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… module
Pure move of the tree-walking and mutation-accumulation helpers out of the
RSV source, so they can be reused for other organisms.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…e configurable
Detect a lineage introduction where node_attrs.<lineage_attr> changes from the
parent node instead of relying on branch_attrs.labels.clade. The SARS-CoV-2
tree only labels Nextstrain clades on branches, Pango lineages are only
available as node_attrs.Nextclade_pango.
For RSV ("clade_membership") this is equivalent: the generated collections
are identical for the current RSV-A and RSV-B trees.
Also expose node_attrs and depth of the introducing node.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…tree
Derive the covid pango lineage collections from the Nextclade SARS-CoV-2
reference tree (nextclade_data, sars-cov-2/wuhan-hu-1/orfs/tree.json) instead
of corneliusroemer/pango-sequences, as we already do for RSV.
- Lineages come from node_attrs.Nextclade_pango. If a lineage is introduced
at several places in the tree, the node closest to the root is used.
- Variants now also contain deletions (like the RSV lineages), the old source
only had substitutions.
- "New" substitutions are those not in the parent lineage's definition.
- Source name, tag, collection names and variant names are unchanged, so
existing collections are updated in place.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…to parent clade
The 'New ... substitutions' variants only contained the mutations on the
branch introducing the clade. Mutations on intermediate nodes between the
parent clade and the clade were missing, although they also distinguish the
clade from its parent. Use the difference to the parent clade's full set
instead, like for the covid pango lineages.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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fhennig
changed the title
refactor(collection-seeding): Switch covid source to nextclade
refactor(website): Switch covid source to nextclade
Oct 1, 2026
… ancestor clade
The parent clade was looked up by name. Since a clade can be introduced at
several nodes of the tree, and only one introduction per name is kept, this
could pick an unrelated introduction: e.g. BA.4 and BA.5 sit below the second
introduction of B.1.1.529 (inside BA.2) and got ~70 "new" mutations instead of
1-3. Affects 15 covid lineages in the current tree.
Compute new_nuc / new_aa during the tree walk instead, carrying the full sets
of the ancestor's introduction along the path. RSV output is unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
These lists now intentionally contain deletions as well as substitutions (the new tests include A21766- and S:H69-), but all four user-facing variant names and descriptions below still call every entry a “substitution.” Rename them to nucleotide/amino-acid “mutations” (or otherwise distinguish deletions) so the generated collection does not misdescribe its filters.
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resolves #1382
Summary
Switch to pulling from nextclade, instead of cornelius' list. We already had the code in place for RSV.
A few definitions changed, some lineages were deleted (early ones) and some were added that were missing.
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