I am trying to initialize polyclonal models using the mutation effects of a different polyclonal model that uses reference sites, rather than sequential sites. To use reference sites, you must specify a list of the reference sites when initializing. However, if you specify a list of sites when initializing, this causes both options "prune_to_data" and "fill_to_data" to fail for "data_mut_escape_overlap", because those options will only work if self.sites is None for some reason (as in, a check for this specifically is coded in). Is there a reason these options check that self.sites is None?
I am trying to initialize polyclonal models using the mutation effects of a different polyclonal model that uses reference sites, rather than sequential sites. To use reference sites, you must specify a list of the reference sites when initializing. However, if you specify a list of sites when initializing, this causes both options "prune_to_data" and "fill_to_data" to fail for "data_mut_escape_overlap", because those options will only work if self.sites is None for some reason (as in, a check for this specifically is coded in). Is there a reason these options check that self.sites is None?