X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=trimflowscommand.cpp;h=296a6fe37d0449bb719d69c4001429583bcb74ee;hb=c9a311f0c621a2e88abf7b2efbe74e9aa1e88a8d;hp=d45f20cae1f0516c014d42cf7e6afaef57d2a1a2;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index d45f20c..296a6fe 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -28,7 +28,7 @@ vector<string> TrimFlowsCommand::setParameters(){
 		CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
 		CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
 		CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
-		CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+		CommandParameter porder("order", "String", "", "TACG", "", "", "",false,false); parameters.push_back(porder);
 		CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -347,7 +347,7 @@ int TrimFlowsCommand::execute(){
 			
 			output.close();
 		}
-		outputTypes["flow.files"].push_back(flowFilesFileName);
+		outputTypes["file"].push_back(flowFilesFileName);
 		outputNames.push_back(flowFilesFileName);
 		
 //		set fasta file as new current fastafile
@@ -423,11 +423,9 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 			string trashCode = "";
 			
 			flowData.getNext(flowFile); 
-			//cout << "driver good bit " << flowFile.good() << endl;	
 			flowData.capFlows(maxFlows);	
 			
 			Sequence currSeq = flowData.getSequence();
-			
 			if(!flowData.hasMinFlows(minFlows)){	//screen to see if sequence is of a minimum number of flows
 				success = 0;
 				trashCode += 'l';
@@ -443,6 +441,8 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                 
             }
             
+            if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
+            
 			if(barcodes.size() != 0){
 				success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 				if(success > bdiffs)		{	trashCode += 'b';	}