Mauricio Carneiro 1b75663178 BQSR Gatherer implementation and integration tests ... * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration		2012-03-27 13:50:22 -05:00
..
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	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00
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 Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00