From 54bb643d1954260661fe103620a2ec88b30cf0c8 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 26 May 2009 15:58:21 +0000
Subject: [PATCH] Validated Mark's assertion that GSA-27 is fixed.  Also did
 some cleanup on the pileup walker so that it doesn't output to System.out.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/ValidatingPileupWalker.java          | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
index 397cd02e1..15a573563 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
@@ -27,7 +27,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         Pileup truePileup = getTruePileup( tracker );
 
         if ( truePileup == null ) {
-            System.out.printf("No truth pileup data available at %s%n", pileup.getPileupString());
+            out.printf("No truth pileup data available at %s%n", pileup.getPileupString());
             if ( ! CONTINUE_AFTER_AN_ERROR ) {
                 Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
                                 context.getLocation(), pileup.getBases()));
@@ -68,6 +68,10 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
      */
     private Pileup getTruePileup( RefMetaDataTracker tracker ) {
         rodSAMPileup pileup = (rodSAMPileup)tracker.lookup("pileup", null);
+
+        if( pileup == null )
+            return null;
+
         if( pileup.hasPointGenotype() )
             return (Pileup)pileup.getPointGenotype();
         else if( pileup.hasIndelGenotype() )