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r174: make max-chain-skip work

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The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
This commit is contained in:
Heng Li
2017-07-12 10:08:06 -04:00
parent 33451aba45
commit eeeb2ffb68
4 changed files with 30 additions and 9 deletions
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14
chain.c
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@@ -42,11 +42,6 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
int64_t dr = ri - a[j].x;
int32_t dq = qi - (int32_t)a[j].y, dd, sc;
if (dr == 0 || dq <= 0 || dq > max_dist) continue;
if (t[j] == i) { // FIXME: never enter this block. i.e. max_skip has no effect at all. This may affect speed.
if (p[j] >= 0) t[p[j]] = i;
if (++n_skip > max_skip) break;
continue;
}
dd = dr > dq? dr - dq : dq - dr;
if (dd > bw) continue;
min_d = dq < dr? dq : dr;
@@ -54,7 +49,14 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
sc -= dd? ilog2_32(dd) * 2 : 0;
if (min_d > q_span) sc -= ilog2_32(min_d) / 2;
sc += f[j];
if (sc > max_f) max_f = sc, max_j = j;
if (sc > max_f) {
max_f = sc, max_j = j;
if (n_skip > 0) --n_skip;
} else if (t[j] == i) {
if (++n_skip > max_skip)
break;
}
if (p[j] >= 0) t[p[j]] = i;
}
if (max_j >= 0) f[i] = max_f, p[i] = max_j;
else f[i] = q_span, p[i] = -1;