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  <ul>
<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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<div class="title">BamTools::BamReader Member List</div>  </div>
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<p>This is the complete list of members for <a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab3902f9802bd9e9b8960d44abe302a58">BamReader</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a9bedadbb878c84d3674eea1c11f981ec">Close</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a050af09369dd60bf0db3168727a201b4">CreateIndex</a>(const BamIndex::IndexType &amp;type=BamIndex::STANDARD)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa8cfff90af216f7f401650db0d1492ca">GetConstSamHeader</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a46a3b08df29f2fb26c7d868816d15c83">GetErrorString</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a111ec8c00050fef5bf5b580e5dcc83cb">GetFilename</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810">GetHeader</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705">GetHeaderText</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae">GetNextAlignment</a>(BamAlignment &amp;alignment)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95">GetNextAlignmentCore</a>(BamAlignment &amp;alignment)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#af595ee6029b3ffffa473797b23806923">GetReferenceCount</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aec1ff34f2718cb7a6f3d17861c58620b">GetReferenceData</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a4fdf1d7b99b134069c8b58fae4a68f8a">GetReferenceID</a>(const std::string &amp;refName) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab79d3d603434f61807820a19c99d51b9">HasIndex</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5">IsOpen</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa62d784c8348662064fe363de2b40381">Jump</a>(int refID, int position=0)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a86dfc39a2d57eb3b665e641e6436b5ee">LocateIndex</a>(const BamIndex::IndexType &amp;preferredType=BamIndex::STANDARD)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a9a863a20a48b960a94b9b9c16471cc02">Open</a>(const std::string &amp;filename)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#ab62b5f370b91e225fd7684d0180bd41d">OpenIndex</a>(const std::string &amp;indexFilename)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a487f2da4d773a1ac17fdab855f3a964c">Rewind</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a89712324427d42091c3a979a426871d5">SetIndex</a>(BamIndex *index)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420">SetRegion</a>(const BamRegion &amp;region)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a1e6edaeac4531846727384dfb43e4eeb">SetRegion</a>(const int &amp;leftRefID, const int &amp;leftPosition, const int &amp;rightRefID, const int &amp;rightPosition)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html#a81b83ee41a37e94b0228125e0b082499">~BamReader</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></td><td class="entry"></td></tr>
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