#include <sampler.hpp>

Inheritance diagram for vg::Sampler:

Public Member Functions
	Sampler (PathPositionHandleGraph *x, int seed=0, bool forward_only=false, bool allow_Ns=false, const vector< string > &source_paths={}, const vector< double > &source_path_ploidies={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={})

Alignment	sample_read ()

pair< Alignment, Alignment >	sample_read_pair ()

void	set_source_paths (const vector< string > &source_paths, const vector< double > &source_path_ploidies, const vector< pair< string, double >> &transcript_expressions, const vector< tuple< string, string, size_t >> &haplotype_transcripts)

pos_t	position (void)

string	sequence (size_t length)

Alignment	alignment (size_t length)

Alignment	alignment_to_graph (size_t length)
	Get an alignment against the whole graph. More...

Alignment	alignment_to_path (const string &source_path, size_t length)
	Get an alignment against the currently set source_path. More...

Alignment	alignment_with_error (size_t length, double base_error, double indel_error)

vector< Alignment >	alignment_pair (size_t read_length, size_t fragment_length, double fragment_std_dev, double base_error, double indel_error)

size_t	node_length (id_t id)

char	pos_char (pos_t pos)

map< pos_t, char >	next_pos_chars (pos_t pos)

Alignment	mutate (const Alignment &aln, double base_error, double indel_error)

vector< Edit >	mutate_edit (const Edit &edit, const pos_t &position, double base_error, double indel_error, const string &bases, vg::uniform_real_distribution< double > &rprob, vg::uniform_int_distribution< int > &rbase)

string	alignment_seq (const Alignment &aln)

bool	is_valid (const Alignment &aln)

Public Member Functions inherited from vg::AbstractReadSampler
virtual	~AbstractReadSampler ()=default

	AbstractReadSampler (PathPositionHandleGraph &graph)
	Make a new sampler using the given graph. More...

Public Attributes
LRUCache< id_t, Node >	node_cache

LRUCache< id_t, vector< Edge > >	edge_cache

mt19937	rng

int64_t	nonce

bool	forward_only

bool	no_Ns

vector< string >	source_paths

vg::discrete_distribution	path_sampler

size_t	total_seq_length = 0

Public Attributes inherited from vg::AbstractReadSampler
bool	multi_position_annotations = false

size_t	max_tries = 100
	What limit should we use for retry loops before giving up or failing? More...

std::unique_ptr< std::function< bool(const path_handle_t &)> >	annotation_path_filter

Additional Inherited Members
Protected Member Functions inherited from vg::AbstractReadSampler
void	annotate_with_path_positions (Alignment &aln)

Protected Attributes inherited from vg::AbstractReadSampler
PathPositionHandleGraph &	graph
	The graph being simulated against. More...

Detailed Description

Generate Alignments (with or without mutations, and in pairs or alone) from an PathPositionHandleGraph index.

Constructor & Destructor Documentation

◆ Sampler()

vg::Sampler::Sampler	(	PathPositionHandleGraph *	x,
		int	seed = `0`,
		bool	forward_only = `false`,
		bool	allow_Ns = `false`,
		const vector< string > &	source_paths = `{}`,
		const vector< double > &	source_path_ploidies = `{}`,
		const vector< pair< string, double >> &	transcript_expressions = `{}`,
		const vector< tuple< string, string, size_t >> &	haplotype_transcripts = `{}`
	)

inline

Make a Sampler to sample from the given graph. If sampling from particular paths, source_paths should contain their names, and source_path_ploidies should either be empty or contain a ploidy value for each source path.

Member Function Documentation

◆ alignment()

Alignment vg::Sampler::alignment ( size_t length )

Get an alignment against the whole graph, or against the source path if one is selected.

◆ alignment_pair()

vector< Alignment > vg::Sampler::alignment_pair	(	size_t	read_length,
		size_t	fragment_length,
		double	fragment_std_dev,
		double	base_error,
		double	indel_error
	)

◆ alignment_seq()

string vg::Sampler::alignment_seq ( const Alignment & aln )

◆ alignment_to_graph()

Alignment vg::Sampler::alignment_to_graph ( size_t length )

Get an alignment against the whole graph.

◆ alignment_to_path()

Alignment vg::Sampler::alignment_to_path	(	const string &	source_path,
		size_t	length
	)

Get an alignment against the currently set source_path.

◆ alignment_with_error()

Alignment vg::Sampler::alignment_with_error	(	size_t	length,
		double	base_error,
		double	indel_error
	)

◆ is_valid()

bool vg::Sampler::is_valid ( const Alignment & aln )

Return true if the alignment is semantically valid against the PathPositionHandleGraph index we wrap, and false otherwise. Checks from_lengths on mappings to make sure all node bases are accounted for. Won't accept alignments with internal jumps between graph locations or regions; all skipped bases need to be accounted for by deletions.

◆ mutate()

Alignment vg::Sampler::mutate	(	const Alignment &	aln,
		double	base_error,
		double	indel_error
	)

◆ mutate_edit()

vector< Edit > vg::Sampler::mutate_edit	(	const Edit &	edit,
		const pos_t &	position,
		double	base_error,
		double	indel_error,
		const string &	bases,
		vg::uniform_real_distribution< double > &	rprob,
		vg::uniform_int_distribution< int > &	rbase
	)

Mutate the given edit, producing a vector of edits that should replace it. Position is the position of the start of the edit, and is updated to point to the next base after the mutated edit.

◆ next_pos_chars()

map< pos_t, char > vg::Sampler::next_pos_chars ( pos_t pos )

◆ node_length()

size_t vg::Sampler::node_length ( id_t id )

◆ pos_char()

char vg::Sampler::pos_char ( pos_t pos )

◆ position()

pos_t vg::Sampler::position ( void )

◆ sample_read()

Alignment vg::Sampler::sample_read ( )

◆ sample_read_pair()

pair<Alignment, Alignment> vg::Sampler::sample_read_pair ( )

◆ sequence()

string vg::Sampler::sequence ( size_t length )

◆ set_source_paths()

void vg::Sampler::set_source_paths	(	const vector< string > &	source_paths,
		const vector< double > &	source_path_ploidies,
		const vector< pair< string, double >> &	transcript_expressions,
		const vector< tuple< string, string, size_t >> &	haplotype_transcripts
	)

Make a path sampling distribution based on relative lengths (weighted by ploidy) or on transcript expressions. (At most one of source_paths and expressions should be non-empty.) If providing a transcript expression profile, can optionally provide a non-empty vector of haplotype transcripts to translate between the embedded path names and the transcript names in the expression profile.

Member Data Documentation

◆ edge_cache

LRUCache<id_t, vector<Edge> > vg::Sampler::edge_cache

◆ forward_only

bool vg::Sampler::forward_only

◆ no_Ns

bool vg::Sampler::no_Ns

◆ node_cache

LRUCache<id_t, Node> vg::Sampler::node_cache

◆ nonce

int64_t vg::Sampler::nonce

◆ path_sampler

vg::discrete_distribution vg::Sampler::path_sampler

◆ rng

mt19937 vg::Sampler::rng

◆ source_paths

vector<string> vg::Sampler::source_paths

◆ total_seq_length

size_t vg::Sampler::total_seq_length = 0

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

src/sampler.hpp
src/sampler.cpp

Public Member Functions

Public Attributes

Additional Inherited Members