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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_1SeqWriter.html">SeqWriter</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="classbtllib_1_1SeqWriter-members.html">List of all members</a> </div>
<div class="headertitle"><div class="title">btllib::SeqWriter Class Reference</div></div>
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<p><code>#include <<a class="el" href="seq__writer_8hpp_source.html">seq_writer.hpp</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-types" name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:abae6e1e28066fa63a8f08ba422ccb9ee" id="r_abae6e1e28066fa63a8f08ba422ccb9ee"><td class="memItemLeft" align="right" valign="top"><a id="abae6e1e28066fa63a8f08ba422ccb9ee" name="abae6e1e28066fa63a8f08ba422ccb9ee"></a>enum  </td><td class="memItemRight" valign="bottom"><b>Format</b> { <b>FASTA</b>
, <b>FASTQ</b>
}</td></tr>
<tr class="separator:abae6e1e28066fa63a8f08ba422ccb9ee"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a6271cffe77701558f0997532a7e58d43" id="r_a6271cffe77701558f0997532a7e58d43"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a6271cffe77701558f0997532a7e58d43">SeqWriter</a> (const std::string &sink_path, Format format=FASTA, bool append=false)</td></tr>
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void </td><td class="memItemRight" valign="bottom"><b>close</b> ()</td></tr>
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<tr class="memitem:ad1202d19b9934405fa0cfa7ee165ccc3" id="r_ad1202d19b9934405fa0cfa7ee165ccc3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#ad1202d19b9934405fa0cfa7ee165ccc3">write</a> (const std::string &id, const std::string &comment, const std::string &seq, const std::string &qual="")</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Write FASTA or FASTQ sequences to a file. Capable of writing gzip (.gz), bzip2 (.bz2), xz (.xz), zip (.zip), 7zip (.7z), and lrzip (.lrz) files. Add the appropriate extension to the output filename to automatically compress. Threadsafe. </p>
<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="seq_writer_8cpp-example.html#_a0">seq_writer.cpp</a>.</dd>
</dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a6271cffe77701558f0997532a7e58d43" name="a6271cffe77701558f0997532a7e58d43"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6271cffe77701558f0997532a7e58d43">◆ </a></span>SeqWriter()</h2>
<div class="memitem">
<div class="memproto">
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<tr>
<td class="memname">btllib::SeqWriter::SeqWriter </td>
<td>(</td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>sink_path</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Format</td> <td class="paramname"><span class="paramname"><em>format</em></span><span class="paramdefsep"> = </span><span class="paramdefval">FASTA</span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>append</em></span><span class="paramdefsep"> = </span><span class="paramdefval">false</span> )</td>
</tr>
</table>
</div><div class="memdoc">
<p>Construct a <a class="el" href="classbtllib_1_1SeqWriter.html">SeqWriter</a> to write sequences to a given path.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">source_path</td><td>Filepath to write to. Pass "-" to write to stdout. </td></tr>
<tr><td class="paramname">format</td><td>Which format to write the output as. </td></tr>
<tr><td class="paramname">append</td><td>Whether to append to the target file or write anew. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="ad1202d19b9934405fa0cfa7ee165ccc3" name="ad1202d19b9934405fa0cfa7ee165ccc3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad1202d19b9934405fa0cfa7ee165ccc3">◆ </a></span>write()</h2>
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<td class="memname">void btllib::SeqWriter::write </td>
<td>(</td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>id</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>comment</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>seq</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>qual</em></span><span class="paramdefsep"> = </span><span class="paramdefval">""</span> )</td>
</tr>
</table>
</div><div class="memdoc">
<p>Write a sequence.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">id</td><td>Sequence ID or name. </td></tr>
<tr><td class="paramname">comment</td><td>Optional comment after the ID/name. </td></tr>
<tr><td class="paramname">seq</td><td>The sequence to write. </td></tr>
<tr><td class="paramname">qual</td><td>Optional quality scores, mandatory if format is FASTQ. </td></tr>
</table>
</dd>
</dl>
<dl class="section examples"><dt>Examples</dt><dd><a class="el" href="seq_writer_8cpp-example.html#a1">seq_writer.cpp</a>.</dd>
</dl>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>include/btllib/<a class="el" href="seq__writer_8hpp_source.html">seq_writer.hpp</a></li>
</ul>
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