These features are deprecated, which means they are no longer maintained and will go away in a future major version of Augur. They are currently still available for backwards compatibility, but should not be used in new code.
Deprecated in version 25.1.0 (July 2024). Planned for removal November 2024 or after.
Deprecated in version 24.2.0 (February 2024). Reordered in version 26.0.0 (September 2024).
Users who have both 'name' and 'strain' fields in their data, and want to favor using the 'name' field should add the following augur parse parameter --output-id-field 'name'.
Deprecated in version 24.0.0 (January 2024). Planned for removal March 2024 or after.
This is part of a larger effort to formalize Augur's Python API.
We recognize the existing usage of this function, so it has been moved to
augur.io.read_strains.
Deprecated in version 22.2.0 (July 2023). Planned for removal January 2024 or after.
augur export v2 was introduced in Augur version 6.0.0. Migrate by following
the official guide.
Deprecated in version 5.2.0 (December 2019). Removed in version 7.0.0 (April 2020).
--output was replaced by --output-node-data to accommodate the addition of
--output-sequences.