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move mark primary to worker1()

This commit is contained in:
Heng Li 2013-02-12 15:54:55 -05:00
parent cd0969332f
commit 325ba8213b
1 changed files with 1 additions and 1 deletions
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2
bwamem.c
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@ -608,7 +608,6 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
kstring_t str;
str.l = str.m = 0; str.s = 0;
if (a->n > 0) {
mem_mark_primary_se(opt, a->n, a->a); // NOTE: mem_sort_and_dedup() called in worker1()
for (k = 0; k < a->n; ++k) {
bwahit_t h;
if (a->a[k].secondary >= 0) continue;
@ -658,6 +657,7 @@ static void *worker1(void *data)
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].n = mem_sort_and_dedup(w->regs[i].n, w->regs[i].a);
mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
}
return 0;
}