added classic parameter to cluster.split. working on make.contigs command. fixed...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 89d78288639e6cca3e8eebca34dd01174c3963da..508e2a90610d1b3705972a976580d90937358427 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -136,7 +136,7 @@ ShhherCommand::ShhherCommand(string option) {
                        flowFileName = validParameter.validFile(parameters, "flow", true);
                        flowFilesFileName = validParameter.validFile(parameters, "file", true);
                        if (flowFileName == "not found" && flowFilesFileName == "not found") {
-                               m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
+                               m->mothurOut("values for either flow or file must be provided for the shhh.flows command.");
                                m->mothurOutEndLine();
                                abort = true; 
                        }
@@ -152,11 +152,11 @@ ShhherCommand::ShhherCommand(string option) {
                 string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
                 
                                //flow.files = 9 character offset
-                               compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -218,7 +218,7 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
-                outputDir += m->hasPath(flowFileName);
+                if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
                 flowFileVector.push_back(flowFileName);
             }
                
@@ -431,6 +431,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -443,6 +445,7 @@ int ShhherCommand::execute(){
 
                                if (m->control_pressed) { break; }
                                
+            
                                for(int i=1;i<ncpus;i++){
                                        MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
                                        MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
@@ -2448,7 +2451,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
                NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
                clusterNameMap->readMap();
                read->read(clusterNameMap);
-               
+        
                ListVector* list = read->getListVector();
                SparseMatrix* matrix = read->getMatrix();
                
@@ -2980,7 +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;
@@ -3088,7 +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);
@@ -3136,7 +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);
@@ -3174,7 +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;
@@ -3199,7 +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);