Improvements `simulate_seq` function

[jovoni]

I and @valerianilucrezia were discussing with @caravagn about what would be useful for the simulate_seq function to return.

As today, it returns only the sequencing results, but we feel like it would be useful if maybe it returned a list containing:

• seq_results (current output)
• sequencing_info (Sequencer, coverage, purity, read_size)
• genome_reference_positions (absolute chromosome position for the reference used, object now return by the get_absolute_chromosome_positions method over a Rcpp_PhylogeneticForest object (which is also the input of the simulate_seq function))

We think that this additional informations could be useful both for keeping track of the sequencing setup and to remove an eventual dependency of genome wide plotting functions over the Rcpp_PhylogeneticForest object.

What do you think?

[caravagn]

I would encapsulate this in an Robject