just importing single function one R6 classes.","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-050-2022-09-28","dir":"Changelog","previous_headings":"","what":"dracarys 0.5.0 (2022-09-28)","title":"dracarys 0.5.0 (2022-09-28)","text":"0.4.0 - 0.5.0 diff move map separate TSV CLI: add option output format (tsv, parquet, ) (pr18). new contributors: @victorskl","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-040-2022-09-12","dir":"Changelog","previous_headings":"","what":"dracarys 0.4.0 (2022-09-12)","title":"dracarys 0.4.0 (2022-09-12)","text":"0.3.0 - 0.4.0 diff also add Quarto HTML report template","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-030-2022-08-28","dir":"Changelog","previous_headings":"","what":"dracarys 0.3.0 (2022-08-28)","title":"dracarys 0.3.0 (2022-08-28)","text":"0.2.0 - 0.3.0 diff ⭐ MultiQC: support DRAGEN ctdna output (pr13).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-020-2022-07-23","dir":"Changelog","previous_headings":"","what":"dracarys 0.2.0 (2022-07-23)","title":"dracarys 0.2.0 (2022-07-23)","text":"0.1.0 - 0.2.0 diff Add MULTIQC_COLUMNS tibble maps raw metric name cleaner name (pr12). Support MultiQC JSONs (bcbio-wts bcbio-wgs).","code":""},{"path":"https://umccr.github.io/dracarys/news/index.html","id":"dracarys-010-2022-07-11","dir":"Changelog","previous_headings":"","what":"dracarys 0.1.0 (2022-07-11)","title":"dracarys 0.1.0 (2022-07-11)","text":"Initial release dracarys. Support MultiQC JSON tidying. Add conda, conda-lock, Docker support (pr11). Initially supporting just MultiQC json input (dragen-alignment, dragen-transcriptome, dragen-tumor-normal, dragen-umccrise, bcbio-umccrise).","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 1835c2e..68575fb 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,264 +1,90 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
-  <url>
-    <loc>https://umccr.github.io/dracarys/404.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/CODE_OF_CONDUCT.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/LICENSE-text.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/LICENSE.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/articles/developers.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/articles/files.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/articles/flames.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/articles/index.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/authors.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/index.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/news/index.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/BcftoolsStatsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/BclconvertReports.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/File.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/FragmentLengthHistFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/MappingMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/MultiqcFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/PcgrJsonFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/PcgrTiersFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/PloidyEstimationMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/ReplayFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/SvMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TimeMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TrimmerMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoAlignCollapseFusionCallerMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoCombinedVariantOutputFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoCopyNumberVariantsVcfFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoFragmentLengthHistFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoFusionsCsvFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsGenomeVcfFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoMergedSmallVariantsVcfFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoMsiFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoSampleAnalysisResultsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoTargetRegionCoverageFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoTmbFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/TsoTmbTraceTsvFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/UmChordTsvFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/UmHrdetectTsvFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/UmQcSumFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/UmSigsSnvFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/VCMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/WgsContigMeanCovFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/WgsCoverageMetricsFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/WgsFineHistFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/WgsHistFile.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/bcftools_parse_vcf.html</loc>
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-    <loc>https://umccr.github.io/dracarys/reference/bcftools_parse_vcf_regions.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/bclconvert_read_adaptermetrics.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/bclconvert_read_demultiplexstats.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/bclconvert_read_indexhoppingcounts.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/bclconvert_read_topunknownbarcodes.html</loc>
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-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/date_log.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/dr_func_eval.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/dr_gds_download.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/dr_output_format_valid.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/dr_s3_download.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/dracarys-package.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/empty_tbl.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/file_regex_getter.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_file_download.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_file_download_api.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_file_presignedurl.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_files_list.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_files_list_filter_relevant.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/gds_volumes_list.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/ica_token_validate.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/index.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/match_regex.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_date_fmt.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_bargraph_plot.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_gen.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_plots.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_raw.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_raw_interop.html</loc>
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