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r395: bugfix - hard clipping not applied on revaln

This commit is contained in:
Heng Li 2013-05-23 12:45:14 -04:00
parent 9441bb7f2a
commit 3d2450ed97
2 changed files with 3 additions and 3 deletions
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4
bwamem.c
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@ -714,8 +714,8 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
} else { // the reverse strand
int i, qb = 0, qe = s->l_seq;
if (p->n_cigar) {
if ((p->cigar[0]&0xf) == 4) qe -= p->cigar[0]>>4;
if ((p->cigar[p->n_cigar-1]&0xf) == 4) qb += p->cigar[p->n_cigar-1]>>4;
if (which && ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3)) qe -= p->cigar[0]>>4;
if (which && ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3)) qb += p->cigar[p->n_cigar-1]>>4;
}
ks_resize(str, str->l + (qe - qb) + 1);
for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.4-r394-beta"
#define PACKAGE_VERSION "0.7.4-r395-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);