sam_flag.hpp File Reference

Provides helper data structures for the seqan3::sam_file_output. More...

#include <seqan3/core/add_enum_bitwise_operators.hpp>
#include <seqan3/core/debug_stream/debug_stream_type.hpp>

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Classes
struct	seqan3::ref_info_not_given
	Type tag which indicates that no reference information has been passed to the alignment file on construction. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.

Enumerations
enum class	seqan3::sam_flag : uint16_t {   seqan3::sam_flag::none = 0 , seqan3::sam_flag::paired = 0x1 , seqan3::sam_flag::proper_pair = 0x2 , seqan3::sam_flag::unmapped = 0x4 ,   seqan3::sam_flag::mate_unmapped = 0x8 , seqan3::sam_flag::on_reverse_strand = 0x10 , seqan3::sam_flag::mate_on_reverse_strand = 0x20 , seqan3::sam_flag::first_in_pair = 0x40 ,   seqan3::sam_flag::second_in_pair = 0x80 , seqan3::sam_flag::secondary_alignment = 0x100 , seqan3::sam_flag::failed_filter = 0x200 , seqan3::sam_flag::duplicate = 0x400 ,   seqan3::sam_flag::supplementary_alignment = 0x800 }
	An enum flag that describes the properties of an aligned read (given as a SAM record). More...

Detailed Description

Provides helper data structures for the seqan3::sam_file_output.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>