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classbtllib_1_1Indexlr.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<li class="navelem"><a class="el" href="namespacebtllib.html">btllib</a></li><li class="navelem"><a class="el" href="classbtllib_1_1Indexlr.html">Indexlr</a></li> </ul>
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<div class="headertitle"><div class="title">btllib::Indexlr Class Reference</div></div>
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Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html">Flag</a></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structbtllib_1_1Indexlr_1_1Minimizer.html">Minimizer</a></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structbtllib_1_1Indexlr_1_1Record.html">Record</a></td></tr>
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using </td><td class="memItemRight" valign="bottom"><b>HashedKmer</b> = <a class="el" href="structbtllib_1_1Indexlr_1_1Minimizer.html">Minimizer</a></td></tr>
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Public Member Functions</h2></td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>output_id</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>output_bx</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>output_seq</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>output_qual</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>filter_in</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>filter_out</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>short_mode</b> () const</td></tr>
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bool </td><td class="memItemRight" valign="bottom"><b>long_mode</b> () const</td></tr>
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<tr class="memitem:a88e89c2c60ff3dea0a151f2fe8cccd00" id="r_a88e89c2c60ff3dea0a151f2fe8cccd00"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structbtllib_1_1Indexlr_1_1Record.html">Record</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a88e89c2c60ff3dea0a151f2fe8cccd00">read</a> ()</td></tr>
<tr class="separator:a88e89c2c60ff3dea0a151f2fe8cccd00"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a16eaf1402422f88cd3a66d03e9e11b85" id="r_a16eaf1402422f88cd3a66d03e9e11b85"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a16eaf1402422f88cd3a66d03e9e11b85">Indexlr</a> (std::string seqfile, size_t k, size_t w, unsigned flags=0, unsigned threads=5, bool verbose=false, const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &bf1=Indexlr::dummy_bf(), const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &bf2=Indexlr::dummy_bf())</td></tr>
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 </td><td class="memItemRight" valign="bottom"><b>Indexlr</b> (std::string seqfile, size_t k, size_t w, size_t q, unsigned flags=0, unsigned threads=5, bool verbose=false, const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &bf1=Indexlr::dummy_bf(), const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &bf2=Indexlr::dummy_bf())</td></tr>
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<tr class="memitem:ad0d2093026f5ad59c2f05d739e82f815" id="r_ad0d2093026f5ad59c2f05d739e82f815"><td class="memItemLeft" align="right" valign="top"><a id="ad0d2093026f5ad59c2f05d739e82f815" name="ad0d2093026f5ad59c2f05d739e82f815"></a>
void </td><td class="memItemRight" valign="bottom"><b>close</b> () noexcept</td></tr>
<tr class="separator:ad0d2093026f5ad59c2f05d739e82f815"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4c28c9cd0832f19fa077a0a4afd1c2f5" id="r_a4c28c9cd0832f19fa077a0a4afd1c2f5"><td class="memItemLeft" align="right" valign="top">RecordIterator </td><td class="memItemRight" valign="bottom"><a class="el" href="#a4c28c9cd0832f19fa077a0a4afd1c2f5">begin</a> ()</td></tr>
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<tr class="memitem:abf96e055bfac6c7f0a30f1c1a3df233e" id="r_abf96e055bfac6c7f0a30f1c1a3df233e"><td class="memItemLeft" align="right" valign="top"><a id="abf96e055bfac6c7f0a30f1c1a3df233e" name="abf96e055bfac6c7f0a30f1c1a3df233e"></a>
RecordIterator </td><td class="memItemRight" valign="bottom"><b>end</b> ()</td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-static-attribs" name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:a9cebcc5048cd4b65f5ef414ecf2cf684" id="r_a9cebcc5048cd4b65f5ef414ecf2cf684"><td class="memItemLeft" align="right" valign="top"><a id="a9cebcc5048cd4b65f5ef414ecf2cf684" name="a9cebcc5048cd4b65f5ef414ecf2cf684"></a>
static const size_t </td><td class="memItemRight" valign="bottom"><b>MAX_SIMULTANEOUS_INDEXLRS</b> = 256</td></tr>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a16eaf1402422f88cd3a66d03e9e11b85" name="a16eaf1402422f88cd3a66d03e9e11b85"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a16eaf1402422f88cd3a66d03e9e11b85">◆ </a></span>Indexlr()</h2>
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<td class="memname">btllib::Indexlr::Indexlr </td>
<td>(</td>
<td class="paramtype">std::string</td> <td class="paramname"><span class="paramname"><em>seqfile</em></span>, </td>
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<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>k</em></span>, </td>
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<td class="paramtype">unsigned</td> <td class="paramname"><span class="paramname"><em>flags</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span>, </td>
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<td class="paramtype">const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &</td> <td class="paramname"><span class="paramname"><em>bf1</em></span><span class="paramdefsep"> = </span><span class="paramdefval">Indexlr::dummy_bf()</span>, </td>
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<td class="paramtype">const <a class="el" href="classbtllib_1_1BloomFilter.html">btllib::BloomFilter</a> &</td> <td class="paramname"><span class="paramname"><em>bf2</em></span><span class="paramdefsep"> = </span><span class="paramdefval">Indexlr::dummy_bf()</span> )</td>
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<p>Construct <a class="el" href="classbtllib_1_1Indexlr.html">Indexlr</a> to calculate minimizers from sequences at the given path.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seqfile</td><td>Filepath to read sequences from. Pass "-" to read from stdin. </td></tr>
<tr><td class="paramname">k</td><td>k-mer size for the minimizer. </td></tr>
<tr><td class="paramname">w</td><td>window size when selecting minimizers. </td></tr>
<tr><td class="paramname">q</td><td>quality threshold to ignore potential minimizers. </td></tr>
<tr><td class="paramname">flags</td><td>Modifier flags. Specifiying either short or long mode flag is mandatory; other flags are optional. </td></tr>
<tr><td class="paramname">threads</td><td>Maximum number of processing threads to use. Must be at least 1. </td></tr>
<tr><td class="paramname">verbose</td><td>Whether to output informational messages during processing. </td></tr>
<tr><td class="paramname">bf1</td><td>A Bloom filter to use for either filtering minimizers in or out, if one of the flags is enabled. If both are enabled, bf1 is used for filtering in. </td></tr>
<tr><td class="paramname">bf2</td><td>A second Bloom filter to use when both filtering minimizers in and out is enabled. bf2 is used for filtering out. </td></tr>
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</dd>
</dl>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a4c28c9cd0832f19fa077a0a4afd1c2f5">◆ </a></span>begin()</h2>
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<td class="memname">RecordIterator btllib::Indexlr::begin </td>
<td>(</td>
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<p>For range-based for loop only. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a88e89c2c60ff3dea0a151f2fe8cccd00">◆ </a></span>read()</h2>
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<td class="memname"><a class="el" href="structbtllib_1_1Indexlr_1_1Record.html">Indexlr::Record</a> btllib::Indexlr::read </td>
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<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
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<p>Read the next <a class="el" href="classbtllib_1_1Indexlr.html">Indexlr</a> record, containing read information and a list of minimizers. </p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>include/btllib/<a class="el" href="indexlr_8hpp_source.html">indexlr.hpp</a></li>
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