ebanks 850f36aa61 Changes to the Unified Genotyper's arguments: ... 1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites. 2. User can cap the base quality by the read's mapping quality (not done yet). 3. Default confidence threshold is now Q30. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-30 16:44:24 +00:00
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alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Changes to the Unified Genotyper's arguments:	2010-04-30 16:44:24 +00:00
playground	Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.	2010-04-29 22:50:17 +00:00
utils	Rev the reservoir downsampler to support partitioning through a functor.	2010-04-21 19:50:26 +00:00
BaseTest.java	Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).	2010-04-09 18:30:59 +00:00
WalkerTest.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00