Package org.monarchinitiative.lirical.exomiser_db_adapter

Class ExomiserMvStoreMetadataServiceFactory

java.lang.Object

org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory

All Implemented Interfaces:

AutoCloseable, VariantMetadataServiceFactory

public class ExomiserMvStoreMetadataServiceFactory
extends Object
implements VariantMetadataServiceFactory, AutoCloseable

Constructor Summary

Constructors

Constructor	Description
ExomiserMvStoreMetadataServiceFactory(Map<GenomeBuild,Path> exomiserDbPaths)	Deprecated, for removal: This API element is subject to removal in a future version. Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores.

Method Summary

Modifier and Type	Method	Description
void	close()
static ExomiserMvStoreMetadataServiceFactory	fromResources(Map<GenomeBuild,ExomiserResources> resources)	Create ExomiserMvStoreMetadataServiceFactory from mappings from ExomiserResources for a GenomeBuild.
Optional<VariantMetadataService>	getVariantMetadataService(GenomeBuild genomeBuild)
static ExomiserMvStoreMetadataServiceFactory	of(Map<GenomeBuild,Path> exomiserDbPaths)	Deprecated, for removal: This API element is subject to removal in a future version. Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ExomiserMvStoreMetadataServiceFactory

@Deprecated(forRemoval=true,
            since="2.0.3")
public ExomiserMvStoreMetadataServiceFactory(Map<GenomeBuild,Path> exomiserDbPaths)

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

Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores. Use fromResources(Map) instead and provide ExomiserResources with paths to variant and clinvar database files for each GenomeBuild. To be removed in 3.0.0.

Parameters:

exomiserDbPaths - map with Path to variant database for a GenomeBuild. Usually, this file is called 2309_hg38_variants.mv.db or similar.

Method Details

of

@Deprecated(forRemoval=true,
            since="2.0.3")
public static ExomiserMvStoreMetadataServiceFactory of(Map<GenomeBuild,Path> exomiserDbPaths)

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

Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores. Use fromResources(Map) instead and provide ExomiserResources with paths to variant and clinvar database files for each GenomeBuild. To be removed in 3.0.0.

fromResources

public static ExomiserMvStoreMetadataServiceFactory fromResources(Map<GenomeBuild,ExomiserResources> resources)

Create ExomiserMvStoreMetadataServiceFactory from mappings from ExomiserResources for a GenomeBuild.

Parameters:

resources - map with ExomiserResources for a GenomeBuild.

Returns:

the newly created factory.

getVariantMetadataService

public Optional<VariantMetadataService> getVariantMetadataService(GenomeBuild genomeBuild)

Specified by:

getVariantMetadataService in interface VariantMetadataServiceFactory

close

public void close()

Specified by:

close in interface AutoCloseable