9f74969e3a
* 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 |
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