The IO module provides stream handling formatted I/O. More...

Collaboration diagram for IO:

Modules
	Alignment File
	Provides files and formats for handling alignment data.

	Sequence File
	Provides files and formats for handling sequence data.

	stream_REMOVEME
	The stream sub-module contains data structures and functions for streaming and tokenization.

	Structure File
	Provides files and formats for handling structure data.

Classes
struct	seqan3::fields< fs >
	A class template that holds a choice of seqan3::field. More...

struct	seqan3::file_open_error
	Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem. More...

struct	seqan3::format_error
	Thrown if information given to output format didn't match expectations. More...

struct	seqan3::io_error
	Thrown if there is an io error in low level io operations such as in std::basic_streambuf operations. More...

struct	seqan3::parse_error
	Thrown if there is a parse error, such as reading an unexpected character from an input stream. More...

struct	seqan3::record< field_types, field_ids >
	The class template that file records are based on; behaves like an std::tuple. More...

struct	seqan3::unexpected_end_of_input
	Thrown if I/O was expecting more input (e.g. a delimiter or a new line), but the end of input was reached. More...

struct	seqan3::unhandled_extension_error
	Thrown if there is no format that accepts a given file extension. More...

Enumerations
enum	seqan3::field { seqan3::field::seq, seqan3::field::id, seqan3::field::qual, seqan3::field::seq_qual, seqan3::field::offset, seqan3::field::bpp, seqan3::field::structure, seqan3::field::structured_seq, seqan3::field::energy, seqan3::field::react, seqan3::field::react_err, seqan3::field::comment, seqan3::field::alignment, seqan3::field::ref_id, seqan3::field::ref_seq, seqan3::field::ref_offset, seqan3::field::header_ptr, seqan3::field::flag, seqan3::field::mate, seqan3::field::mapq, seqan3::field::cigar, seqan3::field::tags, seqan3::field::bit_score, seqan3::field::evalue, seqan3::field::user_defined_0, seqan3::field::user_defined_1, seqan3::field::user_defined_2, seqan3::field::user_defined_3, seqan3::field::user_defined_4, seqan3::field::user_defined_5, seqan3::field::user_defined_6, seqan3::field::user_defined_7, seqan3::field::user_defined_8, seqan3::field::user_defined_9, seqan3::field::SEQ = seq, seqan3::field::ID = id, seqan3::field::QUAL = qual, seqan3::field::SEQ_QUAL = seq_qual, seqan3::field::OFFSET = offset, seqan3::field::BPP = bpp, seqan3::field::STRUCTURE = structure, seqan3::field::STRUCTURED_SEQ = structured_seq, seqan3::field::ENERGY = energy, seqan3::field::REACT = react, seqan3::field::REACT_ERR = react_err, seqan3::field::COMMENT = comment, seqan3::field::ALIGNMENT = alignment, seqan3::field::REF_ID = ref_id, seqan3::field::REF_SEQ = ref_seq, seqan3::field::REF_OFFSET = ref_offset, seqan3::field::HEADER_PTR = header_ptr, seqan3::field::FLAG = flag, seqan3::field::MATE = mate, seqan3::field::MAPQ = mapq, seqan3::field::CIGAR = cigar, seqan3::field::TAGS = tags, seqan3::field::BIT_SCORE = bit_score, seqan3::field::EVALUE = evalue, seqan3::field::USER_DEFINED_0 = user_defined_0, seqan3::field::USER_DEFINED_1 = user_defined_1, seqan3::field::USER_DEFINED_2 = user_defined_2, seqan3::field::USER_DEFINED_3 = user_defined_3, seqan3::field::USER_DEFINED_4 = user_defined_4, seqan3::field::USER_DEFINED_5 = user_defined_5, seqan3::field::USER_DEFINED_6 = user_defined_6, seqan3::field::USER_DEFINED_7 = user_defined_7, seqan3::field::USER_DEFINED_8 = user_defined_8, seqan3::field::USER_DEFINED_9 = user_defined_9 }
	An enumerator for the fields used in file formats. More...

Variables
template<typename t >
SEQAN3_CONCEPT	fields_specialisation = is_value_specialisation_of_v<t, fields>
	Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.

Detailed Description

The IO module provides stream handling formatted I/O.

stream_REMOVEMEs and (de-)compression

SeqAn works with regular iostreams as provided by the standard library, but it also handles compressed streams:

Format	Extension	Dependency	Description
GZip	`.gz`¹	zlib	GNU-Zip, most common format on UNIX
BGZF	`.gz`, `.bgzf`²	zlib	Blocked GZip, compatible extension to GZip, features parallelisation
BZip2	`.bz2`	libbz2	Stronger compression than GZip, slower to compress

¹ SeqAn always assumes GZip and does not handle pure .Z.
² Some file formats like .bam or .bcf are implicitly BGZF-compressed without showing this in the extension.

Support for these compression formats is optional and depends on whether the respective dependency is available when you build your program (if you use CMake, this should happen automatically).

SeqAn file types apply compression/decompression streams transparently, i.e. if the given file-extension or "magic-header" of a file suggest this, the respective stream is automatically (de-)compressed.

The (de)compression stream wrappers are currently only used internally and not part of the API.

Formatted I/O

Files and formats

SeqAn has the notion of files and formats. File is an abstraction level higher than format. A file describes a common use-case and it typically supports multiple formats. The developer needs to know which kind of file they want to read/write, this choice is made at compile-time. The format, on the other hand, is automatically detected based on the file provided by the user to the program.

For example, seqan3::sequence_file_input handles reading sequence files. It can be created directly from an input stream, or from a file name. After opening the file it will detect whether the format is seqan3::format_fasta or seqan3::format_fastq (or another supported format) automatically – normally by comparing the extension.

File	Formats
seqan3::alignment_file_input	seqan3::format_sam, seqan3::format_bam
seqan3::alignment_file_output	seqan3::format_sam, seqan3::format_bam
seqan3::sequence_file_input	seqan3::format_embl, seqan3::format_fasta, seqan3::format_fastq, seqan3::format_genbank, seqan3::format_sam
seqan3::sequence_file_output	seqan3::format_embl, seqan3::format_fasta, seqan3::format_fastq, seqan3::format_genbank, seqan3::format_sam
seqan3::structure_file_input	seqan3::format_vienna
seqan3::structure_file_output	seqan3::format_vienna

Some formats are available in multiple files, e.g. seqan3::format_sam can be read by seqan3::sequence_file_input and by seqan3::alignment_file_input. This represents different use-cases of the same file format.

Typically formats are supported for reading and writing, but this does not always have to be the case. See the above links for more information.

Records and fields

The main file interface that SeqAn offers is record-based, i.e. every file conceptionally is a range of records. And each record in turn behaves as a tuple of fields.

The record type of all files is based on seqan3::record, but the composition of fields is different per file.

In particular this means:

You can iterate over a seqan3::sequence_file_input just like you iterate over a std::vector.
The element type is seqan3::record and for seqan3::sequence_file_input the records typically consist of three fields: ID, sequence and qualities.
Not every format may provide every field (e.g. all three fields can be extracted from a FastQ file, but only ID and sequence can be extracted from a FastA file).
This is not a problem when reading files; the format is detected at run-time and either it provides all desired fields, or some of them will be empty.
When writing files it depends on the format whether it allows certain fields to be unset; e.g. you can convert a FastQ file to a FastA file, but not the other way around (at least not without providing placeholders for the qualitites).

Please have a look the tutorial for Sequence File Input and Output and the API docs for seqan3::sequence_file_input to learn about this design in practice.

Serialisation

Besides formatted I/O which is realised via files and formats, SeqAn also supports object-level serialisation. This enables you to store data structures like indexes or sequences directly to disk.

We use the cereal library to accomplish this. For more information see cereal's documentation or our tutorial on Indexing and searching with SeqAn which contains an example.

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Enumeration Type Documentation

◆ field

enum seqan3::field

strong

An enumerator for the fields used in file formats.

Some of the fields are shared between formats.

The following table shows the usage of fields in the respective files (Note that each valid format for a file must handle all of its fields):

Field	Sequence IO	Alignment IO	Structure IO
seq	✅	✅	✅
id	✅	✅	✅
qual	✅	✅	✅
seq_qual	✅	✅	✅
offset		✅	✅
bpp			✅
structure			✅
structured_seq			✅
energy			✅
react			✅
react_err			✅
comment			✅
alignment		✅
ref_id		✅
ref_seq		✅
ref_offset		✅
header_ptr		✅
flag		✅
mate		✅
mapq		✅
cigar		✅
tags		✅
bit_score		✅
evalue		✅

Enumerator
seq	The "sequence", usually a range of nucleotides or amino acids.
id	The identifier, usually a string.
qual	The qualities, usually in phred-score notation.
seq_qual	Sequence and qualities combined in one range.
offset	Sequence (SEQ) relative start position (0-based), unsigned value.
bpp	Base pair probability matrix of interactions, usually a matrix of float numbers.
structure	Fixed interactions, usually a string of structure alphabet characters.
structured_seq	Sequence and fixed interactions combined in one range.
energy	Energy of a folded sequence, represented by one float number.
react	Reactivity values of the sequence characters given in a vector of float numbers.
react_err	Reactivity error values given in a vector corresponding to REACT.
comment	Comment field of arbitrary content, usually a string.
alignment	The (pairwise) alignment stored in an seqan3::alignment object.
ref_id	The identifier of the (reference) sequence that SEQ was aligned to.
ref_seq	The (reference) "sequence" information, usually a range of nucleotides or amino acids.
ref_offset	Sequence (REF_SEQ) relative start position (0-based), unsigned value.
header_ptr	A pointer to the seqan3::alignment_file_header object storing header information.
flag	The alignment flag (bit information), `uint16_t` value.
mate	The mate pair information given as a std::tuple of reference name, offset and template length.
mapq	The mapping quality of the SEQ alignment, usually a ohred-scaled score.
cigar	The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
tags	The optional tags in the SAM format, stored in a dictionary.
bit_score	The bit score (statistical significance indicator), unsigned value.
evalue	The e-value (length normalized bit score), `double` value.
user_defined_0	Identifier for user defined file formats and specialisations.
user_defined_1	Identifier for user defined file formats and specialisations.
user_defined_2	Identifier for user defined file formats and specialisations.
user_defined_3	Identifier for user defined file formats and specialisations.
user_defined_4	Identifier for user defined file formats and specialisations.
user_defined_5	Identifier for user defined file formats and specialisations.
user_defined_6	Identifier for user defined file formats and specialisations.
user_defined_7	Identifier for user defined file formats and specialisations.
user_defined_8	Identifier for user defined file formats and specialisations.
user_defined_9	Identifier for user defined file formats and specialisations.
SEQ	Please use the field name in lower case.
ID	Please use the field name in lower case.
QUAL	Please use the field name in lower case.
SEQ_QUAL	Please use the field name in lower case.
OFFSET	Please use the field name in lower case.
BPP	Please use the field name in lower case.
STRUCTURE	Please use the field name in lower case.
STRUCTURED_SEQ	Please use the field name in lower case.
ENERGY	Please use the field name in lower case.
REACT	Please use the field name in lower case.
REACT_ERR	Please use the field name in lower case.
COMMENT	Please use the field name in lower case.
ALIGNMENT	Please use the field name in lower case.
REF_ID	Please use the field name in lower case.
REF_SEQ	Please use the field name in lower case.
REF_OFFSET	Please use the field name in lower case.
HEADER_PTR	Please use the field name in lower case.
FLAG	Please use the field name in lower case.
MATE	Please use the field name in lower case.
MAPQ	Please use the field name in lower case.
CIGAR	Please use the field name in lower case.
TAGS	Please use the field name in lower case.
BIT_SCORE	Please use the field name in lower case.
EVALUE	Please use the field name in lower case.
USER_DEFINED_0	Please use the field name in lower case.
USER_DEFINED_1	Please use the field name in lower case.
USER_DEFINED_2	Please use the field name in lower case.
USER_DEFINED_3	Please use the field name in lower case.
USER_DEFINED_4	Please use the field name in lower case.
USER_DEFINED_5	Please use the field name in lower case.
USER_DEFINED_6	Please use the field name in lower case.
USER_DEFINED_7	Please use the field name in lower case.
USER_DEFINED_8	Please use the field name in lower case.
USER_DEFINED_9	Please use the field name in lower case.

Modules

Classes

Enumerations

Variables