some bug fixes

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 69c34016e1c091b2f0a792b6ed990c82a0509fd7..962c15b3134a836b1e2d25fcbeb983a914bb92fe 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -27,7 +27,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("chimera.ccode");
                        map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -228,7 +228,7 @@ int ChimeraCcodeCommand::execute(){
                
                                int pid, end, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<long> MPIPos;
+                               vector<unsigned long int> MPIPos;
                                                                
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -505,7 +505,7 @@ int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filen
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
+int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
        try {
                                
                MPI_Status status;