X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.cpp;h=33349decab52e90be19c928b44b9b07c8f6c710a;hp=aebb16b42a6455693b7c491f83b1740c58acd0e0;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ac663461b19ad1436a06aa63f97221d1ff105482

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b..33349de 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -395,7 +395,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		
 		if(line->start == 0){
 			flowFile >> numFlows; m->gobble(flowFile);
-			scrapFlowFile << maxFlows << endl;
+			scrapFlowFile << numFlows << endl;
 			trimFlowFile << maxFlows << endl;
 			if(allFiles){
 				for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
@@ -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;
 			
@@ -595,6 +599,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 				else if(type == "REVERSE"){
 					string oligoRC = reverseOligo(oligo);
 					revPrimer.push_back(oligoRC);
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
 				}
 				else if(type == "BARCODE"){
 					oligosFile >> group;
@@ -633,8 +638,7 @@ 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(), "");