Validation options. More...

#include <utils_public.hpp>

Public Attributes
bool	parallel_reads = true

hsize_t	hdf5_buffer_size = 10000

std::unordered_map< std::string, std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)> >	custom_validate

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	custom_global_validate

std::unordered_map< std::string, std::function< std::vector< size_t >(const std::filesystem::path &, const ObjectMetadata &, Options &)> >	custom_dimensions

std::unordered_map< std::string, std::function< size_t(const std::filesystem::path &, const ObjectMetadata &m, Options &)> >	custom_height

std::unordered_map< std::string, std::unordered_set< std::string > >	custom_derived_from

std::unordered_map< std::string, std::unordered_set< std::string > >	custom_satisfies_interface

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	bam_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	bcf_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &, bool)>	bed_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	bigbed_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	bigwig_file_strict_check

std::function< bool(const std::filesystem::path &, const ObjectMetadata &, Options &options)>	data_frame_factor_any_duplicated

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &, bool)>	fasta_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &, bool)>	fastq_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &, bool)>	gff_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	gmt_file_strict_check

std::function< void(const std::filesystem::path &, const ObjectMetadata &, Options &)>	rds_file_strict_check

chihaya::Options	delayed_array_options

Detailed Description

Validation options.

Collection of optional parameters to fine-tune the behavior of various takane functions. This can be configured by applications to, e.g., add more validation functions for custom types or to increase the strictness of some checks.

Most takane functions will accept a non-const reference to an Options object. The lack of const-ness is intended to support custom functions that mutate some external variable, e.g., to collect statistics for certain object types. While unusual, it is permissible for a takane function to modify the supplied Options, as long as that modification is reversed upon exiting the function.

The possibility for modification means that calls to takane functions are effectively const but not thread-safe with respect to any single Options instance. If thread safety is needed, it is best achieved by creating a separate Options instance for use in each thread.

Member Data Documentation

◆ bam_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::bam_file_strict_check

Application-specific function to check the validity of a BAM file and its indices in bam_file::validate(). This should accept a path to the directory containing the BAM file and indices, the object metadata, and additional reading options. It should throw an error if the BAM file is not valid, e.g., corrupted file, mismatched indices.

◆ bcf_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::bcf_file_strict_check

Application-specific function to check the validity of a BCF file and its indices in bcf_file::validate(). This should accept a path to the directory containing the BCF file and indices, the object metadata, and additional reading options. It should throw an error if the BCF file is not valid, e.g., corrupted file, mismatched indices.

◆ bed_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&, bool)> takane::Options::bed_file_strict_check

Application-specific function to check the validity of a BED file and its indices in bed_file::validate(). This should accept a path to the directory containing the BED file, the object metadata, additional reading options, and a boolean indicating whether indices are expected to be present in the directory. It should throw an error if the BED file is not valid, e.g., corrupted file, mismatched indices.

◆ bigbed_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::bigbed_file_strict_check

Application-specific function to check the validity of a bigBed file in bigbed_file::validate(). This should accept a path to the directory containing the bigBed file, the object metadata, and additional reading options. It should throw an error if the bigBed file is not valid, e.g., corrupted file, mismatched indices.

◆ bigwig_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::bigwig_file_strict_check

Application-specific function to check the validity of a bigWig file in bigwig_file::validate(). This should accept a path to the directory containing the bigWig file, the object metadata, and additional reading options. It should throw an error if the bigWig file is not valid, e.g., corrupted file, mismatched indices.

◆ custom_derived_from

std::unordered_map<std::string, std::unordered_set<std::string> > takane::Options::custom_derived_from

Custom registry of derived object types and their base types, to be used by derived_from(). Each key is the base object type and each value is the set of its derived types. If a type is specified here, the set of derived types is added to the the default set.

◆ custom_dimensions

std::unordered_map<std::string, std::function<std::vector<size_t>(const std::filesystem::path&, const ObjectMetadata&, Options&)> > takane::Options::custom_dimensions

Custom registry of functions to be used by dimensions(). Each key is an object type and each value is a function that accepts the same arguments as dimensions(). If a type is specified here, the custom function replaces the default.

◆ custom_global_validate

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::custom_global_validate

Addtional validation function to run for all object types during a call to validate(), after running the (default or custom) type-specific validation function. Arguments for this function are as described for validate().

◆ custom_height

std::unordered_map<std::string, std::function<size_t(const std::filesystem::path&, const ObjectMetadata& m, Options&)> > takane::Options::custom_height

Custom registry of functions to be used by height(). Each key is an object type and each value is a function that accepts the same arguments as height(). If a type is specified here, the custom function replaces the default.

◆ custom_satisfies_interface

std::unordered_map<std::string, std::unordered_set<std::string> > takane::Options::custom_satisfies_interface

Custom registry of object types that satisfy a particular object interface. Each key is the interface and each value is the set of all types that satisfy it. If a type is specified here, its set of types is added to the the default set.

◆ custom_validate

std::unordered_map<std::string, std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> > takane::Options::custom_validate

Custom registry of functions to be used by validate(). Each key is an object type and each value is a function that accepts the same arguments as validate(). If a type is specified here, the custom function replaces the default.

◆ data_frame_factor_any_duplicated

std::function<bool(const std::filesystem::path&, const ObjectMetadata&, Options& options)> takane::Options::data_frame_factor_any_duplicated

Application-specific function to determine whether there are duplicated rows in the data frame containing the levels of a data frame factor, to be used in data_frame_factor::validate() This should accept a path to the directory containing the data frame, the object metadata, and additional reading options. It should return a boolean indicating whether any duplicate rows were found.

◆ delayed_array_options

chihaya::Options takane::Options::delayed_array_options

Options to use for validating chihaya specifications in delayed_array::validate().

◆ fasta_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&, bool)> takane::Options::fasta_file_strict_check

Application-specific function to check the validity of a FASTA file and its indices in fasta_file::validate(). This should accept a path to the directory containing the FASTA file, the object metadata, additional reading options, and a boolean indicating whether indices are expected to be present in the directory. It should throw an error if the FASTA file is not valid, e.g., corrupted file, mismatched indices.

◆ fastq_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&, bool)> takane::Options::fastq_file_strict_check

Application-specific function to check the validity of a FASTQ file and its indices in fastq_file::validate(). This should accept a path to the directory containing the FASTQ file, the object metadata, additional reading options, and a boolean indicating whether or not indices are expected to be present in the directory. It should throw an error if the FASTQ file is not valid, e.g., corrupted file, mismatched indices.

◆ gff_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&, bool)> takane::Options::gff_file_strict_check

Application-specific function to check the validity of a GFF file and its indices in gff_file::validate(). This should accept a path to the directory containing the GFF file, the object metadata, additional reading options. and a boolean indicating whether indices are expected to be present in the directory. It should throw an error if the GFF file is not valid, e.g., corrupted file, mismatched indices.

◆ gmt_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::gmt_file_strict_check

Application-specific function to check the validity of a GMT file and its indices in gmt_file::validate(). This should accept a path to the directory containing the GMT file, the object metadata and additional reading options. It should throw an error if the GMT file is not valid, e.g., corrupted file, mismatched indices.

◆ hdf5_buffer_size

hsize_t takane::Options::hdf5_buffer_size = 10000

Buffer size to use when reading data from a HDF5 file.

◆ parallel_reads

bool takane::Options::parallel_reads = true

Whether to parallelize reading from disk and parsing, when available.

◆ rds_file_strict_check

std::function<void(const std::filesystem::path&, const ObjectMetadata&, Options&)> takane::Options::rds_file_strict_check

Application-specific function to check the validity of a RDS file and its indices in rds_file::validate(). This should accept a path to the directory containing the RDS file, the object metadata and additional reading options. It should throw an error if the RDS file is not valid, e.g., corrupted file, mismatched indices.

The documentation for this struct was generated from the following file:

takane/utils_public.hpp

Public Attributes