vg::RecombinatorHaplotype Struct Reference

Public Types
typedef Recombinator::sequence_type	sequence_type

Public Member Functions
void	extend (sequence_type sequence, const Haplotypes::Subchain &subchain, const Recombinator &recombinator, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)
void	take (gbwt::size_type sequence_id, const Recombinator &recombinator, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)
void	finish (const Recombinator &recombinator, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)

Public Attributes
const std::string &	contig_name
size_t	id
size_t	fragment
gbwt::size_type	sequence_id
gbwt::edge_type	position
gbwt::vector_type	path

Private Member Functions
void	connect (gbwt::node_type until, const gbwtgraph::GBWTGraph &graph)
void	prefix (gbwt::size_type sequence_id, gbwt::node_type until, const gbwt::GBWT &index)
void	suffix (const gbwt::GBWT &index)
void	insert (gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)

Member Typedef Documentation

sequence_type

typedef Recombinator::sequence_type vg::RecombinatorHaplotype::sequence_type

Member Function Documentation

connect()

void vg::RecombinatorHaplotype::connect ( gbwt::node_type  until, const gbwtgraph::GBWTGraph &  graph  )

private

extend()

void vg::RecombinatorHaplotype::extend	(	sequence_type	sequence,
		const Haplotypes::Subchain &	subchain,
		const Recombinator &	recombinator,
		gbwt::GBWTBuilder &	builder,
		gbwtgraph::MetadataBuilder &	metadata
	)

finish()

void vg::RecombinatorHaplotype::finish	(	const Recombinator &	recombinator,
		gbwt::GBWTBuilder &	builder,
		gbwtgraph::MetadataBuilder &	metadata
	)

insert()

void vg::RecombinatorHaplotype::insert ( gbwt::GBWTBuilder &  builder, gbwtgraph::MetadataBuilder &  metadata  )

private

prefix()

void vg::RecombinatorHaplotype::prefix ( gbwt::size_type  sequence_id, gbwt::node_type  until, const gbwt::GBWT &  index  )

private

suffix()

void vg::RecombinatorHaplotype::suffix ( const gbwt::GBWT &  index )

private

take()

void vg::RecombinatorHaplotype::take	(	gbwt::size_type	sequence_id,
		const Recombinator &	recombinator,
		gbwt::GBWTBuilder &	builder,
		gbwtgraph::MetadataBuilder &	metadata
	)

the builder. This is intended for fragments that do not contain subchains crossed by the original haplotypes. The call will fail if extend() has been called.

Member Data Documentation

contig_name

const std::string& vg::RecombinatorHaplotype::contig_name

fragment

size_t vg::RecombinatorHaplotype::fragment

id

size_t vg::RecombinatorHaplotype::id

path

gbwt::vector_type vg::RecombinatorHaplotype::path

position

gbwt::edge_type vg::RecombinatorHaplotype::position

sequence_id

gbwt::size_type vg::RecombinatorHaplotype::sequence_id

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The documentation for this struct was generated from the following file:

• src/recombinator.cpp