567dba0f76
-- 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 |
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