Merge remote-tracking branch 'mothur/master'

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 6ef9532790a5fc63905cb598f1e7bc4baa4c9871..32891c333ab5229aec50ed05ff5f03b6799d1396 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -434,6 +434,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -446,6 +448,7 @@ 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);
@@ -2400,7 +2403,8 @@ 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]);          }
         
@@ -2451,7 +2455,7 @@ 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.cpp b/trimflowscommand.cpp
index 0557c71bda3453068175fe3d405ff87972df80e1..86de668b4f57596bf11efb80807b18f932136551 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -392,7 +392,8 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
                
                while(moreSeqs) {
-                               
+                       //cout << "driver " << count << endl;
+       
                        if (m->control_pressed) { break; }
                        
                        int success = 1;

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 2594815f6b763a303382f9730bce36e84060b713..27bafd530cad4a66ef22e41696eef7e2328bde97 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -59,7 +59,9 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
+    int numLinkers, numSpacers;
+
+    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -67,7 +69,6 @@ private:
        
        string flowFileName, oligoFileName, outputDir;
 
-
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;