X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=d8ebe50fb11859367256a28286dec9789cc70d36;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=5c80047681c15640c5926d771536a42ea60a8c9d;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5c80047..d8ebe50 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,9 +176,13 @@ 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 = "";	}
@@ -209,7 +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); 
@@ -238,10 +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) {
@@ -273,9 +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);
 		
@@ -731,7 +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; }
@@ -1204,7 +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
@@ -1246,7 +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);
 					}
@@ -1267,7 +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");
@@ -1305,7 +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);
 				}
@@ -1326,7 +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");
@@ -1346,7 +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");