Binaries compiled with BGAP-C are not meant to be ready to ship programs. The system is not restricted to RNA problems; although this package only deals with them. Thus, compiled programs are equipped with a very generic front end (the *_main.cc files). In order to pass RNA specific command line arguments (e.g. usage of lonely base-pairs) into the computation, we replace some components of the generated C++ code previous to compilation with g++. This task is automated by the Perl script Misc/Applications/addRNAoptions.pl and can be applied via perl Misc/Applications/addRNAoptions.pl out.mf.
"rnaoptions.hh" replaces the BGAP built-in "rtlib/generic_opts.hh" file.

Since this extension of the command line parameters only matters if you want to deploy an application, but not if you are in the process of designing a new BGAP program, the file Extensions/rnaoptions_defaults.hh contains default values for all additional RNA parameters.

Depending on your instances not all arguments will have influence on the results, e.g. if you deal with nested folding pkissinit (the initialization penalty for a kissing hairpin) can be set but won't change anything.