From 5f2b2d860e858bc62849a396dc466fc8a59d7b86 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Jun 2010 21:39:07 +0000
Subject: [PATCH] Final stage of renaming

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3696 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java  | 6 +++---
 .../gatk/walkers/variantutils/FilterLiftedVariants.java    | 7 +++----
 .../sting/gatk/walkers/variantutils/LiftoverVariants.java  | 7 +++----
 3 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index 52e8bc086..95a208350 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -193,11 +193,11 @@ public class VariantContextUtils {
         String name = first.getName();
         GenomeLoc loc = first.getLocation();
 
-        Set<Allele> alleles = new HashSet<Allele>();
-        Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
+        Set<Allele> alleles = new TreeSet<Allele>();
+        Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
         double negLog10PError = -1;
         Set<String> filters = new HashSet<String>();
-        Map<String, String> attributes = new HashMap<String, String>();
+        Map<String, String> attributes = new TreeMap<String, String>();
         int depth = 0;
 
         // filtering values
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index c644dda39..b974a4ebd 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010.
+ * Copyright (c) 2010, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -12,15 +12,14 @@
  *
  * The above copyright notice and this permission notice shall be
  * included in all copies or substantial portions of the Software.
- *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index ca13b5bf6..1308e5283 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010.
+ * Copyright (c) 2010, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -12,15 +12,14 @@
  *
  * The above copyright notice and this permission notice shall be
  * included in all copies or substantial portions of the Software.
- *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;