From d369136bda1cc0e74f0613efded1093f42ce883f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 15 Jul 2009 13:33:03 +0000
Subject: [PATCH] depricate this ROD yet again

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1245 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/refdata/rodGELI.java   | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
index 1c4c0e80b..64bf552df 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
@@ -17,7 +17,7 @@ import net.sf.samtools.util.CloseableIterator;
  *  This class wraps Picard Geli CHiP data and presents it as a ROD.
  */
 
-public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
+public class rodGELI extends BasicReferenceOrderedDatum {
 	// ----------------------------------------------------------------------
 	//
 	// Constructors
@@ -93,6 +93,9 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
 		return new rodGELI.rodGELIIterator(name,file);
 	}
 
+    /****
+     * We no longer want to use this class as truth data (sigh)
+     *
     public List<String> getFWDAlleles() {
         return new ArrayList<String>();
     }
@@ -123,8 +126,8 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
     public double getConsensusConfidence() {
         return gh.getBestToSecondBestLod();
     }
-
-
+    *
+    */
 
     public static void main(String argv[]) {
         String testFile = "NA12878.geli";