Clean the functions that are unused

[XingerTang]

Some functions are written but not used at all, e.g.

• All the functions in Imputation.py except those start with fillIn and the ind_align()
• generate... in Heuristic_Peeling.py

[gregorgorjanc]

@XingerTang perhaps the only thing that should be done for these functions is that they could be moved later in the code and document them that they are not used. I believe that Andrew was testing several approaches, which is where these functions are coming from. They might still be useful in future.