Refactor Phred function and misc changes for release (#132)

* refactor phred func and docs * add aahash component credits * regenerate docs
bcgsc · Nov 29, 2024 · 2c00e7a · 2c00e7a
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diff --git a/README.md b/README.md
@@ -86,6 +86,7 @@ Credits
 - Components:
   - [Hamid Mohamadi](https://github.com/mohamadi) and [Parham Kazemi](https://github.com/parham-k) for [ntHash](https://github.com/bcgsc/ntHash)
   - [Justin Chu](https://github.com/JustinChu) for [MIBloomFilter](https://github.com/bcgsc/btl_bloomfilter)
+  - [Johnathan Wong](https://github.com/jwcodee) for [aaHash](https://github.com/bcgsc/btllib)
 - Included dependencies:
   - [Chase Geigle](https://github.com/skystrife) for [cpptoml](https://github.com/skystrife/cpptoml)
   - Simon Gog, Timo Beller, Alistair Moffat, and Matthias Petri for [sdsl-lite](https://github.com/simongog/sdsl-lite)

diff --git a/docs/aahash_8hpp_source.html b/docs/aahash_8hpp_source.html
diff --git a/docs/annotated.html b/docs/annotated.html
diff --git a/docs/bloom__filter_8hpp_source.html b/docs/bloom__filter_8hpp_source.html
diff --git a/docs/classbtllib_1_1AAHash-members.html b/docs/classbtllib_1_1AAHash-members.html
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-  <div class="headertitle">
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 </div><!--header-->
 <div class="contents">
 
 <p>This is the complete list of members for <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>, including all inherited members.</p>
 <table class="directory">
   <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html#a2edba2dba416e5913a9867fec2fd5444">AAHash</a>(std::string_view seq, uint8_t hash_num, uint16_t k, unsigned level, size_t pos=0)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>AAHash</b>(const AAHash &amp;aahash) (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>AAHash</b>(const AAHash &amp;aahash) (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>AAHash</b>(AAHash &amp;&amp;)=default (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>get_forward_hash</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_hash_num</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>get_k</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_level</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>get_pos</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_seq</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>hashes</b>() const  (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>get_forward_hash</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_hash_num</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>get_k</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_level</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>get_pos</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_seq</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>hashes</b>() const (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html#a94a48eac3e812204810c3182f55b122f">roll</a>()</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"></td></tr>
-  <tr bgcolor="#f0f0f0"><td class="entry"><b>SeedAAHash</b> (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>SeedAAHash</b> (defined in <a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1AAHash.html">btllib::AAHash</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
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