org.gel.models.participant.avro.Pedigree Maven / Gradle / Ivy
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.participant.avro;
@SuppressWarnings("all")
/** This is the concept of a family with associated phenotypes as present in the record RDParticipant */
@org.apache.avro.specific.AvroGenerated
public class Pedigree extends org.apache.avro.specific.SpecificRecordBase implements org.apache.avro.specific.SpecificRecord {
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"record\",\"name\":\"Pedigree\",\"namespace\":\"org.gel.models.participant.avro\",\"doc\":\"This is the concept of a family with associated phenotypes as present in the record RDParticipant\",\"fields\":[{\"name\":\"versionControl\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VersionControl\",\"fields\":[{\"name\":\"GitVersionControl\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"This is the version for the entire set of data models as referred to the Git release tag\",\"default\":\"1.3.0\"}]}],\"doc\":\"Model version number\"},{\"name\":\"LDPCode\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"LDP Code (Local Delivery Partner)\"},{\"name\":\"familyId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Family identifier which internally translate to a sample set\"},{\"name\":\"members\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PedigreeMember\",\"doc\":\"This defines a RD Participant (demographics and pedigree information)\",\"fields\":[{\"name\":\"pedigreeId\",\"type\":[\"null\",\"int\"],\"doc\":\"Numbering used to refer to each member of the pedigree\"},{\"name\":\"isProband\",\"type\":[\"null\",\"boolean\"],\"doc\":\"If this field is true, the member should be considered the proband of this family\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"participantId. This is the human readable ID in GMS\"},{\"name\":\"participantQCState\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ParticipantQCState\",\"doc\":\"QCState Status\",\"symbols\":[\"noState\",\"passedMedicalReviewReadyForInterpretation\",\"passedMedicalReviewNotReadyForInterpretation\",\"queryToGel\",\"queryToGMC\",\"failed\"]}],\"doc\":\"participantQCState\"},{\"name\":\"gelSuperFamilyId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"superFamily id, this id is built as a concatenation of all\\n families id in this superfamily i.e, fam10024_fam100457.\\n NOTE: Retired for GMS\"},{\"name\":\"sex\",\"type\":{\"type\":\"enum\",\"name\":\"Sex\",\"doc\":\"Sex\",\"symbols\":[\"MALE\",\"FEMALE\",\"UNKNOWN\"]},\"doc\":\"Sex of the Participant\"},{\"name\":\"personKaryotypicSex\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"PersonKaryotipicSex\",\"doc\":\"Karyotipic Sex\",\"symbols\":[\"UNKNOWN\",\"XX\",\"XY\",\"XO\",\"XXY\",\"XXX\",\"XXYY\",\"XXXY\",\"XXXX\",\"XYY\",\"OTHER\"]}],\"doc\":\"Karyotypic sex of the participant as previously established or by looking at the GEL genome\"},{\"name\":\"yearOfBirth\",\"type\":[\"null\",\"int\"],\"doc\":\"Year of Birth\"},{\"name\":\"fatherId\",\"type\":[\"null\",\"int\"],\"doc\":\"refers to the pedigreeId of the father\\n Id of the parent, if unknown then no parent is referenced. Parents may need to be entered even if no data is known\\n about them in order to unambiguously reconstruct the pedigree.\"},{\"name\":\"motherId\",\"type\":[\"null\",\"int\"],\"doc\":\"refers to the pedigreeId of the mother\\n Id of the parent, if unknown then no parent is referenced. Parents may need to be entered even if no data is known\\n about them in order to unambiguously reconstruct the pedigree.\"},{\"name\":\"superFatherId\",\"type\":[\"null\",\"int\"],\"doc\":\"this id is built using the original familyId and the original pedigreeId of the father\\n NOTE: retired for GMS\"},{\"name\":\"superMotherId\",\"type\":[\"null\",\"int\"],\"doc\":\"this id is built using the original familyId and the original pedigreeId of the mother\\n NOTE: Retired for GMS\"},{\"name\":\"twinGroup\",\"type\":[\"null\",\"int\"],\"doc\":\"Each twin group is numbered, i.e. all members of a group of multiparous births receive the same number\"},{\"name\":\"monozygotic\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"TernaryOption\",\"doc\":\"This defines a yes/no/unknown case\",\"symbols\":[\"yes\",\"no\",\"unknown\"]}],\"doc\":\"A property of the twinning group but should be entered for all members\"},{\"name\":\"adoptedStatus\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"AdoptedStatus\",\"doc\":\"adoptedin means adopted into the family\\n adoptedout means child belonged to the family and was adopted out\",\"symbols\":[\"notadopted\",\"adoptedin\",\"adoptedout\"]}],\"doc\":\"Adopted Status\"},{\"name\":\"lifeStatus\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"LifeStatus\",\"doc\":\"Life Status\",\"symbols\":[\"ALIVE\",\"ABORTED\",\"DECEASED\",\"UNBORN\",\"STILLBORN\",\"MISCARRIAGE\"]}],\"doc\":\"Life Status\"},{\"name\":\"consanguineousParents\",\"type\":[\"null\",\"TernaryOption\"],\"doc\":\"The parents of this participant has a consanguineous relationship\"},{\"name\":\"affectionStatus\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"AffectionStatus\",\"doc\":\"Affection Status\",\"symbols\":[\"UNAFFECTED\",\"AFFECTED\",\"UNCERTAIN\"]}],\"doc\":\"Affection Status\"},{\"name\":\"disorderList\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Disorder\",\"doc\":\"This is quite GEL specific. This is the way is stored in ModelCatalogue and PanelApp.\\n Currently all specific disease titles are assigned to a disease subgroup so really only specificDisease needs to be\\n completed but we add the others for generality\",\"fields\":[{\"name\":\"diseaseGroup\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"This is Level2 Title for this disorder\"},{\"name\":\"diseaseSubGroup\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"This is Level3 Title for this disorder\"},{\"name\":\"specificDisease\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"This is Level4 Title for this disorder.\\n In GMS, this is the clinicalIndicationFullName/clinicalIndicationCode.\"},{\"name\":\"ageOfOnset\",\"type\":[\"null\",\"float\"],\"doc\":\"Age of onset in years\"}]}}],\"doc\":\"Clinical Data (disorders). If the family member is unaffected as per affectionStatus then this list is empty.\"},{\"name\":\"hpoTermList\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"HpoTerm\",\"doc\":\"This defines an HPO term and its modifiers (possibly multiple)\\n If HPO term presence is unknown we don't have a entry on the list\",\"fields\":[{\"name\":\"term\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Identifier of the HPO term\"},{\"name\":\"termPresence\",\"type\":[\"null\",\"TernaryOption\"],\"doc\":\"This is whether the term is present in the participant (default is unknown) yes=term is present in participant,\\n no=term is not present\"},{\"name\":\"hpoBuildNumber\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"hpoBuildNumber\"},{\"name\":\"modifiers\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"HpoTermModifiers\",\"doc\":\"HPO Modifiers\\n For GMS, hpoModifierCode and hpoModifierVersion will be used\",\"fields\":[{\"name\":\"laterality\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Laterality\",\"symbols\":[\"RIGHT\",\"UNILATERAL\",\"BILATERAL\",\"LEFT\"]}]},{\"name\":\"progression\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Progression\",\"symbols\":[\"PROGRESSIVE\",\"NONPROGRESSIVE\"]}]},{\"name\":\"severity\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Severity\",\"symbols\":[\"BORDERLINE\",\"MILD\",\"MODERATE\",\"SEVERE\",\"PROFOUND\"]}]},{\"name\":\"spatialPattern\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"SpatialPattern\",\"symbols\":[\"DISTAL\",\"GENERALIZED\",\"LOCALIZED\",\"PROXIMAL\"]}]},{\"name\":\"hpoModifierCode\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"hpoModifierVersion\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}],\"doc\":\"Modifier associated with the HPO term\"},{\"name\":\"ageOfOnset\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"AgeOfOnset\",\"symbols\":[\"EMBRYONAL_ONSET\",\"FETAL_ONSET\",\"NEONATAL_ONSET\",\"INFANTILE_ONSET\",\"CHILDHOOD_ONSET\",\"JUVENILE_ONSET\",\"YOUNG_ADULT_ONSET\",\"LATE_ONSET\",\"MIDDLE_AGE_ONSET\"]}],\"doc\":\"Age of onset in months\"}]}}],\"doc\":\"Clinical Data (HPO terms)\"},{\"name\":\"ancestries\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"Ancestries\",\"doc\":\"Ancestries, defined as Ethnic category(ies) and Chi-square test\",\"fields\":[{\"name\":\"mothersEthnicOrigin\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"EthnicCategory\",\"doc\":\"This is the list of ethnicities in ONS16\\n\\n * `D`: Mixed: White and Black Caribbean\\n * `E`: Mixed: White and Black African\\n * `F`: Mixed: White and Asian\\n * `G`: Mixed: Any other mixed background\\n * `A`: White: British\\n * `B`: White: Irish\\n * `C`: White: Any other White background\\n * `L`: Asian or Asian British: Any other Asian background\\n * `M`: Black or Black British: Caribbean\\n * `N`: Black or Black British: African\\n ","* `H`: Asian or Asian British: Indian\\n * `J`: Asian or Asian British: Pakistani\\n * `K`: Asian or Asian British: Bangladeshi\\n * `P`: Black or Black British: Any other Black background\\n * `S`: Other Ethnic Groups: Any other ethnic group\\n * `R`: Other Ethnic Groups: Chinese\\n * `Z`: Not stated\",\"symbols\":[\"D\",\"E\",\"F\",\"G\",\"A\",\"B\",\"C\",\"L\",\"M\",\"N\",\"H\",\"J\",\"K\",\"P\",\"S\",\"R\",\"Z\"]}],\"doc\":\"Mother's Ethnic Origin\"},{\"name\":\"mothersOtherRelevantAncestry\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Mother's Ethnic Origin Description\"},{\"name\":\"fathersEthnicOrigin\",\"type\":[\"null\",\"EthnicCategory\"],\"doc\":\"Father's Ethnic Origin\"},{\"name\":\"fathersOtherRelevantAncestry\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Father's Ethnic Origin Description\"},{\"name\":\"chiSquare1KGenomesPhase3Pop\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"ChiSquare1KGenomesPhase3Pop\",\"doc\":\"Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations\",\"fields\":[{\"name\":\"kgSuperPopCategory\",\"type\":{\"type\":\"enum\",\"name\":\"KgSuperPopCategory\",\"doc\":\"1K Genomes project super populations\",\"symbols\":[\"AFR\",\"AMR\",\"EAS\",\"EUR\",\"SAS\"]},\"doc\":\"1K Super Population\"},{\"name\":\"kgPopCategory\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"KgPopCategory\",\"doc\":\"1K Genomes project populations\",\"symbols\":[\"ACB\",\"ASW\",\"BEB\",\"CDX\",\"CEU\",\"CHB\",\"CHS\",\"CLM\",\"ESN\",\"FIN\",\"GBR\",\"GIH\",\"GWD\",\"IBS\",\"ITU\",\"JPT\",\"KHV\",\"LWK\",\"MSL\",\"MXL\",\"PEL\",\"PJL\",\"PUR\",\"STU\",\"TSI\",\"YRI\"]}],\"doc\":\"1K Population\"},{\"name\":\"chiSquare\",\"type\":\"double\",\"doc\":\"Chi-square test for goodness of fit of this sample to this 1000 Genomes Phase 3 population\"}]}}],\"doc\":\"Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations\"}]}],\"doc\":\"Participant's ancestries, defined as Mother's/Father's Ethnic Origin and Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations.\\n NOTE: for GMS this field has been deprecated in favour of clinicalEthnicities\"},{\"name\":\"consentStatus\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"ConsentStatus\",\"doc\":\"Consent Status for 100k program\",\"fields\":[{\"name\":\"programmeConsent\",\"type\":\"boolean\",\"doc\":\"Is this individual consented to the programme?\\n It could simply be a family member that is not consented but for whom affection status is known\",\"default\":false},{\"name\":\"primaryFindingConsent\",\"type\":\"boolean\",\"doc\":\"Consent for feedback of primary findings?\",\"default\":false},{\"name\":\"secondaryFindingConsent\",\"type\":\"boolean\",\"doc\":\"Consent for secondary finding lookup\",\"default\":false},{\"name\":\"carrierStatusConsent\",\"type\":\"boolean\",\"doc\":\"Consent for carrier status check?\",\"default\":false}]}],\"doc\":\"What has this participant consented to?\\n A participant that has been consented to the programme should also have sequence data associated with them; however\\n this needs to be programmatically checked\"},{\"name\":\"testConsentStatus\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"GmsConsentStatus\",\"doc\":\"Consent Status for GMS\",\"fields\":[{\"name\":\"programmeConsent\",\"type\":{\"type\":\"enum\",\"name\":\"GenericConsent\",\"doc\":\"clinicalEthnicities supersedes Ancestries in GMS\",\"symbols\":[\"yes\",\"no\",\"undefined\",\"not_applicable\"]},\"doc\":\"Is this individual consented to the programme? It could simply be a family member that is not consented\\n but for whom affection status is known\"},{\"name\":\"primaryFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for feedback of primary findings?\\n RD: Primary Findings\\n Cancer: PrimaryFindings is somatic + pertinent germline findings\"},{\"name\":\"researchConsent\",\"type\":\"GenericConsent\",\"doc\":\"Research Consent\"},{\"name\":\"healthRelatedFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for secondary health related findings?\"},{\"name\":\"carrierStatusConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for carrier status check?\"},{\"name\":\"pharmacogenomicsFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for pharmacogenomics consent as secondary findings?\"}]}],\"doc\":\"What has this participant consented in the context of a Genomic Test?\"},{\"name\":\"samples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GermlineSample\",\"doc\":\"A germline sample\",\"fields\":[{\"name\":\"sampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample identifier (e.g, LP00012645_5GH))\"},{\"name\":\"labSampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Lab sample identifier\"},{\"name\":\"LDPCode\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"LDP Code (Local Delivery Partner)\"},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"SampleSource\",\"doc\":\"The source of the sample\\n NOTE: IN GMS, BONE_MARROW_ASPIRATE_TUMOUR_CELLS and BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS are deprecated as they have been separated into their respective biotypes\",\"symbols\":[\"AMNIOTIC_FLUID\",\"BLOOD\",\"BONE_MARROW\",\"BONE_MARROW_ASPIRATE_TUMOUR_CELLS\",\"BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS\",\"BUCCAL_SWAB\",\"CHORIONIC_VILLUS_SAMPLE\",\"FIBROBLAST\",\"FLUID\",\"FRESH_TISSUE_IN_CULTURE_MEDIUM\",\"OTHER\",\"SALIVA\",\"TISSUE\",\"TUMOUR\",\"URINE\"]}],\"doc\":\"Source of the sample\"},{\"name\":\"product\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Product\",\"symbols\":[\"DNA\",\"RNA\"]}],\"doc\":\"Product of the sample\"},{\"name\":\"preparationMethod\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"PreparationMethod\",\"doc\":\"In 100K, preparation Method of sample\\n NOTE: In GMS, this field is deprecated in favour of StorageMedium and Method\",\"symbols\":[\"ASPIRATE\",\"CD128_SORTED_CELLS\",\"CD138_SORTED_CELLS\",\"EDTA\",\"FF\",\"FFPE\",\"LI_HEP\",\"ORAGENE\"]}],\"doc\":\"Preparation method\\n NOTE: In GMS, this has been deprecated in favour of Method and storageMedium\"},{\"name\":\"programmePhase\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ProgrammePhase\",\"symbols\":[\"CRUK\",\"OXFORD\",\"CLL\",\"IIP\",\"MAIN\",\"EXPT\"]}],\"doc\":\"Genomics England programme phase\"},{\"name\":\"clinicalSampleDateTime\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The time when the sample was received. In the format YYYY-MM-DDTHH:MM:SS+0000\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"participantUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Participant UId of the sample\"},{\"name\":\"sampleUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"maskedPid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"method\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Method\",\"doc\":\"In GMS, Method is defined as how the sample was taken directly from the patient\",\"symbols\":[\"ASPIRATE\",\"BIOPSY\",\"NOT_APPLICABLE\",\"RESECTION\",\"SORTED_OTHER\",\"UNKNOWN\",\"UNSORTED\",\"CD138_SORTED\"]}],\"doc\":\"In GMS, this is how the sample was extracted from the participant\"},{\"name\":\"storageMedium\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"StorageMedium\",\"doc\":\"In GMS, storage medium of sample\",\"symbols\":[\"EDTA\",\"FF\",\"LI_HEP\",\"ORAGENE\",\"FFPE\"]}],\"doc\":\"In GMS, this is what solvent/medium the sample was stored in\"},{\"name\":\"sampleType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleType as entered by the clinician in TOMs\"},{\"name\":\"sampleState\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleState as entered by the clinician in TOMs\"}]}}],\"doc\":\"This is an array containing all the samples that belong to this individual, e.g [\\\"LP00002255_GA4\\\"]\"},{\"name\":\"inbreedingCoefficient\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"InbreedingCoefficient\",\"doc\":\"Inbreeding coefficient\",\"fields\":[{\"name\":\"sampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"This is the sample id against which the coefficient was estimated\"},{\"name\":\"program\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Name of program used to calculate the coefficient\"},{\"name\":\"version\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Version of the programme\"},{\"name\":\"estimationMethod\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Where various methods for estimation exist, which method was"," used.\"},{\"name\":\"coefficient\",\"type\":\"double\",\"doc\":\"Inbreeding coefficient ideally a real number in [0,1]\"},{\"name\":\"standardError\",\"type\":[\"null\",\"double\"],\"doc\":\"Standard error of the Inbreeding coefficient\"}]}],\"doc\":\"Inbreeding Coefficient Estimation\"},{\"name\":\"additionalInformation\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"We could add a map here to store additional information for example URIs to images, ECGs, etc\\n Null by default\"},{\"name\":\"lastMenstrualPeriod\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Last Menstrual Period\"},{\"name\":\"diagnosticDetails\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"DiagnosticDetail\",\"fields\":[{\"name\":\"diagnosisCodingSystem\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Diagnosis coding system\"},{\"name\":\"diagnosisCodingSystemVersion\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Diagnosis Coding System Version\"},{\"name\":\"diagnosisCode\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Diagnosis Code\"},{\"name\":\"diagnosisDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Diagnosis description\"},{\"name\":\"diagnosisCertainty\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Diagnosis Certainty\"},{\"name\":\"ageAtOnsetInYears\",\"type\":[\"null\",\"float\"],\"doc\":\"Age at diagnosis\"}]}}],\"doc\":\"Additional set of diagnostic ontology terms\"},{\"name\":\"participantUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"ParticipantGUID in GMS\"},{\"name\":\"clinicalEthnicities\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"enum\",\"name\":\"ClinicalEthnicity\",\"doc\":\"* A British, Mixed British\\n * B Irish\\n * C Any other White background\\n * C2 Northern Irish\\n * C3 Other white, white unspecified\\n * CA English\\n * CB Scottish\\n * CC Welsh\\n * CD Cornish\\n * CE Cypriot (part not stated)\\n * CF Greek\\n * CG Greek Cypriot\\n * CH Turkish\\n * CJ Turkish Cypriot\\n * CK Italian\\n * CL Irish Traveller\\n * CM Traveller\\n * CN Gypsy/Romany\\n * CP Polish\\n * CQ All republics which made up the former USSR\\n * CR Kosovan\\n * CS Albanian\\n * CT Bosnian\\n * CU Croatian\\n * CV Serbian\\n * CW Other republics which made up the former Yugoslavia\\n * CX Mixed white\\n * CY Other white European, European unspecified, European mixed\\n * D White and Black Caribbean\\n * E White and Black African\\n * F White and Asian\\n * G Any other mixed background\\n * GA Black and Asian\\n * GB Black and Chinese\\n * GC Black and White\\n * GD Chinese and White\\n * GE Asian and Chinese\\n * GF Other Mixed, Mixed Unspecified\\n * H Indian or British Indian\\n * J Pakistani or British Pakistani\\n * K Bangladeshi or British Bangladeshi\\n * L Any other Asian background\\n * LA Mixed Asian\\n * LB Punjabi\\n * LC Kashmiri\\n * LD East African Asian\\n * LE Sri Lanka\\n * LF Tamil\\n * LG Sinhalese\\n * LH British Asian\\n * LJ Caribbean Asian\\n * LK Other Asian, Asian unspecified\\n * M Caribbean\\n * N African\\n * P Any other Black background\\n * PA Somali\\n * PB Mixed Black\\n * PC Nigerian\\n * PD Black British\\n * PE Other Black, Black unspecified\\n * R Chinese\\n * S Any other ethnic group\\n * S1 Ashkenazi\\n * S2 Sephardi\\n * SA Vietnamese\\n * SB Japanese\\n * SC Filipino\\n * SD Malaysian\\n * SE Any Other Group\\n * Z Not stated\",\"symbols\":[\"A\",\"B\",\"C\",\"C2\",\"C3\",\"CA\",\"CB\",\"CC\",\"CD\",\"CE\",\"CF\",\"CG\",\"CH\",\"CJ\",\"CK\",\"CL\",\"CM\",\"CN\",\"CP\",\"CQ\",\"CR\",\"CS\",\"CT\",\"CU\",\"CV\",\"CW\",\"CX\",\"CY\",\"D\",\"E\",\"F\",\"G\",\"GA\",\"GB\",\"GC\",\"GD\",\"GE\",\"GF\",\"H\",\"J\",\"K\",\"L\",\"LA\",\"LB\",\"LC\",\"LD\",\"LE\",\"LF\",\"LG\",\"LH\",\"LJ\",\"LK\",\"M\",\"N\",\"P\",\"PA\",\"PB\",\"PC\",\"PD\",\"PE\",\"R\",\"S\",\"S1\",\"S2\",\"SA\",\"SB\",\"SC\",\"SD\",\"SE\",\"Z\"]}}],\"doc\":\"ClinicalEthnicity as defined for GMS\"},{\"name\":\"previousTreatment\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PreviousTreatment\",\"doc\":\"In GMS, Previous Treatment of Patient\",\"fields\":[{\"name\":\"previousTreatmentType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"previousTreatmentName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"previousTreatmentDate\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"Date\",\"doc\":\"This defines a date record\",\"fields\":[{\"name\":\"year\",\"type\":\"int\",\"doc\":\"Format YYYY\"},{\"name\":\"month\",\"type\":[\"null\",\"int\"],\"doc\":\"Format MM. e.g June is 06\"},{\"name\":\"day\",\"type\":[\"null\",\"int\"],\"doc\":\"Format DD e.g. 12th of October is 12\"}]}]}]}}],\"doc\":\"For GMS cases, previous Treatment History\"}]}},\"doc\":\"List of members of a pedigree\"},{\"name\":\"analysisPanels\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AnalysisPanel\",\"doc\":\"An analysis panel\",\"fields\":[{\"name\":\"specificDisease\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The specific disease that a panel tests\"},{\"name\":\"panelName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The name of the panel\"},{\"name\":\"panelId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Id of the panel\"},{\"name\":\"panelVersion\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The version of the panel\"},{\"name\":\"reviewOutcome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Deprecated\"},{\"name\":\"multipleGeneticOrigins\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Deprecated\"}]}}],\"doc\":\"List of panels\"},{\"name\":\"diseasePenetrances\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"DiseasePenetrance\",\"doc\":\"A disease penetrance definition\",\"fields\":[{\"name\":\"specificDisease\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The disease to which the penetrance applies\"},{\"name\":\"penetrance\",\"type\":{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetrance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]},\"doc\":\"The penetrance\"}]}}],\"doc\":\"List of disease penetrances. Moved to referralTest for GMS\"},{\"name\":\"readyForAnalysis\",\"type\":\"boolean\",\"doc\":\"Flag indicating if a pedigree is ready for analysis\"},{\"name\":\"familyQCState\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"FamilyQCState\",\"doc\":\"FamilyQCState\",\"symbols\":[\"noState\",\"passedMedicalReviewReadyForInterpretation\",\"passedMedicalReviewNotReadyForInterpretation\",\"queryToGel\",\"queryToGMC\",\"failed\"]}],\"doc\":\"The family quality control status\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Model version number */
private org.gel.models.participant.avro.VersionControl versionControl;
/** LDP Code (Local Delivery Partner) */
private java.lang.String LDPCode;
/** Family identifier which internally translate to a sample set */
private java.lang.String familyId;
/** List of members of a pedigree */
private java.util.List members;
/** List of panels */
private java.util.List analysisPanels;
/** List of disease penetrances. Moved to referralTest for GMS */
private java.util.List diseasePenetrances;
/** Flag indicating if a pedigree is ready for analysis */
private boolean readyForAnalysis;
/** The family quality control status */
private org.gel.models.participant.avro.FamilyQCState familyQCState;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public Pedigree() {}
/**
* All-args constructor.
*/
public Pedigree(org.gel.models.participant.avro.VersionControl versionControl, java.lang.String LDPCode, java.lang.String familyId, java.util.List members, java.util.List analysisPanels, java.util.List diseasePenetrances, java.lang.Boolean readyForAnalysis, org.gel.models.participant.avro.FamilyQCState familyQCState) {
this.versionControl = versionControl;
this.LDPCode = LDPCode;
this.familyId = familyId;
this.members = members;
this.analysisPanels = analysisPanels;
this.diseasePenetrances = diseasePenetrances;
this.readyForAnalysis = readyForAnalysis;
this.familyQCState = familyQCState;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return versionControl;
case 1: return LDPCode;
case 2: return familyId;
case 3: return members;
case 4: return analysisPanels;
case 5: return diseasePenetrances;
case 6: return readyForAnalysis;
case 7: return familyQCState;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: versionControl = (org.gel.models.participant.avro.VersionControl)value$; break;
case 1: LDPCode = (java.lang.String)value$; break;
case 2: familyId = (java.lang.String)value$; break;
case 3: members = (java.util.List)value$; break;
case 4: analysisPanels = (java.util.List)value$; break;
case 5: diseasePenetrances = (java.util.List)value$; break;
case 6: readyForAnalysis = (java.lang.Boolean)value$; break;
case 7: familyQCState = (org.gel.models.participant.avro.FamilyQCState)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'versionControl' field.
* Model version number */
public org.gel.models.participant.avro.VersionControl getVersionControl() {
return versionControl;
}
/**
* Sets the value of the 'versionControl' field.
* Model version number * @param value the value to set.
*/
public void setVersionControl(org.gel.models.participant.avro.VersionControl value) {
this.versionControl = value;
}
/**
* Gets the value of the 'LDPCode' field.
* LDP Code (Local Delivery Partner) */
public java.lang.String getLDPCode() {
return LDPCode;
}
/**
* Sets the value of the 'LDPCode' field.
* LDP Code (Local Delivery Partner) * @param value the value to set.
*/
public void setLDPCode(java.lang.String value) {
this.LDPCode = value;
}
/**
* Gets the value of the 'familyId' field.
* Family identifier which internally translate to a sample set */
public java.lang.String getFamilyId() {
return familyId;
}
/**
* Sets the value of the 'familyId' field.
* Family identifier which internally translate to a sample set * @param value the value to set.
*/
public void setFamilyId(java.lang.String value) {
this.familyId = value;
}
/**
* Gets the value of the 'members' field.
* List of members of a pedigree */
public java.util.List getMembers() {
return members;
}
/**
* Sets the value of the 'members' field.
* List of members of a pedigree * @param value the value to set.
*/
public void setMembers(java.util.List value) {
this.members = value;
}
/**
* Gets the value of the 'analysisPanels' field.
* List of panels */
public java.util.List getAnalysisPanels() {
return analysisPanels;
}
/**
* Sets the value of the 'analysisPanels' field.
* List of panels * @param value the value to set.
*/
public void setAnalysisPanels(java.util.List value) {
this.analysisPanels = value;
}
/**
* Gets the value of the 'diseasePenetrances' field.
* List of disease penetrances. Moved to referralTest for GMS */
public java.util.List getDiseasePenetrances() {
return diseasePenetrances;
}
/**
* Sets the value of the 'diseasePenetrances' field.
* List of disease penetrances. Moved to referralTest for GMS * @param value the value to set.
*/
public void setDiseasePenetrances(java.util.List value) {
this.diseasePenetrances = value;
}
/**
* Gets the value of the 'readyForAnalysis' field.
* Flag indicating if a pedigree is ready for analysis */
public java.lang.Boolean getReadyForAnalysis() {
return readyForAnalysis;
}
/**
* Sets the value of the 'readyForAnalysis' field.
* Flag indicating if a pedigree is ready for analysis * @param value the value to set.
*/
public void setReadyForAnalysis(java.lang.Boolean value) {
this.readyForAnalysis = value;
}
/**
* Gets the value of the 'familyQCState' field.
* The family quality control status */
public org.gel.models.participant.avro.FamilyQCState getFamilyQCState() {
return familyQCState;
}
/**
* Sets the value of the 'familyQCState' field.
* The family quality control status * @param value the value to set.
*/
public void setFamilyQCState(org.gel.models.participant.avro.FamilyQCState value) {
this.familyQCState = value;
}
/** Creates a new Pedigree RecordBuilder */
public static org.gel.models.participant.avro.Pedigree.Builder newBuilder() {
return new org.gel.models.participant.avro.Pedigree.Builder();
}
/** Creates a new Pedigree RecordBuilder by copying an existing Builder */
public static org.gel.models.participant.avro.Pedigree.Builder newBuilder(org.gel.models.participant.avro.Pedigree.Builder other) {
return new org.gel.models.participant.avro.Pedigree.Builder(other);
}
/** Creates a new Pedigree RecordBuilder by copying an existing Pedigree instance */
public static org.gel.models.participant.avro.Pedigree.Builder newBuilder(org.gel.models.participant.avro.Pedigree other) {
return new org.gel.models.participant.avro.Pedigree.Builder(other);
}
/**
* RecordBuilder for Pedigree instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.participant.avro.VersionControl versionControl;
private java.lang.String LDPCode;
private java.lang.String familyId;
private java.util.List members;
private java.util.List analysisPanels;
private java.util.List diseasePenetrances;
private boolean readyForAnalysis;
private org.gel.models.participant.avro.FamilyQCState familyQCState;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.participant.avro.Pedigree.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.participant.avro.Pedigree.Builder other) {
super(other);
if (isValidValue(fields()[0], other.versionControl)) {
this.versionControl = data().deepCopy(fields()[0].schema(), other.versionControl);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.LDPCode)) {
this.LDPCode = data().deepCopy(fields()[1].schema(), other.LDPCode);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.familyId)) {
this.familyId = data().deepCopy(fields()[2].schema(), other.familyId);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.members)) {
this.members = data().deepCopy(fields()[3].schema(), other.members);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.analysisPanels)) {
this.analysisPanels = data().deepCopy(fields()[4].schema(), other.analysisPanels);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.diseasePenetrances)) {
this.diseasePenetrances = data().deepCopy(fields()[5].schema(), other.diseasePenetrances);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.readyForAnalysis)) {
this.readyForAnalysis = data().deepCopy(fields()[6].schema(), other.readyForAnalysis);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.familyQCState)) {
this.familyQCState = data().deepCopy(fields()[7].schema(), other.familyQCState);
fieldSetFlags()[7] = true;
}
}
/** Creates a Builder by copying an existing Pedigree instance */
private Builder(org.gel.models.participant.avro.Pedigree other) {
super(org.gel.models.participant.avro.Pedigree.SCHEMA$);
if (isValidValue(fields()[0], other.versionControl)) {
this.versionControl = data().deepCopy(fields()[0].schema(), other.versionControl);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.LDPCode)) {
this.LDPCode = data().deepCopy(fields()[1].schema(), other.LDPCode);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.familyId)) {
this.familyId = data().deepCopy(fields()[2].schema(), other.familyId);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.members)) {
this.members = data().deepCopy(fields()[3].schema(), other.members);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.analysisPanels)) {
this.analysisPanels = data().deepCopy(fields()[4].schema(), other.analysisPanels);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.diseasePenetrances)) {
this.diseasePenetrances = data().deepCopy(fields()[5].schema(), other.diseasePenetrances);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.readyForAnalysis)) {
this.readyForAnalysis = data().deepCopy(fields()[6].schema(), other.readyForAnalysis);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.familyQCState)) {
this.familyQCState = data().deepCopy(fields()[7].schema(), other.familyQCState);
fieldSetFlags()[7] = true;
}
}
/** Gets the value of the 'versionControl' field */
public org.gel.models.participant.avro.VersionControl getVersionControl() {
return versionControl;
}
/** Sets the value of the 'versionControl' field */
public org.gel.models.participant.avro.Pedigree.Builder setVersionControl(org.gel.models.participant.avro.VersionControl value) {
validate(fields()[0], value);
this.versionControl = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'versionControl' field has been set */
public boolean hasVersionControl() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'versionControl' field */
public org.gel.models.participant.avro.Pedigree.Builder clearVersionControl() {
versionControl = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'LDPCode' field */
public java.lang.String getLDPCode() {
return LDPCode;
}
/** Sets the value of the 'LDPCode' field */
public org.gel.models.participant.avro.Pedigree.Builder setLDPCode(java.lang.String value) {
validate(fields()[1], value);
this.LDPCode = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'LDPCode' field has been set */
public boolean hasLDPCode() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'LDPCode' field */
public org.gel.models.participant.avro.Pedigree.Builder clearLDPCode() {
LDPCode = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'familyId' field */
public java.lang.String getFamilyId() {
return familyId;
}
/** Sets the value of the 'familyId' field */
public org.gel.models.participant.avro.Pedigree.Builder setFamilyId(java.lang.String value) {
validate(fields()[2], value);
this.familyId = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'familyId' field has been set */
public boolean hasFamilyId() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'familyId' field */
public org.gel.models.participant.avro.Pedigree.Builder clearFamilyId() {
familyId = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'members' field */
public java.util.List getMembers() {
return members;
}
/** Sets the value of the 'members' field */
public org.gel.models.participant.avro.Pedigree.Builder setMembers(java.util.List value) {
validate(fields()[3], value);
this.members = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'members' field has been set */
public boolean hasMembers() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'members' field */
public org.gel.models.participant.avro.Pedigree.Builder clearMembers() {
members = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'analysisPanels' field */
public java.util.List getAnalysisPanels() {
return analysisPanels;
}
/** Sets the value of the 'analysisPanels' field */
public org.gel.models.participant.avro.Pedigree.Builder setAnalysisPanels(java.util.List value) {
validate(fields()[4], value);
this.analysisPanels = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'analysisPanels' field has been set */
public boolean hasAnalysisPanels() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'analysisPanels' field */
public org.gel.models.participant.avro.Pedigree.Builder clearAnalysisPanels() {
analysisPanels = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'diseasePenetrances' field */
public java.util.List getDiseasePenetrances() {
return diseasePenetrances;
}
/** Sets the value of the 'diseasePenetrances' field */
public org.gel.models.participant.avro.Pedigree.Builder setDiseasePenetrances(java.util.List value) {
validate(fields()[5], value);
this.diseasePenetrances = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'diseasePenetrances' field has been set */
public boolean hasDiseasePenetrances() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'diseasePenetrances' field */
public org.gel.models.participant.avro.Pedigree.Builder clearDiseasePenetrances() {
diseasePenetrances = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'readyForAnalysis' field */
public java.lang.Boolean getReadyForAnalysis() {
return readyForAnalysis;
}
/** Sets the value of the 'readyForAnalysis' field */
public org.gel.models.participant.avro.Pedigree.Builder setReadyForAnalysis(boolean value) {
validate(fields()[6], value);
this.readyForAnalysis = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'readyForAnalysis' field has been set */
public boolean hasReadyForAnalysis() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'readyForAnalysis' field */
public org.gel.models.participant.avro.Pedigree.Builder clearReadyForAnalysis() {
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'familyQCState' field */
public org.gel.models.participant.avro.FamilyQCState getFamilyQCState() {
return familyQCState;
}
/** Sets the value of the 'familyQCState' field */
public org.gel.models.participant.avro.Pedigree.Builder setFamilyQCState(org.gel.models.participant.avro.FamilyQCState value) {
validate(fields()[7], value);
this.familyQCState = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'familyQCState' field has been set */
public boolean hasFamilyQCState() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'familyQCState' field */
public org.gel.models.participant.avro.Pedigree.Builder clearFamilyQCState() {
familyQCState = null;
fieldSetFlags()[7] = false;
return this;
}
@Override
public Pedigree build() {
try {
Pedigree record = new Pedigree();
record.versionControl = fieldSetFlags()[0] ? this.versionControl : (org.gel.models.participant.avro.VersionControl) defaultValue(fields()[0]);
record.LDPCode = fieldSetFlags()[1] ? this.LDPCode : (java.lang.String) defaultValue(fields()[1]);
record.familyId = fieldSetFlags()[2] ? this.familyId : (java.lang.String) defaultValue(fields()[2]);
record.members = fieldSetFlags()[3] ? this.members : (java.util.List) defaultValue(fields()[3]);
record.analysisPanels = fieldSetFlags()[4] ? this.analysisPanels : (java.util.List) defaultValue(fields()[4]);
record.diseasePenetrances = fieldSetFlags()[5] ? this.diseasePenetrances : (java.util.List) defaultValue(fields()[5]);
record.readyForAnalysis = fieldSetFlags()[6] ? this.readyForAnalysis : (java.lang.Boolean) defaultValue(fields()[6]);
record.familyQCState = fieldSetFlags()[7] ? this.familyQCState : (org.gel.models.participant.avro.FamilyQCState) defaultValue(fields()[7]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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