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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 1 callersFunctionnet_init

src/utils/htslib/hfile_net.c:48

↓ 1 callersFunctionnew_pool

src/utils/htslib/cram/pooled_alloc.c:82

↓ 1 callersFunctionnew_string_pool

src/utils/htslib/cram/string_alloc.c:73

↓ 1 callersMethodnewline

src/utils/RecordOutputMgr/RecordOutputMgr.h:35

↓ 1 callersFunctionnext_power_2

credit to http://graphics.stanford.edu/~seander/bithacks.html

src/utils/htslib/cram/pooled_alloc.c:45

↓ 1 callersMethodnonNumErrFlagSet

src/utils/KeyListOps/KeyListOpsMethods.h:81

↓ 1 callersFunctionnuc_main

src/nucBed/nucBedMain.cpp:27

↓ 1 callersMethodopen

src/utils/gzstream/gzstream.h:98

↓ 1 callersMethodopenGenomeFile

src/utils/Contexts/ContextBase.cpp:156

↓ 1 callersFunctionopen_path_mfile

* Opens a trace file named 'file'. This is initially looked for as a * pathname relative to a file named "relative_to". This may (for * example) be

src/utils/htslib/cram/open_trace_file.c:315

↓ 1 callersFunctionoverlap_push

Fix overlapping reads. Simple soft-clipping did not give good results. Lowering qualities of unwanted bases is more selective and works better.

src/utils/htslib/sam.c:2572

↓ 1 callersFunctionpairing_score

src/utils/htslib/bcf_sr_sort.c:165

↓ 1 callersFunctionpairtobed_main

src/pairToBed/pairToBedMain.cpp:26

↓ 1 callersFunctionpairtopair_main

src/pairToPair/pairToPairMain.cpp:26

↓ 1 callersMethodparseCmdArgs

src/utils/Contexts/ContextMap.cpp:24

↓ 1 callersFunctionparse_ga4gh_body_json

Returns 'v' (valid value), 'i' (invalid; required GA4GH field missing), or upon encountering an unexpected token, that token's type. Explicit `return

src/utils/htslib/multipart.c:148

↓ 1 callersFunctionparse_ga4gh_redirect_json

Returns 'v' (valid value), 'i' (invalid; required GA4GH field missing), or upon encountering an unexpected token, that token's type. Explicit `return

src/utils/htslib/multipart.c:219

↓ 1 callersFunctionparse_global_args

src/bedtools.cpp:92

↓ 1 callersFunctionparse_regions

src/utils/htslib/tabix.c:92

↓ 1 callersFunctionparse_simple

src/utils/htslib/hfile_s3.c:207

↓ 1 callersFunctionparse_va_list

src/utils/htslib/hfile_libcurl.c:1219

↓ 1 callersMethodpop_front

src/utils/general/BTlist.h:94

↓ 1 callersMethodpopulateScanBuffer

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:147

↓ 1 callersMethodprintFullCols

src/utils/Contexts/ContextGroupBy.h:20

↓ 1 callersMethodprintNull

src/utils/FileRecordTools/Records/VcfRecord.cpp:73

↓ 1 callersMethodprintUnmapped

src/utils/FileRecordTools/Records/BamRecord.cpp:186

↓ 1 callersMethodprocessHits

src/groupBy/groupBy.cpp:84

↓ 1 callersFunctionprocess_messages

src/utils/htslib/hfile_libcurl.c:657

↓ 1 callersFunctionprocess_one_read

* Converts a single bam record into a cram record. * Possibly used within a thread. * * Returns 0 on success; * -1 on failure */

src/utils/htslib/cram/cram_encode.c:2513

↓ 1 callersFunctionpush_vset

src/utils/htslib/bcf_sr_sort.c:244

↓ 1 callersFunctionquery_chroms

src/utils/htslib/tabix.c:229

↓ 1 callersFunctionquery_regions

src/utils/htslib/tabix.c:142

↓ 1 callersFunctionrand_proportion

src/utils/general/Random.cpp:34

↓ 1 callersFunctionrandom_main

src/randomBed/randomBedMain.cpp:27

↓ 1 callersFunctionrans_compress_O1

src/utils/htslib/cram/rANS_static.c:357

↓ 1 callersFunctionrans_uncompress_O0

src/utils/htslib/cram/rANS_static.c:206

↓ 1 callersFunctionrans_uncompress_O1

src/utils/htslib/cram/rANS_static.c:568

↓ 1 callersMethodread

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:110

↓ 1 callersMethodreadEntry

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:34

↓ 1 callersMethodreadIndexFile

src/utils/Fasta/Fasta.cpp:35

↓ 1 callersFunctionread_auth_json

* Read an OAUTH2-style Bearer access token (see * https://tools.ietf.org/html/rfc6750#section-4). * Returns 'v' for valid; 'i' for invalid (token mi

src/utils/htslib/hfile_libcurl.c:393

↓ 1 callersFunctionread_auth_plain

src/utils/htslib/hfile_libcurl.c:454

↓ 1 callersMethodrecordTypeHasName

src/utils/fileType/FileRecordTypeChecker.h:42

↓ 1 callersMethodrecordTypeHasScore

src/utils/fileType/FileRecordTypeChecker.h:43

↓ 1 callersMethodrecordTypeHasStrand

src/utils/fileType/FileRecordTypeChecker.h:44

↓ 1 callersMethodrecordsHaveStrand

src/utils/FileRecordTools/FileRecordMgr.h:62

↓ 1 callersFunctionreg2bins

src/utils/htslib/hts.c:1970

↓ 1 callersFunctionreg2intervals

src/utils/htslib/hts.c:1988

↓ 1 callersFunctionregidx_nregs

src/utils/htslib/regidx.c:72

↓ 1 callersFunctionregidx_seq_names

src/utils/htslib/regidx.c:79

↓ 1 callersFunctionregress_test_main

src/regressTest/regressTestMain.cpp:27

↓ 1 callersFunctionreheader_file

src/utils/htslib/tabix.c:264

↓ 1 callersFunctionreldist_main

src/reldist/reldistMain.cpp:27

↓ 1 callersFunctionrenew_auth_token

src/utils/htslib/hfile_libcurl.c:482

↓ 1 callersMethodresetNonNumErrFlag

src/utils/KeyListOps/KeyListOpsMethods.h:83

↓ 1 callersMethodresetStream

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:320

↓ 1 callersFunctionresolve_cigar2

s->k: the index of the CIGAR operator that has just been processed. s->x: the reference coordinate of the start of s->k s->y: the query coordian

src/utils/htslib/sam.c:2272

↓ 1 callersMethodrunTests

src/regressTest/RegressTest.cpp:104

↓ 1 callersMethodrunToDbEnd

src/utils/Contexts/ContextIntersect.h:108

↓ 1 callersFunctions3_sign

src/utils/htslib/hfile_s3.c:60

↓ 1 callersFunctionsafe_ltf8_get

src/utils/htslib/cram/cram_io.h:301

↓ 1 callersFunctionsam_format1

src/utils/htslib/sam.c:1478

↓ 1 callersFunctionsam_hdr_add

* Adds a single line to a SAM header. * Specify type and one or more key,value pairs, ending with the NULL key. * Eg. sam_hdr_add(h, "SQ", "ID", "fo

src/utils/htslib/cram/sam_header.c:424

↓ 1 callersFunctionsam_hdr_add_lines

* Appends a formatted line to an existing SAM header. * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with * optional new-line. If it

src/utils/htslib/cram/sam_header.c:284

↓ 1 callersFunctionsam_hdr_link_pg

* Fixes any PP links in @PG headers. * If the entries are in order then this doesn't need doing, but incase * our header is out of order this goes t

src/utils/htslib/cram/sam_header.c:1108

↓ 1 callersFunctionsam_hdr_name2ref

* Looks up a reference sequence by name and returns the numerical ID. * Returns -1 if unknown reference. */

src/utils/htslib/cram/sam_header.c:1076

↓ 1 callersFunctionsam_hdr_new

* Creates an empty SAM header, ready to be populated. * * Returns a SAM_hdr struct on success (free with sam_hdr_free()) * NULL on failure

src/utils/htslib/cram/sam_header.c:862

↓ 1 callersFunctionsam_hdr_parse_sort_order

src/utils/htslib/cram/sam_header.c:761

↓ 1 callersFunctionsam_hdr_rebuild

src/utils/BamTools/include/SamHeader.hpp:23

↓ 1 callersFunctionsam_index_build

src/utils/htslib/sam.c:645

↓ 1 callersFunctionsam_index_build2

src/utils/htslib/sam.c:640

↓ 1 callersFunctionsam_index_load

src/utils/htslib/sam.c:792

↓ 1 callersFunctionsam_index_load2

src/utils/htslib/sam.c:771

↓ 1 callersFunctionsam_itr_queryi

src/utils/htslib/sam.c:854

↓ 1 callersFunctionsam_open_mode

src/utils/htslib/sam.c:2070

↓ 1 callersFunctionsam_parse1

src/utils/htslib/sam.c:1197

↓ 1 callersFunctionsample_help

src/sampleFile/sampleHelp.cpp:10

↓ 1 callersMethodscanBuffer

src/utils/fileType/FileRecordTypeChecker.cpp:95

↓ 1 callersFunctionscan_keyword

* Splits str into a prefix, delimiter ('\0' or delim), and suffix, writing * the prefix in lowercase into buf and returning a pointer to the suffix.

src/utils/htslib/hts.c:466

↓ 1 callersMethodsetBam

src/utils/fileType/FileRecordTypeChecker.cpp:446

↓ 1 callersMethodsetBamReader

src/utils/FileRecordTools/FileReaders/BamFileReader.h:32

↓ 1 callersMethodsetColumn

src/utils/KeyListOps/KeyListOpsMethods.h:27

↓ 1 callersMethodsetCram

src/utils/fileType/FileRecordTypeChecker.cpp:454

↓ 1 callersMethodsetEndPosStr

src/utils/FileRecordTools/Records/Record.h:101

↓ 1 callersMethodsetFileName

src/utils/FileRecordTools/FileReaders/FileReader.h:18

↓ 1 callersMethodsetFileRecordManager

src/utils/FileRecordTools/Records/Record.cpp:307

↓ 1 callersMethodsetFilename

src/utils/fileType/FileRecordTypeChecker.h:38

↓ 1 callersMethodsetFullBamFlags

special: For BAM files, our default is to not use all the tag information in a BAM file, which reduces the run time in some cases by more than 50%. Bu

src/utils/FileRecordTools/FileRecordMgr.h:100

↓ 1 callersMethodsetGenomeFile

src/utils/FileRecordTools/FileRecordMgr.h:101

↓ 1 callersMethodsetInputStream

src/utils/FileRecordTools/FileReaders/FileReader.h:22

↓ 1 callersMethodsetIsBam

src/utils/KeyListOps/KeyListOpsMethods.h:25

↓ 1 callersMethodsetIsSorted

src/utils/FileRecordTools/FileRecordMgr.h:106

↓ 1 callersMethodsetKeyList

src/utils/KeyListOps/KeyListOps.h:43

↓ 1 callersMethodsetMaxDistance

src/utils/FileRecordTools/FileRecordMergeMgr.h:43

↓ 1 callersMethodsetNoEnforceCoordSort

src/utils/Contexts/ContextBase.h:300

↓ 1 callersMethodsetNumExpectedItems

src/utils/general/Tokenizer.cpp:19

↓ 1 callersMethodsetNumFixedFields

src/utils/FileRecordTools/Records/BedPlusInterval.cpp:11

↓ 1 callersFunctionsetOneWayOptions

src/regressTest/regressTestMain.cpp:12

↓ 1 callersMethodsetOverlapFractionA

src/utils/Contexts/ContextIntersect.h:76

↓ 1 callersMethodsetPrecision

src/utils/KeyListOps/KeyListOps.h:52

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