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r718: retrieve sequence from the index

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This commit is contained in:
Heng Li
2018-02-23 10:18:26 -05:00
parent 29ed675ee5
commit 24a4808826
9 changed files with 115 additions and 20 deletions
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18
python/cmappy.h
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@@ -112,4 +112,22 @@ static inline char *mappy_revcomp(int len, const uint8_t *seq)
return rev;
}
static char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int en, int *len)
{
int i, rid;
char *s;
*len = 0;
rid = mm_idx_name2id(mi, name);
if (rid < 0) return 0;
if (st >= mi->seq[i].len || st >= en) return 0;
if (en < 0 || en > mi->seq[i].len)
en = mi->seq[i].len;
s = (char*)malloc(en - st + 1);
*len = mm_idx_getseq(mi, rid, st, en, s);
for (i = 0; i < *len; ++i)
s[i] = "ACGTN"[(uint8_t)s[i]];
s[*len] = 0;
return s;
}
#endif