fix: don't count mutations at masked sites towards branch length#1779
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fix: don't count mutations at masked sites towards branch length#1779
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## master #1779 +/- ##
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+ Coverage 73.21% 73.23% +0.02%
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Branches 1713 1715 +2
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Adds a functional test for augur refine's behavior when one or more columns in the alignment are all Ns. In this case, the columns should get ignored in the final branch length calculations as ambiguous positions. This test adds an alternate version of the Zika alignment and the expected branch lengths JSON where the third column of the alignment has been changed to all Ns. Since this column originally had a variant in one sample that would have changed the overall branch lengths, this change produces different a node data JSON output with a shorter branch length.
Adds a comment to clarify why we can break from the loop through all positions in TreeTime's compressed alignment data structure. For people who are not familiar with that data structure, the appearance of a break in the for loop could appear to be a bug.
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Thanks, @huddlej |
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augur refinehas the mode--divergence-units mutationsin which case branch length are given as number of mutations in an ancestral reconstruction. We ignore gaps and ambiguous sites in this calculation as we should, but in the edge case when there is no information at all (site isNeverywhere), we count a large number of spurious mutations. This happens when the root state is picked by from the probability distribution at random, and other states are set to the most likely state. @corneliusroemer discovered this in the case of mpox where about 10k sites are masked. The probability distribution for these 10k states in[0.2, 0.2, 0.2, 0.2, 0.2]. The root was picked at random, other states vianp.argmax([0.2, 0.2, 0.2, 0.2, 0.2]). If these differed, this generated 10k unwanted mutations.This PR excludes those sites from the branch length calculation. A list of all these sites is anyway available within treetime.