X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=0dc15f59ee98d0ee2d93659c4c3ad1f033f8a193;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=253e03e2a1d380cb4d13f360fc9a5fecaaeb0808;hpb=8977d23b7f18d981b14e59c210c97198541ca7b0;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e..0dc15f5 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,7 +176,7 @@ 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);
@@ -213,7 +213,7 @@ 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); 
@@ -242,10 +242,15 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			
 			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) {
@@ -293,7 +298,7 @@ int SeqErrorCommand::execute(){
 		if(qualFileName == "")	{	qLines = lines;	rLines = lines; } //fills with duds
 		
 		int numSeqs = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		if(processors == 1){
 			numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
 		}else{
@@ -361,7 +366,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
 		processIDS.clear();
 		map<char, vector<int> >::iterator it;
 		int num = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -677,7 +682,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 			if(numParentSeqs > 1 && ignoreChimeras == 1)	{	ignoreSeq = 1;	}
 			else											{	ignoreSeq = 0;	}
 			
-			Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
+			Compare minCompare;
+            getErrors(query, referenceSeqs[closestRefIndex], minCompare);
 			
 			if(namesFileName != ""){
 				it = weights.find(query.getName());
@@ -734,7 +740,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
 			
 			index++;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = queryFile.tellg();
 				if ((pos == -1) || (pos >= line.end)) { break; }
 			#else
@@ -834,7 +840,7 @@ void SeqErrorCommand::getReferences(){
 
 //***************************************************************************************************************
 
-Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
+int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){
 	try {
 		if(query.getAlignLength() != reference.getAlignLength()){
 			m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
@@ -845,7 +851,7 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 		string r = reference.getAligned();
 
 		int started = 0;
-		Compare errors;
+		//Compare errors;
 
 		for(int i=0;i<alignLength;i++){
 //			cout << r[i] << '\t' << q[i] << '\t';
@@ -924,7 +930,8 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
 		errors.queryName = query.getName();
 		errors.refName = reference.getName();
 		
-		return errors;
+		//return errors;
+        return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SeqErrorCommand", "getErrors");
@@ -1210,7 +1217,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 
 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)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		//set file positions for fasta file
 		fastaFilePos = m->divideFile(filename, processors);