Clade-I tweaks #278
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Clade-I tweaks #278
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jameshadfield
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Update the geographical inference for Clade-I builds. A number of samples are missing these detailed geo resolutions, but they are still very helpful. Additional lat-longs provided by Dr. Eddy K. Lusamaki (INRB, DRC). These are available to all builds although currently none make use of them.
We don't want an ordering for division & location in the clade-I builds as these are constantly changing and we want to avoid auspice using greys for demes
For clade-i builds run a custom script rather than using `augur clades` as that approach can't reliably identify basal clades due to the stochastic way `augur ancestral` assigns mutations on basal branches.
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I'd like to merge this ASAP and will do so tomorrow if there are no objections. The only changes are to clade-I builds and they fix the currently buggy clade labeling as well as adding metadata to reflect the richness of the newly submitted INRB data. |
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Clade-I specific changes to how geographic metadata is passed through and how clades are assigned.
This PR should use the updated ingest data from #279