X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandoptionparser.cpp;h=dfad533c8898ff3d79067d5f16c6869803e21e12;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=3b45e48f4d992e470867a3071ff8d8f18c519dca;hpb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;p=mothur.git

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index 3b45e48..dfad533 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -22,8 +22,12 @@ CommandOptionParser::CommandOptionParser(string input){
 		optionString = "";
 		commandString = "";
 
-		if(openParen != -1 && closeParen != -1){			
-			commandString = input.substr(0, openParen);   //commandString contains everything before "("
+		if(openParen != -1 && closeParen != -1){	
+            //gobble extra spaces
+            int spot = 0;
+            for (int i = 0; i < input.length(); i++) {  if (!(isspace(input[i]))) { spot = i; break; } }
+            if (spot > openParen) { spot = 0; }
+			commandString = input.substr(spot, openParen-spot);   //commandString contains everything before "("
 			optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
 		}
 		else if (openParen == -1) { m->mothurOut("[ERROR]: You are missing ("); m->mothurOutEndLine(); }