X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=systemcommand.cpp;h=b5b4945b92b6d664e6d81aa2dc6911a2d30414c3;hp=5ace75e3a2d152f27e6483aab2ad4a697f952c79;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=75962c819c16814e5c2340d99af1aa62e564dc20

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 5ace75e..b5b4945 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -12,7 +12,7 @@
 //**********************************************************************************************************************
 vector<string> SystemCommand::setParameters(){	
 	try {
-		CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
+		CommandParameter pcommand("command", "String", "", "", "", "", "","",false,false); parameters.push_back(pcommand);
 				
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -91,23 +91,31 @@ int SystemCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		command += " > ./commandScreen.output 2>&1";
-		system(command.c_str());
+		//if command contains a redirect don't add the redirect
+		bool usedRedirect = false;
+		if ((command.find('>')) == string::npos) {
+			command += " > ./commandScreen.output 2>&1";
+			usedRedirect = true;
+		}
 		
-		ifstream in;
-		string filename = "./commandScreen.output";
-		m->openInputFile(filename, in);
+		system(command.c_str());
 		
-		string output = "";
-		while(char c = in.get()){
-			if(in.eof())		{	break;			}
-			else				{	output += c;	}
+		if (usedRedirect) {
+			ifstream in;
+			string filename = "./commandScreen.output";
+			m->openInputFile(filename, in, "no error");
+			
+			string output = "";
+			while(char c = in.get()){
+				if(in.eof())		{	break;			}
+				else				{	output += c;	}
+			}
+			in.close();
+			
+			m->mothurOut(output); m->mothurOutEndLine();
+			m->mothurRemove(filename);
 		}
-		in.close();
 		
-		m->mothurOut(output); m->mothurOutEndLine();
-		remove(filename.c_str());
-				
 		return 0;		
 	}