Remove schema data #343
Remove schema data #343
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benjeffery
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Yes, looks good. There's a few details to follow up on, but it's the right approach. |
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Rebased |
CHANGELOG.md
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| @@ -4,6 +4,8 @@ | |||
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| - Add support for unindexed (and uncompressed) VCFs (#337) | |||
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| - Remove explicit sample, contig and filter lists from the schema (#343) | |||
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This is a breaking schema format change, so will require existing ICFs to be recreated. I listed these as "Breaking changes" below
bio2zarr/vcz.py
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| self.encode_samples(root) | ||
| self.encode_filter_id(root) | ||
| self.encode_contig_id(root) | ||
| if hasattr(self.source, "samples"): |
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Control flow by hasattr is pretty :vomit: for me - so easy for mistakes to get hidden as code evolves over time.
Every implementation has to have samples anyway, right? And, I would imagine likewise for contigs, so they should both be unconditional.
For filters, I think we should probably define a superclass which defines the interface we require here, and have filters return None by default. That way we can detect if filters (and other optional stuff) makes sense or not.
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I've added a base class for the sources and removed the mapping base class from the icf source. I've kept contigs optional as plink doesn't have them in this PR. |
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Stacked on #339 - clean diff at 9f727a1