From 20601f034e97456ba5f2c5d30b4ca0eca1348d76 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 22 Aug 2012 07:33:10 -0700
Subject: [PATCH] Updating the checkType() function to include the new
 StructuralIndel variant type. Fixes outstanding broken integration test.

---
 .../gatk/walkers/variantrecalibration/VariantDataManager.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index aacd987d5..33a543e39 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -286,6 +286,7 @@ public class VariantDataManager {
             case INDEL:
             case MIXED:
             case SYMBOLIC:
+            case STRUCTURAL_INDEL:
                 return checkVariationClass( evalVC, VariantRecalibratorArgumentCollection.Mode.INDEL );
             default:
                 return false;