void WindowsStorage::add(junction window, Sequence sequence, int status, Germline *germline) {
if (! hasWindow(window)) {
// First time we see that window: init
status_by_window[window].resize(STATS_SIZE);
seqs_by_window[window].init(nb_bins, max_value_bins, &scorer);
seqs_by_window[window].setMaxNbReadsStored(getMaximalNbReadsPerWindow());
}
seqs_by_window[window].add(sequence);
status_by_window[window][status]++;
germline_by_window[window] = germline;
}
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;
}
