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r168: fixed a bug in long join: a[] not sorted

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Also added length requirement for long join and changed -g in the ava mode
This commit is contained in:
Heng Li
2017-07-09 12:14:20 -04:00
parent 1ac48556ae
commit 782449975d
3 changed files with 28 additions and 10 deletions
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chain.c
+22 -6
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@@ -23,8 +23,8 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
{ // TODO: make sure this works when n has more than 32 bits
int32_t st = 0, j, k, *f, *p, *t, *v, n_u, n_v;
int64_t i;
uint64_t *u;
mm128_t *b;
uint64_t *u, *u2;
mm128_t *b, *w;
if (_u) *_u = 0;
f = (int32_t*)kmalloc(km, n * 4);
@@ -99,19 +99,35 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
}
if (k0 == k) n_v = n_v0; // no new chain added, reset
}
n_u = k, *_u = u;
n_u = k, *_u = u; // NB: note that u[] may not be sorted by score here
// free
kfree(km, f); kfree(km, p); kfree(km, t);
// write the result to _a_
// write the result to b[]
b = (mm128_t*)kmalloc(km, n_v * sizeof(mm128_t));
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);
kfree(km, v);
// sort u[] and a[] by a[].x, such that adjacent chains may be joined (required by mm_join_long)
w = (mm128_t*)kmalloc(km, n_u * sizeof(mm128_t));
for (i = k = 0; i < n_u; ++i) {
w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
k += (int32_t)u[i];
}
radix_sort_128x(w, w + n_u);
u2 = (uint64_t*)kmalloc(km, n_u * 8);
for (i = k = 0; i < n_u; ++i) {
int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
u2[i] = u[j];
memcpy(&a[k], &b[w[i].y>>32], n * sizeof(mm128_t));
k += n;
}
memcpy(u, u2, n_u * 8);
kfree(km, b); kfree(km, w); kfree(km, u2);
return n_u;
}