[med-svn] [bamtools] branch upstream updated (1e568fc -> a221884)
Andreas Tille
tille at debian.org
Tue Feb 6 10:31:52 UTC 2018
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tille pushed a change to branch upstream
in repository bamtools.
from 1e568fc New upstream version 2.4.1+dfsg
new a221884 New upstream version 2.5.1+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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(-)
create mode 100644 src/bamtools.pc.in
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