Package org.monarchinitiative.lirical.configuration

Class LiricalBuilder

java.lang.Object

org.monarchinitiative.lirical.configuration.LiricalBuilder

public class LiricalBuilder
extends Object

Method Summary

Modifier and Type	Method	Description
LiricalBuilder	backgroundVariantFrequencyServiceFactory(BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory)
Lirical	build()
static LiricalBuilder	builder(Path liricalDataDirectory)
LiricalBuilder	clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild genomeBuild)
LiricalBuilder	exomiserVariantDbPath(GenomeBuild genomeBuild, Path exomiserVariantDatabase)	Set path to exomiser variant database for given GenomeBuild.
LiricalBuilder	parallelism(int parallelism)	Set the number threads/workers in the LIRICAL worker pool.
LiricalBuilder	phenotypeService(PhenotypeService phenotypeService)
LiricalBuilder	variantMetadataServiceFactory(VariantMetadataServiceFactory variantMetadataServiceFactory)

Methods inherited from class java.lang.Object

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

Method Details

builder

public static LiricalBuilder builder(Path liricalDataDirectory)
                              throws LiricalDataException

Throws:

LiricalDataException

exomiserVariantDbPath

public LiricalBuilder exomiserVariantDbPath(GenomeBuild genomeBuild,
 Path exomiserVariantDatabase)

Set path to exomiser variant database for given GenomeBuild.

Returns:

the builder

clearExomiserVariantDatabaseForGenomeBuild

public LiricalBuilder clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild genomeBuild)

backgroundVariantFrequencyServiceFactory

public LiricalBuilder backgroundVariantFrequencyServiceFactory(BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory)

phenotypeService

public LiricalBuilder phenotypeService(PhenotypeService phenotypeService)

variantMetadataServiceFactory

public LiricalBuilder variantMetadataServiceFactory(VariantMetadataServiceFactory variantMetadataServiceFactory)

parallelism

public LiricalBuilder parallelism(int parallelism)

Set the number threads/workers in the LIRICAL worker pool.

build

public Lirical build()
              throws LiricalDataException

Throws:

LiricalDataException