Mauricio Carneiro 7c3b3650bb BQSR bug triage ... * fixed bug where some keys were using the same recal datum objects * fixed quantization qual calculations when combining multiple reports * fixed rounding error with empirical quality reported when combining reports * fixed combine routine in the gatk reports due to the primary keys being out of order * added auto-recalibration option to BQSR scala script * reduced the size of the recalibration report by ~15% * updated md5's		2012-04-05 09:32:18 -04:00
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datasources	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	Added more primitives to GATK Report Column Type	2012-03-28 09:07:54 -04:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	BQSR bug triage	2012-04-05 09:32:18 -04:00
EngineFeaturesIntegrationTest.java	HierarchicalMicroScheduler no longer attempts to wrap exceptions	2012-03-23 11:27:21 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00