Eric Banks 56f8afab97 Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.		2012-08-01 09:50:00 -04:00
..
R	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -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	Requested by Geraldine: adding a utility to register deprecated walkers (and the major version of the first release since they were removed) so that the User Error printed out for e.g. CountCovariates now states: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0.	2012-08-01 09:50:00 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.	2012-08-01 09:23:04 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00