-- 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>
* if a read starts with insertion, and is part of a read that overlaps both the consensus and the variant region, and the insertion is the first base of this read. Don't try to remove it.
* keep the last header element in a variant region to prevent adjacent reads starting with insertions from breaking when trying to remove the header element before the insertion.
* if a read starts with insertion, and is part of a read that overlaps both the consensus and the variant region, and the insertion is the first base of this read. Don't try to remove it.
*
* 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
* Turn off the post-downsampler by default until new implementation.
* optimized read clipping in consensus regions -- only clip once instead of every time the window slides.
* extracted HeaderElement into it's own class.
* moved RFA to archive
* unified the context size of indels and mismatches
Mark DePristo
Mauricio Carneiro
Eric Banks
Guillermo del Angel
David Roazen
Joel Thibault
Roger Zurawicki
Ryan Poplin