This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository bedtools.
commit 856a5fd43cbb9b4c694cdc1421426a7fb71ef0e7 Merge: 08063ad 4356ace Author: Charles Plessy <[email protected]> Date: Fri Sep 19 10:03:30 2014 +0900 Merge tag 'v2.21.0' into debian/unstable Makefile | 5 +- RELEASE_HISTORY | 86 ++- docs/_static/labibi.css | 9 - docs/bedtools.swiss.png | Bin 0 -> 8133 bytes docs/conf.py | 2 +- docs/content/bedtools-suite.rst | 3 +- docs/content/history.rst | 12 + .../content/images/tool-glyphs/intersect-glyph.png | Bin 34437 -> 94521 bytes docs/content/installation.rst | 48 +- docs/content/overview.rst | 2 +- docs/content/tools/coverage.rst | 9 +- docs/content/tools/fisher.rst | 119 ++++ docs/content/tools/intersect.rst | 222 +++++- docs/templates/page.html | 7 +- docs/templates/sidebar-intro.html | 11 +- genomes/human.hg38.genome | 455 ++++++++++++ src/bedtools.cpp | 3 + src/fisher/Fisher.cpp | 112 +++ src/fisher/Fisher.h | 30 + src/fisher/Makefile | 49 ++ src/fisher/fisherMain.cpp | 72 ++ src/fisher/kfunc.c | 253 +++++++ src/intersectFile/intersectFile.cpp | 14 +- src/intersectFile/intersectFile.h | 6 +- src/intersectFile/intersectMain.cpp | 18 +- src/jaccard/Jaccard.cpp | 12 +- src/jaccard/Jaccard.h | 2 +- src/mapFile/mapFile.cpp | 6 +- src/mapFile/mapFile.h | 4 +- src/mapFile/mapMain.cpp | 3 +- src/mergeFile/mergeFile.cpp | 2 +- src/nekSandbox1/nekSandboxMain.cpp | 2 - src/regressTest/RegressTest.h | 5 +- src/sampleFile/SampleFile.h | 4 +- src/slopBed/slopBed.cpp | 8 +- src/subtractBed/subtractBed.cpp | 2 +- .../BamTools/src/api/internal/io/HostInfo_p.cpp | 3 + .../src/api/internal/io/TcpSocketEngine_unix_p.cpp | 4 +- src/utils/BinTree/BinTree.cpp | 38 +- src/utils/BinTree/BinTree.h | 11 +- src/utils/Contexts/ContextBase.cpp | 99 ++- src/utils/Contexts/ContextBase.h | 51 +- src/utils/Contexts/ContextFisher.cpp | 115 ++++ src/utils/Contexts/ContextFisher.h | 26 + src/utils/Contexts/ContextIntersect.cpp | 58 +- src/utils/Contexts/ContextIntersect.h | 18 +- src/utils/Contexts/ContextMap.cpp | 14 + src/utils/Contexts/ContextMap.h | 2 + src/utils/Contexts/Makefile | 7 +- src/utils/Fasta/Fasta.cpp | 6 +- .../FileRecordTools/FileReaders/BamFileReader.h | 2 - .../FileReaders/BufferedStreamMgr.cpp | 4 +- .../FileReaders/BufferedStreamMgr.h | 7 +- .../FileRecordTools/FileReaders/FileReader.cpp | 2 +- src/utils/FileRecordTools/FileReaders/FileReader.h | 8 +- .../FileRecordTools/FileReaders/InputStreamMgr.h | 4 +- src/utils/FileRecordTools/FileReaders/Makefile | 6 +- .../FileReaders/{Makefile => Makefile~} | 0 .../FileReaders/SingleLineDelimTextFileReader.h | 2 - .../FileReaders/SingleLineDelimTransferBuffer.cpp | 2 + .../FileReaders/SingleLineDelimTransferBuffer.h | 2 - src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 16 +- src/utils/FileRecordTools/FileRecordMergeMgr.h | 8 +- src/utils/FileRecordTools/FileRecordMgr.cpp | 11 +- src/utils/FileRecordTools/FileRecordMgr.h | 18 +- src/utils/FileRecordTools/Records/BamRecord.cpp | 15 +- src/utils/FileRecordTools/Records/BamRecord.h | 10 +- src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 + src/utils/FileRecordTools/Records/BlockMgr.cpp | 38 +- src/utils/FileRecordTools/Records/BlockMgr.h | 19 +- src/utils/FileRecordTools/Records/GffRecord.cpp | 1 + src/utils/FileRecordTools/Records/Makefile | 14 +- src/utils/FileRecordTools/Records/Record.cpp | 34 +- src/utils/FileRecordTools/Records/Record.h | 19 +- src/utils/FileRecordTools/Records/RecordKeyList.h | 13 +- .../FileRecordTools/Records/RecordKeyVector.cpp | 88 +++ .../FileRecordTools/Records/RecordKeyVector.h | 62 ++ src/utils/FileRecordTools/Records/RecordList.cpp | 202 ++++++ src/utils/FileRecordTools/Records/RecordList.h | 117 ++++ src/utils/FileRecordTools/Records/StrandQueue.h | 6 +- src/utils/FileRecordTools/Records/VcfRecord.cpp | 5 +- src/utils/GenomeFile/NewGenomeFile.cpp | 17 +- src/utils/GenomeFile/NewGenomeFile.h | 2 +- src/utils/KeyListOps/KeyListOps.cpp | 2 +- src/utils/KeyListOps/KeyListOps.h | 4 +- src/utils/KeyListOps/KeyListOpsMethods.cpp | 6 +- src/utils/KeyListOps/KeyListOpsMethods.h | 16 +- src/utils/NewChromsweep/NewChromsweep.cpp | 221 +++--- src/utils/NewChromsweep/NewChromsweep.h | 63 +- src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +- src/utils/RecordOutputMgr/RecordOutputMgr.h | 17 +- src/utils/fileType/FileRecordTypeChecker.cpp | 1 + src/utils/fileType/FileRecordTypeChecker.h | 6 +- src/utils/general/CommonHelp.cpp | 17 + src/utils/general/CommonHelp.h | 19 + src/utils/general/CompressionTools.h | 2 - src/utils/general/FreeList.h | 4 +- src/utils/general/Makefile | 7 +- src/utils/general/ParseTools.h | 4 +- src/utils/general/PushBackStreamBuf.h | 6 +- src/utils/general/QuickString.cpp | 5 + src/utils/general/QuickString.h | 4 +- src/utils/general/Tokenizer.h | 4 +- src/utils/version/version_release.txt | 6 +- test/general/test-general.sh | 2 +- test/intersect/multi_intersect/d1.bed | 9 + test/intersect/multi_intersect/d2.bed | 6 + test/intersect/multi_intersect/d3.bed | 3 + test/intersect/multi_intersect/d4.bed | 9 + test/intersect/multi_intersect/d5.bed | 6 + test/intersect/multi_intersect/d6.bed | 3 + test/intersect/multi_intersect/d7.bed | 10 + test/intersect/multi_intersect/d8.bed | 7 + test/intersect/multi_intersect/d9.bed | 4 + test/intersect/multi_intersect/g.bed | 3 + test/intersect/multi_intersect/query.bed | 12 + test/intersect/multi_intersect/query2.bed | 13 + test/intersect/multi_intersect/query3.bed | 13 + .../multi_intersect/test-multi_intersect.sh | 404 +++++++++++ test/intersect/new_test-intersect.sh~ | 766 +++++++++++++++++++++ test/intersect/performanceTest.sh | 2 +- test/intersect/test-intersect.sh | 7 +- test/merge/test-merge.sh | 69 ++ test/slop/test-slop.sh | 8 +- 124 files changed, 4140 insertions(+), 468 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
