some command-line arguments in docs use `-` but should use `_`

[petrelharp]

For instance, here:

When the --add-mutations flag is provided, Threads parsimoniously adds mutations to the converted ARG objects corresponding to those used to infer the ARG. Note that this can result in a high number of mutations when the threading instructions were not inferred with the --fit-to-data flag.

Those arguments should be --add_mutations and --fit_to_data.

(this is very minor, and easy to figure out, of course, but thought you'd like to know)

[ArniFreyrG]

Thanks for flagging, good catch