Separate clade definitions and lineage definitions #71
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This commit separates clade definitions used for mpxv from lineage definitions used for hmpxv1. Additionally, this updates coloring "clade_membership" to have the display name "Lineage" for hmpxv1. Clades displayed for mpxv are: - MPXV Clade 1 - MPXV Clade 2 - MPXV Clade 3 - hMPXV-1 Lineages displayed for hmpxv1 are: - A - A.1 - A.1.1 - A.2 - B.1
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I didn't like how in the the live version we have a mixture of "clades" like
MPXV Clade 1and "lineages" likeB.1and we call all of this "Clade". I think we need to clearly distinguish "clades" vs "lineages".This PR separates clade definitions used for
mpxvfrom lineage definitions used forhmpxv1.Additionally, this updates coloring "clade_membership" to have the display name "Lineage" for
hmpxv1.Clades displayed for
mpxvare:MPXV Clade 1MPXV Clade 2MPXV Clade 3hMPXV-1Lineages displayed for
hmpxv1are:AA.1A.1.1A.2B.1I'd think to use these as two separate columns in nextclade output as well, again labeled as "clade" vs "lineage".
Output can be seen at nextstrain.org/staging/monkeypox/hmpxv1/lineage-labels