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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_alignment.html">BamAlignment</a></li>  </ul>
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<div class="title">BamTools::BamAlignment 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_alignment.html">BamTools::BamAlignment</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_alignment.html#a553f81130bf6e136ae8859bb89011c71">AddTag</a>(const std::string &amp;tag, const std::string &amp;type, const T &amp;value)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ab09155dbfea4f7ab1c86eb31ffdcae47">AddTag</a>(const std::string &amp;tag, const std::vector&lt; T &gt; &amp;values)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a55d27086aca3e321cee411d43633a788">AlignedBases</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a528e10f19aec995e58ec7dbdf1e35b6b">AlignmentFlag</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ac6f09055928c6015a08f76edb0e44e13">BamAlignment</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a11c3bff2252799d68ee6a098b2007462">BamAlignment</a>(const BamAlignment &amp;other)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aa7068d3ba7704dbecb6b47ffbf6f8467">Bin</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a1ea231426b422a70242a44c010894af9">BuildCharData</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ac7ad2244a0e268abdcdf09e97fadee3e">CigarData</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#af70ac92ef127712790dff1cddfb3bccd">EditTag</a>(const std::string &amp;tag, const std::string &amp;type, const T &amp;value)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#afa96020f82b5cd0d4f0e7684026fc820">EditTag</a>(const std::string &amp;tag, const std::vector&lt; T &gt; &amp;values)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#abbac2cbd8b0508c36a6be13ab1aa53c4">Filename</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a9daa40efada5d9879a9024dbdbc45368">GetArrayTagType</a>(const std::string &amp;tag, char &amp;type) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a232702c4461241d839fb3e47900d6a38">GetEndPosition</a>(bool usePadded=false, bool closedInterval=false) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aace1174a346afa5677d67acab34f5be6">GetErrorString</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a89f003c94168e057f0d1cfcf0b8249bc">GetSoftClips</a>(std::vector&lt; int &gt; &amp;clipSizes, std::vector&lt; int &gt; &amp;readPositions, std::vector&lt; int &gt; &amp;genomePositions, bool usePadded=false) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">GetTag</a>(const std::string &amp;tag, T &amp;destination) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a261b3a6e3f41e5d481c4d1d29e9c9371">GetTag</a>(const std::string &amp;tag, std::vector&lt; T &gt; &amp;destination) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a6bb858bf17600167b60710ccc7dc2db0">GetTagNames</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aaec9ad3e43021ca3ab49a136b55aa3d4">GetTagType</a>(const std::string &amp;tag, char &amp;type) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#adb788ab4e95e9d3165cc2eed2c72258c">HasTag</a>(const std::string &amp;tag) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a19c45c67919fb8d22d3487b3f1fcd79d">InsertSize</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a1ff3357da3472115c30e9b3285502bbf">Internal::BamReaderPrivate</a> class</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aa01fcc0bfc0452beb435289c61d8dec8">Internal::BamWriterPrivate</a> class</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ad4277014925ada2128fb1e1b6c63fdbf">IsDuplicate</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a235682b6d81138ed85edd9abe028d695">IsFailedQC</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a3ca1a3d49f8518c0aec28bbdbb9d3e68">IsFirstMate</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a235e9ecbfc71bb4bdff9035ce883ab5b">IsMapped</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a3fc4df5172a701d75fe9d7ebb27551f9">IsMateMapped</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aec5c50e3e03ddcd3d9b48c3cb17d3952">IsMateReverseStrand</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a72609635ae47a972675d02ea05b36e2a">IsPaired</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a2cce9b832f3aec3fd467b6fb04591a53">IsPrimaryAlignment</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a1aba1d59242b6960960215dd04cebc8e">IsProperPair</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a4c05f4d6dc44764cb4189c6ab3b9bd0c">IsReverseStrand</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#af249af81550080de497d7d38409e8bf6">IsSecondMate</a>(void) const</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a4d2ee5aeba57fdffc36e8fb9e01c4bb4">Length</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a96c235eb7645c6e0fcf5da5bfb16a2aa">MapQuality</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aaef8a38689198150d0627a51b53e6352">MatePosition</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#acbfdd5b968249c9c074943b2d1fddca8">MateRefID</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf">Name</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc">Position</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a9af49d39bda11b60eb12ed4162100fd6">Qualities</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#aed5682a27b7bc660d45d705e4411b3d5">QueryBases</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ae794c81d9eee17d830ba3bdb81f33fa2">RemoveTag</a>(const std::string &amp;tag)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a65d3a3de3ca370482998128fdd664027">SetIsDuplicate</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a437aefdb4cce3e6c81fdacf1b235a627">SetIsFailedQC</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ac386dcf67e1f5a38693cba9a88d93222">SetIsFirstMate</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a016f937f85b65bfd0010a1677f86c070">SetIsMapped</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a3ee0485a69f32c29db5fe85fa3833f77">SetIsMateMapped</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ad6ef32dbd31e764a4881c9737281932d">SetIsMateReverseStrand</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#af93cbf0065f171eef11c06a80889f3c4">SetIsPaired</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a6f5609efeed9e780c01d2fd7f046eb4b">SetIsPrimaryAlignment</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a6509aab004e21c61f7a88928bd55fcdf">SetIsProperPair</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#af53274437d257d27bda824c889cde2a2">SetIsReverseStrand</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a8311f972b6358c8a4c6bb6c933d751f4">SetIsSecondMate</a>(bool ok)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#ab3ac5fc4c4f193d0448882e592a31962">TagData</a></td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html#a1341749fe3dcb1801126dcaee72e0817">~BamAlignment</a>(void)</td><td class="entry"><a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></td><td class="entry"></td></tr>
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