Add a validator for input SAM/BAM file

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index e014f8d5915445622841b8ca6f680cdf6b9e413d..12ab087d668966f905a495f4e608a777e157ebc0 100644 (file)
--- 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