X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=fd55edf25ede0b4de807bef17dadb861b44c03a8;hb=89cfcfcc9e648d2f956f2ff419e64ba7907106d2;hp=aebb16b42a6455693b7c491f83b1740c58acd0e0;hpb=ac663461b19ad1436a06aa63f97221d1ff105482;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b..fd55edf 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -435,7 +435,11 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 				success = 0;
 				trashCode += 'l';
 			}
-			
+            if(!flowData.hasGoodHomoP()){	//screen to see if sequence meets the maximum homopolymer limit
+				success = 0;
+				trashCode += 'h';
+			}
+
 			int primerIndex = 0;
 			int barcodeIndex = 0;
 			
@@ -633,8 +637,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 			primers[""] = 0;
 			primerNameVector.push_back("");			
 		}
-		
-		
+
 		outFlowFileNames.resize(barcodeNameVector.size());
 		for(int i=0;i<outFlowFileNames.size();i++){
 			outFlowFileNames[i].assign(primerNameVector.size(), "");