Update geo-fixes #279
Update geo-fixes #279
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I'm going to merge this ASAP (post-merge review welcome) as none of our mpox builds currently have sub-country level metadata included. #278 will add this to the Clade-I build, and we are using it for INRB builds as well. |
| # Note that in our master geolocation rules we replace "Sud-Kivu" with "Sud Kivu" (similarly for "Nord-Kivu") | ||
| # however the INRB tends to use "Sud-Kivu". We can't add a rule here to change it back (`augur curate` doesn't | ||
| # allow it) so we enforce the use of "Sud Kivu" in INRB data as well. |
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I was curious what you meant by "augur curate doesn't allow it"...Because we just concatenate these to the "general" geolocation rules, the conflicting rules raises the CyclicGeolocationRulesError in augur curate apply-geolocation-rules.
Not sure if this is something we should handle within Augur or if the workflow should be improved to not blindly concatenate the geolocation rules...
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Not sure if this is something we should handle within Augur...
If we're going to continue with the pattern of a master-list plus some repo-specific additions it'd be nice if those additions could function as overrides. I.e. if the master list replaces X with Y, we could add an override of Y to X (or Y to Z etc) in a repo-specific manner.
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Yeah, that makes sense! Tracking in nextstrain/augur#1648.
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