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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 1 callersFunctionbam_plp_init_overlaps

src/utils/htslib/sam.c:2392

↓ 1 callersFunctionbam_plp_reset

src/utils/htslib/sam.c:2741

↓ 1 callersFunctionbam_write1

src/utils/htslib/sam.c:519

↓ 1 callersFunctionbamtobed_main

src/bamToBed/bamToBed.cpp:72

↓ 1 callersFunctionbamtofastq_main

src/bamToFastq/bamToFastqMain.cpp:31

↓ 1 callersFunctionbase64_kput

src/utils/htslib/hfile_s3.c:101

↓ 1 callersFunctionbcf_add_filter

src/utils/htslib/vcf.c:3520

↓ 1 callersFunctionbcf_clear

src/utils/htslib/vcf.c:965

↓ 1 callersFunctionbcf_copy

src/utils/htslib/vcf.c:1465

↓ 1 callersFunctionbcf_format_gt

src/utils/htslib/htslib/vcf.h:904

↓ 1 callersFunctionbcf_get_fmt

src/utils/htslib/vcf.c:3675

↓ 1 callersFunctionbcf_get_fmt_id

src/utils/htslib/vcf.c:3689

↓ 1 callersFunctionbcf_get_format_values

src/utils/htslib/vcf.c:3810

↓ 1 callersFunctionbcf_get_info

src/utils/htslib/vcf.c:3682

↓ 1 callersFunctionbcf_get_info_id

src/utils/htslib/vcf.c:3700

↓ 1 callersFunctionbcf_get_info_values

src/utils/htslib/vcf.c:3712

↓ 1 callersFunctionbcf_hdr_check_sanity

src/utils/htslib/vcf.c:615

↓ 1 callersFunctionbcf_hdr_get_version

src/utils/htslib/vcf.c:799

↓ 1 callersFunctionbcf_hdr_register_hrec

returns: 1 when hdr needs to be synced, 0 otherwise

src/utils/htslib/vcf.c:401

↓ 1 callersFunctionbcf_hdr_seqnames

src/utils/htslib/vcf.c:1691

↓ 1 callersFunctionbcf_hdr_set_version

src/utils/htslib/vcf.c:810

↓ 1 callersFunctionbcf_index

src/utils/htslib/vcf.c:2644

↓ 1 callersFunctionbcf_index_build

src/utils/htslib/vcf.c:2735

↓ 1 callersFunctionbcf_read

src/utils/htslib/vcf.c:1261

↓ 1 callersFunctionbcf_record_check

src/utils/htslib/vcf.c:1094

↓ 1 callersFunctionbcf_set_variant_type

src/utils/htslib/vcf.c:3199

↓ 1 callersFunctionbcf_sr_destroy_threads

src/utils/htslib/synced_bcf_reader.c:191

↓ 1 callersFunctionbcf_sr_init_scores

src/utils/htslib/bcf_sr_sort.c:73

↓ 1 callersFunctionbcf_sr_regions_flush

src/utils/htslib/synced_bcf_reader.c:1222

↓ 1 callersFunctionbcf_sr_regions_seek

src/utils/htslib/synced_bcf_reader.c:1031

↓ 1 callersFunctionbcf_sr_seek_start

src/utils/htslib/synced_bcf_reader.c:662

↓ 1 callersFunctionbcf_sr_set_opt

src/utils/htslib/synced_bcf_reader.c:95

↓ 1 callersFunctionbcf_sr_sort_add_active

src/utils/htslib/bcf_sr_sort.c:339

↓ 1 callersFunctionbcf_sr_sort_destroy

src/utils/htslib/bcf_sr_sort.c:654

↓ 1 callersFunctionbcf_sr_sort_init

src/utils/htslib/bcf_sr_sort.c:644

↓ 1 callersFunctionbcf_sr_sort_next

src/utils/htslib/bcf_sr_sort.c:562

↓ 1 callersFunctionbcf_sr_sort_remove_reader

src/utils/htslib/bcf_sr_sort.c:631

↓ 1 callersFunctionbcf_sr_sort_reset

src/utils/htslib/bcf_sr_sort.c:650

↓ 1 callersFunctionbcf_sr_sort_set

src/utils/htslib/bcf_sr_sort.c:346

↓ 1 callersFunctionbcf_sr_sort_set_active

src/utils/htslib/bcf_sr_sort.c:332

↓ 1 callersFunctionbcf_update_alleles_str

src/utils/htslib/vcf.c:3617

↓ 1 callersFunctionbed12tobed6_main

src/bed12ToBed6/bed12ToBed6.cpp:39

↓ 1 callersFunctionbedpetobam_MakeBamHeader

src/bedpeToBam/bedpeToBam.cpp:292

↓ 1 callersFunctionbedpetobam_main

src/bedpeToBam/bedpeToBam.cpp:48

↓ 1 callersFunctionbedtobam_main

src/bedToBam/bedToBam.cpp:47

↓ 1 callersFunctionbedtobam_reg2bin

Taken directly from the SAMTools spec calculate bin given an alignment in [beg,end) (zero-based, half-close, half-open) */

src/bedToBam/bedToBam.cpp:345

↓ 1 callersFunctionbedtoigv_main

src/bedToIgv/bedToIgv.cpp:39

↓ 1 callersFunctionbedtools_faq

src/bedtools.cpp:311

↓ 1 callersFunctionbgzf_block_write

src/utils/htslib/bgzf.c:1593

↓ 1 callersFunctionbgzf_flush_try

src/utils/htslib/bgzf.c:1564

↓ 1 callersFunctionbgzf_gzip_compress

src/utils/htslib/bgzf.c:483

↓ 1 callersFunctionbgzf_hfile

prototype is in hfile_internal.h */

src/utils/htslib/bgzf.c:2091

↓ 1 callersFunctionbgzf_index_dump_hfile

src/utils/htslib/bgzf.c:1877

↓ 1 callersFunctionbgzf_index_load_hfile

src/utils/htslib/bgzf.c:1959

↓ 1 callersFunctionbgzf_mt_read_block

* Reads a compressed block of data using hread and dispatches it to * the thread pool for decompression. This is the analogue of the old * non-thre

src/utils/htslib/bgzf.c:1167

↓ 1 callersFunctionbgzf_raw_read

src/utils/htslib/bgzf.c:1025

↓ 1 callersFunctionbgzf_raw_write

src/utils/htslib/bgzf.c:1622

↓ 1 callersFunctionbgzf_set_cache_size

src/utils/htslib/bgzf.c:1674

↓ 1 callersFunctionbyChromThenStart

src/utils/bedFile/bedFile.cpp:65

↓ 1 callersFunctioncache_block

src/utils/htslib/bgzf.c:683

↓ 1 callersFunctioncal_coef

src/utils/htslib/errmod.c:64

↓ 1 callersMethodcheckForHeader

src/utils/RecordOutputMgr/RecordOutputMgr.cpp:335

↓ 1 callersMethodchromFound

src/utils/Fasta/Fasta.cpp:76

↓ 1 callersMethodclass_def

src/utils/BamTools/mapping/BamAlignment.py:7

↓ 1 callersMethodcleanupHits

src/jaccard/jaccard.cpp:30

↓ 1 callersMethodclear

src/utils/general/QuickString.cpp:65

↓ 1 callersMethodclear

src/utils/general/BTlist.h:198

↓ 1 callersMethodclear

src/utils/general/FreeList.h:33

↓ 1 callersMethodclear

src/utils/FileRecordTools/Records/BamRecord.cpp:80

↓ 1 callersMethodclear

src/utils/BamTools/include/BamAlignment.hpp:219

↓ 1 callersMethodclose

src/utils/BamTools/include/BamReader.hpp:30

↓ 1 callersFunctionclosest_help

src/closestFile/closestHelp.cpp:10

↓ 1 callersFunctioncluster_main

src/clusterBed/clusterMain.cpp:27

↓ 1 callersFunctioncmp_nonblank

src/utils/htslib/hts.c:184

↓ 1 callersFunctioncmp_prefix

src/utils/htslib/hfile.c:841

↓ 1 callersFunctioncomplement_help

src/complementFile/complementHelp.cpp:11

↓ 1 callersFunctioncompress

src/htsutil.cpp:77

↓ 1 callersFunctioncompress_binning

src/utils/htslib/hts.c:1447

↓ 1 callersMethodcoordsValid

src/utils/FileRecordTools/Records/Record.cpp:233

↓ 1 callersMethodcountListHits

src/utils/bedFile/bedFile.cpp:589

↓ 1 callersFunctioncountPattern

src/utils/sequenceUtilities/sequenceUtils.cpp:214

↓ 1 callersFunctioncoverage_help

src/coverageFile/coverageHelp.cpp:15

↓ 1 callersFunctioncram_add_deletion

src/utils/htslib/cram/cram_encode.c:1833

↓ 1 callersFunctioncram_add_hardclip

src/utils/htslib/cram/cram_encode.c:1876

↓ 1 callersFunctioncram_add_insertion

src/utils/htslib/cram/cram_encode.c:1906

↓ 1 callersFunctioncram_add_pad

src/utils/htslib/cram/cram_encode.c:1896

↓ 1 callersFunctioncram_add_skip

src/utils/htslib/cram/cram_encode.c:1886

↓ 1 callersFunctioncram_add_softclip

src/utils/htslib/cram/cram_encode.c:1843

↓ 1 callersFunctioncram_block_append

src/utils/htslib/cram/cram_external.c:212

↓ 1 callersFunctioncram_block_compression_hdr_decoder2encoder

* Converts a cram_block_compression_hdr struct used for decoding to * one used for encoding. Maybe this should be a transparent * operation applied

src/utils/htslib/cram/cram_external.c:163

↓ 1 callersFunctioncram_block_compression_hdr_set_DS

src/utils/htslib/cram/cram_external.c:126

↓ 1 callersFunctioncram_block_compression_hdr_set_rg

src/utils/htslib/cram/cram_external.c:151

↓ 1 callersFunctioncram_block_get_data

src/utils/htslib/cram/cram_external.c:199

↓ 1 callersFunctioncram_block_get_size

src/utils/htslib/cram/cram_external.c:200

↓ 1 callersFunctioncram_block_get_uncomp_size

src/utils/htslib/cram/cram_external.c:197

↓ 1 callersFunctioncram_block_method2str

src/utils/htslib/cram/cram_io.c:1449

↓ 1 callersFunctioncram_block_set_size

src/utils/htslib/cram/cram_external.c:210

↓ 1 callersFunctioncram_block_update_size

src/utils/htslib/cram/cram_external.c:216

↓ 1 callersFunctioncram_check_EOF

src/utils/htslib/cram/cram_io.c:4590

↓ 1 callersFunctioncram_close

* Closes a CRAM file. * Returns 0 on success * -1 on failure */

src/utils/htslib/cram/cram_io.c:4257

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