augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Consolidate dates logic between `curate/format_dates` and `dates/ambiguous_date`
- Support partial ambiguity in `augur curate format-dates`
- filter: Rewrite using SQLite3
- augur clade only partially assigns clade information
- ENH(clades): Validate `clades.tsv`, bad file currently throws uncaught error
- DOC(filter): Surface excellent function level documentation`--exclude-where` for cli help
- filter: Improperly handled `ValueError: not enough values to unpack (expected 2, got 1)` in ` _parse_filter_query`
- Report helpful error if filter query string malformed
- DOC(curate): Improve explanation of what `--seq-field` does
- BUG: Passing unrecognized argument shows general augur not subcommand usage string
- Docs
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