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openvar / variantValidator

Public repository for VariantValidator project
GNU Affero General Public License v3.0
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A genome build is not a reference sequence #502

Closed leicray closed 1 year ago

leicray commented 1 year ago

Describe the bug VariantValidator parses variant descriptions to ensure that a reference sequence is specified and that the reference sequence syntax is valid.

However, an anonymous user has attempted (twice) to submit the variant description GRCh38:27983407:C:T. There was no attempt to specify a chromosome number and the submissions triggered an ERROR message to sysadmin.

Errors such as this also need to be handled gracefully, with feedback to the user.

Peter-J-Freeman commented 1 year ago

Again, banging my head!

Peter-J-Freeman commented 1 year ago 
"validation_warnings": [
            "Insufficient or incorrect VCF elements provided. Elements required are chr-pos-ref-alt"
        ],