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@jsstevenson jsstevenson commented Jan 10, 2026

As of biocommons/anyvar#369, AnyVar now supports bulk additions via HTTP and via Python API, so this PR refactors each respective AnyVar client to transmit variations in bulk.

  • I performed a very unscientific experiment (a single VCF) and it seemed to be something like 20-30% faster in that specific case? It looks like the main remaining bottleneck is variant translation, although bulk inserts to the CAF table will be nice too
  • Also did some cleanup in the HTTP client to move some repeated code into the shared method and move some request-specific code up into the respective functions

@jsstevenson jsstevenson added the priority:medium Medium priority label Jan 10, 2026
@jsstevenson jsstevenson requested a review from a team as a code owner January 10, 2026 02:04
@jsstevenson jsstevenson changed the title feat: use bulk methods for loading AnyVar alleles feat: use bulk methods for loading alleles in AnyVar Jan 10, 2026
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