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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 442 callersMethodc_str

src/utils/general/QuickString.h:61

↓ 242 callersMethodsize

src/utils/bedFile/bedFile.h:165

↓ 171 callersMethodend

src/utils/general/BTlist.h:131

↓ 163 callersMethodappend

src/utils/general/QuickString.cpp:258

↓ 155 callersMethodbegin

src/utils/general/BTlist.h:115

↓ 153 callersMethodpush_back

src/utils/general/BTlist.h:159

↓ 122 callersFunctionkputc

src/utils/htslib/htslib/kstring.h:160

↓ 107 callersFunctionhgetc

Read one character from the stream @return The character read, or `EOF` on end-of-file or error. */

src/utils/htslib/htslib/hfile.h:144

↓ 94 callersFunctionkputs

src/utils/htslib/htslib/kstring.h:155

↓ 72 callersFunctionkputsn

src/utils/htslib/htslib/kstring.h:145

↓ 58 callersMethodfind

if true, pos will be the idx the distance is at. if false, pos will be the idx to insert at.

src/utils/NewChromsweep/CloseSweep.cpp:106

↓ 57 callersMethodempty

src/utils/general/BTlist.h:89

↓ 53 callersMethodOpen

src/utils/tabFile/tabFile.cpp:28

↓ 52 callersFunctionitf8_put

* Stores a value to memory in ITF-8 format. * * Returns the number of bytes required to store the number. * This is a maximum of 5 bytes. */

src/utils/htslib/cram/cram_io.h:97

↓ 51 callersFunctioncram_free_compression_header

src/utils/htslib/cram/cram_io.c:3276

↓ 48 callersMethodclear

src/utils/Fasta/Fasta.cpp:25

↓ 46 callersFunctionbgzf_write

src/utils/htslib/bgzf.c:1570

↓ 46 callersMethodgetKey

src/utils/FileRecordTools/Records/RecordKeyList.cpp:54

↓ 45 callersFunctionsafe_itf8_get

src/utils/htslib/cram/cram_io.h:272

↓ 45 callersMethodstr

src/utils/general/QuickString.h:62

↓ 43 callersMethodgetField

src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:80

↓ 41 callersMethodClose

Close the TAB file

src/utils/tabFile/tabFile.cpp:54

↓ 41 callersFunctioncram_free_block

* Frees a CRAM block, deallocating internal data too. */

src/utils/htslib/cram/cram_io.c:922

↓ 40 callersFunctioncram_free_container

src/utils/htslib/cram/cram_io.c:2752

↓ 38 callersFunctioncram_encoder_init

src/utils/htslib/cram/cram_codecs.c:1845

↓ 38 callersFunctionerror

src/utils/htslib/tabix.c:52

↓ 38 callersMethodgetStartPos

src/utils/FileRecordTools/Records/Record.h:93

↓ 38 callersMethodsize

src/split/splitBed.cpp:59

↓ 37 callersFunctionbgzf_read

src/utils/htslib/bgzf.c:987

↓ 37 callersFunctioncram_stats_add

src/utils/htslib/cram/cram_stats.c:50

↓ 37 callersFunctionksprintf

src/utils/htslib/kstring.c:167

↓ 34 callersFunctionbgzf_close

src/utils/htslib/bgzf.c:1629

↓ 34 callersMethodsize

src/utils/FileRecordTools/Records/StrandQueue.cpp:98

↓ 33 callersFunctioncram_decoder_init

src/utils/htslib/cram/cram_codecs.c:1817

↓ 33 callersFunctioncram_new_block

* Allocates a new cram_block structure with a specified content_type and * id. * * Returns block pointer on success * NULL on failure */

src/utils/htslib/cram/cram_io.c:758

↓ 33 callersMethodresize

src/utils/general/QuickString.cpp:301

↓ 31 callersMethodgetEndPos

src/utils/FileRecordTools/Records/Record.h:98

↓ 30 callersMethodreportBedNewLine

src/utils/bedFile/bedFile.h:1091

↓ 29 callersMethodgetChrName

src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:50

↓ 29 callersMethodgetChromSize

src/utils/GenomeFile/GenomeFile.cpp:99

↓ 28 callersFunctioncram_stats_encoding

* Computes entropy from integer frequencies for various encoding methods and * picks the best encoding. * * FIXME: we could reuse some of the code

src/utils/htslib/cram/cram_stats.c:129

↓ 28 callersMethodreserve

src/utils/general/QuickString.cpp:240

↓ 27 callersFunctionbcf_seqname

src/utils/htslib/htslib/vcf.h:755

↓ 27 callersFunctionhopen

src/utils/htslib/hfile.c:1104

↓ 27 callersFunctionkputw

src/utils/htslib/htslib/kstring.h:186

↓ 26 callersMethodgetStrandVal

src/utils/FileRecordTools/Records/Record.h:118

↓ 25 callersMethodGetNextBed

src/utils/bedFile/bedFile.cpp:206

↓ 25 callersMethodIsMapped

src/utils/BamTools/include/BamAlignment.hpp:318

↓ 25 callersMethodgetElem

src/utils/general/Tokenizer.h:37

↓ 25 callersFunctionitf8_put_blk

* Pushes a value in ITF8 format onto the end of a block. * This shouldn't be used for high-volume data as it is not the fastest * method. * * Retu

src/utils/htslib/cram/cram_io.c:472

↓ 24 callersFunctionToString

src/utils/lineFileUtilities/lineFileUtilities.h:17

↓ 24 callersFunctionstr2chrPos

src/utils/general/ParseTools.cpp:45

↓ 23 callersFunctionhts_close

src/utils/htslib/hts.c:919

↓ 23 callersFunctionisspace_c

src/utils/htslib/textutils_internal.h:166

↓ 22 callersFunctionbcf_enc_size

src/utils/htslib/htslib/vcf.h:927

↓ 22 callersFunctionbgzf_open

src/utils/htslib/bgzf.c:302

↓ 22 callersFunctionhclose

src/utils/htslib/hfile.c:464

↓ 21 callersFunctionTokenize

tokenize into a list of strings.

src/utils/lineFileUtilities/lineFileUtilities.h:25

↓ 21 callersFunctionbcf_unpack

src/utils/htslib/vcf.c:2430

↓ 20 callersFunctionbcf_hdr_id2int

src/utils/htslib/vcf.c:2631

↓ 20 callersFunctionkputc_

src/utils/htslib/htslib/kstring.h:169

↓ 20 callersMethodpush_back

src/utils/FileRecordTools/Records/RecordList.cpp:76

↓ 20 callersMethodsize

src/utils/general/BTlist.h:90

↓ 20 callersFunctionsub_idx

* Returns index of val into key. * Basically strchr(key, val)-key; */

src/utils/htslib/cram/cram_encode.c:63

↓ 19 callersMethoddeleteRecord

src/utils/FileRecordTools/FileRecordMgr.cpp:217

↓ 19 callersFunctionerror

src/utils/htslib/htsfile.c:46

↓ 19 callersFunctionhclose_abruptly

src/utils/htslib/hfile.c:479

↓ 19 callersFunctionhts_json_fnext

src/utils/htslib/textutils.c:283

↓ 19 callersFunctionks_resize

src/utils/htslib/htslib/kstring.h:109

↓ 18 callersFunctionDBG_OUT

src/utils/htslib/thread_pool.c:56

↓ 18 callersMethodSaveAlignment

src/utils/BamTools/include/BamWriter.hpp:50

↓ 18 callersMethodbegin

src/utils/KeyListOps/KeyListOpsMethods.h:118

↓ 18 callersFunctionerror

src/utils/htslib/bgzip.c:47

↓ 17 callersMethodGetNextAlignment

src/utils/BamTools/include/BamReader.hpp:270

↓ 17 callersMethodclose

src/utils/FileRecordTools/FileRecordMgr.cpp:98

↓ 17 callersFunctioncram_compress_block

* Compresses a block using one of two different zlib strategies. If we only * want one choice set strat2 to be -1. * * The logic here is that somet

src/utils/htslib/cram/cram_io.c:1098

↓ 17 callersFunctioncram_free_slice

src/utils/htslib/cram/cram_io.c:3339

↓ 17 callersMethodend

src/utils/NewChromsweep/CloseSweep.h:55

↓ 17 callersMethodgetFile

src/utils/Contexts/ContextBase.h:44

↓ 17 callersFunctionhts_tpool_delete_result

* Frees a result 'r' and if free_data is true also frees * the internal r->data result too. */

src/utils/htslib/thread_pool.c:315

↓ 17 callersFunctionopen

src/utils/gzstream/gzstream.C:149

↓ 17 callersMethodprint

src/utils/FileRecordTools/Records/Record.cpp:295

↓ 16 callersFunctionRansEncPutSymbol

Encodes a given symbol. This is faster than straight RansEnc since we can do multiplications instead of a divide. See RansEncSymbolInit for a descrip

src/utils/htslib/cram/rANS_byte.h:269

↓ 16 callersFunctionbcf_hdr_add_hrec

src/utils/htslib/vcf.c:541

↓ 16 callersFunctioned_swap_4p

src/utils/htslib/htslib/hts.h:856

↓ 16 callersFunctionhts_tpool_process_destroy

Deallocates memory for a thread process-queue. * Must be called before the thread pool is destroyed. */

src/utils/htslib/thread_pool.c:378

↓ 16 callersFunctionle_to_u32

Get a uint32_t value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 32 bit unsigned integer * T

src/utils/htslib/htslib/hts_endian.h:134

↓ 15 callersFunctionbcf_hdr_destroy

src/utils/htslib/vcf.c:852

↓ 15 callersFunctionbgzf_zerr

src/utils/htslib/bgzf.c:176

↓ 15 callersMethodend

src/utils/KeyListOps/KeyListOpsMethods.h:119

↓ 15 callersMethodend

src/utils/FileRecordTools/Records/RecordKeyList.cpp:38

↓ 15 callersMethodeof

src/utils/FileRecordTools/FileRecordMgr.cpp:109

↓ 14 callersMethodc_str

src/utils/BamTools/include/BamAlignment.hpp:217

↓ 14 callersMethodempty

src/utils/FileRecordTools/Records/StrandQueue.cpp:106

↓ 14 callersMethodgetFileIdx

src/utils/FileRecordTools/Records/Record.h:87

↓ 14 callersFunctionkputsn_

src/utils/htslib/htslib/kstring.h:177

↓ 14 callersMethodlength

src/utils/BamTools/include/BamAlignment.hpp:218

↓ 13 callersFunctionbcf_hdr_sync

src/utils/htslib/vcf.c:142

↓ 13 callersFunctionclose

src/utils/gzstream/gzstream.C:154

↓ 13 callersMethoddeleteObj

src/utils/general/FreeList.h:55

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