24646064493
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Ran 20 Apr 2026 02:52AM UTC

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Build # 24646064493

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github

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web-flow

Commit Message

Fix #321: apply HGVS 3'-rule for in-frame deletions in fast (#327)

In a poly-residue stretch (e.g. CFTR ``…PLLL…`` at positions 98–101),
deleting one L codon is biologically ambiguous — the resulting protein
is identical regardless of which L is reported as deleted. HGVS
nomenclature §3.0 prescribes the most 3' (C-terminal) representation
in this case, so the canonical description is ``p.L101del``, not
``p.L99del``.

``ProteinDiffEffectAnnotator`` already produces the canonical form
because its shared-flank trim runs over the whole protein. ``Fast``'s
trim only sees the codon being edited, so its output stayed at the
deleted-codon position.

After computing ``aa_mutation_start_offset``, slide it forward while
the residue immediately after the deletion equals the residue at the
deletion's start (the slide-validity check that lets the deleted
window rotate one position to the right without changing the mutant
protein). Update ``aa_ref`` to the residues at the new position.

Flip the pinned divergence test in
``test_annotator_divergence_scenarios.py`` to an agreement test
(both annotators now produce ``p.L101del``).

Tighten ``_is_known_divergence`` in the parity harness — the
``Deletion`` ambiguity exception no longer applies.

Closes #321. Bump version to 4.0.6.

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