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new code works for SE

This commit is contained in:
Heng Li 2013-03-11 21:59:15 -04:00
parent c7edaa8e84
commit ebb45dc42e
1 changed files with 3 additions and 2 deletions
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5
bwamem.c
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@ -874,7 +874,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
s->sam = str.s; s->sam = str.s;
} }
void mem_aln2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m) void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
{ {
kstring_t str; kstring_t str;
str.l = str.m = 0; str.s = 0; str.l = str.m = 0; str.s = 0;
@ -1024,7 +1024,8 @@ static void *worker2(void *data)
if (!(w->opt->flag&MEM_F_PE)) { if (!(w->opt->flag&MEM_F_PE)) {
for (i = w->start; i < w->n; i += w->step) { for (i = w->start; i < w->n; i += w->step) {
mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a); mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0); //mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
free(w->regs[i].a); free(w->regs[i].a);
} }
} else { } else {