Mark DePristo 9cb3fe3a59 Vastly better way of doing on-demand genotyping loading ... -- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading. -- This new class was replaced all of the old, complex functionality -- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency. This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily -- Misc. bug fixes throughout the system -- Bug fixes for PhaseByTransmission with new GenotypesContext		2011-11-20 08:23:09 -05:00
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datasources	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
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	Merge with master	2011-11-19 09:56:06 -05:00
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	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Vastly better way of doing on-demand genotyping loading	2011-11-20 08:23:09 -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