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blab / cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
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adding indel tests to hamming distance method #26

Closed huddlej closed 1 year ago

nandsra21 commented 1 year ago

@huddlej I think I've fixed the issues outlined above - can you check and let me know?

huddlej commented 1 year ago

@nandsra21 The most recent commits fix the indel counting logic, adding a check that excludes leading and trailing gaps from the total indel-based distances. Can you try updating the MERS workflow to use indel counts and then regenerate the MERS embeddings to see how it works? If it looks ok, we can update the SARS-CoV-2 workflow to use indels, too.