X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=12ab087d668966f905a495f4e608a777e157ebc0;hb=fb2aa1ca9d00710943155ef3abbbdd87df116e4a;hp=e014f8d5915445622841b8ca6f680cdf6b9e413d;hpb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f;p=rsem.git

diff --git a/BamWriter.h b/BamWriter.h
index e014f8d..12ab087 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -113,6 +113,9 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 		cnt += 2;
 		if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
 
+		//mate info is not complete, skip
+		if (!(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)))) continue;
+		//unalignable reads, skip
 		if ((b->core.flag & 0x0004) || (b2->core.flag & 0x0004)) continue;
 
 		//swap if b is mate 2