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r201: fixed a minor chaining issue 

Chaining looked at the end of a chain, but the end may not be the best. We now
go back to find the max.
This commit is contained in:
Heng Li 2017-07-25 18:26:51 -04:00
parent 215e92ed7b
commit 21ca564112
2 changed files with 17 additions and 9 deletions
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24
chain.c
View File

@ -17,6 +17,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
f = (int32_t*)kmalloc(km, n * 4);
p = (int32_t*)kmalloc(km, n * 4);
t = (int32_t*)kmalloc(km, n * 4);
v = (int32_t*)kmalloc(km, n * 4);
memset(t, 0, n * 4);
for (i = 0; i < n; ++i) sum_qspan += a[i].y>>32&0xff;
@ -26,7 +27,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x;
int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32&0xff; // NB: only 8 bits of span is used!!!
int32_t max_f = q_span, max_j = -1, n_skip = 0, min_d;
int32_t max_f = q_span, max_j = -1, n_skip = 0, min_d, max_f_past = -INT32_MAX;
while (st < i && ri - a[st].x > max_dist) ++st;
for (j = i - 1; j >= st; --j) {
int64_t dr = ri - a[j].x;
@ -34,6 +35,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
if (dr == 0 || dq <= 0 || dq > max_dist) continue;
dd = dr > dq? dr - dq : dq - dr;
if (dd > bw) continue;
max_f_past = max_f_past > f[j]? max_f_past : f[j];
min_d = dq < dr? dq : dr;
sc = min_d > q_span? q_span : dq < dr? dq : dr;
sc -= (int)(dd * .01 * avg_qspan);
@ -47,7 +49,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
}
if (p[j] >= 0) t[p[j]] = i;
}
f[i] = max_f, p[i] = max_j;
f[i] = max_f, p[i] = max_j, v[i] = max_f_past; // v[] keeps the max score in the previous chain
}
// find the ending positions of chains
@ -55,16 +57,23 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
for (i = 0; i < n; ++i)
if (p[i] >= 0) t[p[i]] = 1;
for (i = n_u = 0; i < n; ++i)
if (t[i] == 0 && f[i] >= min_sc)
if (t[i] == 0 && v[i] >= min_sc)
++n_u;
if (n_u == 0) {
kfree(km, f); kfree(km, p); kfree(km, t);
kfree(km, f); kfree(km, p); kfree(km, t); kfree(km, v);
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)
u[n_u++] = (uint64_t)f[i] << 32 | i;
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)
}
u[n_u++] = (uint64_t)f[j] << 32 | j;
}
}
radix_sort_64(u, u + n_u);
for (i = 0; i < n_u>>1; ++i) { // reverse, s.t. the highest scoring chain is the first
uint64_t t = u[i];
@ -73,7 +82,6 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
// backtrack
memset(t, 0, n * 4);
v = (int32_t*)kmalloc(km, n * 4);
for (i = n_v = k = 0; i < n_u; ++i) { // starting from the highest score
int32_t n_v0 = n_v, k0 = k;
j = (int32_t)u[i];

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r200-dirty"
#define MM_VERSION "2.0-r201-dirty"
void liftrlimit()
{