fix rarefaction.single

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 78bd73b45bfa6e5bc1337eb81cd783d9a6f1ec82..e6b00bac1361284bd803c5ffc92dfcec27e44f8e 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -67,6 +67,13 @@ ShhherCommand::ShhherCommand(){
 
 ShhherCommand::ShhherCommand(string option) {
        try {
+        
+#ifdef USE_MPI
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+               MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
+        
+               if(pid == 0){
+#endif
                abort = false; calledHelp = false;   
                
                //allow user to run help
@@ -121,8 +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);
@@ -139,13 +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 = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+                               compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -207,17 +218,10 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
+                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;
@@ -314,6 +318,9 @@ ShhherCommand::ShhherCommand(string option) {
                        }
                        
                }
+#ifdef USE_MPI
+               }                               
+#endif
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "ShhherCommand");
@@ -328,9 +335,7 @@ int ShhherCommand::execute(){
                
                int tag = 1976;
                MPI_Status status; 
-               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-               MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
-        
+                       
                if(pid == 0){
 
                        for(int i=1;i<ncpus;i++){
@@ -344,6 +349,22 @@ int ShhherCommand::execute(){
                        getSingleLookUp();      if (m->control_pressed) { return 0; }
                        getJointLookUp();       if (m->control_pressed) { return 0; }
                        
+            vector<string> flowFileVector;
+                       if(flowFilesFileName != "not found"){
+                               string fName;
+                
+                               ifstream flowFilesFile;
+                               m->openInputFile(flowFilesFileName, flowFilesFile);
+                               while(flowFilesFile){
+                                       fName = m->getline(flowFilesFile);
+                                       flowFileVector.push_back(fName);
+                                       m->gobble(flowFilesFile);
+                               }
+                       }
+                       else{
+                               flowFileVector.push_back(flowFileName);
+                       }
+            
                        int numFiles = flowFileVector.size();
 
                        for(int i=1;i<ncpus;i++){
@@ -410,6 +431,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -422,6 +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);
@@ -2427,7 +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();
                
@@ -3042,11 +3066,12 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
                        
                        if(otuCounts[i] > 0){
                                qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-                               
+                       
                                int j=4;        //need to get past the first four bases
                                while(qualities[i][j] != -1){
-                                       qualityFile << qualities[i][j] << ' ';
-                                       j++;
+                    qualityFile << qualities[i][j] << ' ';
+                    if (j > qualities[i].size()) { break; }
+                    j++;
                                }
                                qualityFile << endl;
                        }