Kl/validty updates

[klaricch]

No description provided.

[Copilot]

Pull request overview

Updates federated data validity tooling and associated field requirement documentation to account for additional VEP 115 annotations and improve validation ergonomics.

Changes:

• Document new vep115_globals global annotations and a vep115 row annotation in field requirements (MD + generated HTML).
• Refactor/extend validity checks with helpers for test-partition filtering, row↔global length checks, “extra field” warnings, and populating select info annotations.
• Switch the default public-release input HT to exomes and adjust the default output path accordingly.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 4 comments.

File	Description
gnomad_qc/v5/data_ingestion/field_requirements.md	Adds VEP 115 global/row field specs to the requirements doc.
gnomad_qc/v5/data_ingestion/field_requirements.html	Regenerated HTML to reflect the updated requirements (incl. VEP 115 fields).
gnomad_qc/v5/data_ingestion/federated_validity_checks.py	Adds/refactors validation helpers and updates defaults used by the CLI run.

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[Copilot]

Pull request overview

Copilot reviewed 4 out of 5 changed files in this pull request and generated 6 comments.

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[mike-w-wilson]

A few more comments and also a general one. I know we want to use some of this for v5 but considering the documentation and end goal, this sshould be moved out of v5 and into its own federated directory. A separate script can then call these functions inside v5.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 9 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (2)

gnomad_qc/federated/federated_validity_checks.py:386

• validate_config_fields_in_ht checks for monoallelic/only_het inside ht.info when check_mono_and_only_het is set, but ht.info is only populated later via add_info_annotations. For inputs where those annotations exist as top-level row fields (and are later moved into info), this will incorrectly flag missing fields (or raise if info is empty). Consider either (a) performing this validation after add_info_annotations, or (b) accepting the fields in either location (ht.info or ht.row) and validating accordingly.
  gnomad_qc/federated/federated_validity_checks.py:693
• check_missingness divides by n_sites when computing frac_missing, but n_sites = ht.count() can be 0 (e.g., if filtering to test partitions/intervals yields an empty Table). This will raise a ZeroDivisionError. Add an early return (or skip fraction computation) when n_sites == 0.

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[mike-w-wilson]

A couple very minor things and responses, then LGTM