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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7c8485adfedc0a0c39dc928e50b45fc6bfef2a11..321ae77cf743420284e4dfac274d9c88b9b4557f 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -299,7 +299,7 @@ int ChimeraCcodeCommand::execute(){
                
                                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
@@ -390,7 +390,7 @@ int ChimeraCcodeCommand::execute(){
 
                        outHeader.close();
                        
-                       vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
+                       vector<unsigned long long> 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)]));
@@ -522,7 +522,7 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
                        delete candidateSeq;
                        
                        #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; }
@@ -547,7 +547,7 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
+int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
        try {
                                
                MPI_Status status;