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@theferrit32 theferrit32 commented Jul 22, 2025

  • Update handlers for Allele, CopyNumberCount, CopyNumberChange to use methods in the variation-normalization code
  • Update worker threading to add a per-worker event loop

This does change the prereqs for running this process.

The VICC-customized UTA must be used as it adds a table which is referenced in some operations by the variation-normalization code. The compose.yaml below includes this and it includes a necessary gene-normalizer dynamodb server. Change the local ports as necessary to avoid collisions.

https://github.com/cancervariants/variation-normalization/blob/0.15.0/compose.yaml

It also makes some changes to add an asyncio event loop to each worker process so they can execute calls into the async variation-normalization functions. A future feature here may be to update our code to use asyncio.

@theferrit32 theferrit32 changed the title Refactor to use variation-normalizer programmatically for CopyNumberCount and CopyNumberChange Refactor to use variation-normalizer Python library Jul 28, 2025
@theferrit32 theferrit32 self-assigned this Jul 28, 2025
@theferrit32 theferrit32 marked this pull request as ready for review July 28, 2025 19:00
@theferrit32 theferrit32 merged commit 4fb700d into main Aug 6, 2025
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@theferrit32 theferrit32 deleted the handle-indefinite-ranges branch August 6, 2025 20:36
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2 participants