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optionally output unmapped query in PAF

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Heng Li
2018-07-07 10:26:08 -05:00
parent bcf92b3c46
commit a609a07f8c
4 changed files with 16 additions and 0 deletions
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map.c
+9
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@@ -496,6 +496,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
mm_err_puts(p->str.s);
}
if (s->n_reg[i] == 0) {
if (p->opt->flag & MM_F_OUT_SAM) {
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
mm_err_puts(p->str.s);
} else if (p->opt->flag & MM_F_PAF_NO_HIT) {
mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag);
mm_err_puts(p->str.s);
}
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
mm_err_puts(p->str.s);