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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 2 callersMethodsetOperations

src/utils/KeyListOps/KeyListOps.h:29

↓ 2 callersMethodsetRecordType

src/utils/fileType/FileRecordTypeChecker.h:51

↓ 2 callersMethodsetStartPos

src/utils/FileRecordTools/Records/Record.h:94

↓ 2 callersFunctionsetTwoWayOptions

src/regressTest/regressTestMain.cpp:19

↓ 2 callersMethodset_cram_reqd_fields

src/utils/BamTools/include/BamReader.hpp:92

↓ 2 callersFunctionshift_help

src/shiftBed/shiftBedMain.cpp:133

↓ 2 callersFunctionshuffle_help

src/shuffleBed/shuffleBedMain.cpp:160

↓ 2 callersFunctionskip_value

src/utils/htslib/textutils.c:328

↓ 2 callersFunctionslop_help

src/slopBed/slopBedMain.cpp:147

↓ 2 callersMethodsortVector

src/utils/FileRecordTools/Records/RecordKeyVector.cpp:108

↓ 2 callersFunctionsort_help

src/sortBed/sortMain.cpp:172

↓ 2 callersFunctiontagbam_help

src/tagBam/tagBamMain.cpp:200

↓ 2 callersFunctiontbx_index

src/utils/htslib/tbx.c:211

↓ 2 callersFunctiontbx_index_build

src/utils/htslib/tbx.c:287

↓ 2 callersFunctiontbx_index_build3

src/utils/htslib/tbx.c:266

↓ 2 callersFunctiontest_and_fetch

*** Retrieve index *** **********************/ Returns -1 if index couldn't be opened. -2 on other errors

src/utils/htslib/hts.c:2775

↓ 2 callersFunctiontoLower

src/utils/stringUtilities/stringUtilities.h:22

↓ 2 callersFunctiontoLowerCase

src/utils/sequenceUtilities/sequenceUtils.cpp:159

↓ 2 callersFunctiontoUpperCase

src/utils/sequenceUtilities/sequenceUtils.cpp:169

↓ 2 callersFunctiontoken_type

src/utils/htslib/textutils.c:198

↓ 2 callersFunctiontokenise_search_path

* Tokenises the search path splitting on colons (unix) or semicolons * (windows). * We also explicitly add a "./" to the end of the search path *

src/utils/htslib/cram/open_trace_file.c:96

↓ 2 callersFunctionu64_to_le

Store a uint64_t value in little-endian byte order @param val The value to store * @param buf Where to store it (may be unaligned) */

src/utils/htslib/htslib/hts_endian.h:197

↓ 2 callersFunctionupdate_loff

src/utils/htslib/hts.c:1410

↓ 2 callersFunctionusage

src/regressTest/regressTestMain.cpp:8

↓ 2 callersFunctionview_raw

src/utils/htslib/htsfile.c:156

↓ 2 callersFunctionwake_next_worker

src/utils/htslib/thread_pool.c:594

↓ 2 callersFunctionwindow_help

src/windowBed/windowMain.cpp:207

↓ 2 callersFunctionwindowmaker_help

src/windowMaker/windowMakerMain.cpp:171

↓ 2 callersFunctionzlib_mem_inflate

---------------------------------------------------------------------- * zlib compression code - from Gap5's tg_iface_g.c * They're static here as t

src/utils/htslib/cram/cram_io.c:541

↓ 1 callersMethodAddTag

src/utils/BamTools/include/BamAlignment.hpp:385

↓ 1 callersMethodAnnotateBed

src/annotateBed/annotateBed.cpp:104

↓ 1 callersFunctionBuildCigarString

src/bamToBed/bamToBed.cpp:359

↓ 1 callersMethodCluster

src/multiIntersectBed/multiIntersectBed.cpp:263

↓ 1 callersMethodCollectCoverage

src/multiBamCov/multiBamCov.cpp:106

↓ 1 callersFunctionConvertBamToBed

src/bamToBed/bamToBed.cpp:280

↓ 1 callersFunctionConvertBamToBedpe

Assumptions: 1. The BAM file is grouped/sorted by query name, not alignment position */

src/bamToBed/bamToBed.cpp:317

↓ 1 callersFunctionConvertBedPEToBam

void ConvertBedPEToBam(const BEDPE &bedpe, BamAlignment &bam1,BamAlignment &bam2, map<string, int, std::less<string> > &chromToId, bool isBED12, int m

src/bedpeToBam/bedpeToBam.cpp:211

↓ 1 callersFunctionConvertBedToBam

src/bedToBam/bedToBam.cpp:208

↓ 1 callersFunctionDetermineBedInput

src/bed12ToBed6/bed12ToBed6.cpp:114

↓ 1 callersFunctionDetermineBedInput

src/bedToIgv/bedToIgv.cpp:194

↓ 1 callersFunctionDetermineInput

src/getOverlap/getOverlap.cpp:143

↓ 1 callersFunctionExpand

src/expand/expand.cpp:168

↓ 1 callersMethodGetNextAlignmentCore

src/utils/BamTools/include/BamReader.hpp:280

↓ 1 callersMethodGetNextBedGraph

src/utils/bedGraphFile/bedGraphFile.h:121

↓ 1 callersMethodGetNextTabLine

src/utils/tabFile/tabFile.cpp:59

↓ 1 callersMethodGetReference

src/utils/BamTools/include/BamReader.hpp:380

↓ 1 callersMethodGetReferenceID

src/utils/BamTools/include/BamReader.hpp:317

↓ 1 callersMethodHasIndexes

src/utils/BamTools/include/BamReader.hpp:340

↓ 1 callersMethodInitAdditionalData

src/utils/BamTools/include/BamAlignment.hpp:165

↓ 1 callersFunctionIntersectOutputHelp

src/utils/general/CommonHelp.cpp:9

↓ 1 callersMethodLocateIndexes

src/utils/BamTools/include/BamReader.hpp:329

↓ 1 callersFunctionMakeBamHeader

src/bedToBam/bedToBam.cpp:304

↓ 1 callersMethodMultiIntersect

src/multiIntersectBed/multiIntersectBed.cpp:211

↓ 1 callersFunctionPrintBed

src/bamToBed/bamToBed.cpp:397

↓ 1 callersFunctionPrintBed12

src/bamToBed/bamToBed.cpp:529

↓ 1 callersMethodPrintHeader

src/unionBedGraphs/unionBedGraphs.cpp:134

↓ 1 callersMethodPrintHeader

Dump the header

src/utils/bedFile/bedFile.cpp:201

↓ 1 callersMethodPrintHeader

src/multiIntersectBed/multiIntersectBed.cpp:84

↓ 1 callersFunctionProcessBed

src/bedToBam/bedToBam.cpp:167

↓ 1 callersFunctionProcessBedPE

src/bedpeToBam/bedpeToBam.cpp:161

↓ 1 callersFunctionRansDecAdvance

Advances in the bit stream by "popping" a single symbol with range start "start" and frequency "freq". All frequencies are assumed to sum to "1 << sca

src/utils/htslib/cram/rANS_byte.h:142

↓ 1 callersFunctionRansDecAdvanceStep

Advances in the bit stream by "popping" a single symbol with range start "start" and frequency "freq". All frequencies are assumed to sum to "1 << sca

src/utils/htslib/cram/rANS_byte.h:306

↓ 1 callersFunctionRansEncRenorm

Renormalize the encoder. Internal function.

src/utils/htslib/cram/rANS_byte.h:71

↓ 1 callersMethodSetRegion

src/utils/BamTools/include/BamReader.hpp:350

↓ 1 callersMethodSortBed

src/sortBed/sortBed.cpp:37

↓ 1 callersMethodSortBedByChromThenScoreAsc

src/sortBed/sortBed.cpp:204

↓ 1 callersMethodSortBedByChromThenScoreDesc

src/sortBed/sortBed.cpp:226

↓ 1 callersMethodSortBedByChromThenSizeAsc

src/sortBed/sortBed.cpp:171

↓ 1 callersMethodSortBedByChromThenSizeDesc

src/sortBed/sortBed.cpp:187

↓ 1 callersMethodSortBedBySizeAsc

src/sortBed/sortBed.cpp:118

↓ 1 callersMethodSortBedBySizeDesc

src/sortBed/sortBed.cpp:145

↓ 1 callersMethodSortBedOnFaidx

src/sortBed/sortBed.cpp:51

↓ 1 callersMethodSyncExtraData

src/utils/BamTools/include/BamAlignment.hpp:187

↓ 1 callersMethodTag

src/tagBam/tagBam.cpp:58

↓ 1 callersMethodUnion

src/unionBedGraphs/unionBedGraphs.cpp:56

↓ 1 callersFunction_reader_fill_buffer

* _reader_fill_buffer() - buffers all records with the same coordinate */

src/utils/htslib/synced_bcf_reader.c:482

↓ 1 callersFunction_reader_shift_buffer

* _readers_shift_buffer() - removes the first line and all subsequent lines with the same position */

src/utils/htslib/synced_bcf_reader.c:563

↓ 1 callersFunction_readers_next_region

* _readers_next_region() - jumps to next region if necessary * Returns 0 on success or -1 when there are no more regions left */

src/utils/htslib/synced_bcf_reader.c:457

↓ 1 callersFunction_regidx_build_index

src/utils/htslib/regidx.c:85

↓ 1 callersFunction_regions_match_alleles

src/utils/htslib/synced_bcf_reader.c:1140

↓ 1 callersFunctionadd_read_names

* Adds the reading names. We do this here as a separate pass rather * than per record in the process_one_read calls as that function can * go back

src/utils/htslib/cram/cram_encode.c:1222

↓ 1 callersFunctionalign_mem

src/utils/htslib/vcf.c:1867

↓ 1 callersMethodallClear

src/utils/FileRecordTools/Records/RecordKeyList.h:46

↓ 1 callersMethodallocateAndAssignRecord

src/utils/FileRecordTools/Records/BlockMgr.cpp:123

↓ 1 callersFunctionannotate_main

src/annotateBed/annotateMain.cpp:26

↓ 1 callersMethodassignNoCopy

src/utils/FileRecordTools/Records/RecordList.cpp:120

↓ 1 callersMethodassignWeightsBasedOnSize

src/utils/bedFile/bedFile.cpp:781

↓ 1 callersMethodback

src/utils/general/BTlist.h:93

↓ 1 callersFunctionbam_aux2i

src/utils/htslib/sam.c:2006

↓ 1 callersFunctionbam_cigar2qlen

src/utils/htslib/sam.c:373

↓ 1 callersFunctionbam_cigar2rqlens

src/utils/htslib/sam.c:361

↓ 1 callersFunctionbam_construct_seq

--------------------------------------------------------------------------- * Samtools compatibility portion */

src/utils/htslib/cram/cram_samtools.c:43

↓ 1 callersFunctionbam_hdr_write

src/utils/htslib/sam.c:228

↓ 1 callersFunctionbam_header_to_cram

src/utils/htslib/cram/cram_samtools.c:152

↓ 1 callersFunctionbam_index

src/utils/htslib/sam.c:571

↓ 1 callersFunctionbam_plp_auto

src/utils/htslib/sam.c:2717

↓ 1 callersFunctionbam_plp_constructor

src/utils/htslib/sam.c:2411

↓ 1 callersFunctionbam_plp_destroy

src/utils/htslib/sam.c:2397

↓ 1 callersFunctionbam_plp_destructor

src/utils/htslib/sam.c:2416

↓ 1 callersFunctionbam_plp_init

src/utils/htslib/sam.c:2376

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