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r294: bugfix - -M not working

This commit is contained in:
Heng Li 2013-02-26 13:14:33 -05:00
parent 619ac4f93d
commit 32f2d60a2e
2 changed files with 2 additions and 2 deletions
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2
bwamem.c
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@ -517,7 +517,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
kputs(s->name, str); kputc('\t', str);
if (is_mapped(p)) { // has a coordinate, no matter whether it is mapped or copied from the mate
int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag
if (sam_flag&0x10000) sam_flag |= 0x100;
if (p->flag&0x10000) sam_flag |= 0x100;
if (!copy_mate) {
cigar = bwa_gen_cigar(mat, q, r, w, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar);
p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.6.2-r293-beta"
#define PACKAGE_VERSION "0.6.2-r294-beta"
#endif
static int usage()