<<" -c: Constraint files where constraints are in the same order than the secondary structure and interaction files"<<std::endl
<<" -p: Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)"<<std::endl
<<" -o: Format of output \"d\" (dot-parenthesis, default), \"j\" (JSON) or \"b\" (base pair list format)"<<std::endl
<<" -e: Energy model (0: No energy model; use energies computed by upstream tools, 1: ViennaRNA package model; default, 2: NUPACK model)"<<std::endl
<<" -t: Threshold for compatibility RNA (0->100, default 100)"<<std::endl
<<" -l: Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)"<<std::endl
<<" -u: Upper probing threshold (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)"<<std::endl
<<" -g: Output graph file"<<std::endl
<<" -k: Output cliques predicted"<<std::endl
<<" -q: Output cliques predicted without duplicates"<<std::endl
<<" -m: Maximum number of structures to output"<<std::endl
<<" -c Constraint files where constraints are in the same order than the secondary structure and interaction files"<<std::endl
<<" -p Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)"<<std::endl
<<" -o Format of output \"d\" (dot-parenthesis, default), \"j\" (JSON) or \"b\" (base pair list format)"<<std::endl
<<" -e Energy model (0: No energy model; use energies computed by upstream tools, 1: ViennaRNA package model; default, 2: NUPACK model)"<<std::endl
<<" -t Threshold for compatibility RNA (0->100, default 100)"<<std::endl
<<" -l Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)"<<std::endl
<<" -u Upper probing threshold (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)"<<std::endl
<<" -g Output graph file"<<std::endl
<<" -k Output cliques predicted"<<std::endl
<<" -q Output cliques predicted without duplicates"<<std::endl
<<" -m Maximum number of structures to output"<<std::endl
<<" -h Shows this message"<<std::endl;
}
// Main
...
...
@@ -279,7 +279,7 @@ int main(int argc, char *argv[]) {