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r669: improved self chain extension (#10)

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This has not fully resolved #10, only alleviated the issue.
This commit is contained in:
Heng Li
2018-01-30 20:05:02 -05:00
parent ad18fa490d
commit 12a5a5fa3c
4 changed files with 27 additions and 12 deletions
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align.c
+8
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@@ -499,6 +499,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re0 = re0 > re1? re0 : re1;
} else re0 = re, qe0 = qe;
}
if (a[r->as].y & MM_SEED_SELF) {
int max_ext = r->qs > r->rs? r->qs - r->rs : r->rs - r->qs;
if (r->rs - rs0 > max_ext) rs0 = r->rs - max_ext;
if (r->qs - qs0 > max_ext) qs0 = r->qs - max_ext;
max_ext = r->qe > r->re? r->qe - r->re : r->re - r->qe;
if (re0 - r->re > max_ext) re0 = r->re + max_ext;
if (qe0 - r->qe > max_ext) qe0 = r->qe + max_ext;
}
assert(re0 > rs0);
tseq = (uint8_t*)kmalloc(km, re0 - rs0);