Eric Banks 4fa439d89e Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now		2013-01-09 11:06:10 -05:00
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genotyper	Move around the DiploidGenotype classes (so it can be used by the GATKPaperGenotyper)	2013-01-08 15:53:11 -05:00
pairhmm	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
recalibration	Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now	2013-01-09 11:06:10 -05:00