* field attributesCanBeModified - a null attributes object can't be modified in its current state
* method makeAttributesModifiable() - initialize a null attributes object to empty
-- Added MLEAC and MLEAF format lines to PoolCallerWalker
-- VariantFiltrationWalker now throws an error when JEXL variables cannot be found (XXX < 0.5) but passes through (albeit with a disgusting warning) when a variable is found but its value is a bad type (AF < 0.5) where AF == [0.04,0.00] at multi-allelic variation
-- Allow values to pass assertEquals in VariantContextTestProvider when one file contains X=[null, null] and the other has X missing
-- Update to 2.1.1 from 2.0
-- VariantFiltrationWalker now allows you to run with type unsafe selects, which all default to false when matching. So "AF < 0.5" works even in the presence of multi-allelics now.
--
-- MLAC and MLAF in PoolCaller now use standard MLE_AC and MLE_AF
-- VCFDiffableReader disables onTheFly fixing of VCF header fields so comparisons are easier when headers are changing
-- Flag fields with FLAG_KEY=0 are parsed as though FLAG_KEY were entirely absent in AbstractVCFCodec to fix bug where FLAG_KEY=0 was being translated into FLAG_KEY in output VCF, making a false flag value a true one
-- Fix the GT field value in VariantContextTestProviders so it isn't fixed 1000s of times during testing
-- Keys whose value is null are put into the VariantContext info attributes now
-- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller
-- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers
-- VCF parsers now automatically repair standard VCF header lines when reading the header
-- Updating integration tests to reflect header changes
-- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test
-- SelectHeaders now always updates the header to include the contig lines
-- SelectVariants add UG header lines when in regenotype mode
-- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY
-- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs)
-- Throw error when VCF has unbounded non-flag values that don't have = value bindings
-- By default we no longer allow writing of BCF2 files without contig lines in the header
-- Moved GENOTYPE_KEY vcf header line to VCFConstants. This general migration and cleanup is on Eric's plate now
-- Updated HC to initialize the annotation engine in an order that allows it to write a proper VCF header. Still doesn't work...
-- Updating integration test files. Moved many more files into public/testdata. Updated their headers to all work correctly with new strict VCF header checking.
-- Bugfix for TandemRepeatAnnotation that must be unbounded not A count type as it provides info for the REF as well as each alt
-- No longer add FALSE values to flag values in VCs in VariantAnnotatorEngine. DB = 0 is never seen in the output VCFs now
-- Fixed bug in VCFDiffableReader that didn't differeniate between "." and "PASS" VC filter status
-- Unconditionally add lowQual Filter to UG output VCF files as this is in some cases (EMIT_ALL_SITES) used when the previous check said it wouldn't be
-- VariantsToVCF now properly writes out the GT FORMAT field
-- BCF2 codec explodes when reading symbolic alleles as I literally cannot figure out how to use the allele clipping code. Eric said he and Ami will clean up this whole piece of instructure
-- Fixed bug in BCF2Codec that wasn't setting the phase field correctly. UnitTested now
-- PASS string now added at the end of the BCF2 dictionary after discussion with Heng
-- Fixed bug where I was writing out all field values as BigEndian. Now everything is LittleEndian.
-- VCFHeader detects the case where a count field has size < 0 (some of our files have count = -1) and throws a UserException
-- Cleaned up unused code
-- Fixed bug in BCF2 string encoder that wasn't handling the case of an empty list of strings for encoding
-- Fixed bug where all samples are no called in a VC, in which case we (like the VCFwriter) write out no called diploid genotypes for all samples
-- We always write the number of genotype samples into the BCF2 nSamples header. How we can have a variable number of samples per record isn't clear to me, as we don't have a map from missing samples to header names...
-- Removed old filtersWereAppliedToContext code in VCF as properly handle unfiltered, filtered, and PASS records internally
-- Fastpath function getDisplayBases() in allele that just gives you the raw bytes[] you'd see for an Allele
-- Genotype fields no longer differentiate between unfiltered, filtered, and PASS values. Genotype objects are all PASS implicitly, or explicitly filtered. We only write out the FT values if at least one sample is filtered. Removed interface functions and cleaned up code
-- Refactored padAllele code from createVariantContextWithPaddedAlleles into the function padAllele so that it actually works. In general, **** NEVER COPY CODE **** if you need to share funcitonality make a function, that's why there were invented!
-- Increased the default number of records to read for DiffObjects to 1M
-- The GATK VCFWriter now enforces by default that all INFO, FILTER, and FORMAT fields be properly defined in the header. This helps avoid some of the low-level errors I saw in SelectVariants. This behavior can be disable in the engine with the --allowMissingVCFHeaders argument
-- Fixed broken annotations in TandemRepeat, which were overwriting AD instead of defining RPA
-- Optimizations to VariantEval, removing some obvious low-hanging fruit all in the subsetting of variants by sample
-- SelectVariants header fixes -- Was defining DP for the info field as a FORMAT field, as for AC, AF, and AN original
-- Performance optimizations in BCF2 codec and writer
-- using arrays not lists for intermediate data structures
-- Create once and reuse an array of GenotypeBuilders for the codec, avoiding reallocating this data structure over and over
-- VCFHeader (which needs a complete rewrite, FYI Eric)
-- Warn and fix on the way flag values with counts > 0
-- GenotypeSampleNames are now stored as a List as they are ordered, and the set iteration was slow. Duplicates are detected once at header creation.
-- Explicitly track FILTER fields for efficient lookup in their own hashmap
-- Automatically add PL field when we see a GL field and no PL field
-- Added get and has methods for INFO, FILTER, and FORMAT fields
-- No longer add AC and AF values to the INFO field when there's no ALT allele
-- Memory efficient comparison of VCF and BCF files for shadow BCF testing. Now there's no (memory) constraint on the size of the files we can compare
-- Because of VCF's limited floating point resolution we can only use 1 sig digit for comparing doubles between BCF and VCF
* Sites with more soft clipped bases than regular will force-trigger a variant region
* No more unclipping/reclipping, RR machinery now handles soft clips natively.
* implemented support for base insertion and base deletion quality scores in synthetic and regular reads.
* GATKSAMRecord clone() now creates a fresh object for temporary attributes if one is present.
note: SAMRecords create a shallow copy of the tempAttribute object which was causing multiple reads (that came from the same read) to have their temporary attributes modified by one another inside reduce reads. Beware, if you're not using GATKSAMRecord!
-- Inline encodeString that doesn't go via List<Byte> intermediate
-- Inline encodeString that uses byte[] directly so that we can go from Allele.getBytes() => BCF2
-- Fast paths for Atomic Float and Atomic Integer values avoiding intermediate list creation
-- Final UG integration test update
-- encodeTyped in BCF2Encoder now with specialized versions for int, float, and string, avoiding unnecessary intermediate list creation and dynamic type checking. encodeTypedMissing also includes inline operations now instead of using Collections.emptyList() version. Lots of contracts. User code updated to use specialized versions where possible
-- Misc code refactoring
-- Updated VCF float formating to always include 3 sig digits for values < 1, and 2 for > 1. Updating MD5s accordingly
-- Expanded testing of BCF2Decoder to really use all of the encodeTyped* operations
-- Cleanup a few contracts
-- BCF2FieldManager uses new VCFHeader accessors for specific info and format fields
-- A few simple optimizations
-- VCF header samples stored in String[] in the writer for fast access
-- getCalledChrCount() uses emptySet instead of allocating over and over empty hashset
-- VariantContextWriterStorage now creates a 1MB buffered output writer, which results in 3x performance boost when writing BCF2 files
-- A few editorial comments in VCFHeader
-- Final merge conflicts resolved
-- BCF2Writer now supports case where a sample is present in the header but the sample isn't in the VC, in which case we create an empty sample and encode that
-- 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
Mark DePristo
Roger Zurawicki
Joel Thibault
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Christopher Hartl
Eric Banks