zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
bwamem.c
View File

@ -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;
}
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;
str.l = str.m = 0; str.s = 0;
@ -1024,7 +1024,8 @@ static void *worker2(void *data)
if (!(w->opt->flag&MEM_F_PE)) {
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_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);
}
} else {