X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=0add62e03a99270babfde920acca61a65dcdc2b3;hb=5cbb9328400eabc6689da26738aceee394666dfa;hp=e7704642874d050a3de7625a28ed3fae390fe653;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index e770464..0add62e 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -16,6 +16,7 @@ vector<string> MakeGroupCommand::setParameters(){
 	try {
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
@@ -159,7 +160,7 @@ 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]); }
 					}
 				}
 				
@@ -205,7 +206,7 @@ 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);
@@ -214,7 +215,7 @@ 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;		}
 			}