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r938: added --sam-hit-only; resolved #377

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Heng Li
2019-04-30 22:40:36 -04:00
parent 97f67a2a0a
commit c2aec88b84
4 changed files with 8 additions and 2 deletions
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map.c
+1 -1
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@@ -589,7 +589,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_write_paf3(&p->str, mi, t, r, km, p->opt->flag, s->rep_len[i]);
mm_err_puts(p->str.s);
}
} else if (p->opt->flag & (MM_F_OUT_SAM|MM_F_PAF_NO_HIT)) { // output an empty hit, if requested
} else if ((p->opt->flag & MM_F_PAF_NO_HIT) || ((p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_SAM_HIT_ONLY))) { // output an empty hit, if requested
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam3(&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, s->rep_len[i]);
else