Package org.monarchinitiative.lirical.core

Class Lirical

java.lang.Object

org.monarchinitiative.lirical.core.Lirical

public class Lirical
extends Object

Method Summary

Modifier and Type	Method	Description
AnalysisResultWriterFactory	analysisResultsWriterFactory()
LiricalAnalysisRunner	analysisRunner()
FunctionalVariantAnnotatorService	functionalVariantAnnotatorService()
static Lirical	of(VariantParserFactory variantParserFactory, PhenotypeService phenotypeService, BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory, VariantMetadataServiceFactory variantMetadataService, FunctionalVariantAnnotatorService functionalVariantAnnotatorService, AnalysisResultWriterFactory analysisResultWriterFactory, LiricalOptions options)
PhenotypeService	phenotypeService()
VariantMetadataServiceFactory	variantMetadataServiceFactory()
VariantParserFactory	variantParserFactory()
Optional<String>	version()

Methods inherited from class java.lang.Object

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

Method Details

of

public static Lirical of(VariantParserFactory variantParserFactory,
 PhenotypeService phenotypeService,
 BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory,
 VariantMetadataServiceFactory variantMetadataService,
 FunctionalVariantAnnotatorService functionalVariantAnnotatorService,
 AnalysisResultWriterFactory analysisResultWriterFactory,
 LiricalOptions options)

variantParserFactory

public VariantParserFactory variantParserFactory()

Returns:

variant parser factory for parsing variants for LIRICAL analysis.

phenotypeService

public PhenotypeService phenotypeService()

functionalVariantAnnotatorService

public FunctionalVariantAnnotatorService functionalVariantAnnotatorService()

variantMetadataServiceFactory

public VariantMetadataServiceFactory variantMetadataServiceFactory()

analysisRunner

public LiricalAnalysisRunner analysisRunner()

analysisResultsWriterFactory

public AnalysisResultWriterFactory analysisResultsWriterFactory()

version

public Optional<String> version()