From c2c80dd9469d82d4197bb8f347b6872b04d12be6 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Jul 2009 16:28:39 +0000
Subject: [PATCH] cleanup and moving some things around to more logical
 locations

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1358 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotype/{ => confidence}/ConfidenceScoreComparator.java  | 4 +++-
 .../broadinstitute/sting/utils/genotype/glf/GLFWriter.java    | 2 --
 .../sting/utils/genotype/{ => tabular}/TabularLFWriter.java   | 4 +++-
 3 files changed, 6 insertions(+), 4 deletions(-)
 rename java/src/org/broadinstitute/sting/utils/genotype/{ => confidence}/ConfidenceScoreComparator.java (77%)
 rename java/src/org/broadinstitute/sting/utils/genotype/{ => tabular}/TabularLFWriter.java (92%)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/ConfidenceScoreComparator.java b/java/src/org/broadinstitute/sting/utils/genotype/confidence/ConfidenceScoreComparator.java
similarity index 77%
rename from java/src/org/broadinstitute/sting/utils/genotype/ConfidenceScoreComparator.java
rename to java/src/org/broadinstitute/sting/utils/genotype/confidence/ConfidenceScoreComparator.java
index 7e30e3b00..51f07cc23 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/ConfidenceScoreComparator.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/confidence/ConfidenceScoreComparator.java
@@ -1,4 +1,6 @@
-package org.broadinstitute.sting.utils.genotype;
+package org.broadinstitute.sting.utils.genotype.confidence;
+
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.Comparator;
 
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
index 769e4dc30..fc656649e 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
@@ -60,8 +60,6 @@ public class GLFWriter implements GenotypeWriter {
     // the last position written
     private int lastPos = 1;
 
-    int getRidOfMe = 0;
-
     /**
      * The public constructor for creating a GLF object
      *
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
similarity index 92%
rename from java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java
rename to java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
index 782601d97..2d9823e12 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
@@ -1,6 +1,8 @@
-package org.broadinstitute.sting.utils.genotype;
+package org.broadinstitute.sting.utils.genotype.tabular;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
+import org.broadinstitute.sting.utils.genotype.GenotypeOutput;
 
 import java.io.File;
 import java.io.FileNotFoundException;