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openvar / variantValidator

Public repository for VariantValidator project
GNU Affero General Public License v3.0
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Incorrect warning for a deletion not conforming to the 3' rule #585

Closed leicray closed 4 months ago

leicray commented 4 months ago

Describe the bug Validation of a variant description describing a deletion that does not conform to the 3' rule generates an incorrect warning.

To Reproduce Validate the variant description NM_005445.3:c.717_719del

Expected behaviour The warning that is displayed is NM_005445.3:c.717_719del automapped to NM_005445.3:c.720_722delTGA but should be NM_005445.3:c.717_719del automapped to NM_005445.3:c.720_722del.

This behaviour is observed with the interactive tool and the batch tool.

ifokkema commented 4 months ago

Note that https://github.com/openvar/variantValidator/issues/584 suggests the idea of tossing these "automapping" messages altogether, as they are meant for internal use only.

leicray commented 4 months ago

I'm not sure what you mean by "...they are meant for internal use only."

They are certainly of use to users of the interactive validator who might otherwise not understand that the validated output does not correspond to the submitted variant because of the 3' rule being applied. I would argue that the same is also true for the batch tool. The only place where it is perhaps not needed is tools whose output is intended to be solely machine-readable.

ifokkema commented 4 months ago

I agree that some form of warning should be shown, indicating the original input wasn't correct.

Peter-J-Freeman commented 4 months ago

OK, I see now why we included these warnings. I need to trim them. The thing is though that not all may be perfect.

Peter-J-Freeman commented 4 months ago

Fixed. Needs server update to take effect. Be patient please @leicray :)