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Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING

This commit is contained in:
David Roazen 2014-03-05 19:26:37 -05:00
parent d3de6413c9
commit 53895e15cd
1 changed files with 1 additions and 1 deletions
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protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -433,7 +433,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, 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)