From add9ad97ec7192f3b16acd2be8cf0ac7d6908b5b Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 26 Oct 2011 15:34:23 -0400
Subject: [PATCH] No scatter gather for VQSR or ApplyVQSR.

These walkers should not be scatter gatherable. Annotating them accordingly so that Queue doesn't allow a less than knowledgeable user to try and scatter/gather VQSR.
---
 .../gatk/walkers/variantrecalibration/ApplyRecalibration.java  | 3 +++
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 16f1abf1b..1d5493daf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -32,6 +32,8 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.walkers.PartitionBy;
+import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
@@ -84,6 +86,7 @@ import java.util.*;
  *
  */
 
+@PartitionBy(PartitionType.NONE)
 public class ApplyRecalibration extends RodWalker<Integer, Integer> {
 
     /////////////////////////////
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 89e702b64..d8cc264c2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -29,6 +29,8 @@ import org.broadinstitute.sting.commandline.*;
 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.walkers.PartitionBy;
+import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -94,6 +96,7 @@ import java.util.*;
  *
  */
 
+@PartitionBy(PartitionType.NONE)
 public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {
 
     public static final String VQS_LOD_KEY = "VQSLOD"; // Log odds ratio of being a true variant versus being false under the trained gaussian mixture model