This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository bedtools.
commit e3786564e0811e3a37686f75f8f79e517c5a299b Merge: 9213f1b 1d7b0cd Author: Charles Plessy <[email protected]> Date: Fri Sep 4 16:32:44 2015 +0200 Merge tag 'v2.25.0' into debian/unstable Conflicts: src/utils/FileRecordTools/FileReaders/Makefile~ This file was deleted by mistake in the commit f62bafa2b4b0b91e39fcec94a0c6c825dc3e0ee2. Makefile | 10 +- README.md | 2 +- docs/conf.py | 4 +- docs/content/history.rst | 20 +- docs/content/images/tool-glyphs/random-glyph.ai | 6467 ++++++++++++++++++++ docs/content/images/tool-glyphs/random-glyph.png | Bin 0 -> 30097 bytes docs/content/tools/coverage.rst | 2 + docs/content/tools/intersect.rst | 3 + docs/content/tools/jaccard.rst | 7 +- docs/content/tools/map.rst | 6 +- docs/content/tools/subtract.rst | 6 +- scripts/vcfsort.sh | 13 + src/annotateBed/Makefile | 2 +- src/bamToBed/Makefile | 2 +- src/bamToFastq/Makefile | 2 +- src/bed12ToBed6/Makefile | 2 +- src/bedToBam/Makefile | 2 +- src/bedToIgv/Makefile | 2 +- src/bedpeToBam/Makefile | 2 +- src/bedtools.cpp | 13 +- src/closestFile/Makefile | 2 +- src/clusterBed/Makefile | 2 +- src/complementBed/Makefile | 38 - src/complementBed/complementBed.cpp | 84 - src/complementBed/complementBed.h | 47 - src/complementBed/complementMain.cpp | 114 - src/{jaccard => complementFile}/Makefile | 13 +- src/complementFile/complementFile.cpp | 127 + src/complementFile/complementFile.h | 54 + src/complementFile/complementHelp.cpp | 36 + src/coverageFile/coverageFile.cpp | 43 +- src/coverageFile/coverageFile.h | 1 + src/coverageFile/coverageHelp.cpp | 2 + src/expand/Makefile | 2 +- src/fastaFromBed/Makefile | 2 +- src/fisher/Makefile | 2 +- src/flankBed/Makefile | 2 +- src/genomeCoverageBed/Makefile | 2 +- src/genomeCoverageBed/genomeCoverageBed.cpp | 55 +- src/genomeCoverageBed/genomeCoverageBed.h | 8 +- src/getOverlap/Makefile | 2 +- src/groupBy/Makefile | 38 +- src/groupBy/groupBy.cpp | 728 +-- src/groupBy/groupBy.h | 41 + src/groupBy/groupByHelp.cpp | 92 + src/intersectFile/Makefile | 2 +- src/jaccard/Makefile | 2 +- src/linksBed/Makefile | 2 +- src/mapFile/Makefile | 2 +- src/maskFastaFromBed/Makefile | 2 +- src/mergeFile/Makefile | 2 +- src/multiBamCov/Makefile | 2 +- src/multiIntersectBed/Makefile | 2 +- src/nekSandbox1/Makefile | 2 +- src/nucBed/Makefile | 2 +- src/pairToBed/Makefile | 2 +- src/pairToPair/Makefile | 2 +- src/randomBed/Makefile | 2 +- src/regressTest/Makefile | 6 +- src/reldist/Makefile | 2 +- src/sampleFile/Makefile | 2 +- src/shuffleBed/Makefile | 2 +- src/slopBed/Makefile | 2 +- src/sortBed/Makefile | 2 +- src/sortBed/sortBed.cpp | 24 +- src/spacingFile/Makefile | 2 +- src/spacingFile/spacingFile.cpp | 5 +- src/split/Makefile | 2 +- src/subtractFile/subtractFile.cpp | 2 +- src/tagBam/Makefile | 2 +- src/unionBedGraphs/Makefile | 2 +- src/utils/BamTools-Ancillary/Makefile | 2 +- src/utils/BamTools/Makefile | 2 +- src/utils/BinTree/BinTree.cpp | 12 +- src/utils/BinTree/Makefile | 2 +- src/utils/BlockedIntervals/Makefile | 2 +- src/utils/Contexts/ContextBase.cpp | 30 +- src/utils/Contexts/ContextBase.h | 18 +- src/utils/Contexts/ContextClosest.cpp | 11 - src/utils/Contexts/ContextComplement.cpp | 31 + src/utils/Contexts/ContextComplement.h | 24 + src/utils/Contexts/ContextCoverage.cpp | 18 +- src/utils/Contexts/ContextCoverage.h | 4 +- src/utils/Contexts/ContextGroupBy.cpp | 138 + src/utils/Contexts/ContextGroupBy.h | 40 + src/utils/Contexts/ContextIntersect.cpp | 48 +- src/utils/Contexts/ContextIntersect.h | 23 +- src/utils/Contexts/Makefile | 13 +- src/utils/Fasta/Makefile | 2 +- .../FileReaders/BufferedStreamMgr.cpp | 2 +- .../FileReaders/BufferedStreamMgr.h | 2 +- .../FileRecordTools/FileReaders/InputStreamMgr.h | 5 +- src/utils/FileRecordTools/FileReaders/Makefile | 2 +- .../FileReaders/{Makefile => Makefile~} | 8 +- .../FileReaders/SingleLineDelimTextFileReader.cpp | 13 +- .../FileReaders/SingleLineDelimTextFileReader.h | 3 +- src/utils/FileRecordTools/FileRecordMgr.cpp | 26 +- src/utils/FileRecordTools/FileRecordMgr.h | 6 +- src/utils/FileRecordTools/Makefile | 4 +- src/utils/FileRecordTools/Records/Bed3Interval.h | 2 +- .../FileRecordTools/Records/BedPlusInterval.cpp | 117 +- .../FileRecordTools/Records/BedPlusInterval.h | 24 +- .../FileRecordTools/Records/GffPlusRecord.cpp | 70 + src/utils/FileRecordTools/Records/GffPlusRecord.h | 46 + src/utils/FileRecordTools/Records/GffRecord.cpp | 8 +- src/utils/FileRecordTools/Records/GffRecord.h | 7 +- src/utils/FileRecordTools/Records/Makefile | 21 +- .../FileRecordTools/Records/NoPosPlusRecord.cpp | 42 + .../FileRecordTools/Records/NoPosPlusRecord.h | 41 + src/utils/FileRecordTools/Records/PlusFields.cpp | 40 + src/utils/FileRecordTools/Records/PlusFields.h | 39 + src/utils/FileRecordTools/Records/Record.cpp | 61 +- src/utils/FileRecordTools/Records/Record.h | 14 +- src/utils/FileRecordTools/Records/RecordMgr.cpp | 50 +- src/utils/FileRecordTools/Records/RecordMgr.h | 2 + src/utils/FileRecordTools/Records/VcfRecord.cpp | 39 +- src/utils/FileRecordTools/Records/VcfRecord.h | 8 +- src/utils/GenomeFile/Makefile | 4 +- src/utils/GenomeFile/NewGenomeFile.cpp | 12 + src/utils/GenomeFile/NewGenomeFile.h | 2 + src/utils/KeyListOps/KeyListOps.cpp | 14 + src/utils/KeyListOps/KeyListOps.h | 2 +- src/utils/KeyListOps/KeyListOpsMethods.cpp | 19 +- src/utils/KeyListOps/KeyListOpsMethods.h | 7 +- src/utils/KeyListOps/Makefile | 2 +- src/utils/NewChromsweep/Makefile | 2 +- src/utils/NewChromsweep/NewChromsweep.cpp | 15 +- src/utils/RecordOutputMgr/Makefile | 2 +- src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 26 +- src/utils/RecordOutputMgr/RecordOutputMgr.h | 5 +- src/utils/VectorOps/Makefile | 2 +- src/utils/VectorOps/VectorOps.cpp | 33 +- src/utils/VectorOps/VectorOps.h | 6 +- src/utils/bedFile/Makefile | 2 +- src/utils/bedFilePE/Makefile | 2 +- src/utils/bedGraphFile/Makefile | 2 +- src/utils/chromsweep/Makefile | 2 +- src/utils/{aux => driver}/BedtoolsDriver.cpp | 16 +- src/utils/{aux => driver}/BedtoolsDriver.h | 2 + src/utils/{aux => driver}/Makefile | 2 +- src/utils/fileType/FileRecordTypeChecker.cpp | 61 +- src/utils/fileType/FileRecordTypeChecker.h | 10 +- src/utils/fileType/Makefile | 2 +- src/utils/general/CommonHelp.cpp | 11 +- src/utils/general/Makefile | 4 +- src/utils/general/QuickString.cpp | 39 +- src/utils/general/QuickString.h | 7 +- src/utils/general/Tokenizer.cpp | 4 +- src/utils/general/Tokenizer.h | 2 +- src/utils/gzstream/Makefile | 2 +- src/utils/sequenceUtilities/Makefile | 2 +- src/utils/tabFile/Makefile | 2 +- src/utils/version/Makefile | 2 +- src/utils/version/version_release.txt | 6 +- src/windowBed/Makefile | 2 +- src/windowMaker/Makefile | 2 +- test/coverage/test-coverage.sh | 587 +- test/general/test-general.sh | 2 +- test/genomecov/test-genomecov.sh | 92 +- test/genomecov/y.bam | Bin 0 -> 220 bytes test/genomecov/y.bed | 2 + test/groupBy/a_vcfSVtest.vcf | 5 + test/groupBy/gdc.bam | Bin 0 -> 204 bytes test/groupBy/noPosvalues.header.bed | 13 + test/groupBy/test-groupby.sh | 339 +- test/groupBy/values3.7fields.header.bed | 13 + test/groupBy/values3.no_header.bed | 12 + test/groupBy/values3.unmarked_header.bed | 13 + test/groupBy/values3_case.header.bed | 13 + test/intersect/b.bed | 2 +- test/intersect/bug223_d.vcf | 3 + test/intersect/bug44_a.vcf.gz | Bin 0 -> 32419 bytes test/intersect/bug44_b.bed | 19 + test/intersect/e.bed | 1 + test/intersect/foo | 1 + .../multi_intersect/test-multi_intersect.sh | 2 +- test/intersect/new_test-intersect.sh | 7 +- test/intersect/svlen.vcf | 4 + test/intersect/test-intersect.sh | 148 +- test/intersect/two_blocks_partial.bam.bai | Bin 0 -> 832 bytes test/intersect/x.bam | Bin 0 -> 1755 bytes test/intersect/x.bed | 3 + test/intersect/y.bed | 2 + test/map/bug262_a.bed | 2 + test/map/bug262_b.bed | 2 + test/map/test-map.sh | 29 + test/merge/bug254_c.bed | 4 + test/merge/bug254_d.bed | 4 + test/merge/bug254_e.bed | 4 + test/merge/test-merge.sh | 31 +- test/sample/test-sample.sh | 1 + test/sort/a.bed | 11 + test/sort/names.txt | 3 + test/sort/test-sort.sh | 176 + test/split/test-split.sh | 59 +- test/test.sh | 3 + 196 files changed, 9586 insertions(+), 1672 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 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