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multi-seg working on toy examples

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Heng Li
2017-09-25 13:42:04 -04:00
parent a742f10164
commit 3bb66e1ed3
6 changed files with 62 additions and 16 deletions
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bseq.h
+17 -2
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@@ -24,6 +24,7 @@ mm_bseq1_t *mm_bseq_read_multi(int n_fp, mm_bseq_file_t **fp, int chunk_size, in
int mm_bseq_eof(mm_bseq_file_t *fp);
extern unsigned char seq_nt4_table[256];
extern unsigned char seq_comp_table[256];
static inline int mm_qname_same(const char *s1, const char *s2)
{
@@ -31,11 +32,25 @@ static inline int mm_qname_same(const char *s1, const char *s2)
l1 = strlen(s1);
l2 = strlen(s2);
if (l1 != l2 || l1 < 3) return 0;
if (!(s1[l1-1] >= '1' && s1[l1-1] <= '2' && s1[l1-2] == '/')) return 0;
if (!(s2[l2-1] >= '1' && s2[l2-1] <= '2' && s2[l2-2] == '/')) return 0;
if (!(s1[l1-1] >= '0' && s1[l1-1] <= '9' && s1[l1-2] == '/')) return 0;
if (!(s2[l2-1] >= '0' && s2[l2-1] <= '9' && s2[l2-2] == '/')) return 0;
return (strncmp(s1, s2, l1 - 2) == 0);
}
static inline void mm_revcomp_bseq(mm_bseq1_t *s)
{
int i, t, l = s->l_seq;
for (i = 0; i < l>>1; ++i) {
t = s->seq[l - i - 1];
s->seq[l - i - 1] = seq_comp_table[(uint8_t)s->seq[i]];
s->seq[i] = seq_comp_table[t];
}
if (l&1) s->seq[l>>1] = seq_comp_table[(uint8_t)s->seq[l>>1]];
if (s->qual)
for (i = 0; i < l>>1; ++i)
t = s->qual[l - i - 1], s->qual[l - i - 1] = s->qual[i], s->qual[i] = t;
}
#ifdef __cplusplus
}
#endif