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nextstrain / forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts
https://nextstrain.org/sars-cov-2/forecasts/
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Allow force include of Pango lineages that might not meet threshold #70

Open joverlee521 opened 11 months ago

joverlee521 commented 11 months ago

Context

Requested by @trvrb in today's forecasts-automation meeting :

I’d also like to add functionality to ensure specific Pango lineages are included even if they don’t meet count threshold (important for JN.1 at the moment)

Possible solution

We can use the force-include-clades config for scripts/prepare-data.py to prevent lineages from being added to other.

We will have to update scripts/collapse-lineage-counts.py with a new option to force include lineages and prevent them from being collapsed into their parent lineages.