X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=a90bb7e0588baee4f8d922687f99063c8d961387;hb=ca0785e447ca7aa7e2f0ab8bb1155db126b551ea;hp=54524ba9e6a8aa3fe8b678abf060db68529b7177;hpb=4745a956b3116a719f52f341d2a2db84df4817da;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 54524ba..a90bb7e 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -571,11 +571,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
 		
 		string nextcommand = "";
 		int count = 0;
+		bool ignoreSemiColons = false;
 		
 		//go through string until you reach ; or end
 		while (count < commandString.length()) { 
 			
-			if (commandString[count] == ';') {  break;   }
+			 //you want to ignore any ; until you reach the next '
+			if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+			else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+				
+			if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 			else {		nextcommand += commandString[count];	}
 			
 			count++;