David Roazen 506c0e9c97 Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline ... SnpEff support will remain disabled until SnpEff 2.0.4 has been officially released and we've verified the quality of its annotations.		2011-12-23 19:12:57 -05:00
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datasources	Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.	2011-12-06 10:10:38 -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	Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.	2011-12-06 10:10:38 -05:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
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	Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline	2011-12-23 19:12:57 -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