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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_multi_reader.html">BamMultiReader</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<div class="title">BamTools::BamMultiReader Class Reference</div> </div>
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<p>Convenience class for reading multiple BAM files.
<a href="class_bam_tools_1_1_bam_multi_reader.html#details">More...</a></p>
<p><code>#include <<a class="el" href="_bam_multi_reader_8h_source.html">BamMultiReader.h</a>></code></p>
<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:abf4e4909508f19cc4f733a48aa7d1ed2"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">MergeOrder</a> { <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a84e28c1d03be927b219307f33248f89e">RoundRobinMerge</a> = 0,
<a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a2af00a6dfb052ee8a23319acfd33839b">MergeByCoordinate</a>,
<a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a98ab3051854a1357045117cd1a24e835">MergeByName</a>
}</td></tr>
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</table><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:a18a0708989782f9acb9c05a85b91c913"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a18a0708989782f9acb9c05a85b91c913">BamMultiReader</a> (void)</td></tr>
<tr class="memdesc:a18a0708989782f9acb9c05a85b91c913"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a18a0708989782f9acb9c05a85b91c913">More...</a><br /></td></tr>
<tr class="separator:a18a0708989782f9acb9c05a85b91c913"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa655801419aeeca519109ebac5242722"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#aa655801419aeeca519109ebac5242722">~BamMultiReader</a> (void)</td></tr>
<tr class="memdesc:aa655801419aeeca519109ebac5242722"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#aa655801419aeeca519109ebac5242722">More...</a><br /></td></tr>
<tr class="separator:aa655801419aeeca519109ebac5242722"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac05596504d1c230aa1a32493a1b10216"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ac05596504d1c230aa1a32493a1b10216">Close</a> (void)</td></tr>
<tr class="memdesc:ac05596504d1c230aa1a32493a1b10216"><td class="mdescLeft"> </td><td class="mdescRight">Closes all open BAM files. <a href="#ac05596504d1c230aa1a32493a1b10216">More...</a><br /></td></tr>
<tr class="separator:ac05596504d1c230aa1a32493a1b10216"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a782af28f88e8b91a580ea0f70f32a235"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a782af28f88e8b91a580ea0f70f32a235">CloseFile</a> (const std::string &filename)</td></tr>
<tr class="memdesc:a782af28f88e8b91a580ea0f70f32a235"><td class="mdescLeft"> </td><td class="mdescRight">Closes requested BAM file. <a href="#a782af28f88e8b91a580ea0f70f32a235">More...</a><br /></td></tr>
<tr class="separator:a782af28f88e8b91a580ea0f70f32a235"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2624a904fb20f8c64b6a57176305df93"><td class="memItemLeft" align="right" valign="top">const std::vector< std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a2624a904fb20f8c64b6a57176305df93">Filenames</a> (void) const</td></tr>
<tr class="memdesc:a2624a904fb20f8c64b6a57176305df93"><td class="mdescLeft"> </td><td class="mdescRight">Returns list of filenames for all open BAM files. <a href="#a2624a904fb20f8c64b6a57176305df93">More...</a><br /></td></tr>
<tr class="separator:a2624a904fb20f8c64b6a57176305df93"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a63ecaca57a10920d110693cc0082da8a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a63ecaca57a10920d110693cc0082da8a">GetMergeOrder</a> (void) const</td></tr>
<tr class="memdesc:a63ecaca57a10920d110693cc0082da8a"><td class="mdescLeft"> </td><td class="mdescRight">Returns curent merge order strategy. <a href="#a63ecaca57a10920d110693cc0082da8a">More...</a><br /></td></tr>
<tr class="separator:a63ecaca57a10920d110693cc0082da8a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abbeb7137ba90a1851d424fffd924d7e3"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abbeb7137ba90a1851d424fffd924d7e3">HasOpenReaders</a> (void) const</td></tr>
<tr class="memdesc:abbeb7137ba90a1851d424fffd924d7e3"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if there are any open BAM files. <a href="#abbeb7137ba90a1851d424fffd924d7e3">More...</a><br /></td></tr>
<tr class="separator:abbeb7137ba90a1851d424fffd924d7e3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adabb999cbc393ecf8d268a053d987fb1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1">Jump</a> (int refID, int position=0)</td></tr>
<tr class="memdesc:adabb999cbc393ecf8d268a053d987fb1"><td class="mdescLeft"> </td><td class="mdescRight">Performs a random-access jump within current BAM files. <a href="#adabb999cbc393ecf8d268a053d987fb1">More...</a><br /></td></tr>
<tr class="separator:adabb999cbc393ecf8d268a053d987fb1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a35475e3480ef6886b440deb4e30e9964"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964">Open</a> (const std::vector< std::string > &filenames)</td></tr>
<tr class="memdesc:a35475e3480ef6886b440deb4e30e9964"><td class="mdescLeft"> </td><td class="mdescRight">Opens BAM files. <a href="#a35475e3480ef6886b440deb4e30e9964">More...</a><br /></td></tr>
<tr class="separator:a35475e3480ef6886b440deb4e30e9964"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11ff4c569409990b0a6e3fcdaeaf629e"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a11ff4c569409990b0a6e3fcdaeaf629e">OpenFile</a> (const std::string &filename)</td></tr>
<tr class="memdesc:a11ff4c569409990b0a6e3fcdaeaf629e"><td class="mdescLeft"> </td><td class="mdescRight">Opens a single BAM file. <a href="#a11ff4c569409990b0a6e3fcdaeaf629e">More...</a><br /></td></tr>
<tr class="separator:a11ff4c569409990b0a6e3fcdaeaf629e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a214b9b40f55923fd8bf2141a7f36d7f1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a214b9b40f55923fd8bf2141a7f36d7f1">Rewind</a> (void)</td></tr>
<tr class="memdesc:a214b9b40f55923fd8bf2141a7f36d7f1"><td class="mdescLeft"> </td><td class="mdescRight">Returns the internal file pointers to the beginning of alignment records. <a href="#a214b9b40f55923fd8bf2141a7f36d7f1">More...</a><br /></td></tr>
<tr class="separator:a214b9b40f55923fd8bf2141a7f36d7f1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab5cd0aa4cea16a53954731387d0c4aaf"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ab5cd0aa4cea16a53954731387d0c4aaf">SetExplicitMergeOrder</a> (<a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> order)</td></tr>
<tr class="memdesc:ab5cd0aa4cea16a53954731387d0c4aaf"><td class="mdescLeft"> </td><td class="mdescRight">Sets an explicit merge order, regardless of the BAM files' SO header tag. <a href="#ab5cd0aa4cea16a53954731387d0c4aaf">More...</a><br /></td></tr>
<tr class="separator:ab5cd0aa4cea16a53954731387d0c4aaf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c9c3d1f9882053af4cbfebfb894b8c7"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7">SetRegion</a> (const <a class="el" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a> &region)</td></tr>
<tr class="memdesc:a7c9c3d1f9882053af4cbfebfb894b8c7"><td class="mdescLeft"> </td><td class="mdescRight">Sets a target region of interest. <a href="#a7c9c3d1f9882053af4cbfebfb894b8c7">More...</a><br /></td></tr>
<tr class="separator:a7c9c3d1f9882053af4cbfebfb894b8c7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abcca568dd142e9db91cca5dab8934da8"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abcca568dd142e9db91cca5dab8934da8">SetRegion</a> (const int &leftRefID, const int &leftPosition, const int &rightRefID, const int &rightPosition)</td></tr>
<tr class="memdesc:abcca568dd142e9db91cca5dab8934da8"><td class="mdescLeft"> </td><td class="mdescRight">Sets a target region of interest. <a href="#abcca568dd142e9db91cca5dab8934da8">More...</a><br /></td></tr>
<tr class="separator:abcca568dd142e9db91cca5dab8934da8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8e78819e59b1a5c08c34d56972188a44"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a8e78819e59b1a5c08c34d56972188a44">GetNextAlignment</a> (<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> &alignment)</td></tr>
<tr class="memdesc:a8e78819e59b1a5c08c34d56972188a44"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves next available alignment. <a href="#a8e78819e59b1a5c08c34d56972188a44">More...</a><br /></td></tr>
<tr class="separator:a8e78819e59b1a5c08c34d56972188a44"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c1b307ac78087f8174b1dcac838f6a2"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2">GetNextAlignmentCore</a> (<a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> &alignment)</td></tr>
<tr class="memdesc:a7c1b307ac78087f8174b1dcac838f6a2"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves next available alignment. <a href="#a7c1b307ac78087f8174b1dcac838f6a2">More...</a><br /></td></tr>
<tr class="separator:a7c1b307ac78087f8174b1dcac838f6a2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae17506fe2f4959fdbebf27f05d17c8cd"><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_multi_reader.html#ae17506fe2f4959fdbebf27f05d17c8cd">GetHeader</a> (void) const</td></tr>
<tr class="memdesc:ae17506fe2f4959fdbebf27f05d17c8cd"><td class="mdescLeft"> </td><td class="mdescRight">Returns unified SAM-format header for all files. <a href="#ae17506fe2f4959fdbebf27f05d17c8cd">More...</a><br /></td></tr>
<tr class="separator:ae17506fe2f4959fdbebf27f05d17c8cd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa65c1ed621c41d3e07a99500cd5311ac"><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_multi_reader.html#aa65c1ed621c41d3e07a99500cd5311ac">GetHeaderText</a> (void) const</td></tr>
<tr class="memdesc:aa65c1ed621c41d3e07a99500cd5311ac"><td class="mdescLeft"> </td><td class="mdescRight">Returns unified SAM-format header text for all files. <a href="#aa65c1ed621c41d3e07a99500cd5311ac">More...</a><br /></td></tr>
<tr class="separator:aa65c1ed621c41d3e07a99500cd5311ac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa02252ba82b3e39a4a9527f37688e0bb"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#aa02252ba82b3e39a4a9527f37688e0bb">GetReferenceCount</a> (void) const</td></tr>
<tr class="memdesc:aa02252ba82b3e39a4a9527f37688e0bb"><td class="mdescLeft"> </td><td class="mdescRight">Returns number of reference sequences. <a href="#aa02252ba82b3e39a4a9527f37688e0bb">More...</a><br /></td></tr>
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<tr class="memitem:a5a3ea49b0ad5bc9ca4e599668bcca848"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">BamTools::RefVector</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a5a3ea49b0ad5bc9ca4e599668bcca848">GetReferenceData</a> (void) const</td></tr>
<tr class="memdesc:a5a3ea49b0ad5bc9ca4e599668bcca848"><td class="mdescLeft"> </td><td class="mdescRight">Returns all reference sequence entries. <a href="#a5a3ea49b0ad5bc9ca4e599668bcca848">More...</a><br /></td></tr>
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<tr class="memitem:a0fd0cec7b87ed157e9d9314f62483ed5"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a0fd0cec7b87ed157e9d9314f62483ed5">GetReferenceID</a> (const std::string &refName) const</td></tr>
<tr class="memdesc:a0fd0cec7b87ed157e9d9314f62483ed5"><td class="mdescLeft"> </td><td class="mdescRight">Returns the ID of the reference with this name. <a href="#a0fd0cec7b87ed157e9d9314f62483ed5">More...</a><br /></td></tr>
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<tr class="memitem:adfefc02fd813f5d26325a9eb9299de5a"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adfefc02fd813f5d26325a9eb9299de5a">CreateIndexes</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:adfefc02fd813f5d26325a9eb9299de5a"><td class="mdescLeft"> </td><td class="mdescRight">Creates index files for the current BAM files. <a href="#adfefc02fd813f5d26325a9eb9299de5a">More...</a><br /></td></tr>
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<tr class="memitem:ad5683c81b8e122a867af4982df9bf93f"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ad5683c81b8e122a867af4982df9bf93f">HasIndexes</a> (void) const</td></tr>
<tr class="memdesc:ad5683c81b8e122a867af4982df9bf93f"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if all BAM files have index data available. <a href="#ad5683c81b8e122a867af4982df9bf93f">More...</a><br /></td></tr>
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<tr class="memitem:a9c09a395dd8ecc33f2e6a147ee7fd001"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a9c09a395dd8ecc33f2e6a147ee7fd001">LocateIndexes</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:a9c09a395dd8ecc33f2e6a147ee7fd001"><td class="mdescLeft"> </td><td class="mdescRight">Looks for index files that match current BAM files. <a href="#a9c09a395dd8ecc33f2e6a147ee7fd001">More...</a><br /></td></tr>
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<tr class="memitem:a527fabdd80d8dc7788abd60520048b13"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a527fabdd80d8dc7788abd60520048b13">OpenIndexes</a> (const std::vector< std::string > &indexFilenames)</td></tr>
<tr class="memdesc:a527fabdd80d8dc7788abd60520048b13"><td class="mdescLeft"> </td><td class="mdescRight">Opens index files for current BAM files. <a href="#a527fabdd80d8dc7788abd60520048b13">More...</a><br /></td></tr>
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<tr class="memitem:a67d34b61a514b875661ac11f0cca7dc2"><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_multi_reader.html#a67d34b61a514b875661ac11f0cca7dc2">GetErrorString</a> (void) const</td></tr>
<tr class="memdesc:a67d34b61a514b875661ac11f0cca7dc2"><td class="mdescLeft"> </td><td class="mdescRight">Returns a human-readable description of the last error that occurred. <a href="#a67d34b61a514b875661ac11f0cca7dc2">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Convenience class for reading multiple BAM files. </p>
</div><h2 class="groupheader">Member Enumeration Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#abf4e4909508f19cc4f733a48aa7d1ed2">◆ </a></span>MergeOrder</h2>
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<td class="memname">enum <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamTools::BamMultiReader::MergeOrder</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="abf4e4909508f19cc4f733a48aa7d1ed2a84e28c1d03be927b219307f33248f89e"></a>RoundRobinMerge </td><td class="fielddoc"><p>Merge strategy when BAM files are unsorted, or their sorted status is either unknown or ignored. </p>
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<tr><td class="fieldname"><a id="abf4e4909508f19cc4f733a48aa7d1ed2a2af00a6dfb052ee8a23319acfd33839b"></a>MergeByCoordinate </td><td class="fielddoc"><p>Merge strategy when BAM files are sorted by position ('coordinate') </p>
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<tr><td class="fieldname"><a id="abf4e4909508f19cc4f733a48aa7d1ed2a98ab3051854a1357045117cd1a24e835"></a>MergeByName </td><td class="fielddoc"><p>Merge strategy when BAM files are sorted by read name ('queryname') </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a18a0708989782f9acb9c05a85b91c913">◆ </a></span>BamMultiReader()</h2>
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<td class="memname">BamMultiReader::BamMultiReader </td>
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<p>constructor </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa655801419aeeca519109ebac5242722">◆ </a></span>~BamMultiReader()</h2>
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<td class="memname">BamMultiReader::~BamMultiReader </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="#ac05596504d1c230aa1a32493a1b10216">◆ </a></span>Close()</h2>
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<td class="memname">bool BamMultiReader::Close </td>
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<p>Closes all open BAM files. </p>
<p>Also clears out all header and reference data.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a782af28f88e8b91a580ea0f70f32a235" title="Closes requested BAM file. ">CloseFile()</a>, IsOpen(), <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9bedadbb878c84d3674eea1c11f981ec" title="Closes the current BAM file. ">BamReader::Close()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a782af28f88e8b91a580ea0f70f32a235">◆ </a></span>CloseFile()</h2>
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<td class="memname">bool BamMultiReader::CloseFile </td>
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<p>Closes requested BAM file. </p>
<p>Leaves any other file(s) open, along with header and reference data.</p>
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<tr><td class="paramdir">[in]</td><td class="paramname">filename</td><td>name of specific BAM file to close</td></tr>
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</dd>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ac05596504d1c230aa1a32493a1b10216" title="Closes all open BAM files. ">Close()</a>, IsOpen(), <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9bedadbb878c84d3674eea1c11f981ec" title="Closes the current BAM file. ">BamReader::Close()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#adfefc02fd813f5d26325a9eb9299de5a">◆ </a></span>CreateIndexes()</h2>
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<td class="memname">bool BamMultiReader::CreateIndexes </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 index files for the current BAM files. </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 files created OK </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a9c09a395dd8ecc33f2e6a147ee7fd001" title="Looks for index files that match current BAM files. ">LocateIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a527fabdd80d8dc7788abd60520048b13" title="Opens index files for current BAM files. ">OpenIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a050af09369dd60bf0db3168727a201b4" title="Creates an index file for current BAM file. ">BamReader::CreateIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a2624a904fb20f8c64b6a57176305df93">◆ </a></span>Filenames()</h2>
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<td class="memname">const std::vector< std::string > BamMultiReader::Filenames </td>
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<p>Returns list of filenames for all open BAM files. </p>
<p>Retrieved filenames will contain whatever was passed via <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>. If you need full directory paths here, be sure to include them when you open the BAM files.</p>
<dl class="section return"><dt>Returns</dt><dd>names of open BAM files. If no files are open, returns an empty vector. </dd></dl>
<dl class="section see"><dt>See also</dt><dd>IsOpen(), <a class="el" href="class_bam_tools_1_1_bam_reader.html#a111ec8c00050fef5bf5b580e5dcc83cb" title="Returns name of current BAM file. ">BamReader::GetFilename()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a67d34b61a514b875661ac11f0cca7dc2">◆ </a></span>GetErrorString()</h2>
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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="#ae17506fe2f4959fdbebf27f05d17c8cd">◆ </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> BamMultiReader::GetHeader </td>
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<p>Returns unified SAM-format header for all files. </p>
<dl class="section note"><dt>Note</dt><dd>Modifying the retrieved text does NOT affect the current BAM files. These files have 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>header data wrapped in <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 </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#aa65c1ed621c41d3e07a99500cd5311ac" title="Returns unified SAM-format header text for all files. ">GetHeaderText()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810" title="Returns SAM header data. ">BamReader::GetHeader()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa65c1ed621c41d3e07a99500cd5311ac">◆ </a></span>GetHeaderText()</h2>
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<p>Returns unified SAM-format header text for all files. </p>
<dl class="section note"><dt>Note</dt><dd>Modifying the retrieved text does NOT affect the current BAM files. These files have 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_multi_reader.html#ae17506fe2f4959fdbebf27f05d17c8cd" title="Returns unified SAM-format header for all files. ">GetHeader()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705" title="Returns SAM header data, as SAM-formatted text. ">BamReader::GetHeaderText()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a63ecaca57a10920d110693cc0082da8a">◆ </a></span>GetMergeOrder()</h2>
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<td class="memname"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> BamMultiReader::GetMergeOrder </td>
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<p>Returns curent merge order strategy. </p>
<dl class="section return"><dt>Returns</dt><dd>current merge order enum value </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ab5cd0aa4cea16a53954731387d0c4aaf" title="Sets an explicit merge order, regardless of the BAM files' SO header tag. ">SetExplicitMergeOrder()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a8e78819e59b1a5c08c34d56972188a44">◆ </a></span>GetNextAlignment()</h2>
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<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> & </td>
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<p>Retrieves next available alignment. </p>
<p>Equivalent to <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae" title="Retrieves next available alignment. ">BamReader::GetNextAlignment()</a> with respect to what is a valid overlapping alignment and what data gets populated.</p>
<p>This method takes care of determining which alignment actually is 'next' across multiple files, depending on their sort order.</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_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2" title="Retrieves next available alignment. ">GetNextAlignmentCore()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ab5cd0aa4cea16a53954731387d0c4aaf" title="Sets an explicit merge order, regardless of the BAM files' SO header tag. ">SetExplicitMergeOrder()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" title="Sets a target region of interest. ">SetRegion()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae" title="Retrieves next available alignment. ">BamReader::GetNextAlignment()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a7c1b307ac78087f8174b1dcac838f6a2">◆ </a></span>GetNextAlignmentCore()</h2>
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<td class="memname">bool BamMultiReader::GetNextAlignmentCore </td>
<td>(</td>
<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>Equivalent to <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...">BamReader::GetNextAlignmentCore()</a> with respect to what is a valid overlapping alignment and what data gets populated.</p>
<p>This method takes care of determining which alignment actually is 'next' across multiple files, depending on their sort order.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">alignment</td><td>destination for alignment record data </td></tr>
</table>
</dd>
</dl>
<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_multi_reader.html#a8e78819e59b1a5c08c34d56972188a44" title="Retrieves next available alignment. ">GetNextAlignment()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ab5cd0aa4cea16a53954731387d0c4aaf" title="Sets an explicit merge order, regardless of the BAM files' SO header tag. ">SetExplicitMergeOrder()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" title="Sets a target region of interest. ">SetRegion()</a>, <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...">BamReader::GetNextAlignmentCore()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa02252ba82b3e39a4a9527f37688e0bb">◆ </a></span>GetReferenceCount()</h2>
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<td class="memname">int BamMultiReader::GetReferenceCount </td>
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<p>Returns number of reference sequences. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#af595ee6029b3ffffa473797b23806923" title="Returns number of reference sequences. ">BamReader::GetReferenceCount()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a5a3ea49b0ad5bc9ca4e599668bcca848">◆ </a></span>GetReferenceData()</h2>
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<td class="memname">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">BamTools::RefVector</a> BamMultiReader::GetReferenceData </td>
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<td class="paramtype">void </td>
<td class="paramname"></td><td>)</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>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aec1ff34f2718cb7a6f3d17861c58620b" title="Returns all reference sequence entries. ">BamReader::GetReferenceData()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a0fd0cec7b87ed157e9d9314f62483ed5">◆ </a></span>GetReferenceID()</h2>
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<td class="memname">int BamMultiReader::GetReferenceID </td>
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<td class="paramtype">const std::string & </td>
<td class="paramname"><em>refName</em></td><td>)</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>
<dl class="params"><dt>Parameters</dt><dd>
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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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</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#a4fdf1d7b99b134069c8b58fae4a68f8a" title="Returns the ID of the reference with this name. ">BamReader::GetReferenceID()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ad5683c81b8e122a867af4982df9bf93f">◆ </a></span>HasIndexes()</h2>
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<td class="memname">bool BamMultiReader::HasIndexes </td>
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<td class="paramtype">void </td>
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<p>Returns <code>true</code> if all BAM files have index data available. </p>
<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. ">BamReader::HasIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#abbeb7137ba90a1851d424fffd924d7e3">◆ </a></span>HasOpenReaders()</h2>
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<td class="memname">bool BamMultiReader::HasOpenReaders </td>
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<td class="paramtype">void </td>
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<p>Returns <code>true</code> if there are any open BAM files. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#adabb999cbc393ecf8d268a053d987fb1">◆ </a></span>Jump()</h2>
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<td class="memname">bool BamMultiReader::Jump </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>refID</em>, </td>
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<td class="paramkey"></td>
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<p>Performs a random-access jump within current BAM files. </p>
<p>This is a convenience method, equivalent to calling <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" 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>ID of reference to jump to </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">position</td><td>(0-based) left boundary</td></tr>
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</dd>
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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>HasIndex(), <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381" title="Performs a random-access jump within BAM file. ">BamReader::Jump()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a9c09a395dd8ecc33f2e6a147ee7fd001">◆ </a></span>LocateIndexes()</h2>
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<td class="memname">bool BamMultiReader::LocateIndexes </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 for index files that match current BAM files. </p>
<p>Use this function when you need index files, and perhaps have a preferred index format, but do not depend heavily on which indexes actually get loaded at runtime.</p>
<p>For each BAM file, 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 matches that BAM file.</p>
<p>An example case would look this: </p><div class="fragment"><div class="line"><a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#a18a0708989782f9acb9c05a85b91c913">BamMultiReader</a> reader;</div><div class="line"></div><div class="line"><span class="comment">// do setup...</span></div><div class="line"></div><div class="line"><span class="comment">// ensure that all files have an index</span></div><div class="line"><span class="keywordflow">if</span> ( !reader.LocateIndexes() ) <span class="comment">// opens any existing index files that match our BAM files</span></div><div class="line"> reader.CreateIndexes(); <span class="comment">// creates index files for any BAM files that still lack one</span></div><div class="line"></div><div class="line"><span class="comment">// do interesting stuff using random-access...</span></div></div><!-- fragment --><p>If you want precise control over which index files are loaded, use <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a527fabdd80d8dc7788abd60520048b13" title="Opens index files for current BAM files. ">OpenIndexes()</a> with the desired index filenames. If that function returns false, you can use <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adfefc02fd813f5d26325a9eb9299de5a" title="Creates index files for the current BAM files. ">CreateIndexes()</a> to then build index files of the exact requested format.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<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>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if index files could be found for <b>ALL</b> open BAM files </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. ">BamReader::LocateIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a35475e3480ef6886b440deb4e30e9964">◆ </a></span>Open()</h2>
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<td class="memname">bool BamMultiReader::Open </td>
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<td class="paramtype">const std::vector< std::string > & </td>
<td class="paramname"><em>filenames</em></td><td>)</td>
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<p>Opens BAM files. </p>
<dl class="section note"><dt>Note</dt><dd>Opening BAM files will invalidate any current region set on the multireader. All file pointers will be returned to the beginning of the alignment data. Follow this with <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1" title="Performs a random-access jump within current BAM files. ">Jump()</a> or <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" title="Sets a target region of interest. ">SetRegion()</a> to establish a region of interest.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">filenames</td><td>list of BAM filenames to open </td></tr>
</table>
</dd>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if BAM files were opened successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ac05596504d1c230aa1a32493a1b10216" title="Closes all open BAM files. ">Close()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abbeb7137ba90a1851d424fffd924d7e3" title="Returns true if there are any open BAM files. ">HasOpenReaders()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a11ff4c569409990b0a6e3fcdaeaf629e" title="Opens a single BAM file. ">OpenFile()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a527fabdd80d8dc7788abd60520048b13" title="Opens index files for current BAM files. ">OpenIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02" title="Opens a BAM file. ">BamReader::Open()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a11ff4c569409990b0a6e3fcdaeaf629e">◆ </a></span>OpenFile()</h2>
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<td class="memname">bool BamMultiReader::OpenFile </td>
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<td class="paramtype">const std::string & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>Opens a single BAM file. </p>
<p>Adds another BAM file to multireader "on-the-fly".</p>
<dl class="section note"><dt>Note</dt><dd>Opening a BAM file will invalidate any current region set on the multireader. All file pointers will be returned to the beginning of the alignment data. Follow this with <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1" title="Performs a random-access jump within current BAM files. ">Jump()</a> or <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" title="Sets a target region of interest. ">SetRegion()</a> to establish a region of interest.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">filename</td><td>BAM filename to open </td></tr>
</table>
</dd>
</dl>
<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_multi_reader.html#ac05596504d1c230aa1a32493a1b10216" title="Closes all open BAM files. ">Close()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abbeb7137ba90a1851d424fffd924d7e3" title="Returns true if there are any open BAM files. ">HasOpenReaders()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a527fabdd80d8dc7788abd60520048b13" title="Opens index files for current BAM files. ">OpenIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02" title="Opens a BAM file. ">BamReader::Open()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a527fabdd80d8dc7788abd60520048b13">◆ </a></span>OpenIndexes()</h2>
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<td class="memname">bool BamMultiReader::OpenIndexes </td>
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<td class="paramtype">const std::vector< std::string > & </td>
<td class="paramname"><em>indexFilenames</em></td><td>)</td>
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<p>Opens index files for current BAM files. </p>
<dl class="section note"><dt>Note</dt><dd>Currently assumes that index filenames match the order (and number) of BAM files passed to <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">indexFilenames</td><td>list of BAM index file names </td></tr>
</table>
</dd>
</dl>
<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>LocateIndex(), <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a35475e3480ef6886b440deb4e30e9964" title="Opens BAM files. ">Open()</a>, SetIndex(), <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d" title="Opens a BAM index file. ">BamReader::OpenIndex()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a214b9b40f55923fd8bf2141a7f36d7f1">◆ </a></span>Rewind()</h2>
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<td class="memname">bool BamMultiReader::Rewind </td>
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<p>Returns the internal file pointers to the beginning of alignment records. </p>
<p>Useful for performing multiple sequential passes through BAM files. Calling this function clears any prior region that may have been set.</p>
<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_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1" title="Performs a random-access jump within current BAM files. ">Jump()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7" title="Sets a target region of interest. ">SetRegion()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a487f2da4d773a1ac17fdab855f3a964c" title="Returns the internal file pointer to the first alignment record. ">BamReader::Rewind()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ab5cd0aa4cea16a53954731387d0c4aaf">◆ </a></span>SetExplicitMergeOrder()</h2>
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<td class="memname">bool BamMultiReader::SetExplicitMergeOrder </td>
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<td class="paramtype"><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> </td>
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<p>Sets an explicit merge order, regardless of the BAM files' SO header tag. </p>
<p>The default behavior of the <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html" title="Convenience class for reading multiple BAM files. ">BamMultiReader</a> is to check the SO tag in the BAM files' SAM header text to determine the merge strategy". The merge strategy is used to determine from which BAM file the next alignment should come when either <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a8e78819e59b1a5c08c34d56972188a44" title="Retrieves next available alignment. ">GetNextAlignment()</a> or <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2" title="Retrieves next available alignment. ">GetNextAlignmentCore()</a> are called. If files share a 'coordinate' or 'queryname' value for this tag, then the merge strategy is selected accordingly. If any of them do not match, or if any fileis marked as 'unsorted', then the merge strategy is simply a round-robin.</p>
<p>This method allows client code to explicitly override the lookup behavior. This method can be useful when you know, for example, that your BAM files are sorted by coordinate but upstream processes did not set the header tag properly.</p>
<dl class="section note"><dt>Note</dt><dd>This method should <b>not</b> be called while reading alignments via <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a8e78819e59b1a5c08c34d56972188a44" title="Retrieves next available alignment. ">GetNextAlignment()</a> or <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2" title="Retrieves next available alignment. ">GetNextAlignmentCore()</a>. For proper results, you should call this method before (or immediately after) opening files, rewinding, jumping, etc. but <b>not</b> once alignment fetching has started. There is nothing in the API to prevent you from doing so, but the results may be unexpected.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if merge order could be successfully applied </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a63ecaca57a10920d110693cc0082da8a" title="Returns curent merge order strategy. ">GetMergeOrder()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a8e78819e59b1a5c08c34d56972188a44" title="Retrieves next available alignment. ">GetNextAlignment()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2" title="Retrieves next available alignment. ">GetNextAlignmentCore()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a7c9c3d1f9882053af4cbfebfb894b8c7">◆ </a></span>SetRegion() <span class="overload">[1/2]</span></h2>
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<td class="memname">bool BamMultiReader::SetRegion </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><td>)</td>
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<p>Sets a target region of interest. </p>
<p>Equivalent to calling <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">BamReader::SetRegion()</a> on all open BAM files.</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>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">region</td><td>desired region-of-interest to activate </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if ALL readers set the region successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ad5683c81b8e122a867af4982df9bf93f" title="Returns true if all BAM files have index data available. ">HasIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1" title="Performs a random-access jump within current BAM files. ">Jump()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">BamReader::SetRegion()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#abcca568dd142e9db91cca5dab8934da8">◆ </a></span>SetRegion() <span class="overload">[2/2]</span></h2>
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<td class="memname">bool BamMultiReader::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. Equivalent to calling <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">BamReader::SetRegion()</a> on all open BAM files.</p>
<dl class="section warning"><dt>Warning</dt><dd>This function now 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>
</dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if ALL readers set the region successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#ad5683c81b8e122a867af4982df9bf93f" title="Returns true if all BAM files have index data available. ">HasIndexes()</a>, <a class="el" href="class_bam_tools_1_1_bam_multi_reader.html#adabb999cbc393ecf8d268a053d987fb1" title="Performs a random-access jump within current BAM files. ">Jump()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420" title="Sets a target region of interest. ">BamReader::SetRegion()</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_multi_reader_8h_source.html">BamMultiReader.h</a></li>
<li><a class="el" href="_bam_multi_reader_8cpp.html">BamMultiReader.cpp</a></li>
</ul>
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