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r297: reduce wasteful SW extension 

This is particularly important for long sequences
This commit is contained in:
Heng Li 2013-02-26 16:26:46 -05:00
parent 54ab3bbec7
commit acd1ab607b
2 changed files with 17 additions and 5 deletions
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20
bwamem.c
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@ -648,7 +648,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
{
int i, j;
int i, j, k;
mem_chain_v chn;
mem_alnreg_v regs, tmp;
for (i = 0; i < l_seq; ++i)
@ -658,9 +658,21 @@ mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *
if (bwa_verbose >= 4) mem_print_chain(bns, &chn);
kv_init(regs); kv_init(tmp);
for (i = 0; i < chn.n; ++i) {
mem_chain2aln(opt, bns->l_pac, pac, l_seq, (uint8_t*)seq, &chn.a[i], &tmp);
for (j = 0; j < tmp.n; ++j)
kv_push(mem_alnreg_t, regs, tmp.a[j]);
mem_chain_t *p = &chn.a[i];
for (j = 0; j < regs.n; ++j) { // check if all the seeds are contained in alnreg found previously
mem_alnreg_t *q = &regs.a[j];
for (k = 0; k < p->n; ++k) {
mem_seed_t *s = &p->seeds[k];
if (!(s->qbeg >= q->qb && s->qbeg + s->len <= q->qe && s->rbeg >= q->rb && s->rbeg + s->len <= q->re))
break; // stop if seed is not contained
}
if (k == p->n) break; // if all seeds are contained, stop
}
if (j == regs.n) {
mem_chain2aln(opt, bns->l_pac, pac, l_seq, (uint8_t*)seq, p, &tmp);
for (j = 0; j < tmp.n; ++j)
kv_push(mem_alnreg_t, regs, tmp.a[j]);
}
free(chn.a[i].seeds);
}
free(chn.a); free(tmp.a);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.6.2-r295-beta"
#define PACKAGE_VERSION "0.6.2-r297-beta"
#endif
static int usage()