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r438: fixed a rare case that leads to missing hits

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It is a bug in chaining.
This commit is contained in:
Heng Li
2017-09-25 14:59:34 -04:00
parent 8f25cfa36e
commit 9538c985aa
2 changed files with 5 additions and 4 deletions
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chain.c
+3 -2
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@@ -73,7 +73,8 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
}
if (p[j] >= 0) t[p[j]] = i;
}
f[i] = max_f, p[i] = max_j, v[i] = max_f_past; // v[] keeps the max score in the previous chain
f[i] = max_f, p[i] = max_j;
v[i] = max_f_past > max_f? max_f_past : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
}
// find the ending positions of chains
@@ -91,7 +92,7 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
for (i = n_u = 0; i < n; ++i) {
if (t[i] == 0 && v[i] >= min_sc) {
j = i;
while (j >= 0 && f[j] < v[j]) j = p[j]; // find the point that maximizes f[]
while (j >= 0 && f[j] < v[j]) j = p[j]; // find the peak that maximizes f[]
if (j < 0) j = i; // TODO: this should really be assert(j>=0)
u[n_u++] = (uint64_t)f[j] << 32 | j;
}