rpoplin 5f58492401 A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-07 21:17:39 +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	A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.	2010-01-07 21:17:39 +00:00
playground/gatk/walkers	Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker	2010-01-07 00:03:29 +00:00
utils	Minor interface change for VCFGenotypeRecord.	2010-01-07 16:48:09 +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