Merge remote-tracking branch 'mothur/master'

diff --git a/.gitignore b/.gitignore
index 1a3b8bd98ef0ed25aa2dcfd12fa9671e256d0e5d..c1f854e3d6c22d93a5a03c0e365c472a1da46d68 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,2 @@
 .DS_Store
-/nbproject/private/
\ No newline at end of file
+*.zip

diff --git a/calculator.h b/calculator.h
index 2c41329cff33ff7179054969a2595fcb53d2c717..6791d830f01c69492251b6110ebe5ba3d04a50a0 100644 (file)
--- a/calculator.h
+++ b/calculator.h
@@ -100,7 +100,7 @@ class BrokenStick
                void doBStick(vector<double>);
 };
 
-/**************************************************************************************************/
+//**************************************************************************************************/
 /*This Class calculates the geometric series distribution for the data.
 It prints the D-Statistic and the critical values for the Kolmogorov-Smirnov
 1-sample test at the 95% confidence interval.*/

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();
                

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 2594815f6b763a303382f9730bce36e84060b713..414c73cd1d2e6740b89d5200a5c7e7c704097ed6 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -67,7 +67,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;