-- Molten now supports variableName and valueName so you don't have to use variable and value if you don't want to.
-- Cleanup code, reorganize a bit more.
-- Fix for broken integrationtests
*** 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
-- Added memory and safety optimizations to StratNode and StratificationManager. Fresh, immutable Hashmaps are allocated for final data structures, so they exactly the correct size and cannot be changed by users.
-- Added ability of a stratification to specify incompatible evaluation. The two strats using this are AC and Sample with VariantSummary, as this computes per-sample averages and so combining these results in an O(n^2) memory requirement. Added integration test to cover incompatible strats and evals
-- Renamed and reorganized infrastructure
-- StratificationManager now a Map from List<Object> -> V. All key functions are implemented. Less commonly used TODO
-- Ready for hookup to VE
-- Created a unit tested tree mapping from a List<String> -> integer (StratificationStates). This class is the key infrastructure necessary to create a complete static mapping from all stratification combinations to an offset in a vector of EvalutionContexts for update in map.
-- Minor code cleanup throughout VE (removing unused headers, for example)
VariantEval is overly abusive of the GATKReport (lack of) spec.
1. It converts numeric values (longs, integers and doubles) to string before sending to the Report, then expects it to decipher that those were actually numbers.
2. Worse, the stratification modules somehow instead of sending the actual values to the report table, sends a string with the value "unknown" and then abuses the GATKReport spec to convert those "unknown" placeholder values with numbers. Then again, it expects the report to know those are numbers, not strings.
Now that the GATKReport HAS specs, VariantEval needs to be overhauled to conform with that. In the meantime, I have added special ad-hoc treatment to these wrong contracts. It works, and the integration tests all passed without changing any MD5's, but right after Mark and Ryan commit their VariantEval refactors, I will step in to change the way it interacts with the GATKReport, so we can clean up the GATKReport.
No wonder, the printing needed to be O(n^2).
Mark DePristo
Ryan Poplin
Guillermo del Angel
Eric Banks
Mauricio Carneiro
Menachem Fromer