Package org.monarchinitiative.lirical.io.analysis

Class PhenopacketData

java.lang.Object
org.monarchinitiative.lirical.io.analysis.PhenopacketData
All Implemented Interfaces:
SanitationInputs
public class PhenopacketData extends Object implements SanitationInputs
Phenopacket attributes that are relevant for LIRICAL.

  • Method Details

    • sampleId

      public String sampleId()
      Specified by:
      sampleId in interface SanitationInputs
      Returns:
      a string with the sample ID or null if not available.

    • presentHpoTerms

      public List<String> presentHpoTerms()
      Specified by:
      presentHpoTerms in interface SanitationInputs
      Returns:
      a list with CURIEs of HPO terms that represent the phenotypic features observed in the index patient.

    • presentHpoTermIds

      public Stream<org.monarchinitiative.phenol.ontology.data.TermId> presentHpoTermIds()

    • excludedHpoTerms

      public List<String> excludedHpoTerms()
      Specified by:
      excludedHpoTerms in interface SanitationInputs
      Returns:
      a list with CURIEs of HPO terms that represent the phenotypic features that were investigated and excluded in the index patient.

    • excludedHpoTermIds

      public Stream<org.monarchinitiative.phenol.ontology.data.TermId> excludedHpoTermIds()

    • age

      public String age()
      Specified by:
      age in interface SanitationInputs
      Returns:
      a string with the age or null if not available.

    • parseAge

      public Optional<Age> parseAge()
      Try to parse the age and return an empty optional if the parsing fails.

    • sex

      public String sex()
      Specified by:
      sex in interface SanitationInputs
      Returns:
      a string with the sex or null if not available.

    • parseSex

      public Optional<Sex> parseSex()
      Try to parse the sex and return an empty optional if the parsing fails.

    • vcf

      public Path vcf()
      Specified by:
      vcf in interface SanitationInputs
      Returns:
      a path with the path of the VCF file with variants or null if not available.

    • genomeAssembly

      public Optional<String> genomeAssembly()

    • variants

      public Iterable<GenotypedVariant> variants()

    • diseaseIds

      public List<org.monarchinitiative.phenol.ontology.data.TermId> diseaseIds()

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object