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ingest: potential bug with gene coverage #5

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joverlee521 opened this issue Jan 6, 2025 · 0 comments
Open

ingest: potential bug with gene coverage #5

joverlee521 opened this issue Jan 6, 2025 · 0 comments

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@joverlee521
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Copying over potential issue with extend_metadata.py as seen in nextstrain/rsv#75

the gene coverage columns are added during ingest by extend_metadata.py, which compares for the alignment start and end to the gene coordinates, but does not account for gaps/Ns.

in the long term, we should revisit having Nextclade calculate the cds coverage.
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@joverlee521