Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -301,6 +301,12 @@ public class GenomeAnalysisEngine {
                 str.toUpperCase().endsWith(".PICARD") || str.toUpperCase().endsWith(".INTERVAL_LIST")
                 || str.toUpperCase().endsWith(".INTERVALS"))
             return true;
+
+        if(new File(str).exists())
+            throw new StingException("Interval argument looks like a filename, but does not have one of " +
+                                     "the supported extensions (.bed, .picard, .interval_list, or .intervals).  " +
+                                     "Please rename your file with the appropriate extension.");
+
         else return false;
     }