Eric Banks e370030e6c As requested by Mark, I've broken out the code to pull out the protected subclass when available (and otherwise use the public version) into the GATKLiteUtils class. People should use this code instead of reimplementing all of the java reflection on their own.		2012-07-18 22:44:37 -04:00
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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	As requested by Mark, I've broken out the code to pull out the protected subclass when available (and otherwise use the public version) into the GATKLiteUtils class. People should use this code instead of reimplementing all of the java reflection on their own.	2012-07-18 22:44:37 -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	Updated md5s for DPP test	2012-07-17 21:54:46 -04:00
testdata	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00