Public Member Functions
	seed_info_t (size_t index, bool is_rev, size_t flank, bool right_side, size_t nested_snarl_offset, const size_t &depth, const forest_growing_state_t &forest_state)

pos_t	reverse_seed () const

Public Attributes
pos_t	seed_pos
	The seed at the edge of the chain (first/last) More...

size_t	node_length
	Length of the seed's node. More...

const ZipCode &	zipcode
	The seed's non-reversed zipcode. More...

size_t	flank_offset
	Its offset from the edge (i.e. chain.distances.first/second) More...

bool	right_side
	Whether to use the right/left side of the seed. More...

size_t	rank
	Rank of the seed's chain in the snarl. More...

size_t	nested_snarl_offset

Detailed Description

Store edgemost seeds in chains when creating a snarl's distance matrix We make one pass over each chain, remembering its edge seeds, and then use those seeds to calculate all distances

Constructor & Destructor Documentation

◆ seed_info_t()

vg::ZipCodeForest::seed_info_t::seed_info_t	(	size_t	index,
		bool	is_rev,
		size_t	flank,
		bool	right_side,
		size_t	nested_snarl_offset,
		const size_t &	depth,
		const forest_growing_state_t &	forest_state
	)

Pass the seed's index (which is looked up from forest_state.seeds), whether its position should be reversed, and then a few raw values In addition, snarl depth & forest_state are used to look up seed info

Member Function Documentation

◆ reverse_seed()

pos_t vg::ZipCodeForest::seed_info_t::reverse_seed ( ) const

inline

Member Data Documentation

◆ flank_offset

size_t vg::ZipCodeForest::seed_info_t::flank_offset

Its offset from the edge (i.e. chain.distances.first/second)

◆ nested_snarl_offset

size_t vg::ZipCodeForest::seed_info_t::nested_snarl_offset

If this seed is in a nested snarl, and we're calculating using minimum_distance, then we might need to subtract the offset from inner seed to inner snarl edge

◆ node_length

size_t vg::ZipCodeForest::seed_info_t::node_length

Length of the seed's node.

◆ rank

size_t vg::ZipCodeForest::seed_info_t::rank

Rank of the seed's chain in the snarl.

◆ right_side

bool vg::ZipCodeForest::seed_info_t::right_side

Whether to use the right/left side of the seed.

◆ seed_pos

pos_t vg::ZipCodeForest::seed_info_t::seed_pos

The seed at the edge of the chain (first/last)

◆ zipcode

const ZipCode& vg::ZipCodeForest::seed_info_t::zipcode

The seed's non-reversed zipcode.

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

src/zip_code_tree.hpp
src/zip_code_tree.cpp

Public Member Functions

Public Attributes