Package org.monarchinitiative.lirical.io.output

Interface VisualizableVariant

public interface VisualizableVariant

The variant data for displaying in SVG widget.

Method Summary

Modifier and Type	Method	Description
String	alt()
String	contigName()
List<TranscriptAnnotation>	getAnnotationList()
String	getClinvar()
float	getFrequency()
String	getGenotype()
float	getPathogenicityScore()
String	getUcsc()
boolean	isPassingPathogenicThreshold()
static VisualizableVariant	of(String sampleId, LiricalVariant lv, boolean isPassingPathogenicityThreshold)
int	pos()
String	ref()

Method Details

of

static VisualizableVariant of(String sampleId,
 LiricalVariant lv,
 boolean isPassingPathogenicityThreshold)

contigName

String contigName()

pos

int pos()

ref

String ref()

alt

String alt()

getUcsc

String getUcsc()

isPassingPathogenicThreshold

boolean isPassingPathogenicThreshold()

getPathogenicityScore

float getPathogenicityScore()

getFrequency

float getFrequency()

getGenotype

String getGenotype()

getClinvar

String getClinvar()

getAnnotationList

List<TranscriptAnnotation> getAnnotationList()