Package org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity

Record Class ClinVarData

java.lang.Object
java.lang.Record
org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
public record ClinVarData(String variationId, ClinVarData.ClinSig primaryInterpretation, Map<ClinVarData.ClinSig,Integer> conflictingInterpretationCounts, Set<ClinVarData.ClinSig> secondaryInterpretations, ClinVarData.ReviewStatus reviewStatus, Map<String,ClinVarData.ClinSig> includedAlleles, String geneSymbol, de.charite.compbio.jannovar.annotation.VariantEffect variantEffect, String hgvsCdna, String hgvsProtein) extends Record
Immutable data class representing data from the ClinVar resource, with explanation of the data from https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
Since:
10.1.0
Author:
Jules Jacobsen <j.jacobsen@qmul.ac.uk>

  • Constructor Details

    • ClinVarData

      public ClinVarData(String variationId, ClinVarData.ClinSig primaryInterpretation, Map<ClinVarData.ClinSig,Integer> conflictingInterpretationCounts, Set<ClinVarData.ClinSig> secondaryInterpretations, ClinVarData.ReviewStatus reviewStatus, Map<String,ClinVarData.ClinSig> includedAlleles, String geneSymbol, de.charite.compbio.jannovar.annotation.VariantEffect variantEffect, String hgvsCdna, String hgvsProtein)
      Creates an instance of a ClinVarData record class.
      Parameters:
      variationId - the value for the variationId record component
      primaryInterpretation - the value for the primaryInterpretation record component
      conflictingInterpretationCounts - the value for the conflictingInterpretationCounts record component
      secondaryInterpretations - the value for the secondaryInterpretations record component
      reviewStatus - the value for the reviewStatus record component
      includedAlleles - the value for the includedAlleles record component
      geneSymbol - the value for the geneSymbol record component
      variantEffect - the value for the variantEffect record component
      hgvsCdna - the value for the hgvsCdna record component
      hgvsProtein - the value for the hgvsProtein record component

  • Method Details

    • empty

      public static ClinVarData empty()

    • isEmpty

      public boolean isEmpty()

    • isSecondaryAssociationRiskFactorOrOther

      public boolean isSecondaryAssociationRiskFactorOrOther()
      Returns:
      true if the secondary CLNSIG contains one of 'affects', 'other', 'association', 'risk factor' or 'protective'. These are considered unimportant from the mendelian disease perspective. The category 'drug response' is *not* included here as these are also associated with CFTR alleles known to be pathogenic/likely pathogenic for CF.
      Since:
      13.0.0

    • starRating

      public int starRating()
      Returns the ClinVar star rating. In the VCF CLNREVSTAT the star ratings are mapped as follows: 

       1* criteria_provided,_conflicting_interpretations
 1* criteria_provided,_single_submitter
 2* criteria_provided,_multiple_submitters,_no_conflicts
 3* reviewed_by_expert_panel
 4* practice_guideline
      Returns:
      an integer value between 0 (worst) and 4 (best)
      Since:
      13.0.0

    • toString

      public String toString()
      Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
      Specified by:
      toString in class Record
      Returns:
      a string representation of this object

    • toBuilder

      public ClinVarData.Builder toBuilder()

    • builder

      public static ClinVarData.Builder builder()

    • hashCode

      public final int hashCode()
      Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
      Specified by:
      hashCode in class Record
      Returns:
      a hash code value for this object

    • equals

      public final boolean equals(Object o)
      Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. All components in this record class are compared with Objects::equals(Object,Object).
      Specified by:
      equals in class Record
      Parameters:
      o - the object with which to compare
      Returns:
      true if this object is the same as the o argument; false otherwise.

    • variationId

      public String variationId()
      Returns the value of the variationId record component.
      Returns:
      the value of the variationId record component

    • primaryInterpretation

      public ClinVarData.ClinSig primaryInterpretation()
      Returns the value of the primaryInterpretation record component.
      Returns:
      the value of the primaryInterpretation record component

    • conflictingInterpretationCounts

      public Map<ClinVarData.ClinSig,Integer> conflictingInterpretationCounts()
      Returns the value of the conflictingInterpretationCounts record component.
      Returns:
      the value of the conflictingInterpretationCounts record component

    • secondaryInterpretations

      public Set<ClinVarData.ClinSig> secondaryInterpretations()
      Returns the value of the secondaryInterpretations record component.
      Returns:
      the value of the secondaryInterpretations record component

    • reviewStatus

      public ClinVarData.ReviewStatus reviewStatus()
      Returns the value of the reviewStatus record component.
      Returns:
      the value of the reviewStatus record component

    • includedAlleles

      public Map<String,ClinVarData.ClinSig> includedAlleles()
      Returns the value of the includedAlleles record component.
      Returns:
      the value of the includedAlleles record component

    • geneSymbol

      public String geneSymbol()
      Returns the value of the geneSymbol record component.
      Returns:
      the value of the geneSymbol record component

    • variantEffect

      public de.charite.compbio.jannovar.annotation.VariantEffect variantEffect()
      Returns the value of the variantEffect record component.
      Returns:
      the value of the variantEffect record component

    • hgvsCdna

      public String hgvsCdna()
      Returns the value of the hgvsCdna record component.
      Returns:
      the value of the hgvsCdna record component

    • hgvsProtein

      public String hgvsProtein()
      Returns the value of the hgvsProtein record component.
      Returns:
      the value of the hgvsProtein record component