[med-svn] [bedtools] 01/01: Merge tag 'v2.25.0' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 4 14:37:09 UTC 2015
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 <plessy at debian.org>
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(-)
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