From e691fa3e1985f558e832f6da26960a64ce6c7f7f Mon Sep 17 00:00:00 2001
From: Scott Thibault <sthib@defiant.broadinstitute.org>
Date: Fri, 28 Jun 2013 08:52:09 -0500
Subject: [PATCH] FPGA null pointer bug fix

---
 .../walkers/haplotypecaller/LikelihoodCalculationEngine.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 60abc6a68..3cdad37ea 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -180,7 +180,7 @@ public class LikelihoodCalculationEngine {
 
     private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
         // first, a little set up to get copies of the Haplotypes that are Alleles (more efficient than creating them each time)
-	final BatchPairHMM batchPairHMM = (pairHMM instanceof BatchPairHMM) ? (BatchPairHMM)pairHMM : null;
+	final BatchPairHMM batchPairHMM = (pairHMM.get() instanceof BatchPairHMM) ? (BatchPairHMM)pairHMM.get() : null;
 	final Vector<GATKSAMRecord> batchedReads = new Vector<GATKSAMRecord>(reads.size());
         final int numHaplotypes = haplotypes.size();
         final Map<Haplotype, Allele> alleleVersions = new LinkedHashMap<>(numHaplotypes);
@@ -456,4 +456,4 @@ public class LikelihoodCalculationEngine {
         }
         throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" );
     }
-}
\ No newline at end of file
+}