Mark DePristo 1011f3862b CalibrateGenotypeLikelihoods now emits the position of the variant for debugging ... -- Refactored some duplicated code (FYI, code duplication = root of all evil) into shared functions -- Added long-missing integrationtests -- CHRIS/RYAN -- it would be very good to add an integration test covering external VCF files as I believe we rely on this functionality and it's not tested at all		2012-03-09 16:00:07 -05:00
..
R	Now converts gatkreports to properly typed R data types in gsa.read.gatkreport	2012-03-02 09:11:59 -05:00
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	CalibrateGenotypeLikelihoods now emits the position of the variant for debugging	2012-03-09 16:00:07 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
testdata	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00