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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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format.c
+4
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@@ -259,6 +259,10 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
{
s->l = 0;
if (r == 0) {
mm_sprintf_lite(s, "%s\t%d", t->name, t->l_seq);
return;
}
mm_sprintf_lite(s, "%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) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
else mm_sprintf_lite(s, "%d", r->rid);