From 3d9a83c7595a4519022611f128e1adc04e2901ce Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 29 Jan 2013 22:36:31 -0500
Subject: [PATCH] BaseCoverageDistributions should be 'by reference'

otherwise we miss all the 0 coverage spots.
---
 .../walkers/diagnostics/targets/BaseCoverageDistribution.java  | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
index a12008eb4..281c1c55d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
@@ -51,6 +51,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 
 import java.io.PrintStream;
@@ -62,6 +64,7 @@ import java.util.Map;
  * Date: 1/27/13
  * Time: 11:16 AM
  */
+@By(DataSource.REFERENCE)
 public class BaseCoverageDistribution extends LocusWalker<Integer, Map<Integer, Long>> {
     @Output(required = true)
     private PrintStream out;