4b45a2c99d
*** WAY FASTER *** -- 3x performance for multiple sample analysis with 1000 samples -- Analyzing 1MB of the ESP call set (3100 samples) takes 40 secs, compared to several minutes in the previous version -- According to JProfiler all of the runtime is now spent decoding genotypes, which will only get better when we move to BCF2 -- Remove the TableType system, as this was way too complex. No longer possible to embed what were effectively multiple tables in a single Evaluator. You now have to have 1 table per eval -- Replaced it with @Molten, which allows an evaluator to provide a single Map from variable -> value for analysis. IndelLengthHistogram is now a @Molten data type. GenotypeConcordance is also. -- No longer allow Evaluators to use private and protected variables at @DataPoints. You get an error if you do. -- Simplified entire IO system of VE. Refactored into VariantEvalReportWriter. -- Commented out GenotypePhasingEvaluator, as it uses the retired TableType -- Stratifications are all fully typed, so it's easy for GATKReports to format them. -- Removed old VE work around from GATKReportColumn -- General code cleanup throughout -- Updated integration tests |
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