fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e2a1d380cb4d13f360fc9a5fecaaeb0808..0dc15f59ee98d0ee2d93659c4c3ad1f033f8a193 100644 (file)
--- 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);