ancestral, translate: Error when reference gene length is indivisible by 3 #1901
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victorlin
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Oct 7, 2025
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The check is applicable to all load_features calls, not just for VCF inputs in augur translate. Moved into a validation function to be improved in future commits. The calculation has been updated to use the length of feat.location.
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victorlin
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1901 +/- ##
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… instead of warning and padding with N to translate to 'X'. A protein coding sequence with 1 or 2 extra bases indicates a problem with the data. It doesn't make sense to end the translation with 'X' which implies 3 bases.
This matches the equivalent error message in Auspice.¹ ¹ https://github.com/nextstrain/auspice/blob/22124f8eacec2c46f39806aa95472581f65fc25a/src/util/entropyCreateStateFromJsons.ts#L315
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joverlee521
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Note
Based on #1907
Description of proposed changes
… instead of warning and padding with N to translate to 'X'. A protein coding sequence with 1 or 2 extra bases indicates a problem with the data. It doesn't make sense to end the translation with 'X' which implies 3 bases.
Related issue(s)
Closes #1895
Review threads
load_features()? yesChecklist