some bug fixes

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index ee27776c11912bd9fe346f300ffc867f5164223f..f19810e131b687ea372ae1914ecf3a02d03ef8d8 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -45,7 +45,7 @@ AlignCommand::AlignCommand(string option)  {
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters(); 
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("align.seqs");
                        map<string, string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -261,7 +261,7 @@ int AlignCommand::execute(){
 #ifdef USE_MPI 
                                int pid, end, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<long> MPIPos;
+                               vector<unsigned long int> MPIPos;
                                MPIWroteAccnos = false;
                                
                                MPI_Status status; 
@@ -646,7 +646,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
+int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
        try {
                string outputString = "";
                MPI_Status statusReport;