From 53895e15cd1642eb50fb2c6c00044c13a6c1074a Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 5 Mar 2014 19:26:37 -0500 Subject: [PATCH] Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING --- .../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 33dfa54ce..56f12d020 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.VECTOR_LOGLESS_CACHING; + public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.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)