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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
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5
chain.c
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@ -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) { for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x; 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 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; while (st < i && ri - a[st].x > max_dist) ++st;
for (j = i - 1; j >= st; --j) { for (j = i - 1; j >= st; --j) {
int64_t dr = ri - a[j].x; 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 (p[j] >= 0) t[p[j]] = i;
} }
if (max_j >= 0) f[i] = max_f, p[i] = max_j; f[i] = max_f, p[i] = max_j;
else f[i] = q_span, p[i] = -1;
} }
// find the ending positions of chains // find the ending positions of chains

2
main.c
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@ -8,7 +8,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r199-dirty" #define MM_VERSION "2.0-r200-dirty"
void liftrlimit() void liftrlimit()
{ {