do not set "read 1" if reads are not mapped in the PE mode of maq

[samtools.git] / misc / maq2sam.c

diff --git a/misc/maq2sam.c b/misc/maq2sam.c
index 758a698ed59aba300720599cda96c2759317887f..53a3ef3353d0383d336e4f6fa7ebb338f81f860b 100644 (file)
--- a/misc/maq2sam.c
+++ b/misc/maq2sam.c
@@ -113,7 +113,7 @@ void maq2tam_core(gzFile fp, const char *rg)
                        }
                        flag |= c;
                }
-               if (flag) {
+               if (m1->flag) {
                        int l = strlen(m1->name);
                        if (m1->name[l-2] == '/') {
                                flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;