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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 05ecd46ac6a3e192d834c6f26cdb5e1aa533cb71..960d70229a084923fd1cc8dc368ff4b71d815cbd 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -322,7 +322,7 @@ int AlignCommand::execute(){
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<unsigned long int> MPIPos;
+                               vector<unsigned long long> MPIPos;
                                MPIWroteAccnos = false;
                        
                                MPI_Status status; 
@@ -426,7 +426,7 @@ int AlignCommand::execute(){
                                
 #else
 
-                       vector<unsigned long int> positions; 
+                       vector<unsigned long long> positions; 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        positions = m->divideFile(candidateFileNames[s], processors);
                        for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
@@ -623,7 +623,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        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; }
@@ -650,7 +650,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
+int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
        try {
                string outputString = "";
                MPI_Status statusReport;