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r720: improved overlap hit merging

This commit is contained in:
Heng Li 2014-04-15 16:09:42 -04:00
parent bdb7b000cd
commit 45f24b4ae8
2 changed files with 8 additions and 13 deletions
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19
bwamem.c
View File

@ -369,13 +369,17 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg
for (j = i - 1; j >= 0 && p->rid == a[j].rid && p->rb < a[j].re; --j) {
mem_alnreg_t *q = &a[j];
int64_t or, oq, mr, mq;
int is_merged = 0;
if (q->qe == q->qb) continue; // a[j] has been excluded
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) {
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;
break;
} else q->qe = q->qb;
} else 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;
@ -393,15 +397,6 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg
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) {
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;
break;
} else q->qe = q->qb;
}
}
}
@ -989,7 +984,7 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
free(chn.a[i].seeds);
}
free(chn.a);
if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level, opt->w);
if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level_redun, opt->w);
else regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
if (opt->flag & MEM_F_SELF_OVLP)
regs.n = mem_test_and_remove_exact(opt, regs.n, regs.a, l_seq);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r719-dirty"
#define PACKAGE_VERSION "0.7.8-r720-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);