Uses of Interface
org.monarchinitiative.lirical.core.model.LiricalVariant

Packages that use LiricalVariant

Package	Description
org.monarchinitiative.lirical.core.io	APIs for reading and annotation of genomic variants.
org.monarchinitiative.lirical.core.model	Package with data models.
org.monarchinitiative.lirical.io.output	Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.

Uses of LiricalVariant in org.monarchinitiative.lirical.core.io

Methods in org.monarchinitiative.lirical.core.io that return types with arguments of type LiricalVariant

Modifier and Type	Method	Description
default Stream<LiricalVariant>	VariantParser.variantStream()

Uses of LiricalVariant in org.monarchinitiative.lirical.core.model

Methods in org.monarchinitiative.lirical.core.model that return LiricalVariant

Modifier and Type	Method	Description
static LiricalVariant	LiricalVariant.of(GenotypedVariant variant, List<TranscriptAnnotation> annotations, VariantMetadata metadata)

Methods in org.monarchinitiative.lirical.core.model that return types with arguments of type LiricalVariant

Modifier and Type	Method	Description
Stream<LiricalVariant>	Gene2Genotype.variants()	Get a Stream of variants annotated to this gene.

Method parameters in org.monarchinitiative.lirical.core.model with type arguments of type LiricalVariant

Modifier and Type	Method	Description
static GenesAndGenotypes	GenesAndGenotypes.fromVariants(Collection<String> sampleNames, Iterable<LiricalVariant> variants)
static Gene2Genotype	Gene2Genotype.of(org.monarchinitiative.phenol.annotations.formats.GeneIdentifier geneId, Collection<LiricalVariant> passingVariants, int filteredOutVariantCount)	Create Gene2Genotype from provided data.

Uses of LiricalVariant in org.monarchinitiative.lirical.io.output

Methods in org.monarchinitiative.lirical.io.output that return types with arguments of type LiricalVariant

Modifier and Type	Method	Description
protected Function<LiricalVariant,VisualizableVariant>	LiricalTemplate.toVisualizableVariant()

Methods in org.monarchinitiative.lirical.io.output with parameters of type LiricalVariant

Modifier and Type	Method	Description
static VisualizableVariant	VisualizableVariant.of(String sampleId, LiricalVariant lv, boolean isPassingPathogenicityThreshold)