David Roazen 811f871f78 Do not fail tests that require the GATK private key if the user does not have permission to read it ... Several of the unit tests for the new key authorization feature require read access to the GATK master private key file. Since this file is only readable by members of the group gsagit, this makes it hard for people outside the group to run the test suite. Now, we skip tests that require the master private key if the private key exists (since not existing would be a true error) but is not readable by the user running the test suite Bamboo, of course, will always be able to run these tests.		2012-03-06 15:57:02 -05:00
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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	Do not fail tests that require the GATK private key if the user does not have permission to read it	2012-03-06 15:57:02 -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