[med-svn] [bedtools] 04/05: Merge tag 'upstream/2.19.0'
Charles Plessy
plessy at moszumanska.debian.org
Sun Feb 9 12:52:42 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository bedtools.
commit d238031a211daabb278500458addaa20939dfd61
Merge: 604d443 e07e70c
Author: Charles Plessy <plessy at debian.org>
Date: Sun Feb 9 21:47:34 2014 +0900
Merge tag 'upstream/2.19.0'
Upstream version 2.19.0
# gpg: Signature faite le dim. 09 févr. 2014 21:47:30 JST avec la clef RSA d'identifiant 2295D502
# gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »
.gitignore | 9 +
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README.md | 55 +
README.rst | 47 -
RELEASE_HISTORY | 160 +
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docs/_static/labibi.css | 54 +
docs/_static/labibi.js | 30 +
docs/bedtools.ai | 1251 +-
docs/conf.py | 17 +-
docs/content/advanced-usage.rst | 129 +-
docs/content/annotateBed.rst | 99 -
docs/content/bamToBed.rst | 88 -
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docs/content/bedtools-suite.rst | 84 +-
docs/content/complementBed.rst | 48 -
docs/content/example-usage.rst | 330 +-
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docs/content/overview.rst | 239 +-
docs/content/pairToBed.rst | 378 -
docs/content/quick-start.rst | 69 +-
docs/content/related-tools.rst | 67 +
docs/content/shuffleBed.rst | 155 -
docs/content/slopBed.rst | 84 -
docs/content/subtractBed.rst | 88 -
docs/content/tips-and-tricks.rst | 7 +
docs/content/tools/annotate.rst | 120 +
docs/content/tools/bamtobed.rst | 159 +
docs/content/tools/bamtofastq.rst | 103 +
.../{bed12ToBed6.rst => tools/bed12tobed6.rst} | 19 +-
docs/content/tools/bedpetobam.rst | 5 +
docs/content/{bedToBam.rst => tools/bedtobam.rst} | 13 +-
docs/content/{closestBed.rst => tools/closest.rst} | 17 +-
docs/content/tools/cluster.rst | 123 +
docs/content/tools/complement.rst | 62 +
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docs/content/tools/expand.rst | 5 +
docs/content/tools/flank.rst | 131 +
docs/content/tools/genomecov.rst | 338 +
docs/content/tools/getfasta.rst | 252 +
docs/content/tools/groupby.rst | 237 +
docs/content/tools/igv.rst | 5 +
docs/content/tools/intersect.rst | 670 +
docs/content/tools/jaccard.rst | 110 +
docs/content/{linksBed.rst => tools/links.rst} | 14 +-
docs/content/tools/makewindows.rst | 5 +
docs/content/tools/map.rst | 191 +
docs/content/tools/maskfasta.rst | 115 +
docs/content/tools/merge.rst | 219 +
docs/content/tools/multicov.rst | 98 +
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docs/content/tools/shuffle.rst | 232 +
docs/content/tools/slop.rst | 147 +
docs/content/{sortBed.rst => tools/sort.rst} | 16 +-
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docs/content/tools/tag.rst | 5 +
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docs/content/windowBed.rst | 157 -
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src/bamToBed/bamToBed.cpp | 208 +-
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src/clusterBed/clusterBed.cpp | 3 +-
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src/{mapBed/mapBed.h => mapFile/mapFile.h} | 55 +-
src/{mapBed => mapFile}/mapMain.cpp | 38 +-
src/mergeBed/mergeBed.cpp | 21 +-
src/mergeBed/mergeBed.h | 16 +-
src/mergeBed/mergeMain.cpp | 36 +-
src/multiIntersectBed/Makefile | 2 +-
src/multiIntersectBed/multiIntersectBed.h | 2 +-
src/multiIntersectBed/multiIntersectBedMain.cpp | 2 +-
src/nekSandbox1/FormatGuess.h | 76 +
src/{mapBed => nekSandbox1}/Makefile | 29 +-
src/nekSandbox1/nekSandboxMain.cpp | 338 +
src/nucBed/nucBed.cpp | 19 +-
src/nucBed/nucBed.h | 3 +-
src/nucBed/nucBedMain.cpp | 27 +-
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src/randomBed/Makefile | 2 +-
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src/regressTest/Makefile | 49 +
src/regressTest/RegressTest.cpp | 664 +
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src/regressTest/regressTestMain.cpp | 67 +
src/{intersectBed => reldist}/Makefile | 8 +-
src/reldist/reldist.cpp | 154 +
src/{jaccard/jaccard.h => reldist/reldist.h} | 38 +-
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src/{intersectBed => sampleFile}/Makefile | 26 +-
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src/sampleFile/sampleMain.cpp | 77 +
src/shuffleBed/Makefile | 2 +-
src/shuffleBed/shuffleBed.cpp | 167 +-
src/shuffleBed/shuffleBed.h | 12 +-
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src/subtractBed/subtractBed.cpp | 25 +-
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src/utils/Contexts/ContextSample.cpp | 79 +
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src/utils/Fasta/Fasta.cpp | 37 +-
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src/utils/Fasta/Makefile | 2 +-
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src/utils/FileRecordTools/FileReaders/Makefile | 41 +
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src/utils/FileRecordTools/FileRecordMgr.cpp | 398 +
src/utils/FileRecordTools/FileRecordMgr.h | 193 +
src/utils/FileRecordTools/Makefile | 51 +
src/utils/FileRecordTools/Records/BamRecord.cpp | 176 +
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src/utils/FileRecordTools/Records/GffRecord.cpp | 159 +
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src/utils/GenomeFile/NewGenomeFile.cpp | 124 +
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src/utils/NewChromsweep/NewChromsweep.cpp | 211 +
src/utils/NewChromsweep/NewChromsweep.h | 96 +
src/utils/RecordOutputMgr/Makefile | 39 +
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 430 +
src/utils/RecordOutputMgr/RecordOutputMgr.h | 72 +
src/utils/VectorOps/VectorOps.cpp | 28 +-
src/utils/VectorOps/VectorOps.h | 8 +-
src/utils/bedFile/bedFile.cpp | 56 +-
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src/utils/bedFilePE/bedFilePE.cpp | 10 +-
src/utils/bedGraphFile/bedGraphFile.cpp | 10 +-
src/utils/bedGraphFile/bedGraphFile.h | 3 +
src/utils/chromsweep/chromsweep.cpp | 2 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 387 +
src/utils/fileType/FileRecordTypeChecker.h | 126 +
src/utils/fileType/Makefile | 20 +-
src/utils/general/BTlist.h | 262 +
src/utils/general/BedtoolsTypes.h | 33 +
src/utils/general/CompressionTools.cpp | 45 +
src/utils/general/CompressionTools.h | 25 +
src/utils/general/DualQueue.h | 124 +
src/utils/general/ErrorMsg.h | 14 +
src/utils/general/FreeList.h | 83 +
src/utils/general/InflateStreamBuf.h | 130 +
src/utils/{fileType => general}/Makefile | 17 +-
src/utils/general/ParseTools.cpp | 143 +
src/utils/general/ParseTools.h | 97 +
src/utils/general/PushBackStreamBuf.cpp | 51 +
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src/utils/general/QuickString.cpp | 230 +
src/utils/general/QuickString.h | 72 +
src/utils/genomeFile/Makefile | 32 -
src/utils/tabFile/tabFile.cpp | 15 +-
src/utils/version/version_release.txt | 6 +-
src/windowBed/windowMain.cpp | 2 +-
src/windowMaker/Makefile | 2 +-
src/windowMaker/windowMaker.h | 2 +-
test/bamtobed/test-bamtobed.sh | 65 +-
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test/bed12tobed6/test-bed12tobed6.sh | 2 +-
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test/closest/close-b.bed | 7 +
test/closest/strand-test-a.bed | 2 +
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test/closest/test-closest.sh | 88 +-
test/cluster/test-cluster.sh | 2 +-
test/coverage/test-coverage.sh | 2 +-
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test/getfasta/test-getfasta.sh | 42 +-
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test/intersect/chromOrderB.bed | 12 +
test/intersect/chromsOutOfOrder.bed | 4 +
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test/intersect/gdc_exp | 12 +
test/intersect/gdc_one.bed | 1 +
test/intersect/human.hg19.genome | 94 +
test/intersect/human.hg19.vSort.genome | 93 +
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test/intersect/performanceTest.sh | 138 +
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test/intersect/recordsOutOfOrder.bed | 4 +
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test/intersect/three_blocks_match.bam | Bin 0 -> 1804 bytes
test/intersect/two_blocks_partial.bam | Bin 0 -> 1805 bytes
test/intersect/two_blocks_partial.bed | 1 +
test/jaccard/test-jaccard.sh | 46 +-
test/map/a.vsorted.bed | 5 +
test/map/b.vsorted.bed | 3 +
test/map/genome | 3 +
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test/map/test.gff | 7 +
test/map/test.vcf | 26 +
test/map/three_blocks_match.bed | 1 +
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test/map/values4.bed | 12 +
test/map/values5.bed | 8 +
test/merge/test-merge.sh | 30 +-
test/multicov/test-multicov.sh | 2 +-
test/reldist/test-reldist.sh | 149 +
test/sample/human.hg19.genome | 94 +
test/sample/sample_help_withoutVersion.txt | 33 +
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test/slop/test-slop.sh | 2 +-
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test/subtract/test-subtract.sh | 22 +-
test/test.sh | 41 +-
386 files changed, 33980 insertions(+), 62180 deletions(-)
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