Mark DePristo a3d896d80e Part I of creating a fast state space lookup for VE ... -- Created a unit tested tree mapping from a List<String> -> integer (StratificationStates). This class is the key infrastructure necessary to create a complete static mapping from all stratification combinations to an offset in a vector of EvalutionContexts for update in map. -- Minor code cleanup throughout VE (removing unused headers, for example)		2012-03-30 15:31:53 -04:00
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datasources	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00
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	a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.	2012-02-25 13:57:28 -05:00
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	Part I of creating a fast state space lookup for VE	2012-03-30 15:31:53 -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