feat(prepro): add custom lineage functions

[anna-parker]

resolves #

thanks to claude for writing the tests!

Screenshot

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

🚀 Preview: https://add-custom-lineage-functi.loculus.org

[claude]

Claude finished @anna-parker's task in 3m 10s —— View job

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Code Review

• Gather context and read changed files
• Review processing_functions.py changes
• Review test_assign_custom_lineage.py
• Review values.yaml changes
• Review test_metadata_processing_functions.py changes
• Post final review

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Good addition overall. The new is_variant function is clean and well-tested. A few issues worth addressing:

is_variant

• Lines 1218–1219: direct input_data["key"] access will raise KeyError (not caught by the local except (ValueError, TypeError)) if the key is absent rather than None. Use .get(). → inline comment
• Line 1241: error message says "non-numeric threshold value" but the threshold is computed — the actual non-numeric value is length or numMutations. → inline comment

assign_custom_lineage

• Line 1310: if a segment has no reference_segN key in input (partial genome), extract_regex returns None, which ends up in extracted_subtypes. The reassortant check len(set(...)) > 1 would then count None as a distinct subtype and false-positive. Filtering out Nones fixes it. → inline comment

Tests

• ARGS constant contains unrelated fields (is_insdc_ingest_group, submittedAt, ACCESSION_VERSION). → inline comment
• No test for partial genomes (missing reference for some segments) — the most direct way to exercise the false-reassortant bug above. → inline comment

values.yaml

• The explanatory comment about why totalSubstitutions is used (no private mutations in custom nextclade dataset) was dropped when rewriting the SARS-CoV-2 variant fields. → inline comment

[theosanderson]

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[chatgpt-codex-connector]

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