From ad97099df63c1754d9519b9466c591ee14d30a34 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Jun 2011 03:08:47 +0000
Subject: [PATCH] Getting rid of a few extra, very explicit qualifications so
 that the public/ private bifurcation script doesn't have to discover them.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5956 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffprojects/walkers/IndelCountCovariates/Dinuc.java    | 4 ++--
 .../sting/playground/gatk/walkers/reducereads/BaseCounts.java | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/Dinuc.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/Dinuc.java
index 2d1fc592e..6af404154 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/Dinuc.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/Dinuc.java
@@ -31,7 +31,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates;
  * Date: Nov 16, 2009
  */
 //public class Dinuc implements Comparable<org.broadinstitute.sting.gatk.walkers.recalibration.Dinuc>{
-public class Dinuc implements Comparable<org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Dinuc>{
+public class Dinuc implements Comparable<Dinuc>{
     private byte first;
     private byte second;
 
@@ -50,7 +50,7 @@ public class Dinuc implements Comparable<org.broadinstitute.sting.oneoffprojects
         second = _second;
     }
 
-    public int compareTo(final org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Dinuc that) {
+    public int compareTo(final Dinuc that) {
         if( this.first > that.first ) { return 1; }
         else if( this.first < that.first ) { return -1; }
         else { //this.first equals that.first
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java
index 26fc65291..dd5ace93d 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
 
-import org.broadinstitute.sting.alignment.reference.bwt.Counts;
 import org.broadinstitute.sting.utils.BaseUtils;
 import com.google.java.contract.*;