Mark DePristo 979a84a252 Bugfix for thread unsafe PL cache ... -- See https://getsatisfaction.com/gsa/topics/unifiedgenotyper_error_indel?utm_content=topic_link&utm_medium=email&utm_source=new_topic -- Solution is to use a fixed cache that's never updated on the fly. My changes limit us to having no more than 500 alleles at a site, which I hope is ok but easy enough to up to a ridiculously large number.		2012-03-27 22:42:30 -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	Bugfix for thread unsafe PL cache	2012-03-27 22:42:30 -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