zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Revert "Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING" 

This reverts commit cef03f089fb3f131f3a77664b71feaec51a74cc8.
This commit is contained in:
David Roazen 2014-03-06 10:15:35 -05:00
parent 53895e15cd
commit 3f3df90412
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -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.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)