augur package¶
The top-level augur command which dispatches to subcommands.
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augur.
add_default_command
(parser)¶ Sets the default command to run when none is provided.
-
augur.
add_version_alias
(parser)¶ Add –version as a (hidden) alias for the version command.
It’s not uncommon to blindly run a command with –version as the sole argument, so its useful to make that Just Work.
-
augur.
command_name
(command)¶ Returns a short name for a command module.
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augur.
make_parser
()¶
-
augur.
run
(argv)¶
Submodules¶
- augur.align module
- augur.ancestral module
- augur.clades module
- augur.distance module
- augur.export module
- augur.filenames module
- augur.filter module
- augur.frequencies module
- augur.frequency_estimators module
- augur.lbi module
- augur.mask module
- augur.parse module
- augur.reconstruct_sequences module
- augur.refine module
- augur.sequence_traits module
- augur.titer_model module
- augur.titers module
- augur.traits module
- augur.translate module
- augur.tree module
- augur.utils module
- augur.validate module
- augur.version module