cov-lineages/pangolin v4.3

pangolin v4.3

on GitHub

pangoLEARN analysis mode is now deprecated due to lack of resources for updating the pangoLEARN model. If --analysis-mode fast or --analysis-mode pangolearn is given, pangolin v4.3 will print out a warning and use UShER mode instead, unless --datadir is also given specifying a directory with pangoLEARN model files. The next release of pangolin-data (v1.20) will no longer include the model files which have not been updated since v1.18). (PR #519)

In UShER mode, in the case of multiple equally parsimony-optimal placements (EPPs), the lineage with the most EPPs will no longer override UShER's selected lineage. This "voting" logic was problematic in the case of amplicon dropout (e.g. issue #492). (PR #521)

dependencies: snakemake-minimal is no longer pinned to <=6.8.0 and tabulate is no longer pinned to 0.8.10. (PR #514)