SeqAn3 3.1.0
The Modern C++ library for sequence analysis.
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1// -----------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
4// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5// shipped with this file and also available at:
6// -----------------------------------------------------------------------------------------------------
13#pragma once
18namespace seqan3
75enum class sam_flag : uint16_t
77 none = 0,
78 paired = 0x1,
79 proper_pair = 0x2,
80 unmapped = 0x4,
81 mate_unmapped = 0x8,
82 on_reverse_strand = 0x10,
84 first_in_pair = 0x40,
85 second_in_pair = 0x80,
86 secondary_alignment = 0x100,
87 failed_filter = 0x200,
88 duplicate = 0x400,
96template <>
97constexpr bool add_enum_bitwise_operators<sam_flag> = true;
106template <typename char_t>
107inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, sam_flag const flag)
109 return stream << static_cast<int16_t>(flag);
112} // namespace seqan3
Provides seqan3::add_enum_bitwise_operators.
Provides seqan3::debug_stream and related types.
debug_stream_type< char_t > & operator<<(debug_stream_type< char_t > &stream, alignment_t &&alignment)
Stream operator for alignments, which are represented as tuples of aligned sequences.
Definition: debug_stream_alignment.hpp:101
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:76
@ mate_on_reverse_strand
The mate sequence has been reverse complemented before being mapped (aligned).
@ mate_unmapped
The mate of this read is not mapped to a reference (unaligned).
@ secondary_alignment
This read alignment is an alternative (possibly suboptimal) to the primary.
@ duplicate
The read is marked as a PCR duplicate or optical duplicate.
@ on_reverse_strand
The read sequence has been reverse complemented before being mapped (aligned).
@ none
None of the flags below are set.
@ failed_filter
The read alignment failed a filter, e.g. quality controls.
@ second_in_pair
Indicates the ordering (see details in the seqan3::sam_flag description).
@ first_in_pair
Indicates the ordering (see details in the seqan3::sam_flag description).
@ unmapped
The read is not mapped to a reference (unaligned).
@ supplementary_alignment
This sequence is part of a split alignment and is not the primary alignment.
@ paired
The aligned read is paired (paired-end sequencing).
@ proper_pair
The two aligned reads in a pair have a proper distance between each other.
The main SeqAn3 namespace.
Definition: cigar_operation_table.hpp:2
Type tag which indicates that no reference information has been passed to the alignment file on const...
Definition: sam_flag.hpp:24