Mark DePristo b063bcd38d Removing update0 support in VariantEval ... -- Now the only use for update0, calculating the number of processed loci, is centrally tracked in the walker itself not the evaluations. -- This allows us to avoid calling update0 are every genomic base in 100ks of evaluates when there are a lot of stratifications. -- No need to modify the integration tests, this optimization doesn't change the result of the calculation		2012-03-23 21:02:21 -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	Removing update0 support in VariantEval	2012-03-23 21:02:21 -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	Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-03-13 09:28:16 -04:00
testdata	BQSR with GATKReport implementation	2012-03-23 15:42:32 -04:00