KBF2.hpp

/*************************************************************
* Copyright (c) David Pellow, Darya Filippova, Carl Kingsford
*************************************************************/

#ifndef LIB_KBF_2
#define LIB_KBF_2

#include <bf/all.hpp>

#include "BaseBloomFilter.hpp"
#include "KBFUtil.hpp"

class KBF2 : public BaseBloomFilter {
   private:
    const unsigned extend_len;
    unordered_set<kmer_t> edge_kmers;  //set of kmers on sequence edges - will fail BF contains()
    size_t extended_check = 0;         // # of times checks extensions
    size_t edge_check = 0;             // # of times checks edge set
    size_t edge_pass = 0;              // # of times returns true from edge check
   public:
    // constructor 1:
    // takes in kmer sets - kmers and potential edges (read edges)
    KBF2(const int k, unordered_set<kmer_t>& kmer_set, unordered_set<kmer_t>& edge_set, const unsigned extend_len = 1, const size_t size_factor = 20) : BaseBloomFilter(k, kmer_set.size(), size_factor), extend_len(extend_len) {
        populate(kmer_set);
        getEdges(edge_set);
        // cerr << "Edges: " << edge_kmers.size() << endl;
        extended_check = 0;
        edge_check = 0;
        edge_pass = 0;
    }

    ~KBF2() {
        // cerr << "# of extended checks: " << extended_check << endl;
        // cerr << "# of edge checks: " << edge_check << endl;
        // cerr << "# that pass: " << edge_pass << endl;
    }

    // any read edge kmer that is not in the filter needs
    // to be stored in edge_kmers
    void getEdges(unordered_set<kmer_t>& edges) {
        for (auto km : edges) {
            if (!contains(km))
                edge_kmers.insert(km);
        }
    }

    bool contains(const kmer_t& kmer) {
        if (!bf_.lookup(kmer)) {
            return false;
        }
        extended_check++;
        bool containsLeft = searchLeft(kmer, extend_len, k, &bf_);
        bool containsRight = searchRight(kmer, extend_len, k, &bf_);
        if (containsLeft && containsRight) {
            return true;
        }
        if (containsLeft || containsRight) {
            //assumes read length > k+extend_len
            edge_check++;
            if (edge_kmers.find(kmer) != edge_kmers.end()) {
                edge_pass++;
                return true;
            }
        }
        return false;
    }
};

#endif