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Updates for new reference data structure #4509

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merged 14 commits into from
Dec 4, 2024
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@bpblanken bpblanken commented Dec 3, 2024

Tests are passing!

I made two massive mistakes when starting this:

  1. Fetching globals from the production tables... this helped find the hl.Struct() vs None issue we encountered yesterday but our enums/versions are out of sync enough that this led to test failures.
  2. Annotating the dbnsfp values with:
ht = ht.annotate(dbnsfp=ht.dbnsfp.annotate(PrimateAI_score=ht.primate_ai.score, MPC_score=ht.mpc.MPC, CADD_phred=ht.cadd.PHRED))

dbnsfp was missing for several variants, but CADD was not. The outer missing swallowed up the inner non-missing.

@bpblanken bpblanken marked this pull request as ready for review December 4, 2024 18:33
@bpblanken bpblanken requested review from hanars and jklugherz December 4, 2024 18:39
@bpblanken bpblanken changed the title Benb/updates for new structure Updates for new reference data structure Dec 4, 2024
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this looks good to me!!

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hanars commented Dec 4, 2024

We should probably hold off on merging until we are ready to release the updated annotation tables in prod

@bpblanken bpblanken merged commit 5d48616 into dev Dec 4, 2024
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@bpblanken bpblanken deleted the benb/updates_for_new_structure branch December 4, 2024 20:09
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2 participants