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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Drat, forgot the unit tests again	2012-06-12 19:00:47 -04:00
BaseTest.java	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
MD5DB.java	Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s	2012-05-28 20:20:05 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s	2012-05-28 20:20:05 -04:00