From ed0d0d78faa6ca4cd1f23159e76c99929f8c4f96 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 8 Jul 2010 05:25:03 +0000
Subject: [PATCH] corresponding fix for dealing with insertions

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3739 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/sequenom/PickSequenomProbes.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
index 345105eb5..78f9c0540 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@@ -149,9 +149,9 @@ public class PickSequenomProbes extends RodWalker<String, String> {
 
         String assay_sequence;
         if ( vc.isSNP() )
-            assay_sequence = leading_bases + "[" + ref.getBaseAsChar() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
+            assay_sequence = leading_bases + "[" + (char)ref.getBase() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
         else if ( vc.isInsertion() )
-            assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
+            assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases;
         else if ( vc.isDeletion() )
             assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length()-1);
         else