vg::PhasedGenome Class Reference

#include <phased_genome.hpp>

Classes
class	Haplotype
struct	HaplotypeNode
class	iterator

Public Member Functions
	PhasedGenome (const SnarlManager &snarl_manager)
	Constructor. More...
	~PhasedGenome ()
	PhasedGenome (PhasedGenome &phased_genome)
	overloaded constructor More...
	PhasedGenome (PhasedGenome &&other)=delete
	move assignment ctor More...
PhasedGenome &	operator= (PhasedGenome &&phased_genome)=delete
	move assignment operator More...
PhasedGenome &	operator= (PhasedGenome &phased_genome)
	copy assignment operator More...
template<typename NodeTraversalIterator >
int	add_haplotype (NodeTraversalIterator first, NodeTraversalIterator last)
void	build_indices ()
size_t	num_haplotypes ()
iterator	begin (int which_haplotype)
iterator	end (int which_haplotype)
vector< id_t >	get_haplotypes_with_snarl (const Snarl *snarl_to_find)
	Check which haplotypes a snarl is found in. More...
void	print_phased_genome ()
	Prints out the haplotypes, and node values. More...
void	swap_alleles (const Snarl &site, int haplotype_1, int haplotype_2)
template<typename NodeTraversalIterator >
void	set_allele (const Snarl &site, NodeTraversalIterator first, NodeTraversalIterator last, int which_haplotype)
vector< NodeTraversal >	get_allele (const Snarl &site, int which_haplotype)
int32_t	optimal_score_on_genome (const multipath_alignment_t &multipath_aln, VG &graph)
double	read_log_likelihood (const multipath_alignment_t &multipath_aln, double log_base)

Private Member Functions
void	build_site_indices_internal (const Snarl *snarl)
void	insert_left (NodeTraversal node_traversal, HaplotypeNode *haplo_node)
	Insert a node traversal to the left of this haplotype node and update indices. More...
void	insert_right (NodeTraversal node_traversal, HaplotypeNode *haplo_node)
	Insert a node traversal to the right of this haplotype node and update indices. More...
void	remove (HaplotypeNode *haplo_node)
	Remove this haplotype node from its haplotype and update indices. More...
void	swap_label (const Snarl &site, Haplotype &haplotype_1, Haplotype &haplotype_2)
	Update a subsite's location in indices after swapping its parent allele. More...

Private Attributes
const SnarlManager *	snarl_manager
vector< Haplotype * >	haplotypes
	All haplotypes in the genome (generally 2 per chromosome) More...
unordered_map< int64_t, list< HaplotypeNode * > >	node_locations
	Index of where nodes from the graph occur in the phased genome. More...
unordered_map< int64_t, const Snarl * >	site_starts
	Index of which nodes are starts of Snarls. More...
unordered_map< int64_t, const Snarl * >	site_ends
	Index of which nodes are ends of Snarls. More...

Detailed Description

A collection of haplotypes that represent all of the chromosomes of a genome (including phasing) as walks through a variation graph. Designed for fast editing at a site level, so it maintains indices of sites for that purpose.

Constructor & Destructor Documentation

PhasedGenome() [1/3]

vg::PhasedGenome::PhasedGenome

(

const SnarlManager &

snarl_manager

)

Constructor.

~PhasedGenome()

vg::PhasedGenome::~PhasedGenome

(

)

PhasedGenome() [2/3]

vg::PhasedGenome::PhasedGenome

(

PhasedGenome &

phased_genome

)

overloaded constructor

PhasedGenome() [3/3]

vg::PhasedGenome::PhasedGenome ( PhasedGenome &&  other )

delete

move assignment ctor

Member Function Documentation

add_haplotype()

template<typename NodeTraversalIterator >

int vg::PhasedGenome::add_haplotype	(	NodeTraversalIterator	first,
		NodeTraversalIterator	last
	)

Build a haplotype in place from an iterator that returns NodeTraversal objects from its dereference operator (allows construction without instantiating the haplotype elsewhere) returns the numerical id of the new haplotype

note: the haplotype must have at least one node

begin()

PhasedGenome::iterator vg::PhasedGenome::begin

(

int

which_haplotype

)

Unidirectional iterator starting at the left telomere and moving to the right. Requires a haplotype id as input

build_indices()

void vg::PhasedGenome::build_indices

(

)

Construct the site ends, node locations, and haplotype site location indices. This method is intended to be called one time after building haplotypes. After this, the are maintained automatically during edit operations.

build_site_indices_internal()

void vg::PhasedGenome::build_site_indices_internal ( const Snarl *  snarl )

private

end()

PhasedGenome::iterator vg::PhasedGenome::end

(

int

which_haplotype

)

Iterator representing the past-the-last position of the given haplotype, with the last position being the right telomere node.

get_allele()

vector< NodeTraversal > vg::PhasedGenome::get_allele	(	const Snarl &	site,
		int	which_haplotype
	)

Returns a vector of node traversals representing the allele at the indicated site on the indicated haplotype. The allele is returned in the orientation of the Snarl (start to end), not necessarily the orientation on the haplotype. The start and end nodes of the Snarl are not included in the allele.

get_haplotypes_with_snarl()

vector< id_t > vg::PhasedGenome::get_haplotypes_with_snarl

(

const Snarl *

snarl_to_find

)

Check which haplotypes a snarl is found in.

insert_left()

void vg::PhasedGenome::insert_left ( NodeTraversal  node_traversal, HaplotypeNode *  haplo_node  )

inlineprivate

Insert a node traversal to the left of this haplotype node and update indices.

insert_right()

void vg::PhasedGenome::insert_right ( NodeTraversal  node_traversal, HaplotypeNode *  haplo_node  )

inlineprivate

Insert a node traversal to the right of this haplotype node and update indices.

num_haplotypes()

size_t vg::PhasedGenome::num_haplotypes

(

)

operator=() [1/2]

PhasedGenome& vg::PhasedGenome::operator= ( PhasedGenome &&  phased_genome )

delete

move assignment operator

operator=() [2/2]

PhasedGenome & vg::PhasedGenome::operator=

(

PhasedGenome &

phased_genome

)

copy assignment operator

optimal_score_on_genome()

int32_t vg::PhasedGenome::optimal_score_on_genome	(	const multipath_alignment_t &	multipath_aln,
		VG &	graph
	)

Returns the score of the highest scoring alignment contained in the multipath alignment that is restricted to the phased genome's paths through the variation graph.

Note: assumes that multipath_alignment_t has 'start' field filled in

print_phased_genome()

void vg::PhasedGenome::print_phased_genome

(

)

Prints out the haplotypes, and node values.

read_log_likelihood()

double vg::PhasedGenome::read_log_likelihood	(	const multipath_alignment_t &	multipath_aln,
		double	log_base
	)

Returns the sum of the log-likelihoods of all of the alignments expressed in a multipath alignment, given a

remove()

void vg::PhasedGenome::remove ( HaplotypeNode *  haplo_node )

inlineprivate

Remove this haplotype node from its haplotype and update indices.

set_allele()

template<typename NodeTraversalIterator >

void vg::PhasedGenome::set_allele	(	const Snarl &	site,
		NodeTraversalIterator	first,
		NodeTraversalIterator	last,
		int	which_haplotype
	)

Set the allele at a site with an iterator that yields its node sequence. The allele should be provided in the order indicated by the Snarl (i.e. from start to end) and it should not include the boundary nodes of the Snarl.

Note: This method does not check that the allele path takes only edges that are actually included in the graph, so client must ensure this itself.

swap_alleles()

void vg::PhasedGenome::swap_alleles	(	const Snarl &	site,
		int	haplotype_1,
		int	haplotype_2
	)

Swap the allele from between two haplotypes, maintaining all indices. If a nested site is being swapped, this method should be called only once for the top-most site. Child sites are swapped along with the top-most site automatically.

swap_label()

void vg::PhasedGenome::swap_label ( const Snarl &  site, Haplotype &  haplotype_1, Haplotype &  haplotype_2  )

private

Update a subsite's location in indices after swapping its parent allele.

Member Data Documentation

haplotypes

vector<Haplotype*> vg::PhasedGenome::haplotypes

private

All haplotypes in the genome (generally 2 per chromosome)

node_locations

unordered_map<int64_t, list<HaplotypeNode*> > vg::PhasedGenome::node_locations

private

Index of where nodes from the graph occur in the phased genome.

site_ends

unordered_map<int64_t, const Snarl*> vg::PhasedGenome::site_ends

private

Index of which nodes are ends of Snarls.

site_starts

unordered_map<int64_t, const Snarl*> vg::PhasedGenome::site_starts

private

Index of which nodes are starts of Snarls.

snarl_manager

const SnarlManager* vg::PhasedGenome::snarl_manager

private

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

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