Expose two additional options of TreeTime in augur refine #1203
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flags in augur refine. * --stochastic-resolve was added in TreeTime 0.9.6 (hence update to dependencies in setup.py) and uses a different algorithm for polytomy resolution in TreeTime. Instead of pulling successively merging the two branches the increase the likelihood most, this mode generates random coalescent trees. This is faster and leads to more typical resolutions. * --max-iter controls the number of iterations TreeTime uses to infer time trees. This was previously hard coded to 2.
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1203 +/- ##
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Coverage 68.37% 68.38%
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Files 64 64
Lines 6852 6854 +2
Branches 1662 1662
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+ Hits 4685 4687 +2
Misses 1857 1857
Partials 310 310
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I ran this with a modified seasonal-flu workflow that sets
the new result is
overall, this looks like a more "natural" tree topology. When not setting these flags, the behavior shouldn't have changed. |
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thanks, Tom. I also discussed this with John while he was in Basel. |
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Expose two additional options of TreeTime in augur refine as commandline flags in augur refine.
This PR is completely backwards compatible in that without explicitly setting these flags, the behavior of
refinedoes not change.Testing
I ran the seasonal flu builds with these flags and they finished without problem.
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