fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-30 14:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

mm2-fast-v2.22 init

Browse Source
This commit is contained in:
Saurabh
2021-11-27 10:42:22 -05:00
committed by Heng Li
parent c7cdb758db
commit ba2f19ba37
12 changed files with 3535 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files
align.c
+66
View File
@@ -5,6 +5,13 @@
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
#include "ksw2_extd2_avx.h"
#include <x86intrin.h>
extern uint64_t avg;
extern uint64_t alignment_time;
extern void *km1;
extern uint64_t km_size;// = 500000000; // 500 MB
extern int km_top;
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc_ambi)
{
@@ -313,6 +320,7 @@ static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) //
}
}
#if 0
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const uint8_t *junc, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
{
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
@@ -340,7 +348,65 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
fprintf(stderr, "\n");
}
}
#endif
#if 1
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const uint8_t *junc, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
{
#ifdef MANUAL_PROFILING
uint64_t align_start = __rdtsc();
#endif
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;
fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, flag, opt->zdrop);
for (i = 0; i < tlen; ++i) fputc("ACGTN"[tseq[i]], stderr);
fputc('\n', stderr);
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
fputc('\n', stderr);
}
if (opt->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
ksw_reset_extz(ez);
ez->zdropped = 1;
} else if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag, junc, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
else{
#if defined (ALIGN_AVX) && (defined(__AVX512BW__) || (defined(__AVX2__) && defined(APPLY_AVX2)))
#ifdef __AVX512BW__
ksw_extd2_avx512(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
#elif __AVX2__
avg = 0;
// uint64_t *ptr_km = (uint64_t *) km1;
// for(uint64_t itr = 0; itr < km_size/512; itr++){
// avg+=ptr_km[itr];
// }
//#ifdef MANUAL_PROFILING
// uint64_t align_start = __rdtsc();
//#endif
ksw_extd2_avx2(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
//#ifdef MANUAL_PROFILING
// alignment_time += (__rdtsc() - align_start);
//#endif
#endif
#else
ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
#endif
}
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;
fprintf(stderr, "score=%d, cigar=", ez->score);
for (i = 0; i < ez->n_cigar; ++i)
fprintf(stderr, "%d%c", ez->cigar[i]>>4, "MIDN"[ez->cigar[i]&0xf]);
fprintf(stderr, "\n");
}
#ifdef MANUAL_PROFILING
alignment_time += (__rdtsc() - align_start);
#endif
}
#endif
static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x)
{
int64_t i, off0 = mi->seq[rid].offset, off = off0 + x;