augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- parse: crash on invalid dates "0", "99999" instead of handling gracefully as intended
- Replace use of internal, non-public pandas API in parse.fix_dates
- Missing escape of square brackets causes diff_jsons.py in some cram tests to be false negative
- fix(tests): Fix false negative cram tests
- tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel
- feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation
- feat(ancestral): Add optional Nextclade GFF3 compatibility mode
- Validation regex pattern for `branch_label` display default values in Auspice config JSON is too strict
- CLI help text can't contain rST section headings
- Gff3 file: differences between nextclade datasets and augur ancestral
- Docs
- Python not yet supported