-- Replaced getAttributes with getDP() and not the old style getAttribute, where appropriate
-- Added getAnyAttribute and hasAnyAttribute that actually does the expensive work of seeing if the key is something like GT, AD or another inline datum, and returns it. Very expensive but convenient.
-- Fixed nasty subsetting bug in SelectVariants with excluding samples
-- Generalized VariantsToTable to work with new inline attributes (using getAnyAttribute) as well as GT
-- Bugfix for dropping old style GL field values
-- Added test to VCFWriter to ensure that we have the sample number of samples in the VC as in the header
-- Bugfix for Allele.getBaseString to properly show NO_CALL alleles
-- getGenotypeString in Genotype returns "NA" instead of null for ploidy == 0 genotypes
-- Cleanup some (but not all) VCF3 files. Turns out there are lots so...
-- Refactored gneotype parser from VCFCodec and VCF3Codec into a single shared version in AbstractVCFCodec. Now VCF3 properly handles the new GenotypeBuilder interface
-- Misc. bugfixes in GenotypeBuilder
-- Now only includes leaf nodes in the summary, i.e., summaries of the form "*.*....*.X", which are really the most valuable to see. This calculation can be accomplished in linear time for N differences, rather than the previous O(n^2) algorithm
-- Now computes the max number of elements to read correctly. Counts now the size of the entire element tree, not just the count of the roots, which was painful because the trees vary by orders of magnitude in size.
-- Because of this we can enforce a meaningful, useful value for the max elements in MD5 or 100K, and this works well.
-- Added integration test for new leaf and old pairwise calculations
-- Bugfix for Utils.join(sep, int[]) that was eating the first element of the AD, PL fields
-- BCFFieldEncoder and writers divide up the task of formatting values (atomic or vector, ints, strings, floats, etc) from the task of writing these out at the sites or genotypes level.
-- Allows us to create efficient encoders for specific combinations of header fields, such as int[] encoded values with exactly 3 values
-- Currently only used for INFO fields, but subsequent commit will include optimized genotype field encoder
-- Allowed us to naturally support encoding of lists of strings
-- Bugfixes in VariantContextUtils introduced in genotype -> genotypebuilder conversion
-- Fixes for integration test failures
-- Enabling contig updates
-- WalkerTest now prints out relative paths where possible to make cut/paste/run easier
-- As values in VCs are becoming their native Java types the VCFWriter needs to own proper float formating.
-- Created a smart float formatter in VCFWriter, with unit tests
-- Removed makePrecisionFormatStringFromDenominatorValue and its uses
-- Fix broken contracted
-- Refactored some code from the encoder to utils in BCF2
-- HaplotypeCaller's GenotypingEngine was using old version of subset to context. Replaced with a faster call that I think is correct. Ryan, please confirm.
-- FastGenotypes are the default in the engine. Use --useSlowGenotypes engine argument to return to old representation
-- Cleanup of BCF2Codec. Good error handling. Added contracts and docs.
-- Added a few more contacts and docs to BCF2Decoder
-- Optimized encodePrimitive in BCF2Encoder
-- Removed genotype filter field exceptions
-- Docs and cleanup of BCF2GenotypeFieldDecoders
-- Deleted unused BCF2TestWalker
-- Docs and cleanup of BCF2Types
-- Faster version of decodeInts in VCFCodec
-- BCF2Writer
-- Support for writing a sites only file
-- Lots of TODOs for future optimizations
-- Removed lack of filter field support
-- No longer uses the alleleMap from VCFWriter, which was a Allele -> String, now uses Allele -> Integer which is faster and more natural
-- Lots of docs and contracts
-- Docs for GenotypeBuilder. More filter creation routines (unfiltered, for example)
-- More extensive tests in VariantContextTestProfiler, including variable length strings in genotypes and genotype filters. Better genotype comparisons
-- decodeIntArray in BCF2 decoder allows us to more efficiently read ints and int[] from stream directly into Genotype object
-- Code cleanup / contracts added were appropriate
-- V2 will have a yet more optimized path...
-- 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
-- The way I was handling the contig offset ordering wasn't correct. Now the contigs are always indexed in the order in which their corresponding populate() functions are called, so that the order of the contigs is given by the order in which they are in the file, or in our refDict. It has nothing to do with the contig index itself.
-- SelectVariants no longers prints all samples to the screen if you aren't selecting any explicitly
-- 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
* 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
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.
Mark DePristo
Mauricio Carneiro
Eric Banks
Ryan Poplin
Khalid Shakir