#include <vg_set.hpp>

Public Member Functions
	VGset ()

	VGset (vector< string > &files)

void	transform (std::function< void(MutableHandleGraph *)> lambda)

void	for_each (std::function< void(HandleGraph *)> lambda)

id_t	max_node_id (void)
	Stream through the files and determine the max node id. More...

int64_t	merge_id_space (void)

void	to_xg (xg::XG &index)
	Transforms to a succinct, queryable representation. More...

void	to_xg (xg::XG &index, const function< bool(const string &)> &paths_to_take, map< string, Path > *removed_paths=nullptr)

void	for_each_kmer_parallel (size_t kmer_size, const function< void(const kmer_t &)> &lambda)
	Iterate over all kmers in the graph. More...

void	write_gcsa_kmers_ascii (ostream &out, int kmer_size, nid_t head_id=0, nid_t tail_id=0)

void	write_gcsa_kmers_binary (ostream &out, int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)

vector< string >	write_gcsa_kmers_binary (int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)

Public Attributes
vector< string >	filenames

bool	show_progress = false

bool	progress_bars = true

Constructor & Destructor Documentation

◆ VGset() [1/2]

vg::VGset::VGset ( )

inline

◆ VGset() [2/2]

vg::VGset::VGset ( vector< string > & files )

inline

Member Function Documentation

◆ for_each()

void vg::VGset::for_each ( std::function< void(HandleGraph *)> lambda )

◆ for_each_kmer_parallel()

void vg::VGset::for_each_kmer_parallel	(	size_t	kmer_size,
		const function< void(const kmer_t &)> &	lambda
	)

Iterate over all kmers in the graph.

◆ max_node_id()

id_t vg::VGset::max_node_id ( void )

Stream through the files and determine the max node id.

◆ merge_id_space()

int64_t vg::VGset::merge_id_space ( void )

merges the id space of a set of graphs on-disk necessary when storing many graphs in the same index

◆ to_xg() [1/2]

void vg::VGset::to_xg ( xg::XG & index )

Transforms to a succinct, queryable representation.

◆ to_xg() [2/2]

void vg::VGset::to_xg	(	xg::XG &	index,
		const function< bool(const string &)> &	paths_to_take,
		map< string, Path > *	removed_paths = `nullptr`
	)

As above, except paths with names matching the given predicate are removed. They are returned separately by inserting them into the provided map if not null.

◆ transform()

void vg::VGset::transform ( std::function< void(MutableHandleGraph *)> lambda )

◆ write_gcsa_kmers_ascii()

void vg::VGset::write_gcsa_kmers_ascii	(	ostream &	out,
		int	kmer_size,
		nid_t	head_id = `0`,
		nid_t	tail_id = `0`
	)

Write out kmer lines to GCSA2. size_limit is the maximum space usage for the kmer files in bytes. When the function returns, size_limit is the total size of the kmer files in bytes. If the size limit is exceeded, throws SizeLimitExceededException, and (if relevant) deletes temporary files

◆ write_gcsa_kmers_binary() [1/2]

vector< string > vg::VGset::write_gcsa_kmers_binary	(	int	kmer_size,
		size_t &	size_limit,
		nid_t	head_id = `0`,
		nid_t	tail_id = `0`
	)

◆ write_gcsa_kmers_binary() [2/2]

void vg::VGset::write_gcsa_kmers_binary	(	ostream &	out,
		int	kmer_size,
		size_t &	size_limit,
		nid_t	head_id = `0`,
		nid_t	tail_id = `0`
	)

Member Data Documentation

◆ filenames

vector<string> vg::VGset::filenames

◆ progress_bars

bool vg::VGset::progress_bars = true

◆ show_progress

bool vg::VGset::show_progress = false

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

src/vg_set.hpp
src/vg_set.cpp

Public Member Functions

Public Attributes