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r684: separate end score from min_chain_score

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Heng Li
2018-02-05 11:40:38 -05:00
parent 3df5015668
commit dbf284b2d9
6 changed files with 9 additions and 4 deletions
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align.c
+3 -3
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@@ -307,7 +307,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
if (max - min > l >> 1) *as = i;
l += min;
m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break;
if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
}
*cnt = r->as + r->cnt - *as;
m = l = a[r->as + r->cnt - 1].y >> 32 & 0xff;
@@ -321,7 +321,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
if (max - min > l >> 1) *cnt = i + 1 - *as;
l += min;
m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break;
if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
}
}
@@ -422,7 +422,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (is_splice) {
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
} else {
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score, &as1, &cnt1);
mm_fix_bad_ends(r, a, opt->bw, opt->min_end_match, &as1, &cnt1);
}
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);