depristo 8072e9aed5 should never commit without running intergration tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-12 23:42:37 +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	should never commit without running intergration tests.	2010-02-12 23:42:37 +00:00
oneoffprojects/walkers/varianteval2	Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1	2010-02-12 15:26:52 +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	added root GATKData variable	2010-02-12 15:25:34 +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