Overview
Version 6 is a major release of augur affecting many augur commands. The format
of the exported JSON (v2) has changed and now merges the previously separate
files containing tree and meta information. To maintain backward compatibility,
the export command was split into `export v1` (old) and `export v2` (new).
Detailed release notes are provided in the augur documentation [on
read-the-docs](https://nextstrain-augur.readthedocs.io/en/stable/releases/v6.html).
For a migration guide, consult
[migrating-v5-v6](https://nextstrain-augur.readthedocs.io/en/stable/releases/migrating-v5-v6.html).
Major features / changes
* export: Swap from a separate `_tree.json` and `_meta.json` to a single
"unified" `dataset.json` output file
* export: Include additional command line options to alleviate need for Auspice
config
* export: Include option for reference sequence output
* export: Move to GFF-style annotations
* export: Validate exported JSONs against schema
* ancestral: Allow output of FASTA and JSON files
* import: Include `import beast` command to import labeled BEAST MCC tree
* parse: Include `--prettify-fields` option to cleanup metadata fields
* Documentation improvements
Minor features / changes
* colors.tsv: Allow whitespace, but insist on tab delimiting
* lat_longs.tsv: Allow whitespace, but insist on tab delimiting
* Remove code for old "non-modular" augur, old "non-modular" builds and Python
tests
* Improve test builds
* filter: More interpretable output of how many sequences have been filtered
* filter: Additional flag `--subsample-seed` to seed the random number generator
and thereby make subsampling reproducible
* sequence-traits: Numerical output as originally intended, but required an
Auspice bugfix
* traits: Explanation of what is considered missing data & how it is interpreted
* traits: GTR models are exported in the output JSON for better accountability &
reproducibility