X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=59837dd72d7dc8dbe76ee3125052461a9e7b580a;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=8d0e507a8f35bc7d9ee8664765194c546d736c1b;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 8d0e507..59837dd 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -22,9 +22,16 @@ int main(int argc, char *argv[]){
 
 		Engine* mothur;
 		bool bail = 0;
+		string input;
 
 		if(argc>1){
-			mothur = new BatchEngine(argv[0], argv[1]);
+			input = argv[1];
+
+			if (input[0] == '#') {
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else{
+				mothur = new BatchEngine(argv[0], argv[1]);
+			}
 		}
 		else{
 			mothur = new InteractEngine(argv[0]);