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 <span id="projectnumber">2.4.1</span>
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<div class="title">Class Hierarchy</div> </div>
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<div class="textblock">This inheritance list is sorted roughly, but not completely, alphabetically:</div><div class="directory">
<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span>]</div><table class="directory">
<tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">▼</span><span class="icona"><span class="icon">C</span></span><b>AlignmentSortBase</b></td><td class="desc"></td></tr>
<tr id="row_0_0_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html" target="_self">BamTools::Algorithms::Sort::ByName</a></td><td class="desc">Function object for comparing alignments by name </td></tr>
<tr id="row_0_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html" target="_self">BamTools::Algorithms::Sort::ByPosition</a></td><td class="desc">Function object for comparing alignments by position </td></tr>
<tr id="row_0_2_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html" target="_self">BamTools::Algorithms::Sort::ByTag< T ></a></td><td class="desc">Function object for comparing alignments by tag value </td></tr>
<tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html" target="_self">BamTools::Algorithms::Sort::Unsorted</a></td><td class="desc">Placeholder function object </td></tr>
<tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_bam_alignment.html" target="_self">BamTools::BamAlignment</a></td><td class="desc">The main BAM alignment data structure </td></tr>
<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_bam_index.html" target="_self">BamTools::BamIndex</a></td><td class="desc">Provides methods for generating & loading BAM index files </td></tr>
<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_bam_multi_reader.html" target="_self">BamTools::BamMultiReader</a></td><td class="desc">Convenience class for reading multiple BAM files </td></tr>
<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_bam_reader.html" target="_self">BamTools::BamReader</a></td><td class="desc">Provides read access to BAM files </td></tr>
<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_bam_region.html" target="_self">BamTools::BamRegion</a></td><td class="desc">Represents a sequential genomic region </td></tr>
<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_bam_writer.html" target="_self">BamTools::BamWriter</a></td><td class="desc">Provides write access for generating BAM files </td></tr>
<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_cigar_op.html" target="_self">BamTools::CigarOp</a></td><td class="desc">Represents a CIGAR alignment operation </td></tr>
<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_custom_header_tag.html" target="_self">BamTools::CustomHeaderTag</a></td><td class="desc"></td></tr>
<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_i_bam_i_o_device.html" target="_self">BamTools::IBamIODevice</a></td><td class="desc"></td></tr>
<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_ref_data.html" target="_self">BamTools::RefData</a></td><td class="desc">Represents a reference sequence entry </td></tr>
<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_sam_header.html" target="_self">BamTools::SamHeader</a></td><td class="desc">Represents the SAM-formatted text header that is part of the BAM file header </td></tr>
<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_sam_program.html" target="_self">BamTools::SamProgram</a></td><td class="desc">Represents a SAM program record </td></tr>
<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_sam_program_chain.html" target="_self">BamTools::SamProgramChain</a></td><td class="desc">Sorted container "chain" of <a class="el" href="struct_bam_tools_1_1_sam_program.html" title="Represents a SAM program record. ">SamProgram</a> records </td></tr>
<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_sam_read_group.html" target="_self">BamTools::SamReadGroup</a></td><td class="desc">Represents a SAM read group entry </td></tr>
<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_sam_read_group_dictionary.html" target="_self">BamTools::SamReadGroupDictionary</a></td><td class="desc">Container of <a class="el" href="struct_bam_tools_1_1_sam_read_group.html" title="Represents a SAM read group entry. ">SamReadGroup</a> entries </td></tr>
<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_sam_sequence.html" target="_self">BamTools::SamSequence</a></td><td class="desc">Represents a SAM sequence entry </td></tr>
<tr id="row_17_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html" target="_self">BamTools::SamSequenceDictionary</a></td><td class="desc">Container of <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> entries </td></tr>
<tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="struct_bam_tools_1_1_algorithms_1_1_sort.html" target="_self">BamTools::Algorithms::Sort</a></td><td class="desc">Provides classes & methods related to sorting BamAlignments </td></tr>
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