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Normalise variants with allele remapping - #42

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tomwhite merged 1 commit into
sgkit-dev:mainfrom
tomwhite:remap-alleles
Apr 17, 2026
Merged

tomwhite merged 1 commit into
sgkit-dev:mainfrom
tomwhite:remap-alleles

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This is a step towards #31.

  • Add allele remapping (but don't handle case of new alleles yet)
  • Move normalise logic from zarr_impl into a new normalise module
  • Array creation is also split into two passes (create empty, then fill)
  • Create vcz test data directly rather than converting from vcf files

Still to do (follow ons):

  • Updating the variant chunked arrays chunk-by-chunk
  • Updating variant_alleles in case of new alleles

Add allele remapping (but don't handle case of new alleles yet)

Move normalise logic from zarr_impl into a new normalise module

Array creation is also split into two passes (create empty, then fill)

Create vcz test data directly rather than converting from vcf files
@tomwhite
tomwhite requested a review from jeromekelleher April 17, 2026 11:15
@tomwhite
tomwhite merged commit a82f3e9 into sgkit-dev:main Apr 17, 2026
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@tomwhite
tomwhite deleted the remap-alleles branch April 17, 2026 12:08
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