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Merge branch 'master' into bed-bonus

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Heng Li
2018-10-18 11:13:19 -04:00
parent 0aad789ac4 20268a6068
commit 121731ebde
14 changed files with 72 additions and 25 deletions
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align.c
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@@ -593,9 +593,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qs0 = 0, qe0 = qlen;
l = qs;
l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
l = l < opt->bw? l : opt->bw;
rs0 = rs - l > 0? rs - l : 0;
l = qlen - qe;
l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
l = l < opt->bw? l : opt->bw;
re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
} else {
// compute rs0 and qs0