samtools
VCF4.3 constants and header lines
VCF4.3 support
New specifications for VCF 4.3 suggest that a new VCFCompoundHeaderLine could be implemented for symbolic alternative alleles (VCFAltHeaderLine).
New reserved keys are included in the specs, which could be added to VCFConstants in conjuction with reserved structural variant alleles (DEL, INS, etc.). In addition, other headers that can be supported are "##SAMPLE", "##META" and "##PEDIGREE".
I can work on it if there is interest on this issue.
@magicDGS I think we'd be happy to accept any patch that improves htsjdk support for VCF4.3, and the changes you mention sound good to me.
I will work on this, but I found some related issues (#517, #500, #389, #277, #251, #250). Should I take into account that too, @droazen?
You're welcome to take any or all of those tickets on if you like, @magicDGS, but I recommend making each individual branch/pull request as small and specific as possible, with good tests for each one. With htsjdk we have to be extra-careful about what we merge, and large monolithic branches with many features tend to take months to get in.