ebanks 215e908a11 Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters. ... This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-31 02:16:39 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters.	2009-08-31 02:16:39 +00:00
test/org/broadinstitute/sting	Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).	2009-08-30 19:16:30 +00:00