chartl 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] ... Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output). Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-25 20:25:07 +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	Clean up the code a bit following the introduction of reduceByInterval.	2010-02-25 01:20:22 +00:00
oneoffprojects/walkers	Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt]	2010-02-25 20:25:07 +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