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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 7 callersFunctioncram_codec_to_id

* Returns the content_id used by this codec, also in id2 if byte_array_len. * Returns -1 for the CORE block and -2 for unneeded. * id2 is only fille

src/utils/htslib/cram/cram_codecs.c:1869

↓ 7 callersFunctiongetBin

return the genome "bin" for a feature with this start and end

src/utils/bedFile/bedFile.h:315

↓ 7 callersMethodgetNextRecord

src/groupBy/groupBy.cpp:117

↓ 7 callersMethodgetRecordType

src/utils/FileRecordTools/FileRecordMgr.h:69

↓ 7 callersFunctionhfile_destroy

src/utils/htslib/hfile.c:143

↓ 7 callersFunctionhpeek

src/utils/htslib/hfile.c:278

↓ 7 callersFunctionhts_get_bgzfp

For VCF/BCF backward sweeper. Not exposing these functions because their future is uncertain. Things will probably have to change with hFILE...

src/utils/htslib/hts.c:1114

↓ 7 callersFunctionhts_idx_init

src/utils/htslib/hts.c:1388

↓ 7 callersFunctionhts_tpool_init

* Creates a worker pool with n worker threads. * * Returns pool pointer on success; * NULL on failure */

src/utils/htslib/thread_pool.c:664

↓ 7 callersMethodisUnmapped

"Unmapped" only applies to BamRecord, but for design reasons, it has to be here, because we want to short circuit the intersects method if either reco

src/utils/FileRecordTools/Records/Record.h:147

↓ 7 callersFunctionkftp_send_cmd

src/utils/htslib/knetfile.c:243

↓ 7 callersFunctionkhash_str2int_init

src/utils/htslib/htslib/khash_str2int.h:36

↓ 7 callersFunctionknet_seek

src/utils/htslib/knetfile.c:554

↓ 7 callersFunctionle_to_float

Get a float value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 32 bit floating point value *

src/utils/htslib/htslib/hts_endian.h:300

↓ 7 callersFunctionltf8_put

64-bit itf8 variant */

src/utils/htslib/cram/cram_io.h:129

↓ 7 callersMethodopen

src/utils/Fasta/Fasta.cpp:86

↓ 7 callersMethodreportBedPENewLine

reportBedPENewLine Writes the _original_ BED entry for A. Works for BEDPE only. */

src/utils/bedFilePE/bedFilePE.cpp:138

↓ 6 callersFunctionGetBamBlocks

src/utils/BlockedIntervals/BlockedIntervals.cpp:15

↓ 6 callersMethodSetCompressionMode

src/utils/BamTools/include/BamWriter.hpp:58

↓ 6 callersMethodafter

src/utils/FileRecordTools/Records/Record.cpp:126

↓ 6 callersFunctionappend_header

src/utils/htslib/hfile_libcurl.c:292

↓ 6 callersFunctionbam_cigar2rlen

src/utils/htslib/sam.c:382

↓ 6 callersFunctionbam_destroy1

src/utils/htslib/sam.c:331

↓ 6 callersFunctionbam_endpos

src/utils/htslib/sam.c:391

↓ 6 callersFunctionbcf_hdr_format

src/utils/htslib/vcf.c:1665

↓ 6 callersFunctionbcf_hrec_destroy

src/utils/htslib/vcf.c:166

↓ 6 callersFunctionbcf_hrec_dup

Copies all fields except IDX.

src/utils/htslib/vcf.c:182

↓ 6 callersFunctionbcf_unpack_fmt_core1

src/utils/htslib/vcf.c:2396

↓ 6 callersFunctionbgzf_flush

src/utils/htslib/bgzf.c:1532

↓ 6 callersFunctionbuffer_printf

src/utils/FileRecordTools/Records/Record.h:26

↓ 6 callersMethodclearAll

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

↓ 6 callersFunctioncram_get_ref

* Returns a portion of a reference sequence from start to end inclusive. * The returned pointer is owned by either the cram_file fd or by the * inte

src/utils/htslib/cram/cram_io.c:2462

↓ 6 callersFunctioncram_not_enough_bits

src/utils/htslib/cram/cram_codecs.h:167

↓ 6 callersFunctioncram_seek

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

src/utils/htslib/cram/cram_io.c:4205

↓ 6 callersFunctioned_swap_8p

src/utils/htslib/htslib/hts.h:867

↓ 6 callersMethodempty

src/utils/NewChromsweep/CloseSweep.h:39

↓ 6 callersMethoderase

src/utils/FileRecordTools/Records/RecordKeyVector.cpp:68

↓ 6 callersFunctionfai_destroy

src/utils/htslib/faidx.c:420

↓ 6 callersMethodgetGenomeSize

src/utils/GenomeFile/GenomeFile.cpp:107

↓ 6 callersMethodgetProgram

src/utils/Contexts/ContextBase.h:43

↓ 6 callersMethodgetSplitBlockInfo

src/utils/Contexts/ContextBase.h:154

↓ 6 callersMethodhasGenomeFile

src/utils/Contexts/ContextBase.h:67

↓ 6 callersFunctionhfile_init

src/utils/htslib/hfile.c:96

↓ 6 callersFunctionhts_set_opt

src/utils/htslib/hts.c:1003

↓ 6 callersFunctionhts_tpool_process_flush

* Flushes the process-queue, but doesn't exit. This simply drains the queue * and ensures all worker threads have finished their current tasks * ass

src/utils/htslib/thread_pool.c:819

↓ 6 callersFunctionhts_version

src/utils/htslib/hts.c:57

↓ 6 callersFunctionidx_write_int32

src/utils/htslib/hts.c:1649

↓ 6 callersFunctioninit_add_plugin

src/utils/htslib/hfile.c:991

↓ 6 callersFunctioninsert_to_b

src/utils/htslib/hts.c:1337

↓ 6 callersFunctionkgetline

src/utils/htslib/kstring.c:251

↓ 6 callersFunctionknet_open

src/utils/htslib/knetfile.c:472

↓ 6 callersFunctionle_to_i16

Get an int16_t value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 16 bit signed integer * The

src/utils/htslib/htslib/hts_endian.h:232

↓ 6 callersFunctionle_to_u16

Get a uint16_t value from an unsigned byte array @param buf Pointer to source byte, may be unaligned * @return A 16 bit unsigned integer * The inp

src/utils/htslib/htslib/hts_endian.h:121

↓ 6 callersMethodloadBedFileIntoMap

src/utils/bedFile/bedFile.cpp:661

↓ 6 callersFunctionmfcreate

* For creating existing mFILE pointers directly from memory buffers. */

src/utils/htslib/cram/mFILE.c:198

↓ 6 callersFunctionmulti_errno

src/utils/htslib/hfile_libcurl.c:217

↓ 6 callersMethodsameChrom

src/utils/FileRecordTools/Records/Record.cpp:110

↓ 6 callersMethodtestNameConventions

src/utils/Contexts/ContextBase.cpp:687

↓ 5 callersMethodGetHeaderStruct

src/utils/BamTools/include/SamHeader.hpp:137

↓ 5 callersMethodPrintHeader

src/nucBed/nucBed.cpp:68

↓ 5 callersFunctionPrintTag

src/bamToBed/bamToBed.cpp:379

↓ 5 callersFunction_regions_add

Add a new region into a list sorted by start,end. On input the coordinates are 1-based, stored 0-based, inclusive.

src/utils/htslib/synced_bcf_reader.c:767

↓ 5 callersMethodadd

src/split/splitBed.cpp:54

↓ 5 callersMethodadjustZeroLength

src/utils/FileRecordTools/Records/Record.cpp:241

↓ 5 callersMethodallElems

src/utils/NewChromsweep/CloseSweep.h:58

↓ 5 callersFunctionbam_init1

src/utils/htslib/sam.c:292

↓ 5 callersFunctionbam_tag2cigar

src/utils/htslib/sam.c:399

↓ 5 callersFunctionbcf_dec_size_safe

src/utils/htslib/vcf.c:1070

↓ 5 callersFunctionbcf_hdr_init

src/utils/htslib/vcf.c:829

↓ 5 callersFunctionbcf_hdr_parse

src/utils/htslib/vcf.c:639

↓ 5 callersFunctionbgzf_getline

src/utils/htslib/bgzf.c:1794

↓ 5 callersFunctionbgzf_index_dump

src/utils/htslib/bgzf.c:1906

↓ 5 callersFunctionconvert

src/htsutil.cpp:8

↓ 5 callersFunctioncram_index_query

* Searches the index for the first slice overlapping a reference ID * and position, or one immediately preceding it if none is found in * the index

src/utils/htslib/cram/cram_index.c:354

↓ 5 callersFunctioncram_read_container

* Reads a container header. * * Returns cram_container on success * NULL on failure or no container left (fd->err == 0). */

src/utils/htslib/cram/cram_io.c:2819

↓ 5 callersFunctioncram_stats_del

src/utils/htslib/cram/cram_stats.c:75

↓ 5 callersFunctionfree_headers

src/utils/htslib/hfile_libcurl.c:311

↓ 5 callersMethodgetMaxNumDatabaseFields

src/utils/Contexts/ContextIntersect.h:36

↓ 5 callersMethodgetNumInputFiles

src/utils/Contexts/ContextBase.h:49

↓ 5 callersMethodgetQueryFileIdx

src/utils/Contexts/ContextIntersect.h:26

↓ 5 callersFunctionget_type_name

src/utils/htslib/vcf.c:1085

↓ 5 callersFunctionhts_idx_save_as

src/utils/htslib/hts.c:1740

↓ 5 callersFunctionhts_md5_destroy

src/utils/htslib/md5.c:371

↓ 5 callersFunctionhts_md5_final

src/utils/htslib/md5.c:270

↓ 5 callersFunctionhts_md5_init

src/utils/htslib/md5.c:322

↓ 5 callersFunctionhts_md5_update

src/utils/htslib/md5.c:236

↓ 5 callersFunctionhypergeo_acc

incremental version of hypergenometric distribution

src/utils/htslib/kfunc.c:218

↓ 5 callersFunctionhypergeo_acc

incremental version of hypergenometric distribution

src/fisher/kfunc.cpp:187

↓ 5 callersFunctionidx_write_uint64

src/utils/htslib/hts.c:1661

↓ 5 callersFunctionkget_int32

src/utils/htslib/cram/cram_index.c:87

↓ 5 callersFunctionknet_read

src/utils/htslib/knetfile.c:525

↓ 5 callersFunctionkputd

src/utils/htslib/kstring.c:36

↓ 5 callersFunctionle_int4

src/utils/htslib/cram/os.h:154

↓ 5 callersFunctionoverlap_remove

src/utils/htslib/sam.c:2600

↓ 5 callersFunctionoverlaps

return the amount of overlap between two features. Negative if none and the number of negative bases is the distance between the two.

src/utils/bedFile/bedFile.h:346

↓ 5 callersFunctionpool_destroy

src/utils/htslib/cram/pooled_alloc.c:101

↓ 5 callersFunctionpool_free

src/utils/htslib/cram/pooled_alloc.c:140

↓ 5 callersFunctionpossibly_expand_bam_data

src/utils/htslib/sam.c:320

↓ 5 callersMethodprojectOnGenome

src/utils/GenomeFile/GenomeFile.cpp:85

↓ 5 callersMethodread

src/utils/BamTools/include/BamReader.hpp:21

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