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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 1 callersMethodgetBlockCount

src/utils/FileRecordTools/Records/Bed12Interval.h:42

↓ 1 callersMethodgetCount

return the count of element in the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:190

↓ 1 callersMethodgetCountDistinct

return a the count of _unique_ elements in the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:238

↓ 1 callersMethodgetCramRefs

src/utils/FileRecordTools/FileRecordMgr.cpp:254

↓ 1 callersMethodgetDatabaseRecordType

src/utils/Contexts/ContextIntersect.h:35

↓ 1 callersMethodgetDatabaseTotalRecords

src/utils/NewChromsweep/NewChromsweep.h:55

↓ 1 callersMethodgetDbIdx

src/utils/Contexts/ContextIntersect.h:38

↓ 1 callersMethodgetDelimChar

src/utils/fileType/FileRecordTypeChecker.h:72

↓ 1 callersFunctiongetDnaContent

src/utils/sequenceUtilities/sequenceUtils.cpp:179

↓ 1 callersMethodgetEofHit

src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:45

↓ 1 callersMethodgetErrorMessages

src/utils/Contexts/ContextBase.h:156

↓ 1 callersMethodgetErrors

src/utils/driver/BedtoolsDriver.h:12

↓ 1 callersMethodgetForwardOnly

src/utils/Contexts/ContextSample.h:23

↓ 1 callersMethodgetHits

src/utils/BinTree/BinTree.cpp:36

↓ 1 callersMethodgetMateChrName

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:102

↓ 1 callersMethodgetMax

return the maximum element of the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:153

↓ 1 callersMethodgetMean

return the average value in the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:51

↓ 1 callersMethodgetMedian

return the median value in the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:86

↓ 1 callersMethodgetMin

return the minimum element of the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:140

↓ 1 callersMethodgetMultiDbMode

src/utils/Contexts/ContextClosest.h:41

↓ 1 callersMethodgetNameCheckDisabled

src/utils/Contexts/ContextBase.h:121

↓ 1 callersMethodgetNumFields

src/utils/fileType/FileRecordTypeChecker.h:73

↓ 1 callersMethodgetNumFields

src/utils/FileRecordTools/FileRecordMgr.h:83

↓ 1 callersMethodgetNumOutputRecords

METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER OF OUTPUT RECORDS.

src/utils/Contexts/ContextBase.h:126

↓ 1 callersMethodgetNumTotalElems

src/utils/general/Tokenizer.h:36

↓ 1 callersMethodgetNumberOfChroms

src/utils/GenomeFile/GenomeFile.cpp:115

↓ 1 callersMethodgetOnlyChromsWithBedRecords

src/utils/Contexts/ContextComplement.h:20

↓ 1 callersMethodgetPrintHeader

src/utils/Contexts/ContextBase.h:112

↓ 1 callersMethodgetQueryRecordType

src/utils/Contexts/ContextIntersect.h:34

↓ 1 callersMethodgetQueryTotalRecords

src/utils/NewChromsweep/NewChromsweep.h:54

↓ 1 callersMethodgetReverseOnly

src/utils/Contexts/ContextSample.h:24

↓ 1 callersMethodgetRunToQueryEnd

should every record in the query file be processed when using -sorted? This is relevant when we know that all database records have been processed but

src/utils/Contexts/ContextIntersect.h:102

↓ 1 callersMethodgetSampleStddev

return the standard deviation

src/utils/KeyListOps/KeyListOpsMethods.cpp:72

↓ 1 callersMethodgetScore

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:89

↓ 1 callersMethodgetStddev

return the standard deviation

src/utils/KeyListOps/KeyListOpsMethods.cpp:59

↓ 1 callersMethodgetStrand

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:94

↓ 1 callersMethodgetSum

return the total of the values in the vector

src/utils/KeyListOps/KeyListOpsMethods.cpp:40

↓ 1 callersMethodgetTieMode

src/utils/Contexts/ContextClosest.h:35

↓ 1 callersMethodgetTotalFlattenedLength

src/utils/bedFile/bedFile.cpp:333

↓ 1 callersMethodgetUncompressedBam

src/utils/Contexts/ContextBase.h:94

↓ 1 callersMethodgetUnspecifiedSeed

src/utils/Contexts/ContextBase.cpp:382

↓ 1 callersMethodgetUseDBfileNames

src/utils/Contexts/ContextBase.h:109

↓ 1 callersMethodgetVcfSVlen

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148

↓ 1 callersMethodgetWriteAllOverlap

src/utils/Contexts/ContextIntersect.h:66

↓ 1 callersFunctionget_auth_token

src/utils/htslib/hfile_libcurl.c:589

↓ 1 callersFunctionget_cache_basedir

* Return the cache directory to use, based on the first of these * environment variables to be set to a non-empty value. */

src/utils/htslib/cram/cram_io.c:2004

↓ 1 callersFunctionget_int_threadid

* Return an integer representation of pthread_self(). */

src/utils/htslib/cram/cram_io.c:2027

↓ 1 callersFunctionget_one_bits_MSB

* Count number of successive 0 and 1 bits */

src/utils/htslib/cram/cram_codecs.c:77

↓ 1 callersMethodget_reference

src/utils/BamTools/include/BamReader.hpp:87

↓ 1 callersFunctionget_severity_tag

src/utils/htslib/hts.c:2955

↓ 1 callersFunctionget_zero_bits_MSB

src/utils/htslib/cram/cram_codecs.c:95

↓ 1 callersFunctiongetoverlap_main

src/getOverlap/getOverlap.cpp:35

↓ 1 callersMethodgiveFinalReport

src/fisher/fisher.cpp:46

↓ 1 callersFunctiongroupby_help

src/groupBy/groupByHelp.cpp:3

↓ 1 callersFunctiongrp_create_key

src/utils/htslib/bcf_sr_sort.c:311

↓ 1 callersMethodhadError

src/utils/driver/BedtoolsDriver.h:11

↓ 1 callersMethodhasChrInChromName

src/utils/FileRecordTools/Records/Record.cpp:277

↓ 1 callersMethodhasChrom

src/utils/GenomeFile/NewGenomeFile.h:44

↓ 1 callersMethodhasConstantSeed

SEED OPS FOR APPS WITH RANDOMNESS When a seed has been specified on the command line, srand will have been already been called during command line par

src/utils/Contexts/ContextBase.h:135

↓ 1 callersMethodhasLeadingZeroInChromName

src/utils/FileRecordTools/Records/Record.cpp:288

↓ 1 callersFunctionhas_filter

src/utils/htslib/synced_bcf_reader.c:404

↓ 1 callersFunctionhdr_from_dict

src/utils/htslib/sam.c:101

↓ 1 callersFunctionhfile_mem_get_buffer

src/utils/htslib/hfile.c:909

↓ 1 callersFunctionhfile_oflags

src/utils/htslib/hfile.c:788

↓ 1 callersFunctionhgetc2

Called only from hgetc(), when our buffer is empty. */

src/utils/htslib/hfile.c:214

↓ 1 callersFunctionhgetdelim

src/utils/htslib/hfile.c:219

↓ 1 callersFunctionhopen_fd_stdinout

src/utils/htslib/hfile.c:779

↓ 1 callersFunctionhopen_htsget_redirect

src/utils/htslib/multipart.c:240

↓ 1 callersFunctionhpreload

Loads the contents of filename to produced a read-only, in memory, immobile hfile. fp is the already opened file. We always close this input fp, irr

src/utils/htslib/hfile.c:708

↓ 1 callersFunctionhputc2

Called only from hputc(), when our buffer is already full. */

src/utils/htslib/hfile.c:364

↓ 1 callersFunctionhputs2

Called only from hputs(), when our buffer is already full. */

src/utils/htslib/hfile.c:402

↓ 1 callersFunctionhread2

Called only from hread(); when called, our buffer is empty and nread bytes have already been placed in the destination buffer. */

src/utils/htslib/hfile.c:295

↓ 1 callersFunctionhts_base64_decoded_length

src/utils/htslib/textutils.c:71

↓ 1 callersFunctionhts_bin_bot

src/utils/htslib/htslib/hts.h:826

↓ 1 callersFunctionhts_decode_base64

src/utils/htslib/textutils.c:77

↓ 1 callersFunctionhts_decode_percent

src/utils/htslib/textutils.c:43

↓ 1 callersFunctionhts_erand48

src/utils/htslib/os/rand.c:77

↓ 1 callersFunctionhts_format_description

src/utils/htslib/hts.c:315

↓ 1 callersFunctionhts_hfile

src/utils/htslib/hts.c:992

↓ 1 callersFunctionhts_idx_get_meta

src/utils/htslib/hts.c:1916

↓ 1 callersFunctionhts_idx_load_local

src/utils/htslib/hts.c:1825

↓ 1 callersFunctionhts_idx_save

src/utils/htslib/hts.c:1719

↓ 1 callersFunctionhts_idx_save_core

src/utils/htslib/hts.c:1676

↓ 1 callersFunctionhts_idx_set_meta

src/utils/htslib/hts.c:1894

↓ 1 callersFunctionhts_json_alloc_token

src/utils/htslib/textutils.c:218

↓ 1 callersFunctionhts_json_free_token

src/utils/htslib/textutils.c:226

↓ 1 callersFunctionhts_json_snext

src/utils/htslib/textutils.c:234

↓ 1 callersFunctionhts_json_token_str

src/utils/htslib/textutils.c:230

↓ 1 callersFunctionhts_json_token_type

src/utils/htslib/textutils.c:222

↓ 1 callersFunctionhts_md5_reset

src/utils/htslib/md5.c:225

↓ 1 callersFunctionhts_open_format

src/utils/htslib/hts.c:443

↓ 1 callersFunctionhts_opt_add

* Parses arg and appends it to the option list. * * Returns 0 on success; * -1 on failure. */

src/utils/htslib/hts.c:485

↓ 1 callersFunctionhts_parse_reg

src/utils/htslib/hts.c:2533

↓ 1 callersFunctionhts_path_itr_next

src/utils/htslib/plugin.c:104

↓ 1 callersFunctionhts_path_itr_setup

src/utils/htslib/plugin.c:69

↓ 1 callersFunctionhts_process_opts

* Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could

src/utils/htslib/hts.c:780

↓ 1 callersFunctionhts_readlines

src/utils/htslib/hts.c:1209

↓ 1 callersFunctionhts_reglist_free

src/utils/htslib/hts.c:2457

↓ 1 callersFunctionhts_set_cache_size

src/utils/htslib/hts.c:1090

↓ 1 callersFunctionhts_set_thread_pool

src/utils/htslib/hts.c:1081

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