X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=PairedEndRead.h;h=6504e610141e9db33d027bdb47cff33fb2af95a9;hb=5fd66ada6c610981dcecd50e5e41436e0458b110;hp=9c81f9e780d8375bda56babd549aea6069d7b84c;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/PairedEndRead.h b/PairedEndRead.h
index 9c81f9e..6504e61 100644
--- a/PairedEndRead.h
+++ b/PairedEndRead.h
@@ -61,6 +61,7 @@ void PairedEndRead::write(int argc, std::ostream *argv[]) {
 
 void PairedEndRead::calc_lq() {
 	low_quality = mate1.isLowQuality() && mate2.isLowQuality();
+	if (mate1.getReadLength() < OLEN || mate2.getReadLength() < OLEN) low_quality = true;
 }
 
 #endif