depristo c66861746a improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-10 16:12:29 +00:00
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alignment	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
gatk	CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard	2010-02-10 15:52:20 +00:00
oneoffprojects/walkers/varianteval2	improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started	2010-02-10 16:12:29 +00:00
playground/gatk/walkers	Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names.	2010-02-02 00:22:15 +00:00
utils	Updated VCF Reader to parse VCFs according to the VCFv3.3 spec. Column headers are tab separated since sample names might have spaces.	2010-02-08 22:55:59 +00:00
BaseTest.java	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00