misc.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 <seqan3/core/add_enum_bitwise_operators.hpp>
#include <seqan3/core/detail/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 <>
constexpr bool add_enum_bitwise_operators<sam_flag> = true;
 
template <typename char_t>
inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, sam_flag const flag)
{
    return stream << static_cast<int16_t>(flag);
}
 
} // namespace seqan3