Mark DePristo 3e01a76590 Clean up AlleleFrequencyCalculation classes ... -- Added a true base class that only does truly common tasks (like manage call logging) -- This base class provides the only public method (getLog10PNonRef) and calls into a protected compute function that's abstract -- Split ExactAF into superclass ExactAF with common data structures and two subclasses: DiploidExact and GeneralPloidyExact -- Added an abstract reduceScope function that manages the simplification of the input VariantContext in the case where there are too many alleles or other constraints require us to only attempt a smaller computation -- All unit tests pass		2012-10-03 19:55:11 -07:00
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bqsr	updating BQSR integration tests	2012-09-19 14:10:34 -04:00
compression/reducereads	Turn off RR tests while I debug	2012-09-21 17:26:00 -04:00
genotyper	Clean up AlleleFrequencyCalculation classes	2012-10-03 19:55:11 -07:00
haplotypecaller	Adding HC integration test for _structural_ insertions and deletions.	2012-09-12 12:23:00 -04:00