-- 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!
-- Created new clean FastGenotype and GenotypeBuilder classes with contracts to enforce expected behavior and correctness. Tested utility of this approach by rewritting -- and then commenting out -- a path in BCF2Codec that could use this new code. Much cleaner interface now, but not yet hooked up to anything
-- Disabled SHADOW_BCF generation and generating contigs in the output VCFs automatically to ensure that the current code bases integration tests, before switching the code to new Genotype class
-- Code cleanup. Moved "AD" to VCFConstants under GENOTYPE_ALLELIC_DEPTHS. Uses in code replaced with constant
-- Refactored BCF2Codec into a LazyGenotypesDecoder object that provides on-demand genotype decoding of BCF2 data blocks a la VCFCodec.
-- VCFHeader has getters for sampleNamesInOrder and sampleNameToOffset instead of protected variables directly accessed by vcfcodec
This is in response to a request from Mauricio to make it easier
to use the downsamplers with GATKSAMRecords (as opposed to SAMRecords)
without having to do any cumbersome typecasting. Sadly, Java
language limitations make this sort of solution the best choice.
Thanks to Khalid for his feedback on this issue.
Also:
-added a unit test to verify GATKSAMRecord support with no typecasting required
-added some unit tests for the FractionalDownsampler that Mauricio will/might be using
-moved classes from private to public to better sync up with my local development
branch for engine integration
Moved some stuff in the DiagnoseTargets walker to the more general ThresHolder class
Minor tweaks
FindCoveredIntervals supports Gathering
FindCoveredIntervals outputs an interval list instead of GATKReport
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* Re-wrote the sliding window approach to allow the variant region not to clip the reads that overlap it.
* Updated consensus to include only reads that were not passed on by the variant region, header counts are updated on the fly to avoid recompute
* Added soft clipped bases to ReduceReads analysis by unclipping high quality soft-clips then re-clipping after reduce reads
* Updated all integration tests
Mark DePristo
Mauricio Carneiro
Eric Banks
Guillermo del Angel
David Roazen
Roger Zurawicki
Ryan Poplin