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<li class="navelem"><a class="el" href="namespace_bam_tools.html">BamTools</a></li><li class="navelem"><a class="el" href="namespace_bam_tools_1_1_algorithms.html">Algorithms</a></li><li class="navelem"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html">Sort</a></li> </ul>
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<div class="header">
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<div class="title">BamTools::Algorithms::Sort Struct Reference</div> </div>
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<p>Provides classes & methods related to sorting BamAlignments.
<a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#details">More...</a></p>
<p><code>#include <<a class="el" href="_sort_8h_source.html">Sort.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
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="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html">ByName</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Function object for comparing alignments by name. <a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html">ByPosition</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Function object for comparing alignments by position. <a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html">ByTag</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Function object for comparing alignments by tag value. <a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html">Unsorted</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Placeholder function object. <a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:ab00bd07c176b33933717ca362b716f61"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Order</a> { <a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">AscendingOrder</a> = 0,
<a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd">DescendingOrder</a>
}<tr class="memdesc:ab00bd07c176b33933717ca362b716f61"><td class="mdescLeft"> </td><td class="mdescRight">Provides explicit values for specifying desired sort ordering. <a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">More...</a><br /></td></tr>
</td></tr>
<tr class="separator:ab00bd07c176b33933717ca362b716f61"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a978c463fbbacae4a0369f8681f7b00d2"><td class="memTemplParams" colspan="2">template<typename Compare > </td></tr>
<tr class="memitem:a978c463fbbacae4a0369f8681f7b00d2"><td class="memTemplItemLeft" align="right" valign="top">static void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2">SortAlignments</a> (std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > &data, const Compare &comp=Compare())</td></tr>
<tr class="separator:a978c463fbbacae4a0369f8681f7b00d2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9b8bd9b54fbc591462d46a502d8489d1"><td class="memTemplParams" colspan="2">template<typename Compare > </td></tr>
<tr class="memitem:a9b8bd9b54fbc591462d46a502d8489d1"><td class="memTemplItemLeft" align="right" valign="top">static std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a9b8bd9b54fbc591462d46a502d8489d1">SortAlignments</a> (const std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > &input, const Compare &comp=Compare())</td></tr>
<tr class="separator:a9b8bd9b54fbc591462d46a502d8489d1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa564c7366c033d59d81d7a58d0fb6e05"><td class="memTemplParams" colspan="2">template<typename Compare > </td></tr>
<tr class="memitem:aa564c7366c033d59d81d7a58d0fb6e05"><td class="memTemplItemLeft" align="right" valign="top">static std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05">GetSortedRegion</a> (<a class="el" href="class_bam_tools_1_1_bam_reader.html">BamReader</a> &reader, const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> &region, const Compare &comp=Compare())</td></tr>
<tr class="separator:aa564c7366c033d59d81d7a58d0fb6e05"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acaaab81442cd152a6460af9ffd8244d2"><td class="memTemplParams" colspan="2">template<typename Compare > </td></tr>
<tr class="memitem:acaaab81442cd152a6460af9ffd8244d2"><td class="memTemplItemLeft" align="right" valign="top">static std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#acaaab81442cd152a6460af9ffd8244d2">GetSortedRegion</a> (<a class="el" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a> &reader, const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> &region, const Compare &comp=Compare())</td></tr>
<tr class="separator:acaaab81442cd152a6460af9ffd8244d2"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Provides classes & methods related to sorting BamAlignments. </p>
</div><h2 class="groupheader">Member Enumeration Documentation</h2>
<a id="ab00bd07c176b33933717ca362b716f61"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ab00bd07c176b33933717ca362b716f61">◆ </a></span>Order</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">enum <a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">BamTools::Algorithms::Sort::Order</a></td>
</tr>
</table>
</div><div class="memdoc">
<p>Provides explicit values for specifying desired sort ordering. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0"></a>AscendingOrder </td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd"></a>DescendingOrder </td><td class="fielddoc"></td></tr>
</table>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="aa564c7366c033d59d81d7a58d0fb6e05"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa564c7366c033d59d81d7a58d0fb6e05">◆ </a></span>GetSortedRegion() <span class="overload">[1/2]</span></h2>
<div class="memitem">
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<div class="memtemplate">
template<typename Compare > </div>
<table class="mlabels">
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<td class="mlabels-left">
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<td class="memname">static std::vector<<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>> BamTools::Algorithms::Sort::GetSortedRegion </td>
<td>(</td>
<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamReader</a> & </td>
<td class="paramname"><em>reader</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> & </td>
<td class="paramname"><em>region</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const Compare & </td>
<td class="paramname"><em>comp</em> = <code>Compare()</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<p>Reads a region of alignments from a position-sorted BAM file, then sorts by the provided compare function</p>
<div class="fragment"><div class="line">BamReader reader;</div><div class="line"><span class="comment">// open BAM file & index file</span></div><div class="line"></div><div class="line">BamRegion region;</div><div class="line"><span class="comment">// define a region of interest (i.e. a exon or some other feature)</span></div><div class="line"></div><div class="line"><span class="comment">// get all alignments covering that region, sorted by read group name</span></div><div class="line">std::vector<BamAlignments> a;</div><div class="line">a = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05">Sort::GetSortedRegion</a>(reader, region, Sort::ByTag<std::string>(<span class="stringliteral">"RG"</span>));</div></div><!-- fragment --><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">reader</td><td><a class="el" href="class_bam_tools_1_1_bam_reader.html" title="Provides read access to BAM files. ">BamReader</a> opened on desired BAM file </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">region</td><td>desired region-of-interest </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">comp</td><td>comparison function object </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>sorted vector of the region's alignments </dd></dl>
</div>
</div>
<a id="acaaab81442cd152a6460af9ffd8244d2"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acaaab81442cd152a6460af9ffd8244d2">◆ </a></span>GetSortedRegion() <span class="overload">[2/2]</span></h2>
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template<typename Compare > </div>
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">static std::vector<<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>> BamTools::Algorithms::Sort::GetSortedRegion </td>
<td>(</td>
<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a> & </td>
<td class="paramname"><em>reader</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> & </td>
<td class="paramname"><em>region</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const Compare & </td>
<td class="paramname"><em>comp</em> = <code>Compare()</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<p>Reads a region of alignments from position-sorted BAM files, then sorts by the provided compare function</p>
<div class="fragment"><div class="line">BamMultiReader reader;</div><div class="line"><span class="comment">// open BAM files & index files</span></div><div class="line"></div><div class="line">BamRegion region;</div><div class="line"><span class="comment">// define a region of interest (i.e. a exon or some other feature)</span></div><div class="line"></div><div class="line"><span class="comment">// get all alignments covering that region, sorted by read group name</span></div><div class="line">std::vector<BamAlignments> a;</div><div class="line">a = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05">Sort::GetSortedRegion</a>(reader, region, Sort::ByTag<std::string>(<span class="stringliteral">"RG"</span>));</div></div><!-- fragment --><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">reader</td><td><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html" title="Convenience class for reading multiple BAM files. ">BamMultiReader</a> opened on desired BAM files </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">region</td><td>desired region-of-interest </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">comp</td><td>comparison function object </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>sorted vector of the region's alignments </dd></dl>
</div>
</div>
<a id="a978c463fbbacae4a0369f8681f7b00d2"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a978c463fbbacae4a0369f8681f7b00d2">◆ </a></span>SortAlignments() <span class="overload">[1/2]</span></h2>
<div class="memitem">
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<div class="memtemplate">
template<typename Compare > </div>
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<td class="memname">static void BamTools::Algorithms::Sort::SortAlignments </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > & </td>
<td class="paramname"><em>data</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const Compare & </td>
<td class="paramname"><em>comp</em> = <code>Compare()</code> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>Sorts a std::vector of alignments (in-place), using the provided compare function.</p>
<div class="fragment"><div class="line">std::vector<BamAlignemnt> a;</div><div class="line"><span class="comment">// populate data</span></div><div class="line"></div><div class="line"><span class="comment">// sort our alignment list by edit distance</span></div><div class="line"><a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2">Sort::SortAlignments</a>(a, Sort::ByTag<int>(<span class="stringliteral">"NM"</span>));</div></div><!-- fragment --><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in,out]</td><td class="paramname">data</td><td>vector of alignments to be sorted </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">comp</td><td>comparison function object </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a9b8bd9b54fbc591462d46a502d8489d1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a9b8bd9b54fbc591462d46a502d8489d1">◆ </a></span>SortAlignments() <span class="overload">[2/2]</span></h2>
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template<typename Compare > </div>
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
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<td class="memname">static std::vector<<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>> BamTools::Algorithms::Sort::SortAlignments </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> > & </td>
<td class="paramname"><em>input</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const Compare & </td>
<td class="paramname"><em>comp</em> = <code>Compare()</code> </td>
</tr>
<tr>
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<td>)</td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<p>Returns a sorted copy of the input alignments, using the provided compare function.</p>
<div class="fragment"><div class="line">std::vector<BamAlignemnt> a;</div><div class="line"><span class="comment">// populate data</span></div><div class="line"></div><div class="line"><span class="comment">// get a copy of our original data, sorted by edit distance (descending order)</span></div><div class="line">std::vector<BamAligment> sortedData;</div><div class="line">sortedData = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2">Sort::SortAlignments</a>(a, Sort::ByTag<int>(<span class="stringliteral">"NM"</span>, <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd">Sort::DescendingOrder</a>));</div></div><!-- fragment --><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">input</td><td>vector of alignments to be sorted </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">comp</td><td>comparison function object </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>sorted copy of the input data </dd></dl>
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<hr/>The documentation for this struct was generated from the following file:<ul>
<li><a class="el" href="_sort_8h_source.html">Sort.h</a></li>
</ul>
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