X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergefilecommand.cpp;h=04c92fae9a0d2189cb8f1ed69c9c53572fcfee2e;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=cece52d9cd06b78950f5b197c19d2e9574b7daa8;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index cece52d..04c92fa 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -64,7 +64,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
 		if(option == "help") {
 			help();
 			abort = true; calledHelp = true;
-		}
+		}else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		else {
 			vector<string> myArray = setParameters();
 			
@@ -140,7 +140,7 @@ int MergeFileCommand::execute(){
 			m->openInputFile(fileNames[i], inputFile);
 			
 			while(!inputFile.eof()){	
-				if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
+				if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); m->mothurRemove(outputFileName); return 0;  }
 			
 				c = inputFile.get(); 
 				//-1 is eof char
@@ -152,7 +152,7 @@ int MergeFileCommand::execute(){
 		
 		outputFile.close();
 		
-		if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0;  }
+		if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0;  }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();