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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mark DePristo dede3a30e9 Improvements to the validation report of VariantEval 
-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status.  This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF.  The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
 		2012-07-18 16:07:47 -04:00
..
datasources Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
downsampling Make downsampler classes themselves generic (instead of just the Downsampler interface) 2012-06-13 16:43:39 -04:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
iterators Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort. 2012-06-15 15:55:03 -04:00
refdata Minor bugfix -- now that the testfile is in our testdata regenerate the idx file as needed to pass tests 2012-06-26 15:28:32 -04:00
report Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
samples Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
traversals First pass of the asynchronous block loader. 2011-11-18 15:02:59 -05:00
walkers Improvements to the validation report of VariantEval 2012-07-18 16:07:47 -04:00
EngineFeaturesIntegrationTest.java Nearing final BCF commit 2012-06-14 16:42:32 -04:00
GenomeAnalysisEngineUnitTest.java Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding. 2012-06-27 01:15:22 -04:00
WalkerManagerUnitTest.java Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant. 2011-08-10 12:20:18 -04:00