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Commit 1644b431 authored by Cyprien Borée's avatar Cyprien Borée
Browse files

Display FineSegmenter informations from vidjil.cpp

The Filter's informations are displayed for each germline at the end of execution.

For more informations, see #3259.
parent 3960b025
Pipeline #31538 passed with stages
in 55 minutes and 2 seconds
......@@ -1622,7 +1622,21 @@ int main (int argc, char **argv)
cerr << "Ooops... unknown command. I don't know what to do apart from exiting!" << endl;
return 1;
}
if(kmer_threshold != NO_LIMIT_VALUE){
cout << "FineSegmenter:" << endl;
for(list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it){
FilterWithACAutomaton *f = (*it)->getFilter_5();
int original_bioreader_size = (*it)->rep_5.size();
int total_sequences_filtered = (f) ? f->filtered_sequences_nb : 0;
int total_filtered_calls = (f) ? f->filtered_sequences_calls : 0;
int total_sequences_original = total_filtered_calls * original_bioreader_size;
float aligned_rate = ((float)total_sequences_filtered/(float)total_sequences_original) * 100;
cout << '\t'<< (*it)->code << "\taligned\t" << total_sequences_filtered;
cout << "/" << total_sequences_original << " (" << aligned_rate << "%)";
cout << endl;
}
}
//$ Output json
cout << " ==> " << f_json << "\t(data file for the web application)" << endl ;
ofstream out_json(f_json.c_str()) ;
......
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