X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=d8ebe50fb11859367256a28286dec9789cc70d36;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=6ce944ef21189948519310e372907580d8ac1400;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 6ce944e..d8ebe50 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -13,6 +13,7 @@
 #include "refchimeratest.h"
 #include "filterseqscommand.h"
 
+
 //**********************************************************************************************************************
 vector<string> SeqErrorCommand::setParameters(){	
 	try {
@@ -24,6 +25,7 @@ vector<string> SeqErrorCommand::setParameters(){
 		CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
 		CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
 		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+		CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -41,6 +43,15 @@ string SeqErrorCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
+		helpString += "The fasta parameter...\n";
+		helpString += "The reference parameter...\n";
+		helpString += "The qfile parameter...\n";
+		helpString += "The report parameter...\n";
+		helpString += "The name parameter...\n";
+		helpString += "The ignorechimeras parameter...\n";
+		helpString += "The threshold parameter...\n";
+		helpString += "The processors parameter...\n";
+		helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
 		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";
@@ -55,6 +66,7 @@ string SeqErrorCommand::getHelpString(){
 SeqErrorCommand::SeqErrorCommand(){	
 	try {
 		abort = true; calledHelp = true; 
+		setParameters();
 		vector<string> tempOutNames;
 		outputTypes["error.summary"] = tempOutNames;
 		outputTypes["error.seq"] = tempOutNames;
@@ -77,6 +89,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 	try {
 		
 		abort = false; calledHelp = false;   
+		rdb = ReferenceDB::getInstance();
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
@@ -163,22 +176,24 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 				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; }	
+			else if (queryFileName == "not open") { queryFileName = ""; abort = true; }	
+			else { m->setFastaFile(queryFileName); }
 			
 			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; }	
 			
-
 			//check for optional parameters
 			namesFileName = validParameter.validFile(parameters, "name", true);
 			if(namesFileName == "not found"){	namesFileName = "";	}
 			else if (namesFileName == "not open") { namesFileName = ""; abort = true; }	
+			else { m->setNameFile(namesFileName); }
 			
 			qualFileName = validParameter.validFile(parameters, "qfile", true);
 			if(qualFileName == "not found"){	qualFileName = "";	}
 			else if (qualFileName == "not open") { qualFileName = ""; abort = true; }	
-
+			else { m->setQualFile(qualFileName); }
+			
 			reportFileName = validParameter.validFile(parameters, "report", true);
 			if(reportFileName == "not found"){	reportFileName = "";	}
 			else if (reportFileName == "not open") { reportFileName = ""; abort = true; }	
@@ -198,17 +213,44 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			//check for optional parameter and set defaults
 			// ...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);  
+			m->mothurConvert(temp, threshold);  
+			
+			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
+			save = m->isTrue(temp); 
+			rdb->save = save; 
+			if (save) { //clear out old references
+				rdb->clearMemory();	
+			}
+			
+			//this has to go after save so that if the user sets save=t and provides no reference we abort
+			referenceFileName = validParameter.validFile(parameters, "reference", true);
+			if (referenceFileName == "not found") { 
+				//check for saved reference sequences
+				if (rdb->referenceSeqs.size() != 0) {
+					referenceFileName = "saved";
+				}else {
+					m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); 
+					m->mothurOutEndLine();
+					abort = true; 
+				}
+			}else if (referenceFileName == "not open") { abort = true; }	
+			else {	if (save) {	rdb->setSavedReference(referenceFileName);	}	}
+			
 			
 			temp = validParameter.validFile(parameters, "ignorechimeras", false);	if (temp == "not found") { temp = "T"; }
 			ignoreChimeras = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 
 			substitutionMatrix.resize(6);
 			for(int i=0;i<6;i++){	substitutionMatrix[i].resize(6,0);	}
+			
+			if ((namesFileName == "") && (queryFileName != "")){
+				vector<string> files; files.push_back(queryFileName); 
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {
@@ -240,9 +282,9 @@ int SeqErrorCommand::execute(){
 
 		if(namesFileName != ""){	weights = getWeights();	}
 		
-		vector<unsigned long int> fastaFilePos;
-		vector<unsigned long int> qFilePos;
-		vector<unsigned long int> reportFilePos;
+		vector<unsigned long long> fastaFilePos;
+		vector<unsigned long long> qFilePos;
+		vector<unsigned long long> reportFilePos;
 		
 		setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos);
 		
@@ -273,7 +315,7 @@ int SeqErrorCommand::execute(){
 		
 		printErrorFRFile(errorForward, errorReverse);
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
 		string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
 		ofstream errorCountFile;
@@ -288,7 +330,7 @@ int SeqErrorCommand::execute(){
 		}
 		errorCountFile.close();
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
 		printSubMatrix();
 				
@@ -445,11 +487,11 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 			m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 			
 			m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName);
-			remove((summaryFileName + toString(processIDS[i]) + ".temp").c_str());
+			m->mothurRemove((summaryFileName + toString(processIDS[i]) + ".temp"));
 			m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName);
-			remove((errorOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+			m->mothurRemove((errorOutputFileName + toString(processIDS[i]) + ".temp"));
 			m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName);
-			remove((chimeraOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+			m->mothurRemove((chimeraOutputFileName + toString(processIDS[i]) + ".temp"));
 			
 			ifstream in;
 			string tempFile =  filename + toString(processIDS[i]) + ".info.temp";
@@ -544,7 +586,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 			}
 			m->gobble(in);
 			
-			in.close(); remove(tempFile.c_str());
+			in.close(); m->mothurRemove(tempFile);
 			
 		}
 #endif		
@@ -655,8 +697,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 				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;				
+					if(letter != 'r'){
+						errorForward[letter][i] += minCompare.weight;
+						errorReverse[letter][minCompare.total-i-1] += minCompare.weight;				
+					}
 				}
 			}
 			
@@ -670,9 +714,13 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 				quality = QualityScores(qualFile);
 				
 				if(!ignoreSeq){
+//					cout << query.getName() << '\t';
+					
 					quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
 					quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
 					quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
+
+//					cout << endl;
 				}
 			}			
 			
@@ -692,7 +740,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 			index++;
 			
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				unsigned long int pos = queryFile.tellg();
+				unsigned long long pos = queryFile.tellg();
 				if ((pos == -1) || (pos >= line.end)) { break; }
 			#else
 				if (queryFile.eof()) { break; }
@@ -719,32 +767,59 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 
 void SeqErrorCommand::getReferences(){
 	try {
-		
-		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++;	}
-			
-//			int startPos = currentSeq.getStartPos();
-//			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
-//
-//			int endPos = currentSeq.getEndPos();
-//			if(endPos < minEndPos)		{	minEndPos = endPos;		}
-			referenceSeqs.push_back(currentSeq);
+		if (referenceFileName == "saved") {
+			int start = time(NULL);
+			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
+			
+			for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
+				int numAmbigs = rdb->referenceSeqs[i].getAmbigBases();
+				if(numAmbigs > 0){	numAmbigSeqs++;	}
+				
+				//			int startPos = rdb->referenceSeqs[i].getStartPos();
+				//			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
+				//
+				//			int endPos = rdb->referenceSeqs[i].getEndPos();
+				//			if(endPos < minEndPos)		{	minEndPos = endPos;		}				
+				
+				referenceSeqs.push_back(rdb->referenceSeqs[i]);
+			}
+			referenceFileName = rdb->getSavedReference();
+			
+			m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
+		
+		}else {
+			int start = time(NULL);
+
+			ifstream referenceFile;
+			m->openInputFile(referenceFileName, referenceFile);
+			
+			while(referenceFile){
+				Sequence currentSeq(referenceFile);
+				int numAmbigs = currentSeq.getAmbigBases();
+				if(numAmbigs > 0){	numAmbigSeqs++;	}
 				
-			m->gobble(referenceFile);
+	//			int startPos = currentSeq.getStartPos();
+	//			if(startPos > maxStartPos)	{	maxStartPos = startPos;	}
+	//
+	//			int endPos = currentSeq.getEndPos();
+	//			if(endPos < minEndPos)		{	minEndPos = endPos;		}
+				referenceSeqs.push_back(currentSeq);
+				
+				if (rdb->save) { rdb->referenceSeqs.push_back(currentSeq); }
+					
+				m->gobble(referenceFile);
+			}
+			referenceFile.close();
+			
+			m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
 		}
-		referenceFile.close();
+		
 		numRefs = referenceSeqs.size();
-
 		
 		for(int i=0;i<numRefs;i++){
 			referenceSeqs[i].padToPos(maxStartPos);
@@ -753,7 +828,7 @@ void SeqErrorCommand::getReferences(){
 		
 		if(numAmbigSeqs != 0){
 			m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
-		}		
+		}	
 		
 	}
 	catch(exception& e) {
@@ -778,53 +853,65 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 		Compare errors;
 
 		for(int i=0;i<alignLength;i++){
-			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'){
-					if(r[i] == 'A'){	errors.AA++;	errors.matches++;	errors.sequence += 'm';	}
-					if(r[i] == 'T'){	errors.AT++;	errors.sequence += 's';	}
-					if(r[i] == 'G'){	errors.AG++;	errors.sequence += 's';	}
-					if(r[i] == 'C'){	errors.AC++;	errors.sequence += 's';	}
-					if(r[i] == '-'){	errors.Ai++;	errors.sequence += 'i';	}
-				}
-				else if(q[i] == 'T'){
-					if(r[i] == 'A'){	errors.TA++;	errors.sequence += 's';	}
-					if(r[i] == 'T'){	errors.TT++;	errors.matches++;	errors.sequence += 'm';	}
-					if(r[i] == 'G'){	errors.TG++;	errors.sequence += 's';	}
-					if(r[i] == 'C'){	errors.TC++;	errors.sequence += 's';	}
-					if(r[i] == '-'){	errors.Ti++;	errors.sequence += 'i';	}
-				}
-				else if(q[i] == 'G'){
-					if(r[i] == 'A'){	errors.GA++;	errors.sequence += 's';	}
-					if(r[i] == 'T'){	errors.GT++;	errors.sequence += 's';	}
-					if(r[i] == 'G'){	errors.GG++;	errors.matches++;	errors.sequence += 'm';	}
-					if(r[i] == 'C'){	errors.GC++;	errors.sequence += 's';	}
-					if(r[i] == '-'){	errors.Gi++;	errors.sequence += 'i';	}
-				}
-				else if(q[i] == 'C'){
-					if(r[i] == 'A'){	errors.CA++;	errors.sequence += 's';	}
-					if(r[i] == 'T'){	errors.CT++;	errors.sequence += 's';	}
-					if(r[i] == 'G'){	errors.CG++;	errors.sequence += 's';	}
-					if(r[i] == 'C'){	errors.CC++;	errors.matches++;	errors.sequence += 'm';	}
-					if(r[i] == '-'){	errors.Ci++;	errors.sequence += 'i';	}
-				}
-				else if(q[i] == 'N'){
-					if(r[i] == 'A'){	errors.NA++;	errors.sequence += 'a';	}
-					if(r[i] == 'T'){	errors.NT++;	errors.sequence += 'a';	}
-					if(r[i] == 'G'){	errors.NG++;	errors.sequence += 'a';	}
-					if(r[i] == 'C'){	errors.NC++;	errors.sequence += 'a';	}
-					if(r[i] == '-'){	errors.Ni++;	errors.sequence += 'a';	}
+//			cout << r[i] << '\t' << q[i] << '\t';
+			if(q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){			//	no missing data and no double gaps
+				if(r[i] != 'N'){
+					started = 1;
+					
+					if(q[i] == 'A'){
+						if(r[i] == 'A'){	errors.AA++;	errors.matches++;	errors.sequence += 'm';	}
+						if(r[i] == 'T'){	errors.AT++;	errors.sequence += 's';	}
+						if(r[i] == 'G'){	errors.AG++;	errors.sequence += 's';	}
+						if(r[i] == 'C'){	errors.AC++;	errors.sequence += 's';	}
+						if(r[i] == '-'){	errors.Ai++;	errors.sequence += 'i';	}
+					}
+					else if(q[i] == 'T'){
+						if(r[i] == 'A'){	errors.TA++;	errors.sequence += 's';	}
+						if(r[i] == 'T'){	errors.TT++;	errors.matches++;	errors.sequence += 'm';	}
+						if(r[i] == 'G'){	errors.TG++;	errors.sequence += 's';	}
+						if(r[i] == 'C'){	errors.TC++;	errors.sequence += 's';	}
+						if(r[i] == '-'){	errors.Ti++;	errors.sequence += 'i';	}
+					}
+					else if(q[i] == 'G'){
+						if(r[i] == 'A'){	errors.GA++;	errors.sequence += 's';	}
+						if(r[i] == 'T'){	errors.GT++;	errors.sequence += 's';	}
+						if(r[i] == 'G'){	errors.GG++;	errors.matches++;	errors.sequence += 'm';	}
+						if(r[i] == 'C'){	errors.GC++;	errors.sequence += 's';	}
+						if(r[i] == '-'){	errors.Gi++;	errors.sequence += 'i';	}
+					}
+					else if(q[i] == 'C'){
+						if(r[i] == 'A'){	errors.CA++;	errors.sequence += 's';	}
+						if(r[i] == 'T'){	errors.CT++;	errors.sequence += 's';	}
+						if(r[i] == 'G'){	errors.CG++;	errors.sequence += 's';	}
+						if(r[i] == 'C'){	errors.CC++;	errors.matches++;	errors.sequence += 'm';	}
+						if(r[i] == '-'){	errors.Ci++;	errors.sequence += 'i';	}
+					}
+					else if(q[i] == 'N'){
+						if(r[i] == 'A'){	errors.NA++;	errors.sequence += 'a';	}
+						if(r[i] == 'T'){	errors.NT++;	errors.sequence += 'a';	}
+						if(r[i] == 'G'){	errors.NG++;	errors.sequence += 'a';	}
+						if(r[i] == 'C'){	errors.NC++;	errors.sequence += 'a';	}
+						if(r[i] == '-'){	errors.Ni++;	errors.sequence += 'a';	}
+					}
+					else if(q[i] == '-' && r[i] != '-'){
+						if(r[i] == 'A'){	errors.dA++;	errors.sequence += 'd';	}
+						if(r[i] == 'T'){	errors.dT++;	errors.sequence += 'd';	}
+						if(r[i] == 'G'){	errors.dG++;	errors.sequence += 'd';	}
+						if(r[i] == 'C'){	errors.dC++;	errors.sequence += 'd';	}
+					}
+					errors.total++;	
 				}
-				else if(q[i] == '-' && r[i] != '-'){
-					if(r[i] == 'A'){	errors.dA++;	errors.sequence += 'd';	}
-					if(r[i] == 'T'){	errors.dT++;	errors.sequence += 'd';	}
-					if(r[i] == 'G'){	errors.dG++;	errors.sequence += 'd';	}
-					if(r[i] == 'C'){	errors.dC++;	errors.sequence += 'd';	}
+				else{
+					
+					if(q[i] == '-'){
+						errors.sequence += 'd';	errors.total++;
+					}						
+					else{
+						errors.sequence += 'r';
+					}
 				}
-				errors.total++;	
-				
 			}
+				
 			else if(q[i] == '.' && r[i] != '.'){		//	reference extends beyond query
 				if(started == 1){	break;	}
 			}
@@ -834,8 +921,9 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 			else if(q[i] == '.' && r[i] == '.'){		//	both are missing data
 				if(started == 1){	break;	}			
 			}
-			
+//			cout << errors.sequence[errors.sequence.length()-1] << endl;
 		}
+//		cout << errors.sequence << endl;
 		errors.mismatches = errors.total-errors.matches;
 		errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total;
 		errors.queryName = query.getName();
@@ -1125,7 +1213,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 }
 /**************************************************************************************************/
 
-int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos, vector<unsigned long int>& rfileFilePos) {
+int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		//set file positions for fasta file
@@ -1167,7 +1255,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 					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(); 
+						unsigned long long pos = inQual.tellg(); 
 						qfileFilePos.push_back(pos - input.length() - 1);	
 						firstSeqNames.erase(it);
 					}
@@ -1188,7 +1276,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 		
 		//get last file position of qfile
 		FILE * pFile;
-		unsigned long int size;
+		unsigned long long size;
 		
 		//get num bytes in file
 		pFile = fopen (qfilename.c_str(),"rb");
@@ -1226,7 +1314,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 				map<string, int>::iterator it = firstSeqNamesReport.find(sname);
 			
 				if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk
-					unsigned long int pos = inR.tellg(); 
+					unsigned long long pos = inR.tellg(); 
 					rfileFilePos.push_back(pos - input.length() - 1);	
 					firstSeqNamesReport.erase(it);
 				}
@@ -1247,7 +1335,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 		
 		//get last file position of qfile
 		FILE * rFile;
-		unsigned long int sizeR;
+		unsigned long long sizeR;
 		
 		//get num bytes in file
 		rFile = fopen (rfilename.c_str(),"rb");
@@ -1267,7 +1355,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 		fastaFilePos.push_back(0); qfileFilePos.push_back(0);
 		//get last file position of fastafile
 		FILE * pFile;
-		unsigned long int size;
+		unsigned long long size;
 		
 		//get num bytes in file
 		pFile = fopen (filename.c_str(),"rb");