-- 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).
* when gathering, be aware that some keys will be missing from some tables.
* when a gatktable has no elements, it should still output the header so we know it had no records
- The Integer column type now accepts byte and shorts
- Updated Unit Tests and added a new testParse() test
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* 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
-- Minor refactoring of state key iteration in VEW.map to make the dependencies more clear
-- Long discussion about the performance problems with StateKey, and how to fix it, which I have run out of time to address before ESP meeting.
Mark DePristo
Eric Banks
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Roger Zurawicki