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Add VEP cache source metadata mode#162

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mwiewior wants to merge 1 commit into
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feature/add-vep-cache-source-mode
Open

Add VEP cache source metadata mode#162
mwiewior wants to merge 1 commit into
masterfrom
feature/add-vep-cache-source-mode

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@mwiewior
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Summary

  • require VEP cache source metadata (bio.vep.cache_source_type) and reject legacy options_json source selectors
  • carry explicit cache source mode through annotate_vep, VCF output, transcript filtering, RefSeq hydration, and cache-builder export paths
  • add OpenSpec proposal/design/tasks and tests for metadata parsing, rejected selectors, source mismatch, RefSeq/merged CSQ fields, and RefSeq MT handling

Verification

  • cargo fmt --check
  • openspec validate add-vep-cache-source-mode --strict
  • cargo test -p datafusion-bio-function-vep --lib
  • cargo test -p datafusion-bio-function-vep --features cache-builder cache_builder
  • cargo clippy -p datafusion-bio-function-vep --all-targets --features cache-builder -- -D warnings
  • git diff --check

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