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code backup

This commit is contained in:
Heng Li 2014-04-16 12:00:13 -04:00
parent 00a07f61bf
commit 48847af2fc
2 changed files with 15 additions and 9 deletions
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22
bwamem.c
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@ -358,6 +358,11 @@ KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)
#define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash)) #define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))
KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt)
int mem_chain_reg(const bntseq_t *bns, const uint8_t *pac, mem_alnreg_t *a, mem_alnreg_t *b, int merge_bw, int max_gap)
{
return 0;
}
int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw) int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw)
{ {
int m, i, j; int m, i, j;
@ -389,14 +394,15 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun, int merge
l1 = p->qe - q->qb, l2 = p->re - q->rb; 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); 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); 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 if (flag == 2) { // merge p into q; don't merge q into p as this breaks sorting
mem_alnreg_t t = *p; mem_alnreg_t t = *q;
*p = *q; *q = *p;
p->qe = t.qe, p->re = t.re; q->qe = t.qe, q->re = t.re;
p->truesc = p->score = (q_s + r_s) >> 1; q->truesc = q->score = (q_s + r_s) >> 1;
p->w = p->w > t.w? p->w : t.w; q->w = q->w > t.w? q->w : t.w;
p->w = p->w > abs(l1 - l2) + 50? p->w : abs(l1 - l2) + 50; q->w = q->w > abs(l1 - l2) + 50? q->w : abs(l1 - l2) + 50;
q->qb = q->qe; p->qb = p->qe;
break;
} }
} }
} }

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r721-dirty" #define PACKAGE_VERSION "0.7.8-r722-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);