Khalid Shakir 91cb654791 AggregateMetrics: ... - By porting from jython to java now accessible to Queue via automatic extension generation. - Better handling for problematic sample names by using PicardAggregationUtils. GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name. CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering. Added SelectHeaders walker for filtering headers for dbGAP submission. Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter. Latest WholeGenomePipeline. Other minor cleanup to utility methods.		2012-04-17 11:45:32 -04:00
..
R	Improve variantCallQC.R	2012-04-13 17:00:37 -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	AggregateMetrics:	2012-04-17 11:45:32 -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	AggregateMetrics:	2012-04-17 11:45:32 -04:00
testdata	continuing the BQSR triage...	2012-04-05 14:34:15 -04:00