working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0732bc20c3bf534c249a0193409dbf72d874aa0f..0958630862ebf3e61c9d2ec23e5618ddaa868ef1 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -509,7 +509,7 @@ int ChimeraSlayerCommand::execute(){
                        string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
                        
                        //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows.
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
                        if (templatefile != "self") { //you want to run slayer with a reference template
                                chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());      
                        }else {
@@ -546,7 +546,7 @@ int ChimeraSlayerCommand::execute(){
                #ifdef USE_MPI  
                        int pid, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<unsigned long int> MPIPos;
+                               vector<unsigned long long> MPIPos;
                                
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -659,7 +659,7 @@ int ChimeraSlayerCommand::execute(){
                                
                #else
                        //break up file
-                       vector<unsigned long int> positions; 
+                       vector<unsigned long long> positions; 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        positions = m->divideFile(fastaFileNames[s], processors);
                        for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
@@ -716,7 +716,7 @@ int ChimeraSlayerCommand::execute(){
                        
                #endif
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
                        delete chimera;
                        #endif
                        
@@ -849,7 +849,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = inFASTA.tellg();
+                               unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (inFASTA.eof()) { break; }
@@ -876,7 +876,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long long>& MPIPos){
        try {                           
                MPI_Status status; 
                int pid;