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Add function and CLI command to normalise variants with a store - #34

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tomwhite merged 2 commits into
sgkit-dev:mainfrom
tomwhite:normalise
Apr 15, 2026
Merged

tomwhite merged 2 commits into
sgkit-dev:mainfrom
tomwhite:normalise

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@tomwhite

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Fixes #30

@jeromekelleher

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Can you give a bit of context as to the scope of this please @tomwhite? From my reading this will pad out missing variants, but assumes the full genotype matrix fits into memory and doesn't do anything with allele remapping?

@tomwhite

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Can you give a bit of context as to the scope of this please @tomwhite? From my reading this will pad out missing variants, but assumes the full genotype matrix fits into memory and doesn't do anything with allele remapping?

Yes, that's right. Allele remapping has quite a few details, and will be added as a follow on to this. Also the memory limitation will obviously need improving too.

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OK, happy to commit this as a work in progress to be build upon

@tomwhite
tomwhite merged commit 7e2750a into sgkit-dev:main Apr 15, 2026
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@tomwhite
tomwhite deleted the normalise branch April 15, 2026 16:12
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Append samples with variant subset

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