X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=ff11397e3539d8662f31e85d6a9e8d09309e51f8;hb=cb94fd597b180aa7cb01ae84c9d1025201b98d8e;hp=b0aeee026bb7525df2446639c5702ad843eea209;hpb=946f9a6adb2a82048c8453d44693cd3838d32939;p=rsem.git

diff --git a/BamWriter.h b/BamWriter.h
index b0aeee0..ff11397 100644
--- 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) {