From 7ef5ce28cc35eb93c2267643244d2afa9bc2b238 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 25 Jun 2012 20:56:00 -0400
Subject: [PATCH] VariantRecalibrator test currently doesn't work with
 shadowBCF

---
 .../VariantRecalibrationWalkersIntegrationTest.java              | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 8d6a18de0..857032579 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -70,6 +70,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -tranchesFile " + getMd5DB().getMD5FilePath(params.tranchesMD5, null) +
                         " -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
                 Arrays.asList(params.cutVCFMD5));
+        spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
         executeTest("testApplyRecalibration-"+params.inVCF, spec);
     }