Index (LIRICAL 2.1.1-SNAPSHOT API)

A B C D E F G H I J K 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

ac() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
AC_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
addAllFrequencies(Iterable<? extends AlleleProto.Frequency>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addAllPathogenicityScores(Iterable<? extends AlleleProto.PathogenicityScore>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
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
addFrequencies(int, AlleleProto.Frequency) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequencies(int, AlleleProto.Frequency.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequencies(AlleleProto.Frequency) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequencies(AlleleProto.Frequency.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequenciesBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequenciesBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
addFrequency(FrequencySource, float) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData.Builder
addFrequency(FrequencySource, int, int, int) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData.Builder
addPathogenicityScores(int, AlleleProto.PathogenicityScore) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
addPathogenicityScores(int, AlleleProto.PathogenicityScore.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
addPathogenicityScores(AlleleProto.PathogenicityScore) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
addPathogenicityScores(AlleleProto.PathogenicityScore.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
addPathogenicityScoresBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
addPathogenicityScoresBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
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
addRepeatedField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
addRepeatedField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.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;
addTargetDiseases(Collection<TermId>) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
addTargetDiseases(TermId...) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
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.
ALFA_AFA - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_AFA = 57;
ALFA_AFA - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_AFA_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_AFA = 57;
ALFA_AFO - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: reserved 68-75 for ALFA
ALFA_AFO - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_AFO_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: reserved 68-75 for ALFA
ALFA_AFR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_AFR = 58;
ALFA_AFR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_AFR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_AFR = 58;
ALFA_ASN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_ASN = 64;
ALFA_ASN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_ASN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_ASN = 64;
ALFA_EAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_EAS = 63;
ALFA_EAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_EAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_EAS = 63;
ALFA_EUR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_EUR = 59;
ALFA_EUR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_EUR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_EUR = 59;
ALFA_LAC - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_LAC = 60;
ALFA_LAC - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_LAC_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_LAC = 60;
ALFA_LEN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_LEN = 61;
ALFA_LEN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_LEN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_LEN = 61;
ALFA_OAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_OAS = 65;
ALFA_OAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_OAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_OAS = 65;
ALFA_OTR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_OTR = 66;
ALFA_OTR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_OTR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_OTR = 66;
ALFA_SAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_SAS = 62;
ALFA_SAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_SAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_SAS = 62;
ALFA_TOT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_TOT = 67;
ALFA_TOT - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ALFA_TOT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ALFA_TOT = 67;
ALL_ALFA_SOURCES - Static variable in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
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
ALL_GNOMAD_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_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.
AllelePropertiesDataType - Class in org.monarchinitiative.lirical.exomiser_db_adapter.serializers: Specialised DataType for (de)serialising AlleleProto.AlleleProperties objects into and out of the MVStore.
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.ClinVar.ReviewStatus - Enum Class in org.monarchinitiative.exomiser.core.proto: Protobuf enum ClinVar.ReviewStatus
AlleleProto.ClinVarOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProto.Frequency - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type Frequency
AlleleProto.Frequency.Builder - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type Frequency
AlleleProto.FrequencyOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProto.FrequencySource - Enum Class in org.monarchinitiative.exomiser.core.proto: Protobuf enum FrequencySource
AlleleProto.PathogenicityScore - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type PathogenicityScore
AlleleProto.PathogenicityScore.Builder - Class in org.monarchinitiative.exomiser.core.proto: Protobuf type PathogenicityScore
AlleleProto.PathogenicityScoreOrBuilder - Interface in org.monarchinitiative.exomiser.core.proto
AlleleProto.PathogenicitySource - Enum Class in org.monarchinitiative.exomiser.core.proto: Protobuf enum PathogenicitySource
AlleleProto.VariantEffect - Enum Class in org.monarchinitiative.exomiser.core.proto: Protobuf enum VariantEffect
AlleleProtoAdaptor - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model
ALPHA_MISSENSE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: ALPHA_MISSENSE = 11;
ALPHA_MISSENSE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
ALPHA_MISSENSE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: ALPHA_MISSENSE = 11;
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
an() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
AN_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
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. settings that need to be changed for analysis of each sample.
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.PhenopacketCommand: 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.exomiser.core.proto.AlleleProto.Frequency.Builder
build() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.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.frequency.FrequencyData.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.frequency.FrequencyData
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.frequency.FrequencyData.Builder
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
buildPartial() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
buildPartial() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
BundledBackgroundVariantFrequencyServiceFactory - Class in org.monarchinitiative.lirical.configuration.impl

C

CADD - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: CADD = 6;
CADD - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
CADD_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: CADD = 6;
CaddScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: CADD info - see {@link http://cadd.gs.washington.edu/info}
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.PhenopacketCommand
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
CHROMOSOME_NUMBER_VARIATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CHROMOSOME_NUMBER_VARIATION = 1;
CHROMOSOME_NUMBER_VARIATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CHROMOSOME_NUMBER_VARIATION = 1;
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
clear() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
clear() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
clearAc() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: AF doesn't need storing as it is calculated as AC/AN
clearAlleleId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
clearAlt() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: string alt = 4;
clearAn() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1-3 bytes (Varint - 2^24 = 16777216 max)
clearChr() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder: int32 chr = 1;
clearClinSigCounts() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
clearClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
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
clearField(Descriptors.FieldDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
clearField(Descriptors.FieldDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
clearFrequencies() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
clearFrequency() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 4 bytes
clearFrequencySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte (Varint)
clearGeneId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_id = 8;
clearGeneSymbol() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_symbol = 7;
clearHgvsCdna() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_cdna = 10;
clearHgvsProtein() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_protein = 11;
clearHom() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte
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
clearOneof(Descriptors.OneofDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
clearOneof(Descriptors.OneofDescriptor) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
clearPathogenicityScores() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
clearPathogenicitySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: .PathogenicitySource pathogenicitySource = 1;
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: Deprecated.
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: .ClinVar.ReviewStatus reviewStatus = 4;
clearRsId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: string rs_id = 1;
clearScore() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: float score = 2;
clearSecondaryInterpretations() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: repeated .ClinVar.ClinSig secondaryInterpretations = 3;
clearTargetDiseases() - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
clearVariantEffect() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .VariantEffect variant_effect = 9;
clearVariationId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string variationId = 6;
CLIN_SIG_COUNTS_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
CLINVAR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: CLINVAR = 15;
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
CLINVAR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: CLINVAR = 15;
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() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData: Returns a ClinVarData object.
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
ClinVarData.ReviewStatus - Enum Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: Enum for the ClinVar review status field.
ClinVarDataType - Class in org.monarchinitiative.lirical.exomiser_db_adapter.serializers
ClinVarDataType() - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ClinVarDataType
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
clone() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
clone() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
close() - Method in class org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl
close() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory
CODING_SEQUENCE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_SEQUENCE_VARIANT = 58;
CODING_SEQUENCE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_SEQUENCE_VARIANT = 58;
CODING_TRANSCRIPT_INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_TRANSCRIPT_INTRON_VARIANT = 34;
CODING_TRANSCRIPT_INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_TRANSCRIPT_INTRON_VARIANT = 34;
CODING_TRANSCRIPT_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_TRANSCRIPT_VARIANT = 63;
CODING_TRANSCRIPT_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CODING_TRANSCRIPT_VARIANT = 63;
compare(AlleleProto.AlleleKey, AlleleProto.AlleleKey) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType: Sorts variants according to their natural ordering of genome position.
compare(AlleleProto.AlleleProperties, AlleleProto.AlleleProperties) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
compare(AlleleProto.ClinVar, AlleleProto.ClinVar) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ClinVarDataType
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.
COMPLEX_SUBSTITUTION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: COMPLEX_SUBSTITUTION = 15;
COMPLEX_SUBSTITUTION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: COMPLEX_SUBSTITUTION = 15;
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;
conflictingInterpretationCounts(Map<ClinVarData.ClinSig, Integer>) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
CONSERVED_INTERGENIC_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CONSERVED_INTERGENIC_VARIANT = 56;
CONSERVED_INTERGENIC_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CONSERVED_INTERGENIC_VARIANT = 56;
CONSERVED_INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CONSERVED_INTRON_VARIANT = 54;
CONSERVED_INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: CONSERVED_INTRON_VARIANT = 54;
containsClinSigCounts(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
containsClinSigCounts(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: CLNSIGCONF
containsClinSigCounts(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: CLNSIGCONF
containsFrequencySource(FrequencySource) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Checks whether the instance contains a given FrequencySource.
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: Deprecated.
containsProperties(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
containsProperties(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
contigName() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
COPY_NUMBER_CHANGE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: COPY_NUMBER_CHANGE = 13;
COPY_NUMBER_CHANGE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: COPY_NUMBER_CHANGE = 13;
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
createStorage(int) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
createStorage(int) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
createStorage(int) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ClinVarDataType
CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = 4;
CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = 4;
CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 5;
CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 5;
CRITERIA_PROVIDED_SINGLE_SUBMITTER - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3;
CRITERIA_PROVIDED_SINGLE_SUBMITTER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
CRITERIA_PROVIDED_SINGLE_SUBMITTER_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3;
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.PhenopacketCommand
DBVAR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SV data sources
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
DBVAR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SV data sources
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.
DIRECT_TANDEM_DUPLICATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DIRECT_TANDEM_DUPLICATION = 42;
DIRECT_TANDEM_DUPLICATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DIRECT_TANDEM_DUPLICATION = 42;
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
DISRUPTIVE_INFRAME_DELETION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DISRUPTIVE_INFRAME_DELETION = 26;
DISRUPTIVE_INFRAME_DELETION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DISRUPTIVE_INFRAME_DELETION = 26;
DISRUPTIVE_INFRAME_INSERTION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DISRUPTIVE_INFRAME_INSERTION = 24;
DISRUPTIVE_INFRAME_INSERTION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DISRUPTIVE_INFRAME_INSERTION = 24;
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
DOWNSTREAM_GENE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DOWNSTREAM_GENE_VARIANT = 46;
DOWNSTREAM_GENE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: DOWNSTREAM_GENE_VARIANT = 46;
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.TsvDifferential
EMPTY_STRING - Static variable in class org.monarchinitiative.lirical.io.output.LiricalTemplate
ENSEMBL - Enum constant in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase: Transcripts sourced from ENSEMBL.
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.exomiser.core.proto.AlleleProto.Frequency
equals(Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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 record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Indicates whether some other object is "equal to" this one.
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.MutationTasterScore
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.CaddScore
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_AA - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_AA = 5;
ESP_AA - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ESP_AA_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_AA = 5;
ESP_ALL - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_ALL = 6;
ESP_ALL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ESP_ALL_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_ALL = 6;
ESP_EA - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_EA = 4;
ESP_EA - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
ESP_EA_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: ESP_EA = 4;
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.
EVE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: EVE = 12;
EVE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
EVE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: EVE = 12;
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.PhenopacketCommand
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
exomiserAlleleDb() - Method in record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Returns the value of the exomiserAlleleDb record component.
exomiserClinvarDb() - Method in record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Returns the value of the exomiserClinvarDb record component.
ExomiserMvStoreMetadataServiceFactory - Class in org.monarchinitiative.lirical.exomiser_db_adapter
ExomiserMvStoreMetadataServiceFactory(Map<GenomeBuild, Path>) - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory: Deprecated, for removal: This API element is subject to removal in a future version.
Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores. Use ExomiserMvStoreMetadataServiceFactory.fromResources(Map) instead and provide ExomiserResources with paths to variant and clinvar database files for each GenomeBuild. To be removed in 3.0.0.
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
exomiserResources(GenomeBuild, ExomiserResources) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder: Add paths for Exomiser resources required to support the genomeBuild.
ExomiserResources - Record Class in org.monarchinitiative.lirical.exomiser_db_adapter: Paths to Exomiser resources needed to support LIRICAL analysis for a GenomeBuild.
ExomiserResources(Path, Path) - Constructor for record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Creates an instance of a ExomiserResources record class.
exomiserVariantDbPath(GenomeBuild, Path) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder: Deprecated, for removal: This API element is subject to removal in a future version.
use LiricalBuilder.exomiserResources(GenomeBuild, ExomiserResources) instead
EXON_LOSS_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: EXON_LOSS_VARIANT = 3;
EXON_LOSS_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: EXON_LOSS_VARIANT = 3;
EXON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: EXON_VARIANT = 60;
EXON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: EXON_VARIANT = 60;
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
FEATURE_TRUNCATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FEATURE_TRUNCATION = 11;
FEATURE_TRUNCATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FEATURE_TRUNCATION = 11;
FEMALE - Enum constant in enum class org.monarchinitiative.lirical.core.model.Sex
figureOutExomiserPath() - Method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
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.
filterSources(Set<FrequencySource>) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData.Builder: Removes any frequency data not in the argument set of FrequencySource.
FIVE_PRIME_UTR_EXON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_EXON_VARIANT = 36;
FIVE_PRIME_UTR_EXON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_EXON_VARIANT = 36;
FIVE_PRIME_UTR_INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_INTRON_VARIANT = 38;
FIVE_PRIME_UTR_INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_INTRON_VARIANT = 38;
FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT = 35;
FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT = 35;
FIVE_PRIME_UTR_TRUNCATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_TRUNCATION = 27;
FIVE_PRIME_UTR_TRUNCATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FIVE_PRIME_UTR_TRUNCATION = 27;
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
forNumber(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
forNumber(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
forNumber(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
forNumber(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
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_ELONGATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_ELONGATION = 7;
FRAMESHIFT_ELONGATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_ELONGATION = 7;
FRAMESHIFT_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore: Assumed pathogenicity score for a frameshift mutation.
FRAMESHIFT_TRUNCATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_TRUNCATION = 8;
FRAMESHIFT_TRUNCATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_TRUNCATION = 8;
FRAMESHIFT_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_VARIANT = 9;
FRAMESHIFT_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: FRAMESHIFT_VARIANT = 9;
frequencies() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Returns a list of Frequency objects.
FREQUENCIES_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
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() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
frequency(FrequencySource) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
Frequency - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency
FREQUENCY_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.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.
FrequencyData.Builder - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency
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.
frequencyScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
FrequencySource - Enum Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency: Enum describing where the frequency data has originated.
FREQUENCYSOURCE_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
fromResources(Map<GenomeBuild, ExomiserResources>) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory: Create ExomiserMvStoreMetadataServiceFactory from mappings from ExomiserResources for a GenomeBuild.
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

GENE_ID_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
GENE_SYMBOL_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
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.TsvDifferential
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.
geneSymbol(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
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.
getAc() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: AF doesn't need storing as it is calculated as AC/AN
getAc() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: AF doesn't need storing as it is calculated as AC/AN
getAc() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: AF doesn't need storing as it is calculated as AC/AN
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: Deprecated.
getAlleleId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: Deprecated.
getAlleleId() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: Deprecated.
getAlleleId() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData: Get ClinVar allele ID.
getAlleleIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getAlleleIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: Deprecated.
getAlleleIdBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: Deprecated.
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;
getAn() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1-3 bytes (Varint - 2^24 = 16777216 max)
getAn() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: 1-3 bytes (Varint - 2^24 = 16777216 max)
getAn() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: 1-3 bytes (Varint - 2^24 = 16777216 max)
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;
getClinSigCounts() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
getClinSigCounts() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: Deprecated.
getClinSigCounts() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: Deprecated.
getClinSigCountsCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder
getClinSigCountsCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
getClinSigCountsCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: CLNSIGCONF
getClinSigCountsMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
getClinSigCountsMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: CLNSIGCONF
getClinSigCountsMap() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: CLNSIGCONF
getClinSigCountsOrDefault(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
getClinSigCountsOrDefault(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: CLNSIGCONF
getClinSigCountsOrDefault(String, int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: CLNSIGCONF
getClinSigCountsOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
getClinSigCountsOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: CLNSIGCONF
getClinSigCountsOrThrow(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: CLNSIGCONF
getClinvar() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
getClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: .ClinVar clinVar = 3;
getClinVar() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: .ClinVar clinVar = 3;
getClinVarBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
getClinvarClnSig() - Method in class org.monarchinitiative.lirical.core.model.ClinVarAlleleData
getClinVarOrBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
getClinVarOrBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: .ClinVar clinVar = 3;
getClinVarOrBuilder() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: .ClinVar clinVar = 3;
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.TsvDifferential
getConflictingInterpretationCounts() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
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
getDefaultInstance() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getDefaultInstance() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
getDefaultInstanceForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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 enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getDescriptor() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
getDescriptor() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
getDescriptor() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
getDescriptor() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
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
getDescriptorForType() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
getDescriptorForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
getDescriptorForType() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
getDescriptorForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
getDescriptorForType() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
getDescriptorForType() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
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.TsvDifferential
getDiseaseId() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getDiseaseName() - Method in class org.monarchinitiative.lirical.io.output.TsvDifferential
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.TsvDifferential
getExcludedPhenotypeRatio(int) - Method in class org.monarchinitiative.lirical.core.analysis.TestResult
getExomiserPath() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getFrequencies(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequencies(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .Frequency frequencies = 4;
getFrequencies(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .Frequency frequencies = 4;
getFrequenciesBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .Frequency frequencies = 4;
getFrequenciesCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .Frequency frequencies = 4;
getFrequenciesList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .Frequency frequencies = 4;
getFrequenciesList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilder(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .Frequency frequencies = 4;
getFrequenciesOrBuilderList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .Frequency frequencies = 4;
getFrequency() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 4 bytes
getFrequency() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: 4 bytes
getFrequency() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: 4 bytes
getFrequency() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getFrequencySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte (Varint)
getFrequencySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: 1 byte (Varint)
getFrequencySource() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: 1 byte (Varint)
getFrequencySourceValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte (Varint)
getFrequencySourceValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: 1 byte (Varint)
getFrequencySourceValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: 1 byte (Varint)
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 class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_id = 8;
getGeneId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string gene_id = 8;
getGeneId() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string gene_id = 8;
getGeneId() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getGeneIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_id = 8;
getGeneIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string gene_id = 8;
getGeneIdBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string gene_id = 8;
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.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_symbol = 7;
getGeneSymbol() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string gene_symbol = 7;
getGeneSymbol() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string gene_symbol = 7;
getGeneSymbol() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getGeneSymbol() - Method in class org.monarchinitiative.lirical.io.output.TsvDifferential
getGeneSymbol() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getGeneSymbolBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_symbol = 7;
getGeneSymbolBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string gene_symbol = 7;
getGeneSymbolBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string gene_symbol = 7;
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 class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_cdna = 10;
getHgvsCdna() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string hgvs_cdna = 10;
getHgvsCdna() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string hgvs_cdna = 10;
getHgvsCdna() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getHgvsCdna() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getHgvsCdnaBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_cdna = 10;
getHgvsCdnaBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string hgvs_cdna = 10;
getHgvsCdnaBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string hgvs_cdna = 10;
getHgvsProtein() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_protein = 11;
getHgvsProtein() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string hgvs_protein = 11;
getHgvsProtein() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string hgvs_protein = 11;
getHgvsProtein() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getHgvsProtein() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getHgvsProteinBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_protein = 11;
getHgvsProteinBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string hgvs_protein = 11;
getHgvsProteinBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string hgvs_protein = 11;
getHom() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte
getHom() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency: 1 byte
getHom() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencyOrBuilder: 1 byte
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
getLiricalPath() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
getLiricalVersion() - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
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(T) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ProtobufDataType
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
getMostPathogenicVariantEffect() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getMutableClinSigCounts() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
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
getNumber() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
getNumber() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
getNumber() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
getNumber() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
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
getParserForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getParserForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
getPathogenicityScore() - Method in interface org.monarchinitiative.lirical.io.output.VisualizableVariant
getPathogenicityScores(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScores(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScores(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilder(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilder(int) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilderList() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicityScoresOrBuilderList() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: repeated .PathogenicityScore pathogenicityScores = 5;
getPathogenicitySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: .PathogenicitySource pathogenicitySource = 1;
getPathogenicitySource() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore: .PathogenicitySource pathogenicitySource = 1;
getPathogenicitySource() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScoreOrBuilder: .PathogenicitySource pathogenicitySource = 1;
getPathogenicitySourceValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: .PathogenicitySource pathogenicitySource = 1;
getPathogenicitySourceValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore: .PathogenicitySource pathogenicitySource = 1;
getPathogenicitySourceValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScoreOrBuilder: .PathogenicitySource pathogenicitySource = 1;
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.TsvDifferential
getPosttestProbability() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getPretestprob() - Method in class org.monarchinitiative.lirical.io.output.TsvDifferential
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: Deprecated.
getPropertiesCount() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
getPropertiesCount() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
getPropertiesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
getPropertiesMap() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
getPropertiesMap() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
getPropertiesOrDefault(String, float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
getPropertiesOrDefault(String, float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
getPropertiesOrDefault(String, float) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
getPropertiesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
getPropertiesOrThrow(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: Deprecated.
getPropertiesOrThrow(String) - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: Deprecated.
getRank() - Method in class org.monarchinitiative.lirical.io.output.TsvDifferential
getRank() - Method in class org.monarchinitiative.lirical.io.output.SparklinePacket
getRawScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
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.CaddScore
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: .ClinVar.ReviewStatus reviewStatus = 4;
getReviewStatus() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .ClinVar.ReviewStatus reviewStatus = 4;
getReviewStatus() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .ClinVar.ReviewStatus reviewStatus = 4;
getReviewStatus() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getReviewStatusValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ReviewStatus reviewStatus = 4;
getReviewStatusValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .ClinVar.ReviewStatus reviewStatus = 4;
getReviewStatusValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .ClinVar.ReviewStatus 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.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: float score = 2;
getScore() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore: float score = 2;
getScore() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScoreOrBuilder: float score = 2;
getScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
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
getSerializedSize() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getSerializedSize() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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.MutationTasterScore
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.CaddScore
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
getUnknownFields() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
getUnknownFields() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
getUrl() - Method in class org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
getValueDescriptor() - Method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
getVarcount() - Method in class org.monarchinitiative.lirical.io.output.ImprobableDifferential
getVariantEffect() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .VariantEffect variant_effect = 9;
getVariantEffect() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .VariantEffect variant_effect = 9;
getVariantEffect() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .VariantEffect variant_effect = 9;
getVariantEffect() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getVariantEffect() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getVariantEffects() - Method in interface org.monarchinitiative.lirical.core.model.TranscriptAnnotation
getVariantEffectValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .VariantEffect variant_effect = 9;
getVariantEffectValue() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: .VariantEffect variant_effect = 9;
getVariantEffectValue() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: .VariantEffect variant_effect = 9;
getVariantMetadataService(GenomeBuild) - Method in interface org.monarchinitiative.lirical.core.service.VariantMetadataServiceFactory
getVariantMetadataService(GenomeBuild) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory
getVariationId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string variationId = 6;
getVariationId() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string variationId = 6;
getVariationId() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string variationId = 6;
getVariationId() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
getVariationIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string variationId = 6;
getVariationIdBytes() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar: string variationId = 6;
getVariationIdBytes() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder: string variationId = 6;
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.exomiser.core.proto.AlleleProto.FrequencySource: reserved 16-35 GNOMAD_E
GNOMAD_E_AFR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_AFR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: reserved 16-35 GNOMAD_E
GNOMAD_E_AMR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_AMR = 17;
GNOMAD_E_AMR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_AMR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_AMR = 17;
GNOMAD_E_ASJ - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_ASJ = 18;
GNOMAD_E_ASJ - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_ASJ_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_ASJ = 18;
GNOMAD_E_EAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_EAS = 19;
GNOMAD_E_EAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_EAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_EAS = 19;
GNOMAD_E_FIN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_FIN = 20;
GNOMAD_E_FIN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_FIN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_FIN = 20;
GNOMAD_E_MID - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_MID = 24;
GNOMAD_E_MID - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_MID_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_MID = 24;
GNOMAD_E_NFE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_NFE = 21;
GNOMAD_E_NFE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_NFE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_NFE = 21;
GNOMAD_E_OTH - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_OTH = 22;
GNOMAD_E_OTH - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_OTH_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_OTH = 22;
GNOMAD_E_SAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_SAS = 23;
GNOMAD_E_SAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_E_SAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_E_SAS = 23;
GNOMAD_G_AFR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: reserved 36-55 GNOMAD_G
GNOMAD_G_AFR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_AFR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: reserved 36-55 GNOMAD_G
GNOMAD_G_AMI - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_AMI = 44;
GNOMAD_G_AMI - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_AMI_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_AMI = 44;
GNOMAD_G_AMR - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_AMR = 37;
GNOMAD_G_AMR - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_AMR_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_AMR = 37;
GNOMAD_G_ASJ - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_ASJ = 38;
GNOMAD_G_ASJ - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_ASJ_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_ASJ = 38;
GNOMAD_G_EAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_EAS = 39;
GNOMAD_G_EAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_EAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_EAS = 39;
GNOMAD_G_FIN - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_FIN = 40;
GNOMAD_G_FIN - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_FIN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_FIN = 40;
GNOMAD_G_MID - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_MID = 45;
GNOMAD_G_MID - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_MID_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_MID = 45;
GNOMAD_G_NFE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_NFE = 41;
GNOMAD_G_NFE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_NFE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_NFE = 41;
GNOMAD_G_OTH - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_OTH = 42;
GNOMAD_G_OTH - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_OTH_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_OTH = 42;
GNOMAD_G_SAS - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_SAS = 43;
GNOMAD_G_SAS - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
GNOMAD_G_SAS_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: GNOMAD_G_SAS = 43;
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: .ClinVar clinVar = 3;
hasClinVar() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties: .ClinVar clinVar = 3;
hasClinVar() - Method in interface org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder: .ClinVar clinVar = 3;
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 if 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
hasGnomadData() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
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.exomiser.core.proto.AlleleProto.Frequency
hashCode() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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 record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Returns a hash code value for this object.
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.MutationTasterScore
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.CaddScore
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.TsvDifferential: 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
hg19EnsemblTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
hg19RefseqCuratedTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
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
hg38EnsemblTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
hg38RefseqCuratedTxDatabase() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
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
HGVS_CDNA_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
HGVS_PROTEIN_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
hgvsCdna(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
hgvsProtein(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
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.
HOM_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
homs() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
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.
INFRAME_DELETION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INFRAME_DELETION = 25;
INFRAME_DELETION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INFRAME_DELETION = 25;
INFRAME_INSERTION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INFRAME_INSERTION = 23;
INFRAME_INSERTION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INFRAME_INSERTION = 23;
INITIATOR_CODON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INITIATOR_CODON_VARIANT = 32;
INITIATOR_CODON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INITIATOR_CODON_VARIANT = 32;
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
INSERTION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INSERTION = 5;
INSERTION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INSERTION = 5;
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
INSTANCE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ClinVarDataType
INTERGENIC_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTERGENIC_VARIANT = 47;
INTERGENIC_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTERGENIC_VARIANT = 47;
INTERNAL_FEATURE_ELONGATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTERNAL_FEATURE_ELONGATION = 10;
INTERNAL_FEATURE_ELONGATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTERNAL_FEATURE_ELONGATION = 10;
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
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
internalGetFieldAccessorTable() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
internalGetValueMap() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
internalGetValueMap() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
internalGetValueMap() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
internalGetValueMap() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
INTRAGENIC_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTRAGENIC_VARIANT = 55;
INTRAGENIC_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTRAGENIC_VARIANT = 55;
INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTRON_VARIANT = 59;
INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INTRON_VARIANT = 59;
InvalidAlleleProtoException - Exception in org.monarchinitiative.lirical.exomiser_db_adapter.serializers
InvalidAlleleProtoException(Exception) - Constructor for exception org.monarchinitiative.lirical.exomiser_db_adapter.serializers.InvalidAlleleProtoException
INVERSION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INVERSION = 4;
INVERSION_SCORE - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
INVERSION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: INVERSION = 4;
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.FrequencyData: Checks if there are any frequencies present.
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
isGnomadSource() - Method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
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
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
isInitialized() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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

K

KG - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: KG = 1;
KG_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: KG = 1;

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: Build Lirical from provided resources.
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: A convenience class for accessing resources from LIRICAL data directory.
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.exomiser.core.proto.AlleleProto.FrequencySource: LOCAL = 7;
LOCAL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
LOCAL_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: LOCAL = 7;
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

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
maxFreq() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Returns the maximum frequency - if there are no known frequencies/ no frequency data it will return 0.
maxFreqForPopulation(Set<FrequencySource>) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData: Returns the highest frequency in percent for a given set of FrequencySource.
maxFrequency() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
mergeClinVar(AlleleProto.ClinVar) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
mergeFrequencyData(FrequencyData) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData.Builder: Merges the frequency data from the input frequencyData into the builder instance.
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(CodedInputStream, ExtensionRegistryLite) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.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(Message) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
mergeFrom(Message) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.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
mergeFrom(AlleleProto.Frequency) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
mergeFrom(AlleleProto.PathogenicityScore) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.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
mergeUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
mergeUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
message() - Method in record class org.monarchinitiative.lirical.core.sanitize.SanityIssue: Returns the value of the message record component.
messageParser() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType
messageParser() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType
messageParser() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ClinVarDataType
messageParser() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ProtobufDataType
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.
MIRNA - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MIRNA = 62;
MIRNA_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MIRNA = 62;
MISSENSE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MISSENSE_VARIANT = 22;
MISSENSE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MISSENSE_VARIANT = 22;
mkdirIfNotExist(Path) - Static method in class org.monarchinitiative.lirical.io.output.LiricalTemplate
MNV - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MNV = 14;
MNV_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MNV = 14;
MOBILE_ELEMENT_DELETION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MOBILE_ELEMENT_DELETION = 43;
MOBILE_ELEMENT_DELETION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MOBILE_ELEMENT_DELETION = 43;
MOBILE_ELEMENT_INSERTION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MOBILE_ELEMENT_INSERTION = 44;
MOBILE_ELEMENT_INSERTION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: MOBILE_ELEMENT_INSERTION = 44;
MORE_PATHOGENIC - Static variable in interface org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
mostPathogenicScore() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
MTASTER_THRESHOLD - Static variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
MUTATION_TASTER - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: MUTATION_TASTER = 4;
MUTATION_TASTER - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
MUTATION_TASTER_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: MUTATION_TASTER = 4;
MutationTasterScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
MVP - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: MVP = 9;
MVP - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
MVP_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: MVP = 9;
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() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
newBuilder() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
newBuilder(AlleleProto.Frequency) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
newBuilder(AlleleProto.PathogenicityScore) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
newBuilderForType() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
newBuilderForType(GeneratedMessageV3.BuilderParent) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
newBuilderForType(GeneratedMessageV3.BuilderParent) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
newInstance(GeneratedMessageV3.UnusedPrivateParameter) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
newInstance(GeneratedMessageV3.UnusedPrivateParameter) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
nFilteredVariants() - Method in record class org.monarchinitiative.lirical.core.model.FilteringStats: Returns the value of the nFilteredVariants record component.
NO_ASSERTION_CRITERIA_PROVIDED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: NO_ASSERTION_CRITERIA_PROVIDED = 1;
NO_ASSERTION_CRITERIA_PROVIDED - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
NO_ASSERTION_CRITERIA_PROVIDED_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: NO_ASSERTION_CRITERIA_PROVIDED = 1;
NO_ASSERTION_PROVIDED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: default value
NO_ASSERTION_PROVIDED - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
NO_ASSERTION_PROVIDED_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: default value
NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT = 2;
NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT = 2;
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_CODING_TRANSCRIPT_EXON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_EXON_VARIANT = 40;
NON_CODING_TRANSCRIPT_EXON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_EXON_VARIANT = 40;
NON_CODING_TRANSCRIPT_INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_INTRON_VARIANT = 41;
NON_CODING_TRANSCRIPT_INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_INTRON_VARIANT = 41;
NON_CODING_TRANSCRIPT_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_VARIANT = 64;
NON_CODING_TRANSCRIPT_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: NON_CODING_TRANSCRIPT_VARIANT = 64;
NON_FOUNDER_POPS - Static variable in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource: Returns the set of non-founder/bottle-necked populations for use in frequency filtering.
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.TsvDifferential
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.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) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SpliceAiScore
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: Deprecated, for removal: This API element is subject to removal in a future version.
Since Exomiser 14.0.0, the pathogenicity scores, allele frequencies data and clinvar are distributed in separate MV stores. Use ExomiserMvStoreMetadataServiceFactory.fromResources(Map) instead and provide ExomiserResources with paths to variant and clinvar database files for each GenomeBuild. To be removed in 3.0.0.
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(FrequencySource, int, int, int) - 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.
openClinVarMVMap(MVStore) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.MvStoreUtil: Opens the 'clinvar' 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
orpha2gene() - Method in class org.monarchinitiative.lirical.io.LiricalDataResolver
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) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseDelimitedFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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[]) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(byte[]) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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(byte[], ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(byte[], ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(ByteString) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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(ByteString, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(CodedInputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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(CodedInputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(InputStream) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(ByteBuffer) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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
parseFrom(ByteBuffer, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parseFrom(ByteBuffer, ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
parseGenomeBuild(String) - Method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
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
parser() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
parser() - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
parseReviewStatus(String) - Static method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
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() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
pathogenicityScore(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.
PathogenicityScore - Interface in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
pathogenicityScoreOf(VariantEffect) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
pathogenicityScores() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
PATHOGENICITYSCORES_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties
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.
PATHOGENICITYSOURCE_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
pathogenicityThreshold() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
percentageFrequency(int, int) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency: Returns the frequency of ac/an as a percentage frequency.
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(MinimalOntology, HpoDiseases) 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.exomiser.core.proto.AlleleProto.PathogenicitySource: POLYPHEN = 3;
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).
POLYPHEN_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: POLYPHEN = 3;
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
PRACTICE_GUIDELINE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: PRACTICE_GUIDELINE = 7;
PRACTICE_GUIDELINE - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
PRACTICE_GUIDELINE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: PRACTICE_GUIDELINE = 7;
prefix() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
prepareAnalysisOptions(Lirical, GenomeBuild, TranscriptDatabase) - Method in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
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
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;
ProtobufDataType<T extends com.google.protobuf.Message> - Class in org.monarchinitiative.lirical.exomiser_db_adapter.serializers
ProtobufDataType() - Constructor for class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ProtobufDataType
putAllClinSigCounts(Map<String, Integer>) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
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: Deprecated.
putClinSigCounts(String, int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
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: Deprecated.

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
RARE_AMINO_ACID_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: RARE_AMINO_ACID_VARIANT = 21;
RARE_AMINO_ACID_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: RARE_AMINO_ACID_VARIANT = 21;
rawScore - Variable in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.CaddScore
read(InputStream) - Method in interface org.monarchinitiative.lirical.io.analysis.PhenopacketImporter
read(ByteBuffer) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ProtobufDataType
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.PhenopacketCommand
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: RefSeq transcripts, including curated transcripts (NM_) as well as the transcripts that are based on gene predictions (XM_).
REFSEQ_CURATED - Enum constant in enum class org.monarchinitiative.lirical.core.model.TranscriptDatabase: RefSeq with curated transcripts only (NM_) and excluding the transcripts that are based on gene predictions (XM_).
registerAllExtensions(ExtensionRegistry) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
registerAllExtensions(ExtensionRegistryLite) - Static method in class org.monarchinitiative.exomiser.core.proto.AlleleProto
REGULATORY_REGION_ABLATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_ABLATION = 52;
REGULATORY_REGION_ABLATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_ABLATION = 52;
REGULATORY_REGION_AMPLIFICATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_AMPLIFICATION = 53;
REGULATORY_REGION_AMPLIFICATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_AMPLIFICATION = 53;
REGULATORY_REGION_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_VARIANT = 51;
REGULATORY_REGION_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: REGULATORY_REGION_VARIANT = 51;
REMM - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: REMM = 7;
REMM - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
REMM_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: REMM = 7;
RemmScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity: REMM info - see {@link ...}
removeClinSigCounts(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: CLNSIGCONF
removeFrequencies(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
removeIncludedAlleles(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: map<string, .ClinVar.ClinSig> includedAlleles = 5;
removePathogenicityScores(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
removeProperties(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: Deprecated.
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.PhenopacketCommand
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.exomiser.core.proto.AlleleProto.PathogenicitySource: REVEL = 8;
REVEL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
REVEL_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: REVEL = 8;
REVIEWED_BY_EXPERT_PANEL - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: REVIEWED_BY_EXPERT_PANEL = 6;
REVIEWED_BY_EXPERT_PANEL - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
REVIEWED_BY_EXPERT_PANEL_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: REVIEWED_BY_EXPERT_PANEL = 6;
reviewStatus(ClinVarData.ReviewStatus) - 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(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData.Builder
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.PhenopacketCommand

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.TsvDifferential
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.TsvDifferential
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.MutationTasterScore
SCORE_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
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.PhenopacketCommand
SEQUENCE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: n.b. this is the LOWEST value in the jannovar enum
SEQUENCE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: n.b. this is the LOWEST value in the jannovar enum
setAc(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: AF doesn't need storing as it is calculated as AC/AN
setAge(String) - Method in class org.monarchinitiative.lirical.cli.yaml.YamlConfig
setAlleleId(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
setAlleleIdBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: Deprecated.
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;
setAn(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1-3 bytes (Varint - 2^24 = 16777216 max)
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: .ClinVar clinVar = 3;
setClinVar(AlleleProto.ClinVar.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: .ClinVar clinVar = 3;
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
setField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
setField(Descriptors.FieldDescriptor, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
setFrequencies(int, AlleleProto.Frequency) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
setFrequencies(int, AlleleProto.Frequency.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .Frequency frequencies = 4;
setFrequency(float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 4 bytes
setFrequencySource(AlleleProto.FrequencySource) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte (Varint)
setFrequencySourceValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte (Varint)
setGeneId(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_id = 8;
setGeneIdBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_id = 8;
setGenesWithVar(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setGenesWithVar(long) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setGeneSymbol(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_symbol = 7;
setGeneSymbolBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string gene_symbol = 7;
setGlobalMode(boolean) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
setGlobalMode(boolean) - Method in class org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
setHgvsCdna(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_cdna = 10;
setHgvsCdnaBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_cdna = 10;
setHgvsProtein(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_protein = 11;
setHgvsProteinBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string hgvs_protein = 11;
setHom(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder: 1 byte
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
setPathogenicityScores(int, AlleleProto.PathogenicityScore) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
setPathogenicityScores(int, AlleleProto.PathogenicityScore.Builder) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder: repeated .PathogenicityScore pathogenicityScores = 5;
setPathogenicitySource(AlleleProto.PathogenicitySource) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: .PathogenicitySource pathogenicitySource = 1;
setPathogenicitySourceValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: .PathogenicitySource pathogenicitySource = 1;
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
setRepeatedField(Descriptors.FieldDescriptor, int, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
setRepeatedField(Descriptors.FieldDescriptor, int, Object) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
setReviewStatus(AlleleProto.ClinVar.ReviewStatus) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ReviewStatus reviewStatus = 4;
setReviewStatusValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .ClinVar.ReviewStatus 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
setScore(float) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder: float score = 2;
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
setTargetDiseases(Collection<TermId>) - Method in class org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
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
setUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency.Builder
setUnknownFields(UnknownFieldSet) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore.Builder
setVariantEffect(AlleleProto.VariantEffect) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .VariantEffect variant_effect = 9;
setVariantEffectValue(int) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: .VariantEffect variant_effect = 9;
setVariationId(String) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string variationId = 6;
setVariationIdBytes(ByteString) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder: string variationId = 6;
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.
shouldLoadOrpha2Gene(boolean) - Method in class org.monarchinitiative.lirical.configuration.LiricalBuilder
showDiseasesWithNoDeleteriousVariants() - Method in class org.monarchinitiative.lirical.core.output.OutputOptions
SIFT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SIFT = 5;
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
SIFT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SIFT = 5;
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
size() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
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.MutationTasterScore
source() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
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_ACCEPTOR_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_ACCEPTOR_VARIANT = 19;
SPLICE_ACCEPTOR_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_ACCEPTOR_VARIANT = 19;
SPLICE_AI - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SPLICE_AI = 10;
SPLICE_AI - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
SPLICE_AI_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: SPLICE_AI = 10;
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_DONOR_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_DONOR_VARIANT = 20;
SPLICE_DONOR_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_DONOR_VARIANT = 20;
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.
SPLICE_REGION_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_REGION_VARIANT = 30;
SPLICE_REGION_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICE_REGION_VARIANT = 30;
SpliceAiScore - Class in org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity
SPLICING_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICING_VARIANT = 61;
SPLICING_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SPLICING_VARIANT = 61;
starRating() - Method in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ReviewStatus
starRating() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData: Returns the ClinVar star rating.
START_LOST - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: START_LOST = 18;
START_LOST_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: START_LOST = 18;
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.
STOP_GAINED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_GAINED = 16;
STOP_GAINED_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_GAINED = 16;
STOP_LOST - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_LOST = 17;
STOP_LOST_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_LOST = 17;
STOP_RETAINED_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_RETAINED_VARIANT = 31;
STOP_RETAINED_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STOP_RETAINED_VARIANT = 31;
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.
STRUCTURAL_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STRUCTURAL_VARIANT = 57;
STRUCTURAL_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: STRUCTURAL_VARIANT = 57;
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.PhenopacketCommand
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.
SYNONYMOUS_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SYNONYMOUS_VARIANT = 33;
SYNONYMOUS_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: SYNONYMOUS_VARIANT = 33;

T

targetDiseases() - Method in interface org.monarchinitiative.lirical.core.analysis.AnalysisOptions: Limit the analysis to specific diseases.
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.exomiser.core.proto.AlleleProto.PathogenicitySource: An unspecified source for use in testing new pathogenicity scores
TEST - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
TEST_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: An unspecified source for use in testing new pathogenicity scores
TestResult - Class in org.monarchinitiative.lirical.core.analysis: This class organizes information about the result of a test.
TF_BINDING_SITE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TF_BINDING_SITE_VARIANT = 50;
TF_BINDING_SITE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TF_BINDING_SITE_VARIANT = 50;
TFBS_ABLATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TFBS_ABLATION = 48;
TFBS_ABLATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TFBS_ABLATION = 48;
TFBS_AMPLIFICATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TFBS_AMPLIFICATION = 49;
TFBS_AMPLIFICATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TFBS_AMPLIFICATION = 49;
THOUSAND_GENOMES - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
THREE_PRIME_UTR_EXON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_EXON_VARIANT = 37;
THREE_PRIME_UTR_EXON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_EXON_VARIANT = 37;
THREE_PRIME_UTR_INTRON_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_INTRON_VARIANT = 39;
THREE_PRIME_UTR_INTRON_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_INTRON_VARIANT = 39;
THREE_PRIME_UTR_TRUNCATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_TRUNCATION = 28;
THREE_PRIME_UTR_TRUNCATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: THREE_PRIME_UTR_TRUNCATION = 28;
toAlleleKey(int, int, String, String) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
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
toBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
toBuilder() - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore
toBuilder() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
toBuilder() - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
toClinVarData(AlleleProto.ClinVar) - Static method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
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.exomiser.core.proto.AlleleProto.FrequencySource: TOPMED = 2;
TOPMED - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
TOPMED_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: TOPMED = 2;
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 record class org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResources: Returns a string representation of this record class.
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.CaddScore
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
TRANSCRIPT_ABLATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSCRIPT_ABLATION = 2;
TRANSCRIPT_ABLATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSCRIPT_ABLATION = 2;
TRANSCRIPT_AMPLIFICATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSCRIPT_AMPLIFICATION = 12;
TRANSCRIPT_AMPLIFICATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSCRIPT_AMPLIFICATION = 12;
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: Transcript database provides a collection of transcript definitions to use for functional variant annotation.
transcriptDb - Variable in class org.monarchinitiative.lirical.background.BackgroundFrequencyCommand
TRANSLOCATION - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSLOCATION = 6;
TRANSLOCATION_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: TRANSLOCATION = 6;
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: Transcripts sourced from UCSC Genome Browser.
UK10K - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: UK10K = 3;
UK10K - Enum constant in enum class org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
UK10K_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: UK10K = 3;
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_PATH_SOURCE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: UNKNOWN_PATH_SOURCE = 0;
UNKNOWN_PATH_SOURCE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: UNKNOWN_PATH_SOURCE = 0;
UNKNOWN_VERSION_PLACEHOLDER - Static variable in class org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource
UNRECOGNIZED - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect
UNSPECIFIED_FREQUENCY_SOURCE - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: UNSPECIFIED_FREQUENCY_SOURCE = 0;
UNSPECIFIED_FREQUENCY_SOURCE_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: UNSPECIFIED_FREQUENCY_SOURCE = 0;
UNUSUAL_BACKGROUND_FREQUENCY - Enum constant in enum class org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
UPSTREAM_GENE_VARIANT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: UPSTREAM_GENE_VARIANT = 45;
UPSTREAM_GENE_VARIANT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: UPSTREAM_GENE_VARIANT = 45;
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(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: Deprecated.
valueOf(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: Deprecated.
valueOf(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: Deprecated.
valueOf(int) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: 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(Descriptors.EnumValueDescriptor) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: Returns the enum constant of this class with the specified name.
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: Returns the enum constant of this class with the specified name.
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: Returns the enum constant of this class with the specified name.
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: 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.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: 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.ClinVarData.ReviewStatus: 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.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.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.exomiser.core.proto.AlleleProto.PathogenicitySource: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect: 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.ClinVarData.ReviewStatus: 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_EFFECT - Enum constant in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: A default score derived from the predicted variant effect
VARIANT_EFFECT_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
VARIANT_EFFECT_VALUE - Static variable in enum class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource: A default score derived from the predicted variant effect
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
variantEffect(VariantEffect) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.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.TsvDifferential
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
variationId(String) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
VARIATIONID_FIELD_NUMBER - Static variable in class org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar
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.PhenopacketCommand
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, T) - Method in class org.monarchinitiative.lirical.exomiser_db_adapter.serializers.ProtobufDataType
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
writeTo(CodedOutputStream) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency
writeTo(CodedOutputStream) - Method in class org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore

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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