string Analyzer::getTestResuls(){
string results = "";
NumberSystem* best;
float bestAvg = 1000000;
int min = pow(10,DIGITS-1);
int max = pow(10,DIGITS) - 1;
float avgLength = 0;
NumberSystem* currSystem;
results.append("MIN:");
results.append(AlphaConverter::integerToString(min));
results.append(" MAX:");
results.append(AlphaConverter::integerToString(max));
results += '\n';
for(unsigned int i = 0; i < systems.size(); i++){
currSystem = &(systems.at(i));
avgLength = getAverageLength(min,max,currSystem);
results.append(currSystem->getDescription());
results.append(" avgBitsPerDigit = ");
avgLength /= (float)DIGITS;
results.append(AlphaConverter::floatToString(avgLength));
results += '\n';
if(avgLength < bestAvg){
bestAvg = avgLength;
best = currSystem;
}
}
results.append("Best System: ");
results.append(best->getDescription());
results.append(" avgBitsPerDigit = ");
results.append(AlphaConverter::floatToString(bestAvg));
return results;
}
KmerRepresentativeComputer WindowsStorage::getRepresentativeComputer(junction window,
string seed, size_t min_cover,
float percent_cover,
size_t nb_sampled) {
assert(! hasLimitForReadsPerWindow() || nb_sampled <= getMaximalNbReadsPerWindow());
list<Sequence> auditioned_sequences
= getSample(window,nb_sampled);
KmerRepresentativeComputer repComp(auditioned_sequences, seed);
repComp.setRevcomp(true);
repComp.setMinCover((! isInterestingJunction(window)) ? min_cover : 1);
repComp.setPercentCoverage(percent_cover);
repComp.setRequiredSequence(window);
repComp.setCoverageReferenceLength(getAverageLength(window));
repComp.compute(*scorer);
// We should always have a representative, because either the junction is labelled (thus setMinCover(1)), or:
// - there is at least min('min_reads_clone', 'max_auditioned') sequences in auditioned_sequences
// - and 'min_cover' = min('min_reads_clone', 'max_auditioned')
// - and these sequence are at least as long as the seed
if (!repComp.hasRepresentative())
throw invalid_argument("No representative for junction " + window);
return repComp;
}
