1.12.1

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 3784c3deab49a0c4302101372247f48f5ec3e89b..7ab00a7822f7a7fc7ddd1ef0de00d2d24b8c51de 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -28,7 +28,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("filter.seqs");
                        map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -258,12 +258,12 @@ int FilterSeqsCommand::filterSequences() {
 #ifdef USE_MPI 
                                int pid, start, end, numSeqsPerProcessor, num; 
                                int tag = 2001;
-                               vector<long>MPIPos;
+                               vector<unsigned long int>MPIPos;
                                                
                                MPI_Status status; 
                                MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-                               
+       cout << pid << "is in create filter " << endl;                  
                                MPI_File outMPI;
                                MPI_File tempMPI;
                                MPI_File inMPI;
@@ -393,7 +393,7 @@ int FilterSeqsCommand::filterSequences() {
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {     
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {        
        try {
                string outputString = "";
                int count = 0;
@@ -569,7 +569,7 @@ string FilterSeqsCommand::createFilter() {
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;
-                               vector<long> MPIPos;
+                               vector<unsigned long int> MPIPos;
                                
                                MPI_Status status; 
                                MPI_File inMPI; 
@@ -797,7 +797,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {        
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {   
        try {
                
                MPI_Status status;