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Heng Li
2017-06-23 22:42:15 -04:00
parent 523a8832ad
commit 35b84f88c6
3 changed files with 90 additions and 33 deletions
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map.c
+7 -4
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@@ -16,7 +16,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->sdust_thres = 0;
opt->min_score = 40;
opt->bw = 500;
opt->bw = 1000;
opt->max_gap = 10000;
opt->max_skip = 15;
@@ -381,11 +381,14 @@ static void *worker_pipeline(void *shared, int step, void *in)
printf("%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
if (mi->seq[r->rid].name) fputs(mi->seq[r->rid].name, stdout);
else printf("%d", r->rid + 1);
printf("\t%d\t%d\t%d\t%d\t%d\t255\tcm:i:%d", mi->seq[r->rid].len, r->rs, r->re, r->score,
r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs, r->cnt);
printf("\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
if (r->p) printf("\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
else printf("\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
printf("\tcm:i:%d", r->cnt);
if (r->parent == j) printf("\tss:i:%d", r->subsc);
if (r->p) printf("\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
putchar('\n');
free(r->cigar);
free(r->p);
}
free(s->reg[i]);
free(s->seq[i].seq); free(s->seq[i].name);