From c6ef81b611931bc4aa37db7b70f1fd20844ce7b2 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Thu, 23 Jun 2016 10:48:22 -0400
Subject: [PATCH] Change HashMap to LinkedHashMap for predictable ordering

---
 .../gatk/tools/walkers/variantutils/SelectVariants.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index 899346924..68351b0f8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -627,7 +627,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     private Map<String, VCFHeader> vcfRods;
 
     private final List<Allele> diploidNoCallAlleles = GATKVariantContextUtils.noCallAlleles(2);
-    private final Map<Integer, Integer> ploidyToNumberOfAlleles = new HashMap<Integer, Integer>();
+    private final Map<Integer, Integer> ploidyToNumberOfAlleles = new LinkedHashMap<Integer, Integer>();
 
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher