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Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
[samtools.git]
/
misc
/
maq2sam.c
diff --git
a/misc/maq2sam.c
b/misc/maq2sam.c
index 758a698ed59aba300720599cda96c2759317887f..2bfbe2a3b328e276b52f1a443dbc6500d81122e8 100644
(file)
--- a/
misc/maq2sam.c
+++ b/
misc/maq2sam.c
@@
-5,7
+5,7
@@
#include <stdlib.h>
#include <assert.h>
#include <stdlib.h>
#include <assert.h>
-#define PACKAGE_VERSION "
0.1.2 (20090521)
"
+#define PACKAGE_VERSION "
r439
"
//#define MAQ_LONGREADS
//#define MAQ_LONGREADS
@@
-111,9
+111,9
@@
void maq2tam_core(gzFile fp, const char *rg)
else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
else c = m1->pos&1;
}
else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
else c = m1->pos&1;
}
-
flag |= c
;
+
if (c) flag |= 0x20
;
}
}
- if (flag) {
+ if (
m1->
flag) {
int l = strlen(m1->name);
if (m1->name[l-2] == '/') {
flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;
int l = strlen(m1->name);
if (m1->name[l-2] == '/') {
flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;