some bug fixes

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 44696cbbf883c3cde0814c8a615d69d01986a67c..264eb4c4ade8cfa2fd9f56246436b799ecb9d709 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -26,7 +26,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("chimera.check");
                        map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -262,7 +262,7 @@ int ChimeraCheckCommand::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
@@ -490,7 +490,7 @@ int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filen
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
+int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos){
        try {
                MPI_File outAccMPI;
                MPI_Status status;