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Check whether naive was sampled #290

Closed eharkins closed 4 years ago

eharkins commented 5 years ago

This could happen in the same code as checking for similar sampled sequences to inferred ancestors (#186).

However, this step would come after inferring ancestors and so this would not get reflected in the cluster's metadata (in things like multiplicity counts / sampled sequence counts). Although that case can also be made for discovering that we sampled an inferred ancestor (but for some reason it didn't cluster with the original leaves - if we think that is possible).

@metasoarous suggested doing it separately in bin/process_partis.py so that we can reflect the fact that we sampled the naive in the cluster metadata (multiplicity, etc) being counted there.

eharkins commented 4 years ago

Closing this since we achieved the goal of

Check whether naive was sampled

in #296. If we want to add the sampled multiplicity to an inferred sequence's metadata (for viewing in Olmsted) in cases where there is an exact BLAST match, we should open a separate issue for that.