When hard-clipping predict when the read is going to be fully hard clipped to the point where only soft/hard-clips are left in the read and preemptively eliminate the read before the SAMRecord mathematics on malformed cigars kills the GATK.
-- GenotypeBuilder now sorts the list of filter strings so that the output is in a consistent order
-- calculateChromosomeCounts removes the AC/AF fields entirely when there are no alt alleles, to be on VCF spec for A defined info field values
-- Fixed bug in VariantDataManager that this validation mode was intended to detect going forward
-- Still no VariantRecalibrationWalkersIntegrationTest for indels with BCF2 but that's because LowQual is missing from test VCF
-- Bugfix for VCFDiffableReader: don't add null filters to object
-- BCF2Codec uses new VCFAlleleClipper to handle clipping / unclipping of alleles
-- AbstractVCFCodec: decodeLoc uses full decode() [still doesn't decode genotypes] to avoid dangerous code duplication. Refactored code that clipped alleles and determined end position into updateBuilderAllelesAndStop method that uses new VCFAlleleClipper. Fixed bug by ensuring the VCF codec always uses the END field in the INFO when it's provided, not just in the case where the there's a biallelic symbolic allele
-- Brand new home for allele clipping / padding routines in VCFAlleleClipper. Actually documented this code, which results in lots of **** negative comments on the code quality. Eric has promised that he and Ami are going to rethink this code from scratch. Fixed many nasty bugs in here, cleaning up unnecessary branches, etc. Added UnitTests in VCFAlleleClipper that actually test the code full. In the process of testing I discovered lots of edge cases that don't work, and I've commented out failing tests or manually skipped them, noting how this tests need to be fixed. Even introduced some minor optimizations
-- VariantContext: validateAllele was broken in the case where there were mixed symbolic and concrete alleles, failing validation for no reason. Fixed.
-- Added computeEndFromAlleles() function to VariantContextUtils and VariantContextBuilder for convenience calculating where the VC really ends given alleles
--
-- refactored allele clipping / padding code into VCFAlleleClipping class, and added much needed docs and TODOs for methods dev guys
-- Added real unit tests for (some) clipping operations in VCFUtilsUnitTest
-- Previous version was reading the size of the encoded genotypes vector for each genotype. This only worked because I never wrote out genotype field values with > 15 elements. Mauricio's killer DiagnoseTargets VCF uncovered the bug. Unfortunately since symbolic allele clipping is still busted those tests are still diabled
-- GenotypeContext getMaxPloidy was returning -1 in the case where there are no genotypes, but the answer should be 0.
-- They now throw an error, as its really unsafe to write out ./. as a special case in the VCFWriter as occurred previously.
-- Added convenience method in VariantContextUtils.addMissingSamples(vc, allSamples) that returns a complete VC where samples are given ./. Genotype objects
-- This allows us to properly pass tests of creating / writing / reading VCFs and BCFs, which previously differed because the VC from the VCF would actually be different from its original VC
-- Updated UG, UGEngine, GenotypeAndValidateWalker, CombineVariants, and VariantsToVCF to manage the master list of samples they are writing out and addMissingSamples via the VCU function
-- Don't use DP for average interval depth but rather AVG_INTERVAL_DP, which is a float now, not an int
-- Don't add PASS filter value to genotypes, as this is actually considered failing filters in the GATK. Genotype filters should be empty for PASSing sites
Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals.
IntervalUtils return unmodifiable lists so that utilities don't mutate the collections.
Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus.
Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values.
JobRunInfo handles the null done times when jobs crash with strange errors.
-- Previously VCF header lines of count type G assumed that the sample would be diploid.
-- Generalized the code to take a VariantContext and return the right result for G count types by calling into the correct numGenotypes in GenotypeLikelihoods class
-- renamed calcNumGenotypes to numGenotypes, which uses a static cache in the class
-- calcNumGenotypes is private, and is used to build the static cache or to compute on the fly for uncached No. allele / ploidy combinations
-- VariantContext calls into getMaxPloidy in GenotypesContext, which caches the max ploidy among samples
-- Added extensive unit tests that compare A and G type values in genotypes
-- Previous bugfix ensures that header fixing is always on in the GATK by default, even after integration tests that failed and when through the VCFDiffableReader. Updating md5s to reflect this.
-- allowMissingVCFHeaders is now part of -U argument. If you want specifically unsafe VCF processing you need -U LENIENT_VCF_PROCESSING. Updated lots of files to use this
-- LENIENT_VCF_PROCESSING disables on the fly VCF header cleanup. This is now implemented via a member variable, not a class variable, which I believe was changing the GATK behavior during integration tests, causing some files to fail that pass when run as a single test because the header reading behavior was changing depending on previous failures.
-- Just completely wrong.
-- BCF2 shadowBCF now checks that the shadow bcf can be written to avoid /dev/null.bcf problem
-- Added samtools ex2.bcf file for decoding to our integrationtests
* field attributesCanBeModified - a null attributes object can't be modified in its current state
* method makeAttributesModifiable() - initialize a null attributes object to empty
Mauricio Carneiro
Mark DePristo
Guillermo del Angel
Khalid Shakir
Eric Banks
Roger Zurawicki
Joel Thibault
Ryan Poplin