Functions — github.com/arq5x/bedtools2

CodeHub MCPcopy Index your code

hub / github.com/arq5x/bedtools2 / functions

Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 13 callersFunctioneasy_errno

src/utils/htslib/hfile_libcurl.c:139

↓ 13 callersFunctionhfile_add_scheme_handler

src/utils/htslib/hfile.c:981

↓ 13 callersFunctionhts_open

src/utils/htslib/hts.c:455

↓ 13 callersFunctionhts_parse_decimal

src/utils/htslib/hts.c:2488

↓ 13 callersFunctionint2str

src/utils/general/ParseTools.h:44

↓ 13 callersMethodnewObj

src/utils/general/FreeList.h:38

↓ 13 callersMethodprintRecord

src/complementFile/complementFile.cpp:127

↓ 13 callersFunctiontoupper_c

src/utils/htslib/textutils_internal.h:169

↓ 13 callersFunctionu32_to_le

Store a uint32_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:182

↓ 12 callersMethodGetEndPosition

src/utils/BamTools/include/BamAlignment.hpp:338

↓ 12 callersMethodHtsObj2

src/utils/BamTools/include/BamAlignment.hpp:135

↓ 12 callersMethodbegin

src/utils/FileRecordTools/Records/RecordKeyList.cpp:29

↓ 12 callersMethodbegin

used to be a map iter, trying not to change interface too much.

src/utils/NewChromsweep/CloseSweep.h:54

↓ 12 callersFunctioned_is_big

src/utils/htslib/htslib/hts.h:837

↓ 12 callersFunctionhtell

Report the current stream offset @return The offset within the stream, starting from zero. */

src/utils/htslib/htslib/hfile.h:136

↓ 12 callersFunctionhts_tpool_result_data

* Returns the data portion of a hts_tpool_result, corresponding * to the actual "result" itself. */

src/utils/htslib/thread_pool.c:329

↓ 12 callersFunctionitf8_decode_crc

src/utils/htslib/cram/cram_io.c:180

↓ 12 callersFunctionkbs_exists

Test whether the bit set contains the element.

src/utils/htslib/htslib/kbitset.h:119

↓ 12 callersFunctionle_to_i32

Get an int32_t value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 32 bit signed integer * The

src/utils/htslib/htslib/hts_endian.h:243

↓ 12 callersMethodnext

src/utils/general/BTlist.h:123

↓ 12 callersFunctionpool_alloc

src/utils/htslib/cram/pooled_alloc.c:111

↓ 12 callersMethodreportBedPETab

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

src/utils/bedFilePE/bedFilePE.cpp:91

↓ 12 callersFunctionreverseComplement

Performs an in-place reverse complement conversion

src/utils/sequenceUtilities/sequenceUtils.cpp:21

↓ 12 callersMethodtop

src/utils/FileRecordTools/Records/StrandQueue.cpp:28

↓ 11 callersMethodGetTag

src/utils/BamTools/include/BamAlignment.hpp:349

↓ 11 callersFunctionbam_aux_get

src/utils/htslib/sam.c:1747

↓ 11 callersMethodclear

src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:69

↓ 11 callersMethodgetFileType

src/utils/FileRecordTools/FileRecordMgr.h:66

↓ 11 callersFunctionhseek

src/utils/htslib/hfile.c:407

↓ 11 callersFunctionhts_tpool_dispatch

* Adds an item to the work pool. * * Returns 0 on success * -1 on failure */

src/utils/htslib/thread_pool.c:719

↓ 11 callersFunctionisNumeric

This functions recognizes only numbers with digits, plus sign, minus sign, decimal point, e, or E. Hexadecimal and pointers not currently supported.

src/utils/general/ParseTools.cpp:12

↓ 11 callersFunctionrand_range

src/utils/general/Random.cpp:11

↓ 11 callersFunctionreverseSequence

Performs an in-place sequence reversal

src/utils/sequenceUtilities/sequenceUtils.cpp:16

↓ 11 callersFunctionu16_to_le

Store a uint16_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:169

↓ 10 callersFunctionallToolsCommonHelp

src/utils/general/CommonHelp.cpp:103

↓ 10 callersFunctionbam_hdr_destroy

src/utils/htslib/sam.c:60

↓ 10 callersFunctionbcf_hdr_parse_line

src/utils/htslib/vcf.c:288

↓ 10 callersFunctionbcf_hrec_find_key

src/utils/htslib/vcf.c:273

↓ 10 callersFunctioncram_add_feature

* Adds a feature code to a read within a slice. For purposes of minimising * memory allocations and fragmentation we have one array of features for a

src/utils/htslib/cram/cram_encode.c:1748

↓ 10 callersFunctioncram_read_block

* Reads a block from a cram file. * Returns cram_block pointer on success. * NULL on failure */

src/utils/htslib/cram/cram_io.c:781

↓ 10 callersFunctiondehex

src/utils/htslib/textutils.c:35

↓ 10 callersMethodgetObeySplits

split handling.

src/utils/Contexts/ContextBase.h:86

↓ 10 callersFunctionhts_idx_destroy

src/utils/htslib/hts.c:1619

↓ 10 callersMethodpush

src/utils/FileRecordTools/Records/StrandQueue.cpp:82

↓ 10 callersMethodsubstr

src/utils/general/QuickString.cpp:313

↓ 9 callersFunctionRansDecRenormSafe

Renormalize, with extra checks for falling off the end of the input.

src/utils/htslib/cram/rANS_byte.h:339

↓ 9 callersMethodanyHits

src/utils/bedFile/bedFile.cpp:398

↓ 9 callersFunctionbcf_enc_vint

src/utils/htslib/vcf.c:1729

↓ 9 callersFunctionbgzf_getc

src/utils/htslib/bgzf.c:1768

↓ 9 callersFunctioncram_get_block_by_id

src/utils/htslib/cram/cram_io.h:477

↓ 9 callersFunctionhts_getline

src/utils/htslib/hts.c:1136

↓ 9 callersFunctionhts_tpool_process_init

* Initialises a thread process-queue. * * In_only, if true, indicates that the process generates does not need to * hold any output. Otherwise an

src/utils/htslib/thread_pool.c:343

↓ 9 callersFunctionisInteger

// isInteger(s): Tests if string s is a valid integer *****************************************************/

src/utils/bedFile/bedFile.h:335

↓ 9 callersFunctionisdigit_c

src/utils/htslib/textutils_internal.h:162

↓ 9 callersFunctionkhash_str2int_get

* Returns 0 on success and -1 when the key is not present. On success, * *value is set, unless NULL is passed. */

src/utils/htslib/htslib/khash_str2int.h:78

↓ 9 callersFunctionks_len

src/utils/htslib/htslib/kstring.h:128

↓ 9 callersFunctionks_release

Give ownership of the underlying buffer away to something else (making that something else responsible for freeing it), leaving the kstring_t empty an

src/utils/htslib/htslib/kstring.h:137

↓ 9 callersFunctionks_str

src/utils/htslib/htslib/kstring.h:123

↓ 9 callersMethodpop

src/utils/FileRecordTools/Records/StrandQueue.cpp:35

↓ 9 callersMethodreportBedTab

src/utils/bedFile/bedFile.h:924

↓ 9 callersMethodsetKey

src/utils/FileRecordTools/Records/RecordKeyList.cpp:58

↓ 9 callersFunctiontbx_destroy

src/utils/htslib/tbx.c:252

↓ 9 callersMethodtokenize

src/utils/general/Tokenizer.cpp:37

↓ 9 callersMethodvalue

src/utils/FileRecordTools/Records/RecordList.h:39

↓ 8 callersMethodGetReferenceData

src/utils/BamTools/include/BamReader.hpp:251

↓ 8 callersFunctionRansDecInit

Initializes a rANS decoder. Unlike the encoder, the decoder works forwards as you'd expect.

src/utils/htslib/cram/rANS_byte.h:118

↓ 8 callersFunctionRansDecRenorm

src/utils/htslib/cram/rANS_byte.h:322

↓ 8 callersFunctionRansEncFlush

Flushes the rANS encoder.

src/utils/htslib/cram/rANS_byte.h:102

↓ 8 callersFunctionRansEncInit

Initialize a rANS encoder.

src/utils/htslib/cram/rANS_byte.h:65

↓ 8 callersFunctionbcf_enc_int1

src/utils/htslib/htslib/vcf.h:955

↓ 8 callersFunctionbcf_hdr_get_hrec

* Note that while querying of FLT,INFO,FMT,CTG lines is fast (the keys are hashed), * the STR,GEN lines are searched for linearly in a linked list

src/utils/htslib/vcf.c:585

↓ 8 callersFunctionbcf_hdr_read

src/utils/htslib/vcf.c:875

↓ 8 callersFunctionbgzf_read_block

src/utils/htslib/bgzf.c:752

↓ 8 callersMethodclear

src/utils/FileRecordTools/Records/Record.cpp:35

↓ 8 callersFunctioncram_compress_by_method

src/utils/htslib/cram/cram_io.c:1025

↓ 8 callersFunctioncram_ref_decr

src/utils/htslib/cram/cram_io.c:2294

↓ 8 callersFunctioncram_uncompress_block

* Uncompresses a CRAM block, if compressed. */

src/utils/htslib/cram/cram_io.c:933

↓ 8 callersFunctioncram_write_block

* Writes a CRAM block. * Returns 0 on success * -1 on failure */

src/utils/htslib/cram/cram_io.c:873

↓ 8 callersFunctioned_swap_4

src/utils/htslib/htslib/hts.h:851

↓ 8 callersMethodgetChromList

src/utils/GenomeFile/GenomeFile.cpp:111

↓ 8 callersMethodgetType

src/utils/FileRecordTools/Records/Record.h:131

↓ 8 callersFunctionhflush

src/utils/htslib/hfile.c:354

↓ 8 callersFunctionhts_tpool_destroy

* Destroys a thread pool. The threads are joined into the main * thread so they will finish their current work load. */

src/utils/htslib/thread_pool.c:926

↓ 8 callersFunctionhts_tpool_next_result_wait

* Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This will wait for *

src/utils/htslib/thread_pool.c:206

↓ 8 callersFunctionkf_lgamma

Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */

src/utils/htslib/kfunc.c:37

↓ 8 callersFunctionkf_lgamma

src/fisher/kfunc.cpp:10

↓ 8 callersFunctionkstrtok

src/utils/htslib/kstring.c:177

↓ 8 callersMethodnext

src/utils/FileRecordTools/Records/RecordList.cpp:40

↓ 8 callersMethodprintFields

src/utils/FileRecordTools/Records/PlusFields.cpp:34

↓ 8 callersFunctionstring_ndup

src/utils/htslib/cram/string_alloc.c:146

↓ 8 callersMethodundoZeroLength

src/utils/FileRecordTools/Records/Record.cpp:250

↓ 7 callersMethodGetHeaderText

src/utils/BamTools/include/BamReader.hpp:261

↓ 7 callersMethodGetNextBedPE

src/utils/bedFilePE/bedFilePE.cpp:61

↓ 7 callersFunctionIntersectCommonHelp

src/utils/general/CommonHelp.cpp:55

↓ 7 callersMethodallHits

src/utils/bedFile/bedFile.cpp:337

↓ 7 callersFunctionaux_type2size

src/utils/htslib/sam.c:435

↓ 7 callersFunctionbam_copy1

src/utils/htslib/sam.c:337

↓ 7 callersFunctionbcf_enc_vchar

src/utils/htslib/vcf.c:1802

↓ 7 callersMethodclear

src/utils/NewChromsweep/CloseSweep.cpp:37

↓ 7 callersMethodclearVector

src/utils/FileRecordTools/Records/RecordKeyVector.cpp:99

← previous next →101–200 of 2,929, ranked by callers