[med-svn] [bamtools] branch master updated (16dcfcd -> c075d28)
Andreas Tille
tille at debian.org
Tue Feb 6 10:31:49 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository bamtools.
from 16dcfcd releasing package bamtools version 2.4.1+dfsg-2
new a221884 New upstream version 2.5.1+dfsg
new 0565185 Update upstream source from tag 'upstream/2.5.1+dfsg'
new f76c001 New upstream version, refresh patches
new 5a11f5a cme fix dpkg-control
new c075d28 debhelper 11
The 5 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 +-
debian/changelog | 8 +
debian/compat | 2 +-
debian/control | 4 +-
.../0001-ignore-thirdparty-and-fix-jsoncpp.patch | 8 +-
.../patches/0002-support-out-of-source-build.patch | 35 +-
...om-ExportHeader-function-use-install-inst.patch | 109 +-
...bamtools-to-lib.-Installing-libraries-to-.patch | 25 -
debian/patches/0006-Doxygen-reproducibility | 2 -
debian/patches/0007-Big_Endian.patch | 23 -
debian/patches/0008_Cmake_Test.patch | 14 +-
debian/patches/doxygen-tweak | 47 +-
.../patches/non-deprecated-jsoncpp-function-names | 15 -
debian/patches/series | 5 +-
debian/patches/spelling | 12 +-
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 +-
153 files changed, 12475 insertions(+), 11095 deletions(-)
delete mode 100644 debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
delete mode 100644 debian/patches/0007-Big_Endian.patch
delete mode 100644 debian/patches/non-deprecated-jsoncpp-function-names
create mode 100644 src/bamtools.pc.in
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