From 05834598390bd957871acf1d1af3cfa2896a7e07 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 12 Jun 2009 19:53:21 +0000
Subject: [PATCH] Another formatting change to make Hapmap sites more clearly
 visible.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/PileupWithContextWalker.java        | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java
index 77384d7fd..d28f3fd7a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.rodGFF;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.Utils;
@@ -80,9 +81,15 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
 
         String rodString = "";
         for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
+            /*
             if ( datum != null && ! (datum instanceof rodDbSNP)) {
                 rodString += datum.toSimpleString() + " ";
             }
+            */
+
+            if ( datum != null && (datum instanceof rodGFF)) {
+                rodString += "Hapmap: " + datum.toSimpleString() + " ";
+            }
         }
 
         rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);