int main(int argc, char *argv[])
{
if (argc == 1) usage(); // Print usage
for (int i=0; i<argc; i++)
{
cerr << argv[i] << ' ';
cerr << endl;
}
Initial_Time();
cerr<<"Start at: "<<Curr_Time()<<endl;
int noptions = mGetOptions(argc, argv);
// Mutltithreads part
#if defined (_OPENMP)
if (param.ncpu) omp_set_num_threads(param.ncpu);
#endif
fin_db.open(ref_file.c_str());
if (!fin_db)
{
cerr << "fatal error: failed to open ref file\n";
exit(1);
}
ref.Run_ConvertBinseq(fin_db);
cerr << "Load in " << ref.total_num << " reference seqs, total size " << ref.sum_length << " bp. " << Cal_AllTime() << " secs passed" << endl;
ref.CreateIndex(); // Qgram_Index();
cerr << "Create refseq k-mer index table. " << Cal_AllTime() << " secs passed" << endl;
RunProcess();
return 0;
}
void Do_Formatdb()
{
ref.CreateIndex();
cout<<"Create seed table. "<<Cal_AllTime()<<" secs passed"<<endl;
};