Eric Banks 0dd571928d Let's not have the indel model emit more than the max possible number of genotypable alt alleles (since we may not be able to subset down to the best ones).		2012-04-12 15:16:29 -04:00
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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	Let's not have the indel model emit more than the max possible number of genotypable alt alleles (since we may not be able to subset down to the best ones).	2012-04-12 15:16:29 -04:00
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