Release 0.5.0

chrovis · Oct 16, 2024 · 4846f78 · 4846f78
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,18 @@
 # Changelog
 
+## [0.5.0] - TBD
+
+### BREAKING
+
+- Fix uncertain bases and amino acids format of ins and delins because HGVS nomenclature was updated.
+  - DNA: `ins(10)` -> `insN[10]`
+  - RNA: `ins(10)` -> `insn[10]`
+  - Protein: `ins10` -> `insX[10]`
+
+### Fixed
+
+- Fix uncertain insertion. [#10](https://github.com/chrovis/clj-hgvs/pull/10)
+
 ## [0.4.7] - 2023-04-25
 
 ### Fixed
@@ -126,7 +139,8 @@
 
 ## 0.1.0 - 2017-04-17
 
-[Unreleased]: https://github.com/chrovis/clj-hgvs/compare/0.4.7...HEAD
+[Unreleased]: https://github.com/chrovis/clj-hgvs/compare/0.5.0...HEAD
+[0.5.0]: https://github.com/chrovis/clj-hgvs/compare/0.4.7...0.5.0
 [0.4.7]: https://github.com/chrovis/clj-hgvs/compare/0.4.6...0.4.7
 [0.4.6]: https://github.com/chrovis/clj-hgvs/compare/0.4.5...0.4.6
 [0.4.5]: https://github.com/chrovis/clj-hgvs/compare/0.4.4...0.4.5

diff --git a/README.md b/README.md
@@ -19,18 +19,25 @@ clj-hgvs provides:
 Clojure CLI/deps.edn:
 
 ```clojure
-clj-hgvs {:mvn/version "0.4.7"}
+clj-hgvs {:mvn/version "0.5.0"}
 ```
 
 Leiningen/Boot:
 
 ```clojure
-[clj-hgvs "0.4.7"]
+[clj-hgvs "0.5.0"]
 ```
 
 To use clj-hgvs with Clojure 1.8, you must include a dependency on
 [clojure-future-spec](https://github.com/tonsky/clojure-future-spec).
 
+## Breaking Changes in 0.5.0
+
+- Fix uncertain bases and amino acids format of ins and delins because HGVS nomenclature was updated.
+  - DNA: `ins(10)` -> `insN[10]`
+  - RNA: `ins(10)` -> `insn[10]`
+  - Protein: `ins10` -> `insX[10]`
+
 ## Breaking Changes in 0.4.0
 
 - HGVS data structure changes from map to record (`clj-hgvs.core/HGVS`).
@@ -170,6 +177,6 @@ You may supply custom repair rules to the second argument:
 
 ## License
 
-Copyright 2017-2023 [Xcoo, Inc.](https://xcoo.jp/)
+Copyright 2017-2024 [Xcoo, Inc.](https://xcoo.jp/)
 
 Licensed under the [Apache License, Version 2.0](LICENSE).
diff --git a/docs/clj-hgvs.coordinate.html b/docs/clj-hgvs.coordinate.html
diff --git a/docs/clj-hgvs.core.html b/docs/clj-hgvs.core.html
diff --git a/docs/clj-hgvs.mutation.html b/docs/clj-hgvs.mutation.html
diff --git a/docs/clj-hgvs.repairer.html b/docs/clj-hgvs.repairer.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC ""
     "">
-<html><head><meta charset="UTF-8" /><title>clj-hgvs.repairer 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">clj-hgvs</span> <span class="project-version">0.4.7</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>clj-hgvs</span></div></div></li><li class="depth-2 branch"><a href="clj-hgvs.coordinate.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>coordinate</span></div></a></li><li class="depth-2 branch"><a href="clj-hgvs.core.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>core</span></div></a></li><li class="depth-2 branch"><a href="clj-hgvs.mutation.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>mutation</span></div></a></li><li class="depth-2 current"><a href="clj-hgvs.repairer.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>repairer</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="clj-hgvs.repairer.html#var-built-in-repairers"><div class="inner"><span>built-in-repairers</span></div></a></li><li class="depth-1"><a href="clj-hgvs.repairer.html#var-infer-kind"><div class="inner"><span>infer-kind</span></div></a></li></ul></div><div class="namespace-docs" id="content"><h1 class="anchor" id="top">clj-hgvs.repairer</h1><div class="doc"><pre class="plaintext">HGVS repair functions.
+<html><head><meta charset="UTF-8" /><title>clj-hgvs.repairer 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">clj-hgvs</span> <span class="project-version">0.5.0</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 "><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>clj-hgvs</span></div></div></li><li class="depth-2 branch"><a href="clj-hgvs.coordinate.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>coordinate</span></div></a></li><li class="depth-2 branch"><a href="clj-hgvs.core.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>core</span></div></a></li><li class="depth-2 branch"><a href="clj-hgvs.mutation.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>mutation</span></div></a></li><li class="depth-2 current"><a href="clj-hgvs.repairer.html"><div class="inner"><span class="tree"><span class="top"></span><span class="bottom"></span></span><span>repairer</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="clj-hgvs.repairer.html#var-built-in-repairers"><div class="inner"><span>built-in-repairers</span></div></a></li><li class="depth-1"><a href="clj-hgvs.repairer.html#var-infer-kind"><div class="inner"><span>infer-kind</span></div></a></li></ul></div><div class="namespace-docs" id="content"><h1 class="anchor" id="top">clj-hgvs.repairer</h1><div class="doc"><pre class="plaintext">HGVS repair functions.
 </pre></div><div class="public anchor" id="var-built-in-repairers"><h3>built-in-repairers</h3><div class="usage"></div><div class="doc"><pre class="plaintext">The built-in repair functions.
 
 A repair fn must take a HGVS string and an inferred kind, and return a
@@ -13,5 +13,5 @@
       s))
 
 The built-in rules are based on frequent mistakes in popular public-domain
-databases such as dbSNP and ClinVar.</pre></div><div class="src-link"><a href="https://github.com/chrovis/clj-hgvs/blob/0.4.7/src/clj_hgvs/repairer.cljc#L288">view source</a></div></div><div class="public anchor" id="var-infer-kind"><h3>infer-kind</h3><div class="usage"><code>(infer-kind s)</code></div><div class="doc"><pre class="plaintext">Infers a kind from the provided string, returning the kind keyword.
-</pre></div><div class="src-link"><a href="https://github.com/chrovis/clj-hgvs/blob/0.4.7/src/clj_hgvs/repairer.cljc#L6">view source</a></div></div></div></body></html>
+databases such as dbSNP and ClinVar.</pre></div><div class="src-link"><a href="https://github.com/chrovis/clj-hgvs/blob/0.5.0/src/clj_hgvs/repairer.cljc#L302">view source</a></div></div><div class="public anchor" id="var-infer-kind"><h3>infer-kind</h3><div class="usage"><code>(infer-kind s)</code></div><div class="doc"><pre class="plaintext">Infers a kind from the provided string, returning the kind keyword.
+</pre></div><div class="src-link"><a href="https://github.com/chrovis/clj-hgvs/blob/0.5.0/src/clj_hgvs/repairer.cljc#L6">view source</a></div></div></div></body></html>
diff --git a/docs/index.html b/docs/index.html
diff --git a/project.clj b/project.clj
@@ -1,4 +1,4 @@
-(defproject clj-hgvs "0.5.0-SNAPSHOT"
+(defproject clj-hgvs "0.5.0"
   :description "Clojure(Script) library for handling HGVS"
   :url "https://github.com/chrovis/clj-hgvs"
   :license {:name "Apache License, Version 2.0"