-- 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
-- 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
-- integration tests now write out mismatches file, which this script reads in, walks the file system to find files with these md5s, and updates them in the files.
-- Should be run like: python private/python/updateMD5s.py integrationtests/md5mismatches.txt public/java/test
-- Note that before using this code you should really commit your code for safety
-- Note also that you ***MUST*** review the differences before running this code. It's not ok to just update md5s willy-nilly
-- Doc from the code:
Update the MD5s across multiple files.
The first argument is the database of MD5 updates produced automatically by the
integrationtests, which lives in integrationtest/md5mismatches.txt.
The second (and more) argument(s) is the path to the source directory containing the java / scala
code with md5s to update. This program crawls that directory looking for .java
and .scala files to update, id's those with MD5s in the md5mismatches.txt files and
updates these files.
It is highly recommended that you commit your code before updating the MD5s to ensure
that if things go wrong with this script that you don't lose any work.
-- This file is in integrationtests/md5mismatches.txt, and looks like:
expected observed test
7fd0d0c2d1af3b16378339c181e40611 2339d841d3c3c7233ebba9a6ace895fd test BeagleOutputToVCF
43865f3f0d975ee2c5912b31393842f8 1b9c4734274edd3142a05033e520beac testBeagleChangesSitesToRef
daead9bfab1a5df72c5e3a239366118e 27be14f9fc951c4e714b4540b045c2df testDiffObjects:master=/local/dev/depristo/itest/public/testdata/diffTestMaster.vcf,test=/local/dev/depristo/itest/public/testdata/diffTestTest.vcf,md5=daead9bfab1a5df72c5e3a239366118e
-- Associated cleanup with making md5db an instantiated object, rather than a bunch of static methods
Eric Banks
Guillermo del Angel
Mark DePristo