Adds a mutually exclusive input argument, --distance-matrix, to the pathogen-cluster command and corresponding logic to load this matrix and find clusters from its using HDBSCAN's precomputed metric option. When an embedding is provided instead, pathogen-cluster runs HDBSCAN with the default Euclidean distance metric.
Adds a mutually exclusive input argument,
--distance-matrix, to thepathogen-clustercommand and corresponding logic to load this matrix and find clusters from its using HDBSCAN's precomputed metric option. When an embedding is provided instead,pathogen-clusterruns HDBSCAN with the default Euclidean distance metric.