-- 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
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