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Viewing all changes in revision 11.

Committer: Package Import Robot
Author(s): Charles Plessy
Date: 2012-11-04 17:59:41 UTC
mfrom: (1.1.9)
Revision ID: package-import@ubuntu.com-20121104175941-hahqzy1w8uy650z0

Tags: 2.17.0-1

bb9012e Imported Upstream version 2.16.2.
9006b23 Imported Upstream version 2.17.0.
9112569 Documented BEDTools license as a whole.
325689c Removed Pre-Depends: dpkg (>= 1.15.6).
a781b14 Conforms with Policy 3.9.4.
84b1167 Use Debhelper 9.
0bf572d Distribute the test suite.
422cd34 Bash completion for BEDTools.

files added:
.pc/.quilt_patches

.pc/.quilt_series

debian/bash_completion

debian/bash_completion/bedtools

docs

docs/Makefile

docs/bedtools.ai

docs/bedtools.png

docs/build.sh

docs/conf.py

docs/content

docs/content/advanced-usage.rst

docs/content/annotateBed.rst

docs/content/bamToBed.rst

docs/content/bed12ToBed6.rst

docs/content/bedToBam.rst

docs/content/bedToIgv.rst

docs/content/bedtools-suite.rst

docs/content/closestBed.rst

docs/content/complementBed.rst

docs/content/coverageBed.rst

docs/content/example-usage.rst

docs/content/fastafromBed.rst

docs/content/general-usage.rst

docs/content/genomecoverageBed.rst

docs/content/groupBy.rst

docs/content/installation.rst

docs/content/intersectBed.rst

docs/content/linksBed.rst

docs/content/maskfastafromBed.rst

docs/content/mergeBed.rst

docs/content/overlap.rst

docs/content/overview.rst

docs/content/pairToBed.rst

docs/content/pairToPair.rst

docs/content/quick-start.rst

docs/content/shuffleBed.rst

docs/content/slopBed.rst

docs/content/sortBed.rst

docs/content/subtractBed.rst

docs/content/unionBedGraphs.rst

docs/content/windowBed.rst

docs/index.rst

docs/make.bat

docs/themes

docs/themes/rtd

docs/themes/rtd/static

docs/themes/rtd/static/rtd.css_t

docs/themes/rtd/theme.conf

src/jaccard

src/jaccard/Makefile

src/jaccard/jaccard.cpp

src/jaccard/jaccard.h

src/jaccard/jaccardMain.cpp

test/closest

test/closest/a.bed

test/closest/a.names.bed

test/closest/b-one-bp-closer.bed

test/closest/b.bed

test/closest/b.names.bed

test/closest/test-closest.sh

test/coverage

test/coverage/one_block.bam.bai

test/coverage/one_block.sam

test/coverage/sam-w-del.bam.bai

test/coverage/sam-w-del.sam

test/coverage/test-coverage.sh

test/coverage/three_blocks.bam.bai

test/coverage/three_blocks.sam

test/coverage/three_blocks_match.bed

test/coverage/three_blocks_match_1bp.bed

test/coverage/three_blocks_nomatch.bed

test/coverage/two_blocks.bam.bai

test/coverage/two_blocks.sam

test/getfasta

test/getfasta/blocks.bed

test/getfasta/t.bed

test/getfasta/t.fa

test/getfasta/t.fa.fai

test/getfasta/test-getfasta.sh

test/groupBy

test/groupBy/test-groupby.sh

test/groupBy/values3.header.bed

test/intersect/c.bed

test/intersect/mapped_and_unmapped.sam

test/jaccard

test/jaccard/a.bed

test/jaccard/b.bed

test/jaccard/c.bed

test/jaccard/d.bed

test/jaccard/test-jaccard.sh

test/merge/a.full.bed

test/multicov

test/multicov/multicov.bed

test/multicov/one_block.bam.bai

test/multicov/one_block.sam

test/multicov/test-multicov.sh

test/multicov/two_blocks.bam.bai

test/multicov/two_blocks.sam

test/subtract

test/subtract/a.bed

test/subtract/b.bed

test/subtract/test-subtract.sh

files removed:
bin

obj

src/utils/gzstream/gzstream.o

src/utils/gzstream/test_gunzip.o

src/utils/gzstream/test_gzip.o

src/utils/version/version_git.h

test.bed

test.bed.collapsed

files modified:
Makefile

debian/changelog

debian/compat

debian/control

debian/copyright

debian/install

debian/rules

scripts/makeBashScripts.py

src/annotateBed/annotateBed.cpp

src/bamToBed/bamToBed.cpp

src/bedToBam/bedToBam.cpp

src/bedtools.cpp

src/closestBed/closestBed.cpp

src/closestBed/closestBed.h

src/closestBed/closestMain.cpp

src/complementBed/complementBed.cpp

src/coverageBed/coverageBed.cpp

src/fastaFromBed/Makefile

src/fastaFromBed/fastaFromBed.cpp

src/fastaFromBed/fastaFromBed.h

src/fastaFromBed/fastaFromBedMain.cpp

src/flankBed/flankBed.cpp

src/genomeCoverageBed/genomeCoverageBed.cpp

src/groupBy/Makefile

src/groupBy/groupBy.cpp

src/intersectBed/intersectBed.cpp

src/intersectBed/intersectMain.cpp

src/mapBed/mapBed.cpp

src/mergeBed/mergeBed.cpp

src/multiBamCov/Makefile

src/multiBamCov/multiBamCov.cpp

src/multiBamCov/multiBamCov.h

src/multiBamCov/multiBamCovMain.cpp

src/pairToBed/pairToBed.cpp

src/randomBed/randomBed.cpp

src/shuffleBed/Makefile

src/shuffleBed/shuffleBed.cpp

src/shuffleBed/shuffleBed.h

src/shuffleBed/shuffleBedMain.cpp

src/subtractBed/subtractBed.cpp

src/subtractBed/subtractBed.h

src/subtractBed/subtractMain.cpp

src/tagBam/tagBam.cpp

src/utils/BamTools/src/api/internal/io/NetUnix_p.h

src/utils/VectorOps/VectorOps.cpp

src/utils/VectorOps/VectorOps.h

src/utils/bedFile/bedFile.cpp

src/utils/bedFile/bedFile.h

src/utils/chromsweep/chromsweep.cpp

src/utils/chromsweep/chromsweep.h

src/utils/genomeFile/genomeFile.cpp

src/utils/lineFileUtilities/lineFileUtilities.h

src/utils/version/version_release.txt

src/windowBed/windowBed.cpp

src/windowMaker/windowMaker.cpp

test/intersect/test-intersect.sh

test/merge/test-merge.sh

test/test.sh

Show diffs side-by-side

added added

removed removed

.pc/.quilt_patches

.pc/.quilt_series

debian/bash_completion/

debian/bash_completion/bedtools

debian/changelog

debian/copyright

docs/bedtools.ai

docs/bedtools.png

docs/content/advanced-usage.rst

docs/content/annotateBed.rst

docs/content/bamToBed.rst

docs/content/bed12ToBed6.rst

docs/content/bedToBam.rst

docs/content/bedToIgv.rst

docs/content/bedtools-suite.rst

docs/content/closestBed.rst

docs/content/complementBed.rst

docs/content/coverageBed.rst

docs/content/example-usage.rst

docs/content/fastafromBed.rst

docs/content/general-usage.rst

docs/content/genomecoverageBed.rst

docs/content/groupBy.rst

docs/content/installation.rst

docs/content/intersectBed.rst

docs/content/linksBed.rst

docs/content/maskfastafromBed.rst

docs/content/mergeBed.rst

docs/content/overlap.rst

docs/content/overview.rst

docs/content/pairToBed.rst

docs/content/pairToPair.rst

docs/content/quick-start.rst

docs/content/shuffleBed.rst

docs/content/slopBed.rst

docs/content/sortBed.rst

docs/content/subtractBed.rst

docs/content/unionBedGraphs.rst

docs/content/windowBed.rst

docs/themes/rtd/

docs/themes/rtd/static/

docs/themes/rtd/static/rtd.css_t

docs/themes/rtd/theme.conf

scripts/makeBashScripts.py

src/annotateBed/annotateBed.cpp

src/bamToBed/bamToBed.cpp

src/bedToBam/bedToBam.cpp

src/bedtools.cpp

src/closestBed/closestBed.cpp

src/closestBed/closestBed.h

src/closestBed/closestMain.cpp

src/complementBed/complementBed.cpp

src/coverageBed/coverageBed.cpp

src/fastaFromBed/Makefile

src/fastaFromBed/fastaFromBed.cpp

src/fastaFromBed/fastaFromBed.h

src/fastaFromBed/fastaFromBedMain.cpp

src/flankBed/flankBed.cpp

src/genomeCoverageBed/genomeCoverageBed.cpp

src/groupBy/Makefile

src/groupBy/groupBy.cpp

src/intersectBed/intersectBed.cpp

src/intersectBed/intersectMain.cpp

src/jaccard/Makefile

src/jaccard/jaccard.cpp

src/jaccard/jaccard.h

src/jaccard/jaccardMain.cpp

src/mapBed/mapBed.cpp

src/mergeBed/mergeBed.cpp

src/multiBamCov/Makefile

src/multiBamCov/multiBamCov.cpp

src/multiBamCov/multiBamCov.h

src/multiBamCov/multiBamCovMain.cpp

src/pairToBed/pairToBed.cpp

src/randomBed/randomBed.cpp

src/shuffleBed/Makefile

src/shuffleBed/shuffleBed.cpp

src/shuffleBed/shuffleBed.h

src/shuffleBed/shuffleBedMain.cpp

src/subtractBed/subtractBed.cpp

src/subtractBed/subtractBed.h

src/subtractBed/subtractMain.cpp

src/tagBam/tagBam.cpp

src/utils/BamTools/src/api/internal/io/NetUnix_p.h

src/utils/VectorOps/VectorOps.cpp

src/utils/VectorOps/VectorOps.h

src/utils/bedFile/bedFile.cpp

src/utils/bedFile/bedFile.h

src/utils/chromsweep/chromsweep.cpp

src/utils/chromsweep/chromsweep.h

src/utils/genomeFile/genomeFile.cpp

src/utils/gzstream/gzstream.o

src/utils/gzstream/test_gunzip.o

src/utils/gzstream/test_gzip.o

src/utils/lineFileUtilities/lineFileUtilities.h

src/utils/version/version_git.h

src/utils/version/version_release.txt

src/windowBed/windowBed.cpp

src/windowMaker/windowMaker.cpp

test.bed.collapsed

test/closest/a.bed

test/closest/a.names.bed

test/closest/b-one-bp-closer.bed

test/closest/b.bed

test/closest/b.names.bed

test/closest/test-closest.sh

test/coverage/one_block.bam.bai

test/coverage/one_block.sam

test/coverage/sam-w-del.bam.bai

test/coverage/sam-w-del.sam

test/coverage/test-coverage.sh

test/coverage/three_blocks.bam.bai

test/coverage/three_blocks.sam

test/coverage/three_blocks_match.bed

test/coverage/three_blocks_match_1bp.bed

test/coverage/three_blocks_nomatch.bed

test/coverage/two_blocks.bam.bai

test/coverage/two_blocks.sam

test/getfasta/blocks.bed

test/getfasta/t.bed

test/getfasta/t.fa

test/getfasta/t.fa.fai

test/getfasta/test-getfasta.sh

test/groupBy/test-groupby.sh

test/intersect/c.bed

test/intersect/mapped_and_unmapped.sam

test/intersect/test-intersect.sh

test/jaccard/a.bed

test/jaccard/b.bed

test/jaccard/c.bed

test/jaccard/d.bed

test/jaccard/test-jaccard.sh

test/merge/a.full.bed

test/merge/test-merge.sh

test/multicov/multicov.bed

test/multicov/one_block.bam.bai

test/multicov/one_block.sam

test/multicov/test-multicov.sh

test/multicov/two_blocks.bam.bai

test/multicov/two_blocks.sam

test/subtract/a.bed

test/subtract/b.bed

test/subtract/test-subtract.sh

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