vg::Haplotypes::Subchain Struct Reference

Representation of a subchain. More...

#include <recombinator.hpp>

Public Types
enum	subchain_t : std::uint64_t { normal = 0 , prefix = 1 , suffix = 2 , full_haplotype = 3 }
	Subchain types. More...
typedef gbwtgraph::Key64::value_type	kmer_type
	An encoded kmer.

Public Member Functions
handle_t	start_handle () const
	Returns the start node as a GBWTGraph handle.
handle_t	end_handle () const
	Returns the end node as a GBWTGraph handle.
bool	has_start () const
	Returns true if the subchain has a start node.
bool	has_end () const
	Returns true if the subchain has an end node.
std::string	to_string () const
	Returns a string representation of the type and the boundary nodes.
void	simple_sds_serialize (std::ostream &out) const
	Serializes the object to a stream in the simple-sds format.
void	simple_sds_load (std::istream &in)
	Loads the object from a stream in the simple-sds format.
size_t	simple_sds_size () const
	Returns the size of the object in elements.

Public Attributes
subchain_t	type
	The type of this subchain.
gbwt::node_type	start
	Boundary nodes, or gbwt::ENDMARKER if not present.
gbwt::node_type	end
std::vector< std::pair< kmer_type, size_t > >	kmers
std::vector< sequence_type >	sequences
	Sequences as (GBWT sequence id, offset in the relevant node).
sdsl::bit_vector	kmers_present

Detailed Description

Representation of a subchain.

Member Typedef Documentation

kmer_type

typedef gbwtgraph::Key64::value_type vg::Haplotypes::Subchain::kmer_type

An encoded kmer.

Member Enumeration Documentation

subchain_t

enum vg::Haplotypes::Subchain::subchain_t : std::uint64_t

Subchain types.

Enumerator
normal	Normal subchain with two boundary nodes.
prefix	A prefix with only an end node.
suffix	A suffix with only a start node.
full_haplotype	A full haplotype with no boundary nodes.

Member Function Documentation

end_handle()

handle_t vg::Haplotypes::Subchain::end_handle ( ) const

inline

Returns the end node as a GBWTGraph handle.

has_end()

bool vg::Haplotypes::Subchain::has_end ( ) const

inline

Returns true if the subchain has an end node.

has_start()

bool vg::Haplotypes::Subchain::has_start ( ) const

inline

Returns true if the subchain has a start node.

simple_sds_load()

void vg::Haplotypes::Subchain::simple_sds_load

(

std::istream &

in

)

Loads the object from a stream in the simple-sds format.

simple_sds_serialize()

void vg::Haplotypes::Subchain::simple_sds_serialize

(

std::ostream &

out

)

const

Serializes the object to a stream in the simple-sds format.

simple_sds_size()

size_t vg::Haplotypes::Subchain::simple_sds_size

(

)

const

Returns the size of the object in elements.

start_handle()

handle_t vg::Haplotypes::Subchain::start_handle ( ) const

inline

Returns the start node as a GBWTGraph handle.

to_string()

std::string vg::Haplotypes::Subchain::to_string

(

)

const

Returns a string representation of the type and the boundary nodes.

Member Data Documentation

end

gbwt::node_type vg::Haplotypes::Subchain::end

kmers

std::vector<std::pair<kmer_type, size_t> > vg::Haplotypes::Subchain::kmers

A vector of distinct kmers. For each kmer, list the kmer itself and the number of haplotypes it appears in.

kmers_present

sdsl::bit_vector vg::Haplotypes::Subchain::kmers_present

sequences

std::vector<sequence_type> vg::Haplotypes::Subchain::sequences

Sequences as (GBWT sequence id, offset in the relevant node).

start

gbwt::node_type vg::Haplotypes::Subchain::start

Boundary nodes, or gbwt::ENDMARKER if not present.

type

subchain_t vg::Haplotypes::Subchain::type

The type of this subchain.

---

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

• src/recombinator.hpp
• src/recombinator.cpp