vg::RecombinatorHaplotype Struct Reference

Public Types
typedef Recombinator::sequence_type	sequence_type

Public Member Functions
	RecombinatorHaplotype (const Recombinator &recombinator, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const std::string &contig_name, bool wrap, size_t id)
void	extend (sequence_type sequence, const Haplotypes::Subchain &subchain, bool is_last_subchain)
void	take (gbwt::size_type sequence_id)
void	finish (bool with_suffix, bool is_final=true)

Public Attributes
const Recombinator &	recombinator
gbwt::GBWTBuilder &	builder
gbwtgraph::MetadataBuilder &	metadata
const std::string &	contig_name
bool	wrap
gbwt::vector_type	origin_fragment
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)
void	prefix (gbwt::node_type until)
void	suffix ()
void	insert (bool is_final)

Member Typedef Documentation

sequence_type

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

Constructor & Destructor Documentation

RecombinatorHaplotype()

vg::RecombinatorHaplotype::RecombinatorHaplotype ( const Recombinator & recombinator, gbwt::GBWTBuilder & builder, gbwtgraph::MetadataBuilder & metadata, const std::string & contig_name, bool wrap, size_t id )

inline

Member Function Documentation

connect()

void vg::RecombinatorHaplotype::connect ( gbwt::node_type until )

private

extend()

void vg::RecombinatorHaplotype::extend	(	sequence_type	sequence,
		const Haplotypes::Subchain &	subchain,
		bool	is_last_subchain )

finish()

void vg::RecombinatorHaplotype::finish	(	bool	with_suffix,
		bool	is_final = true )

insert()

void vg::RecombinatorHaplotype::insert ( bool is_final )

private

prefix()

void vg::RecombinatorHaplotype::prefix ( gbwt::node_type until )

private

suffix()

void vg::RecombinatorHaplotype::suffix ( )

private

take()

void vg::RecombinatorHaplotype::take

(

gbwt::size_type

sequence_id

)

Member Data Documentation

builder

gbwt::GBWTBuilder& vg::RecombinatorHaplotype::builder

contig_name

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

fragment

size_t vg::RecombinatorHaplotype::fragment

id

size_t vg::RecombinatorHaplotype::id

metadata

gbwtgraph::MetadataBuilder& vg::RecombinatorHaplotype::metadata

origin_fragment

gbwt::vector_type vg::RecombinatorHaplotype::origin_fragment

path

gbwt::vector_type vg::RecombinatorHaplotype::path

position

gbwt::edge_type vg::RecombinatorHaplotype::position

recombinator

const Recombinator& vg::RecombinatorHaplotype::recombinator

sequence_id

gbwt::size_type vg::RecombinatorHaplotype::sequence_id

wrap

bool vg::RecombinatorHaplotype::wrap

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

• src/recombinator.cpp