[med-svn] [bedtools] 07/07: Merge branch 'master' of https://github.com/arq5x/bedtools2
Andreas Tille
tille at debian.org
Mon Jul 18 12:43:12 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstream
in repository bedtools.
commit 8e1a406712900bad39ae8b17a9014048b47c164b
Merge: 5d6f024 1e16d52
Author: Charles Plessy <plessy at debian.org>
Date: Thu Jul 7 13:46:59 2016 +0900
Merge branch 'master' of https://github.com/arq5x/bedtools2
Makefile | 29 +--
docs/conf.py | 6 +-
docs/content/bedtools-suite.rst | 1 +
docs/content/history.rst | 21 +++
docs/content/images/tool-glyphs/closest-glyph.png | Bin 138680 -> 138349 bytes
docs/content/overview.rst | 1 +
docs/content/tools/genomecov.rst | 3 +-
docs/content/tools/getfasta.rst | 54 ++++--
docs/content/tools/shift.rst | 118 ++++++++++++
docs/index.rst | 4 +-
scripts/makeBashScripts.py | 1 +
src/annotateBed/annotateBed.cpp | 2 +-
src/bedToBam/bedToBam.cpp | 2 +-
src/bedpeToBam/bedpeToBam.cpp | 2 +-
src/bedtools.cpp | 9 +-
src/closestFile/Makefile | 1 +
src/complementFile/Makefile | 1 +
src/complementFile/complementFile.cpp | 33 +++-
src/complementFile/complementFile.h | 5 +-
src/coverageFile/Makefile | 1 +
src/coverageFile/coverageFile.cpp | 3 -
src/coverageFile/coverageFile.h | 1 +
src/fastaFromBed/fastaFromBed.cpp | 103 ++++++----
src/fastaFromBed/fastaFromBed.h | 6 +-
src/fastaFromBed/fastaFromBedMain.cpp | 35 ++--
src/fisher/fisher.cpp | 2 +-
src/fisher/kfunc.cpp | 2 +-
src/groupBy/Makefile | 1 +
src/intersectFile/Makefile | 1 +
src/intersectFile/intersectFile.cpp | 20 +-
src/jaccard/Makefile | 1 +
src/mapFile/Makefile | 1 +
src/mergeFile/Makefile | 1 +
src/regressTest/RegressTest.cpp | 2 +-
src/sampleFile/Makefile | 1 +
src/sampleFile/sampleFile.cpp | 2 +-
src/shiftBed/Makefile | 35 ++++
src/shiftBed/shiftBed.cpp | 77 ++++++++
src/shiftBed/shiftBed.h | 57 ++++++
src/shiftBed/shiftBedMain.cpp | 179 ++++++++++++++++++
src/shuffleBed/shuffleBed.cpp | 112 +++++------
src/shuffleBed/shuffleBed.h | 6 +-
src/shuffleBed/shuffleBedMain.cpp | 2 +
src/slopBed/slopBed.cpp | 75 +++++---
src/spacingFile/Makefile | 1 +
src/subtractFile/Makefile | 2 +-
src/subtractFile/subtractFile.cpp | 16 +-
src/utils/BinTree/BinTree.cpp | 5 +-
src/utils/BinTree/BinTree.h | 4 +-
src/utils/BinTree/Makefile | 1 +
src/utils/Contexts/ContextBase.cpp | 11 +-
src/utils/Contexts/ContextBase.h | 3 +-
src/utils/Contexts/ContextCoverage.cpp | 1 +
src/utils/Contexts/ContextGroupBy.cpp | 2 +-
src/utils/Contexts/ContextIntersect.cpp | 23 ++-
src/utils/Contexts/ContextIntersect.h | 10 +
src/utils/Contexts/Makefile | 1 +
.../FileReaders/BufferedStreamMgr.cpp | 2 +-
src/utils/FileRecordTools/FileReaders/Makefile | 3 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 98 +++++-----
.../FileReaders/SingleLineDelimTextFileReader.h | 2 +
src/utils/FileRecordTools/Makefile | 1 +
.../FileRecordTools/Records/Bed12Interval.cpp | 16 +-
src/utils/FileRecordTools/Records/Bed12Interval.h | 3 +-
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 -
src/utils/FileRecordTools/Records/BlockMgr.cpp | 18 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 3 +-
src/utils/FileRecordTools/Records/GffPlusRecord.h | 2 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 2 +-
src/utils/FileRecordTools/Records/GffRecord.h | 1 +
src/utils/FileRecordTools/Records/Makefile | 3 +-
src/utils/FileRecordTools/Records/Record.cpp | 3 -
src/utils/FileRecordTools/Records/Record.h | 3 +
.../FileRecordTools/Records/RecordKeyList.cpp | 6 +-
src/utils/FileRecordTools/Records/RecordKeyList.h | 6 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 6 +-
.../FileRecordTools/Records/RecordKeyVector.h | 6 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 1 +
src/utils/GenomeFile/NewGenomeFile.cpp | 4 +-
src/utils/KeyListOps/KeyListOps.cpp | 7 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 36 ++--
src/utils/KeyListOps/Makefile | 1 +
src/utils/NewChromsweep/CloseSweep.cpp | 13 +-
src/utils/NewChromsweep/Makefile | 1 +
src/utils/NewChromsweep/NewChromsweep.cpp | 20 +-
src/utils/RecordOutputMgr/Makefile | 1 +
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 123 ++++++------
src/utils/RecordOutputMgr/RecordOutputMgr.h | 3 +-
src/utils/ToolBase/Makefile | 1 +
src/utils/bedFile/bedFile.cpp | 123 ++++++------
src/utils/bedFile/bedFile.h | 11 +-
src/utils/bedFilePE/bedFilePE.cpp | 8 -
src/utils/driver/Makefile | 1 +
src/utils/fileType/FileRecordTypeChecker.cpp | 41 ++--
src/utils/fileType/FileRecordTypeChecker.h | 1 +
src/utils/general/ParseTools.cpp | 3 +-
src/utils/general/ParseTools.h | 2 +-
src/utils/general/Tokenizer.cpp | 150 ++++++++-------
src/utils/general/Tokenizer.h | 9 +-
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMaker.cpp | 36 +++-
src/windowMaker/windowMakerMain.cpp | 7 +-
test/closest/dmr.bed | 1 +
test/closest/islands.2.bed | 1 +
test/closest/islands.bed | 1 +
test/closest/kclosest/test-kclosest.sh | 4 +-
test/closest/null_a.bed | 4 +
test/closest/null_b.bed | 1 +
test/closest/null_c.bed | 1 +
test/closest/shores.bed | 1 +
test/closest/test-closest.sh | 50 +++++
test/closest/tfbs.bed | 1 +
test/complement/test-complement.sh | 116 ++++++++++++
test/coverage/c.bed | 2 +
test/coverage/one_block.bam | Bin 0 -> 234 bytes
test/coverage/sam-w-del.bam | Bin 0 -> 225 bytes
test/coverage/test-coverage.sh | 209 ++++++++++++++++++++-
test/coverage/three_blocks.bam | Bin 0 -> 239 bytes
test/coverage/three_blocks_match.bam | Bin 0 -> 1804 bytes
test/coverage/two_blocks.bam | Bin 0 -> 237 bytes
test/coverage/x.bed | 3 +
test/coverage/y.bed | 1 +
test/fisher/get.sh | 2 +
test/fisher/test-fisher.sh | 2 +-
test/general/test-general.sh | 19 +-
test/genomecov/genome.txt | 3 +
test/genomecov/test-genomecov.sh | 2 -
test/getfasta/test-getfasta.sh | 58 ++++--
test/intersect/a.issue311.bed | 1 +
test/intersect/b.issue311.gff | 1 +
test/intersect/b.issue311.vcf | 3 +
test/intersect/blocks.bed12 | 4 +
test/intersect/bug223_e.vcf | 3 +-
test/intersect/gdc.gff | 24 +--
test/intersect/new_test-intersect.sh | 82 +++++++-
test/intersect/null_a.bed | 4 +
test/intersect/null_b.bed | 1 +
test/intersect/null_c.bed | 1 +
test/intersect/test-intersect.sh | 185 ++++++++++++++++--
test/makewindows/a.19bp.bed | 1 +
test/makewindows/a.20bp.bed | 1 +
test/makewindows/a.33bp.bed | 1 +
test/makewindows/test-makewindows.sh | 84 +++++++--
test/map/.RData | Bin 0 -> 77 bytes
test/map/.Rhistory | 6 +
test/map/test-map.sh | 20 +-
test/map/test.gff | 12 +-
test/merge/test-merge.sh | 16 +-
test/{slop => shift}/a.bed | 0
test/shift/test-shift.sh | 115 ++++++++++++
test/shift/tiny.genome | 1 +
test/shuffle/incl.sizedif.bed | 4 +
test/shuffle/test-shuffle.sh | 9 +
test/slop/a.bed | 1 -
test/test.sh | 3 +
tutorial/bedtools.html | 2 +-
156 files changed, 2246 insertions(+), 714 deletions(-)
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