Ignore version validation for BCF in VCFHeaderReader because we only need the header#1707
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lindenb wants to merge 2 commits intosamtools:masterfrom
Open
Ignore version validation for BCF in VCFHeaderReader because we only need the header#1707lindenb wants to merge 2 commits intosamtools:masterfrom
lindenb wants to merge 2 commits intosamtools:masterfrom
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Description
For now HTSJDK does not support BCF2.2 but sometimes you just want to only get the VCF header in a BCF file while you don't care about the variants . e.g:
So this PR, overrides
BCF2Codec.validateVersionCompatibilityin VCFheaderReader so the validation is just ignored.VCFheaderReader is then used in SamSequenceDictionaryExtractor instead of VCFReader so we can extract a dictionary from a BCF2.2 file
I added tests.
Things to think about before submitting: