From 63ad71cca6cebd4a9f60585ad63f868b5acc162d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Jun 2010 05:01:48 +0000
Subject: [PATCH] Fix busted code.  Note for all: String.valueOf(byte[])
 doesn't work.  You must use new String(byte[]).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3533 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/VariantContextAdaptors.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 973a89e2c..0cb24c573 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -156,7 +156,7 @@ public class VariantContextAdaptors {
                 if ( vcf.isDeletion() && refAllele.length() > alt.getLength() ) {
                     byte[] semiDeletion = new byte[refAllele.length() - alt.getLength()];
                     System.arraycopy(ref.getBases(), alt.getLength(), semiDeletion, 0, refAllele.length() - alt.getLength());
-                    allele = Allele.create(String.valueOf(semiDeletion), false);
+                    allele = Allele.create(new String(semiDeletion), false);
                 } else {
                     allele = Allele.create(alt.getBases(), false);
                 }