vg::WFAExtender::ErrorModel Struct Reference

#include <gbwt_extender.hpp>

Classes
struct	Event

Static Public Member Functions
constexpr static Event	default_mismatches ()
	Default error model for mismatches. More...
constexpr static Event	default_gaps ()
	Default error model for gaps. More...
constexpr static Event	default_gap_length ()
	Default error model for gap length. More...
constexpr static Event	default_distance ()
	Default error model for distance. More...

Public Attributes
Event	mismatches
	Limits for mismatches. More...
Event	gaps
	Limits for total gaps (not gap opens; a gap open uses 1 gap and 1 gap length) More...
Event	gap_length
	Limits for total gap length (gap extends plus gap opens) More...
Event	distance
	Limits for alignments that have fallen too far behind. More...

Detailed Description

Defines how many of what kind of errors the WFA alignment algorithm should tolerate, as a function of sequence length.

The WFA alignment can't actually limit edits by type, but it can limit the score such that you can't exceed all the limits on different event types at once.

Member Function Documentation

default_distance()

constexpr static Event vg::WFAExtender::ErrorModel::default_distance ( )

inlinestaticconstexpr

Default error model for distance.

default_gap_length()

constexpr static Event vg::WFAExtender::ErrorModel::default_gap_length ( )

inlinestaticconstexpr

Default error model for gap length.

default_gaps()

constexpr static Event vg::WFAExtender::ErrorModel::default_gaps ( )

inlinestaticconstexpr

Default error model for gaps.

default_mismatches()

constexpr static Event vg::WFAExtender::ErrorModel::default_mismatches ( )

inlinestaticconstexpr

Default error model for mismatches.

Member Data Documentation

distance

Event vg::WFAExtender::ErrorModel::distance

Limits for alignments that have fallen too far behind.

gap_length

Event vg::WFAExtender::ErrorModel::gap_length

Limits for total gap length (gap extends plus gap opens)

gaps

Event vg::WFAExtender::ErrorModel::gaps

Limits for total gaps (not gap opens; a gap open uses 1 gap and 1 gap length)

mismatches

Event vg::WFAExtender::ErrorModel::mismatches

Limits for mismatches.

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

• src/gbwt_extender.hpp