Add standard_dimensions for VCZ

[jeromekelleher]

Fixes #368 and also consolidates dimension handling to some degree

[coveralls]

coverage: 98.185% (+0.006%) from 98.179%
when pulling c314c2f on jeromekelleher:change-default-chunksize
into 21d0224 on sgkit-dev:main.

[jeromekelleher]

Note that this changes the schema output so that we always explicitly list the chunk size for all dimensions:

{
    "format_version": "0.6",
    "dimensions": {
        "variants": {
            "size": 9,
            "chunk_size": 9
        },
        "samples": {
            "size": 3,
            "chunk_size": 3
        },
        "alleles": {
            "size": 4,
            "chunk_size": 4
        },
        "alt_alleles": {
            "size": 3,
            "chunk_size": 3
        },
        "filters": {
            "size": 3,
            "chunk_size": 3
        },
        "ploidy": {
            "size": 2,
            "chunk_size": 2
        },
        "genotypes": {
            "size": 10,
            "chunk_size": 10
        },
        "INFO_AC_dim": {
            "size": 2,
            "chunk_size": 2
        },
        "INFO_AF_dim": {
            "size": 2,
            "chunk_size": 2
        },
        "FORMAT_HQ_dim": {
            "size": 2,
            "chunk_size": 2
        }
    },
    "fields": [
        {
            "name": "variant_contig",
            "dtype": "i1",
            "dimensions": [
                "variants"
            ],
            "description": "An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file",
            "compressor": null,
            "filters": null,
            "source": null
        },

I think this is better for now, as the logic around initialisation and defaults was quite tricky. We can always revert back to "no chunk size means chunk_size = size" for just JSON deserialisation later, if we want to make things a bit more concise.

[benjeffery]

Looks good - I don't think that we need a schema version bump right? These changes look backward compatible.

[jeromekelleher]

Looks good - I don't think that we need a schema version bump right? These changes look backward compatible.

Looks like we're still on 0.4 without the dimensions for the released version, so I think we're OK.