augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- `augur db` with import/export of metadata
- ENH: Allow multiple metadata files to save need to merge manually
- BUG(refine/utils): Uncaught `TypeError: '<' not supported between instances of 'NoneType' and 'str'`
- curate normalize-strings: allow field form overrides
- sequence-traits: Validate features file
- ENH: Allow export of clock deviation from refine
- Refine throw `ValueError: x and y arrays must have at least 2 entries`
- Refine throws: `ERROR: 'NoneType' object has no attribute 'shape'`
- Odd pandas error coming from augur export
- BUG(refine): With `--use-fft`, refine occasionally fails with `ERROR: No module named 'ipdb'`
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- Python not yet supported