zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r200: reduce long gaps in chaining 

Every seed can initiate a chain.
This commit is contained in:
Heng Li 2017-07-25 17:32:54 -04:00
parent b530ade333
commit 215e92ed7b
2 changed files with 3 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
chain.c
View File

@ -26,7 +26,7 @@ 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 = -INT32_MAX, max_j = -1, n_skip = 0, min_d;
int32_t max_f = q_span, max_j = -1, n_skip = 0, min_d;
while (st < i && ri - a[st].x > max_dist) ++st;
for (j = i - 1; j >= st; --j) {
int64_t dr = ri - a[j].x;
@ -47,8 +47,7 @@ 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;
}
if (max_j >= 0) f[i] = max_f, p[i] = max_j;
else f[i] = q_span, p[i] = -1;
f[i] = max_f, p[i] = max_j;
}
// find the ending positions of chains

2
main.c
View File

@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r199-dirty"
#define MM_VERSION "2.0-r200-dirty"
void liftrlimit()
{