vg::Deconstructor Class Reference

#include <deconstructor.hpp>

Public Member Functions
	Deconstructor ()
	~Deconstructor ()
void	deconstruct (vector< string > refpaths, const PathPositionHandleGraph *grpah, SnarlManager *snarl_manager, bool path_restricted_traversals, int ploidy, bool include_nested, const unordered_map< string, string > *path_to_sample=nullptr)

Private Member Functions
bool	deconstruct_site (const Snarl *site)
vector< int >	get_alleles (vcflib::Variant &v, const vector< SnarlTraversal > &travs, int ref_path_idx, char prev_char, bool use_start)
void	get_genotypes (vcflib::Variant &v, const vector< string > &names, const vector< int > &trav_to_allele)
pair< vector< int >, bool >	choose_traversals (const vector< int > &travs, const vector< int > &trav_to_allele, const vector< string > &trav_to_name)
bool	check_max_nodes (const Snarl *snarl)
vector< SnarlTraversal >	explicit_exhaustive_traversals (const Snarl *snarl)

Private Attributes
vcflib::VariantCallFile	outvcf
bool	path_restricted = false
int	ploidy
const PathPositionHandleGraph *	graph
SnarlManager *	snarl_manager
unique_ptr< PathTraversalFinder >	path_trav_finder
unique_ptr< TraversalFinder >	trav_finder
set< string >	ref_paths
set< string >	sample_names
const unordered_map< string, string > *	path_to_sample
int	max_nodes_for_exhaustive = 100

Constructor & Destructor Documentation

Deconstructor()

vg::Deconstructor::Deconstructor

(

)

~Deconstructor()

vg::Deconstructor::~Deconstructor

(

)

Member Function Documentation

check_max_nodes()

bool vg::Deconstructor::check_max_nodes ( const Snarl *  snarl )

private

choose_traversals()

pair< vector< int >, bool > vg::Deconstructor::choose_traversals ( const vector< int > &  travs, const vector< int > &  trav_to_allele, const vector< string > &  trav_to_name  )

private

deconstruct()

void vg::Deconstructor::deconstruct	(	vector< string >	ref_paths,
		const PathPositionHandleGraph *	graph,
		SnarlManager *	snarl_manager,
		bool	path_restricted_traversals,
		int	ploidy,
		bool	include_nested,
		const unordered_map< string, string > *	path_to_sample = nullptr
	)

Convenience wrapper function for deconstruction of multiple paths.

deconstruct_site()

bool vg::Deconstructor::deconstruct_site ( const Snarl *  site )

private

explicit_exhaustive_traversals()

vector< SnarlTraversal > vg::Deconstructor::explicit_exhaustive_traversals ( const Snarl *  snarl )

private

get_alleles()

vector< int > vg::Deconstructor::get_alleles ( vcflib::Variant &  v, const vector< SnarlTraversal > &  travs, int  ref_path_idx, char  prev_char, bool  use_start  )

private

Takes in a vector of snarltraversals returns their sequences as a vector<string> returns a boolean hasRef if a reference path is present, hasRef is set to true and the first string in the vector is the reference allele otherwise, hasRef is set to false and all strings are alt alleles.

get_genotypes()

void vg::Deconstructor::get_genotypes ( vcflib::Variant &  v, const vector< string > &  names, const vector< int > &  trav_to_allele  )

private

Member Data Documentation

graph

const PathPositionHandleGraph* vg::Deconstructor::graph

private

max_nodes_for_exhaustive

int vg::Deconstructor::max_nodes_for_exhaustive = 100

private

outvcf

vcflib::VariantCallFile vg::Deconstructor::outvcf

private

path_restricted

bool vg::Deconstructor::path_restricted = false

private

path_to_sample

const unordered_map<string, string>* vg::Deconstructor::path_to_sample

private

path_trav_finder

unique_ptr<PathTraversalFinder> vg::Deconstructor::path_trav_finder

private

ploidy

int vg::Deconstructor::ploidy

private

ref_paths

set<string> vg::Deconstructor::ref_paths

private

sample_names

set<string> vg::Deconstructor::sample_names

private

snarl_manager

SnarlManager* vg::Deconstructor::snarl_manager

private

trav_finder

unique_ptr<TraversalFinder> vg::Deconstructor::trav_finder

private

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

• src/deconstructor.hpp
• src/deconstructor.cpp