fixed minor issue with sub.sample command.

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d3f62826dce1d75e03e70c8614de2465ded64302..253e03e2a1d380cb4d13f360fc9a5fecaaeb0808 100644 (file)
--- 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 = "";     }