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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

src/utils/VectorOps/VectorOps.cpp:135

src/utils/VectorOps/VectorOps.cpp:163

MethodGetReferenceData

src/utils/BamTools/include/SamHeader.hpp:116

MethodGetSstddev

src/utils/VectorOps/VectorOps.cpp:99

MethodGetStddev

src/utils/VectorOps/VectorOps.cpp:85

src/utils/VectorOps/VectorOps.cpp:71

MethodGffPlusRecord

src/utils/FileRecordTools/Records/GffPlusRecord.cpp:4

MethodGffRecord

src/utils/FileRecordTools/Records/GffRecord.cpp:5

src/groupBy/groupBy.cpp:13

FunctionHTS_RESULT_USED hgetln

Read a line from the stream, up to a maximum length @param buffer The buffer into which bytes will be written @param size The size of the buff

src/utils/htslib/htslib/hfile.h:174

FunctionHTS_RESULT_USED hread

Read a block of characters from the file @return The number of bytes read, or negative if an error occurred. The full _nbytes_ requested will be ret

src/utils/htslib/htslib/hfile.h:211

FunctionHTS_RESULT_USED hwrite

Write a block of characters to the file @return Either _nbytes_, or negative if an error occurred. In the absence of I/O errors, the full _nbytes_ w

src/utils/htslib/htslib/hfile.h:253

src/utils/BamTools/include/BamAlignment.hpp:376

MethodHasVersion

src/utils/BamTools/include/SamHeader.hpp:132

MethodInflateStreamBuf

src/utils/general/InflateStreamBuf.h:34

MethodInitCigarData

src/utils/BamTools/include/BamAlignment.hpp:144

MethodInitializeMainFile

src/annotateBed/annotateBed.cpp:78

MethodInputStreamMgr

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:17

MethodIntersectBamPE

src/pairToBed/pairToBed.cpp:377

MethodIntersectBedPE

src/pairToBed/pairToBed.cpp:338

MethodIntersectFile

src/intersectFile/intersectFile.cpp:20

MethodIntersectPairs

src/pairToPair/pairToPair.cpp:46

FunctionIsCorrectMappingForBEDPE

src/pairToBed/pairToBed.cpp:16

MethodIsValidHit

src/utils/chromsweep/chromsweep.cpp:140

src/jaccard/jaccard.cpp:10

MethodKeyListOps

src/utils/KeyListOps/KeyListOps.cpp:13

MethodKeyListOpsMethods

src/utils/KeyListOps/KeyListOpsMethods.cpp:14

MethodLoadBamFileMap

src/multiBamCov/multiBamCov.cpp:220

MethodLoadMidpoints

src/reldist/reldist.cpp:37

MethodLoadNextBedgraphItem

src/unionBedGraphs/unionBedGraphs.cpp:169

MethodLoadNextItem

src/multiIntersectBed/multiIntersectBed.cpp:151

FunctionMakeAbsDouble

functor to convert the abs() of single string to a double

src/utils/VectorOps/VectorOps.cpp:29

MethodMakeBEDWindow

src/windowMaker/windowMaker.cpp:73

FunctionMakeBedFromBam

src/utils/BamTools-Ancillary/BamAncillary.cpp:77

FunctionMakeDouble

functor to convert a single string to a double

src/utils/VectorOps/VectorOps.cpp:18

MethodMakeFixedCountWindow

src/windowMaker/windowMaker.cpp:103

MethodMakeFixedSizeWindow

src/windowMaker/windowMaker.cpp:89

MethodMakeWindowsFromBED

src/windowMaker/windowMaker.cpp:61

MethodMakeWindowsFromGenome

src/windowMaker/windowMaker.cpp:45

src/mapFile/mapFile.cpp:10

MethodMaskFasta

Mask the Fasta file based on the coordinates in the BED file.

src/maskFastaFromBed/maskFastaFromBed.cpp:40

MethodMaskFastaFromBed

src/maskFastaFromBed/maskFastaFromBed.cpp:16

MethodMergeFile

src/mergeFile/mergeFile.cpp:10

MethodMultiCovBam

src/multiBamCov/multiBamCov.cpp:20

MethodMultiIntersectBed

src/multiIntersectBed/multiIntersectBed.cpp:25

MethodNewChromSweep

src/utils/NewChromsweep/NewChromsweep.cpp:17

MethodNewGenomeFile

src/utils/GenomeFile/NewGenomeFile.cpp:17

src/utils/chromsweep/chromsweep.cpp:171

MethodNextDatabase

src/utils/chromsweep/chromsweep.cpp:70

MethodNextQuery

src/utils/chromsweep/chromsweep.cpp:63

MethodNoPosPlusRecord

src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp:4

src/nucBed/nucBed.cpp:16

Open the BEDGRAPH file

src/utils/bedGraphFile/bedGraphFile.cpp:29

src/utils/bedFilePE/bedFilePE.cpp:28

src/utils/BamTools/include/BamReader.hpp:215

src/utils/BamTools/include/BamWriter.hpp:21

src/utils/bedFile/bedFile.cpp:115

MethodOpenAnnoFiles

src/tagBam/tagBam.cpp:40

MethodOpenAnnoFiles

src/annotateBed/annotateBed.cpp:38

MethodOpenBedgraphFiles

src/unionBedGraphs/unionBedGraphs.cpp:235

MethodOpenFiles

src/multiIntersectBed/multiIntersectBed.cpp:190

FunctionPLUGIN_GLOBAL(hfile_plugin_init,_gcs)

src/utils/htslib/hfile_gcs.c:118

FunctionPLUGIN_GLOBAL(hfile_plugin_init,_libcurl)

src/utils/htslib/hfile_libcurl.c:1331

FunctionPLUGIN_GLOBAL(hfile_plugin_init,_s3)

src/utils/htslib/hfile_s3.c:448

MethodPairToPair

src/pairToPair/pairToPair.cpp:19

MethodPairedFastq

src/bamToFastq/bamToFastq.cpp:69

MethodPairedFastqUseTags

src/bamToFastq/bamToFastq.cpp:252

MethodPlusFields

src/utils/FileRecordTools/Records/PlusFields.cpp:4

src/utils/Point/Point.h:33

MethodPointWithDepth

src/utils/Point/Point.h:83

MethodPrettyPrintChrom

src/maskFastaFromBed/maskFastaFromBed.cpp:149

MethodPrintCoverage

src/unionBedGraphs/unionBedGraphs.cpp:142

MethodPrintCoverage

src/multiIntersectBed/multiIntersectBed.cpp:98

MethodPrintEmptyChromosomes

src/genomeCoverageBed/genomeCoverageBed.cpp:222

MethodPrintEmptyCoverage

src/unionBedGraphs/unionBedGraphs.cpp:157

MethodPrintEmptyCoverage

src/multiIntersectBed/multiIntersectBed.cpp:138

MethodPrintFinalCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:246

MethodPrintHeader

src/annotateBed/annotateBed.cpp:56

MethodPrintTrackDefinitionLine

src/genomeCoverageBed/genomeCoverageBed.cpp:68

MethodProcessBamBlock

src/pairToBed/pairToBed.cpp:445

MethodProfileDNA

src/nucBed/nucBed.cpp:99

MethodPushBackStreamBuf

src/utils/general/PushBackStreamBuf.cpp:13

FunctionRansDecAdvanceSymbol

Equivalent to RansDecAdvance that takes a symbol.

src/utils/htslib/cram/rANS_byte.h:298

FunctionRansDecAdvanceSymbolStep

Equivalent to RansDecAdvanceStep that takes a symbol.

src/utils/htslib/cram/rANS_byte.h:316

FunctionRansEncPut

Encodes a single symbol with range start "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits", and the resulting byte

src/utils/htslib/cram/rANS_byte.h:92

MethodRecDistList

src/utils/NewChromsweep/CloseSweep.cpp:11

src/utils/FileRecordTools/Records/Record.cpp:4

MethodRecordKeyList

src/utils/FileRecordTools/Records/RecordKeyList.cpp:3

MethodRecordKeyVector

src/utils/FileRecordTools/Records/RecordKeyVector.cpp:12

MethodRecordList

src/utils/FileRecordTools/Records/RecordList.cpp:10

MethodRecordListNode

src/utils/FileRecordTools/Records/RecordList.h:37

MethodRecordMgr

src/utils/FileRecordTools/Records/RecordMgr.cpp:5

MethodRecordOutputMgr

src/utils/RecordOutputMgr/RecordOutputMgr.cpp:31

src/utils/BamTools/include/api/BamAux.h:13

MethodRegressTest

src/regressTest/RegressTest.cpp:22

MethodRelativeDistance

src/reldist/reldist.cpp:18

MethodReportAnnotations

src/annotateBed/annotateBed.cpp:134

MethodReportChromCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:378

MethodReportChromCoverageBedGraph

src/genomeCoverageBed/genomeCoverageBed.cpp:486

MethodReportCounts

src/multiBamCov/multiBamCov.cpp:228

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