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move sort_and_dedup() to worker1()

This commit is contained in:
Heng Li 2013-02-10 12:55:19 -05:00
parent c310fb7424
commit f4c0672800
1 changed files with 4 additions and 3 deletions
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7
bwamem.c
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@ -512,8 +512,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
char *seq; char *seq;
str.l = str.m = 0; str.s = 0; str.l = str.m = 0; str.s = 0;
a->n = mem_sort_and_dedup(a->n, a->a); a->n = mem_choose_alnreg_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1()
a->n = mem_choose_alnreg_se(opt, a->n, a->a);
seq = malloc(s->l_seq); seq = malloc(s->l_seq);
if (a->n == 0) { // no seeds found if (a->n == 0) { // no seeds found
for (i = 0; i < s->l_seq; ++i) seq[i] = "ACGTN"[(int)s->seq[i]]; for (i = 0; i < s->l_seq; ++i) seq[i] = "ACGTN"[(int)s->seq[i]];
@ -600,8 +599,10 @@ static void *worker1(void *data)
{ {
worker_t *w = (worker_t*)data; worker_t *w = (worker_t*)data;
int i; int i;
for (i = w->start; i < w->n; i += w->step) for (i = w->start; i < w->n; i += w->step) {
w->regs[i] = find_alnreg(w->opt, w->bwt, w->bns, w->pac, &w->seqs[i]); w->regs[i] = find_alnreg(w->opt, w->bwt, w->bns, w->pac, &w->seqs[i]);
mem_sort_and_dedup(w->regs[i].n, w->regs[i].a);
}
return 0; return 0;
} }