fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-01 23:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r221: output SA in the SAM output

Browse Source
This commit is contained in:
Heng Li
2017-07-28 23:08:39 -04:00
parent 84922cfe41
commit 2179e9e24b
4 changed files with 32 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+3 -3
View File
@@ -346,15 +346,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r);
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
else mm_write_paf(&p->str, mi, t, r);
puts(p->str.s);
free(r->p);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam(&p->str, 0, t, 0);
mm_write_sam(&p->str, 0, t, 0, 0, 0);
puts(p->str.s);
}
for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);
free(s->reg[i]);
free(s->seq[i].seq); free(s->seq[i].name);
if (s->seq[i].qual) free(s->seq[i].qual);