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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

↓ 3 callersFunctionsam_hdr_read

src/utils/htslib/sam.c:1008

↓ 3 callersFunctionsam_hdr_sanitise

Minimal sanitisation of a header to ensure. - null terminated string. - all lines start with @ (also implies no blank lines). Much more could be done

src/utils/htslib/sam.c:944

↓ 3 callersFunctionsam_hdr_str

src/utils/htslib/cram/sam_header.c:1068

↓ 3 callersFunctionsam_hdr_vadd

* sam_hdr_add with a va_list interface. * * Note: this function invokes va_arg at least once, making the value * of ap indeterminate after the retu

src/utils/htslib/cram/sam_header.c:437

↓ 3 callersFunctionsam_read1

src/utils/htslib/sam.c:1434

↓ 3 callersFunctionsam_write1

src/utils/htslib/sam.c:1613

↓ 3 callersMethodsbumpc

src/utils/general/PushBackStreamBuf.cpp:24

↓ 3 callersFunctionserialize_float_array

src/utils/htslib/vcf.c:1777

↓ 3 callersMethodsetChrName

src/utils/FileRecordTools/Records/Record.h:84

↓ 3 callersMethodsetColumns

src/utils/KeyListOps/KeyListOps.h:24

↓ 3 callersMethodsetEndPos

src/utils/FileRecordTools/Records/Record.h:99

↓ 3 callersMethodsetFileIdx

src/utils/FileRecordTools/Records/Record.h:88

↓ 3 callersMethodsetNumPrintFields

src/utils/FileRecordTools/Records/GffPlusRecord.h:33

↓ 3 callersMethodsignDistance

src/utils/Contexts/ContextClosest.h:29

↓ 3 callersFunctionskip_aux

src/utils/htslib/sam.c:1721

↓ 3 callersFunctionsocket_connect

src/utils/htslib/knetfile.c:93

↓ 3 callersFunctionsocket_wait

This function tests if the file handler is ready for reading (or * writing if is_read==0). */

src/utils/htslib/knetfile.c:64

↓ 3 callersFunctionsortedHelp

src/utils/general/CommonHelp.cpp:50

↓ 3 callersFunctionsw_seek

src/utils/htslib/vcf_sweep.c:133

↓ 3 callersFunctionswap_data

src/utils/htslib/sam.c:453

↓ 3 callersFunctionunionbedgraphs_help

src/unionBedGraphs/unionBedGraphsMain.cpp:163

↓ 3 callersFunctionusage

src/utils/htslib/htsfile.c:173

↓ 3 callersFunctionwritebuffer_is_nonempty

src/utils/htslib/hfile.c:151

↓ 2 callersFunctionComputeOverlaps

src/getOverlap/getOverlap.cpp:159

↓ 2 callersMethodFilename

src/utils/BamTools/include/SamHeader.hpp:142

↓ 2 callersMethodGetErrorString

src/utils/BamTools/include/BamReader.hpp:265

↓ 2 callersFunctionGetTotalBlockLength

src/utils/BlockedIntervals/BlockedIntervals.cpp:110

↓ 2 callersMethodIsOpen

src/utils/BamTools/include/BamReader.hpp:246

↓ 2 callersFunctionKeyListOpsHelp

src/utils/KeyListOps/KeyListOps.cpp:344

↓ 2 callersMethodOpenStream

src/utils/BamTools/include/BamReader.hpp:232

↓ 2 callersMethodParseHeaderText

src/utils/BamTools/include/SamHeader.hpp:105

↓ 2 callersFunctionPrintBedPE

src/bamToBed/bamToBed.cpp:591

↓ 2 callersFunctionProcessBed

src/bed12ToBed6/bed12ToBed6.cpp:133

↓ 2 callersFunctionProcessBed

src/bedToIgv/bedToIgv.cpp:214

↓ 2 callersFunctionRansDecSymbolInit

Initialize a decoder symbol to start "start" and frequency "freq"

src/utils/htslib/cram/rANS_byte.h:257

↓ 2 callersFunctionRansEncSymbolInit

Initializes an encoder symbol to start "start" and frequency "freq"

src/utils/htslib/cram/rANS_byte.h:183

↓ 2 callersFunction_bcf1_sync_alleles

src/utils/htslib/vcf.c:3567

↓ 2 callersFunction_bcf_hrec_format

src/utils/htslib/vcf.c:1640

↓ 2 callersFunction_dorand48

src/utils/htslib/os/rand.c:45

↓ 2 callersFunction_kf_gammap

regularized lower incomplete gamma function, by series expansion

src/utils/htslib/kfunc.c:101

↓ 2 callersFunction_kf_gammap

regularized lower incomplete gamma function, by series expansion

src/fisher/kfunc.cpp:74

↓ 2 callersFunction_kf_gammaq

regularized upper incomplete gamma function, by continued fraction

src/utils/htslib/kfunc.c:112

↓ 2 callersFunction_kf_gammaq

regularized upper incomplete gamma function, by continued fraction

src/fisher/kfunc.cpp:85

↓ 2 callersFunction_normalize_coord

src/slopBed/slopBed.cpp:70

↓ 2 callersFunction_reader_next_line

src/utils/htslib/synced_bcf_reader.c:579

↓ 2 callersFunction_reader_seek

src/utils/htslib/synced_bcf_reader.c:421

↓ 2 callersFunction_regions_init_string

File name or a list of genomic locations. If file name, NULL is returned.

src/utils/htslib/synced_bcf_reader.c:818

↓ 2 callersFunctionadd_auth_header

src/utils/htslib/hfile_libcurl.c:526

↓ 2 callersFunctionadd_callback_headers

src/utils/htslib/hfile_libcurl.c:338

↓ 2 callersFunctionafter

is A after (to the right of) B?

src/utils/bedFile/bedFile.h:352

↓ 2 callersFunctionannotate_help

src/annotateBed/annotateMain.cpp:139

↓ 2 callersFunctionappend_sub32

src/utils/htslib/cram/cram_io.h:589

↓ 2 callersFunctionappend_uint64

src/utils/htslib/cram/cram_io.h:603

↓ 2 callersFunctionaux_to_le

src/utils/htslib/sam.c:1645

↓ 2 callersFunctionbam_auxB_len

src/utils/htslib/sam.c:2040

↓ 2 callersFunctionbam_hdr_read

src/utils/htslib/sam.c:120

↓ 2 callersFunctionbam_index_build

src/utils/htslib/sam.c:652

↓ 2 callersFunctionbam_name2id

src/utils/htslib/sam.c:271

↓ 2 callersFunctionbam_plp_push

src/utils/htslib/sam.c:2676

↓ 2 callersFunctionbamtobed_help

src/bamToBed/bamToBed.cpp:233

↓ 2 callersFunctionbamtofastq_help

src/bamToFastq/bamToFastqMain.cpp:121

↓ 2 callersFunctionbcf1_sync

src/utils/htslib/vcf.c:1323

↓ 2 callersFunctionbcf1_sync_alleles

src/utils/htslib/vcf.c:1285

↓ 2 callersFunctionbcf1_sync_filter

src/utils/htslib/vcf.c:1293

↓ 2 callersFunctionbcf1_sync_id

src/utils/htslib/vcf.c:1279

↓ 2 callersFunctionbcf1_sync_info

src/utils/htslib/vcf.c:1300

↓ 2 callersFunctionbcf_destroy

src/utils/htslib/vcf.c:1007

↓ 2 callersFunctionbcf_enc_vfloat

src/utils/htslib/vcf.c:1795

↓ 2 callersFunctionbcf_float_set

src/utils/htslib/htslib/vcf.h:883

↓ 2 callersFunctionbcf_fmt_sized_array

src/utils/htslib/vcf.c:1848

↓ 2 callersFunctionbcf_get_variant_types

src/utils/htslib/vcf.c:3279

↓ 2 callersFunctionbcf_hdr_add_sample

src/utils/htslib/vcf.c:89

↓ 2 callersFunctionbcf_hdr_name2id

* bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID * bcf_hdr_id2name() - Translates numeric ID to sequence name

src/utils/htslib/htslib/vcf.h:753

↓ 2 callersFunctionbcf_hdr_parse_sample_line

src/utils/htslib/vcf.c:120

↓ 2 callersFunctionbcf_hdr_set_idx

src/utils/htslib/vcf.c:378

↓ 2 callersFunctionbcf_hdr_write

src/utils/htslib/vcf.c:929

↓ 2 callersFunctionbcf_hrec_add_key

src/utils/htslib/vcf.c:230

↓ 2 callersFunctionbcf_hrec_set_val

src/utils/htslib/vcf.c:242

↓ 2 callersFunctionbcf_index_build3

src/utils/htslib/vcf.c:2691

↓ 2 callersFunctionbcf_init

src/utils/htslib/vcf.c:958

↓ 2 callersFunctionbcf_read1_core

src/utils/htslib/vcf.c:1014

↓ 2 callersFunctionbcf_remove_allele_set

src/utils/htslib/vcfutils.c:236

↓ 2 callersFunctionbcf_set_variant_types

src/utils/htslib/vcf.c:3260

↓ 2 callersFunctionbcf_sr_destroy1

src/utils/htslib/synced_bcf_reader.c:332

↓ 2 callersFunctionbcf_sr_regions_init

src/utils/htslib/synced_bcf_reader.c:938

↓ 2 callersFunctionbcf_sr_regions_overlap

src/utils/htslib/synced_bcf_reader.c:1194

↓ 2 callersFunctionbcf_subset_format

src/utils/htslib/vcf.c:1220

↓ 2 callersFunctionbcf_update_info

src/utils/htslib/vcf.c:3290

↓ 2 callersFunctionbcf_write

src/utils/htslib/vcf.c:1501

↓ 2 callersFunctionbed12tobed6_help

src/bed12ToBed6/bed12ToBed6.cpp:96

↓ 2 callersFunctionbedpetobam_help

src/bedpeToBam/bedpeToBam.cpp:138

↓ 2 callersFunctionbedpetobam_reg2bin

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

src/bedpeToBam/bedpeToBam.cpp:331

↓ 2 callersFunctionbedtobam_help

src/bedToBam/bedToBam.cpp:140

↓ 2 callersFunctionbedtoigv_help

src/bedToIgv/bedToIgv.cpp:148

↓ 2 callersFunctionbedtools_help

src/bedtools.cpp:215

↓ 2 callersFunctionbgzf_check_EOF_common

src/utils/htslib/bgzf.c:1224

↓ 2 callersFunctionbgzf_compress

src/utils/htslib/bgzf.c:364

↓ 2 callersFunctionbgzf_compression

src/utils/htslib/bgzf.c:1763

↓ 2 callersFunctionbgzf_index_destroy

src/utils/htslib/bgzf.c:1828

↓ 2 callersFunctionbgzf_mt_eof

* Checks EOF from the reader thread. */

src/utils/htslib/bgzf.c:1243

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