Eric Banks 9c1ab1b0c0 Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency.		2012-07-18 21:11:33 -04:00
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src/org/broadinstitute/sting	Pool Caller refactoring in preparation of GATK 2.0: a) PoolCallerUnifiedArgumentCollection disappeared, and arguments moved to UnifiedArgumentCollection. b) PoolCallerWalker is no longer needed and redundant, all functionality subsumed by UG. UG now checks if GATK is lite - if so, don't allow ploidy > 2. c) Moved pool classes from private to protected. d) Changed the way to specify ploidy. Instead of specifying samples per pool and having ploidy = 2*samplesPerPool, have user specify ploidy directly, which is cleaner. Update tests accordingly. We can now call triploid seedless grape genotypes correctly in theory. e) Renamed argument -reference to -reference_sample_calls since the former is ambiguous and it's not clear what it refers to.	2012-07-17 15:27:04 -04:00
test/org/broadinstitute/sting/gatk/walkers	Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency.	2012-07-18 21:11:33 -04:00