Add prefix argument variant_id to plink conversion #390
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plink1.9 --bfile example --recode vcf-iid --out tmp mv tmp example.vcf
jeromekelleher
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benjeffery and
tomwhite
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benjeffery
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This is ready for a look now and should get us to full initial plink support. I think the definition of correctness here being equivalent to running plink's own VCF conversion through vcf2zarr makes things much easier, and it fairly clear we're doing the correct thing now. |
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Ok, I think that's plink support done now. The coverage misses are incidental I think and we can ignore them. |
| # bed and bim files, but should share a .fam | ||
| self.prefix = str(prefix) | ||
| paths = PlinkPaths( | ||
| self.prefix + ".bed", |
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Might be nicer to have the PlinkPaths __init__ just take the prefix?
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Pros and cons - I tend to try and keep these dataclasses as simple as possible for reasoning about serialising and so on.
| ("tests/data", 5045032), | ||
| # NOTE: removed this after additional plink files broke it in #390. | ||
| # It's not worth the trouble - see #330 | ||
| # ("tests/data", 5053610), |
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Ha, glad you removed this. Was driving me potty.
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Looks like CI is complaining about a missing docs section |
Fixup tests for plink Covert some corner cases in the plink outout
Disable the top-level test as it's not working well. Not clear we want this tbh
Add the docs files
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Ha, whoops, forgot to add the docs files! |
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Docs look good. |
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