chopper::configuration Struct Reference

#include <chopper/configuration.hpp>

Public Member Functions
void	read_from (std::istream &stream)
void	write_to (std::ostream &stream) const

Public Attributes
seqan::hibf::config	hibf_config
	The HIBF config which will be used to compute the layout within the HIBF lib. More...
seqan::hibf::concurrent_timer	compute_sketches_timer {}
seqan::hibf::concurrent_timer	union_estimation_timer {}
seqan::hibf::concurrent_timer	rearrangement_timer {}
seqan::hibf::concurrent_timer	dp_algorithm_timer {}
General Configuration
std::filesystem::path	data_file
	The input file to chopper. Should contain one file path per line. More...
bool	debug {false}
	Internal parameter that triggers some verbose debug output. More...
std::filesystem::path	output_filename {"layout.txt"}
	The name of the layout file to write. More...
std::filesystem::path	output_timings {}
	If specified, layout timings are written to the specified file. More...
uint8_t	k {19}
	The kmer size to hash the input sequences before computing a HyperLogLog sketch from them. More...
uint8_t	window_size {k}
	The window size to compute minimizers before computing a HyperLogLog sketch from them. More...
bool	precomputed_files {false}
	Whether the input files are precomputed files (.minimiser) instead of sequence files. More...
Configuration of size estimates
std::filesystem::path	sketch_directory {}
	The name for the output directory when writing sketches to disk. More...
bool	disable_sketch_output {false}
	Do not write the sketches into a dedicated directory. More...
Statistics configuration
bool	determine_best_tmax {false}
	Whether the program should determine the best number of IBF bins by doing multiple binning runs. More...
bool	force_all_binnings {false}
	Whether the programm should compute all binnings up to the given t_max. More...
bool	output_verbose_statistics {false}
	Whether to print verbose output when computing the statistics when computing the layout. More...

Private Member Functions
template<typename archive_t >
void	serialize (archive_t &archive)

Friends
class	cereal::access

Member Function Documentation

read_from()

void chopper::configuration::read_from

(

std::istream &

stream

)

serialize()

template<typename archive_t >

void chopper::configuration::serialize ( archive_t &  archive )

inlineprivate

write_to()

void chopper::configuration::write_to

(

std::ostream &

stream

)

const

Friends And Related Function Documentation

cereal::access

friend class cereal::access

friend

Member Data Documentation

compute_sketches_timer

seqan::hibf::concurrent_timer chopper::configuration::compute_sketches_timer {}

mutable

data_file

std::filesystem::path chopper::configuration::data_file

The input file to chopper. Should contain one file path per line.

debug

bool chopper::configuration::debug {false}

Internal parameter that triggers some verbose debug output.

determine_best_tmax

bool chopper::configuration::determine_best_tmax {false}

Whether the program should determine the best number of IBF bins by doing multiple binning runs.

disable_sketch_output

bool chopper::configuration::disable_sketch_output {false}

Do not write the sketches into a dedicated directory.

dp_algorithm_timer

seqan::hibf::concurrent_timer chopper::configuration::dp_algorithm_timer {}

mutable

force_all_binnings

bool chopper::configuration::force_all_binnings {false}

Whether the programm should compute all binnings up to the given t_max.

hibf_config

seqan::hibf::config chopper::configuration::hibf_config

The HIBF config which will be used to compute the layout within the HIBF lib.

k

uint8_t chopper::configuration::k {19}

The kmer size to hash the input sequences before computing a HyperLogLog sketch from them.

output_filename

std::filesystem::path chopper::configuration::output_filename {"layout.txt"}

The name of the layout file to write.

output_timings

std::filesystem::path chopper::configuration::output_timings {}

If specified, layout timings are written to the specified file.

output_verbose_statistics

bool chopper::configuration::output_verbose_statistics {false}

Whether to print verbose output when computing the statistics when computing the layout.

precomputed_files

bool chopper::configuration::precomputed_files {false}

Whether the input files are precomputed files (.minimiser) instead of sequence files.

rearrangement_timer

seqan::hibf::concurrent_timer chopper::configuration::rearrangement_timer {}

mutable

sketch_directory

std::filesystem::path chopper::configuration::sketch_directory {}

The name for the output directory when writing sketches to disk.

union_estimation_timer

seqan::hibf::concurrent_timer chopper::configuration::union_estimation_timer {}

mutable

window_size

uint8_t chopper::configuration::window_size {k}

The window size to compute minimizers before computing a HyperLogLog sketch from them.

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

• include/chopper/configuration.hpp
• src/configuration.cpp