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r345: bugfix in mem - wrong mate strand for unmap 

Received a clean bill from Picard
This commit is contained in:
Heng Li 2013-03-08 13:15:43 -05:00
parent af7b4d8980
commit 66c9783daf
2 changed files with 2 additions and 1 deletions
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1
bwamem.c
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@ -628,6 +628,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
} }
p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand
p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand
if (is_mapped(p) && m && !is_mapped(m) && (p->flag&0x10)) p->flag |= 0x20; // if mate is unmapped, it takes the strand of the current read
kputs(s->name, str); kputc('\t', str); 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 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 int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.0-r343-beta" #define PACKAGE_VERSION "0.7.0-r345-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);