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

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index f751525b6b1fa6211ab6017063ba6c7090f6e484..d5f2a6c20126dc2a6d8d9d15e0e5d7a15c2ef8bc 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -261,7 +261,7 @@ int ScreenSeqsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //if the user want to optimize we need to know the 90% mark
-               vector<unsigned long int> positions;
+               vector<unsigned long long> positions;
                if (optimize.size() != 0) {  //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
                        //use the namefile to optimize correctly
                        if (namefile != "") { nameMap = m->readNames(namefile); }
@@ -284,7 +284,7 @@ int ScreenSeqsCommand::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
@@ -629,7 +629,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
        }
 }
 //***************************************************************************************************************
-int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
+int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
        try {
                
                vector<int> startPosition;
@@ -638,7 +638,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
                vector<int> ambigBases;
                vector<int> longHomoPolymer;
                
-               vector<unsigned long int> positions = m->divideFile(fastafile, processors);
+               vector<unsigned long long> positions = m->divideFile(fastafile, processors);
                                
                for (int i = 0; i < (positions.size()-1); i++) {
                        lines.push_back(new linePair(positions[i], positions[(i+1)]));
@@ -724,7 +724,7 @@ int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        }
                        
                        #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; }
@@ -1050,7 +1050,7 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc
                        }
                        
                        #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; }
@@ -1076,7 +1076,7 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
+int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
        try {
                string outputString = "";
                MPI_Status statusGood;