Completes path name on fopen calls

source/commands/makecontigscommand.cpp

@@ -769,7 +769,7 @@ unsigned long long MakeContigsCommand::processSingleFileOption(map<string, int>&
                 
                 ofstream out;
                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
-                cout << variables["[filename]"] << endl;
+                //cout << variables["[filename]"] << endl;
                 string thisGroupName = getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
                 
                 m->openOutputFile(thisGroupName, out);
@@ -2652,6 +2652,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
         unsigned long long size;
         
         //get num bytes in file
+        fasta[1] = m->getFullPathName(fasta[1]);
         pFile = fopen (fasta[1].c_str(),"rb");
         if (pFile==NULL) perror ("Error opening file");
         else{
@@ -2723,6 +2724,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
                 unsigned long long size;
                 
                 //get num bytes in file
+                qual[0] = m->getFullPathName(qual[0]);
                 pFile = fopen (qual[0].c_str(),"rb");
                 if (pFile==NULL) perror ("Error opening file");
                 else{
@@ -2781,6 +2783,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
                 FILE * pFile2;
                 
                 //get num bytes in file
+                qual[1] = m->getFullPathName(qual[1]);
                 pFile2 = fopen (qual[1].c_str(),"rb");
                 if (pFile2==NULL) perror ("Error opening file");
                 else{

source/commands/makefilecommand.cpp

@@ -31,7 +31,7 @@ string MakeFileCommand::getHelpString(){
     try {
         string helpString = "";
         helpString += "The make.file command takes a input directory and creates a file file containing the fastq or gz files in the directory.\n";
-        helpString += "The make.fastq command parameters are inputdir, numcols and type.  inputdir is required.\n";
+        helpString += "The make.file command parameters are inputdir, numcols and type.  inputdir is required.\n";
         helpString += "May create more than one file. Mothur will attempt to match paired files. \n";
         helpString += "The type parameter allows you to set the type of files to look for. Options are fastq or gz.  Default=fastq. \n";
         helpString += "The numcols parameter allows you to set number of columns you mothur to make in the file.  Default=3, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first '_' or if no '_' is found then the root of the forwardFastq filename.\n";

source/commands/seqerrorcommand.cpp

@@ -1374,6 +1374,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                 unsigned long long size;
                 
                 //get num bytes in file
+                qfilename = m->getFullPathName(qfilename);
                 pFile = fopen (qfilename.c_str(),"rb");
                 if (pFile==NULL) perror ("Error opening file");
                 else{
@@ -1436,6 +1437,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                 unsigned long long sizeR;
                 
                 //get num bytes in file
+                rfilename = m->getFullPathName(rfilename);
                 rFile = fopen (rfilename.c_str(),"rb");
                 if (rFile==NULL) perror ("Error opening file");
                 else{
@@ -1455,6 +1457,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 		unsigned long long size;
 		
 		//get num bytes in file
+        filename = m->getFullPathName(filename);
 		pFile = fopen (filename.c_str(),"rb");
 		if (pFile==NULL) perror ("Error opening file");
 		else{
@@ -1469,6 +1472,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
             FILE * qFile;
             
             //get num bytes in file
+            qfilename = m->getFullPathName(qfilename);
             qFile = fopen (qfilename.c_str(),"rb");
             if (qFile==NULL) perror ("Error opening file");
             else{
@@ -1486,6 +1490,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
              FILE * rFile;
              
              //get num bytes in file
+             rfilename = m->getFullPathName(rfilename);
              rFile = fopen (rfilename.c_str(),"rb");
              if (rFile==NULL) perror ("Error opening file");
              else{

source/commands/trimflowscommand.cpp

@@ -341,6 +341,7 @@ int TrimFlowsCommand::execute(){
                                 unsigned long long size;
                                 
                                 //get num bytes in file
+                                barcodePrimerComboFileNames[i][j] = m->getFullPathName(barcodePrimerComboFileNames[i][j]);
                                 pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
                                 if (pFile==NULL) perror ("Error opening file");
                                 else{
@@ -777,6 +778,7 @@ vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 		unsigned long long size;
 		
 		//get num bytes in file
+        flowFileName = m->getFullPathName(flowFileName);
 		pFile = fopen (flowFileName.c_str(),"rb");
 		if (pFile==NULL) perror ("Error opening file");
 		else{

source/commands/trimseqscommand.cpp

@@ -1646,6 +1646,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
             unsigned long long size;
             
             //get num bytes in file
+            qfilename = m->getFullPathName(qfilename);
             pFile = fopen (qfilename.c_str(),"rb");
             if (pFile==NULL) perror ("Error opening file");
             else{

source/mothurout.cpp

@@ -1356,6 +1356,8 @@ vector<bool> MothurOut::isGZ(string filename){
         
         int ableToOpen = openInputFileBinary(filename, fileHandle, gzin, ""); //no error
         
+        if (debug) { if (ableToOpen == 1) { mothurOut("[DEBUG]: unable to open gz file. \n"); } }
+        
         if (ableToOpen == 1) { return results; } // results[0] = false; results[1] = false;
         else {  results[0] = true;  }