X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=1d70fb17d7fd7391de4a147ea73367c67f96f786;hb=8c616f2509abd2fb9485a38607c1b439d243b85c;hp=537992584660b29696b602f09285aff6279aea73;hpb=c7f1abdd8b8d24f186320880515a848039ce051a;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5379925..1d70fb1 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -16,6 +16,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 	try {
 		
 		abort = false;
+		comboStarts = 0;
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; }
@@ -23,7 +24,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 		else {
 			//valid paramters for this command
 			string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", 
-									"qthreshold", "qaverage", "allfiles", "qtrim","diffs", "processors", "outputdir","inputdir"};
+									"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
 			
 			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 			
@@ -46,7 +47,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 				it = parameters.find("fasta");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
 				}
@@ -54,7 +55,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 				it = parameters.find("oligos");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["oligos"] = inputDir + it->second;		}
 				}
@@ -62,7 +63,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 				it = parameters.find("qfile");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["qfile"] = inputDir + it->second;		}
 				}
@@ -77,15 +78,16 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
 				outputDir = "";	
-				outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it	
 			}
 		
+			
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "flip", false);
 			if (temp == "not found"){	flip = 0;	}
-			else if(isTrue(temp))	{	flip = 1;	}
+			else if(m->isTrue(temp))	{	flip = 1;	}
 		
 			temp = validParameter.validFile(parameters, "oligos", true);
 			if (temp == "not found"){	oligoFile = "";		}
@@ -104,8 +106,16 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			temp = validParameter.validFile(parameters, "maxlength", false);	if (temp == "not found") { temp = "0"; }
 			convert(temp, maxLength);
 			
-			temp = validParameter.validFile(parameters, "diffs", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, diffs);
+			temp = validParameter.validFile(parameters, "bdiffs", false);		if (temp == "not found") { temp = "0"; }
+			convert(temp, bdiffs);
+			
+			temp = validParameter.validFile(parameters, "pdiffs", false);		if (temp == "not found") { temp = "0"; }
+			convert(temp, pdiffs);
+			
+			temp = validParameter.validFile(parameters, "tdiffs", false);		if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
+			convert(temp, tdiffs);
+			
+			if(tdiffs == 0){	tdiffs = bdiffs + pdiffs;	}
 			
 			temp = validParameter.validFile(parameters, "qfile", true);	
 			if (temp == "not found")	{	qFileName = "";		}
@@ -115,16 +125,28 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			temp = validParameter.validFile(parameters, "qthreshold", false);	if (temp == "not found") { temp = "0"; }
 			convert(temp, qThreshold);
 			
-			temp = validParameter.validFile(parameters, "qtrim", false);	if (temp == "not found") { temp = "F"; }
-			qtrim = isTrue(temp);
+			temp = validParameter.validFile(parameters, "qtrim", false);		if (temp == "not found") { temp = "F"; }
+			qtrim = m->isTrue(temp);
+
+			temp = validParameter.validFile(parameters, "rollaverage", false);	if (temp == "not found") { temp = "0"; }
+			convert(temp, qRollAverage);
+
+			temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
+			convert(temp, qWindowAverage);
+
+			temp = validParameter.validFile(parameters, "qwindowsize", false);	if (temp == "not found") { temp = "100"; }
+			convert(temp, qWindowSize);
+
+			temp = validParameter.validFile(parameters, "qstepsize", false);		if (temp == "not found") { temp = "10"; }
+			convert(temp, qWindowStep);
 
 			temp = validParameter.validFile(parameters, "qaverage", false);		if (temp == "not found") { temp = "0"; }
 			convert(temp, qAverage);
 			
 			temp = validParameter.validFile(parameters, "allfiles", false);		if (temp == "not found") { temp = "F"; }
-			allFiles = isTrue(temp);
+			allFiles = m->isTrue(temp);
 			
-			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = "1";				}
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found") { temp = "1"; }
 			convert(temp, processors); 
 			
 			if(allFiles && oligoFile == ""){
@@ -154,13 +176,15 @@ void TrimSeqsCommand::help(){
 		m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 		m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 		m->mothurOut("The fasta parameter is required.\n");
-		m->mothurOut("The flip parameter .... The default is 0.\n");
+		m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 		m->mothurOut("The oligos parameter .... The default is "".\n");
 		m->mothurOut("The maxambig parameter .... The default is -1.\n");
 		m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 		m->mothurOut("The minlength parameter .... The default is 0.\n");
 		m->mothurOut("The maxlength parameter .... The default is 0.\n");
-		m->mothurOut("The diffs parameter .... The default is 0.\n");
+		m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
+		m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
+		m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 		m->mothurOut("The qfile parameter .....\n");
 		m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 		m->mothurOut("The qaverage parameter .... The default is 0.\n");
@@ -195,97 +219,173 @@ int TrimSeqsCommand::execute(){
 		numFPrimers = 0;  //this needs to be initialized
 		numRPrimers = 0;
 		
-		string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
+		string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
 		outputNames.push_back(trimSeqFile);
-		string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
+		string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
 		outputNames.push_back(scrapSeqFile);
-		string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
+		string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
+		string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+		if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  }
+		string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
 		
 		vector<string> fastaFileNames;
+		vector<string> qualFileNames;
 		if(oligoFile != ""){
 			outputNames.push_back(groupFile);
-			getOligos(fastaFileNames);
+			getOligos(fastaFileNames, qualFileNames);
 		}
-		
-		if(qFileName != "")	{	setLines(qFileName, qLines);	}
 
+		vector<unsigned long int> fastaFilePos;
+		vector<unsigned long int> qFilePos;
+		
+		setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
+		
+		for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+			lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
+			if (qFileName != "") {  qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)]));  }
+		}	
+		if(qFileName == "")	{	qLines = lines;	} //files with duds
 		
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
-					ifstream inFASTA;
-					openInputFile(fastaFile, inFASTA);
-					int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
-					inFASTA.close();
-					
-					lines.push_back(new linePair(0, numSeqs));
-					
-					driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+										
+					driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 					
 					for (int j = 0; j < fastaFileNames.size(); j++) {
 						rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 					}
+					if(qFileName != ""){
+						for (int j = 0; j < qualFileNames.size(); j++) {
+							rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
+						}
+					}						
 
 				}else{
-					setLines(fastaFile, lines);	
-					if(qFileName == "")	{	qLines = lines;	}	
-								
-					createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames); 
+					createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames); 
 					
 					rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 					rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 					rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
+					
+					if(qFileName != ""){
+						rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
+						rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
+					}
+					
+					
 					for (int j = 0; j < fastaFileNames.size(); j++) {
 						rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 					}
+					if(qFileName != ""){
+						for (int j = 0; j < qualFileNames.size(); j++) {
+							rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
+						}
+					}						
+					
 					//append files
 					for(int i=1;i<processors;i++){
-						appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
+						m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 						remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
-						appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
+						m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 						remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
-						appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+
+						m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
+						remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
+						m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
+						remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
+						
+						m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 						remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 						for (int j = 0; j < fastaFileNames.size(); j++) {
-							appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
+							m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 							remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 						}
+						
+						if(qFileName != ""){
+							for (int j = 0; j < qualFileNames.size(); j++) {
+								m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
+								remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
+							}
+						}						
+						
+						
 					}
 				}
 				
 				if (m->control_pressed) {  return 0; }
 		#else
-				ifstream inFASTA;
-				openInputFile(fastafileNames[s], inFASTA);
-				numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
-				inFASTA.close();
-				
-				lines.push_back(new linePair(0, numSeqs));
-				
-				driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 				
+				for (int j = 0; j < fastaFileNames.size(); j++) {
+					rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
+				}
+				if(qFileName != ""){
+					for (int j = 0; j < qualFileNames.size(); j++) {
+						rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
+					}
+				}
+									
 				if (m->control_pressed) {  return 0; }
 		#endif
 						
 										
 		for(int i=0;i<fastaFileNames.size();i++){
-			ifstream inFASTA;
-			string seqName;
-			openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
-			ofstream outGroups;
-			openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
-			outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
-			
-			while(!inFASTA.eof()){
-				if(inFASTA.get() == '>'){
-					inFASTA >> seqName;
-					outGroups << seqName << '\t' << groupVector[i] << endl;
-				}
-				while (!inFASTA.eof())	{	char c = inFASTA.get(); if (c == 10 || c == 13){	break;	}	}
+			if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str());	}
+			else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
+			else {
+				ifstream inFASTA;
+				string seqName;
+				m->openInputFile(fastaFileNames[i], inFASTA);
+				ofstream outGroups;
+				string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+				m->openOutputFile(outGroupFilename, outGroups);
+				outputNames.push_back(outGroupFilename);
+				
+				string thisGroup = "";
+				if (i > comboStarts) {
+					map<string, int>::iterator itCombo;
+					for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
+						if(itCombo->second == i){	thisGroup = itCombo->first;	combos.erase(itCombo);  break;  }
+					}
+				}else{ thisGroup = groupVector[i]; }
+				
+				while(!inFASTA.eof()){
+					if(inFASTA.get() == '>'){
+						inFASTA >> seqName;
+						outGroups << seqName << '\t' << thisGroup << endl;
+					}
+					while (!inFASTA.eof())	{	char c = inFASTA.get(); if (c == 10 || c == 13){	break;	}	}
+				}
+				outGroups.close();
+				inFASTA.close();
+			}
+		}
+		
+		if(qFileName != ""){
+			for(int i=0;i<qualFileNames.size();i++){
+				if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str());	}
+				else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
+				else {
+					ifstream inQual;
+					string seqName;
+					m->openInputFile(qualFileNames[i], inQual);
+//					ofstream outGroups;
+//					
+//					string thisGroup = "";
+//					if (i > comboStarts) {
+//						map<string, int>::iterator itCombo;
+//						for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
+//							if(itCombo->second == i){	thisGroup = itCombo->first;	combos.erase(itCombo);  break;  }
+//						}
+//					}
+//					else{ thisGroup = groupVector[i]; }
+					
+					inQual.close();
+				}
 			}
-			outGroups.close();
-			inFASTA.close();
 		}
 		
+		
 		if (m->control_pressed) { 
 			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }
 			return 0;
@@ -306,137 +406,215 @@ int TrimSeqsCommand::execute(){
 }
 		
 /**************************************************************************************/
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {	
+
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames, linePair* line, linePair* qline) {	
+		
 	try {
 		
 		ofstream outFASTA;
-		int able = openOutputFile(trimFile, outFASTA);
+		int able = m->openOutputFile(trimFile, outFASTA);
 		
 		ofstream scrapFASTA;
-		openOutputFile(scrapFile, scrapFASTA);
+		m->openOutputFile(scrapFile, scrapFASTA);
+		
+		ofstream outQual;
+		ofstream scrapQual;
+		if(qFileName != ""){
+			m->openOutputFile(trimQFile, outQual);
+			m->openOutputFile(scrapQFile, scrapQual);
+		}
 		
 		ofstream outGroups;
 		vector<ofstream*> fastaFileNames;
+		vector<ofstream*> qualFileNames;
+		
 		if (oligoFile != "") {		
-			openOutputFile(groupFile, outGroups);   
+			m->openOutputFile(groupFile, outGroups);   
 			for (int i = 0; i < fastaNames.size(); i++) {
+
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+				if(qFileName != ""){
+					qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); 
+				}
+			#else
+				fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate)); 			
+				if(qFileName != ""){
+					qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate)); 			
+				}
+			#endif
 			}
 		}
 		
 		ifstream inFASTA;
-		openInputFile(filename, inFASTA);
+		m->openInputFile(filename, inFASTA);
+		inFASTA.seekg(line->start);
 		
 		ifstream qFile;
-		if(qFileName != "")	{	openInputFile(qFileName, qFile);	}
-		
-		qFile.seekg(qline->start);
-		inFASTA.seekg(line->start);
+		if(qFileName != "")	{	m->openInputFile(qFileName, qFile);	qFile.seekg(qline->start);  }
 		
-		for(int i=0;i<line->num;i++){
+		bool done = false;
+		int count = 0;
+	
+		while (!done) {
 				
 			if (m->control_pressed) { 
-				inFASTA.close(); 
-				outFASTA.close();
-				scrapFASTA.close();
+				inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 				if (oligoFile != "") {	 outGroups.close();   }
-				if(qFileName != "")	{	qFile.close();	}
-				for(int i=0;i<fastaFileNames.size();i++){
-					fastaFileNames[i]->close();
-					delete fastaFileNames[i];
-				}	
+				
+				for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }	
+
+				if(qFileName != ""){
+					qFile.close();
+					for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }	
+				}
 				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }
+
 				return 0;
 			}
 			
-			bool success = 1;
+			int success = 1;
 			
-			Sequence currSeq(inFASTA);
 
+			Sequence currSeq(inFASTA); m->gobble(inFASTA);
+
+			QualityScores currQual;
+			if(qFileName != ""){
+				currQual = QualityScores(qFile, currSeq.getNumBases());  m->gobble(qFile);
+			}
+			
 			string origSeq = currSeq.getUnaligned();
 			if (origSeq != "") {
-				int group;
+				int groupBar, groupPrime;
 				string trashCode = "";
-				
+				int currentSeqsDiffs = 0;
+
 				if(qFileName != ""){
-					if(qThreshold != 0)		{	success = stripQualThreshold(currSeq, qFile);	}
-					else if(qAverage != 0)	{	success = cullQualAverage(currSeq, qFile);		}
-					if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) { 
+					if(qThreshold != 0)			{	success = currQual.stripQualThreshold(currSeq, qThreshold);			}
+					else if(qAverage != 0)		{	success = currQual.cullQualAverage(currSeq, qAverage);				}
+					else if(qRollAverage != 0)	{	success = currQual.stripQualRollingAverage(currSeq, qRollAverage);	}
+					else if(qWindowAverage != 0){	success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);	}
+
+					if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) { 
 						success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 					}
-					if(!success)			{	trashCode += 'q';								}
+
+					if(!success)				{	trashCode += 'q';	}
 				}
 			
 				if(barcodes.size() != 0){
-					success = stripBarcode(currSeq, group);
-					if(!success){	trashCode += 'b';	}
+					success = stripBarcode(currSeq, currQual, groupBar);
+					if(success > bdiffs)		{	trashCode += 'b';	}
+					else{ currentSeqsDiffs += success;  }
 				}
-			
+
 				if(numFPrimers != 0){
-					success = stripForward(currSeq);
-					if(!success){	trashCode += 'f';	}
+					success = stripForward(currSeq, currQual, groupPrime);
+					if(success > pdiffs)		{	trashCode += 'f';	}
+					else{ currentSeqsDiffs += success;  }
 				}
-					
+				
+				if (currentSeqsDiffs > tdiffs)	{	trashCode += 't';   }
+
 				if(numRPrimers != 0){
-					success = stripReverse(currSeq);
-					if(!success){	trashCode += 'r';	}
+					success = stripReverse(currSeq, currQual);
+					if(!success)				{	trashCode += 'r';	}
 				}
 		
 				if(minLength > 0 || maxLength > 0){
 					success = cullLength(currSeq);
-					if(!success){	trashCode += 'l'; }
+					if(!success)				{	trashCode += 'l';	}
 				}
 				if(maxHomoP > 0){
 					success = cullHomoP(currSeq);
-					if(!success){	trashCode += 'h';	}
+					if(!success)				{	trashCode += 'h';	}
 				}
 				if(maxAmbig != -1){
 					success = cullAmbigs(currSeq);
-					if(!success){	trashCode += 'n';	}
+					if(!success)				{	trashCode += 'n';	}
 				}
 				
-				if(flip){	currSeq.reverseComplement();	}		// should go last			
+				if(flip){	currSeq.reverseComplement();		currQual.flipQScores();	}		// should go last			
 				
 				if(trashCode.length() == 0){
-					currSeq.setAligned(currSeq.getUnaligned());  //this is because of a modification we made to the sequence class to fix a bug.  all seqs have an aligned version, which is the version that gets printed.
+					currSeq.setAligned(currSeq.getUnaligned());
 					currSeq.printSequence(outFASTA);
+					currQual.printQScores(outQual);
+					
 					if(barcodes.size() != 0){
-						outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
-						
+						string thisGroup = groupVector[groupBar];
+						int indexToFastaFile = groupBar;
+						if (primers.size() != 0){
+							//does this primer have a group
+							if (groupVector[groupPrime] != "") {  
+								thisGroup += "." + groupVector[groupPrime]; 
+								indexToFastaFile = combos[thisGroup];
+							}
+						}
+						outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 						if(allFiles){
-							currSeq.printSequence(*fastaFileNames[group]);					
+							currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
+							
+							if(qFileName != ""){
+								currQual.printQScores(*qualFileNames[indexToFastaFile]);							
+							}
 						}
 					}
 				}
 				else{
 					currSeq.setName(currSeq.getName() + '|' + trashCode);
 					currSeq.setUnaligned(origSeq);
+					currSeq.setAligned(origSeq);
 					currSeq.printSequence(scrapFASTA);
+					currQual.printQScores(scrapQual);
 				}
+				count++;
 			}
-			gobble(inFASTA);
+			
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				unsigned long int pos = inFASTA.tellg();
+				if ((pos == -1) || (pos >= line->end)) { break; }
+			#else
+				if (inFASTA.eof()) { break; }
+			#endif
+				
+			//report progress
+			if((count) % 1000 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+			
 		}
+		//report progress
+		if((count) % 1000 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+
 		
 		inFASTA.close();
 		outFASTA.close();
 		scrapFASTA.close();
 		if (oligoFile != "") {	 outGroups.close();   }
-		if(qFileName != "")	{	qFile.close();	}
+		if(qFileName != "")	{	qFile.close();	scrapQual.close(); outQual.close();	}
 		
 		for(int i=0;i<fastaFileNames.size();i++){
 			fastaFileNames[i]->close();
 			delete fastaFileNames[i];
 		}		
 		
-		return 0;
+		if(qFileName != ""){
+			for(int i=0;i<qualFileNames.size();i++){
+				qualFileNames[i]->close();
+				delete qualFileNames[i];
+			}		
+		}			
+		
+		return count;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 		exit(1);
 	}
 }
+
 /**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
+
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 0;
@@ -451,7 +629,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
+				driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
 				exit(0);
 			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 		}
@@ -470,35 +648,73 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 		exit(1);
 	}
 }
+
 /**************************************************************************************************/
 
-int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
+int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 	try {
 		
-		lines.clear();
+		//set file positions for fasta file
+		fastaFilePos = m->divideFile(filename, processors);
 		
-		vector<long int> positions;
+		if (qfilename == "") { return processors; }
 		
-		ifstream inFASTA;
-		openInputFile(filename, inFASTA);
+		//get name of first sequence in each chunk
+		map<string, int> firstSeqNames;
+		for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+			ifstream in;
+			m->openInputFile(filename, in);
+			in.seekg(fastaFilePos[i]);
+		
+			Sequence temp(in); 
+			firstSeqNames[temp.getName()] = i;
+		
+			in.close();
+		}
+				
+		//seach for filePos of each first name in the qfile and save in qfileFilePos
+		ifstream inQual;
+		m->openInputFile(qfilename, inQual);
 			
 		string input;
-		while(!inFASTA.eof()){	
-			input = getline(inFASTA);
+		while(!inQual.eof()){	
+			input = m->getline(inQual);
 
 			if (input.length() != 0) {
-				if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+				if(input[0] == '>'){ //this is a sequence name line
+					istringstream nameStream(input);
+					
+					string sname = "";  nameStream >> sname;
+					sname = sname.substr(1);
+					
+					map<string, int>::iterator it = firstSeqNames.find(sname);
+					
+					if(it != firstSeqNames.end()) { //this is the start of a new chunk
+						unsigned long int pos = inQual.tellg(); 
+						qfileFilePos.push_back(pos - input.length() - 1);	
+						firstSeqNames.erase(it);
+					}
+				}
 			}
+			
+			if (firstSeqNames.size() == 0) { break; }
 		}
-		inFASTA.close();
+		inQual.close();
 		
-		int numFastaSeqs = positions.size();
-	
+		if (firstSeqNames.size() != 0) { 
+			for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+				m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
+			}
+			qFileName = "";
+			return processors;
+		}
+
+		//get last file position of qfile
 		FILE * pFile;
-		long size;
+		unsigned long int size;
 		
 		//get num bytes in file
-		pFile = fopen (filename.c_str(),"rb");
+		pFile = fopen (qfilename.c_str(),"rb");
 		if (pFile==NULL) perror ("Error opening file");
 		else{
 			fseek (pFile, 0, SEEK_END);
@@ -506,20 +722,9 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 			fclose (pFile);
 		}
 		
-		int numSeqsPerProcessor = numFastaSeqs / processors;
+		qfileFilePos.push_back(size);
 		
-		for (int i = 0; i < processors; i++) {
-
-			long int startPos = positions[ i * numSeqsPerProcessor ];
-			if(i == processors - 1){
-				numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
-			}else{  
-				long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
-			}
-			lines.push_back(new linePair(startPos, numSeqsPerProcessor));
-		}
-		
-		return numFastaSeqs;
+		return processors;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "TrimSeqsCommand", "setLines");
@@ -528,23 +733,27 @@ int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 }
 //***************************************************************************************************************
 
-void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
+void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 	try {
 		ifstream inOligos;
-		openInputFile(oligoFile, inOligos);
+		m->openInputFile(oligoFile, inOligos);
 		
 		ofstream test;
 		
 		string type, oligo, group;
 		int index=0;
+		//int indexPrimer = 0;
 		
 		while(!inOligos.eof()){
 			inOligos >> type;
-			
+		 			
 			if(type[0] == '#'){
 				while (!inOligos.eof())	{	char c = inOligos.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
 			}
 			else{
+				//make type case insensitive
+				for(int i=0;i<type.length();i++){	type[i] = toupper(type[i]);  }
+				
 				inOligos >> oligo;
 				
 				for(int i=0;i<oligo.length();i++){
@@ -552,31 +761,93 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 					if(oligo[i] == 'U')	{	oligo[i] = 'T';	}
 				}
 				
-				if(type == "forward"){
-					forPrimer.push_back(oligo);
+				if(type == "FORWARD"){
+					group = "";
+					
+					// get rest of line in case there is a primer name
+					while (!inOligos.eof())	{	
+						char c = inOligos.get(); 
+						if (c == 10 || c == 13){	break;	}
+						else if (c == 32 || c == 9){;} //space or tab
+						else { 	group += c;  }
+					} 
+					
+					//check for repeat barcodes
+					map<string, int>::iterator itPrime = primers.find(oligo);
+					if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
+					
+					primers[oligo]=index; index++;
+					groupVector.push_back(group);
+					
+					if(allFiles){
+						outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+						if(qFileName != ""){
+							outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+						}
+						if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+							filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+							if(qFileName != ""){
+								filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+							}
+						}else {
+							outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+							if(qFileName != ""){
+								outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+							}							
+						}
+					}
+
 				}
-				else if(type == "reverse"){
+				else if(type == "REVERSE"){
 					Sequence oligoRC("reverse", oligo);
 					oligoRC.reverseComplement();
 					revPrimer.push_back(oligoRC.getUnaligned());
 				}
-				else if(type == "barcode"){
+				else if(type == "BARCODE"){
 					inOligos >> group;
-					barcodes[oligo]=index++;
+					
+					//check for repeat barcodes
+					map<string, int>::iterator itBar = barcodes.find(oligo);
+					if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
+					
+					barcodes[oligo]=index; index++;
 					groupVector.push_back(group);
 					
 					if(allFiles){
-						//outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
-						outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
-						outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+						outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+						outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+						if(qFileName != ""){
+							outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+							outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+						}							
 					}
-				}
+				}else{	m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 			}
+			m->gobble(inOligos);
 		}
 		
 		inOligos.close();
 		
-		numFPrimers = forPrimer.size();
+		//add in potential combos
+		if(allFiles){
+			comboStarts = outFASTAVec.size()-1;
+			for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
+				for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
+					if (groupVector[itPrime->second] != "") { //there is a group for this primer
+						outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+						outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+						combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
+						
+						if(qFileName != ""){
+							outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+							outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+						}
+					}
+				}
+			}
+		}
+		
+		numFPrimers = primers.size();
 		numRPrimers = revPrimer.size();
 		
 	}
@@ -587,69 +858,122 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
 	try {
+		
 		string rawSequence = seq.getUnaligned();
-		bool success = 0;	//guilty until proven innocent
+		int success = bdiffs + 1;	//guilty until proven innocent
 		
 		//can you find the barcode
 		for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 			string oligo = it->first;
 			if(rawSequence.length() < oligo.length()){	//let's just assume that the barcodes are the same length
-				success = 0;
-				break;
+				success = bdiffs + 10;					//if the sequence is shorter than the barcode then bail out
+				break;	
 			}
 			
 			if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 				group = it->second;
 				seq.setUnaligned(rawSequence.substr(oligo.length()));
-				success = 1;
+				
+				if(qual.getName() != ""){
+					qual.trimQScores(oligo.length(), -1);
+				}
+				
+				success = 0;
 				break;
 			}
 		}
 		
 		//if you found the barcode or if you don't want to allow for diffs
-		if ((diffs == 0) || (success == 1)) { return success;  }
+//		cout << success;
+		if ((bdiffs == 0) || (success == 0)) { return success;  }
 		
 		else { //try aligning and see if you can find it
-			
+//			cout << endl;
+
+			int maxLength = 0;
+
 			Alignment* alignment;
-			if (barcodes.size() > 0) { //assumes barcodes are all the same length
+			if (barcodes.size() > 0) {
 				map<string,int>::iterator it=barcodes.begin();
-				string temp = it->first;
-				
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));  
+
+				for(it;it!=barcodes.end();it++){
+					if(it->first.length() > maxLength){
+						maxLength = it->first.length();
+					}
+				}
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));  
+
 			}else{ alignment = NULL; } 
 			
-
 			//can you find the barcode
+			int minDiff = 1e6;
+			int minCount = 1;
+			int minGroup = -1;
+			int minPos = 0;
+			
 			for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 				string oligo = it->first;
-				int length = oligo.length();
+//				int length = oligo.length();
 				
-				if(rawSequence.length() < oligo.length()){	//let's just assume that the barcodes are the same length
-					success = 0;
+				if(rawSequence.length() < maxLength){	//let's just assume that the barcodes are the same length
+					success = bdiffs + 10;
 					break;
 				}
 				
 				//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
-				alignment->align(oligo, rawSequence.substr(0,length+diffs));
+				alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 				oligo = alignment->getSeqAAln();
 				string temp = alignment->getSeqBAln();
-		cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;			
+		
+				int alnLength = oligo.length();
+				
+				for(int i=oligo.length()-1;i>=0;i--){
+					if(oligo[i] != '-'){	alnLength = i+1;	break;	}
+				}
+				oligo = oligo.substr(0,alnLength);
+				temp = temp.substr(0,alnLength);
 				
 				int newStart=0;
-				if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
-		cout << "found match" << endl;
-					group = it->second;
-					seq.setUnaligned(rawSequence.substr(newStart));
-					success = 1;
-					break;
+				int numDiff = countDiffs(oligo, temp);
+				
+//				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
+				
+				if(numDiff < minDiff){
+					minDiff = numDiff;
+					minCount = 1;
+					minGroup = it->second;
+					minPos = 0;
+					for(int i=0;i<alnLength;i++){
+						if(temp[i] != '-'){
+							minPos++;
+						}
+					}
+				}
+				else if(numDiff == minDiff){
+					minCount++;
+				}
+
+			}
+
+			if(minDiff > bdiffs)	{	success = minDiff;		}	//no good matches
+			else if(minCount > 1)	{	success = bdiffs + 100;	}	//can't tell the difference between multiple barcodes
+			else{													//use the best match
+				group = minGroup;
+				seq.setUnaligned(rawSequence.substr(minPos));
+				
+				if(qual.getName() != ""){
+					qual.trimQScores(minPos, -1);
 				}
+				success = minDiff;
 			}
 			
 			if (alignment != NULL) {  delete alignment;  }
+			
 		}
+//		cout << success << endl;
+		
 		return success;
 		
 	}
@@ -662,63 +986,120 @@ bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
 	try {
 		string rawSequence = seq.getUnaligned();
-		bool success = 0;	//guilty until proven innocent
+		int success = pdiffs + 1;	//guilty until proven innocent
 		
-		for(int i=0;i<numFPrimers;i++){
-			string oligo = forPrimer[i];
-			
-			if(rawSequence.length() < oligo.length()){
-				success = 0;
-				break;
+		//can you find the primer
+		for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+			string oligo = it->first;
+			if(rawSequence.length() < oligo.length()){	//let's just assume that the primers are the same length
+				success = pdiffs + 10;					//if the sequence is shorter than the barcode then bail out
+				break;	
 			}
 			
 			if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+				group = it->second;
 				seq.setUnaligned(rawSequence.substr(oligo.length()));
-				success = 1;
+				if(qual.getName() != ""){
+					qual.trimQScores(oligo.length(), -1);
+					
+				}
+				success = 0;
 				break;
 			}
 		}
-		
-		//if you found the primer or if you don't want to allow for diffs
-		if ((diffs == 0) || (success == 1)) { return success;  }
+
+		//if you found the barcode or if you don't want to allow for diffs
+//		cout << success;
+		if ((pdiffs == 0) || (success == 0)) { return success;  }
 		
 		else { //try aligning and see if you can find it
-			
-			
+//			cout << endl;
+
+			int maxLength = 0;
+
 			Alignment* alignment;
-			if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+diffs+1));  } //assumes primers are all the same length
-			else{ alignment = NULL; } 
+			if (primers.size() > 0) {
+				map<string,int>::iterator it=primers.begin();
+
+				for(it;it!=primers.end();it++){
+					if(it->first.length() > maxLength){
+						maxLength = it->first.length();
+					}
+				}
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));  
+
+			}else{ alignment = NULL; } 
+			
+			//can you find the barcode
+			int minDiff = 1e6;
+			int minCount = 1;
+			int minGroup = -1;
+			int minPos = 0;
 			
-			//can you find the primer
-			for(int i=0;i<numFPrimers;i++){
-				string oligo = forPrimer[i];
-				int length = oligo.length();
+			for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+				string oligo = it->first;
+//				int length = oligo.length();
 				
-				if(rawSequence.length() < oligo.length()){	
-					success = 0;
+				if(rawSequence.length() < maxLength){	
+					success = pdiffs + 100;
 					break;
 				}
 				
-				//use needleman to align first primer.length()+numdiffs of sequence to each primer
-				alignment->align(oligo, rawSequence.substr(0,length+diffs));
+				//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+				alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 				oligo = alignment->getSeqAAln();
+				string temp = alignment->getSeqBAln();
+		
+				int alnLength = oligo.length();
 				
-				int newStart = 0;
-				if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
-					seq.setUnaligned(rawSequence.substr(newStart));
-					success = 1;
-					break;
+				for(int i=oligo.length()-1;i>=0;i--){
+					if(oligo[i] != '-'){	alnLength = i+1;	break;	}
 				}
+				oligo = oligo.substr(0,alnLength);
+				temp = temp.substr(0,alnLength);
+				
+				int newStart=0;
+				int numDiff = countDiffs(oligo, temp);
+				
+//				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
+				
+				if(numDiff < minDiff){
+					minDiff = numDiff;
+					minCount = 1;
+					minGroup = it->second;
+					minPos = 0;
+					for(int i=0;i<alnLength;i++){
+						if(temp[i] != '-'){
+							minPos++;
+						}
+					}
+				}
+				else if(numDiff == minDiff){
+					minCount++;
+				}
+
+			}
+
+			if(minDiff > pdiffs)	{	success = minDiff;		}	//no good matches
+			else if(minCount > 1)	{	success = pdiffs + 10;	}	//can't tell the difference between multiple primers
+			else{													//use the best match
+				group = minGroup;
+				seq.setUnaligned(rawSequence.substr(minPos));
+				if(qual.getName() != ""){
+					qual.trimQScores(minPos, -1);
+				}
+				success = minDiff;
 			}
 			
 			if (alignment != NULL) {  delete alignment;  }
+			
 		}
 		
 		return success;
-		
+
 	}
 	catch(exception& e) {
 		m->errorOut(e, "TrimSeqsCommand", "stripForward");
@@ -728,7 +1109,7 @@ bool TrimSeqsCommand::stripForward(Sequence& seq){
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripReverse(Sequence& seq){
+bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
 	try {
 		string rawSequence = seq.getUnaligned();
 		bool success = 0;	//guilty until proven innocent
@@ -743,6 +1124,9 @@ bool TrimSeqsCommand::stripReverse(Sequence& seq){
 			
 			if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 				seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+				if(qual.getName() != ""){
+					qual.trimQScores(-1, rawSequence.length()-oligo.length());
+				}
 				success = 1;
 				break;
 			}
@@ -856,24 +1240,14 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
+int TrimSeqsCommand::countDiffs(string oligo, string seq){
 	try {
-		bool success = 1;
+
 		int length = oligo.length();
-		end = length;
-		int countBases = 0;
 		int countDiffs = 0;
 		
-		if (length != 0) {
-			if ((oligo[0] == '-') || (oligo[0] == '.')) {  success = 0; return success;  } //no gaps allowed at beginning
-		}
-		
 		for(int i=0;i<length;i++){
-			
-			if ((oligo[i] != '-') && (oligo[i] != '.'))  { countBases++; } 
-			
-	//cout << oligo[i] << " " << seq[i] << " diffs = " << countDiffs << " countBases = " << countBases << endl; 	
-		
+								
 			if(oligo[i] != seq[i]){
 				if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')	{	countDiffs++; 	}
 				else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))				{	countDiffs++;	}
@@ -886,98 +1260,91 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int&
 				else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))	{	countDiffs++;	}
 				else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))	{	countDiffs++;	}
 				else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))	{	countDiffs++;	}
-				else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))	{	countDiffs++;	}			
-				
-				if(countDiffs > diffs)	{	success = 0; break;	 }
-			}
-			else{
-				success = 1;
+				else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))	{	countDiffs++;	}	
 			}
 			
-			if (countBases >= numBases) { end = i; break; } //stop checking after end of barcode or primer
 		}
-	
-		return success;
+		
+		return countDiffs;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+		m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 		exit(1);
 	}
 
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
-	try {
-		string rawSequence = seq.getUnaligned();
-		int seqLength;  // = rawSequence.length();
-		string name, temp, temp2;
-		
-		qFile >> name >> temp;
-	
-		splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
-		convert(temp, seqLength); //converts string to int
-	
-		if (name.length() != 0) {  if(name.substr(1) != seq.getName())	{	m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine();	}  } 
-		while (!qFile.eof())	{	char c = qFile.get(); if (c == 10 || c == 13){	break;	}	}
-		
-		int score;
-		int end = seqLength;
-		
-		for(int i=0;i<seqLength;i++){
-			qFile >> score;
-			
-			if(score <= qThreshold){
-				end = i;
-				break;
-			}
-		}
-		for(int i=end+1;i<seqLength;i++){
-			qFile >> score;
-		}
-		
-		seq.setUnaligned(rawSequence.substr(0,end));
-		
-		return 1;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
-		exit(1);
-	}
-}
+//bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
+//	try {
+//		
+//		string rawSequence = seq.getUnaligned();
+//		int seqLength = seq.getNumBases();
+//		bool success = 0;	//guilty until proven innocent
+//		string name;
+//		
+//		qFile >> name;
+//		if (name[0] == '>') {  if(name.substr(1) != seq.getName())	{	m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine();	}  }
+//		
+//		while (!qFile.eof())	{	char c = qFile.get(); if (c == 10 || c == 13){	break;	}	}
+//		
+//		int score;
+//		int end = seqLength;
+//		
+//		for(int i=0;i<seqLength;i++){
+//			qFile >> score;
+//			
+//			if(score < qThreshold){
+//				end = i;
+//				break;
+//			}
+//		}
+//		for(int i=end+1;i<seqLength;i++){
+//			qFile >> score;
+//		}
+//		
+//		seq.setUnaligned(rawSequence.substr(0,end));
+//		
+//		return 1;
+//	}
+//	catch(exception& e) {
+//		m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+//		exit(1);
+//	}
+//}
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
-	try {
-		string rawSequence = seq.getUnaligned();
-		int seqLength = seq.getNumBases();
-		bool success = 0;	//guilty until proven innocent
-		string name;
-		
-		qFile >> name;
-		if (name[0] == '>') {  if(name.substr(1) != seq.getName())	{	m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine();	}  }
-		
-		while (!qFile.eof())	{	char c = qFile.get(); if (c == 10 || c == 13){	break;	}	}
-		
-		float score;	
-		float average = 0;
-		
-		for(int i=0;i<seqLength;i++){
-			qFile >> score;
-			average += score;
-		}
-		average /= seqLength;
-
-		if(average >= qAverage)	{	success = 1;	}
-		else					{	success = 0;	}
-		
-		return success;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
-		exit(1);
-	}
-}
+//bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
+//	try {
+//		string rawSequence = seq.getUnaligned();
+//		int seqLength = seq.getNumBases();
+//		bool success = 0;	//guilty until proven innocent
+//		string name;
+//		
+//		qFile >> name;
+//		if (name[0] == '>') {  if(name.substr(1) != seq.getName())	{	m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine();	}  }
+//		
+//		while (!qFile.eof())	{	char c = qFile.get(); if (c == 10 || c == 13){	break;	}	}
+//		
+//		float score;	
+//		float average = 0;
+//		
+//		for(int i=0;i<seqLength;i++){
+//			qFile >> score;
+//			average += score;
+//		}
+//		average /= seqLength;
+//
+//		if(average >= qAverage)	{	success = 1;	}
+//		else					{	success = 0;	}
+//		
+//		return success;
+//	}
+//	catch(exception& e) {
+//		m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+//		exit(1);
+//	}
+//}
 
 //***************************************************************************************************************