modifications to commands to add headers to list file.

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b42a6455693b7c491f83b1740c58acd0e0..fd55edf25ede0b4de807bef17dadb861b44c03a8 100644 (file)
--- 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(), "");