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r469: first step towards PE SAM

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This commit is contained in:
Heng Li
2017-10-05 10:38:09 -04:00
parent 16e6e589a8
commit 7cc4f6f965
5 changed files with 83 additions and 37 deletions
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16
bseq.h
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@@ -26,15 +26,19 @@ 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_len(const char *s)
{
int l;
l = strlen(s);
return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;
}
static inline int mm_qname_same(const char *s1, const char *s2)
{
int l1, l2;
l1 = strlen(s1);
l2 = strlen(s2);
if (l1 != l2 || l1 < 3) 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);
l1 = mm_qname_len(s1);
l2 = mm_qname_len(s2);
return (l1 == l2 && strncmp(s1, s2, l1) == 0);
}
static inline void mm_revcomp_bseq(mm_bseq1_t *s)