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Add input validation for _from_gnomad #147

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korikuzma opened this issue Jan 13, 2023 · 2 comments · Fixed by #148
Closed

Add input validation for _from_gnomad #147

korikuzma opened this issue Jan 13, 2023 · 2 comments · Fixed by #148
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@korikuzma
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I made a similar issue for translator validation in our hackathon repo.

7-7-helloworld-T is not a valid gnomAD VCF, but we're still able to translate to a VRS Allele as seen below:

Screen Shot 2023-01-13 at 9 23 12 AM

We should add some additional validation checks for the input

@korikuzma korikuzma added the bug Something isn't working label Jan 13, 2023
@korikuzma korikuzma self-assigned this Jan 13, 2023
@korikuzma
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@ahwagner In the notebooks, I saw this description:

Screen Shot 2023-01-16 at 10 21 34 AM

I'm now wondering if we should provide a parameter on whether or not to do validation rather than always requiring valid input.

@ahwagner
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I think we should check and throw a warning. If somebody provides a reference nucleotide for translation, and that reference does not match the sequence and location provided, it is an indication something may be wrong in their workflow. I think it is okay to parameterize this check if people want to suppress that behavior, but I think it should be active by default.

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