Mark DePristo c97a361b5d Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF ... -- Helped ID more bugs in the ActivityProfile, necessitating a new algorithm for popping off active regions. This new algorithm requires that at least maxRegionSize + prob. propagation distance states have been examined. This ensures that the incremental results are the same as you get reading in an entire profile and running getRegions on the full profile -- TODO is to remove incremental search start algorithm, as this is no longer necessary, and nicely eliminates a state variable I was always uncomfortable with		2013-01-27 14:10:08 -05:00
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writer	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
AlleleUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GenotypeLikelihoodsUnitTest.java	The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases.	2013-01-16 10:22:43 -05:00
GenotypeUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GenotypesContextUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
VariantContextBenchmark.java	Updating to latest google caliper code	2013-01-11 15:17:16 -05:00
VariantContextTestProvider.java	Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF	2013-01-27 14:10:08 -05:00
VariantContextUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
VariantContextUtilsUnitTest.java	In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample).	2013-01-25 15:49:51 -05:00
VariantJEXLContextUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00