Mauricio Carneiro d561914d4f Revert "First implementation of GATKReportGatherer" ... premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport. This reverts commit aea0de314220810c2666055dc75f04f9010436ad.		2012-02-08 23:28:55 -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	Revert "First implementation of GATKReportGatherer"	2012-02-08 23:28:55 -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	Fixed discordance bug reported by Brad Chapman	2012-01-30 09:50:45 -05:00
EngineFeaturesIntegrationTest.java	Bugfix for incorrect error messages for missing BAMs and VCFs	2012-01-23 09:52:07 -05:00
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