hanna 8d2c14b29c Update Picard / sam-jdk at Tim's request. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-03 02:17:25 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Unit test fixed - Tribble codecs aren't designed to be stateless, but I was	2010-12-31 17:47:52 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.	2010-12-10 19:35:12 +00:00
refdata	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
traversals	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
walkers	No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...	2010-12-29 22:06:19 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00