feat(collection-seeder): add RSV-A/B Nextclade lineages from nextclade_data tree.json#1268
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feat(collection-seeder): add RSV-A/B Nextclade lineages from nextclade_data tree.json#1268fhennig wants to merge 5 commits into
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…e_data tree.json Closes #1256. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…t for RSV Nextclade clades Each clade collection now has four variants (matching COVID Pango shape): - Nucleotide/AA substitutions: full set from reference root (all mutations accumulated along the path root → this clade) - New nucleotide/AA substitutions: branch-only delta (what this clade step introduces relative to its parent) The accumulation handles multi-hop mutations (A→C→G becomes A→G) and reversions (A→C→A is removed from the accumulated set). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…wn by call depth Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…eference base Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
fengelniederhammer
approved these changes
Jun 11, 2026
…ades Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Closes #1256
Summary
RsvANextcladeLineagesSourceandRsvBNextcladeLineagesSourcethat walk the Nextclade reference tree JSON to produce one collection per RSV clade_RsvNextcladeLineagesBasehandles the HTTP fetch; subclasses point at the hardcoded April 2026 snapshots fromnextstrain/nextclade_dataREF_BASE + POSITION + CURRENT_BASE(e.g.A982T)GENE:REF_AA + POSITION + CURRENT_AA(e.g.F:T8A)registry.pyand included in the default runTest plan
pixi run -e test test— all 95 tests pass🤖 Generated with Claude Code