OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("chimera.slayer");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
convert(temp, minBS);
- temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; }
convert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
- m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+ m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n");
m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n");
m->mothurOut("The chimera.slayer command should be in the following format: \n");
#ifdef USE_MPI
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
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
try {
MPI_Status status;
int pid;