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Functions2,929 in github.com/arq5x/bedtools2

⨍ Functions 2,929◇ Types & classes 454

Functionbam_auxB2i

src/utils/htslib/sam.c:2049

Functionbam_aux_update_array

src/utils/htslib/sam.c:1935

Functionbam_aux_update_float

src/utils/htslib/sam.c:1899

Functionbam_aux_update_int

src/utils/htslib/sam.c:1833

Functionbam_aux_update_str

src/utils/htslib/sam.c:1798

Functionbam_dup1

src/utils/htslib/sam.c:353

Functionbam_flag2str

src/utils/htslib/sam.c:2181

Functionbam_hdr_dup

src/utils/htslib/sam.c:75

Functionbam_mplp_auto

src/utils/htslib/sam.c:2811

Functionbam_mplp_constructor

src/utils/htslib/sam.c:2848

Functionbam_mplp_destroy

src/utils/htslib/sam.c:2803

Functionbam_mplp_destructor

src/utils/htslib/sam.c:2855

Functionbam_mplp_init

src/utils/htslib/sam.c:2771

Functionbam_mplp_init_overlaps

src/utils/htslib/sam.c:2789

Functionbam_mplp_reset

src/utils/htslib/sam.c:2836

Functionbam_mplp_set_maxcnt

src/utils/htslib/sam.c:2796

Functionbam_plp_set_maxcnt

src/utils/htslib/sam.c:2754

Functionbam_pseek

src/utils/htslib/sam.c:732

Functionbam_ptell

src/utils/htslib/sam.c:739

Functionbam_readrec

src/utils/htslib/sam.c:657

Functionbam_str2flag

src/utils/htslib/sam.c:2152

Functionbamtobed_IsCorrectMappingForBEDPE

src/bamToBed/bamToBed.cpp:694

Functionbcf_acgt2int

src/utils/htslib/htslib/vcfutils.h:114

Functionbcf_add_id

src/utils/htslib/vcf.c:3647

Functionbcf_calc_ac

src/utils/htslib/vcfutils.c:30

Functionbcf_dup

src/utils/htslib/vcf.c:1495

Functionbcf_empty

src/utils/htslib/vcf.c:997

Functionbcf_enc_inttype

src/utils/htslib/htslib/vcf.h:948

Functionbcf_get_format_string

src/utils/htslib/vcf.c:3771

Functionbcf_get_variant_type

src/utils/htslib/vcf.c:3284

Functionbcf_gt2alleles

src/utils/htslib/htslib/vcf.h:617

Functionbcf_gt_type

src/utils/htslib/vcfutils.c:120

Functionbcf_has_filter

src/utils/htslib/vcf.c:3552

Functionbcf_hdr_combine

src/utils/htslib/vcf.c:2744

Functionbcf_hdr_dup

src/utils/htslib/vcf.c:3005

Functionbcf_hdr_fmt_text

src/utils/htslib/vcf.c:1683

Functionbcf_hdr_id2name

src/utils/htslib/htslib/vcf.h:754

Functionbcf_hdr_merge

src/utils/htslib/vcf.c:2810

Functionbcf_hdr_printf

src/utils/htslib/vcf.c:776

Functionbcf_hdr_remove

src/utils/htslib/vcf.c:703

Functionbcf_hdr_set

src/utils/htslib/vcf.c:1621

Functionbcf_hdr_set_samples

src/utils/htslib/vcf.c:3074

Functionbcf_hdr_subset

src/utils/htslib/vcf.c:3022

Functionbcf_header_debug

src/utils/htslib/vcf.c:212

Functionbcf_hrec_debug

src/utils/htslib/vcf.c:203

Functionbcf_hrec_format

src/utils/htslib/vcf.c:1660

Functionbcf_index_build2

src/utils/htslib/vcf.c:2730

Functionbcf_index_load2

src/utils/htslib/vcf.c:2686

Functionbcf_is_snp

src/utils/htslib/vcf.c:3181

Functionbcf_readrec

src/utils/htslib/vcf.c:1270

Functionbcf_remove_alleles

src/utils/htslib/vcfutils.c:225

Functionbcf_remove_filter

src/utils/htslib/vcf.c:3538

Functionbcf_sr_add_reader

src/utils/htslib/synced_bcf_reader.c:200

Functionbcf_sr_destroy

src/utils/htslib/synced_bcf_reader.c:348

Functionbcf_sr_init

src/utils/htslib/synced_bcf_reader.c:324

Functionbcf_sr_next_line

src/utils/htslib/synced_bcf_reader.c:635

Functionbcf_sr_remove_reader

src/utils/htslib/synced_bcf_reader.c:366

Functionbcf_sr_seek

src/utils/htslib/synced_bcf_reader.c:672

Functionbcf_sr_set_regions

src/utils/htslib/synced_bcf_reader.c:147

Functionbcf_sr_set_samples

src/utils/htslib/synced_bcf_reader.c:691

Functionbcf_sr_set_targets

src/utils/htslib/synced_bcf_reader.c:161

Functionbcf_sr_set_threads

src/utils/htslib/synced_bcf_reader.c:175

Functionbcf_sr_strerror

src/utils/htslib/synced_bcf_reader.c:67

Functionbcf_subset

src/utils/htslib/vcf.c:3154

Functionbcf_sweep_bwd

src/utils/htslib/vcf_sweep.c:174

Functionbcf_sweep_destroy

src/utils/htslib/vcf_sweep.c:121

Functionbcf_sweep_fwd

src/utils/htslib/vcf_sweep.c:145

Functionbcf_sweep_hdr

src/utils/htslib/vcf_sweep.c:182

Functionbcf_sweep_init

src/utils/htslib/vcf_sweep.c:107

Functionbcf_translate

src/utils/htslib/vcf.c:2889

Functionbcf_trim_alleles

src/utils/htslib/vcfutils.c:171

Functionbcf_update_alleles

src/utils/htslib/vcf.c:3590

Functionbcf_update_filter

src/utils/htslib/vcf.c:3507

Functionbcf_update_format_string

src/utils/htslib/vcf.c:3378

Functionbcf_update_id

src/utils/htslib/vcf.c:3634

MethodbeforeLeftClosestEndPos

src/utils/NewChromsweep/CloseSweep.cpp:634

src/utils/FileRecordTools/Records/RecordList.h:69

Functionbgzf_decode_func

Our input block has already been decoded by bgzf_mt_read_block(). We need to split that into a fetch block (compressed) and make this do the actual de

src/utils/htslib/bgzf.c:1083

Functionbgzf_dopen

src/utils/htslib/bgzf.c:324

Functionbgzf_encode_func

src/utils/htslib/bgzf.c:1034

Functionbgzf_encode_level0_func

Optimisation for compression level 0 (uncompressed deflate blocks) Avoids memcpy of the data from uncompressed to compressed buffer.

src/utils/htslib/bgzf.c:1049

Functionbgzf_is_bgzf

src/utils/htslib/bgzf.c:1751

Functionbgzf_mt_reader

src/utils/htslib/bgzf.c:1274

Functionbgzf_mt_writer

* Takes compressed blocks off the results queue and calls hwrite to * punt them to the output stream. * * Returns NULL when no more are left, or -1

src/utils/htslib/bgzf.c:1107

Functionbgzf_nul_func

* Nul function so we can dispatch a job with the correct serial * to mark failure or to indicate an empty read (EOF). */

src/utils/htslib/bgzf.c:1099

Functionbuf_write

src/utils/BamTools/include/SamHeader.hpp:15

src/utils/general/QuickString.cpp:56

MethodbuildCigarStr

src/utils/FileRecordTools/Records/BamRecord.cpp:267

MethodcalcMemoryStats

src/regressTest/RegressTest.cpp:593

src/groupBy/groupBy.cpp:139

src/utils/general/QuickString.h:29

src/utils/general/FreeList.h:63

Functioncb_close

src/utils/htslib/hfile.c:650

Functioncb_flush

src/utils/htslib/hfile.c:643

Functioncb_read

src/utils/htslib/hfile.c:597

Functioncb_seek

src/utils/htslib/hfile.c:633

Functioncb_write

src/utils/htslib/hfile.c:615

MethodcheckCoordinatesAgainstChromLength

src/complementFile/complementFile.cpp:63

MethodcheckMultiDbs

src/utils/NewChromsweep/CloseSweep.cpp:446

MethodcheckSplits

src/intersectFile/intersectFile.cpp:120

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