cerr << "layout.PLACEMENT\n";
cerr << "layout.PLACEMENT" << endl;
int main (int argc, char ** argv){  Mapping_t mapping;  Assembly_t assembly;  //-- COMMAND  ParseArgs (argc, argv);          // parse the command line arguments  srand (OPT_Seed);  //-- INPUT  cerr << "layout.INPUT\n";  ParseAlign (mapping);            // parse the alignment data  ChainAligns (mapping);           // build the LAS chains for each read  if ( OPT_Matepair )    ParseMates (mapping);          // parse the matepair data  //-- READ PLACEMENT  cerr << "layout.PLACEMENT\n";  PlaceUnambiguous (mapping);      // place unambiguous reads  if ( OPT_Matepair )    PlaceHappyMates (mapping);     // place 'happy' matepairs  if ( OPT_Random )    PlaceRandom (mapping);         // randomly place all unplaced reads  sort (mapping.reads.begin( ), mapping.reads.end( ), ReadPlaceCmp_t( ));  //-- CONFLICT DETECTION  cerr << "layout.CONFLICT\n";  FindConflicts (mapping);         // find conflicts btwn reads and refs  RefineConflicts (mapping);       // assess, combine and select conflicts  //-- ASSEMBLY  if ( OPT_PrintTigr  ||  OPT_PrintUMD )    {      cerr << "layout.ASSEMBLY\n";      Assemble (mapping, assembly);// layout the reads to form the assembly      CleanContigs (assembly);     // clean up the contigs    }  //-- OUTPUT  cerr << "layout.OUTPUT\n";  if ( OPT_PrintConflicts )    PrintConflicts (mapping);      // print conflicts  if ( OPT_PrintMaps )    PrintMapping (mapping);        // print read mapping  if ( OPT_PrintTigr )    PrintTigr (assembly);          // print TIGR contigs    if ( OPT_PrintUMD )    PrintUMD (assembly);           // print UMD contigs  return EXIT_SUCCESS;}