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r199: changed to linear gap cost for chaining 

The old cost doesn't penalize long gaps enough. Will also drop seeds close to
the edge in the next commit.
This commit is contained in:
Heng Li 2017-07-25 15:35:10 -04:00
parent 4bd7ebc39c
commit b530ade333
2 changed files with 9 additions and 20 deletions
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27
chain.c
View File

@ -5,25 +5,12 @@
#include "mmpriv.h"
#include "kalloc.h"
static const char LogTable256[256] = {
#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),
LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7)
};
static inline int ilog2_32(uint32_t v)
{
register uint32_t t, tt;
if ((tt = v>>16)) return (t = tt>>8) ? 24 + LogTable256[t] : 16 + LogTable256[tt];
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km)
{ // 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, *u2;
int32_t st = 0, k, *f, *p, *t, *v, n_u, n_v;
int64_t i, j;
uint64_t *u, *u2, sum_qspan = 0;
float avg_qspan;
mm128_t *b, *w;
if (_u) *_u = 0;
@ -32,6 +19,9 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
t = (int32_t*)kmalloc(km, n * 4);
memset(t, 0, n * 4);
for (i = 0; i < n; ++i) sum_qspan += a[i].y>>32&0xff;
avg_qspan = (float)sum_qspan / n;
// fill the score and backtrack arrays
for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x;
@ -46,8 +36,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
if (dd > bw) continue;
min_d = dq < dr? dq : dr;
sc = min_d > q_span? q_span : dq < dr? dq : dr;
sc -= dd? ilog2_32(dd) * 2 : 0;
if (min_d > q_span) sc -= ilog2_32(min_d) / 2;
sc -= (int)(dd * .01 * avg_qspan);
sc += f[j];
if (sc > max_f) {
max_f = sc, max_j = j;

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r197-dirty"
#define MM_VERSION "2.0-r199-dirty"
void liftrlimit()
{