X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=392f5877d9099308593d0cba26a8ff7baddd1d3b;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=ea049544c818f217f84931577b604af9e24e4d6e;hpb=85af0d7ce5839dfd39981811f149157c305dd31a;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index ea04954..392f587 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -8,53 +8,64 @@
  */
 
 #include "seqerrorcommand.h"
+#include "reportfile.h"
+#include "qualityscores.h"
+#include "refchimeratest.h"
 
 //**********************************************************************************************************************
-vector<string> SeqErrorCommand::getValidParameters(){	
+vector<string> SeqErrorCommand::setParameters(){	
 	try {
-		string Array[] =  {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery);
+		CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference);
+		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile);
+		CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+		CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
+		CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SeqErrorCommand", "getValidParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-SeqErrorCommand::SeqErrorCommand(){	
-	try {
-		abort = true;
-		//initialize outputTypes
-		vector<string> tempOutNames;
-		outputTypes["error"] = tempOutNames;
-		outputTypes["count"] = tempOutNames;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
+		m->errorOut(e, "SeqErrorCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> SeqErrorCommand::getRequiredParameters(){	
+string SeqErrorCommand::getHelpString(){	
 	try {
-		string Array[] =  {"query","reference"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
+		string helpString = "";
+		helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
+		helpString += "Example seq.error(...).\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+		helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SeqErrorCommand", "getRequiredParameters");
+		m->errorOut(e, "SeqErrorCommand", "getHelpString");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> SeqErrorCommand::getRequiredFiles(){	
+SeqErrorCommand::SeqErrorCommand(){	
 	try {
-		vector<string> myArray;
-		return myArray;
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["error.summary"] = tempOutNames;
+		outputTypes["error.seq"] = tempOutNames;
+		outputTypes["error.quality"] = tempOutNames;
+		outputTypes["error.qual.forward"] = tempOutNames;
+		outputTypes["error.qual.reverse"] = tempOutNames;
+		outputTypes["error.forward"] = tempOutNames;
+		outputTypes["error.reverse"] = tempOutNames;
+		outputTypes["error.count"] = tempOutNames;
+		outputTypes["error.matrix"] = tempOutNames;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SeqErrorCommand", "getRequiredFiles");
+		m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
 		exit(1);
 	}
 }
@@ -63,20 +74,14 @@ vector<string> SeqErrorCommand::getRequiredFiles(){
 SeqErrorCommand::SeqErrorCommand(string option)  {
 	try {
 		
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			string temp;
-			
-			//valid paramters for this command
-			string AlignArray[] =  {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
-			
-//need to implement name file option
-			
-			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -91,20 +96,28 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			
 			//initialize outputTypes
 			vector<string> tempOutNames;
-			outputTypes["error"] = tempOutNames;
-			outputTypes["count"] = tempOutNames;
+			outputTypes["error.summary"] = tempOutNames;
+			outputTypes["error.seq"] = tempOutNames;
+			outputTypes["error.quality"] = tempOutNames;
+			outputTypes["error.qual.forward"] = tempOutNames;
+			outputTypes["error.qual.reverse"] = tempOutNames;
+			outputTypes["error.forward"] = tempOutNames;
+			outputTypes["error.reverse"] = tempOutNames;
+			outputTypes["error.count"] = tempOutNames;
+			outputTypes["error.matrix"] = tempOutNames;
+
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
 			if (inputDir == "not found"){	inputDir = "";		}
 			else {
 				string path;
-				it = parameters.find("query");
+				it = parameters.find("fasta");
 				//user has given a template file
 				if(it != parameters.end()){ 
 					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["query"] = inputDir + it->second;		}
+					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
 				}
 				
 				it = parameters.find("reference");
@@ -116,27 +129,62 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 				}
 				
 				it = parameters.find("name");
-				//user has given a template file
+				//user has given a names file
 				if(it != parameters.end()){ 
 					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["name"] = inputDir + it->second;		}
 				}
+
+				it = parameters.find("qfile");
+				//user has given a quality score file
+				if(it != parameters.end()){ 
+					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;		}
+				}
+				
+				it = parameters.find("report");
+				//user has given a alignment report file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["report"] = inputDir + it->second;		}
+				}
 				
 			}
 			//check for required parameters
-			queryFileName = validParameter.validFile(parameters, "query", true);
-			if (queryFileName == "not found") { m->mothurOut("query is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
+			queryFileName = validParameter.validFile(parameters, "fasta", true);
+			if (queryFileName == "not found") { 
+				queryFileName = m->getFastaFile(); 
+				if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}
 			else if (queryFileName == "not open") { abort = true; }	
 			
 			referenceFileName = validParameter.validFile(parameters, "reference", true);
 			if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
 			else if (referenceFileName == "not open") { abort = true; }	
 			
-			//if the user changes the output directory command factory will send this info to us in the output parameter 
+
+			//check for optional parameters
 			namesFileName = validParameter.validFile(parameters, "name", true);
 			if(namesFileName == "not found"){	namesFileName = "";	}
-			cout << namesFileName << endl;
+			else if (namesFileName == "not open") { namesFileName = ""; abort = true; }	
+			
+			qualFileName = validParameter.validFile(parameters, "qfile", true);
+			if(qualFileName == "not found"){	qualFileName = "";	}
+			else if (qualFileName == "not open") { qualFileName = ""; abort = true; }	
+
+			reportFileName = validParameter.validFile(parameters, "report", true);
+			if(reportFileName == "not found"){	reportFileName = "";	}
+			else if (reportFileName == "not open") { reportFileName = ""; abort = true; }	
+			
+			if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
+				m->mothurOut("if you use either a qual file or a report file, you have to have both.");
+				m->mothurOutEndLine();
+				abort = true; 
+			}
 			
 			outputDir = validParameter.validFile(parameters, "outputdir", false);
 			if (outputDir == "not found"){	
@@ -148,17 +196,12 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found") { temp = "1.00"; }
 			convert(temp, threshold);  
-						
-			errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
-			m->openOutputFile(errorSummaryFileName, errorSummaryFile);
-			outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
-			printErrorHeader();
-
-			errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
-			m->openOutputFile(errorSeqFileName, errorSeqFile);
-			outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
-			printErrorHeader();
 			
+			temp = validParameter.validFile(parameters, "ignorechimeras", false);	if (temp == "not found") { temp = "1"; }
+			convert(temp, ignoreChimeras);  
+
+			substitutionMatrix.resize(6);
+			for(int i=0;i<6;i++){	substitutionMatrix[i].resize(6,0);	}
 		}
 	}
 	catch(exception& e) {
@@ -166,37 +209,22 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 		exit(1);
 	}
 }
-
-//**********************************************************************************************************************
-
-void SeqErrorCommand::help(){
-	try {
-		m->mothurOut("The seq.error command reads a query alignment file and a reference alignment file and creates .....\n");
-		
-		
-		
-		m->mothurOut("Example seq.error(...).\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/seq.error .\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SeqErrorCommand", "help");
-		exit(1);
-	}
-}
-
-//***************************************************************************************************************
-
-SeqErrorCommand::~SeqErrorCommand(){
-	errorSummaryFile.close();	
-	errorSeqFile.close();	
-}
-
 //***************************************************************************************************************
 
 int SeqErrorCommand::execute(){
 	try{
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+
+		maxLength = 2000;
+		
+		string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
+		m->openOutputFile(errorSummaryFileName, errorSummaryFile);
+		outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
+		printErrorHeader();
+		
+		string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
+		m->openOutputFile(errorSeqFileName, errorSeqFile);
+		outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
 
 		getReferences();	//read in reference sequences - make sure there's no ambiguous bases
 
@@ -205,7 +233,27 @@ int SeqErrorCommand::execute(){
 		
 		ifstream queryFile;
 		m->openInputFile(queryFileName, queryFile);
-				
+		
+		ifstream reportFile;
+		ifstream qualFile;
+
+		ReportFile report;
+		QualityScores quality;
+		vector<vector<int> > qualForwardMap;
+		vector<vector<int> > qualReverseMap;
+		
+		if(qualFileName != "" && reportFileName != ""){
+			m->openInputFile(qualFileName, qualFile);
+			report = ReportFile(reportFile, reportFileName);
+			
+			qualForwardMap.resize(maxLength);
+			qualReverseMap.resize(maxLength);
+			for(int i=0;i<maxLength;i++){
+				qualForwardMap[i].assign(41,0);
+				qualReverseMap[i].assign(41,0);
+			}				
+		}
+		
 		int totalBases = 0;
 		int totalMatches = 0;
 		
@@ -214,32 +262,85 @@ int SeqErrorCommand::execute(){
 		int numSeqs = 0;
 		
 		map<string, int>::iterator it;
+		map<char, vector<int> > qScoreErrorMap;
+		qScoreErrorMap['m'].assign(41, 0);
+		qScoreErrorMap['s'].assign(41, 0);
+		qScoreErrorMap['i'].assign(41, 0);
+		qScoreErrorMap['a'].assign(41, 0);
+		
+		map<char, vector<int> > errorForward;
+		errorForward['m'].assign(maxLength,0);
+		errorForward['s'].assign(maxLength,0);
+		errorForward['i'].assign(maxLength,0);
+		errorForward['d'].assign(maxLength,0);
+		errorForward['a'].assign(maxLength,0);
+		
+		map<char, vector<int> > errorReverse;
+		errorReverse['m'].assign(maxLength,0);
+		errorReverse['s'].assign(maxLength,0);
+		errorReverse['i'].assign(maxLength,0);
+		errorReverse['d'].assign(maxLength,0);
+		errorReverse['a'].assign(maxLength,0);	
+		
+
+		string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
+		RefChimeraTest chimeraTest(referenceSeqs, errorChimeraFileName);
+		outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
+		
+		vector<string> megaAlignVector(numRefs, "");
+
+		int index = 0;
+		bool ignoreSeq = 0;
 		
 		while(queryFile){
-			Compare minCompare;
-			
+
+			if (m->control_pressed) { errorSummaryFile.close();	errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+		
 			Sequence query(queryFile);
 			
-			for(int i=0;i<numRefs;i++){
-				Compare currCompare = getErrors(query, referenceSeqs[i]);
-				
-				if(currCompare.errorRate < minCompare.errorRate){
-					minCompare = currCompare;
-				}
-				
-			}
+			int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
+			int closestRefIndex = chimeraTest.getClosestRefIndex();
+
+			if(numParentSeqs > 1 && ignoreChimeras == 1)	{	ignoreSeq = 1;	}
+			else											{	ignoreSeq = 0;	}
 
+			Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
+			
 			if(namesFileName != ""){
 				it = weights.find(query.getName());
 				minCompare.weight = it->second;
 			}
-			else {
-				minCompare.weight = 1;
+			else{	minCompare.weight = 1;	}
+
+			printErrorData(minCompare, numParentSeqs);
+		
+			if(!ignoreSeq){
+
+				for(int i=0;i<minCompare.sequence.length();i++){
+					char letter = minCompare.sequence[i];
+
+					errorForward[letter][i] += minCompare.weight;
+					errorReverse[letter][minCompare.total-i-1] += minCompare.weight;				
+				}
 			}
 
-			printErrorData(minCompare);
+			if(qualFileName != "" && reportFileName != ""){
+				report = ReportFile(reportFile);
+				
+//				int origLength = report.getQueryLength();
+				int startBase = report.getQueryStart();
+				int endBase = report.getQueryEnd();
+
+				quality = QualityScores(qualFile);
 
-			if(minCompare.errorRate < threshold){
+				if(!ignoreSeq){
+					quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
+					quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
+					quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
+				}
+			}			
+
+			if(minCompare.errorRate < threshold && !ignoreSeq){
 				totalBases += (minCompare.total * minCompare.weight);
 				totalMatches += minCompare.matches * minCompare.weight;
 				if(minCompare.mismatches > maxMismatch){
@@ -248,28 +349,59 @@ int SeqErrorCommand::execute(){
 				}				
 				misMatchCounts[minCompare.mismatches] += minCompare.weight;
 				numSeqs++;
+				
+				megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
 			}
+
+			index++;
 			
+			if(index % 1000 == 0){	m->mothurOut(toString(index) + '\n');	}
 		}
 		queryFile.close();
+		errorSummaryFile.close();	
+		errorSeqFile.close();
+
+		if(qualFileName != "" && reportFileName != ""){		
+			printErrorQuality(qScoreErrorMap);
+			printQualityFR(qualForwardMap, qualReverseMap);
+		}
 		
-		int total = 0;
-		
+		printErrorFRFile(errorForward, errorReverse);
 		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
 		string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
 		ofstream errorCountFile;
 		m->openOutputFile(errorCountFileName, errorCountFile);
 		outputNames.push_back(errorCountFileName);  outputTypes["error.count"].push_back(errorCountFileName);
-		
-		m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n\n");
+		m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
 		m->mothurOut("Errors\tSequences\n");
-		
-		errorCountFile << "Errors\tSequences\n";
-		
+		errorCountFile << "Errors\tSequences\n";		
 		for(int i=0;i<misMatchCounts.size();i++){
 			m->mothurOut(toString(i) + '\t' + toString(misMatchCounts[i]) + '\n');
 			errorCountFile << i << '\t' << misMatchCounts[i] << endl;
 		}
+		errorCountFile.close();
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+		printSubMatrix();
+				
+		string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
+		ofstream megAlignmentFile;
+		m->openOutputFile(megAlignmentFileName, megAlignmentFile);
+		outputNames.push_back(megAlignmentFileName);  outputTypes["error.ref-query"].push_back(megAlignmentFileName);
+		
+		for(int i=0;i<numRefs;i++){
+			megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
+			megAlignmentFile << megaAlignVector[i] << endl;
+		}
+		
+		
+		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;	
 	}
@@ -287,20 +419,38 @@ void SeqErrorCommand::getReferences(){
 		ifstream referenceFile;
 		m->openInputFile(referenceFileName, referenceFile);
 		
+		int numAmbigSeqs = 0;
+		
+		int maxStartPos = 0;
+		int minEndPos = 100000;
+		
 		while(referenceFile){
 			Sequence currentSeq(referenceFile);
 			int numAmbigs = currentSeq.getAmbigBases();
+			if(numAmbigs > 0){	numAmbigSeqs++;	}
 			
-			if(numAmbigs != 0){
-				m->mothurOut("Warning: " + toString(currentSeq.getName()) + " has " + toString(numAmbigs) + " ambiguous bases, these bases will be removed\n");
-				currentSeq.removeAmbigBases();
-			}
+//			int startPos = currentSeq.getStartPos();
+//			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
+//
+//			int endPos = currentSeq.getEndPos();
+//			if(endPos < minEndPos)		{	minEndPos = endPos;		}
 			referenceSeqs.push_back(currentSeq);
+				
 			m->gobble(referenceFile);
 		}
+		referenceFile.close();
 		numRefs = referenceSeqs.size();
+
+		
+		for(int i=0;i<numRefs;i++){
+			referenceSeqs[i].padToPos(maxStartPos);
+			referenceSeqs[i].padFromPos(minEndPos);
+		}
+		
+		if(numAmbigSeqs != 0){
+			m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
+		}		
 		
-		referenceFile.close();
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SeqErrorCommand", "getReferences");
@@ -320,12 +470,11 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 		string q = query.getAligned();
 		string r = reference.getAligned();
 
-		
 		int started = 0;
 		Compare errors;
 
 		for(int i=0;i<alignLength;i++){
-			if(q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){			//	no missing data and no double gaps
+			if(r[i] != 'N' && q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){			//	no missing data and no double gaps
 				started = 1;
 				
 				if(q[i] == 'A'){
@@ -376,7 +525,6 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 				if(started == 1){	break;	}
 			}
 			else if(q[i] != '.' && r[i] == '.'){		//	query extends beyond reference
-				m->mothurOut("Warning: " + toString(query.getName()) + " extend beyond " + toString(reference.getName()) + ".  Ignoring the extra bases in the query\n");
 				if(started == 1){	break;	}
 			}
 			else if(q[i] == '.' && r[i] == '.'){		//	both are missing data
@@ -422,7 +570,7 @@ void SeqErrorCommand::printErrorHeader(){
 	try {
 		errorSummaryFile << "query\treference\tweight\t";
 		errorSummaryFile << "AA\tAT\tAG\tAC\tTA\tTT\tTG\tTC\tGA\tGT\tGG\tGC\tCA\tCT\tCG\tCC\tNA\tNT\tNG\tNC\tAi\tTi\tGi\tCi\tNi\tdA\tdT\tdG\tdC\t";
-		errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\n";
+		errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\tnumparents\n";
 		
 		errorSummaryFile << setprecision(6);
 		errorSummaryFile.setf(ios::fixed);
@@ -435,24 +583,64 @@ void SeqErrorCommand::printErrorHeader(){
 
 //***************************************************************************************************************
 
-void SeqErrorCommand::printErrorData(Compare error){
+void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs){
 	try {
+
 		errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
 		errorSummaryFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
 		errorSummaryFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
 		errorSummaryFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
 		errorSummaryFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
 		errorSummaryFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
-		errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t' ;
+		errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t';
 		errorSummaryFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
 		
 		errorSummaryFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t';			//insertions
 		errorSummaryFile << error.dA + error.dT + error.dG + error.dC << '\t';			//deletions
 		errorSummaryFile << error.mismatches - (error.Ai + error.Ti + error.Gi + error.Ci) - (error.dA + error.dT + error.dG + error.dC) - (error.NA + error.NT + error.NG + error.NC + error.Ni) << '\t';	//substitutions
 		errorSummaryFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t';	//ambiguities
-		errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << endl;
-		
+		errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << '\t' << numParentSeqs << endl;
+
 		errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
+		
+		int a=0;		int t=1;		int g=2;		int c=3;
+		int gap=4;		int n=5;
+
+		if(numParentSeqs == 1 || ignoreChimeras == 0){
+			substitutionMatrix[a][a] += error.weight * error.AA;
+			substitutionMatrix[a][t] += error.weight * error.TA;
+			substitutionMatrix[a][g] += error.weight * error.GA;
+			substitutionMatrix[a][c] += error.weight * error.CA;
+			substitutionMatrix[a][gap] += error.weight * error.dA;
+			substitutionMatrix[a][n] += error.weight * error.NA;
+			
+			substitutionMatrix[t][a] += error.weight * error.AT;
+			substitutionMatrix[t][t] += error.weight * error.TT;
+			substitutionMatrix[t][g] += error.weight * error.GT;
+			substitutionMatrix[t][c] += error.weight * error.CT;
+			substitutionMatrix[t][gap] += error.weight * error.dT;
+			substitutionMatrix[t][n] += error.weight * error.NT;
+
+			substitutionMatrix[g][a] += error.weight * error.AG;
+			substitutionMatrix[g][t] += error.weight * error.TG;
+			substitutionMatrix[g][g] += error.weight * error.GG;
+			substitutionMatrix[g][c] += error.weight * error.CG;
+			substitutionMatrix[g][gap] += error.weight * error.dG;
+			substitutionMatrix[g][n] += error.weight * error.NG;
+
+			substitutionMatrix[c][a] += error.weight * error.AC;
+			substitutionMatrix[c][t] += error.weight * error.TC;
+			substitutionMatrix[c][g] += error.weight * error.GC;
+			substitutionMatrix[c][c] += error.weight * error.CC;
+			substitutionMatrix[c][gap] += error.weight * error.dC;
+			substitutionMatrix[c][n] += error.weight * error.NC;
+
+			substitutionMatrix[gap][a] += error.weight * error.Ai;
+			substitutionMatrix[gap][t] += error.weight * error.Ti;
+			substitutionMatrix[gap][g] += error.weight * error.Gi;
+			substitutionMatrix[gap][c] += error.weight * error.Ci;
+			substitutionMatrix[gap][n] += error.weight * error.Ni;
+		}
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SeqErrorCommand", "printErrorData");
@@ -462,9 +650,174 @@ void SeqErrorCommand::printErrorData(Compare error){
 
 //***************************************************************************************************************
 
+void SeqErrorCommand::printSubMatrix(){
+	try {
+		string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
+		ofstream subMatrixFile;
+		m->openOutputFile(subMatrixFileName, subMatrixFile);
+		outputNames.push_back(subMatrixFileName);  outputTypes["error.matrix"].push_back(subMatrixFileName);
+		vector<string> bases(6);
+		bases[0] = "A";
+		bases[1] = "T";
+		bases[2] = "G";
+		bases[3] = "C";
+		bases[4] = "Gap";
+		bases[5] = "N";
+		vector<int> refSums(5,1);
+
+		for(int i=0;i<5;i++){
+			subMatrixFile << "\tr" << bases[i];
+			
+			for(int j=0;j<6;j++){
+				refSums[i] += substitutionMatrix[i][j];				
+			}
+		}
+		subMatrixFile << endl;
+		
+		for(int i=0;i<6;i++){
+			subMatrixFile << 'q' << bases[i];
+			for(int j=0;j<5;j++){
+				subMatrixFile << '\t' << substitutionMatrix[j][i];				
+			}
+			subMatrixFile << endl;
+		}
+
+		subMatrixFile << "total";
+		for(int i=0;i<5;i++){
+			subMatrixFile << '\t' << refSums[i];
+		}
+		subMatrixFile << endl;
+		subMatrixFile.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SeqErrorCommand", "printSubMatrix");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+
+void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
+	try{
+		string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward";
+		ofstream errorForwardFile;
+		m->openOutputFile(errorForwardFileName, errorForwardFile);
+		outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
+
+		errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
+		for(int i=0;i<maxLength;i++){
+			float match = (float)errorForward['m'][i];
+			float subst = (float)errorForward['s'][i];
+			float insert = (float)errorForward['i'][i];
+			float del = (float)errorForward['d'][i];
+			float amb = (float)errorForward['a'][i];
+			float total = match + subst + insert + del + amb;
+			if(total == 0){	break;	}
+			errorForwardFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
+		}
+		errorForwardFile.close();
+
+		string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
+		ofstream errorReverseFile;
+		m->openOutputFile(errorReverseFileName, errorReverseFile);
+		outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
+
+		errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
+		for(int i=0;i<maxLength;i++){
+			float match = (float)errorReverse['m'][i];
+			float subst = (float)errorReverse['s'][i];
+			float insert = (float)errorReverse['i'][i];
+			float del = (float)errorReverse['d'][i];
+			float amb = (float)errorReverse['a'][i];
+			float total = match + subst + insert + del + amb;
+			if(total == 0){	break;	}
+			errorReverseFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
+		}
+		errorReverseFile.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
+		exit(1);
+	}
+}
+
+//***************************************************************************************************************
+
+void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
+	try{
+
+		string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
+		ofstream errorQualityFile;
+		m->openOutputFile(errorQualityFileName, errorQualityFile);
+		outputNames.push_back(errorQualityFileName);  outputTypes["error.quality"].push_back(errorQualityFileName);
+
+		errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
+		for(int i=0;i<41;i++){
+			errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
+		}
+		errorQualityFile.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
+		exit(1);
+	}
+}
+
+
+//***************************************************************************************************************
+
+void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
 
+	try{
+		int numRows = 0;
+		int numColumns = qualForwardMap[0].size();
+
+		for(int i=0;i<qualForwardMap.size();i++){
+			for(int j=0;j<numColumns;j++){
+				if(qualForwardMap[i][j] != 0){
+					if(numRows < i)		{	numRows = i+20;		}
+				}
+			}
+		}
 
+		string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward";
+		ofstream qualityForwardFile;
+		m->openOutputFile(qualityForwardFileName, qualityForwardFile);
+		outputNames.push_back(qualityForwardFileName);  outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
 
+		for(int i=0;i<numColumns;i++){	qualityForwardFile << '\t' << i;	}	qualityForwardFile << endl;
 
+		for(int i=0;i<numRows;i++){
+			qualityForwardFile << i+1;
+			for(int j=0;j<numColumns;j++){
+				qualityForwardFile << '\t' << qualForwardMap[i][j];
+			}
 
+			qualityForwardFile << endl;
+		}
+		qualityForwardFile.close();
 
+		
+		string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse";
+		ofstream qualityReverseFile;
+		m->openOutputFile(qualityReverseFileName, qualityReverseFile);
+		outputNames.push_back(qualityReverseFileName);  outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
+		
+		for(int i=0;i<numColumns;i++){	qualityReverseFile << '\t' << i;	}	qualityReverseFile << endl;
+		for(int i=0;i<numRows;i++){
+			
+			qualityReverseFile << i+1;
+			for(int j=0;j<numColumns;j++){
+				qualityReverseFile << '\t' << qualReverseMap[i][j];
+			}
+			qualityReverseFile << endl;
+		}
+		qualityReverseFile.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
+		exit(1);
+	}
+	
+}
+
+//***************************************************************************************************************