SeqAn3  3.0.1
The Modern C++ library for sequence analysis.
Alignment File

Provides files and formats for handling alignment data. More...

+ Collaboration diagram for Alignment File:

Classes

class  seqan3::alignment_file_header< ref_ids_type >
 Stores the header information of alignment files. More...
 
class  seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >
 A class for reading alignment files, e.g. SAM, BAM, BLAST ... More...
 
struct  seqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t >
 The default traits for seqan3::alignment_file_input. More...
 
interface  seqan3::alignment_file_input_format
 The generic concept for alignment file input formats. More...
 
struct  seqan3::alignment_file_input_options< sequence_legal_alphabet >
 The options type defines various option members that influence the behaviour of all or some formats. More...
 
interface  seqan3::alignment_file_input_traits
 The requirements a traits_type for seqan3::alignment_file_input must meet. More...
 
class  seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
 A class for writing alignment files, e.g. SAM, BAL, BLAST, ... More...
 
interface  seqan3::alignment_file_output_format
 The generic concept for alignment file out formats. More...
 
struct  seqan3::alignment_file_output_options
 The options type defines various option members that influence the behavior of all or some formats. More...
 
class  seqan3::format_bam
 The BAM format. More...
 
class  seqan3::format_sam
 The SAM format (tag). More...
 
struct  std::tuple_element< elem_no, seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > >
 Obtains the type of the specified element. More...
 
struct  std::tuple_size< seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > >
 Provides access to the number of elements in a tuple as a compile-time constant expression. More...
 

Enumerations

enum  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).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. More...
 

Detailed Description

Provides files and formats for handling alignment data.

Enumeration Type Documentation

◆ sam_flag

enum seqan3::sam_flag : uint16_t
strong

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.

Example:

#include <iostream>
#include <sstream>
auto sam_file_raw = R"(@HD VN:1.6 SO:coordinate GO:none
@SQ SN:ref LN:45
r001 99 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTG !!!!!!!!!!!!!!!!!
r003 0 ref 29 30 5S6M * 0 0 GCCTAAGCTAA !!!!!!!!!!! SA:Z:ref,29,-,6H5M,17,0;
r003 4 * 29 17 * * 0 0 TAGGC @@@@@ SA:Z:ref,9,+,5S6M,30,1;
r001 147 ref 237 30 9M = 7 -39 CAGCGGCAT !!!!!!!!! NM:i:1
)";
int main()
{
for (auto & rec : fin)
{
// Check if a certain flag value (bit) is set:
if (static_cast<bool>(seqan3::get<seqan3::field::flag>(rec) & seqan3::sam_flag::unmapped))
std::cout << "Read " << seqan3::get<seqan3::field::id>(rec) << " is unmapped\n";
if (seqan3::get<seqan3::field::qual>(rec)[0] < seqan3::assign_char_to('@', seqan3::phred42{})) // low quality
{
// Set a flag value (bit):
seqan3::get<seqan3::field::flag>(rec) &= seqan3::sam_flag::failed_filter;
// Note that this does not affect other flag values (bits),
// e.g. `seqan3::get<seqan3::field::flag>(rec) & seqan3::sam_flag::unmapped` may still be true
}
// Unset a flag value (bit):
seqan3::get<seqan3::field::flag>(rec) &= ~seqan3::sam_flag::duplicate; // not marked as a duplicate anymore
}
}

Adapted from the SAM specifications are the following additional information to some flag values:

See also
https://broadinstitute.github.io/picard/explain-flags.html
Enumerator
none 

None of the flags below are set.

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.

unmapped 

The read is not mapped to a reference (unaligned).

mate_unmapped 

The mate of this read is not mapped to a reference (unaligned).

on_reverse_strand 

The read sequence has been reverse complemented before being mapped (aligned).

mate_on_reverse_strand 

The mate sequence has been reverse complemented before being mapped (aligned).

first_in_pair 

Indicates the ordering (see details in the seqan3::sam_flag description).

second_in_pair 

Indicates the ordering (see details in the seqan3::sam_flag description).

secondary_alignment 

This read alignment is an alternative (possibly suboptimal) to the primary.

failed_filter 

The read alignment failed a filter, e.g. quality controls.

duplicate 

The read is marked as a PCR duplicate or optical duplicate.

supplementary_alignment 

This sequence is part of a split alignment and is not the primary alignment.