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SPDI normalization with refseq files #76

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Commits on May 16, 2024

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  2. WIP

    mihaitodor committed May 16, 2024
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  5. Fix bit mask bug

    mihaitodor committed May 16, 2024
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  13. Fix CI/CD pipeline

    mihaitodor committed May 16, 2024
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  19. Fix bug in get_variant and fix tests

    Need to run the Flask server in a background thread so the
    seqfetcher endpoint is available for the hgvs library to call.
    Details here: https://stackoverflow.com/questions/77676757/run-a-full-flask-server-under-pytest-to-handle-http-requests-on-a-given-port
    
    Also need to pick the relevat transcript in `process_NC_HGVS()` in
    such a way that we select the one with the most up to date version
    so we don't end up unable to find the RefSeq data because it looks
    like we don't have all the RNA transcripts that UTA knows about.
    mihaitodor committed May 16, 2024
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  21. Disable HGVS strict bounds checks

    This is a workaround for some liftover failures: biocommons/hgvs#717
    mihaitodor committed May 16, 2024
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  23. Re-enable test

    mihaitodor committed May 16, 2024
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  27. Add implication identifiers

    Also remove them from the variants
    mihaitodor committed May 16, 2024
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