Merge remote-tracking branch 'mothur/master'

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index d8f538b56109e2faa290cb060c314186e8be318a..803b6cb7955af18d441d6c160e5aafb797c3a057 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -128,8 +128,10 @@ ShhherCommand::ShhherCommand(string option) {
                                        if (path == "") {       parameters["file"] = inputDir + it->second;             }
                                }
                        }
-                       
-                       
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
+            
                        //check for required parameters
                        flowFileName = validParameter.validFile(parameters, "flow", true);
                        flowFilesFileName = validParameter.validFile(parameters, "file", true);
@@ -146,13 +148,15 @@ ShhherCommand::ShhherCommand(string option) {
                        }
                        else{
                                ofstream temp;
-
+                
+                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                
                                //flow.files = 9 character offset
-                               compositeFASTAFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -214,17 +218,10 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
+                if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
                 flowFileVector.push_back(flowFileName);
             }
-
-                       
-                       //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
-                               outputDir = ""; 
-                               outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it    
-                       }
-                       
-                       
+               
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
@@ -1772,7 +1769,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
         
         
         if(compositeNamesFileName != ""){
-            m->appendFiles(nameFileName, uchimecompositeNamesFileName);
+            m->appendFiles(nameFileName, compositeNamesFileName);
         }              
     }
     catch(exception& e) {
@@ -2403,8 +2400,7 @@ int ShhherCommand::getUniques(int numSeqs, int numFlowCells, vector<short>& uniq
                }
                uniqueFlowDataIntI.resize(numFlowCells * numUniques);
                uniqueLengths.resize(numUniques);       
-               uniqueFlowgrams.resize(numFlowCells * numUniques);
-        
+               
                flowDataPrI.resize(numSeqs * numFlowCells, 0);
                for(int i=0;i<flowDataPrI.size();i++)   {       if (m->control_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);          }
         
@@ -2987,7 +2983,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
        
        try {
                string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+               if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
                string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.qual";
         
                ofstream qualityFile;
@@ -3095,7 +3091,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
 void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
        try {
                string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+               if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
                string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.fasta";
                ofstream fastaFile;
                m->openOutputFile(fastaFileName, fastaFile);
@@ -3143,7 +3139,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU
 void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string filename, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
        try {
                string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+               if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
                string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.names";
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
@@ -3181,7 +3177,7 @@ void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, s
 void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& seqNameVector){
        try {
                string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+               if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
                string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
                string groupFileName = fileRoot + "shhh.groups";
                ofstream groupFile;
@@ -3206,7 +3202,7 @@ void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& se
 void ShhherCommand::writeClusters(string filename, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
        try {
                string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(filename);  }
+               if (outputDir == "") {  thisOutputDir = m->hasPath(filename);  }
                string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.counts";
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);