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dp chaining mostly works, but fails sometimes

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which means there are bugs that need to be fixed
This commit is contained in:
Heng Li
2017-06-06 14:19:50 -04:00
parent 1a9fc04cf0
commit 6d4348db44
6 changed files with 60 additions and 25 deletions
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chain.c
+17 -12
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@@ -19,11 +19,13 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, int32_t **_v, void *km)
int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
{
int32_t st = 0, i, j, k, *p, *f, *t, *idx, *v, n_u, n_v;
int32_t st = 0, i, j, k, *p, *f, *t, *v, n_u, n_v;
uint64_t *u;
mm128_t *b;
if (_u) *_u = 0;
f = (int32_t*)kmalloc(km, n * 4);
p = (int32_t*)kmalloc(km, n * 4);
t = (int32_t*)kmalloc(km, n * 4);
@@ -54,12 +56,6 @@ int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, i
else f[i] = match_len, p[i] = -1;
}
// free the a[] array
for (i = 0; i < n; ++i) t[i] = a[i].y>>32;
kfree(km, a);
idx = (int32_t*)kmalloc(km, n * 4);
for (i = 0; i < n; ++i) idx[i] = t[i];
// find the ending positions of chains
memset(t, 0, n * 4);
for (i = 0; i < n; ++i)
@@ -67,6 +63,7 @@ int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, i
for (i = n_u = 0; i < n; ++i)
if (t[i] == 0 && f[i] >= min_sc)
++n_u;
if (n_u == 0) return 0;
u = (uint64_t*)kmalloc(km, n_u * 8);
for (i = n_u = 0; i < n; ++i)
if (t[i] == 0 && f[i] >= min_sc)
@@ -80,22 +77,30 @@ int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, i
int32_t n_v0 = n_v;
j = (int32_t)u[i];
do {
v[n_v++] = idx[j];
v[n_v++] = j;
t[j] = 1;
j = p[j];
} while (j >= 0 && t[j] == 0);
if (j < 0) u[k++] = u[i]>>32<<32 | (n_v - n_v0);
else if ((u[i]>>32) - f[j] >= min_sc) u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
else n_v0 = n_v;
for (j = 0; j < (n_v - n_v0) >> 1; ++j) {
for (j = 0; j < (n_v - n_v0) >> 1; ++j) { // reverse v[] such that the smallest index comes the first
int32_t t = v[n_v0 + j];
v[n_v0 + j] = v[n_v - 1 - j];
v[n_v - 1 - j] = t;
}
}
n_u = k, *_u = u, *_v = v;
n_u = k, *_u = u;
// free
kfree(km, f); kfree(km, p); kfree(km, t); kfree(km, idx);
kfree(km, f); kfree(km, p); kfree(km, t);
// write the result to _a_
b = kmalloc(km, n_v * sizeof(mm128_t));
for (i = 0, k = 0; i < n_u; ++i)
for (j = 0; j < (int32_t)u[i]; ++j)
b[k] = a[v[k]], ++k;
memcpy(a, b, n_v * sizeof(mm128_t));
kfree(km, b);
return n_u;
}