From f1affa9fbb061720a7b67d2e26083006f206aeb7 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 28 May 2013 14:58:50 -0400
Subject: [PATCH] Turn off downsampling for DiagnoseTargets

Diagnose targets should never be downsampled. (and I didn't know there was a default downsampling going on for locus walkers)
---
 .../walkers/diagnostics/diagnosetargets/DiagnoseTargets.java    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
index 4bd08294b..bde324e3c 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
@@ -52,6 +52,7 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -110,6 +111,7 @@ import java.util.*;
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
 @By(value = DataSource.READS)
 @PartitionBy(PartitionType.INTERVAL)
+@Downsample(by = DownsampleType.NONE)
 public class DiagnoseTargets extends LocusWalker<Long, Long> {
 
     private static final String AVG_INTERVAL_DP_KEY = "IDP";