From 3f3df904121797773858886cf897a1dce095b4ef Mon Sep 17 00:00:00 2001 From: David Roazen Date: Thu, 6 Mar 2014 10:15:35 -0500 Subject: [PATCH] Revert "Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING" This reverts commit cef03f089fb3f131f3a77664b71feaec51a74cc8. --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 56f12d020..33dfa54ce 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -433,7 +433,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @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.LOGLESS_CACHING; + public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING; @Hidden @Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)