raptor Namespace Reference

Namespaces
namespace	detail
namespace	hibf
	Must be first include.
namespace	index_structure
namespace	logspace
namespace	threshold

Classes
class	bin_validator
struct	build_arguments
struct	dna4_traits
class	hierarchical_interleaved_bloom_filter
	The HIBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins. More...
class	index_factory
struct	pattern_size
class	positive_integer_validator
struct	power_of_two_validator
class	raptor_index
struct	search_arguments
class	size_validator
class	sync_out
struct	upgrade_arguments
struct	window
	Strong type for passing the window size. More...

Functions
void	build_parsing (sharg::parser &parser, bool const is_socks)
void	init_shared_meta (sharg::parser &parser)
void	parse_bin_path (build_arguments &arguments)
void	parse_bin_path (upgrade_arguments &arguments)
void	search_parsing (sharg::parser &parser, bool const is_socks)
void	upgrade_parsing (sharg::parser &parser)
template<bool compressed>
void	build_from_files (build_arguments const &arguments)
void	build_from_minimiser (build_arguments const &arguments)
template<typename algorithm_t >
void	call_parallel_on_bins (algorithm_t &&worker, build_arguments const &arguments)
void	compute_minimiser (build_arguments const &arguments)
void	raptor_build (build_arguments const &arguments)
void	init_top_level_parser (sharg::parser &parser)
void	run_build (sharg::parser &parser)
void	run_search (sharg::parser &parser)
template<typename algorithm_t >
void	do_parallel (algorithm_t &&worker, size_t const num_records, size_t const threads, double &compute_time)
template<typename index_t >
void	load_index (index_t &index, search_arguments const &arguments, size_t const part, double &index_io_time)
template<typename index_t >
void	load_index (index_t &index, search_arguments const &arguments, double &index_io_time)
template<typename index_t >
void	load_index (index_t &index, std::filesystem::path const &path, double &index_io_time)
void	raptor_search (search_arguments const &arguments)
template<bool compressed>
void	search_hibf (search_arguments const &arguments)
template<bool compressed>
void	search_ibf (search_arguments const &arguments)
template<bool compressed>
void	search_multiple (search_arguments const &arguments)
template<typename index_t >
void	search_single (search_arguments const &arguments, index_t &&index)
template<bool compressed>
void	search_socks (search_arguments const &arguments)
void	raptor_upgrade (upgrade_arguments const &arguments)
template<bool compressed>
void	upgrade_index (upgrade_arguments const &arguments)
std::ostream &	operator<< (std::ostream &s, window const &)
std::istream &	operator>> (std::istream &s, window &window_)
void	init_build_parser (sharg::parser &parser, build_arguments &arguments)
std::ostream &	operator<< (std::ostream &s, pattern_size const &)
std::istream &	operator>> (std::istream &s, pattern_size &pattern_size_)
void	init_search_parser (sharg::parser &parser, search_arguments &arguments)
void	init_upgrade_parser (sharg::parser &parser, upgrade_arguments &arguments)
bool	check_for_fasta_format (std::vector< std::string > const &valid_extensions, std::string const &file_path)
template void	search_hibf< false > (search_arguments const &arguments)
template void	search_hibf< true > (search_arguments const &arguments)
template void	search_ibf< false > (search_arguments const &arguments)
template void	search_ibf< true > (search_arguments const &arguments)
template void	search_multiple< false > (search_arguments const &arguments)
template void	search_multiple< true > (search_arguments const &arguments)
template void	search_socks< false > (search_arguments const &arguments)
template void	search_socks< true > (search_arguments const &arguments)

Function Documentation

build_from_files()

template<bool compressed>

void raptor::build_from_files

(

build_arguments const &

arguments

)

build_from_minimiser()

void raptor::build_from_minimiser

(

build_arguments const &

arguments

)

build_parsing()

void raptor::build_parsing	(	sharg::parser &	parser,
		bool const	is_socks
	)

call_parallel_on_bins()

template<typename algorithm_t >

void raptor::call_parallel_on_bins	(	algorithm_t &&	worker,
		build_arguments const &	arguments
	)

check_for_fasta_format()

bool raptor::check_for_fasta_format	(	std::vector< std::string > const &	valid_extensions,
		std::string const &	file_path
	)

compute_minimiser()

void raptor::compute_minimiser

(

build_arguments const &

arguments

)

do_parallel()

template<typename algorithm_t >

void raptor::do_parallel	(	algorithm_t &&	worker,
		size_t const	num_records,
		size_t const	threads,
		double &	compute_time
	)

init_build_parser()

void raptor::init_build_parser	(	sharg::parser &	parser,
		build_arguments &	arguments
	)

init_search_parser()

void raptor::init_search_parser	(	sharg::parser &	parser,
		search_arguments &	arguments
	)

init_shared_meta()

void raptor::init_shared_meta

(

sharg::parser &

parser

)

init_top_level_parser()

void raptor::init_top_level_parser

(

sharg::parser &

parser

)

init_upgrade_parser()

void raptor::init_upgrade_parser	(	sharg::parser &	parser,
		upgrade_arguments &	arguments
	)

load_index() [1/3]

template<typename index_t >

void raptor::load_index	(	index_t &	index,
		search_arguments const &	arguments,
		double &	index_io_time
	)

load_index() [2/3]

template<typename index_t >

void raptor::load_index	(	index_t &	index,
		search_arguments const &	arguments,
		size_t const	part,
		double &	index_io_time
	)

load_index() [3/3]

template<typename index_t >

void raptor::load_index	(	index_t &	index,
		std::filesystem::path const &	path,
		double &	index_io_time
	)

operator<<() [1/2]

std::ostream & raptor::operator<<	(	std::ostream &	s,
		pattern_size const &
	)

operator<<() [2/2]

std::ostream & raptor::operator<<	(	std::ostream &	s,
		window const &
	)

operator>>() [1/2]

std::istream & raptor::operator>>	(	std::istream &	s,
		pattern_size &	pattern_size_
	)

operator>>() [2/2]

std::istream & raptor::operator>>	(	std::istream &	s,
		window &	window_
	)

parse_bin_path() [1/2]

void raptor::parse_bin_path

(

build_arguments &

arguments

)

parse_bin_path() [2/2]

void raptor::parse_bin_path

(

upgrade_arguments &

arguments

)

raptor_build()

void raptor::raptor_build

(

build_arguments const &

arguments

)

raptor_search()

void raptor::raptor_search

(

search_arguments const &

arguments

)

raptor_upgrade()

void raptor::raptor_upgrade

(

upgrade_arguments const &

arguments

)

run_build()

void raptor::run_build

(

sharg::parser &

parser

)

run_search()

void raptor::run_search

(

sharg::parser &

parser

)

search_hibf()

template<bool compressed>

void raptor::search_hibf

(

search_arguments const &

arguments

)

search_hibf< false >()

template void raptor::search_hibf< false >

(

search_arguments const &

arguments

)

search_hibf< true >()

template void raptor::search_hibf< true >

(

search_arguments const &

arguments

)

search_ibf()

template<bool compressed>

void raptor::search_ibf

(

search_arguments const &

arguments

)

search_ibf< false >()

template void raptor::search_ibf< false >

(

search_arguments const &

arguments

)

search_ibf< true >()

template void raptor::search_ibf< true >

(

search_arguments const &

arguments

)

search_multiple()

template<bool compressed>

void raptor::search_multiple

(

search_arguments const &

arguments

)

search_multiple< false >()

template void raptor::search_multiple< false >

(

search_arguments const &

arguments

)

search_multiple< true >()

template void raptor::search_multiple< true >

(

search_arguments const &

arguments

)

search_parsing()

void raptor::search_parsing	(	sharg::parser &	parser,
		bool const	is_socks
	)

search_single()

template<typename index_t >

void raptor::search_single	(	search_arguments const &	arguments,
		index_t &&	index
	)

search_socks()

template<bool compressed>

void raptor::search_socks

(

search_arguments const &

arguments

)

search_socks< false >()

template void raptor::search_socks< false >

(

search_arguments const &

arguments

)

search_socks< true >()

template void raptor::search_socks< true >

(

search_arguments const &

arguments

)

upgrade_index()

template<bool compressed>

void raptor::upgrade_index

(

upgrade_arguments const &

arguments

)

upgrade_parsing()

void raptor::upgrade_parsing

(

sharg::parser &

parser

)