droazen 8d5b4af8ca Binomial and Multinomial interfaces for probability and coefficients in log and real space. Passed all unit tests. ... BinomialCumulativeProbability was reformatted to follow the now standard parameter order. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6057 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-22 22:55:15 +00:00
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alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	Fixing broken walker as per GS; adding integration test to cover it.	2011-06-22 22:54:04 +00:00
jna	Added an integration test showing how to use LSF C API to get LSF parameters.	2011-06-21 22:54:55 +00:00
oneoffprojects/walkers	Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.	2011-05-23 18:06:05 +00:00
playground/gatk/walkers	Fixed up md5s	2011-06-16 16:20:41 +00:00
utils	Binomial and Multinomial interfaces for probability and coefficients in log and real space. Passed all unit tests.	2011-06-22 22:55:15 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	The previous version of the UG was always creating BAQ'd pileups for the underlying site QUAL calculation. This resulted in some slowdown in the code. But as far as I can tell, the code actually didn't apply the BAQ'd base quality anywhere when the BAQ field wasn't in the read, so this just saves us 20% of the runtime when BAQ isn't enabled from heading into the BAQ subsystem when we don't actually want to get the BAQ'd base qualities.	2011-05-27 14:00:52 +00:00