├── .github └── workflows │ └── main.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── data ├── aluY.chr1.bed.gz ├── gerp.chr1.bed.gz ├── knownGene.hg18.chr21.bed ├── knownGene.hg18.chr21.short.bed ├── refseq.chr1.exons.bed.gz └── simpleRepeats.chr1.bed.gz ├── docs ├── Makefile ├── _static │ ├── labibi.css │ └── labibi.js ├── bedtools.ai ├── bedtools.png ├── bedtools.swiss.png ├── build.sh ├── conf.py ├── content │ ├── advanced-usage.rst │ ├── bedtools-suite.rst │ ├── example-usage.rst │ ├── faq.rst │ ├── general-usage.rst │ ├── history.rst │ ├── images │ │ ├── bedtoolsMenu.png │ │ ├── fisher │ │ │ └── res-genes.png │ │ ├── galaxy-bedtools.png │ │ ├── github-zip-button.png │ │ ├── memory-comparo.png │ │ ├── speed-comparo.png │ │ └── tool-glyphs │ │ │ ├── barski_binding_site.png │ │ │ ├── closest-glyph.png │ │ │ ├── cluster-glyph.png │ │ │ ├── complement-glyph.png │ │ │ ├── flank-glyph.png │ │ │ ├── genomecov-glyph.png │ │ │ ├── getfasta-glyph.png │ │ │ ├── intersect-glyph.png │ │ │ ├── jaccard-glyph.ai │ │ │ ├── jaccard-glyph.png │ │ │ ├── map-glyph.png │ │ │ ├── map-glyph.svg │ │ │ ├── map-speed-comparo.png │ │ │ ├── maskfasta-glyph.png │ │ │ ├── maskfasta-glyph.svg │ │ │ ├── merge-glyph.png │ │ │ ├── multiinter-glyph.png │ │ │ ├── random-glyph.ai │ │ │ ├── random-glyph.png │ │ │ ├── reldist-glyph.ai │ │ │ ├── reldist-glyph.png │ │ │ ├── reldist-plot.png │ │ │ ├── shuffle-glyph.png │ │ │ ├── slop-glyph.png │ │ │ ├── subtract-glyph.png │ │ │ ├── summary.png │ │ │ └── window-glyph.png │ ├── installation.rst │ ├── overview.rst │ ├── quick-start.rst │ ├── related-tools.rst │ ├── tips-and-tricks.rst │ └── tools │ │ ├── annotate.rst │ │ ├── bamtobed.rst │ │ ├── bamtofastq.rst │ │ ├── bed12tobed6.rst │ │ ├── bedpetobam.rst │ │ ├── bedtobam.rst │ │ ├── closest.rst │ │ ├── cluster.rst │ │ ├── complement.rst │ │ ├── coverage.rst │ │ ├── expand.rst │ │ ├── fisher.rst │ │ ├── flank.rst │ │ ├── genomecov.rst │ │ ├── getfasta.rst │ │ ├── groupby.rst │ │ ├── igv.rst │ │ ├── intersect.rst │ │ ├── jaccard.rst │ │ ├── links.rst │ │ ├── makewindows.rst │ │ ├── map.rst │ │ ├── maskfasta.rst │ │ ├── merge.rst │ │ ├── multicov.rst │ │ ├── multiinter.rst │ │ ├── nuc.rst │ │ ├── overlap.rst │ │ ├── pairtobed.rst │ │ ├── pairtopair.rst │ │ ├── random.rst │ │ ├── reldist.rst │ │ ├── shift.rst │ │ ├── shuffle.rst │ │ ├── slop.rst │ │ ├── sort.rst │ │ ├── subtract.rst │ │ ├── summary.rst │ │ ├── tag.rst │ │ ├── unionbedg.rst │ │ └── window.rst ├── index.rst ├── make.bat ├── templates │ ├── page.html │ └── sidebar-intro.html └── themes │ └── rtd │ ├── static │ └── rtd.css_t │ └── theme.conf ├── genomes ├── human.hg18.genome ├── human.hg19.genome ├── human.hg38.genome ├── mouse.mm10.genome ├── mouse.mm8.genome └── mouse.mm9.genome ├── scripts ├── makeBashScripts.py └── vcfsort.sh ├── src ├── annotateBed │ ├── Makefile.frag │ ├── annotateBed.cpp │ ├── annotateBed.h │ └── annotateMain.cpp ├── bamToBed │ ├── Makefile.frag │ └── bamToBed.cpp ├── bamToFastq │ ├── Makefile.frag │ ├── bamToFastq.cpp │ ├── bamToFastq.h │ └── bamToFastqMain.cpp ├── bed12ToBed6 │ ├── Makefile.frag │ └── bed12ToBed6.cpp ├── bedToBam │ ├── Makefile.frag │ └── bedToBam.cpp ├── bedToIgv │ ├── Makefile.frag │ └── bedToIgv.cpp ├── bedpeToBam │ ├── Makefile.frag │ ├── bedpeToBam.cpp │ └── notes.txt ├── bedtools.cpp ├── closestFile │ ├── Makefile.frag │ ├── closestFile.cpp │ ├── closestFile.h │ └── closestHelp.cpp ├── clusterBed │ ├── Makefile.frag │ ├── clusterBed.cpp │ ├── clusterBed.h │ └── clusterMain.cpp ├── complementFile │ ├── Makefile.frag │ ├── complementFile.cpp │ ├── complementFile.h │ └── complementHelp.cpp ├── coverageFile │ ├── Makefile.frag │ ├── coverageFile.cpp │ ├── coverageFile.h │ └── coverageHelp.cpp ├── expand │ ├── Makefile.frag │ └── expand.cpp ├── fastaFromBed │ ├── Makefile.frag │ ├── fastaFromBed.cpp │ ├── fastaFromBed.h │ └── fastaFromBedMain.cpp ├── fisher │ ├── Makefile.frag │ ├── fisher.cpp │ ├── fisher.h │ ├── fisherHelp.cpp │ ├── kfunc.cpp │ └── kfunc.h ├── flankBed │ ├── Makefile.frag │ ├── flankBed.cpp │ ├── flankBed.h │ ├── flankBedMain.cpp │ ├── test.fa │ ├── test.fa.fai │ └── test.gff ├── genomeCoverageBed │ ├── Makefile.frag │ ├── genomeCoverageBed.cpp │ ├── genomeCoverageBed.h │ └── genomeCoverageMain.cpp ├── getOverlap │ ├── Makefile.frag │ └── getOverlap.cpp ├── groupBy │ ├── Makefile.frag │ ├── groupBy.cpp │ ├── groupBy.h │ └── groupByHelp.cpp ├── htsutil.cpp ├── intersectFile │ ├── Makefile.frag │ ├── intersectFile.cpp │ ├── intersectFile.h │ └── intersectHelp.cpp ├── jaccard │ ├── Makefile.frag │ ├── jaccard.cpp │ ├── jaccard.h │ └── jaccardHelp.cpp ├── linksBed │ ├── Makefile.frag │ ├── linksBed.cpp │ ├── linksBed.h │ └── linksMain.cpp ├── mapFile │ ├── Makefile.frag │ ├── mapFile.cpp │ ├── mapFile.h │ └── mapHelp.cpp ├── maskFastaFromBed │ ├── Makefile.frag │ ├── maskFastaFromBed.cpp │ ├── maskFastaFromBed.h │ └── maskFastaFromBedMain.cpp ├── mergeFile │ ├── Makefile.frag │ ├── mergeFile.cpp │ ├── mergeFile.h │ └── mergeHelp.cpp ├── multiBamCov │ ├── Makefile.frag │ ├── multiBamCov.cpp │ ├── multiBamCov.h │ └── multiBamCovMain.cpp ├── multiIntersectBed │ ├── Makefile.frag │ ├── multiIntersectBed.cpp │ ├── multiIntersectBed.h │ └── multiIntersectBedMain.cpp ├── nekSandbox1 │ ├── FormatGuess.h │ ├── Makefile │ └── nekSandboxMain.cpp ├── nucBed │ ├── LargeFileSupport.h │ ├── Makefile.frag │ ├── nucBed.cpp │ ├── nucBed.h │ └── nucBedMain.cpp ├── pairToBed │ ├── Makefile.frag │ ├── pairToBed.cpp │ ├── pairToBed.h │ └── pairToBedMain.cpp ├── pairToPair │ ├── Makefile.frag │ ├── pairToPair.cpp │ ├── pairToPair.h │ └── pairToPairMain.cpp ├── randomBed │ ├── Makefile.frag │ ├── randomBed.cpp │ ├── randomBed.h │ └── randomBedMain.cpp ├── regressTest │ ├── Makefile.frag │ ├── RegressTest.cpp │ ├── RegressTest.h │ └── regressTestMain.cpp ├── reldist │ ├── Makefile.frag │ ├── reldist.cpp │ ├── reldist.h │ └── reldistMain.cpp ├── sampleFile │ ├── Makefile.frag │ ├── sampleFile.cpp │ ├── sampleFile.h │ └── sampleHelp.cpp ├── shiftBed │ ├── Makefile.frag │ ├── shiftBed.cpp │ ├── shiftBed.h │ └── shiftBedMain.cpp ├── shuffleBed │ ├── Makefile.frag │ ├── shuffleBed.cpp │ ├── shuffleBed.h │ └── shuffleBedMain.cpp ├── slopBed │ ├── Makefile.frag │ ├── slopBed.cpp │ ├── slopBed.h │ └── slopBedMain.cpp ├── sortBed │ ├── Makefile.frag │ ├── sortBed.cpp │ ├── sortBed.h │ └── sortMain.cpp ├── spacingFile │ ├── Makefile.frag │ ├── spacingFile.cpp │ ├── spacingFile.h │ └── spacingHelp.cpp ├── split │ ├── Makefile.frag │ ├── splitBed.cpp │ ├── splitBed.h │ └── splitBedMain.cpp ├── subtractFile │ ├── Makefile.frag │ ├── subtractFile.cpp │ ├── subtractFile.h │ └── subtractHelp.cpp ├── summaryFile │ ├── Makefile.frag │ ├── summaryFile.cpp │ ├── summaryFile.h │ └── summaryHelp.cpp ├── tagBam │ ├── Makefile.frag │ ├── tagBam.cpp │ ├── tagBam.h │ └── tagBamMain.cpp ├── unionBedGraphs │ ├── Makefile.frag │ ├── unionBedGraphs.cpp │ ├── unionBedGraphs.h │ └── unionBedGraphsMain.cpp ├── utils │ ├── BamTools-Ancillary │ │ ├── BamAncillary.cpp │ │ ├── BamAncillary.h │ │ └── Makefile.frag │ ├── BamTools │ │ ├── .gitignore │ │ ├── Makefile.frag │ │ ├── include │ │ │ ├── BamAlignment.hpp │ │ │ ├── BamAlignment.mapping.hpp │ │ │ ├── BamAncillary.h │ │ │ ├── BamReader.hpp │ │ │ ├── BamWriter.hpp │ │ │ ├── SamHeader.hpp │ │ │ └── api │ │ │ │ ├── BamAlignment.h │ │ │ │ ├── BamAux.h │ │ │ │ ├── BamMultiReader.h │ │ │ │ ├── BamReader.h │ │ │ │ ├── BamWriter.h │ │ │ │ └── SamConstants.h │ │ └── mapping │ │ │ ├── BamAlignment.map │ │ │ └── BamAlignment.py │ ├── BinTree │ │ ├── BinTree.cpp │ │ ├── BinTree.h │ │ └── Makefile.frag │ ├── BlockedIntervals │ │ ├── BlockedIntervals.cpp │ │ ├── BlockedIntervals.h │ │ └── Makefile.frag │ ├── Contexts │ │ ├── ContextBase.cpp │ │ ├── ContextBase.h │ │ ├── ContextClosest.cpp │ │ ├── ContextClosest.h │ │ ├── ContextComplement.cpp │ │ ├── ContextComplement.h │ │ ├── ContextCoverage.cpp │ │ ├── ContextCoverage.h │ │ ├── ContextFisher.cpp │ │ ├── ContextFisher.h │ │ ├── ContextGroupBy.cpp │ │ ├── ContextGroupBy.h │ │ ├── ContextIntersect.cpp │ │ ├── ContextIntersect.h │ │ ├── ContextJaccard.cpp │ │ ├── ContextJaccard.h │ │ ├── ContextMap.cpp │ │ ├── ContextMap.h │ │ ├── ContextMerge.cpp │ │ ├── ContextMerge.h │ │ ├── ContextSample.cpp │ │ ├── ContextSample.h │ │ ├── ContextSpacing.cpp │ │ ├── ContextSpacing.h │ │ ├── ContextSubtract.cpp │ │ ├── ContextSubtract.h │ │ ├── ContextSummary.cpp │ │ ├── ContextSummary.h │ │ └── Makefile.frag │ ├── Fasta │ │ ├── Fasta.cpp │ │ ├── Fasta.h │ │ ├── LargeFileSupport.h │ │ ├── Makefile.frag │ │ ├── split.cpp │ │ └── split.h │ ├── FileRecordTools │ │ ├── FileReaders │ │ │ ├── BamFileReader.cpp │ │ │ ├── BamFileReader.h │ │ │ ├── BufferedStreamMgr.cpp │ │ │ ├── BufferedStreamMgr.h │ │ │ ├── FileReader.cpp │ │ │ ├── FileReader.h │ │ │ ├── InputStreamMgr.cpp │ │ │ ├── InputStreamMgr.h │ │ │ ├── Makefile.frag │ │ │ ├── SingleLineDelimTextFileReader.cpp │ │ │ ├── SingleLineDelimTextFileReader.h │ │ │ ├── SingleLineDelimTransferBuffer.cpp │ │ │ └── SingleLineDelimTransferBuffer.h │ │ ├── FileRecordMergeMgr.cpp │ │ ├── FileRecordMergeMgr.h │ │ ├── FileRecordMgr.cpp │ │ ├── FileRecordMgr.h │ │ ├── Makefile.frag │ │ └── Records │ │ │ ├── BamRecord.cpp │ │ │ ├── BamRecord.h │ │ │ ├── Bed12Interval.cpp │ │ │ ├── Bed12Interval.h │ │ │ ├── Bed3Interval.cpp │ │ │ ├── Bed3Interval.h │ │ │ ├── Bed4Interval.cpp │ │ │ ├── Bed4Interval.h │ │ │ ├── Bed5Interval.cpp │ │ │ ├── Bed5Interval.h │ │ │ ├── Bed6Interval.cpp │ │ │ ├── Bed6Interval.h │ │ │ ├── BedGraphInterval.cpp │ │ │ ├── BedGraphInterval.h │ │ │ ├── BedPlusInterval.cpp │ │ │ ├── BedPlusInterval.h │ │ │ ├── BlockMgr.cpp │ │ │ ├── BlockMgr.h │ │ │ ├── EmptyRecord.cpp │ │ │ ├── EmptyRecord.h │ │ │ ├── GffPlusRecord.cpp │ │ │ ├── GffPlusRecord.h │ │ │ ├── GffRecord.cpp │ │ │ ├── GffRecord.h │ │ │ ├── Makefile.frag │ │ │ ├── NoPosPlusRecord.cpp │ │ │ ├── NoPosPlusRecord.h │ │ │ ├── PlusFields.cpp │ │ │ ├── PlusFields.h │ │ │ ├── Record.cpp │ │ │ ├── Record.h │ │ │ ├── RecordKeyList.cpp │ │ │ ├── RecordKeyList.h │ │ │ ├── RecordKeyVector.cpp │ │ │ ├── RecordKeyVector.h │ │ │ ├── RecordList.cpp │ │ │ ├── RecordList.h │ │ │ ├── RecordMgr.cpp │ │ │ ├── RecordMgr.h │ │ │ ├── StrandQueue.cpp │ │ │ ├── StrandQueue.h │ │ │ ├── VcfRecord.cpp │ │ │ └── VcfRecord.h │ ├── GenomeFile │ │ ├── GenomeFile.cpp │ │ ├── GenomeFile.h │ │ ├── Makefile.frag │ │ ├── NewGenomeFile.cpp │ │ └── NewGenomeFile.h │ ├── KeyListOps │ │ ├── KeyListOps.cpp │ │ ├── KeyListOps.h │ │ ├── KeyListOpsMethods.cpp │ │ ├── KeyListOpsMethods.h │ │ └── Makefile.frag │ ├── NewChromsweep │ │ ├── CloseSweep.cpp │ │ ├── CloseSweep.h │ │ ├── Makefile.frag │ │ ├── NewChromsweep.cpp │ │ └── NewChromsweep.h │ ├── Point │ │ └── Point.h │ ├── RecordOutputMgr │ │ ├── Makefile.frag │ │ ├── RecordOutputMgr.cpp │ │ └── RecordOutputMgr.h │ ├── ToolBase │ │ ├── Makefile.frag │ │ ├── ToolBase.cpp │ │ └── ToolBase.h │ ├── VectorOps │ │ ├── Makefile.frag │ │ ├── VectorOps.cpp │ │ └── VectorOps.h │ ├── bedFile │ │ ├── Makefile.frag │ │ ├── bedFile.cpp │ │ └── bedFile.h │ ├── bedFilePE │ │ ├── Makefile.frag │ │ ├── bedFilePE.cpp │ │ └── bedFilePE.h │ ├── bedGraphFile │ │ ├── Makefile.frag │ │ ├── bedGraphFile.cpp │ │ └── bedGraphFile.h │ ├── chromsweep │ │ ├── Makefile.frag │ │ ├── chromsweep.cpp │ │ └── chromsweep.h │ ├── driver │ │ ├── BedtoolsDriver.cpp │ │ ├── BedtoolsDriver.h │ │ └── Makefile.frag │ ├── fileType │ │ ├── FileRecordTypeChecker.cpp │ │ ├── FileRecordTypeChecker.h │ │ ├── Makefile.frag │ │ ├── fileType.cpp │ │ └── fileType.h │ ├── general │ │ ├── BTlist.h │ │ ├── BedtoolsTypes.h │ │ ├── CommonHelp.cpp │ │ ├── CommonHelp.h │ │ ├── CompressionTools.cpp │ │ ├── CompressionTools.h │ │ ├── ErrorMsg.cpp │ │ ├── ErrorMsg.h │ │ ├── FreeList.h │ │ ├── InflateStreamBuf.h │ │ ├── Makefile.frag │ │ ├── ParseTools.cpp │ │ ├── ParseTools.h │ │ ├── PushBackStreamBuf.cpp │ │ ├── PushBackStreamBuf.h │ │ ├── QuickString.cpp │ │ ├── QuickString.h │ │ ├── Random.cpp │ │ ├── Random.h │ │ ├── Tokenizer.cpp │ │ └── Tokenizer.h │ ├── gzstream │ │ ├── COPYING.LIB │ │ ├── Makefile.frag │ │ ├── README │ │ ├── gzstream.C │ │ ├── gzstream.h │ │ └── version.txt │ ├── htslib │ │ ├── INSTALL │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── NEWS │ │ ├── README │ │ ├── bcf_sr_sort.c │ │ ├── bcf_sr_sort.h │ │ ├── bgzf.c │ │ ├── bgzip.1 │ │ ├── bgzip.c │ │ ├── config.mk.in │ │ ├── configure.ac │ │ ├── cram │ │ │ ├── cram.h │ │ │ ├── cram_codecs.c │ │ │ ├── cram_codecs.h │ │ │ ├── cram_decode.c │ │ │ ├── cram_decode.h │ │ │ ├── cram_encode.c │ │ │ ├── cram_encode.h │ │ │ ├── cram_external.c │ │ │ ├── cram_index.c │ │ │ ├── cram_index.h │ │ │ ├── cram_io.c │ │ │ ├── cram_io.h │ │ │ ├── cram_samtools.c │ │ │ ├── cram_samtools.h │ │ │ ├── cram_stats.c │ │ │ ├── cram_stats.h │ │ │ ├── cram_structs.h │ │ │ ├── files.c │ │ │ ├── mFILE.c │ │ │ ├── mFILE.h │ │ │ ├── misc.h │ │ │ ├── open_trace_file.c │ │ │ ├── open_trace_file.h │ │ │ ├── os.h │ │ │ ├── pooled_alloc.c │ │ │ ├── pooled_alloc.h │ │ │ ├── rANS_byte.h │ │ │ ├── rANS_static.c │ │ │ ├── rANS_static.h │ │ │ ├── sam_header.c │ │ │ ├── sam_header.h │ │ │ ├── string_alloc.c │ │ │ └── string_alloc.h │ │ ├── errmod.c │ │ ├── faidx.5 │ │ ├── faidx.c │ │ ├── hfile.c │ │ ├── hfile_gcs.c │ │ ├── hfile_internal.h │ │ ├── hfile_libcurl.c │ │ ├── hfile_net.c │ │ ├── hfile_s3.c │ │ ├── hts.c │ │ ├── hts_internal.h │ │ ├── hts_os.c │ │ ├── htsfile.1 │ │ ├── htsfile.c │ │ ├── htslib.mk │ │ ├── htslib.pc.in │ │ ├── htslib │ │ │ ├── bgzf.h │ │ │ ├── cram.h │ │ │ ├── faidx.h │ │ │ ├── hfile.h │ │ │ ├── hts.h │ │ │ ├── hts_defs.h │ │ │ ├── hts_endian.h │ │ │ ├── hts_log.h │ │ │ ├── hts_os.h │ │ │ ├── kbitset.h │ │ │ ├── kfunc.h │ │ │ ├── khash.h │ │ │ ├── khash_str2int.h │ │ │ ├── klist.h │ │ │ ├── knetfile.h │ │ │ ├── kseq.h │ │ │ ├── ksort.h │ │ │ ├── kstring.h │ │ │ ├── regidx.h │ │ │ ├── sam.h │ │ │ ├── synced_bcf_reader.h │ │ │ ├── tbx.h │ │ │ ├── thread_pool.h │ │ │ ├── vcf.h │ │ │ ├── vcf_sweep.h │ │ │ └── vcfutils.h │ │ ├── htslib_vars.mk │ │ ├── kfunc.c │ │ ├── knetfile.c │ │ ├── kstring.c │ │ ├── m4 │ │ │ └── hts_prog_cc_warnings.m4 │ │ ├── md5.c │ │ ├── multipart.c │ │ ├── os │ │ │ ├── lzma_stub.h │ │ │ └── rand.c │ │ ├── plugin.c │ │ ├── probaln.c │ │ ├── realn.c │ │ ├── regidx.c │ │ ├── sam.5 │ │ ├── sam.c │ │ ├── synced_bcf_reader.c │ │ ├── tabix.1 │ │ ├── tabix.c │ │ ├── tbx.c │ │ ├── textutils.c │ │ ├── textutils_internal.h │ │ ├── thread_pool.c │ │ ├── thread_pool_internal.h │ │ ├── vcf.5 │ │ ├── vcf.c │ │ ├── vcf_sweep.c │ │ ├── vcfutils.c │ │ └── version.sh │ ├── lineFileUtilities │ │ └── lineFileUtilities.h │ ├── sequenceUtilities │ │ ├── Makefile.frag │ │ ├── sequenceUtils.cpp │ │ └── sequenceUtils.h │ ├── stringUtilities │ │ └── stringUtilities.h │ ├── tabFile │ │ ├── Makefile.frag │ │ ├── tabFile.cpp │ │ └── tabFile.h │ └── version │ │ ├── Makefile.frag │ │ ├── version.cpp │ │ ├── version.h │ │ └── version_release.txt ├── windowBed │ ├── Makefile.frag │ ├── windowBed.cpp │ ├── windowBed.h │ └── windowMain.cpp └── windowMaker │ ├── Makefile.frag │ ├── windowMaker.cpp │ ├── windowMaker.h │ └── windowMakerMain.cpp ├── test ├── bamtobed │ ├── extra-long-header.sam.gz │ ├── numeric_tag.sam │ ├── one_block.sam │ ├── test-bamtobed.sh │ ├── three_blocks.sam │ ├── two_blocks.sam │ └── two_blocks_w_D.sam ├── bamtofastq │ ├── golden.fq │ ├── golden.fq2 │ ├── test-bamtofastq.sh │ ├── test.sam │ └── test2.sam ├── bed12tobed6 │ ├── bed6.bed │ ├── one_blocks.bed │ ├── test-bed12tobed6.sh │ ├── three_blocks.bed │ └── two_blocks.bed ├── bedtobam │ ├── chrsize.tmp │ └── test-bedtobam.sh ├── bigchroms │ ├── abig.bed │ ├── big4.bed │ ├── big4c.bed │ ├── bigx.bed │ ├── make-big-chrom.py │ └── test-bigchroms.sh ├── closest │ ├── a.bed │ ├── a.names.bed │ ├── a2.bed │ ├── b-one-bp-closer.bed │ ├── b.bed │ ├── b.names.bed │ ├── b2.bed │ ├── bug157_a.bed │ ├── bug157_b.bed │ ├── bug281_a.flip.medium.bed │ ├── bug281_a.medium.bed │ ├── bug281_b.bed │ ├── bug281_b.flip.bed │ ├── close-a.bed │ ├── close-b.bed │ ├── d.bed │ ├── d4.bed │ ├── d_d1F.bed │ ├── d_d1R.bed │ ├── d_d2F.bed │ ├── d_d2R.bed │ ├── d_id.bed │ ├── d_iu.bed │ ├── d_q1.bed │ ├── d_q2.bed │ ├── dmr.bed │ ├── islands.2.bed │ ├── islands.bed │ ├── kclosest │ │ ├── bug471_a.bed │ │ ├── bug471_b.bed │ │ ├── d1.bed │ │ ├── d2.bed │ │ ├── d3.bed │ │ ├── q1.bed │ │ ├── q2.bed │ │ └── test-kclosest.sh │ ├── mdb1.bed │ ├── mdb2.bed │ ├── mdb3.bed │ ├── mq1.bed │ ├── null_a.bed │ ├── null_b.bed │ ├── null_c.bed │ ├── shores.bed │ ├── sortAndNaming │ │ ├── alpha_all.bed │ │ ├── alpha_missing.bed │ │ ├── db1_gls.bed │ │ ├── db1_leadingZero.txt │ │ ├── db1_noChr.bed │ │ ├── db1_num.bed │ │ ├── db2_num.bed │ │ ├── db2_numBackwards.bed │ │ ├── db3_numBackwards.bed │ │ ├── num_all.bed │ │ ├── num_missing.bed │ │ ├── q1_gls.bed │ │ ├── q1_num.bed │ │ ├── q1a_num.bed │ │ ├── sdb1.bed │ │ ├── sq1.bed │ │ └── test-sort-and-naming.sh │ ├── strand-test-a.bed │ ├── strand-test-b.bed │ ├── strand-test-c.bed │ ├── strand-test-d.bed │ ├── test-closest.sh │ └── tfbs.bed ├── cluster │ ├── in.bed │ └── test-cluster.sh ├── complement │ ├── issue_503.bed │ ├── issue_503.genome │ └── test-complement.sh ├── coverage │ ├── a.bed │ ├── b.bed │ ├── c.bed │ ├── chr_0-100.bed │ ├── one_block.bam.bai │ ├── one_block.sam │ ├── sam-w-del.bam.bai │ ├── sam-w-del.sam │ ├── test-coverage.sh │ ├── three_blocks.bam.bai │ ├── three_blocks.sam │ ├── three_blocks_match.bam │ ├── three_blocks_match.bed │ ├── three_blocks_match_1bp.bed │ ├── three_blocks_nomatch.bed │ ├── two_blocks.bam.bai │ ├── two_blocks.sam │ ├── x.bed │ └── y.bed ├── expand │ ├── expand.txt │ └── test-expand.sh ├── fisher │ ├── README.md │ ├── a.bed │ ├── a_merge.bed │ ├── b.bed │ ├── cmp.sh │ ├── dm6.fai │ ├── get.sh │ ├── issue954.genome │ ├── issue954_a.bed │ ├── issue954_b.bed │ ├── plot.py │ ├── shuf.sh │ ├── sim.py │ ├── t.500.genome │ ├── t.60.genome │ ├── test-fisher.sh │ ├── test.bed │ └── tumor.gff ├── flank │ ├── a.bed │ ├── test-flank.sh │ └── tiny.genome ├── general │ ├── a.chromheader.bed │ ├── a.trackheader.bed │ ├── empty.bed │ ├── hg19.fa.fai │ ├── non-empty.bed.gz │ ├── t.bed │ └── test-general.sh ├── genomecov │ ├── chip.sam │ ├── empty.bam │ ├── empty.cram │ ├── genome.txt │ ├── mk-deep.py │ ├── one_block.sam │ ├── pair-chip.sam │ ├── sam-w-del.sam │ ├── test-genomecov.sh │ ├── test_ref.fa │ ├── test_ref.fa.fai │ ├── three_blocks.sam │ ├── three_blocks_match.bed │ ├── three_blocks_match_1bp.bed │ ├── three_blocks_nomatch.bed │ ├── two_blocks.sam │ ├── y.bam │ └── y.bed ├── getfasta │ ├── blocks.bed │ ├── rna.bed │ ├── rna.fasta │ ├── t.bed │ ├── t.fa │ ├── t.fa.fai │ ├── t.fa.gz │ ├── t_fH.fa │ ├── t_fH.fa.fai │ ├── test-getfasta.sh │ ├── test.iupac.bed │ └── test.iupac.fa ├── groupby │ ├── a_vcfSVtest.vcf │ ├── bug569_problem.txt │ ├── gdc.bam │ ├── noPosvalues.header.bed │ ├── test-groupby.sh │ ├── test.bed │ ├── values3.7fields.header.bed │ ├── values3.header.bed │ ├── values3.no_header.bed │ ├── values3.unmarked_header.bed │ ├── values3.unmarked_header.bed.2 │ └── values3_case.header.bed ├── intersect │ ├── a.bam │ ├── a.bed │ ├── a.cram │ ├── a.issue311.bed │ ├── aVSb.bam │ ├── aWithHeaderVsB.txt │ ├── a_bgzipped.bed.gz │ ├── a_gzipped.bed.gz │ ├── a_testZeroLen.bed │ ├── a_vcfSVtest.vcf │ ├── a_withLargeHeader.bed │ ├── a_withLargeHeader_bgzipped.bed.gz │ ├── a_withLargeHeader_gzipped.bed.gz │ ├── a_with_bothUnmapped.bam │ ├── b.bed │ ├── b.cram │ ├── b.issue311.gff │ ├── b.issue311.vcf │ ├── b_testZeroLen.bed │ ├── b_vcfSVtest.vcf │ ├── bed3.bed │ ├── bed4.bed │ ├── bed5.bed │ ├── bed6.bed │ ├── bed6.strand.bed │ ├── bed6.strand2.bed │ ├── bedplus.bed │ ├── blocks.bed12 │ ├── bug150_a.bed │ ├── bug150_b.bed │ ├── bug167_strandSweep.bed │ ├── bug187_a.bed │ ├── bug187_b.bed │ ├── bug223_d.vcf │ ├── bug223_e.vcf │ ├── bug223_f.vcf │ ├── bug223_sv1_a.vcf │ ├── bug223_sv1_b.vcf │ ├── bug44_a.vcf.gz │ ├── bug44_b.bed │ ├── c.bed │ ├── chromOrderA.bed │ ├── chromOrderB.bed │ ├── chromsOutOfOrder.bed │ ├── d.bed │ ├── dosLineCharWithExtraTab_b.bed │ ├── dosLineChar_a.bed │ ├── e.bed │ ├── exons.issue750.bed │ ├── foo │ ├── gdc.bam │ ├── gdc.gff │ ├── gdc_exp │ ├── gdc_one.bed │ ├── headerOnly.vcf │ ├── human.hg19.genome │ ├── human.hg19.vSort.genome │ ├── issue-919.bed │ ├── issue-919.region.bed │ ├── issue_773_b.bed │ ├── issue_773_y.bed │ ├── j1.bed │ ├── jim.bed │ ├── jim.vcf │ ├── large_a.bed │ ├── large_b.bed │ ├── mapped_and_unmapped.sam │ ├── multi_intersect │ │ ├── d1.bed │ │ ├── d2.bed │ │ ├── d3.bed │ │ ├── d4.bed │ │ ├── d5.bed │ │ ├── d6.bed │ │ ├── d7.bed │ │ ├── d8.bed │ │ ├── d9.bed │ │ ├── g.bed │ │ ├── query.bed │ │ ├── query2.bed │ │ ├── query3.bed │ │ └── test-multi_intersect.sh │ ├── new_test-intersect.sh │ ├── nonamecheck_a.bed │ ├── nonamecheck_b.bed │ ├── notexthdr.bam │ ├── null_a.bed │ ├── null_b.bed │ ├── null_c.bed │ ├── oneRecordNoNewline.bed │ ├── oneUnmapped.bam │ ├── one_block.sam │ ├── performanceTest.sh │ ├── queryUnmappedMateMappedCoordsInvalid.bam │ ├── recordsOutOfOrder.bed │ ├── sortAndNaming │ │ ├── alpha_all.bed │ │ ├── alpha_missing.bed │ │ ├── bigTests │ │ │ ├── 2.21_500Kvs500K.txt │ │ │ ├── 2.21_5v5.txt │ │ │ ├── 2.21_chr1.txt │ │ │ ├── curr500Kvs500K.txt │ │ │ ├── curr5v5.txt │ │ │ ├── currChr1.txt │ │ │ ├── db500K.bed │ │ │ ├── dbchr1.bed │ │ │ ├── diffs.txt │ │ │ ├── q500K.bed │ │ │ └── qchr1.bed │ │ ├── db1_gls.bed │ │ ├── db1_leadingZero.txt │ │ ├── db1_noChr.bed │ │ ├── db1_num.bed │ │ ├── db2_num.bed │ │ ├── db2_numBackwards.bed │ │ ├── db3_numBackwards.bed │ │ ├── diffs.txt │ │ ├── exp1 │ │ ├── num_all.bed │ │ ├── num_missing.bed │ │ ├── q1_gls.bed │ │ ├── q1_num.bed │ │ ├── q1a_num.bed │ │ ├── sdb1.bed │ │ ├── sq1.bed │ │ └── test-sort-and-naming.sh │ ├── split.issue750.bam │ ├── split.issue750.sam │ ├── splitBug155_a.bed │ ├── splitBug155_b.bed │ ├── strand_with_star.a.bed │ ├── strand_with_star.b.bed │ ├── svlen.vcf │ ├── test-intersect.sh │ ├── test_ref.fa │ ├── test_ref.fa.fai │ ├── three_blocks.sam │ ├── three_blocks_match.bam │ ├── three_blocks_match.bed │ ├── three_blocks_match_1bp.bed │ ├── three_blocks_nomatch.bed │ ├── two_blocks.sam │ ├── two_blocks_partial.bam │ ├── two_blocks_partial.bam.bai │ ├── two_blocks_partial.bed │ ├── ultra-long-bed4.bed │ ├── x.bam │ ├── x.bed │ └── y.bed ├── jaccard │ ├── a.bam │ ├── a.bed │ ├── a645.bed │ ├── aMixedStrands.bed │ ├── b.bed │ ├── b645.bed │ ├── bMixedStrands.bed │ ├── c.bed │ ├── e.bed │ ├── long.bed │ ├── short.bed │ ├── test-jaccard.sh │ ├── three_blocks_match.bam │ └── three_blocks_match.bed ├── makewindows │ ├── a.19bp.bed │ ├── a.20bp.bed │ ├── a.33bp.bed │ ├── input.bed │ └── test-makewindows.sh ├── map │ ├── .RData │ ├── .Rhistory │ ├── a.vsorted.bed │ ├── b.vsorted.bed │ ├── bug262_a.bed │ ├── bug262_b.bed │ ├── d.bed │ ├── fullFields.bam │ ├── genome │ ├── ivls.bed │ ├── ivls2.bed │ ├── t.bed │ ├── test-map.sh │ ├── test.gff │ ├── test.vcf │ ├── three_blocks_match.bed │ ├── three_blocks_nomatch.bed │ ├── values.bam │ ├── values.bed │ ├── values2.bed │ ├── values3.bed │ ├── values4.bed │ └── values5.bed ├── merge │ ├── a.bed │ ├── a.full.bam │ ├── a.full.bed │ ├── a.gff │ ├── a.names.bed │ ├── b.bed │ ├── bamCol10Collapse.txt │ ├── bamCol11Collapse.txt │ ├── bamCol1Collapse.txt │ ├── bamCol3Collapse.txt │ ├── bamCol4Mean.txt │ ├── bamCol5Mean.txt │ ├── bamCol6Collapse.txt │ ├── bamCol7Collapse.txt │ ├── bamCol8Mean.txt │ ├── bamCol9Mean.txt │ ├── bug254_c.bed │ ├── bug254_d.bed │ ├── bug254_e.bed │ ├── chained.bed.gz │ ├── expFormat.bed │ ├── fullFields.bam │ ├── mergeBugTest.bed │ ├── mixedStrands.bed │ ├── precisionTest.bed │ ├── precisionTest2.bed │ ├── test-merge.sh │ ├── testA.vcf │ ├── unsorted.bed │ └── vcfSVtest.vcf ├── multicov │ ├── multicov.bed │ ├── one_block.sam │ ├── test-multi.2.sam │ ├── test-multi.bed │ ├── test-multi.sam │ ├── test-multicov.sh │ └── two_blocks.sam ├── negativecontrol │ └── test-negativecontrol.sh ├── reldist │ ├── issue_711.a.bed │ ├── issue_711.b.bed │ └── test-reldist.sh ├── sample │ ├── human.hg19.genome │ └── test-sample.sh ├── shift │ ├── a.bed │ ├── b.bed │ ├── huge.genome │ ├── issue_807.bed │ ├── issue_807.genomesize │ ├── test-shift.sh │ └── tiny.genome ├── shuffle │ ├── excl.bed │ ├── incl.bed │ ├── incl.sizedif.bed │ ├── simrep.bed │ └── test-shuffle.sh ├── slop │ ├── a.bed │ ├── test-slop.sh │ └── tiny.genome ├── sort │ ├── a.bed │ ├── b.bed │ ├── names.txt │ └── test-sort.sh ├── spacing │ ├── a.bed │ └── test-spacing.sh ├── split │ ├── randData.bed │ └── test-split.sh ├── subtract │ ├── a.bed │ ├── b.bed │ ├── b2.bed │ ├── c.bed │ ├── d.bed │ └── test-subtract.sh └── test.sh └── tutorial ├── Makefile ├── answers.html ├── answers.md ├── bedtools.html ├── bedtools.md ├── bootstrap.css ├── template.class.html └── template.html /.github/workflows/main.yml: -------------------------------------------------------------------------------- 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