├── .github └── workflows │ └── build.yml ├── CMakeLists.txt ├── LICENSE ├── README ├── docs └── Doxyfile ├── src ├── CMakeLists.txt ├── api │ ├── BamAlgorithms.h │ ├── BamAlignment.cpp │ ├── BamAlignment.h │ ├── BamAux.h │ ├── BamConstants.h │ ├── BamIndex.h │ ├── BamMultiReader.cpp │ ├── BamMultiReader.h │ ├── BamReader.cpp │ ├── BamReader.h │ ├── BamWriter.cpp │ ├── BamWriter.h │ ├── CMakeLists.txt │ ├── IBamIODevice.h │ ├── SamConstants.h │ ├── SamHeader.cpp │ ├── SamHeader.h │ ├── SamProgram.cpp │ ├── SamProgram.h │ ├── SamProgramChain.cpp │ ├── SamProgramChain.h │ ├── SamReadGroup.cpp │ ├── SamReadGroup.h │ ├── SamReadGroupDictionary.cpp │ ├── SamReadGroupDictionary.h │ ├── SamSequence.cpp │ ├── SamSequence.h │ ├── SamSequenceDictionary.cpp │ ├── SamSequenceDictionary.h │ ├── algorithms │ │ └── Sort.h │ ├── api_global.h │ └── internal │ │ ├── bam │ │ ├── BamHeader_p.cpp │ │ ├── BamHeader_p.h │ │ ├── BamMultiMerger_p.h │ │ ├── BamMultiReader_p.cpp │ │ ├── BamMultiReader_p.h │ │ ├── BamRandomAccessController_p.cpp │ │ ├── BamRandomAccessController_p.h │ │ ├── BamReader_p.cpp │ │ ├── BamReader_p.h │ │ ├── BamWriter_p.cpp │ │ └── BamWriter_p.h │ │ ├── index │ │ ├── BamIndexFactory_p.cpp │ │ ├── BamIndexFactory_p.h │ │ ├── BamStandardIndex_p.cpp │ │ ├── BamStandardIndex_p.h │ │ ├── BamToolsIndex_p.cpp │ │ └── BamToolsIndex_p.h │ │ ├── io │ │ ├── BamDeviceFactory_p.cpp │ │ ├── BamDeviceFactory_p.h │ │ ├── BamFile_p.cpp │ │ ├── BamFile_p.h │ │ ├── BamFtp_p.cpp │ │ ├── BamFtp_p.h │ │ ├── BamHttp_p.cpp │ │ ├── BamHttp_p.h │ │ ├── BamPipe_p.cpp │ │ ├── BamPipe_p.h │ │ ├── BgzfStream_p.cpp │ │ ├── BgzfStream_p.h │ │ ├── ByteArray_p.cpp │ │ ├── ByteArray_p.h │ │ ├── HostAddress_p.cpp │ │ ├── HostAddress_p.h │ │ ├── HostInfo_p.cpp │ │ ├── HostInfo_p.h │ │ ├── HttpHeader_p.cpp │ │ ├── HttpHeader_p.h │ │ ├── ILocalIODevice_p.cpp │ │ ├── ILocalIODevice_p.h │ │ ├── NetUnix_p.h │ │ ├── NetWin_p.h │ │ ├── RollingBuffer_p.cpp │ │ ├── RollingBuffer_p.h │ │ ├── TcpSocketEngine_p.cpp │ │ ├── TcpSocketEngine_p.h │ │ ├── TcpSocketEngine_unix_p.cpp │ │ ├── TcpSocketEngine_win_p.cpp │ │ ├── TcpSocket_p.cpp │ │ └── TcpSocket_p.h │ │ ├── sam │ │ ├── SamFormatParser_p.cpp │ │ ├── SamFormatParser_p.h │ │ ├── SamFormatPrinter_p.cpp │ │ ├── SamFormatPrinter_p.h │ │ ├── SamHeaderValidator_p.cpp │ │ ├── SamHeaderValidator_p.h │ │ └── SamHeaderVersion_p.h │ │ └── utils │ │ ├── BamException_p.cpp │ │ └── BamException_p.h ├── bamtools.pc.in ├── shared │ └── bamtools_global.h ├── third_party │ ├── CMakeLists.txt │ └── jsoncpp │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── json │ │ ├── json-forwards.h │ │ └── json.h │ │ └── jsoncpp.cpp ├── toolkit │ ├── bamtools.cpp │ ├── bamtools_convert.cpp │ ├── bamtools_convert.h │ ├── bamtools_count.cpp │ ├── bamtools_count.h │ ├── bamtools_coverage.cpp │ ├── bamtools_coverage.h │ ├── bamtools_filter.cpp │ ├── bamtools_filter.h │ ├── bamtools_header.cpp │ ├── bamtools_header.h │ ├── bamtools_index.cpp │ ├── bamtools_index.h │ ├── bamtools_merge.cpp │ ├── bamtools_merge.h │ ├── bamtools_random.cpp │ ├── bamtools_random.h │ ├── bamtools_resolve.cpp │ ├── bamtools_resolve.h │ ├── bamtools_revert.cpp │ ├── bamtools_revert.h │ ├── bamtools_sort.cpp │ ├── bamtools_sort.h │ ├── bamtools_split.cpp │ ├── bamtools_split.h │ ├── bamtools_stats.cpp │ ├── bamtools_stats.h │ ├── bamtools_tool.h │ └── bamtools_version.h.in └── utils │ ├── bamtools_fasta.cpp │ ├── bamtools_fasta.h │ ├── bamtools_filter_engine.h │ ├── bamtools_filter_properties.h │ ├── bamtools_filter_ruleparser.h │ ├── bamtools_options.cpp │ ├── bamtools_options.h │ ├── bamtools_pileup_engine.cpp │ ├── bamtools_pileup_engine.h │ ├── bamtools_utilities.cpp │ ├── bamtools_utilities.h │ ├── bamtools_variant.h │ └── utils_global.h └── tests ├── CMakeLists.txt └── data └── sam_spec_example.bam /.github/workflows/build.yml: -------------------------------------------------------------------------------- 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