diff --git a/404.html b/404.html
index 06aa799..37b931b 100644
--- a/404.html
+++ b/404.html
@@ -10,7 +10,7 @@
 <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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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)">
+<!-- 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>
@@ -20,11 +20,11 @@
     <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"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -41,6 +41,7 @@
   <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>
 </li>
       </ul>
@@ -77,13 +78,11 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<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>
+  <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></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 16ecefe..eb70fa1 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -124,11 +125,11 @@ <h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#att
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 8245156..78d7c6f 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -51,38 +52,19 @@
       
     </div>
 
-<pre>MIT License
-
-Copyright (c) 2022 University of Melbourne Centre for Cancer Research (UMCCR)
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+<pre>YEAR: 2024
+COPYRIGHT HOLDER: University of Melbourne Centre for Cancer Research - Genomics Platform Group
 </pre>
 
   </main></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/LICENSE.html b/LICENSE.html
new file mode 100644
index 0000000..7d580bc
--- /dev/null
+++ b/LICENSE.html
@@ -0,0 +1,81 @@
+<!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>
+    <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">
+    
+    <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>
+
+    
+    <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">
+  <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>
+      </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>
+    </div>
+
+<div id="mit-license" class="section level1">
+
+<p>Copyright (c) 2024 University of Melbourne Centre for Cancer Research - Genomics Platform Group</p>
+<p>Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:</p>
+<p>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.</p>
+<p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
+</div>
+
+  </main></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> 2.0.9.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/articles/developers.html b/articles/developers.html
index 7454754..8010e1d 100644
--- a/articles/developers.html
+++ b/articles/developers.html
@@ -11,7 +11,7 @@
 <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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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">
+<!-- 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>
@@ -22,11 +22,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -43,6 +43,7 @@
   <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>
@@ -205,13 +206,11 @@ <h3 id="pkgdown">pkgdown<a class="anchor" aria-label="anchor" href="#pkgdown"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<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>
+  <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></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/files.html b/articles/files.html
index 0b3932b..edef3eb 100644
--- a/articles/files.html
+++ b/articles/files.html
@@ -11,7 +11,7 @@
 <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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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">
+<!-- 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>
@@ -22,11 +22,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -38,11 +38,12 @@
 <li class="nav-item">
   <a class="nav-link" href="../index.html">Intro</a>
 </li>
-<li class="nav-item dropdown">
+<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>
 </li>
       </ul>
@@ -69,15 +70,8 @@
 
 
 
-<script src="files_files/htmlwidgets-1.6.4/htmlwidgets.js"></script><link href="files_files/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet">
-<script src="files_files/datatables-binding-0.32/datatables.js"></script><link href="files_files/dt-core-1.13.6/css/jquery.dataTables.min.css" rel="stylesheet">
-<link href="files_files/dt-core-1.13.6/css/jquery.dataTables.extra.css" rel="stylesheet">
-<script src="files_files/dt-core-1.13.6/js/jquery.dataTables.min.js"></script><link href="files_files/dt-ext-scroller-1.13.6/css/scroller.dataTables.min.css" rel="stylesheet">
-<script src="files_files/dt-ext-scroller-1.13.6/js/dataTables.scroller.min.js"></script><link href="files_files/dt-ext-keytable-1.13.6/css/keyTable.dataTables.min.css" rel="stylesheet">
-<script src="files_files/dt-ext-keytable-1.13.6/js/dataTables.keyTable.min.js"></script><link href="files_files/nouislider-7.0.10/jquery.nouislider.min.css" rel="stylesheet">
-<script src="files_files/nouislider-7.0.10/jquery.nouislider.min.js"></script><link href="files_files/selectize-0.12.0/selectize.bootstrap3.css" rel="stylesheet">
-<script src="files_files/selectize-0.12.0/selectize.min.js"></script><link href="files_files/crosstalk-1.2.1/css/crosstalk.min.css" rel="stylesheet">
-<script src="files_files/crosstalk-1.2.1/js/crosstalk.min.js"></script><div class="row">
+
+<div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Files Supported</h1>
             
@@ -90,20 +84,922 @@
     
 <p>Below are the files output from UMCCR workflows that are supported by
 {dracarys}.</p>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-a520eebc5b8e563fe953" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-a520eebc5b8e563fe953">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div style=\"margin-bottom: auto;\">\n      <input type=\"text\" placeholder=\"All\" style=\"width: 100%;\"/>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div style=\"margin-bottom: auto;\">\n      <input type=\"text\" placeholder=\"All\" style=\"width: 100%;\"/>\n    <\/div>\n  <\/td>\n<\/tr>","extensions":["Scroller","KeyTable"],"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35"],["bcftools_stats\\.txt$","fastqc_metrics\\.csv$","fragment_length_hist\\.csv$","mapping_metrics\\.csv$","multiqc_data\\.json","somatic\\.pcgr\\.json\\.gz$","somatic\\.pcgr\\.snvs_indels\\.tiers\\.tsv$","ploidy_estimation_metrics\\.csv$","replay\\.json$","sv_metrics\\.csv$","time_metrics\\.csv$","trimmer_metrics\\.csv$","AlignCollapseFusionCaller_metrics\\.json\\.gz$","CombinedVariantOutput\\.tsv$","CopyNumberVariants\\.vcf\\.gz$","CopyNumberVariants\\.vcf\\.gz\\.tbi$","fragment_length_hist\\.json\\.gz$","_Fusions\\.csv$","MergedSmallVariants\\.vcf\\.gz$","MergedSmallVariants\\.vcf\\.gz\\.tbi$","msi\\.json\\.gz$","SampleAnalysisResults\\.json\\.gz$","TargetRegionCoverage\\.json\\.gz$","tmb\\.json\\.gz$","TMB_Trace\\.tsv$","chord\\.tsv\\.gz$","hrdetect\\.tsv\\.gz$","-qc_summary\\.tsv\\.gz$","snv_2015\\.tsv\\.gz$","snv_2020\\.tsv\\.gz$","vc_metrics\\.csv$","wgs_contig_mean_cov(_tumor|_normal|)\\.csv$","wgs_coverage_metrics(_tumor|_normal|)\\.csv$","wgs_fine_hist(_tumor|_normal|)\\.csv$","wgs_hist(_tumor|_normal|)\\.csv$"],["BcftoolsStatsFile","FastqcMetricsFile","FragmentLengthHistFile","MappingMetricsFile","MultiqcFile","PcgrJsonFile","PcgrTiersFile","PloidyEstimationMetricsFile","ReplayFile","SvMetricsFile","TimeMetricsFile","TrimmerMetricsFile","TsoAlignCollapseFusionCallerMetricsFile","TsoCombinedVariantOutputFile","TsoCopyNumberVariantsVcfFile","TsoCopyNumberVariantsVcfIndexFile","TsoFragmentLengthHistFile","TsoFusionsCsvFile","TsoMergedSmallVariantsVcfFile","TsoMergedSmallVariantsVcfIndexFile","TsoMsiFile","TsoSampleAnalysisResultsFile","TsoTargetRegionCoverageFile","TsoTmbFile","TsoTmbTraceTsvFile","UmChordTsvFile","UmHrdetectTsvFile","UmQcSumFile","UmSigsSnvFile","UmSigsSnvFile","VCMetricsFile","WgsContigMeanCovFile","WgsCoverageMetricsFile","WgsFineHistFile","WgsHistFile"]],"container":"<table class=\"cell-border display compact\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>regex<\/th>\n      <th>fun<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"scroller":true,"scrollY":600,"scrollX":true,"autoWidth":false,"keys":true,"dom":"lfrtip","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"regex","targets":1},{"name":"fun","targets":2}],"order":[],"orderClasses":false,"orderCellsTop":true}},"evals":[],"jsHooks":[]}</script></main>
+<div class="section level2 tabset tabset-pills">
+<h2 class="tabset tabset-pills" id="workflows">Workflows<a class="anchor" aria-label="anchor" href="#workflows"></a>
+</h2>
+
+
+
+
+
+
+
+
+
+
+<ul class="nav nav-pills" id="workflows" role="tablist">
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#wgs_alignment_qc" id="wgs_alignment_qc-tab" type="button" role="tab" aria-controls="wgs_alignment_qc" aria-selected="true" class="active nav-link">wgs_alignment_qc</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#wts_alignment_qc" id="wts_alignment_qc-tab" type="button" role="tab" aria-controls="wts_alignment_qc" aria-selected="false" class="nav-link">wts_alignment_qc</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#wts_tumor_only" id="wts_tumor_only-tab" type="button" role="tab" aria-controls="wts_tumor_only" aria-selected="false" class="nav-link">wts_tumor_only</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#wgs_tumor_normal-germ" id="wgs_tumor_normal-germ-tab" type="button" role="tab" aria-controls="wgs_tumor_normal-germ" aria-selected="false" class="nav-link">wgs_tumor_normal-germ</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#wgs_tumor_normal-som" id="wgs_tumor_normal-som-tab" type="button" role="tab" aria-controls="wgs_tumor_normal-som" aria-selected="false" class="nav-link">wgs_tumor_normal-som</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#umccrise" id="umccrise-tab" type="button" role="tab" aria-controls="umccrise" aria-selected="false" class="nav-link">umccrise</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#oncoanalyser_wgs" id="oncoanalyser_wgs-tab" type="button" role="tab" aria-controls="oncoanalyser_wgs" aria-selected="false" class="nav-link">oncoanalyser_wgs</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#oncoanalyser_wts" id="oncoanalyser_wts-tab" type="button" role="tab" aria-controls="oncoanalyser_wts" aria-selected="false" class="nav-link">oncoanalyser_wts</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#oncoanalyser_wgts" id="oncoanalyser_wgts-tab" type="button" role="tab" aria-controls="oncoanalyser_wgts" aria-selected="false" class="nav-link">oncoanalyser_wgts</button></li>
+<li role="presentation" class="nav-item"><button data-bs-toggle="tab" data-bs-target="#sash" id="sash-tab" type="button" role="tab" aria-controls="sash" aria-selected="false" class="nav-link">sash</button></li>
+</ul>
+<div class="tab-content">
+<div class="active  tab-pane" id="wgs_alignment_qc" role="tabpanel" aria-labelledby="wgs_alignment_qc-tab">
+
+<table class="table">
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">replay.json</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">fastqc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">fragment_length_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">mapping_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">ploidy_estimation_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">time_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">trimmer_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">wgs_contig_mean_cov.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">wgs_coverage_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">wgs_fine_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">wgs_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="wts_alignment_qc" role="tabpanel" aria-labelledby="wts_alignment_qc-tab">
+
+<table class="table">
+<colgroup>
+<col width="2%">
+<col width="33%">
+<col width="64%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">replay.json</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">fastqc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">fragment_length_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">mapping_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">ploidy_estimation_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">time_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">trimmer_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">wgs_contig_mean_cov.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">wgs_coverage_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">wgs_fine_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">wgs_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">fusion_metrics.csv</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="odd">
+<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">
+<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">
+<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">
+<td align="right">16</td>
+<td align="left">saturation.txt</td>
+<td align="left">
+<strong>TODO</strong>: sequencing saturation, num of
+unique splice junctions observed</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="wts_tumor_only" role="tabpanel" aria-labelledby="wts_tumor_only-tab">
+
+<table class="table">
+<colgroup>
+<col width="2%">
+<col width="33%">
+<col width="64%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">replay.json</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">fastqc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">fragment_length_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">mapping_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">ploidy_estimation_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">time_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">trimmer_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">wgs_contig_mean_cov.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">wgs_coverage_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">wgs_fine_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">wgs_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">fusion_metrics.csv</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="odd">
+<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">
+<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">
+<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">
+<td align="right">16</td>
+<td align="left">saturation.txt</td>
+<td align="left">
+<strong>TODO</strong>: sequencing saturation, num of
+unique splice junctions observed</td>
+</tr>
+</tbody>
+</table>
+</div>
+<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">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">replay.json</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">fastqc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">fragment_length_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">mapping_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">ploidy_estimation_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">roh.bed</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">roh_metrics.csv</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">time_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">trimmer_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">wgs_contig_mean_cov.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">wgs_coverage_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">wgs_fine_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">13</td>
+<td align="left">wgs_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">14</td>
+<td align="left">vc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<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">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">replay.json</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">cnv_metrics.csv</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">fastqc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">fragment_length_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">hrdscore.csv</td>
+<td align="left"><strong>TODO</strong></td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">mapping_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">ploidy_estimation_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">sv_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">time_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">trimmer_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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">
+<td align="right">12</td>
+<td align="left">wgs_coverage_metrics_(tumor/normal).csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">13</td>
+<td align="left">wgs_fine_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">14</td>
+<td align="left">wgs_hist.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">15</td>
+<td align="left">vc_metrics.csv</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="umccrise" role="tabpanel" aria-labelledby="umccrise-tab">
+
+<table class="table">
+<colgroup>
+<col width="2%">
+<col width="53%">
+<col width="43%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<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">
+<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">
+<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">
+<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">
+<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">
+<td align="right">6</td>
+<td align="left">coverage/(tumor/normal).mosdepth.summary.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">coverage/(tumor/normal).samtools_stats.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">oncoviruses/oncoviral_breakpoints.vcf</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">oncoviruses/prioritized_oncoviruses.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">purple/purple.cnv.gene.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">purple/purple.cnv.somatic.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">purple/purple.purity.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">13</td>
+<td align="left">purple/purple.qc</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">14</td>
+<td align="left">small_variants/stats/bcftools_stats.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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">
+<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">
+<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">
+<td align="right">18</td>
+<td align="left">small_variants/somatic.pcgr.json.gz</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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
+dir</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="oncoanalyser_wgs" role="tabpanel" aria-labelledby="oncoanalyser_wgs-tab">
+
+<table class="table">
+<colgroup>
+<col width="3%">
+<col width="46%">
+<col width="50%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">pipeline_info/execution_trace.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">pipeline_info/software_versions.yml</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">amber/amber.homozygousregion.tsv</td>
+<td align="left">For BAF gaps</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">amber/amber.qc</td>
+<td align="left">Includes ConsanguinityProportion, Contamination</td>
+</tr>
+<tr class="odd">
+<td align="right">5</td>
+<td align="left">bamtools/wgsmetrics</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">chord/chord_prediction.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">7</td>
+<td align="left">cuppa/cup.data.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">8</td>
+<td align="left">cuppa/cuppa.conclusion.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">9</td>
+<td align="left">flagstats/flagstat</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">lilac/lilac.candidates.coverage.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">lilac/lilac.qc.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">lilac/lilac.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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">
+<td align="right">14</td>
+<td align="left">purple/purple.cnv.gene.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">15</td>
+<td align="left">purple/purple.cnv.somatic.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">16</td>
+<td align="left">purple/purple.purity.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">17</td>
+<td align="left">purple/purple.qc</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">18</td>
+<td align="left">sigs/sig.allocation.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">19</td>
+<td align="left">sigs/sig.snv_counts.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">20</td>
+<td align="left">virusbreakend/virusbreakend.vcf</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">21</td>
+<td align="left">virusbreakend/virusbreakend.vcf.summary.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">22</td>
+<td align="left">virusinterpreter/virus.annotated.tsv</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="oncoanalyser_wts" role="tabpanel" aria-labelledby="oncoanalyser_wts-tab">
+
+<table class="table">
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">pipeline_info/execution_trace.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">pipeline_info/software_versions.yml</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">cuppa/cup.data.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">4</td>
+<td align="left">isofox/isf.summary.csv</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="oncoanalyser_wgts" role="tabpanel" aria-labelledby="oncoanalyser_wgts-tab">
+
+<table class="table">
+<colgroup>
+<col width="3%">
+<col width="40%">
+<col width="56%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">lilac/lilac.candidates.coverage.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">lilac/lilac.qc.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">3</td>
+<td align="left">lilac/lilac.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<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">
+<td align="right">5</td>
+<td align="left">cuppa/cup.data.csv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">6</td>
+<td align="left">cuppa/cuppa.conclusion.txt</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="tab-pane" id="sash" role="tabpanel" aria-labelledby="sash-tab">
+
+<table class="table">
+<colgroup>
+<col width="3%">
+<col width="81%">
+<col width="15%">
+</colgroup>
+<thead><tr class="header">
+<th align="right">N</th>
+<th align="left">file</th>
+<th align="left">description</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="right">1</td>
+<td align="left">pipeline_info/execution_trace.txt</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">2</td>
+<td align="left">pipeline_info/software_versions.yml</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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">
+<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">
+<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">
+<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">
+<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">
+<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">
+<td align="right">9</td>
+<td align="left">purple/purple.cnv.gene.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">10</td>
+<td align="left">purple/purple.cnv.somatic.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<td align="right">11</td>
+<td align="left">purple/purple.purity.tsv</td>
+<td align="left">NA</td>
+</tr>
+<tr class="even">
+<td align="right">12</td>
+<td align="left">purple/purple.qc</td>
+<td align="left">NA</td>
+</tr>
+<tr class="odd">
+<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">
+<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">
+<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">
+<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">
+<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">
+<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">
+<td align="right">19</td>
+<td align="left">smlv_germline/report/germline.variant_counts_type.yaml</td>
+<td align="left">NA</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+</div>
+  </main>
 </div>
 
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<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>
+  <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></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/files_files/crosstalk-1.2.1/css/crosstalk.min.css b/articles/files_files/crosstalk-1.2.1/css/crosstalk.min.css
deleted file mode 100644
index 6b45382..0000000
--- a/articles/files_files/crosstalk-1.2.1/css/crosstalk.min.css
+++ /dev/null
@@ -1 +0,0 @@
-.container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px}
diff --git a/articles/files_files/crosstalk-1.2.1/js/crosstalk.js b/articles/files_files/crosstalk-1.2.1/js/crosstalk.js
deleted file mode 100644
index fd9eb53..0000000
--- a/articles/files_files/crosstalk-1.2.1/js/crosstalk.js
+++ /dev/null
@@ -1,1474 +0,0 @@
-(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()({1:[function(require,module,exports){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-var Events = function () {
-  function Events() {
-    _classCallCheck(this, Events);
-
-    this._types = {};
-    this._seq = 0;
-  }
-
-  _createClass(Events, [{
-    key: "on",
-    value: function on(eventType, listener) {
-      var subs = this._types[eventType];
-      if (!subs) {
-        subs = this._types[eventType] = {};
-      }
-      var sub = "sub" + this._seq++;
-      subs[sub] = listener;
-      return sub;
-    }
-
-    // Returns false if no match, or string for sub name if matched
-
-  }, {
-    key: "off",
-    value: function off(eventType, listener) {
-      var subs = this._types[eventType];
-      if (typeof listener === "function") {
-        for (var key in subs) {
-          if (subs.hasOwnProperty(key)) {
-            if (subs[key] === listener) {
-              delete subs[key];
-              return key;
-            }
-          }
-        }
-        return false;
-      } else if (typeof listener === "string") {
-        if (subs && subs[listener]) {
-          delete subs[listener];
-          return listener;
-        }
-        return false;
-      } else {
-        throw new Error("Unexpected type for listener");
-      }
-    }
-  }, {
-    key: "trigger",
-    value: function trigger(eventType, arg, thisObj) {
-      var subs = this._types[eventType];
-      for (var key in subs) {
-        if (subs.hasOwnProperty(key)) {
-          subs[key].call(thisObj, arg);
-        }
-      }
-    }
-  }]);
-
-  return Events;
-}();
-
-exports.default = Events;
-
-},{}],2:[function(require,module,exports){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.FilterHandle = undefined;
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _events = require("./events");
-
-var _events2 = _interopRequireDefault(_events);
-
-var _filterset = require("./filterset");
-
-var _filterset2 = _interopRequireDefault(_filterset);
-
-var _group = require("./group");
-
-var _group2 = _interopRequireDefault(_group);
-
-var _util = require("./util");
-
-var util = _interopRequireWildcard(_util);
-
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-function getFilterSet(group) {
-  var fsVar = group.var("filterset");
-  var result = fsVar.get();
-  if (!result) {
-    result = new _filterset2.default();
-    fsVar.set(result);
-  }
-  return result;
-}
-
-var id = 1;
-function nextId() {
-  return id++;
-}
-
-/**
- * Use this class to contribute to, and listen for changes to, the filter set
- * for the given group of widgets. Filter input controls should create one
- * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that
- * wish to displayed filtered data should create one `FilterHandle` and use
- * the {@link FilterHandle#filteredKeys} property and listen for change
- * events.
- *
- * If two (or more) `FilterHandle` instances in the same webpage share the
- * same group name, they will contribute to a single "filter set". Each
- * `FilterHandle` starts out with a `null` value, which means they take
- * nothing away from the set of data that should be shown. To make a
- * `FilterHandle` actually remove data from the filter set, set its value to
- * an array of keys which should be displayed. Crosstalk will aggregate the
- * various key arrays by finding their intersection; only keys that are
- * present in all non-null filter handles are considered part of the filter
- * set.
- *
- * @param {string} [group] - The name of the Crosstalk group, or if none,
- *   null or undefined (or any other falsy value). This can be changed later
- *   via the {@link FilterHandle#setGroup} method.
- * @param {Object} [extraInfo] - An object whose properties will be copied to
- *   the event object whenever an event is emitted.
- */
-
-var FilterHandle = exports.FilterHandle = function () {
-  function FilterHandle(group, extraInfo) {
-    _classCallCheck(this, FilterHandle);
-
-    this._eventRelay = new _events2.default();
-    this._emitter = new util.SubscriptionTracker(this._eventRelay);
-
-    // Name of the group we're currently tracking, if any. Can change over time.
-    this._group = null;
-    // The filterSet that we're tracking, if any. Can change over time.
-    this._filterSet = null;
-    // The Var we're currently tracking, if any. Can change over time.
-    this._filterVar = null;
-    // The event handler subscription we currently have on var.on("change").
-    this._varOnChangeSub = null;
-
-    this._extraInfo = util.extend({ sender: this }, extraInfo);
-
-    this._id = "filter" + nextId();
-
-    this.setGroup(group);
-  }
-
-  /**
-   * Changes the Crosstalk group membership of this FilterHandle. If `set()` was
-   * previously called on this handle, switching groups will clear those keys
-   * from the old group's filter set. These keys will not be applied to the new
-   * group's filter set either. In other words, `setGroup()` effectively calls
-   * `clear()` before switching groups.
-   *
-   * @param {string} group - The name of the Crosstalk group, or null (or
-   *   undefined) to clear the group.
-   */
-
-
-  _createClass(FilterHandle, [{
-    key: "setGroup",
-    value: function setGroup(group) {
-      var _this = this;
-
-      // If group is unchanged, do nothing
-      if (this._group === group) return;
-      // Treat null, undefined, and other falsy values the same
-      if (!this._group && !group) return;
-
-      if (this._filterVar) {
-        this._filterVar.off("change", this._varOnChangeSub);
-        this.clear();
-        this._varOnChangeSub = null;
-        this._filterVar = null;
-        this._filterSet = null;
-      }
-
-      this._group = group;
-
-      if (group) {
-        group = (0, _group2.default)(group);
-        this._filterSet = getFilterSet(group);
-        this._filterVar = (0, _group2.default)(group).var("filter");
-        var sub = this._filterVar.on("change", function (e) {
-          _this._eventRelay.trigger("change", e, _this);
-        });
-        this._varOnChangeSub = sub;
-      }
-    }
-
-    /**
-     * Combine the given `extraInfo` (if any) with the handle's default
-     * `_extraInfo` (if any).
-     * @private
-     */
-
-  }, {
-    key: "_mergeExtraInfo",
-    value: function _mergeExtraInfo(extraInfo) {
-      return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null);
-    }
-
-    /**
-     * Close the handle. This clears this handle's contribution to the filter set,
-     * and unsubscribes all event listeners.
-     */
-
-  }, {
-    key: "close",
-    value: function close() {
-      this._emitter.removeAllListeners();
-      this.clear();
-      this.setGroup(null);
-    }
-
-    /**
-     * Clear this handle's contribution to the filter set.
-     *
-     * @param {Object} [extraInfo] - Extra properties to be included on the event
-     *   object that's passed to listeners (in addition to any options that were
-     *   passed into the `FilterHandle` constructor).
-     * 
-     * @fires FilterHandle#change
-     */
-
-  }, {
-    key: "clear",
-    value: function clear(extraInfo) {
-      if (!this._filterSet) return;
-      this._filterSet.clear(this._id);
-      this._onChange(extraInfo);
-    }
-
-    /**
-     * Set this handle's contribution to the filter set. This array should consist
-     * of the keys of the rows that _should_ be displayed; any keys that are not
-     * present in the array will be considered _filtered out_. Note that multiple
-     * `FilterHandle` instances in the group may each contribute an array of keys,
-     * and only those keys that appear in _all_ of the arrays make it through the
-     * filter.
-     *
-     * @param {string[]} keys - Empty array, or array of keys. To clear the
-     *   filter, don't pass an empty array; instead, use the
-     *   {@link FilterHandle#clear} method.
-     * @param {Object} [extraInfo] - Extra properties to be included on the event
-     *   object that's passed to listeners (in addition to any options that were
-     *   passed into the `FilterHandle` constructor).
-     * 
-     * @fires FilterHandle#change
-     */
-
-  }, {
-    key: "set",
-    value: function set(keys, extraInfo) {
-      if (!this._filterSet) return;
-      this._filterSet.update(this._id, keys);
-      this._onChange(extraInfo);
-    }
-
-    /**
-     * @return {string[]|null} - Either: 1) an array of keys that made it through
-     *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter
-     *   is being applied (all data should be displayed).
-     */
-
-  }, {
-    key: "on",
-
-
-    /**
-     * Subscribe to events on this `FilterHandle`.
-     *
-     * @param {string} eventType - Indicates the type of events to listen to.
-     *   Currently, only `"change"` is supported.
-     * @param {FilterHandle~listener} listener - The callback function that
-     *   will be invoked when the event occurs.
-     * @return {string} - A token to pass to {@link FilterHandle#off} to cancel
-     *   this subscription.
-     */
-    value: function on(eventType, listener) {
-      return this._emitter.on(eventType, listener);
-    }
-
-    /**
-     * Cancel event subscriptions created by {@link FilterHandle#on}.
-     *
-     * @param {string} eventType - The type of event to unsubscribe.
-     * @param {string|FilterHandle~listener} listener - Either the callback
-     *   function previously passed into {@link FilterHandle#on}, or the
-     *   string that was returned from {@link FilterHandle#on}.
-     */
-
-  }, {
-    key: "off",
-    value: function off(eventType, listener) {
-      return this._emitter.off(eventType, listener);
-    }
-  }, {
-    key: "_onChange",
-    value: function _onChange(extraInfo) {
-      if (!this._filterSet) return;
-      this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));
-    }
-
-    /**
-     * @callback FilterHandle~listener
-     * @param {Object} event - An object containing details of the event. For
-     *   `"change"` events, this includes the properties `value` (the new
-     *   value of the filter set, or `null` if no filter set is active),
-     *   `oldValue` (the previous value of the filter set), and `sender` (the
-     *   `FilterHandle` instance that made the change).
-     */
-
-  }, {
-    key: "filteredKeys",
-    get: function get() {
-      return this._filterSet ? this._filterSet.value : null;
-    }
-  }]);
-
-  return FilterHandle;
-}();
-
-/**
- * @event FilterHandle#change
- * @type {object}
- * @property {object} value - The new value of the filter set, or `null`
- *   if no filter set is active.
- * @property {object} oldValue - The previous value of the filter set.
- * @property {FilterHandle} sender - The `FilterHandle` instance that
- *   changed the value.
- */
-
-},{"./events":1,"./filterset":3,"./group":4,"./util":11}],3:[function(require,module,exports){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _util = require("./util");
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-function naturalComparator(a, b) {
-  if (a === b) {
-    return 0;
-  } else if (a < b) {
-    return -1;
-  } else if (a > b) {
-    return 1;
-  }
-}
-
-/**
- * @private
- */
-
-var FilterSet = function () {
-  function FilterSet() {
-    _classCallCheck(this, FilterSet);
-
-    this.reset();
-  }
-
-  _createClass(FilterSet, [{
-    key: "reset",
-    value: function reset() {
-      // Key: handle ID, Value: array of selected keys, or null
-      this._handles = {};
-      // Key: key string, Value: count of handles that include it
-      this._keys = {};
-      this._value = null;
-      this._activeHandles = 0;
-    }
-  }, {
-    key: "update",
-    value: function update(handleId, keys) {
-      if (keys !== null) {
-        keys = keys.slice(0); // clone before sorting
-        keys.sort(naturalComparator);
-      }
-
-      var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys),
-          added = _diffSortedLists.added,
-          removed = _diffSortedLists.removed;
-
-      this._handles[handleId] = keys;
-
-      for (var i = 0; i < added.length; i++) {
-        this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;
-      }
-      for (var _i = 0; _i < removed.length; _i++) {
-        this._keys[removed[_i]]--;
-      }
-
-      this._updateValue(keys);
-    }
-
-    /**
-     * @param {string[]} keys Sorted array of strings that indicate
-     * a superset of possible keys.
-     * @private
-     */
-
-  }, {
-    key: "_updateValue",
-    value: function _updateValue() {
-      var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys;
-
-      var handleCount = Object.keys(this._handles).length;
-      if (handleCount === 0) {
-        this._value = null;
-      } else {
-        this._value = [];
-        for (var i = 0; i < keys.length; i++) {
-          var count = this._keys[keys[i]];
-          if (count === handleCount) {
-            this._value.push(keys[i]);
-          }
-        }
-      }
-    }
-  }, {
-    key: "clear",
-    value: function clear(handleId) {
-      if (typeof this._handles[handleId] === "undefined") {
-        return;
-      }
-
-      var keys = this._handles[handleId];
-      if (!keys) {
-        keys = [];
-      }
-
-      for (var i = 0; i < keys.length; i++) {
-        this._keys[keys[i]]--;
-      }
-      delete this._handles[handleId];
-
-      this._updateValue();
-    }
-  }, {
-    key: "value",
-    get: function get() {
-      return this._value;
-    }
-  }, {
-    key: "_allKeys",
-    get: function get() {
-      var allKeys = Object.keys(this._keys);
-      allKeys.sort(naturalComparator);
-      return allKeys;
-    }
-  }]);
-
-  return FilterSet;
-}();
-
-exports.default = FilterSet;
-
-},{"./util":11}],4:[function(require,module,exports){
-(function (global){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
-
-exports.default = group;
-
-var _var2 = require("./var");
-
-var _var3 = _interopRequireDefault(_var2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-// Use a global so that multiple copies of crosstalk.js can be loaded and still
-// have groups behave as singletons across all copies.
-global.__crosstalk_groups = global.__crosstalk_groups || {};
-var groups = global.__crosstalk_groups;
-
-function group(groupName) {
-  if (groupName && typeof groupName === "string") {
-    if (!groups.hasOwnProperty(groupName)) {
-      groups[groupName] = new Group(groupName);
-    }
-    return groups[groupName];
-  } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) {
-    // Appears to already be a group object
-    return groupName;
-  } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") {
-    return group(groupName[0]);
-  } else {
-    throw new Error("Invalid groupName argument");
-  }
-}
-
-var Group = function () {
-  function Group(name) {
-    _classCallCheck(this, Group);
-
-    this.name = name;
-    this._vars = {};
-  }
-
-  _createClass(Group, [{
-    key: "var",
-    value: function _var(name) {
-      if (!name || typeof name !== "string") {
-        throw new Error("Invalid var name");
-      }
-
-      if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name);
-      return this._vars[name];
-    }
-  }, {
-    key: "has",
-    value: function has(name) {
-      if (!name || typeof name !== "string") {
-        throw new Error("Invalid var name");
-      }
-
-      return this._vars.hasOwnProperty(name);
-    }
-  }]);
-
-  return Group;
-}();
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./var":12}],5:[function(require,module,exports){
-(function (global){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _group = require("./group");
-
-var _group2 = _interopRequireDefault(_group);
-
-var _selection = require("./selection");
-
-var _filter = require("./filter");
-
-var _input = require("./input");
-
-require("./input_selectize");
-
-require("./input_checkboxgroup");
-
-require("./input_slider");
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var defaultGroup = (0, _group2.default)("default");
-
-function var_(name) {
-  return defaultGroup.var(name);
-}
-
-function has(name) {
-  return defaultGroup.has(name);
-}
-
-if (global.Shiny) {
-  global.Shiny.addCustomMessageHandler("update-client-value", function (message) {
-    if (typeof message.group === "string") {
-      (0, _group2.default)(message.group).var(message.name).set(message.value);
-    } else {
-      var_(message.name).set(message.value);
-    }
-  });
-}
-
-var crosstalk = {
-  group: _group2.default,
-  var: var_,
-  has: has,
-  SelectionHandle: _selection.SelectionHandle,
-  FilterHandle: _filter.FilterHandle,
-  bind: _input.bind
-};
-
-/**
- * @namespace crosstalk
- */
-exports.default = crosstalk;
-
-global.crosstalk = crosstalk;
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){
-(function (global){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.register = register;
-exports.bind = bind;
-var $ = global.jQuery;
-
-var bindings = {};
-
-function register(reg) {
-  bindings[reg.className] = reg;
-  if (global.document && global.document.readyState !== "complete") {
-    $(function () {
-      bind();
-    });
-  } else if (global.document) {
-    setTimeout(bind, 100);
-  }
-}
-
-function bind() {
-  Object.keys(bindings).forEach(function (className) {
-    var binding = bindings[className];
-    $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) {
-      bindInstance(binding, el);
-    });
-  });
-}
-
-// Escape jQuery identifier
-function $escape(val) {
-  return val.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g, "\\$1");
-}
-
-function bindEl(el) {
-  var $el = $(el);
-  Object.keys(bindings).forEach(function (className) {
-    if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) {
-      var binding = bindings[className];
-      bindInstance(binding, el);
-    }
-  });
-}
-
-function bindInstance(binding, el) {
-  var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']");
-  var data = JSON.parse(jsonEl[0].innerText);
-
-  var instance = binding.factory(el, data);
-  $(el).data("crosstalk-instance", instance);
-  $(el).addClass("crosstalk-input-bound");
-}
-
-if (global.Shiny) {
-  var inputBinding = new global.Shiny.InputBinding();
-  var _$ = global.jQuery;
-  _$.extend(inputBinding, {
-    find: function find(scope) {
-      return _$(scope).find(".crosstalk-input");
-    },
-    initialize: function initialize(el) {
-      if (!_$(el).hasClass("crosstalk-input-bound")) {
-        bindEl(el);
-      }
-    },
-    getId: function getId(el) {
-      return el.id;
-    },
-    getValue: function getValue(el) {},
-    setValue: function setValue(el, value) {},
-    receiveMessage: function receiveMessage(el, data) {},
-    subscribe: function subscribe(el, callback) {
-      _$(el).data("crosstalk-instance").resume();
-    },
-    unsubscribe: function unsubscribe(el) {
-      _$(el).data("crosstalk-instance").suspend();
-    }
-  });
-  global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding");
-}
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{}],7:[function(require,module,exports){
-(function (global){
-"use strict";
-
-var _input = require("./input");
-
-var input = _interopRequireWildcard(_input);
-
-var _filter = require("./filter");
-
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
-
-var $ = global.jQuery;
-
-input.register({
-  className: "crosstalk-input-checkboxgroup",
-
-  factory: function factory(el, data) {
-    /*
-     * map: {"groupA": ["keyA", "keyB", ...], ...}
-     * group: "ct-groupname"
-     */
-    var ctHandle = new _filter.FilterHandle(data.group);
-
-    var lastKnownKeys = void 0;
-    var $el = $(el);
-    $el.on("change", "input[type='checkbox']", function () {
-      var checked = $el.find("input[type='checkbox']:checked");
-      if (checked.length === 0) {
-        lastKnownKeys = null;
-        ctHandle.clear();
-      } else {
-        var keys = {};
-        checked.each(function () {
-          data.map[this.value].forEach(function (key) {
-            keys[key] = true;
-          });
-        });
-        var keyArray = Object.keys(keys);
-        keyArray.sort();
-        lastKnownKeys = keyArray;
-        ctHandle.set(keyArray);
-      }
-    });
-
-    return {
-      suspend: function suspend() {
-        ctHandle.clear();
-      },
-      resume: function resume() {
-        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
-      }
-    };
-  }
-});
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./filter":2,"./input":6}],8:[function(require,module,exports){
-(function (global){
-"use strict";
-
-var _input = require("./input");
-
-var input = _interopRequireWildcard(_input);
-
-var _util = require("./util");
-
-var util = _interopRequireWildcard(_util);
-
-var _filter = require("./filter");
-
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
-
-var $ = global.jQuery;
-
-input.register({
-  className: "crosstalk-input-select",
-
-  factory: function factory(el, data) {
-    /*
-     * items: {value: [...], label: [...]}
-     * map: {"groupA": ["keyA", "keyB", ...], ...}
-     * group: "ct-groupname"
-     */
-
-    var first = [{ value: "", label: "(All)" }];
-    var items = util.dataframeToD3(data.items);
-    var opts = {
-      options: first.concat(items),
-      valueField: "value",
-      labelField: "label",
-      searchField: "label"
-    };
-
-    var select = $(el).find("select")[0];
-
-    var selectize = $(select).selectize(opts)[0].selectize;
-
-    var ctHandle = new _filter.FilterHandle(data.group);
-
-    var lastKnownKeys = void 0;
-    selectize.on("change", function () {
-      if (selectize.items.length === 0) {
-        lastKnownKeys = null;
-        ctHandle.clear();
-      } else {
-        var keys = {};
-        selectize.items.forEach(function (group) {
-          data.map[group].forEach(function (key) {
-            keys[key] = true;
-          });
-        });
-        var keyArray = Object.keys(keys);
-        keyArray.sort();
-        lastKnownKeys = keyArray;
-        ctHandle.set(keyArray);
-      }
-    });
-
-    return {
-      suspend: function suspend() {
-        ctHandle.clear();
-      },
-      resume: function resume() {
-        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
-      }
-    };
-  }
-});
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){
-(function (global){
-"use strict";
-
-var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }();
-
-var _input = require("./input");
-
-var input = _interopRequireWildcard(_input);
-
-var _filter = require("./filter");
-
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
-
-var $ = global.jQuery;
-var strftime = global.strftime;
-
-input.register({
-  className: "crosstalk-input-slider",
-
-  factory: function factory(el, data) {
-    /*
-     * map: {"groupA": ["keyA", "keyB", ...], ...}
-     * group: "ct-groupname"
-     */
-    var ctHandle = new _filter.FilterHandle(data.group);
-
-    var opts = {};
-    var $el = $(el).find("input");
-    var dataType = $el.data("data-type");
-    var timeFormat = $el.data("time-format");
-    var round = $el.data("round");
-    var timeFormatter = void 0;
-
-    // Set up formatting functions
-    if (dataType === "date") {
-      timeFormatter = strftime.utc();
-      opts.prettify = function (num) {
-        return timeFormatter(timeFormat, new Date(num));
-      };
-    } else if (dataType === "datetime") {
-      var timezone = $el.data("timezone");
-      if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime;
-
-      opts.prettify = function (num) {
-        return timeFormatter(timeFormat, new Date(num));
-      };
-    } else if (dataType === "number") {
-      if (typeof round !== "undefined") opts.prettify = function (num) {
-        var factor = Math.pow(10, round);
-        return Math.round(num * factor) / factor;
-      };
-    }
-
-    $el.ionRangeSlider(opts);
-
-    function getValue() {
-      var result = $el.data("ionRangeSlider").result;
-
-      // Function for converting numeric value from slider to appropriate type.
-      var convert = void 0;
-      var dataType = $el.data("data-type");
-      if (dataType === "date") {
-        convert = function convert(val) {
-          return formatDateUTC(new Date(+val));
-        };
-      } else if (dataType === "datetime") {
-        convert = function convert(val) {
-          // Convert ms to s
-          return +val / 1000;
-        };
-      } else {
-        convert = function convert(val) {
-          return +val;
-        };
-      }
-
-      if ($el.data("ionRangeSlider").options.type === "double") {
-        return [convert(result.from), convert(result.to)];
-      } else {
-        return convert(result.from);
-      }
-    }
-
-    var lastKnownKeys = null;
-
-    $el.on("change.crosstalkSliderInput", function (event) {
-      if (!$el.data("updating") && !$el.data("animating")) {
-        var _getValue = getValue(),
-            _getValue2 = _slicedToArray(_getValue, 2),
-            from = _getValue2[0],
-            to = _getValue2[1];
-
-        var keys = [];
-        for (var i = 0; i < data.values.length; i++) {
-          var val = data.values[i];
-          if (val >= from && val <= to) {
-            keys.push(data.keys[i]);
-          }
-        }
-        keys.sort();
-        ctHandle.set(keys);
-        lastKnownKeys = keys;
-      }
-    });
-
-    // let $el = $(el);
-    // $el.on("change", "input[type="checkbox"]", function() {
-    //   let checked = $el.find("input[type="checkbox"]:checked");
-    //   if (checked.length === 0) {
-    //     ctHandle.clear();
-    //   } else {
-    //     let keys = {};
-    //     checked.each(function() {
-    //       data.map[this.value].forEach(function(key) {
-    //         keys[key] = true;
-    //       });
-    //     });
-    //     let keyArray = Object.keys(keys);
-    //     keyArray.sort();
-    //     ctHandle.set(keyArray);
-    //   }
-    // });
-
-    return {
-      suspend: function suspend() {
-        ctHandle.clear();
-      },
-      resume: function resume() {
-        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
-      }
-    };
-  }
-});
-
-// Convert a number to a string with leading zeros
-function padZeros(n, digits) {
-  var str = n.toString();
-  while (str.length < digits) {
-    str = "0" + str;
-  }return str;
-}
-
-// Given a Date object, return a string in yyyy-mm-dd format, using the
-// UTC date. This may be a day off from the date in the local time zone.
-function formatDateUTC(date) {
-  if (date instanceof Date) {
-    return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2);
-  } else {
-    return null;
-  }
-}
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./filter":2,"./input":6}],10:[function(require,module,exports){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.SelectionHandle = undefined;
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _events = require("./events");
-
-var _events2 = _interopRequireDefault(_events);
-
-var _group = require("./group");
-
-var _group2 = _interopRequireDefault(_group);
-
-var _util = require("./util");
-
-var util = _interopRequireWildcard(_util);
-
-function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-/**
- * Use this class to read and write (and listen for changes to) the selection
- * for a Crosstalk group. This is intended to be used for linked brushing.
- *
- * If two (or more) `SelectionHandle` instances in the same webpage share the
- * same group name, they will share the same state. Setting the selection using
- * one `SelectionHandle` instance will result in the `value` property instantly
- * changing across the others, and `"change"` event listeners on all instances
- * (including the one that initiated the sending) will fire.
- *
- * @param {string} [group] - The name of the Crosstalk group, or if none,
- *   null or undefined (or any other falsy value). This can be changed later
- *   via the [SelectionHandle#setGroup](#setGroup) method.
- * @param {Object} [extraInfo] - An object whose properties will be copied to
- *   the event object whenever an event is emitted.
- */
-var SelectionHandle = exports.SelectionHandle = function () {
-  function SelectionHandle() {
-    var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
-    var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
-
-    _classCallCheck(this, SelectionHandle);
-
-    this._eventRelay = new _events2.default();
-    this._emitter = new util.SubscriptionTracker(this._eventRelay);
-
-    // Name of the group we're currently tracking, if any. Can change over time.
-    this._group = null;
-    // The Var we're currently tracking, if any. Can change over time.
-    this._var = null;
-    // The event handler subscription we currently have on var.on("change").
-    this._varOnChangeSub = null;
-
-    this._extraInfo = util.extend({ sender: this }, extraInfo);
-
-    this.setGroup(group);
-  }
-
-  /**
-   * Changes the Crosstalk group membership of this SelectionHandle. The group
-   * being switched away from (if any) will not have its selection value
-   * modified as a result of calling `setGroup`, even if this handle was the
-   * most recent handle to set the selection of the group.
-   *
-   * The group being switched to (if any) will also not have its selection value
-   * modified as a result of calling `setGroup`. If you want to set the
-   * selection value of the new group, call `set` explicitly.
-   *
-   * @param {string} group - The name of the Crosstalk group, or null (or
-   *   undefined) to clear the group.
-   */
-
-
-  _createClass(SelectionHandle, [{
-    key: "setGroup",
-    value: function setGroup(group) {
-      var _this = this;
-
-      // If group is unchanged, do nothing
-      if (this._group === group) return;
-      // Treat null, undefined, and other falsy values the same
-      if (!this._group && !group) return;
-
-      if (this._var) {
-        this._var.off("change", this._varOnChangeSub);
-        this._var = null;
-        this._varOnChangeSub = null;
-      }
-
-      this._group = group;
-
-      if (group) {
-        this._var = (0, _group2.default)(group).var("selection");
-        var sub = this._var.on("change", function (e) {
-          _this._eventRelay.trigger("change", e, _this);
-        });
-        this._varOnChangeSub = sub;
-      }
-    }
-
-    /**
-     * Retrieves the current selection for the group represented by this
-     * `SelectionHandle`.
-     *
-     * - If no selection is active, then this value will be falsy.
-     * - If a selection is active, but no data points are selected, then this
-     *   value will be an empty array.
-     * - If a selection is active, and data points are selected, then the keys
-     *   of the selected data points will be present in the array.
-     */
-
-  }, {
-    key: "_mergeExtraInfo",
-
-
-    /**
-     * Combines the given `extraInfo` (if any) with the handle's default
-     * `_extraInfo` (if any).
-     * @private
-     */
-    value: function _mergeExtraInfo(extraInfo) {
-      // Important incidental effect: shallow clone is returned
-      return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null);
-    }
-
-    /**
-     * Overwrites the current selection for the group, and raises the `"change"`
-     * event among all of the group's '`SelectionHandle` instances (including
-     * this one).
-     *
-     * @fires SelectionHandle#change
-     * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see
-     *   {@link SelectionHandle#value}).
-     * @param {Object} [extraInfo] - Extra properties to be included on the event
-     *   object that's passed to listeners (in addition to any options that were
-     *   passed into the `SelectionHandle` constructor).
-     */
-
-  }, {
-    key: "set",
-    value: function set(selectedKeys, extraInfo) {
-      if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));
-    }
-
-    /**
-     * Overwrites the current selection for the group, and raises the `"change"`
-     * event among all of the group's '`SelectionHandle` instances (including
-     * this one).
-     *
-     * @fires SelectionHandle#change
-     * @param {Object} [extraInfo] - Extra properties to be included on the event
-     *   object that's passed to listeners (in addition to any that were passed
-     *   into the `SelectionHandle` constructor).
-     */
-
-  }, {
-    key: "clear",
-    value: function clear(extraInfo) {
-      if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo));
-    }
-
-    /**
-     * Subscribes to events on this `SelectionHandle`.
-     *
-     * @param {string} eventType - Indicates the type of events to listen to.
-     *   Currently, only `"change"` is supported.
-     * @param {SelectionHandle~listener} listener - The callback function that
-     *   will be invoked when the event occurs.
-     * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel
-     *   this subscription.
-     */
-
-  }, {
-    key: "on",
-    value: function on(eventType, listener) {
-      return this._emitter.on(eventType, listener);
-    }
-
-    /**
-     * Cancels event subscriptions created by {@link SelectionHandle#on}.
-     *
-     * @param {string} eventType - The type of event to unsubscribe.
-     * @param {string|SelectionHandle~listener} listener - Either the callback
-     *   function previously passed into {@link SelectionHandle#on}, or the
-     *   string that was returned from {@link SelectionHandle#on}.
-     */
-
-  }, {
-    key: "off",
-    value: function off(eventType, listener) {
-      return this._emitter.off(eventType, listener);
-    }
-
-    /**
-     * Shuts down the `SelectionHandle` object.
-     *
-     * Removes all event listeners that were added through this handle.
-     */
-
-  }, {
-    key: "close",
-    value: function close() {
-      this._emitter.removeAllListeners();
-      this.setGroup(null);
-    }
-  }, {
-    key: "value",
-    get: function get() {
-      return this._var ? this._var.get() : null;
-    }
-  }]);
-
-  return SelectionHandle;
-}();
-
-/**
- * @callback SelectionHandle~listener
- * @param {Object} event - An object containing details of the event. For
- *   `"change"` events, this includes the properties `value` (the new
- *   value of the selection, or `undefined` if no selection is active),
- *   `oldValue` (the previous value of the selection), and `sender` (the
- *   `SelectionHandle` instance that made the change).
- */
-
-/**
- * @event SelectionHandle#change
- * @type {object}
- * @property {object} value - The new value of the selection, or `undefined`
- *   if no selection is active.
- * @property {object} oldValue - The previous value of the selection.
- * @property {SelectionHandle} sender - The `SelectionHandle` instance that
- *   changed the value.
- */
-
-},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
-
-exports.extend = extend;
-exports.checkSorted = checkSorted;
-exports.diffSortedLists = diffSortedLists;
-exports.dataframeToD3 = dataframeToD3;
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-function extend(target) {
-  for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) {
-    sources[_key - 1] = arguments[_key];
-  }
-
-  for (var i = 0; i < sources.length; i++) {
-    var src = sources[i];
-    if (typeof src === "undefined" || src === null) continue;
-
-    for (var key in src) {
-      if (src.hasOwnProperty(key)) {
-        target[key] = src[key];
-      }
-    }
-  }
-  return target;
-}
-
-function checkSorted(list) {
-  for (var i = 1; i < list.length; i++) {
-    if (list[i] <= list[i - 1]) {
-      throw new Error("List is not sorted or contains duplicate");
-    }
-  }
-}
-
-function diffSortedLists(a, b) {
-  var i_a = 0;
-  var i_b = 0;
-
-  if (!a) a = [];
-  if (!b) b = [];
-
-  var a_only = [];
-  var b_only = [];
-
-  checkSorted(a);
-  checkSorted(b);
-
-  while (i_a < a.length && i_b < b.length) {
-    if (a[i_a] === b[i_b]) {
-      i_a++;
-      i_b++;
-    } else if (a[i_a] < b[i_b]) {
-      a_only.push(a[i_a++]);
-    } else {
-      b_only.push(b[i_b++]);
-    }
-  }
-
-  if (i_a < a.length) a_only = a_only.concat(a.slice(i_a));
-  if (i_b < b.length) b_only = b_only.concat(b.slice(i_b));
-  return {
-    removed: a_only,
-    added: b_only
-  };
-}
-
-// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }
-// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]
-function dataframeToD3(df) {
-  var names = [];
-  var length = void 0;
-  for (var name in df) {
-    if (df.hasOwnProperty(name)) names.push(name);
-    if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") {
-      throw new Error("All fields must be arrays");
-    } else if (typeof length !== "undefined" && length !== df[name].length) {
-      throw new Error("All fields must be arrays of the same length");
-    }
-    length = df[name].length;
-  }
-  var results = [];
-  var item = void 0;
-  for (var row = 0; row < length; row++) {
-    item = {};
-    for (var col = 0; col < names.length; col++) {
-      item[names[col]] = df[names[col]][row];
-    }
-    results.push(item);
-  }
-  return results;
-}
-
-/**
- * Keeps track of all event listener additions/removals and lets all active
- * listeners be removed with a single operation.
- *
- * @private
- */
-
-var SubscriptionTracker = exports.SubscriptionTracker = function () {
-  function SubscriptionTracker(emitter) {
-    _classCallCheck(this, SubscriptionTracker);
-
-    this._emitter = emitter;
-    this._subs = {};
-  }
-
-  _createClass(SubscriptionTracker, [{
-    key: "on",
-    value: function on(eventType, listener) {
-      var sub = this._emitter.on(eventType, listener);
-      this._subs[sub] = eventType;
-      return sub;
-    }
-  }, {
-    key: "off",
-    value: function off(eventType, listener) {
-      var sub = this._emitter.off(eventType, listener);
-      if (sub) {
-        delete this._subs[sub];
-      }
-      return sub;
-    }
-  }, {
-    key: "removeAllListeners",
-    value: function removeAllListeners() {
-      var _this = this;
-
-      var current_subs = this._subs;
-      this._subs = {};
-      Object.keys(current_subs).forEach(function (sub) {
-        _this._emitter.off(current_subs[sub], sub);
-      });
-    }
-  }]);
-
-  return SubscriptionTracker;
-}();
-
-},{}],12:[function(require,module,exports){
-(function (global){
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-
-var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
-
-var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
-
-var _events = require("./events");
-
-var _events2 = _interopRequireDefault(_events);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-
-var Var = function () {
-  function Var(group, name, /*optional*/value) {
-    _classCallCheck(this, Var);
-
-    this._group = group;
-    this._name = name;
-    this._value = value;
-    this._events = new _events2.default();
-  }
-
-  _createClass(Var, [{
-    key: "get",
-    value: function get() {
-      return this._value;
-    }
-  }, {
-    key: "set",
-    value: function set(value, /*optional*/event) {
-      if (this._value === value) {
-        // Do nothing; the value hasn't changed
-        return;
-      }
-      var oldValue = this._value;
-      this._value = value;
-      // Alert JavaScript listeners that the value has changed
-      var evt = {};
-      if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") {
-        for (var k in event) {
-          if (event.hasOwnProperty(k)) evt[k] = event[k];
-        }
-      }
-      evt.oldValue = oldValue;
-      evt.value = value;
-      this._events.trigger("change", evt, this);
-
-      // TODO: Make this extensible, to let arbitrary back-ends know that
-      // something has changed
-      if (global.Shiny && global.Shiny.onInputChange) {
-        global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value);
-      }
-    }
-  }, {
-    key: "on",
-    value: function on(eventType, listener) {
-      return this._events.on(eventType, listener);
-    }
-  }, {
-    key: "off",
-    value: function off(eventType, listener) {
-      return this._events.off(eventType, listener);
-    }
-  }]);
-
-  return Var;
-}();
-
-exports.default = Var;
-
-}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
-
-},{"./events":1}]},{},[5])
-//# sourceMappingURL=crosstalk.js.map
diff --git a/articles/files_files/crosstalk-1.2.1/js/crosstalk.js.map b/articles/files_files/crosstalk-1.2.1/js/crosstalk.js.map
deleted file mode 100644
index cff94f0..0000000
--- a/articles/files_files/crosstalk-1.2.1/js/crosstalk.js.map
+++ /dev/null
@@ -1,37 +0,0 @@
-{
-  "version": 3,
-  "sources": [
-    "node_modules/browser-pack/_prelude.js",
-    "javascript/src/events.js",
-    "javascript/src/filter.js",
-    "javascript/src/filterset.js",
-    "javascript/src/group.js",
-    "javascript/src/index.js",
-    "javascript/src/input.js",
-    "javascript/src/input_checkboxgroup.js",
-    "javascript/src/input_selectize.js",
-    "javascript/src/input_slider.js",
-    "javascript/src/selection.js",
-    "javascript/src/util.js",
-    "javascript/src/var.js"
-  ],
-  "names": [],
-  "mappings": 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-  "file": "generated.js",
-  "sourceRoot": "",
-  "sourcesContent": [
-    "(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()",
-    "export default class Events {\n  constructor() {\n    this._types = {};\n    this._seq = 0;\n  }\n\n  on(eventType, listener) {\n    let subs = this._types[eventType];\n    if (!subs) {\n      subs = this._types[eventType] = {};\n    }\n    let sub = \"sub\" + (this._seq++);\n    subs[sub] = listener;\n    return sub;\n  }\n\n  // Returns false if no match, or string for sub name if matched\n  off(eventType, listener) {\n    let subs = this._types[eventType];\n    if (typeof(listener) === \"function\") {\n      for (let key in subs) {\n        if (subs.hasOwnProperty(key)) {\n          if (subs[key] === listener) {\n            delete subs[key];\n            return key;\n          }\n        }\n      }\n      return false;\n    } else if (typeof(listener) === \"string\") {\n      if (subs && subs[listener]) {\n        delete subs[listener];\n        return listener;\n      }\n      return false;\n    } else {\n      throw new Error(\"Unexpected type for listener\");\n    }\n  }\n\n  trigger(eventType, arg, thisObj) {\n    let subs = this._types[eventType];\n    for (let key in subs) {\n      if (subs.hasOwnProperty(key)) {\n        subs[key].call(thisObj, arg);\n      }\n    }\n  }\n}\n",
-    "import Events from \"./events\";\nimport FilterSet from \"./filterset\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nfunction getFilterSet(group) {\n  let fsVar = group.var(\"filterset\");\n  let result = fsVar.get();\n  if (!result) {\n    result = new FilterSet();\n    fsVar.set(result);\n  }\n  return result;\n}\n\nlet id = 1;\nfunction nextId() {\n  return id++;\n}\n\n/**\n * Use this class to contribute to, and listen for changes to, the filter set\n * for the given group of widgets. Filter input controls should create one\n * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that\n * wish to displayed filtered data should create one `FilterHandle` and use\n * the {@link FilterHandle#filteredKeys} property and listen for change\n * events.\n *\n * If two (or more) `FilterHandle` instances in the same webpage share the\n * same group name, they will contribute to a single \"filter set\". Each\n * `FilterHandle` starts out with a `null` value, which means they take\n * nothing away from the set of data that should be shown. To make a\n * `FilterHandle` actually remove data from the filter set, set its value to\n * an array of keys which should be displayed. Crosstalk will aggregate the\n * various key arrays by finding their intersection; only keys that are\n * present in all non-null filter handles are considered part of the filter\n * set.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the {@link FilterHandle#setGroup} method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class FilterHandle {\n  constructor(group, extraInfo) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The filterSet that we're tracking, if any. Can change over time.\n    this._filterSet = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._filterVar = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this._id = \"filter\" + nextId();\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this FilterHandle. If `set()` was\n   * previously called on this handle, switching groups will clear those keys\n   * from the old group's filter set. These keys will not be applied to the new\n   * group's filter set either. In other words, `setGroup()` effectively calls\n   * `clear()` before switching groups.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._filterVar) {\n      this._filterVar.off(\"change\", this._varOnChangeSub);\n      this.clear();\n      this._varOnChangeSub = null;\n      this._filterVar = null;\n      this._filterSet = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      group = grp(group);\n      this._filterSet = getFilterSet(group);\n      this._filterVar = grp(group).var(\"filter\");\n      let sub = this._filterVar.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Combine the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Close the handle. This clears this handle's contribution to the filter set,\n   * and unsubscribes all event listeners.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.clear();\n    this.setGroup(null);\n  }\n\n  /**\n   * Clear this handle's contribution to the filter set.\n   *\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  clear(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.clear(this._id);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * Set this handle's contribution to the filter set. This array should consist\n   * of the keys of the rows that _should_ be displayed; any keys that are not\n   * present in the array will be considered _filtered out_. Note that multiple\n   * `FilterHandle` instances in the group may each contribute an array of keys,\n   * and only those keys that appear in _all_ of the arrays make it through the\n   * filter.\n   *\n   * @param {string[]} keys - Empty array, or array of keys. To clear the\n   *   filter, don't pass an empty array; instead, use the\n   *   {@link FilterHandle#clear} method.\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  set(keys, extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.update(this._id, keys);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * @return {string[]|null} - Either: 1) an array of keys that made it through\n   *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n   *   is being applied (all data should be displayed).\n   */\n  get filteredKeys() {\n    return this._filterSet ? this._filterSet.value : null;\n  }\n\n  /**\n   * Subscribe to events on this `FilterHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {FilterHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancel event subscriptions created by {@link FilterHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|FilterHandle~listener} listener - Either the callback\n   *   function previously passed into {@link FilterHandle#on}, or the\n   *   string that was returned from {@link FilterHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  _onChange(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * @callback FilterHandle~listener\n   * @param {Object} event - An object containing details of the event. For\n   *   `\"change\"` events, this includes the properties `value` (the new\n   *   value of the filter set, or `null` if no filter set is active),\n   *   `oldValue` (the previous value of the filter set), and `sender` (the\n   *   `FilterHandle` instance that made the change).\n   */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n *   if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n *   changed the value.\n */\n",
-    "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n  if (a === b) {\n    return 0;\n  } else if (a < b) {\n    return -1;\n  } else if (a > b) {\n    return 1;\n  }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n  constructor() {\n    this.reset();\n  }\n\n  reset() {\n    // Key: handle ID, Value: array of selected keys, or null\n    this._handles = {};\n    // Key: key string, Value: count of handles that include it\n    this._keys = {};\n    this._value = null;\n    this._activeHandles = 0;\n  }\n\n  get value() {\n    return this._value;\n  }\n\n  update(handleId, keys) {\n    if (keys !== null) {\n      keys = keys.slice(0); // clone before sorting\n      keys.sort(naturalComparator);\n    }\n\n    let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n    this._handles[handleId] = keys;\n\n    for (let i = 0; i < added.length; i++) {\n      this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n    }\n    for (let i = 0; i < removed.length; i++) {\n      this._keys[removed[i]]--;\n    }\n\n    this._updateValue(keys);\n  }\n\n  /**\n   * @param {string[]} keys Sorted array of strings that indicate\n   * a superset of possible keys.\n   * @private\n   */\n  _updateValue(keys = this._allKeys) {\n    let handleCount = Object.keys(this._handles).length;\n    if (handleCount === 0) {\n      this._value = null;\n    } else {\n      this._value = [];\n      for (let i = 0; i < keys.length; i++) {\n        let count = this._keys[keys[i]];\n        if (count === handleCount) {\n          this._value.push(keys[i]);\n        }\n      }\n    }\n  }\n\n  clear(handleId) {\n    if (typeof(this._handles[handleId]) === \"undefined\") {\n      return;\n    }\n\n    let keys = this._handles[handleId];\n    if (!keys) {\n      keys = [];\n    }\n\n    for (let i = 0; i < keys.length; i++) {\n      this._keys[keys[i]]--;\n    }\n    delete this._handles[handleId];\n\n    this._updateValue();\n  }\n\n  get _allKeys() {\n    let allKeys = Object.keys(this._keys);\n    allKeys.sort(naturalComparator);\n    return allKeys;\n  }\n}\n",
-    "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n  if (groupName && typeof(groupName) === \"string\") {\n    if (!groups.hasOwnProperty(groupName)) {\n      groups[groupName] = new Group(groupName);\n    }\n    return groups[groupName];\n  } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n    // Appears to already be a group object\n    return groupName;\n  } else if (Array.isArray(groupName) &&\n      groupName.length == 1 &&\n      typeof(groupName[0]) === \"string\") {\n    return group(groupName[0]);\n  } else {\n    throw new Error(\"Invalid groupName argument\");\n  }\n}\n\nclass Group {\n  constructor(name) {\n    this.name = name;\n    this._vars = {};\n  }\n\n  var(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    if (!this._vars.hasOwnProperty(name))\n      this._vars[name] = new Var(this, name);\n    return this._vars[name];\n  }\n\n  has(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    return this._vars.hasOwnProperty(name);\n  }\n}\n",
-    "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n  return defaultGroup.var(name);\n}\n\nfunction has(name) {\n  return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n  global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n    if (typeof(message.group) === \"string\") {\n      group(message.group).var(message.name).set(message.value);\n    } else {\n      var_(message.name).set(message.value);\n    }\n  });\n}\n\nconst crosstalk = {\n  group: group,\n  var: var_,\n  has: has,\n  SelectionHandle: SelectionHandle,\n  FilterHandle: FilterHandle,\n  bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n",
-    "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n  bindings[reg.className] = reg;\n  if (global.document && global.document.readyState !== \"complete\") {\n    $(() => {\n      bind();\n    });\n  } else if (global.document) {\n    setTimeout(bind, 100);\n  }\n}\n\nexport function bind() {\n  Object.keys(bindings).forEach(function(className) {\n    let binding = bindings[className];\n    $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n      bindInstance(binding, el);\n    });\n  });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n  return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n  let $el = $(el);\n  Object.keys(bindings).forEach(function(className) {\n    if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n      let binding = bindings[className];\n      bindInstance(binding, el);\n    }\n  });\n}\n\nfunction bindInstance(binding, el) {\n  let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n  let data = JSON.parse(jsonEl[0].innerText);\n\n  let instance = binding.factory(el, data);\n  $(el).data(\"crosstalk-instance\", instance);\n  $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n  let inputBinding = new global.Shiny.InputBinding();\n  let $ = global.jQuery;\n  $.extend(inputBinding, {\n    find: function(scope) {\n      return $(scope).find(\".crosstalk-input\");\n    },\n    initialize: function(el) {\n      if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n        bindEl(el);\n      }\n    },\n    getId: function(el) {\n      return el.id;\n    },\n    getValue: function(el) {\n\n    },\n    setValue: function(el, value) {\n\n    },\n    receiveMessage: function(el, data) {\n\n    },\n    subscribe: function(el, callback) {\n      $(el).data(\"crosstalk-instance\").resume();\n    },\n    unsubscribe: function(el) {\n      $(el).data(\"crosstalk-instance\").suspend();\n    }\n  });\n  global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n",
-    "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-checkboxgroup\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    let $el = $(el);\n    $el.on(\"change\", \"input[type='checkbox']\", function() {\n      let checked = $el.find(\"input[type='checkbox']:checked\");\n      if (checked.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        checked.each(function() {\n          data.map[this.value].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n",
-    "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-select\",\n\n  factory: function(el, data) {\n    /*\n     * items: {value: [...], label: [...]}\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n\n    let first = [{value: \"\", label: \"(All)\"}];\n    let items = util.dataframeToD3(data.items);\n    let opts = {\n      options: first.concat(items),\n      valueField: \"value\",\n      labelField: \"label\",\n      searchField: \"label\"\n    };\n\n    let select = $(el).find(\"select\")[0];\n\n    let selectize = $(select).selectize(opts)[0].selectize;\n\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    selectize.on(\"change\", function() {\n      if (selectize.items.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        selectize.items.forEach(function(group) {\n          data.map[group].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n",
-    "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n  className: \"crosstalk-input-slider\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let opts = {};\n    let $el = $(el).find(\"input\");\n    let dataType = $el.data(\"data-type\");\n    let timeFormat = $el.data(\"time-format\");\n    let round = $el.data(\"round\");\n    let timeFormatter;\n\n    // Set up formatting functions\n    if (dataType === \"date\") {\n      timeFormatter = strftime.utc();\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n\n    } else if (dataType === \"datetime\") {\n      let timezone = $el.data(\"timezone\");\n      if (timezone)\n        timeFormatter = strftime.timezone(timezone);\n      else\n        timeFormatter = strftime;\n\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n    } else if (dataType === \"number\") {\n      if (typeof round !== \"undefined\")\n        opts.prettify = function(num) {\n          let factor = Math.pow(10, round);\n          return Math.round(num * factor) / factor;\n        };\n    }\n\n    $el.ionRangeSlider(opts);\n\n    function getValue() {\n      let result = $el.data(\"ionRangeSlider\").result;\n\n      // Function for converting numeric value from slider to appropriate type.\n      let convert;\n      let dataType = $el.data(\"data-type\");\n      if (dataType === \"date\") {\n        convert = function(val) {\n          return formatDateUTC(new Date(+val));\n        };\n      } else if (dataType === \"datetime\") {\n        convert = function(val) {\n          // Convert ms to s\n          return +val / 1000;\n        };\n      } else {\n        convert = function(val) { return +val; };\n      }\n\n      if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n        return [convert(result.from), convert(result.to)];\n      } else {\n        return convert(result.from);\n      }\n    }\n\n    let lastKnownKeys = null;\n\n    $el.on(\"change.crosstalkSliderInput\", function(event) {\n      if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n        let [from, to] = getValue();\n        let keys = [];\n        for (let i = 0; i < data.values.length; i++) {\n          let val = data.values[i];\n          if (val >= from && val <= to) {\n            keys.push(data.keys[i]);\n          }\n        }\n        keys.sort();\n        ctHandle.set(keys);\n        lastKnownKeys = keys;\n      }\n    });\n\n\n    // let $el = $(el);\n    // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n    //   let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n    //   if (checked.length === 0) {\n    //     ctHandle.clear();\n    //   } else {\n    //     let keys = {};\n    //     checked.each(function() {\n    //       data.map[this.value].forEach(function(key) {\n    //         keys[key] = true;\n    //       });\n    //     });\n    //     let keyArray = Object.keys(keys);\n    //     keyArray.sort();\n    //     ctHandle.set(keyArray);\n    //   }\n    // });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n  let str = n.toString();\n  while (str.length < digits)\n    str = \"0\" + str;\n  return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n  if (date instanceof Date) {\n    return date.getUTCFullYear() + \"-\" +\n           padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n           padZeros(date.getUTCDate(), 2);\n\n  } else {\n    return null;\n  }\n}\n",
-    "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n  constructor(group = null, extraInfo = null) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._var = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this SelectionHandle. The group\n   * being switched away from (if any) will not have its selection value\n   * modified as a result of calling `setGroup`, even if this handle was the\n   * most recent handle to set the selection of the group.\n   *\n   * The group being switched to (if any) will also not have its selection value\n   * modified as a result of calling `setGroup`. If you want to set the\n   * selection value of the new group, call `set` explicitly.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._var) {\n      this._var.off(\"change\", this._varOnChangeSub);\n      this._var = null;\n      this._varOnChangeSub = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      this._var = grp(group).var(\"selection\");\n      let sub = this._var.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Retrieves the current selection for the group represented by this\n   * `SelectionHandle`.\n   *\n   * - If no selection is active, then this value will be falsy.\n   * - If a selection is active, but no data points are selected, then this\n   *   value will be an empty array.\n   * - If a selection is active, and data points are selected, then the keys\n   *   of the selected data points will be present in the array.\n   */\n  get value() {\n    return this._var ? this._var.get() : null;\n  }\n\n  /**\n   * Combines the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    // Important incidental effect: shallow clone is returned\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n   *   {@link SelectionHandle#value}).\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `SelectionHandle` constructor).\n   */\n  set(selectedKeys, extraInfo) {\n    if (this._var)\n      this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any that were passed\n   *   into the `SelectionHandle` constructor).\n   */\n  clear(extraInfo) {\n    if (this._var)\n      this.set(void 0, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Subscribes to events on this `SelectionHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {SelectionHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancels event subscriptions created by {@link SelectionHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|SelectionHandle~listener} listener - Either the callback\n   *   function previously passed into {@link SelectionHandle#on}, or the\n   *   string that was returned from {@link SelectionHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  /**\n   * Shuts down the `SelectionHandle` object.\n   *\n   * Removes all event listeners that were added through this handle.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.setGroup(null);\n  }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n *   `\"change\"` events, this includes the properties `value` (the new\n *   value of the selection, or `undefined` if no selection is active),\n *   `oldValue` (the previous value of the selection), and `sender` (the\n *   `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n *   if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n *   changed the value.\n */\n",
-    "export function extend(target, ...sources) {\n  for (let i = 0; i < sources.length; i++) {\n    let src = sources[i];\n    if (typeof(src) === \"undefined\" || src === null)\n      continue;\n\n    for (let key in src) {\n      if (src.hasOwnProperty(key)) {\n        target[key] = src[key];\n      }\n    }\n  }\n  return target;\n}\n\nexport function checkSorted(list) {\n  for (let i = 1; i < list.length; i++) {\n    if (list[i] <= list[i-1]) {\n      throw new Error(\"List is not sorted or contains duplicate\");\n    }\n  }\n}\n\nexport function diffSortedLists(a, b) {\n  let i_a = 0;\n  let i_b = 0;\n\n  if (!a) a = [];\n  if (!b) b = [];\n\n  let a_only = [];\n  let b_only = [];\n\n  checkSorted(a);\n  checkSorted(b);\n\n  while (i_a < a.length && i_b < b.length) {\n    if (a[i_a] === b[i_b]) {\n      i_a++;\n      i_b++;\n    } else if (a[i_a] < b[i_b]) {\n      a_only.push(a[i_a++]);\n    } else {\n      b_only.push(b[i_b++]);\n    }\n  }\n\n  if (i_a < a.length)\n    a_only = a_only.concat(a.slice(i_a));\n  if (i_b < b.length)\n    b_only = b_only.concat(b.slice(i_b));\n  return {\n    removed: a_only,\n    added: b_only\n  };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n  let names = [];\n  let length;\n  for (let name in df) {\n    if (df.hasOwnProperty(name))\n      names.push(name);\n    if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n      throw new Error(\"All fields must be arrays\");\n    } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n      throw new Error(\"All fields must be arrays of the same length\");\n    }\n    length = df[name].length;\n  }\n  let results = [];\n  let item;\n  for (let row = 0; row < length; row++) {\n    item = {};\n    for (let col = 0; col < names.length; col++) {\n      item[names[col]] = df[names[col]][row];\n    }\n    results.push(item);\n  }\n  return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n  constructor(emitter) {\n    this._emitter = emitter;\n    this._subs = {};\n  }\n\n  on(eventType, listener) {\n    let sub = this._emitter.on(eventType, listener);\n    this._subs[sub] = eventType;\n    return sub;\n  }\n\n  off(eventType, listener) {\n    let sub = this._emitter.off(eventType, listener);\n    if (sub) {\n      delete this._subs[sub];\n    }\n    return sub;\n  }\n\n  removeAllListeners() {\n    let current_subs = this._subs;\n    this._subs = {};\n    Object.keys(current_subs).forEach((sub) => {\n      this._emitter.off(current_subs[sub], sub);\n    });\n  }\n}\n",
-    "import Events from \"./events\";\n\nexport default class Var {\n  constructor(group, name, /*optional*/ value) {\n    this._group = group;\n    this._name = name;\n    this._value = value;\n    this._events = new Events();\n  }\n\n  get() {\n    return this._value;\n  }\n\n  set(value, /*optional*/ event) {\n    if (this._value === value) {\n      // Do nothing; the value hasn't changed\n      return;\n    }\n    let oldValue = this._value;\n    this._value = value;\n    // Alert JavaScript listeners that the value has changed\n    let evt = {};\n    if (event && typeof(event) === \"object\") {\n      for (let k in event) {\n        if (event.hasOwnProperty(k))\n          evt[k] = event[k];\n      }\n    }\n    evt.oldValue = oldValue;\n    evt.value = value;\n    this._events.trigger(\"change\", evt, this);\n\n    // TODO: Make this extensible, to let arbitrary back-ends know that\n    // something has changed\n    if (global.Shiny && global.Shiny.onInputChange) {\n      global.Shiny.onInputChange(\n        \".clientValue-\" +\n          (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n          this._name,\n        typeof(value) === \"undefined\" ? null : value\n      );\n    }\n  }\n\n  on(eventType, listener) {\n    return this._events.on(eventType, listener);\n  }\n\n  off(eventType, listener) {\n    return this._events.off(eventType, listener);\n  }\n}\n"
-  ]
-}
\ No newline at end of file
diff --git a/articles/files_files/crosstalk-1.2.1/js/crosstalk.min.js b/articles/files_files/crosstalk-1.2.1/js/crosstalk.min.js
deleted file mode 100644
index b7ec0ac..0000000
--- a/articles/files_files/crosstalk-1.2.1/js/crosstalk.min.js
+++ /dev/null
@@ -1,2 +0,0 @@
-!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e<l.length;e++)s(l[e]);return s}({1:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(){function r(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(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}();var i=function(){function e(){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,e),this._types={},this._seq=0}return r(e,[{key:"on",value:function(e,t){var n=this._types[e];n||(n=this._types[e]={});var r="sub"+this._seq++;return n[r]=t,r}},{key:"off",value:function(e,t){var n=this._types[e];if("function"==typeof t){for(var r in n)if(n.hasOwnProperty(r)&&n[r]===t)return delete n[r],r;return!1}if("string"==typeof t)return!(!n||!n[t])&&(delete n[t],t);throw new Error("Unexpected type for listener")}},{key:"trigger",value:function(e,t,n){var r=this._types[e];for(var i in r)r.hasOwnProperty(i)&&r[i].call(n,t)}}]),e}();n.default=i},{}],2:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0}),n.FilterHandle=void 0;var r=function(){function r(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(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),i=l(e("./events")),o=l(e("./filterset")),u=l(e("./group")),a=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(e("./util"));function l(e){return e&&e.__esModule?e:{default:e}}var s=1;n.FilterHandle=function(){function n(e,t){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,n),this._eventRelay=new i.default,this._emitter=new a.SubscriptionTracker(this._eventRelay),this._group=null,this._filterSet=null,this._filterVar=null,this._varOnChangeSub=null,this._extraInfo=a.extend({sender:this},t),this._id="filter"+s++,this.setGroup(e)}return r(n,[{key:"setGroup",value:function(e){var t,n,r=this;if(this._group!==e&&((this._group||e)&&(this._filterVar&&(this._filterVar.off("change",this._varOnChangeSub),this.clear(),this._varOnChangeSub=null,this._filterVar=null,this._filterSet=null),this._group=e))){e=(0,u.default)(e),this._filterSet=(t=e.var("filterset"),(n=t.get())||(n=new o.default,t.set(n)),n),this._filterVar=(0,u.default)(e).var("filter");var i=this._filterVar.on("change",function(e){r._eventRelay.trigger("change",e,r)});this._varOnChangeSub=i}}},{key:"_mergeExtraInfo",value:function(e){return a.extend({},this._extraInfo?this._extraInfo:null,e||null)}},{key:"close",value:function(){this._emitter.removeAllListeners(),this.clear(),this.setGroup(null)}},{key:"clear",value:function(e){this._filterSet&&(this._filterSet.clear(this._id),this._onChange(e))}},{key:"set",value:function(e,t){this._filterSet&&(this._filterSet.update(this._id,e),this._onChange(t))}},{key:"on",value:function(e,t){return this._emitter.on(e,t)}},{key:"off",value:function(e,t){return this._emitter.off(e,t)}},{key:"_onChange",value:function(e){this._filterSet&&this._filterVar.set(this._filterSet.value,this._mergeExtraInfo(e))}},{key:"filteredKeys",get:function(){return this._filterSet?this._filterSet.value:null}}]),n}()},{"./events":1,"./filterset":3,"./group":4,"./util":11}],3:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(){function r(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(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),a=e("./util");function l(e,t){return e===t?0:e<t?-1:t<e?1:void 0}var i=function(){function e(){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,e),this.reset()}return r(e,[{key:"reset",value:function(){this._handles={},this._keys={},this._value=null,this._activeHandles=0}},{key:"update",value:function(e,t){null!==t&&(t=t.slice(0)).sort(l);var n=(0,a.diffSortedLists)(this._handles[e],t),r=n.added,i=n.removed;this._handles[e]=t;for(var o=0;o<r.length;o++)this._keys[r[o]]=(this._keys[r[o]]||0)+1;for(var u=0;u<i.length;u++)this._keys[i[u]]--;this._updateValue(t)}},{key:"_updateValue",value:function(){var e=0<arguments.length&&void 0!==arguments[0]?arguments[0]:this._allKeys,t=Object.keys(this._handles).length;if(0===t)this._value=null;else{this._value=[];for(var n=0;n<e.length;n++){this._keys[e[n]]===t&&this._value.push(e[n])}}}},{key:"clear",value:function(e){if(void 0!==this._handles[e]){var t=this._handles[e];t||(t=[]);for(var n=0;n<t.length;n++)this._keys[t[n]]--;delete this._handles[e],this._updateValue()}}},{key:"value",get:function(){return this._value}},{key:"_allKeys",get:function(){var e=Object.keys(this._keys);return e.sort(l),e}}]),e}();n.default=i},{"./util":11}],4:[function(l,e,s){(function(e){"use strict";Object.defineProperty(s,"__esModule",{value:!0});var n=function(){function r(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(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),r="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};s.default=function e(t){{if(t&&"string"==typeof t)return u.hasOwnProperty(t)||(u[t]=new a(t)),u[t];if("object"===(void 0===t?"undefined":r(t))&&t._vars&&t.var)return t;if(Array.isArray(t)&&1==t.length&&"string"==typeof t[0])return e(t[0]);throw new Error("Invalid groupName argument")}};var t,i=l("./var"),o=(t=i)&&t.__esModule?t:{default:t};e.__crosstalk_groups=e.__crosstalk_groups||{};var u=e.__crosstalk_groups;var a=function(){function t(e){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,t),this.name=e,this._vars={}}return n(t,[{key:"var",value:function(e){if(!e||"string"!=typeof e)throw new Error("Invalid var name");return this._vars.hasOwnProperty(e)||(this._vars[e]=new o.default(this,e)),this._vars[e]}},{key:"has",value:function(e){if(!e||"string"!=typeof e)throw new Error("Invalid var name");return 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e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()","export default class Events {\n  constructor() {\n    this._types = {};\n    this._seq = 0;\n  }\n\n  on(eventType, listener) {\n    let subs = this._types[eventType];\n    if (!subs) {\n      subs = this._types[eventType] = {};\n    }\n    let sub = \"sub\" + (this._seq++);\n    subs[sub] = listener;\n    return sub;\n  }\n\n  // Returns false if no match, or string for sub name if matched\n  off(eventType, listener) {\n    let subs = this._types[eventType];\n    if (typeof(listener) === \"function\") {\n      for (let key in subs) {\n        if (subs.hasOwnProperty(key)) {\n          if (subs[key] === listener) {\n            delete subs[key];\n            return key;\n          }\n        }\n      }\n      return false;\n    } else if (typeof(listener) === \"string\") {\n      if (subs && subs[listener]) {\n        delete subs[listener];\n        return listener;\n      }\n      return false;\n    } else {\n      throw new Error(\"Unexpected type for listener\");\n    }\n  }\n\n  trigger(eventType, arg, thisObj) {\n    let subs = this._types[eventType];\n    for (let key in subs) {\n      if (subs.hasOwnProperty(key)) {\n        subs[key].call(thisObj, arg);\n      }\n    }\n  }\n}\n","import Events from \"./events\";\nimport FilterSet from \"./filterset\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nfunction getFilterSet(group) {\n  let fsVar = group.var(\"filterset\");\n  let result = fsVar.get();\n  if (!result) {\n    result = new FilterSet();\n    fsVar.set(result);\n  }\n  return result;\n}\n\nlet id = 1;\nfunction nextId() {\n  return id++;\n}\n\n/**\n * Use this class to contribute to, and listen for changes to, the filter set\n * for the given group of widgets. Filter input controls should create one\n * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that\n * wish to displayed filtered data should create one `FilterHandle` and use\n * the {@link FilterHandle#filteredKeys} property and listen for change\n * events.\n *\n * If two (or more) `FilterHandle` instances in the same webpage share the\n * same group name, they will contribute to a single \"filter set\". Each\n * `FilterHandle` starts out with a `null` value, which means they take\n * nothing away from the set of data that should be shown. To make a\n * `FilterHandle` actually remove data from the filter set, set its value to\n * an array of keys which should be displayed. Crosstalk will aggregate the\n * various key arrays by finding their intersection; only keys that are\n * present in all non-null filter handles are considered part of the filter\n * set.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the {@link FilterHandle#setGroup} method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class FilterHandle {\n  constructor(group, extraInfo) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The filterSet that we're tracking, if any. Can change over time.\n    this._filterSet = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._filterVar = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this._id = \"filter\" + nextId();\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this FilterHandle. If `set()` was\n   * previously called on this handle, switching groups will clear those keys\n   * from the old group's filter set. These keys will not be applied to the new\n   * group's filter set either. In other words, `setGroup()` effectively calls\n   * `clear()` before switching groups.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._filterVar) {\n      this._filterVar.off(\"change\", this._varOnChangeSub);\n      this.clear();\n      this._varOnChangeSub = null;\n      this._filterVar = null;\n      this._filterSet = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      group = grp(group);\n      this._filterSet = getFilterSet(group);\n      this._filterVar = grp(group).var(\"filter\");\n      let sub = this._filterVar.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Combine the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Close the handle. This clears this handle's contribution to the filter set,\n   * and unsubscribes all event listeners.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.clear();\n    this.setGroup(null);\n  }\n\n  /**\n   * Clear this handle's contribution to the filter set.\n   *\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  clear(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.clear(this._id);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * Set this handle's contribution to the filter set. This array should consist\n   * of the keys of the rows that _should_ be displayed; any keys that are not\n   * present in the array will be considered _filtered out_. Note that multiple\n   * `FilterHandle` instances in the group may each contribute an array of keys,\n   * and only those keys that appear in _all_ of the arrays make it through the\n   * filter.\n   *\n   * @param {string[]} keys - Empty array, or array of keys. To clear the\n   *   filter, don't pass an empty array; instead, use the\n   *   {@link FilterHandle#clear} method.\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  set(keys, extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.update(this._id, keys);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * @return {string[]|null} - Either: 1) an array of keys that made it through\n   *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n   *   is being applied (all data should be displayed).\n   */\n  get filteredKeys() {\n    return this._filterSet ? this._filterSet.value : null;\n  }\n\n  /**\n   * Subscribe to events on this `FilterHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {FilterHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancel event subscriptions created by {@link FilterHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|FilterHandle~listener} listener - Either the callback\n   *   function previously passed into {@link FilterHandle#on}, or the\n   *   string that was returned from {@link FilterHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  _onChange(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * @callback FilterHandle~listener\n   * @param {Object} event - An object containing details of the event. For\n   *   `\"change\"` events, this includes the properties `value` (the new\n   *   value of the filter set, or `null` if no filter set is active),\n   *   `oldValue` (the previous value of the filter set), and `sender` (the\n   *   `FilterHandle` instance that made the change).\n   */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n *   if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n *   changed the value.\n */\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n  if (a === b) {\n    return 0;\n  } else if (a < b) {\n    return -1;\n  } else if (a > b) {\n    return 1;\n  }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n  constructor() {\n    this.reset();\n  }\n\n  reset() {\n    // Key: handle ID, Value: array of selected keys, or null\n    this._handles = {};\n    // Key: key string, Value: count of handles that include it\n    this._keys = {};\n    this._value = null;\n    this._activeHandles = 0;\n  }\n\n  get value() {\n    return this._value;\n  }\n\n  update(handleId, keys) {\n    if (keys !== null) {\n      keys = keys.slice(0); // clone before sorting\n      keys.sort(naturalComparator);\n    }\n\n    let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n    this._handles[handleId] = keys;\n\n    for (let i = 0; i < added.length; i++) {\n      this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n    }\n    for (let i = 0; i < removed.length; i++) {\n      this._keys[removed[i]]--;\n    }\n\n    this._updateValue(keys);\n  }\n\n  /**\n   * @param {string[]} keys Sorted array of strings that indicate\n   * a superset of possible keys.\n   * @private\n   */\n  _updateValue(keys = this._allKeys) {\n    let handleCount = Object.keys(this._handles).length;\n    if (handleCount === 0) {\n      this._value = null;\n    } else {\n      this._value = [];\n      for (let i = 0; i < keys.length; i++) {\n        let count = this._keys[keys[i]];\n        if (count === handleCount) {\n          this._value.push(keys[i]);\n        }\n      }\n    }\n  }\n\n  clear(handleId) {\n    if (typeof(this._handles[handleId]) === \"undefined\") {\n      return;\n    }\n\n    let keys = this._handles[handleId];\n    if (!keys) {\n      keys = [];\n    }\n\n    for (let i = 0; i < keys.length; i++) {\n      this._keys[keys[i]]--;\n    }\n    delete this._handles[handleId];\n\n    this._updateValue();\n  }\n\n  get _allKeys() {\n    let allKeys = Object.keys(this._keys);\n    allKeys.sort(naturalComparator);\n    return allKeys;\n  }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n  if (groupName && typeof(groupName) === \"string\") {\n    if (!groups.hasOwnProperty(groupName)) {\n      groups[groupName] = new Group(groupName);\n    }\n    return groups[groupName];\n  } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n    // Appears to already be a group object\n    return groupName;\n  } else if (Array.isArray(groupName) &&\n      groupName.length == 1 &&\n      typeof(groupName[0]) === \"string\") {\n    return group(groupName[0]);\n  } else {\n    throw new Error(\"Invalid groupName argument\");\n  }\n}\n\nclass Group {\n  constructor(name) {\n    this.name = name;\n    this._vars = {};\n  }\n\n  var(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    if (!this._vars.hasOwnProperty(name))\n      this._vars[name] = new Var(this, name);\n    return this._vars[name];\n  }\n\n  has(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    return this._vars.hasOwnProperty(name);\n  }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n  return defaultGroup.var(name);\n}\n\nfunction has(name) {\n  return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n  global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n    if (typeof(message.group) === \"string\") {\n      group(message.group).var(message.name).set(message.value);\n    } else {\n      var_(message.name).set(message.value);\n    }\n  });\n}\n\nconst crosstalk = {\n  group: group,\n  var: var_,\n  has: has,\n  SelectionHandle: SelectionHandle,\n  FilterHandle: FilterHandle,\n  bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n  bindings[reg.className] = reg;\n  if (global.document && global.document.readyState !== \"complete\") {\n    $(() => {\n      bind();\n    });\n  } else if (global.document) {\n    setTimeout(bind, 100);\n  }\n}\n\nexport function bind() {\n  Object.keys(bindings).forEach(function(className) {\n    let binding = bindings[className];\n    $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n      bindInstance(binding, el);\n    });\n  });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n  return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n  let $el = $(el);\n  Object.keys(bindings).forEach(function(className) {\n    if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n      let binding = bindings[className];\n      bindInstance(binding, el);\n    }\n  });\n}\n\nfunction bindInstance(binding, el) {\n  let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n  let data = JSON.parse(jsonEl[0].innerText);\n\n  let instance = binding.factory(el, data);\n  $(el).data(\"crosstalk-instance\", instance);\n  $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n  let inputBinding = new global.Shiny.InputBinding();\n  let $ = global.jQuery;\n  $.extend(inputBinding, {\n    find: function(scope) {\n      return $(scope).find(\".crosstalk-input\");\n    },\n    initialize: function(el) {\n      if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n        bindEl(el);\n      }\n    },\n    getId: function(el) {\n      return el.id;\n    },\n    getValue: function(el) {\n\n    },\n    setValue: function(el, value) {\n\n    },\n    receiveMessage: function(el, data) {\n\n    },\n    subscribe: function(el, callback) {\n      $(el).data(\"crosstalk-instance\").resume();\n    },\n    unsubscribe: function(el) {\n      $(el).data(\"crosstalk-instance\").suspend();\n    }\n  });\n  global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-checkboxgroup\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    let $el = $(el);\n    $el.on(\"change\", \"input[type='checkbox']\", function() {\n      let checked = $el.find(\"input[type='checkbox']:checked\");\n      if (checked.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        checked.each(function() {\n          data.map[this.value].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-select\",\n\n  factory: function(el, data) {\n    /*\n     * items: {value: [...], label: [...]}\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n\n    let first = [{value: \"\", label: \"(All)\"}];\n    let items = util.dataframeToD3(data.items);\n    let opts = {\n      options: first.concat(items),\n      valueField: \"value\",\n      labelField: \"label\",\n      searchField: \"label\"\n    };\n\n    let select = $(el).find(\"select\")[0];\n\n    let selectize = $(select).selectize(opts)[0].selectize;\n\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    selectize.on(\"change\", function() {\n      if (selectize.items.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        selectize.items.forEach(function(group) {\n          data.map[group].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n  className: \"crosstalk-input-slider\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let opts = {};\n    let $el = $(el).find(\"input\");\n    let dataType = $el.data(\"data-type\");\n    let timeFormat = $el.data(\"time-format\");\n    let round = $el.data(\"round\");\n    let timeFormatter;\n\n    // Set up formatting functions\n    if (dataType === \"date\") {\n      timeFormatter = strftime.utc();\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n\n    } else if (dataType === \"datetime\") {\n      let timezone = $el.data(\"timezone\");\n      if (timezone)\n        timeFormatter = strftime.timezone(timezone);\n      else\n        timeFormatter = strftime;\n\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n    } else if (dataType === \"number\") {\n      if (typeof round !== \"undefined\")\n        opts.prettify = function(num) {\n          let factor = Math.pow(10, round);\n          return Math.round(num * factor) / factor;\n        };\n    }\n\n    $el.ionRangeSlider(opts);\n\n    function getValue() {\n      let result = $el.data(\"ionRangeSlider\").result;\n\n      // Function for converting numeric value from slider to appropriate type.\n      let convert;\n      let dataType = $el.data(\"data-type\");\n      if (dataType === \"date\") {\n        convert = function(val) {\n          return formatDateUTC(new Date(+val));\n        };\n      } else if (dataType === \"datetime\") {\n        convert = function(val) {\n          // Convert ms to s\n          return +val / 1000;\n        };\n      } else {\n        convert = function(val) { return +val; };\n      }\n\n      if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n        return [convert(result.from), convert(result.to)];\n      } else {\n        return convert(result.from);\n      }\n    }\n\n    let lastKnownKeys = null;\n\n    $el.on(\"change.crosstalkSliderInput\", function(event) {\n      if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n        let [from, to] = getValue();\n        let keys = [];\n        for (let i = 0; i < data.values.length; i++) {\n          let val = data.values[i];\n          if (val >= from && val <= to) {\n            keys.push(data.keys[i]);\n          }\n        }\n        keys.sort();\n        ctHandle.set(keys);\n        lastKnownKeys = keys;\n      }\n    });\n\n\n    // let $el = $(el);\n    // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n    //   let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n    //   if (checked.length === 0) {\n    //     ctHandle.clear();\n    //   } else {\n    //     let keys = {};\n    //     checked.each(function() {\n    //       data.map[this.value].forEach(function(key) {\n    //         keys[key] = true;\n    //       });\n    //     });\n    //     let keyArray = Object.keys(keys);\n    //     keyArray.sort();\n    //     ctHandle.set(keyArray);\n    //   }\n    // });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n  let str = n.toString();\n  while (str.length < digits)\n    str = \"0\" + str;\n  return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n  if (date instanceof Date) {\n    return date.getUTCFullYear() + \"-\" +\n           padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n           padZeros(date.getUTCDate(), 2);\n\n  } else {\n    return null;\n  }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n  constructor(group = null, extraInfo = null) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._var = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this SelectionHandle. The group\n   * being switched away from (if any) will not have its selection value\n   * modified as a result of calling `setGroup`, even if this handle was the\n   * most recent handle to set the selection of the group.\n   *\n   * The group being switched to (if any) will also not have its selection value\n   * modified as a result of calling `setGroup`. If you want to set the\n   * selection value of the new group, call `set` explicitly.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._var) {\n      this._var.off(\"change\", this._varOnChangeSub);\n      this._var = null;\n      this._varOnChangeSub = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      this._var = grp(group).var(\"selection\");\n      let sub = this._var.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Retrieves the current selection for the group represented by this\n   * `SelectionHandle`.\n   *\n   * - If no selection is active, then this value will be falsy.\n   * - If a selection is active, but no data points are selected, then this\n   *   value will be an empty array.\n   * - If a selection is active, and data points are selected, then the keys\n   *   of the selected data points will be present in the array.\n   */\n  get value() {\n    return this._var ? this._var.get() : null;\n  }\n\n  /**\n   * Combines the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    // Important incidental effect: shallow clone is returned\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n   *   {@link SelectionHandle#value}).\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `SelectionHandle` constructor).\n   */\n  set(selectedKeys, extraInfo) {\n    if (this._var)\n      this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any that were passed\n   *   into the `SelectionHandle` constructor).\n   */\n  clear(extraInfo) {\n    if (this._var)\n      this.set(void 0, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Subscribes to events on this `SelectionHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {SelectionHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancels event subscriptions created by {@link SelectionHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|SelectionHandle~listener} listener - Either the callback\n   *   function previously passed into {@link SelectionHandle#on}, or the\n   *   string that was returned from {@link SelectionHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  /**\n   * Shuts down the `SelectionHandle` object.\n   *\n   * Removes all event listeners that were added through this handle.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.setGroup(null);\n  }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n *   `\"change\"` events, this includes the properties `value` (the new\n *   value of the selection, or `undefined` if no selection is active),\n *   `oldValue` (the previous value of the selection), and `sender` (the\n *   `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n *   if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n *   changed the value.\n */\n","export function extend(target, ...sources) {\n  for (let i = 0; i < sources.length; i++) {\n    let src = sources[i];\n    if (typeof(src) === \"undefined\" || src === null)\n      continue;\n\n    for (let key in src) {\n      if (src.hasOwnProperty(key)) {\n        target[key] = src[key];\n      }\n    }\n  }\n  return target;\n}\n\nexport function checkSorted(list) {\n  for (let i = 1; i < list.length; i++) {\n    if (list[i] <= list[i-1]) {\n      throw new Error(\"List is not sorted or contains duplicate\");\n    }\n  }\n}\n\nexport function diffSortedLists(a, b) {\n  let i_a = 0;\n  let i_b = 0;\n\n  if (!a) a = [];\n  if (!b) b = [];\n\n  let a_only = [];\n  let b_only = [];\n\n  checkSorted(a);\n  checkSorted(b);\n\n  while (i_a < a.length && i_b < b.length) {\n    if (a[i_a] === b[i_b]) {\n      i_a++;\n      i_b++;\n    } else if (a[i_a] < b[i_b]) {\n      a_only.push(a[i_a++]);\n    } else {\n      b_only.push(b[i_b++]);\n    }\n  }\n\n  if (i_a < a.length)\n    a_only = a_only.concat(a.slice(i_a));\n  if (i_b < b.length)\n    b_only = b_only.concat(b.slice(i_b));\n  return {\n    removed: a_only,\n    added: b_only\n  };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n  let names = [];\n  let length;\n  for (let name in df) {\n    if (df.hasOwnProperty(name))\n      names.push(name);\n    if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n      throw new Error(\"All fields must be arrays\");\n    } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n      throw new Error(\"All fields must be arrays of the same length\");\n    }\n    length = df[name].length;\n  }\n  let results = [];\n  let item;\n  for (let row = 0; row < length; row++) {\n    item = {};\n    for (let col = 0; col < names.length; col++) {\n      item[names[col]] = df[names[col]][row];\n    }\n    results.push(item);\n  }\n  return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n  constructor(emitter) {\n    this._emitter = emitter;\n    this._subs = {};\n  }\n\n  on(eventType, listener) {\n    let sub = this._emitter.on(eventType, listener);\n    this._subs[sub] = eventType;\n    return sub;\n  }\n\n  off(eventType, listener) {\n    let sub = this._emitter.off(eventType, listener);\n    if (sub) {\n      delete this._subs[sub];\n    }\n    return sub;\n  }\n\n  removeAllListeners() {\n    let current_subs = this._subs;\n    this._subs = {};\n    Object.keys(current_subs).forEach((sub) => {\n      this._emitter.off(current_subs[sub], sub);\n    });\n  }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n  constructor(group, name, /*optional*/ value) {\n    this._group = group;\n    this._name = name;\n    this._value = value;\n    this._events = new Events();\n  }\n\n  get() {\n    return this._value;\n  }\n\n  set(value, /*optional*/ event) {\n    if (this._value === value) {\n      // Do nothing; the value hasn't changed\n      return;\n    }\n    let oldValue = this._value;\n    this._value = value;\n    // Alert JavaScript listeners that the value has changed\n    let evt = {};\n    if (event && typeof(event) === \"object\") {\n      for (let k in event) {\n        if (event.hasOwnProperty(k))\n          evt[k] = event[k];\n      }\n    }\n    evt.oldValue = oldValue;\n    evt.value = value;\n    this._events.trigger(\"change\", evt, this);\n\n    // TODO: Make this extensible, to let arbitrary back-ends know that\n    // something has changed\n    if (global.Shiny && global.Shiny.onInputChange) {\n      global.Shiny.onInputChange(\n        \".clientValue-\" +\n          (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n          this._name,\n        typeof(value) === \"undefined\" ? null : value\n      );\n    }\n  }\n\n  on(eventType, listener) {\n    return this._events.on(eventType, listener);\n  }\n\n  off(eventType, listener) {\n    return this._events.off(eventType, listener);\n  }\n}\n"]}
\ No newline at end of file
diff --git a/articles/files_files/crosstalk-1.2.1/scss/crosstalk.scss b/articles/files_files/crosstalk-1.2.1/scss/crosstalk.scss
deleted file mode 100644
index 3566561..0000000
--- a/articles/files_files/crosstalk-1.2.1/scss/crosstalk.scss
+++ /dev/null
@@ -1,75 +0,0 @@
-/* Adjust margins outwards, so column contents line up with the edges of the
-   parent of container-fluid. */
-.container-fluid.crosstalk-bscols {
-  margin-left: -30px;
-  margin-right: -30px;
-  white-space: normal;
-}
-
-/* But don't adjust the margins outwards if we're directly under the body,
-   i.e. we were the top-level of something at the console. */
-body > .container-fluid.crosstalk-bscols {
-  margin-left: auto;
-  margin-right: auto;
-}
-
-.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
-  display: inline-block;
-  padding-right: 12px;
-  vertical-align: top;
-}
-
-@media only screen and (max-width:480px) {
-  .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
-    display: block;
-    padding-right: inherit;
-  }
-}
-
-/* Relevant BS3 styles to make filter_checkbox() look reasonable without Bootstrap */
-.crosstalk-input {
-  margin-bottom: 15px; /* a la .form-group */
-  .control-label {
-    margin-bottom: 0;
-    vertical-align: middle;
-  }
-  input[type="checkbox"] {
-    margin: 4px 0 0;
-    margin-top: 1px;
-    line-height: normal;
-  }
-  .checkbox {
-    position: relative;
-    display: block;
-    margin-top: 10px;
-    margin-bottom: 10px;
-  }
-  .checkbox > label{
-    padding-left: 20px;
-    margin-bottom: 0;
-    font-weight: 400;
-    cursor: pointer;
-  }
-  .checkbox input[type="checkbox"],
-  .checkbox-inline input[type="checkbox"] {
-    position: absolute;
-    margin-top: 2px;
-    margin-left: -20px;
-  }
-  .checkbox + .checkbox {
-    margin-top: -5px;
-  }
-  .checkbox-inline {
-    position: relative;
-    display: inline-block;
-    padding-left: 20px;
-    margin-bottom: 0;
-    font-weight: 400;
-    vertical-align: middle;
-    cursor: pointer;
-  }
-  .checkbox-inline + .checkbox-inline {
-    margin-top: 0;
-    margin-left: 10px;
-  }
-}
diff --git a/articles/files_files/datatables-binding-0.32/datatables.js b/articles/files_files/datatables-binding-0.32/datatables.js
deleted file mode 100644
index 6a3c3d5..0000000
--- a/articles/files_files/datatables-binding-0.32/datatables.js
+++ /dev/null
@@ -1,1536 +0,0 @@
-(function() {
-
-// some helper functions: using a global object DTWidget so that it can be used
-// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's
-// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects
-// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made
-// a global object
-var DTWidget = {};
-
-// 123456666.7890 -> 123,456,666.7890
-var markInterval = function(d, digits, interval, mark, decMark, precision) {
-  x = precision ? d.toPrecision(digits) : d.toFixed(digits);
-  if (!/^-?[\d.]+$/.test(x)) return x;
-  var xv = x.split('.');
-  if (xv.length > 2) return x;  // should have at most one decimal point
-  xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark);
-  return xv.join(decMark);
-};
-
-DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before, zeroPrint) {
-  var d = parseFloat(data);
-  if (isNaN(d)) return '';
-  if (zeroPrint !== null && d === 0.0) return zeroPrint;
-  var res = markInterval(d, digits, interval, mark, decMark);
-  res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) :
-    res + currency;
-  return res;
-};
-
-DTWidget.formatString = function(data, prefix, suffix) {
-  var d = data;
-  if (d === null) return '';
-  return prefix + d + suffix;
-};
-
-DTWidget.formatPercentage = function(data, digits, interval, mark, decMark, zeroPrint) {
-  var d = parseFloat(data);
-  if (isNaN(d)) return '';
-  if (zeroPrint !== null && d === 0.0) return zeroPrint;
-  return markInterval(d * 100, digits, interval, mark, decMark) + '%';
-};
-
-DTWidget.formatRound = function(data, digits, interval, mark, decMark, zeroPrint) {
-  var d = parseFloat(data);
-  if (isNaN(d)) return '';
-  if (zeroPrint !== null && d === 0.0) return zeroPrint;
-  return markInterval(d, digits, interval, mark, decMark);
-};
-
-DTWidget.formatSignif = function(data, digits, interval, mark, decMark, zeroPrint) {
-  var d = parseFloat(data);
-  if (isNaN(d)) return '';
-  if (zeroPrint !== null && d === 0.0) return zeroPrint;
-  return markInterval(d, digits, interval, mark, decMark, true);
-};
-
-DTWidget.formatDate = function(data, method, params) {
-  var d = data;
-  if (d === null) return '';
-  // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the
-  // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)',
-  // i.e. the date-only string is treated as UTC time instead of local time
-  if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) {
-    d = d.split(/\D/);
-    d = new Date(d[0], d[1] - 1, d[2]);
-  } else {
-    d = new Date(d);
-  }
-  return d[method].apply(d, params);
-};
-
-window.DTWidget = DTWidget;
-
-// A helper function to update the properties of existing filters
-var setFilterProps = function(td, props) {
-  // Update enabled/disabled state
-  var $input = $(td).find('input').first();
-  var searchable = $input.data('searchable');
-  $input.prop('disabled', !searchable || props.disabled);
-
-  // Based on the filter type, set its new values
-  var type = td.getAttribute('data-type');
-  if (['factor', 'logical'].includes(type)) {
-    // Reformat the new dropdown options for use with selectize
-    var new_vals = props.params.options.map(function(item) {
-      return { text: item, value: item };
-    });
-
-    // Find the selectize object
-    var dropdown = $(td).find('.selectized').eq(0)[0].selectize;
-
-    // Note the current values
-    var old_vals = dropdown.getValue();
-
-    // Remove the existing values
-    dropdown.clearOptions();
-
-    // Add the new options
-    dropdown.addOption(new_vals);
-
-    // Preserve the existing values
-    dropdown.setValue(old_vals);
-
-  } else if (['number', 'integer', 'date', 'time'].includes(type)) {
-    // Apply internal scaling to new limits. Updating scale not yet implemented.
-    var slider = $(td).find('.noUi-target').eq(0);
-    var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0));
-    var new_vals = [props.params.min * scale, props.params.max * scale];
-
-    // Note what the new limits will be just for this filter
-    var new_lims = new_vals.slice();
-
-    // Determine the current values and limits
-    var old_vals = slider.val().map(Number);
-    var old_lims = slider.noUiSlider('options').range;
-    old_lims = [old_lims.min, old_lims.max];
-
-    // Preserve the current values if filters have been applied; otherwise, apply no filtering
-    if (old_vals[0] != old_lims[0]) {
-      new_vals[0] = Math.max(old_vals[0], new_vals[0]);
-    }
-
-    if (old_vals[1] != old_lims[1]) {
-      new_vals[1] = Math.min(old_vals[1], new_vals[1]);
-    }
-
-    // Update the endpoints of the slider
-    slider.noUiSlider({
-      start: new_vals,
-      range: {'min': new_lims[0], 'max': new_lims[1]}
-    }, true);
-  }
-};
-
-var transposeArray2D = function(a) {
-  return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a);
-};
-
-var crosstalkPluginsInstalled = false;
-
-function maybeInstallCrosstalkPlugins() {
-  if (crosstalkPluginsInstalled)
-    return;
-  crosstalkPluginsInstalled = true;
-
-  $.fn.dataTable.ext.afnFiltering.push(
-    function(oSettings, aData, iDataIndex) {
-      var ctfilter = oSettings.nTable.ctfilter;
-      if (ctfilter && !ctfilter[iDataIndex])
-        return false;
-
-      var ctselect = oSettings.nTable.ctselect;
-      if (ctselect && !ctselect[iDataIndex])
-        return false;
-
-      return true;
-    }
-  );
-}
-
-HTMLWidgets.widget({
-  name: "datatables",
-  type: "output",
-  renderOnNullValue: true,
-  initialize: function(el, width, height) {
-    // in order that the type=number inputs return a number
-    $.valHooks.number = {
-      get: function(el) {
-        var value = parseFloat(el.value);
-        return isNaN(value) ? "" : value;
-      }
-    };
-    $(el).html('&nbsp;');
-    return {
-      data: null,
-      ctfilterHandle: new crosstalk.FilterHandle(),
-      ctfilterSubscription: null,
-      ctselectHandle: new crosstalk.SelectionHandle(),
-      ctselectSubscription: null
-    };
-  },
-  renderValue: function(el, data, instance) {
-    if (el.offsetWidth === 0 || el.offsetHeight === 0) {
-      instance.data = data;
-      return;
-    }
-    instance.data = null;
-    var $el = $(el);
-    $el.empty();
-
-    if (data === null) {
-      $el.append('&nbsp;');
-      // clear previous Shiny inputs (if any)
-      for (var i in instance.clearInputs) instance.clearInputs[i]();
-      instance.clearInputs = {};
-      return;
-    }
-
-    var crosstalkOptions = data.crosstalkOptions;
-    if (!crosstalkOptions) crosstalkOptions = {
-      'key': null, 'group': null
-    };
-    if (crosstalkOptions.group) {
-      maybeInstallCrosstalkPlugins();
-      instance.ctfilterHandle.setGroup(crosstalkOptions.group);
-      instance.ctselectHandle.setGroup(crosstalkOptions.group);
-    }
-
-    // if we are in the viewer then we always want to fillContainer and
-    // and autoHideNavigation (unless the user has explicitly set these)
-    if (window.HTMLWidgets.viewerMode) {
-      if (!data.hasOwnProperty("fillContainer"))
-        data.fillContainer = true;
-      if (!data.hasOwnProperty("autoHideNavigation"))
-        data.autoHideNavigation = true;
-    }
-
-    // propagate fillContainer to instance (so we have it in resize)
-    instance.fillContainer = data.fillContainer;
-
-    var cells = data.data;
-
-    if (cells instanceof Array) cells = transposeArray2D(cells);
-
-    $el.append(data.container);
-    var $table = $el.find('table');
-    if (data.class) $table.addClass(data.class);
-    if (data.caption) $table.prepend(data.caption);
-
-    if (!data.selection) data.selection = {
-      mode: 'none', selected: null, target: 'row', selectable: null
-    };
-    if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' &&
-        data.selection.target === 'row+column') {
-      if ($table.children('tfoot').length === 0) {
-        $table.append($('<tfoot>'));
-        $table.find('thead tr').clone().appendTo($table.find('tfoot'));
-      }
-    }
-
-    // column filters
-    var filterRow;
-    switch (data.filter) {
-      case 'top':
-        $table.children('thead').append(data.filterHTML);
-        filterRow = $table.find('thead tr:last td');
-        break;
-      case 'bottom':
-        if ($table.children('tfoot').length === 0) {
-          $table.append($('<tfoot>'));
-        }
-        $table.children('tfoot').prepend(data.filterHTML);
-        filterRow = $table.find('tfoot tr:first td');
-        break;
-    }
-
-    var options = { searchDelay: 1000 };
-    if (cells !== null) $.extend(options, {
-      data: cells
-    });
-
-    // options for fillContainer
-    var bootstrapActive = typeof($.fn.popover) != 'undefined';
-    if (instance.fillContainer) {
-
-      // force scrollX/scrollY and turn off autoWidth
-      options.scrollX = true;
-      options.scrollY = "100px"; // can be any value, we'll adjust below
-
-      // if we aren't paginating then move around the info/filter controls
-      // to save space at the bottom and rephrase the info callback
-      if (data.options.paging === false) {
-
-        // we know how to do this cleanly for bootstrap, not so much
-        // for other themes/layouts
-        if (bootstrapActive) {
-          options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" +
-                        "<'row'<'col-sm-12'tr>>";
-        }
-
-        options.fnInfoCallback = function(oSettings, iStart, iEnd,
-                                           iMax, iTotal, sPre) {
-          return Number(iTotal).toLocaleString() + " records";
-        };
-      }
-    }
-
-    // auto hide navigation if requested
-    // Note, this only works on client-side processing mode as on server-side,
-    // cells (data.data) is null; In addition, we require the pageLength option
-    // being provided explicitly to enable this. Despite we may be able to deduce
-    // the default value of pageLength, it may complicate things so we'd rather
-    // put this responsiblity to users and warn them on the R side.
-    if (data.autoHideNavigation === true && data.options.paging !== false) {
-      // strip all nav if length >= cells
-      if ((cells instanceof Array) && data.options.pageLength >= cells.length)
-        options.dom = bootstrapActive ? "<'row'<'col-sm-12'tr>>" : "t";
-      // alternatively lean things out for flexdashboard mobile portrait
-      else if (bootstrapActive && window.FlexDashboard && window.FlexDashboard.isMobilePhone())
-        options.dom = "<'row'<'col-sm-12'f>>" +
-                      "<'row'<'col-sm-12'tr>>"  +
-                      "<'row'<'col-sm-12'p>>";
-    }
-
-    $.extend(true, options, data.options || {});
-
-    var searchCols = options.searchCols;
-    if (searchCols) {
-      searchCols = searchCols.map(function(x) {
-        return x === null ? '' : x.search;
-      });
-      // FIXME: this means I don't respect the escapeRegex setting
-      delete options.searchCols;
-    }
-
-    // server-side processing?
-    var server = options.serverSide === true;
-
-    // use the dataSrc function to pre-process JSON data returned from R
-    var DT_rows_all = [], DT_rows_current = [];
-    if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' &&
-        /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) {
-      options.ajax.dataSrc = function(json) {
-        DT_rows_all = $.makeArray(json.DT_rows_all);
-        DT_rows_current = $.makeArray(json.DT_rows_current);
-        var data = json.data;
-        if (!colReorderEnabled()) return data;
-        var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row;
-        for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false;
-        if (flag) return data;
-        for (i = 0; i < data.length; ++i) {
-          row = data[i].slice();
-          for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]];
-        }
-        return data;
-      };
-    }
-
-    var thiz = this;
-    if (instance.fillContainer) $table.on('init.dt', function(e) {
-      thiz.fillAvailableHeight(el, $(el).innerHeight());
-    });
-    // If the page contains serveral datatables and one of which enables colReorder,
-    // the table.colReorder.order() function will exist but throws error when called.
-    // So it seems like the only way to know if colReorder is enabled or not is to
-    // check the options.
-    var colReorderEnabled = function() { return "colReorder" in options; };
-    var table = $table.DataTable(options);
-    $el.data('datatable', table);
-
-    if ('rowGroup' in options) {
-      // Maintain RowGroup dataSrc when columns are reordered (#1109)
-      table.on('column-reorder', function(e, settings, details) {
-        var oldDataSrc = table.rowGroup().dataSrc();
-        var newDataSrc = details.mapping[oldDataSrc];
-        table.rowGroup().dataSrc(newDataSrc);
-      });
-    }
-
-    // Unregister previous Crosstalk event subscriptions, if they exist
-    if (instance.ctfilterSubscription) {
-      instance.ctfilterHandle.off("change", instance.ctfilterSubscription);
-      instance.ctfilterSubscription = null;
-    }
-    if (instance.ctselectSubscription) {
-      instance.ctselectHandle.off("change", instance.ctselectSubscription);
-      instance.ctselectSubscription = null;
-    }
-
-    if (!crosstalkOptions.group) {
-      $table[0].ctfilter = null;
-      $table[0].ctselect = null;
-    } else {
-      var key = crosstalkOptions.key;
-      function keysToMatches(keys) {
-        if (!keys) {
-          return null;
-        } else {
-          var selectedKeys = {};
-          for (var i = 0; i < keys.length; i++) {
-            selectedKeys[keys[i]] = true;
-          }
-          var matches = {};
-          for (var j = 0; j < key.length; j++) {
-            if (selectedKeys[key[j]])
-              matches[j] = true;
-          }
-          return matches;
-        }
-      }
-
-      function applyCrosstalkFilter(e) {
-        $table[0].ctfilter = keysToMatches(e.value);
-        table.draw();
-      }
-      instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter);
-      applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys});
-
-      function applyCrosstalkSelection(e) {
-        if (e.sender !== instance.ctselectHandle) {
-          table
-            .rows('.' + selClass, {search: 'applied'})
-            .nodes()
-            .to$()
-            .removeClass(selClass);
-          if (selectedRows)
-            changeInput('rows_selected', selectedRows(), void 0, true);
-        }
-
-        if (e.sender !== instance.ctselectHandle && e.value && e.value.length) {
-          var matches = keysToMatches(e.value);
-
-          // persistent selection with plotly (& leaflet)
-          var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {};
-          if (ctOpts.persistent === true) {
-            var matches = $.extend(matches, $table[0].ctselect);
-          }
-
-          $table[0].ctselect = matches;
-          table.draw();
-        } else {
-          if ($table[0].ctselect) {
-            $table[0].ctselect = null;
-            table.draw();
-          }
-        }
-      }
-      instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection);
-      // TODO: This next line doesn't seem to work when renderDataTable is used
-      applyCrosstalkSelection({value: instance.ctselectHandle.value});
-    }
-
-    var inArray = function(val, array) {
-      return $.inArray(val, $.makeArray(array)) > -1;
-    };
-
-    // search the i-th column
-    var searchColumn = function(i, value) {
-      var regex = false, ci = true;
-      if (options.search) {
-        regex = options.search.regex,
-        ci = options.search.caseInsensitive !== false;
-      }
-      // need to transpose the column index when colReorder is enabled
-      if (table.colReorder) i = table.colReorder.transpose(i);
-      return table.column(i).search(value, regex, !regex, ci);
-    };
-
-    if (data.filter !== 'none') {
-      if (!data.hasOwnProperty('filterSettings')) data.filterSettings = {};
-
-      filterRow.each(function(i, td) {
-
-        var $td = $(td), type = $td.data('type'), filter;
-        var $input = $td.children('div').first().children('input');
-        var disabled = $input.prop('disabled');
-        var searchable = table.settings()[0].aoColumns[i].bSearchable;
-        $input.prop('disabled', !searchable || disabled);
-        $input.data('searchable', searchable); // for updating later
-        $input.on('input blur', function() {
-          $input.next('span').toggle(Boolean($input.val()));
-        });
-        // Bootstrap sets pointer-events to none and we won't be able to click
-        // the clear button
-        $input.next('span').css('pointer-events', 'auto').hide().click(function() {
-          $(this).hide().prev('input').val('').trigger('input').focus();
-        });
-        var searchCol;  // search string for this column
-        if (searchCols && searchCols[i]) {
-          searchCol = searchCols[i];
-          $input.val(searchCol).trigger('input');
-        }
-        var $x = $td.children('div').last();
-
-        // remove the overflow: hidden attribute of the scrollHead
-        // (otherwise the scrolling table body obscures the filters)
-        // The workaround and the discussion from
-        // https://github.com/rstudio/DT/issues/554#issuecomment-518007347
-        // Otherwise the filter selection will not be anchored to the values
-        // when the columns number is many and scrollX is enabled.
-        var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot');
-        var cssOverflowHead = scrollHead.css('overflow');
-        var scrollBody = $(el).find('.dataTables_scrollBody');
-        var cssOverflowBody = scrollBody.css('overflow');
-        var scrollTable = $(el).find('.dataTables_scroll');
-        var cssOverflowTable = scrollTable.css('overflow');
-        if (cssOverflowHead === 'hidden') {
-          $x.on('show hide', function(e) {
-            if (e.type === 'show') {
-              scrollHead.css('overflow', 'visible');
-              scrollBody.css('overflow', 'visible');
-              scrollTable.css('overflow-x', 'scroll');
-            } else {
-              scrollHead.css('overflow', cssOverflowHead);
-              scrollBody.css('overflow', cssOverflowBody);
-              scrollTable.css('overflow-x', cssOverflowTable);
-            }
-          });
-          $x.css('z-index', 25);
-        }
-
-        if (inArray(type, ['factor', 'logical'])) {
-          $input.on({
-            click: function() {
-              $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus();
-            },
-            input: function() {
-              var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val();
-              if (v1 === '[]') v1 = '';
-              if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2));
-            }
-          });
-          var $input2 = $x.children('select');
-          filter = $input2.selectize($.extend({
-            options: $input2.data('options').map(function(v, i) {
-              return ({text: v, value: v});
-            }),
-            plugins: ['remove_button'],
-            hideSelected: true,
-            onChange: function(value) {
-              if (value === null) value = []; // compatibility with jQuery 3.0
-              $input.val(value.length ? JSON.stringify(value) : '');
-              if (value.length) $input.trigger('input');
-              $input.attr('title', $input.val());
-              if (server) {
-                searchColumn(i, value.length ? JSON.stringify(value) : '').draw();
-                return;
-              }
-              // turn off filter if nothing selected
-              $td.data('filter', value.length > 0);
-              table.draw();  // redraw table, and filters will be applied
-            }
-          }, data.filterSettings.select));
-          filter[0].selectize.on('blur', function() {
-            $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur');
-          });
-          filter.next('div').css('margin-bottom', 'auto');
-        } else if (type === 'character') {
-          var fun = function() {
-            searchColumn(i, $input.val()).draw();
-          };
-          // throttle searching for server-side processing
-          var throttledFun = $.fn.dataTable.util.throttle(fun, options.searchDelay);
-          $input.on('input', function(e, immediate) {
-            // always bypass throttling when immediate = true (via the updateSearch method)
-            (immediate || !server) ? fun() : throttledFun();
-          });
-        } else if (inArray(type, ['number', 'integer', 'date', 'time'])) {
-          var $x0 = $x;
-          $x = $x0.children('div').first();
-          $x0.css({
-            'background-color': '#fff',
-            'border': '1px #ddd solid',
-            'border-radius': '4px',
-            'padding': data.vertical ? '35px 20px': '20px 20px 10px 20px'
-          });
-          var $spans = $x0.children('span').css({
-            'margin-top': data.vertical ? '0' : '10px',
-            'white-space': 'nowrap'
-          });
-          var $span1 = $spans.first(), $span2 = $spans.last();
-          var r1 = +$x.data('min'), r2 = +$x.data('max');
-          // when the numbers are too small or have many decimal places, the
-          // slider may have numeric precision problems (#150)
-          var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0));
-          r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale);
-          var scaleBack = function(x, scale) {
-            if (scale === 1) return x;
-            var d = Math.round(Math.log(scale) / Math.log(10));
-            // to avoid problems like 3.423/100 -> 0.034230000000000003
-            return (x / scale).toFixed(d);
-          };
-          var slider_min = function() {
-            return filter.noUiSlider('options').range.min;
-          };
-          var slider_max = function() {
-            return filter.noUiSlider('options').range.max;
-          };
-          $input.on({
-            focus: function() {
-              $x0.show().trigger('show');
-              // first, make sure the slider div leaves at least 20px between
-              // the two (slider value) span's
-              $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20));
-              // then, if the input is really wide or slider is vertical,
-              // make the slider the same width as the input
-              if ($x0.outerWidth() < $input.outerWidth() || data.vertical) {
-                $x0.outerWidth($input.outerWidth());
-              }
-              // make sure the slider div does not reach beyond the right margin
-              if ($(window).width() < $x0.offset().left + $x0.width()) {
-                $x0.offset({
-                  'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth()
-                });
-              }
-            },
-            blur: function() {
-              $x0.hide().trigger('hide');
-            },
-            input: function() {
-              if ($input.val() === '') filter.val([slider_min(), slider_max()]);
-            },
-            change: function() {
-              var v = $input.val().replace(/\s/g, '');
-              if (v === '') return;
-              v = v.split('...');
-              if (v.length !== 2) {
-                $input.parent().addClass('has-error');
-                return;
-              }
-              if (v[0] === '') v[0] = slider_min();
-              if (v[1] === '') v[1] = slider_max();
-              $input.parent().removeClass('has-error');
-              // treat date as UTC time at midnight
-              var strTime = function(x) {
-                var s = type === 'date' ? 'T00:00:00Z' : '';
-                var t = new Date(x + s).getTime();
-                // add 10 minutes to date since it does not hurt the date, and
-                // it helps avoid the tricky floating point arithmetic problems,
-                // e.g. sometimes the date may be a few milliseconds earlier
-                // than the midnight due to precision problems in noUiSlider
-                return type === 'date' ? t + 3600000 : t;
-              };
-              if (inArray(type, ['date', 'time'])) {
-                v[0] = strTime(v[0]);
-                v[1] = strTime(v[1]);
-              }
-              if (v[0] != slider_min()) v[0] *= scale;
-              if (v[1] != slider_max()) v[1] *= scale;
-              filter.val(v);
-            }
-          });
-          var formatDate = function(d) {
-            d = scaleBack(d, scale);
-            if (type === 'number') return d;
-            if (type === 'integer') return parseInt(d);
-            var x = new Date(+d);
-            if (type === 'date') {
-              var pad0 = function(x) {
-                return ('0' + x).substr(-2, 2);
-              };
-              return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth())
-                      + '-' + pad0(x.getUTCDate());
-            } else {
-              return x.toISOString();
-            }
-          };
-          var opts = type === 'date' ? { step: 60 * 60 * 1000 } :
-                     type === 'integer' ? { step: 1 } : {};
-
-          opts.orientation = data.vertical ? 'vertical': 'horizontal';
-          opts.direction = data.vertical ? 'rtl': 'ltr';
-
-          filter = $x.noUiSlider($.extend({
-            start: [r1, r2],
-            range: {min: r1, max: r2},
-            connect: true
-          }, opts, data.filterSettings.slider));
-          if (scale > 1) (function() {
-            var t1 = r1, t2 = r2;
-            var val = filter.val();
-            while (val[0] > r1 || val[1] < r2) {
-              if (val[0] > r1) {
-                t1 -= val[0] - r1;
-              }
-              if (val[1] < r2) {
-                t2 += r2 - val[1];
-              }
-              filter = $x.noUiSlider($.extend({
-                start: [t1, t2],
-                range: {min: t1, max: t2},
-                connect: true
-              }, opts, data.filterSettings.slider), true);
-              val = filter.val();
-            }
-            r1  = t1; r2 = t2;
-          })();
-          // format with active column renderer, if defined
-          var colDef = data.options.columnDefs.find(function(def) {
-            return (def.targets === i || inArray(i, def.targets)) && 'render' in def;
-          });
-          var updateSliderText = function(v1, v2) {
-            // we only know how to use function renderers
-            if (colDef && typeof colDef.render === 'function') {
-              var restore = function(v) {
-                v = scaleBack(v, scale);
-                return inArray(type, ['date', 'time']) ? new Date(+v) : v;
-              }
-              $span1.text(colDef.render(restore(v1), 'display'));
-              $span2.text(colDef.render(restore(v2), 'display'));
-            } else {
-              $span1.text(formatDate(v1));
-              $span2.text(formatDate(v2));
-            }
-          };
-          updateSliderText(r1, r2);
-          var updateSlider = function(e) {
-            var val = filter.val();
-            // turn off filter if in full range
-            $td.data('filter', val[0] > slider_min() || val[1] < slider_max());
-            var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival;
-            if ($td.data('filter')) {
-              ival = v1 + ' ... ' + v2;
-              $input.attr('title', ival).val(ival).trigger('input');
-            } else {
-              $input.attr('title', '').val('');
-            }
-            updateSliderText(val[0], val[1]);
-            if (e.type === 'slide') return;  // no searching when sliding only
-            if (server) {
-              searchColumn(i, $td.data('filter') ? ival : '').draw();
-              return;
-            }
-            table.draw();
-          };
-          filter.on({
-            set: updateSlider,
-            slide: updateSlider
-          });
-        }
-
-        // server-side processing will be handled by R (or whatever server
-        // language you use); the following code is only needed for client-side
-        // processing
-        if (server) {
-          // if a search string has been pre-set, search now
-          if (searchCol) $input.trigger('input').trigger('change');
-          return;
-        }
-
-        var customFilter = function(settings, data, dataIndex) {
-          // there is no way to attach a search function to a specific table,
-          // and we need to make sure a global search function is not applied to
-          // all tables (i.e. a range filter in a previous table should not be
-          // applied to the current table); we use the settings object to
-          // determine if we want to perform searching on the current table,
-          // since settings.sTableId will be different to different tables
-          if (table.settings()[0] !== settings) return true;
-          // no filter on this column or no need to filter this column
-          if (typeof filter === 'undefined' || !$td.data('filter')) return true;
-
-          var r = filter.val(), v, r0, r1;
-          var i_data = function(i) {
-            if (!colReorderEnabled()) return i;
-            var order = table.colReorder.order(), k;
-            for (k = 0; k < order.length; ++k) if (order[k] === i) return k;
-            return i; // in theory it will never be here...
-          }
-          v = data[i_data(i)];
-          if (type === 'number' || type === 'integer') {
-            v = parseFloat(v);
-            // how to handle NaN? currently exclude these rows
-            if (isNaN(v)) return(false);
-            r0 = parseFloat(scaleBack(r[0], scale))
-            r1 = parseFloat(scaleBack(r[1], scale));
-            if (v >= r0 && v <= r1) return true;
-          } else if (type === 'date' || type === 'time') {
-            v = new Date(v);
-            r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale);
-            if (v >= r0 && v <= r1) return true;
-          } else if (type === 'factor') {
-            if (r.length === 0 || inArray(v, r)) return true;
-          } else if (type === 'logical') {
-            if (r.length === 0) return true;
-            if (inArray(v === '' ? 'na' : v, r)) return true;
-          }
-          return false;
-        };
-
-        $.fn.dataTable.ext.search.push(customFilter);
-
-        // search for the preset search strings if it is non-empty
-        if (searchCol) $input.trigger('input').trigger('change');
-
-      });
-
-    }
-
-    // highlight search keywords
-    var highlight = function() {
-      var body = $(table.table().body());
-      // removing the old highlighting first
-      body.unhighlight();
-
-      // don't highlight the "not found" row, so we get the rows using the api
-      if (table.rows({ filter: 'applied' }).data().length === 0) return;
-      // highlight global search keywords
-      body.highlight($.trim(table.search()).split(/\s+/));
-      // then highlight keywords from individual column filters
-      if (filterRow) filterRow.each(function(i, td) {
-        var $td = $(td), type = $td.data('type');
-        if (type !== 'character') return;
-        var $input = $td.children('div').first().children('input');
-        var column = table.column(i).nodes().to$(),
-            val = $.trim($input.val());
-        if (type !== 'character' || val === '') return;
-        column.highlight(val.split(/\s+/));
-      });
-    };
-
-    if (options.searchHighlight) {
-      table
-      .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight)
-      .on('destroy', function() {
-        // remove event handler
-        table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth');
-      });
-
-      // Set the option for escaping regex characters in our search string.  This will be used
-      // for all future matching.
-      jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex);
-
-      // initial highlight for state saved conditions and initial states
-      highlight();
-    }
-
-    // run the callback function on the table instance
-    if (typeof data.callback === 'function') data.callback(table);
-
-    // double click to edit the cell, row, column, or all cells
-    if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) {
-      // only bring up the editor when the cell itself is dbclicked, and ignore
-      // other dbclick events bubbled up (e.g. from the <input>)
-      if (e.target !== this) return;
-      var target = [], immediate = false;
-      switch (data.editable.target) {
-        case 'cell':
-          target = [this];
-          immediate = true;  // edit will take effect immediately
-          break;
-        case 'row':
-          target = table.cells(table.cell(this).index().row, '*').nodes();
-          break;
-        case 'column':
-          target = table.cells('*', table.cell(this).index().column).nodes();
-          break;
-        case 'all':
-          target = table.cells().nodes();
-          break;
-        default:
-          throw 'The editable parameter must be "cell", "row", "column", or "all"';
-      }
-      var disableCols = data.editable.disable ? data.editable.disable.columns : null;
-      var numericCols = data.editable.numeric;
-      var areaCols = data.editable.area;
-      var dateCols = data.editable.date;
-      for (var i = 0; i < target.length; i++) {
-        (function(cell, current) {
-          var $cell = $(cell), html = $cell.html();
-          var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column;
-          var $input;
-          if (inArray(index, numericCols)) {
-            $input = $('<input type="number">');
-          } else if (inArray(index, areaCols)) {
-            $input = $('<textarea></textarea>');
-          } else if (inArray(index, dateCols)) {
-            $input = $('<input type="date">');
-          } else {
-            $input = $('<input type="text">');
-          }
-          if (!immediate) {
-            $cell.data('input', $input).data('html', html);
-            $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel');
-          }
-          $input.val(value);
-          if (inArray(index, disableCols)) {
-            $input.attr('readonly', '').css('filter', 'invert(25%)');
-          }
-          $cell.empty().append($input);
-          if (cell === current) $input.focus();
-          $input.css('width', '100%');
-
-          if (immediate) $input.on('blur', function(e) {
-            var valueNew = $input.val();
-            if (valueNew !== value) {
-              _cell.data(valueNew);
-              if (HTMLWidgets.shinyMode) {
-                changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'});
-              }
-              // for server-side processing, users have to call replaceData() to update the table
-              if (!server) table.draw(false);
-            } else {
-              $cell.html(html);
-            }
-          }).on('keyup', function(e) {
-            // hit Escape to cancel editing
-            if (e.keyCode === 27) $input.trigger('blur');
-          });
-
-          // bulk edit (row, column, or all)
-          if (!immediate) $input.on('keyup', function(e) {
-            var removeInput = function($cell, restore) {
-              $cell.data('input').remove();
-              if (restore) $cell.html($cell.data('html'));
-            }
-            if (e.keyCode === 27) {
-              for (var i = 0; i < target.length; i++) {
-                removeInput($(target[i]), true);
-              }
-            } else if (e.keyCode === 13 && e.ctrlKey) {
-              // Ctrl + Enter
-              var cell, $cell, _cell, cellData = [];
-              for (var i = 0; i < target.length; i++) {
-                cell = target[i]; $cell = $(cell); _cell = table.cell(cell);
-                _cell.data($cell.data('input').val());
-                HTMLWidgets.shinyMode && cellData.push(cellInfo(cell));
-                removeInput($cell, false);
-              }
-              if (HTMLWidgets.shinyMode) {
-                changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"});
-              }
-              if (!server) table.draw(false);
-            }
-          });
-        })(target[i], this);
-      }
-    });
-
-    // interaction with shiny
-    if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return;
-
-    var methods = {};
-    var shinyData = {};
-
-    methods.updateCaption = function(caption) {
-      if (!caption) return;
-      $table.children('caption').replaceWith(caption);
-    }
-
-    // register clear functions to remove input values when the table is removed
-    instance.clearInputs = {};
-
-    var changeInput = function(id, value, type, noCrosstalk, opts) {
-      var event = id;
-      id = el.id + '_' + id;
-      if (type) id = id + ':' + type;
-      // do not update if the new value is the same as old value
-      if (event !== 'cell_edit' && !/_clicked$/.test(event) && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value))
-        return;
-      shinyData[id] = JSON.stringify(value);
-      if (HTMLWidgets.shinyMode && Shiny.setInputValue) {
-        Shiny.setInputValue(id, value, opts);
-        if (!instance.clearInputs[id]) instance.clearInputs[id] = function() {
-          Shiny.setInputValue(id, null);
-        }
-      }
-
-      // HACK
-      if (event === "rows_selected" && !noCrosstalk) {
-        if (crosstalkOptions.group) {
-          var keys = crosstalkOptions.key;
-          var selectedKeys = null;
-          if (value) {
-            selectedKeys = [];
-            for (var i = 0; i < value.length; i++) {
-              // The value array's contents use 1-based row numbers, so we must
-              // convert to 0-based before indexing into the keys array.
-              selectedKeys.push(keys[value[i] - 1]);
-            }
-          }
-          instance.ctselectHandle.set(selectedKeys);
-        }
-      }
-    };
-
-    var addOne = function(x) {
-      return x.map(function(i) { return 1 + i; });
-    };
-
-    var unique = function(x) {
-      var ux = [];
-      $.each(x, function(i, el){
-        if ($.inArray(el, ux) === -1) ux.push(el);
-      });
-      return ux;
-    }
-
-    // change the row index of a cell
-    var tweakCellIndex = function(cell) {
-      var info = cell.index();
-      // some cell may not be valid. e.g, #759
-      // when using the RowGroup extension, datatables will
-      // generate the row label and the cells are not part of
-      // the data thus contain no row/col info
-      if (info === undefined)
-        return {row: null, col: null};
-      if (server) {
-        info.row = DT_rows_current[info.row];
-      } else {
-        info.row += 1;
-      }
-      return {row: info.row, col: info.column};
-    }
-
-    var cleanSelectedValues = function() {
-      changeInput('rows_selected', []);
-      changeInput('columns_selected', []);
-      changeInput('cells_selected', transposeArray2D([]), 'shiny.matrix');
-    }
-    // #828 we should clean the selection on the server-side when the table reloads
-    cleanSelectedValues();
-
-    // a flag to indicates if select extension is initialized or not
-    var flagSelectExt = table.settings()[0]._select !== undefined;
-    // the Select extension should only be used in the client mode and
-    // when the selection.mode is set to none
-    if (data.selection.mode === 'none' && !server && flagSelectExt) {
-      var updateRowsSelected = function() {
-        var rows = table.rows({selected: true});
-        var selected = [];
-        $.each(rows.indexes().toArray(), function(i, v) {
-          selected.push(v + 1);
-        });
-        changeInput('rows_selected', selected);
-      }
-      var updateColsSelected = function() {
-        var columns = table.columns({selected: true});
-        changeInput('columns_selected', columns.indexes().toArray());
-      }
-      var updateCellsSelected = function() {
-        var cells = table.cells({selected: true});
-        var selected = [];
-        cells.every(function() {
-          var row = this.index().row;
-          var col = this.index().column;
-          selected = selected.concat([[row + 1, col]]);
-        });
-        changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix');
-      }
-      table.on('select deselect', function(e, dt, type, indexes) {
-        updateRowsSelected();
-        updateColsSelected();
-        updateCellsSelected();
-      })
-    }
-
-    var selMode = data.selection.mode, selTarget = data.selection.target;
-    var selDisable = data.selection.selectable === false;
-    if (inArray(selMode, ['single', 'multiple'])) {
-      var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected';
-      // selected1: row indices; selected2: column indices
-      var initSel = function(x) {
-        if (x === null || typeof x === 'boolean' || selTarget === 'cell') {
-          return {rows: [], cols: []};
-        } else if (selTarget === 'row') {
-          return {rows: $.makeArray(x), cols: []};
-        } else if (selTarget === 'column') {
-          return {rows: [], cols: $.makeArray(x)};
-        } else if (selTarget === 'row+column') {
-          return {rows: $.makeArray(x.rows), cols: $.makeArray(x.cols)};
-        }
-      }
-      var selected = data.selection.selected;
-      var selected1 = initSel(selected).rows, selected2 = initSel(selected).cols;
-      // selectable should contain either all positive or all non-positive values, not both
-      // positive values indicate "selectable" while non-positive values means "nonselectable"
-      // the assertion is performed on R side. (only column indicides could be zero which indicates
-      // the row name)
-      var selectable = data.selection.selectable;
-      var selectable1 = initSel(selectable).rows, selectable2 = initSel(selectable).cols;
-
-      // After users reorder the rows or filter the table, we cannot use the table index
-      // directly. Instead, we need this function to find out the rows between the two clicks.
-      // If user filter the table again between the start click and the end click, the behavior
-      // would be undefined, but it should not be a problem.
-      var shiftSelRowsIndex = function(start, end) {
-        var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray();
-        start = indexes.indexOf(start); end = indexes.indexOf(end);
-        // if start is larger than end, we need to swap
-        if (start > end) {
-          var tmp = end; end = start; start = tmp;
-        }
-        return indexes.slice(start, end + 1);
-      }
-
-      var serverRowIndex = function(clientRowIndex) {
-        return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1;
-      }
-
-      // row, column, or cell selection
-      var lastClickedRow;
-      if (inArray(selTarget, ['row', 'row+column'])) {
-        // Get the current selected rows. It will also
-        // update the selected1's value based on the current row selection state
-        // Note we can't put this function inside selectRows() directly,
-        // the reason is method.selectRows() will override selected1's value but this
-        // function will add rows to selected1 (keep the existing selection), which is
-        // inconsistent with column and cell selection.
-        var selectedRows = function() {
-          var rows = table.rows('.' + selClass);
-          var idx = rows.indexes().toArray();
-          if (!server) {
-            selected1 = addOne(idx);
-            return selected1;
-          }
-          idx = idx.map(function(i) {
-            return DT_rows_current[i];
-          });
-          selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx;
-          return selected1;
-        }
-        // Change selected1's value based on selectable1, then refresh the row state
-        var onlyKeepSelectableRows = function() {
-          if (selDisable) { // users can't select; useful when only want backend select
-            selected1 = [];
-            return;
-          }
-          if (selectable1.length === 0) return;
-          var nonselectable = selectable1[0] <= 0;
-          if (nonselectable) {
-            // should make selectable1 positive
-            selected1 = $(selected1).not(selectable1.map(function(i) { return -i; })).get();
-          } else {
-            selected1 = $(selected1).filter(selectable1).get();
-          }
-        }
-        // Change selected1's value based on selectable1, then
-        // refresh the row selection state according to values in selected1
-        var selectRows = function(ignoreSelectable) {
-          if (!ignoreSelectable) onlyKeepSelectableRows();
-          table.$('tr.' + selClass).removeClass(selClass);
-          if (selected1.length === 0) return;
-          if (server) {
-            table.rows({page: 'current'}).every(function() {
-              if (inArray(DT_rows_current[this.index()], selected1)) {
-                $(this.node()).addClass(selClass);
-              }
-            });
-          } else {
-            var selected0 = selected1.map(function(i) { return i - 1; });
-            $(table.rows(selected0).nodes()).addClass(selClass);
-          }
-        }
-        table.on('mousedown.dt', 'tbody tr', function(e) {
-          var $this = $(this), thisRow = table.row(this);
-          if (selMode === 'multiple') {
-            if (e.shiftKey && lastClickedRow !== undefined) {
-              // select or de-select depends on the last clicked row's status
-              var flagSel = !$this.hasClass(selClass);
-              var crtClickedRow = serverRowIndex(thisRow.index());
-              if (server) {
-                var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow);
-                // update current page's selClass
-                rowsIndex.map(function(i) {
-                  var rowIndex = DT_rows_current.indexOf(i);
-                  if (rowIndex >= 0) {
-                    var row = table.row(rowIndex).nodes().to$();
-                    var flagRowSel = !row.hasClass(selClass);
-                    if (flagSel === flagRowSel) row.toggleClass(selClass);
-                  }
-                });
-                // update selected1
-                if (flagSel) {
-                  selected1 = unique(selected1.concat(rowsIndex));
-                } else {
-                  selected1 = selected1.filter(function(index) {
-                    return !inArray(index, rowsIndex);
-                  });
-                }
-              } else {
-                // js starts from 0
-                shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) {
-                  var row = table.row(value).nodes().to$();
-                  var flagRowSel = !row.hasClass(selClass);
-                  if (flagSel === flagRowSel) row.toggleClass(selClass);
-                });
-              }
-              e.preventDefault();
-            } else {
-              $this.toggleClass(selClass);
-            }
-          } else {
-            if ($this.hasClass(selClass)) {
-              $this.removeClass(selClass);
-            } else {
-              table.$('tr.' + selClass).removeClass(selClass);
-              $this.addClass(selClass);
-            }
-          }
-          if (server && !$this.hasClass(selClass)) {
-            var id = DT_rows_current[thisRow.index()];
-            // remove id from selected1 since its class .selected has been removed
-            if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1);
-          }
-          selectedRows(); // update selected1's value based on selClass
-          selectRows(false); // only keep the selectable rows
-          changeInput('rows_selected', selected1);
-          changeInput('row_last_clicked', serverRowIndex(thisRow.index()), null, null, {priority: 'event'});
-          lastClickedRow = serverRowIndex(thisRow.index());
-        });
-        selectRows(false);  // in case users have specified pre-selected rows
-        // restore selected rows after the table is redrawn (e.g. sort/search/page);
-        // client-side tables will preserve the selections automatically; for
-        // server-side tables, we have to *real* row indices are in `selected1`
-        changeInput('rows_selected', selected1);
-        if (server) table.on('draw.dt', function(e) { selectRows(false); });
-        methods.selectRows = function(selected, ignoreSelectable) {
-          selected1 = $.makeArray(selected);
-          selectRows(ignoreSelectable);
-          changeInput('rows_selected', selected1);
-        }
-      }
-
-      if (inArray(selTarget, ['column', 'row+column'])) {
-        if (selTarget === 'row+column') {
-          $(table.columns().footer()).css('cursor', 'pointer');
-        }
-        // update selected2's value based on selectable2
-        var onlyKeepSelectableCols = function() {
-          if (selDisable) { // users can't select; useful when only want backend select
-            selected2 = [];
-            return;
-          }
-          if (selectable2.length === 0) return;
-          var nonselectable = selectable2[0] <= 0;
-          if (nonselectable) {
-            // need to make selectable2 positive
-            selected2 = $(selected2).not(selectable2.map(function(i) { return -i; })).get();
-          } else {
-            selected2 = $(selected2).filter(selectable2).get();
-          }
-        }
-        // update selected2 and then
-        // refresh the col selection state according to values in selected2
-        var selectCols = function(ignoreSelectable) {
-          if (!ignoreSelectable) onlyKeepSelectableCols();
-          // if selected2 is not a valide index (e.g., larger than the column number)
-          // table.columns(selected2) will fail and result in a blank table
-          // this is different from the table.rows(), where the out-of-range indexes
-          // doesn't affect at all
-          selected2 = $(selected2).filter(table.columns().indexes()).get();
-          table.columns().nodes().flatten().to$().removeClass(selClass);
-          if (selected2.length > 0)
-            table.columns(selected2).nodes().flatten().to$().addClass(selClass);
-        }
-        var callback = function() {
-          var colIdx = selTarget === 'column' ? table.cell(this).index().column :
-              $.inArray(this, table.columns().footer()),
-              thisCol = $(table.column(colIdx).nodes());
-          if (colIdx === -1) return;
-          if (thisCol.hasClass(selClass)) {
-            thisCol.removeClass(selClass);
-            selected2.splice($.inArray(colIdx, selected2), 1);
-          } else {
-            if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass);
-            thisCol.addClass(selClass);
-            selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx]));
-          }
-          selectCols(false); // update selected2 based on selectable
-          changeInput('columns_selected', selected2);
-        }
-        if (selTarget === 'column') {
-          $(table.table().body()).on('click.dt', 'td', callback);
-        } else {
-          $(table.table().footer()).on('click.dt', 'tr th', callback);
-        }
-        selectCols(false);  // in case users have specified pre-selected columns
-        changeInput('columns_selected', selected2);
-        if (server) table.on('draw.dt', function(e) { selectCols(false); });
-        methods.selectColumns = function(selected, ignoreSelectable) {
-          selected2 = $.makeArray(selected);
-          selectCols(ignoreSelectable);
-          changeInput('columns_selected', selected2);
-        }
-      }
-
-      if (selTarget === 'cell') {
-        var selected3 = [], selectable3 = [];
-        if (selected !== null) selected3 = selected;
-        if (selectable !== null && typeof selectable !== 'boolean') selectable3 = selectable;
-        var findIndex = function(ij, sel) {
-          for (var i = 0; i < sel.length; i++) {
-            if (ij[0] === sel[i][0] && ij[1] === sel[i][1]) return i;
-          }
-          return -1;
-        }
-         // Change selected3's value based on selectable3, then refresh the cell state
-        var onlyKeepSelectableCells = function() {
-          if (selDisable) { // users can't select; useful when only want backend select
-            selected3 = [];
-            return;
-          }
-          if (selectable3.length === 0) return;
-          var nonselectable = selectable3[0][0] <= 0;
-          var out = [];
-          if (nonselectable) {
-            selected3.map(function(ij) {
-              // should make selectable3 positive
-              if (findIndex([-ij[0], -ij[1]], selectable3) === -1) { out.push(ij); }
-            });
-          } else {
-            selected3.map(function(ij) {
-              if (findIndex(ij, selectable3) > -1) { out.push(ij); }
-            });
-          }
-          selected3 = out;
-        }
-        // Change selected3's value based on selectable3, then
-        // refresh the cell selection state according to values in selected3
-        var selectCells = function(ignoreSelectable) {
-          if (!ignoreSelectable) onlyKeepSelectableCells();
-          table.$('td.' + selClass).removeClass(selClass);
-          if (selected3.length === 0) return;
-          if (server) {
-            table.cells({page: 'current'}).every(function() {
-              var info = tweakCellIndex(this);
-              if (findIndex([info.row, info.col], selected3) > -1)
-                $(this.node()).addClass(selClass);
-            });
-          } else {
-            selected3.map(function(ij) {
-              $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass);
-            });
-          }
-        };
-        table.on('click.dt', 'tbody td', function() {
-          var $this = $(this), info = tweakCellIndex(table.cell(this));
-          if ($this.hasClass(selClass)) {
-            $this.removeClass(selClass);
-            selected3.splice(findIndex([info.row, info.col], selected3), 1);
-          } else {
-            if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass);
-            $this.addClass(selClass);
-            selected3 = selMode === 'single' ? [[info.row, info.col]] :
-              unique(selected3.concat([[info.row, info.col]]));
-          }
-          selectCells(false); // must call this to update selected3 based on selectable3
-          changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
-        });
-        selectCells(false);  // in case users have specified pre-selected columns
-        changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
-
-        if (server) table.on('draw.dt', function(e) { selectCells(false); });
-        methods.selectCells = function(selected, ignoreSelectable) {
-          selected3 = selected ? selected : [];
-          selectCells(ignoreSelectable);
-          changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
-        }
-      }
-    }
-
-    // expose some table info to Shiny
-    var updateTableInfo = function(e, settings) {
-      // TODO: is anyone interested in the page info?
-      // changeInput('page_info', table.page.info());
-      var updateRowInfo = function(id, modifier) {
-        var idx;
-        if (server) {
-          idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all;
-        } else {
-          var rows = table.rows($.extend({
-            search: 'applied',
-            page: 'all'
-          }, modifier));
-          idx = addOne(rows.indexes().toArray());
-        }
-        changeInput('rows' + '_' + id, idx);
-      };
-      updateRowInfo('current', {page: 'current'});
-      updateRowInfo('all', {});
-    }
-    table.on('draw.dt', updateTableInfo);
-    updateTableInfo();
-
-    // state info
-    table.on('draw.dt column-visibility.dt', function() {
-      changeInput('state', table.state());
-    });
-    changeInput('state', table.state());
-
-    // search info
-    var updateSearchInfo = function() {
-      changeInput('search', table.search());
-      if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) {
-        return $(td).find('input').first().val();
-      }));
-    }
-    table.on('draw.dt', updateSearchInfo);
-    updateSearchInfo();
-
-    var cellInfo = function(thiz) {
-      var info = tweakCellIndex(table.cell(thiz));
-      info.value = table.cell(thiz).data();
-      return info;
-    }
-    // the current cell clicked on
-    table.on('click.dt', 'tbody td', function() {
-      changeInput('cell_clicked', cellInfo(this), null, null, {priority: 'event'});
-    })
-    changeInput('cell_clicked', {});
-
-    // do not trigger table selection when clicking on links unless they have classes
-    table.on('mousedown.dt', 'tbody td a', function(e) {
-      if (this.className === '') e.stopPropagation();
-    });
-
-    methods.addRow = function(data, rowname, resetPaging) {
-      var n = table.columns().indexes().length, d = n - data.length;
-      if (d === 1) {
-        data = rowname.concat(data)
-      } else if (d !== 0) {
-        console.log(data);
-        console.log(table.columns().indexes());
-        throw 'New data must be of the same length as current data (' + n + ')';
-      };
-      table.row.add(data).draw(resetPaging);
-    }
-
-    methods.updateSearch = function(keywords) {
-      if (keywords.global !== null)
-        $(table.table().container()).find('input[type=search]').first()
-             .val(keywords.global).trigger('input');
-      var columns = keywords.columns;
-      if (!filterRow || columns === null) return;
-      filterRow.toArray().map(function(td, i) {
-        var v = typeof columns === 'string' ? columns : columns[i];
-        if (typeof v === 'undefined') {
-          console.log('The search keyword for column ' + i + ' is undefined')
-          return;
-        }
-        // Update column search string and values on linked filter widgets.
-        // 'input' for factor and char filters, 'change' for numeric filters.
-        $(td).find('input').first().val(v).trigger('input', [true]).trigger('change');
-      });
-      table.draw();
-    }
-
-    methods.hideCols = function(hide, reset) {
-      if (reset) table.columns().visible(true, false);
-      table.columns(hide).visible(false);
-    }
-
-    methods.showCols = function(show, reset) {
-      if (reset) table.columns().visible(false, false);
-      table.columns(show).visible(true);
-    }
-
-    methods.colReorder = function(order, origOrder) {
-      table.colReorder.order(order, origOrder);
-    }
-
-    methods.selectPage = function(page) {
-      if (table.page.info().pages < page || page < 1) {
-        throw 'Selected page is out of range';
-      };
-      table.page(page - 1).draw(false);
-    }
-
-    methods.reloadData = function(resetPaging, clearSelection) {
-      // empty selections first if necessary
-      if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]);
-      if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]);
-      if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]);
-      table.ajax.reload(null, resetPaging);
-    }
-
-    // update table filters (set new limits of sliders)
-    methods.updateFilters = function(newProps) {
-      // loop through each filter in the filter row
-      filterRow.each(function(i, td) {
-        var k = i;
-        if (filterRow.length > newProps.length) {
-          if (i === 0) return;  // first column is row names
-          k = i - 1;
-        }
-        // Update the filters to reflect the updated data.
-        // Allow "falsy" (e.g. NULL) to signify a no-op.
-        if (newProps[k]) {
-          setFilterProps(td, newProps[k]);
-        }
-      });
-    };
-
-    table.shinyMethods = methods;
-  },
-  resize: function(el, width, height, instance) {
-    if (instance.data) this.renderValue(el, instance.data, instance);
-
-    // dynamically adjust height if fillContainer = TRUE
-    if (instance.fillContainer)
-      this.fillAvailableHeight(el, height);
-
-    this.adjustWidth(el);
-  },
-
-  // dynamically set the scroll body to fill available height
-  // (used with fillContainer = TRUE)
-  fillAvailableHeight: function(el, availableHeight) {
-
-    // see how much of the table is occupied by header/footer elements
-    // and use that to compute a target scroll body height
-    var dtWrapper = $(el).find('div.dataTables_wrapper');
-    var dtScrollBody = $(el).find($('div.dataTables_scrollBody'));
-    var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight();
-    var scrollBodyHeight = availableHeight - framingHeight;
-
-    // we need to set `max-height` to none as datatables library now sets this
-    // to a fixed height, disabling the ability to resize to fill the window,
-    // as it will be set to a fixed 100px under such circumstances, e.g., RStudio IDE,
-    // or FlexDashboard
-    // see https://github.com/rstudio/DT/issues/951#issuecomment-1026464509
-    dtScrollBody.css('max-height', 'none');
-    // set the height
-    dtScrollBody.height(scrollBodyHeight + 'px');
-  },
-
-  // adjust the width of columns; remove the hard-coded widths on table and the
-  // scroll header when scrollX/Y are enabled
-  adjustWidth: function(el) {
-    var $el = $(el), table = $el.data('datatable');
-    if (table) table.columns.adjust();
-    $el.find('.dataTables_scrollHeadInner').css('width', '')
-        .children('table').css('margin-left', '');
-  }
-});
-
-  if (!HTMLWidgets.shinyMode) return;
-
-  Shiny.addCustomMessageHandler('datatable-calls', function(data) {
-    var id = data.id;
-    var el = document.getElementById(id);
-    var table = el ? $(el).data('datatable') : null;
-    if (!table) {
-      console.log("Couldn't find table with id " + id);
-      return;
-    }
-
-    var methods = table.shinyMethods, call = data.call;
-    if (methods[call.method]) {
-      methods[call.method].apply(table, call.args);
-    } else {
-      console.log("Unknown method " + call.method);
-    }
-  });
-
-})();
diff --git a/articles/files_files/datatables-css-0.0.0/datatables-crosstalk.css b/articles/files_files/datatables-css-0.0.0/datatables-crosstalk.css
deleted file mode 100644
index bd1159c..0000000
--- a/articles/files_files/datatables-css-0.0.0/datatables-crosstalk.css
+++ /dev/null
@@ -1,32 +0,0 @@
-.dt-crosstalk-fade {
-  opacity: 0.2;
-}
-
-html body div.DTS div.dataTables_scrollBody {
-  background: none;
-}
-
-
-/*
-Fix https://github.com/rstudio/DT/issues/563
-If the `table.display` is set to "block" (e.g., pkgdown), the browser will display
-datatable objects strangely. The search panel and the page buttons will still be
-in full-width but the table body will be "compact" and shorter.
-In therory, having this attributes will affect `dom="t"`
-with `display: block` users. But in reality, there should be no one.
-We may remove the below lines in the future if the upstream agree to have this there.
-See https://github.com/DataTables/DataTablesSrc/issues/160
-*/
-
-table.dataTable {
-  display: table;
-}
-
-
-/*
-When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height).
-*/
-
-.html-fill-container > .html-fill-item.datatables {
-  flex-basis: 400px;
-}
diff --git a/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.extra.css b/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
deleted file mode 100644
index b2dd141..0000000
--- a/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
+++ /dev/null
@@ -1,28 +0,0 @@
-/* Selected rows/cells */
-table.dataTable tr.selected td, table.dataTable td.selected {
-  background-color: #b0bed9 !important;
-}
-/* In case of scrollX/Y or FixedHeader */
-.dataTables_scrollBody .dataTables_sizing {
-  visibility: hidden;
-}
-
-/* The datatables' theme CSS file doesn't define
-the color but with white background. It leads to an issue that
-when the HTML's body color is set to 'white', the user can't
-see the text since the background is white. One case happens in the
-RStudio's IDE when inline viewing the DT table inside an Rmd file,
-if the IDE theme is set to "Cobalt".
-
-See https://github.com/rstudio/DT/issues/447 for more info
-
-This fixes should have little side-effects because all the other elements
-of the default theme use the #333 font color.
-
-TODO: The upstream may use relative colors for both the table background
-and the color. It means the table can display well without this patch
-then. At that time, we need to remove the below CSS attributes.
-*/
-div.datatables {
-  color: #333;
-}
diff --git a/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.min.css b/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.min.css
deleted file mode 100644
index ad59f84..0000000
--- a/articles/files_files/dt-core-1.13.6/css/jquery.dataTables.min.css
+++ /dev/null
@@ -1 +0,0 @@
-:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11;--dt-row-stripe: 0, 0, 0;--dt-row-hover: 0, 0, 0;--dt-column-ordering: 0, 0, 0;--dt-html-background: white}:root.dark{--dt-html-background: rgb(33, 37, 41)}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{display:inline-block;color:rgba(0, 0, 0, 0.5);content:"►"}table.dataTable tr.dt-hasChild td.dt-control:before{content:"▼"}html.dark table.dataTable td.dt-control:before{color:rgba(255, 255, 255, 0.5)}html.dark table.dataTable tr.dt-hasChild td.dt-control:before{color:rgba(255, 255, 255, 0.5)}table.dataTable thead>tr>th.sorting,table.dataTable thead>tr>th.sorting_asc,table.dataTable thead>tr>th.sorting_desc,table.dataTable thead>tr>th.sorting_asc_disabled,table.dataTable thead>tr>th.sorting_desc_disabled,table.dataTable thead>tr>td.sorting,table.dataTable thead>tr>td.sorting_asc,table.dataTable thead>tr>td.sorting_desc,table.dataTable thead>tr>td.sorting_asc_disabled,table.dataTable thead>tr>td.sorting_desc_disabled{cursor:pointer;position:relative;padding-right:26px}table.dataTable thead>tr>th.sorting:before,table.dataTable thead>tr>th.sorting:after,table.dataTable thead>tr>th.sorting_asc:before,table.dataTable thead>tr>th.sorting_asc:after,table.dataTable thead>tr>th.sorting_desc:before,table.dataTable thead>tr>th.sorting_desc:after,table.dataTable thead>tr>th.sorting_asc_disabled:before,table.dataTable thead>tr>th.sorting_asc_disabled:after,table.dataTable thead>tr>th.sorting_desc_disabled:before,table.dataTable thead>tr>th.sorting_desc_disabled:after,table.dataTable thead>tr>td.sorting:before,table.dataTable thead>tr>td.sorting:after,table.dataTable thead>tr>td.sorting_asc:before,table.dataTable thead>tr>td.sorting_asc:after,table.dataTable thead>tr>td.sorting_desc:before,table.dataTable thead>tr>td.sorting_desc:after,table.dataTable thead>tr>td.sorting_asc_disabled:before,table.dataTable thead>tr>td.sorting_asc_disabled:after,table.dataTable thead>tr>td.sorting_desc_disabled:before,table.dataTable thead>tr>td.sorting_desc_disabled:after{position:absolute;display:block;opacity:.125;right:10px;line-height:9px;font-size:.8em}table.dataTable thead>tr>th.sorting:before,table.dataTable thead>tr>th.sorting_asc:before,table.dataTable thead>tr>th.sorting_desc:before,table.dataTable thead>tr>th.sorting_asc_disabled:before,table.dataTable thead>tr>th.sorting_desc_disabled:before,table.dataTable thead>tr>td.sorting:before,table.dataTable thead>tr>td.sorting_asc:before,table.dataTable thead>tr>td.sorting_desc:before,table.dataTable thead>tr>td.sorting_asc_disabled:before,table.dataTable thead>tr>td.sorting_desc_disabled:before{bottom:50%;content:"▲";content:"▲"/""}table.dataTable thead>tr>th.sorting:after,table.dataTable thead>tr>th.sorting_asc:after,table.dataTable thead>tr>th.sorting_desc:after,table.dataTable 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index 13f17b6..0000000
--- a/articles/files_files/dt-ext-keytable-1.13.6/css/keyTable.dataTables.min.css
+++ /dev/null
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deleted file mode 100644
index d750f80..0000000
--- a/articles/files_files/dt-ext-keytable-1.13.6/js/dataTables.keyTable.min.js
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\ No newline at end of file
diff --git a/articles/files_files/dt-ext-scroller-1.13.6/css/scroller.dataTables.min.css b/articles/files_files/dt-ext-scroller-1.13.6/css/scroller.dataTables.min.css
deleted file mode 100644
index 693e998..0000000
--- a/articles/files_files/dt-ext-scroller-1.13.6/css/scroller.dataTables.min.css
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/articles/files_files/dt-ext-scroller-1.13.6/js/dataTables.scroller.min.js b/articles/files_files/dt-ext-scroller-1.13.6/js/dataTables.scroller.min.js
deleted file mode 100644
index e801f5b..0000000
--- a/articles/files_files/dt-ext-scroller-1.13.6/js/dataTables.scroller.min.js
+++ /dev/null
@@ -1,4 +0,0 @@
-/*! Scroller 2.2.0
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0!==this.s.dt.oLoadedState.scroller?((r=!(!this.s.dt.sAjaxSource&&!s.s.dt.ajax||this.s.dt.oFeatures.bServerSide))&&2<=this.s.dt.iDraw||!r&&1<=this.s.dt.iDraw)&&setTimeout(function(){f(s.dom.scroller).scrollTop(s.s.dt.oLoadedState.scroller.scrollTop),setTimeout(function(){s.s.ingnoreScroll=!1},0)},0):s.s.ingnoreScroll=!1),this.s.dt.oFeatures.bInfo&&setTimeout(function(){s._info.call(s)},0),f(this.s.dt.nTable).triggerHandler("position.dts.dt",n),this.dom.loader&&this.s.loaderVisible&&(this.dom.loader.css("display","none"),this.s.loaderVisible=!1)},_domain:function(s,t){var o,e=this.s.heights,l=1e4;return e.virtual===e.scroll||t<l?t:"virtualToPhysical"===s&&t>=e.virtual-l?(o=e.virtual-t,e.scroll-o):"physicalToVirtual"===s&&t>=e.scroll-l?(o=e.scroll-t,e.virtual-o):(e=l-(o=(e.virtual-l-l)/(e.scroll-l-l))*l,"virtualToPhysical"===s?(t-e)/o:o*t+e)},_info:function(){if(this.s.dt.oFeatures.bInfo){var s=this.s.dt,t=s.oLanguage,o=this.dom.scroller.scrollTop,e=Math.floor(this.pixelsToRow(o,!1,this.s.ani)+1),l=s.fnRecordsTotal(),r=s.fnRecordsDisplay(),o=Math.ceil(this.pixelsToRow(o+this.s.heights.viewport,!1,this.s.ani)),o=r<o?r:o,i=s.fnFormatNumber(e),a=s.fnFormatNumber(o),n=s.fnFormatNumber(l),h=s.fnFormatNumber(r),c=0===s.fnRecordsDisplay()&&s.fnRecordsDisplay()==s.fnRecordsTotal()?t.sInfoEmpty+t.sInfoPostFix:0===s.fnRecordsDisplay()?t.sInfoEmpty+" "+t.sInfoFiltered.replace("_MAX_",n)+t.sInfoPostFix:s.fnRecordsDisplay()==s.fnRecordsTotal()?t.sInfo.replace("_START_",i).replace("_END_",a).replace("_MAX_",n).replace("_TOTAL_",h)+t.sInfoPostFix:t.sInfo.replace("_START_",i).replace("_END_",a).replace("_MAX_",n).replace("_TOTAL_",h)+" "+t.sInfoFiltered.replace("_MAX_",s.fnFormatNumber(s.fnRecordsTotal()))+t.sInfoPostFix,i=t.fnInfoCallback,d=(i&&(c=i.call(s.oInstance,s,e,o,l,r,c)),s.aanFeatures.i);if(void 0!==d)for(var p=0,u=d.length;p<u;p++)f(d[p]).html(c);f(s.nTable).triggerHandler("info.dt")}},_parseHeight:function(s){var t,o,s=/^([+-]?(?:\d+(?:\.\d+)?|\.\d+))(px|em|rem|vh)$/.exec(s);return null!==s&&(o=parseFloat(s[1]),"px"===(s=s[2])?t=o:"vh"===s?t=o/100*f(i).height():"rem"===s?t=o*parseFloat(f(":root").css("font-size")):"em"===s&&(t=o*parseFloat(f("body").css("font-size"))),t)||0},_scroll:function(){var s,t=this,o=this.s.heights,e=this.dom.scroller.scrollTop;this.s.skip||this.s.ingnoreScroll||e!==this.s.lastScrollTop&&(this.s.dt.bFiltered||this.s.dt.bSorted?this.s.lastScrollTop=0:(this._info(),clearTimeout(this.s.stateTO),this.s.stateTO=setTimeout(function(){t.s.dtApi.state.save()},250),this.s.scrollType=Math.abs(e-this.s.lastScrollTop)>o.viewport?"jump":"cont",this.s.topRowFloat="cont"===this.s.scrollType?this.pixelsToRow(e,!1,!1):this._domain("physicalToVirtual",e)/o.row,this.s.topRowFloat<0&&(this.s.topRowFloat=0),this.s.forceReposition||e<this.s.redrawTop||e>this.s.redrawBottom?(s=Math.ceil((this.s.displayBuffer-1)/2*this.s.viewportRows),s=parseInt(this.s.topRowFloat,10)-s,this.s.forceReposition=!1,s<=0?s=0:s+this.s.dt._iDisplayLength>this.s.dt.fnRecordsDisplay()?(s=this.s.dt.fnRecordsDisplay()-this.s.dt._iDisplayLength)<0&&(s=0):s%2!=0&&s++,(this.s.targetTop=s)!=this.s.dt._iDisplayStart&&(this.s.tableTop=f(this.s.dt.nTable).offset().top,this.s.tableBottom=f(this.s.dt.nTable).height()+this.s.tableTop,s=function(){t.s.dt._iDisplayStart=t.s.targetTop,t.s.dt.oApi._fnDraw(t.s.dt)},this.s.dt.oFeatures.bServerSide?(this.s.forceReposition=!0,clearTimeout(this.s.drawTO),this.s.drawTO=setTimeout(s,this.s.serverWait)):s(),this.dom.loader)&&!this.s.loaderVisible&&(this.dom.loader.css("display","block"),this.s.loaderVisible=!0)):this.s.topRowFloat=this.pixelsToRow(e,!1,!0),this.s.lastScrollTop=e,this.s.stateSaveThrottle(),"jump"===this.s.scrollType&&this.s.mousedown&&(this.s.labelVisible=!0),this.s.labelVisible&&(s=(o.viewport-o.labelHeight-o.xbar)/o.scroll,this.dom.label.html(this.s.dt.fnFormatNumber(parseInt(this.s.topRowFloat,10)+1)).css("top",e+e*s).css("display","block"))))},_scrollForce:function(){var s=this.s.heights;s.virtual=s.row*this.s.dt.fnRecordsDisplay(),s.scroll=s.virtual,1e6<s.scroll&&(s.scroll=1e6),this.dom.force.style.height=s.scroll>this.s.heights.row?s.scroll+"px":this.s.heights.row+"px"}}),l.oDefaults=l.defaults={boundaryScale:.5,displayBuffer:9,loadingIndicator:!1,rowHeight:"auto",serverWait:200},l.version="2.2.0",f(o).on("preInit.dt.dtscroller",function(s,t){var o,e;"dt"===s.namespace&&(s=t.oInit.scroller,o=r.defaults.scroller,s||o)&&(e=f.extend({},s,o),!1!==s)&&new l(t,e)}),f.fn.dataTable.Scroller=l,f.fn.DataTable.Scroller=l,f.fn.dataTable.Api);return s.register("scroller()",function(){return this}),s.register("scroller().rowToPixels()",function(s,t,o){var e=this.context;if(e.length&&e[0].oScroller)return e[0].oScroller.rowToPixels(s,t,o)}),s.register("scroller().pixelsToRow()",function(s,t,o){var e=this.context;if(e.length&&e[0].oScroller)return e[0].oScroller.pixelsToRow(s,t,o)}),s.register(["scroller().scrollToRow()","scroller.toPosition()"],function(t,o){return this.iterator("table",function(s){s.oScroller&&s.oScroller.scrollToRow(t,o)}),this}),s.register("row().scrollTo()",function(o){var e=this;return this.iterator("row",function(s,t){s.oScroller&&(t=e.rows({order:"applied",search:"applied"}).indexes().indexOf(t),s.oScroller.scrollToRow(t,o))}),this}),s.register("scroller.measure()",function(t){return this.iterator("table",function(s){s.oScroller&&s.oScroller.measure(t)}),this}),s.register("scroller.page()",function(){var s=this.context;if(s.length&&s[0].oScroller)return s[0].oScroller.pageInfo()}),r});
\ No newline at end of file
diff --git a/articles/files_files/htmlwidgets-1.6.4/htmlwidgets.js b/articles/files_files/htmlwidgets-1.6.4/htmlwidgets.js
deleted file mode 100644
index 1067d02..0000000
--- a/articles/files_files/htmlwidgets-1.6.4/htmlwidgets.js
+++ /dev/null
@@ -1,901 +0,0 @@
-(function() {
-  // If window.HTMLWidgets is already defined, then use it; otherwise create a
-  // new object. This allows preceding code to set options that affect the
-  // initialization process (though none currently exist).
-  window.HTMLWidgets = window.HTMLWidgets || {};
-
-  // See if we're running in a viewer pane. If not, we're in a web browser.
-  var viewerMode = window.HTMLWidgets.viewerMode =
-      /\bviewer_pane=1\b/.test(window.location);
-
-  // See if we're running in Shiny mode. If not, it's a static document.
-  // Note that static widgets can appear in both Shiny and static modes, but
-  // obviously, Shiny widgets can only appear in Shiny apps/documents.
-  var shinyMode = window.HTMLWidgets.shinyMode =
-      typeof(window.Shiny) !== "undefined" && !!window.Shiny.outputBindings;
-
-  // We can't count on jQuery being available, so we implement our own
-  // version if necessary.
-  function querySelectorAll(scope, selector) {
-    if (typeof(jQuery) !== "undefined" && scope instanceof jQuery) {
-      return scope.find(selector);
-    }
-    if (scope.querySelectorAll) {
-      return scope.querySelectorAll(selector);
-    }
-  }
-
-  function asArray(value) {
-    if (value === null)
-      return [];
-    if ($.isArray(value))
-      return value;
-    return [value];
-  }
-
-  // Implement jQuery's extend
-  function extend(target /*, ... */) {
-    if (arguments.length == 1) {
-      return target;
-    }
-    for (var i = 1; i < arguments.length; i++) {
-      var source = arguments[i];
-      for (var prop in source) {
-        if (source.hasOwnProperty(prop)) {
-          target[prop] = source[prop];
-        }
-      }
-    }
-    return target;
-  }
-
-  // IE8 doesn't support Array.forEach.
-  function forEach(values, callback, thisArg) {
-    if (values.forEach) {
-      values.forEach(callback, thisArg);
-    } else {
-      for (var i = 0; i < values.length; i++) {
-        callback.call(thisArg, values[i], i, values);
-      }
-    }
-  }
-
-  // Replaces the specified method with the return value of funcSource.
-  //
-  // Note that funcSource should not BE the new method, it should be a function
-  // that RETURNS the new method. funcSource receives a single argument that is
-  // the overridden method, it can be called from the new method. The overridden
-  // method can be called like a regular function, it has the target permanently
-  // bound to it so "this" will work correctly.
-  function overrideMethod(target, methodName, funcSource) {
-    var superFunc = target[methodName] || function() {};
-    var superFuncBound = function() {
-      return superFunc.apply(target, arguments);
-    };
-    target[methodName] = funcSource(superFuncBound);
-  }
-
-  // Add a method to delegator that, when invoked, calls
-  // delegatee.methodName. If there is no such method on
-  // the delegatee, but there was one on delegator before
-  // delegateMethod was called, then the original version
-  // is invoked instead.
-  // For example:
-  //
-  // var a = {
-  //   method1: function() { console.log('a1'); }
-  //   method2: function() { console.log('a2'); }
-  // };
-  // var b = {
-  //   method1: function() { console.log('b1'); }
-  // };
-  // delegateMethod(a, b, "method1");
-  // delegateMethod(a, b, "method2");
-  // a.method1();
-  // a.method2();
-  //
-  // The output would be "b1", "a2".
-  function delegateMethod(delegator, delegatee, methodName) {
-    var inherited = delegator[methodName];
-    delegator[methodName] = function() {
-      var target = delegatee;
-      var method = delegatee[methodName];
-
-      // The method doesn't exist on the delegatee. Instead,
-      // call the method on the delegator, if it exists.
-      if (!method) {
-        target = delegator;
-        method = inherited;
-      }
-
-      if (method) {
-        return method.apply(target, arguments);
-      }
-    };
-  }
-
-  // Implement a vague facsimilie of jQuery's data method
-  function elementData(el, name, value) {
-    if (arguments.length == 2) {
-      return el["htmlwidget_data_" + name];
-    } else if (arguments.length == 3) {
-      el["htmlwidget_data_" + name] = value;
-      return el;
-    } else {
-      throw new Error("Wrong number of arguments for elementData: " +
-        arguments.length);
-    }
-  }
-
-  // http://stackoverflow.com/questions/3446170/escape-string-for-use-in-javascript-regex
-  function escapeRegExp(str) {
-    return str.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g, "\\$&");
-  }
-
-  function hasClass(el, className) {
-    var re = new RegExp("\\b" + escapeRegExp(className) + "\\b");
-    return re.test(el.className);
-  }
-
-  // elements - array (or array-like object) of HTML elements
-  // className - class name to test for
-  // include - if true, only return elements with given className;
-  //   if false, only return elements *without* given className
-  function filterByClass(elements, className, include) {
-    var results = [];
-    for (var i = 0; i < elements.length; i++) {
-      if (hasClass(elements[i], className) == include)
-        results.push(elements[i]);
-    }
-    return results;
-  }
-
-  function on(obj, eventName, func) {
-    if (obj.addEventListener) {
-      obj.addEventListener(eventName, func, false);
-    } else if (obj.attachEvent) {
-      obj.attachEvent(eventName, func);
-    }
-  }
-
-  function off(obj, eventName, func) {
-    if (obj.removeEventListener)
-      obj.removeEventListener(eventName, func, false);
-    else if (obj.detachEvent) {
-      obj.detachEvent(eventName, func);
-    }
-  }
-
-  // Translate array of values to top/right/bottom/left, as usual with
-  // the "padding" CSS property
-  // https://developer.mozilla.org/en-US/docs/Web/CSS/padding
-  function unpackPadding(value) {
-    if (typeof(value) === "number")
-      value = [value];
-    if (value.length === 1) {
-      return {top: value[0], right: value[0], bottom: value[0], left: value[0]};
-    }
-    if (value.length === 2) {
-      return {top: value[0], right: value[1], bottom: value[0], left: value[1]};
-    }
-    if (value.length === 3) {
-      return {top: value[0], right: value[1], bottom: value[2], left: value[1]};
-    }
-    if (value.length === 4) {
-      return {top: value[0], right: value[1], bottom: value[2], left: value[3]};
-    }
-  }
-
-  // Convert an unpacked padding object to a CSS value
-  function paddingToCss(paddingObj) {
-    return paddingObj.top + "px " + paddingObj.right + "px " + paddingObj.bottom + "px " + paddingObj.left + "px";
-  }
-
-  // Makes a number suitable for CSS
-  function px(x) {
-    if (typeof(x) === "number")
-      return x + "px";
-    else
-      return x;
-  }
-
-  // Retrieves runtime widget sizing information for an element.
-  // The return value is either null, or an object with fill, padding,
-  // defaultWidth, defaultHeight fields.
-  function sizingPolicy(el) {
-    var sizingEl = document.querySelector("script[data-for='" + el.id + "'][type='application/htmlwidget-sizing']");
-    if (!sizingEl)
-      return null;
-    var sp = JSON.parse(sizingEl.textContent || sizingEl.text || "{}");
-    if (viewerMode) {
-      return sp.viewer;
-    } else {
-      return sp.browser;
-    }
-  }
-
-  // @param tasks Array of strings (or falsy value, in which case no-op).
-  //   Each element must be a valid JavaScript expression that yields a
-  //   function. Or, can be an array of objects with "code" and "data"
-  //   properties; in this case, the "code" property should be a string
-  //   of JS that's an expr that yields a function, and "data" should be
-  //   an object that will be added as an additional argument when that
-  //   function is called.
-  // @param target The object that will be "this" for each function
-  //   execution.
-  // @param args Array of arguments to be passed to the functions. (The
-  //   same arguments will be passed to all functions.)
-  function evalAndRun(tasks, target, args) {
-    if (tasks) {
-      forEach(tasks, function(task) {
-        var theseArgs = args;
-        if (typeof(task) === "object") {
-          theseArgs = theseArgs.concat([task.data]);
-          task = task.code;
-        }
-        var taskFunc = tryEval(task);
-        if (typeof(taskFunc) !== "function") {
-          throw new Error("Task must be a function! Source:\n" + task);
-        }
-        taskFunc.apply(target, theseArgs);
-      });
-    }
-  }
-
-  // Attempt eval() both with and without enclosing in parentheses.
-  // Note that enclosing coerces a function declaration into
-  // an expression that eval() can parse
-  // (otherwise, a SyntaxError is thrown)
-  function tryEval(code) {
-    var result = null;
-    try {
-      result = eval("(" + code + ")");
-    } catch(error) {
-      if (!(error instanceof SyntaxError)) {
-        throw error;
-      }
-      try {
-        result = eval(code);
-      } catch(e) {
-        if (e instanceof SyntaxError) {
-          throw error;
-        } else {
-          throw e;
-        }
-      }
-    }
-    return result;
-  }
-
-  function initSizing(el) {
-    var sizing = sizingPolicy(el);
-    if (!sizing)
-      return;
-
-    var cel = document.getElementById("htmlwidget_container");
-    if (!cel)
-      return;
-
-    if (typeof(sizing.padding) !== "undefined") {
-      document.body.style.margin = "0";
-      document.body.style.padding = paddingToCss(unpackPadding(sizing.padding));
-    }
-
-    if (sizing.fill) {
-      document.body.style.overflow = "hidden";
-      document.body.style.width = "100%";
-      document.body.style.height = "100%";
-      document.documentElement.style.width = "100%";
-      document.documentElement.style.height = "100%";
-      cel.style.position = "absolute";
-      var pad = unpackPadding(sizing.padding);
-      cel.style.top = pad.top + "px";
-      cel.style.right = pad.right + "px";
-      cel.style.bottom = pad.bottom + "px";
-      cel.style.left = pad.left + "px";
-      el.style.width = "100%";
-      el.style.height = "100%";
-
-      return {
-        getWidth: function() { return cel.getBoundingClientRect().width; },
-        getHeight: function() { return cel.getBoundingClientRect().height; }
-      };
-
-    } else {
-      el.style.width = px(sizing.width);
-      el.style.height = px(sizing.height);
-
-      return {
-        getWidth: function() { return cel.getBoundingClientRect().width; },
-        getHeight: function() { return cel.getBoundingClientRect().height; }
-      };
-    }
-  }
-
-  // Default implementations for methods
-  var defaults = {
-    find: function(scope) {
-      return querySelectorAll(scope, "." + this.name);
-    },
-    renderError: function(el, err) {
-      var $el = $(el);
-
-      this.clearError(el);
-
-      // Add all these error classes, as Shiny does
-      var errClass = "shiny-output-error";
-      if (err.type !== null) {
-        // use the classes of the error condition as CSS class names
-        errClass = errClass + " " + $.map(asArray(err.type), function(type) {
-          return errClass + "-" + type;
-        }).join(" ");
-      }
-      errClass = errClass + " htmlwidgets-error";
-
-      // Is el inline or block? If inline or inline-block, just display:none it
-      // and add an inline error.
-      var display = $el.css("display");
-      $el.data("restore-display-mode", display);
-
-      if (display === "inline" || display === "inline-block") {
-        $el.hide();
-        if (err.message !== "") {
-          var errorSpan = $("<span>").addClass(errClass);
-          errorSpan.text(err.message);
-          $el.after(errorSpan);
-        }
-      } else if (display === "block") {
-        // If block, add an error just after the el, set visibility:none on the
-        // el, and position the error to be on top of the el.
-        // Mark it with a unique ID and CSS class so we can remove it later.
-        $el.css("visibility", "hidden");
-        if (err.message !== "") {
-          var errorDiv = $("<div>").addClass(errClass).css("position", "absolute")
-            .css("top", el.offsetTop)
-            .css("left", el.offsetLeft)
-            // setting width can push out the page size, forcing otherwise
-            // unnecessary scrollbars to appear and making it impossible for
-            // the element to shrink; so use max-width instead
-            .css("maxWidth", el.offsetWidth)
-            .css("height", el.offsetHeight);
-          errorDiv.text(err.message);
-          $el.after(errorDiv);
-
-          // Really dumb way to keep the size/position of the error in sync with
-          // the parent element as the window is resized or whatever.
-          var intId = setInterval(function() {
-            if (!errorDiv[0].parentElement) {
-              clearInterval(intId);
-              return;
-            }
-            errorDiv
-              .css("top", el.offsetTop)
-              .css("left", el.offsetLeft)
-              .css("maxWidth", el.offsetWidth)
-              .css("height", el.offsetHeight);
-          }, 500);
-        }
-      }
-    },
-    clearError: function(el) {
-      var $el = $(el);
-      var display = $el.data("restore-display-mode");
-      $el.data("restore-display-mode", null);
-
-      if (display === "inline" || display === "inline-block") {
-        if (display)
-          $el.css("display", display);
-        $(el.nextSibling).filter(".htmlwidgets-error").remove();
-      } else if (display === "block"){
-        $el.css("visibility", "inherit");
-        $(el.nextSibling).filter(".htmlwidgets-error").remove();
-      }
-    },
-    sizing: {}
-  };
-
-  // Called by widget bindings to register a new type of widget. The definition
-  // object can contain the following properties:
-  // - name (required) - A string indicating the binding name, which will be
-  //   used by default as the CSS classname to look for.
-  // - initialize (optional) - A function(el) that will be called once per
-  //   widget element; if a value is returned, it will be passed as the third
-  //   value to renderValue.
-  // - renderValue (required) - A function(el, data, initValue) that will be
-  //   called with data. Static contexts will cause this to be called once per
-  //   element; Shiny apps will cause this to be called multiple times per
-  //   element, as the data changes.
-  window.HTMLWidgets.widget = function(definition) {
-    if (!definition.name) {
-      throw new Error("Widget must have a name");
-    }
-    if (!definition.type) {
-      throw new Error("Widget must have a type");
-    }
-    // Currently we only support output widgets
-    if (definition.type !== "output") {
-      throw new Error("Unrecognized widget type '" + definition.type + "'");
-    }
-    // TODO: Verify that .name is a valid CSS classname
-
-    // Support new-style instance-bound definitions. Old-style class-bound
-    // definitions have one widget "object" per widget per type/class of
-    // widget; the renderValue and resize methods on such widget objects
-    // take el and instance arguments, because the widget object can't
-    // store them. New-style instance-bound definitions have one widget
-    // object per widget instance; the definition that's passed in doesn't
-    // provide renderValue or resize methods at all, just the single method
-    //   factory(el, width, height)
-    // which returns an object that has renderValue(x) and resize(w, h).
-    // This enables a far more natural programming style for the widget
-    // author, who can store per-instance state using either OO-style
-    // instance fields or functional-style closure variables (I guess this
-    // is in contrast to what can only be called C-style pseudo-OO which is
-    // what we required before).
-    if (definition.factory) {
-      definition = createLegacyDefinitionAdapter(definition);
-    }
-
-    if (!definition.renderValue) {
-      throw new Error("Widget must have a renderValue function");
-    }
-
-    // For static rendering (non-Shiny), use a simple widget registration
-    // scheme. We also use this scheme for Shiny apps/documents that also
-    // contain static widgets.
-    window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || [];
-    // Merge defaults into the definition; don't mutate the original definition.
-    var staticBinding = extend({}, defaults, definition);
-    overrideMethod(staticBinding, "find", function(superfunc) {
-      return function(scope) {
-        var results = superfunc(scope);
-        // Filter out Shiny outputs, we only want the static kind
-        return filterByClass(results, "html-widget-output", false);
-      };
-    });
-    window.HTMLWidgets.widgets.push(staticBinding);
-
-    if (shinyMode) {
-      // Shiny is running. Register the definition with an output binding.
-      // The definition itself will not be the output binding, instead
-      // we will make an output binding object that delegates to the
-      // definition. This is because we foolishly used the same method
-      // name (renderValue) for htmlwidgets definition and Shiny bindings
-      // but they actually have quite different semantics (the Shiny
-      // bindings receive data that includes lots of metadata that it
-      // strips off before calling htmlwidgets renderValue). We can't
-      // just ignore the difference because in some widgets it's helpful
-      // to call this.renderValue() from inside of resize(), and if
-      // we're not delegating, then that call will go to the Shiny
-      // version instead of the htmlwidgets version.
-
-      // Merge defaults with definition, without mutating either.
-      var bindingDef = extend({}, defaults, definition);
-
-      // This object will be our actual Shiny binding.
-      var shinyBinding = new Shiny.OutputBinding();
-
-      // With a few exceptions, we'll want to simply use the bindingDef's
-      // version of methods if they are available, otherwise fall back to
-      // Shiny's defaults. NOTE: If Shiny's output bindings gain additional
-      // methods in the future, and we want them to be overrideable by
-      // HTMLWidget binding definitions, then we'll need to add them to this
-      // list.
-      delegateMethod(shinyBinding, bindingDef, "getId");
-      delegateMethod(shinyBinding, bindingDef, "onValueChange");
-      delegateMethod(shinyBinding, bindingDef, "onValueError");
-      delegateMethod(shinyBinding, bindingDef, "renderError");
-      delegateMethod(shinyBinding, bindingDef, "clearError");
-      delegateMethod(shinyBinding, bindingDef, "showProgress");
-
-      // The find, renderValue, and resize are handled differently, because we
-      // want to actually decorate the behavior of the bindingDef methods.
-
-      shinyBinding.find = function(scope) {
-        var results = bindingDef.find(scope);
-
-        // Only return elements that are Shiny outputs, not static ones
-        var dynamicResults = results.filter(".html-widget-output");
-
-        // It's possible that whatever caused Shiny to think there might be
-        // new dynamic outputs, also caused there to be new static outputs.
-        // Since there might be lots of different htmlwidgets bindings, we
-        // schedule execution for later--no need to staticRender multiple
-        // times.
-        if (results.length !== dynamicResults.length)
-          scheduleStaticRender();
-
-        return dynamicResults;
-      };
-
-      // Wrap renderValue to handle initialization, which unfortunately isn't
-      // supported natively by Shiny at the time of this writing.
-
-      shinyBinding.renderValue = function(el, data) {
-        Shiny.renderDependencies(data.deps);
-        // Resolve strings marked as javascript literals to objects
-        if (!(data.evals instanceof Array)) data.evals = [data.evals];
-        for (var i = 0; data.evals && i < data.evals.length; i++) {
-          window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]);
-        }
-        if (!bindingDef.renderOnNullValue) {
-          if (data.x === null) {
-            el.style.visibility = "hidden";
-            return;
-          } else {
-            el.style.visibility = "inherit";
-          }
-        }
-        if (!elementData(el, "initialized")) {
-          initSizing(el);
-
-          elementData(el, "initialized", true);
-          if (bindingDef.initialize) {
-            var rect = el.getBoundingClientRect();
-            var result = bindingDef.initialize(el, rect.width, rect.height);
-            elementData(el, "init_result", result);
-          }
-        }
-        bindingDef.renderValue(el, data.x, elementData(el, "init_result"));
-        evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]);
-      };
-
-      // Only override resize if bindingDef implements it
-      if (bindingDef.resize) {
-        shinyBinding.resize = function(el, width, height) {
-          // Shiny can call resize before initialize/renderValue have been
-          // called, which doesn't make sense for widgets.
-          if (elementData(el, "initialized")) {
-            bindingDef.resize(el, width, height, elementData(el, "init_result"));
-          }
-        };
-      }
-
-      Shiny.outputBindings.register(shinyBinding, bindingDef.name);
-    }
-  };
-
-  var scheduleStaticRenderTimerId = null;
-  function scheduleStaticRender() {
-    if (!scheduleStaticRenderTimerId) {
-      scheduleStaticRenderTimerId = setTimeout(function() {
-        scheduleStaticRenderTimerId = null;
-        window.HTMLWidgets.staticRender();
-      }, 1);
-    }
-  }
-
-  // Render static widgets after the document finishes loading
-  // Statically render all elements that are of this widget's class
-  window.HTMLWidgets.staticRender = function() {
-    var bindings = window.HTMLWidgets.widgets || [];
-    forEach(bindings, function(binding) {
-      var matches = binding.find(document.documentElement);
-      forEach(matches, function(el) {
-        var sizeObj = initSizing(el, binding);
-
-        var getSize = function(el) {
-          if (sizeObj) {
-            return {w: sizeObj.getWidth(), h: sizeObj.getHeight()}
-          } else {
-            var rect = el.getBoundingClientRect();
-            return {w: rect.width, h: rect.height}
-          }
-        };
-
-        if (hasClass(el, "html-widget-static-bound"))
-          return;
-        el.className = el.className + " html-widget-static-bound";
-
-        var initResult;
-        if (binding.initialize) {
-          var size = getSize(el);
-          initResult = binding.initialize(el, size.w, size.h);
-          elementData(el, "init_result", initResult);
-        }
-
-        if (binding.resize) {
-          var lastSize = getSize(el);
-          var resizeHandler = function(e) {
-            var size = getSize(el);
-            if (size.w === 0 && size.h === 0)
-              return;
-            if (size.w === lastSize.w && size.h === lastSize.h)
-              return;
-            lastSize = size;
-            binding.resize(el, size.w, size.h, initResult);
-          };
-
-          on(window, "resize", resizeHandler);
-
-          // This is needed for cases where we're running in a Shiny
-          // app, but the widget itself is not a Shiny output, but
-          // rather a simple static widget. One example of this is
-          // an rmarkdown document that has runtime:shiny and widget
-          // that isn't in a render function. Shiny only knows to
-          // call resize handlers for Shiny outputs, not for static
-          // widgets, so we do it ourselves.
-          if (window.jQuery) {
-            window.jQuery(document).on(
-              "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets",
-              resizeHandler
-            );
-            window.jQuery(document).on(
-              "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets",
-              resizeHandler
-            );
-          }
-
-          // This is needed for the specific case of ioslides, which
-          // flips slides between display:none and display:block.
-          // Ideally we would not have to have ioslide-specific code
-          // here, but rather have ioslides raise a generic event,
-          // but the rmarkdown package just went to CRAN so the
-          // window to getting that fixed may be long.
-          if (window.addEventListener) {
-            // It's OK to limit this to window.addEventListener
-            // browsers because ioslides itself only supports
-            // such browsers.
-            on(document, "slideenter", resizeHandler);
-            on(document, "slideleave", resizeHandler);
-          }
-        }
-
-        var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']");
-        if (scriptData) {
-          var data = JSON.parse(scriptData.textContent || scriptData.text);
-          // Resolve strings marked as javascript literals to objects
-          if (!(data.evals instanceof Array)) data.evals = [data.evals];
-          for (var k = 0; data.evals && k < data.evals.length; k++) {
-            window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]);
-          }
-          binding.renderValue(el, data.x, initResult);
-          evalAndRun(data.jsHooks.render, initResult, [el, data.x]);
-        }
-      });
-    });
-
-    invokePostRenderHandlers();
-  }
-
-
-  function has_jQuery3() {
-    if (!window.jQuery) {
-      return false;
-    }
-    var $version = window.jQuery.fn.jquery;
-    var $major_version = parseInt($version.split(".")[0]);
-    return $major_version >= 3;
-  }
-
-  /*
-  / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's
-  / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now
-  / really means $(setTimeout(fn)).
-  / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous
-  /
-  / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny
-  / one tick later than it did before, which means staticRender() is
-  / called renderValue() earlier than (advanced) widget authors might be expecting.
-  / https://github.com/rstudio/shiny/issues/2630
-  /
-  / For a concrete example, leaflet has some methods (e.g., updateBounds)
-  / which reference Shiny methods registered in initShiny (e.g., setInputValue).
-  / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to
-  / delay execution of those methods (until Shiny methods are ready)
-  / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268
-  /
-  / Ideally widget authors wouldn't need to use this setTimeout() hack that
-  / leaflet uses to call Shiny methods on a staticRender(). In the long run,
-  / the logic initShiny should be broken up so that method registration happens
-  / right away, but binding happens later.
-  */
-  function maybeStaticRenderLater() {
-    if (shinyMode && has_jQuery3()) {
-      window.jQuery(window.HTMLWidgets.staticRender);
-    } else {
-      window.HTMLWidgets.staticRender();
-    }
-  }
-
-  if (document.addEventListener) {
-    document.addEventListener("DOMContentLoaded", function() {
-      document.removeEventListener("DOMContentLoaded", arguments.callee, false);
-      maybeStaticRenderLater();
-    }, false);
-  } else if (document.attachEvent) {
-    document.attachEvent("onreadystatechange", function() {
-      if (document.readyState === "complete") {
-        document.detachEvent("onreadystatechange", arguments.callee);
-        maybeStaticRenderLater();
-      }
-    });
-  }
-
-
-  window.HTMLWidgets.getAttachmentUrl = function(depname, key) {
-    // If no key, default to the first item
-    if (typeof(key) === "undefined")
-      key = 1;
-
-    var link = document.getElementById(depname + "-" + key + "-attachment");
-    if (!link) {
-      throw new Error("Attachment " + depname + "/" + key + " not found in document");
-    }
-    return link.getAttribute("href");
-  };
-
-  window.HTMLWidgets.dataframeToD3 = function(df) {
-    var names = [];
-    var length;
-    for (var name in df) {
-        if (df.hasOwnProperty(name))
-            names.push(name);
-        if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") {
-            throw new Error("All fields must be arrays");
-        } else if (typeof(length) !== "undefined" && length !== df[name].length) {
-            throw new Error("All fields must be arrays of the same length");
-        }
-        length = df[name].length;
-    }
-    var results = [];
-    var item;
-    for (var row = 0; row < length; row++) {
-        item = {};
-        for (var col = 0; col < names.length; col++) {
-            item[names[col]] = df[names[col]][row];
-        }
-        results.push(item);
-    }
-    return results;
-  };
-
-  window.HTMLWidgets.transposeArray2D = function(array) {
-      if (array.length === 0) return array;
-      var newArray = array[0].map(function(col, i) {
-          return array.map(function(row) {
-              return row[i]
-          })
-      });
-      return newArray;
-  };
-  // Split value at splitChar, but allow splitChar to be escaped
-  // using escapeChar. Any other characters escaped by escapeChar
-  // will be included as usual (including escapeChar itself).
-  function splitWithEscape(value, splitChar, escapeChar) {
-    var results = [];
-    var escapeMode = false;
-    var currentResult = "";
-    for (var pos = 0; pos < value.length; pos++) {
-      if (!escapeMode) {
-        if (value[pos] === splitChar) {
-          results.push(currentResult);
-          currentResult = "";
-        } else if (value[pos] === escapeChar) {
-          escapeMode = true;
-        } else {
-          currentResult += value[pos];
-        }
-      } else {
-        currentResult += value[pos];
-        escapeMode = false;
-      }
-    }
-    if (currentResult !== "") {
-      results.push(currentResult);
-    }
-    return results;
-  }
-  // Function authored by Yihui/JJ Allaire
-  window.HTMLWidgets.evaluateStringMember = function(o, member) {
-    var parts = splitWithEscape(member, '.', '\\');
-    for (var i = 0, l = parts.length; i < l; i++) {
-      var part = parts[i];
-      // part may be a character or 'numeric' member name
-      if (o !== null && typeof o === "object" && part in o) {
-        if (i == (l - 1)) { // if we are at the end of the line then evalulate
-          if (typeof o[part] === "string")
-            o[part] = tryEval(o[part]);
-        } else { // otherwise continue to next embedded object
-          o = o[part];
-        }
-      }
-    }
-  };
-
-  // Retrieve the HTMLWidget instance (i.e. the return value of an
-  // HTMLWidget binding's initialize() or factory() function)
-  // associated with an element, or null if none.
-  window.HTMLWidgets.getInstance = function(el) {
-    return elementData(el, "init_result");
-  };
-
-  // Finds the first element in the scope that matches the selector,
-  // and returns the HTMLWidget instance (i.e. the return value of
-  // an HTMLWidget binding's initialize() or factory() function)
-  // associated with that element, if any. If no element matches the
-  // selector, or the first matching element has no HTMLWidget
-  // instance associated with it, then null is returned.
-  //
-  // The scope argument is optional, and defaults to window.document.
-  window.HTMLWidgets.find = function(scope, selector) {
-    if (arguments.length == 1) {
-      selector = scope;
-      scope = document;
-    }
-
-    var el = scope.querySelector(selector);
-    if (el === null) {
-      return null;
-    } else {
-      return window.HTMLWidgets.getInstance(el);
-    }
-  };
-
-  // Finds all elements in the scope that match the selector, and
-  // returns the HTMLWidget instances (i.e. the return values of
-  // an HTMLWidget binding's initialize() or factory() function)
-  // associated with the elements, in an array. If elements that
-  // match the selector don't have an associated HTMLWidget
-  // instance, the returned array will contain nulls.
-  //
-  // The scope argument is optional, and defaults to window.document.
-  window.HTMLWidgets.findAll = function(scope, selector) {
-    if (arguments.length == 1) {
-      selector = scope;
-      scope = document;
-    }
-
-    var nodes = scope.querySelectorAll(selector);
-    var results = [];
-    for (var i = 0; i < nodes.length; i++) {
-      results.push(window.HTMLWidgets.getInstance(nodes[i]));
-    }
-    return results;
-  };
-
-  var postRenderHandlers = [];
-  function invokePostRenderHandlers() {
-    while (postRenderHandlers.length) {
-      var handler = postRenderHandlers.shift();
-      if (handler) {
-        handler();
-      }
-    }
-  }
-
-  // Register the given callback function to be invoked after the
-  // next time static widgets are rendered.
-  window.HTMLWidgets.addPostRenderHandler = function(callback) {
-    postRenderHandlers.push(callback);
-  };
-
-  // Takes a new-style instance-bound definition, and returns an
-  // old-style class-bound definition. This saves us from having
-  // to rewrite all the logic in this file to accomodate both
-  // types of definitions.
-  function createLegacyDefinitionAdapter(defn) {
-    var result = {
-      name: defn.name,
-      type: defn.type,
-      initialize: function(el, width, height) {
-        return defn.factory(el, width, height);
-      },
-      renderValue: function(el, x, instance) {
-        return instance.renderValue(x);
-      },
-      resize: function(el, width, height, instance) {
-        return instance.resize(width, height);
-      }
-    };
-
-    if (defn.find)
-      result.find = defn.find;
-    if (defn.renderError)
-      result.renderError = defn.renderError;
-    if (defn.clearError)
-      result.clearError = defn.clearError;
-
-    return result;
-  }
-})();
diff --git a/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.css b/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.css
deleted file mode 100644
index fadef03..0000000
--- a/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.css
+++ /dev/null
@@ -1,4 +0,0 @@
-/*! noUiSlider - 7.0.10 - 2015-03-17 17:30:22 */
-
-
-.noUi-target,.noUi-target *{-webkit-touch-callout:none;-webkit-user-select:none;-ms-touch-action:none;-ms-user-select:none;-moz-user-select:none;-moz-box-sizing:border-box;box-sizing:border-box}.noUi-target{position:relative;direction:ltr}.noUi-base{width:100%;height:100%;position:relative}.noUi-origin{position:absolute;right:0;top:0;left:0;bottom:0}.noUi-handle{position:relative;z-index:1}.noUi-stacking .noUi-handle{z-index:10}.noUi-state-tap .noUi-origin{-webkit-transition:left .3s,top .3s;transition:left .3s,top .3s}.noUi-state-drag *{cursor:inherit!important}.noUi-base{-webkit-transform:translate3d(0,0,0);transform:translate3d(0,0,0)}.noUi-horizontal{height:10px}.noUi-horizontal .noUi-handle{width:24px;height:18px;left:-12px;top:-6px}.noUi-vertical{width:10px}.noUi-vertical .noUi-handle{width:18px;height:24px;left:-5px;top:-12px}.noUi-background{background:#FAFAFA;box-shadow:inset 0 1px 1px #f0f0f0}.noUi-connect{background:#3FB8AF;box-shadow:inset 0 0 3px rgba(51,51,51,.45);-webkit-transition:background 450ms;transition:background 450ms}.noUi-origin{border-radius:2px}.noUi-target{border-radius:4px;border:1px solid #D3D3D3;box-shadow:inset 0 1px 1px #F0F0F0,0 3px 6px -5px #BBB}.noUi-target.noUi-connect{box-shadow:inset 0 0 3px rgba(51,51,51,.45),0 3px 6px -5px #BBB}.noUi-dragable{cursor:w-resize}.noUi-vertical .noUi-base{height:135px;}.noUi-vertical .noUi-dragable{cursor:n-resize}.noUi-handle{border:1px solid #D9D9D9;border-radius:3px;background:#FFF;cursor:default;box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #EBEBEB,0 3px 6px -3px #BBB}.noUi-active{box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #DDD,0 3px 6px -3px #BBB}.noUi-handle:after,.noUi-handle:before{content:"";display:block;position:absolute;height:9px;width:1px;background:#E8E7E6;left:9px;top:3.5px}.noUi-handle:after{left:12px}.noUi-vertical .noUi-handle:after,.noUi-vertical .noUi-handle:before{width:9px;height:1px;left:3.5px;top:9px}.noUi-vertical .noUi-handle:after{top:12px}[disabled] .noUi-connect,[disabled].noUi-connect{background:#B8B8B8}[disabled] .noUi-handle{cursor:not-allowed}
diff --git a/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.js b/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.js
deleted file mode 100644
index 03b5244..0000000
--- a/articles/files_files/nouislider-7.0.10/jquery.nouislider.min.js
+++ /dev/null
@@ -1,3 +0,0 @@
-/*! noUiSlider - 7.0.10 - 2015-03-17 17:30:22 */
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diff --git a/articles/files_files/selectize-0.12.0/selectize.bootstrap3.css b/articles/files_files/selectize-0.12.0/selectize.bootstrap3.css
deleted file mode 100644
index 6779260..0000000
--- a/articles/files_files/selectize-0.12.0/selectize.bootstrap3.css
+++ /dev/null
@@ -1,401 +0,0 @@
-/**
- * selectize.bootstrap3.css (v0.12.0) - Bootstrap 3 Theme
- * Copyright (c) 2013–2015 Brian Reavis & contributors
- *
- * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
- * file except in compliance with the License. You may obtain a copy of the License at:
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software distributed under
- * the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
- * ANY KIND, either express or implied. See the License for the specific language
- * governing permissions and limitations under the License.
- *
- * @author Brian Reavis <brian@thirdroute.com>
- */
-.selectize-control.plugin-drag_drop.multi > .selectize-input > div.ui-sortable-placeholder {
-  visibility: visible !important;
-  background: #f2f2f2 !important;
-  background: rgba(0, 0, 0, 0.06) !important;
-  border: 0 none !important;
-  -webkit-box-shadow: inset 0 0 12px 4px #ffffff;
-  box-shadow: inset 0 0 12px 4px #ffffff;
-}
-.selectize-control.plugin-drag_drop .ui-sortable-placeholder::after {
-  content: '!';
-  visibility: hidden;
-}
-.selectize-control.plugin-drag_drop .ui-sortable-helper {
-  -webkit-box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2);
-  box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2);
-}
-.selectize-dropdown-header {
-  position: relative;
-  padding: 3px 12px;
-  border-bottom: 1px solid #d0d0d0;
-  background: #f8f8f8;
-  -webkit-border-radius: 4px 4px 0 0;
-  -moz-border-radius: 4px 4px 0 0;
-  border-radius: 4px 4px 0 0;
-}
-.selectize-dropdown-header-close {
-  position: absolute;
-  right: 12px;
-  top: 50%;
-  color: #333333;
-  opacity: 0.4;
-  margin-top: -12px;
-  line-height: 20px;
-  font-size: 20px !important;
-}
-.selectize-dropdown-header-close:hover {
-  color: #000000;
-}
-.selectize-dropdown.plugin-optgroup_columns .optgroup {
-  border-right: 1px solid #f2f2f2;
-  border-top: 0 none;
-  float: left;
-  -webkit-box-sizing: border-box;
-  -moz-box-sizing: border-box;
-  box-sizing: border-box;
-}
-.selectize-dropdown.plugin-optgroup_columns .optgroup:last-child {
-  border-right: 0 none;
-}
-.selectize-dropdown.plugin-optgroup_columns .optgroup:before {
-  display: none;
-}
-.selectize-dropdown.plugin-optgroup_columns .optgroup-header {
-  border-top: 0 none;
-}
-.selectize-control.plugin-remove_button [data-value] {
-  position: relative;
-  padding-right: 24px !important;
-}
-.selectize-control.plugin-remove_button [data-value] .remove {
-  z-index: 1;
-  /* fixes ie bug (see #392) */
-  position: absolute;
-  top: 0;
-  right: 0;
-  bottom: 0;
-  width: 17px;
-  text-align: center;
-  font-weight: bold;
-  font-size: 12px;
-  color: inherit;
-  text-decoration: none;
-  vertical-align: middle;
-  display: inline-block;
-  padding: 1px 0 0 0;
-  border-left: 1px solid rgba(0, 0, 0, 0);
-  -webkit-border-radius: 0 2px 2px 0;
-  -moz-border-radius: 0 2px 2px 0;
-  border-radius: 0 2px 2px 0;
-  -webkit-box-sizing: border-box;
-  -moz-box-sizing: border-box;
-  box-sizing: border-box;
-}
-.selectize-control.plugin-remove_button [data-value] .remove:hover {
-  background: rgba(0, 0, 0, 0.05);
-}
-.selectize-control.plugin-remove_button [data-value].active .remove {
-  border-left-color: rgba(0, 0, 0, 0);
-}
-.selectize-control.plugin-remove_button .disabled [data-value] .remove:hover {
-  background: none;
-}
-.selectize-control.plugin-remove_button .disabled [data-value] .remove {
-  border-left-color: rgba(77, 77, 77, 0);
-}
-.selectize-control {
-  position: relative;
-}
-.selectize-dropdown,
-.selectize-input,
-.selectize-input input {
-  color: #333333;
-  font-family: inherit;
-  font-size: inherit;
-  line-height: 20px;
-  -webkit-font-smoothing: inherit;
-}
-.selectize-input,
-.selectize-control.single .selectize-input.input-active {
-  background: #ffffff;
-  cursor: text;
-  display: inline-block;
-}
-.selectize-input {
-  border: 1px solid #cccccc;
-  padding: 6px 12px;
-  display: inline-block;
-  width: 100%;
-  overflow: hidden;
-  position: relative;
-  z-index: 1;
-  -webkit-box-sizing: border-box;
-  -moz-box-sizing: border-box;
-  box-sizing: border-box;
-  -webkit-box-shadow: none;
-  box-shadow: none;
-  -webkit-border-radius: 4px;
-  -moz-border-radius: 4px;
-  border-radius: 4px;
-}
-.selectize-control.multi .selectize-input.has-items {
-  padding: 5px 12px 2px;
-}
-.selectize-input.full {
-  background-color: #ffffff;
-}
-.selectize-input.disabled,
-.selectize-input.disabled * {
-  cursor: default !important;
-}
-.selectize-input.focus {
-  -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.15);
-  box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.15);
-}
-.selectize-input.dropdown-active {
-  -webkit-border-radius: 4px 4px 0 0;
-  -moz-border-radius: 4px 4px 0 0;
-  border-radius: 4px 4px 0 0;
-}
-.selectize-input > * {
-  vertical-align: baseline;
-  display: -moz-inline-stack;
-  display: inline-block;
-  zoom: 1;
-  *display: inline;
-}
-.selectize-control.multi .selectize-input > div {
-  cursor: pointer;
-  margin: 0 3px 3px 0;
-  padding: 1px 3px;
-  background: #efefef;
-  color: #333333;
-  border: 0 solid rgba(0, 0, 0, 0);
-}
-.selectize-control.multi .selectize-input > div.active {
-  background: #428bca;
-  color: #ffffff;
-  border: 0 solid rgba(0, 0, 0, 0);
-}
-.selectize-control.multi .selectize-input.disabled > div,
-.selectize-control.multi .selectize-input.disabled > div.active {
-  color: #808080;
-  background: #ffffff;
-  border: 0 solid rgba(77, 77, 77, 0);
-}
-.selectize-input > input {
-  display: inline-block !important;
-  padding: 0 !important;
-  min-height: 0 !important;
-  max-height: none !important;
-  max-width: 100% !important;
-  margin: 0 !important;
-  text-indent: 0 !important;
-  border: 0 none !important;
-  background: none !important;
-  line-height: inherit !important;
-  -webkit-user-select: auto !important;
-  -webkit-box-shadow: none !important;
-  box-shadow: none !important;
-}
-.selectize-input > input::-ms-clear {
-  display: none;
-}
-.selectize-input > input:focus {
-  outline: none !important;
-}
-.selectize-input::after {
-  content: ' ';
-  display: block;
-  clear: left;
-}
-.selectize-input.dropdown-active::before {
-  content: ' ';
-  display: block;
-  position: absolute;
-  background: #ffffff;
-  height: 1px;
-  bottom: 0;
-  left: 0;
-  right: 0;
-}
-.selectize-dropdown {
-  position: absolute;
-  z-index: 10;
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deleted file mode 100644
index fe955bc..0000000
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b=this,c=b.isFull(),d=b.isLocked;b.$wrapper.toggleClass("rtl",b.rtl),b.$control.toggleClass("focus",b.isFocused).toggleClass("disabled",b.isDisabled).toggleClass("required",b.isRequired).toggleClass("invalid",b.isInvalid).toggleClass("locked",d).toggleClass("full",c).toggleClass("not-full",!c).toggleClass("input-active",b.isFocused&&!b.isInputHidden).toggleClass("dropdown-active",b.isOpen).toggleClass("has-options",!a.isEmptyObject(b.options)).toggleClass("has-items",b.items.length>0),b.$control_input.data("grow",!c&&!d)},isFull:function(){return null!==this.settings.maxItems&&this.items.length>=this.settings.maxItems},updateOriginalInput:function(a){var b,c,d,e,f=this;if(a=a||{},f.tagType===v){for(d=[],b=0,c=f.items.length;c>b;b++)e=f.options[f.items[b]][f.settings.labelField]||"",d.push('<option value="'+A(f.items[b])+'" selected="selected">'+A(e)+"</option>");d.length||this.$input.attr("multiple")||d.push('<option value="" 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a=this.$control,b="body"===this.settings.dropdownParent?a.offset():a.position();b.top+=a.outerHeight(!0),this.$dropdown.css({width:a.outerWidth(),top:b.top,left:b.left})},clear:function(a){var b=this;b.items.length&&(b.$control.children(":not(input)").remove(),b.items=[],b.lastQuery=null,b.setCaret(0),b.setActiveItem(null),b.updatePlaceholder(),b.updateOriginalInput({silent:a}),b.refreshState(),b.showInput(),b.trigger("clear"))},insertAtCaret:function(b){var c=Math.min(this.caretPos,this.items.length);0===c?this.$control.prepend(b):a(this.$control[0].childNodes[c]).before(b),this.setCaret(c+1)},deleteSelection:function(b){var 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c,d,e=this;0!==a&&(c=a>0?"next":"prev",e.isShiftDown?(d=e.$control_input[c](),d.length&&(e.hideInput(),e.setActiveItem(d),b&&b.preventDefault())):e.setCaret(e.caretPos+a))},setCaret:function(b){var c=this;if(b="single"===c.settings.mode?c.items.length:Math.max(0,Math.min(c.items.length,b)),!c.isPending){var d,e,f,g;for(f=c.$control.children(":not(input)"),d=0,e=f.length;e>d;d++)g=a(f[d]).detach(),b>d?c.$control_input.before(g):c.$control.append(g)}c.caretPos=b},lock:function(){this.close(),this.isLocked=!0,this.refreshState()},unlock:function(){this.isLocked=!1,this.refreshState()},disable:function(){var a=this;a.$input.prop("disabled",!0),a.$control_input.prop("disabled",!0).prop("tabindex",-1),a.isDisabled=!0,a.lock()},enable:function(){var a=this;a.$input.prop("disabled",!1),a.$control_input.prop("disabled",!1).prop("tabindex",a.tabIndex),a.isDisabled=!1,a.unlock()},destroy:function(){var 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c=a.fn.selectize.defaults,d=a.extend({},c,b),e=d.dataAttr,f=d.labelField,g=d.valueField,h=d.optgroupField,i=d.optgroupLabelField,j=d.optgroupValueField,k=function(b,c){var h,i,j,k,l=b.attr(e);if(l)for(c.options=JSON.parse(l),h=0,i=c.options.length;i>h;h++)c.items.push(c.options[h][g]);else{var m=a.trim(b.val()||"");if(!d.allowEmptyOption&&!m.length)return;for(j=m.split(d.delimiter),h=0,i=j.length;i>h;h++)k={},k[f]=j[h],k[g]=j[h],c.options.push(k);c.items=j}},l=function(b,c){var k,l,m,n,o=c.options,p={},q=function(a){var b=e&&a.attr(e);return"string"==typeof b&&b.length?JSON.parse(b):null},r=function(b,e){b=a(b);var i=z(b.attr("value"));if(i||d.allowEmptyOption)if(p.hasOwnProperty(i)){if(e){var j=p[i][h];j?a.isArray(j)?j.push(e):p[i][h]=[j,e]:p[i][h]=e}}else{var k=q(b)||{};k[f]=k[f]||b.text(),k[g]=k[g]||i,k[h]=k[h]||e,p[i]=k,o.push(k),b.is(":selected")&&c.items.push(i)}},s=function(b){var d,e,f,g,h;for(b=a(b),f=b.attr("label"),f&&(g=q(b)||{},g[i]=f,g[j]=f,c.optgroups.push(g)),h=a("option",b),d=0,e=h.length;e>d;d++)r(h[d],f)};for(c.maxItems=b.attr("multiple")?null:1,n=b.children(),k=0,l=n.length;l>k;k++)m=n[k].tagName.toLowerCase(),"optgroup"===m?s(n[k]):"option"===m&&r(n[k])};return this.each(function(){if(!this.selectize){var e,f=a(this),g=this.tagName.toLowerCase(),h=f.attr("placeholder")||f.attr("data-placeholder");h||d.allowEmptyOption||(h=f.children('option[value=""]').text());var i={placeholder:h,options:[],optgroups:[],items:[]};"select"===g?l(f,i):k(f,i),e=new L(f,a.extend(!0,{},c,i,b))}})},a.fn.selectize.defaults=L.defaults,a.fn.selectize.support={validity:x},L.define("drag_drop",function(){if(!a.fn.sortable)throw new Error('The "drag_drop" plugin requires jQuery UI "sortable".');if("multi"===this.settings.mode){var b=this;b.lock=function(){var a=b.lock;return function(){var c=b.$control.data("sortable");return c&&c.disable(),a.apply(b,arguments)}}(),b.unlock=function(){var a=b.unlock;return function(){var c=b.$control.data("sortable");return c&&c.enable(),a.apply(b,arguments)}}(),b.setup=function(){var c=b.setup;return function(){c.apply(this,arguments);var d=b.$control.sortable({items:"[data-value]",forcePlaceholderSize:!0,disabled:b.isLocked,start:function(a,b){b.placeholder.css("width",b.helper.css("width")),d.css({overflow:"visible"})},stop:function(){d.css({overflow:"hidden"});var c=b.$activeItems?b.$activeItems.slice():null,e=[];d.children("[data-value]").each(function(){e.push(a(this).attr("data-value"))}),b.setValue(e),b.setActiveItem(c)}})}}()}}),L.define("dropdown_header",function(b){var c=this;b=a.extend({title:"Untitled",headerClass:"selectize-dropdown-header",titleRowClass:"selectize-dropdown-header-title",labelClass:"selectize-dropdown-header-label",closeClass:"selectize-dropdown-header-close",html:function(a){return'<div class="'+a.headerClass+'"><div class="'+a.titleRowClass+'"><span class="'+a.labelClass+'">'+a.title+'</span><a href="javascript:void(0)" class="'+a.closeClass+'">&times;</a></div></div>'}},b),c.setup=function(){var d=c.setup;return function(){d.apply(c,arguments),c.$dropdown_header=a(b.html(b)),c.$dropdown.prepend(c.$dropdown_header)}}()}),L.define("optgroup_columns",function(b){var c=this;b=a.extend({equalizeWidth:!0,equalizeHeight:!0},b),this.getAdjacentOption=function(b,c){var d=b.closest("[data-group]").find("[data-selectable]"),e=d.index(b)+c;return e>=0&&e<d.length?d.eq(e):a()},this.onKeyDown=function(){var a=c.onKeyDown;return function(b){var d,e,f,g;return!this.isOpen||b.keyCode!==j&&b.keyCode!==m?a.apply(this,arguments):(c.ignoreHover=!0,g=this.$activeOption.closest("[data-group]"),d=g.find("[data-selectable]").index(this.$activeOption),g=b.keyCode===j?g.prev("[data-group]"):g.next("[data-group]"),f=g.find("[data-selectable]"),e=f.eq(Math.min(f.length-1,d)),void(e.length&&this.setActiveOption(e)))}}();var d=function(){var a,b=d.width,c=document;return"undefined"==typeof b&&(a=c.createElement("div"),a.innerHTML='<div style="width:50px;height:50px;position:absolute;left:-50px;top:-50px;overflow:auto;"><div style="width:1px;height:100px;"></div></div>',a=a.firstChild,c.body.appendChild(a),b=d.width=a.offsetWidth-a.clientWidth,c.body.removeChild(a)),b},e=function(){var e,f,g,h,i,j,k;if(k=a("[data-group]",c.$dropdown_content),f=k.length,f&&c.$dropdown_content.width()){if(b.equalizeHeight){for(g=0,e=0;f>e;e++)g=Math.max(g,k.eq(e).height());k.css({height:g})}b.equalizeWidth&&(j=c.$dropdown_content.innerWidth()-d(),h=Math.round(j/f),k.css({width:h}),f>1&&(i=j-h*(f-1),k.eq(f-1).css({width:i})))}};(b.equalizeHeight||b.equalizeWidth)&&(C.after(this,"positionDropdown",e),C.after(this,"refreshOptions",e))}),L.define("remove_button",function(b){if("single"!==this.settings.mode){b=a.extend({label:"&times;",title:"Remove",className:"remove",append:!0},b);var c=this,d='<a href="javascript:void(0)" class="'+b.className+'" tabindex="-1" title="'+A(b.title)+'">'+b.label+"</a>",e=function(a,b){var c=a.search(/(<\/[^>]+>\s*)$/);return a.substring(0,c)+b+a.substring(c)};this.setup=function(){var f=c.setup;return function(){if(b.append){var g=c.settings.render.item;c.settings.render.item=function(){return e(g.apply(this,arguments),d)}}f.apply(this,arguments),this.$control.on("click","."+b.className,function(b){if(b.preventDefault(),!c.isLocked){var d=a(b.currentTarget).parent();c.setActiveItem(d),c.deleteSelection()&&c.setCaret(c.items.length)}})}}()}}),L.define("restore_on_backspace",function(a){var b=this;a.text=a.text||function(a){return a[this.settings.labelField]},this.onKeyDown=function(){var c=b.onKeyDown;return function(b){var d,e;return b.keyCode===p&&""===this.$control_input.val()&&!this.$activeItems.length&&(d=this.caretPos-1,d>=0&&d<this.items.length)?(e=this.options[this.items[d]],this.deleteSelection(b)&&(this.setTextboxValue(a.text.apply(this,[e])),this.refreshOptions(!0)),void b.preventDefault()):c.apply(this,arguments)}}()}),L});
\ No newline at end of file
diff --git a/articles/flames.html b/articles/flames.html
index b48599d..11be1aa 100644
--- a/articles/flames.html
+++ b/articles/flames.html
@@ -11,7 +11,7 @@
 <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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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">
+<!-- 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>
@@ -22,11 +22,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -43,6 +43,7 @@
   <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>
@@ -137,13 +138,11 @@ <h3 id="germline-duplication-rate">Germline duplication rate<a class="anchor" ar
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<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>
+  <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></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/index.html b/articles/index.html
index 01eccf9..6bd9039 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -52,7 +53,7 @@
 
     <div class="section ">
       <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+      <div class="section-desc"></div>
 
       <dl><dt><a href="developers.html">Developers</a></dt>
         <dd>
@@ -65,11 +66,11 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/authors.html b/authors.html
index 73f5134..a2b12d1 100644
--- a/authors.html
+++ b/authors.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -83,11 +84,11 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
index 5524910..7204d3a 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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#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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.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-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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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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(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 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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, ".") 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";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 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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' 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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: 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#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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.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-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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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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(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 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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, ".") 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";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 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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' 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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: 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#3f79bc;background:linear-gradient(var(--bg-gradient-deg, 140deg), #029acf var(--bg-gradient-start, 36%), #9b479f var(--bg-gradient-end, 180%)) #3f79bc;color:#fff}.bg-gradient-cyan-pink{--bslib-color-fg: #fff;--bslib-color-bg: #5e75b4;background:linear-gradient(var(--bg-gradient-deg, 140deg), #029acf var(--bg-gradient-start, 36%), #e83e8c var(--bg-gradient-end, 180%)) #5e75b4;color:#fff}.bg-gradient-cyan-red{--bslib-color-fg: #fff;--bslib-color-bg: #586a82;background:linear-gradient(var(--bg-gradient-deg, 140deg), #029acf var(--bg-gradient-start, 36%), #d9230f var(--bg-gradient-end, 180%)) #586a82;color:#fff}.bg-gradient-cyan-orange{--bslib-color-fg: #fff;--bslib-color-bg: #589189;background:linear-gradient(var(--bg-gradient-deg, 140deg), #029acf var(--bg-gradient-start, 36%), #d9831f var(--bg-gradient-end, 180%)) #589189;color:#fff}.bg-gradient-cyan-yellow{--bslib-color-fg: #000;--bslib-color-bg: #67aa7f;background:linear-gradient(var(--bg-gradient-deg, 140deg), #029acf 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#bd1e0d}.btn-secondary,.btn-default:not(.btn-primary):not(.btn-info):not(.btn-success):not(.btn-warning):not(.btn-danger):not(.btn-dark):not(.btn-light):not([class*='btn-outline-']),.btn-secondary:hover{background-image:linear-gradient(#fff, #fff 6%, #f0f0f0);filter:none;border:1px solid #dedede}.btn-secondary:focus,.btn-default:focus:not(.btn-primary):not(.btn-info):not(.btn-success):not(.btn-warning):not(.btn-danger):not(.btn-dark):not(.btn-light):not([class*='btn-outline-']),.btn-secondary:not([disabled]):not(.disabled):active,.btn-default:not([disabled]):not(.disabled):active:not(.btn-primary):not(.btn-info):not(.btn-success):not(.btn-warning):not(.btn-danger):not(.btn-dark):not(.btn-light):not([class*='btn-outline-']),.btn-secondary:not([disabled]):not(.disabled).active,.btn-default:not([disabled]):not(.disabled).active:not(.btn-primary):not(.btn-info):not(.btn-success):not(.btn-warning):not(.btn-danger):not(.btn-dark):not(.btn-light):not([class*='btn-outline-']){box-shadow:0 0 0 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solid #dedede}.pagination .page-link:hover{text-decoration:none}.badge.bg-secondary,.badge.bg-light{color:#373a3c}.row>main{max-width:50rem}@media (min-width: 1200px) and (max-width: 1399.98px){.container .row{justify-content:space-evenly}}@media (min-width: 1400px){body{font-size:18px}.col-md-3{margin-left:5rem}}.navbar-nav .nav-item>.nav-link{border-radius:.375rem;padding:0.5rem}.navbar>.container{align-items:baseline;-webkit-align-items:baseline}.navbar-light .navbar-nav .active>.nav-link{background:#ddd;color:#212529}.navbar-dark .navbar-nav .active>.nav-link{background:#373a3c;color:#fcfcfc}.navbar-dark .navbar-nav .nav-item>.nav-link:hover,.navbar-light .navbar-nav .nav-item>.nav-link:hover{background:rgba(217,35,15,0.1)}.navbar-dark input[type="search"]{border-color:#777;background-color:#212529;color:#ddd}input[type="search"]{border-color:#ccc;width:12rem}.headroom{will-change:transform;transition:transform 400ms ease}.headroom--pinned{transform:translateY(0%)}.headroom--unpinned{transform:translateY(-100%)}.row>main,.row>aside{margin-top:100px}html,body{scroll-padding:100px}@media (min-width: 576px){#toc{position:sticky;top:100px;max-height:calc(100vh - 100px - 1rem);overflow-y:auto}}aside h2,aside .h2{margin-top:1.5rem;font-size:1.25rem}aside .roles{color:#4d5053}aside .list-unstyled li{margin-bottom:0.5rem}aside .dev-status .list-unstyled li{margin-bottom:0.1rem}@media (max-width: 575.98px){aside{margin:0.5rem;width:calc(100vw - 1rem);background-color:#f8f9fa;border-color:#ccc;border-radius:.375rem}aside h2:first-child,aside .h2:first-child{margin-top:1rem}}body{position:relative}#toc>.nav{margin-bottom:1rem}#toc>.nav a.nav-link{color:inherit;padding:0.25rem 0.5rem;margin-bottom:2px;border-radius:.375rem;border:0 solid #ccc}#toc>.nav a.nav-link:hover,#toc>.nav a.nav-link:focus{background-color:rgba(217,35,15,0.1);color:#000}#toc>.nav a.nav-link.active{background-color:#e6e7e7;color:#000}#toc>.nav .nav a.nav-link{margin-left:0.5rem}#toc>.nav .nav{display:none !important}#toc>.nav a.active+.nav{display:flex !important}footer{margin:1rem 0 1rem 0;padding-top:1rem;font-size:.875em;border-top:1px solid #ccc;background:rgba(0,0,0,0);color:#4d5053;display:flex;column-gap:1rem}@media (max-width: 575.98px){footer{flex-direction:column}}@media (min-width: 576px){footer .pkgdown-footer-right{text-align:right}}footer div{flex:1 1 auto}html,body{height:100%}body>.container{min-height:100%;display:flex;flex-direction:column}body>.container .row{flex:1 0 auto}::selection{background-color:#f5d1cd}main img{max-width:100%;height:auto}main table{display:block;overflow:auto}body{font-display:fallback}.page-header{border-bottom:1px solid #ccc;padding-bottom:0.5rem;margin-bottom:0.5rem;margin-top:1.5rem}dd{margin-left:1.5rem}summary{margin-bottom:0.5rem}details{margin-bottom:1rem}.html-widget{margin-bottom:1rem}a.anchor{display:none;margin-left:5px;width:Min(0.9em, 20px);height:Min(0.9em, 20px);background-image:url(../../link.svg);background-repeat:no-repeat;background-size:Min(0.9em, 20px) Min(0.9em, 20px);background-position:center center}h2:hover .anchor,.h2:hover .anchor,h3:hover .anchor,.h3:hover .anchor,h4:hover .anchor,.h4:hover .anchor,h5:hover .anchor,.h5:hover .anchor,h6:hover .anchor,.h6:hover .anchor{display:inline-block}.orcid{color:#A6CE39;margin-right:4px}.fab{font-family:"Font Awesome 5 Brands" !important}img.logo{float:right;width:100px;margin-left:30px}.template-home img.logo{width:120px}@media (max-width: 575.98px){img.logo{width:80px}}@media (min-width: 576px){.page-header{min-height:88px}.template-home .page-header{min-height:104px}}.line-block{margin-bottom:1rem}.template-reference-index 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diff --git a/deps/bootstrap-5.3.1/font.css b/deps/bootstrap-5.3.1/font.css
index e1ef484..3c41ba7 100644
--- a/deps/bootstrap-5.3.1/font.css
+++ b/deps/bootstrap-5.3.1/font.css
@@ -1,16 +1,200 @@
+/* cyrillic-ext */
 @font-face {
   font-family: 'Open Sans';
   font-style: normal;
   font-weight: 400;
-  font-stretch: normal;
+  font-stretch: 100%;
   font-display: swap;
-  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff) format('woff');
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
 }
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2) format('woff2');
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F, U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2) format('woff2');
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2) format('woff2');
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2) format('woff2');
+  unicode-range: U+0370-0377, U+037A-037F, U+0384-038A, U+038C, U+038E-03A1, U+03A3-03FF;
+}
+/* hebrew */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2) format('woff2');
+  unicode-range: U+0590-05FF, U+200C-2010, U+20AA, U+25CC, U+FB1D-FB4F;
+}
+/* math */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2) format('woff2');
+  unicode-range: U+0302-0303, U+0305, U+0307-0308, U+0330, U+0391-03A1, U+03A3-03A9, U+03B1-03C9, U+03D1, U+03D5-03D6, U+03F0-03F1, U+03F4-03F5, U+2034-2037, U+2057, U+20D0-20DC, U+20E1, U+20E5-20EF, U+2102, U+210A-210E, U+2110-2112, U+2115, U+2119-211D, U+2124, U+2128, U+212C-212D, U+212F-2131, U+2133-2138, U+213C-2140, U+2145-2149, U+2190, U+2192, U+2194-21AE, U+21B0-21E5, U+21F1-21F2, U+21F4-2211, U+2213-2214, U+2216-22FF, U+2308-230B, U+2310, U+2319, U+231C-2321, U+2336-237A, U+237C, U+2395, U+239B-23B6, U+23D0, U+23DC-23E1, U+2474-2475, U+25AF, U+25B3, U+25B7, U+25BD, U+25C1, U+25CA, U+25CC, U+25FB, U+266D-266F, U+27C0-27FF, U+2900-2AFF, U+2B0E-2B11, U+2B30-2B4C, U+2BFE, U+FF5B, U+FF5D, U+1D400-1D7FF, U+1EE00-1EEFF;
+}
+/* symbols */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2) format('woff2');
+  unicode-range: U+0001-000C, U+000E-001F, U+007F-009F, U+20DD-20E0, U+20E2-20E4, U+2150-218F, U+2190, U+2192, U+2194-2199, U+21AF, U+21E6-21F0, U+21F3, U+2218-2219, U+2299, U+22C4-22C6, U+2300-243F, U+2440-244A, U+2460-24FF, U+25A0-27BF, U+2800-28FF, U+2921-2922, U+2981, U+29BF, U+29EB, U+2B00-2BFF, U+4DC0-4DFF, U+FFF9-FFFB, U+10140-1018E, U+10190-1019C, U+101A0, U+101D0-101FD, U+102E0-102FB, U+10E60-10E7E, U+1D2C0-1D2D3, U+1D2E0-1D37F, U+1F000-1F0FF, U+1F100-1F1AD, U+1F1E6-1F1FF, U+1F30D-1F30F, U+1F315, U+1F31C, U+1F31E, U+1F320-1F32C, U+1F336, U+1F378, U+1F37D, U+1F382, U+1F393-1F39F, U+1F3A7-1F3A8, U+1F3AC-1F3AF, U+1F3C2, U+1F3C4-1F3C6, U+1F3CA-1F3CE, U+1F3D4-1F3E0, U+1F3ED, U+1F3F1-1F3F3, U+1F3F5-1F3F7, U+1F408, U+1F415, U+1F41F, U+1F426, U+1F43F, U+1F441-1F442, U+1F444, U+1F446-1F449, U+1F44C-1F44E, U+1F453, U+1F46A, U+1F47D, U+1F4A3, U+1F4B0, U+1F4B3, U+1F4B9, U+1F4BB, U+1F4BF, U+1F4C8-1F4CB, U+1F4D6, U+1F4DA, U+1F4DF, U+1F4E3-1F4E6, U+1F4EA-1F4ED, U+1F4F7, U+1F4F9-1F4FB, U+1F4FD-1F4FE, U+1F503, U+1F507-1F50B, U+1F50D, U+1F512-1F513, U+1F53E-1F54A, U+1F54F-1F5FA, U+1F610, U+1F650-1F67F, U+1F687, U+1F68D, U+1F691, U+1F694, U+1F698, U+1F6AD, U+1F6B2, U+1F6B9-1F6BA, U+1F6BC, U+1F6C6-1F6CF, U+1F6D3-1F6D7, U+1F6E0-1F6EA, U+1F6F0-1F6F3, U+1F6F7-1F6FC, U+1F700-1F7FF, U+1F800-1F80B, U+1F810-1F847, U+1F850-1F859, U+1F860-1F887, U+1F890-1F8AD, U+1F8B0-1F8B1, U+1F900-1F90B, U+1F93B, U+1F946, U+1F984, U+1F996, U+1F9E9, U+1FA00-1FA6F, U+1FA70-1FA7C, U+1FA80-1FA88, U+1FA90-1FABD, U+1FABF-1FAC5, U+1FACE-1FADB, U+1FAE0-1FAE8, U+1FAF0-1FAF8, U+1FB00-1FBFF;
+}
+/* vietnamese */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2) format('woff2');
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: 100%;
+  font-display: swap;
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2) format('woff2');
+  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20C0, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
 @font-face {
   font-family: 'Open Sans';
   font-style: normal;
   font-weight: 700;
-  font-stretch: normal;
+  font-stretch: 100%;
   font-display: swap;
-  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff) format('woff');
+  src: url(fonts/memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
 }
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diff --git a/index.html b/index.html
index ba14655..8b5778f 100644
--- a/index.html
+++ b/index.html
@@ -11,7 +11,7 @@
 <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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Post-processing DRAGEN workflows">
+<!-- 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="Post-processing DRAGEN workflows">
 <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]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -22,11 +22,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -43,6 +43,7 @@
   <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>
@@ -91,7 +92,7 @@
 <div class="section level2">
 <h2 id="id_-aim">🏆 Aim<a class="anchor" aria-label="anchor" href="#id_-aim"></a>
 </h2>
-<p>Given a <a href="https://developer.illumina.com/illumina-connected-analytics" class="external-link">ICA GDS</a> 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>
+<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>
@@ -129,11 +130,11 @@ <h2 id="id_-installation">🍕 Installation<a class="anchor" aria-label="anchor"
 <div class="section level2">
 <h2 id="id_-supported-workflows">✨ Supported Workflows<a class="anchor" aria-label="anchor" href="#id_-supported-workflows"></a>
 </h2>
-<p>{dracarys} supports most outputs from the following UMCCR workflows, including their <a href="https://multiqc.info/" class="external-link">MultiQC</a> JSON output.</p>
+<p>{dracarys} supports most outputs from the following UMCCR workflows:</p>
 <table class="table">
 <colgroup>
-<col width="12%">
-<col width="87%">
+<col width="13%">
+<col width="86%">
 </colgroup>
 <thead><tr class="header">
 <th>Workflow</th>
@@ -142,31 +143,53 @@ <h2 id="id_-supported-workflows">✨ Supported Workflows<a class="anchor" aria-l
 <tbody>
 <tr class="odd">
 <td>bcl_convert</td>
-<td>BCLConvert workflow (only MultiQC JSON)</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">
 <td>tso_ctdna_tumor_only</td>
-<td>UMCCR <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>
+<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">
 <td>wgs_alignment_qc</td>
-<td>UMCCR <a href="https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/GPipelineIntro_fDG.htm" class="external-link">DRAGEN DNA</a> (alignment)</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">
-<td>wts_tumor_only</td>
-<td></td>
+<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">
-<td>wgs_tumor_normal</td>
-<td>UMCCR Tumor/Normal DRAGEN workflow</td>
+<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">
-<td>umccrise</td>
-<td>UMCCR <a href="https://github.com/umccr/umccrise" class="external-link">umccrise</a> workflow</td>
+<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">
+<td>umccrise</td>
+<td>
+<a href="https://github.com/umccr/umccrise" class="external-link">umccrise</a> workflow</td>
+</tr>
+<tr class="even">
 <td>rnasum</td>
-<td>UMCCR <a href="rnasum-web">RNAsum</a> workflow</td>
+<td>
+<a href="https://github.com/umccr/RNAsum" class="external-link">RNAsum</a> workflow</td>
+</tr>
+<tr class="odd">
+<td>sash</td>
+<td>
+<a href="https://github.com/scwatts/sash" class="external-link">sash</a> workflow</td>
+</tr>
+<tr class="even">
+<td>oncoanalyser</td>
+<td>
+<a href="https://github.com/nf-core/oncoanalyser" class="external-link">oncoanalyser</a> workflow</td>
 </tr>
 </tbody>
 </table>
@@ -184,7 +207,7 @@ <h2 id="id_-cli">🌀 CLI<a class="anchor" aria-label="anchor" href="#id_-cli"><
 <div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="va">dracarys_cli</span><span class="op">=</span><span class="va">$(</span><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'x = system.file("cli", package = "dracarys"); cat(x, "\n")'</span> <span class="kw">|</span> <span class="fu">xargs</span><span class="va">)</span></span>
 <span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="bu">export</span> <span class="va">PATH</span><span class="op">=</span><span class="st">"</span><span class="va">${dracarys_cli}</span><span class="st">:</span><span class="va">${PATH}</span><span class="st">"</span></span></code></pre></div>
 <div class="sourceCode" id="cb6"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a>dracarys.R <span class="sc">--</span>version</span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>dracarys.R <span class="dv">0</span>.<span class="fl">10.0</span></span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>dracarys.R <span class="dv">0</span>.<span class="fl">14.0</span></span>
 <span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
 <span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co">#-----------------------------------#</span></span>
 <span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>dracarys.R <span class="sc">--</span>help</span>
@@ -204,24 +227,24 @@ <h2 id="id_-cli">🌀 CLI<a class="anchor" aria-label="anchor" href="#id_-cli"><
 <span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a><span class="st">#------- Tidy ----------------------#</span></span>
 <span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a><span class="st">dracarys.R tidy --help</span></span>
 <span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="st">usage: dracarys.R tidy [-h] -i IN_DIR -o OUT_DIR -p PREFIX [-t TOKEN]</span></span>
-<span id="cb6-22"><a href="#cb6-22" tabindex="-1"></a><span class="st">                       [-g GDS_LOCAL_DIR] [-f {tsv,parquet,both}] [-n] [-q]</span></span>
+<span id="cb6-22"><a href="#cb6-22" tabindex="-1"></a><span class="st">                       [-l LOCAL_DIR] [-f FORMAT] [-n] [-q]</span></span>
 <span id="cb6-23"><a href="#cb6-23" tabindex="-1"></a></span>
 <span id="cb6-24"><a href="#cb6-24" tabindex="-1"></a><span class="st">options:</span></span>
 <span id="cb6-25"><a href="#cb6-25" tabindex="-1"></a><span class="st">  -h, --help            show this help message and exit</span></span>
 <span id="cb6-26"><a href="#cb6-26" tabindex="-1"></a><span class="st">  -i IN_DIR, --in_dir IN_DIR</span></span>
 <span id="cb6-27"><a href="#cb6-27" tabindex="-1"></a><span class="st">                        ⛄️ Directory with untidy UMCCR workflow results. Can</span></span>
-<span id="cb6-28"><a href="#cb6-28" tabindex="-1"></a><span class="st">                        be GDS or local.</span></span>
+<span id="cb6-28"><a href="#cb6-28" tabindex="-1"></a><span class="st">                        be GDS, S3 or local.</span></span>
 <span id="cb6-29"><a href="#cb6-29" tabindex="-1"></a><span class="st">  -o OUT_DIR, --out_dir OUT_DIR</span></span>
 <span id="cb6-30"><a href="#cb6-30" tabindex="-1"></a><span class="st">                        🔥 Directory to output tidy results.</span></span>
 <span id="cb6-31"><a href="#cb6-31" tabindex="-1"></a><span class="st">  -p PREFIX, --prefix PREFIX</span></span>
 <span id="cb6-32"><a href="#cb6-32" tabindex="-1"></a><span class="st">                        🎻 Prefix string used for all results.</span></span>
 <span id="cb6-33"><a href="#cb6-33" tabindex="-1"></a><span class="st">  -t TOKEN, --token TOKEN</span></span>
 <span id="cb6-34"><a href="#cb6-34" tabindex="-1"></a><span class="st">                        🙈 ICA access token. Default: ICA_ACCESS_TOKEN env var.</span></span>
-<span id="cb6-35"><a href="#cb6-35" tabindex="-1"></a><span class="st">  -g GDS_LOCAL_DIR, --gds_local_dir GDS_LOCAL_DIR</span></span>
-<span id="cb6-36"><a href="#cb6-36" tabindex="-1"></a><span class="st">                        📥 If input is a GDS directory, download the</span></span>
+<span id="cb6-35"><a href="#cb6-35" tabindex="-1"></a><span class="st">  -l LOCAL_DIR, --local_dir LOCAL_DIR</span></span>
+<span id="cb6-36"><a href="#cb6-36" tabindex="-1"></a><span class="st">                        📥 If input is a GDS/S3 directory, download the</span></span>
 <span id="cb6-37"><a href="#cb6-37" tabindex="-1"></a><span class="st">                        recognisable files to this directory. Default:</span></span>
-<span id="cb6-38"><a href="#cb6-38" tabindex="-1"></a><span class="st">                        '</span><span class="sc">&lt;</span>out_dir<span class="sc">&gt;</span><span class="er">/</span>dracarys_gds_sync<span class="st">'.</span></span>
-<span id="cb6-39"><a href="#cb6-39" tabindex="-1"></a><span class="st">  -f {tsv,parquet,both}, --format {tsv,parquet,both}</span></span>
+<span id="cb6-38"><a href="#cb6-38" tabindex="-1"></a><span class="st">                        '</span><span class="sc">&lt;</span>out_dir<span class="sc">&gt;</span><span class="er">/</span>dracarys_<span class="sc">&lt;</span>gds<span class="sc">|</span>s3<span class="sc">&gt;</span>_sync<span class="st">'.</span></span>
+<span id="cb6-39"><a href="#cb6-39" tabindex="-1"></a><span class="st">  -f FORMAT, --format FORMAT</span></span>
 <span id="cb6-40"><a href="#cb6-40" tabindex="-1"></a><span class="st">                        🎨 Format of output. Default: tsv.</span></span>
 <span id="cb6-41"><a href="#cb6-41" tabindex="-1"></a><span class="st">  -n, --dryrun          🐫 Dry run - just show files to be tidied.</span></span>
 <span id="cb6-42"><a href="#cb6-42" tabindex="-1"></a><span class="st">  -q, --quiet           😴 Shush all the logs.</span></span></code></pre></div>
@@ -273,9 +296,8 @@ <h2 data-toc-skip>Links</h2>
 <div class="license">
 <h2 data-toc-skip>License</h2>
 <ul class="list-unstyled">
-<li>
-<a href="https://opensource.org/licenses/mit-license.php" class="external-link">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
+<li><a href="LICENSE.html">Full license</a></li>
+<li><small><a href="https://opensource.org/licenses/mit-license.php" class="external-link">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a></small></li>
 </ul>
 </div>
 
@@ -310,13 +332,11 @@ <h2 data-toc-skip>Developers</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<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>
+  <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></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/news/index.html b/news/index.html
index 0946839..518dbcb 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -51,6 +52,18 @@
       <small>Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.14.0" id="dracarys-0140-2024-05-13">dracarys 0.14.0 (2024-05-13)<a class="anchor" aria-label="anchor" href="#dracarys-0140-2024-05-13"></a></h2>
+<p><a href="https://github.com/umccr/dracarys/compare/v0.13.0...v0.14.0" class="external-link">0.13.0 - 0.14.0 diff</a></p>
+</div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.13.0" id="dracarys-0130-2024-03-15">dracarys 0.13.0 (2024-03-15)<a class="anchor" aria-label="anchor" href="#dracarys-0130-2024-03-15"></a></h2>
+<p><a href="https://github.com/umccr/dracarys/compare/v0.12.0...v0.13.0" class="external-link">0.12.0 - 0.13.0 diff</a></p>
+</div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.12.0" id="dracarys-0120-2023-12-12">dracarys 0.12.0 (2023-12-12)<a class="anchor" aria-label="anchor" href="#dracarys-0120-2023-12-12"></a></h2>
+<p><a href="https://github.com/umccr/dracarys/compare/v0.11.0...v0.12.0" class="external-link">0.11.0 - 0.12.0 diff</a></p>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.11.0" id="dracarys-0110-2023-08-22">dracarys 0.11.0 (2023-08-22)<a class="anchor" aria-label="anchor" href="#dracarys-0110-2023-08-22"></a></h2>
 <p><a href="https://github.com/umccr/dracarys/compare/v0.10.0...v0.11.0" class="external-link">0.10.0 - 0.11.0 diff</a></p>
@@ -195,11 +208,11 @@ <h2 class="pkg-version" data-toc-text="0.1.0" id="dracarys-010-2022-07-11">draca
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/pkgdown.js b/pkgdown.js
index 5fccd9c..9bd6621 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -30,10 +30,10 @@
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
+    var tooltipOriginalTitle=element.getAttribute('data-bs-original-title');
+    element.setAttribute('data-bs-original-title', msg);
     $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    element.setAttribute('data-bs-original-title', tooltipOriginalTitle);
   }
 
   if(ClipboardJS.isSupported()) {
@@ -60,7 +60,7 @@
         e.clearSelection();
       });
 
-      clipboard.on('error', function() {
+      clipboard.on('error', function(e) {
         changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
       });
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 91c0ba3..bfd5597 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,11 +1,11 @@
-pandoc: 3.1.12.2
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   developers: developers.html
   files: files.html
   flames: flames.html
-last_built: 2024-03-14T23:57Z
+last_built: 2024-05-13T13:16Z
 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 31f70ae..8737394 100644
--- a/reference/BcftoolsStatsFile.html
+++ b/reference/BcftoolsStatsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -163,11 +164,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/BclconvertReports.html b/reference/BclconvertReports.html
new file mode 100644
index 0000000..16a54fb
--- /dev/null
+++ b/reference/BclconvertReports.html
@@ -0,0 +1,220 @@
+<!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>
+    <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">
+    
+    <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>
+
+    
+    <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">
+  <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>
+      </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>
+      <div class="d-none name"><code>BclconvertReports.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Reads and writes tidy versions of files within the <code>Reports</code> directory output
+from BCLConvert.</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>path</code></dt>
+<dd><p>Path to the <code>Reports</code> directory.</p></dd>
+
+
+<dt><code>contents</code></dt>
+<dd><p>Tibble with file path, basename, and size.</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-BclconvertReports-new"><code>BclconvertReports$new()</code></a></p></li>
+<li><p><a href="#method-BclconvertReports-print"><code>BclconvertReports$print()</code></a></p></li>
+<li><p><a href="#method-BclconvertReports-read"><code>BclconvertReports$read()</code></a></p></li>
+<li><p><a href="#method-BclconvertReports-write"><code>BclconvertReports$write()</code></a></p></li>
+<li><p><a href="#method-BclconvertReports-clone"><code>BclconvertReports$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-BclconvertReports-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+<p>Create a new BclconvertReports object.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/BclconvertReports.html">BclconvertReports</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span>path <span class="op">=</span> <span class="cn">NULL</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>path</code></dt>
+<dd><p>Path to the <code>Reports</code> directory.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-BclconvertReports-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 BclconvertReports directory.</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">BclconvertReports</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>...</code></dt>
+<dd><p>(ignored).</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-BclconvertReports-read"></a><div class="section">
+<h3 id="method-read-">Method <code><a href="read.html">read()</a></code><a class="anchor" aria-label="anchor" href="#method-read-"></a></h3>
+<p>Reads contents of <code>Reports</code> directory output by BCLConvert.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">BclconvertReports</span><span class="op">$</span><span class="fu">read</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="returns">Returns<a class="anchor" aria-label="anchor" href="#returns"></a></h4>
+<p>A list of tibbles.</p>
+</div>
+
+</div><p></p><hr><a id="method-BclconvertReports-write"></a><div class="section">
+<h3 id="method-write-">Method <code><a href="https://rdrr.io/r/base/write.html" class="external-link">write()</a></code><a class="anchor" aria-label="anchor" href="#method-write-"></a></h3>
+<p>Writes tidied contents of <code>Reports</code> directory output by BCLConvert.</p><div class="section">
+<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">BclconvertReports</span><span class="op">$</span><span class="fu">write</span><span class="op">(</span></span>
+<span>  <span class="va">d</span>,</span>
+<span>  out_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  <span class="va">prefix</span>,</span>
+<span>  out_format <span class="op">=</span> <span class="st">"tsv"</span>,</span>
+<span>  drid <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>d</code></dt>
+<dd><p>Parsed object from <code>self$read()</code>.</p></dd>
+
+
+<dt><code>out_dir</code></dt>
+<dd><p>Output directory.</p></dd>
+
+
+<dt><code>prefix</code></dt>
+<dd><p>Prefix of output file(s).</p></dd>
+
+
+<dt><code>out_format</code></dt>
+<dd><p>Format of output file(s).</p></dd>
+
+
+<dt><code>drid</code></dt>
+<dd><p>dracarys ID to use for the dataset (e.g. <code>wfrid.123</code>, <code>prid.456</code>).</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-BclconvertReports-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-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">BclconvertReports</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="va">BclconvertReports</span><span class="op">$</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></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc"><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> 2.0.9.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/FastqcMetricsFile.html b/reference/FastqcMetricsFile.html
index 555d04a..086db75 100644
--- a/reference/FastqcMetricsFile.html
+++ b/reference/FastqcMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -163,11 +164,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/File.html b/reference/File.html
index daa3821..3f002fc 100644
--- a/reference/File.html
+++ b/reference/File.html
@@ -1,8 +1,8 @@
 <!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
-a DRAGEN 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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 DRAGEN workflow.
+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 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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -30,6 +30,7 @@
   <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">
@@ -58,7 +59,7 @@
 
     <div class="ref-description section level2">
     <p>File is a base R6 class representing a TSV/CSV/JSON output from
-a DRAGEN workflow.</p>
+a UMCCR workflow.</p>
 <p>A File has a path, a basename, a type, and can be a presigned URL.</p>
     </div>
 
@@ -185,11 +186,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/FragmentLengthHistFile.html b/reference/FragmentLengthHistFile.html
index e1a388e..b6fc4ed 100644
--- a/reference/FragmentLengthHistFile.html
+++ b/reference/FragmentLengthHistFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -193,11 +194,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/MappingMetricsFile.html b/reference/MappingMetricsFile.html
index 9fd8a5f..04991db 100644
--- a/reference/MappingMetricsFile.html
+++ b/reference/MappingMetricsFile.html
@@ -6,7 +6,7 @@
 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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)."><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
 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
@@ -20,11 +20,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -40,6 +40,7 @@
   <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">
@@ -180,11 +181,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/MultiqcFile.html b/reference/MultiqcFile.html
index 820580e..13e510a 100644
--- a/reference/MultiqcFile.html
+++ b/reference/MultiqcFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -172,11 +173,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/PcgrJsonFile.html b/reference/PcgrJsonFile.html
index b0c8222..989fc31 100644
--- a/reference/PcgrJsonFile.html
+++ b/reference/PcgrJsonFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -153,11 +154,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/PcgrTiersFile.html b/reference/PcgrTiersFile.html
index 9b84530..3b3ca6b 100644
--- a/reference/PcgrTiersFile.html
+++ b/reference/PcgrTiersFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -153,11 +154,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/PloidyEstimationMetricsFile.html b/reference/PloidyEstimationMetricsFile.html
index 729abcf..f5ed74d 100644
--- a/reference/PloidyEstimationMetricsFile.html
+++ b/reference/PloidyEstimationMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -162,11 +163,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/ReplayFile.html b/reference/ReplayFile.html
index 5b1ce26..1c9203b 100644
--- a/reference/ReplayFile.html
+++ b/reference/ReplayFile.html
@@ -1,7 +1,7 @@
 <!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 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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
 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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -30,6 +30,7 @@
   <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">
@@ -158,11 +159,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/SvMetricsFile.html b/reference/SvMetricsFile.html
index 46e83f2..441eefd 100644
--- a/reference/SvMetricsFile.html
+++ b/reference/SvMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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"><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -156,11 +157,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TimeMetricsFile.html b/reference/TimeMetricsFile.html
index 05fa720..b90a9b2 100644
--- a/reference/TimeMetricsFile.html
+++ b/reference/TimeMetricsFile.html
@@ -1,7 +1,7 @@
 <!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 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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
 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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -30,6 +30,7 @@
   <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">
@@ -164,11 +165,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TrimmerMetricsFile.html b/reference/TrimmerMetricsFile.html
index 261abe2..8aa7b93 100644
--- a/reference/TrimmerMetricsFile.html
+++ b/reference/TrimmerMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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"><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -162,11 +163,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoAlignCollapseFusionCallerMetricsFile.html b/reference/TsoAlignCollapseFusionCallerMetricsFile.html
index c03df8a..9fe0def 100644
--- a/reference/TsoAlignCollapseFusionCallerMetricsFile.html
+++ b/reference/TsoAlignCollapseFusionCallerMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -199,11 +200,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoCombinedVariantOutputFile.html b/reference/TsoCombinedVariantOutputFile.html
index df45b56..4edd037 100644
--- a/reference/TsoCombinedVariantOutputFile.html
+++ b/reference/TsoCombinedVariantOutputFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -163,11 +164,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoCopyNumberVariantsVcfFile.html b/reference/TsoCopyNumberVariantsVcfFile.html
index b00a3e1..c93e8df 100644
--- a/reference/TsoCopyNumberVariantsVcfFile.html
+++ b/reference/TsoCopyNumberVariantsVcfFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -175,11 +176,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoFragmentLengthHistFile.html b/reference/TsoFragmentLengthHistFile.html
index 6f1e81f..2f92ccd 100644
--- a/reference/TsoFragmentLengthHistFile.html
+++ b/reference/TsoFragmentLengthHistFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -191,11 +192,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoFusionsCsvFile.html b/reference/TsoFusionsCsvFile.html
index 987b970..633936e 100644
--- a/reference/TsoFusionsCsvFile.html
+++ b/reference/TsoFusionsCsvFile.html
@@ -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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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
+"><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
 Fusions.csv file output from TSO.
 Returns a tibble where the columns are (based on the input file header metadata):
 Sample: input sample ID.
@@ -40,11 +40,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -60,6 +60,7 @@
   <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">
@@ -205,11 +206,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoMergedSmallVariantsGenomeVcfFile.html b/reference/TsoMergedSmallVariantsGenomeVcfFile.html
index 7a6284d..940d89b 100644
--- a/reference/TsoMergedSmallVariantsGenomeVcfFile.html
+++ b/reference/TsoMergedSmallVariantsGenomeVcfFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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]>
 <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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -174,11 +175,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoMergedSmallVariantsVcfFile.html b/reference/TsoMergedSmallVariantsVcfFile.html
index a914689..e396a78 100644
--- a/reference/TsoMergedSmallVariantsVcfFile.html
+++ b/reference/TsoMergedSmallVariantsVcfFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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]>
 <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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -175,11 +176,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoMsiFile.html b/reference/TsoMsiFile.html
index ca00100..340a4f6 100644
--- a/reference/TsoMsiFile.html
+++ b/reference/TsoMsiFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -154,11 +155,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoSampleAnalysisResultsFile.html b/reference/TsoSampleAnalysisResultsFile.html
index 81f5687..d354543 100644
--- a/reference/TsoSampleAnalysisResultsFile.html
+++ b/reference/TsoSampleAnalysisResultsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -161,11 +162,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoTargetRegionCoverageFile.html b/reference/TsoTargetRegionCoverageFile.html
index 338b1f3..75e335e 100644
--- a/reference/TsoTargetRegionCoverageFile.html
+++ b/reference/TsoTargetRegionCoverageFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -191,11 +192,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoTmbFile.html b/reference/TsoTmbFile.html
index f4e28e3..872ed72 100644
--- a/reference/TsoTmbFile.html
+++ b/reference/TsoTmbFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -161,11 +162,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/TsoTmbTraceTsvFile.html b/reference/TsoTmbTraceTsvFile.html
index b7b455d..cef7008 100644
--- a/reference/TsoTmbTraceTsvFile.html
+++ b/reference/TsoTmbTraceTsvFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -160,11 +161,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/UmChordTsvFile.html b/reference/UmChordTsvFile.html
index 210bd07..9fa3500 100644
--- a/reference/UmChordTsvFile.html
+++ b/reference/UmChordTsvFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -162,11 +163,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/UmHrdetectTsvFile.html b/reference/UmHrdetectTsvFile.html
index 59468b6..0581878 100644
--- a/reference/UmHrdetectTsvFile.html
+++ b/reference/UmHrdetectTsvFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -156,11 +157,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/UmQcSumFile.html b/reference/UmQcSumFile.html
index c7d3035..7f80ec2 100644
--- a/reference/UmQcSumFile.html
+++ b/reference/UmQcSumFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -157,11 +158,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/UmSigsSnvFile.html b/reference/UmSigsSnvFile.html
index 39d3b23..1191577 100644
--- a/reference/UmSigsSnvFile.html
+++ b/reference/UmSigsSnvFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -156,11 +157,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/VCMetricsFile.html b/reference/VCMetricsFile.html
index 7118a1e..6cf5875 100644
--- a/reference/VCMetricsFile.html
+++ b/reference/VCMetricsFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -156,11 +157,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/WgsContigMeanCovFile.html b/reference/WgsContigMeanCovFile.html
index b960261..afd230a 100644
--- a/reference/WgsContigMeanCovFile.html
+++ b/reference/WgsContigMeanCovFile.html
@@ -2,7 +2,7 @@
 <!-- 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_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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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
 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]>
@@ -12,11 +12,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -32,6 +32,7 @@
   <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">
@@ -214,11 +215,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/WgsCoverageMetricsFile.html b/reference/WgsCoverageMetricsFile.html
index f60bd45..bb5b5b0 100644
--- a/reference/WgsCoverageMetricsFile.html
+++ b/reference/WgsCoverageMetricsFile.html
@@ -1,7 +1,7 @@
 <!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_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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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
 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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -30,6 +30,7 @@
   <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">
@@ -169,11 +170,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/WgsFineHistFile.html b/reference/WgsFineHistFile.html
index 4b601ca..85210fd 100644
--- a/reference/WgsFineHistFile.html
+++ b/reference/WgsFineHistFile.html
@@ -3,7 +3,7 @@
 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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
 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
@@ -14,11 +14,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -34,6 +34,7 @@
   <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">
@@ -205,11 +206,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/WgsHistFile.html b/reference/WgsHistFile.html
index d0ee412..2139bea 100644
--- a/reference/WgsHistFile.html
+++ b/reference/WgsHistFile.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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"><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -156,11 +157,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/bcftools_parse_vcf.html b/reference/bcftools_parse_vcf.html
index 5702476..412d7f0 100644
--- a/reference/bcftools_parse_vcf.html
+++ b/reference/bcftools_parse_vcf.html
@@ -1,7 +1,7 @@
 <!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.
 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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.
 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>
@@ -10,11 +10,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -30,6 +30,7 @@
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     <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">
@@ -99,11 +100,11 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/bcftools_parse_vcf_regions.html b/reference/bcftools_parse_vcf_regions.html
index aaf3ecd..ea1785b 100644
--- a/reference/bcftools_parse_vcf_regions.html
+++ b/reference/bcftools_parse_vcf_regions.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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]>
 <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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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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+    <a class="dropdown-item" href="../articles/files.html">Files</a>
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 </li>
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@@ -101,11 +102,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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>
 
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/bclconvert_read_adaptermetrics.html b/reference/bclconvert_read_adaptermetrics.html
new file mode 100644
index 0000000..9164cae
--- /dev/null
+++ b/reference/bclconvert_read_adaptermetrics.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"><meta name="description" content="Reads the Adapter_Metrics.csv file in the Reports directory
+output by BCLConvert."><title>BCLConvert Adapter Metrics — bclconvert_read_adaptermetrics • 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 Adapter Metrics — bclconvert_read_adaptermetrics"><meta property="og:description" content="Reads the Adapter_Metrics.csv file in the Reports directory
+output by 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>
+    <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">
+    
+    <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>
+
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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>
+    </button>
+
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+</li>
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+    <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>
+      </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>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>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Reads the <code>Adapter_Metrics.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_adaptermetrics</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>Adapter_Metrics.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/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>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc"><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> 2.0.9.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/meta_rnasum.html b/reference/bclconvert_read_demultiplexstats.html
similarity index 56%
rename from reference/meta_rnasum.html
rename to reference/bclconvert_read_demultiplexstats.html
index 6b75c73..d828528 100644
--- a/reference/meta_rnasum.html
+++ b/reference/bclconvert_read_demultiplexstats.html
@@ -1,16 +1,18 @@
 <!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="Metadata for rnasum workflow"><title>Metadata for rnasum workflow — meta_rnasum • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for rnasum workflow — meta_rnasum"><meta property="og:description" content="Metadata for rnasum workflow"><!-- 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]>
+<!-- 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
+output by BCLConvert."><title>BCLConvert Demultiplex Stats — bclconvert_read_demultiplexstats • 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 Demultiplex Stats — bclconvert_read_demultiplexstats"><meta property="og:description" content="Reads the Demultiplex_Stats.csv file in the Reports directory
+output by 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +28,7 @@
   <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">
@@ -47,42 +50,40 @@
 </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>Metadata for rnasum workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_rnasum.Rd</code></div>
+      <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>Metadata for rnasum workflow</p>
+    <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">meta_rnasum</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</span><span class="op">)</span></span></code></pre></div>
+    <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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</p></dd>
+    <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>A tibble with metadata per workflow run.</p>
+<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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_rnasum</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</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></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>
@@ -90,11 +91,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/bclconvert_read_indexhoppingcounts.html b/reference/bclconvert_read_indexhoppingcounts.html
new file mode 100644
index 0000000..a8c62fb
--- /dev/null
+++ b/reference/bclconvert_read_indexhoppingcounts.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"><meta name="description" content="Reads the Index_Hopping_Counts.csv file in the Reports directory
+output by BCLConvert."><title>BCLConvert Index Hopping Counts — bclconvert_read_indexhoppingcounts • 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 Index Hopping Counts — bclconvert_read_indexhoppingcounts"><meta property="og:description" content="Reads the Index_Hopping_Counts.csv file in the Reports directory
+output by 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>
+    <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">
+    
+    <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>
+
+    
+    <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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+    </button>
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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>
+<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>
+  </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>
+      </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>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>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Reads the <code>Index_Hopping_Counts.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_indexhoppingcounts</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>Index_Hopping_Counts.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/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>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc"><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> 2.0.9.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/bclconvert_read_topunknownbarcodes.html b/reference/bclconvert_read_topunknownbarcodes.html
new file mode 100644
index 0000000..3f8c067
--- /dev/null
+++ b/reference/bclconvert_read_topunknownbarcodes.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"><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
+output by 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>
+    <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">
+    
+    <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>
+
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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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+    </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">
+  <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>
+      </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>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>
+
+
+    <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> 2.0.9.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/date_log.html b/reference/date_log.html
index 52f8340..d8d8851 100644
--- a/reference/date_log.html
+++ b/reference/date_log.html
@@ -1,16 +1,16 @@
 <!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="Print current timestamp for logging"><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><!-- 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Print current timestamp for logging — date_log"><meta property="og:description" content="Print current timestamp for logging"><!-- 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]>
+<!-- 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="Print current timestamp for logging"><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><!-- 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="Print current timestamp for logging — date_log"><meta property="og:description" content="Print current timestamp for logging"><!-- 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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -73,11 +74,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/dr_func_eval.html b/reference/dr_func_eval.html
index d07e185..0b6ad45 100644
--- a/reference/dr_func_eval.html
+++ b/reference/dr_func_eval.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -94,11 +95,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/dr_gds_download.html b/reference/dr_gds_download.html
index 987d500..d64112b 100644
--- a/reference/dr_gds_download.html
+++ b/reference/dr_gds_download.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -65,7 +66,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  page_size <span class="op">=</span> <span class="fl">100</span>,</span>
 <span>  pattern <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  dryrun <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  regexes <span class="op">=</span> <span class="va">DR_FILE_REGEX</span></span>
+<span>  regexes <span class="op">=</span> <span class="va">DR_FILE_REGEX</span>,</span>
+<span>  recursive <span class="op">=</span> <span class="cn">NULL</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -99,6 +101,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dt>regexes</dt>
 <dd><p>Tibble with regex and function name.</p></dd>
 
+
+<dt>recursive</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>
@@ -106,11 +113,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/dr_output_format_valid.html b/reference/dr_output_format_valid.html
index 0d0cc72..7f32ad2 100644
--- a/reference/dr_output_format_valid.html
+++ b/reference/dr_output_format_valid.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></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"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -73,11 +74,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/meta_wts_tumor_only.html b/reference/dr_s3_download.html
similarity index 53%
rename from reference/meta_wts_tumor_only.html
rename to reference/dr_s3_download.html
index a0b51ce..96e8253 100644
--- a/reference/meta_wts_tumor_only.html
+++ b/reference/dr_s3_download.html
@@ -1,16 +1,16 @@
 <!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="Metadata for wts_tumor_only workflow"><title>Metadata for wts_tumor_only workflow — meta_wts_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><!-- 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for wts_tumor_only workflow — meta_wts_tumor_only"><meta property="og:description" content="Metadata for wts_tumor_only workflow"><!-- 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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -47,42 +48,63 @@
 </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>Metadata for wts_tumor_only workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_wts_tumor_only.Rd</code></div>
+      <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>
+      <div class="d-none name"><code>dr_s3_download.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>Metadata for wts_tumor_only workflow</p>
+    <p>Download only S3 files that can be processed by dracarys.</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">meta_wts_tumor_only</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">dr_s3_download</span><span class="op">(</span></span>
+<span>  <span class="va">s3dir</span>,</span>
+<span>  <span class="va">outdir</span>,</span>
+<span>  page_size <span class="op">=</span> <span class="fl">100</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>  dryrun <span class="op">=</span> <span class="cn">FALSE</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
+    <dl><dt>s3dir</dt>
+<dd><p>Full path to S3 directory.</p></dd>
 
 
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</p></dd>
+<dt>outdir</dt>
+<dd><p>Path to output directory.</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 metadata per workflow run.</p>
-    </div>
+<dt>page_size</dt>
+<dd><p>Page size (def: 100).</p></dd>
+
+
+<dt>pattern</dt>
+<dd><p>Pattern to further filter the returned file type tibble.</p></dd>
+
+
+<dt>regexes</dt>
+<dd><p>Tibble with regex and function name.</p></dd>
+
+
+<dt>dryrun</dt>
+<dd><p>If TRUE, just list the files that will be downloaded (don't
+download them).</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_wts_tumor_only</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">s3dir</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>
+<span class="r-in"><span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">outdir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">"s3:/"</span>, <span class="st">"~/s3"</span>, <span class="va">s3dir</span><span class="op">)</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>
@@ -90,11 +112,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/dracarys-package.html b/reference/dracarys-package.html
index 9bd7d3f..1529a7a 100644
--- a/reference/dracarys-package.html
+++ b/reference/dracarys-package.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -75,11 +76,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/empty_tbl.html b/reference/empty_tbl.html
index ee2357c..07b0156 100644
--- a/reference/empty_tbl.html
+++ b/reference/empty_tbl.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -86,11 +87,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/file_regex_getter.html b/reference/file_regex_getter.html
index 3032f99..0e184cd 100644
--- a/reference/file_regex_getter.html
+++ b/reference/file_regex_getter.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -73,11 +74,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_file_download.html b/reference/gds_file_download.html
index 98c329a..db5ce0b 100644
--- a/reference/gds_file_download.html
+++ b/reference/gds_file_download.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -81,11 +82,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_file_download_api.html b/reference/gds_file_download_api.html
index e5e5f55..64415e0 100644
--- a/reference/gds_file_download_api.html
+++ b/reference/gds_file_download_api.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -90,11 +91,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_file_presignedurl.html b/reference/gds_file_presignedurl.html
index 9b74ae7..095da59 100644
--- a/reference/gds_file_presignedurl.html
+++ b/reference/gds_file_presignedurl.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></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"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -83,11 +84,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_files_list.html b/reference/gds_files_list.html
index 036b6fc..4b3a283 100644
--- a/reference/gds_files_list.html
+++ b/reference/gds_files_list.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -58,7 +59,15 @@
 
     <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</span><span class="op">(</span><span class="va">gdsdir</span>, <span class="va">token</span>, page_size <span class="op">=</span> <span class="fl">100</span>, include <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">gds_files_list</span><span class="op">(</span></span>
+<span>  <span class="va">gdsdir</span>,</span>
+<span>  <span class="va">token</span>,</span>
+<span>  page_size <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  include_url <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  no_recurse <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  page_token <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  recursive <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -72,12 +81,25 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>page_size</dt>
-<dd><p>Page size (def: 100).</p></dd>
+<dd><p>Page size (def: 10).</p></dd>
 
 
-<dt>include</dt>
-<dd><p>Use PresignedUrl to include presigned URLs to all files within
-the GDS directory.</p></dd>
+<dt>include_url</dt>
+<dd><p>Include presigned URLs to all files within the GDS directory (def: FALSE).</p></dd>
+
+
+<dt>no_recurse</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>
+<dd><p>Page token (def: NULL). Used internally for recursion.</p></dd>
+
+
+<dt>recursive</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">
@@ -87,16 +109,41 @@ <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>
     </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">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>
+<span class="r-in"><span><span class="op">)</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://bssh.acddbfda498038ed99fa94fe79523959/Runs"</span>,</span></span>
+<span class="r-in"><span>  <span class="st">"240322_A00130_0290_BH5HLLDSXC_r.3TbcOsEKZUyetygkqIOXcg/InterOp"</span></span></span>
+<span class="r-in"><span><span class="op">)</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/analysis_data/SBJ00699/umccrise"</span>,</span></span>
+<span class="r-in"><span>  <span class="st">"202203277dcf8562/L2200352__L2100146/SBJ00699__MDX220105/coverage"</span></span></span>
+<span class="r-in"><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="ica_token_validate.html">ica_token_validate</a></span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">page_size</span> <span class="op">&lt;-</span> <span class="fl">11</span></span></span>
+<span class="r-in"><span><span class="va">include_url</span> <span class="op">&lt;-</span> <span class="cn">TRUE</span></span></span>
+<span class="r-in"><span><span class="va">page_token</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span></span>
+<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>
+</code></pre></div>
+    </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_files_list_filter_relevant.html b/reference/gds_files_list_filter_relevant.html
index 960fb98..197fad4 100644
--- a/reference/gds_files_list_filter_relevant.html
+++ b/reference/gds_files_list_filter_relevant.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -62,7 +63,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  <span class="va">gdsdir</span>,</span>
 <span>  <span class="va">token</span>,</span>
 <span>  pattern <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  include <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  include_url <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  page_size <span class="op">=</span> <span class="fl">100</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>
@@ -82,13 +83,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>Pattern to further filter the returned file type tibble.</p></dd>
 
 
-<dt>include</dt>
-<dd><p>Use PresignedUrl to include presigned URLs to all files within</p></dd>
+<dt>include_url</dt>
+<dd><p>Include presigned URLs to all files within the GDS directory (def: FALSE).</p></dd>
 
 
 <dt>page_size</dt>
-<dd><p>Page size (def: 100).
-the GDS directory.</p></dd>
+<dd><p>Page size (def: 100).</p></dd>
 
 
 <dt>regexes</dt>
@@ -107,11 +107,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/gds_volumes_list.html b/reference/gds_volumes_list.html
index a57e398..b918196 100644
--- a/reference/gds_volumes_list.html
+++ b/reference/gds_volumes_list.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -83,11 +84,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/glims_excel_read.html b/reference/glims_excel_read.html
deleted file mode 100644
index 8b006f4..0000000
--- a/reference/glims_excel_read.html
+++ /dev/null
@@ -1,90 +0,0 @@
-<!DOCTYPE html>
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-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>glims_excel_read.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads UMCCR's Google LIMS spreadsheet.</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">glims_excel_read</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Tibble with all columns and rows from the Google LIMS spreadsheet.</p>
-    </div>
-
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
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-  <p></p><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/glims_portal_read.html b/reference/glims_portal_read.html
deleted file mode 100644
index 156f39a..0000000
--- a/reference/glims_portal_read.html
+++ /dev/null
@@ -1,100 +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 rows from the data portal's limsrow table, given a set of LibraryIDs
-to query."><title>Read Portal Limsrow Table — glims_portal_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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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 Portal Limsrow Table — glims_portal_read"><meta property="og:description" content="Reads rows from the data portal's limsrow table, given a set of LibraryIDs
-to query."><!-- 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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-    
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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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-</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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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Read Portal Limsrow Table</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>glims_portal_read.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads rows from the data portal's limsrow table, given a set of <code>LibraryID</code>s
-to query.</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">glims_portal_read</span><span class="op">(</span><span class="va">libids</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>libids</dt>
-<dd><p>Character vector of LibraryID values to query for.</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 all rows from the data portal limsrow table where
-there are hits with the <code>library_id</code> column.</p>
-    </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">
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diff --git a/reference/ica_token_validate.html b/reference/ica_token_validate.html
index fb26218..79c2cbf 100644
--- a/reference/ica_token_validate.html
+++ b/reference/ica_token_validate.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -79,11 +80,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/index.html b/reference/index.html
index b999681..12f4923 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -68,6 +69,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>BcftoolsStatsFile R6 Class</dd>
       </dl><dl><dt>
           
+          <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> 
         </dt>
         <dd>FastqcMetrics R6 Class</dd>
@@ -243,6 +249,26 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Parse VCF regions with bcftools</dd>
       </dl><dl><dt>
           
+          <code><a href="bclconvert_read_adaptermetrics.html">bclconvert_read_adaptermetrics()</a></code> 
+        </dt>
+        <dd>BCLConvert Adapter Metrics</dd>
+      </dl><dl><dt>
+          
+          <code><a href="bclconvert_read_demultiplexstats.html">bclconvert_read_demultiplexstats()</a></code> 
+        </dt>
+        <dd>BCLConvert Demultiplex Stats</dd>
+      </dl><dl><dt>
+          
+          <code><a href="bclconvert_read_indexhoppingcounts.html">bclconvert_read_indexhoppingcounts()</a></code> 
+        </dt>
+        <dd>BCLConvert Index Hopping Counts</dd>
+      </dl><dl><dt>
+          
+          <code><a href="bclconvert_read_topunknownbarcodes.html">bclconvert_read_topunknownbarcodes()</a></code> 
+        </dt>
+        <dd>BCLConvert Top Unknown Barcodes</dd>
+      </dl><dl><dt>
+          
           <code><a href="date_log.html">date_log()</a></code> 
         </dt>
         <dd>Print current timestamp for logging</dd>
@@ -263,6 +289,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Output Format is Valid</dd>
       </dl><dl><dt>
           
+          <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> 
         </dt>
         <dd>Create Empty Tibble Given Column Names</dd>
@@ -303,16 +334,6 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>List GDS Volumes</dd>
       </dl><dl><dt>
           
-          <code><a href="glims_excel_read.html">glims_excel_read()</a></code> 
-        </dt>
-        <dd>Read Google LIMS</dd>
-      </dl><dl><dt>
-          
-          <code><a href="glims_portal_read.html">glims_portal_read()</a></code> 
-        </dt>
-        <dd>Read Portal Limsrow Table</dd>
-      </dl><dl><dt>
-          
           <code><a href="ica_token_validate.html">ica_token_validate()</a></code> 
         </dt>
         <dd>Validate ICA access token</dd>
@@ -323,71 +344,6 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Match File to Regex</dd>
       </dl><dl><dt>
           
-          <code><a href="meta_bcl_convert.html">meta_bcl_convert()</a></code> 
-        </dt>
-        <dd>Metadata for bcl_convert workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_oncoanalyser_wgs.html">meta_oncoanalyser_wgs()</a></code> 
-        </dt>
-        <dd>Metadata for oncoanalyser_wgs workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_oncoanalyser_wgts_existing_both.html">meta_oncoanalyser_wgts_existing_both()</a></code> 
-        </dt>
-        <dd>Metadata for oncoanalyser_wgts_existing_both workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_oncoanalyser_wts.html">meta_oncoanalyser_wts()</a></code> 
-        </dt>
-        <dd>Metadata for oncoanalyser_wts workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_rnasum.html">meta_rnasum()</a></code> 
-        </dt>
-        <dd>Metadata for rnasum workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_sash.html">meta_sash()</a></code> 
-        </dt>
-        <dd>Metadata for sash workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_star_alignment.html">meta_star_alignment()</a></code> 
-        </dt>
-        <dd>Metadata for star_alignment workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_tso_ctdna_tumor_only.html">meta_tso_ctdna_tumor_only()</a></code> 
-        </dt>
-        <dd>Metadata for tso_ctdna_tumor_only workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_umccrise.html">meta_umccrise()</a></code> 
-        </dt>
-        <dd>Metadata for umccrise workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_wgs_alignment_qc.html">meta_wgs_alignment_qc()</a></code> 
-        </dt>
-        <dd>Metadata for wgs_alignment_qc workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_wgs_tumor_normal.html">meta_wgs_tumor_normal()</a></code> 
-        </dt>
-        <dd>Metadata for wgs_tumor_normal workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_wts_alignment_qc.html">meta_wts_alignment_qc()</a></code> 
-        </dt>
-        <dd>Metadata for wts_alignment_qc workflow</dd>
-      </dl><dl><dt>
-          
-          <code><a href="meta_wts_tumor_only.html">meta_wts_tumor_only()</a></code> 
-        </dt>
-        <dd>Metadata for wts_tumor_only workflow</dd>
-      </dl><dl><dt>
-          
           <code><a href="multiqc_column_map_append.html">multiqc_column_map_append()</a></code> 
         </dt>
         <dd>Append New MultiQC Workflow Columns</dd>
@@ -418,6 +374,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <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> 
+        </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> 
         </dt>
         <dd>MultiQC Extract XY Line Plot Data</dd>
@@ -433,16 +394,6 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Tidy MultiQC JSON</dd>
       </dl><dl><dt>
           
-          <code><a href="portal_meta_read.html">portal_meta_read()</a></code> 
-        </dt>
-        <dd>Read ICA Workflows Metadata via Portal API</dd>
-      </dl><dl><dt>
-          
-          <code><a href="portal_meta_read_athena.html">portal_meta_read_athena()</a></code> 
-        </dt>
-        <dd>Read ICA Workflows Metadata via Athena</dd>
-      </dl><dl><dt>
-          
           <code><a href="rdf2tab.html">rdf2tab()</a></code> 
         </dt>
         <dd>Write Local R Dataframe to Spark-backed Table</dd>
@@ -486,11 +437,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/match_regex.html b/reference/match_regex.html
index 767d9fd..0db7c4a 100644
--- a/reference/match_regex.html
+++ b/reference/match_regex.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -96,11 +97,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/meta_bcl_convert.html b/reference/meta_bcl_convert.html
deleted file mode 100644
index d231ad2..0000000
--- a/reference/meta_bcl_convert.html
+++ /dev/null
@@ -1,107 +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="Metadata for bcl_convert workflow"><title>Metadata for bcl_convert workflow — meta_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><!-- 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for bcl_convert workflow — meta_bcl_convert"><meta property="og:description" content="Metadata for bcl_convert workflow"><!-- 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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
-
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="../index.html">dracarys</a>
-
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-    </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">
-  <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>
-  </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>
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-  <a class="external-link nav-link" href="https://github.com/umccr/dracarys/" aria-label="github">
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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>Metadata for bcl_convert workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_bcl_convert.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for bcl_convert workflow</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">meta_bcl_convert</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_bcl_convert</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</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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diff --git a/reference/meta_oncoanalyser_wgs.html b/reference/meta_oncoanalyser_wgs.html
deleted file mode 100644
index 9e23c5f..0000000
--- a/reference/meta_oncoanalyser_wgs.html
+++ /dev/null
@@ -1,107 +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="Metadata for oncoanalyser_wgs workflow"><title>Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs"><meta property="og:description" content="Metadata for oncoanalyser_wgs workflow"><!-- 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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-      <img src="" class="logo" alt=""><h1>Metadata for oncoanalyser_wgs workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_oncoanalyser_wgs.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for oncoanalyser_wgs workflow</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">meta_oncoanalyser_wgs</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_oncoanalyser_wgs</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
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-  <p></p><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>
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diff --git a/reference/meta_oncoanalyser_wgts_existing_both.html b/reference/meta_oncoanalyser_wgts_existing_both.html
deleted file mode 100644
index 2e79fc2..0000000
--- a/reference/meta_oncoanalyser_wgts_existing_both.html
+++ /dev/null
@@ -1,107 +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="Metadata for oncoanalyser_wgts_existing_both workflow"><title>Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both"><meta property="og:description" content="Metadata for oncoanalyser_wgts_existing_both workflow"><!-- 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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-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Metadata for oncoanalyser_wgts_existing_both workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_oncoanalyser_wgts_existing_both.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for oncoanalyser_wgts_existing_both workflow</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">meta_oncoanalyser_wgts_existing_both</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_oncoanalyser_wgts_existing_both</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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diff --git a/reference/meta_oncoanalyser_wts.html b/reference/meta_oncoanalyser_wts.html
deleted file mode 100644
index 7076282..0000000
--- a/reference/meta_oncoanalyser_wts.html
+++ /dev/null
@@ -1,107 +0,0 @@
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-      <img src="" class="logo" alt=""><h1>Metadata for oncoanalyser_wts workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_oncoanalyser_wts.Rd</code></div>
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-    <p>Metadata for oncoanalyser_wts workflow</p>
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-    <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">meta_oncoanalyser_wts</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</span><span class="op">)</span></span></code></pre></div>
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-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_oncoanalyser_wts</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
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-  <p></p><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>
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diff --git a/reference/meta_sash.html b/reference/meta_sash.html
deleted file mode 100644
index 56a4db3..0000000
--- a/reference/meta_sash.html
+++ /dev/null
@@ -1,107 +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="Metadata for sash workflow"><title>Metadata for sash workflow — meta_sash • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for sash workflow — meta_sash"><meta property="og:description" content="Metadata for sash workflow"><!-- 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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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Metadata for sash workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_sash.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for sash workflow</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">meta_sash</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_sash</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/reference/meta_star_alignment.html b/reference/meta_star_alignment.html
deleted file mode 100644
index 59b6263..0000000
--- a/reference/meta_star_alignment.html
+++ /dev/null
@@ -1,107 +0,0 @@
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-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Metadata for star_alignment workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_star_alignment.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for star_alignment workflow</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">meta_star_alignment</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_star_alignment</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
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-  </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">
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-</div>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/reference/meta_tso_ctdna_tumor_only.html b/reference/meta_tso_ctdna_tumor_only.html
deleted file mode 100644
index 275189a..0000000
--- a/reference/meta_tso_ctdna_tumor_only.html
+++ /dev/null
@@ -1,107 +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="Metadata for tso_ctdna_tumor_only workflow"><title>Metadata for tso_ctdna_tumor_only workflow — meta_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><!-- 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only"><meta property="og:description" content="Metadata for tso_ctdna_tumor_only workflow"><!-- 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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-</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>Metadata for tso_ctdna_tumor_only workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_tso_ctdna_tumor_only.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for tso_ctdna_tumor_only workflow</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">meta_tso_ctdna_tumor_only</span><span class="op">(</span><span class="va">pmeta</span>, status <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">"Succeeded"</span><span class="op">)</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_tso_ctdna_tumor_only</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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-    </footer></div>
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-  
-
-  </body></html>
-
diff --git a/reference/meta_umccrise.html b/reference/meta_umccrise.html
deleted file mode 100644
index 23dc7bd..0000000
--- a/reference/meta_umccrise.html
+++ /dev/null
@@ -1,107 +0,0 @@
-<!DOCTYPE html>
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-      <img src="" class="logo" alt=""><h1>Metadata for umccrise workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_umccrise.Rd</code></div>
-    </div>
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-    <div class="ref-description section level2">
-    <p>Metadata for umccrise workflow</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">meta_umccrise</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_umccrise</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
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-  </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">
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-</div>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/reference/meta_wgs_alignment_qc.html b/reference/meta_wgs_alignment_qc.html
deleted file mode 100644
index ef03399..0000000
--- a/reference/meta_wgs_alignment_qc.html
+++ /dev/null
@@ -1,107 +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="Metadata for wgs_alignment_qc workflow"><title>Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc"><meta property="og:description" content="Metadata for wgs_alignment_qc workflow"><!-- 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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-    
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</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>Metadata for wgs_alignment_qc workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_wgs_alignment_qc.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for wgs_alignment_qc workflow</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">meta_wgs_alignment_qc</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_wgs_alignment_qc</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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diff --git a/reference/meta_wgs_tumor_normal.html b/reference/meta_wgs_tumor_normal.html
deleted file mode 100644
index 64e1338..0000000
--- a/reference/meta_wgs_tumor_normal.html
+++ /dev/null
@@ -1,107 +0,0 @@
-<!DOCTYPE html>
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-      <img src="" class="logo" alt=""><h1>Metadata for wgs_tumor_normal workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_wgs_tumor_normal.Rd</code></div>
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-    <div class="ref-description section level2">
-    <p>Metadata for wgs_tumor_normal workflow</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">meta_wgs_tumor_normal</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_wgs_tumor_normal</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
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-    </nav></aside></div>
-
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-</div>
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diff --git a/reference/meta_wts_alignment_qc.html b/reference/meta_wts_alignment_qc.html
deleted file mode 100644
index d996010..0000000
--- a/reference/meta_wts_alignment_qc.html
+++ /dev/null
@@ -1,107 +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="Metadata for wts_alignment_qc workflow"><title>Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc"><meta property="og:description" content="Metadata for wts_alignment_qc workflow"><!-- 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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-    
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-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
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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>
-</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>
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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>Metadata for wts_alignment_qc workflow</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>meta_wts_alignment_qc.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Metadata for wts_alignment_qc workflow</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">meta_wts_alignment_qc</span><span class="op">(</span><span class="va">pmeta</span>, status <span class="op">=</span> <span class="st">"Succeeded"</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>pmeta</dt>
-<dd><p>Path to portal workflows metadata table, or tibble with already parsed data.</p></dd>
-
-
-<dt>status</dt>
-<dd><p>Workflow status to keep (default: Succeeded).</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 metadata per workflow run.</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="va">pmeta</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/portal_meta_top4.csv"</span>, package <span class="op">=</span> <span class="st">"dracarys"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="op">(</span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu">meta_wts_alignment_qc</span><span class="op">(</span><span class="va">pmeta</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in portal_meta_read(pmeta):</span> pmeta should be an already parsed dataframe or a local file.</span>
-</code></pre></div>
-    </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
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diff --git a/reference/multiqc_column_map_append.html b/reference/multiqc_column_map_append.html
index 5b175b5..bd27d87 100644
--- a/reference/multiqc_column_map_append.html
+++ b/reference/multiqc_column_map_append.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -81,11 +82,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/multiqc_date_fmt.html b/reference/multiqc_date_fmt.html
index 5c464be..a9cdbfc 100644
--- a/reference/multiqc_date_fmt.html
+++ b/reference/multiqc_date_fmt.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -91,11 +92,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/multiqc_parse_bargraph_plot.html b/reference/multiqc_parse_bargraph_plot.html
index c91abb3..9490b8a 100644
--- a/reference/multiqc_parse_bargraph_plot.html
+++ b/reference/multiqc_parse_bargraph_plot.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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:"><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
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     <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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 </li>
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@@ -107,11 +108,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/multiqc_parse_gen.html b/reference/multiqc_parse_gen.html
index 2fd40ea..4838f0a 100644
--- a/reference/multiqc_parse_gen.html
+++ b/reference/multiqc_parse_gen.html
@@ -1,6 +1,6 @@
 <!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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 <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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
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     <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">
@@ -82,11 +83,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/multiqc_parse_plots.html b/reference/multiqc_parse_plots.html
index 103edb3..1b0e0d1 100644
--- a/reference/multiqc_parse_plots.html
+++ b/reference/multiqc_parse_plots.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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]>
 <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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -94,11 +95,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/multiqc_parse_raw.html b/reference/multiqc_parse_raw.html
index 1aeaa08..c108405 100644
--- a/reference/multiqc_parse_raw.html
+++ b/reference/multiqc_parse_raw.html
@@ -1,16 +1,16 @@
 <!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_saved_raw_data' JSON Element."><title>Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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 MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw"><meta property="og:description" content="Parses MultiQC 'report_saved_raw_data' JSON Element."><!-- 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]>
+<!-- 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_saved_raw_data' JSON Element."><title>Parse MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw • 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 MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw"><meta property="og:description" content="Parses MultiQC 'report_saved_raw_data' JSON Element."><!-- 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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -71,7 +72,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>A list.</p>
+<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>
@@ -79,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/multiqc_parse_raw_interop.html b/reference/multiqc_parse_raw_interop.html
new file mode 100644
index 0000000..d17f8b5
--- /dev/null
+++ b/reference/multiqc_parse_raw_interop.html
@@ -0,0 +1,97 @@
+<!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 Interop MultiQC 'report_saved_raw_data' JSON Element."><title>Parse Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop • 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 Interop MultiQC 'report_saved_raw_data' JSON Element — multiqc_parse_raw_interop"><meta property="og:description" content="Parses Interop MultiQC 'report_saved_raw_data' JSON Element."><!-- 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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+  <a class="nav-link" href="../reference/index.html">Reference</a>
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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>
+      <div class="d-none name"><code>multiqc_parse_raw_interop.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Parses Interop MultiQC 'report_saved_raw_data' JSON Element.</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">multiqc_parse_raw_interop</span><span class="op">(</span><span class="va">p</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>p</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>
+    </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/multiqc_parse_xyline_plot.html b/reference/multiqc_parse_xyline_plot.html
index a24f210..a1ffd12 100644
--- a/reference/multiqc_parse_xyline_plot.html
+++ b/reference/multiqc_parse_xyline_plot.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
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     <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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 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
@@ -84,11 +85,11 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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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 0810366..5d77959 100644
--- a/reference/multiqc_parse_xyline_plot_contig_cvg.html
+++ b/reference/multiqc_parse_xyline_plot_contig_cvg.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -79,11 +80,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/multiqc_tidy_json.html b/reference/multiqc_tidy_json.html
index 83b419b..6c8f25b 100644
--- a/reference/multiqc_tidy_json.html
+++ b/reference/multiqc_tidy_json.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -83,11 +84,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/portal_meta_read.html b/reference/portal_meta_read.html
deleted file mode 100644
index 446af16..0000000
--- a/reference/portal_meta_read.html
+++ /dev/null
@@ -1,119 +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 ICA Workflows Metadata via Portal API using awscurl. See
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-      <img src="" class="logo" alt=""><h1>Read ICA Workflows Metadata via Portal API</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>portal_meta_read.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads ICA Workflows Metadata via Portal API using awscurl. See
-https://github.com/okigan/awscurl for required <code>AWS_</code> environment variables.</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">portal_meta_read</span><span class="op">(</span>pmeta <span class="op">=</span> <span class="cn">NULL</span>, rows <span class="op">=</span> <span class="fl">100</span>, params <span class="op">=</span> <span class="st">""</span>, account <span class="op">=</span> <span class="st">"prod"</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>pmeta</dt>
-<dd><p>Path to downloaded portal metadata file, or already parsed metadata tibble.</p></dd>
-
-
-<dt>rows</dt>
-<dd><p>Number of rows to return.</p></dd>
-
-
-<dt>params</dt>
-<dd><p>String containing additional params to pass to the <code>/workflows</code>
-endpoint, e.g. <code>'&amp;type_name=bclconvert'</code>.</p></dd>
-
-
-<dt>account</dt>
-<dd><p>UMCCR portal account (one of "prod", "dev", "stg").</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 of the results from the given query.</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="fu">portal_meta_read</span><span class="op">(</span>params <span class="op">=</span> <span class="st">"&amp;type_name=rnasum"</span>, rows <span class="op">=</span> <span class="fl">4</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/portal_meta_read_athena.html b/reference/portal_meta_read_athena.html
deleted file mode 100644
index a78dec3..0000000
--- a/reference/portal_meta_read_athena.html
+++ /dev/null
@@ -1,104 +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 ICA Workflows Metadata for the given workflow run IDs."><title>Read ICA Workflows Metadata via Athena — portal_meta_read_athena • 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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 ICA Workflows Metadata via Athena — portal_meta_read_athena"><meta property="og:description" content="Reads the ICA Workflows Metadata for the given workflow run IDs."><!-- 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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-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Read ICA Workflows Metadata via Athena</h1>
-      <small class="dont-index">Source: <a href="https://github.com/umccr/dracarys/blob/HEAD/R/portal_meta.R" class="external-link"><code>R/portal_meta.R</code></a></small>
-      <div class="d-none name"><code>portal_meta_read_athena.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>Reads the ICA Workflows Metadata for the given workflow run IDs.</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">portal_meta_read_athena</span><span class="op">(</span>wfrids <span class="op">=</span> <span class="cn">NULL</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>wfrids</dt>
-<dd><p>Character vector of wfr IDs to query.</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 a row per wfr ID.</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">wfrids</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">"wfr.1e764ca00e7a43a69e2424f250a34868"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">portal_meta_read_athena</span><span class="op">(</span><span class="va">wfrids</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>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/reference/rdf2tab.html b/reference/rdf2tab.html
index 14b90ae..1110dc5 100644
--- a/reference/rdf2tab.html
+++ b/reference/rdf2tab.html
@@ -1,6 +1,6 @@
 <!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,
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+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]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">dracarys</a>
 
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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>
 
     
     <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="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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 </li>
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@@ -96,11 +97,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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">
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diff --git a/reference/read.File.html b/reference/read.File.html
index 24c6249..2363137 100644
--- a/reference/read.File.html
+++ b/reference/read.File.html
@@ -1,16 +1,16 @@
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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"><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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
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     <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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 </li>
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@@ -78,11 +79,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/read.html b/reference/read.html
index 00453d8..96efcc1 100644
--- a/reference/read.html
+++ b/reference/read.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -83,11 +84,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/s3_files_list_filter_relevant.html b/reference/s3_files_list_filter_relevant.html
index 386d44b..82a8bd3 100644
--- a/reference/s3_files_list_filter_relevant.html
+++ b/reference/s3_files_list_filter_relevant.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></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"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -71,7 +72,7 @@ <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>
-<dd><p>GDS directory.</p></dd>
+<dd><p>S3 directory.</p></dd>
 
 
 <dt>pattern</dt>
@@ -114,11 +115,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/s3_search.html b/reference/s3_search.html
index bbc6717..9c41fc7 100644
--- a/reference/s3_search.html
+++ b/reference/s3_search.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -94,11 +95,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/session_info_kable.html b/reference/session_info_kable.html
index 1367f7e..be0b0a5 100644
--- a/reference/session_info_kable.html
+++ b/reference/session_info_kable.html
@@ -1,16 +1,16 @@
 <!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="Session information kables for vignettes."><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><!-- 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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Session Information Kable — session_info_kable"><meta property="og:description" content="Session information kables for vignettes."><!-- 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]>
+<!-- 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="Session information kables for vignettes."><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><!-- 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="Session Information Kable — session_info_kable"><meta property="og:description" content="Session information kables for vignettes."><!-- 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 href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -80,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/time_metrics_process.html b/reference/time_metrics_process.html
index e8e4f84..a989e71 100644
--- a/reference/time_metrics_process.html
+++ b/reference/time_metrics_process.html
@@ -1,16 +1,16 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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]>
+<!-- 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>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -26,6 +26,7 @@
   <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">
@@ -105,11 +106,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/umccr_tidy.html b/reference/umccr_tidy.html
index 6502f62..2a385ba 100644
--- a/reference/umccr_tidy.html
+++ b/reference/umccr_tidy.html
@@ -1,6 +1,6 @@
 <!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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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."><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>
@@ -8,11 +8,11 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><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="">0.13.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.14.0</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">
@@ -28,6 +28,7 @@
   <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">
@@ -65,7 +66,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  in_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  out_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  prefix <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  gds_local_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  local_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <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>
@@ -76,7 +77,7 @@ <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>in_dir</dt>
-<dd><p>Directory path to UMCCR workflow results (can be GDS or local).</p></dd>
+<dd><p>Directory path to UMCCR workflow results (can be GDS, S3 or local).</p></dd>
 
 
 <dt>out_dir</dt>
@@ -87,8 +88,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>Prefix of output file(s).</p></dd>
 
 
-<dt>gds_local_dir</dt>
-<dd><p>If <code>indir</code> is a GDS directory, 'recognisable' files
+<dt>local_dir</dt>
+<dd><p>If <code>indir</code> is a GDS or S3 directory, 'recognisable' files
 will be first downloaded to this directory.</p></dd>
 
 
@@ -119,16 +120,23 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <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">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>
+<span class="r-in"><span><span class="op">)</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/paste.html" class="external-link">paste0</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="st">"gds://production/analysis_data/SBJ01639/tso_ctdna_tumor_only/"</span>,</span></span>
 <span class="r-in"><span>  <span class="st">"202204045ad5743c/L2200214/Results/PRJ220425_L2200214"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">o1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">"^gds://"</span>, <span class="st">""</span>, <span class="va">in_dir</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">o1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">"s3:/"</span>, <span class="st">"~/s3"</span>, <span class="va">in_dir</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">out_dir</span> <span class="op">&lt;-</span> <span class="va">o1</span></span></span>
 <span class="r-in"><span><span class="va">out_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 class="fu">fs</span><span class="fu">::</span><span class="fu"><a href="https://fs.r-lib.org/reference/path_expand.html" class="external-link">path_home</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"icav1/g"</span>, <span class="va">o1</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co"># in_dir &lt;- file.path(out_dir, "dracarys_gds_sync")</span></span></span>
 <span class="r-in"><span><span class="va">prefix</span> <span class="op">&lt;-</span> <span class="st">"SBJ01639"</span></span></span>
+<span class="r-in"><span><span class="va">prefix</span> <span class="op">&lt;-</span> <span class="st">"PTC_SSqCMM05pc_L2100067"</span></span></span>
 <span class="r-in"><span><span class="va">out_format</span> <span class="op">&lt;-</span> <span class="st">"rds"</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>, out_format <span class="op">=</span> <span class="va">out_format</span>, dryrun <span class="op">=</span> <span class="cn">T</span><span class="op">)</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>, out_format <span class="op">=</span> <span class="va">out_format</span>, dryrun <span class="op">=</span> <span class="cn">F</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">in_dir</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="fu">glue</span><span class="op">(</span><span class="st">"nogit/tso/2022-12-13/SBJ02858/dracarys_gds_sync"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">out_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 class="va">in_dir</span>, <span class="st">"../out"</span><span class="op">)</span></span></span>
@@ -144,11 +152,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><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>
+  <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></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/search.json b/search.json
index 5d69747..7d88495 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":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"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 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, including MultiQC JSON output. 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 0.10.0  #-----------------------------------# 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]                        [-g GDS_LOCAL_DIR] [-f {tsv,parquet,both}] [-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 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.   -g GDS_LOCAL_DIR, --gds_local_dir GDS_LOCAL_DIR                         📥 If input is a GDS directory, download the                         recognisable files to this directory. Default:                         '<out_dir>/dracarys_gds_sync'.   -f {tsv,parquet,both}, --format {tsv,parquet,both}                         🎨 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$write(d_parsed, out_dir = tempdir(), prefix = \"sample123\", out_format = \"tsv\") }"},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":null,"dir":"Reference","previous_headings":"","what":"FastqcMetrics R6 Class — FastqcMetricsFile","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"Contains methods reading displaying contents fastqc_metrics.csv file output DRAGEN.","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File -> FastqcMetricsFile","code":""},{"path":"https://umccr.github.io/dracarys/reference/FastqcMetricsFile.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"FastqcMetrics R6 Class — FastqcMetricsFile","text":"dracarys::File$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 DRAGEN 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/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 )"},{"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.","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/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 = 100, include = 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: 100). include Use PresignedUrl include presigned URLs files within GDS directory.","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_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 = NULL,   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 Use PresignedUrl include presigned URLs files within page_size Page size (def: 100). GDS directory. 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/glims_excel_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Google LIMS — glims_excel_read","title":"Read Google LIMS — glims_excel_read","text":"Reads UMCCR's Google LIMS spreadsheet.","code":""},{"path":"https://umccr.github.io/dracarys/reference/glims_excel_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Google LIMS — glims_excel_read","text":"","code":"glims_excel_read()"},{"path":"https://umccr.github.io/dracarys/reference/glims_excel_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Google LIMS — glims_excel_read","text":"Tibble columns rows Google LIMS spreadsheet.","code":""},{"path":"https://umccr.github.io/dracarys/reference/glims_portal_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Portal Limsrow Table — glims_portal_read","title":"Read Portal Limsrow Table — glims_portal_read","text":"Reads rows data portal's limsrow table, given set LibraryIDs query.","code":""},{"path":"https://umccr.github.io/dracarys/reference/glims_portal_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Portal Limsrow Table — glims_portal_read","text":"","code":"glims_portal_read(libids)"},{"path":"https://umccr.github.io/dracarys/reference/glims_portal_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Portal Limsrow Table — glims_portal_read","text":"libids Character vector LibraryID values query .","code":""},{"path":"https://umccr.github.io/dracarys/reference/glims_portal_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Portal Limsrow Table — glims_portal_read","text":"Tibble rows data portal limsrow table hits library_id column.","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/meta_bcl_convert.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for bcl_convert workflow — meta_bcl_convert","title":"Metadata for bcl_convert workflow — meta_bcl_convert","text":"Metadata bcl_convert workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_bcl_convert.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for bcl_convert workflow — meta_bcl_convert","text":"","code":"meta_bcl_convert(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_bcl_convert.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for bcl_convert workflow — meta_bcl_convert","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_bcl_convert.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for bcl_convert workflow — meta_bcl_convert","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_bcl_convert.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for bcl_convert workflow — meta_bcl_convert","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_bcl_convert(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","title":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","text":"Metadata oncoanalyser_wgs workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","text":"","code":"meta_oncoanalyser_wgs(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for oncoanalyser_wgs workflow — meta_oncoanalyser_wgs","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_oncoanalyser_wgs(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","title":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","text":"Metadata oncoanalyser_wgts_existing_both workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","text":"","code":"meta_oncoanalyser_wgts_existing_both(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for oncoanalyser_wgts_existing_both workflow — meta_oncoanalyser_wgts_existing_both","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_oncoanalyser_wgts_existing_both(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","title":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","text":"Metadata oncoanalyser_wts workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","text":"","code":"meta_oncoanalyser_wts(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for oncoanalyser_wts workflow — meta_oncoanalyser_wts","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_oncoanalyser_wts(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_rnasum.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for rnasum workflow — meta_rnasum","title":"Metadata for rnasum workflow — meta_rnasum","text":"Metadata rnasum workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_rnasum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for rnasum workflow — meta_rnasum","text":"","code":"meta_rnasum(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_rnasum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for rnasum workflow — meta_rnasum","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_rnasum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for rnasum workflow — meta_rnasum","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_rnasum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for rnasum workflow — meta_rnasum","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_rnasum(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_sash.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for sash workflow — meta_sash","title":"Metadata for sash workflow — meta_sash","text":"Metadata sash workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_sash.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for sash workflow — meta_sash","text":"","code":"meta_sash(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_sash.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for sash workflow — meta_sash","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_sash.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for sash workflow — meta_sash","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_sash.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for sash workflow — meta_sash","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_sash(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_star_alignment.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for star_alignment workflow — meta_star_alignment","title":"Metadata for star_alignment workflow — meta_star_alignment","text":"Metadata star_alignment workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_star_alignment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for star_alignment workflow — meta_star_alignment","text":"","code":"meta_star_alignment(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_star_alignment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for star_alignment workflow — meta_star_alignment","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_star_alignment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for star_alignment workflow — meta_star_alignment","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_star_alignment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for star_alignment workflow — meta_star_alignment","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_star_alignment(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","title":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","text":"Metadata tso_ctdna_tumor_only workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","text":"","code":"meta_tso_ctdna_tumor_only(pmeta, status = c(\"Succeeded\"))"},{"path":"https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for tso_ctdna_tumor_only workflow — meta_tso_ctdna_tumor_only","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_tso_ctdna_tumor_only(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_umccrise.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for umccrise workflow — meta_umccrise","title":"Metadata for umccrise workflow — meta_umccrise","text":"Metadata umccrise workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_umccrise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for umccrise workflow — meta_umccrise","text":"","code":"meta_umccrise(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_umccrise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for umccrise workflow — meta_umccrise","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_umccrise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for umccrise workflow — meta_umccrise","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_umccrise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for umccrise workflow — meta_umccrise","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_umccrise(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","title":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","text":"Metadata wgs_alignment_qc workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","text":"","code":"meta_wgs_alignment_qc(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for wgs_alignment_qc workflow — meta_wgs_alignment_qc","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_wgs_alignment_qc(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","title":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","text":"Metadata wgs_tumor_normal workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","text":"","code":"meta_wgs_tumor_normal(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for wgs_tumor_normal workflow — meta_wgs_tumor_normal","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_wgs_tumor_normal(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","title":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","text":"Metadata wts_alignment_qc workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","text":"","code":"meta_wts_alignment_qc(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for wts_alignment_qc workflow — meta_wts_alignment_qc","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_wts_alignment_qc(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","title":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","text":"Metadata wts_tumor_only workflow","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","text":"","code":"meta_wts_tumor_only(pmeta, status = \"Succeeded\")"},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","text":"pmeta Path portal workflows metadata table, tibble already parsed data. status Workflow status keep (default: Succeeded).","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","text":"tibble metadata per workflow run.","code":""},{"path":"https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata for wts_tumor_only workflow — meta_wts_tumor_only","text":"","code":"pmeta <- system.file(\"extdata/portal_meta_top4.csv\", package = \"dracarys\") (m <- meta_wts_tumor_only(pmeta)) #> Error in portal_meta_read(pmeta): pmeta should be an already parsed dataframe or a local file."},{"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.","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/portal_meta_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Read ICA Workflows Metadata via Portal API — portal_meta_read","title":"Read ICA Workflows Metadata via Portal API — portal_meta_read","text":"Reads ICA Workflows Metadata via Portal API using awscurl. See https://github.com/okigan/awscurl required AWS_ environment variables.","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read ICA Workflows Metadata via Portal API — portal_meta_read","text":"","code":"portal_meta_read(pmeta = NULL, rows = 100, params = \"\", account = \"prod\")"},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read ICA Workflows Metadata via Portal API — portal_meta_read","text":"pmeta Path downloaded portal metadata file, already parsed metadata tibble. rows Number rows return. params String containing additional params pass /workflows endpoint, e.g. '&type_name=bclconvert'. account UMCCR portal account (one \"prod\", \"dev\", \"stg\").","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read ICA Workflows Metadata via Portal API — portal_meta_read","text":"tibble results given query.","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read ICA Workflows Metadata via Portal API — portal_meta_read","text":"","code":"if (FALSE) { portal_meta_read(params = \"&type_name=rnasum\", rows = 4) }"},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html","id":null,"dir":"Reference","previous_headings":"","what":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","title":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","text":"Reads ICA Workflows Metadata given workflow run IDs.","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","text":"","code":"portal_meta_read_athena(wfrids = NULL)"},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","text":"wfrids Character vector wfr IDs query.","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","text":"Tibble row per wfr ID.","code":""},{"path":"https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read ICA Workflows Metadata via Athena — portal_meta_read_athena","text":"","code":"if (FALSE) { wfrids <- c(\"wfr.1e764ca00e7a43a69e2424f250a34868\") portal_meta_read_athena(wfrids) }"},{"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 GDS 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,   gds_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 local). out_dir Output directory. prefix Prefix output file(s). gds_local_dir indir GDS 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 <- paste0(   \"gds://production/analysis_data/SBJ01639/tso_ctdna_tumor_only/\",   \"202204045ad5743c/L2200214/Results/PRJ220425_L2200214\" ) o1 <- sub(\"^gds://\", \"\", in_dir) out_dir <- file.path(fs::path_home(), \"icav1/g\", o1) # in_dir <- file.path(out_dir, \"dracarys_gds_sync\") prefix <- \"SBJ01639\" out_format <- \"rds\" umccr_tidy(in_dir = in_dir, out_dir = out_dir, prefix = prefix, out_format = out_format, dryrun = T)  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-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. 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":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 99a3c3c..1835c2e 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -9,6 +9,9 @@
   <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>
@@ -33,6 +36,9 @@
   <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>
@@ -138,6 +144,18 @@
   <url>
     <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>
+  </url>
   <url>
     <loc>https://umccr.github.io/dracarys/reference/date_log.html</loc>
   </url>
@@ -150,6 +168,9 @@
   <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>
@@ -177,12 +198,6 @@
   <url>
     <loc>https://umccr.github.io/dracarys/reference/gds_volumes_list.html</loc>
   </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/glims_excel_read.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/glims_portal_read.html</loc>
-  </url>
   <url>
     <loc>https://umccr.github.io/dracarys/reference/ica_token_validate.html</loc>
   </url>
@@ -192,45 +207,6 @@
   <url>
     <loc>https://umccr.github.io/dracarys/reference/match_regex.html</loc>
   </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_bcl_convert.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgs.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wgts_existing_both.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_oncoanalyser_wts.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_rnasum.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_sash.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_star_alignment.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_tso_ctdna_tumor_only.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_umccrise.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_wgs_alignment_qc.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_wgs_tumor_normal.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_wts_alignment_qc.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/meta_wts_tumor_only.html</loc>
-  </url>
   <url>
     <loc>https://umccr.github.io/dracarys/reference/multiqc_column_map_append.html</loc>
   </url>
@@ -249,6 +225,9 @@
   <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>
+  </url>
   <url>
     <loc>https://umccr.github.io/dracarys/reference/multiqc_parse_xyline_plot.html</loc>
   </url>
@@ -258,12 +237,6 @@
   <url>
     <loc>https://umccr.github.io/dracarys/reference/multiqc_tidy_json.html</loc>
   </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/portal_meta_read.html</loc>
-  </url>
-  <url>
-    <loc>https://umccr.github.io/dracarys/reference/portal_meta_read_athena.html</loc>
-  </url>
   <url>
     <loc>https://umccr.github.io/dracarys/reference/rdf2tab.html</loc>
   </url>