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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 2 callersFunctionbgzf_mt_seek

* Performs the seek (called by reader thread). * * This simply drains the entire queue, throwing away blocks, seeks, * and starts it up again. Bru

src/utils/htslib/bgzf.c:1259

↓ 2 callersFunctionbgzf_uncompress

src/utils/htslib/bgzf.c:527

↓ 2 callersFunctionblksize

src/utils/htslib/hfile.c:662

↓ 2 callersFunctioncigar_iref2iseq_next

src/utils/htslib/sam.c:2471

↓ 2 callersFunctioncigar_iref2iseq_set

* cigar_iref2iseq_set() - find the first CMATCH setting the ref and the read index * cigar_iref2iseq_next() - get the next CMATCH base * @cigar:

src/utils/htslib/sam.c:2436

↓ 2 callersMethodclose

src/utils/general/InflateStreamBuf.h:50

↓ 2 callersFunctionclose_plugin

src/utils/htslib/plugin.c:178

↓ 2 callersFunctioncluster_help

src/clusterBed/clusterMain.cpp:103

↓ 2 callersFunctionconfirm_overwrite

src/utils/htslib/bgzip.c:56

↓ 2 callersFunctioncopy_auth_headers

src/utils/htslib/hfile_s3.c:231

↓ 2 callersFunctioncram_add_base

src/utils/htslib/cram/cram_encode.c:1807

↓ 2 callersFunctioncram_add_bases

src/utils/htslib/cram/cram_encode.c:1794

↓ 2 callersFunctioncram_add_substitution

src/utils/htslib/cram/cram_encode.c:1771

↓ 2 callersFunctioncram_block_size

* Computes the size of a cram block, including the block * header itself. */

src/utils/htslib/cram/cram_io.c:852

↓ 2 callersFunctioncram_decode_slice_header

* Decodes a CRAM (un)mapped slice header block. * Returns slice header ptr on success * NULL on failure */

src/utils/htslib/cram/cram_decode.c:1071

↓ 2 callersFunctioncram_dopen

Opens an existing stream for reading or writing. * * Returns file handle on success; * NULL on failure. */

src/utils/htslib/cram/cram_io.c:4078

↓ 2 callersFunctioncram_drain_rqueue

* Drains and frees the decode read-queue for a multi-threaded reader. */

src/utils/htslib/cram/cram_decode.c:3351

↓ 2 callersFunctioncram_ds_unique

* Checks whether an external block is used solely by a single data series. * Returns the codec type if so (EXTERNAL, BYTE_ARRAY_LEN, BYTE_ARRAY_STOP)

src/utils/htslib/cram/cram_decode.c:993

↓ 2 callersFunctioncram_encode_compression_header

* Encodes a compression header block into a generic cram_block structure. * * Returns cram_block ptr on success * NULL on failure */

src/utils/htslib/cram/cram_encode.c:76

↓ 2 callersFunctioncram_encode_container

* Encodes all slices in a container into blocks. * Returns 0 on success * -1 on failure */

src/utils/htslib/cram/cram_encode.c:1250

↓ 2 callersFunctioncram_encoding2str

src/utils/htslib/cram/cram_codecs.c:1784

↓ 2 callersFunctioncram_extract_block

* Returns the next 'size' bytes from a block, or NULL if insufficient * data left.This is just a pointer into the block data and not an * allocated

src/utils/htslib/cram/cram_codecs.c:301

↓ 2 callersFunctioncram_flush_container

* Flushes a completely or partially full container to disk, writing * container structure, header and blocks. This also calls the encoder * function

src/utils/htslib/cram/cram_io.c:3115

↓ 2 callersFunctioncram_flush_container2

common component shared by cram_flush_container{,_mt}

src/utils/htslib/cram/cram_io.c:3075

↓ 2 callersFunctioncram_flush_result

src/utils/htslib/cram/cram_io.c:3140

↓ 2 callersFunctioncram_free_file_def

src/utils/htslib/cram/cram_io.c:3607

↓ 2 callersFunctioncram_free_slice_header

src/utils/htslib/cram/cram_io.c:3327

↓ 2 callersFunctioncram_load_reference

* If fd has been opened for reading, it may be permitted to specify 'fn' * as NULL and let the code auto-detect the reference by parsing the * SAM h

src/utils/htslib/cram/cram_io.c:2658

↓ 2 callersFunctioncram_new_metrics

src/utils/htslib/cram/cram_io.c:1436

↓ 2 callersFunctioncram_read_slice

* Loads an entire slice. * FIXME: In 1.0 the native unit of slices within CRAM is broken * as slices contain references to objects in other slices.

src/utils/htslib/cram/cram_io.c:3476

↓ 2 callersFunctioncram_set_voption

* Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success *

src/utils/htslib/cram/cram_io.c:4408

↓ 2 callersFunctioncreate_hfile_mem

src/utils/htslib/hfile.c:850

↓ 2 callersFunctiondebug_vsets

src/utils/htslib/bcf_sr_sort.c:274

↓ 2 callersFunctiondeflate_block

Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.

src/utils/htslib/bgzf.c:506

↓ 2 callersMethoddeleteCurrent

src/utils/general/BTlist.h:133

↓ 2 callersMethoddeleteMergedRecord

src/utils/FileRecordTools/FileRecordMergeMgr.cpp:194

↓ 2 callersFunctiondo_realloc_bam_data

src/utils/htslib/sam.c:297

↓ 2 callersFunctiondup_stdout

src/utils/htslib/htsfile.c:61

↓ 2 callersFunctionencode_utf8

src/utils/htslib/textutils.c:101

↓ 2 callersFunctionexpand_cache_path

* Converts a directory and a filename into an expanded path, replacing %s * in directory with the filename and %[0-9]+s with portions of the filename

src/utils/htslib/cram/cram_io.c:1914

↓ 2 callersFunctionexpand_path

* Takes a dirname possibly including % rules and appends the filename * to it. * * Returns expanded pathname or NULL for malloc failure. */

src/utils/htslib/cram/open_trace_file.c:218

↓ 2 callersFunctionexpand_tilde_open

src/utils/htslib/hfile_s3.c:148

↓ 2 callersFunctionfai_build3_core

src/utils/htslib/faidx.c:432

↓ 2 callersFunctionfai_get_val

src/utils/htslib/faidx.c:727

↓ 2 callersFunctionfai_load3_core

src/utils/htslib/faidx.c:539

↓ 2 callersFunctionfaidx_adjust_position

src/utils/htslib/faidx.c:863

↓ 2 callersFunctionfastafrombed_help

src/fastaFromBed/fastaFromBedMain.cpp:155

↓ 2 callersFunctionfile_type

src/utils/htslib/tabix.c:70

↓ 2 callersMethodfindBlockedOverlaps

src/utils/FileRecordTools/Records/BlockMgr.cpp:218

↓ 2 callersFunctionfind_file_dir

* Searches for file in the directory 'dirname'. If it finds it, it opens * it. This also searches for compressed versions of the file in dirname * t

src/utils/htslib/cram/open_trace_file.c:282

↓ 2 callersFunctionfind_file_url

src/utils/htslib/cram/open_trace_file.c:171

↓ 2 callersFunctionfind_scheme_handler

Returns the appropriate handler, or NULL if the string isn't an URL. */

src/utils/htslib/hfile.c:1078

↓ 2 callersFunctionflank_help

src/flankBed/flankBedMain.cpp:145

↓ 2 callersFunctionflush_buffer

src/utils/gzstream/gzstream.C:103

↓ 2 callersFunctionfree_all_parts

src/utils/htslib/multipart.c:65

↓ 2 callersFunctionfree_auth

src/utils/htslib/hfile_libcurl.c:257

↓ 2 callersFunctionfree_auth_data

src/utils/htslib/hfile_s3.c:246

↓ 2 callersFunctionfree_part

src/utils/htslib/multipart.c:52

↓ 2 callersFunctiongcs_rewrite

src/utils/htslib/hfile_gcs.c:40

↓ 2 callersFunctiongenomecoverage_help

src/genomeCoverageBed/genomeCoverageMain.cpp:241

↓ 2 callersMethodgetAnyHit

src/utils/Contexts/ContextIntersect.h:42

↓ 2 callersMethodgetBlocks

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

↓ 2 callersMethodgetChromId

src/utils/GenomeFile/NewGenomeFile.cpp:153

↓ 2 callersMethodgetCoverageType

src/utils/Contexts/ContextCoverage.h:23

↓ 2 callersMethodgetCurrChromdId

this is an abstract base class.

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

↓ 2 callersMethodgetDatabaseFile

src/utils/Contexts/ContextIntersect.h:25

↓ 2 callersMethodgetEitherFraction

src/utils/Contexts/ContextIntersect.h:84

↓ 2 callersMethodgetExcludeFile

src/utils/Contexts/ContextFisher.h:20

↓ 2 callersMethodgetLength

src/utils/FileRecordTools/Records/Record.cpp:302

↓ 2 callersMethodgetLine

src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:98

↓ 2 callersMethodgetMaxLeftEndPos

src/utils/NewChromsweep/CloseSweep.cpp:126

↓ 2 callersMethodgetNoHit

src/utils/Contexts/ContextIntersect.h:45

↓ 2 callersMethodgetNumFields

src/utils/FileRecordTools/Records/GffRecord.h:31

↓ 2 callersMethodgetOverlapFractionB

src/utils/Contexts/ContextIntersect.h:78

↓ 2 callersMethodgetRemoveAll

src/utils/Contexts/ContextSubtract.h:23

↓ 2 callersMethodgetSortOutput

src/utils/Contexts/ContextBase.h:103

↓ 2 callersMethodgetUseBufferedOutput

src/utils/Contexts/ContextBase.h:97

↓ 2 callersMethodgetUseDBnameTags

src/utils/Contexts/ContextBase.h:106

↓ 2 callersMethodgetWriteCount

src/utils/Contexts/ContextIntersect.h:57

↓ 2 callersMethodgetWriteCountsPerDatabase

src/utils/Contexts/ContextIntersect.h:60

↓ 2 callersMethodgetWriteOverlap

src/utils/Contexts/ContextIntersect.h:63

↓ 2 callersFunctionget_header_list

src/utils/htslib/hfile_libcurl.c:326

↓ 2 callersFunctionget_intv

src/utils/htslib/tbx.c:146

↓ 2 callersFunctionget_name_suffix

src/utils/htslib/bgzf.c:1868

↓ 2 callersMethodhasIntersectMethods

src/utils/Contexts/ContextMap.h:18

↓ 2 callersFunctionhfile_init_fixed

src/utils/htslib/hfile.c:123

↓ 2 callersFunctionhfile_set_blksize

* Changes the buffer size for an hFILE. Ideally this is done * immediately after opening. If performed later, this function may * fail if we are r

src/utils/htslib/hfile.c:192

↓ 2 callersFunctionhisremote

src/utils/htslib/hfile.c:1129

↓ 2 callersFunctionhopen_callback

src/utils/htslib/hfile.c:673

↓ 2 callersFunctionhputc

Write a character to the stream @return The character written, or `EOF` if an error occurred. */

src/utils/htslib/htslib/hfile.h:226

↓ 2 callersFunctionhts_idx_load

src/utils/htslib/hts.c:2871

↓ 2 callersFunctionhts_itr_off

src/utils/htslib/hts.c:2044

↓ 2 callersFunctionhts_itr_query

src/utils/htslib/hts.c:2097

↓ 2 callersFunctionhts_itr_querys

src/utils/htslib/hts.c:2553

↓ 2 callersFunctionhts_itr_regions

src/utils/htslib/hts.c:2585

↓ 2 callersFunctionhts_log

src/utils/htslib/hts.c:2975

↓ 2 callersFunctionhts_md5_hex

src/utils/htslib/md5.c:379

↓ 2 callersFunctionhts_open_callback

src/utils/htslib/hts.c:448

↓ 2 callersFunctionhts_open_format_impl

src/utils/htslib/hts.c:393

↓ 2 callersFunctionhts_opt_apply

* Applies an hts_opt option list to a given htsFile. * * Returns 0 on success * -1 on failure */

src/utils/htslib/hts.c:647

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