From 9d7d5f174780bd619263a9962996eba133e84383 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Jun 2010 20:24:27 +0000
Subject: [PATCH] Continuing the renaming nightmare...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3694 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/CombineVariants.java      | 4 ++--
 .../sting/gatk/walkers/variantutils/FilterLiftedVCF.java      | 4 ++--
 .../sting/gatk/walkers/variantutils/LiftoverVCF.java          | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 8ef032f35..1fae7a85a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.vcf;
+package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
@@ -48,7 +48,7 @@ import java.util.*;
  *   priority list (if provided), emits a single record instance at every position represented in the rods.
  */
 @Requires(value={})
-public class VCFCombine extends RodWalker<Integer, Integer> {
+public class CombineVariants extends RodWalker<Integer, Integer> {
     // the types of combinations we currently allow
     public enum ComboType { UNION, MERGE }
     @Argument(fullName="combination_type", shortName="type", doc="combination type; MERGE are supported", required=true)
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java
index c30dc1ee2..c644dda39 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.vcf;
+package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -39,7 +39,7 @@ import java.util.List;
  * Filters a lifted-over VCF file for ref bases that have been changed.
  */
 @Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
-public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
+public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
 
     private VCFWriter writer;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java
index d2700f1a4..ca13b5bf6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.vcf;
+package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
@@ -46,7 +46,7 @@ import net.sf.samtools.SAMFileReader;
  * Lifts a VCF file over from one build to another.  Note that the resulting VCF could be mis-sorted.
  */
 @Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
-public class LiftoverVCF extends RodWalker<Integer, Integer> {
+public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
     @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
     protected File CHAIN = null;