Merge remote-tracking branch 'mothur/master'

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 89d78288639e6cca3e8eebca34dd01174c3963da..2214c5ea8b4b5f124393067ff2d59dcc3acf931c 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -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 = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+                               compositeNamesFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }
@@ -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);
@@ -1766,7 +1769,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
         
         
         if(compositeNamesFileName != ""){
-            m->appendFiles(nameFileName, compositeNamesFileName);
+            m->appendFiles(nameFileName, uchimecompositeNamesFileName);
         }              
     }
     catch(exception& e) {
@@ -2397,7 +2400,8 @@ 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]);          }
         
@@ -2448,7 +2452,7 @@ 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();