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

⨍ Functions 263◇ Types & classes 31

↓ 124 callersFunction__rdtsc

↓ 43 callersFunctionkputc

src/kstring.h:80

↓ 31 callersFunctionfind_opt

src/profiling.cpp:36

↓ 26 callersFunction_mm_blendv_epi8

src/bandedSWA.cpp:4152

↓ 23 callersFunction_mm_blendv_epi16

SSE2 =- 16 bit version

src/bandedSWA.cpp:3364

↓ 16 callersFunction_err_fatal_simple

src/utils.cpp:112

↓ 15 callersFunctionkputsn

src/kstring.h:62

↓ 15 callersFunctionkputw

src/kstring.h:92

↓ 14 callersFunction_mm_realloc

src/bwamem.cpp:1834

↓ 13 callersFunctionerr_fread_noeof

src/utils.cpp:132

↓ 11 callersFunctionkv_push

src/bwamem.cpp:564

↓ 11 callersFunctionmem_reg2aln

src/bwamem.cpp:1732

↓ 10 callersFunctionerr_fatal

src/utils.cpp:90

↓ 10 callersFunctionerr_fclose

src/utils.cpp:271

↓ 10 callersFunctiongetBuckets

↓ 9 callersFunctionkputs

src/kstring.h:75

↓ 8 callersFunctiongetCounts

↓ 8 callersFunctionrevseq

src/ksw.cpp:340

↓ 8 callersFunctionsortPairsId

src/bandedSWA.cpp:393

↓ 7 callersFunctionerr_fprintf

src/utils.cpp:188

↓ 7 callersFunctionerr_gzclose

src/utils.cpp:278

↓ 7 callersFunctionmem_approx_mapq_se

src/bwamem.cpp:1470

↓ 7 callersMethodscalarBandedSWAWrapper

------------------------------------------------------------- Banded SWA, wrapper function -----------------------------------------------------------

src/bandedSWA.cpp:242

↓ 6 callersFunctionbns_depos

src/bntseq.h:87

↓ 6 callersFunctionbns_pos2rid

src/bntseq.cpp:378

↓ 6 callersFunctionerr_printf

src/utils.cpp:176

↓ 6 callersFunctionksw_qinit

* Initialize the query data structure * * @param size Number of bytes used to store a score; valid valures are 1 or 2 * @param qlen Length of t

↓ 6 callersFunctionmem_aln2sam

src/bwamem.cpp:1592

↓ 6 callersFunctionmem_infer_dir

src/bwamem_pair.cpp:58

↓ 6 callersFunctionmem_mark_primary_se

src/bwamem.cpp:1420

↓ 6 callersFunctionmemcpy_bwamem

src/memcpy_bwamem.cpp:32

↓ 6 callersFunctionsortPairsLen

src/bwamem.cpp:2025

↓ 6 callersFunctionsortPairsLen

---------------------------------------------------------------------------------- B-SWA - Vector code ------------------------- AVX2 - 8 bit SIMD_LAN

src/bandedSWA.cpp:356

↓ 5 callersFunctionerr_fputs

src/utils.cpp:222

↓ 5 callersMethodgetScores16

Vectorized Code 16 bit *****************************/ 16 bit lanes

src/kswv.cpp:713

↓ 5 callersMethodgetScores8

src/kswv.cpp:164

↓ 5 callersFunctionkftp_send_cmd

src/kopen.cpp:215

↓ 5 callersFunctionkputl

src/kstring.h:126

↓ 5 callersFunctionks_resize

src/kstring.h:53

↓ 5 callersFunctionksprintf

src/kstring.cpp:34

↓ 5 callersFunctionksw_align2

src/ksw.cpp:347

↓ 5 callersFunctionmem_reg2sam

TODO (future plan): group hits into a uint64_t[] array. This will be cleaner and more flexible

src/bwamem.cpp:1521

↓ 5 callersFunctionmem_reorder_primary5

src/bwamem.cpp:1496

↓ 5 callersFunctionmem_sort_dedup_patch

src/bwamem.cpp:292

↓ 5 callersFunctionpush_cigar

src/ksw.cpp:546

↓ 5 callersFunctiontest_and_launch

src/runsimd.cpp:152

↓ 4 callersFunctionbns_fetch_seq

src/bntseq.cpp:453

↓ 4 callersFunctioncal_max_gap

src/bwamem.cpp:66

↓ 4 callersFunctionerr_fgets

src/utils.cpp:211

↓ 4 callersFunctionkclose

src/kopen.cpp:386

↓ 4 callersFunctionkseq2bseq1

↓ 4 callersFunctionrevseq

src/bwamem_pair.cpp:604

↓ 4 callersMethodsortSMEMs

src/FMI_search.cpp:1008

↓ 4 callersFunctionsort_alnreg_re

src/bwamem.cpp:162

↓ 4 callersFunctionsort_alnreg_score

src/bwamem.cpp:166

↓ 4 callersFunctionstage1sort

↓ 4 callersFunctionstage3sort

↓ 4 callersFunctiontrim_readno

↓ 3 callersFunction__cpuid

src/fastmap.cpp:51

↓ 3 callersFunction__cpuidex

adapted from https://github.com/01org/linux-sgx/blob/master/common/inc/internal/linux/cpuid_gnu.h

src/runsimd.cpp:58

↓ 3 callersFunctionbns_destroy

src/bntseq.cpp:230

↓ 3 callersFunctionbwa_fill_scmat

src/bwa.cpp:248

↓ 3 callersFunctionbwa_gen_cigar2

Generate CIGAR when the alignment end points are known

src/bwa.cpp:260

↓ 3 callersFunctionbwa_insert_header

src/bwa.cpp:612

↓ 3 callersFunctionerr_fflush

src/utils.cpp:244

↓ 3 callersFunctionerr_fwrite

src/utils.cpp:124

↓ 3 callersFunctionkftp_get_response

src/kopen.cpp:191

↓ 3 callersFunctionkopen

src/kopen.cpp:312

↓ 3 callersFunctionkt_for

src/kthread.cpp:80

↓ 3 callersFunctionmem_gen_alt

Okay, returning strings is bad, but this has happened a lot elsewhere. If I have time, I need serious code cleanup.

src/bwamem_extra.cpp:130

↓ 3 callersFunctionmem_process_seqs

src/bwamem.cpp:1338

↓ 3 callersFunctionsocket_connect

src/kopen.cpp:80

↓ 2 callersFunctionLMSsort2

↓ 2 callersFunctionadd_cigar

src/bwamem.cpp:1579

↓ 2 callersFunctionbns_fasta2bntseq

src/bntseq.cpp:298

↓ 2 callersFunctionbns_get_seq

src/bntseq.cpp:427

↓ 2 callersFunctionbns_restore

src/bntseq.cpp:188

↓ 2 callersFunctionbseq_read_one_fasta_file

src/bwa.cpp:218

↓ 2 callersFunctionbseq_read_orig

src/bwa.cpp:170

↓ 2 callersFunctionbwa_escape

src/bwa.cpp:567

↓ 2 callersFunctionbwa_idx_infer_prefix

src/bwa.cpp:358

↓ 2 callersMethodbwtSeedStrategyAllPosOneThread

src/FMI_search.cpp:726

↓ 2 callersFunctioncal_sub

src/bwamem_pair.cpp:67

↓ 2 callersFunctioncputime

src/utils.cpp:293

↓ 2 callersFunctionerr_fputc

src/utils.cpp:200

↓ 2 callersFunctionfind_stats

profiling stats

test/main_banded.cpp:171

↓ 2 callersFunctionfind_stats

profiling stats

src/kswv.cpp:1738

↓ 2 callersMethodgetSMEMsAllPosOneThread

src/FMI_search.cpp:672

↓ 2 callersMethodgetSMEMsOnePosOneThread

src/FMI_search.cpp:496

↓ 2 callersFunctionget_pri_idx

src/bwamem_extra.cpp:122

↓ 2 callersFunctionget_rlen

src/bwamem.cpp:1820

↓ 2 callersMethodget_sa_entries

src/FMI_search.cpp:1062

↓ 2 callersFunctionhash_64

src/utils.h:117

↓ 2 callersFunctioninfer_bw

src/bwamem.cpp:1811

↓ 2 callersFunctionks_getuntil

↓ 2 callersFunctionksw_align

src/ksw.cpp:419

↓ 2 callersFunctionksw_global2

src/ksw.cpp:558

↓ 2 callersFunctionloadPairs

test/main_banded.cpp:117

↓ 2 callersFunctionloadPairs

src/kswv.cpp:1686

↓ 2 callersMethodload_index

src/FMI_search.cpp:384

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