{
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "MyOme json report",
   "description": "MyOme report object",
   "type": "object",
   "allOf": [
      {
         "$ref": "base.json"
      },
      {
         "properties": {
            "report_type": {
               "const": "NDD_CNA",
               "type": "string"
            },
            "results": {
               "$ref": "#/definitions/NDDCNAReportResults"
            }
         }
      }
   ],
   "definitions": {
      "NDDCNAVariationClassification": {
         "type": "object",
         "additionalProperties": false,
         "required": [
            "classification"
         ],
         "properties": {
            "variantfinding_id": {
               "$ref": "../../ids.json#/definitions/VariantFindingId"
            },
            "finding_type": {
               "$ref": "../../core.json#/definitions/FindingType"
            },
            "classification": {
               "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
            },
            "evidence": {
               "type": "array",
               "items": {
                  "type": "string"
               },
               "examples": [
                  "A pathogenic duplication of the chromosome 22q11.21 region was identified which may be consistent with the clinical signs and symptoms reported for this individual."
               ]
            },
            "genetic_event": {
               "$ref": "../../core.json#/definitions/GeneticEventType"
            },
            "gene_symbol": {
               "type": "string"
            },
            "variation": {
               "type": "object",
               "properties": {
                  "chromosome_region": {
                     "$ref": "../../core.json#/definitions/ChromosomeRegion"
                  },
                  "hgvs_g_37": {
                     "$ref": "../../core.json#/definitions/HGVSExpressionOrNone"
                  },
                  "hgvs_g_38": {
                     "$ref": "../../core.json#/definitions/HGVSExpressionOrNone"
                  },
                  "display": {
                     "type": "string"
                  }
               }
            },
            "inheritance": {
               "type": "object",
               "properties": {
                  "mode": {
                     "title": "Mode of Inheritance",
                     "$ref": "../../core.json#/definitions/Inheritance"
                  },
                  "zygosity": {
                     "title": "Zygosity",
                     "$ref": "../../core.json#/definitions/Zygosity"
                  },
                  "pattern": {
                     "title": "Inherited From",
                     "$ref": "../../core.json#/definitions/VariantInheritance"
                  }
               }
            },
            "variant_description": {
               "type": [
                  "string",
                  "null"
               ]
            },
            "condition": {
               "type": "string"
            },
            "cytoband": {
               "$ref": "../../core.json#/definitions/Cytoband"
            },
            "iscn_nomenclature": {
               "$ref": "../../core.json#/definitions/ISCNNomenclature"
            },
            "size_mb": {
               "type": "number",
               "examples": [
                  0.65,
                  2.35
               ]
            },
            "number_of_genes": {
               "type": "integer",
               "examples": [
                  6,
                  25
               ]
            },
            "alleles": {
               "title": "Pathogenic TRE Alleles",
               "type": "array",
               "minItems": 1,
               "maxItems": 2,
               "items": {
                  "type": "object",
                  "additionalProperties": false,
                  "required": [
                     "event",
                     "classification"
                  ],
                  "properties": {
                     "event": {
                        "title": "TRE Event",
                        "type": "string"
                     },
                     "classification": {
                        "title": "ACMG Classification",
                        "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
                     },
                     "number": {
                        "type": "integer"
                     }
                  }
               }
            }
         },
         "if": {
            "required": [
               "finding_type"
            ],
            "properties": {
               "finding_type": {
                  "const": "NDD_CNA_TRE"
               }
            }
         },
         "then": {
            "required": [
               "gene_symbol",
               "condition",
               "inheritance",
               "alleles"
            ]
         }
      },
      "NDDCNAReportResults": {
         "description": "ReportResults is the editable, versioned component of a MyOme lab report. ",
         "type": "object",
         "additionalProperties": false,
         "required": [
            "toplines",
            "next_steps",
            "classifications"
         ],
         "properties": {
            "classifications": {
               "minItems": 1,
               "type": "array",
               "items": {
                  "$ref": "#/definitions/NDDCNAVariationClassification"
               }
            },
            "hpo_terms": {
               "type": "array",
               "items": {
                  "type": "string"
               },
               "examples": [
                  "Seizure",
                  "Hypertelorism"
               ]
            },
            "next_steps": {
               "$ref": "../../structs.json#/definitions/ReportNextSteps"
            },
            "toplines": {
               "$ref": "#/definitions/NDDCNATopline"
            },
            "sample_limitations": {
               "type": "array",
               "items": {
                  "type": "string"
               }
            }
         }
      },
      "NDDCNATopline": {
         "description": "Uses topline finding definition from structs.json.",
         "type": "array",
         "minItems": 1,
         "maxItems": 5,
         "items": {
            "allOf": [
               {
                  "$ref": "../../structs.json#/definitions/ToplineFinding"
               },
               {
                  "properties": {
                     "finding": {
                        "$ref": "../../core.json#/definitions/RareDiseaseToplineFinding"
                     }
                  }
               }
            ]
         },
         "example": {
            "finding": "POSITIVE",
            "text": "A pathogenic variant was identified on chromosome chr1."
         }
      }
   }
}