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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

src/shiftBed/shiftBed.cpp:13

MethodBedShuffle

src/shuffleBed/shuffleBed.cpp:17

src/slopBed/slopBed.cpp:16

src/sortBed/sortBed.cpp:19

src/split/splitBed.cpp:67

MethodBedSplitItems

src/split/splitBed.cpp:48

MethodBedWindow

src/windowBed/windowBed.cpp:19

MethodBedtoolsDriver

src/utils/driver/BedtoolsDriver.cpp:32

src/utils/BinTree/BinTree.cpp:5

src/utils/FileRecordTools/Records/BlockMgr.cpp:16

MethodBufferedStreamMgr

src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:13

MethodCalculateRelativeDistance

src/reldist/reldist.cpp:87

MethodCalculateWindows

src/windowMaker/windowMaker.cpp:81

MethodChooseLocus

src/shuffleBed/shuffleBed.cpp:318

MethodChooseLocusFromInclusionFile

src/shuffleBed/shuffleBed.cpp:447

MethodChoosePairedLocus

src/shuffleBed/shuffleBed.cpp:395

MethodChromChange

src/utils/chromsweep/chromsweep.cpp:101

MethodChromSweep

// constructor using existing BedFile pointers */

src/utils/chromsweep/chromsweep.cpp:21

src/utils/BamTools/include/BamAlignment.hpp:41

Close the BEDGRAPH file

src/utils/bedGraphFile/bedGraphFile.cpp:56

Close the BEDPE file

src/utils/bedFilePE/bedFilePE.cpp:56

src/utils/BamTools/include/BamReader.hpp:297

src/utils/BamTools/include/BamWriter.hpp:45

Close the BED file

src/utils/bedFile/bedFile.cpp:163

MethodCloseAnnoFiles

src/tagBam/tagBam.cpp:49

MethodCloseAnnoFiles

src/annotateBed/annotateBed.cpp:47

MethodCloseBedgraphFiles

src/unionBedGraphs/unionBedGraphs.cpp:247

MethodCloseFiles

src/multiIntersectBed/multiIntersectBed.cpp:201

MethodCloseSweep

src/utils/NewChromsweep/CloseSweep.cpp:144

MethodClosestFile

src/closestFile/closestFile.cpp:11

MethodClusterBed

= Cluster overlapping or nearby BED entries =

src/clusterBed/clusterBed.cpp:38

MethodClusterBedStranded

= Cluster overlapping BED entries, accounting for strandedness =

src/clusterBed/clusterBed.cpp:69

MethodComplementFile

src/complementFile/complementFile.cpp:4

MethodConsumeNextCoordinate

src/unionBedGraphs/unionBedGraphs.cpp:98

MethodContextBase

src/utils/Contexts/ContextBase.cpp:14

MethodContextClosest

src/utils/Contexts/ContextClosest.cpp:10

MethodContextComplement

src/utils/Contexts/ContextComplement.cpp:10

MethodContextCoverage

src/utils/Contexts/ContextCoverage.cpp:10

MethodContextFisher

src/utils/Contexts/ContextFisher.cpp:8

MethodContextGroupBy

src/utils/Contexts/ContextGroupBy.cpp:11

MethodContextIntersect

src/utils/Contexts/ContextIntersect.cpp:10

MethodContextJaccard

src/utils/Contexts/ContextJaccard.cpp:10

MethodContextMap

src/utils/Contexts/ContextMap.cpp:10

MethodContextMerge

src/utils/Contexts/ContextMerge.cpp:11

MethodContextSample

src/utils/Contexts/ContextSample.cpp:9

MethodContextSpacing

src/utils/Contexts/ContextSpacing.cpp:9

MethodContextSubtract

src/utils/Contexts/ContextSubtract.cpp:10

MethodContextSummary

src/utils/Contexts/ContextSummary.cpp:9

MethodConvertBamToBedPE

src/pairToBed/pairToBed.h:81

MethodCoverageBam

src/genomeCoverageBed/genomeCoverageBed.cpp:254

MethodCoverageBed

src/genomeCoverageBed/genomeCoverageBed.cpp:157

MethodCoverageFile

src/coverageFile/coverageFile.cpp:11

MethodCreateLinks

src/linksBed/linksBed.cpp:81

MethodDetermineNextChrom

src/unionBedGraphs/unionBedGraphs.cpp:196

MethodDetermineNextChrom

src/multiIntersectBed/multiIntersectBed.cpp:174

MethodEmptyRecord

src/utils/FileRecordTools/Records/EmptyRecord.cpp:15

MethodExtractSeq

Extract sequence

src/fastaFromBed/fastaFromBed.cpp:111

MethodFastaIndex

src/utils/Fasta/Fasta.cpp:31

MethodFastaIndexEntry

src/utils/Fasta/Fasta.cpp:14

MethodFastaReference

src/utils/Fasta/Fasta.h:64

MethodFileReader

src/utils/FileRecordTools/FileReaders/FileReader.cpp:6

MethodFileRecordMergeMgr

src/utils/FileRecordTools/FileRecordMergeMgr.cpp:11

MethodFileRecordMgr

src/utils/FileRecordTools/FileRecordMgr.cpp:7

MethodFileRecordTypeChecker

src/utils/fileType/FileRecordTypeChecker.cpp:6

MethodFindBlockedOverlaps

src/multiBamCov/multiBamCov.cpp:52

MethodFindHitsOnBothEnds

src/pairToPair/pairToPair.cpp:136

MethodFindHitsOnEitherEnd

src/pairToPair/pairToPair.cpp:175

MethodFindOneOrMoreOverlaps

src/pairToBed/pairToBed.cpp:195

MethodFindOneOrMoreSpanningOverlaps

src/pairToBed/pairToBed.cpp:306

MethodFindOneOrMoreWindowOverlaps

src/windowBed/windowBed.cpp:113

MethodFindOverlaps

src/pairToBed/pairToBed.cpp:70

MethodFindOverlaps

src/pairToPair/pairToPair.cpp:70

MethodFindSpanningOverlaps

src/pairToBed/pairToBed.cpp:250

MethodFindWindowOverlaps

src/windowBed/windowBed.cpp:60

src/fisher/fisher.cpp:10

src/flankBed/flankBed.cpp:42

src/utils/general/FreeList.h:20

src/randomBed/randomBed.cpp:40

MethodGenerateID

src/windowMaker/windowMaker.cpp:145

MethodGenomeFile

src/utils/GenomeFile/GenomeFile.cpp:16

MethodGetAbsMax

src/utils/VectorOps/VectorOps.cpp:156

MethodGetAbsMin

src/utils/VectorOps/VectorOps.cpp:142

MethodGetAlignmentFlag

src/utils/BamTools/include/BamAlignment.hpp:301

MethodGetAntiMode

src/utils/VectorOps/VectorOps.cpp:194

MethodGetCollapse

src/utils/VectorOps/VectorOps.cpp:236

MethodGetConcat

src/utils/VectorOps/VectorOps.cpp:247

src/utils/VectorOps/VectorOps.cpp:224

MethodGetCountDistinct

src/utils/VectorOps/VectorOps.cpp:229

MethodGetDistinct

src/utils/VectorOps/VectorOps.cpp:255

MethodGetDistinctSortNum

src/utils/VectorOps/VectorOps.cpp:271

src/utils/VectorOps/VectorOps.cpp:367

MethodGetFreqAsc

src/utils/VectorOps/VectorOps.cpp:331

MethodGetFreqDesc

src/utils/VectorOps/VectorOps.cpp:295

MethodGetHeader

src/utils/BamTools/include/BamReader.hpp:256

MethodGetHeader

Extract and store the header for the file.

src/utils/bedFile/bedFile.cpp:169

MethodGetHeaderText

src/utils/BamTools/include/SamHeader.hpp:100

src/utils/VectorOps/VectorOps.cpp:373

src/utils/VectorOps/VectorOps.cpp:149

src/utils/VectorOps/VectorOps.cpp:78

MethodGetMedian

src/utils/VectorOps/VectorOps.cpp:113

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