Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects ... -- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples -- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type. -- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name) -- Integrationtests updated and all pass		2011-11-11 15:00:35 -05:00
..
datasources	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
refdata	Fix for dynamic type determination for bgzip files	2011-09-21 15:39:19 -04:00
report	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
samples	Fixed bad expected value in PedReaderUnitTest	2011-10-06 08:16:47 -07:00
traversals	BugFix for unit test	2011-09-07 14:54:10 -04:00
walkers	VariantContext genotypes are now stored as GenotypeMap objects	2011-11-11 15:00:35 -05:00
EngineFeaturesIntegrationTest.java	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -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