Rate confidence arguments passed down to treetime

[rneher]

Description of proposed changes

@pauloluniyi ran into an issue where augur failed during refine due to inconsistent arguments handed off to treetime. (requesting confidence intervals with rate uncertainty for a fixed rate without specifying uncertainty for the rate).

This commit checks that no rate is provided, i.e. the rate is estimated from the data, before requesting confidence intervals with rate uncertainty.

Related issue(s)

Fixes #547
Related to neherlab/treetime#118

Testing

What steps should be taken to test the changes you've proposed?
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?

Thank you for contributing to Nextstrain!

[codecov]

Codecov Report

Merging #548 into master will not change coverage.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##           master     #548   +/-   ##
=======================================
  Coverage   19.16%   19.16%           
=======================================
  Files          31       31           
  Lines        5072     5072           
  Branches     1289     1289           
=======================================
  Hits          972      972           
  Misses       4077     4077           
  Partials       23       23           

Impacted Files	Coverage Δ
augur/refine.py	5.52% <0.00%> (ø)

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