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Cargo, data, firmware, help: add the structural and copy number variant slots - #43

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karalabe merged 3 commits into
dark-bio:mainfrom
karalabe:genome-tree
Oct 19, 2026
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karalabe merged 3 commits into
dark-bio:mainfrom
karalabe:genome-tree

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Moves ark to darkbio-wire 0.17.0 and the six dataset slots of ArkOS v0.13.0, which adds Structural Variants and Copy Number Variants beside Small Variants.

  • ark data names all six slots: reference-genome, gene-annotations, small-variants, variant-catalog, structural-variants and copy-number-variants. snp-indel-calls is gone.
  • An upload or fetch into a slot whose required slot is empty fails with dependency-missing, exit 5, before the owner is asked.
  • ark data fetch --sample NAME fills a public 1000 Genomes person's three personal slots in order, each with its own pin check and approval, and refuses before any download while a personal slot holds data.
  • ark requires firmware v0.13.0, and a develop build published from that release on.

The help topics describe the new slots. Not run against a live Ark yet.

karalabe and others added 3 commits October 17, 2026 12:43
Co-authored-by: Astra <noreply@openai.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Astra <noreply@openai.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Astra <noreply@openai.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
@karalabe
karalabe merged commit 29c0be2 into dark-bio:main Oct 19, 2026
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