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fixed a bug

This commit is contained in:
Heng Li 2017-06-07 11:40:13 -04:00
parent 77c76c1e14
commit c01f2dd757
2 changed files with 7 additions and 10 deletions
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15
chain.c
View File

@ -90,12 +90,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *
} while (j >= 0 && t[j] == 0);
if (j < 0) u[k++] = u[i]>>32<<32 | (n_v - n_v0);
else if ((int32_t)(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) { // 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;
}
else n_v = n_v0;
}
n_u = k, *_u = u;
@ -104,9 +99,11 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *
// write the result to _a_
b = (mm128_t*)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;
for (i = 0, k = 0; i < n_u; ++i) {
int32_t k0 = k, ni = (int32_t)u[i];
for (j = 0; j < ni; ++j)
b[k] = a[v[k0 + (ni - j - 1)]], ++k;
}
memcpy(a, b, n_v * sizeof(mm128_t));
kfree(km, v); kfree(km, b);
return n_u;

2
map.c
View File

@ -227,7 +227,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
for (i = 0; i < n; ++i)
if (m[i].is_alloc) kfree(b->km_fixed, m[i].x.r);
kfree(b->km_fixed, m);
//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x, (uint32_t)a[i].y);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_score, n_a, a, &u, b->km_fixed);
printf("%s\t%d", qname, n_u);