vg::PhasedGenome::Haplotype Class Reference

#include <phased_genome.hpp>

Public Member Functions
	Haplotype (NodeTraversal node_traversal)
	Construct a haplotype with a single node. More...
template<typename NodeTraversalIterator >
	Haplotype (NodeTraversalIterator first, NodeTraversalIterator last)
	Construct a haplotype with an iterator that yields NodeTraversals. More...
	~Haplotype ()
HaplotypeNode *	append_left (NodeTraversal node_traversal)
HaplotypeNode *	append_right (NodeTraversal node_traversal)

Private Attributes
PhasedGenome::HaplotypeNode *	left_telomere_node
	Leftmost node in walk. More...
PhasedGenome::HaplotypeNode *	right_telomere_node
	Rightmost node in walk. More...
unordered_map< const Snarl *, pair< HaplotypeNode *, HaplotypeNode * > >	sites

Friends
class	PhasedGenome
class	HaplotypeNode

Detailed Description

Specialized linked list that tracks a walk through the variation graph and maintains an index of sites.

Constructor & Destructor Documentation

Haplotype() [1/2]

vg::PhasedGenome::Haplotype::Haplotype

(

NodeTraversal

node_traversal

)

Construct a haplotype with a single node.

Haplotype() [2/2]

template<typename NodeTraversalIterator >

vg::PhasedGenome::Haplotype::Haplotype	(	NodeTraversalIterator	first,
		NodeTraversalIterator	last
	)

Construct a haplotype with an iterator that yields NodeTraversals.

~Haplotype()

vg::PhasedGenome::Haplotype::~Haplotype

(

)

Member Function Documentation

append_left()

PhasedGenome::HaplotypeNode * vg::PhasedGenome::Haplotype::append_left ( NodeTraversal  node_traversal )

inline

Add a haplotype node for this node traversal to left end of haplotye and return new node. Does not maintain indices; intended for use by the PhasedGenome for initial haplotype build.

append_right()

PhasedGenome::HaplotypeNode * vg::PhasedGenome::Haplotype::append_right ( NodeTraversal  node_traversal )

inline

Add a haplotype node for this node traversal to right end of haplotye and return new node. Does not maintain indices; intended for use by the PhasedGenome for initial haplotype build.

Friends And Related Function Documentation

HaplotypeNode

friend class HaplotypeNode

friend

PhasedGenome

friend class PhasedGenome

friend

Member Data Documentation

left_telomere_node

PhasedGenome::HaplotypeNode* vg::PhasedGenome::Haplotype::left_telomere_node

private

Leftmost node in walk.

right_telomere_node

PhasedGenome::HaplotypeNode* vg::PhasedGenome::Haplotype::right_telomere_node

private

Rightmost node in walk.

sites

unordered_map<const Snarl*, pair<HaplotypeNode*, HaplotypeNode*> > vg::PhasedGenome::Haplotype::sites

private

Index of the location in the haplotype of nested sites. Locations of sites are stored as the nodes on haplotype that correspond to the start and end node of the site. The pair of haplotype nodes is stored in left-to-right order along the haplotype (i.e. .first->prev and .second->next are outside the bubble).

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

• src/phased_genome.hpp
• src/phased_genome.cpp