#include <primer_filter.hpp>

Public Member Functions
	PrimerFinder (const unique_ptr< handlegraph::PathPositionHandleGraph > &graph_param, const SnarlDistanceIndex distance_index_param, ifstream &primers_file_handle, const gbwtgraph::GBWTGraph &gbwt_graph, const gbwt::GBWT &gbwt_index, const gbwt::FastLocate &r_index, MinimizerMapper giraffe_mapper_param=nullptr)

	~PrimerFinder ()

void	add_primer_pair (const string &path_name, const size_t &left_primer_starting_node_id, const size_t &left_primer_offset, const size_t &left_primer_length, const size_t &right_primer_starting_node_id, const size_t &right_primer_offset, const size_t &right_primer_length)

void	load_primers (ifstream &file_handle)

const vector< PrimerPair > &	get_primer_pairs_of_chrom (const string &chrom_name) const

const size_t	total_reference_paths () const

vector< string >	get_reference_paths ()

Private Member Functions
std::pair< string, size_t >	get_graph_coordinates_from_sequence (const string &seq)

void	update_min_max_product_size (PrimerPair &primer_pair)

void	make_primer (Primer &primer, const string &path_name, const size_t &starting_node_id, const size_t &offset, const size_t &length, const bool &is_left)

void	map_to_nodes (Primer &primer, const string &path_name)

size_t	longest_match_len (Primer &primer, const string &left_seq, const string &right_seq, const bool &first_node)

const string	strip (const string &s) const

void	update_variation (PrimerPair &primer_pair, const string &path_name)

vector< string >	split (const string &str)

vector< string >	split (const string &str, const char &delim)

bool	startswith (const string &str, const string &prefix)

Private Attributes
unordered_map< string, vector< PrimerPair > >	chroms

const PathPositionHandleGraph *	graph

const SnarlDistanceIndex *	distance_index

MinimizerMapper *	giraffe_mapper

const gbwtgraph::GBWTGraph &	gbwt_graph

const gbwt::GBWT &	gbwt_index

const gbwt::FastLocate &	r_index

Constructor & Destructor Documentation

◆ PrimerFinder()

vg::PrimerFinder::PrimerFinder	(	const unique_ptr< handlegraph::PathPositionHandleGraph > &	graph_param,
		const SnarlDistanceIndex *	distance_index_param,
		ifstream &	primers_file_handle,
		const gbwtgraph::GBWTGraph &	gbwt_graph,
		const gbwt::GBWT &	gbwt_index,
		const gbwt::FastLocate &	r_index,
		MinimizerMapper *	giraffe_mapper_param = `nullptr`
	)

Construct Primer finder given PathPositionHandleGraph, reference graph name and pointer to SnarlDistanceIndex

◆ ~PrimerFinder()

vg::PrimerFinder::~PrimerFinder ( )

Destructor

Member Function Documentation

◆ add_primer_pair()

void vg::PrimerFinder::add_primer_pair	(	const string &	path_name,
		const size_t &	left_primer_starting_node_id,
		const size_t &	left_primer_offset,
		const size_t &	left_primer_length,
		const size_t &	right_primer_starting_node_id,
		const size_t &	right_primer_offset,
		const size_t &	right_primer_length
	)

Add a Primer_pair object given primers' starting node id, offset relative to the starting node, and length, all in the POSTIVE orientation. The new primer_pair object is automatically added to primer_pairs vector - and selected_primer_pairs if conditions are met. Mainly used for unit testing.

◆ get_graph_coordinates_from_sequence()

std::pair< string, size_t > vg::PrimerFinder::get_graph_coordinates_from_sequence ( const string & seq )

private

Private functions used by public or private functions. Get the graph coordinates by mapping and surjecting the template To be used if the chromosome_name isn't a valid path Returns a pair of the path/chromosome name and the offset of the template in the path Used in: load_primers

◆ get_primer_pairs_of_chrom()

const vector< PrimerPair > & vg::PrimerFinder::get_primer_pairs_of_chrom ( const string & chrom_name ) const

return vector of Primer pairs

◆ get_reference_paths()

vector< string > vg::PrimerFinder::get_reference_paths ( )

◆ load_primers()

void vg::PrimerFinder::load_primers ( ifstream & file_handle )

Read the path to the primer3 output. Primers information is parsed, processed, and stored in primer_pairs vector - and selected_primer_pairs if conditions are met.

◆ longest_match_len()

size_t vg::PrimerFinder::longest_match_len	(	Primer &	primer,
		const string &	left_seq,
		const string &	right_seq,
		const bool &	first_node
	)

private

Find the length of the longest match between two sequences. Also find and store offset in Primer object. Used in: map_to_nodes

◆ make_primer()

void vg::PrimerFinder::make_primer	(	Primer &	primer,
		const string &	path_name,
		const size_t &	starting_node_id,
		const size_t &	offset,
		const size_t &	length,
		const bool &	is_left
	)

private

Update a Primer object given starting node id, offset relative to the starting node, and the length of primer. Used in: add_primer_pair

◆ map_to_nodes()

void vg::PrimerFinder::map_to_nodes	(	Primer &	primer,
		const string &	path_name
	)

private

Find and store corresponding node ids to Primer object. Used in: make_primer load_primers

◆ split() [1/2]

vector< string > vg::PrimerFinder::split ( const string & str )

private

Split a string into vectors. Used in: load_primers

◆ split() [2/2]

vector< string > vg::PrimerFinder::split	(	const string &	str,
		const char &	delim
	)

private

Split a string into vectors given delimiter.

◆ startswith()

bool vg::PrimerFinder::startswith	(	const string &	str,
		const string &	prefix
	)

private

Works like str.startswith(prefix) in python Used in: load_primers

◆ strip()

const string vg::PrimerFinder::strip ( const string & s ) const

private

Strip empty spaces on the sides of a string. Used in: load_primers

◆ total_reference_paths()

const size_t vg::PrimerFinder::total_reference_paths ( ) const

return the total number of reference paths

◆ update_min_max_product_size()

void vg::PrimerFinder::update_min_max_product_size ( PrimerPair & primer_pair )

private

Update minimum and maximum prodcut to a primer pair object. Used in: add_primer_pair load_primers

◆ update_variation()

void vg::PrimerFinder::update_variation	(	PrimerPair &	primer_pair,
		const string &	path_name
	)

private

Check if primers in a primer_pair object have variations on the pangenome. Used in: add_primer_node load_primers

Member Data Documentation

◆ chroms

unordered_map<string, vector<PrimerPair> > vg::PrimerFinder::chroms

private

◆ distance_index

const SnarlDistanceIndex* vg::PrimerFinder::distance_index

private

◆ gbwt_graph

const gbwtgraph::GBWTGraph& vg::PrimerFinder::gbwt_graph

private

◆ gbwt_index

const gbwt::GBWT& vg::PrimerFinder::gbwt_index

private

◆ giraffe_mapper

MinimizerMapper* vg::PrimerFinder::giraffe_mapper

private

◆ graph

const PathPositionHandleGraph* vg::PrimerFinder::graph

private

◆ r_index

const gbwt::FastLocate& vg::PrimerFinder::r_index

private

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

src/primer_filter.hpp
src/primer_filter.cpp

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ PrimerFinder()

◆ ~PrimerFinder()

Member Function Documentation

◆ add_primer_pair()

◆ get_graph_coordinates_from_sequence()

◆ get_primer_pairs_of_chrom()

◆ get_reference_paths()

◆ load_primers()

◆ longest_match_len()

◆ make_primer()

◆ map_to_nodes()

◆ split() [1/2]

◆ split() [2/2]

◆ startswith()

◆ strip()

◆ total_reference_paths()

◆ update_min_max_product_size()

◆ update_variation()

Member Data Documentation

◆ chroms

◆ distance_index

◆ gbwt_graph

◆ gbwt_index

◆ giraffe_mapper

◆ graph

◆ r_index