Eric Banks 533c283783 Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine.		2012-03-30 10:37:14 -04:00
..
R	Further cleanup of R	2012-03-22 21:24:37 -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	Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine.	2012-03-30 10:37:14 -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	Added more primitives to GATK Report Column Type	2012-03-28 09:07:54 -04:00
testdata	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00