Mauricio Carneiro 9f74969e3a BQSR with GATKReport implementation ... * restructured BQSR to report recalibrated tables. * implemented empirical quality calculation to the BQSR stage (instead of on-the-fly recalibration) * linked quality score quantization to the BQSR stage, outputting a quantization histogram * included the arguments used in BQSR to the GATK Report * included all three tables (RG, QUAL and COVARIATES) to the GATK Report with empirical qualities On-the-fly recalibration with GATK Report * loads all tables from the GATKReport using existing infrastructure (with minor updates) * implemented initialiazation of the covariates using BQSR's argument list * reduced memory usage significantly by loading only the empirical quality and estimated quality reported for each bit set key * applied quality quantization to the base recalibration * excluded low quality bases from on-the-fly recalibration for mismatches, insertions or deletions		2012-03-23 15:42:32 -04:00
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	BQSR with GATKReport implementation	2012-03-23 15:42:32 -04:00
test	BQSR with GATKReport implementation	2012-03-23 15:42:32 -04:00