sam_flag.hpp

Go to the documentation of this file.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <seqan3/core/add_enum_bitwise_operators.hpp>
#include <seqan3/core/debug_stream/debug_stream_type.hpp>
 
namespace seqan3
{
 
struct ref_info_not_given
{};
 
enum class sam_flag : uint16_t
{
    none = 0,                       
    paired = 0x1,                   
    proper_pair = 0x2,              
    unmapped = 0x4,                 
    mate_unmapped = 0x8,            
    on_reverse_strand = 0x10,       
    mate_on_reverse_strand = 0x20,  
    first_in_pair = 0x40,           
    second_in_pair = 0x80,          
    secondary_alignment = 0x100,    
    failed_filter = 0x200,          
    duplicate = 0x400,              
    supplementary_alignment = 0x800 
};
 
template <>
inline constexpr bool add_enum_bitwise_operators<sam_flag> = true;
 
template <>
struct sam_flag_printer<sam_flag>
{
    template <typename stream_t>
    constexpr void operator()(stream_t & stream, sam_flag const arg) const
    {
        stream << static_cast<int16_t>(arg);
    }
};
 
} // namespace seqan3