-- Created a new Genotype interface with a more limited set of operations
-- Old genotype object is now SlowGenotype. New genotype object is FastGenotype. They can be used interchangable
-- There's no way to create Genotypes directly any longer. You have to use GenotypeBuilder just like VariantContextBuilder
-- Modified lots and lots of code to use GenotypeBuilder
-- Added a temporary hidden argument to engine to use FastGenotype by default. Current default is SlowGenotype
-- Lots of bug fixes to BCF2 codec and encoder.
-- Feature additions
-- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes
-- Cleaned up semantics of subContextFromSamples. There's one function that either rederives or not the alleles from the subsetted genotypes
-- MASSIVE BUGFIX in SelectVariants. The code has been decoding genotypes always, even if you were not subsetting down samples. Fixed!
This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
Mark DePristo
Laurent Francioli
Christopher Hartl
David Roazen