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r819: mappy to support cs/MD

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Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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4
python/cmappy.h
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@@ -126,8 +126,8 @@ static char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int e
*len = 0;
rid = mm_idx_name2id(mi, name);
if (rid < 0) return 0;
if (st >= mi->seq[rid].len || st >= en) return 0;
if (en < 0 || en > mi->seq[rid].len)
if ((uint32_t)st >= mi->seq[rid].len || st >= en) return 0;
if (en < 0 || (uint32_t)en > mi->seq[rid].len)
en = mi->seq[rid].len;
s = (char*)malloc(en - st + 1);
*len = mm_idx_getseq(mi, rid, st, en, (uint8_t*)s);