X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=PairedEndQModel.h;h=cbc5475588d19996154d892cc99af336b75ddbde;hb=86e650e9577999a7ba00ab454d1f6bf674b0ea70;hp=64e486b66b98d19fafc98bce67ef0a5bd85131ad;hpb=5b867894f164d9fa3fbc1a8e659b34890b977716;p=rsem.git

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index 64e486b..cbc5475 100644
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -243,16 +243,21 @@ void PairedEndQModel::estimateFromReads(const char* readFN) {
     			SingleReadQ mate1 = read.getMate1();
     			SingleReadQ mate2 = read.getMate2();
 
-    			mld->update(mate1.getReadLength(), 1.0);
-    			mld->update(mate2.getReadLength(), 1.0);
-
-    			qd->update(mate1.getQScore());
-    			qd->update(mate2.getQScore());
-
-    			if (i == 0) {
-    				nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
-    				nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
-    			}
+			if (!read.isLowQuality()) {
+			  mld->update(mate1.getReadLength(), 1.0);
+			  mld->update(mate2.getReadLength(), 1.0);
+
+			  qd->update(mate1.getQScore());
+			  qd->update(mate2.getQScore());
+			  
+			  if (i == 0) {
+			    nqpro->updateC(mate1.getReadSeq(), mate1.getQScore());
+			    nqpro->updateC(mate2.getReadSeq(), mate2.getQScore());
+			  }
+			}
+			else if (verbose && (mate1.getReadLength() < OLEN || mate2.getReadLength() < OLEN)) { 
+			  printf("Warning: Read %s is ignored due to at least one of the mates' length < %d!\n", read.getName().c_str(), OLEN);
+			}
 
     			++cnt;
     			if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }