Uses of Enum Class
org.monarchinitiative.lirical.core.model.GenomeBuild

Packages that use GenomeBuild

Package	Description
org.monarchinitiative.lirical.configuration
org.monarchinitiative.lirical.configuration.impl
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.
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.core.service	Package with services used across LIRICAL.
org.monarchinitiative.lirical.exomiser_db_adapter
org.monarchinitiative.lirical.io	Parsers for LIRICAL.
org.monarchinitiative.lirical.io.background
org.monarchinitiative.lirical.io.service
org.monarchinitiative.lirical.io.vcf

Uses of GenomeBuild in org.monarchinitiative.lirical.configuration

Methods in org.monarchinitiative.lirical.configuration with parameters of type GenomeBuild

Modifier and Type	Method	Description
LiricalBuilder	LiricalBuilder.clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild genomeBuild)
LiricalBuilder	LiricalBuilder.exomiserVariantDbPath(GenomeBuild genomeBuild, Path exomiserVariantDatabase)	Set path to exomiser variant database for given GenomeBuild.

Uses of GenomeBuild in org.monarchinitiative.lirical.configuration.impl

Methods in org.monarchinitiative.lirical.configuration.impl with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<BackgroundVariantFrequencyService>	BundledBackgroundVariantFrequencyServiceFactory.forGenomeBuild(GenomeBuild genomeBuild, double defaultVariantBackgroundFrequency)

Uses of GenomeBuild in org.monarchinitiative.lirical.core.analysis

Methods in org.monarchinitiative.lirical.core.analysis that return GenomeBuild

Modifier and Type	Method	Description
GenomeBuild	AnalysisOptions.genomeBuild()

Methods in org.monarchinitiative.lirical.core.analysis with parameters of type GenomeBuild

Modifier and Type	Method	Description
AnalysisOptions.Builder	AnalysisOptions.Builder.genomeBuild(GenomeBuild genomeBuild)

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

Methods in org.monarchinitiative.lirical.core.io with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<VariantParser>	VariantParserFactory.forPath(Path variantResource, GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)

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

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

Modifier and Type	Method	Description
GenomeBuild	GenotypedVariant.genomeBuild()
static GenomeBuild	GenomeBuild.valueOf(String name)	Returns the enum constant of this class with the specified name.
static GenomeBuild[]	GenomeBuild.values()	Returns an array containing the constants of this enum class, in the order they are declared.

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

Modifier and Type	Method	Description
static Optional<GenomeBuild>	GenomeBuild.parse(String payload)

Methods in org.monarchinitiative.lirical.core.model with parameters of type GenomeBuild

Modifier and Type	Method	Description
static GenotypedVariant	GenotypedVariant.of(GenomeBuild genomeBuild, org.monarchinitiative.svart.GenomicVariant variant, Collection<SampleAlleleCount> alleleCounts, boolean passedFilters)

Uses of GenomeBuild in org.monarchinitiative.lirical.core.service

Methods in org.monarchinitiative.lirical.core.service with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<BackgroundVariantFrequencyService>	BackgroundVariantFrequencyServiceFactory.forGenomeBuild(GenomeBuild genomeBuild, double defaultVariantBackgroundFrequency)
Optional<FunctionalVariantAnnotator>	FunctionalVariantAnnotatorService.getFunctionalAnnotator(GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)	Get FunctionalVariantAnnotator for a combination of GenomeBuild and TranscriptDatabase.
Optional<VariantMetadataService>	VariantMetadataServiceFactory.getVariantMetadataService(GenomeBuild genomeBuild)

Uses of GenomeBuild in org.monarchinitiative.lirical.exomiser_db_adapter

Methods in org.monarchinitiative.lirical.exomiser_db_adapter with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<VariantMetadataService>	ExomiserMvStoreMetadataServiceFactory.getVariantMetadataService(GenomeBuild genomeBuild)

Method parameters in org.monarchinitiative.lirical.exomiser_db_adapter with type arguments of type GenomeBuild

Modifier and Type	Method	Description
static ExomiserMvStoreMetadataServiceFactory	ExomiserMvStoreMetadataServiceFactory.of(Map<GenomeBuild,Path> exomiserDbPaths)

Constructor parameters in org.monarchinitiative.lirical.exomiser_db_adapter with type arguments of type GenomeBuild

Modifier	Constructor	Description
	ExomiserMvStoreMetadataServiceFactory(Map<GenomeBuild,Path> exomiserDbPaths)

Uses of GenomeBuild in org.monarchinitiative.lirical.io

Methods in org.monarchinitiative.lirical.io with parameters of type GenomeBuild

Modifier and Type	Method	Description
Path	LiricalDataResolver.transcriptCacheFor(GenomeBuild genomeBuild, TranscriptDatabase txDb)

Uses of GenomeBuild in org.monarchinitiative.lirical.io.background

Methods in org.monarchinitiative.lirical.io.background with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<BackgroundVariantFrequencyService>	CustomBackgroundVariantFrequencyServiceFactory.forGenomeBuild(GenomeBuild genomeBuild, double defaultVariantBackgroundFrequency)

Method parameters in org.monarchinitiative.lirical.io.background with type arguments of type GenomeBuild

Modifier and Type	Method	Description
static CustomBackgroundVariantFrequencyServiceFactory	CustomBackgroundVariantFrequencyServiceFactory.of(Map<GenomeBuild,Path> backgroundFilePaths)

Uses of GenomeBuild in org.monarchinitiative.lirical.io.service

Methods in org.monarchinitiative.lirical.io.service with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<FunctionalVariantAnnotator>	JannovarFunctionalVariantAnnotatorService.getFunctionalAnnotator(GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)

Uses of GenomeBuild in org.monarchinitiative.lirical.io.vcf

Methods in org.monarchinitiative.lirical.io.vcf with parameters of type GenomeBuild

Modifier and Type	Method	Description
Optional<VariantParser>	VcfVariantParserFactory.forPath(Path path, GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase)

Constructors in org.monarchinitiative.lirical.io.vcf with parameters of type GenomeBuild

Modifier	Constructor	Description
	VcfGenotypedVariantParser(org.monarchinitiative.svart.assembly.GenomicAssembly assembly, GenomeBuild genomeBuild, htsjdk.variant.vcf.VCFFileReader reader)