aaron d8fedd59be docs, cleanup, and some improvements to the iterators. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-26 22:36:04 +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	docs, cleanup, and some improvements to the iterators.	2010-02-26 22:36:04 +00:00
oneoffprojects/walkers	Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample.	2010-02-26 16:39:47 +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	adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255.	2010-02-22 22:27:39 +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