OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("classify.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+ string RippedTaxName = getRootName(getSimpleName(taxonomyFileName));
+ RippedTaxName = getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
+ if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
+ RippedTaxName += ".";
+
if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
- string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
+ string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
- string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
+ string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
outputNames.push_back(newTaxonomyFile);
outputNames.push_back(taxSummary);
#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 ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<long>& MPIPos){
+int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
try {
MPI_Status statusNew;
MPI_Status statusTemp;