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openvar / variantValidator

Public repository for VariantValidator project
GNU Affero General Public License v3.0
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Protein-level variant validation is not trapping invalid single-letter amino acid codes #551

Closed leicray closed 3 months ago

leicray commented 8 months ago

Describe the bug A user has submitted the variant descriptionNP_000483.3:p.Z1335P but the invalid reference amino acid (Z) is not being trapped and flagged as invalid. The variant fails to validate and an error email is sent to the sysops.

The system ought to be trapping "Z" and pointing out that it is not a valid amino acid.

Peter-J-Freeman commented 3 months ago

In the next release cycle this will not give

        "validation_warnings": [
            "Invalid amino acid Z stated in description NP_000483.3:p.Z1335P"
        ],
        "variant_exonic_positions": null