Package org.monarchinitiative.lirical.cli.yaml

Class YamlConfig

java.lang.Object
org.monarchinitiative.lirical.cli.yaml.YamlConfig
All Implemented Interfaces:
SanitationInputs
public class YamlConfig extends Object implements SanitationInputs
This class is used to input the YAML configuration file.
Author:
Peter Robinson

  • Constructor Details

    • YamlConfig

      public YamlConfig()

  • Method Details

    • setSampleId

      public void setSampleId(String sampleId)

    • setHpoIds

      public void setHpoIds(List<String> hpoIds)

    • setNegatedHpoIds

      public void setNegatedHpoIds(List<String> negatedHpoIds)

    • setAge

      public void setAge(String age)

    • setSex

      public void setSex(String sex)

    • setVcf

      public void setVcf(String vcf)

    • getSampleId

      public String getSampleId()

    • getHpoIds

      public List<String> getHpoIds()
      Returns:
      list of HPO ids observed in the proband.

    • getNegatedHpoIds

      public List<String> getNegatedHpoIds()

    • 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.

    • 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.

    • age

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

    • sex

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

    • vcf

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

    • vcfPath

      public Optional<Path> vcfPath()