add new files

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index b0aeee026bb7525df2446639c5702ad843eea209..ff11397e3539d8662f31e85d6a9e8d09309e51f8 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -123,7 +123,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
                cnt += 2;
                if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
 
-               if (!((b->core.flag & 0x0002) && (b2->core.flag & 0x0002))) continue;
+               if ((b->core.flag & 0x0004) || (b2->core.flag & 0x0004)) continue;
 
                //swap if b is mate 2
                if (b->core.flag & 0x0080) {