X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fmaq2sam.c;h=2bfbe2a3b328e276b52f1a443dbc6500d81122e8;hb=0b3418cf166ce4a58cedf0d9a2df5ec3dd4cc5fa;hp=53a3ef3353d0383d336e4f6fa7ebb338f81f860b;hpb=d89ec29105e36257fe27067d350ebbe879378c8d;p=samtools.git

diff --git a/misc/maq2sam.c b/misc/maq2sam.c
index 53a3ef3..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
 
@@ -111,7 +111,7 @@ 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 (m1->flag) {
 			int l = strlen(m1->name);