<< "-c            Circular reference sequence\n"
void PrintHelp (const char * s){  PrintUsage (s);  cerr    << "-b path       Set path of the AMOS bank to use for mate-pair info\n"    << "-c            Circular reference sequence\n"    << "-C            Print conflict positions and support counts\n"    << "-e            Exclude all segmented and partial read mappings\n"    << "-g uint       Set maximum alignment gap length, default "    << OPT_MaxGap << endl    << "-h            Display help information\n"    << "-i float      Set the minimum alignment identity, default "    << OPT_MinIdentity << endl    << "-I float      Set the identity tolerance between repeats, default "    << OPT_MaxIdentityDiff << endl    << "-M            Print read mappings\n"    << "-o uint       Set minimum overlap length for assembly, default "    << OPT_MinOverlap << endl    << "-r            Randomly place repetitive reads into one of their copy\n"    << "              locations if they cannot be placed via mate-pair info\n"    << "-s uint       Set random generator seed to unsigned int. Default\n"    << "              seed is generated by the system clock\n"    << "-t uint       Set maximum ignorable trim length, default "    << OPT_MaxTrimLen << endl    << "-T            Print TIGR contig\n"    << "-U            Print UMD contig\n"    << "-v float      Set the minimum alignment coverage, default "    << OPT_MinCoverage << endl    << "-V float      Set the coverage tolerance between repeats, default "    << OPT_MaxCoverageDiff << endl    << endl;  cerr    << "  Position query sequences on a reference based on the alignment\n"    << "information contained in the deltafile. Can utilize mate-pair\n"    << "information to place repetitive sequences, or random placement\n"    << "to simulate even coverage.\n\n";  return;}