header.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, 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/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <deque>
#include <seqan3/std/ranges>
#include <unordered_map>
#include <vector>
 
#include <seqan3/alphabet/concept.hpp>
#include <seqan3/io/sam_file/detail/cigar.hpp>
#include <seqan3/range/hash.hpp>
#include <seqan3/range/views/type_reduce.hpp>
#include <seqan3/utility/type_traits/pre.hpp>
 
namespace seqan3
{
 
template <std::ranges::forward_range ref_ids_type = std::deque<std::string>>
class sam_file_header
{
public:
    sam_file_header() = default;
    sam_file_header(sam_file_header const &) = default;
    sam_file_header & operator=(sam_file_header const &) = default;
    sam_file_header(sam_file_header &&) = default;
    sam_file_header & operator=(sam_file_header &&) = default;
    ~sam_file_header() = default;
 
    sam_file_header(ref_ids_type & ref_ids) :
        ref_ids_ptr{&ref_ids, ref_ids_deleter_noop}
    {}
 
    sam_file_header(ref_ids_type && ref_ids) :
        ref_ids_ptr{new ref_ids_type{std::move(ref_ids)}, ref_ids_deleter_default}
    {}
 
    struct program_info_t
    {
        std::string id;                
        std::string name;              
        std::string command_line_call; 
        std::string previous;          
        std::string description;       
        std::string version;           
    };
 
    std::string format_version; 
    std::string sorting;        
    std::string subsorting;     
    std::string grouping;       
 
    std::vector<program_info_t> program_infos; 
 
    std::vector<std::string> comments;         
 
private:
    using ref_ids_ptr_t = std::unique_ptr<ref_ids_type, std::function<void(ref_ids_type*)>>;
    static void ref_ids_deleter_noop(ref_ids_type *) {}
    static void ref_ids_deleter_default(ref_ids_type * ptr) { delete ptr; }
    using key_type = std::conditional_t<std::ranges::contiguous_range<std::ranges::range_reference_t<ref_ids_type>>,
                        std::span<range_innermost_value_t<ref_ids_type> const>,
                        type_reduce_view<std::ranges::range_reference_t<ref_ids_type>>>;
    ref_ids_ptr_t ref_ids_ptr{new ref_ids_type{}, ref_ids_deleter_default};
 
public:
    ref_ids_type & ref_ids()
    {
        return *ref_ids_ptr;
    }
 
    std::vector<std::tuple<int32_t, std::string>> ref_id_info{};
 
    std::unordered_map<key_type, int32_t, std::hash<key_type>, detail::view_equality_fn> ref_dict{};
 
    std::vector<std::pair<std::string, std::string>> read_groups;
};
 
} // namespace seqan3