* fixed the loading of the new reduced size reports
* reduced BQSR scala script memory to 2Gb
* removed dcov parameter from BQSR scala script
* fixed estimatedQReported calculation from -log10(pe) to -10*log10(pe).
* updated md5's with the proper PHRED scaled EstimatedQReported
* fixed bug where some keys were using the same recal datum objects
* fixed quantization qual calculations when combining multiple reports
* fixed rounding error with empirical quality reported when combining reports
* fixed combine routine in the gatk reports due to the primary keys being out of order
* added auto-recalibration option to BQSR scala script
* reduced the size of the recalibration report by ~15%
* updated md5's
* 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
* 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
* Added standard pipeline test for the DPP
* Added a full BWA pipeline test for the DPP
* Included the extra files for the reference needed by BWA (to be used by DPP and PPP tests)
* added a pipeline test to the Pacbio Processing Pipeline.
* updated exampleBAM with more complete RG information so we can use it in a wider variety of pipeline tests
* added exampleDBSNP.vcf file with only chromosome 1 in the range of the exampleFASTA.fasta reference for pipeline tests
Mauricio Carneiro
Mark DePristo
David Roazen