pathogen-cluster: Export table of mutations per cluster

[huddlej]

For the cartography paper, we generated a table of mutations per cluster to get a sense of what distinguishes clusters from each other and whether those cluster differences could be biologically meaningful. We implemented this logic in a standalone script, but it seems natural to want this information as an optional output of the pathogen-cluster command. This way users could interrogate their clusters in detail and use the mutations table to refine the cluster thresholds and other parameters for their pathogens.

I can imagine adding this support to pathogen-cluster as a subsection of optional arguments that mostly copy from the cluster mutations script linked above. The arguments we'd want to keep would be:

• --reference-sequence
• --alignment
• --ignored-clusters
• --valid-characters
• --min-allele-count
• --min-allele-frequency

Then we would add an output argument like --output-mutation-table for the mutation table.

I think we could copy most of the original script's code into the pathogen-cluster logic except for the bits where we load cluster labels from different metadata input files.