Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Release 0.10.0 #84

Merged
merged 2 commits into from
Dec 27, 2023
Merged

Release 0.10.0 #84

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
bd55f59
chore: update change log
nokara26 Dec 25, 2023
ca31e2e
chore(release): Release 0.10.0
nokara26 Dec 25, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,12 @@
# Changelog

## [0.10.0] - date TBD

### Fixed

- Fix upstream and downstream sequence of sequence-info and delins process. [#81](https://github.com/chrovis/varity/pull/81)
- Fix boundary of exon/intron determining process. [#82](https://github.com/chrovis/varity/pull/82)

## [0.9.3] - 2023-07-03

### Fixed
Expand Down Expand Up @@ -333,7 +340,8 @@ Strand representation is changed from string (`+`, `-`) to keyword (`:forward`,

First release.

[Unreleased]: https://github.com/chrovis/varity/compare/0.9.3...HEAD
[Unreleased]: https://github.com/chrovis/varity/compare/0.10.0...HEAD
[0.10.0]: https://github.com/chrovis/varity/compare/0.9.3...0.10.0
[0.9.3]: https://github.com/chrovis/varity/compare/0.9.2...0.9.3
[0.9.2]: https://github.com/chrovis/varity/compare/0.9.1...0.9.2
[0.9.1]: https://github.com/chrovis/varity/compare/0.9.0...0.9.1
Expand Down
19 changes: 17 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,18 +17,33 @@ Variant translation library for Clojure.
Clojure CLI/deps.edn:

```clojure
varity/varity {:mvn/version "0.9.3"}
varity/varity {:mvn/version "0.10.0"}
```

Leiningen/Boot:

```clojure
[varity "0.9.3"]
[varity "0.10.0"]
```

To use varity with Clojure 1.8, you must include a dependency on
[clojure-future-spec](https://github.com/tonsky/clojure-future-spec).

## Breaking changes in 0.10.0

We introduced enhancements to the description of protein changes by `varity.vcf-to-hgvs`, specifically making deletions more clinically meaningful:

1. exon-intron boundary deletions:

The deletion that overlaps the exon-intron boundary will trigger an Exception because alterations affecting the splice sites are predicted to be splicing abnormalities.

2. stop codon deletions:

In cases where deletions contain a stop codon, `varity.vcf-to-hgvs` generates the following outputs based on the alteration sequence:

- If the alteration sequence contains a stop codon, varity outputs as deletion-insertion.
- Otherwise, this outputs `p.?`.

## Breaking changes in 0.9.0

The default value of `:prefer-deletion?` option is changed to `false`.
Expand Down
2 changes: 1 addition & 1 deletion docs/index.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<!DOCTYPE html PUBLIC ""
"">
<html><head><meta charset="UTF-8" /><title>varity 0.9.3</title><link rel="stylesheet" type="text/css" href="css/default.css" /><link rel="stylesheet" type="text/css" href="highlight/solarized-light.css" /><script type="text/javascript" src="highlight/highlight.min.js"></script><script type="text/javascript" src="js/jquery.min.js"></script><script type="text/javascript" src="js/page_effects.js"></script><script>hljs.initHighlightingOnLoad();</script></head><body><div id="header"><h2>Generated by <a href="https://github.com/weavejester/codox">Codox</a> with <a href="https://github.com/xsc/codox-theme-rdash">RDash UI</a> theme</h2><h1><a href="index.html"><span class="project-title"><span class="project-name">varity</span> <span class="project-version">0.9.3</span></span></a></h1></div><div class="sidebar primary"><h3 class="no-link"><span class="inner">Project</span></h3><ul class="index-link"><li class="depth-1 current"><a href="index.html"><div class="inner">Index</div></a></li></ul><h3 class="no-link"><span class="inner">Namespaces</span></h3><ul><li class="depth-1"><div class="no-link"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>varity</span></div></div></li><li class="depth-2 branch"><a href="varity.chain.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>chain</span></div></a></li><li class="depth-2 branch"><a href="varity.codon.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>codon</span></div></a></li><li class="depth-2 branch"><a href="varity.fusion.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>fusion</span></div></a></li><li class="depth-2 branch"><a href="varity.hgvs.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>hgvs</span></div></a></li><li class="depth-2 branch"><a href="varity.hgvs-to-vcf.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>hgvs-to-vcf</span></div></a></li><li class="depth-2 branch"><a href="varity.lift.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>lift</span></div></a></li><li class="depth-2 branch"><a href="varity.ref-gene.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>ref-gene</span></div></a></li><li class="depth-2 branch"><a href="varity.util.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>util</span></div></a></li><li class="depth-2 branch"><a href="varity.vcf-lift.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>vcf-lift</span></div></a></li><li class="depth-2"><a href="varity.vcf-to-hgvs.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>vcf-to-hgvs</span></div></a></li></ul></div><div class="namespace-index" id="content"><h1><span class="project-title"><span class="project-name">varity</span> <span class="project-version">0.9.3</span></span></h1><h5 class="license">Released under the <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a></h5><div class="doc"><p>Variant translation library for Clojure.</p></div><h2>Installation</h2><p>To install, add the following dependency to your project or build file:</p><pre class="deps">[varity "0.9.3"]</pre><h2>Namespaces</h2><div class="namespace"><h3><a href="varity.chain.html">varity.chain</a></h3><div class="doc"><pre class="plaintext">Functions to read, index, and search the chain format. See
<html><head><meta charset="UTF-8" /><title>varity 0.10.0</title><link rel="stylesheet" type="text/css" href="css/default.css" /><link rel="stylesheet" type="text/css" href="highlight/solarized-light.css" /><script type="text/javascript" src="highlight/highlight.min.js"></script><script type="text/javascript" src="js/jquery.min.js"></script><script type="text/javascript" src="js/page_effects.js"></script><script>hljs.initHighlightingOnLoad();</script></head><body><div id="header"><h2>Generated by <a href="https://github.com/weavejester/codox">Codox</a> with <a href="https://github.com/xsc/codox-theme-rdash">RDash UI</a> theme</h2><h1><a href="index.html"><span class="project-title"><span class="project-name">varity</span> <span class="project-version">0.10.0</span></span></a></h1></div><div class="sidebar primary"><h3 class="no-link"><span class="inner">Project</span></h3><ul class="index-link"><li class="depth-1 current"><a href="index.html"><div class="inner">Index</div></a></li></ul><h3 class="no-link"><span class="inner">Namespaces</span></h3><ul><li class="depth-1"><div class="no-link"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>varity</span></div></div></li><li class="depth-2 branch"><a href="varity.chain.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>chain</span></div></a></li><li class="depth-2 branch"><a href="varity.codon.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>codon</span></div></a></li><li class="depth-2 branch"><a href="varity.fusion.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>fusion</span></div></a></li><li class="depth-2 branch"><a href="varity.hgvs.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>hgvs</span></div></a></li><li class="depth-2 branch"><a href="varity.hgvs-to-vcf.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>hgvs-to-vcf</span></div></a></li><li class="depth-2 branch"><a href="varity.lift.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>lift</span></div></a></li><li class="depth-2 branch"><a href="varity.ref-gene.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>ref-gene</span></div></a></li><li class="depth-2 branch"><a href="varity.util.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>util</span></div></a></li><li class="depth-2 branch"><a href="varity.vcf-lift.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>vcf-lift</span></div></a></li><li class="depth-2"><a href="varity.vcf-to-hgvs.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>vcf-to-hgvs</span></div></a></li></ul></div><div class="namespace-index" id="content"><h1><span class="project-title"><span class="project-name">varity</span> <span class="project-version">0.10.0</span></span></h1><h5 class="license">Released under the <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a></h5><div class="doc"><p>Variant translation library for Clojure.</p></div><h2>Installation</h2><p>To install, add the following dependency to your project or build file:</p><pre class="deps">[varity "0.10.0"]</pre><h2>Namespaces</h2><div class="namespace"><h3><a href="varity.chain.html">varity.chain</a></h3><div class="doc"><pre class="plaintext">Functions to read, index, and search the chain format. See
<a href="https://genome.ucsc.edu/goldenPath/help/chain.html">https://genome.ucsc.edu/goldenPath/help/chain.html</a> for the detail chain format
specifications.</pre></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="varity.chain.html#var-index">index</a> </li><li> <a href="varity.chain.html#var-load-chain">load-chain</a> </li><li> <a href="varity.chain.html#var-search-chains">search-chains</a> </li><li> <a href="varity.chain.html#var-search-containing-chains">search-containing-chains</a> </li><li> <a href="varity.chain.html#var-search-overlap-blocks">search-overlap-blocks</a> </li></ul></div></div><div class="namespace"><h3><a href="varity.codon.html">varity.codon</a></h3><div class="doc"><pre class="plaintext">Handles codon.</pre></div><div class="index"><p>Public variables and functions:</p><ul><li> <a href="varity.codon.html#var-amino-acid-.3Ecodons">amino-acid-&gt;codons</a> </li><li> <a href="varity.codon.html#var-amino-acid-sequence">amino-acid-sequence</a> </li><li> <a href="varity.codon.html#var-codon-.3Eamino-acid">codon-&gt;amino-acid</a> </li></ul></div></div><div class="namespace"><h3><a href="varity.fusion.html">varity.fusion</a></h3><div class="doc"><pre class="plaintext">NOTE: This algorithm was initially developed at Cancer Precision
Medicine Center, Japanese Foundation for Cancer Research and Xcoo
Expand Down
Loading