Add function for creating reference index column

[alxndrkalinin]

Adding the reference index column (constant for perturbation profiles, index for controls) is currently used for phenotypic activity calculations to avoid: (i) forming positive pairs across controls (by pos diffby = ["pert_id", "ref_index"]), (ii) forming negative pairs between perturbation profiles (by neg diffby=["pert_id", "ref_index"]).

We found that adding this column manually can be a source of errors and confusion, so it would be more convenient to add a function that takes a condition as a parameter, which indicates where controls are, and returns a dataframe with the added reference index column.