adds group parameter to chimera.uchime so you can check for chimeras with template...

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 7ca4aa64d28f9ec23bcc93c37e42c753ef6a8137..e32af2152e1bd3d420a0a94dac738a97c19c24af 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -69,6 +69,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -158,7 +159,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
-                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
+                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
                                        }
                                }
                                
@@ -204,7 +205,7 @@ int MakeGroupCommand::execute(){
                
                for (int i = 0; i < fastaFileNames.size(); i++) {
                
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
                        
                        ifstream in;
                        m->openInputFile(fastaFileNames[i], in);
@@ -213,7 +214,7 @@ int MakeGroupCommand::execute(){
                                
                                Sequence seq(in, "no align"); m->gobble(in);
                                
-                               if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); m->mothurRemove(filename); return 0; }
                                
                                if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
                        }