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r280: output introns as "N" in the cdna mode

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Heng Li
2017-08-09 11:45:02 -04:00
parent 7429b12164
commit c59b0781bc
5 changed files with 27 additions and 13 deletions
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map.c
+8 -3
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@@ -344,19 +344,24 @@ static void *worker_pipeline(void *shared, int step, void *in)
void *km = 0;
step_t *s = (step_t*)in;
const mm_idx_t *mi = p->mi;
int intron_thres = -1;
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
free(s->buf);
if (p->opt->flag & MM_F_CDNA)
intron_thres = (int)((float)(p->opt->q2 - p->opt->q) / p->opt->e + 0.999f);
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
for (i = 0; i < s->n_seq; ++i) {
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, s->n_reg[i], s->reg[i]);
else mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i], intron_thres);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag, intron_thres);
puts(p->str.s);
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
mm_write_sam(&p->str, 0, t, 0, 0, 0);
mm_write_sam(&p->str, 0, t, 0, 0, 0, 0);
puts(p->str.s);
}
for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);