CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2054 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java

@@ -114,6 +114,11 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
             System.exit( 0 ); // early exit here because user requested it
         }
 
+        // Warn the user if no dbSNP file was specified
+        if( this.getToolkit().getArguments().DBSNPFile == null ) {
+            Utils.warnUser("This calculation is critically dependent on being able to skip over known variant sites. Are you sure you want to be running without a dbSNP rod specified?");
+        }
+
         // Initialize the requested covariates by parsing the -cov argument
         requestedCovariates = new ArrayList<Covariate>();
         if( validateOldRecalibrator ) {