-- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private.
-- Throw an exception if its required bintag argument is missing
-- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate
-- Show the type (Required, Experimental, Standard) of the covariates when running --list
-- When merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion.
* No reads with Hard/Soft clips in the middle of the cigar
* No reads starting with deletions (with or without preceding clips)
* No reads ending in deletions (with or without follow-up clips)
* No reads that are fully hard or soft clipped
* No reads that have consecutive indels in the cigar (II, DD, ID or DI)
Also added systematic test for good cigars and iterative test for bad cigars.
-- Removed REFERENCE_BASES option. You only have REFERENCE now. There's no efficiency savings for the REFERENCE_BASES option any longer, since the reference bases are loaded lazy so if you don't use them there's effectively no cost to making the RefContext that could load them.
-- The GATK sort of handles this now, but only if you have the exactly correct sequence dictionary and FAI files associated with the reference. If you do, the file can be .gz. If not, the GATK will fail on creating the FAI and DICT files. Added an error message that handles this case and clearly says what to do.
-- Now blows up if an argument begins with -. Implementation isn't pretty, as it actually blows up during Queue extension creation with a somewhat obscure error message but at least its something.
-- Keep reading from BCF2 input stream when read(byte[]) returns < number of needed bytes
-- It's possible (I think) that the failure in GSA-484 is due to multi-threading writing/reading of BCF2 records where the underlying stream is not yet flushed so read(byte[]) returns a partial result. No loops until we get all of the needed bytes or EOF is encounted
-- Removed half-a*ssed attempt to automatically repair VCF files with bad headers, which allowed users to provide a replacement header overwriting the file's actually header on the fly. Not a good idea, really. Eric has promised to create a utility that walks through a VCF file and creates a meaningful header field based on the file's contents (if this ever becomes a priority)
-- Now possible to do -o /dev/stdout -bcf -l DEBUG > tmp.bcf and create a valid BCF2 file
-- Cleanup code to make sure extensions easier by moving to a setX model in VariantContextWriterStub
-- BCF2 is failing for some reason when merging tmp. files with parallel combine variants. ThreadLocalOutputTracker no longer sets deleteOnExit on the tmp file, as this prevents debugging. And it's unnecessary because each mergeInto was deleting files as appropriate
-- MergeInfo in VariantContextWriterStorage only deletes the intermediate output if an error occurs
-- All tests but one (using old bad VCF3 input) run unmodified with parallel code.
-- Disabled UNSAFE_VCF_PROCESSING for all but that test, which changes md5s because the output files have fixed headers
-- Minor optimizations to simpleMerge
-- BCF2 now determines whether it can safely write out raw genotype blocks, which is true in the case where the VCF header of the input is a complete, ordered subset of the output header. Added utilities to determine this and extensive unit tests (headerLinesAreOrderedConsistently)
-- Cleanup collapseStringList and exploreStringList for new unit tests of BCF2Utils. Fixed bug in edge case that never occurred in practice
-- VCFContigHeaderLine now provides its own key (VCFHeader.CONTIG_KEY) directly instead of requiring the user to provide it (and hoping its right)
-- More ways to access the data in VCFHeader
-- BCF2Writer uses a cache to avoid recomputing unnecessarily whether raw genotype blocks can be emitted directly into the output
-- Optimization of fullyDecodeAttributes -- attributes.size() is expensive and unnecessary. We just guess that on average we need ~10 elements for the attribute map
-- CombineVariants optimization -- filters are online HashSet but are sorted at the end by creating a TreeSet
-- makeCombinations is now makePermutations, and you can request to create the permutations with or without replacement
-- CombineVariants is now TreeReducible!
-- Integration tests running in parallel all pass except one (will fix) due to incorrect use of db=0 flag on input from old VCF format
-- Previous IO stub was hardcoded to write VCF. So when you ran -nt 2 -o my.bcf you actually created intermediate VCF files that were then encoded single threaded as BCF. Now we emit natively per thread BCF, and use the fast mergeInfo code to read BCF -> write BCF. Upcoming optimizations to avoid decoding genotype data unnecessarily will enable us to really quickly process BCF2 in parallel
-- VariantContextWriterStub forces BCF output for intermediate files
-- Nicer debug log message in BCF2Codec
-- Turn off debug logging of BCF2LazyGenotypesDecoder
-- BCF2FieldWriterManager now uses .debug not .info, so you won't see all of that field manager debugging info with BCF2 any longer
-- VariantContextWriterFactory.isBCFOutput now has version that accepts just a file path, not path + options
-- Expanded unit tests
-- Support for clean logging of results to logger
-- Refactored MyTime into AutoFormattingTime in Utils, out of TraversalEngine, for cleanliness and reuse
-- Added docs and contracts to StateMonitoringThreadFactory
Ryan Poplin
Eric Banks
Mark DePristo
Mauricio Carneiro