testing 1.22.0

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 74eddbee75d7021b3ee8584da6b8236df52eca4c..4b04529af1f8181efff2dff2986cf0ab52065a58 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -227,7 +227,7 @@ int PreClusterCommand::execute(){
                                
                                if (m->control_pressed) {  delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 
-                               m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+                               m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
                                m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); 
                                printData(newFastaFile, newNamesFile);
                                
@@ -253,9 +253,8 @@ int PreClusterCommand::execute(){
                        
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                        
-                       newNamesFile = filenames["name"][0];
-                       newFastaFile = filenames["fasta"][0];
-                       
+                       m->renameFile(filenames["fasta"][0], newFastaFile);
+                               
                }else {
                        if (namefile != "") { readNameFile(); }
                
@@ -436,7 +435,7 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
                                if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
                                else{
                                        //get number of reps
-                                       int numReps = 0;
+                                       int numReps = 1;
                                        for(int j=0;j<(it->second).length();j++){
                                                if((it->second)[j] == ','){     numReps++;      }
                                        }