// Copyright 2017 Ryan Wick

// This file is part of Filtlong

// Filtlong is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
// version.

// Filtlong is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
// details.

// You should have received a copy of the GNU General Public License along with Filtlong.  If not, see
// <http://www.gnu.org/licenses/>.

#ifndef KMERS_H
#define KMERS_H


#include <cstdint>
#include <string>
#include <vector>
#include <unordered_set>
#include <unordered_map>
#include "bloom_filter.h"


class Kmers
{
public:
    Kmers();
    ~Kmers();

    bool empty() {return m_kmers.size() == 0;}

    void add_read_fastqs(std::vector<std::string> filenames);
    void add_assembly_fasta(std::string filename);
    bool is_kmer_present(uint32_t kmer);

    uint32_t starting_kmer_to_bits_forward(char * sequence);
    uint32_t starting_kmer_to_bits_reverse(char * sequence);

    uint32_t base_to_bits_forward(char base);
    uint32_t base_to_bits_reverse(char base);

private:
    std::unordered_set<uint32_t> m_kmers;
    std::unordered_map<uint32_t, int> m_kmer_counts;
    bloom_filter * bloom;
    int required_kmer_copies;

    int add_reference(std::string filename, bool require_two_kmer_copies);
    void add_kmer_require_one_copy(uint32_t kmer);
    void add_kmer_require_multiple_copies(uint32_t kmer);
};


#endif // KMERS_H