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commit 0565185d57289bfa36f112980c7c2697cdfb6422 Merge: 16dcfcd a221884 Author: Andreas Tille <[email protected]> Date: Tue Feb 6 10:08:31 2018 +0100 Update upstream source from tag 'upstream/2.5.1+dfsg' Update to upstream version '2.5.1+dfsg' with Debian dir 2a35f6d5c843b88e901df0bd6230f9d708b310b4 CMakeLists.txt | 71 +- docs/Doxyfile | 2 +- src/CMakeLists.txt | 4 + src/ExportHeader.cmake | 4 +- src/api/BamAlgorithms.h | 2 +- src/api/BamAlignment.cpp | 612 ++++++----- src/api/BamAlignment.h | 442 ++++---- src/api/BamAux.h | 1000 ++++++++--------- src/api/BamConstants.h | 383 ++++--- src/api/BamIndex.h | 88 +- src/api/BamMultiReader.cpp | 109 +- src/api/BamMultiReader.h | 190 ++-- src/api/BamReader.cpp | 105 +- src/api/BamReader.h | 236 ++--- src/api/BamWriter.cpp | 307 +++--- src/api/BamWriter.h | 139 +-- src/api/CMakeLists.txt | 38 +- src/api/IBamIODevice.h | 94 +- src/api/SamConstants.h | 92 +- src/api/SamHeader.cpp | 88 +- src/api/SamHeader.h | 57 +- src/api/SamProgram.cpp | 62 +- src/api/SamProgram.h | 51 +- src/api/SamProgramChain.cpp | 185 ++-- src/api/SamProgramChain.h | 89 +- src/api/SamReadGroup.cpp | 104 +- src/api/SamReadGroup.h | 72 +- src/api/SamReadGroupDictionary.cpp | 142 +-- src/api/SamReadGroupDictionary.h | 94 +- src/api/SamSequence.cpp | 75 +- src/api/SamSequence.h | 55 +- src/api/SamSequenceDictionary.cpp | 146 +-- src/api/SamSequenceDictionary.h | 95 +- src/api/algorithms/Sort.h | 155 +-- src/api/api_global.h | 6 +- src/api/internal/bam/BamHeader_p.cpp | 61 +- src/api/internal/bam/BamHeader_p.h | 63 +- src/api/internal/bam/BamMultiMerger_p.h | 268 ++--- src/api/internal/bam/BamMultiReader_p.cpp | 491 +++++---- src/api/internal/bam/BamMultiReader_p.h | 123 ++- .../internal/bam/BamRandomAccessController_p.cpp | 163 +-- src/api/internal/bam/BamRandomAccessController_p.h | 94 +- src/api/internal/bam/BamReader_p.cpp | 341 ++++-- src/api/internal/bam/BamReader_p.h | 136 +-- src/api/internal/bam/BamWriter_p.cpp | 414 +++++--- src/api/internal/bam/BamWriter_p.h | 63 +- src/api/internal/index/BamIndexFactory_p.cpp | 80 +- src/api/internal/index/BamIndexFactory_p.h | 50 +- src/api/internal/index/BamStandardIndex_p.cpp | 572 +++++----- src/api/internal/index/BamStandardIndex_p.h | 263 +++-- src/api/internal/index/BamToolsIndex_p.cpp | 371 ++++--- src/api/internal/index/BamToolsIndex_p.h | 191 ++-- src/api/internal/io/BamDeviceFactory_p.cpp | 13 +- src/api/internal/io/BamDeviceFactory_p.h | 15 +- src/api/internal/io/BamFile_p.cpp | 38 +- src/api/internal/io/BamFile_p.h | 31 +- src/api/internal/io/BamFtp_p.cpp | 291 ++--- src/api/internal/io/BamFtp_p.h | 92 +- src/api/internal/io/BamHttp_p.cpp | 300 +++--- src/api/internal/io/BamHttp_p.h | 99 +- src/api/internal/io/BamPipe_p.cpp | 42 +- src/api/internal/io/BamPipe_p.h | 25 +- src/api/internal/io/BgzfStream_p.cpp | 301 +++--- src/api/internal/io/BgzfStream_p.h | 98 +- src/api/internal/io/ByteArray_p.cpp | 75 +- src/api/internal/io/ByteArray_p.h | 59 +- src/api/internal/io/HostAddress_p.cpp | 237 ++--- src/api/internal/io/HostAddress_p.h | 109 +- src/api/internal/io/HostInfo_p.cpp | 111 +- src/api/internal/io/HostInfo_p.h | 66 +- src/api/internal/io/HttpHeader_p.cpp | 309 +++--- src/api/internal/io/HttpHeader_p.h | 140 +-- src/api/internal/io/ILocalIODevice_p.cpp | 39 +- src/api/internal/io/ILocalIODevice_p.h | 29 +- src/api/internal/io/NetUnix_p.h | 14 +- src/api/internal/io/NetWin_p.h | 42 +- src/api/internal/io/RollingBuffer_p.cpp | 157 +-- src/api/internal/io/RollingBuffer_p.h | 93 +- src/api/internal/io/TcpSocketEngine_p.cpp | 98 +- src/api/internal/io/TcpSocketEngine_p.h | 102 +- src/api/internal/io/TcpSocketEngine_unix_p.cpp | 82 +- src/api/internal/io/TcpSocketEngine_win_p.cpp | 85 +- src/api/internal/io/TcpSocket_p.cpp | 230 ++-- src/api/internal/io/TcpSocket_p.h | 160 +-- src/api/internal/sam/SamFormatParser_p.cpp | 223 ++-- src/api/internal/sam/SamFormatParser_p.h | 39 +- src/api/internal/sam/SamFormatPrinter_p.cpp | 144 ++- src/api/internal/sam/SamFormatPrinter_p.h | 35 +- src/api/internal/sam/SamHeaderValidator_p.cpp | 270 ++--- src/api/internal/sam/SamHeaderValidator_p.h | 116 +- src/api/internal/sam/SamHeaderVersion_p.h | 136 ++- src/api/internal/utils/BamException_p.cpp | 3 +- src/api/internal/utils/BamException_p.h | 34 +- src/bamtools.pc.in | 10 + src/shared/bamtools_global.h | 82 +- src/toolkit/CMakeLists.txt | 11 +- src/toolkit/bamtools.cpp | 203 ++-- src/toolkit/bamtools_convert.cpp | 934 ++++++++-------- src/toolkit/bamtools_convert.h | 43 +- src/toolkit/bamtools_count.cpp | 138 +-- src/toolkit/bamtools_count.h | 43 +- src/toolkit/bamtools_coverage.cpp | 208 ++-- src/toolkit/bamtools_coverage.h | 43 +- src/toolkit/bamtools_filter.cpp | 1027 ++++++++++-------- src/toolkit/bamtools_filter.h | 41 +- src/toolkit/bamtools_header.cpp | 95 +- src/toolkit/bamtools_header.h | 41 +- src/toolkit/bamtools_index.cpp | 81 +- src/toolkit/bamtools_index.h | 41 +- src/toolkit/bamtools_merge.cpp | 162 +-- src/toolkit/bamtools_merge.h | 41 +- src/toolkit/bamtools_random.cpp | 209 ++-- src/toolkit/bamtools_random.h | 41 +- src/toolkit/bamtools_resolve.cpp | 1119 +++++++++++--------- src/toolkit/bamtools_resolve.h | 37 +- src/toolkit/bamtools_revert.cpp | 146 +-- src/toolkit/bamtools_revert.h | 41 +- src/toolkit/bamtools_sort.cpp | 276 ++--- src/toolkit/bamtools_sort.h | 41 +- src/toolkit/bamtools_split.cpp | 755 +++++++------ src/toolkit/bamtools_split.h | 41 +- src/toolkit/bamtools_stats.cpp | 301 +++--- src/toolkit/bamtools_stats.h | 41 +- src/toolkit/bamtools_tool.h | 33 +- src/toolkit/bamtools_version.h.in | 2 +- src/utils/CMakeLists.txt | 3 +- src/utils/bamtools_fasta.cpp | 552 +++++----- src/utils/bamtools_fasta.h | 49 +- src/utils/bamtools_filter_engine.h | 579 +++++----- src/utils/bamtools_filter_properties.h | 219 ++-- src/utils/bamtools_filter_ruleparser.h | 426 ++++---- src/utils/bamtools_options.cpp | 174 +-- src/utils/bamtools_options.h | 241 ++--- src/utils/bamtools_pileup_engine.cpp | 319 +++--- src/utils/bamtools_pileup_engine.h | 73 +- src/utils/bamtools_utilities.cpp | 294 ++--- src/utils/bamtools_utilities.h | 67 +- src/utils/bamtools_variant.h | 212 ++-- src/utils/utils_global.h | 6 +- 139 files changed, 12381 insertions(+), 10880 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
