vg::HaplotypePartitioner::Subchain Struct Reference

#include <recombinator.hpp>

Public Member Functions
bool	has_start () const
	Returns true if the subchain has a start node. More...
bool	has_end () const
	Returns true if the subchain has an end node. More...

Public Attributes
Haplotypes::Subchain::subchain_t	type
	The type of this subchain. More...
handle_t	start
	Start node. More...
handle_t	end
	End node. More...
std::uint32_t	length
std::uint32_t	extra_snarls

Detailed Description

A subchain is a substring of a top-level chain defined by at most two boundary nodes.

Normal subchains have two boundary nodes, which are assumed to be the start node of a snarl and the end node of a possibly different snarl. There are assumed to be haplotypes crossing the subchain. Prefixes and suffixes lack one of the boundary nodes, while full haplotypes lack both.

When a top-level chain is partitioned into subchains, the boundary nodes may either overlap or be connected by unary paths. If a snarl is not connected, it may be presented as a suffix and a prefix.

Member Function Documentation

has_end()

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

inline

Returns true if the subchain has an end node.

has_start()

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

inline

Returns true if the subchain has a start node.

Member Data Documentation

end

handle_t vg::HaplotypePartitioner::Subchain::end

End node.

extra_snarls

std::uint32_t vg::HaplotypePartitioner::Subchain::extra_snarls

Number of additional snarls included in the subchain to keep reversals within the subchain.

length

std::uint32_t vg::HaplotypePartitioner::Subchain::length

Shortest distance from the last base of start to the first base of end, if both are present.

start

handle_t vg::HaplotypePartitioner::Subchain::start

Start node.

type

Haplotypes::Subchain::subchain_t vg::HaplotypePartitioner::Subchain::type

The type of this subchain.

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

• src/recombinator.hpp