X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=489a2f11f7c3a13df14bedf42a05339e86fcaeb2;hb=81276c241b984898f8d30ad123c00592ee6db7b8;hp=f341d0a03e3d35177895ab49696f7fb4f1f7ad20;hpb=348a7bac1d3c5d17ae0e4a93b78f69f4e200a190;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index f341d0a..489a2f1 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -20,7 +20,17 @@ SystemCommand::SystemCommand(string option){
 		
 		else {
 			if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
-			else { command = option; }
+			else { 
+				//check for outputdir and inputdir parameters
+				int commaPos = option.find_first_of(',');
+				
+				//if there is a comma then grab string up to that pos
+				if (commaPos != option.npos) {
+					option = option.substr(0, commaPos);
+				}
+			
+				command = option;
+			}
 		}	
 
 	}