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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

MethodReportDistanceSummary

src/reldist/reldist.cpp:58

MethodReportDnaProfile

src/nucBed/nucBed.cpp:40

MethodReportGenomeCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:441

MethodReportSeq

src/fastaFromBed/fastaFromBed.cpp:69

MethodResetChromCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:91

Rewind the pointer back to the beginning of the file

src/utils/bedFile/bedFile.cpp:145

MethodSamHeader

src/utils/BamTools/include/SamHeader.hpp:62

MethodSampleFile

src/sampleFile/sampleFile.cpp:8

FunctionSampleRecordLtFn

src/sampleFile/sampleFile.cpp:4

MethodScanCache

src/utils/chromsweep/chromsweep.cpp:84

Jump to a specific byte in the file

src/utils/bedFile/bedFile.cpp:153

MethodSetAlignmentFlag

src/utils/BamTools/include/BamAlignment.hpp:306

MethodSetCramReqdFieldsCode

src/utils/BamTools/include/BamReader.hpp:370

src/shiftBed/shiftBed.cpp:32

src/shuffleBed/shuffleBed.cpp:103

MethodShuffleWithExclusions

src/shuffleBed/shuffleBed.cpp:144

MethodShuffleWithInclusions

src/shuffleBed/shuffleBed.cpp:243

MethodShuffleWithInclusionsAndExclusions

src/shuffleBed/shuffleBed.cpp:274

MethodSimpleSplitInfo

src/split/splitBed.cpp:210

MethodSingleFastq

src/bamToFastq/bamToFastq.cpp:38

MethodSingleLineDelimTextFileReader

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:9

MethodSingleLineDelimTransferBuffer

src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:9

src/slopBed/slopBed.cpp:41

MethodSpacingFile

src/spacingFile/spacingFile.cpp:9

MethodStartNewChrom

src/genomeCoverageBed/genomeCoverageBed.cpp:98

MethodStrandQueue

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

MethodSubtractFile

src/subtractFile/subtractFile.cpp:4

MethodSummaryFile

src/summaryFile/summaryFile.cpp:17

src/utils/tabFile/tabFile.cpp:20

src/tagBam/tagBam.cpp:16

src/utils/BamTools/include/SamHeader.hpp:126

FunctionTokenizeColumns

tokenize a column string into a list of integers.

src/utils/lineFileUtilities/lineFileUtilities.h:66

MethodTokenizer

src/utils/general/Tokenizer.cpp:11

src/utils/ToolBase/ToolBase.h:20

MethodUnionBedGraphs

src/unionBedGraphs/unionBedGraphs.cpp:25

MethodUpdateDistanceSummary

src/reldist/reldist.cpp:78

MethodUpdateInformation

src/unionBedGraphs/unionBedGraphs.cpp:112

MethodVcfRecord

src/utils/FileRecordTools/Records/VcfRecord.h:19

MethodVectorOps

src/utils/VectorOps/VectorOps.cpp:58

MethodWindowIntersectBam

src/windowBed/windowBed.cpp:152

MethodWindowIntersectBed

src/windowBed/windowBed.cpp:127

MethodWindowMaker

src/windowMaker/windowMaker.cpp:14

MethodWritePairs

src/bamToFastq/bamToFastq.cpp:113

src/linksBed/linksBed.cpp:36

Method_MetaData

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

Method_Open_impl

src/utils/BamTools/include/BamReader.hpp:172

src/utils/BamTools/include/BamReader.hpp:42

Method_SupportData

TODO(haohou): populate the string data */ TODO(haohou): Tag2Cigar? Real Cigar ? */

src/utils/BamTools/include/BamAlignment.hpp:223

Method_TagGetter

src/utils/BamTools/include/BamAlignment.hpp:84

Method_TagGetter

src/utils/BamTools/include/BamAlignment.hpp:98

Method_TagGetterBase

src/utils/BamTools/include/BamAlignment.hpp:74

Function__ac_Wang_hash

src/utils/htslib/htslib/khash.h:412

Function__ac_X31_hash_string

! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */

src/utils/htslib/htslib/khash.h:395

(self, *args, **kwargs)

docs/conf.py:232

Method__getattr__

docs/conf.py:236

src/utils/BamTools/mapping/BamAlignment.py:3

src/utils/BamTools/mapping/BamAlignment.py:24

(self, *args, **kwargs)

docs/conf.py:229

Method_ensure_data_chunk

src/utils/BamTools/include/BamAlignment.hpp:110

Function_mk_numeric

src/utils/BamTools/include/BamAlignment.hpp:12

src/utils/BamTools/include/BamAlignment.hpp:10

src/utils/BamTools/include/BamAlignment.mapping.hpp:9

src/utils/BamTools/include/BamAlignment.mapping.hpp:21

src/utils/BamTools/include/BamAlignment.mapping.hpp:33

src/utils/BamTools/include/BamAlignment.mapping.hpp:45

src/utils/BamTools/include/BamAlignment.mapping.hpp:57

src/utils/BamTools/include/BamAlignment.mapping.hpp:69

src/utils/BamTools/include/BamAlignment.mapping.hpp:81

src/utils/BamTools/include/BamAlignment.mapping.hpp:93

src/utils/BamTools/include/BamAlignment.mapping.hpp:105

src/utils/BamTools/include/BamAlignment.mapping.hpp:117

src/utils/BamTools/include/BamAlignment.mapping.hpp:129

src/utils/BamTools/include/BamAlignment.mapping.hpp:141

Method_read_sam_file

src/utils/BamTools/include/BamReader.hpp:139

Functionabs_cmp

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:7

MethodaddColumns

src/utils/KeyListOps/KeyListOps.h:25

MethodaddDatabaseNameTag

src/utils/Contexts/ContextIntersect.h:39

MethodaddDbFileId

src/utils/RecordOutputMgr/RecordOutputMgr.cpp:490

MethodaddOperations

src/utils/KeyListOps/KeyListOps.h:30

MethodaddRecordToTree

src/utils/BinTree/BinTree.cpp:99

MethodaddRecsToRetList

src/utils/NewChromsweep/CloseSweep.cpp:417

MethodaddSingleRec

src/utils/NewChromsweep/CloseSweep.cpp:440

MethodaddToStorage

src/utils/FileRecordTools/FileRecordMergeMgr.cpp:165

MethodadjustStrandVal

src/utils/FileRecordTools/Records/Record.h:114

MethodallCachesEmpty

src/utils/NewChromsweep/NewChromsweep.cpp:318

src/utils/FileRecordTools/Records/RecordKeyVector.h:51

MethodallCurrDBrecsNull

src/utils/NewChromsweep/NewChromsweep.cpp:327

MethodallHitsRightOfQueryIgnored

src/utils/NewChromsweep/CloseSweep.cpp:723

MethodallocateFileReader

src/utils/FileRecordTools/FileRecordMgr.cpp:225

src/utils/general/QuickString.h:68

MethodappendField

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:97

MethodassignChromId

src/utils/FileRecordTools/FileRecordMgr.cpp:152

MethodassignNoCopy

src/utils/general/BTlist.h:226

MethodassignPrevFields

src/groupBy/groupBy.cpp:133

Functionauth_header_callback

src/utils/htslib/hfile_s3.c:255

src/utils/FileRecordTools/Records/RecordList.h:67

Functionbam_aux2A

src/utils/htslib/sam.c:2022

Functionbam_aux2Z

src/utils/htslib/sam.c:2031

Functionbam_aux2f

src/utils/htslib/sam.c:2013

Functionbam_auxB2f

src/utils/htslib/sam.c:2059

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