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Added before index_sequences because no sequence-based filters are used.
Removing some filters that are now redundant with the previous filter step.
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Update cut.py to infer gene coordinates from the last matching gene or CDS, the same way as newreference.py.
The trimmed Nextclade alignment is sufficient for all other genes.
To support proximal subsampling, sequences must be aligned and trimmed to reference coordinates prior to subsampling. Done via several changes: - A new rule `nextclade_align` replaces the former `genome_align` and `align_pre_subsample_sequences` and is run after the initial `filter`. - A new rule `filter_f_translations` subsets the output of `nextclade_align` with respect to `filter_for_f_antibody_escape` to retain the behavior of `align_pre_subsample_sequences`. - The rule `cut` is moved before subsampling to trim aligned sequences for gene builds. - A new rule `cut_G` replaces the former `cut` and is only used for genome builds to prepare for MAFFT realignment. - The rule `realign` is renamed to `realign_G` and only applies to `genome` and `G` builds. - `hybrid_align` is renamed to `hybrid_align_genome` and is only used for genome builds. The underlying script has been simplified for this single use case.
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Description of proposed changes
This PR contains 4 prep commits and 1 main commit, and 3 to-be-dropped testing commits. Commits to review: 7d91d8f...73c2e25
Some trial run links:
Partial DAG for
a/genome/all-time, before:after:
commands
AI disclosure: ideas and code via Gemini 3.8 Flash
Related issue(s)
https://phylo-lab.slack.com/archives/C01G4B4UY31/p1791912750475389
Checklist