do_simulation: Simulation code
In TransmissibleCancerGroup/dftdLowCov:

Simulation code

do_simulation(input_data, chrlengths, simulation_name, nsims, base_outdir,
  plot_every = 100, write_output = FALSE,
  keep_to_original_chrom = FALSE, hard_bounds = FALSE,
  parametric = FALSE)

`input_data`	data.table; table of CNVs
`chrlengths`	data.table; table of the Devil chromosome lengths
`simulation_name`	string; used in name of output files
`nsims`	int; number of simulation replicates
`base_outdir`	path; output will be written under this path
`plot_every`	int; draw a chromosome map every 'plot_every' reps
`write_output`	bool; write output to disk?
`keep_to_original_chrom`	bool; should shuffled CNV segments be restricted to their original chromosome, or be allowed to move genome wide?
`hard_bounds`	bool; should chromosome ends act as hard boundaries for shuffled CNVs? Or should CNVs be allowed to straddle over chromosome ends?
`parametric`	bool; if TRUE, then CNV widths are drawn from a Gamma distribution, fitted to the observed widths in the input data. If FALSE, the original widths are used.