Index (LIRICAL 2.0.3-SNAPSHOT API)

A B C D E F G H I J L M N O P Q R S T U V W Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addAllSecondaryInterpretations(Iterable<? extends AlleleProto.ClinVar.ClinSig>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
addAllSecondaryInterpretationsValue(Iterable<Integer>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
addDiseaseDatabases(Collection<DiseaseDatabase>) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
addDiseaseDatabases(DiseaseDatabase...) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
addRepeatedField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
addRepeatedField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
addRepeatedField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
addSecondaryInterpretations(AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
addSecondaryInterpretationsValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
AFFECTS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Non-ACMG-based
AFFECTS - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
AFFECTS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
AFFECTS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Non-ACMG-based
age - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
age() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
age() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
age() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
age() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
age() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
Age - Class in org.monarchinitiative.lirical.core.model: Convenience class to represent the age of a subject.
ageInDays(int) - Static method in class org.monarchinitiative.lirical.core.model.Age: Create a postnatal age to represent d days of age.
ageInMonths(int) - Static method in class org.monarchinitiative.lirical.core.model.Age: Create a postnatal age to represent m months of age.
ageInYears(int) - Static method in class org.monarchinitiative.lirical.core.model.Age: Create a postnatal age to represent y years of age.
ALL_ESP_SOURCES - Static variable in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALL_EXAC_SOURCES - Static variable in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALL_EXTERNAL_FREQ_SOURCES - Static variable in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
alleleCount(String) - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant: Get allele count for given sample.
AlleleCount - Class in org.monarchinitiative.lirical.core.model
alleleId(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
ALLELEID_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
AlleleKeyDataType - Class in org.monarchinitiative.lirical.exomiser_db_adapter.serializers: Specialised DataType for (de)serialising AlleleProto.AlleleKey objects into and out of the MVStore.
AlleleKeyDataType() - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
AllelePropertiesDataType - Class in org.monarchinitiative.lirical.exomiser_db_adapter.serializers: Specialised DataType for (de)serialising AlleleProto.AlleleProperties objects into and out of the MVStore.
AllelePropertiesDataType() - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
AlleleProto - Class in org.monarchinitiative.exomiser.core.proto
AlleleProto.AlleleKey - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type AlleleKey
AlleleProto.AlleleKey.Builder - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type AlleleKey
AlleleProto.AlleleKeyOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProto.AlleleProperties - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type AlleleProperties
AlleleProto.AlleleProperties.Builder - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type AlleleProperties
AlleleProto.AllelePropertiesOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProto.ClinVar - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type ClinVar
AlleleProto.ClinVar.Builder - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type ClinVar
AlleleProto.ClinVar.ClinSig - Enum Class in org.monarchinitiative.exomiser.core.proto: Protobuf enum ClinVar.ClinSig
AlleleProto.ClinVarOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProtoAdaptor - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model
alt() - Method in class org.monarchinitiative.lirical.core.model.AlleleCount
alt() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
ALT_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
AnalysisData - Interface in org.monarchinitiative.lirical.core.analysis: Representation of subject data required by LIRICAL analysis.
AnalysisOptions - Interface in org.monarchinitiative.lirical.core.analysis: A container for analysis-specific settings, i.e.
AnalysisOptions.Builder - Class in org.monarchinitiative.lirical.core.analysis: A builder for AnalysisOptions.
AnalysisResults - Interface in org.monarchinitiative.lirical.core.analysis: A container for the likelihood ratio test results.
AnalysisResultsMetadata - Class in org.monarchinitiative.lirical.core.output
AnalysisResultsMetadata.Builder - Class in org.monarchinitiative.lirical.core.output
AnalysisResultsWriter - Interface in org.monarchinitiative.lirical.core.output: The implementors can store results of LIRICAL analysis in some OutputFormat.
analysisResultsWriterFactory() - Method in class org.monarchinitiative.lirical.core.Lirical
AnalysisResultWriterFactory - Interface in org.monarchinitiative.lirical.core.output: Factory class for getting AnalysisResultsWriters.
analysisRunner() - Method in class org.monarchinitiative.lirical.core.Lirical
annotate(GenomicVariant) - Method in interface org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotator
annotate(GenomicVariant) - Method in class org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotator
annotations() - Method in interface org.monarchinitiative.lirical.core.model.FunctionalAnnotationAware
ASSOCIATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: ASSOCIATION = 10;
ASSOCIATION - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
ASSOCIATION - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
ASSOCIATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: ASSOCIATION = 10;
associationData() - Method in interface org.monarchinitiative.lirical.core.service.PhenotypeService

B

BackgroundFrequencyCommand - Class in org.monarchinitiative.lirical.background: This command is used to generate the background frequency files.
BackgroundFrequencyCommand() - Constructor for class org.monarchinitiative.lirical.background.BackgroundFrequencyCommand
BackgroundVariantFrequencyParser - Class in org.monarchinitiative.lirical.io.background: This class coordinates the input of the background frequency file.
BackgroundVariantFrequencyService - Interface in org.monarchinitiative.lirical.core.service
backgroundVariantFrequencyServiceFactory(BackgroundVariantFrequencyServiceFactory) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
BackgroundVariantFrequencyServiceFactory - Interface in org.monarchinitiative.lirical.core.service
BenchmarkCommand - Class in org.monarchinitiative.lirical.cli.cmd: Benchmark command runs LIRICAL on one or more phenopackets and writes prioritization results into a CSV table.
BenchmarkCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
BENIGN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: ACMG/AMP-based
BENIGN - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
BENIGN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
BENIGN_OR_LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: BENIGN_OR_LIKELY_BENIGN = 2;
BENIGN_OR_LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
BENIGN_OR_LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
BENIGN_OR_LIKELY_BENIGN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: BENIGN_OR_LIKELY_BENIGN = 2;
BENIGN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: ACMG/AMP-based
binarySearch(T[], Function<T, U>, Comparator<? super U>, U) - Static method in class org.monarchinitiative.lirical.core.util.BinarySearch: Perform a binary search on an array of sorted BinarySearchs using the keyExtractor function for extracting the key for comparison.
binarySearch(T[], Function<T, U>, U) - Static method in class org.monarchinitiative.lirical.core.util.BinarySearch: Perform a binary search on an array of sorted BinarySearchs using the keyExtractor function for extracting the key for comparison.
BinarySearch - Class in org.monarchinitiative.lirical.core.util: Static utility class with the binary search implementation for arrays of items with custom key extractor function.
BLACK - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
BLUE - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
bootstrapLirical(GenomeBuild) - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand: Build Lirical for a GenomeBuild based on LiricalConfigurationCommand.DataSection and LiricalConfigurationCommand.RunConfiguration sections.
BOX_HEIGHT - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
BOX_OFFSET - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg: distance between two adjacent "boxes"
BRIGHT_GREEN - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
BROWN - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
build() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
build() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
build() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
build() - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
build() - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
build() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
build() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
builder() - Static method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
builder() - Static method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
builder() - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
builder(Path) - Static method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
Builder() - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
buildPartial() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
buildPartial() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
buildPartial() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
BundledBackgroundVariantFrequencyServiceFactory - Class in org.monarchinitiative.lirical.configuration.impl

C

CADD - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
CaddScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: CADD info - see here.
call() - Method in class org.monarchinitiative.lirical.background.BackgroundFrequencyCommand
call() - Method in class org.monarchinitiative.lirical.background.Main
call() - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
call() - Method in class org.monarchinitiative.lirical.cli.cmd.experimental.ExperimentalCommand
call() - Method in class org.monarchinitiative.lirical.cli.Main
cfg - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate: FreeMarker configuration object.
checkInput() - Method in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
checkInput() - Method in class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
checkInput() - Method in class org.monarchinitiative.lirical.cli.cmd.OutputCommand
CHR_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
clear() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
clear() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
clear() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
clearAlleleId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string alleleId = 1;
clearAlt() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
clearChr() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 chr = 1;
clearClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
clearDiseaseDatabases() - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
clearExomiserVariantDatabaseForGenomeBuild(GenomeBuild) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
clearField(Descriptors.FieldDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
clearField(Descriptors.FieldDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
clearField(Descriptors.FieldDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
clearIncludedAlleles() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
clearOneof(Descriptors.OneofDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
clearOneof(Descriptors.OneofDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
clearOneof(Descriptors.OneofDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
clearPosition() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 position = 2;
clearPrimaryInterpretation() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ClinSig primaryInterpretation = 2;
clearProperties() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
clearRef() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string ref = 3;
clearReviewStatus() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string reviewStatus = 4;
clearRsId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
clearSecondaryInterpretations() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
CLINVAR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
CLINVAR_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
clinVarAlleleData() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata
ClinVarAlleleData - Class in org.monarchinitiative.lirical.core.model: A subset of ClinVar allele data relevant for LIRICAL analysis.
clinvarClnSig() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: Deprecated, for removal: This API element is subject to removal in a future version.
since 2.0.0-RC3 and will be removed in v3.0.0. Use VariantMetadata.clinVarAlleleData() instead.
clinvarClnSig() - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
ClinvarClnSig - Enum Class in org.monarchinitiative.lirical.core.model: Clinvar clinical significance categories.
ClinVarData - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: Immutable data class representing data from the ClinVar resource, with explanation of the data from https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
ClinVarData.Builder - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
ClinVarData.ClinSig - Enum Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
clone() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
clone() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
clone() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
close() - Method in class org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl
compare(Object, Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType: Sorts variants according to their natural ordering of genome position.
compare(Object, Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
compare(PathogenicityScore, PathogenicityScore) - Static method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore: For the purposes of this comparator scores are ranked on a scale of 0 to 1 where 0 is considered probably non-pathogenic and 1 probably pathogenic.
compareByPathogenicity(VariantMetadata, VariantMetadata) - Static method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: Deprecated, for removal: This API element is subject to removal in a future version.
the function has been deprecated without replacement and will be removed in v3.0.0.
compareTo(TestResult) - Method in class org.monarchinitiative.lirical.core.analysis.TestResult: Compare two TestResult objects based on their TestResult.compositeLR value.
compareTo(LrWithExplanation) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation: Sort the LrWithExplanation objects in decreasing order according to likelihood ratio score.
compareTo(PathogenicityScore) - Method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore: For the purposes of this comparator scores are ranked on a scale of 0 to 1 where 0 is considered probably non-pathogenic and 1 probably pathogenic.
COMPREHENSIVE - Enum constant in enum class org.monarchinitiative.lirical.core.sanitize.SanitizerType: Comprehensive sanitizer performs the broadest array of checks to point out all errors and warnings.
computeFilteringStats() - Method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
CONFLICTING_PATHOGENICITY_INTERPRETATIONS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: CONFLICTING_PATHOGENICITY_INTERPRETATIONS = 8;
CONFLICTING_PATHOGENICITY_INTERPRETATIONS - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
CONFLICTING_PATHOGENICITY_INTERPRETATIONS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
CONFLICTING_PATHOGENICITY_INTERPRETATIONS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: CONFLICTING_PATHOGENICITY_INTERPRETATIONS = 8;
containsIncludedAlleles(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
containsIncludedAlleles(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
containsIncludedAlleles(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
containsProperties(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
containsProperties(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: map<string, float> properties = 2;
containsProperties(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: map<string, float> properties = 2;
contigName() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
create(HpoDisease, MinimalOntology) - Static method in class org.monarchinitiative.lirical.core.likelihoodratio.InducedDiseaseGraph
create(TermId, LrMatchType, double) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanationFactory
create(TermId, TermId, LrMatchType, double) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanationFactory
createOutputFile(Path, String, String) - Static method in class org.monarchinitiative.lirical.io.output.LiricalTemplate
createOutputOptions(String) - Method in class org.monarchinitiative.lirical.cli.cmd.OutputCommand
CustomBackgroundVariantFrequencyServiceFactory - Class in org.monarchinitiative.lirical.io.background: A BackgroundVariantFrequencyServiceFactory implementation that uses user-provided frequency files.

D

DARKBLUE - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
datadir - Variable in class org.monarchinitiative.lirical.cli.cmd.DownloadCommand
dataDirectory() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
dataSection - Variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
DBVAR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
DBVAR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
DECIPHER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
DEFAULT_FREQUENCY - Static variable in interface org.monarchinitiative.lirical.core.service.VariantMetadataService: We will assume a frequency of 1:100,000 if no frequency data is available.
DEFAULT_HIGH_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
DEFAULT_MISSENSE_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: This is the pathogenicity value we will give to missense (nonsynonymous) variants for which we cannot find values for mutationTaster, polyphen2, or SIFT.
DEFAULT_TERM_FREQUENCY - Static variable in class org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio: The default frequency of a term in a disease if the explicit frequency is not available.
defaultVariantBackgroundFrequency() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
defaultVariantBackgroundFrequency() - Method in interface org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyService
defaultVariantBackgroundFrequency(double) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
deleteriousAlleleCount(String, float) - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get the count of alleles of predicted pathogenic/deleterious variants in the gene for the sampleId.
DGV - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
DifferentialDiagnosis - Class in org.monarchinitiative.lirical.io.output: This class stores all the information we need for a detailed differential diagnosis -- the major candidates.
DISEASE_TERM_SUBCLASS_OF_QUERY - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
diseaseDatabases() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
diseaseId() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
diseaseIds() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
diseases() - Method in interface org.monarchinitiative.lirical.core.service.PhenotypeService
displayAllVariants - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
displayAllVariants() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
DownloadCommand - Class in org.monarchinitiative.lirical.cli.cmd: Download a number of files needed for the analysis.
DownloadCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.DownloadCommand
DRUG_RESPONSE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: DRUG_RESPONSE = 11;
DRUG_RESPONSE - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
DRUG_RESPONSE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
DRUG_RESPONSE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: DRUG_RESPONSE = 11;

E

empty() - Static method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
empty() - Static method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
empty() - Static method in interface org.monarchinitiative.lirical.core.model.VariantMetadata
empty() - Static method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
empty() - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
empty() - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId: Returns an instance of an empty value.
empty() - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
empty() - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
EMPTY_STRING - Static variable in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
EMPTY_STRING - Static variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate
EQUAL - Static variable in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
equals(Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
equals(Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
equals(Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
equals(Object) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
equals(Object) - Method in class org.monarchinitiative.lirical.core.model.Age
equals(Object) - Method in class org.monarchinitiative.lirical.core.model.AlleleCount
equals(Object) - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
equals(Object) - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
equals(Object) - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
equals(Object) - Method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
equals(Object) - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
equals(Object) - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
equals(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
equals(Object) - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
error(String, String) - Static method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue
ERROR - Enum constant in enum class org.monarchinitiative.lirical.core.sanitize.SanityLevel: Serious issues in the input data and the analysis cannot be carried on.
escapedExplanation() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation
ESP_AFRICAN_AMERICAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ESP_ALL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ESP_EUROPEAN_AMERICAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
evaluateGenotype(String, Gene2Genotype, List<TermId>) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLikelihoodRatio: Calculate the genotype likelihood ratio using lambda_disease=1 for autosomal dominant and lambda_disease=2 for autosomal recessive.
EXAC_AFRICAN_INC_AFRICAN_AMERICAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_AMERICAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_EAST_ASIAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_FINNISH - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_NON_FINNISH_EUROPEAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_OTHER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXAC_SOUTH_ASIAN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
EXACT_MATCH - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
EXCLUDED_QUERY_TERM_EXCLUDED_IN_DISEASE - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
EXCLUDED_QUERY_TERM_NOT_PRESENT_IN_DISEASE - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
EXCLUDED_QUERY_TERM_PRESENT_IN_DISEASE - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
excludedHpoTermIds() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
excludedHpoTerms() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
excludedHpoTerms() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
excludedHpoTerms() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
excludedHpoTerms() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
excludedResults() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
excludedTerms() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
execute() - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
execute() - Method in class org.monarchinitiative.lirical.cli.cmd.OutputCommand
execute() - Method in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
execute() - Method in class org.monarchinitiative.lirical.cli.cmd.DownloadCommand
execute() - Method in class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
ExomiserMvStoreMetadataServiceFactory - Class in org.monarchinitiative.lirical.exomiser_db_adapter
ExomiserMvStoreMetadataServiceFactory(Map<GenomeBuild, Path>) - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory
ExomiserResourceException - Exception in org.monarchinitiative.lirical.exomiser_db_adapter
ExomiserResourceException() - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceException(String) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceException(Throwable) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
ExomiserResourceRuntimeException - Exception in org.monarchinitiative.lirical.exomiser_db_adapter
ExomiserResourceRuntimeException() - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceRuntimeException
ExomiserResourceRuntimeException(String) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceRuntimeException
ExomiserResourceRuntimeException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceRuntimeException
ExomiserResourceRuntimeException(Throwable) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceRuntimeException
exomiserVariantDbPath(GenomeBuild, Path) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder: Set path to exomiser variant database for given GenomeBuild.
ExperimentalCommand - Class in org.monarchinitiative.lirical.cli.cmd.experimental
ExperimentalCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.experimental.ExperimentalCommand
explanation() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
explanation() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation

F

failedFilters() - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
FEMALE - Enum constant in enum class org.monarchinitiative.lirical.core.model.Sex
figureOutExomiserPath() - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
filteredOutVariantCount() - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get the count of variants annotated to this gene which failed the filtering.
FilteringStats - Record Class in org.monarchinitiative.lirical.core.model: A summary of variant input and functional annotation.
FilteringStats(long, long, long) - Constructor for record class org.monarchinitiative.lirical.core.model.FilteringStats: Creates an instance of a FilteringStats record class.
FOOTER - Static variable in class org.monarchinitiative.lirical.cli.Main
forGenomeBuild(GenomeBuild, double) - Method in class org.monarchinitiative.lirical.configuration.impl.BundledBackgroundVariantFrequencyServiceFactory
forGenomeBuild(GenomeBuild, double) - Method in interface org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyServiceFactory
forGenomeBuild(GenomeBuild, double) - Method in class org.monarchinitiative.lirical.io.background.CustomBackgroundVariantFrequencyServiceFactory
forNumber(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
forPath(Path, GenomeBuild, TranscriptDatabase) - Method in interface org.monarchinitiative.lirical.core.io.VariantParserFactory
forPath(Path, GenomeBuild, TranscriptDatabase) - Method in class org.monarchinitiative.lirical.io.vcf.VcfVariantParserFactory
forType(SanitizerType) - Method in class org.monarchinitiative.lirical.core.sanitize.InputSanitizerFactory
FRAMESHIFT_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a frameshift mutation.
frequency() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: Get variant frequency as a percentage or an empty optional if the variant has not been observed in any available variant database.
Frequency - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency
FrequencyData - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency: Frequency data for the variant from the Thousand Genomes, the Exome Server Project and Broad ExAC datasets.
frequencyForGene(TermId) - Method in interface org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyService
frequencyScore() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: This is the frequency factor used for the Exomiser like pathogenicity score.
FrequencySource - Enum Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency: Enum describing where the frequency data has originated.
fromVariants(Collection<String>, Iterable<LiricalVariant>) - Static method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
FunctionalAnnotationAware - Interface in org.monarchinitiative.lirical.core.model
FunctionalVariantAnnotator - Interface in org.monarchinitiative.lirical.core.service
functionalVariantAnnotatorService() - Method in class org.monarchinitiative.lirical.core.Lirical
FunctionalVariantAnnotatorService - Interface in org.monarchinitiative.lirical.core.service: FunctionalVariantAnnotatorService knows about FunctionalVariantAnnotators for all genome build and transcript database combinations that have been configured for a given Lirical instance.

G

Gene2Genotype - Interface in org.monarchinitiative.lirical.core.model: Gene2Genotype represents variants that have been annotated to a single gene.
geneById - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate
geneId - Variable in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
geneId() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation: Get the gene identifier for this genotype LR.
geneId() - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get the credentials of the gene.
genes() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
genes() - Method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
GenesAndGenotypes - Interface in org.monarchinitiative.lirical.core.model: Container for Gene2Genotypes present in the analysis.
genesWithVariants() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns the value of the genesWithVariants record component.
GenicIntoleranceCalculator - Class in org.monarchinitiative.lirical.background.backgroundfrequency: This class calculates the relative proportions of variants assessed as having a certain degree of pathogenicity by Exomiser.
GenicIntoleranceCalculator(GenomicAssembly, FunctionalVariantAnnotator, MVStore, boolean) - Constructor for class org.monarchinitiative.lirical.background.backgroundfrequency.GenicIntoleranceCalculator
genomeAssembly() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
genomeBuild - Variable in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
genomeBuild - Variable in class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
genomeBuild - Variable in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
genomeBuild - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
genomeBuild - Variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
genomeBuild() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
genomeBuild() - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
genomeBuild(GenomeBuild) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
GenomeBuild - Enum Class in org.monarchinitiative.lirical.core.model
GenotypedVariant - Interface in org.monarchinitiative.lirical.core.model: A description of variant coordinates, sample genotypes, and filtering status for LIRICAL analysis.
GenotypedVariantParser - Interface in org.monarchinitiative.lirical.core.io
GenotypeLikelihoodRatio - Class in org.monarchinitiative.lirical.core.likelihoodratio: This class is responsible for calculating the likelihood ratio for genotypes, as described in the Material and Methods | Likelihood Ratio for Genotypes section of the LIRICAL manuscript.
GenotypeLikelihoodRatio(BackgroundVariantFrequencyService, GenotypeLikelihoodRatio.Options) - Constructor for class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLikelihoodRatio
GenotypeLikelihoodRatio.Options - Class in org.monarchinitiative.lirical.core.likelihoodratio
genotypeLr() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
GenotypeLrMatchType - Enum Class in org.monarchinitiative.lirical.core.likelihoodratio: The enum for representing the type of the genotype likelihood ratio analysis performed for a gene.
GenotypeLrWithExplanation - Class in org.monarchinitiative.lirical.core.likelihoodratio: Results of genotype likelihood ratio evaluation for a single gene.
gestationalAge(int, int) - Static method in class org.monarchinitiative.lirical.core.model.Age: Create a gestational age to represent weeks and days.
getAccession() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getAlleleCount() - Method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
getAlleleId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string alleleId = 1;
getAlleleId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string alleleId = 1;
getAlleleId() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string alleleId = 1;
getAlleleId() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData: Get ClinVar allele ID.
getAlleleId() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getAlleleIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string alleleId = 1;
getAlleleIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string alleleId = 1;
getAlleleIdBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string alleleId = 1;
getAlleleIdString() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
getAlt() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
getAlt() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: string alt = 4;
getAlt() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: string alt = 4;
getAltBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
getAltBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: string alt = 4;
getAltBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: string alt = 4;
getAnalysisDate() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getAnchor() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getAnnotationList() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getChr() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 chr = 1;
getChr() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: int32 chr = 1;
getChr() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: int32 chr = 1;
getClinvar() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinVar() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinVarBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinvarClnSig() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
getClinVarData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData: Returns a ClinVarData object.
getClinVarOrBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinVarOrBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: TODO: move to model or somewhere and then import here - this is also needed for output in results
getClinVarOrBuilder() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: TODO: move to model or somewhere and then import here - this is also needed for output in results
getCompositeLikelihoodRatio() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getCompositeLR() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
getCompositeLR() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getDays() - Method in class org.monarchinitiative.lirical.core.model.Age
getDefaultInstance() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getDefaultInstance() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getDefaultInstance() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
getDescriptor() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
getDescriptorForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
getDescriptorForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
getDescriptorForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
getDescriptorForType() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
getDisease() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.InducedDiseaseGraph
getDiseaseAnchor() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getDiseaseCurie() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getDiseaseId() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getDiseaseName() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getDiseaseName() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getDiseaseName() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getEntrezGeneId() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getExcludedPhenotypeRatio(int) - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
getExomiserPath() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getFrequency() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
getFrequency() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getFrequencyForSource(FrequencySource) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
getFunctionalAnnotator(GenomeBuild, TranscriptDatabase) - Method in interface org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotatorService: Get FunctionalVariantAnnotator for a combination of GenomeBuild and TranscriptDatabase.
getFunctionalAnnotator(GenomeBuild, TranscriptDatabase) - Method in class org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotatorService
getGeneId() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getGeneName() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getGeneSparklineSvg() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getGeneSparklineSvg(AnalysisResults, TermId, String) - Method in class org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg
getGenesWithVar() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getGeneSymbol() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getGeneSymbol() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getGeneUrl() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.OutputCommand
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
getGenomeBuild() - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
getGenotype() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getGenotypeExplanation() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getGlobalMode() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getHgvsCdna() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getHgvsProtein() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getHpoIds() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
getHpoVersion() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getId() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId
getIncludedAlleles() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getIncludedAlleles() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: Deprecated.
getIncludedAlleles() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: Deprecated.
getIncludedAlleles() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getIncludedAllelesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
getIncludedAllelesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getIncludedAllelesCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesMap() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrDefault(String, AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrDefault(String, AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrDefault(String, AlleleProto.ClinVar.ClinSig) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesOrThrow(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getIncludedAllelesValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: Deprecated.
getIncludedAllelesValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: Deprecated.
getIncludedAllelesValueMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueMap() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrDefault(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrDefault(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrDefault(String, int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getIncludedAllelesValueOrThrow(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
getInstance() - Static method in class org.monarchinitiative.lirical.configuration.impl.BundledBackgroundVariantFrequencyServiceFactory
getKnownFrequencies() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Returns a list of Frequency objects.
getLiricalPath() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getLiricalVersion() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getMaxFreq() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Returns a the maximum frequency - if there are no known frequencies/ no frequency data it will return 0.
getMaximumIndividualLR() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult: Calculate the maximum absolute value of any individual likelihood ratio.
getMean() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.poisson.PoissonDistribution: Get the mean for the distribution.
getMemory(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
getMemory(Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
getMinimumToShowInThresholdMode() - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
getMinToShow() - Method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
getMonths() - Method in class org.monarchinitiative.lirical.core.model.Age
getMostPathogenicScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
getMostPathogenicVariantEffect() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getMutableIncludedAlleles() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getMutableIncludedAllelesValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getMutableProperties() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
getNegatedHpoIds() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
getnFilteredVariants() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getnPassingVariants() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getNumber() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
getNumberOfTests() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
getNumDifferentialsToShowSVG() - Method in class org.monarchinitiative.lirical.io.output.svg.Posttest2Svg
getObservedPhenotypeRatio(int) - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
getParserForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getParserForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getParserForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getPathogenicityScore() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getPathogenicityScoreOf(VariantEffect) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
getPosition() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 position = 2;
getPosition() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: int32 position = 2;
getPosition() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: int32 position = 2;
getPosttestBar(double) - Method in class org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg
getPosttestBarSvg() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getPosttestprob() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getPosttestProbability() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getPredictedPathogenicityScores() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
getPredictedScore(PathogenicitySource) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData: Returns the PathogenicityScore from the requested source, or null if not present.
getPretestprob() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getPrimaryInterpretation() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ClinSig primaryInterpretation = 2;
getPrimaryInterpretation() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .ClinVar.ClinSig primaryInterpretation = 2;
getPrimaryInterpretation() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .ClinVar.ClinSig primaryInterpretation = 2;
getPrimaryInterpretation() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getPrimaryInterpretationValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ClinSig primaryInterpretation = 2;
getPrimaryInterpretationValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .ClinVar.ClinSig primaryInterpretation = 2;
getPrimaryInterpretationValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .ClinVar.ClinSig primaryInterpretation = 2;
getProperties() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
getProperties() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
getProperties() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
getPropertiesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
getPropertiesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getPropertiesCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: map<string, float> properties = 2;
getPropertiesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
getPropertiesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: map<string, float> properties = 2;
getPropertiesMap() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: map<string, float> properties = 2;
getPropertiesOrDefault(String, float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
getPropertiesOrDefault(String, float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: map<string, float> properties = 2;
getPropertiesOrDefault(String, float) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: map<string, float> properties = 2;
getPropertiesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
getPropertiesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: map<string, float> properties = 2;
getPropertiesOrThrow(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: map<string, float> properties = 2;
getRank() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getRank() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getRawScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
getRawScore() - Method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore: In cases such as SIFT or CADD the raw scores as contained in that data source require scaling in order to fit the 0-1 scale used in exomiser.
getRawScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
getRef() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string ref = 3;
getRef() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: string ref = 3;
getRef() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: string ref = 3;
getRefBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string ref = 3;
getRefBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey: string ref = 3;
getRefBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder: string ref = 3;
getReviewStatus() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string reviewStatus = 4;
getReviewStatus() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string reviewStatus = 4;
getReviewStatus() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string reviewStatus = 4;
getReviewStatus() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getReviewStatusBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string reviewStatus = 4;
getReviewStatusBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string reviewStatus = 4;
getReviewStatusBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string reviewStatus = 4;
getRsId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
getRsId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: string rs_id = 1;
getRsId() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: string rs_id = 1;
getRsId() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
getRsIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
getRsIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: string rs_id = 1;
getRsIdBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: string rs_id = 1;
getSampleId() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
getSampleId() - Method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
getSampleName() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
getScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
getScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
getScore() - Method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore: A score in the range of 0-1 where 0 is considered benign and 1 to be pathogenic.
getSecondaryInterpretations() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getSecondaryInterpretations(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretations(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretations(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValue(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValueList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValueList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSecondaryInterpretationsValueList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
getSerializedSize() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getSerializedSize() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getSerializedSize() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getSource() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
getSource() - Method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
getSource() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
getSource() - Method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
getSource() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
getSparklineSvg() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getSparklineSvg(String, TestResult) - Method in class org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg
getSparklineSvg(TestResult) - Method in class org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg: This is used by Phenotype only output.
getSumOfPathBinScores(String, float) - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype
getSvg() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getSvgString() - Method in class org.monarchinitiative.lirical.io.output.svg.Lr2Svg
getSvgString() - Method in class org.monarchinitiative.lirical.io.output.svg.Posttest2Svg
getThreshold() - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
getTranscriptDatabase() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getUcsc() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getUnknownFields() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
getUnknownFields() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
getUnknownFields() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getUrl() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
getVarcount() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getVariantEffect() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getVariantEffects() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getVariantMetadataService(GenomeBuild) - Method in interface org.monarchinitiative.lirical.core.service.VariantMetadataServiceFactory
getVariantMetadataService(GenomeBuild) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory
getVarString() - Method in class org.monarchinitiative.lirical.io.output.TsvDifferential
getVisualizableVariants() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getWeeks() - Method in class org.monarchinitiative.lirical.core.model.Age
getWriter(OutputFormat) - Method in interface org.monarchinitiative.lirical.core.output.AnalysisResultWriterFactory: Get AnalysisResultsWriter or an empty Optional if the factory does not know about an AnalysisResultsWriter for the given OutputFormat.
getYears() - Method in class org.monarchinitiative.lirical.core.model.Age
GNOMAD_E_AFR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_AMR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_ASJ - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_EAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_FIN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_NFE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_OTH - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_SAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_AFR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_AMR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_ASJ - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_EAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_FIN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_NFE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_OTH - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_SAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_SV - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GONL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GREEN - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

H

hasClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
hasClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: TODO: move to model or somewhere and then import here - this is also needed for output in results
hasClinVar() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: TODO: move to model or somewhere and then import here - this is also needed for output in results
hasClinVarData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData: Method used to check whether there is any real ClinVar data associated with this object.
hasDbSnpData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hasDbSnpRsID() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hasDeleteriousVariants() - Method in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Returns true if the genotype LR match indicates that the enclosing GenotypeLrWithExplanation was created for a gene that contains deleterious variants.
hasErrorOrWarnings() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationResult
hasErrors() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationResult
hasEspData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hasExacData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hasFrequencyOverPercentageValue(float) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: This function tests whether or not this FrequencyData object contains a Frequency object which has a frequency greater than the maximum frequency provided.
hasGenotypeExplanation() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
hashCode() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
hashCode() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
hashCode() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
hashCode() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
hashCode() - Method in class org.monarchinitiative.lirical.core.model.Age
hashCode() - Method in class org.monarchinitiative.lirical.core.model.AlleleCount
hashCode() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
hashCode() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns a hash code value for this object.
hashCode() - Method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
hashCode() - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
hashCode() - Method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
hashCode() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
hashCode() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns a hash code value for this object.
hashCode() - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
hashCode() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
hashCode() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
hasKnownFrequency() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
hasPredictedScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
hasPredictedScore(PathogenicitySource) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
hasVariants() - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype
hasVariants() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis: The answer to this string is used by the FreeMarker template to determine whether or not to show a table with variants.
HG19 - Enum constant in enum class org.monarchinitiative.lirical.core.model.GenomeBuild
hg19RefseqTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
hg19UcscTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
HG38 - Enum constant in enum class org.monarchinitiative.lirical.core.model.GenomeBuild
hg38RefseqTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
hg38UcscTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
hgncCompleteSet() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
HIGH_NUMBER_OF_OBSERVED_PREDICTED_PATHOGENIC_VARIANTS - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Heuristic for the case where we have more called pathogenic variants than we should have in a gene without a high background count -- we will model this as technical error and will take the observed path weighted count to not be more than λ_disease.
hpo() - Method in interface org.monarchinitiative.lirical.core.service.PhenotypeService
hpoJson() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
HpoTermSanitizer - Class in org.monarchinitiative.lirical.core.service
HpoTermSanitizer(MinimalOntology) - Constructor for class org.monarchinitiative.lirical.core.service.HpoTermSanitizer
HTML - Enum constant in enum class org.monarchinitiative.lirical.core.output.OutputFormat
HtmlTemplate - Class in org.monarchinitiative.lirical.io.output: This class coordinates getting the data from the analysis into the FreeMark org.monarchinitiative.lirical.output templates.

I

ImprobableDifferential - Class in org.monarchinitiative.lirical.io.output: This class arranges data for genes that do not have a probable differential diagnosis.
ImprobableDifferential(String, String, String, double, int) - Constructor for class org.monarchinitiative.lirical.io.output.ImprobableDifferential: Construct a data opbject for display in FreeMarker template (which requires a public constructor)
includedAlleles(Map<String, ClinVarData.ClinSig>) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
INCLUDEDALLELES_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
includeDiseasesWithNoDeleteriousVariants() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions: Include a disease if no known or predicted deleterious variants are found in the gene associated with the disease.
includeDiseasesWithNoDeleteriousVariants(boolean) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
InducedDiseaseGraph - Class in org.monarchinitiative.lirical.core.likelihoodratio: For some calculations of the phenotype likelihood ratio, we need to traverse the graph induced by the HPO terms to which a disease is annotated.
InputSanitizer - Interface in org.monarchinitiative.lirical.core.sanitize: Sanitize the user input before running the analysis.
InputSanitizerFactory - Class in org.monarchinitiative.lirical.core.sanitize: Get the input sanitizer with required level
InputSanitizerFactory(MinimalOntology) - Constructor for class org.monarchinitiative.lirical.core.sanitize.InputSanitizerFactory
instance() - Static method in class org.monarchinitiative.lirical.core.service.NoOpVariantMetadataService
INSTANCE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
INSTANCE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
internalGetMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
internalGetMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
internalGetMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
internalGetMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
internalGetMutableMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
internalGetMutableMapField(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
internalGetValueMap() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
InvalidAlleleProtoException - Exception in org.monarchinitiative.lirical.exomiser_db_adapter.serializers
InvalidAlleleProtoException(Exception) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.serializers.InvalidAlleleProtoException
INVERSION_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
isBenignOrLikelyBenign() - Method in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
isEmpty() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
isEmpty() - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
isEmpty() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId
isEmpty() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
isEmpty() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
isExactExcludedMatch(TermId) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.InducedDiseaseGraph: See comments about InducedDiseaseGraph.inducedNegativeGraph.
isGestational() - Method in class org.monarchinitiative.lirical.core.model.Age
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
isOverThreshold(float) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
isPassingPathogenicThreshold() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
isPathogenicOrLikelyPathogenic() - Method in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
isPostnatal() - Method in class org.monarchinitiative.lirical.core.model.Age
isRepresentedInDatabase() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
isSecondaryAssociationRiskFactorOrOther() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
isSetByUser() - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
isSetByUser() - Method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
issues() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationResult
iterator() - Method in class org.monarchinitiative.lirical.io.vcf.VcfGenotypedVariantParser

J

JannovarFunctionalVariantAnnotator - Class in org.monarchinitiative.lirical.io.service
JannovarFunctionalVariantAnnotatorService - Class in org.monarchinitiative.lirical.io.service
JSON - Enum constant in enum class org.monarchinitiative.lirical.core.output.OutputFormat
JsonAnalysisResultWriter - Class in org.monarchinitiative.lirical.io.output

L

LENIENT - Enum constant in enum class org.monarchinitiative.lirical.cli.cmd.ValidationPolicy: Run the analysis if the user input contains non-controversial issues that can be fixed automatically.
LESS_PATHOGENIC - Static variable in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
level() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns the value of the level record component.
LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: LIKELY_BENIGN = 3;
LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
LIKELY_BENIGN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
LIKELY_BENIGN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: LIKELY_BENIGN = 3;
LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: LIKELY_PATHOGENIC = 5;
LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
LIKELY_PATHOGENIC_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: LIKELY_PATHOGENIC = 5;
Lirical - Class in org.monarchinitiative.lirical.core
LIRICAL_GT_MODEL - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Gene scored using LIRICAL genotype LR model.
Lirical2Svg - Class in org.monarchinitiative.lirical.io.output.svg
Lirical2Svg() - Constructor for class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
LiricalAnalysisException - Exception in org.monarchinitiative.lirical.core.analysis: An exception thrown by LiricalAnalysisRunner if the analysis cannot be run.
LiricalAnalysisException() - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisException(String) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisException(Throwable) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
LiricalAnalysisRunner - Interface in org.monarchinitiative.lirical.core.analysis: The analysis runner runs LIRICAL analysis on provided analysis subject (AnalysisData).
LiricalAnalysisRunnerImpl - Class in org.monarchinitiative.lirical.core.analysis.impl
LiricalBuilder - Class in org.monarchinitiative.lirical.configuration
LiricalDataException - Exception in org.monarchinitiative.lirical.io: An exception thrown when data error (missing resource, invalid resource file, etc.) is detected.
LiricalDataException() - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataException(String) - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataException(Throwable) - Constructor for exception org.monarchinitiative.lirical.io.LiricalDataException
LiricalDataResolver - Class in org.monarchinitiative.lirical.io
LiricalException - Exception in org.monarchinitiative.lirical.core.exception
LiricalException() - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalException(String) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalException(Throwable) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalException
LiricalOptions - Class in org.monarchinitiative.lirical.core: Global options to parameterize LIRICAL execution.
LiricalOptions(String, int) - Constructor for class org.monarchinitiative.lirical.core.LiricalOptions
LiricalParseException - Exception in org.monarchinitiative.lirical.core.analysis: An exception thrown when user-provided input is invalid.
LiricalParseException() - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalParseException(String) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalParseException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalParseException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalParseException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalParseException(Throwable) - Constructor for exception org.monarchinitiative.lirical.core.analysis.LiricalParseException
LiricalRuntimeException - Exception in org.monarchinitiative.lirical.core.exception
LiricalRuntimeException() - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalRuntimeException
LiricalRuntimeException(String) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalRuntimeException
LiricalRuntimeException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalRuntimeException
LiricalRuntimeException(Throwable) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalRuntimeException
LiricalTemplate - Class in org.monarchinitiative.lirical.io.output: This is the superclass for TsvTemplate and HtmlTemplate, and provides common methods for setting up the data prior to output as either tab-separated values (TSV) or HTML.
LiricalTemplate(MinimalOntology, AnalysisData, AnalysisResultsMetadata, OutputOptions) - Constructor for class org.monarchinitiative.lirical.io.output.LiricalTemplate
LiricalTermFrequencyException - Exception in org.monarchinitiative.lirical.core.exception
LiricalTermFrequencyException() - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalTermFrequencyException
LiricalTermFrequencyException(String) - Constructor for exception org.monarchinitiative.lirical.core.exception.LiricalTermFrequencyException
LiricalVariant - Interface in org.monarchinitiative.lirical.core.model
LOCAL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
log() - Method in class org.monarchinitiative.lirical.core.analysis.ProgressReporter: Log processing of an item.
log10Lr() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation: Get the log₁₀ LR for the gene.
lr() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation: Get the genotype likelihood ratio for the gene.
lr() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation
Lr2Svg - Class in org.monarchinitiative.lirical.io.output.svg: This class creates an SVG file representing the results of likelihood ratio analysis of an HPO case.
Lr2Svg(TestResult, int, TermId, String, MinimalOntology, String) - Constructor for class org.monarchinitiative.lirical.io.output.svg.Lr2Svg: Constructor to draw an SVG representation of the phenotype and genotype likelihood ratios
lrForExcludedTerm(TermId, InducedDiseaseGraph) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio: Calculate and return the likelihood ratio of an EXCLUDED HPO feature tid in an individual with the disease "diseaseId"
lrForObservedTerm(TermId, InducedDiseaseGraph) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio: Calculate and return the likelihood ratio of observing the HPO feature queryTid in an individual with the disease idg (note that the InducedDiseaseGraph contains information about the annotations of the disease that we use to calculate the likelihood ratios).
LrMatchType - Enum Class in org.monarchinitiative.lirical.core.likelihoodratio
lrThreshold - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
lrThreshold() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
LrThreshold - Class in org.monarchinitiative.lirical.core.output: This class encapsulates the likelihood ratio threshold, which is an optional user argument (-t).
LrWithExplanation - Class in org.monarchinitiative.lirical.core.likelihoodratio: There are five possible ways that a query term can match a disease term.
LrWithExplanationFactory - Class in org.monarchinitiative.lirical.core.likelihoodratio
LrWithExplanationFactory(MinimalOntology) - Constructor for class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanationFactory

M

M_CAP - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
main(String[]) - Static method in class org.monarchinitiative.lirical.background.Main
main(String[]) - Static method in class org.monarchinitiative.lirical.cli.Main
Main - Class in org.monarchinitiative.lirical.background
Main - Class in org.monarchinitiative.lirical.cli
Main() - Constructor for class org.monarchinitiative.lirical.background.Main
Main() - Constructor for class org.monarchinitiative.lirical.cli.Main
MALE - Enum constant in enum class org.monarchinitiative.lirical.core.model.Sex
matchingTerm() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation
matchType() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation: Get the genotype LR match type.
matchType() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation
mergeClinVar(AlleleProto.ClinVar) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
mergeFrom(Message) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
mergeFrom(Message) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
mergeFrom(Message) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
mergeFrom(AlleleProto.AlleleKey) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
mergeFrom(AlleleProto.AlleleProperties) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
mergeFrom(AlleleProto.ClinVar) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
mergeUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
mergeUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
mergeUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
message() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns the value of the message record component.
metadata(GenomicVariant, List<VariantEffect>) - Method in class org.monarchinitiative.lirical.core.service.NoOpVariantMetadataService
metadata(GenomicVariant, List<VariantEffect>) - Method in interface org.monarchinitiative.lirical.core.service.VariantMetadataService
mim2geneMedgen() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
MIN_VERTICAL_OFFSET - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg: minimum distance to top of image of graphic elements
minDiagnosisCount() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
MinDiagnosisCount - Class in org.monarchinitiative.lirical.core.output: This class encapsulates the minimum number of diagnoses to show, which is an optional user argument (-m).
minDifferentialsToShow - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
MINIMAL - Enum constant in enum class org.monarchinitiative.lirical.cli.cmd.ValidationPolicy: Run the bare minimum of checks required to run the analysis but not even a bit more.
MINIMAL - Enum constant in enum class org.monarchinitiative.lirical.core.sanitize.SanitizerType: Minimal sanitizer performs the minimal checks required for the analysis to runnable.
mkdirIfNotExist(Path) - Static method in class org.monarchinitiative.lirical.io.output.LiricalTemplate
MORE_PATHOGENIC - Static variable in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
MPC - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
MpcScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: A deleteriousness prediction score for missense variants based on regional missense constraint.
MTASTER_THRESHOLD - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
MUTATION_TASTER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
MutationTasterScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
MVP - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
MvStoreUtil - Class in org.monarchinitiative.lirical.exomiser_db_adapter: Utility class for helping read and write Alleles to the MVStore

N

negated - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
negatedPhenotypeTerms() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
newBuilder() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
newBuilder() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
newBuilder() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
newBuilder(AlleleProto.AlleleKey) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
newBuilder(AlleleProto.AlleleProperties) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
newBuilder(AlleleProto.ClinVar) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
newBuilderForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
newBuilderForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
newBuilderForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
newBuilderForType(GeneratedMessageV3.BuilderParent) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
newBuilderForType(GeneratedMessageV3.BuilderParent) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
newBuilderForType(GeneratedMessageV3.BuilderParent) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
newInstance(GeneratedMessageV3.UnusedPrivateParameter) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
newInstance(GeneratedMessageV3.UnusedPrivateParameter) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
newInstance(GeneratedMessageV3.UnusedPrivateParameter) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
nFilteredVariants() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns the value of the nFilteredVariants record component.
NO_MATCH_BELOW_ROOT - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
NO_VARIANTS_DETECTED_AD - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: No variants were detected in a gene associated with a disease with autosomal dominant inheritance.
NO_VARIANTS_DETECTED_AR - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: No variants were detected in a gene associated with a disease with autosomal recessive inheritance.
NON_PATHOGENIC_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Pathogenicity score for a mutation class such as INTERGENIC where we are entirely sure it is nonpathogenic (for the purposes of this software).
NON_ROOT_COMMON_ANCESTOR - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
NONFRAMESHIFT_INDEL_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a nonframeshift indel mutation.
NONSENSE_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a nonsense mutation.
noOpFactory() - Static method in interface org.monarchinitiative.lirical.core.io.VariantParserFactory: Get a factory that can be used when LIRICAL seems to be configured for phenotype only analyses.
noOpFactory() - Static method in interface org.monarchinitiative.lirical.core.service.VariantMetadataServiceFactory
NoOpVariantMetadataService - Class in org.monarchinitiative.lirical.core.service: A VariantMetadataService implementation used when the variant data is not available.
NOT_AVAILABLE - Static variable in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
NOT_PROVIDED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: default
NOT_PROVIDED - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
NOT_PROVIDED - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
NOT_PROVIDED_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: default
notBenignOrLikelyBenign() - Method in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
notInitialized() - Static method in class org.monarchinitiative.lirical.core.output.LrThreshold
notInitialized() - Static method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
nPassingVariants() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns the value of the nPassingVariants record component.

O

observed - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
observedResults() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
observedTerms() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
of() - Static method in class org.monarchinitiative.lirical.io.output.JsonAnalysisResultWriter
of(byte, byte) - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.CaddScore: Creates a CaddScore from the input PHRED scaled score.
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore: Static factory for creating MpcScore objects.
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
of(float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SiftScore
of(float, float, ClinVarAlleleData) - Static method in interface org.monarchinitiative.lirical.core.model.VariantMetadata
of(float, ClinvarClnSig) - Static method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
of(int) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId: Returns new RsId from the integer provided.
of(int, int) - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount
of(int, int, int) - Static method in class org.monarchinitiative.lirical.core.model.Age: Create a postnatal age from given inputs.
of(JannovarData, GeneIdentifiers) - Static method in class org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotator
of(String) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId: Parses rs ids from their VCF representation - can be in the form "rs123456", "123456" or "." for an empty value.
of(String, Collection<Frequency>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(String, Age, Sex, Collection<TermId>, Collection<TermId>, GenesAndGenotypes) - Static method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData: Construct analysis data from the inputs.
of(String, AlleleCount) - Static method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
of(String, LiricalVariant, boolean) - Static method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
of(String, Frequency) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(String, Frequency...) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(Path) - Static method in class org.monarchinitiative.lirical.io.LiricalDataResolver
of(Collection<String>, Collection<Gene2Genotype>) - Static method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
of(Collection<Frequency>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(Collection<PathogenicityScore>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(List<TestResult>) - Static method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
of(Map<GenomeBuild, Path>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory
of(Map<GenomeBuild, Path>) - Static method in class org.monarchinitiative.lirical.io.background.CustomBackgroundVariantFrequencyServiceFactory
of(Map<TermId, Double>) - Static method in interface org.monarchinitiative.lirical.core.analysis.probability.PretestDiseaseProbability
of(Map<TermId, Double>, double) - Static method in interface org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyService
of(VariantParserFactory, PhenotypeService, BackgroundVariantFrequencyServiceFactory, VariantMetadataServiceFactory, FunctionalVariantAnnotatorService, AnalysisResultWriterFactory, LiricalOptions) - Static method in class org.monarchinitiative.lirical.core.Lirical
of(ClinvarClnSig, Long) - Static method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
of(GenomeBuild, GenomicVariant, Collection<SampleAlleleCount>, boolean) - Static method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
of(GenotypedVariant, List<TranscriptAnnotation>, VariantMetadata) - Static method in interface org.monarchinitiative.lirical.core.model.LiricalVariant
of(FunctionalVariantAnnotatorService, VariantMetadataServiceFactory) - Static method in class org.monarchinitiative.lirical.io.vcf.VcfVariantParserFactory
of(PhenotypeService, BackgroundVariantFrequencyServiceFactory, int) - Static method in class org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl
of(Frequency) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(Frequency...) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
of(FrequencySource, float) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
of(ClinVarData, Collection<PathogenicityScore>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(ClinVarData, PathogenicityScore) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(ClinVarData, PathogenicityScore...) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(PathogenicityScore) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(PathogenicityScore...) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
of(PathogenicitySource, float) - Static method in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore: Static factory constructor to simplify creation of new PathogenicityScore objects.
of(LiricalDataResolver, GeneIdentifiers) - Static method in class org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotatorService
of(GeneIdentifier, double, String) - Static method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation: Deprecated, for removal: This API element is subject to removal in a future version.
the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrWithExplanation.of(GeneIdentifier, GenotypeLrMatchType, double, String) instead.
of(GeneIdentifier, Collection<LiricalVariant>, int) - Static method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Create Gene2Genotype from provided data.
of(GeneIdentifier, GenotypeLrMatchType, double, String) - Static method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
of(MinimalOntology, HpoDiseases, HpoAssociationData) - Static method in interface org.monarchinitiative.lirical.core.service.PhenotypeService
of(TermId, double, List<LrWithExplanation>, List<LrWithExplanation>, GenotypeLrWithExplanation) - Static method in class org.monarchinitiative.lirical.core.analysis.TestResult
of(TermId, TermId, LrMatchType, double, String) - Static method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation
ONE_DELETERIOUS_CLINVAR_VARIANT_IN_AD - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Deprecated, for removal: This API element is subject to removal in a future version.
the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD instead.
ONE_DELETERIOUS_VARIANT_IN_AR - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: One deleterious allele detected with autosomal recessive disease.
ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: One ClinVar pathogenic or likely pathogenic allele discovered in a disease with autosomal dominant inheritance.
oneOne() - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount
openAlleleMVMap(MVStore) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.MvStoreUtil: Opens the 'alleles' map from the MVStore.
Options(float, boolean) - Constructor for class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLikelihoodRatio.Options
ORANGE - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
org.monarchinitiative.exomiser.core.proto - package org.monarchinitiative.exomiser.core.proto
org.monarchinitiative.lirical.background - package org.monarchinitiative.lirical.background
org.monarchinitiative.lirical.background.backgroundfrequency - package org.monarchinitiative.lirical.background.backgroundfrequency: Classes related to calculating the distribution of pathogenicity scores of ClinVar or all GNOMAD variants.
org.monarchinitiative.lirical.cli - package org.monarchinitiative.lirical.cli
org.monarchinitiative.lirical.cli.cmd - package org.monarchinitiative.lirical.cli.cmd: Commands to run LIRICAL in different configurations.
org.monarchinitiative.lirical.cli.cmd.experimental - package org.monarchinitiative.lirical.cli.cmd.experimental: Package with experimental LIRICAL commands.
org.monarchinitiative.lirical.cli.cmd.util - package org.monarchinitiative.lirical.cli.cmd.util
org.monarchinitiative.lirical.cli.yaml - package org.monarchinitiative.lirical.cli.yaml: Read user input formatted into YAML file.
org.monarchinitiative.lirical.configuration - package org.monarchinitiative.lirical.configuration
org.monarchinitiative.lirical.configuration.impl - package org.monarchinitiative.lirical.configuration.impl
org.monarchinitiative.lirical.core - package org.monarchinitiative.lirical.core: Core functionality of the LIRICAL algorithm.
org.monarchinitiative.lirical.core.analysis - package org.monarchinitiative.lirical.core.analysis: A high-level representation of LIRICAL analysis.
org.monarchinitiative.lirical.core.analysis.impl - package org.monarchinitiative.lirical.core.analysis.impl: Default LIRICAL analysis implementation.
org.monarchinitiative.lirical.core.analysis.probability - package org.monarchinitiative.lirical.core.analysis.probability: Model of pretest probability of diseases.
org.monarchinitiative.lirical.core.exception - package org.monarchinitiative.lirical.core.exception: Top-level exceptions.
org.monarchinitiative.lirical.core.io - package org.monarchinitiative.lirical.core.io: APIs for reading and annotation of genomic variants.
org.monarchinitiative.lirical.core.likelihoodratio - package org.monarchinitiative.lirical.core.likelihoodratio: Package with logic for calculation of likelihood ratios for phenotypic or genotypic test results.
org.monarchinitiative.lirical.core.likelihoodratio.poisson - package org.monarchinitiative.lirical.core.likelihoodratio.poisson: Classes in this package were slightly adapted from the Apache Math version 3 library and remain under the Apache License, Version 2.0.
org.monarchinitiative.lirical.core.model - package org.monarchinitiative.lirical.core.model: Package with data models.
org.monarchinitiative.lirical.core.output - package org.monarchinitiative.lirical.core.output: Base data model for writing out the results of LIRICAL analysis.
org.monarchinitiative.lirical.core.sanitize - package org.monarchinitiative.lirical.core.sanitize: Sanitize the user-provided SanitationInputs.
org.monarchinitiative.lirical.core.service - package org.monarchinitiative.lirical.core.service: Package with services used across LIRICAL.
org.monarchinitiative.lirical.core.util - package org.monarchinitiative.lirical.core.util: Package with utility methods such as binary search with custom comparator for extracting the sorting key.
org.monarchinitiative.lirical.exomiser_db_adapter - package org.monarchinitiative.lirical.exomiser_db_adapter
org.monarchinitiative.lirical.exomiser_db_adapter.model - package org.monarchinitiative.lirical.exomiser_db_adapter.model
org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency - package org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency
org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity - package org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
org.monarchinitiative.lirical.exomiser_db_adapter.serializers - package org.monarchinitiative.lirical.exomiser_db_adapter.serializers
org.monarchinitiative.lirical.io - package org.monarchinitiative.lirical.io: Parsers for LIRICAL.
org.monarchinitiative.lirical.io.analysis - package org.monarchinitiative.lirical.io.analysis: Read user input formatted as a v1 or v2 phenopacket.
org.monarchinitiative.lirical.io.background - package org.monarchinitiative.lirical.io.background
org.monarchinitiative.lirical.io.output - package org.monarchinitiative.lirical.io.output: Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.
org.monarchinitiative.lirical.io.output.svg - package org.monarchinitiative.lirical.io.output.svg: Classes to create an SVG graphic representing the result of likelihood raio analysis of one HPO Case.
org.monarchinitiative.lirical.io.service - package org.monarchinitiative.lirical.io.service
org.monarchinitiative.lirical.io.vcf - package org.monarchinitiative.lirical.io.vcf
OTHER - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: OTHER = 12;
OTHER - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
OTHER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
OTHER_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: OTHER = 12;
outdir - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
outfilePrefix - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output: Prefix of the output file.
output - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand
Output() - Constructor for class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
OutputCommand - Class in org.monarchinitiative.lirical.cli.cmd
OutputCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.OutputCommand
OutputCommand.Output - Class in org.monarchinitiative.lirical.cli.cmd
outputDirectory() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
outputFile() - Method in class org.monarchinitiative.lirical.io.output.HtmlTemplate
outputFile() - Method in class org.monarchinitiative.lirical.io.output.TsvTemplate
OutputFormat - Enum Class in org.monarchinitiative.lirical.core.output: LIRICAL supports writing results in these formats.
outputFormats - Variable in class org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
outputFormatString() - Method in class org.monarchinitiative.lirical.io.output.HtmlTemplate
outputFormatString() - Method in class org.monarchinitiative.lirical.io.output.LiricalTemplate
outputFormatString() - Method in class org.monarchinitiative.lirical.io.output.TsvTemplate
OutputOptions - Class in org.monarchinitiative.lirical.core.output
OutputOptions(LrThreshold, MinDiagnosisCount, float, boolean, boolean, Path, String) - Constructor for class org.monarchinitiative.lirical.core.output.OutputOptions
outputPath - Variable in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
outputPath - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate
overwrite - Variable in class org.monarchinitiative.lirical.cli.cmd.DownloadCommand

P

parallelism() - Method in class org.monarchinitiative.lirical.core.LiricalOptions
parallelism(int) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder: Set the number threads/workers in the LIRICAL worker pool.
parse(BufferedReader) - Static method in class org.monarchinitiative.lirical.io.background.BackgroundVariantFrequencyParser: symbol geneID freqsum-benign count-benign freqsum-path count-path
parse(InputStream) - Static method in class org.monarchinitiative.lirical.cli.yaml.YamlParser
parse(String) - Static method in enum class org.monarchinitiative.lirical.core.model.GenomeBuild
parse(String) - Static method in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase
parse(String) - Static method in enum class org.monarchinitiative.lirical.core.output.OutputFormat
parse(Path) - Static method in class org.monarchinitiative.lirical.cli.yaml.YamlParser
parse(Period) - Static method in class org.monarchinitiative.lirical.core.model.Age
parseAge() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData: Try to parse the age and return an empty optional if the parsing fails.
parseDelimitedFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseDelimitedFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseDelimitedFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(byte[]) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(byte[]) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(byte[]) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(byte[], ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(byte[], ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(byte[], ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(ByteString) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(ByteString) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(ByteString) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(CodedInputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(CodedInputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(CodedInputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(ByteBuffer) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(ByteBuffer) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(ByteBuffer) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseFrom(ByteBuffer, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parseFrom(ByteBuffer, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parseFrom(ByteBuffer, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseGenomeBuild(String) - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
parser() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
parser() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
parser() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
parseSex() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData: Try to parse the sex and return an empty optional if the parsing fails.
passedFilters() - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
PATHOGENIC - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PATHOGENIC = 7;
PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
PATHOGENIC_OR_LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PATHOGENIC_OR_LIKELY_PATHOGENIC = 6;
PATHOGENIC_OR_LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
PATHOGENIC_OR_LIKELY_PATHOGENIC - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
PATHOGENIC_OR_LIKELY_PATHOGENIC_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PATHOGENIC_OR_LIKELY_PATHOGENIC = 6;
PATHOGENIC_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PATHOGENIC = 7;
pathogenicClinVarAlleleCount(String) - Method in interface org.monarchinitiative.lirical.core.model.LiricalVariant: Count the number of ClinVar-pathogenic alleles.
pathogenicClinVarCount(String) - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get the number of predicted pathogenic/deleterious alleles in the gene for the sampleId.
pathogenicity() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: Get estimate of the overall variant pathogenicity.
pathogenicity() - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
PathogenicityData - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: Container for Pathogenicity data about a variant.
pathogenicityScore() - Method in interface org.monarchinitiative.lirical.core.model.VariantMetadata: Get aggregated variant pathogenicity score.
PathogenicityScore - Interface in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
PathogenicitySource - Enum Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: Enum representing the pathogenicity prediction method/database used to calculate a given score.
pathogenicityThreshold() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
PhenopacketCommand - Class in org.monarchinitiative.lirical.cli.cmd: Run LIRICAL from a Phenopacket -- with or without accompanying VCF file.
PhenopacketCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
PhenopacketData - Class in org.monarchinitiative.lirical.io.analysis: Phenopacket attributes that are relevant for LIRICAL.
PhenopacketImporter - Interface in org.monarchinitiative.lirical.io.analysis: Decode phenopacket data from an input stream.
PhenopacketImporters - Class in org.monarchinitiative.lirical.io.analysis: Get PhenopacketImporters to ingest v1 or v2 phenopackets.
PhenopacketImportException - Exception in org.monarchinitiative.lirical.io.analysis
PhenopacketImportException() - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
PhenopacketImportException(String) - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
PhenopacketImportException(String, Exception) - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
PhenopacketImportException(String, Throwable) - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
PhenopacketImportException(String, Throwable, boolean, boolean) - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
PhenopacketImportException(Throwable) - Constructor for exception org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
phenopacketIsEligibleForAnalysis(SanitationResult, ValidationPolicy) - Static method in class org.monarchinitiative.lirical.cli.cmd.util.Util
phenopacketPath - Variable in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
phenopacketPaths - Variable in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
phenopacketPaths - Variable in class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
PhenopacketsCommand - Class in org.monarchinitiative.lirical.cli.cmd.experimental: Run LIRICAL in phenotype-only mode on a collection of phenopackets.
PhenopacketsCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
PhenopacketUtil - Class in org.monarchinitiative.lirical.cli.cmd
phenotypeAnnotations() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
PhenotypeLikelihoodRatio - Class in org.monarchinitiative.lirical.core.likelihoodratio: This class is designed to calculate the background and foreground frequencies of any HPO term in any disease (This is calculated by PhenotypeLikelihoodRatio.initializeFrequencyMap() and stored in PhenotypeLikelihoodRatio.hpoTerm2OverallFrequency).
PhenotypeLikelihoodRatio(MinimalOntology, HpoDiseases) - Constructor for class org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio
phenotypeOnly - Variable in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
phenotypeService() - Method in class org.monarchinitiative.lirical.core.Lirical
phenotypeService(PhenotypeService) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
PhenotypeService - Interface in org.monarchinitiative.lirical.core.service
PoissonDistribution - Class in org.monarchinitiative.lirical.core.likelihoodratio.poisson: This class and the other classes in this package were adapted and mainly copied from the Apache Math package.
PoissonDistribution(double) - Constructor for class org.monarchinitiative.lirical.core.likelihoodratio.poisson.PoissonDistribution
POLYPHEN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
POLYPHEN_PROB_DAMAGING_THRESHOLD - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore: A polyphen2 score above this threshold is probably damaging
POLYPHEN_THRESHOLD - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore: Possibly damaging is > 0.446 with Polyphen2 (this is an intermediate category, thus, we are not being extremely strict with the polyphen filter).
PolyPhenScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: PolyPhen (polymorphism phenotyping) score.
pos() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
POSITION_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
Posttest2Svg - Class in org.monarchinitiative.lirical.io.output.svg
Posttest2Svg(AnalysisResults, HpoDiseases, double, int) - Constructor for class org.monarchinitiative.lirical.io.output.svg.Posttest2Svg
posttestOdds() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
posttestProbability() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
prefix() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
prepareAnalysisOptions(Lirical, GenomeBuild, TranscriptDatabase) - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
presentHpoTermIds() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
presentHpoTerms() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
presentHpoTerms() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
presentHpoTerms() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
presentHpoTerms() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
presentPhenotypeTerms() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
PretestDiseaseProbabilities - Class in org.monarchinitiative.lirical.core.analysis.probability: A collection of PretestDiseaseProbability instances.
pretestDiseaseProbability() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
PretestDiseaseProbability - Interface in org.monarchinitiative.lirical.core.analysis.probability: Implementors provide pretest probability for observing a disease.
pretestOdds() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
pretestProbability() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
pretestProbability(PretestDiseaseProbability) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
pretestProbability(TermId) - Method in interface org.monarchinitiative.lirical.core.analysis.probability.PretestDiseaseProbability
prettifyDiseaseName(String) - Method in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg: This method shortens items such as #101200 APERT SYNDROME;;ACROCEPHALOSYNDACTYLY, TYPE I; ACS1;;ACS IAPERT-CROUZON DISEASE, INCLUDED;; to simply APERT SYNDROME
primaryInterpretation(ClinVarData.ClinSig) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
PRIMARYINTERPRETATION_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
PRIMATE_AI - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
PrioritizeCommand - Class in org.monarchinitiative.lirical.cli.cmd
PrioritizeCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
probability(double) - Method in class org.monarchinitiative.lirical.core.likelihoodratio.poisson.PoissonDistribution
process(AnalysisData, AnalysisResults, AnalysisResultsMetadata, OutputOptions) - Method in interface org.monarchinitiative.lirical.core.output.AnalysisResultsWriter: Write the provided AnalysisData, AnalysisResults and AnalysisResultsMetadata into some OutputFormat as guided by OutputOptions.
process(AnalysisData, AnalysisResults, AnalysisResultsMetadata, OutputOptions) - Method in class org.monarchinitiative.lirical.io.output.JsonAnalysisResultWriter
process(AnalysisData, AnalysisResults, AnalysisResultsMetadata, OutputOptions) - Method in class org.monarchinitiative.lirical.io.output.TemplateBasedAnalysisResultsWriter
procureSanitationInputs() - Method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
procureSanitationInputs() - Method in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
procureSanitationInputs() - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
ProgressReporter - Class in org.monarchinitiative.lirical.core.analysis: Class for pretty progress reporting using logger.
ProgressReporter() - Constructor for class org.monarchinitiative.lirical.core.analysis.ProgressReporter: Report each 5,000-th item using ProgressReporter.DEFAULT_COLLECTION_ITEM_NAME.
ProgressReporter(int) - Constructor for class org.monarchinitiative.lirical.core.analysis.ProgressReporter: Report each n-th item using ProgressReporter.DEFAULT_COLLECTION_ITEM_NAME.
ProgressReporter(int, String) - Constructor for class org.monarchinitiative.lirical.core.analysis.ProgressReporter: Report each n-th item using provided progress message template.
PROPERTIES_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
PROTECTIVE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PROTECTIVE = 13;
PROTECTIVE - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
PROTECTIVE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
PROTECTIVE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: PROTECTIVE = 13;
putAllIncludedAlleles(Map<String, AlleleProto.ClinVar.ClinSig>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
putAllIncludedAllelesValue(Map<String, Integer>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
putAllProperties(Map<String, Float>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
putIncludedAlleles(String, AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
putIncludedAllelesValue(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
putProperties(String, float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;

Q

QUERY_TERM_PRESENT_BUT_EXCLUDED_IN_DISEASE - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
QUERY_TERM_SUBCLASS_OF_DISEASE_TERM - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
queryTerm() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation

R

rank() - Method in class org.monarchinitiative.lirical.io.output.svg.Lr2Svg
rawScore - Variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
read(InputStream) - Method in interface org.monarchinitiative.lirical.io.analysis.PhenopacketImporter
read(ByteBuffer) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
read(ByteBuffer) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
read(ByteBuffer, Object[], int, boolean) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
read(ByteBuffer, Object[], int, boolean) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
readPhenopacketData(Path) - Static method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketUtil
readVariantsFromVcfFile(String, Path, GenomeBuild, TranscriptDatabase, VariantParserFactory) - Static method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
RED - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
ref() - Method in class org.monarchinitiative.lirical.core.model.AlleleCount
ref() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
REF_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
REFSEQ - Enum constant in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase
registerAllExtensions(ExtensionRegistry) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
registerAllExtensions(ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
REMM - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
RemmScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: REMM info.
removeIncludedAlleles(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
removeProperties(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: map<string, float> properties = 2;
replaceIfObsolete(TermId) - Method in class org.monarchinitiative.lirical.core.service.HpoTermSanitizer: The method performs 2 things: drops termId if it's absent from current HPO, and replaces the termId with current term if termId is obsolete.
reportElapsedTime(long, long) - Static method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
resultByDiseaseId(TermId) - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
results() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
resultsWithDescendingPostTestProbability() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
REVEL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
reviewStatus(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
REVIEWSTATUS_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
RISK_FACTOR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: RISK_FACTOR = 14;
RISK_FACTOR - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
RISK_FACTOR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
RISK_FACTOR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: RISK_FACTOR = 14;
RS_ID_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
RsId - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency: Immutable value Class representing an NCBI dbSNP reference SNP rsID.
run(Path) - Method in class org.monarchinitiative.lirical.background.backgroundfrequency.GenicIntoleranceCalculator: This function inputs the data from the MV store, bins each variant into one of four categories, normalizes the frequencies, and writes the results to a file that can be used elsewhere.
run(AnalysisData, AnalysisOptions) - Method in class org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl
run(AnalysisData, AnalysisOptions) - Method in interface org.monarchinitiative.lirical.core.analysis.LiricalAnalysisRunner: Run analysis parametrized by analysisOptions on analysisData.
runConfiguration - Variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand

S

SampleAlleleCount - Class in org.monarchinitiative.lirical.core.model: A container for associating sample id and the AlleleCount.
sampleId - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
sampleId - Variable in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
sampleId() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
sampleId() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
sampleId() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
sampleId() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
sampleId() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
sampleId() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
sampleNames() - Method in interface org.monarchinitiative.lirical.core.io.VariantParser
sampleNames() - Method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
sampleNames() - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
SanitationInputs - Interface in org.monarchinitiative.lirical.core.sanitize: The sanitation requirements.
SanitationResult - Interface in org.monarchinitiative.lirical.core.sanitize: Result of the input sanitation.
sanitize(SanitationInputs) - Method in interface org.monarchinitiative.lirical.core.sanitize.InputSanitizer
sanitizedInputs() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationResult
SanitizedInputs - Class in org.monarchinitiative.lirical.core.sanitize: Result of input sanitation.
SanitizerType - Enum Class in org.monarchinitiative.lirical.core.sanitize: Enum to represent the existing sanitizer types.
SanityIssue - Record Class in org.monarchinitiative.lirical.core.sanitize: An issue that was found in the analysis input.
SanityIssue(SanityLevel, String, String) - Constructor for record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Creates an instance of a SanityIssue record class.
SanityLevel - Enum Class in org.monarchinitiative.lirical.core.sanitize: Represents the severity of an issue found during input data sanitation.
score - Variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
secondaryInterpretations(Set<ClinVarData.ClinSig>) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
SECONDARYINTERPRETATIONS_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
selectSanitizer(InputSanitizerFactory) - Method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
setAge(String) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setAlleleId(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string alleleId = 1;
setAlleleIdBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string alleleId = 1;
setAlt(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
setAltBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
setAnalysisDate(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setAnalysisDate(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setAnchor(String) - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
setChr(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 chr = 1;
setClinVar(AlleleProto.ClinVar) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
setClinVar(AlleleProto.ClinVar.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: TODO: move to model or somewhere and then import here - this is also needed for output in results
setDiseaseDatabases(Collection<DiseaseDatabase>) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
setExomiserPath(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setExomiserPath(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
setField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
setField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
setGenesWithVar(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setGenesWithVar(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setGlobalMode(boolean) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setGlobalMode(boolean) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setHpoIds(List<String>) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setHpoVersion(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setHpoVersion(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setLiricalPath(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setLiricalPath(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setLiricalVersion(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setNegatedHpoIds(List<String>) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setnFilteredVariants(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setnFilteredVariants(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setnPassingVariants(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setnPassingVariants(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setPosition(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 position = 2;
setPrimaryInterpretation(AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ClinSig primaryInterpretation = 2;
setPrimaryInterpretationValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ClinSig primaryInterpretation = 2;
setRef(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string ref = 3;
setRefBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string ref = 3;
setRepeatedField(Descriptors.FieldDescriptor, int, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
setRepeatedField(Descriptors.FieldDescriptor, int, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
setRepeatedField(Descriptors.FieldDescriptor, int, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
setReviewStatus(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string reviewStatus = 4;
setReviewStatusBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string reviewStatus = 4;
setRsId(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
setRsIdBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
setSampleId(String) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setSampleName(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setSampleName(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setSecondaryInterpretations(int, AlleleProto.ClinVar.ClinSig) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
setSecondaryInterpretationsValue(int, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
setSex(String) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setToUserDefinedMinCount(int) - Static method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
setToUserDefinedThreshold(double) - Static method in class org.monarchinitiative.lirical.core.output.LrThreshold
setTranscriptDatabase(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setTranscriptDatabase(String) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder
setUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder
setUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
setVcf(String) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
sex - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
sex() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
sex() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisData
sex() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
sex() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
sex() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
Sex - Enum Class in org.monarchinitiative.lirical.core.model
shortName(String) - Method in class org.monarchinitiative.lirical.io.output.LiricalTemplate: Some of our name strings contain multiple synonyms.
showDiseasesWithNoDeleteriousVariants() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
SIFT - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
SIFT_THRESHOLD - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SiftScore: A SIFT score below this threshold is considered to be pathogenic
SiftScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: The score is the normalized probability that the amino acid change is tolerated.
size() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisResults
size() - Method in interface org.monarchinitiative.lirical.core.model.GenesAndGenotypes
solution() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns the value of the solution record component.
sortByValue(Map<K, V>) - Static method in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
source - Variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
Sparkline2Svg - Class in org.monarchinitiative.lirical.io.output.svg: Make a set of sparklines for the top of the page.
Sparkline2Svg(TestResult, boolean, MinimalOntology) - Constructor for class org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg: Set up the Sparkline2Svg generator by sorting the HPO terms according to their likelihood ratios in the top diagnosis (diseaseId).
sparklineFactory(AnalysisResults, HpoDiseases, MinimalOntology, boolean, int) - Static method in class org.monarchinitiative.lirical.io.output.SparklinePacket: Factory method for genotype-phenotype analysis.
SparklinePacket - Class in org.monarchinitiative.lirical.io.output: This class encapsulates all of the information we need to produce one row of the sparkline table.
SPLICE_DONOR_ACCEPTOR_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a splice site mutation.
SPLICE_REGION_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Default pathogenicity score for variants in the a splice region, but not a donor or acceptor.
starRating() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData: Returns the ClinVar star rating according to the criteria provided at https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/#revstat_def
STARTLOSS_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a variant that causes the start codon to be lost.
STOPLOSS_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a stoploss mutation.
STRICT - Enum constant in enum class org.monarchinitiative.lirical.cli.cmd.ValidationPolicy: Only run the analysis if no errors or warnings are found.
summarize() - Method in class org.monarchinitiative.lirical.core.analysis.ProgressReporter: Log summary after processing.
summarizeSanitationResult(SanitationResult) - Static method in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
symbolsWithoutGeneIds - Variable in class org.monarchinitiative.lirical.io.output.HtmlTemplate: There are gene symbols returned by Jannovar for which we cannot find a geneId.
SYNONYMOUS_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a synonymous mutation.

T

TemplateBasedAnalysisResultsWriter - Class in org.monarchinitiative.lirical.io.output
TemplateBasedAnalysisResultsWriter(OutputFormat, MinimalOntology, HpoDiseases) - Constructor for class org.monarchinitiative.lirical.io.output.TemplateBasedAnalysisResultsWriter
templateData - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate: Map of data that will be used for the FreeMark template.
TEST - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
TestResult - Class in org.monarchinitiative.lirical.core.analysis: This class organizes information about the result of a test.
THOUSAND_GENOMES - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
toAlleleKey(GenomicVariant) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
toBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
toBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
toBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
toFrequencyData(AlleleProto.AlleleProperties) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
toPathogenicityData(AlleleProto.AlleleProperties) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
topDiagnosisAnchors - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate: Anchors that are used in the HTML output to navigate to the top differential diagnoses.
topDiagnosisMap - Variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate: This map contains the names of the top differential diagnoses that we will show as a list at the top of the page together with anchors to navigate to the detailed analysis.
TOPMED - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
toString() - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
toString() - Method in class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
toString() - Method in class org.monarchinitiative.lirical.core.model.Age
toString() - Method in class org.monarchinitiative.lirical.core.model.AlleleCount
toString() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
toString() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns a string representation of this record class.
toString() - Method in class org.monarchinitiative.lirical.core.model.SampleAlleleCount
toString() - Method in enum class org.monarchinitiative.lirical.core.model.Sex
toString() - Method in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase
toString() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
toString() - Method in class org.monarchinitiative.lirical.core.output.LrThreshold
toString() - Method in class org.monarchinitiative.lirical.core.output.MinDiagnosisCount
toString() - Method in enum class org.monarchinitiative.lirical.core.output.OutputFormat
toString() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
toString() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
toString() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns a string representation of this record class.
toString() - Method in class org.monarchinitiative.lirical.core.service.VariantPathogenicity
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId: Returns an rsID formatted string - 'rs123456' or '.' for an empty value.
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
toString() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SiftScore
toString() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
toVisualizableVariant() - Method in class org.monarchinitiative.lirical.io.output.LiricalTemplate
TranscriptAnnotation - Interface in org.monarchinitiative.lirical.core.model: The interface represents variant functional annotation data required by LIRICAL.
transcriptCacheFor(GenomeBuild, TranscriptDatabase) - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
transcriptDatabase() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
transcriptDatabase(TranscriptDatabase) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
TranscriptDatabase - Enum Class in org.monarchinitiative.lirical.core.model
transcriptDb - Variable in class org.monarchinitiative.lirical.background.BackgroundFrequencyCommand
TSV - Enum constant in enum class org.monarchinitiative.lirical.core.output.OutputFormat
TsvDifferential - Class in org.monarchinitiative.lirical.io.output
TsvDifferential(String, TermId, String, TestResult, int, List<VisualizableVariant>) - Constructor for class org.monarchinitiative.lirical.io.output.TsvDifferential
TsvTemplate - Class in org.monarchinitiative.lirical.io.output: This class coordinates the output of a TSV file that contains a suymmary of the analysis results.
TWO_DELETERIOUS_CLINVAR_VARIANTS_IN_AR - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Deprecated, for removal: This API element is subject to removal in a future version.
the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR instead.
TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Two ClinVar pathogenic or likely pathogenic alleles discovered in a disease with autosomal recessive inheritance.

U

UCSC - Enum constant in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase
UK10K - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
UNCERTAIN_SIGNIFICANCE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: UNCERTAIN_SIGNIFICANCE = 4;
UNCERTAIN_SIGNIFICANCE - Enum constant in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig
UNCERTAIN_SIGNIFICANCE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
UNCERTAIN_SIGNIFICANCE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: UNCERTAIN_SIGNIFICANCE = 4;
uniform(Collection<TermId>) - Static method in class org.monarchinitiative.lirical.core.analysis.probability.PretestDiseaseProbabilities: Prepare uniform pretest disease probabilities for given disease identifiers.
UNKNOWN - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Deprecated, for removal: This API element is subject to removal in a future version.
the field will be removed in v3.0.0.
UNKNOWN - Enum constant in enum class org.monarchinitiative.lirical.core.model.Sex
UNKNOWN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
UNKNOWN_VERSION_PLACEHOLDER - Static variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
UNUSUAL_BACKGROUND_FREQUENCY - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
useGlobal() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
useGlobal(boolean) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
useStrictPenalties() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
useStrictPenalties(boolean) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
Util - Class in org.monarchinitiative.lirical.cli.cmd.util

V

v1() - Static method in class org.monarchinitiative.lirical.io.analysis.PhenopacketImporters
v2() - Static method in class org.monarchinitiative.lirical.io.analysis.PhenopacketImporters
ValidationPolicy - Enum Class in org.monarchinitiative.lirical.cli.cmd: What to do in case of errors or imperfections in the input data.
valueOf(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Deprecated.
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.cli.cmd.ValidationPolicy: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.model.GenomeBuild: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.model.Sex: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.output.OutputFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.sanitize.SanitizerType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.core.sanitize.SanityLevel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.cli.cmd.ValidationPolicy: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.model.ClinvarClnSig: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.model.GenomeBuild: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.model.Sex: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.output.OutputFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.sanitize.SanitizerType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.core.sanitize.SanityLevel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource: Returns an array containing the constants of this enum class, in the order they are declared.
variant() - Method in interface org.monarchinitiative.lirical.core.model.GenotypedVariant
VARIANT_TYPE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
variantCount() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats
variantCount() - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get the count of variants annotated to this gene that passed the filtering.
variantDeleteriousnessThreshold() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions
variantDeleteriousnessThreshold(float) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
VariantEffectPathogenicityScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: Set of constants for use as default pathogenicity scores for a given VariantEffect.
VariantMetadata - Interface in org.monarchinitiative.lirical.core.model
VariantMetadataService - Interface in org.monarchinitiative.lirical.core.service
variantMetadataServiceFactory() - Method in class org.monarchinitiative.lirical.core.Lirical
variantMetadataServiceFactory(VariantMetadataServiceFactory) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
VariantMetadataServiceFactory - Interface in org.monarchinitiative.lirical.core.service: VariantMetadataServiceFactory knows about VariantMetadataServices for all genome builds that have been configured for a given Lirical instance.
VariantParser - Interface in org.monarchinitiative.lirical.core.io
variantParserFactory() - Method in class org.monarchinitiative.lirical.core.Lirical
VariantParserFactory - Interface in org.monarchinitiative.lirical.core.io
VariantPathogenicity - Class in org.monarchinitiative.lirical.core.service: Class to represent pathogenicity data available for a genomic variant.
variants - Variable in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
variants() - Method in interface org.monarchinitiative.lirical.core.model.Gene2Genotype: Get a Stream of variants annotated to this gene.
variants() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
variantStream() - Method in interface org.monarchinitiative.lirical.core.io.GenotypedVariantParser
variantStream() - Method in interface org.monarchinitiative.lirical.core.io.VariantParser
vcf() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
vcf() - Method in interface org.monarchinitiative.lirical.core.sanitize.SanitationInputs
vcf() - Method in class org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
vcf() - Method in class org.monarchinitiative.lirical.io.analysis.PhenopacketData
VcfGenotypedVariantParser - Class in org.monarchinitiative.lirical.io.vcf
VcfGenotypedVariantParser(GenomicAssembly, GenomeBuild, VCFFileReader) - Constructor for class org.monarchinitiative.lirical.io.vcf.VcfGenotypedVariantParser
vcfPath - Variable in class org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
vcfPath - Variable in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
vcfPath - Variable in class org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
vcfPath() - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
VcfVariantParserFactory - Class in org.monarchinitiative.lirical.io.vcf
verbosity - Variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand
version() - Method in class org.monarchinitiative.lirical.core.Lirical
version() - Method in class org.monarchinitiative.lirical.core.LiricalOptions
VERSION - Static variable in class org.monarchinitiative.lirical.cli.Main
VIOLET - Static variable in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
VisualizableVariant - Interface in org.monarchinitiative.lirical.io.output: The variant data for displaying in SVG widget.

W

warning(String, String) - Static method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue
WARNING - Enum constant in enum class org.monarchinitiative.lirical.core.sanitize.SanityLevel: Something is not right, and you probably should not proceed.
WIDTH - Static variable in class org.monarchinitiative.lirical.cli.Main
write(WriteBuffer, Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
write(WriteBuffer, Object) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
write(WriteBuffer, Object[], int, boolean) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
write(WriteBuffer, Object[], int, boolean) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
writeDiamond(Writer, int, int) - Method in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg: We use a diamond symbol to show a value that would be too small to appear as a visible box.
writeDiamond(Writer, int, int, String) - Method in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg: We use a diamond symbol to show a value that would be too small to appear as a visible box.
writeFooter(Writer) - Method in class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
writeSvg(String) - Method in class org.monarchinitiative.lirical.io.output.svg.Lr2Svg
writeTo(CodedOutputStream) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey
writeTo(CodedOutputStream) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
writeTo(CodedOutputStream) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar

Y

YamlCommand - Class in org.monarchinitiative.lirical.cli.cmd: This class coordinates the main analysis of a VCF file plus list of observed HPO terms.
YamlCommand() - Constructor for class org.monarchinitiative.lirical.cli.cmd.YamlCommand
YamlConfig - Class in org.monarchinitiative.lirical.cli.yaml: This class is used to input the YAML configuration file.
YamlConfig() - Constructor for class org.monarchinitiative.lirical.cli.yaml.YamlConfig
YamlParser - Class in org.monarchinitiative.lirical.cli.yaml: This class ingests a YAML file with parameters that will be used for the analysis.
yamlPath - Variable in class org.monarchinitiative.lirical.cli.cmd.YamlCommand

Z

zeroOne() - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount
zeroTwo() - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount
zeroZero() - Static method in class org.monarchinitiative.lirical.core.model.AlleleCount

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