Package org.monarchinitiative.lirical.core.model

Interface VariantMetadata

All Known Subinterfaces:

LiricalVariant

public interface VariantMetadata

Method Summary

Modifier and Type	Method	Description
Optional<ClinVarAlleleData>	clinVarAlleleData()
default ClinvarClnSig	clinvarClnSig()	Deprecated, for removal: This API element is subject to removal in a future version. since 2.0.0-RC3 and will be removed in v3.0.0.
static int	compareByPathogenicity(VariantMetadata left, VariantMetadata right)	Deprecated, for removal: This API element is subject to removal in a future version. the function has been deprecated without replacement and will be removed in v3.0.0.
static VariantMetadata	empty()
Optional<Float>	frequency()	Get variant frequency as a percentage or an empty optional if the variant has not been observed in any available variant database.
default Optional<Float>	frequencyScore()	This is the frequency factor used for the Exomiser like pathogenicity score.
static VariantMetadata	of(float frequency, float pathogenicity, ClinVarAlleleData clinVarAlleleData)
float	pathogenicity()	Get estimate of the overall variant pathogenicity.
default Optional<Float>	pathogenicityScore()	Get aggregated variant pathogenicity score.

Method Details

empty

static VariantMetadata empty()

of

static VariantMetadata of(float frequency,
 float pathogenicity,
 ClinVarAlleleData clinVarAlleleData)

frequency

Optional<Float> frequency()

Get variant frequency as a percentage or an empty optional if the variant has not been observed in any available variant database.

For instance, 0.5 for a variant with frequency 1/500.

Returns:

optional variant frequency as a percentage.

pathogenicity

float pathogenicity()

Get estimate of the overall variant pathogenicity.

The estimate must be in range [0, 1] where 0 and 1 represent the least and the most deleterious variants.

The estimate can be an aggregate of multiple scoring tools or a product of a single tool.

Returns:

the overall variant pathogenicity estimate.

pathogenicityScore

default Optional<Float> pathogenicityScore()

Get aggregated variant pathogenicity score.

The Clinvar pathogenic or likely pathogenic variants are assigned a score of 1. The other variants are assigned a product of the frequencyScore() and pathogenicity(). An empty optional is returned if the frequencyScore() is missing.

Returns:

optional pathogenicity score.

clinvarClnSig

@Deprecated(forRemoval=true,
            since="2.0.0-RC3")
default ClinvarClnSig clinvarClnSig()

Deprecated, for removal: This API element is subject to removal in a future version.

since 2.0.0-RC3 and will be removed in v3.0.0. Use clinVarAlleleData() instead.

Returns:

Clinvar clinical significance category.

clinVarAlleleData

Optional<ClinVarAlleleData> clinVarAlleleData()

Returns:

ClinvarData for the variant, if available.

frequencyScore

default Optional<Float> frequencyScore()

This is the frequency factor used for the Exomiser like pathogenicity score. It penalizes variants that have a higher population frequency, with anything above 2% getting a factor of zero.

Returns:

The Exomiser-style frequency factor

compareByPathogenicity

@Deprecated(forRemoval=true,
            since="2.0.0-RC3")
static int compareByPathogenicity(VariantMetadata left,
 VariantMetadata right)

Deprecated, for removal: This API element is subject to removal in a future version.

the function has been deprecated without replacement and will be removed in v3.0.0.