Commit 84b59d7a authored by Mathieu Giraud's avatar Mathieu Giraud

core/filter.cpp, vidjil.cpp: bikeshed filter statistics

See #3259.
parent f2a71a4b
Pipeline #31589 passed with stages
in 56 minutes and 38 seconds
......@@ -133,8 +133,11 @@ ostream &operator<<(ostream &out, const FilterWithACAutomaton& obj){
int total_filtered_calls = obj.filtered_sequences_calls;
int total_sequences_origin = total_filtered_calls * origin_bioreader_size;
float aligned_rate = ((float)total_sequences_filtered/(float)total_sequences_origin) * 100;
out << "aligned\t" << total_sequences_filtered;
out << "/" << total_sequences_origin << " (" << aligned_rate << "%)";
out << endl;
return out;
out << fixed << setw(8) << total_sequences_filtered << "/"
<< fixed << setw(8) << total_sequences_origin << " "
<< fixed << setprecision(1) << setw(6) << aligned_rate << "%"
<< endl ;
return out ;
}
......@@ -1622,14 +1622,17 @@ int main (int argc, char **argv)
cerr << "Ooops... unknown command. I don't know what to do apart from exiting!" << endl;
return 1;
}
//$ Output statistics on filter()
if(kmer_threshold != NO_LIMIT_VALUE){
cout << "FineSegmenter:" << endl;
cout << "Statistics on clone analysis (-Z):" << endl;
for(list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it){
FilterWithACAutomaton *f = (*it)->getFilter_5();
if(f){
cout << "\t" << (*it)->code << "\t" << *f;
}
if (f)
if (f->filtered_sequences_nb)
cout << "\t" << (*it)->code << "\t" << *f;
}
cout << endl;
}
//$ Output json
......
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