[med-svn] [bedtools] branch master updated (03e594d -> e8f87ef)
Charles Plessy
plessy at moszumanska.debian.org
Sun Feb 9 12:52:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bedtools.
from 03e594d Work in progress.
new afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
new 604d443 Work in progress.
new e07e70c Imported Upstream version 2.19.0
new d238031 Merge tag 'upstream/2.19.0'
new e8f87ef New upstream releases; no new copyright nor license notice.
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 9 +
.travis.yml | 5 +
Makefile | 26 +-
README.md | 55 +
README.rst | 47 -
RELEASE_HISTORY | 160 +
data/aluY.chr1.bed.gz | Bin 0 -> 129766 bytes
data/gerp.chr1.bed.gz | Bin 0 -> 1128077 bytes
data/knownGene.hg18.chr21.short.bed | 828 +
data/refseq.chr1.exons.bed.gz | Bin 0 -> 456335 bytes
data/rmsk.hg18.chr21.bed | 57261 -------------------
data/simpleRepeats.chr1.bed.gz | Bin 0 -> 614807 bytes
debian/changelog | 4 +-
debian/copyright | 2 +-
debian/watch | 4 +-
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 -
docs/content/bedToIgv.rst | 68 -
docs/content/bedtools-suite.rst | 84 +-
docs/content/complementBed.rst | 48 -
docs/content/example-usage.rst | 330 +-
docs/content/faq.rst | 169 +
docs/content/fastafromBed.rst | 126 -
docs/content/general-usage.rst | 165 +-
docs/content/genomecoverageBed.rst | 122 -
docs/content/groupBy.rst | 194 -
docs/content/images/bedtoolsMenu.png | Bin 0 -> 23256 bytes
docs/content/images/galaxy-bedtools.png | Bin 0 -> 23492 bytes
docs/content/images/github-zip-button.png | Bin 0 -> 45691 bytes
docs/content/images/memory-comparo.png | Bin 0 -> 47395 bytes
docs/content/images/speed-comparo.png | Bin 0 -> 46622 bytes
docs/content/images/tool-glyphs/cluster-glyph.png | Bin 0 -> 45077 bytes
.../images/tool-glyphs/complement-glyph.png | Bin 0 -> 20223 bytes
docs/content/images/tool-glyphs/flank-glyph.png | Bin 0 -> 19718 bytes
.../content/images/tool-glyphs/genomecov-glyph.png | Bin 0 -> 41644 bytes
docs/content/images/tool-glyphs/getfasta-glyph.png | Bin 0 -> 13714 bytes
.../content/images/tool-glyphs/intersect-glyph.png | Bin 0 -> 34437 bytes
docs/content/images/tool-glyphs/jaccard-glyph.ai | 2189 +
docs/content/images/tool-glyphs/jaccard-glyph.png | Bin 0 -> 43088 bytes
docs/content/images/tool-glyphs/map-glyph.png | Bin 0 -> 39209 bytes
docs/content/images/tool-glyphs/map-glyph.svg | 463 +
.../content/images/tool-glyphs/maskfasta-glyph.png | Bin 0 -> 14514 bytes
.../content/images/tool-glyphs/maskfasta-glyph.svg | 171 +
docs/content/images/tool-glyphs/merge-glyph.png | Bin 0 -> 37072 bytes
docs/content/images/tool-glyphs/reldist-glyph.ai | 1137 +
docs/content/images/tool-glyphs/reldist-glyph.png | Bin 0 -> 16670 bytes
docs/content/images/tool-glyphs/reldist-plot.png | Bin 0 -> 206397 bytes
docs/content/images/tool-glyphs/shuffle-glyph.png | Bin 0 -> 31657 bytes
docs/content/images/tool-glyphs/slop-glyph.png | Bin 0 -> 21452 bytes
docs/content/images/tool-glyphs/subtract-glyph.png | Bin 0 -> 23353 bytes
docs/content/images/tool-glyphs/window-glyph.png | Bin 0 -> 25915 bytes
docs/content/installation.rst | 112 +-
docs/content/intersectBed.rst | 385 -
docs/content/maskfastafromBed.rst | 70 -
docs/content/mergeBed.rst | 120 -
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 +
.../{coverageBed.rst => tools/coverage.rst} | 32 +-
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 +
docs/content/tools/multiinter.rst | 5 +
docs/content/tools/nuc.rst | 5 +
docs/content/{ => tools}/overlap.rst | 11 +-
docs/content/tools/pairtobed.rst | 5 +
.../{pairToPair.rst => tools/pairtopair.rst} | 16 +-
docs/content/tools/random.rst | 157 +
docs/content/tools/reldist.rst | 197 +
docs/content/tools/shuffle.rst | 232 +
docs/content/tools/slop.rst | 147 +
docs/content/{sortBed.rst => tools/sort.rst} | 16 +-
docs/content/tools/subtract.rst | 157 +
docs/content/tools/tag.rst | 5 +
.../{unionBedGraphs.rst => tools/unionbedg.rst} | 27 +-
docs/content/tools/window.rst | 210 +
docs/content/windowBed.rst | 157 -
docs/index.rst | 95 +-
docs/templates/page.html | 140 +
docs/templates/sidebar-intro.html | 22 +
docs/themes/rtd/static/rtd.css_t | 3 +
src/annotateBed/annotateBed.cpp | 9 +-
src/bamToBed/bamToBed.cpp | 208 +-
src/bedToBam/Makefile | 2 +-
src/bedToBam/bedToBam.cpp | 2 +-
src/bedToIgv/Makefile | 2 +-
src/bedToIgv/bedToIgv.cpp | 2 +-
src/bedpeToBam/Makefile | 2 +-
src/bedpeToBam/bedpeToBam.cpp | 2 +-
src/bedtools.cpp | 19 +-
src/closestBed/closestBed.cpp | 99 +-
src/closestBed/closestBed.h | 2 +-
src/clusterBed/clusterBed.cpp | 3 +-
src/complementBed/Makefile | 2 +-
src/complementBed/complementBed.h | 2 +-
src/coverageBed/coverageMain.cpp | 2 +-
src/fastaFromBed/fastaFromBed.cpp | 9 +-
src/fastaFromBed/fastaFromBed.h | 3 +-
src/fastaFromBed/fastaFromBedMain.cpp | 9 +-
src/flankBed/Makefile | 2 +-
src/flankBed/flankBed.h | 2 +-
src/genomeCoverageBed/Makefile | 2 +-
src/genomeCoverageBed/genomeCoverageBed.h | 2 +-
src/intersectBed/intersectBed.cpp | 401 -
src/intersectBed/intersectBed.h | 102 -
src/intersectBed/intersectMain.cpp | 326 -
src/intersectFile/Makefile | 45 +
src/intersectFile/intersectFile.cpp | 105 +
src/intersectFile/intersectFile.h | 46 +
src/intersectFile/intersectMain.cpp | 130 +
src/jaccard/jaccard.cpp | 66 +-
src/jaccard/jaccard.h | 6 +-
src/jaccard/jaccardMain.cpp | 7 +-
src/mapBed/mapBed.cpp | 122 -
src/mapFile/Makefile | 56 +
src/mapFile/mapFile.cpp | 120 +
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 +-
src/pairToBed/pairToBedMain.cpp | 2 +-
src/randomBed/Makefile | 2 +-
src/randomBed/randomBed.h | 2 +-
src/regressTest/Makefile | 49 +
src/regressTest/RegressTest.cpp | 664 +
src/regressTest/RegressTest.h | 93 +
src/regressTest/regressTestMain.cpp | 67 +
src/{intersectBed => reldist}/Makefile | 8 +-
src/reldist/reldist.cpp | 154 +
src/{jaccard/jaccard.h => reldist/reldist.h} | 38 +-
.../jaccardMain.cpp => reldist/reldistMain.cpp} | 80 +-
src/{jaccard => sampleFile}/Makefile | 26 +-
src/sampleFile/SampleFile.cpp | 121 +
src/sampleFile/SampleFile.h | 43 +
src/sampleFile/sampleMain.cpp | 77 +
src/shuffleBed/Makefile | 2 +-
src/shuffleBed/shuffleBed.cpp | 167 +-
src/shuffleBed/shuffleBed.h | 12 +-
src/shuffleBed/shuffleBedMain.cpp | 41 +-
src/slopBed/Makefile | 2 +-
src/slopBed/slopBed.h | 2 +-
src/subtractBed/subtractBed.cpp | 25 +-
src/subtractBed/subtractBed.h | 3 +-
src/subtractBed/subtractMain.cpp | 17 +-
src/tagBam/tagBam.cpp | 3 +-
src/tagBam/tagBam.h | 1 -
src/unionBedGraphs/Makefile | 2 +-
src/unionBedGraphs/unionBedGraphs.h | 2 +-
src/unionBedGraphs/unionBedGraphsMain.cpp | 2 +-
src/utils/BamTools/.gitignore | 2 +
src/utils/BamTools/src/api/BamAlignment.h | 5 +-
src/utils/BamTools/src/api/BamReader.cpp | 5 +
src/utils/BamTools/src/api/BamReader.h | 2 +
.../BamTools/src/api/internal/bam/BamReader_p.cpp | 29 +
.../BamTools/src/api/internal/bam/BamReader_p.h | 1 +
.../src/api/internal/io/BamDeviceFactory_p.cpp | 8 +
.../src/api/internal/io/BamDeviceFactory_p.h | 1 +
.../BamTools/src/api/internal/io/BgzfStream_p.cpp | 24 +
.../BamTools/src/api/internal/io/BgzfStream_p.h | 2 +
src/utils/BamTools/src/api/internal/io/NetUnix_p.h | 1 -
.../src/api/internal/io/StdStreamDevice_p.h | 54 +
src/utils/BinTree/BinTree.cpp | 220 +
src/utils/BinTree/BinTree.h | 75 +
src/utils/{fileType => BinTree}/Makefile | 21 +-
src/utils/BlockedIntervals/Makefile | 4 +-
src/utils/Contexts/ContextBase.cpp | 365 +
src/utils/Contexts/ContextBase.h | 236 +
src/utils/Contexts/ContextIntersect.cpp | 318 +
src/utils/Contexts/ContextIntersect.h | 98 +
src/utils/Contexts/ContextMap.cpp | 118 +
src/utils/Contexts/ContextMap.h | 39 +
src/utils/Contexts/ContextSample.cpp | 79 +
src/utils/Contexts/ContextSample.h | 31 +
src/utils/Contexts/Makefile | 42 +
src/utils/Fasta/Fasta.cpp | 37 +-
src/utils/Fasta/Fasta.h | 13 +-
src/utils/Fasta/Makefile | 2 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 100 +
.../FileRecordTools/FileReaders/BamFileReader.h | 67 +
.../FileReaders/BufferedStreamMgr.cpp | 132 +
.../FileReaders/BufferedStreamMgr.h | 53 +
.../FileRecordTools/FileReaders/FileReader.cpp | 33 +
src/utils/FileRecordTools/FileReaders/FileReader.h | 42 +
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 269 +
.../FileRecordTools/FileReaders/InputStreamMgr.h | 74 +
src/utils/FileRecordTools/FileReaders/Makefile | 41 +
.../FileReaders/SingleLineDelimTextFileReader.cpp | 135 +
.../FileReaders/SingleLineDelimTextFileReader.h | 46 +
.../FileReaders/SingleLineDelimTransferBuffer.cpp | 72 +
.../FileReaders/SingleLineDelimTransferBuffer.h | 31 +
src/utils/FileRecordTools/FileRecordMgr.cpp | 398 +
src/utils/FileRecordTools/FileRecordMgr.h | 193 +
src/utils/FileRecordTools/Makefile | 51 +
src/utils/FileRecordTools/Records/BamRecord.cpp | 176 +
src/utils/FileRecordTools/Records/BamRecord.h | 55 +
.../FileRecordTools/Records/Bed12Interval.cpp | 148 +
src/utils/FileRecordTools/Records/Bed12Interval.h | 77 +
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 81 +
src/utils/FileRecordTools/Records/Bed3Interval.h | 43 +
src/utils/FileRecordTools/Records/Bed4Interval.cpp | 62 +
src/utils/FileRecordTools/Records/Bed4Interval.h | 38 +
src/utils/FileRecordTools/Records/Bed5Interval.cpp | 72 +
src/utils/FileRecordTools/Records/Bed5Interval.h | 36 +
src/utils/FileRecordTools/Records/Bed6Interval.cpp | 83 +
src/utils/FileRecordTools/Records/Bed6Interval.h | 36 +
.../FileRecordTools/Records/BedGraphInterval.cpp | 62 +
.../FileRecordTools/Records/BedGraphInterval.h | 36 +
.../FileRecordTools/Records/BedPlusInterval.cpp | 119 +
.../FileRecordTools/Records/BedPlusInterval.h | 54 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 217 +
src/utils/FileRecordTools/Records/BlockMgr.h | 65 +
src/utils/FileRecordTools/Records/GffRecord.cpp | 159 +
src/utils/FileRecordTools/Records/GffRecord.h | 51 +
src/utils/FileRecordTools/Records/Makefile | 45 +
src/utils/FileRecordTools/Records/Record.cpp | 203 +
src/utils/FileRecordTools/Records/Record.h | 155 +
.../FileRecordTools/Records/RecordKeyList.cpp | 68 +
src/utils/FileRecordTools/Records/RecordKeyList.h | 60 +
src/utils/FileRecordTools/Records/RecordMgr.cpp | 277 +
src/utils/FileRecordTools/Records/RecordMgr.h | 47 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 111 +
src/utils/FileRecordTools/Records/VcfRecord.h | 40 +
.../FileRecordTools/Records/recordsTar.tar.gz | Bin 0 -> 54443 bytes
.../genomeFile.cpp => GenomeFile/GenomeFile.cpp} | 4 +-
.../genomeFile.h => GenomeFile/GenomeFile.h} | 2 +-
src/utils/GenomeFile/Makefile | 34 +
src/utils/GenomeFile/NewGenomeFile.cpp | 124 +
src/utils/GenomeFile/NewGenomeFile.h | 65 +
src/utils/NewChromsweep/Makefile | 39 +
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 +-
src/utils/bedFile/bedFile.h | 16 +
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/{sequenceUtilities => general}/Makefile | 17 +-
src/utils/general/ParseTools.cpp | 143 +
src/utils/general/ParseTools.h | 97 +
src/utils/general/PushBackStreamBuf.cpp | 51 +
src/utils/general/PushBackStreamBuf.h | 39 +
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 +-
test/bamtobed/two_blocks_w_D.sam | 6 +
test/bed12tobed6/test-bed12tobed6.sh | 2 +-
test/closest/close-a.bed | 8 +
test/closest/close-b.bed | 7 +
test/closest/strand-test-a.bed | 2 +
test/closest/strand-test-b.bed | 3 +
test/closest/test-closest.sh | 88 +-
test/cluster/test-cluster.sh | 2 +-
test/coverage/test-coverage.sh | 2 +-
test/expand/test-expand.sh | 2 +-
test/flank/test-flank.sh | 2 +-
test/{getfasta/t.bed => general/empty.bed} | 0
test/general/non-empty.bed.gz | Bin 0 -> 53 bytes
test/general/test-general.sh | 33 +-
test/genomecov/test-genomecov.sh | 2 +-
test/getfasta/{t.fa => t_fH.fa} | 2 +-
test/getfasta/t_fH.fa.fai | 1 +
test/getfasta/test-getfasta.sh | 42 +-
test/groupBy/test-groupby.sh | 14 +-
test/intersect/a.bam | Bin 0 -> 1739 bytes
test/intersect/aVSb.bam | Bin 0 -> 1735 bytes
test/intersect/aWithHeaderVsB.txt | 4002 ++
test/intersect/a_bgzipped.bed.gz | Bin 0 -> 85 bytes
test/intersect/a_gzipped.bed.gz | Bin 0 -> 63 bytes
test/intersect/a_withLargeHeader.bed | 4002 ++
test/intersect/a_withLargeHeader_bgzipped.bed.gz | Bin 0 -> 10624 bytes
test/intersect/a_withLargeHeader_gzipped.bed.gz | Bin 0 -> 10384 bytes
test/intersect/a_with_bothUnmapped.bam | Bin 0 -> 2911 bytes
test/{closest/a.bed => intersect/bed3.bed} | 0
test/intersect/bed4.bed | 1 +
test/intersect/bed5.bed | 1 +
test/intersect/bed6.bed | 1 +
test/intersect/bed6.strand.bed | 1 +
test/intersect/bed6.strand2.bed | 2 +
test/intersect/bedplus.bed | 1 +
test/intersect/chromOrderA.bed | 6 +
test/intersect/chromOrderB.bed | 12 +
test/intersect/chromsOutOfOrder.bed | 4 +
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test/intersect/gdc.gff | 12 +
test/intersect/gdc_exp | 12 +
test/intersect/gdc_one.bed | 1 +
{genomes => test/intersect}/human.hg19.genome | 128 +-
.../intersect/human.hg19.vSort.genome | 111 +-
test/intersect/j1.bed | 1 +
test/intersect/new_test-intersect.sh | 668 +
test/intersect/oneUnmapped.bam | Bin 0 -> 2564 bytes
test/intersect/performanceTest.sh | 138 +
.../queryUnmappedMateMappedCoordsInvalid.bam | Bin 0 -> 1051 bytes
test/intersect/recordsOutOfOrder.bed | 4 +
test/intersect/test-intersect.sh | 152 +-
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 +
test/map/ivls.bed | 1 +
test/map/ivls2.bed | 3 +
test/{closest/a.bed => map/t.bed} | 0
test/map/test-map.sh | 553 +-
test/map/test.gff | 7 +
test/map/test.vcf | 26 +
test/map/three_blocks_match.bed | 1 +
test/map/three_blocks_nomatch.bed | 1 +
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test/map/values.bed | 2 +-
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 +
{genomes => test/sample}/human.hg19.genome | 128 +-
test/sample/sample_help_withoutVersion.txt | 33 +
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test/slop/test-slop.sh | 2 +-
test/subtract/c.bed | 1 +
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test/subtract/test-subtract.sh | 22 +-
test/test.sh | 41 +-
389 files changed, 33881 insertions(+), 62369 deletions(-)
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