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

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 173227f372f4d4cbf7445e5f3fea440220e70b4a..e96b7fd3762fa69c5930066729e867ff69705b3d 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -341,7 +341,7 @@ int FilterSeqsCommand::filterSequences() {
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;
-                               vector<unsigned long int>MPIPos;
+                               vector<unsigned long long>MPIPos;
                                                
                                MPI_Status status; 
                                MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
@@ -420,7 +420,7 @@ int FilterSeqsCommand::filterSequences() {
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
-                       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)]));
@@ -462,7 +462,7 @@ int FilterSeqsCommand::filterSequences() {
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {        
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {       
        try {
                string outputString = "";
                int count = 0;
@@ -568,7 +568,7 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = in.tellg();
+                               unsigned long long pos = in.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (in.eof()) { break; }
@@ -676,7 +676,7 @@ string FilterSeqsCommand::createFilter() {
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;
-                               vector<unsigned long int> MPIPos;
+                               vector<unsigned long long> MPIPos;
                                
                                MPI_Status status; 
                                MPI_File inMPI; 
@@ -736,7 +736,7 @@ string FilterSeqsCommand::createFilter() {
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
-               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)]));
@@ -877,7 +877,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = in.tellg();
+                               unsigned long long pos = in.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (in.eof()) { break; }
@@ -899,7 +899,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {   
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {  
        try {
                
                MPI_Status status;