The function add_individuals_to_tree_sequence only adds new edges to an existing tree sequence but not new mutations. A separate function needs to be implemented to add new mutations that occur above newly added sample nodes of the individuals.
It should be as simple as getting the inherited state of the parent node and checking whether it is identical to the observed state of the sample at each site.
The function
add_individuals_to_tree_sequence
only adds new edges to an existing tree sequence but not new mutations. A separate function needs to be implemented to add new mutations that occur above newly added sample nodes of the individuals.