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feat: plug in caf storage to ingest function #48

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jsstevenson merged 2 commits into from
Jan 7, 2026
Merged

feat: plug in caf storage to ingest function #48

jsstevenson merged 2 commits into from
Jan 7, 2026
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@jsstevenson jsstevenson commented Jan 6, 2026 •
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close #46

  • Plug AnyVLM storage class into CAF ingest function, so that CAF fields are associated with ingested alleles
  • Add FILTER field extraction (there's a discussion to be had in the future about whether/how to ingest the full item and not just the ID)

@jsstevenson jsstevenson requested a review from a team as a code owner January 6, 2026 21:37
@jsstevenson jsstevenson added the priority:high High priority label Jan 6, 2026
@jsstevenson jsstevenson marked this pull request as draft January 6, 2026 21:37
theferrit32
theferrit32 reviewed Jan 6, 2026
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src/anyvlm/functions/ingest_vcf.py


AfData = namedtuple("AfData", ("ac", "an", "ac_het", "ac_hom", "ac_hemi"))
AfData = namedtuple("AfData", ("ac", "an", "ac_het", "ac_hom", "ac_hemi", "filters"))
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@theferrit32 theferrit32 Jan 6, 2026

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Not exactly "AfData" now

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@jsstevenson jsstevenson Jan 6, 2026

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haha, I mean, it still more or less is -- although I do wonder if we should double-check whether these are meaningful for the gregor VCFs specifically

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I think we will need to change a few things when we genericize but it looks good for now. I've got things running locally now

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@jsstevenson jsstevenson Jan 7, 2026

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Yeah, I'm unsure of how to best handle variation in things like INFO field naming...

@jsstevenson jsstevenson requested a review from a team January 6, 2026 23:08
@jsstevenson jsstevenson marked this pull request as ready for review January 6, 2026 23:08
@jsstevenson jsstevenson merged commit 9532ab6 into main Jan 7, 2026
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@jsstevenson jsstevenson deleted the feat/46-fill-in-caf-store branch January 7, 2026 16:29
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Store CAFs from input VCF

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