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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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Renamed NO_HEADER to the more accurate no_cmdline_in_header	2012-05-24 10:57:08 -04:00
testdata	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00