gatk-disable-vectorloglesscaching.patch

From 569f593a141befd88e21ce66edc62e42988c8c80 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 14 Jan 2018 23:42:32 +0100
Subject: [PATCH] Disable VectorLoglessCaching.

---
 .../walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
index 8daffb915..61b0bdff1 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
@@ -71,7 +71,7 @@ public class LikelihoodEngineArgumentCollection {
      */
     @Hidden
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
 
     /**
      * This argument is intended for use in the test suite only. It gives developers the ability to select of the
-- 
2.15.1