#include <chain_items.hpp>

Public Attributes
int	item_bonus = 0
	Score bonus for each item collected. More...

double	gap_scale = 1.0
	Scale to apply to the scores of gaps. More...

int	recombination_penalty = 0
	Penalize this many points per recombination. More...

int	consistency_bonus = 0

Detailed Description

Represents the scoring scheme for chains, to determine which are best. Doesn't cover the parameters that really belong to an alignment scoring scheme (like gap open and extend).

Member Data Documentation

◆ consistency_bonus

int vg::algorithms::ChainScoringScheme::consistency_bonus = 0

Apply a bonus during alternative selection (but not to actual DP scores) of this many points when matching haplotype paths are preserved, scaled by fraction of haplotypes preserved.

◆ gap_scale

double vg::algorithms::ChainScoringScheme::gap_scale = 1.0

Scale to apply to the scores of gaps.

◆ item_bonus

int vg::algorithms::ChainScoringScheme::item_bonus = 0

Score bonus for each item collected.

◆ recombination_penalty

int vg::algorithms::ChainScoringScheme::recombination_penalty = 0

Penalize this many points per recombination.

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

src/algorithms/chain_items.hpp