This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository bedtools.
commit 854dcc20c00ca7139e502cd68d52b050e215d41a Merge: b0cdd10 1e16d52 Author: Charles Plessy <[email protected]> Date: Thu Jul 7 13:52:21 2016 +0900 Merge tag 'v2.26.0' into debian/unstable Makefile | 29 +- README.md | 15 +- docs/conf.py | 8 +- docs/content/bedtools-suite.rst | 1 + docs/content/history.rst | 21 + .../images/tool-glyphs/barski_binding_site.png | Bin 0 -> 346688 bytes docs/content/images/tool-glyphs/closest-glyph.png | Bin 138680 -> 138349 bytes docs/content/installation.rst | 22 +- docs/content/overview.rst | 1 + docs/content/tools/genomecov.rst | 28 +- docs/content/tools/getfasta.rst | 54 +- docs/content/tools/shift.rst | 118 ++++ docs/index.rst | 4 +- genomes/human.hg18.genome | 1 + genomes/human.hg19.genome | 1 + genomes/human.hg38.genome | 1 + genomes/mouse.mm10.genome | 67 +++ genomes/mouse.mm10.genome.txt | 66 --- genomes/mouse.mm8.genome | 1 + genomes/mouse.mm9.genome | 2 +- scripts/makeBashScripts.py | 1 + src/annotateBed/annotateBed.cpp | 2 +- src/bedToBam/bedToBam.cpp | 2 +- src/bedpeToBam/bedpeToBam.cpp | 2 +- src/bedtools.cpp | 9 +- src/closestFile/Makefile | 1 + src/complementFile/Makefile | 1 + src/complementFile/complementFile.cpp | 33 +- src/complementFile/complementFile.h | 5 +- src/coverageFile/Makefile | 1 + src/coverageFile/coverageFile.cpp | 3 - src/coverageFile/coverageFile.h | 1 + src/fastaFromBed/fastaFromBed.cpp | 103 ++-- src/fastaFromBed/fastaFromBed.h | 6 +- src/fastaFromBed/fastaFromBedMain.cpp | 35 +- src/fisher/fisher.cpp | 2 +- src/fisher/kfunc.cpp | 2 +- src/genomeCoverageBed/genomeCoverageBed.cpp | 57 +- src/genomeCoverageBed/genomeCoverageBed.h | 5 + src/genomeCoverageBed/genomeCoverageMain.cpp | 27 + src/groupBy/Makefile | 1 + src/groupBy/groupBy.cpp | 8 +- src/intersectFile/Makefile | 1 + src/intersectFile/intersectFile.cpp | 28 +- src/jaccard/Makefile | 1 + src/mapFile/Makefile | 1 + src/mergeFile/Makefile | 1 + src/regressTest/RegressTest.cpp | 2 +- src/sampleFile/Makefile | 1 + src/sampleFile/sampleFile.cpp | 2 +- src/shiftBed/Makefile | 35 ++ src/shiftBed/shiftBed.cpp | 77 +++ src/shiftBed/shiftBed.h | 57 ++ src/shiftBed/shiftBedMain.cpp | 179 ++++++ src/shuffleBed/shuffleBed.cpp | 112 ++-- src/shuffleBed/shuffleBed.h | 6 +- src/shuffleBed/shuffleBedMain.cpp | 2 + src/slopBed/slopBed.cpp | 75 ++- src/spacingFile/Makefile | 1 + src/split/splitBed.cpp | 11 +- src/subtractFile/Makefile | 2 +- src/subtractFile/subtractFile.cpp | 16 +- src/utils/BinTree/BinTree.cpp | 5 +- src/utils/BinTree/BinTree.h | 4 +- src/utils/BinTree/Makefile | 1 + src/utils/Contexts/ContextBase.cpp | 43 +- src/utils/Contexts/ContextBase.h | 5 +- src/utils/Contexts/ContextCoverage.cpp | 1 + src/utils/Contexts/ContextGroupBy.cpp | 2 +- src/utils/Contexts/ContextIntersect.cpp | 27 +- src/utils/Contexts/ContextIntersect.h | 10 + src/utils/Contexts/ContextJaccard.cpp | 20 - src/utils/Contexts/ContextMerge.cpp | 11 +- src/utils/Contexts/Makefile | 1 + .../FileReaders/BufferedStreamMgr.cpp | 2 +- src/utils/FileRecordTools/FileReaders/Makefile | 3 +- .../FileReaders/SingleLineDelimTextFileReader.cpp | 98 ++-- .../FileReaders/SingleLineDelimTextFileReader.h | 2 + src/utils/FileRecordTools/FileRecordMgr.cpp | 11 +- src/utils/FileRecordTools/FileRecordMgr.h | 2 + src/utils/FileRecordTools/Makefile | 1 + .../FileRecordTools/Records/Bed12Interval.cpp | 16 +- src/utils/FileRecordTools/Records/Bed12Interval.h | 3 +- src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 - src/utils/FileRecordTools/Records/Bed4Interval.cpp | 2 +- src/utils/FileRecordTools/Records/BlockMgr.cpp | 18 +- src/utils/FileRecordTools/Records/BlockMgr.h | 3 +- src/utils/FileRecordTools/Records/GffPlusRecord.h | 2 +- src/utils/FileRecordTools/Records/GffRecord.cpp | 2 +- src/utils/FileRecordTools/Records/GffRecord.h | 1 + src/utils/FileRecordTools/Records/Makefile | 3 +- src/utils/FileRecordTools/Records/PlusFields.h | 4 +- src/utils/FileRecordTools/Records/Record.cpp | 3 - src/utils/FileRecordTools/Records/Record.h | 3 + .../FileRecordTools/Records/RecordKeyList.cpp | 6 +- src/utils/FileRecordTools/Records/RecordKeyList.h | 6 +- .../FileRecordTools/Records/RecordKeyVector.cpp | 6 +- .../FileRecordTools/Records/RecordKeyVector.h | 6 +- src/utils/FileRecordTools/Records/VcfRecord.h | 1 + src/utils/GenomeFile/NewGenomeFile.cpp | 4 +- src/utils/KeyListOps/KeyListOps.cpp | 11 +- src/utils/KeyListOps/KeyListOpsMethods.cpp | 28 +- src/utils/KeyListOps/Makefile | 1 + src/utils/NewChromsweep/CloseSweep.cpp | 326 ++++++----- src/utils/NewChromsweep/CloseSweep.h | 39 +- src/utils/NewChromsweep/Makefile | 1 + src/utils/NewChromsweep/NewChromsweep.cpp | 623 +++++++++++---------- src/utils/RecordOutputMgr/Makefile | 1 + src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 130 ++--- src/utils/RecordOutputMgr/RecordOutputMgr.h | 3 +- src/utils/ToolBase/Makefile | 1 + src/utils/bedFile/bedFile.cpp | 123 ++-- src/utils/bedFile/bedFile.h | 11 +- src/utils/bedFilePE/bedFilePE.cpp | 8 - src/utils/driver/Makefile | 1 + src/utils/fileType/FileRecordTypeChecker.cpp | 58 +- src/utils/fileType/FileRecordTypeChecker.h | 1 + src/utils/general/ParseTools.cpp | 18 +- src/utils/general/ParseTools.h | 3 +- src/utils/general/Tokenizer.cpp | 150 ++--- src/utils/general/Tokenizer.h | 9 +- src/utils/version/version_release.txt | 6 +- src/windowMaker/windowMaker.cpp | 36 +- src/windowMaker/windowMakerMain.cpp | 7 +- test/closest/bug281_a.flip.medium.bed | 2 + test/closest/bug281_a.medium.bed | 2 + test/closest/bug281_b.bed | 4 + test/closest/bug281_b.flip.bed | 4 + test/closest/dmr.bed | 1 + test/closest/islands.2.bed | 1 + test/closest/islands.bed | 1 + test/closest/kclosest/test-kclosest.sh | 4 +- test/closest/null_a.bed | 4 + test/closest/null_b.bed | 1 + test/closest/null_c.bed | 1 + test/closest/shores.bed | 1 + test/closest/test-closest.sh | 148 +++++ test/closest/tfbs.bed | 1 + test/complement/test-complement.sh | 116 ++++ test/coverage/c.bed | 2 + test/coverage/one_block.bam | Bin 0 -> 234 bytes test/coverage/sam-w-del.bam | Bin 0 -> 225 bytes test/coverage/test-coverage.sh | 209 ++++++- test/coverage/three_blocks.bam | Bin 0 -> 239 bytes test/coverage/three_blocks_match.bam | Bin 0 -> 1804 bytes test/coverage/two_blocks.bam | Bin 0 -> 237 bytes test/coverage/x.bed | 3 + test/coverage/y.bed | 1 + test/fisher/get.sh | 2 + test/fisher/test-fisher.sh | 2 +- test/general/test-general.sh | 19 +- test/genomecov/chip.sam | 4 + test/genomecov/genome.txt | 3 + test/genomecov/pair-chip.sam | 4 + test/genomecov/test-genomecov.sh | 23 +- test/getfasta/test-getfasta.sh | 58 +- test/groupBy/test-groupby.sh | 9 + test/intersect/a.issue311.bed | 1 + test/intersect/b.issue311.gff | 1 + test/intersect/b.issue311.vcf | 3 + test/intersect/blocks.bed12 | 4 + test/intersect/bug223_e.vcf | 3 +- test/intersect/gdc.gff | 24 +- test/intersect/new_test-intersect.sh | 82 ++- test/intersect/null_a.bed | 4 + test/intersect/null_b.bed | 1 + test/intersect/null_c.bed | 1 + test/intersect/test-intersect.sh | 185 +++++- test/makewindows/a.19bp.bed | 1 + test/makewindows/a.20bp.bed | 1 + test/makewindows/a.33bp.bed | 1 + test/makewindows/test-makewindows.sh | 84 ++- test/map/.RData | Bin 0 -> 77 bytes test/map/.Rhistory | 6 + test/map/test-map.sh | 20 +- test/map/test.gff | 12 +- test/merge/test-merge.sh | 16 +- test/{slop => shift}/a.bed | 0 test/shift/test-shift.sh | 115 ++++ test/shift/tiny.genome | 1 + test/shuffle/incl.sizedif.bed | 4 + test/shuffle/test-shuffle.sh | 9 + test/slop/a.bed | 1 - test/test.sh | 3 + tutorial/bedtools.html | 2 +- 185 files changed, 3232 insertions(+), 1274 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
