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r486: treat "U" as "T" for RNA reads (#33)

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Heng Li
2017-10-07 18:53:25 -04:00
parent 47b86e765b
commit bf2d4f7aec
4 changed files with 23 additions and 16 deletions
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bseq.c
+4
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@@ -55,8 +55,12 @@ void mm_bseq_close(mm_bseq_file_t *fp)
static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual)
{
int i;
s->name = strdup(ks->name.s);
s->seq = strdup(ks->seq.s);
for (i = 0; i < ks->seq.l; ++i) // convert U to T
if (s->seq[i] == 'u' || s->seq[i] == 'U')
--s->seq[i];
s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
s->l_seq = ks->seq.l;
}