Request: a script to figure out input parameters

[lskatz]

This is kind of a long-term request since it is so difficult but probably very useful. I feel like it is possible to estimate many of the parameters in the config file.

Many of these parameters could be estimated from the original data using, I believe, ClonalFrameML on the genome assemblies, standard read metrics from the original fastq files, and a profile that ART generates.

This would be a separate script but I think worth having in the TTR package long-term.