ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. ... This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all. The major changes here are that 1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes 2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called). The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-06 03:12:41 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
test/org/broadinstitute/sting	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00