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r202: trim bad chain ends before extension

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This fixes a few more FP long INDELs towards the end of alignments.
This commit is contained in:
Heng Li
2017-07-25 19:53:19 -04:00
parent 21ca564112
commit f2ef48878a
3 changed files with 47 additions and 18 deletions
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6
chain.c
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@@ -67,10 +67,8 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
for (i = n_u = 0; i < n; ++i) {
if (t[i] == 0 && v[i] >= min_sc) {
j = i;
if (f[j] < v[j]) { // find the point that maximizes f[]
while (j >= 0 && f[j] < v[j]) j = p[j];
if (j < 0) j = i; // TODO: this should really be assert(j>=0)
}
while (j >= 0 && f[j] < v[j]) j = p[j]; // find the point 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;
}
}