-- Eliminated the large intermediate map from field name to list of list<Integer> values needed to create genotypes without the GenotypeBuilder. The new code is cleaner and simply fills in an array of GenotypeBuilders as it moves through the column layout in BCF2
-- Now we create once decoders specialized for each GT field (GT, AD, etc) that can be optimized for putting data into the GenotypeBuilder. In a subsequent commit these will actually use lower level BCF2 decoders to create the low-level ints and int[], avoiding the intermediate List<Integer> form
-- Reduced the amount of data further to be computed in the DiffEngine. The DiffEngine algorithm needs to be rethought to be efficient...
-- Builder now provides a depreciated log10pError function to make a new GQ value
-- Genotype is an abstract class, with most of the associated functions implemented here and not in the derived Fast and Slow versions
-- Lots of contracts
-- Bugfixes throughout
-- 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
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
Instead of creating a supposed network temporary directory locally which then fails when remote nodes try to access the non-existant dir, now checking to see if they network directory is available and throwing a SkipException to bypass the test when it cannot be run.
TODO: Throw similar SkipExceptions when fastas are not available. Right now instead of skipping the test or failing fast the REQUIRE_NETWORK_CONNECTION=false means that the errors popup later when the networked fastas aren't found.
- Merged Roger's metrics with Mauricio's optimizations
- Added Stats for DiagnoseTargets
- now has functions to find the median depth, and upper/lower quartile
- the REF_N callable status is implemented
- The walker now runs efficiently
- Diagnose Targets accepts overlapping intervals
- Diagnose Targets now checks for bad mates
- The read mates are checked in a memory efficient manner
- The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker.
- Fixed some bugs
- Removed rod binding
Added more Unit tests
- Test callable statuses on the locus level
- Test bad mates
- Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
-- VCFWriter / codec now passes the same rigorous UnitTest as the BCF2 writer / codec. As part of this we now can only test doubles for equivalence in VCFs to 1e-2 (not exactly impressive)
-- This version of BCF should actually work properly for most files, assuming headers are properly defined.
-- Lots of bug fixes to BCF2 codec
-- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL. NOTE THIS SEMANTICS change
-- Equals() method for GenotypeLikelihoods, using PLs.
-- VCFCodec now longer adds empty bindings to missing input field values. NOTE THIS CHANGE
-- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work. The BCF2 codec now makes VCs marked as fully decoded
-- stringToBytes returns empty list for null or "" string in BCF2Encoder
-- Proper handling of genotype ordering in BCF2 reader / writer
-- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily
-- Many failing MD5s now due to double -> int change in GQ, will update later
-- Added a new parameter to control the maximum number of pairwise differences to generate, which previously could expand to a very large number when there were lots of differences among genotypes, resulting in a n^2 algorithm running with n > 1,000,000
-- Cut down the size of a few large files in public/testdata that were only used in part
-- Refactor vcf Filename => shadow BCF filename to BCF2Utils. Fix bug in WalkerTest due to the way this was handled previously
-- Fully working version
-- Use -generateShadowBCF to write out foo.bcf as well as foo.vcf anywhere you use -o foo.vcf
-- Moved MedianUnitTest to its proper home in Utils
-- Added reportng to ivy and testng, so build/report/X/html/ is a nicely formatted output for Unit and Integration tests. From this website it's easy to see md5 diffs, etc. This is a vastly better way to manage unit and integration test output
--handle entirely missing GT in a sample in decodeGenotypeAlleles
--Create MAX_ALLELES_IN_GENOTYPES constant in BCF2Utils, and extracted its use inline from the code
-- Generalized genotype writing code to handle ploidy != 2 and variable ploidy among samples
-- Remove special case inline treatment of case where all samples have no GT field values, and moved this into calcVCFGenotypeKeys
-- Removed restriction on getPloidy requiring ploidy > 1. It's logically find to return 0 for a no called sample
-- getMaxPloidy() in VC that does what it says
-- Support for padding / depadding of generic genotype fields
-- fixed final bugs with PL encoding / decoding
-- Ready for testing by other members of the group
-- Current performance numbers aren't so great, but they will improve in the next phase of BCF2 optimizations
-- Fixed a nasty bug in the filter field
-- Not that some (many?) GATK tools won't work with BCF because they internally assume values are Strings not their true types
Read 1500 genotypes file in VCF -> VCF : 11 seconds
Read 1500 genotypes file in VCF -> BCF : 9.5 seconds
VariantEval 1500 genotypes file in VCF : 3 seconds
VariantEval 1500 genotypes file in BCF : 3 seconds
-- Trivial import changes in some walkers
-- SelectVariants has a new hidden mode to fully decode a VCF file
-- DepthPerAlleleBySample (AD) changed to have not UNBOUNDED by A type, which is actually the right type
-- GenotypeLikelihoods now implements List<Double> for convenience. The PL duality here is going to be removed in a subsequent commit
-- BugFixes in BCF2Writer. Proper handling of padding. Bugfix for nFields for a field
-- padAllele function in VariantContextUtils
-- Much better tests for VariantContextTestProvider, including loading parts of dbSNP 135 and the Phase II 1000G call set with genotypes to test encoding / decoding of fields.
-- List<String> is converted inside of the codec to a collapsed string, and exploded in the decoder.
-- Unified the type conversion code in BCFWriter to simply the mapping from VCF type => BCF type and special value recoding
-- Code cleanup and renaming
-- Convenience routine for creating alleles from strings of bases
-- Convenience constructor for VCFFilterHeader line whose description is the same as name
-- VariantContextTestProvider creates all sorts of types of VariantContexts for testing purposes. Can be reused throughtout code for BCF, VCF, etc.
-- Created basic BCF2WriterCodec tests that consumes VariantContextTestProvider contexts, writes them to disk with BCF2 writer, and checks that they come back equals to the original VariantContexts. Actually worked for some complex tests in the first go
-- Moved VCF and BCF writers to variantcontext.writers
-- Updated vcf.jar build path
-- Refactored VCFWriter and other code. Now the best (and soon to be only) way to create these files is through a factory method called VariantContextWriterFactory. Renamed the general VCFWriter interface to VariantContextWriter which is implemented by VCFWriter and BCF2Writer.
-- Refactored VCF writers into vcf.writers package
-- Moved BCF2Writer to bcf2.writer
-- Updates to all of the walkers using VCFWriter to reflect new packages
-- A large number of files had their headers cleaned up because of this as well
Mark DePristo
Eric Banks
David Roazen
Ryan Poplin
Khalid Shakir
Roger Zurawicki
Guillermo del Angel