David Roazen 0550b27799 Make downsampler classes themselves generic (instead of just the Downsampler interface) ... This is in response to a request from Mauricio to make it easier to use the downsamplers with GATKSAMRecords (as opposed to SAMRecords) without having to do any cumbersome typecasting. Sadly, Java language limitations make this sort of solution the best choice. Thanks to Khalid for his feedback on this issue. Also: -added a unit test to verify GATKSAMRecord support with no typecasting required -added some unit tests for the FractionalDownsampler that Mauricio will/might be using -moved classes from private to public to better sync up with my local development branch for engine integration		2012-06-13 16:43:39 -04:00
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datasources	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Bugfixes and testdata cleanup	2012-05-24 13:26:05 -04:00
report	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
samples	Added function to get founders IDs in SampleDB	2012-04-25 12:49:36 -04:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Drat, forgot the unit tests again	2012-06-12 19:00:47 -04:00
EngineFeaturesIntegrationTest.java	More extensive testing of type of error thrown in multi-threaded walker test	2012-04-13 09:23:33 -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