takane validation functions. More...

Classes
struct	ObjectMetadata
	Object metadata, including the type and other fields. More...

struct	Options
	Validation options. More...

Functions
bool	derived_from (const std::string &type, const std::string &base, const Options &options)

std::vector< std::size_t >	dimensions (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< size_t >	dimensions (const std::filesystem::path &path, const Options &options)

std::vector< size_t >	dimensions (const std::filesystem::path &path)

std::size_t	height (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height (const std::filesystem::path &path, const Options &options)

std::size_t	height (const std::filesystem::path &path)

bool	satisfies_interface (const std::string &type, const std::string &interface, const Options &options)

void	validate (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate (const std::filesystem::path &path, const Options &options)

void	validate (const std::filesystem::path &path)

void	validate_atomic_vector (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_atomic_vector (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_atomic_vector_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_atomic_vector_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bam_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bcf_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bed_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bigbed_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bigwig_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bumpy_atomic_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_bumpy_atomic_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_bumpy_atomic_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_bumpy_data_frame_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_bumpy_data_frame_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_bumpy_data_frame_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_compressed_sparse_matrix (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_compressed_sparse_matrix (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< size_t >	dimensions_of_compressed_sparse_matrix (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_data_frame (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_data_frame (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_data_frame (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_data_frame_factor (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_data_frame_factor (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_data_frame_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_data_frame_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_delayed_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_delayed_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_delayed_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_dense_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_dense_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_dense_array (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_fasta_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_fastq_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_genomic_ranges (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_genomic_ranges (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_genomic_ranges_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_genomic_ranges_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_gff_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_gmt_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_image_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_multi_sample_dataset (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_ranged_summarized_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_rds_file (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_sequence_information (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_sequence_string_set (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_sequence_string_set (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_simple_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_simple_list (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_single_cell_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_spatial_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_string_factor (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_string_factor (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

void	validate_summarized_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_summarized_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_summarized_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

ObjectMetadata	reformat_object_metadata (millijson::Base *raw)

ObjectMetadata	read_object_metadata (const std::filesystem::path &path)

void	validate_vcf_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::size_t	height_of_vcf_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

std::vector< std::size_t >	dimensions_of_vcf_experiment (const std::filesystem::path &path, const ObjectMetadata &metadata, const Options &options)

Detailed Description

takane validation functions.

Function Documentation

◆ derived_from()

bool takane::derived_from	(	const std::string &	type,
		const std::string &	base,
		const Options &	options )

inline

Check whether a particular object type is derived from a base object type. Derived types satisfy the same file requirements of the base type, but usually add more files to represent additional functionality. This can be used by specifications to check whether arbitrary objects satisfy the file structure expectations for a particular base type.

Applications can add their own derived types for a given base class in Options::custom_derived_from. This extends the default relationships whereby derived_from() will take the union of all derived object types in the default and custom sets. Note that derived types must be manually included in every base type's set, e.g., if B is derived from A and C is derived from B, C must be added to the sets for both A and B.

Parameters

type	Object type.
base	Base object type.
options	Validation options, containing custom derived/base relationships.

Returns: Whether type is derived from base or is equal to base.

◆ dimensions() [1/3]

std::vector< size_t > takane::dimensions ( const std::filesystem::path & path )

inline

Overload of dimensions() with default settings.

Parameters

path	Path to a directory containing an object.

Returns: The object's dimensions.

◆ dimensions() [2/3]

std::vector< std::size_t > takane::dimensions	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Get the dimensions of a multi-dimensional object in a subdirectory, based on the supplied object type.

Applications can supply custom dimension functions for a given type via Options::custom_dimensions. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

Returns: Vector containing the object's dimensions.

◆ dimensions() [3/3]

std::vector< size_t > takane::dimensions	(	const std::filesystem::path &	path,
		const Options &	options )

inline

Get the dimensions of an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

Returns: The object's dimensions.

◆ dimensions_of_bumpy_atomic_array()

std::vector< std::size_t > takane::dimensions_of_bumpy_atomic_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an bumpy atomic array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Vector containing the dimensions of the array.

◆ dimensions_of_bumpy_data_frame_array()

std::vector< std::size_t > takane::dimensions_of_bumpy_data_frame_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an bumpy data frame array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Vector containing the dimensions of the array.

◆ dimensions_of_compressed_sparse_matrix()

std::vector< size_t > takane::dimensions_of_compressed_sparse_matrix	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a compressed sparse matrix.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Dimensions of the matrix.

◆ dimensions_of_data_frame()

std::vector< std::size_t > takane::dimensions_of_data_frame	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a data frame.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: A vector of length 2 containing the number of rows and columns in the data frame.

◆ dimensions_of_delayed_array()

std::vector< std::size_t > takane::dimensions_of_delayed_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a delayed array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Dimensions of the array.

◆ dimensions_of_dense_array()

std::vector< std::size_t > takane::dimensions_of_dense_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a dense array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Dimensions of the array.

◆ dimensions_of_summarized_experiment()

std::vector< std::size_t > takane::dimensions_of_summarized_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a summarized experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: A vector of length 2 containing the dimensions of the summarized experiment.

◆ dimensions_of_vcf_experiment()

std::vector< std::size_t > takane::dimensions_of_vcf_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a VCF experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: A vector of length 2 containing the dimensions of the VCF experiment.

◆ height() [1/3]

std::size_t takane::height ( const std::filesystem::path & path )

inline

Overload of height() with default settings.

Parameters

path	Path to a directory containing an object.

Returns: The object's height.

◆ height() [2/3]

std::size_t takane::height	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Get the height of an object in a subdirectory, based on the supplied object type.

height() is used to check the shape of objects stored in vertical containers, e.g., columns of a data_frame. For vectors or other 1-dimensional objects, the height is usually just the length of the object (for some object-specific definition of "length"). For higher-dimensional objects, the height is usually the extent of the first dimension.

Applications can supply custom height functions for a given type via Options::custom_height. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

Returns: The object's height.

◆ height() [3/3]

std::size_t takane::height	(	const std::filesystem::path &	path,
		const Options &	options )

inline

Get the height of an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

Returns: The object's height.

◆ height_of_atomic_vector()

std::size_t takane::height_of_atomic_vector	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the atomic vector.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Length of the vector.

◆ height_of_atomic_vector_list()

std::size_t takane::height_of_atomic_vector_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an atomic vector list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The length of the list.

◆ height_of_bumpy_atomic_array()

std::size_t takane::height_of_bumpy_atomic_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an bumpy atomic array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The height (i.e., first dimension extent) of the array.

◆ height_of_bumpy_data_frame_array()

std::size_t takane::height_of_bumpy_data_frame_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an bumpy data frame array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The height (i.e., first dimension extent) of the array.

◆ height_of_compressed_sparse_matrix()

std::size_t takane::height_of_compressed_sparse_matrix	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a compressed sparse matrix.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Number of rows in the matrix.

◆ height_of_data_frame()

std::size_t takane::height_of_data_frame	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a data frame.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The number of rows.

◆ height_of_data_frame_factor()

std::size_t takane::height_of_data_frame_factor	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the data frame factor.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Length of the factor.

◆ height_of_data_frame_list()

std::size_t takane::height_of_data_frame_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an data frame list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The length of the list.

◆ height_of_delayed_array()

std::size_t takane::height_of_delayed_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a delayed array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Extent of the first dimension.

◆ height_of_dense_array()

std::size_t takane::height_of_dense_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a dense array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Extent of the first dimension.

◆ height_of_genomic_ranges()

std::size_t takane::height_of_genomic_ranges	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing genomic ranges.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The number of ranges.

◆ height_of_genomic_ranges_list()

std::size_t takane::height_of_genomic_ranges_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing an genomic ranges list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The length of the list.

◆ height_of_sequence_string_set()

std::size_t takane::height_of_sequence_string_set	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a sequence string set.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The number of sequences.

◆ height_of_simple_list()

std::size_t takane::height_of_simple_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the simple list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: The number of list elements.

◆ height_of_string_factor()

std::size_t takane::height_of_string_factor	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the string factor.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Length of the factor.

◆ height_of_summarized_experiment()

std::size_t takane::height_of_summarized_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a summarized experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Number of rows in the summarized experiment.

◆ height_of_vcf_experiment()

std::size_t takane::height_of_vcf_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a VCF experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Returns: Number of rows in the VCF experiment.

◆ read_object_metadata()

ObjectMetadata takane::read_object_metadata ( const std::filesystem::path & path )

inline

Reads the OBJECT file inside a directory to determine the object type.

Parameters

path	Path to a directory containing an object.

Returns: Object metadata, including the type and other fields.

◆ reformat_object_metadata()

ObjectMetadata takane::reformat_object_metadata ( millijson::Base * raw )

inline

Parses a JSON object to obtain the object metadata.

Parameters

raw	Raw JSON object, typically obtained by `millijson::parse_file`. Note that `raw` is consumed by this function and should no longer be used by the caller.

Returns: Object metadata, including the type and other fields.

◆ satisfies_interface()

bool takane::satisfies_interface	(	const std::string &	type,
		const std::string &	interface,
		const Options &	options )

inline

Check whether a particular object type satisfies a particular object interface. This can be used by specifications to check that child components satisfy certain user-level expectations for an abstract object (e.g., data frames, lists).

Applications can extend the takane framework by adding custom types to Options::custom_satisfies_interface. This extends the default relationships whereby satisfies_interface() will take the union of all object types in the default and custom sets. Note that, if a type is included in a particular set, it is not necessary to add its derived types, as satisfies_interface() will automatically call derived_from().

Parameters

type	Object type.
interface	Interface type.
options	Validation options, containing custom object interface relationships.

Returns: Whether type satisfies interface.

◆ validate() [1/3]

void takane::validate ( const std::filesystem::path & path )

inline

Overload of validate() with default settings.

Parameters

path	Path to a directory containing an object.

◆ validate() [2/3]

void takane::validate	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Validate an object in a subdirectory, based on the supplied object type.

Applications can supply custom validation functions for a given type via Options::custom_validate. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

◆ validate() [3/3]

void takane::validate	(	const std::filesystem::path &	path,
		const Options &	options )

inline

Validate an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

◆ validate_atomic_vector()

void takane::validate_atomic_vector	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the atomic vector.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_atomic_vector_list()

void takane::validate_atomic_vector_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the atomic vector list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bam_file()

void takane::validate_bam_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::bam_file_strict_check is provided, it is used to perform stricter checking of the BAM file contents and indices. By default, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.

Parameters

path	Path to the directory containing the BAM file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bcf_file()

void takane::validate_bcf_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::bcf_file_strict_check is provided, it is used to perform stricter checking of the BCF file contents and indices. By default, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.

Parameters

path	Path to the directory containing the BCF file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bed_file()

void takane::validate_bed_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::bed_file_strict_check is provided, it is used to perform stricter checking of the BED file contents and indices. Currently, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.

Parameters

path	Path to the directory containing the BED file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bigbed_file()

void takane::validate_bigbed_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::bigbed_file_strict_check is provided, it is used to perform stricter checking of the bigBed file contents. By default, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.

Parameters

path	Path to the directory containing the bigBed file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bigwig_file()

void takane::validate_bigwig_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::bigwig_file_strict_check is provided, it is used to perform stricter checking of the bigWig file contents. By default, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.

Parameters

path	Path to the directory containing the bigWig file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bumpy_atomic_array()

void takane::validate_bumpy_atomic_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the bumpy atomic array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_bumpy_data_frame_array()

void takane::validate_bumpy_data_frame_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the bumpy data frame array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_compressed_sparse_matrix()

void takane::validate_compressed_sparse_matrix	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a compressed sparse matrix.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_data_frame()

void takane::validate_data_frame	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the data frame.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_data_frame_factor()

void takane::validate_data_frame_factor	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::data_frame_factor_any_duplicated is set, it enables stricter checking of the uniqueness of the data frame levels. Currently, we don't provide a default method for data_frame objects, as it's kind of tedious and we haven't gotten around to it yet.

Parameters

path	Path to the directory containing the data frame factor.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_data_frame_list()

void takane::validate_data_frame_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the data frame list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_delayed_array()

void takane::validate_delayed_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a delayed array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_dense_array()

void takane::validate_dense_array	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing a dense array.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_fasta_file()

void takane::validate_fasta_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::fasta_file_strict_check is provided, this enables stricter checking of the FASTA file contents and indices. By default, we just look at the first few bytes to verify the files.

Parameters

path	Path to the directory containing the FASTA file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_fastq_file()

void takane::validate_fastq_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::fastq_file_strict_check is provided, this enables stricter checking of the FASTQ file contents and indices. By default, we just look at the first few bytes to verify the files.

Parameters

path	Path to the directory containing the FASTQ file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_genomic_ranges()

void takane::validate_genomic_ranges	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the genomic ranges.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_genomic_ranges_list()

void takane::validate_genomic_ranges_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the genomic ranges list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_gff_file()

void takane::validate_gff_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::gff_file_strict_check is provided, this enables stricter checking of the GFF file contents. By default, we just look at the first few bytes to verify the files.

Parameters

path	Path to the directory containing the GFF file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_gmt_file()

void takane::validate_gmt_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::gmt_file_strict_check is provided, this enables stricter checking of the GMT file contents. By default, we just look at the first few bytes to verify the files.

Parameters

path	Path to the directory containing the GMT file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_image_file()

void takane::validate_image_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::image_file_strict_check is provided, it is used to perform stricter checking of the image file contents. By default, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., Magick.

Parameters

path	Path to the directory containing the image file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_multi_sample_dataset()

void takane::validate_multi_sample_dataset	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the multi-sample dataset.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_ranged_summarized_experiment()

void takane::validate_ranged_summarized_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the ranged summarized experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_rds_file()

void takane::validate_rds_file	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

If Options::rds_file_strict_check is provided, this enables stricter checking of the RDS file contents. By default, we just look at the first few bytes to verify the files.

Parameters

path	Path to the directory containing the RDS file.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_sequence_information()

void takane::validate_sequence_information	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the data frame.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_sequence_string_set()

void takane::validate_sequence_string_set	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to a directory containing a sequence string set.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_simple_list()

void takane::validate_simple_list	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the simple list.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_single_cell_experiment()

void takane::validate_single_cell_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the single cell experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_spatial_experiment()

void takane::validate_spatial_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the spatial experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_string_factor()

void takane::validate_string_factor	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the string factor.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_summarized_experiment()

void takane::validate_summarized_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the summarized experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

◆ validate_vcf_experiment()

void takane::validate_vcf_experiment	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		const Options &	options )

inline

Parameters

path	Path to the directory containing the VCF experiment.
metadata	Metadata for the object, typically read from its `OBJECT` file.
options	Validation options.

Classes

Functions

Detailed Description

Function Documentation

◆ derived_from()

◆ dimensions() [1/3]

◆ dimensions() [2/3]

◆ dimensions() [3/3]

◆ dimensions_of_bumpy_atomic_array()

◆ dimensions_of_bumpy_data_frame_array()

◆ dimensions_of_compressed_sparse_matrix()

◆ dimensions_of_data_frame()

◆ dimensions_of_delayed_array()

◆ dimensions_of_dense_array()

◆ dimensions_of_summarized_experiment()

◆ dimensions_of_vcf_experiment()

◆ height() [1/3]

◆ height() [2/3]

◆ height() [3/3]

◆ height_of_atomic_vector()

◆ height_of_atomic_vector_list()

◆ height_of_bumpy_atomic_array()

◆ height_of_bumpy_data_frame_array()

◆ height_of_compressed_sparse_matrix()

◆ height_of_data_frame()

◆ height_of_data_frame_factor()

◆ height_of_data_frame_list()

◆ height_of_delayed_array()

◆ height_of_dense_array()

◆ height_of_genomic_ranges()

◆ height_of_genomic_ranges_list()

◆ height_of_sequence_string_set()

◆ height_of_simple_list()

◆ height_of_string_factor()

◆ height_of_summarized_experiment()

◆ height_of_vcf_experiment()

◆ read_object_metadata()

◆ reformat_object_metadata()

◆ satisfies_interface()

◆ validate() [1/3]

◆ validate() [2/3]

◆ validate() [3/3]

◆ validate_atomic_vector()

◆ validate_atomic_vector_list()

◆ validate_bam_file()

◆ validate_bcf_file()

◆ validate_bed_file()

◆ validate_bigbed_file()

◆ validate_bigwig_file()

◆ validate_bumpy_atomic_array()

◆ validate_bumpy_data_frame_array()

◆ validate_compressed_sparse_matrix()

◆ validate_data_frame()

◆ validate_data_frame_factor()

◆ validate_data_frame_list()

◆ validate_delayed_array()

◆ validate_dense_array()

◆ validate_fasta_file()

◆ validate_fastq_file()

◆ validate_genomic_ranges()

◆ validate_genomic_ranges_list()

◆ validate_gff_file()

◆ validate_gmt_file()

◆ validate_image_file()

◆ validate_multi_sample_dataset()

◆ validate_ranged_summarized_experiment()

◆ validate_rds_file()

◆ validate_sequence_information()

◆ validate_sequence_string_set()

◆ validate_simple_list()

◆ validate_single_cell_experiment()

◆ validate_spatial_experiment()

◆ validate_string_factor()

◆ validate_summarized_experiment()

◆ validate_vcf_experiment()