This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository bedtools.
commit 7b6b2d6f0d1c5cd226f6baa6df52facb25ae76eb Merge: 68dfd72 4122ba1 Author: Charles Plessy <[email protected]> Date: Sat May 24 21:48:23 2014 +0900 Merge tag 'v2.20.1' into debian/unstable Makefile | 7 +- README.md | 4 +- RELEASE_HISTORY | 7 + docs/conf.py | 6 +- RELEASE_HISTORY => docs/content/history.rst | 482 +++++----- docs/content/installation.rst | 2 +- docs/content/tools/jaccard.rst | 3 + docs/content/tools/map.rst | 2 - docs/content/tools/merge.rst | 169 ++-- docs/content/tools/unionbedg.rst | 28 +- docs/index.rst | 3 +- src/intersectFile/intersectFile.cpp | 3 +- src/jaccard/Jaccard.cpp | 94 ++ src/{mapFile/mapFile.h => jaccard/Jaccard.h} | 38 +- src/jaccard/Makefile | 29 +- src/jaccard/jaccard.cpp | 110 --- src/jaccard/jaccard.h | 70 -- src/jaccard/jaccardMain.cpp | 240 +++-- src/mapFile/mapFile.h | 1 - src/mapFile/mapMain.cpp | 18 +- src/mergeBed/Makefile | 35 - src/mergeBed/mergeBed.cpp | 359 ------- src/mergeBed/mergeBed.h | 72 -- src/mergeBed/mergeMain.cpp | 184 ---- src/mergeFile/Makefile | 46 + src/mergeFile/mergeFile.cpp | 39 + src/mergeFile/mergeFile.h | 37 + src/mergeFile/mergeMain.cpp | 80 ++ src/nekSandbox1/nekSandboxMain.cpp | 6 +- src/nucBed/nucBed.cpp | 6 +- src/sampleFile/SampleFile.cpp | 2 +- src/shuffleBed/shuffleBed.cpp | 51 +- src/shuffleBed/shuffleBedMain.cpp | 2 - src/slopBed/slopBed.cpp | 34 +- src/utils/BamTools/src/api/BamAlignment.h | 2 +- src/utils/BamTools/src/api/SamHeader.h | 4 +- .../src/api/internal/io/TcpSocketEngine_p.h | 2 +- .../src/api/internal/sam/SamHeaderValidator_p.h | 4 +- src/utils/BinTree/BinTree.cpp | 9 +- src/utils/BlockedIntervals/BlockedIntervals.cpp | 6 +- src/utils/Contexts/ContextBase.cpp | 66 +- src/utils/Contexts/ContextBase.h | 47 +- src/utils/Contexts/ContextJaccard.cpp | 109 +++ src/utils/Contexts/ContextJaccard.h | 25 + src/utils/Contexts/ContextMap.cpp | 10 - src/utils/Contexts/ContextMap.h | 5 - src/utils/Contexts/ContextMerge.cpp | 176 ++++ src/utils/Contexts/ContextMerge.h | 31 + src/utils/Contexts/Makefile | 9 +- .../FileRecordTools/FileReaders/BamFileReader.cpp | 10 + .../FileRecordTools/FileReaders/BamFileReader.h | 4 +- .../FileReaders/BufferedStreamMgr.cpp | 30 +- .../FileRecordTools/FileReaders/InputStreamMgr.cpp | 21 +- .../FileRecordTools/FileReaders/InputStreamMgr.h | 7 +- .../FileReaders/SingleLineDelimTextFileReader.cpp | 6 +- src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 217 +++++ src/utils/FileRecordTools/FileRecordMergeMgr.h | 58 ++ src/utils/FileRecordTools/FileRecordMgr.cpp | 186 +--- src/utils/FileRecordTools/FileRecordMgr.h | 79 +- src/utils/FileRecordTools/Makefile | 10 +- src/utils/FileRecordTools/Records/BamRecord.cpp | 209 ++-- src/utils/FileRecordTools/Records/BamRecord.h | 27 +- src/utils/FileRecordTools/Records/BlockMgr.cpp | 16 +- src/utils/FileRecordTools/Records/BlockMgr.h | 3 + src/utils/FileRecordTools/Records/EmptyRecord.cpp | 34 + src/utils/FileRecordTools/Records/EmptyRecord.h | 30 + src/utils/FileRecordTools/Records/Makefile | 12 +- src/utils/FileRecordTools/Records/Record.h | 5 +- src/utils/FileRecordTools/Records/RecordMgr.cpp | 24 + src/utils/FileRecordTools/Records/RecordMgr.h | 1 + src/utils/FileRecordTools/Records/StrandQueue.cpp | 131 +++ src/utils/FileRecordTools/Records/StrandQueue.h | 47 + .../FileRecordTools/Records/recordsTar.tar.gz | Bin 54443 -> 0 bytes src/utils/GenomeFile/NewGenomeFile.cpp | 12 +- src/utils/KeyListOps/KeyListOps.cpp | 142 ++- src/utils/KeyListOps/KeyListOps.h | 20 + src/utils/KeyListOps/KeyListOpsMethods.cpp | 21 +- src/utils/KeyListOps/KeyListOpsMethods.h | 13 +- src/utils/NewChromsweep/NewChromsweep.cpp | 10 +- src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +- src/utils/RecordOutputMgr/RecordOutputMgr.h | 1 + src/utils/bedFile/bedFile.cpp | 14 + src/utils/bedFile/bedFile.h | 4 + src/utils/fileType/FileRecordTypeChecker.cpp | 56 +- src/utils/fileType/FileRecordTypeChecker.h | 19 +- src/utils/fileType/fileType.cpp | 2 +- src/utils/general/DualQueue.h | 124 --- src/utils/general/Makefile | 6 +- src/utils/general/ParseTools.cpp | 34 +- src/utils/general/ParseTools.h | 4 +- src/utils/general/QuickString.h | 1 + src/utils/general/Tokenizer.cpp | 102 ++ src/utils/general/Tokenizer.h | 57 ++ src/utils/version/version_release.txt | 6 +- test/general/test-general.sh | 204 +++- test/intersect/dosLineCharWithExtraTab_b.bed | 4 + test/intersect/dosLineChar_a.bed | 3 + test/intersect/headerOnly.vcf | 121 +++ test/intersect/new_test-intersect.sh | 104 +- test/intersect/oneRecordNoNewline.bed | 1 + test/jaccard/a.bam | Bin 0 -> 1796 bytes test/jaccard/aMixedStrands.bed | 12 + test/jaccard/bMixedStrands.bed | 6 + test/jaccard/e.bed | 1 + test/jaccard/test-jaccard.sh | 82 +- test/jaccard/three_blocks_match.bam | Bin 0 -> 1804 bytes test/jaccard/three_blocks_match.bed | 1 + test/map/d.bed | 2 + test/map/fullFields.bam | Bin 0 -> 25813 bytes test/map/test-map.sh | 44 +- test/merge/a.full.bam | Bin 0 -> 1836 bytes test/merge/a.gff | 6 + test/merge/b.bed | 7 + test/merge/bamCol10Collapse.txt | 112 +++ test/merge/bamCol11Collapse.txt | 112 +++ test/merge/bamCol1Collapse.txt | 112 +++ test/merge/bamCol3Collapse.txt | 112 +++ test/merge/bamCol4Mean.txt | 112 +++ test/merge/bamCol5Mean.txt | 112 +++ test/merge/bamCol6Collapse.txt | 112 +++ test/merge/bamCol7Collapse.txt | 112 +++ test/merge/bamCol8Mean.txt | 112 +++ test/merge/bamCol9Mean.txt | 112 +++ test/merge/fullFields.bam | Bin 0 -> 25813 bytes test/merge/mergeBugTest.bed | 12 + test/merge/mixedStrands.bed | 12 + test/merge/precisionTest.bed | 10 + test/merge/test-merge.sh | 391 ++++++-- test/merge/testA.vcf | 129 +++ test/merge/unsorted.bed | 7 + test/sample/test-sample.sh | 11 +- test/shuffle/excl.bed | 9 + test/shuffle/incl.bed | 9 + test/shuffle/simrep.bed | 1000 ++++++++++++++++++++ test/shuffle/test-shuffle.sh | 127 +++ test/slop/test-slop.sh | 21 + test/test.sh | 3 + 137 files changed, 5966 insertions(+), 2116 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
