bool Process() {
if (is_selected)
{
return kmc->Process();
}
else
return app_1->Process();
}
//----------------------------------------------------------------------------------
// Main function
int _tmain(int argc, _TCHAR* argv[])
{
CStopWatch w0, w1;
double time1, time2, time3;
uint64 n_unique, n_cutoff_min, n_cutoff_max, n_total, n_reads, tmp_size, tmp_size_strict_mem, max_disk_usage, n_total_super_kmers;
omp_set_num_threads(1);
#ifdef WIN32
_setmaxstdio(2040);
#endif
if(!parse_parameters(argc, argv))
{
usage();
return 0;
}
if(Params.p_quake)
{
CApplication<CKmerQuake, KMER_WORDS, true> *app = new CApplication<CKmerQuake, KMER_WORDS, true>(Params);
if(!app->Process())
{
cout << "Not enough memory or some other error\n";
delete app;
return 0;
}
app->GetStats(time1, time2, time3, n_unique, n_cutoff_min, n_cutoff_max, n_total, n_reads, tmp_size, tmp_size_strict_mem, max_disk_usage, n_total_super_kmers);
delete app;
}
else
{
CApplication<CKmer, KMER_WORDS, false> *app = new CApplication<CKmer, KMER_WORDS, false>(Params);
if(!app->Process())
{
cout << "Not enough memory or some other error\n";
delete app;
return 0;
}
app->GetStats(time1, time2, time3, n_unique, n_cutoff_min, n_cutoff_max, n_total, n_reads, tmp_size, tmp_size_strict_mem, max_disk_usage, n_total_super_kmers);
delete app;
}
cout << "1st stage: " << time1 << "s\n";
cout << "2nd stage: " << time2 << "s\n";
if (Params.p_strict_mem)
cout << "3rd stage: " << time3 << "s\n";
if (Params.p_strict_mem)
cout << "Total : " << (time1 + time2 + time3) << "s\n";
else
cout << "Total : " << (time1+time2) << "s\n";
if (Params.p_strict_mem)
{
cout << "Tmp size : " << tmp_size / 1000000 << "MB\n";
cout << "Tmp size strict memory : " << tmp_size_strict_mem / 1000000 << "MB\n";
//cout << "Tmp total: " << (tmp_size + tmp_size_strict_mem) / 1000000 << "MB\n";
cout << "Tmp total: " << max_disk_usage / 1000000 << "MB\n";
}
else
cout << "Tmp size : " << tmp_size / 1000000 << "MB\n";
cout << "\nStats:\n";
cout << " No. of k-mers below min. threshold : " << setw(12) << n_cutoff_min << "\n";
cout << " No. of k-mers above max. threshold : " << setw(12) << n_cutoff_max << "\n";
cout << " No. of unique k-mers : " << setw(12) << n_unique << "\n";
cout << " No. of unique counted k-mers : " << setw(12) << n_unique-n_cutoff_min-n_cutoff_max << "\n";
cout << " Total no. of k-mers : " << setw(12) << n_total << "\n";
if(Params.p_file_type != multiline_fasta)
cout << " Total no. of reads : " << setw(12) << n_reads << "\n";
else
cout << " Total no. of sequences : " << setw(12) << n_reads << "\n";
cout << " Total no. of super-k-mers : " << setw(12) << n_total_super_kmers << "\n";
return 0;
}
