Mark DePristo 804caf7a45 HaplotypeCaller Optimization: return a inactive (p = 0.0) activity if the context has no bases in the pileup ... -- Allows us to avoid doing a lot of misc. work to set up the genotype when we don't have any data to genotype. Valuable in the case where we are passing through large regions without any data		2013-01-27 14:10:06 -05:00
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annotator	Moving lots of walkers back from protected to public (along with several of the VA annotations).	2013-01-24 11:42:49 -05:00
bqsr	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
compression/reducereads	Merged bug fix from Stable into Unstable	2013-01-11 11:05:27 -05:00
diagnostics/targets	ActivityProfile now cuts intelligently at the best local minimum when in a larger than max size active region	2013-01-24 13:48:00 -05:00
genotyper	Don't let users play with the different exact model implementations.	2013-01-25 10:52:02 -05:00
haplotypecaller	HaplotypeCaller Optimization: return a inactive (p = 0.0) activity if the context has no bases in the pileup	2013-01-27 14:10:06 -05:00
indels	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	Moving lots of walkers back from protected to public (along with several of the VA annotations).	2013-01-24 11:42:49 -05:00
variantrecalibration	Moving lots of walkers back from protected to public (along with several of the VA annotations).	2013-01-24 11:42:49 -05:00
variantutils	Pulled out the --regenotype functionality from SelectVariants into its own tool: RegenotypeVariants.	2013-01-25 09:42:04 -05:00