Pat's testing

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 537821134edebcf9dcad70f8c1f38be0da39b121..1ad0b27390421d2bf43049d398c3375786077b93 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -386,6 +386,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -398,6 +400,7 @@ 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);
@@ -1111,7 +1114,8 @@ void ShhherCommand::getUniques(){
                }
                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]);          }
        }
@@ -1368,7 +1372,7 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
                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 77dacfe711ea694d7d81cb7536fd15d14cb0ec97..6a26fac949a335999be1cf7c1355f9c5c4f7d48c 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -198,6 +198,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
                        numFPrimers = 0;
                        numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
                }
                
        }
@@ -382,7 +384,6 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                
                while(moreSeqs) {
                        //cout << "driver " << count << endl;
-                       
        
                        if (m->control_pressed) { break; }