[med-svn] [bedtools] 03/07: Merge https://github.com/arq5x/bedtools2
Andreas Tille
tille at debian.org
Mon Jul 18 12:43:11 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 81797798a80c960d4824f19021051f6b22bb14f9
Merge: 32c26d8 b0bc5b7
Author: Andreas Tille <andreas at sputnik.fam-tille.de>
Date: Tue Jul 7 13:33:06 2015 +0200
Merge https://github.com/arq5x/bedtools2
Makefile | 53 +-
README.md | 2 +-
docs/conf.py | 12 +-
docs/content/history.rst | 45 ++
docs/content/tools/closest.rst | 8 +
docs/content/tools/coverage.rst | 207 +++---
docs/content/tools/merge.rst | 14 +-
src/bedtools.cpp | 155 +++--
src/closestFile/Makefile | 12 +-
src/closestFile/closestFile.cpp | 80 +--
src/closestFile/closestFile.h | 63 +-
.../{closestMain.cpp => closestHelp.cpp} | 199 +++---
src/complementBed/Makefile | 38 --
src/complementBed/complementBed.cpp | 84 ---
src/complementBed/complementBed.h | 47 --
src/complementBed/complementMain.cpp | 114 ----
src/{intersectFile => complementFile}/Makefile | 14 +-
src/complementFile/complementFile.cpp | 127 ++++
src/complementFile/complementFile.h | 54 ++
src/complementFile/complementHelp.cpp | 36 ++
src/coverageBed/Makefile | 35 -
src/coverageBed/coverageBed.cpp | 341 ----------
src/coverageBed/coverageBed.h | 83 ---
src/coverageBed/coverageMain.cpp | 180 ------
src/{jaccard => coverageFile}/Makefile | 18 +-
src/coverageFile/coverageFile.cpp | 218 +++++++
src/coverageFile/coverageFile.h | 55 ++
src/coverageFile/coverageHelp.cpp | 52 ++
src/fisher/Fisher.h | 39 --
src/fisher/Makefile | 40 +-
src/fisher/{Fisher.cpp => fisher.cpp} | 102 ++-
src/fisher/fisher.h | 37 ++
src/fisher/fisherHelp.cpp | 29 +
src/fisher/fisherMain.cpp | 71 ---
src/fisher/{kfunc.c => kfunc.cpp} | 22 +-
src/fisher/kfunc.h | 40 ++
src/genomeCoverageBed/genomeCoverageBed.cpp | 2 +-
src/groupBy/groupBy.cpp | 49 +-
src/intersectFile/Makefile | 7 +-
src/intersectFile/intersectFile.cpp | 137 ++--
src/intersectFile/intersectFile.h | 44 +-
src/intersectFile/intersectHelp.cpp | 47 ++
src/intersectFile/intersectMain.cpp | 146 -----
src/jaccard/Jaccard.cpp | 94 ---
src/jaccard/Jaccard.h | 39 --
src/jaccard/Makefile | 11 +-
src/jaccard/jaccard.cpp | 79 +++
src/jaccard/jaccard.h | 41 ++
src/jaccard/jaccardHelp.cpp | 40 ++
src/jaccard/jaccardMain.cpp | 191 ------
src/mapFile/Makefile | 25 +-
src/mapFile/mapFile.cpp | 64 +-
src/mapFile/mapFile.h | 52 +-
src/mapFile/mapHelp.cpp | 36 ++
src/mapFile/mapMain.cpp | 91 ---
src/mergeFile/Makefile | 10 +-
src/mergeFile/mergeFile.cpp | 61 +-
src/mergeFile/mergeFile.h | 57 +-
src/mergeFile/{mergeMain.cpp => mergeHelp.cpp} | 42 +-
src/nekSandbox1/nekSandboxMain.cpp | 22 +-
src/sampleFile/Makefile | 9 +-
src/sampleFile/SampleFile.h | 43 --
src/sampleFile/{SampleFile.cpp => sampleFile.cpp} | 61 +-
src/sampleFile/sampleFile.h | 47 ++
src/sampleFile/{sampleMain.cpp => sampleHelp.cpp} | 37 +-
src/slopBed/slopBed.cpp | 8 +-
src/sortBed/sortBed.cpp | 91 ++-
src/sortBed/sortBed.h | 7 +-
src/sortBed/sortMain.cpp | 30 +-
src/{sampleFile => spacingFile}/Makefile | 11 +-
src/spacingFile/spacingFile.cpp | 82 +++
src/spacingFile/spacingFile.h | 43 ++
src/spacingFile/spacingHelp.cpp | 43 ++
src/{subtractBed => split}/Makefile | 7 +-
src/split/splitBed.cpp | 359 +++++++++++
src/split/splitBed.h | 50 ++
src/split/splitBedMain.cpp | 20 +
src/subtractBed/subtractBed.cpp | 191 ------
src/subtractBed/subtractBed.h | 57 --
src/subtractBed/subtractMain.cpp | 173 -----
src/{intersectFile => subtractFile}/Makefile | 13 +-
src/subtractFile/subtractFile.cpp | 134 ++++
src/subtractFile/subtractFile.h | 36 ++
src/subtractFile/subtractHelp.cpp | 43 ++
src/utils/BinTree/BinTree.cpp | 136 +---
src/utils/BinTree/BinTree.h | 40 +-
src/utils/Contexts/ContextBase.cpp | 136 +++-
src/utils/Contexts/ContextBase.h | 33 +-
src/utils/Contexts/ContextClosest.cpp | 63 +-
src/utils/Contexts/ContextClosest.h | 10 +-
src/utils/Contexts/ContextComplement.cpp | 31 +
src/utils/Contexts/ContextComplement.h | 24 +
src/utils/Contexts/ContextCoverage.cpp | 93 +++
src/utils/Contexts/ContextCoverage.h | 44 ++
src/utils/Contexts/ContextFisher.cpp | 98 +--
src/utils/Contexts/ContextFisher.h | 11 +-
src/utils/Contexts/ContextIntersect.cpp | 12 -
src/utils/Contexts/ContextIntersect.h | 5 +-
src/utils/Contexts/ContextJaccard.cpp | 18 -
src/utils/Contexts/ContextJaccard.h | 2 +-
src/utils/Contexts/ContextMap.cpp | 11 -
src/utils/Contexts/ContextMerge.cpp | 8 -
src/utils/Contexts/ContextSample.cpp | 12 -
src/utils/Contexts/ContextSpacing.cpp | 29 +
src/utils/Contexts/ContextSpacing.h | 25 +
src/utils/Contexts/ContextSubtract.cpp | 89 +++
src/utils/Contexts/ContextSubtract.h | 37 ++
src/utils/Contexts/Makefile | 12 +-
src/utils/Fasta/Fasta.cpp | 9 +-
.../FileReaders/BufferedStreamMgr.cpp | 2 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 5 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 48 +-
src/utils/FileRecordTools/Makefile | 9 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 20 +
src/utils/FileRecordTools/Records/BamRecord.h | 3 +
.../FileRecordTools/Records/Bed12Interval.cpp | 20 +
src/utils/FileRecordTools/Records/Bed12Interval.h | 1 +
src/utils/FileRecordTools/Records/Bed3Interval.h | 2 +-
.../FileRecordTools/Records/BedPlusInterval.cpp | 140 ++--
.../FileRecordTools/Records/BedPlusInterval.h | 28 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 10 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 7 +-
.../FileRecordTools/Records/GffPlusRecord.cpp | 70 ++
src/utils/FileRecordTools/Records/GffPlusRecord.h | 46 ++
src/utils/FileRecordTools/Records/GffRecord.cpp | 8 +-
src/utils/FileRecordTools/Records/GffRecord.h | 7 +-
src/utils/FileRecordTools/Records/Makefile | 18 +-
src/utils/FileRecordTools/Records/PlusFields.cpp | 40 ++
src/utils/FileRecordTools/Records/PlusFields.h | 39 ++
src/utils/FileRecordTools/Records/Record.cpp | 19 +-
src/utils/FileRecordTools/Records/Record.h | 3 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 55 +-
.../FileRecordTools/Records/RecordKeyVector.h | 8 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 29 +-
src/utils/FileRecordTools/Records/RecordMgr.h | 1 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 51 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 13 +-
src/utils/GenomeFile/NewGenomeFile.cpp | 12 +
src/utils/GenomeFile/NewGenomeFile.h | 2 +
src/utils/KeyListOps/KeyListOps.cpp | 21 +
src/utils/KeyListOps/KeyListOps.h | 2 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 19 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 7 +-
src/utils/NewChromsweep/CloseSweep.cpp | 702 ++++++++++++++-------
src/utils/NewChromsweep/CloseSweep.h | 98 ++-
src/utils/NewChromsweep/NewChromsweep.cpp | 9 +-
src/utils/NewChromsweep/NewChromsweep.h | 6 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 47 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 16 +-
src/utils/ToolBase/Makefile | 41 ++
src/utils/ToolBase/ToolBase.cpp | 4 +
src/utils/ToolBase/ToolBase.h | 35 +
src/utils/VectorOps/VectorOps.cpp | 33 +-
src/utils/VectorOps/VectorOps.h | 6 +-
src/utils/aux/BedtoolsDriver.cpp | 152 +++++
src/utils/aux/BedtoolsDriver.h | 18 +
src/utils/aux/Makefile | 93 +++
src/utils/bedFile/bedFile.h | 36 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 63 +-
src/utils/fileType/FileRecordTypeChecker.h | 14 +-
src/utils/general/CommonHelp.cpp | 96 ++-
src/utils/general/CommonHelp.h | 12 +-
src/utils/general/ErrorMsg.cpp | 2 +
src/utils/general/ErrorMsg.h | 1 -
src/utils/general/Makefile | 5 +-
src/utils/general/ParseTools.cpp | 2 +-
src/utils/general/ParseTools.h | 44 +-
src/utils/general/QuickString.cpp | 14 +
src/utils/general/QuickString.h | 3 +
src/utils/general/Tokenizer.cpp | 4 +-
src/utils/general/Tokenizer.h | 2 +-
src/utils/sequenceUtilities/sequenceUtils.cpp | 89 +++
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMaker.cpp | 37 +-
src/windowMaker/windowMaker.h | 8 +-
src/windowMaker/windowMakerMain.cpp | 35 +-
test/closest/a.bed | 1 +
test/closest/a2.bed | 1 +
test/closest/b2.bed | 2 +
test/closest/d4.bed | 2 +
test/closest/kclosest/d1.bed | 7 +
test/closest/kclosest/d2.bed | 9 +
test/closest/kclosest/d3.bed | 18 +
test/closest/kclosest/q1.bed | 1 +
test/closest/kclosest/q2.bed | 2 +
test/closest/kclosest/test-kclosest.sh | 654 +++++++++++++++++++
test/closest/sortAndNaming/test-sort-and-naming.sh | 8 +-
test/closest/test-closest.sh | 16 +
test/coverage/a.bed | 6 +
test/coverage/b.bed | 20 +
test/coverage/test-coverage.sh | 485 +++++++++++++-
test/fisher/a_merge.bed | 4 +
test/fisher/test-fisher.sh | 42 ++
test/general/test-general.sh | 8 +-
test/getfasta/test-getfasta.sh | 45 +-
test/getfasta/test.iupac.bed | 2 +
test/getfasta/test.iupac.fa | 4 +
test/intersect/bug167_strandSweep.bed | 10 +
test/intersect/bug187_a.bed | 1 +
test/intersect/bug187_b.bed | 2 +
test/intersect/bug223_d.vcf | 3 +
test/intersect/bug223_e.vcf | 3 +
test/intersect/bug223_f.vcf | 3 +
test/intersect/bug223_sv1_a.vcf | 3 +
test/intersect/bug223_sv1_b.vcf | 3 +
test/intersect/bug44_a.vcf.gz | Bin 0 -> 32419 bytes
test/intersect/bug44_b.bed | 19 +
test/intersect/new_test-intersect.sh | 1 -
.../{closest/a.bed => intersect/nonamecheck_a.bed} | 0
test/intersect/nonamecheck_b.bed | 1 +
.../sortAndNaming/test-sort-and-naming.sh | 8 +-
test/intersect/test-intersect.sh | 131 ++++
test/jaccard/a.bed | 1 +
test/jaccard/test-jaccard.sh | 7 +-
test/makewindows/input.bed | 4 +
test/makewindows/test-makewindows.sh | 128 ++++
test/map/bug262_a.bed | 2 +
test/map/bug262_b.bed | 2 +
test/map/test-map.sh | 29 +
test/merge/bug254_c.bed | 4 +
test/merge/bug254_d.bed | 4 +
test/merge/bug254_e.bed | 4 +
test/merge/test-merge.sh | 29 +-
test/sample/sample_help_withoutVersion.txt | 33 -
test/sample/test-sample.sh | 6 +-
test/sort/a.bed | 11 +
test/sort/names.txt | 3 +
test/sort/test-sort.sh | 176 ++++++
test/spacing/a.bed | 8 +
test/spacing/test-spacing.sh | 28 +
test/split/test-split.sh | 25 +
test/subtract/b2.bed | 2 +
test/subtract/d.bed | 1 +
test/subtract/test-subtract.sh | 144 ++++-
test/test.sh | 8 +
235 files changed, 7507 insertions(+), 3871 deletions(-)
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