From 7cf9a54b6485ea7319c3eddf098a3b7106c499ad Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 27 Aug 2009 23:47:56 +0000
Subject: [PATCH] change for new char/byte in BaseUtils

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1467 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/recalibration/CovariateCounter.java  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java
index 3d9214bc0..4d511bce0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounter.java
@@ -121,9 +121,9 @@ public class CovariateCounter {
         char prevBase = (char)bases[offset - 1];
 
         if (read.getReadNegativeStrandFlag()) {
-            ref = (char)BaseUtils.simpleComplement(ref);
-            base = (char)BaseUtils.simpleComplement(base);
-            prevBase = (char)BaseUtils.simpleComplement((char)bases[offset+1]);
+            ref = BaseUtils.simpleComplement(ref);
+            base = BaseUtils.simpleComplement(base);
+            prevBase = BaseUtils.simpleComplement((char)bases[offset+1]);
             cycle = read.getReadLength() - (offset + 1);
         }