Remove VCF header

[tomwhite]

Fixes sgkit-dev/bio2zarr#184

This needs sgkit-dev/bio2zarr#352 (from bio2zarr). This is not working yet as it exposes some corner cases in the VCF conversion that may be bugs. I'll open issues for these in bio2zarr.

[jeromekelleher]

This would be a great step forward!

I wonder if we should try and get the rest of the header fields in to Zarr first in bio2zarr, so that we can more-or-less round-trip?

• Add non-redundant header entries as a list of name-value tuples vcf-zarr-spec#29
• Clarify purpose of the vcf_header attribute and/or refine? vcf-zarr-spec#15

[tomwhite]

Here are the bugs I found:

• alt_alleles dimension is not always being added for Number=A fields bio2zarr#353
• Type=Character fields are converted to String #199
• SB field Number is changed from 4 to 1 during conversion bio2zarr#355
• alt_alleles dimension is not picked up when max_number is zero bio2zarr#359

[tomwhite]

I wonder if we should try and get the rest of the header fields in to Zarr first in bio2zarr, so that we can more-or-less round-trip?

We don't need to tie them together - would be OK to do them separately I think.

[jeromekelleher]

Looks like you've dug out enough bugs to keep us going for a while in any case!

[tomwhite]

All tests pass locally with the latest changes from sgkit-dev/bio2zarr#360

[tomwhite]

This can go in once there is a new release of bio2zarr.

[tomwhite]

Superceded by #208