Imported Upstream version 0.1.6~dfsg

[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>
 
-#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;