From bd11060e7218e111aed395059f31916ad12dd429 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 27 Jan 2010 21:51:54 +0000
Subject: [PATCH] Ups, I did it again. Fixing the bug introduced in a previous
 commit: use correct length of the indel event.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2713 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/fasta/PickSequenomProbes.java            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
index 965ee935c..85cedf520 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
@@ -100,7 +100,7 @@ public class PickSequenomProbes extends RefWalker<String, String> {
         else if ( variant.isInsertion() )
             assay_sequence = leading_bases + refBase + "[-/" + Utils.join("",variant.getAlleleList()) + "]" + trailing_bases;
         else if ( variant.isDeletion() )
-            assay_sequence = leading_bases + refBase + "[" + Utils.join("",variant.getAlleleList()) + "/-]" + trailing_bases.substring(variant.getAlleleList().size());
+            assay_sequence = leading_bases + refBase + "[" + Utils.join("",variant.getAlleleList()) + "/-]" + trailing_bases.substring(variant.getAlleleList().get(0).length());
         else
             return "";