X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=b430624838594e4185233f7e946733a94469303b;hb=bbdb72971ea4cd171abe34985af89f97bc2a31d3;hp=ef0c06649af1afb64458bf153457bdadda566999;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index ef0c066..b430624 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -8,20 +8,23 @@
  */
 
 #include "trimseqscommand.h"
+#include "needlemanoverlap.hpp"
 
 //***************************************************************************************************************
 
-TrimSeqsCommand::TrimSeqsCommand(string option){
+TrimSeqsCommand::TrimSeqsCommand(string option)  {
 	try {
 		
 		abort = false;
+		comboStarts = 0;
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; }
 		
 		else {
 			//valid paramters for this command
-			string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles"};
+			string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", 
+									"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
 			
 			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 			
@@ -29,18 +32,56 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 			map<string,string> parameters = parser.getParameters();
 			
 			ValidParameters validParameter;
+			map<string,string>::iterator it;
 			
 			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//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);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("fasta");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = 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;		}
+				}
+				
+				it = parameters.find("oligos");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = 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;		}
+				}
+				
+				it = parameters.find("qfile");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = 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;		}
+				}
+			}
+
+			
 			//check for required parameters
 			fastaFile = validParameter.validFile(parameters, "fasta", true);
-			if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
+			if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
 			else if (fastaFile == "not open") { abort = true; }	
+			
+			//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	
+			}
 		
-		
+			
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			string temp;
@@ -65,13 +106,39 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 			temp = validParameter.validFile(parameters, "maxlength", false);	if (temp == "not found") { temp = "0"; }
 			convert(temp, maxLength);
 			
+			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 = "";		}
-			else if(temp == "not open")	{	abort = 0;		}
+			else if(temp == "not open")	{	abort = true;		}
 			else						{	qFileName = temp;	}
 			
 			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, "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);
@@ -79,23 +146,26 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 			temp = validParameter.validFile(parameters, "allfiles", false);		if (temp == "not found") { temp = "F"; }
 			allFiles = isTrue(temp);
 			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found") { temp = "1"; }
+			convert(temp, processors); 
+			
 			if(allFiles && oligoFile == ""){
-				mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); mothurOutEndLine();
+				m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 			}
 			if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
-				mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
+				m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 				qAverage=0;
 				qThreshold=0;
 			}
 			if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){		
-				mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
+				m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 				abort = true;
 			}
 		}
 
 	}
 	catch(exception& e) {
-		errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+		m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 		exit(1);
 	}
 }
@@ -103,24 +173,33 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
 
 void TrimSeqsCommand::help(){
 	try {
-		mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
-		mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength.\n");
-		mothurOut("The fasta parameter is required.\n");
-		mothurOut("The flip parameter .... The default is 0.\n");
-		mothurOut("The oligos parameter .... The default is "".\n");
-		mothurOut("The maxambig parameter .... The default is -1.\n");
-		mothurOut("The maxhomop parameter .... The default is 0.\n");
-		mothurOut("The minlength parameter .... The default is 0.\n");
-		mothurOut("The maxlength parameter .... The default is 0.\n");
-		mothurOut("The trim.seqs command should be in the following format: \n");
-		mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
-		mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");	
-		mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
-		mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+		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 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 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");
+		m->mothurOut("The allfiles parameter .... The default is F.\n");
+		m->mothurOut("The qtrim parameter .... The default is F.\n");
+		m->mothurOut("The trim.seqs command should be in the following format: \n");
+		m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
+		m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");	
+		m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
+		m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 
 	}
 	catch(exception& e) {
-		errorOut(e, "TrimSeqsCommand", "help");
+		m->errorOut(e, "TrimSeqsCommand", "help");
 		exit(1);
 	}
 }
@@ -136,385 +215,1105 @@ int TrimSeqsCommand::execute(){
 	try{
 	
 		if (abort == true) { return 0; }
+		
+		numFPrimers = 0;  //this needs to be initialized
+		numRPrimers = 0;
+		
+		string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
+		outputNames.push_back(trimSeqFile);
+		string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
+		outputNames.push_back(scrapSeqFile);
+		string trimQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.qual";
+		outputNames.push_back(trimQualFile);
+		string scrapQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.qual";
+		outputNames.push_back(scrapQualFile);
+		string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
+		
+		vector<string> fastaFileNames;
+		vector<string> qualFileNames;
+		if(oligoFile != ""){
+			outputNames.push_back(groupFile);
+			getOligos(fastaFileNames, qualFileNames);
+		}
+		
+		if(qFileName != "")	{	setLines(qFileName, qLines);	}
 
-		ifstream inFASTA;
-		openInputFile(fastaFile, inFASTA);
+		
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					ifstream inFASTA;
+					int numSeqs;
+					openInputFile(fastaFile, inFASTA);
+					getNumSeqs(inFASTA, numSeqs);
+					inFASTA.close();
+					
+					lines.push_back(new linePair(0, numSeqs));
+					
+					driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[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, 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);
+						remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
+						appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
+						remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
+
+						appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
+						remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
+						appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
+						remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
+						
+						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]);
+							remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
+						}
+						
+						if(qFileName != ""){
+							for (int j = 0; j < qualFileNames.size(); j++) {
+								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;
+				int numSeqs;
+				openInputFile(fastaFile, inFASTA);
+				getNumSeqs(inFASTA, numSeqs);
+				inFASTA.close();
+				
+				lines.push_back(new linePair(0, numSeqs));
+				
+				driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[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++){
+			if (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;
+				openInputFile(fastaFileNames[i], inFASTA);
+				ofstream outGroups;
+				string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
+				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 (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;
+					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();
+				}
+			}
+		}
+		
+		
+		if (m->control_pressed) { 
+			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }
+			return 0;
+		}
+
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOutEndLine();
+		
+		return 0;	
+			
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "execute");
+		exit(1);
+	}
+}
+		
+/**************************************************************************************/
+
+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;
-		string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
-		openOutputFile(trimSeqFile, outFASTA);
+		int able = openOutputFile(trimFile, outFASTA);
+		
+		ofstream scrapFASTA;
+		openOutputFile(scrapFile, scrapFASTA);
+		
+		ofstream outQual;
+		ofstream scrapQual;
+		if(qFileName != ""){
+			openOutputFile(trimQFile, outQual);
+			openOutputFile(scrapQFile, scrapQual);
+		}
 		
 		ofstream outGroups;
 		vector<ofstream*> fastaFileNames;
-		if(oligoFile != ""){
-			string groupFile = getRootName(fastaFile) + "groups"; 
-			openOutputFile(groupFile, outGroups);
-			getOligos(fastaFileNames);
+		vector<ofstream*> qualFileNames;
+		
+		
+		if (oligoFile != "") {		
+			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
+			}
 		}
 		
-		ofstream scrapFASTA;
-		string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
-		openOutputFile(scrapSeqFile, scrapFASTA);
+		ifstream inFASTA;
+		openInputFile(filename, inFASTA);
 		
 		ifstream qFile;
 		if(qFileName != "")	{	openInputFile(qFileName, qFile);	}
 		
-		bool success;
+		qFile.seekg(qline->start);
+		inFASTA.seekg(line->start);
 		
-		while(!inFASTA.eof()){
-			Sequence currSeq(inFASTA);
-			string origSeq = currSeq.getUnaligned();
-			int group;
-			string trashCode = "";
+		for(int i=0;i<line->num;i++){
+				
+			if (m->control_pressed) { 
+				inFASTA.close(); outFASTA.close(); scrapFASTA.close();
+				if (oligoFile != "") {	 outGroups.close();   }
+				
+				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;
+			}
+			
+			int success = 1;
 			
+			Sequence currSeq(inFASTA);
+			QualityScores currQual;
 			if(qFileName != ""){
-				if(qThreshold != 0)		{	success = stripQualThreshold(currSeq, qFile);	}
-				else if(qAverage != 0)	{	success = cullQualAverage(currSeq, qFile);		}
-				if(!success)			{	trashCode += 'q';								}
-				qFile.close();
-			}
-			if(barcodes.size() != 0){
-				success = stripBarcode(currSeq, group);
-				if(!success){	trashCode += 'b';	}
-			}
-			if(numFPrimers != 0){
-				success = stripForward(currSeq);
-				if(!success){	trashCode += 'f';	}
-			}
-			if(numRPrimers != 0){
-				success = stripReverse(currSeq);
-				if(!success){	trashCode += 'r';	}
-			}
-			if(minLength > 0 || maxLength > 0){
-				success = cullLength(currSeq);
-				if(!success){	trashCode += 'l';	}
-			}
-			if(maxHomoP > 0){
-				success = cullHomoP(currSeq);
-				if(!success){	trashCode += 'h';	}
-			}
-			if(maxAmbig != -1){
-				success = cullAmbigs(currSeq);
-				if(!success){	trashCode += 'n';	}
+				currQual = QualityScores(qFile, currSeq.getNumBases());
 			}
 			
-			if(flip){	currSeq.reverseComplement();	}		// should go last			
+			string origSeq = currSeq.getUnaligned();
+			if (origSeq != "") {
+				int groupBar, groupPrime;
+				string trashCode = "";
+				int currentSeqsDiffs = 0;
+
+				if(qFileName != ""){
+					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(trashCode.length() == 0){
-				currSeq.printSequence(outFASTA);
 				if(barcodes.size() != 0){
-					outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+					success = stripBarcode(currSeq, currQual, groupBar);
+					if(success > bdiffs)		{	trashCode += 'b';	}
+					else{ currentSeqsDiffs += success;  }
+				}
+
+				if(numFPrimers != 0){
+					success = stripForward(currSeq, currQual, groupPrime);
+					if(success > pdiffs)		{	trashCode += 'f';	}
+					else{ currentSeqsDiffs += success;  }
+				}
+				
+				if (currentSeqsDiffs > tdiffs)	{	trashCode += 't';   }
+
+				if(numRPrimers != 0){
+					success = stripReverse(currSeq, currQual);
+					if(!success)				{	trashCode += 'r';	}
+				}
+		
+				if(minLength > 0 || maxLength > 0){
+					success = cullLength(currSeq);
+					if(!success)				{	trashCode += 'l';	}
+				}
+				if(maxHomoP > 0){
+					success = cullHomoP(currSeq);
+					if(!success)				{	trashCode += 'h';	}
+				}
+				if(maxAmbig != -1){
+					success = cullAmbigs(currSeq);
+					if(!success)				{	trashCode += 'n';	}
+				}
+				
+				if(flip){	currSeq.reverseComplement();		currQual.flipQScores();	}		// should go last			
+				
+				if(trashCode.length() == 0){
+					currSeq.setAligned(currSeq.getUnaligned());
+					currSeq.printSequence(outFASTA);
+					currQual.printQScores(outQual);
 					
-					if(allFiles){
-						currSeq.printSequence(*fastaFileNames[group]);					
+					if(barcodes.size() != 0){
+						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[indexToFastaFile]);
+							
+							if(qFileName != ""){
+								currQual.printQScores(*qualFileNames[indexToFastaFile]);							
+							}
+						}
 					}
 				}
-			}
-			else{
-				currSeq.setName(currSeq.getName() + '|' + trashCode);
-				currSeq.setUnaligned(origSeq);
-				currSeq.printSequence(scrapFASTA);
+				else{
+					currSeq.setName(currSeq.getName() + '|' + trashCode);
+					currSeq.setUnaligned(origSeq);
+					currSeq.setAligned(origSeq);
+					currSeq.printSequence(scrapFASTA);
+					currQual.printQScores(scrapQual);
+				}
 			}
 			gobble(inFASTA);
+			gobble(qFile);
 		}
+		
 		inFASTA.close();
 		outFASTA.close();
 		scrapFASTA.close();
-		outGroups.close();
+		if (oligoFile != "") {	 outGroups.close();   }
+		if(qFileName != "")	{	qFile.close();	scrapQual.close(); outQual.close();	}
 		
 		for(int i=0;i<fastaFileNames.size();i++){
 			fastaFileNames[i]->close();
 			delete fastaFileNames[i];
 		}		
 		
-		for(int i=0;i<fastaFileNames.size();i++){
-			string seqName;
-			openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
-			ofstream outGroups;
-			openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
+		if(qFileName != ""){
+			for(int i=0;i<qualFileNames.size();i++){
+				qualFileNames[i]->close();
+				delete qualFileNames[i];
+			}		
+		}			
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+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;
+		int exitCommand = 1;
+		processIDS.clear();
+		
+		//loop through and create all the processes you want
+		while (process != processors) {
+			int pid = fork();
 			
-			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;	}	}
-			}
-			outGroups.close();
-			inFASTA.close();
+			if (pid > 0) {
+				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"), (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); }
 		}
 		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processors;i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
 		
-		return 0;		
+		return exitCommand;
+#endif		
 	}
 	catch(exception& e) {
-		errorOut(e, "TrimSeqsCommand", "execute");
+		m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 		exit(1);
 	}
 }
 
-//***************************************************************************************************************
-
-void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
-	
-	ifstream inOligos;
-	openInputFile(oligoFile, inOligos);
-
-	ofstream test;
-	
-	string type, oligo, group;
-	int index=0;
+/**************************************************************************************************/
 
-	while(!inOligos.eof()){
-		inOligos >> type;
+int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
+	try {
+		
+		lines.clear();
+		
+		vector<unsigned long int> positions;
+		
+		ifstream inFASTA;
+		openInputFile(filename, inFASTA);
+			
+		string input;
+		while(!inFASTA.eof()){	
+			input = getline(inFASTA);
 
-		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
+			if (input.length() != 0) {
+				if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+			}
 		}
+		inFASTA.close();
+		
+		int numFastaSeqs = positions.size();
+	
+		FILE * pFile;
+		unsigned long int size;
+		
+		//get num bytes in file
+		pFile = fopen (filename.c_str(),"rb");
+		if (pFile==NULL) perror ("Error opening file");
 		else{
-			inOligos >> oligo;
-			
-			for(int i=0;i<oligo.length();i++){
-				oligo[i] = toupper(oligo[i]);
-				if(oligo[i] == 'U')	{	oligo[i] = 'T';	}
-			}
-			
-			if(type == "forward"){
-				forPrimer.push_back(oligo);
+			fseek (pFile, 0, SEEK_END);
+			size=ftell (pFile);
+			fclose (pFile);
+		}
+		
+		int numSeqsPerProcessor = numFastaSeqs / processors;
+		
+		for (int i = 0; i < processors; i++) {
+
+			unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
+			if(i == processors - 1){
+				numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+			}else{  
+				unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 			}
-			else if(type == "reverse"){
-				revPrimer.push_back(oligo);
+			lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+		}
+		
+		return numFastaSeqs;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "setLines");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+
+void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
+	try {
+		ifstream inOligos;
+		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 if(type == "barcode"){
-				inOligos >> group;
-				barcodes[oligo]=index++;
-				groupVector.push_back(group);
+			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++){
+					oligo[i] = toupper(oligo[i]);
+					if(oligo[i] == 'U')	{	oligo[i] = 'T';	}
+				}
+				
+				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();  }
 					
-				if(allFiles){
-					outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
+					primers[oligo]=index; index++;
+					groupVector.push_back(group);
+					
+					if(allFiles){
+						outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+						if(qFileName != ""){
+							outQualVec.push_back((outputDir + getRootName(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 + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+							if(qFileName != ""){
+								filesToRemove.insert((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+							}
+						}else {
+							outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+							if(qFileName != ""){
+								outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+							}							
+						}
+					}
+
+				}
+				else if(type == "REVERSE"){
+					Sequence oligoRC("reverse", oligo);
+					oligoRC.reverseComplement();
+					revPrimer.push_back(oligoRC.getUnaligned());
+				}
+				else if(type == "BARCODE"){
+					inOligos >> group;
+					
+					//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){
+						outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+						outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+						if(qFileName != ""){
+							outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+							outputNames.push_back((outputDir + getRootName(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();  }
+			}
+			gobble(inOligos);
+		}
+		
+		inOligos.close();
+		
+		//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 + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+						outFASTAVec.push_back((outputDir + getRootName(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 + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+							outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+						}
+					}
 				}
 			}
 		}
+		
+		numFPrimers = primers.size();
+		numRPrimers = revPrimer.size();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "getOligos");
+		exit(1);
 	}
-	
-	inOligos.close();
-	
-	numFPrimers = forPrimer.size();
-	numRPrimers = revPrimer.size();
 }
-
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
-	
-	string rawSequence = seq.getUnaligned();
-	bool success = 0;	//guilty until proven innocent
-	
-	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;
+int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
+	try {
+		
+		string rawSequence = seq.getUnaligned();
+		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 = 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()));
+				
+				if(qual.getName() != ""){
+					qual.trimQScores(oligo.length(), -1);
+				}
+				
+				success = 0;
+				break;
+			}
 		}
 		
-		if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
-			group = it->second;
-			seq.setUnaligned(rawSequence.substr(oligo.length()));
-			success = 1;
-			break;
+		//if you found the barcode or if you don't want to allow for diffs
+//		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) {
+				map<string,int>::iterator it=barcodes.begin();
+
+				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();
+				
+				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,oligo.length()+bdiffs));
+				oligo = alignment->getSeqAAln();
+				string temp = alignment->getSeqBAln();
+		
+				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;
+				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;
+		
 	}
-	return success;
-	
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
+		exit(1);
+	}
+
 }
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripForward(Sequence& seq){
-	
-	string rawSequence = seq.getUnaligned();
-	bool success = 0;	//guilty until proven innocent
-	
-	for(int i=0;i<numFPrimers;i++){
-		string oligo = forPrimer[i];
+int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
+	try {
+		string rawSequence = seq.getUnaligned();
+		int success = pdiffs + 1;	//guilty until proven innocent
 		
-		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()));
+				if(qual.getName() != ""){
+					qual.trimQScores(oligo.length(), -1);
+					
+				}
+				success = 0;
+				break;
+			}
 		}
 
-		if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
-			seq.setUnaligned(rawSequence.substr(oligo.length()));
-			success = 1;
-			break;
+		//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 (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;
+			
+			for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
+				string oligo = it->first;
+//				int length = oligo.length();
+				
+				if(rawSequence.length() < maxLength){	
+					success = pdiffs + 100;
+					break;
+				}
+				
+				//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();
+				
+				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");
+		exit(1);
 	}
-	
-	return success;
-	
 }
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripReverse(Sequence& seq){
-	
-	string rawSequence = seq.getUnaligned();
-	bool success = 0;	//guilty until proven innocent
-	
-	for(int i=0;i<numRPrimers;i++){
-		string oligo = revPrimer[i];
+bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
+	try {
+		string rawSequence = seq.getUnaligned();
+		bool success = 0;	//guilty until proven innocent
 		
-		if(rawSequence.length() < oligo.length()){
-			success = 0;
-			break;
-		}
+		for(int i=0;i<numRPrimers;i++){
+			string oligo = revPrimer[i];
+			
+			if(rawSequence.length() < oligo.length()){
+				success = 0;
+				break;
+			}
+			
+			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;
+			}
+		}	
+		return success;
 		
-		if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
-			seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
-			success = 1;
-			break;
-		}
-	}	
-	return success;
-	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "stripReverse");
+		exit(1);
+	}
 }
 
 //***************************************************************************************************************
 
 bool TrimSeqsCommand::cullLength(Sequence& seq){
+	try {
 	
-	int length = seq.getNumBases();
-	bool success = 0;	//guilty until proven innocent
-	
-	if(length >= minLength && maxLength == 0)			{	success = 1;	}
-	else if(length >= minLength && length <= maxLength)	{	success = 1;	}
-	else												{	success = 0;	}
+		int length = seq.getNumBases();
+		bool success = 0;	//guilty until proven innocent
+		
+		if(length >= minLength && maxLength == 0)			{	success = 1;	}
+		else if(length >= minLength && length <= maxLength)	{	success = 1;	}
+		else												{	success = 0;	}
+		
+		return success;
 	
-	return success;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "cullLength");
+		exit(1);
+	}
 	
 }
 
 //***************************************************************************************************************
 
 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
-	
-	int longHomoP = seq.getLongHomoPolymer();
-	bool success = 0;	//guilty until proven innocent
-	
-	if(longHomoP <= maxHomoP){	success = 1;	}
-	else					{	success = 0;	}
-	
-	return success;
+	try {
+		int longHomoP = seq.getLongHomoPolymer();
+		bool success = 0;	//guilty until proven innocent
+		
+		if(longHomoP <= maxHomoP){	success = 1;	}
+		else					{	success = 0;	}
+		
+		return success;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
+		exit(1);
+	}
 	
 }
 
 //***************************************************************************************************************
 
 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
-	
-	int numNs = seq.getAmbigBases();
-	bool success = 0;	//guilty until proven innocent
-	
-	if(numNs <= maxAmbig)	{	success = 1;	}
-	else					{	success = 0;	}
-	
-	return success;
+	try {
+		int numNs = seq.getAmbigBases();
+		bool success = 0;	//guilty until proven innocent
+		
+		if(numNs <= maxAmbig)	{	success = 1;	}
+		else					{	success = 0;	}
+		
+		return success;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
+		exit(1);
+	}
 	
 }
 
 //***************************************************************************************************************
 
 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
-	
-	bool success = 1;
-	int length = oligo.length();
-	
-	for(int i=0;i<length;i++){
-		
-		if(oligo[i] != seq[i]){
-			if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')	{	success = 0;	}
-			else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))				{	success = 0;	}
-			else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))					{	success = 0;	}
-			else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))					{	success = 0;	}
-			else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))					{	success = 0;	}
-			else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))					{	success = 0;	}
-			else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))					{	success = 0;	}
-			else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))					{	success = 0;	}
-			else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))	{	success = 0;	}
-			else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))	{	success = 0;	}
-			else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))	{	success = 0;	}
-			else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))	{	success = 0;	}			
-			
-			if(success == 0)	{	break;	}
-		}
-		else{
-			success = 1;
+	try {
+		bool success = 1;
+		int length = oligo.length();
+		
+		for(int i=0;i<length;i++){
+			
+			if(oligo[i] != seq[i]){
+				if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')	{	success = 0; 	}
+				else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))				{	success = 0;	}
+				else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))					{	success = 0;	}
+				else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))					{	success = 0;	}
+				else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))					{	success = 0;	}
+				else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))					{	success = 0;	}
+				else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))					{	success = 0;	}
+				else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))					{	success = 0;	}
+				else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))	{	success = 0;	}
+				else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))	{	success = 0;	}
+				else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))	{	success = 0;	}
+				else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))	{	success = 0;	}			
+				
+				if(success == 0)	{	break;	 }
+			}
+			else{
+				success = 1;
+			}
 		}
+		
+		return success;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+		exit(1);
 	}
-	
-	return success;
-}
 
+}
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
-	
-	string rawSequence = seq.getUnaligned();
-	int seqLength = rawSequence.length();
-	string name;
-	
-	qFile >> name;
-	if(name.substr(1) != seq.getName())	{	mothurOut("sequence name mismatch btwn fasta and qual file"); 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;
+int TrimSeqsCommand::countDiffs(string oligo, string seq){
+	try {
 
-		if(score <= qThreshold){
-			end = i;
-			break;
+		int length = oligo.length();
+		int countDiffs = 0;
+		
+		for(int i=0;i<length;i++){
+								
+			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++;	}
+				else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))					{	countDiffs++;	}
+				else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))					{	countDiffs++;	}
+				else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))					{	countDiffs++;	}
+				else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))					{	countDiffs++;	}
+				else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))					{	countDiffs++;	}
+				else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))					{	countDiffs++;	}
+				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++;	}	
+			}
+			
 		}
+		
+		return countDiffs;
 	}
-	for(int i=end+1;i<seqLength;i++){
-		qFile >> score;
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "countDiffs");
+		exit(1);
 	}
 
-	seq.setUnaligned(rawSequence.substr(0,end));
-
-	return 1;
 }
-
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
-	
-	string rawSequence = seq.getUnaligned();
-	int seqLength = seq.getNumBases();
-	bool success = 0;	//guilty until proven innocent
-	string name;
-	
-	qFile >> name;
-	if(name.substr(1) != seq.getName())	{	mothurOut("sequence name mismatch btwn fasta and qual file"); 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;
-}
+//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);
+//	}
+//}
 
+//***************************************************************************************************************