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Ran 09 Jul 2026 02:20AM UTC

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Build # 28989302506

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push

github

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web-flow

Commit Message

Add selenocysteine (Sec/U) regression tests (#42) (#401)

#42 (2015) observed varcode treating selenocysteines as stop codons,
producing spurious StopLoss / UTR effects for selenoproteins. That no
longer happens: varcode annotates against Ensembl's reference
protein_sequence (full-length, with U at the recoded UGA) rather than
re-translating the CDS with the standard table.

Verified on GPX1 (ENST00000419783, Sec at residue 49) and locked in with
regression tests covering the three paths:
- substitution AT the Sec codon -> Substitution p.U49C (aa_ref="U"),
  not StopLoss/UTR;
- substitution downstream -> p.R100W with correct numbering (read-through);
- in-frame deletion upstream -> full-length mutant protein that retains U.

Passes under both the fast and protein_diff annotators.

Closes #42

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