From 3e52ce5fa8d6f8ec80c73b65959b6604f035bcef Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Thu, 10 Jan 2013 11:44:24 -0500
Subject: [PATCH] Remove DepthOfCoverage.java because it is no longer public -
 Move Pileup.java and PrintReads.java to their new homes

---
 public/packages/GATKEngine.xml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index 27d2afa47..42b3a4d6e 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -53,11 +53,10 @@
     <file name="public/testdata/exampleFASTA.fasta.fai" />
     <file name="public/testdata/exampleFASTA.dict" />
     <!-- GATK sample code and build scripts -->
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java" />
   </resources>
 </package>