ebanks 4e85416af1 [Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6008 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 17:35:37 +00:00
..
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	[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).	2011-06-16 17:35:37 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +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	No one should be calling the createHeader method(s) directly, but instead should be going through the full readHeader method (because it first sets the version); therefore I made them package protected and merged them. Updated the various unit tests that were using createHeader and were dangerously assuming that the header version was defaulting to 4.0 (which it no longer does).	2011-06-03 02:17:37 +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