97 template <
typename char_t>
100 return stream << static_cast<int16_t>(
flag);
The mate sequence has been reverse complemented before being mapped (aligned).
Provides seqan3::add_enum_bitwise_operators.
Indicates the ordering (see details in the seqan3::sam_flag description).
Provides seqan3::debug_stream and related types.
The aligned read is paired (paired-end sequencing).
The main SeqAn3 namespace.
The alignment flag (bit information), uint16_t value.
The read sequence has been reverse complemented before being mapped (aligned).
This read alignment is an alternative (possibly suboptimal) to the primary.
constexpr bool add_enum_bitwise_operators< sam_flag >
Enables bitwise operations for seqan3::sam_flags.
Definition: misc.hpp:89
The read is marked as a PCR duplicate or optical duplicate.
None of the flags below are set.
The mate of this read is not mapped to a reference (unaligned).
Indicates the ordering (see details in the seqan3::sam_flag description).
Type tag which indicates that no reference information has been passed to the alignment file on const...
Definition: misc.hpp:22
The two aligned reads in a pair have a proper distance between each other.
This sequence is part of a split alignment and is not the primary alignment.
The read is not mapped to a reference (unaligned).
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).The SAM flag are bitwise flags, which means that each value corresponds to a specific bit that is set and that they can be combined and tested using binary operations. See this tutorial for an introduction on bitwise operations on enum flags.
Definition: misc.hpp:70
A "pretty printer" for most SeqAn data structures and related types.
Definition: debug_stream_type.hpp:70
The read alignment failed a filter, e.g. quality controls.