Commit 951facdc authored by Mikaël Salson's avatar Mikaël Salson
Browse files

automaton.hpp: Count kmers even if they are not new

This seem weird and is a bit hacky. But the purpose is
not to disadvantage a real germline (eg. IGH) compared
to a fake germline (unexpected).

As there are more ambiguous k-mers in the unexpected germline
there will be less IGH k-mers hence a smaller index load for
IGH in the unexpected germline rather than the real one.

See also #2651.
parent 726b0f82
Pipeline #6793 failed with stages
in 1 minute and 56 seconds
......@@ -183,10 +183,8 @@ void PointerACAutomaton<Info>::insert(const seqtype &seq, Info info) {
}
state->is_final = true;
assert(info.getLength() <= MAX_KMER_SIZE);
if (state->informations.front().isNull()) {
this->nb_kmers_inserted++;
this->kmers_inserted[info]++;
}
this->nb_kmers_inserted++;
this->kmers_inserted[info]++;
state->informations.front() += info;
}
......
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