Feature request: pass custom settings to mappy/minimap

[billytcl]

Just in megalodon, where you can pass custom settings to guppy, it would be nice to be able to pass custom mapping settings to minimap/mappy. For example, for things like spliced alignment and tuning settings.

[sklages]

I'd love to see this as well. Not necessarily direct passing of arguments to minimap2, but some more named parameters for bonito to modify some key behavior of minimap, e.g. sth like --secondary-alignments (-N INT option of minimap2).
See also #318