Deprecated API

Contents

• Terminally Deprecated
• Methods
• Enum Constants

Terminally Deprecated Elements

Element	Description
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.ONE_DELETERIOUS_CLINVAR_VARIANT_IN_AD	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD instead.
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.TWO_DELETERIOUS_CLINVAR_VARIANTS_IN_AR	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR instead.
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.UNKNOWN	the field will be removed in v3.0.0.
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation.of(GeneIdentifier, double, String)	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrWithExplanation.of(GeneIdentifier, GenotypeLrMatchType, double, String) instead.
org.monarchinitiative.lirical.core.model.VariantMetadata.clinvarClnSig()	since 2.0.0-RC3 and will be removed in v3.0.0. Use VariantMetadata.clinVarAlleleData() instead.
org.monarchinitiative.lirical.core.model.VariantMetadata.compareByPathogenicity(VariantMetadata, VariantMetadata)	the function has been deprecated without replacement and will be removed in v3.0.0.

Deprecated Methods

Method	Description
org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder.getMutableProperties()
org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder.getProperties()
org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.getProperties()
org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder.getProperties()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder.getIncludedAlleles()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder.getIncludedAllelesValue()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder.getMutableIncludedAlleles()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder.getMutableIncludedAllelesValue()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig.valueOf(int)
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.getIncludedAlleles()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.getIncludedAllelesValue()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder.getIncludedAlleles()
org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder.getIncludedAllelesValue()
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation.of(GeneIdentifier, double, String)	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrWithExplanation.of(GeneIdentifier, GenotypeLrMatchType, double, String) instead.
org.monarchinitiative.lirical.core.model.VariantMetadata.clinvarClnSig()	since 2.0.0-RC3 and will be removed in v3.0.0. Use VariantMetadata.clinVarAlleleData() instead.
org.monarchinitiative.lirical.core.model.VariantMetadata.compareByPathogenicity(VariantMetadata, VariantMetadata)	the function has been deprecated without replacement and will be removed in v3.0.0.

Deprecated Enum Constants

Enum Constant	Description
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.ONE_DELETERIOUS_CLINVAR_VARIANT_IN_AD	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD instead.
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.TWO_DELETERIOUS_CLINVAR_VARIANTS_IN_AR	the method has been deprecated and will be removed in v3.0.0. Use GenotypeLrMatchType.TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR instead.
org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType.UNKNOWN	the field will be removed in v3.0.0.