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sam output

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This commit is contained in:
Heng Li
2017-06-25 22:05:20 -04:00
parent 39083be9ab
commit b1077ff14c
5 changed files with 71 additions and 8 deletions
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map.c
+8 -2
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@@ -306,7 +306,6 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, m
if (opt->sdust_thres > 0)
mm_dust_minier(&b->mini, l_seq, seq, opt->sdust_thres, b->sdb);
regs = mm_map_frag(opt, mi, b, 0, b->mini.n, qname, l_seq, seq, n_regs);
// mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
return regs;
}
@@ -368,7 +367,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
mm_write_paf(&p->str, mi, t, j, r);
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, j, r);
else mm_write_paf(&p->str, mi, t, j, r);
puts(p->str.s);
free(r->p);
}
@@ -389,7 +389,13 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
if (pl.fp == 0) return -1;
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
if (opt->flag & MM_F_OUT_SAM) {
uint32_t i;
for (i = 0; i < idx->n_seq; ++i)
printf("@SQ\tID:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
}
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
free(pl.str.s);
bseq_close(pl.fp);
return 0;
}