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VCFHeader drops sequence dictionary attributes #730

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cmnbroad opened this issue Oct 26, 2016 · 0 comments
Open

VCFHeader drops sequence dictionary attributes #730

cmnbroad opened this issue Oct 26, 2016 · 0 comments
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VCFHeader Refactor Issues fixed by the header/line refactoring branch

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cmnbroad commented Oct 26, 2016 •
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Both:

  • VCFHeader.setSequenceDictionary
  • the VCFContigHeaderLine constructor VCFContigHeaderLine(final SAMSequenceRecord sequenceRecord, final String assembly)

drop all SAMSequenceRecord attributes except ID, length, and assembly (i.e. they drop MD5/UR). If these are allowed in the vcf (AFAICT they are) then both of these classes should be fixed up to propagate any attributes in and out.
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