Eric Banks dd571d9aa0 Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.		2012-07-04 01:22:20 -04:00
..
R	Bugfix for R 2.15 not including reshape	2012-06-14 16:42:29 -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	Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.	2012-07-04 01:22:20 -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	Pass the original GATK unsafe parameter to the VcfGatherFunction	2012-07-02 16:03:11 -04:00
testdata	Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.	2012-07-04 00:21:21 -04:00