Merge pull request #101 from bcgsc/nthash-randseq

Update ntHash and RandSeq

docs/aahash_8hpp_source.html

@@ -294,7 +294,7 @@
 <div class="ttc" id="aclassbtllib_1_1SeedAAHash_html_a920b6430467869782159dc3b6906d8fb"><div class="ttname"><a href="classbtllib_1_1SeedAAHash.html#a920b6430467869782159dc3b6906d8fb">btllib::SeedAAHash::SeedAAHash</a></div><div class="ttdeci">SeedAAHash(const char *seq, const std::vector&lt; SpacedSeed &gt; &amp;seeds, unsigned hash_num_per_seed, unsigned k, size_t pos=0)</div><div class="ttdef"><b>Definition:</b> aahash.hpp:172</div></div>
 <div class="ttc" id="aclassbtllib_1_1SeedAAHash_html_ac189ce494d185b0e224b05902d4b7a54"><div class="ttname"><a href="classbtllib_1_1SeedAAHash.html#ac189ce494d185b0e224b05902d4b7a54">btllib::SeedAAHash::roll</a></div><div class="ttdeci">bool roll()</div></div>
 <div class="ttc" id="anamespacebtllib_html"><div class="ttname"><a href="namespacebtllib.html">btllib</a></div><div class="ttdef"><b>Definition:</b> aahash.hpp:15</div></div>
-<div class="ttc" id="anamespacebtllib_html_a3d172327f4a061736fa3788a476da88f"><div class="ttname"><a href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">btllib::srol</a></div><div class="ttdeci">uint64_t srol(const uint64_t x)</div><div class="ttdef"><b>Definition:</b> nthash_lowlevel.hpp:51</div></div>
+<div class="ttc" id="anamespacebtllib_html_a3d172327f4a061736fa3788a476da88f"><div class="ttname"><a href="namespacebtllib.html#a3d172327f4a061736fa3788a476da88f">btllib::srol</a></div><div class="ttdeci">uint64_t srol(const uint64_t x)</div><div class="ttdef"><b>Definition:</b> nthash_lowlevel.hpp:54</div></div>
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docs/classbtllib_1_1RandSeq-members.html

@@ -83,6 +83,7 @@
   <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>Masking</b> enum name (defined in <a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html#a5d704c9e95d04018daac74489e3dca1c">RandSeq</a>(SeqType type, Masking masking=Masking::NONE)</td><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a></td><td class="entry"></td></tr>
   <tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>SeqType</b> enum name (defined in <a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">set_seed</a>(unsigned long seed)</td><td class="entry"><a class="el" href="classbtllib_1_1RandSeq.html">btllib::RandSeq</a></td><td class="entry"></td></tr>
 </table></div><!-- contents -->
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docs/classbtllib_1_1RandSeq.html

@@ -98,6 +98,8 @@
 Public Member Functions</h2></td></tr>
 <tr class="memitem:a5d704c9e95d04018daac74489e3dca1c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RandSeq.html#a5d704c9e95d04018daac74489e3dca1c">RandSeq</a> (SeqType type, Masking masking=Masking::NONE)</td></tr>
 <tr class="separator:a5d704c9e95d04018daac74489e3dca1c"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0a481fe231a3ca8021aa807f2bd7d97b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">set_seed</a> (unsigned long seed)</td></tr>
+<tr class="separator:a0a481fe231a3ca8021aa807f2bd7d97b"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a8d530883472e225d971cac14b40a0571"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RandSeq.html#a8d530883472e225d971cac14b40a0571">generate</a> (size_t length)</td></tr>
 <tr class="separator:a8d530883472e225d971cac14b40a0571"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
@@ -162,6 +164,31 @@ <h2 class="memtitle"><span class="permalink"><a href="#a8d530883472e225d971cac14
   </dd>
 </dl>
 
+</div>
+</div>
+<a id="a0a481fe231a3ca8021aa807f2bd7d97b" name="a0a481fe231a3ca8021aa807f2bd7d97b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0a481fe231a3ca8021aa807f2bd7d97b">&#9670;&#160;</a></span>set_seed()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void btllib::RandSeq::set_seed </td>
+          <td>(</td>
+          <td class="paramtype">unsigned long&#160;</td>
+          <td class="paramname"><em>seed</em></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<p >Set the seed of the random string generator</p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">seed</td><td>Random generator seed </td></tr>
+  </table>
+  </dd>
+</dl>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>

docs/counting__bloom__filter-inl_8hpp_source.html

@@ -555,7 +555,7 @@
 <div class="ttc" id="aclassbtllib_1_1KmerCountingBloomFilter_html_a9f5ab29059b0fa1cc5b076520639f14c"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#a9f5ab29059b0fa1cc5b076520639f14c">btllib::KmerCountingBloomFilter::insert</a></div><div class="ttdeci">void insert(const char *seq, size_t seq_len)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:304</div></div>
 <div class="ttc" id="aclassbtllib_1_1KmerCountingBloomFilter_html_aab2f78777fa04950abd2197bd12bf6cb"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#aab2f78777fa04950abd2197bd12bf6cb">btllib::KmerCountingBloomFilter::contains_insert</a></div><div class="ttdeci">T contains_insert(const char *seq, size_t seq_len)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:346</div></div>
 <div class="ttc" id="aclassbtllib_1_1KmerCountingBloomFilter_html_af5073e09146d1b029e4f6be38ec644bc"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#af5073e09146d1b029e4f6be38ec644bc">btllib::KmerCountingBloomFilter::KmerCountingBloomFilter</a></div><div class="ttdeci">KmerCountingBloomFilter()</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter.hpp:301</div></div>
-<div class="ttc" id="aclassbtllib_1_1NtHash_html"><div class="ttname"><a href="classbtllib_1_1NtHash.html">btllib::NtHash</a></div><div class="ttdef"><b>Definition:</b> nthash.hpp:59</div></div>
+<div class="ttc" id="aclassbtllib_1_1NtHash_html"><div class="ttname"><a href="classbtllib_1_1NtHash.html">btllib::NtHash</a></div><div class="ttdef"><b>Definition:</b> nthash.hpp:60</div></div>
 <div class="ttc" id="aclassbtllib_1_1NtHash_html_a244c0c11655b6e1c52dd7c4528b8ed05"><div class="ttname"><a href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">btllib::NtHash::roll</a></div><div class="ttdeci">bool roll()</div></div>
 <div class="ttc" id="anamespacebtllib_html"><div class="ttname"><a href="namespacebtllib.html">btllib</a></div><div class="ttdef"><b>Definition:</b> aahash.hpp:15</div></div>
 <div class="ttc" id="anamespacebtllib_html_a540bce0213b7718e519ddc4466361bf7"><div class="ttname"><a href="namespacebtllib.html#a540bce0213b7718e519ddc4466361bf7">btllib::check_error</a></div><div class="ttdeci">void check_error(bool condition, const std::string &amp;msg)</div></div>

docs/functions.html

@@ -175,6 +175,7 @@ <h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
 <li>SEQ&#160;:&#160;<a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html#a1071f9e151bc7b70631263f8e3eea180">btllib::Indexlr::Flag</a></li>
 <li>SeqReader()&#160;:&#160;<a class="el" href="classbtllib_1_1SeqReader.html#a03cc4e39fffc556a2f05c30bc6d3731d">btllib::SeqReader</a></li>
 <li>SeqWriter()&#160;:&#160;<a class="el" href="classbtllib_1_1SeqWriter.html#a6271cffe77701558f0997532a7e58d43">btllib::SeqWriter</a></li>
+<li>set_seed()&#160;:&#160;<a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">btllib::RandSeq</a></li>
 <li>SHORT_MODE&#160;:&#160;<a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html#ad901a6d96362ce4b250fa144fe9a76ef">btllib::Indexlr::Flag</a>, <a class="el" href="structbtllib_1_1SeqReader_1_1Flag.html#ab0aba3f99ab4159205621e2242c6e18f">btllib::SeqReader::Flag</a></li>
 </ul>
 

docs/functions_func.html

@@ -155,6 +155,7 @@ <h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
 <li>SeedBloomFilter()&#160;:&#160;<a class="el" href="classbtllib_1_1SeedBloomFilter.html#ad13884cf28a0e94978ac5005be628f3b">btllib::SeedBloomFilter</a></li>
 <li>SeqReader()&#160;:&#160;<a class="el" href="classbtllib_1_1SeqReader.html#a03cc4e39fffc556a2f05c30bc6d3731d">btllib::SeqReader</a></li>
 <li>SeqWriter()&#160;:&#160;<a class="el" href="classbtllib_1_1SeqWriter.html#a6271cffe77701558f0997532a7e58d43">btllib::SeqWriter</a></li>
+<li>set_seed()&#160;:&#160;<a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">btllib::RandSeq</a></li>
 </ul>
 
 

docs/index.html

@@ -171,7 +171,7 @@ <h2><a class="anchor" id="autotoc_md4"></a>
 <li><code>ninja sanitize-undefined</code> runs undefined sanitization.</li>
 <li><code>ninja test-wrappers</code> tests whether wrappers work.</li>
 <li><code>ninja docs</code> generates code documentation from comments (requires Doxygen).</li>
-<li><code>ninja quality-assurance</code> runs <code>clang-format</code>, <code>wrap</code>, <code>clang-tidy</code>, <code>test</code>, <code>sanitize-undefined</code>, and <code>test-wrappers</code>. These are all checked at the CI test.</li>
+<li><code>ninja quality-assurance</code> runs <code>clang-format</code>, <code>wrap</code>, <code>clang-tidy</code>, <code>test</code>, <code>code-coverage</code>, <code>sanitize-undefined</code>, and <code>test-wrappers</code>. These are all checked at the CI test.</li>
 </ul>
 <h2><a class="anchor" id="autotoc_md5"></a>
 Credits</h2>