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r875: invalid SAM output for ALT hits

This commit is contained in:
Heng Li 2014-09-26 15:29:08 -04:00
parent 8d61316cc8
commit dae4ca3ced
2 changed files with 3 additions and 3 deletions
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4
bwamem.c
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@ -858,7 +858,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
kputsn("*\t*", 3, str); kputsn("*\t*", 3, str);
} else if (!p->is_rev) { // the forward strand } else if (!p->is_rev) { // the forward strand
int i, qb = 0, qe = s->l_seq; int i, qb = 0, qe = s->l_seq;
if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP)) { // have cigar && not the primary alignment && not softclip all if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt) { // have cigar && not the primary alignment && not softclip all
if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qb += p->cigar[0]>>4; if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qb += p->cigar[0]>>4;
if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qe -= p->cigar[p->n_cigar-1]>>4; if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qe -= p->cigar[p->n_cigar-1]>>4;
} }
@ -872,7 +872,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
} else kputc('*', str); } else kputc('*', str);
} else { // the reverse strand } else { // the reverse strand
int i, qb = 0, qe = s->l_seq; int i, qb = 0, qe = s->l_seq;
if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP)) { if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt) {
if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qe -= p->cigar[0]>>4; if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qe -= p->cigar[0]>>4;
if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qb += p->cigar[p->n_cigar-1]>>4; if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qb += p->cigar[p->n_cigar-1]>>4;
} }

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r868-dirty" #define PACKAGE_VERSION "0.7.10-r875-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);