changes for 1.12.2

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index a20a383b6125e135fc1aefeec47e2bc6b892f1e9..a95f436dd7ffdf4403d316be77a1f8ab580f21f5 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -32,7 +32,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        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
@@ -399,10 +399,15 @@ int ClassifySeqsCommand::execute(){
                
                        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);
@@ -414,7 +419,7 @@ int ClassifySeqsCommand::execute(){
 #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
@@ -841,7 +846,7 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 }
 //**********************************************************************************************************************
 #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;