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jeromekelleher / sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Remove `epi_isl_map` #210

Closed szhan closed 1 month ago

szhan commented 1 month ago

Since we don't really use GISAID sequences at the moment, this snippet in utils.py when creating a TreeInfo object is not needed anymore, and shouldn't be required in the metadata.

self.epi_isl_map[md["gisaid_epi_isl"]] = node.id
if md["gisaid_epi_isl"] is not None:
    if "." in md["gisaid_epi_isl"]:
        self.epi_isl_map[md["gisaid_epi_isl"].split(".")[0]] = node.id
szhan commented 1 month ago

I think that the strain map we got suffices for now.