cerr<<"Usage: "<<PROGRAM_NAME<<" [OPTIONS] -a <a.bed> -b <b.bed>"<<endl<<endl;
cerr<<"OPTIONS: "<<endl;
cerr<<"\t"<<"-w (e.g. 100000)\t"<<"Base pairs added before and after each entry in A when searching for overlaps in B"<<endl<<endl;
cerr<<"\t"<<"-w (e.g. 100000)\t"<<"Base pairs added before and after each entry in A when searching for overlaps in B (default=0)"<<endl<<endl;
cerr<<"\t"<<"-u\t\t\t"<<"Write ORIGINAL a.bed entry ONCE if ANY overlap with B.bed."<<endl<<"\t\t\t\tIn other words, just report the fact >=1 hit was found."<<endl<<endl;
cerr<<"\t"<<"-v \t\t\t"<<"Only report those entries in A that have NO OVERLAP in B within the requested window."<<endl<<"\t\t\t\tSimilar to grep -v."<<endl<<endl;
cerr<<"\t"<<"-c \t\t\t"<<"For each entry in A, report the number of hits in B within the requested window."<<endl<<"\t\t\t\tReports 0 for A entries that have no overlap with B."<<endl<<endl;