Method getKmers

src/rnabloom/bloom/hash/HashFunction.java:55–85

(final String seq, final int numHash, BloomFilterDeBruijnGraph graph)

    }
    
    public ArrayList<Kmer> getKmers(final String seq, final int numHash, BloomFilterDeBruijnGraph graph) {
        boolean containsInvalidChar = containsInvalidNucleotides(seq);
        ArrayList<Kmer> result = new ArrayList<>();
        
        int seqLength = seq.length();
        
        if (seqLength >= k) {
            byte[] bytes = stringToBytes(seq, seqLength);

            NTHashIterator itr = new NTHashIterator(k, numHash);
            itr.start(seq);
            long[] hVals = itr.hVals;
            int i;
            float c;
            while (itr.hasNext()) {                
                itr.next();                
                i = itr.getPos();
                
                if (containsInvalidChar && containsInvalidNucleotides(seq, i, i+k)) {
                    c = 0;
                }
                else {
                    c = graph.getCount(hVals);
                }
                
                result.add(new Kmer(Arrays.copyOfRange(bytes, i, i+k), c, hVals[0]));
            }
        }
        
        return result;
    }

    public ArrayList<Kmer> getKmers(final String seq, final int numHash, BloomFilterDeBruijnGraph graph, float minCoverage) {
        boolean containsInvalidChar = containsInvalidNucleotides(seq);