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r515: more conservative hit exclusion 

When a hit covers a long query subsequence that has not been covered by better
primary hits, this hit is more likely to become a new primary hit.
This commit is contained in:
Heng Li 2017-10-16 13:58:01 -04:00
parent b24c9c90c7
commit addb61bcb2
2 changed files with 31 additions and 6 deletions
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35
hit.c
View File

@ -107,19 +107,42 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff) // and compute mm_reg1_t::subsc
{
int i, j, k, *w;
uint64_t *cov;
if (n <= 0) return;
for (i = 0; i < n; ++i) r[i].id = i;
cov = (uint64_t*)kmalloc(km, n * sizeof(uint64_t));
w = (int*)kmalloc(km, n * sizeof(int));
w[0] = 0, r[0].parent = 0;
for (i = 1, k = 1; i < n; ++i) {
mm_reg1_t *ri = &r[i];
int si = ri->qs, ei = ri->qe;
for (j = 0; j < k; ++j) {
int si = ri->qs, ei = ri->qe, n_cov = 0, uncov_len = 0;
for (j = 0; j < k; ++j) { // traverse existing primary hits to find overlapping hits
mm_reg1_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe;
int min = ej - sj < ei - si? ej - sj : ei - si;
int ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si);
if (ol > mask_level * min) {
if (ej <= si || sj >= ei) continue;
if (sj < si) sj = si;
if (ej > ei) ej = ei;
cov[n_cov++] = (uint64_t)sj<<32 | ej;
}
if (n_cov == 0) {
goto set_parent_test; // no overlapping primary hits; then i is a new primary hit
} else if (n_cov > 0) { // there are overlapping primary hits; find the length not covered by existing primary hits
int j, x = si;
radix_sort_64(cov, cov + n_cov);
for (j = 0; j < n_cov; ++j) {
if (cov[j]>>32 > x) uncov_len += (cov[j]>>32) - x;
x = (int32_t)cov[j] > x? (int32_t)cov[j] : x;
}
if (ei > x) uncov_len += ei - x;
}
for (j = 0; j < k; ++j) { // traverse existing primary hits again
mm_reg1_t *rp = &r[w[j]];
int sj = rp->qs, ej = rp->qe, min, max, ol;
if (ej <= si || sj >= ei) continue; // no overlap
min = ej - sj < ei - si? ej - sj : ei - si;
max = ej - sj > ei - si? ej - sj : ei - si;
ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si); // overlap length
if ((float)ol / min - (float)uncov_len / max > mask_level) {
int cnt_sub = 0;
ri->parent = rp->parent;
rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
@ -132,8 +155,10 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
break;
}
}
set_parent_test:
if (j == k) w[k++] = i, ri->parent = i, ri->n_sub = 0;
}
kfree(km, cov);
kfree(km, w);
}

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r513-dirty"
#define MM_VERSION "2.2-r515-dirty"
#ifdef __linux__
#include <sys/resource.h>