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Merge pull request #78 from chrovis/chore/release-0.9.3
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Release 0.9.3
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@totakke
totakke authored Jul 3, 2023
2 parents 71dad6b + 96f97f3 commit 1f7b5ac
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10 changes: 9 additions & 1 deletion CHANGELOG.md
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# Changelog

## [0.9.3] - date TBD

### Fixed

- Fix 3'-rule errors for certain sequence patterns. [#75](https://github.com/chrovis/varity/pull/75)
- Fix overlapping condition of boundary of exon/intron. [#77](https://github.com/chrovis/varity/pull/77)

## [0.9.2] - 2023-02-08

### Fixed
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First release.

[Unreleased]: https://github.com/chrovis/varity/compare/0.9.2...HEAD
[Unreleased]: https://github.com/chrovis/varity/compare/0.9.3...HEAD
[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
[0.9.0]: https://github.com/chrovis/varity/compare/0.8.0...0.9.0
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -17,13 +17,13 @@ Variant translation library for Clojure.
Clojure CLI/deps.edn:

```clojure
varity/varity {:mvn/version "0.9.2"}
varity/varity {:mvn/version "0.9.3"}
```

Leiningen/Boot:

```clojure
[varity "0.9.2"]
[varity "0.9.3"]
```

To use varity with Clojure 1.8, you must include a dependency on
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6 changes: 3 additions & 3 deletions docs/index.html
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12 changes: 6 additions & 6 deletions docs/varity.chain.html
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<!DOCTYPE html PUBLIC ""
"">
<html><head><meta charset="UTF-8" /><title>varity.chain documentation</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">0.9.2</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 "><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 current"><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.check.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>check</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.hgvs-vcf-check.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>hgvs-vcf-check</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="sidebar secondary"><h3><a href="#top"><span class="inner">Public Vars</span></a></h3><ul><li class="depth-1"><a href="varity.chain.html#var-index"><div class="inner"><span>index</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-load-chain"><div class="inner"><span>load-chain</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-chains"><div class="inner"><span>search-chains</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-containing-chains"><div class="inner"><span>search-containing-chains</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-overlap-blocks"><div class="inner"><span>search-overlap-blocks</span></div></a></li></ul></div><div class="namespace-docs" id="content"><h1 class="anchor" id="top">varity.chain</h1><div class="doc"><pre class="plaintext">Functions to read, index, and search the chain format. See
<html><head><meta charset="UTF-8" /><title>varity.chain documentation</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 "><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 current"><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="sidebar secondary"><h3><a href="#top"><span class="inner">Public Vars</span></a></h3><ul><li class="depth-1"><a href="varity.chain.html#var-index"><div class="inner"><span>index</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-load-chain"><div class="inner"><span>load-chain</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-chains"><div class="inner"><span>search-chains</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-containing-chains"><div class="inner"><span>search-containing-chains</span></div></a></li><li class="depth-1"><a href="varity.chain.html#var-search-overlap-blocks"><div class="inner"><span>search-overlap-blocks</span></div></a></li></ul></div><div class="namespace-docs" id="content"><h1 class="anchor" id="top">varity.chain</h1><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="public anchor" id="var-index"><h3>index</h3><div class="usage"><code>(index chains)</code></div><div class="doc"><pre class="plaintext">Creates chain index for search.
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.2/src/varity/chain.clj#L102">view source</a></div></div><div class="public anchor" id="var-load-chain"><h3>load-chain</h3><div class="usage"><code>(load-chain f)</code></div><div class="doc"><pre class="plaintext">Loads f (e.g. hg19ToHg38.over.chain(.gz)), returning the all contents as a
sequence.</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.2/src/varity/chain.clj#L62">view source</a></div></div><div class="public anchor" id="var-search-chains"><h3>search-chains</h3><div class="usage"><code>(search-chains chr pos chain-idx)</code></div><div class="doc"><pre class="plaintext">Searches chain entries with chr and pos using the index, returning the
results as a sequence. See also varity.chain/index.</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.2/src/varity/chain.clj#L122">view source</a></div></div><div class="public anchor" id="var-search-containing-chains"><h3>search-containing-chains</h3><div class="usage"><code>(search-containing-chains chr start end chain-idx)</code></div><div class="doc"><pre class="plaintext">Calculates a list of chains that contain the given interval.
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.2/src/varity/chain.clj#L129">view source</a></div></div><div class="public anchor" id="var-search-overlap-blocks"><h3>search-overlap-blocks</h3><div class="usage"><code>(search-overlap-blocks start end blocks-idx)</code></div><div class="doc"><pre class="plaintext">Calculates a list of blocks that overlap the given interval.
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.2/src/varity/chain.clj#L137">view source</a></div></div></div></body></html>
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.3/src/varity/chain.clj#L102">view source</a></div></div><div class="public anchor" id="var-load-chain"><h3>load-chain</h3><div class="usage"><code>(load-chain f)</code></div><div class="doc"><pre class="plaintext">Loads f (e.g. hg19ToHg38.over.chain(.gz)), returning the all contents as a
sequence.</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.3/src/varity/chain.clj#L62">view source</a></div></div><div class="public anchor" id="var-search-chains"><h3>search-chains</h3><div class="usage"><code>(search-chains chr pos chain-idx)</code></div><div class="doc"><pre class="plaintext">Searches chain entries with chr and pos using the index, returning the
results as a sequence. See also varity.chain/index.</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.3/src/varity/chain.clj#L122">view source</a></div></div><div class="public anchor" id="var-search-containing-chains"><h3>search-containing-chains</h3><div class="usage"><code>(search-containing-chains chr start end chain-idx)</code></div><div class="doc"><pre class="plaintext">Calculates a list of chains that contain the given interval.
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.3/src/varity/chain.clj#L129">view source</a></div></div><div class="public anchor" id="var-search-overlap-blocks"><h3>search-overlap-blocks</h3><div class="usage"><code>(search-overlap-blocks start end blocks-idx)</code></div><div class="doc"><pre class="plaintext">Calculates a list of blocks that overlap the given interval.
</pre></div><div class="src-link"><a href="https://github.com/chrovis/varity/blob/0.9.3/src/varity/chain.clj#L137">view source</a></div></div></div></body></html>
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