From 17d5e897343610e384016d6b2c9d63c0113eea33 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 Aug 2010 21:00:37 +0000
Subject: [PATCH] Now --list annotates which modules are Standard

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3927 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/varianteval/VariantEvalWalker.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 3f387c6a4..2d3f1cb68 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -345,7 +345,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     private void listModulesAndExit() {
         List<Class<? extends VariantEvaluator>> veClasses = PackageUtils.getClassesImplementingInterface(VariantEvaluator.class);
         out.println("\nAvailable eval modules:");
-        for (Class<? extends VariantEvaluator> veClass : veClasses) out.println("\t" + veClass.getSimpleName());
+        out.println("(Standard modules are starred)");
+        for (Class<? extends VariantEvaluator> veClass : veClasses)
+            out.println("\t" + veClass.getSimpleName() + (StandardEval.class.isAssignableFrom(veClass) ? "*" : ""));
         out.println();
         System.exit(0);
     }