X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=misc%2Fmaq2sam.c;h=2bfbe2a3b328e276b52f1a443dbc6500d81122e8;hp=758a698ed59aba300720599cda96c2759317887f;hb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906;ds=sidebyside

diff --git a/misc/maq2sam.c b/misc/maq2sam.c
index 758a698..2bfbe2a 100644
--- a/misc/maq2sam.c
+++ b/misc/maq2sam.c
@@ -5,7 +5,7 @@
 #include <stdlib.h>
 #include <assert.h>
 
-#define PACKAGE_VERSION "0.1.2 (20090521)"
+#define PACKAGE_VERSION "r439"
 
 //#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;
 			}
-			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;