This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository bedtools.
commit 1ee79d373e2a5f238690afc16aac9f1b21237658 Merge: 4272686 c6cc550 Author: Andreas Tille <[email protected]> Date: Sat Feb 10 07:48:07 2018 +0100 Update upstream source from tag '2.27.1+dfsg' Update to upstream version '2.27.1+dfsg' with Debian dir 5bf3e8aa8b60d0efe025e96453d9e9ebd3a14405 .travis.yml | 5 + Makefile | 11 +- docs/conf.py | 6 +- docs/content/advanced-usage.rst | 10 +- docs/content/faq.rst | 7 + docs/content/general-usage.rst | 2 + docs/content/history.rst | 52 +- docs/content/installation.rst | 2 +- docs/content/tools/bamtobed.rst | 1 + docs/content/tools/bed12tobed6.rst | 2 + docs/content/tools/bedtobam.rst | 3 + docs/content/tools/closest.rst | 2 +- docs/content/tools/coverage.rst | 2 +- docs/content/tools/genomecov.rst | 2 +- docs/content/tools/getfasta.rst | 2 +- docs/content/tools/intersect.rst | 4 +- docs/content/tools/links.rst | 4 + docs/content/tools/overlap.rst | 3 + docs/content/tools/pairtopair.rst | 4 + docs/content/tools/sort.rst | 39 +- docs/content/tools/subtract.rst | 5 +- docs/content/tools/unionbedg.rst | 1 + docs/content/tools/window.rst | 4 +- docs/index.rst | 11 + docs/templates/sidebar-intro.html | 2 +- src/annotateBed/annotateBed.cpp | 4 +- src/bed12ToBed6/bed12ToBed6.cpp | 3 +- src/bedtools.cpp | 35 +- src/closestFile/closestHelp.cpp | 2 - src/clusterBed/clusterBed.h | 1 + src/clusterBed/clusterMain.cpp | 18 +- src/complementFile/complementFile.cpp | 18 +- src/complementFile/complementFile.h | 6 +- src/complementFile/complementHelp.cpp | 2 - src/coverageFile/coverageFile.cpp | 183 +- src/coverageFile/coverageFile.h | 9 +- src/coverageFile/coverageHelp.cpp | 2 - src/fastaFromBed/fastaFromBed.cpp | 94 +- src/fastaFromBed/fastaFromBed.h | 9 +- src/fastaFromBed/fastaFromBedMain.cpp | 18 +- src/fisher/fisher.cpp | 17 +- src/fisher/fisherHelp.cpp | 4 - src/genomeCoverageBed/genomeCoverageBed.cpp | 2 +- src/genomeCoverageBed/genomeCoverageMain.cpp | 4 + src/groupBy/Makefile | 1 + src/groupBy/groupBy.cpp | 74 +- src/groupBy/groupBy.h | 10 +- src/intersectFile/intersectFile.cpp | 15 +- src/intersectFile/intersectFile.h | 10 +- src/intersectFile/intersectHelp.cpp | 5 +- src/jaccard/jaccard.cpp | 6 +- src/jaccard/jaccard.h | 8 +- src/jaccard/jaccardHelp.cpp | 4 - src/mapFile/mapHelp.cpp | 4 - src/maskFastaFromBed/Makefile | 3 +- src/maskFastaFromBed/maskFastaFromBed.cpp | 26 +- src/maskFastaFromBed/maskFastaFromBed.h | 7 +- src/maskFastaFromBed/maskFastaFromBedMain.cpp | 33 +- src/mergeFile/mergeHelp.cpp | 4 - src/multiBamCov/multiBamCov.cpp | 4 +- src/nekSandbox1/nekSandboxMain.cpp | 14 +- src/regressTest/regressTestMain.cpp | 4 +- src/reldist/reldist.cpp | 12 +- src/sampleFile/sampleHelp.cpp | 5 - src/shiftBed/shiftBed.cpp | 6 +- src/shuffleBed/shuffleBed.cpp | 102 +- src/shuffleBed/shuffleBed.h | 6 + src/slopBed/slopBed.cpp | 65 +- src/sortBed/sortBed.h | 1 + src/sortBed/sortMain.cpp | 27 +- src/spacingFile/spacingFile.cpp | 9 +- src/spacingFile/spacingFile.h | 8 +- src/spacingFile/spacingHelp.cpp | 12 +- src/subtractFile/subtractFile.cpp | 14 +- src/subtractFile/subtractHelp.cpp | 4 - src/utils/BamTools/src/api/BamConstants.h | 6 +- .../src/api/internal/bam/BamMultiReader_p.cpp | 4 +- .../BamTools/src/api/internal/io/HostAddress_p.cpp | 2 +- src/utils/BinTree/BinTree.cpp | 20 +- src/utils/BinTree/BinTree.h | 10 +- src/utils/Contexts/ContextBase.cpp | 45 +- src/utils/Contexts/ContextBase.h | 44 +- src/utils/Contexts/ContextClosest.cpp | 6 +- src/utils/Contexts/ContextGroupBy.cpp | 10 +- src/utils/Contexts/ContextGroupBy.h | 8 +- src/utils/Contexts/ContextIntersect.cpp | 9 - src/utils/Contexts/ContextIntersect.h | 8 +- src/utils/Contexts/ContextMerge.cpp | 8 +- src/utils/Contexts/ContextMerge.h | 2 +- src/utils/Contexts/ContextSubtract.cpp | 19 +- src/utils/Contexts/ContextSubtract.h | 2 +- src/utils/Contexts/Makefile | 2 +- .../FileRecordTools/FileReaders/BamFileReader.cpp | 8 +- .../FileRecordTools/FileReaders/BamFileReader.h | 14 +- .../FileReaders/BufferedStreamMgr.cpp | 6 +- .../FileReaders/BufferedStreamMgr.h | 10 +- src/utils/FileRecordTools/FileReaders/FileReader.h | 4 +- .../FileRecordTools/FileReaders/InputStreamMgr.cpp | 10 +- .../FileRecordTools/FileReaders/InputStreamMgr.h | 12 +- src/utils/FileRecordTools/FileReaders/Makefile | 8 +- src/utils/FileRecordTools/FileReaders/Makefile~ | 2 +- .../FileReaders/SingleLineDelimTextFileReader.cpp | 22 +- .../FileReaders/SingleLineDelimTextFileReader.h | 18 +- src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 8 +- src/utils/FileRecordTools/FileRecordMergeMgr.h | 2 +- src/utils/FileRecordTools/FileRecordMgr.cpp | 34 +- src/utils/FileRecordTools/FileRecordMgr.h | 18 +- src/utils/FileRecordTools/Makefile | 18 +- src/utils/FileRecordTools/Records/BamRecord.cpp | 112 +- src/utils/FileRecordTools/Records/BamRecord.h | 30 +- .../FileRecordTools/Records/Bed12Interval.cpp | 48 +- src/utils/FileRecordTools/Records/Bed12Interval.h | 31 +- src/utils/FileRecordTools/Records/Bed3Interval.cpp | 38 +- src/utils/FileRecordTools/Records/Bed3Interval.h | 12 +- src/utils/FileRecordTools/Records/Bed4Interval.cpp | 18 +- src/utils/FileRecordTools/Records/Bed4Interval.h | 10 +- src/utils/FileRecordTools/Records/Bed5Interval.cpp | 22 +- src/utils/FileRecordTools/Records/Bed5Interval.h | 10 +- src/utils/FileRecordTools/Records/Bed6Interval.cpp | 28 +- src/utils/FileRecordTools/Records/Bed6Interval.h | 10 +- .../FileRecordTools/Records/BedGraphInterval.cpp | 16 +- .../FileRecordTools/Records/BedGraphInterval.h | 10 +- .../FileRecordTools/Records/BedPlusInterval.cpp | 24 +- .../FileRecordTools/Records/BedPlusInterval.h | 14 +- src/utils/FileRecordTools/Records/BlockMgr.cpp | 36 +- src/utils/FileRecordTools/Records/BlockMgr.h | 9 +- .../FileRecordTools/Records/GffPlusRecord.cpp | 10 +- src/utils/FileRecordTools/Records/GffPlusRecord.h | 10 +- src/utils/FileRecordTools/Records/GffRecord.cpp | 74 +- src/utils/FileRecordTools/Records/GffRecord.h | 24 +- src/utils/FileRecordTools/Records/Makefile | 18 +- .../FileRecordTools/Records/NoPosPlusRecord.cpp | 4 +- .../FileRecordTools/Records/NoPosPlusRecord.h | 4 +- src/utils/FileRecordTools/Records/PlusFields.cpp | 7 +- src/utils/FileRecordTools/Records/PlusFields.h | 9 +- src/utils/FileRecordTools/Records/Record.cpp | 28 +- src/utils/FileRecordTools/Records/Record.h | 65 +- .../FileRecordTools/Records/RecordKeyList.cpp | 8 +- src/utils/FileRecordTools/Records/RecordKeyList.h | 6 +- .../FileRecordTools/Records/RecordKeyVector.cpp | 28 +- .../FileRecordTools/Records/RecordKeyVector.h | 15 +- src/utils/FileRecordTools/Records/RecordList.cpp | 5 +- src/utils/FileRecordTools/Records/RecordList.h | 12 +- src/utils/FileRecordTools/Records/StrandQueue.cpp | 18 +- src/utils/FileRecordTools/Records/StrandQueue.h | 14 +- src/utils/FileRecordTools/Records/VcfRecord.cpp | 33 +- src/utils/FileRecordTools/Records/VcfRecord.h | 16 +- src/utils/GenomeFile/NewGenomeFile.cpp | 16 +- src/utils/GenomeFile/NewGenomeFile.h | 24 +- src/utils/KeyListOps/KeyListOps.cpp | 100 +- src/utils/KeyListOps/KeyListOps.h | 38 +- src/utils/KeyListOps/KeyListOpsMethods.cpp | 77 +- src/utils/KeyListOps/KeyListOpsMethods.h | 54 +- src/utils/NewChromsweep/CloseSweep.cpp | 177 +- src/utils/NewChromsweep/CloseSweep.h | 35 +- src/utils/NewChromsweep/NewChromsweep.cpp | 61 +- src/utils/NewChromsweep/NewChromsweep.h | 18 +- src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 81 +- src/utils/RecordOutputMgr/RecordOutputMgr.h | 14 +- src/utils/bedFile/bedFile.cpp | 50 +- src/utils/bedFile/bedFile.h | 23 +- src/utils/driver/BedtoolsDriver.cpp | 6 +- src/utils/driver/BedtoolsDriver.h | 9 +- src/utils/fileType/FileRecordTypeChecker.cpp | 22 +- src/utils/fileType/FileRecordTypeChecker.h | 6 +- src/utils/fileType/Makefile | 2 +- src/utils/general/BTlist.h | 16 +- src/utils/general/BedtoolsTypes.h | 2 +- src/utils/general/Makefile | 6 +- src/utils/general/ParseTools.cpp | 42 +- src/utils/general/ParseTools.h | 15 +- src/utils/general/QuickString.cpp | 96 +- src/utils/general/QuickString.h | 78 +- src/utils/general/Tokenizer.cpp | 9 +- src/utils/general/Tokenizer.h | 9 +- src/utils/stringUtilities/stringUtilities.h | 18 +- src/utils/version/version_release.txt | 6 +- src/windowBed/windowMain.cpp | 2 +- test/bamtobed/test-bamtobed.sh | 35 +- test/bamtofastq/test-bamtofastq.sh | 7 +- test/bed12tobed6/test-bed12tobed6.sh | 19 +- test/closest/kclosest/bug471_a.bed | 5 + test/closest/kclosest/bug471_b.bed | 9 + test/closest/kclosest/test-kclosest.sh | 262 +- test/closest/sortAndNaming/test-sort-and-naming.sh | 71 +- test/closest/test-closest.sh | 168 +- test/cluster/test-cluster.sh | 17 +- test/complement/test-complement.sh | 29 +- test/coverage/chr_0-100.bed | 2 + test/coverage/test-coverage.sh | 89 +- test/expand/test-expand.sh | 17 +- test/fisher/test-fisher.sh | 19 +- test/flank/test-flank.sh | 35 +- test/general/a.chromheader.bed | 2 + test/general/a.trackheader.bed | 2 + test/general/hg19.fa.fai | 1 + test/general/t.bed | 5 + test/general/test-general.sh | 171 +- test/genomecov/test-genomecov.sh | 37 +- test/getfasta/test-getfasta.sh | 78 +- test/{groupBy => groupby}/a_vcfSVtest.vcf | 0 test/groupby/bug569_problem.txt | 4 + test/{groupBy => groupby}/gdc.bam | Bin test/{groupBy => groupby}/noPosvalues.header.bed | 0 test/{groupBy => groupby}/test-groupby.sh | 89 +- test/groupby/test.bed | 3 + .../values3.7fields.header.bed | 0 test/{groupBy => groupby}/values3.header.bed | 0 test/{groupBy => groupby}/values3.no_header.bed | 0 .../values3.unmarked_header.bed | 2 +- .../values3.unmarked_header.bed.2} | 2 +- test/{groupBy => groupby}/values3_case.header.bed | 0 test/intersect/jim.bed | 1 + test/intersect/jim.vcf | 3 + .../multi_intersect/test-multi_intersect.sh | 47 +- test/intersect/new_test-intersect.sh | 185 +- ...ew_test-intersect.sh => new_test-intersect.sh~} | 142 +- .../sortAndNaming/test-sort-and-naming.sh | 73 +- test/intersect/test-intersect.sh | 231 +- test/jaccard/test-jaccard.sh | 31 +- test/makewindows/test-makewindows.sh | 27 +- test/map/test-map.sh | 121 +- test/merge/test-merge.sh | 201 +- test/multicov/test-multicov.sh | 27 +- test/negativecontrol/test-negativecontrol.sh | 2 + test/reldist/test-reldist.sh | 13 +- test/sample/test-sample.sh | 41 +- test/shift/b.bed | 2 + test/shift/huge.genome | 1 + test/shift/test-shift.sh | 51 +- test/shuffle/test-shuffle.sh | 145 +- test/slop/test-slop.sh | 106 +- test/sort/b.bed | 4 + test/sort/test-sort.sh | 38 +- test/spacing/a.bed | 3 +- test/spacing/test-spacing.sh | 18 +- test/split/randData.bed | 10000 +++++++++++++++++++ test/split/test-split.sh | 32 +- test/subtract/test-subtract.sh | 51 +- test/test.sh | 99 +- 240 files changed, 13592 insertions(+), 2800 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
