zzh
/
bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r401: bugfix - forgot to change sampe 

some changes to samse should also be applied to sampe
This commit is contained in:
Heng Li 2013-05-27 22:24:35 -04:00
parent 6fed8fa0b4
commit 73619754f8
3 changed files with 6 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
bwape.c
View File

@ -296,7 +296,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
int strand;
int max_diff = gopt->fnr > 0.0? bwa_cal_maxdiff(p[j]->len, BWA_AVG_ERR, gopt->fnr) : gopt->max_diff;
p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len, &strand);
p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len + p[j]->ref_shift, &strand);
p[j]->strand = strand;
}
}
@ -345,7 +345,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
z->a = (bwtint_t*)malloc(sizeof(bwtint_t) * z->n);
for (l = r->k; l <= r->l; ++l) {
int strand;
z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand)<<1;
z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand)<<1;
z->a[l - r->k] |= strand;
}
}
@ -357,7 +357,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
} else { // then calculate on the fly
for (l = r->k; l <= r->l; ++l) {
int strand;
x.x = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand);
x.x = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand);
x.y = k<<2 | strand<<1 | j;
kv_push(pair64_t, d->arr, x);
}
@ -377,7 +377,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
for (k = 0, n_multi = 0; k < p[j]->n_multi; ++k) {
int strand;
bwt_multi1_t *q = p[j]->multi + k;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len, &strand);
q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
q->strand = strand;
if (q->pos != p[j]->pos)
p[j]->multi[n_multi++] = *q;

2
bwase.c
View File

@ -155,7 +155,7 @@ void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_se
bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
for (j = n_multi = 0; j < p->n_multi; ++j) {
bwt_multi1_t *q = p->multi + j;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + p->ref_shift, &strand);
q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + q->ref_shift, &strand);
q->strand = strand;
if (q->pos != p->pos && q->pos != (bwtint_t)-1)
p->multi[n_multi++] = *q;

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.4-r397-beta"
#define PACKAGE_VERSION "0.7.4-r401-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);