KmerIterator undefined behaviour if string starts with N

[kreldjarn]

When iterating over a string that contains N, the KmerIterator should spool over the N and continue iterating from there. This works for the general case, but if the string starts with an N the KmerIterator returns a Kmer consisting of only A's, even though the next Kmer is a valid one containing no N's.

See reproducible example here:

int main(int argc, char* argv[]) {
    CompactedDBG<void> dbg(31);
    std::string seq1 = "NCATCACACACAGGGCTATTCCTTTCCTCCAATGAACCAA";
    std::string seq2 = "CNATCACACACAGGGCTATTCCTTTCCTCCAATGAACCAA";

    KmerIterator kit1(seq1.c_str());
    std::cout << kit1->first.toString() << std::endl;
    // AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    KmerIterator kit2(seq2.c_str());
    std::cout << kit2->first.toString() << std::endl;
    // ATCACACACAGGGCTATTCCTTTCCTCCAAT

    return 0;
}

[kreldjarn]

Should be fixed in 4b2917b

[GuillaumeHolley]

Hi @kreldjarn,

This is a very good catch, thanks! The issue stems from a modification I have made some time ago to the way the Kmer object is initialized and checked for "emptyness". I'll approve your PR asap.

Guillaume