Use defaultdict where possible

[jstoja]

Description of proposed changes

Use defaultdict where possible

Testing

What steps should be taken to test the changes you've proposed? Automated tests should be enough.
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this? -> didn't change behaviour, only simplified the code.

[codecov]

Codecov Report

Merging #533 into master will increase coverage by 0.52%.
The diff coverage is 22.22%.

@@            Coverage Diff             @@
##           master     #533      +/-   ##
==========================================
+ Coverage   18.68%   19.21%   +0.52%     
==========================================
  Files          31       31              
  Lines        5053     5070      +17     
  Branches     1281     1286       +5     
==========================================
+ Hits          944      974      +30     
+ Misses       4082     4073       -9     
+ Partials       27       23       -4     

Impacted Files	Coverage Δ
augur/import_beast.py	7.11% <20.00%> (+0.36%)	⬆️
augur/clades.py	12.37% <25.00%> (+1.03%)	⬆️
augur/titer_model.py	18.61% <0.00%> (-0.30%)	⬇️
augur/utils.py	22.89% <0.00%> (-0.18%)	⬇️
augur/frequency_estimators.py	33.71% <0.00%> (-0.13%)	⬇️
augur/refine.py	5.52% <0.00%> (+0.49%)	⬆️
augur/mask.py	100.00% <0.00%> (+13.63%)	⬆️

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[groutr]

You should probably set the default_factory to None after adding all your items to the defaultdict. Otherwise, future lookups to non-existent keys will create the key instead of raising a KeyError.

[jstoja]

Thanks @groutr , that's a very good remark!