Description:
Transforms a delegation dependency from HC to UG genotyping engine into a reusage by inhertance where HC and UG engines inherit from a common superclass GenotyperEngine
that implements the common parts. A side-effect some of the code is now more clear and redundant code has been removed.
Changes have a few consequence for the end user. HC has now a few more user arguments, those that control the functionality that HC was borrowing directly from UGE.
Added -ploidy argument although it is contraint to be 2 for now.
Added -out_mode EMIT_ALL_SITES|EMIT_VARIANTS_ONLY ...
Added -allSitePLs flag.
Stories:
https://www.pivotaltracker.com/story/show/68017394
Changes:
- Moved (HC's) GenotyperEngine to HaplotypeCallerGenotyperEngine (HCGE). Then created a engine superclass class GenotypingEngine (GE) that contains common parts between HCGE and the UG counterpart 'UnifiedGenotypingEngine' (UGE). Simplified the code and applied the template pattern to accomodate for small diferences in behaviour between both caller
engines. (There is still room for improvement though).
- Moved inner classes and enums to top-level components for various reasons including making them shorter and simpler names to refer to them.
- Create a HomoSpiens class for Human specific constants; even if they are good default for most users we need to clearly identify the human assumption across the code if we want to make
GATK work with any species in general; i.e. any reference to HomoSapiens, except as a default value for a user argument, should smell.
- Fixed a bug deep in the genotyping calculation we were taking on fixed values for snp and indel heterozygisity to be the default for Human ignoring user arguments.
- GenotypingLikehooldCalculationCModel.Model to Gen.*Like.*Calc.*Model.Name; not a definitive solution though as names are used often in conditionals that perhaps should be member methods of the
GenLikeCalc classes.
- Renamed LikelihoodCalculationEngine to ReadLikelihoodCalculationEngine to distinguish them clearly from Genotype likelihood calculation engines.
- Changed copy by explicity argument listing to a clone/reflexion solution for casting between genotypers argument collection classes.
- Created GenotypeGivenAllelesUtils to collect methods needed nearly exclusively by the GGA mode.
Tests :
- StandardCallerArgumentCollectionUnitTest (check copy by cloning/reflexion).
- All existing integration and unit tests for modified classes.
08203b516e