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

Merge pull request #48 from srl147/master 

ensure bwa_sa2pos does not return without setting strand
This commit is contained in:
Heng Li 2016-02-23 11:05:35 -05:00
parent cc9eef2d33 099c24f5fc
commit f9a7869079
2 changed files with 2 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
bwape.c
View File

@ -379,7 +379,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
bwt_multi1_t *q = p[j]->multi + k;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
q->strand = strand;
if (q->pos != p[j]->pos)
if (q->pos != p[j]->pos && q->pos != (bwtint_t)-1)
p[j]->multi[n_multi++] = *q;
}
p[j]->n_multi = n_multi;

1
bwase.c
View File

@ -113,6 +113,7 @@ bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int r
{
bwtint_t pos_f;
int is_rev;
*strand = 0; // initialise strand to 0 otherwise we could return without setting it
pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base