Clarify default values for inference of ambiguous bases #613
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Description of proposed changes
This commit makes the following changes to clarify what the defaults are for inferring ambiguous bases both for the user and maintainers:
--keep-ambiguous
flag has an implicit default ofFalse
because of its action type (the usual behavior for this type of opt-in flag)--infer-ambiguous
flag has an explicit default ofTrue
to properly document the default behavior in the help output and communicate to us as developers that this flag is essentially redundantRelated issue(s)
Resolves #612
Testing
Added minimal functional tests for
augur ancestral
prior to making the changes in this PR, to confirm that the new code does not break the existing user interface.