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VCFFileReader can't read BCF files with IDX fields in the header #507
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Any thoughts on how to fix this @lbergelson, @droazen? |
@tomwhite htsjdk does not support the latest BCF spec -- we should probably change the parser to throw if it encounters an unsupported BCF. I suspect that there are ways in which htsjdk is not fully compliant with the latest VCF spec, either -- we may need to allocate an engineer next quarter to go in and make sure we're fully VCF 4.3-compliant, and bring us up to spec if we're not. |
OK, thanks for the update. I was surprised because a test file in the htsjdk source tree cannot be parsed by the htsjdk parser... |
Your surprise is very justified! |
Related to: #628. |
IDX fields have been allowed since BCF v 2.2 (see end of http://samtools.github.io/hts-specs/VCFv4.3.pdf). The file ex2.uncompressed.bcf in the htsjdk source has IDX fields and cannot be parsed by VCFFileReader, see:
I've written a unit test to reproduce: tomwhite@fffc1d5
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