X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupcommand.cpp;h=194e8e16b1e388bdb8d01ac372fbc884cbc92e43;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=6b76bf2d74a1c3443111dade5d7ceaad7a1c75a2;hpb=d4429ccc354708f3c9a13c809ba9b57c22908d2b;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 6b76bf2..194e8e1 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -62,6 +62,7 @@ GetgroupCommand::GetgroupCommand(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();
@@ -102,7 +103,7 @@ GetgroupCommand::GetgroupCommand(string option)  {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -145,13 +146,13 @@ int GetgroupCommand::execute(){
 			in >> inputData;
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+		if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); m->mothurRemove(outputFile);   return 0; }
 
 		if (in.eof() != true) { in >> nextLabel; }
 		
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (in.eof() != true)) {
-			if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); m->mothurRemove(outputFile);   return 0; }
 			
 			in >> groupN >> num;
 			count++;
@@ -171,7 +172,7 @@ int GetgroupCommand::execute(){
 		in.close();
 		out.close();
 		
-		if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
+		if (m->control_pressed) {  m->mothurRemove(outputFile);   return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();