ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. ... - Reimplemented optimization in UG to not call when there are no non-ref bases. - Compute reference confidence accurately in UG for ref calls. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-26 21:56:33 +00:00
..
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	- Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads.	2010-01-26 21:56:33 +00:00
playground/gatk/walkers	Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly.	2010-01-21 17:35:20 +00:00
utils	Looks bigger than it is:	2010-01-15 00:14:35 +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