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;
}
int main(int argc, char *argv[])
{
//print usage
if (argc == 1)
{
usage();
}
Initial_Time();
cout<<"Start at: "<<Curr_Time()<<endl;
int noptions;
noptions=mGetOptions(argc, argv);
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);
cout<<"Load in "<<ref.total_num<<" db seqs, total size "<<ref.sum_length<<" bp. "<<Cal_AllTime()<<" secs passed"<<endl;
//single command:
if(noptions==argc) {
Do_Formatdb();
RunProcess();
}
else {
int old_seed_size=0;
char * margv[1000];
for(int i=0; i<1000; i++) {
margv[i] = new char[1000];
}
char ch[10000];
ifstream fin_batch(argv[noptions]);
while(!fin_batch.eof()) {
fin_batch.getline(ch, 10000);
if(fin_batch.eof())
break;
cout<<"Line of options: "<<ch<<endl;
bool is_word=0;
int margc=0;
char *q=margv[margc];
for(int i=0; ch[i]!='\0'; i++) {
if((ch[i]>=33)&&(ch[i]<=126)) {
if(!is_word) {
*q='\0';
margc++;
q=margv[margc];
}
is_word=1;
*q++=ch[i];
}
else {
is_word=0;
}
}
*q='\0';
margc++;
mGetOptions(margc, margv);
if(param.seed_size!=old_seed_size) {
if(ref.total_kmers>0)
ref.ReleaseIndex();
Do_Formatdb();
old_seed_size=param.seed_size;
}
RunProcess();
}
fin_batch.close();
}
return 0;
}