added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 115e930969323ba4655e0b5ba5c2a8e1166a1397..c40963999f953e2cfc534afcfdaec1a1e56b8c72 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -802,7 +802,7 @@ string ShhherCommand::createNamesFile(){
                        duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
                }
                
-               string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName) + getOutputFileNameTag("name");
+               string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
                
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
@@ -1039,7 +1039,12 @@ void ShhherCommand::getFlowData(){
         
         float intensity;
         
-        flowFile >> numFlowCells;
+        string numFlowTest;
+        flowFile >> numFlowTest;
+        
+        if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+        else { convert(numFlowTest, numFlowCells); }
+        
         int index = 0;//pcluster
         while(!flowFile.eof()){
             
@@ -1376,17 +1381,17 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
     try {
         
         ReadMatrix* read = new ReadColumnMatrix(distFileName);         
-        read->setCutoff(cutoff);
-        
-        NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
-        clusterNameMap->readMap();
-        read->read(clusterNameMap);
-        
-        ListVector* list = read->getListVector();
-        SparseMatrix* matrix = read->getMatrix();
+               read->setCutoff(cutoff);
+               
+               NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
+               clusterNameMap->readMap();
+               read->read(clusterNameMap);
         
-        delete read; 
-        delete clusterNameMap; 
+               ListVector* list = read->getListVector();
+               SparseDistanceMatrix* matrix = read->getDMatrix();
+               
+               delete read; 
+               delete clusterNameMap; 
         
         RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
         
@@ -2029,7 +2034,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                //Windows version shared memory, so be careful when passing variables through the shhhFlowsData struct. 
                //Above fork() will clone, so memory is separate, but that's not the case with windows, 
                //////////////////////////////////////////////////////////////////////////////////////////////////////
-               
+               /*
                vector<shhhFlowsData*> pDataArray; 
                DWORD   dwThreadIdArray[processors-1];
                HANDLE  hThreadArray[processors-1]; 
@@ -2060,7 +2065,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
-               
+               */
         #endif
         
         for (int i=0;i<processIDS.size();i++) { 
@@ -2309,7 +2314,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 if (m->control_pressed) { break; }
                 
                 vector<int> otuCounts(numOTUs, 0);
-                for(int i=0;i<numSeqs;i++)     {       otuCounts[otuData[i]]++;        }
+                for(int j=0;j<numSeqs;j++)     {       otuCounts[otuData[j]]++;        }
                 
                 calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);        
                 
@@ -2382,7 +2387,12 @@ int ShhherCommand::getFlowData(string filename, vector<string>& thisSeqNameVecto
                thisFlowDataIntI.clear();
                thisNameMap.clear();
                
-               flowFile >> numFlowCells;
+               string numFlowTest;
+        flowFile >> numFlowTest;
+        
+        if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+        else { convert(numFlowTest, numFlowCells); }
+        
         if (m->debug) { m->mothurOut("[DEBUG]: numFlowCells = " + toString(numFlowCells) + ".\n"); }
                int index = 0;//pcluster
                while(!flowFile.eof()){
@@ -2632,7 +2642,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
                read->read(clusterNameMap);
         
                ListVector* list = read->getListVector();
-               SparseMatrix* matrix = read->getMatrix();
+               SparseDistanceMatrix* matrix = read->getDMatrix();
                
                delete read; 
                delete clusterNameMap;