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r719: more stringent overlap merge 

Will consider to make it the default
This commit is contained in:
Heng Li 2014-04-15 14:52:17 -04:00
parent 4e22270eba
commit bdb7b000cd
2 changed files with 12 additions and 8 deletions
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18
bwamem.c
View File

@ -371,28 +371,32 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg
int64_t or, oq, mr, mq;
int is_merged = 0;
if (q->qe == q->qb) continue; // a[j] has been excluded
if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re) {
int flag = 0;
or = q->re - p->rb; // overlap length on the reference
oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re && fabs((float)oq / (p->qe - q->qb) - (float)or / (p->re - q->rb)) < .05) {
int flag = 0, q_s, r_s;
int64_t l1, l2;
l1 = p->qb - q->qb, l2 = p->rb - q->rb;
if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
l1 = p->qe - q->qe, l2 = p->re - q->re;
if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
l1 = p->qe - q->qb, l2 = p->re - q->rb;
q_s = (int)((double)(p->qe - q->qb) / ((p->qe - p->qb) + (q->qe - q->qb)) * (p->score + q->score) + .499);
r_s = (int)((double)(p->re - q->rb) / ((p->re - p->rb) + (q->re - q->rb)) * (p->score + q->score) + .499);
if (flag == 2) { // merge q into p
mem_alnreg_t t = *p;
*p = *q;
p->qe = t.qe, p->re = t.re;
p->score = p->score > t.score? p->score : t.score;
p->truesc = p->score = (q_s + r_s) >> 1;
p->w = p->w > t.w? p->w : t.w;
p->w = p->w > abs(l1 - l2) + 50? p->w : abs(l1 - l2) + 50;
q->qb = q->qe;
is_merged = 1;
}
}
if (is_merged == 0) {
or = q->re - p->rb; // overlap length on the reference
oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
if (p->score < q->score) {
p->qe = p->qb;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r718-dirty"
#define PACKAGE_VERSION "0.7.8-r719-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);