Mauricio Carneiro e39a59594a BQSR triage and test routines ... * updated BQSR queue script for faster turnaround * implemented plot generation for scatter/gatherered runs * adjusted output file names to be cooperative with the queue script * added the recalibration report file to the argument table in the report * added ReadCovariates unit test -- guarantees that all the covariates are being generated for every base in the read * added RecalibrationReport unit test -- guarantees the integrity of the delta tables		2012-04-23 11:23:00 -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	BQSR triage and test routines	2012-04-23 11:23:00 -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