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Functions263 in github.com/bwa-mem2/bwa-mem2

⨍ Functions 263◇ Types & classes 31

↓ 2 callersFunctionmem_chain_weight

src/bwamem.cpp:429

↓ 2 callersFunctionmem_dedup_patch

src/bwamem.cpp:239

↓ 2 callersFunctionmem_mark_primary_se_core

src/bwamem.cpp:1392

↓ 2 callersFunctionmem_matesw

src/bwamem_pair.cpp:150

↓ 2 callersFunctionmem_matesw_batch_post

src/bwamem_pair.cpp:1095

↓ 2 callersFunctionmem_pair

src/bwamem_pair.cpp:285

↓ 2 callersFunctionmem_patch_reg

src/bwamem.cpp:175

↓ 2 callersFunctionrealtime

src/utils.cpp:300

↓ 2 callersFunctionsocket_wait

src/kopen.cpp:65

↓ 2 callersFunctionsortPairsLenExt

src/bwamem.cpp:1926

↓ 2 callersFunctionsuffixsort

↓ 2 callersFunctionwrite_bytes

src/kopen.cpp:102

↓ 1 callersFunctionHTStatus

src/fastmap.cpp:63

↓ 1 callersFunctionLMSpostproc1

↓ 1 callersFunctionLMSpostproc2

↓ 1 callersFunctionLMSsort1

↓ 1 callersFunctionadd1

src/bntseq.cpp:249

↓ 1 callersFunctionbns_dump

src/bntseq.cpp:73

↓ 1 callersFunctionbns_fetch_seq_v2

src/bwamem.cpp:1890

↓ 1 callersFunctionbns_get_seq_v2

src/bwamem.cpp:1851

↓ 1 callersFunctionbns_intv2rid

src/bntseq.cpp:394

↓ 1 callersFunctionbns_restore_core

src/bntseq.cpp:106

↓ 1 callersFunctionbseq_classify

src/bwa.cpp:226

↓ 1 callersMethodbuild_index

src/FMI_search.cpp:306

↓ 1 callersFunctionbwa_fill_scmat

test/main_banded.cpp:56

↓ 1 callersFunctionbwa_idx_build

src/bwtindex.cpp:61

↓ 1 callersFunctionbwa_idx_load_bwt

src/bwa.cpp:384

↓ 1 callersFunctionbwa_idx_load_from_disk

src/bwa.cpp:402

↓ 1 callersFunctionbwa_index

src/bwtindex.cpp:43

↓ 1 callersFunctionbwa_mem2idx

src/bwa.cpp:452

↓ 1 callersFunctionbwa_print_sam_hdr

src/bwa.cpp:523

↓ 1 callersFunctionbwa_set_rg

src/bwa.cpp:583

↓ 1 callersFunctioncmd2argv

src/kopen.cpp:278

↓ 1 callersFunctioncomputeBWT

↓ 1 callersFunctiondisplay_stats

src/profiling.cpp:54

↓ 1 callersFunctionerr_fseek

src/utils.cpp:156

↓ 1 callersFunctionerr_ftell

src/utils.cpp:166

↓ 1 callersFunctionexe_path

src/runsimd.cpp:95

↓ 1 callersFunctionftp_open

src/kopen.cpp:222

↓ 1 callersMethodget_sa_entries_prefetch

src/FMI_search.cpp:1257

↓ 1 callersFunctionhttp_open

src/kopen.cpp:117

↓ 1 callersFunctioninduceSA

↓ 1 callersFunctionksw_extend2

src/ksw.cpp:432

↓ 1 callersMethodkswvScalarWrapper

------------------------------------------------------------- kswc scalar, wrapper function, the interface. ------------------------------------------

src/kswv.cpp:1550

↓ 1 callersFunctionkt_pipeline

src/fastmap.cpp:189

↓ 1 callersFunctionloadData

test/sa2ref_test.cpp:47

↓ 1 callersFunctionmain_mem

src/fastmap.cpp:616

↓ 1 callersFunctionmem_chain2aln_across_reads_V2

src/bwamem.cpp:2069

↓ 1 callersFunctionmem_chain_flt

src/bwamem.cpp:506

↓ 1 callersFunctionmem_chain_seeds

src/bwamem.cpp:806

↓ 1 callersFunctionmem_collect_smem

src/bwamem.cpp:626

↓ 1 callersFunctionmem_flt_chained_seeds

src/bwamem.cpp:472

↓ 1 callersFunctionmem_kernel1_core

src/bwamem.cpp:976

↓ 1 callersFunctionmem_kernel2_core

src/bwamem.cpp:1093

↓ 1 callersFunctionmem_matesw_batch_pre

src/bwamem_pair.cpp:930

↓ 1 callersFunctionmem_opt_init

src/bwamem.cpp:107

↓ 1 callersFunctionmem_pestat

src/bwamem_pair.cpp:81

↓ 1 callersFunctionmem_sam_pe

src/bwamem_pair.cpp:353

↓ 1 callersFunctionmem_sam_pe_batch

This function is equivalent to align2() for axv512

src/bwamem_pair.cpp:612

↓ 1 callersFunctionmem_sam_pe_batch_post

src/bwamem_pair.cpp:713

↓ 1 callersFunctionmem_sam_pe_batch_pre

src/bwamem_pair.cpp:553

↓ 1 callersFunctionmem_seed_sw

src/bwamem.cpp:401

↓ 1 callersFunctionmemoryAlloc

Memory pre-allocations ***/

src/fastmap.cpp:100

↓ 1 callersFunctionparseCmdLine

test/main_banded.cpp:67

↓ 1 callersFunctionparseCmdLine

src/kswv.cpp:1636

↓ 1 callersFunctionprocess

src/fastmap.cpp:368

↓ 1 callersFunctionread_smem2_input

test/smem2_test.cpp:46

↓ 1 callersFunctionsaisxx

↓ 1 callersFunctionsort_classify

src/bwamem.cpp:1216

↓ 1 callersFunctionsteal_work

src/kthread.cpp:41

↓ 1 callersFunctiontest_and_merge

return 1 if the seed is merged into the chain

src/bwamem.cpp:357

↓ 1 callersFunctionupdate_a

src/fastmap.cpp:547

↓ 1 callersFunctionusage

src/fastmap.cpp:563

↓ 1 callersFunctionusage

src/main.cpp:43

↓ 1 callersFunctionx86_simd

src/runsimd.cpp:72

MethodBandedPairWiseSW

----------------------------------------------------------------------------------- constructor

src/bandedSWA.cpp:50

MethodFMI_search

src/FMI_search.cpp:44

Function__ac_Wang_hash

src/khash.h:400

Function__ac_X31_hash_string

! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */

src/khash.h:383

Function_err_fatal_simple_core

src/utils.cpp:118

Function_mm_countbits_64

src/FMI_search.h:61

src/bwamem.h:114

MethodbackwardExt

src/FMI_search.cpp:1025

Functionbns_cnt_ambi

src/bntseq.cpp:404

Functionbseq_read

Customized for MPI processing */

Methodbuild_fm_index

src/FMI_search.cpp:144

Functionbwa_fa2pac

src/bntseq.cpp:359

Methodbwa_fill_scmat

src/kswv.cpp:1231

Functionbwa_gen_cigar

src/bwa.cpp:349

Functionbwa_idx2mem

src/bwa.cpp:477

Functionbwa_idx_destroy

src/bwa.cpp:438

Methodbwa_idx_infer_prefix

src/read_index_ele.cpp:96

Functionbwa_idx_load

src/bwa.cpp:433

Methodbwa_idx_load_ele

src/read_index_ele.cpp:60

Methodcall_one_step

SA_COPMRESSION w/ PREFETCH

src/FMI_search.cpp:1202

Functioncompare_smem

src/FMI_search.cpp:987

Functionerr_fatal_core

src/utils.cpp:101

Functionerr_gzread

src/utils.cpp:142

Functionerr_puts

src/utils.cpp:233

Functionerr_xopen_core

src/utils.cpp:56

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