shared.hpp

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// ---------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/chopper/blob/main/LICENSE.md
// ---------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <cstdint>
#include <filesystem>
#include <string>
#include <vector>
 
#include <hibf/contrib/robin_hood.hpp>
#include <hibf/sketch/hyperloglog.hpp>
 
struct config
{
    std::filesystem::path input{};
    std::filesystem::path output{};
    bool output_shared_kmers{false};
    uint8_t threads{1u};
};
 
void execute_general(config const & cfg);
void execute_sizes(config const & cfg);
 
void process_file(std::string const & filename,
                  std::vector<uint64_t> & current_kmers,
                  uint8_t const kmer_size,
                  uint8_t const window_size);
 
void process_file(std::string const & filename,
                  robin_hood::unordered_set<uint64_t> & current_kmer_set,
                  std::vector<uint64_t> & current_kmers,
                  seqan::hibf::sketch::hyperloglog & sketch,
                  bool const fill_current_kmers,
                  uint8_t const kmer_size,
                  uint8_t const window_size);