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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 1 callersMethodsetPrintHeader

src/utils/Contexts/ContextBase.h:113

↓ 1 callersMethodsetStartPosStr

src/utils/FileRecordTools/Records/Record.h:96

↓ 1 callersMethodsetStrandType

src/utils/FileRecordTools/FileRecordMergeMgr.h:42

↓ 1 callersMethodsetSubtractFraction

src/utils/Contexts/ContextSubtract.h:21

↓ 1 callersMethodsetUseTags

setUseTags will tell the BamReader to give us all the extra tag information in a BAM record. By default, this is set to false, so not using them, whic

src/utils/FileRecordTools/FileReaders/BamFileReader.h:31

↓ 1 callersMethodset_range

src/utils/BamTools/include/BamReader.hpp:70

↓ 1 callersFunctionshift_main

src/shiftBed/shiftBedMain.cpp:25

↓ 1 callersMethodshouldRunToDbEnd

src/utils/Contexts/ContextIntersect.h:107

↓ 1 callersFunctionshowErrors

src/bedtools.cpp:354

↓ 1 callersFunctionshowHelp

src/bedtools.cpp:324

↓ 1 callersFunctionshuffle_main

src/shuffleBed/shuffleBedMain.cpp:27

↓ 1 callersMethodsize

src/utils/general/QuickString.h:28

↓ 1 callersMethodsizeWeightedSearch

src/utils/bedFile/bedFile.cpp:806

↓ 1 callersFunctionslop_main

src/slopBed/slopBedMain.cpp:27

↓ 1 callersMethodsort

src/utils/FileRecordTools/Records/RecordList.h:85

↓ 1 callersFunctionsort_main

src/sortBed/sortMain.cpp:27

↓ 1 callersFunctionspacing_help

src/spacingFile/spacingHelp.cpp:10

↓ 1 callersFunctionsplit

src/utils/Fasta/split.cpp:12

↓ 1 callersFunctionsplit_main

src/split/splitBedMain.cpp:14

↓ 1 callersFunctionsscan_string

src/utils/htslib/textutils.c:123

↓ 1 callersFunctionstring_alloc

src/utils/htslib/cram/string_alloc.c:110

↓ 1 callersFunctionstrtoint64

src/utils/htslib/knetfile.c:136

↓ 1 callersMethodsubMain

src/utils/driver/BedtoolsDriver.cpp:55

↓ 1 callersFunctionsubtract_help

src/subtractFile/subtractHelp.cpp:11

↓ 1 callersFunctionsummary_help

src/summaryFile/summaryHelp.cpp:10

↓ 1 callersMethodsupports

src/utils/driver/BedtoolsDriver.cpp:50

↓ 1 callersFunctionsw_fill_buffer

src/utils/htslib/vcf_sweep.c:83

↓ 1 callersFunctionsw_rec_equal

src/utils/htslib/vcf_sweep.c:55

↓ 1 callersFunctionsw_rec_save

src/utils/htslib/vcf_sweep.c:69

↓ 1 callersFunctionswap_bins

src/utils/htslib/hts.c:1667

↓ 1 callersFunctionsync

src/utils/gzstream/gzstream.C:125

↓ 1 callersFunctiontagbam_main

src/tagBam/tagBamMain.cpp:26

↓ 1 callersFunctiontbx_index_load2

src/utils/htslib/tbx.c:292

↓ 1 callersFunctiontbx_name2id

src/utils/htslib/tbx.c:78

↓ 1 callersFunctiontbx_parse1

src/utils/htslib/tbx.c:83

↓ 1 callersFunctiontbx_set_meta

src/utils/htslib/tbx.c:180

↓ 1 callersMethodtestCmdArgs

src/utils/Contexts/ContextBase.cpp:166

↓ 1 callersFunctiontestDualQueue

src/nekSandbox1/nekSandboxMain.cpp:295

↓ 1 callersFunctiontest_pipe

src/utils/htslib/thread_pool.c:1320

↓ 1 callersFunctiontest_square

src/utils/htslib/thread_pool.c:1060

↓ 1 callersFunctiontest_squareB

src/utils/htslib/thread_pool.c:1146

↓ 1 callersFunctiontest_square_u

src/utils/htslib/thread_pool.c:1018

↓ 1 callersFunctiontest_streams

src/nekSandbox1/nekSandboxMain.cpp:333

↓ 1 callersMethodtoStr

this method will convert the contents of the list into a string. It assumes that the templated type of the listNode can be converted to a char using t

src/utils/general/BTlist.h:239

↓ 1 callersMethodto_htslib_repr

src/utils/BamTools/include/BamAlignment.hpp:47

↓ 1 callersFunctiontrimNewlines

src/utils/general/ParseTools.cpp:37

↓ 1 callersFunctiontweak_overlap_quality

src/utils/htslib/sam.c:2496

↓ 1 callersFunctionunionbedgraphs_main

src/unionBedGraphs/unionBedGraphsMain.cpp:44

↓ 1 callersFunctionunionbedgraphs_showexamples

src/unionBedGraphs/unionBedGraphsMain.cpp:197

↓ 1 callersMethodupdate_range

src/utils/BamTools/include/BamReader.hpp:80

↓ 1 callersFunctionvcf_hdr_read

src/utils/htslib/vcf.c:1542

↓ 1 callersFunctionvcf_hdr_write

src/utils/htslib/vcf.c:1711

↓ 1 callersFunctionvcf_parse_format

src/utils/htslib/vcf.c:1878

↓ 1 callersFunctionvcf_read

src/utils/htslib/vcf.c:2388

↓ 1 callersFunctionvcf_write

src/utils/htslib/vcf.c:2614

↓ 1 callersFunctionview_sam

src/utils/htslib/htsfile.c:68

↓ 1 callersFunctionview_vcf

src/utils/htslib/htsfile.c:112

↓ 1 callersFunctionwindow_main

src/windowBed/windowMain.cpp:27

↓ 1 callersFunctionwindowmaker_main

src/windowMaker/windowMakerMain.cpp:27

↓ 1 callersFunctionzlib_mem_deflate

src/utils/htslib/cram/cram_io.c:603

MethodAddBlockedCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:145

MethodAddCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:133

src/flankBed/flankBed.cpp:75

MethodAddInterval

src/unionBedGraphs/unionBedGraphs.cpp:212

MethodAddInterval

src/multiIntersectBed/multiIntersectBed.cpp:61

src/shiftBed/shiftBed.cpp:50

src/slopBed/slopBed.cpp:75

MethodAddStrandedFlank

src/flankBed/flankBed.cpp:131

MethodAddWindow

src/windowBed/windowBed.cpp:235

MethodAllFilesDone

src/unionBedGraphs/unionBedGraphs.cpp:188

MethodAllFilesDone

src/multiIntersectBed/multiIntersectBed.cpp:166

src/utils/bedFile/bedFile.h:93

constructors Null

src/utils/bedFile/bedFile.h:213

MethodBEDCOVLIST

constructors Null

src/utils/bedFile/bedFile.h:260

src/utils/bedGraphFile/bedGraphFile.h:61

src/utils/general/BTlist.h:61

MethodBTlistNode

src/utils/general/BTlist.h:41

MethodBamAlignment

src/utils/BamTools/include/BamAlignment.hpp:238

MethodBamFileReader

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:4

MethodBamRecord

src/utils/FileRecordTools/Records/BamRecord.cpp:13

MethodBamRegion

src/utils/BamTools/include/api/BamAux.h:27

MethodBamToFastq

src/bamToFastq/bamToFastq.cpp:18

MethodBed12Interval

src/utils/FileRecordTools/Records/Bed12Interval.cpp:5

src/fastaFromBed/fastaFromBed.cpp:17

MethodBed3Interval

src/utils/FileRecordTools/Records/Bed3Interval.cpp:6

MethodBed4Interval

src/utils/FileRecordTools/Records/Bed4Interval.cpp:5

MethodBed5Interval

src/utils/FileRecordTools/Records/Bed5Interval.cpp:5

MethodBed6Interval

src/utils/FileRecordTools/Records/Bed6Interval.cpp:5

MethodBedAnnotate

src/annotateBed/annotateBed.cpp:16

MethodBedCluster

= Constructor =

src/clusterBed/clusterBed.cpp:16

src/utils/bedFile/bedFile.cpp:85

MethodBedFilePE

src/utils/bedFilePE/bedFilePE.cpp:20

src/flankBed/flankBed.cpp:16

MethodBedGenomeCoverage

src/genomeCoverageBed/genomeCoverageBed.cpp:16

MethodBedGraphFile

src/utils/bedGraphFile/bedGraphFile.cpp:16

MethodBedGraphInterval

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

MethodBedIntersectPE

src/pairToBed/pairToBed.cpp:36

src/linksBed/linksBed.cpp:18

MethodBedPlusInterval

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

MethodBedRandom

src/randomBed/randomBed.cpp:16

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