printer for boost::program_options::variables_map
use to_ptree memfn if it exists, fall back to ptree ctor
use values from variables_map directly
dead code
single to_ptree function
moved Mutation support code into Contig_Entry class
added Mutation::to_stream; simple methods into header
added methods to enable deallocation
enable disposing code; more logging
added Hap_Hop::to_stream method
cli code moved to separate TU