X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=296a6fe37d0449bb719d69c4001429583bcb74ee;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=86de668b4f57596bf11efb80807b18f932136551;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 86de668..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);
@@ -56,7 +56,28 @@ string TrimFlowsCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "flow")            {   outputFileName =  "flow";   }
+            else if (type == "fasta")            {   outputFileName =  "flow.fasta";   }
+            else if (type == "file")            {   outputFileName =  "flow.files";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimFlowsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 TrimFlowsCommand::TrimFlowsCommand(){	
@@ -66,6 +87,7 @@ TrimFlowsCommand::TrimFlowsCommand(){
 		vector<string> tempOutNames;
 		outputTypes["flow"] = tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
+        outputTypes["file"] = tempOutNames;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
@@ -103,6 +125,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 			vector<string> tempOutNames;
 			outputTypes["flow"] = tempOutNames;
 			outputTypes["fasta"] = tempOutNames;
+            outputTypes["file"] = tempOutNames;
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
@@ -225,13 +248,13 @@ int TrimFlowsCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
-		string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
+		string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
 		outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 		
-		string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
+		string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
 		outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 
-		string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
+		string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
 		if(fasta){
 			outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
 		}
@@ -284,7 +307,7 @@ int TrimFlowsCommand::execute(){
 		
 		if(allFiles){
 			set<string> namesAlreadyProcessed;
-			flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+			flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
 			m->openOutputFile(flowFilesFileName, output);
 
 			for(int i=0;i<barcodePrimerComboFileNames.size();i++){
@@ -317,14 +340,14 @@ int TrimFlowsCommand::execute(){
 			output.close();
 		}
 		else{
-			flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+			flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
 			m->openOutputFile(flowFilesFileName, output);
 			
 			output << m->getFullPathName(trimFlowFileName) << endl;
 			
 			output.close();
 		}
-		outputTypes["flow.files"].push_back(flowFilesFileName);
+		outputTypes["file"].push_back(flowFilesFileName);
 		outputNames.push_back(flowFilesFileName);
 		
 //		set fasta file as new current fastafile
@@ -392,8 +415,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 		
 		while(moreSeqs) {
-			//cout << "driver " << count << endl;
-	
+				
 			if (m->control_pressed) { break; }
 			
 			int success = 1;
@@ -401,11 +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';
@@ -421,6 +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';	}