X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=253e03e2a1d380cb4d13f360fc9a5fecaaeb0808;hb=8977d23b7f18d981b14e59c210c97198541ca7b0;hp=d3f62826dce1d75e03e70c8614de2465ded64302;hpb=65e21482d022d12f7a78a8d436fb51f322603e41;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d3f6282..253e03e 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -178,7 +178,11 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			}
 			else if (queryFileName == "not open") { abort = true; }	
 			else { m->setFastaFile(queryFileName); }
-
+			
+			referenceFileName = validParameter.validFile(parameters, "reference", true);
+			if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
+			else if (referenceFileName == "not open") { abort = true; }	
+			
 			//check for optional parameters
 			namesFileName = validParameter.validFile(parameters, "name", true);
 			if(namesFileName == "not found"){	namesFileName = "";	}