vg::PrimerFinder Class Reference

#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