Fix vcf2zarr tests

[tomwhite]

• Fixes ImportError: cannot import name 'vcf2zarr' from 'bio2zarr' #1308

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  Coverage   100.00%   100.00%           
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  Files           46        46           
  Lines         2992      2992           
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[tomwhite]

I got ValueError: Zarr schema format version mismatch: 0.4 != 0.5, so I regenerated the schema, see 3cae0f6.

But now the docs build is failing with

"'alleles' is not a valid dimension or coordinate for Dataset with dimensions FrozenMappingWarningOnValuesAccess({'variants': 10879, 'samples': 250, 'FORMAT_AD_dim': 2})"

I noticed that for call_AD the dimension is now FORMAT_AD_dim, not alleles.

Any idea why that's happening @benjeffery?

[jeromekelleher]

I noticed that for call_AD the dimension is now FORMAT_AD_dim, not alleles.

That's a good catch @tomwhite, I think we can regard that as bug. Probably something simple happened in the generalisation code, I'll investigate

[jeromekelleher]

This is weird @tomwhite, I don't see what would have changed here. The number in VCF is "." in the 1000G files I'm looking at, and I assume it's the same here, so I don't see how we'd ever have gotten "alleles" in there. There was never any special case for AD, and I don't think we should overrule the header anyway.

Did you manually edit the schema to fix this problem before by any chance?

[tomwhite]

This is weird @tomwhite, I don't see what would have changed here. The number in VCF is "." in the 1000G files I'm looking at, and I assume it's the same here, so I don't see how we'd ever have gotten "alleles" in there. There was never any special case for AD, and I don't think we should overrule the header anyway.

Did you manually edit the schema to fix this problem before by any chance?

Yes, that was it. Sorry!

[jeromekelleher]

Great! LGTM