// count up occurrences of kmers within each read
final KMerCounter counter = new KMerCounter(kmerSize);
final int stopPosition = seqForKmers.stop - kmerSize;
for ( int i = 0; i <= stopPosition; i++ ) {
final Kmer kmer = new Kmer(seqForKmers.sequence, i, kmerSize);
counter.addKmer(kmer, 1);
}
return counter.getKmersWithCountsAtLeast(2);
}