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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="class_bam_tools_1_1_bam_reader.html">BamReader</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
<a href="class_bam_tools_1_1_bam_reader-members.html">List of all members</a> </div>
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<div class="title">BamTools::BamReader Class Reference</div> </div>
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<p>Provides read access to BAM files.
<a href="class_bam_tools_1_1_bam_reader.html#details">More...</a></p>
<p><code>#include <<a class="el" href="_bam_reader_8h_source.html">BamReader.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ab3902f9802bd9e9b8960d44abe302a58"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab3902f9802bd9e9b8960d44abe302a58">BamReader</a> (void)</td></tr>
<tr class="memdesc:ab3902f9802bd9e9b8960d44abe302a58"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#ab3902f9802bd9e9b8960d44abe302a58">More...</a><br /></td></tr>
<tr class="separator:ab3902f9802bd9e9b8960d44abe302a58"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a81b83ee41a37e94b0228125e0b082499"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a81b83ee41a37e94b0228125e0b082499">~BamReader</a> (void)</td></tr>
<tr class="memdesc:a81b83ee41a37e94b0228125e0b082499"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a81b83ee41a37e94b0228125e0b082499">More...</a><br /></td></tr>
<tr class="separator:a81b83ee41a37e94b0228125e0b082499"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9bedadbb878c84d3674eea1c11f981ec"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a9bedadbb878c84d3674eea1c11f981ec">Close</a> (void)</td></tr>
<tr class="memdesc:a9bedadbb878c84d3674eea1c11f981ec"><td class="mdescLeft"> </td><td class="mdescRight">Closes the current BAM file. <a href="#a9bedadbb878c84d3674eea1c11f981ec">More...</a><br /></td></tr>
<tr class="separator:a9bedadbb878c84d3674eea1c11f981ec"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a111ec8c00050fef5bf5b580e5dcc83cb"><td class="memItemLeft" align="right" valign="top">const std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a111ec8c00050fef5bf5b580e5dcc83cb">GetFilename</a> (void) const</td></tr>
<tr class="memdesc:a111ec8c00050fef5bf5b580e5dcc83cb"><td class="mdescLeft"> </td><td class="mdescRight">Returns name of current BAM file. <a href="#a111ec8c00050fef5bf5b580e5dcc83cb">More...</a><br /></td></tr>
<tr class="separator:a111ec8c00050fef5bf5b580e5dcc83cb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab29989c9627f2a379d4b80f9a7f349c5"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5">IsOpen</a> (void) const</td></tr>
<tr class="memdesc:ab29989c9627f2a379d4b80f9a7f349c5"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if a BAM file is open for reading. <a href="#ab29989c9627f2a379d4b80f9a7f349c5">More...</a><br /></td></tr>
<tr class="separator:ab29989c9627f2a379d4b80f9a7f349c5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa62d784c8348662064fe363de2b40381"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381">Jump</a> (int refID, int position=0)</td></tr>
<tr class="memdesc:aa62d784c8348662064fe363de2b40381"><td class="mdescLeft"> </td><td class="mdescRight">Performs a random-access jump within BAM file. <a href="#aa62d784c8348662064fe363de2b40381">More...</a><br /></td></tr>
<tr class="separator:aa62d784c8348662064fe363de2b40381"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a863a20a48b960a94b9b9c16471cc02"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02">Open</a> (const std::string &filename)</td></tr>
<tr class="memdesc:a9a863a20a48b960a94b9b9c16471cc02"><td class="mdescLeft"> </td><td class="mdescRight">Opens a BAM file. <a href="#a9a863a20a48b960a94b9b9c16471cc02">More...</a><br /></td></tr>
<tr class="separator:a9a863a20a48b960a94b9b9c16471cc02"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a487f2da4d773a1ac17fdab855f3a964c"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a487f2da4d773a1ac17fdab855f3a964c">Rewind</a> (void)</td></tr>
<tr class="memdesc:a487f2da4d773a1ac17fdab855f3a964c"><td class="mdescLeft"> </td><td class="mdescRight">Returns the internal file pointer to the first alignment record. <a href="#a487f2da4d773a1ac17fdab855f3a964c">More...</a><br /></td></tr>
<tr class="separator:a487f2da4d773a1ac17fdab855f3a964c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1273d2e1da19861ffdc1bddeb9152420"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420">SetRegion</a> (const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> &region)</td></tr>
<tr class="memdesc:a1273d2e1da19861ffdc1bddeb9152420"><td class="mdescLeft"> </td><td class="mdescRight">Sets a target region of interest. <a href="#a1273d2e1da19861ffdc1bddeb9152420">More...</a><br /></td></tr>
<tr class="separator:a1273d2e1da19861ffdc1bddeb9152420"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1e6edaeac4531846727384dfb43e4eeb"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a1e6edaeac4531846727384dfb43e4eeb">SetRegion</a> (const int &leftRefID, const int &leftPosition, const int &rightRefID, const int &rightPosition)</td></tr>
<tr class="memdesc:a1e6edaeac4531846727384dfb43e4eeb"><td class="mdescLeft"> </td><td class="mdescRight">Sets a target region of interest. <a href="#a1e6edaeac4531846727384dfb43e4eeb">More...</a><br /></td></tr>
<tr class="separator:a1e6edaeac4531846727384dfb43e4eeb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa19d6b5effb5b840946a611b7ae039ae"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae">GetNextAlignment</a> (<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> &alignment)</td></tr>
<tr class="memdesc:aa19d6b5effb5b840946a611b7ae039ae"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves next available alignment. <a href="#aa19d6b5effb5b840946a611b7ae039ae">More...</a><br /></td></tr>
<tr class="separator:aa19d6b5effb5b840946a611b7ae039ae"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac95d20470a02a104990f5a8cf9868f95"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95">GetNextAlignmentCore</a> (<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> &alignment)</td></tr>
<tr class="memdesc:ac95d20470a02a104990f5a8cf9868f95"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves next available alignment, without populating the alignment's string data fields. <a href="#ac95d20470a02a104990f5a8cf9868f95">More...</a><br /></td></tr>
<tr class="separator:ac95d20470a02a104990f5a8cf9868f95"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa8cfff90af216f7f401650db0d1492ca"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa8cfff90af216f7f401650db0d1492ca">GetConstSamHeader</a> (void) const</td></tr>
<tr class="memdesc:aa8cfff90af216f7f401650db0d1492ca"><td class="mdescLeft"> </td><td class="mdescRight">Returns const reference to SAM header data. <a href="#aa8cfff90af216f7f401650db0d1492ca">More...</a><br /></td></tr>
<tr class="separator:aa8cfff90af216f7f401650db0d1492ca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa12c15ad26839fd2daa4d5fa1d483810"><td class="memItemLeft" align="right" valign="top"><a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810">GetHeader</a> (void) const</td></tr>
<tr class="memdesc:aa12c15ad26839fd2daa4d5fa1d483810"><td class="mdescLeft"> </td><td class="mdescRight">Returns SAM header data. <a href="#aa12c15ad26839fd2daa4d5fa1d483810">More...</a><br /></td></tr>
<tr class="separator:aa12c15ad26839fd2daa4d5fa1d483810"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab22109b6db2999ea99fc4511b963d705"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705">GetHeaderText</a> (void) const</td></tr>
<tr class="memdesc:ab22109b6db2999ea99fc4511b963d705"><td class="mdescLeft"> </td><td class="mdescRight">Returns SAM header data, as SAM-formatted text. <a href="#ab22109b6db2999ea99fc4511b963d705">More...</a><br /></td></tr>
<tr class="separator:ab22109b6db2999ea99fc4511b963d705"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af595ee6029b3ffffa473797b23806923"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#af595ee6029b3ffffa473797b23806923">GetReferenceCount</a> (void) const</td></tr>
<tr class="memdesc:af595ee6029b3ffffa473797b23806923"><td class="mdescLeft"> </td><td class="mdescRight">Returns number of reference sequences. <a href="#af595ee6029b3ffffa473797b23806923">More...</a><br /></td></tr>
<tr class="separator:af595ee6029b3ffffa473797b23806923"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aec1ff34f2718cb7a6f3d17861c58620b"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aec1ff34f2718cb7a6f3d17861c58620b">GetReferenceData</a> (void) const</td></tr>
<tr class="memdesc:aec1ff34f2718cb7a6f3d17861c58620b"><td class="mdescLeft"> </td><td class="mdescRight">Returns all reference sequence entries. <a href="#aec1ff34f2718cb7a6f3d17861c58620b">More...</a><br /></td></tr>
<tr class="separator:aec1ff34f2718cb7a6f3d17861c58620b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4fdf1d7b99b134069c8b58fae4a68f8a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a4fdf1d7b99b134069c8b58fae4a68f8a">GetReferenceID</a> (const std::string &refName) const</td></tr>
<tr class="memdesc:a4fdf1d7b99b134069c8b58fae4a68f8a"><td class="mdescLeft"> </td><td class="mdescRight">Returns the ID of the reference with this name. <a href="#a4fdf1d7b99b134069c8b58fae4a68f8a">More...</a><br /></td></tr>
<tr class="separator:a4fdf1d7b99b134069c8b58fae4a68f8a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a050af09369dd60bf0db3168727a201b4"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a050af09369dd60bf0db3168727a201b4">CreateIndex</a> (const <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> &type=<a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a>)</td></tr>
<tr class="memdesc:a050af09369dd60bf0db3168727a201b4"><td class="mdescLeft"> </td><td class="mdescRight">Creates an index file for current BAM file. <a href="#a050af09369dd60bf0db3168727a201b4">More...</a><br /></td></tr>
<tr class="separator:a050af09369dd60bf0db3168727a201b4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab79d3d603434f61807820a19c99d51b9"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab79d3d603434f61807820a19c99d51b9">HasIndex</a> (void) const</td></tr>
<tr class="memdesc:ab79d3d603434f61807820a19c99d51b9"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if index data is available. <a href="#ab79d3d603434f61807820a19c99d51b9">More...</a><br /></td></tr>
<tr class="separator:ab79d3d603434f61807820a19c99d51b9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86dfc39a2d57eb3b665e641e6436b5ee"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a86dfc39a2d57eb3b665e641e6436b5ee">LocateIndex</a> (const <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> &preferredType=<a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a>)</td></tr>
<tr class="memdesc:a86dfc39a2d57eb3b665e641e6436b5ee"><td class="mdescLeft"> </td><td class="mdescRight">Looks in BAM file's directory for a matching index file. <a href="#a86dfc39a2d57eb3b665e641e6436b5ee">More...</a><br /></td></tr>
<tr class="separator:a86dfc39a2d57eb3b665e641e6436b5ee"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab62b5f370b91e225fd7684d0180bd41d"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d">OpenIndex</a> (const std::string &indexFilename)</td></tr>
<tr class="memdesc:ab62b5f370b91e225fd7684d0180bd41d"><td class="mdescLeft"> </td><td class="mdescRight">Opens a BAM index file. <a href="#ab62b5f370b91e225fd7684d0180bd41d">More...</a><br /></td></tr>
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<tr class="memitem:a89712324427d42091c3a979a426871d5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a89712324427d42091c3a979a426871d5">SetIndex</a> (<a class="el" href="class_bam_tools_1_1_bam_index.html">BamIndex</a> *index)</td></tr>
<tr class="memdesc:a89712324427d42091c3a979a426871d5"><td class="mdescLeft"> </td><td class="mdescRight">Sets a custom <a class="el" href="class_bam_tools_1_1_bam_index.html" title="Provides methods for generating & loading BAM index files. ">BamIndex</a> on this reader. <a href="#a89712324427d42091c3a979a426871d5">More...</a><br /></td></tr>
<tr class="separator:a89712324427d42091c3a979a426871d5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a46a3b08df29f2fb26c7d868816d15c83"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a46a3b08df29f2fb26c7d868816d15c83">GetErrorString</a> (void) const</td></tr>
<tr class="memdesc:a46a3b08df29f2fb26c7d868816d15c83"><td class="mdescLeft"> </td><td class="mdescRight">Returns a human-readable description of the last error that occurred. <a href="#a46a3b08df29f2fb26c7d868816d15c83">More...</a><br /></td></tr>
<tr class="separator:a46a3b08df29f2fb26c7d868816d15c83"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Provides read access to BAM files. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ab3902f9802bd9e9b8960d44abe302a58">◆ </a></span>BamReader()</h2>
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<td class="memname">BamReader::BamReader </td>
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<p>constructor </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a81b83ee41a37e94b0228125e0b082499">◆ </a></span>~BamReader()</h2>
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<td class="memname">BamReader::~BamReader </td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9bedadbb878c84d3674eea1c11f981ec">◆ </a></span>Close()</h2>
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<td class="memname">bool BamReader::Close </td>
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<p>Closes the current BAM file. </p>
<p>Also clears out all header and reference data.</p>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if file closed OK </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5" title="Returns true if a BAM file is open for reading. ">IsOpen()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02" title="Opens a BAM file. ">Open()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a050af09369dd60bf0db3168727a201b4">◆ </a></span>CreateIndex()</h2>
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<td class="memname">bool BamReader::CreateIndex </td>
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<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> & </td>
<td class="paramname"><em>type</em> = <code><a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a></code></td><td>)</td>
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<p>Creates an index file for current BAM file. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">type</td><td>file format to create, see <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> for available formats </td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if index created OK </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a86dfc39a2d57eb3b665e641e6436b5ee" title="Looks in BAM file's directory for a matching index file. ">LocateIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d" title="Opens a BAM index file. ">OpenIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa8cfff90af216f7f401650db0d1492ca">◆ </a></span>GetConstSamHeader()</h2>
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<td class="memname">const <a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> & BamReader::GetConstSamHeader </td>
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<p>Returns const reference to SAM header data. </p>
<p>Allows for read-only queries of SAM header data.</p>
<p>If you do not need to modify the SAM header, use this method to avoid the potentially expensive copy used by <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810" title="Returns SAM header data. ">GetHeader()</a>.</p>
<dl class="section note"><dt>Note</dt><dd></dd></dl>
<dl class="section return"><dt>Returns</dt><dd>const reference to header data object </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810" title="Returns SAM header data. ">GetHeader()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705" title="Returns SAM header data, as SAM-formatted text. ">GetHeaderText()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a46a3b08df29f2fb26c7d868816d15c83">◆ </a></span>GetErrorString()</h2>
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<td class="memname">string BamReader::GetErrorString </td>
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<p>Returns a human-readable description of the last error that occurred. </p>
<p>This method allows elimination of STDERR pollution. Developers of client code may choose how the messages are displayed to the user, if at all.</p>
<dl class="section return"><dt>Returns</dt><dd>error description </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a111ec8c00050fef5bf5b580e5dcc83cb">◆ </a></span>GetFilename()</h2>
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<td class="memname">const std::string BamReader::GetFilename </td>
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<p>Returns name of current BAM file. </p>
<p>Retrieved filename will contain whatever was passed via <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02" title="Opens a BAM file. ">Open()</a>. If you need full directory paths here, be sure to include them when you open the BAM file.</p>
<dl class="section return"><dt>Returns</dt><dd>name of open BAM file. If no file is open, returns an empty string. </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5" title="Returns true if a BAM file is open for reading. ">IsOpen()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa12c15ad26839fd2daa4d5fa1d483810">◆ </a></span>GetHeader()</h2>
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<td class="memname"><a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> BamReader::GetHeader </td>
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<p>Returns SAM header data. </p>
<p>Header data is wrapped in a <a class="el" href="struct_bam_tools_1_1_sam_header.html" title="Represents the SAM-formatted text header that is part of the BAM file header. ">SamHeader</a> object that can be conveniently queried and/or modified. If you only need read access, consider using <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa8cfff90af216f7f401650db0d1492ca" title="Returns const reference to SAM header data. ">GetConstSamHeader()</a> instead.</p>
<dl class="section note"><dt>Note</dt><dd>Modifying the retrieved <a class="el" href="struct_bam_tools_1_1_sam_header.html" title="Represents the SAM-formatted text header that is part of the BAM file header. ">SamHeader</a> object does NOT affect the current BAM file. This file has been opened in a read-only mode. However, your modified <a class="el" href="struct_bam_tools_1_1_sam_header.html" title="Represents the SAM-formatted text header that is part of the BAM file header. ">SamHeader</a> object can be used in conjunction with <a class="el" href="class_bam_tools_1_1_bam_writer.html" title="Provides write access for generating BAM files. ">BamWriter</a> to generate a new BAM file with the appropriate header information.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>header data object </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa8cfff90af216f7f401650db0d1492ca" title="Returns const reference to SAM header data. ">GetConstSamHeader()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705" title="Returns SAM header data, as SAM-formatted text. ">GetHeaderText()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ab22109b6db2999ea99fc4511b963d705">◆ </a></span>GetHeaderText()</h2>
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<td class="memname">std::string BamReader::GetHeaderText </td>
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<p>Returns SAM header data, as SAM-formatted text. </p>
<dl class="section note"><dt>Note</dt><dd>Modifying the retrieved text does NOT affect the current BAM file. This file has been opened in a read-only mode. However, your modified header text can be used in conjunction with <a class="el" href="class_bam_tools_1_1_bam_writer.html" title="Provides write access for generating BAM files. ">BamWriter</a> to generate a new BAM file with the appropriate header information.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>SAM-formatted header text </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810" title="Returns SAM header data. ">GetHeader()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa19d6b5effb5b840946a611b7ae039ae">◆ </a></span>GetNextAlignment()</h2>
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<td class="memname">bool BamReader::GetNextAlignment </td>
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<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> & </td>
<td class="paramname"><em>alignment</em></td><td>)</td>
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<p>Retrieves next available alignment. </p>
<p>Attempts to read the next alignment record from BAM file, and checks to see if it overlaps the current region. If no region is currently set, then the next alignment available is always considered valid.</p>
<p>If a region has been set, via <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381" title="Performs a random-access jump within BAM file. ">Jump()</a> or <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">SetRegion()</a>, an alignment is only considered valid if it overlaps the region. If the actual 'next' alignment record in the BAM file does not overlap this region, then this function will read sequentially through the file until the next alignment that overlaps this region is found. Once the region has been exhausted (i.e. the next alignment loaded is beyond the region), the function aborts and returns <code>false</code>. In this case, there is no point to continue reading, assuming properly sorted alignments.</p>
<p>This function fully populates all of the alignment's available data fields, including the string data fields (read name, bases, qualities, tags, filename). If only positional data (refID, position, CIGAR ops, alignment flags, etc.) are required, consider using <a class="el" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95" title="Retrieves next available alignment, without populating the alignment's string data fields...">GetNextAlignmentCore()</a> for a significant performance boost.</p>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if a valid alignment was found </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ac95d20470a02a104990f5a8cf9868f95">◆ </a></span>GetNextAlignmentCore()</h2>
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<p>Retrieves next available alignment, without populating the alignment's string data fields. </p>
<p>Equivalent to <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae" title="Retrieves next available alignment. ">GetNextAlignment()</a> with respect to what is a valid overlapping alignment.</p>
<p>However, this method does NOT populate the alignment's string data fields (read name, bases, qualities, tags, filename). This provides a boost in speed when these fields are not required for every alignment. These fields, excluding filename, can be populated 'lazily' (as needed) by calling <a class="el" href="class_bam_tools_1_1_bam_alignment.html#a1ea231426b422a70242a44c010894af9" title="Populates alignment string fields (read name, bases, qualities, tag data). ">BamAlignment::BuildCharData()</a> later.</p>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if a valid alignment was found </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">SetRegion()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#af595ee6029b3ffffa473797b23806923">◆ </a></span>GetReferenceCount()</h2>
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<td class="memname">int BamReader::GetReferenceCount </td>
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<p>Returns number of reference sequences. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aec1ff34f2718cb7a6f3d17861c58620b">◆ </a></span>GetReferenceData()</h2>
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<td class="memname">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> & BamReader::GetReferenceData </td>
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<p>Returns all reference sequence entries. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="struct_bam_tools_1_1_ref_data.html" title="Represents a reference sequence entry. ">RefData</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a4fdf1d7b99b134069c8b58fae4a68f8a">◆ </a></span>GetReferenceID()</h2>
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<td class="memname">int BamReader::GetReferenceID </td>
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<p>Returns the ID of the reference with this name. </p>
<p>If <em>refName</em> is not found, returns -1.</p>
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<tr><td class="paramdir">[in]</td><td class="paramname">refName</td><td>name of reference to look up </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#ab79d3d603434f61807820a19c99d51b9">◆ </a></span>HasIndex()</h2>
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<td class="memname">bool BamReader::HasIndex </td>
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<p>Returns <code>true</code> if index data is available. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab29989c9627f2a379d4b80f9a7f349c5">◆ </a></span>IsOpen()</h2>
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<p>Returns <code>true</code> if a BAM file is open for reading. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa62d784c8348662064fe363de2b40381">◆ </a></span>Jump()</h2>
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<td class="memname">bool BamReader::Jump </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>refID</em>, </td>
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<p>Performs a random-access jump within BAM file. </p>
<p>This is a convenience method, equivalent to calling <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">SetRegion()</a> with only a left boundary specified.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">refID</td><td>left-bound reference ID </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">position</td><td>left-bound position</td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if jump was successful </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab79d3d603434f61807820a19c99d51b9" title="Returns true if index data is available. ">HasIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a86dfc39a2d57eb3b665e641e6436b5ee">◆ </a></span>LocateIndex()</h2>
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<td class="memname">bool BamReader::LocateIndex </td>
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<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> & </td>
<td class="paramname"><em>preferredType</em> = <code><a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a></code></td><td>)</td>
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<p>Looks in BAM file's directory for a matching index file. </p>
<p>Use this function when you need an index file, and perhaps have a preferred index format, but do not depend heavily on which format actually gets loaded at runtime.</p>
<p>This function will defer to your <em>preferredType</em> whenever possible. However, if an index file of <em>preferredType</em> can not be found, then it will look for any other index file that corresponds to this BAM file.</p>
<p>If you want precise control over which index file is loaded, use <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d" title="Opens a BAM index file. ">OpenIndex()</a> with the desired index filename. If that function returns false, you can use <a class="el" href="class_bam_tools_1_1_bam_reader.html#a050af09369dd60bf0db3168727a201b4" title="Creates an index file for current BAM file. ">CreateIndex()</a> to then build an index of the exact requested format.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">preferredType</td><td>desired index file format, see <a class="el" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> for available formats</td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if (any) index file could be found </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a9a863a20a48b960a94b9b9c16471cc02">◆ </a></span>Open()</h2>
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<td class="memname">bool BamReader::Open </td>
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<td class="paramtype">const std::string & </td>
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<p>Opens a BAM file. </p>
<p>If <a class="el" href="class_bam_tools_1_1_bam_reader.html" title="Provides read access to BAM files. ">BamReader</a> is already opened on another file, this function closes that file, then attempts to open requested <em>filename</em>.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">filename</td><td>name of BAM file to open</td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if BAM file was opened successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a9bedadbb878c84d3674eea1c11f981ec" title="Closes the current BAM file. ">Close()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5" title="Returns true if a BAM file is open for reading. ">IsOpen()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d" title="Opens a BAM index file. ">OpenIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ab62b5f370b91e225fd7684d0180bd41d">◆ </a></span>OpenIndex()</h2>
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<td class="memname">bool BamReader::OpenIndex </td>
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<td class="paramtype">const std::string & </td>
<td class="paramname"><em>indexFilename</em></td><td>)</td>
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<p>Opens a BAM index file. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">indexFilename</td><td>name of BAM index file to open</td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if BAM index file was opened & data loaded successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a86dfc39a2d57eb3b665e641e6436b5ee" title="Looks in BAM file's directory for a matching index file. ">LocateIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02" title="Opens a BAM file. ">Open()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a89712324427d42091c3a979a426871d5" title="Sets a custom BamIndex on this reader. ">SetIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a487f2da4d773a1ac17fdab855f3a964c">◆ </a></span>Rewind()</h2>
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<td class="memname">bool BamReader::Rewind </td>
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<p>Returns the internal file pointer to the first alignment record. </p>
<p>Useful for performing multiple sequential passes through a BAM file. Calling this function clears any prior region that may have been set.</p>
<dl class="section note"><dt>Note</dt><dd>This function sets the file pointer to first alignment record in the BAM file, NOT the beginning of the file.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if rewind operation was successful </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381" title="Performs a random-access jump within BAM file. ">Jump()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">SetRegion()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a89712324427d42091c3a979a426871d5">◆ </a></span>SetIndex()</h2>
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<td class="memname">void BamReader::SetIndex </td>
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<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_index.html">BamIndex</a> * </td>
<td class="paramname"><em>index</em></td><td>)</td>
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<p>Sets a custom <a class="el" href="class_bam_tools_1_1_bam_index.html" title="Provides methods for generating & loading BAM index files. ">BamIndex</a> on this reader. </p>
<p>Only necessary for custom <a class="el" href="class_bam_tools_1_1_bam_index.html" title="Provides methods for generating & loading BAM index files. ">BamIndex</a> subclasses. Most clients should never have to use this function.</p>
<p>Example: </p><div class="fragment"><div class="line"><a class="code" href="class_bam_tools_1_1_bam_reader.html#ab3902f9802bd9e9b8960d44abe302a58">BamReader</a> reader;</div><div class="line">reader.SetIndex(<span class="keyword">new</span> MyCustomBamIndex);</div></div><!-- fragment --><dl class="section note"><dt>Note</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html" title="Provides read access to BAM files. ">BamReader</a> takes ownership of <em>index</em> - i.e. the <a class="el" href="class_bam_tools_1_1_bam_reader.html" title="Provides read access to BAM files. ">BamReader</a> will take care of deleting it when the reader is destructed, when the current BAM file is closed, or when a new index is requested.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">index</td><td>custom <a class="el" href="class_bam_tools_1_1_bam_index.html" title="Provides methods for generating & loading BAM index files. ">BamIndex</a> subclass created by client </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a050af09369dd60bf0db3168727a201b4" title="Creates an index file for current BAM file. ">CreateIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a86dfc39a2d57eb3b665e641e6436b5ee" title="Looks in BAM file's directory for a matching index file. ">LocateIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d" title="Opens a BAM index file. ">OpenIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a1273d2e1da19861ffdc1bddeb9152420">◆ </a></span>SetRegion() <span class="overload">[1/2]</span></h2>
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<td class="memname">bool BamReader::SetRegion </td>
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<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><td>)</td>
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<p>Sets a target region of interest. </p>
<p>Requires that index data be available. Attempts a random-access jump in the BAM file, near <em>region</em> left boundary position.</p>
<p>Subsequent calls to <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae" title="Retrieves next available alignment. ">GetNextAlignment()</a> or <a class="el" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95" title="Retrieves next available alignment, without populating the alignment's string data fields...">GetNextAlignmentCore()</a> will only return <code>true</code> when alignments can be found that overlap this <em>region</em>.</p>
<p>A <em>region</em> with no right boundary is considered open-ended, meaning that all alignments that lie downstream of the left boundary are considered valid, continuing to the end of the BAM file.</p>
<dl class="section warning"><dt>Warning</dt><dd><a class="el" href="struct_bam_tools_1_1_bam_region.html" title="Represents a sequential genomic region. ">BamRegion</a> now represents a zero-based, HALF-OPEN interval. In previous versions of <a class="el" href="namespace_bam_tools.html" title="Contains all BamTools classes & methods. ">BamTools</a> (0.x & 1.x) all intervals were treated as zero-based, CLOSED.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">region</td><td>desired region-of-interest to activate</td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if reader was able to jump successfully to the region's left boundary </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab79d3d603434f61807820a19c99d51b9" title="Returns true if index data is available. ">HasIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381" title="Performs a random-access jump within BAM file. ">Jump()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a1e6edaeac4531846727384dfb43e4eeb">◆ </a></span>SetRegion() <span class="overload">[2/2]</span></h2>
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<td class="memname">bool BamReader::SetRegion </td>
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<td class="paramtype">const int & </td>
<td class="paramname"><em>leftRefID</em>, </td>
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<td class="paramtype">const int & </td>
<td class="paramname"><em>leftPosition</em>, </td>
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<td class="paramtype">const int & </td>
<td class="paramname"><em>rightRefID</em>, </td>
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<td class="paramtype">const int & </td>
<td class="paramname"><em>rightPosition</em> </td>
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<p>Sets a target region of interest. </p>
<p>This is an overloaded function.</p>
<dl class="section warning"><dt>Warning</dt><dd>This function expects a zero-based, HALF-OPEN interval. In previous versions of <a class="el" href="namespace_bam_tools.html" title="Contains all BamTools classes & methods. ">BamTools</a> (0.x & 1.x) all intervals were treated as zero-based, CLOSED.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">leftRefID</td><td>referenceID of region's left boundary </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">leftPosition</td><td>position of region's left boundary </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">rightRefID</td><td>reference ID of region's right boundary </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">rightPosition</td><td>position of region's right boundary</td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if reader was able to jump successfully to the region's left boundary </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab79d3d603434f61807820a19c99d51b9" title="Returns true if index data is available. ">HasIndex()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381" title="Performs a random-access jump within BAM file. ">Jump()</a> </dd></dl>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="_bam_reader_8h_source.html">BamReader.h</a></li>
<li><a class="el" href="_bam_reader_8cpp.html">BamReader.cpp</a></li>
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