25683129499
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Ran 11 May 2026 04:34PM UTC

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Build # 25683129499

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push

github

Committed by

web-flow

Commit Message

Remove stale mitochondrial codon-table limitation note (closes #365, #44) (#366)

The vertebrate mitochondrial codon table (NCBI table 2) has been
applied automatically to chrM transcripts since #294 / #300 (commit
d255d18) via `codon_table_for_transcript`. Threads through every
translation path including the germline-aware pipeline (which goes
through `apply_variant_to_transcript` -> `_translate_from_cds`).

The limitation note in docs/germline.md and the matching out-of-scope
comment in varcode/germline.py were copy-pasted from the original
germline design doc and never refreshed when #294 landed. Removed
both. Added a germline+mt integration test that locks in the
table-2 dispatch on the germline-aware path so a regression here
shows up loudly.

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