-- 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
--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.
From tribble logs:
Binary feature support in tribble
-- Massive refactoring and cleanup
-- Many bug fixes throughout
-- FeatureCodec is now general, with decode etc. taking a PositionBufferedStream
as an argument not a String
-- See ExampleBinaryCodec for an example binary codec
-- AbstractAsciiFeatureCodec provides to its subclass the same String decode,
readHeader functionality before. Old ASCII codecs should inherit from this base
class, and will work without additional modifications
-- Split AsciiLineReader into a position tracking stream
(PositionalBufferedStream). The new AsciiLineReader takes as an argument a
PositionalBufferedStream and provides the readLine() functionality of before.
Could potentially use optimizations (its a TODO in the code)
-- The Positional interface includes some more functionality that's now
necessary to support the more general decoding of binary features
-- FeatureReaders now work using the general FeatureCodec interface, so they can
index binary features
-- Bugfixes to LinearIndexCreator off by 1 error in setting the end block
position
-- Deleted VariantType, since this wasn't used anywhere and it's a particularly
clean why of thinking about the problem
-- Moved DiploidGenotype, which is specific to Gelitext, to the gelitext package
-- TabixReader requires an AsciiFeatureCodec as it's currently only implemented
to handle line oriented records
-- Renamed AsciiFeatureReader to TribbleIndexedFeatureReader now that it handles
Ascii and binary features
-- Removed unused functions here and there as encountered
-- Fixed build.xml to be truly headless
-- FeatureCodec readHeader returns a FeatureCodecHeader obtain that contains a
value and the position in the file where the header ends (not inclusive).
TribbleReaders now skip the header if the position is set, so its no longer
necessary, if one implements the general readHeader(PositionalBufferedStream)
version to see header lines in the decode functions. Necessary for binary
codecs but a nice side benefit for ascii codecs as well
-- Cleaned up the IndexFactory interface so there's a truly general createIndex
function that takes the enumerated index type. Added a writeIndex() function
that writes an index to disk.
-- Vastly expanded the index unit tests and reader tests to really test linear,
interval, and tabix indexed files. Updated test.bed, and created a tabix
version of it as well.
-- Significant BinaryFeaturesTest suite.
-- Some test files have indent changes
Returns true iff VC is an non-complex indel where every allele represents an expansion or
contraction of a series of identical bases in the reference.
The logic of this function is pretty simple. Take all of the non-null alleles in VC. For
each insertion allele of n bases, check if that allele matches the next n reference bases.
For each deletion allele of n bases, check if this matches the reference bases at n - 2 n,
as it must necessarily match the first n bases. If this test returns true for all
alleles you are a tandem repeat, otherwise you are not. Note that in this context n is the
base differences between the ref and alt alleles
-- Now properly handles the case where a sample isn't present (no longer adds a null to the genotypes list)
-- Fix for logic failure where if the number of requested samples equals the number of known genotypes then all of the records were returned, which isn't correct when there are missing samples.
-- Unit tests added to handle these cases
-- Now you provide a LazyParsing object
-- LazyGenotypesContext now knows nothing about the VCF parser itself. The parser holds all of the necessary data to parse the VCF genotypes when necessarily, and the LGC only has a pointer to this object
-- Using new interface added LazyGenotypesContext to unit tests with a simple lazy version
-- Deleted VCFParser interface, as it was no longer necessary
-- We should no longer have md5s changing because of hashmaps changing their sort order on us
-- Added GenotypeLikelihoodsUnitTests
-- Refactored ExactAFCaclculation to put the PL -> QUAL calculation in the GenotypeLikelihoods class to avoid the code copy.
-- New approach to making VariantContexts modeled on StringBuilder
-- No more modify routines -- use VariantContextBuilder
-- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono
-- getChromosomeCount -> getCalledChrCount
-- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain
-- VCFCodec now uses optimized cached information to create GenotypesContext.
-- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2.
-- Naming changes for getSamplesNameInOrder()
-- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4
-- 1.3 VC and associated utilities copied wholesale into test directory under v13
-- I have no idea why I named this InferredGeneticContext, a totally meaningless term
-- Renamed to CommonInfo.
-- Made package protected, as no one should use this outside of VariantContext and Genotype
-- UGEngine was using IGC constant, but it's now using the public one in VariantContext.
Mark DePristo
Guillermo del Angel
Eric Banks
Ryan Poplin
Laurent Francioli