[med-svn] [freebayes] branch master updated (e6a790b -> c60831b)
Andreas Tille
tille at debian.org
Wed May 28 17:27:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository freebayes.
from e6a790b Merge branch 'master' of ssh://git.debian.org/git/debian-med/freebayes
new cedd7db Fix d/watch; remove bamtools from source
new 28bfd02 Imported Upstream version 0.9.14+dfsg
new c60831b Merge tag 'upstream/0.9.14+dfsg'
The 3 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:
.gitmodules | 6 +-
Makefile | 8 +-
README.md | 2 +-
bamtools/CMakeLists.txt | 65 -
bamtools/LICENSE | 22 -
bamtools/README | 60 -
bamtools/docs/Doxyfile | 1605 --
bamtools/src/CMakeLists.txt | 16 -
bamtools/src/ExportHeader.cmake | 27 -
bamtools/src/api/BamAlgorithms.h | 21 -
bamtools/src/api/BamAlignment.cpp | 1083 -
bamtools/src/api/BamAlignment.h | 638 -
bamtools/src/api/BamAux.h | 468 -
bamtools/src/api/BamConstants.h | 282 -
bamtools/src/api/BamIndex.h | 90 -
bamtools/src/api/BamMultiReader.cpp | 421 -
bamtools/src/api/BamMultiReader.h | 127 -
bamtools/src/api/BamReader.cpp | 383 -
bamtools/src/api/BamReader.h | 119 -
bamtools/src/api/BamWriter.cpp | 152 -
bamtools/src/api/BamWriter.h | 69 -
bamtools/src/api/CMakeLists.txt | 83 -
bamtools/src/api/IBamIODevice.h | 98 -
bamtools/src/api/SamConstants.h | 97 -
bamtools/src/api/SamHeader.cpp | 236 -
bamtools/src/api/SamHeader.h | 74 -
bamtools/src/api/SamProgram.cpp | 139 -
bamtools/src/api/SamProgram.h | 61 -
bamtools/src/api/SamProgramChain.cpp | 354 -
bamtools/src/api/SamProgramChain.h | 85 -
bamtools/src/api/SamReadGroup.cpp | 221 -
bamtools/src/api/SamReadGroup.h | 68 -
bamtools/src/api/SamReadGroupDictionary.cpp | 297 -
bamtools/src/api/SamReadGroupDictionary.h | 85 -
bamtools/src/api/SamSequence.cpp | 161 -
bamtools/src/api/SamSequence.h | 60 -
bamtools/src/api/SamSequenceDictionary.cpp | 301 -
bamtools/src/api/SamSequenceDictionary.h | 86 -
bamtools/src/api/algorithms/Sort.h | 335 -
bamtools/src/api/api_global.h | 21 -
bamtools/src/api/internal/CMakeLists.txt | 25 -
bamtools/src/api/internal/bam/BamHeader_p.cpp | 125 -
bamtools/src/api/internal/bam/BamHeader_p.h | 71 -
bamtools/src/api/internal/bam/BamMultiMerger_p.h | 266 -
bamtools/src/api/internal/bam/BamMultiReader_p.cpp | 872 -
bamtools/src/api/internal/bam/BamMultiReader_p.h | 105 -
.../internal/bam/BamRandomAccessController_p.cpp | 289 -
.../api/internal/bam/BamRandomAccessController_p.h | 94 -
bamtools/src/api/internal/bam/BamReader_p.cpp | 470 -
bamtools/src/api/internal/bam/BamReader_p.h | 119 -
bamtools/src/api/internal/bam/BamWriter_p.cpp | 475 -
bamtools/src/api/internal/bam/BamWriter_p.h | 73 -
bamtools/src/api/internal/bam/CMakeLists.txt | 19 -
.../src/api/internal/index/BamIndexFactory_p.cpp | 107 -
.../src/api/internal/index/BamIndexFactory_p.h | 49 -
.../src/api/internal/index/BamStandardIndex_p.cpp | 965 -
.../src/api/internal/index/BamStandardIndex_p.h | 237 -
.../src/api/internal/index/BamToolsIndex_p.cpp | 642 -
bamtools/src/api/internal/index/BamToolsIndex_p.h | 186 -
bamtools/src/api/internal/index/CMakeLists.txt | 17 -
.../src/api/internal/io/BamDeviceFactory_p.cpp | 37 -
bamtools/src/api/internal/io/BamDeviceFactory_p.h | 37 -
bamtools/src/api/internal/io/BamFile_p.cpp | 69 -
bamtools/src/api/internal/io/BamFile_p.h | 51 -
bamtools/src/api/internal/io/BamFtp_p.cpp | 490 -
bamtools/src/api/internal/io/BamFtp_p.h | 91 -
bamtools/src/api/internal/io/BamHttp_p.cpp | 544 -
bamtools/src/api/internal/io/BamHttp_p.h | 91 -
bamtools/src/api/internal/io/BamPipe_p.cpp | 69 -
bamtools/src/api/internal/io/BamPipe_p.h | 46 -
bamtools/src/api/internal/io/BgzfStream_p.cpp | 469 -
bamtools/src/api/internal/io/BgzfStream_p.h | 93 -
bamtools/src/api/internal/io/ByteArray_p.cpp | 111 -
bamtools/src/api/internal/io/ByteArray_p.h | 69 -
bamtools/src/api/internal/io/CMakeLists.txt | 48 -
bamtools/src/api/internal/io/HostAddress_p.cpp | 396 -
bamtools/src/api/internal/io/HostAddress_p.h | 100 -
bamtools/src/api/internal/io/HostInfo_p.cpp | 224 -
bamtools/src/api/internal/io/HostInfo_p.h | 76 -
bamtools/src/api/internal/io/HttpHeader_p.cpp | 395 -
bamtools/src/api/internal/io/HttpHeader_p.h | 132 -
bamtools/src/api/internal/io/ILocalIODevice_p.cpp | 56 -
bamtools/src/api/internal/io/ILocalIODevice_p.h | 50 -
bamtools/src/api/internal/io/NetUnix_p.h | 39 -
bamtools/src/api/internal/io/NetWin_p.h | 60 -
bamtools/src/api/internal/io/RollingBuffer_p.cpp | 314 -
bamtools/src/api/internal/io/RollingBuffer_p.h | 87 -
bamtools/src/api/internal/io/TcpSocketEngine_p.cpp | 196 -
bamtools/src/api/internal/io/TcpSocketEngine_p.h | 103 -
.../src/api/internal/io/TcpSocketEngine_unix_p.cpp | 216 -
.../src/api/internal/io/TcpSocketEngine_win_p.cpp | 241 -
bamtools/src/api/internal/io/TcpSocket_p.cpp | 430 -
bamtools/src/api/internal/io/TcpSocket_p.h | 128 -
bamtools/src/api/internal/sam/CMakeLists.txt | 17 -
.../src/api/internal/sam/SamFormatParser_p.cpp | 202 -
bamtools/src/api/internal/sam/SamFormatParser_p.h | 61 -
.../src/api/internal/sam/SamFormatPrinter_p.cpp | 219 -
bamtools/src/api/internal/sam/SamFormatPrinter_p.h | 59 -
.../src/api/internal/sam/SamHeaderValidator_p.cpp | 524 -
.../src/api/internal/sam/SamHeaderValidator_p.h | 105 -
bamtools/src/api/internal/sam/SamHeaderVersion_p.h | 134 -
bamtools/src/api/internal/utils/BamException_p.cpp | 15 -
bamtools/src/api/internal/utils/BamException_p.h | 51 -
bamtools/src/api/internal/utils/CMakeLists.txt | 15 -
bamtools/src/shared/bamtools_global.h | 97 -
bamtools/src/third_party/CMakeLists.txt | 9 -
bamtools/src/third_party/gtest-1.6.0/CHANGES | 130 -
.../src/third_party/gtest-1.6.0/CMakeLists.txt | 240 -
bamtools/src/third_party/gtest-1.6.0/CONTRIBUTORS | 37 -
bamtools/src/third_party/gtest-1.6.0/COPYING | 28 -
bamtools/src/third_party/gtest-1.6.0/README | 424 -
.../gtest-1.6.0/cmake/internal_utils.cmake | 216 -
.../gtest-1.6.0/fused-src/gtest/gtest-all.cc | 9118 ---------
.../gtest-1.6.0/fused-src/gtest/gtest.h | 19537 -------------------
.../gtest-1.6.0/fused-src/gtest/gtest_main.cc | 39 -
.../src/third_party/gtest-1.6.0/src/gtest-all.cc | 48 -
.../gtest-1.6.0/src/gtest-death-test.cc | 1234 --
.../third_party/gtest-1.6.0/src/gtest-filepath.cc | 380 -
.../gtest-1.6.0/src/gtest-internal-inl.h | 1038 -
.../src/third_party/gtest-1.6.0/src/gtest-port.cc | 746 -
.../third_party/gtest-1.6.0/src/gtest-printers.cc | 356 -
.../third_party/gtest-1.6.0/src/gtest-test-part.cc | 110 -
.../gtest-1.6.0/src/gtest-typed-test.cc | 110 -
bamtools/src/third_party/gtest-1.6.0/src/gtest.cc | 4898 -----
.../src/third_party/gtest-1.6.0/src/gtest_main.cc | 39 -
bamtools/src/third_party/jsoncpp/CMakeLists.txt | 23 -
bamtools/src/third_party/jsoncpp/LICENSE | 55 -
bamtools/src/third_party/jsoncpp/json.h | 15 -
.../src/third_party/jsoncpp/json_batchallocator.h | 130 -
bamtools/src/third_party/jsoncpp/json_config.h | 42 -
bamtools/src/third_party/jsoncpp/json_features.h | 47 -
bamtools/src/third_party/jsoncpp/json_forwards.h | 42 -
.../src/third_party/jsoncpp/json_internalarray.inl | 453 -
.../src/third_party/jsoncpp/json_internalmap.inl | 612 -
bamtools/src/third_party/jsoncpp/json_reader.cpp | 870 -
bamtools/src/third_party/jsoncpp/json_reader.h | 201 -
bamtools/src/third_party/jsoncpp/json_tool.h | 93 -
bamtools/src/third_party/jsoncpp/json_value.cpp | 1701 --
bamtools/src/third_party/jsoncpp/json_value.h | 1059 -
.../src/third_party/jsoncpp/json_valueiterator.inl | 297 -
bamtools/src/third_party/jsoncpp/json_writer.cpp | 819 -
bamtools/src/third_party/jsoncpp/json_writer.h | 179 -
bamtools/src/toolkit/CMakeLists.txt | 44 -
bamtools/src/toolkit/bamtools.cpp | 163 -
bamtools/src/toolkit/bamtools_convert.cpp | 919 -
bamtools/src/toolkit/bamtools_convert.h | 37 -
bamtools/src/toolkit/bamtools_count.cpp | 210 -
bamtools/src/toolkit/bamtools_count.h | 37 -
bamtools/src/toolkit/bamtools_coverage.cpp | 197 -
bamtools/src/toolkit/bamtools_coverage.h | 37 -
bamtools/src/toolkit/bamtools_filter.cpp | 955 -
bamtools/src/toolkit/bamtools_filter.h | 37 -
bamtools/src/toolkit/bamtools_header.cpp | 141 -
bamtools/src/toolkit/bamtools_header.h | 38 -
bamtools/src/toolkit/bamtools_index.cpp | 126 -
bamtools/src/toolkit/bamtools_index.h | 37 -
bamtools/src/toolkit/bamtools_merge.cpp | 241 -
bamtools/src/toolkit/bamtools_merge.h | 37 -
bamtools/src/toolkit/bamtools_random.cpp | 285 -
bamtools/src/toolkit/bamtools_random.h | 37 -
bamtools/src/toolkit/bamtools_resolve.cpp | 1414 --
bamtools/src/toolkit/bamtools_resolve.h | 42 -
bamtools/src/toolkit/bamtools_revert.cpp | 194 -
bamtools/src/toolkit/bamtools_revert.h | 37 -
bamtools/src/toolkit/bamtools_sort.cpp | 375 -
bamtools/src/toolkit/bamtools_sort.h | 37 -
bamtools/src/toolkit/bamtools_split.cpp | 600 -
bamtools/src/toolkit/bamtools_split.h | 38 -
bamtools/src/toolkit/bamtools_stats.cpp | 307 -
bamtools/src/toolkit/bamtools_stats.h | 37 -
bamtools/src/toolkit/bamtools_tool.h | 35 -
bamtools/src/toolkit/bamtools_version.h.in | 20 -
bamtools/src/utils/CMakeLists.txt | 30 -
bamtools/src/utils/bamtools_fasta.cpp | 623 -
bamtools/src/utils/bamtools_fasta.h | 47 -
bamtools/src/utils/bamtools_filter_engine.h | 552 -
bamtools/src/utils/bamtools_filter_properties.h | 195 -
bamtools/src/utils/bamtools_filter_ruleparser.h | 319 -
bamtools/src/utils/bamtools_options.cpp | 287 -
bamtools/src/utils/bamtools_options.h | 213 -
bamtools/src/utils/bamtools_pileup_engine.cpp | 346 -
bamtools/src/utils/bamtools_pileup_engine.h | 95 -
bamtools/src/utils/bamtools_utilities.cpp | 333 -
bamtools/src/utils/bamtools_utilities.h | 65 -
bamtools/src/utils/bamtools_variant.h | 128 -
bamtools/src/utils/utils_global.h | 21 -
debian/copyright | 1 +
debian/rules | 4 +
debian/watch | 8 +-
intervaltree/.gitignore | 1 -
intervaltree/IntervalTree.h | 215 -
intervaltree/LICENSE | 19 -
intervaltree/Makefile | 7 -
intervaltree/README | 41 -
intervaltree/interval_tree_test.cpp | 81 -
src/Allele.cpp | 3 +-
src/AlleleParser.cpp | 3 +
src/Ewens.cpp | 4 +-
src/version_git.h | 2 +-
src/version_release.txt | 6 +-
vcflib/.gitignore | 107 -
vcflib/.gitmodules | 21 -
vcflib/LICENSE | 19 -
vcflib/Makefile | 154 -
vcflib/README.md | 639 -
vcflib/bin/plot_roc.r | 153 -
vcflib/bin/vcf2sqlite.py | 130 -
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vcflib/bin/vcfmultiallelic | 20 -
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vcflib/bin/vcfsort | 3 -
vcflib/bin/vcfvarstats | 225 -
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vcflib/fastahack/FastaHack.cpp | 179 -
vcflib/fastahack/LargeFileSupport.h | 16 -
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vcflib/fastahack/README | 63 -
vcflib/fastahack/Region.h | 51 -
vcflib/fastahack/disorder.c | 192 -
vcflib/fastahack/disorder.h | 62 -
vcflib/fastahack/libdisorder.LICENSE | 339 -
vcflib/fastahack/split.cpp | 33 -
vcflib/fastahack/split.h | 20 -
vcflib/fastahack/tests/correct.fasta | 30 -
vcflib/fastahack/tests/embedded_newline.fasta | 35 -
vcflib/fastahack/tests/mismatched_lines.fasta | 30 -
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vcflib/filevercmp/Makefile | 13 -
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vcflib/fsom/Makefile | 5 -
vcflib/fsom/README | 0
vcflib/fsom/convert.h | 22 -
vcflib/fsom/example.c | 121 -
vcflib/fsom/fsom.c | 988 -
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vcflib/smithwaterman/libdisorder.LICENSE | 339 -
vcflib/smithwaterman/smithwaterman.cpp | 246 -
vcflib/src/BedReader.h | 176 -
vcflib/src/Variant.cpp | 2199 ---
vcflib/src/Variant.h | 495 -
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vcflib/src/ssw_cpp.cpp | 399 -
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vcflib/src/vcf2fasta.cpp | 264 -
vcflib/src/vcf2tsv.cpp | 241 -
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vcflib/src/vcfallelicprimitives.cpp | 341 -
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vcflib/src/vcfcheck.cpp | 139 -
vcflib/src/vcfclassify.cpp | 162 -
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vcflib/src/vcfevenregions.cpp | 202 -
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vcflib/src/vcfsamplediff.cpp | 200 -
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vcflib/src/vcfsitesummarize.cpp | 94 -
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vcflib/src/vcfstats.cpp | 570 -
vcflib/src/vcfstreamsort.cpp | 143 -
vcflib/src/vcfuniq.cpp | 49 -
vcflib/src/vcfuniqalleles.cpp | 54 -
vcflib/tabixpp/ChangeLog | 593 -
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vcflib/tabixpp/TabixReader.java | 395 -
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vcflib/tabixpp/example.gtf.gz | Bin 3778 -> 0 bytes
vcflib/tabixpp/example.gtf.gz.tbi | Bin 259 -> 0 bytes
vcflib/tabixpp/index.c | 998 -
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411 files changed, 29 insertions(+), 109186 deletions(-)
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delete mode 100644 vcflib/tabixpp/perl/Tabix.xs
delete mode 100644 vcflib/tabixpp/perl/TabixIterator.pm
delete mode 100644 vcflib/tabixpp/perl/t/01local.t
delete mode 100644 vcflib/tabixpp/perl/t/02remote.t
delete mode 100644 vcflib/tabixpp/perl/typemap
delete mode 100644 vcflib/tabixpp/python/setup.py
delete mode 100644 vcflib/tabixpp/python/tabixmodule.c
delete mode 100755 vcflib/tabixpp/python/test.py
delete mode 100644 vcflib/tabixpp/tabix.1
delete mode 100644 vcflib/tabixpp/tabix.cpp
delete mode 100644 vcflib/tabixpp/tabix.h
delete mode 100644 vcflib/tabixpp/tabix.hpp
delete mode 100755 vcflib/tabixpp/tabix.py
delete mode 100644 vcflib/tabixpp/tabix.tex
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