[med-svn] [bedtools] 01/01: Merge tag 'v2.22.1' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Mon Jan 5 01:05:06 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 b7570497a8196c86f671e96067031e060db1ef46
Merge: 6835466 a596d5a
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jan 5 10:04:52 2015 +0900
Merge tag 'v2.22.1' into debian/unstable
.gitignore | 5 +
Makefile | 10 +-
README.md | 2 +-
docs/conf.py | 4 +-
docs/content/images/fisher/res-genes.png | Bin 0 -> 72950 bytes
docs/content/images/tool-glyphs/closest-glyph.png | Bin 0 -> 138680 bytes
.../content/images/tool-glyphs/genomecov-glyph.png | Bin 41644 -> 43832 bytes
docs/content/tools/closest.rst | 457 +-
docs/content/tools/fisher.rst | 94 +-
docs/content/tools/intersect.rst | 369 +-
docs/index.rst | 11 +-
src/bamToFastq/bamToFastq.cpp | 14 +-
src/bedtools.cpp | 12 +-
src/closestBed/Makefile | 32 -
src/closestBed/closestBed.cpp | 289 -
src/closestBed/closestBed.h | 66 -
src/closestBed/closestMain.cpp | 245 -
src/{fisher => closestFile}/Makefile | 93 +-
src/closestFile/closestFile.cpp | 45 +
src/closestFile/closestFile.h | 31 +
src/closestFile/closestMain.cpp | 112 +
src/fisher/Fisher.cpp | 171 +-
src/fisher/Fisher.h | 9 +
src/fisher/Makefile | 35 +-
src/fisher/fisherMain.cpp | 11 +-
src/groupBy/groupBy.cpp | 55 +-
src/intersectFile/intersectFile.cpp | 3 +
src/intersectFile/intersectMain.cpp | 6 +-
src/jaccard/jaccardMain.cpp | 2 +-
src/mapFile/mapMain.cpp | 2 +-
src/mergeFile/mergeMain.cpp | 2 +-
src/pairToPair/pairToPair.cpp | 4 +-
src/sampleFile/sampleMain.cpp | 2 +-
src/slopBed/slopBed.cpp | 12 +-
src/tagBam/tagBam.cpp | 6 +-
src/tagBam/tagBamMain.cpp | 4 +
src/utils/BinTree/BinTree.cpp | 2 +
src/utils/Contexts/ContextBase.cpp | 119 +-
src/utils/Contexts/ContextBase.h | 23 +-
src/utils/Contexts/ContextClosest.cpp | 222 +
src/utils/Contexts/ContextClosest.h | 65 +
src/utils/Contexts/ContextFisher.cpp | 25 +-
src/utils/Contexts/ContextFisher.h | 7 +
src/utils/Contexts/ContextIntersect.cpp | 5 +
src/utils/Contexts/ContextMerge.cpp | 14 +-
src/utils/Contexts/Makefile | 10 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 17 +
.../FileReaders/SingleLineDelimTextFileReader.h | 12 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 7 +-
src/utils/FileRecordTools/Records/Record.cpp | 46 +-
src/utils/FileRecordTools/Records/Record.h | 4 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 24 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 2 +-
src/utils/KeyListOps/KeyListOps.cpp | 29 +-
src/utils/KeyListOps/KeyListOps.h | 6 +
src/utils/NewChromsweep/CloseSweep.cpp | 525 +
src/utils/NewChromsweep/CloseSweep.h | 57 +
src/utils/NewChromsweep/Makefile | 80 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 707 +-
src/utils/NewChromsweep/NewChromsweep.h | 62 +-
src/utils/RecordOutputMgr/Makefile | 78 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 978 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 148 +-
src/utils/bedFile/bedFile.cpp | 18 +-
src/utils/bedFile/bedFile.h | 1 +
src/utils/general/ParseTools.cpp | 29 +-
src/utils/general/ParseTools.h | 8 +-
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMakerMain.cpp | 4 +
test/bamtofastq/golden.fq | 8 +
test/bamtofastq/golden.fq2 | 8 +
test/bamtofastq/test-bamtofastq.sh | 20 +
test/bamtofastq/test.sam | 7 +
test/closest/bug157_a.bed | 1 +
test/closest/bug157_b.bed | 2 +
test/closest/close-b.bed | 3 -
test/closest/d.bed | 1 +
test/closest/d_d1F.bed | 1 +
test/closest/d_d1R.bed | 1 +
test/closest/d_d2F.bed | 1 +
test/closest/d_d2R.bed | 1 +
test/closest/d_id.bed | 2 +
test/closest/d_iu.bed | 2 +
test/closest/d_q1.bed | 1 +
test/closest/d_q2.bed | 1 +
test/closest/mdb1.bed | 4 +
test/closest/mdb2.bed | 3 +
test/closest/mdb3.bed | 2 +
test/closest/mq1.bed | 1 +
test/closest/sortAndNaming/alpha_all.bed | 5 +
test/closest/sortAndNaming/alpha_missing.bed | 3 +
test/closest/sortAndNaming/db1_gls.bed | 12 +
test/closest/sortAndNaming/db1_leadingZero.txt | 10 +
test/closest/sortAndNaming/db1_noChr.bed | 10 +
test/closest/sortAndNaming/db1_num.bed | 6 +
test/closest/sortAndNaming/db2_num.bed | 6 +
test/closest/sortAndNaming/db2_numBackwards.bed | 6 +
test/closest/sortAndNaming/db3_numBackwards.bed | 4 +
test/closest/sortAndNaming/num_all.bed | 5 +
test/closest/sortAndNaming/num_missing.bed | 3 +
test/closest/sortAndNaming/q1_gls.bed | 12 +
test/closest/sortAndNaming/q1_num.bed | 10 +
test/closest/sortAndNaming/q1a_num.bed | 11 +
test/closest/sortAndNaming/sdb1.bed | 2 +
test/closest/sortAndNaming/sq1.bed | 2 +
test/closest/sortAndNaming/test-sort-and-naming.sh | 320 +
test/closest/strand-test-c.bed | 2 +
test/closest/strand-test-d.bed | 2 +
test/closest/test-closest.sh | 519 +-
test/fisher/README.md | 20 +
test/fisher/a.bed | 3 +
test/fisher/b.bed | 2 +
test/fisher/cmp.sh | 9 +
test/fisher/plot.py | 46 +
test/fisher/shuf.sh | 14 +
test/fisher/sim.py | 31 +
test/fisher/t.500.genome | 1 +
test/fisher/t.60.genome | 1 +
test/fisher/test-fisher.sh | 53 +
test/groupBy/test-groupby.sh | 29 +
test/intersect/a_testZeroLen.bed | 3 +
test/intersect/a_vcfSVtest.vcf | 5 +
test/intersect/b_testZeroLen.bed | 2 +
test/intersect/b_vcfSVtest.vcf | 5 +
test/intersect/bug150_a.bed | 1 +
test/intersect/bug150_b.bed | 2 +
test/intersect/new_test-intersect.sh | 59 +-
test/intersect/sortAndNaming/alpha_all.bed | 5 +
test/intersect/sortAndNaming/alpha_missing.bed | 3 +
.../sortAndNaming/bigTests/2.21_500Kvs500K.txt | 15821 +
test/intersect/sortAndNaming/bigTests/2.21_5v5.txt | 15821 +
.../intersect/sortAndNaming/bigTests/2.21_chr1.txt | 1173 +
.../sortAndNaming/bigTests/curr500Kvs500K.txt | 15575 +
test/intersect/sortAndNaming/bigTests/curr5v5.txt | 15821 +
test/intersect/sortAndNaming/bigTests/currChr1.txt | 1173 +
test/intersect/sortAndNaming/bigTests/db500K.bed | 500000 ++++++++++++++++++
test/intersect/sortAndNaming/bigTests/dbchr1.bed | 39409 ++
test/intersect/sortAndNaming/bigTests/diffs.txt | 34 +
test/intersect/sortAndNaming/bigTests/q500K.bed | 500000 ++++++++++++++++++
test/intersect/sortAndNaming/bigTests/qchr1.bed | 39544 ++
test/intersect/sortAndNaming/db1_gls.bed | 12 +
test/intersect/sortAndNaming/db1_leadingZero.txt | 10 +
test/intersect/sortAndNaming/db1_noChr.bed | 10 +
test/intersect/sortAndNaming/db1_num.bed | 6 +
test/intersect/sortAndNaming/db2_num.bed | 6 +
test/intersect/sortAndNaming/db2_numBackwards.bed | 6 +
test/intersect/sortAndNaming/db3_numBackwards.bed | 4 +
test/intersect/sortAndNaming/diffs.txt | 489 +
test/intersect/sortAndNaming/exp1 | 2 +
test/intersect/sortAndNaming/num_all.bed | 5 +
test/intersect/sortAndNaming/num_missing.bed | 3 +
test/intersect/sortAndNaming/q1_gls.bed | 12 +
test/intersect/sortAndNaming/q1_num.bed | 10 +
test/intersect/sortAndNaming/q1a_num.bed | 11 +
test/intersect/sortAndNaming/sdb1.bed | 2 +
test/intersect/sortAndNaming/sq1.bed | 2 +
.../sortAndNaming/test-sort-and-naming.sh | 315 +
test/intersect/splitBug155_a.bed | 1 +
test/intersect/splitBug155_b.bed | 1 +
test/intersect/test-intersect.sh | 52 +-
test/jaccard/d.bed | 1 -
test/jaccard/test-jaccard.sh | 11 +-
test/map/test-map.sh | 10 +-
test/merge/bamCol4Mean.txt | 14 +-
test/merge/bamCol5Mean.txt | 14 +-
test/merge/bamCol8Mean.txt | 32 +-
test/merge/bamCol9Mean.txt | 18 +-
test/merge/expFormat.bed | 1 +
test/merge/precisionTest2.bed | 5 +
test/merge/test-merge.sh | 64 +
test/merge/vcfSVtest.vcf | 5 +
test/test.sh | 3 +
tutorial/Makefile | 3 +
tutorial/answers.html | 148 +
tutorial/answers.md | 140 +
tutorial/bedtools.html | 582 +
tutorial/bedtools.md | 716 +
tutorial/bootstrap.css | 4480 +
tutorial/template.class.html | 65 +
tutorial/template.html | 75 +
180 files changed, 1156469 insertions(+), 2117 deletions(-)
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