From 3a42c375d4b42b77f1a25b6288f7d367af9f3abb Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 4 Aug 2009 21:16:51 +0000
Subject: [PATCH] fixed a SERIOUS bug in setting 0x20 flag

---
 misc/maq2sam.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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);
-- 
2.39.2