getHammingCounts

Compares the kmers of two KmerMultiSets, set1 and set2.

For every kmer in set1 we assign it a value based on Hamming distance: 0: if the kmer is also present in set2 1: if the most similar kmer in set2 is hamming distance 1 from this kmer 2: if the most similar kmer in set2 is hamming distance 2 or more from this kmer We do the same in reverse for all sequences in set2. Then we count how many kmers falls into each category of HammingCounts

h1KmerCount: number of kmers that had a max Hamming distance value of 1 hManyKmerCount: number of kmers that had a max Hamming distance value of 2 copyNumberCount: of the kmers that appeared in both sets, how many had a different number of counts copyNumberDifference: of the kmers that appeared in both sets, the total difference in their counts

Compares the kmers of two KmerMultiSets, set1 and set2. Also takes one hashmap for each set, hashmap1 and hashmap2.