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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.
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:We should add some additional validation checks for the input
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