From 150a9692797744d4b0147d6f49b07d3522b8ec22 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 29 Aug 2012 15:13:28 -0400
Subject: [PATCH] Be careful with String manipulation when constructing alleles
 in SomaticIndelDetector

---
 .../sting/gatk/walkers/indels/SomaticIndelDetector.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index b0c09f78e..3965a63fb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
@@ -1181,10 +1181,10 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
         if ( event_length == 0 ) { // insertion
 
             l.add( Allele.create(referencePaddingBase,true) );
-            l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), false ));
+            l.add( Allele.create((char)referencePaddingBase + new String(call.getVariant().getBases()), false ));
 
         } else { //deletion:
-            l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), true ));
+            l.add( Allele.create((char)referencePaddingBase + new String(call.getVariant().getBases()), true ));
             l.add( Allele.create(referencePaddingBase,false) );
         }
     }