@molgenis/vip-report-template 2.7.1 → 3.0.0-beta

package/src/mocks/GRCh38/decisionTree.json

@@ -0,0 +1,369 @@
+{
+  "files": {
+    "panel": {
+      "path": ""
+    }
+  },
+  "rootNode": "MT",
+  "nodes": {
+    "MT": {
+      "type": "BOOL",
+      "description": "VariantonMTchrom",
+      "query": {
+        "field": "#CHROM",
+        "operator": "==",
+        "value": "chrM"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "blaat"
+      },
+      "outcomeMissing": {
+        "nextNode": "blaat"
+      }
+    },
+    "blaat": {
+      "type": "EXISTS",
+      "description": "blaatannotationexists",
+      "field": "INFO/CSQ/blaat",
+      "outcomeTrue": {
+        "nextNode": "csq_exists"
+      },
+      "outcomeFalse": {
+        "nextNode": "csq_exists"
+      }
+    },
+    "csq_exists": {
+      "type": "EXISTS",
+      "description": "CSQannotationexists",
+      "field": "INFO/CSQ/Gene",
+      "outcomeTrue": {
+        "nextNode": "genepanel"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      }
+    },
+    "genepanel": {
+      "type": "BOOL",
+      "description": "genepanel",
+      "query": {
+        "field": "INFO/CSQ/Gene",
+        "operator": "in",
+        "value": "file:panel"
+      },
+      "outcomeTrue": {
+        "nextNode": "mvl"
+      },
+      "outcomeFalse": {
+        "nextNode": "phenotype_match"
+      }
+    },
+    "phenotype_match": {
+      "type": "EXISTS",
+      "description": "Phenotypematch",
+      "field": "INFO/CSQ/HPO",
+      "outcomeTrue": {
+        "nextNode": "mvl"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      }
+    },
+    "mvl": {
+      "type": "CATEGORICAL",
+      "description": "ManagedVariantListclassification",
+      "field": "INFO/VKGL_UMCG",
+      "outcomeMap": {
+        "P": {
+          "nextNode": "exit_t"
+        },
+        "LP": {
+          "nextNode": "exit_t"
+        },
+        "LB": {
+          "nextNode": "exit_f"
+        },
+        "B": {
+          "nextNode": "exit_f"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "vkgl"
+      },
+      "outcomeDefault": {
+        "nextNode": "vkgl"
+      }
+    },
+    "vkgl": {
+      "type": "CATEGORICAL",
+      "description": "VKGLclassification",
+      "field": "INFO/VKGL",
+      "outcomeMap": {
+        "P": {
+          "nextNode": "exit_t"
+        },
+        "LP": {
+          "nextNode": "exit_t"
+        },
+        "LB": {
+          "nextNode": "exit_f"
+        },
+        "B": {
+          "nextNode": "exit_f"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "filter"
+      },
+      "outcomeDefault": {
+        "nextNode": "filter"
+      }
+    },
+    "filter": {
+      "type": "BOOL",
+      "description": "Allfilterspassed",
+      "query": {
+        "field": "FILTER",
+        "operator": "==",
+        "value": [
+          "PASS"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "artefact"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "artefact"
+      }
+    },
+    "artefact": {
+      "type": "BOOL",
+      "description": "Variantonartefactlist",
+      "query": {
+        "field": "INFO/MVLA",
+        "operator": "==",
+        "value": "DUMMY"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "capice"
+      }
+    },
+    "capice": {
+      "type": "BOOL",
+      "description": "CAPICEscore>=0.2",
+      "query": {
+        "field": "INFO/CAP",
+        "operator": ">=",
+        "value": 0.2
+      },
+      "outcomeTrue": {
+        "nextNode": "gnomad"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "gnomad"
+      }
+    },
+    "gnomad": {
+      "type": "BOOL",
+      "description": "gnomAD_AF<0.02",
+      "query": {
+        "field": "INFO/CSQ/gnomAD_AF",
+        "operator": "<",
+        "value": 0.02
+      },
+      "outcomeTrue": {
+        "nextNode": "HLA"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "HLA"
+      }
+    },
+    "HLA": {
+      "type": "BOOL",
+      "description": "HLA",
+      "query": {
+        "field": "INFO/CSQ/SYMBOL",
+        "operator": "in",
+        "value": [
+          "HLA-A",
+          "HLA-B",
+          "HLA-C",
+          "HLA-DRB1",
+          "HLA-DRB5",
+          "HLA-DQA1",
+          "HLA-DQB1"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "five_prime"
+      },
+      "outcomeMissing": {
+        "nextNode": "five_prime"
+      }
+    },
+    "five_prime": {
+      "type": "BOOL",
+      "description": "5primeUTR",
+      "query": {
+        "field": "INFO/CSQ/Consequence",
+        "operator": "contains",
+        "value": [
+          "5_prime_UTR_variant"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "inframe"
+      },
+      "outcomeMissing": {
+        "nextNode": "inframe"
+      }
+    },
+    "inframe": {
+      "type": "BOOL",
+      "description": "inframeinsertionordeletion",
+      "query": {
+        "field": "INFO/CSQ/Consequence",
+        "operator": "contains_any",
+        "value": [
+          "inframe_deletion",
+          "inframe_insertion"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "splice_acceptor"
+      },
+      "outcomeMissing": {
+        "nextNode": "splice_acceptor"
+      }
+    },
+    "splice_acceptor": {
+      "type": "BOOL",
+      "description": "Spliceacceptor",
+      "query": {
+        "field": "INFO/CSQ/Consequence",
+        "operator": "contains_any",
+        "value": [
+          "splice_acceptor_variant",
+          "splice_donor_variant",
+          "splice_region_variant"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_t"
+      },
+      "outcomeFalse": {
+        "nextNode": "intron"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_t"
+      }
+    },
+    "intron": {
+      "type": "BOOL",
+      "description": "Intron",
+      "query": {
+        "field": "INFO/CSQ/Consequence",
+        "operator": "contains_any",
+        "value": [
+          "intron_variant",
+          "synonymous_variant"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_f"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_t"
+      },
+      "outcomeMissing": {
+        "nextNode": "my_multi"
+      }
+    },
+    "my_multi": {
+      "type": "BOOL_MULTI",
+      "fields": [
+        "my_multi_1",
+        "my_multi_2"
+      ],
+      "outcomeDefault": {
+        "nextNode": "exit_t"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_f"
+      },
+      "outcomes": [
+        {
+          "operator": "AND",
+          "queries": [
+            {
+              "field": "my_multi_1",
+              "operator": ">",
+              "value": 0.1
+            },
+            {
+              "field": "my_multi_1",
+              "operator": "<=",
+              "value": 0.2
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_f"
+          }
+        },
+        {
+          "operator": "OR",
+          "queries": [
+            {
+              "field": "my_multi_2",
+              "operator": "<",
+              "value": 0.1
+            },
+            {
+              "field": "my_multi_2",
+              "operator": ">",
+              "value": 0.2
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_t"
+          }
+        }
+      ]
+    },
+    "exit_t": {
+      "type": "LEAF",
+      "class": "T"
+    },
+    "exit_f": {
+      "type": "LEAF",
+      "class": "F"
+    }
+  }
+}

package/src/mocks/GRCh38/static.ts

@@ -0,0 +1,170 @@
+import bamUrl from "./alignment.bam.blob";
+import fastaUrl_chr1_9982230_9982730 from "./fasta/chr1-9982230-9982730.fasta.gz.blob";
+import fastaUrl_chr1_16049667_16050167 from "./fasta/chr1-16049667-16050167.fasta.gz.blob";
+import fastaUrl_chr1_17022474_17022974 from "./fasta/chr1-17022474-17022974.fasta.gz.blob";
+import fastaUrl_chr1_152548062_152548562 from "./fasta/chr1-152548062-152548562.fasta.gz.blob";
+import fastaUrl_chr2_47408278_47408778 from "./fasta/chr2-47408278-47408778.fasta.gz.blob";
+import fastaUrl_chr4_105398887_105399387 from "./fasta/chr4-105398887-105399387.fasta.gz.blob";
+import fastaUrl_chr7_41977462_41977962 from "./fasta/chr7-41977462-41977962.fasta.gz.blob";
+import fastaUrl_chr7_42025108_42025608 from "./fasta/chr7-42025108-42025608.fasta.gz.blob";
+import fastaUrl_chr8_60852334_60852834 from "./fasta/chr8-60852334-60852834.fasta.gz.blob";
+import fastaUrl_chr8_144085347_144085847 from "./fasta/chr8-144085347-144085847.fasta.gz.blob";
+import fastaUrl_chr9_104784102_104784602 from "./fasta/chr9-104784102-104784602.fasta.gz.blob";
+import fastaUrl_chr10_124402680_124403180 from "./fasta/chr10-124402680-124403180.fasta.gz.blob";
+import fastaUrl_chr11_134144080_134144580 from "./fasta/chr11-134144080-134144580.fasta.gz.blob";
+import fastaUrl_chr13_76995743_76996243 from "./fasta/chr13-76995743-76996243.fasta.gz.blob";
+import fastaUrl_chr14_88869813_88870313 from "./fasta/chr14-88869813-88870313.fasta.gz.blob";
+import fastaUrl_chr14_104701273_104701773 from "./fasta/chr14-104701273-104701773.fasta.gz.blob";
+import fastaUrl_chr17_31228796_31229296 from "./fasta/chr17-31228796-31229296.fasta.gz.blob";
+import fastaUrl_chr17_31336611_31337111 from "./fasta/chr17-31336611-31337111.fasta.gz.blob";
+import fastaUrl_chr19_11105220_11105720 from "./fasta/chr19-11105220-11105720.fasta.gz.blob";
+import fastaUrl_chr19_17340938_17341438 from "./fasta/chr19-17340938-17341438.fasta.gz.blob";
+import fastaUrl_chr20_63695389_63695889 from "./fasta/chr20-63695389-63695889.fasta.gz.blob";
+import fastaUrl_chr22_50188914_50189414 from "./fasta/chr22-50188914-50189414.fasta.gz.blob";
+import fastaUrl_chr22_50282867_50283367 from "./fasta/chr22-50282867-50283367.fasta.gz.blob";
+import fastaUrl_chrM_15075_15575 from "./fasta/chrM-15075-15575.fasta.gz.blob";
+import fastaUrl_chrX_49075112_49075612 from "./fasta/chrX-49075112-49075612.fasta.gz.blob";
+import fastaUrl_chrY_2787350_2787850 from "./fasta/chrY-2787350-2787850.fasta.gz.blob";
+import genesUrl from "./genes.txt.gz.blob";
+import vcfUrlFamily from "./vcf/family.vcf.blob";
+import vcfUrlNoVep from "./vcf/no_vep.vcf.blob";
+import vcfUrlSamples0 from "./vcf/samples_0.vcf.blob";
+import vcfUrlSamples1 from "./vcf/samples_1.vcf.blob";
+import vcfUrlSamples100 from "./vcf/samples_100.vcf.blob";
+
+import { fetchAsBytes } from "../utils";
+import decisionTreeJson from "./decisionTree.json";
+import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
+
+export const bam = await fetchAsBytes(bamUrl as string);
+
+export const decisionTree: DecisionTree = decisionTreeJson as DecisionTree;
+
+export const fastaGz = {
+  "chr1:9982230-9982730": await fetchAsBytes(fastaUrl_chr1_9982230_9982730 as string),
+  "chr1:16049667-16050167": await fetchAsBytes(fastaUrl_chr1_16049667_16050167 as string),
+  "chr1:17022474-17022974": await fetchAsBytes(fastaUrl_chr1_17022474_17022974 as string),
+  "chr1:152548062-152548562": await fetchAsBytes(fastaUrl_chr1_152548062_152548562 as string),
+  "chr2:47408278-47408778": await fetchAsBytes(fastaUrl_chr2_47408278_47408778 as string),
+  "chr4:105398887-105399387": await fetchAsBytes(fastaUrl_chr4_105398887_105399387 as string),
+  "chr7:41977462-41977962": await fetchAsBytes(fastaUrl_chr7_41977462_41977962 as string),
+  "chr7:42025108-42025608": await fetchAsBytes(fastaUrl_chr7_42025108_42025608 as string),
+  "chr8:60852334-60852834": await fetchAsBytes(fastaUrl_chr8_60852334_60852834 as string),
+  "chr8:144085347-144085847": await fetchAsBytes(fastaUrl_chr8_144085347_144085847 as string),
+  "chr9:104784102-104784602": await fetchAsBytes(fastaUrl_chr9_104784102_104784602 as string),
+  "chr10:124402680-124403180": await fetchAsBytes(fastaUrl_chr10_124402680_124403180 as string),
+  "chr11:134144080-134144580": await fetchAsBytes(fastaUrl_chr11_134144080_134144580 as string),
+  "chr13:76995743-76996243": await fetchAsBytes(fastaUrl_chr13_76995743_76996243 as string),
+  "chr14:88869813-88870313": await fetchAsBytes(fastaUrl_chr14_88869813_88870313 as string),
+  "chr14:104701273-104701773": await fetchAsBytes(fastaUrl_chr14_104701273_104701773 as string),
+  "chr17:31228796-31229296": await fetchAsBytes(fastaUrl_chr17_31228796_31229296 as string),
+  "chr17:31336611-31337111": await fetchAsBytes(fastaUrl_chr17_31336611_31337111 as string),
+  "chr19:11105220-11105720": await fetchAsBytes(fastaUrl_chr19_11105220_11105720 as string),
+  "chr19:17340938-17341438": await fetchAsBytes(fastaUrl_chr19_17340938_17341438 as string),
+  "chr20:63695389-63695889": await fetchAsBytes(fastaUrl_chr20_63695389_63695889 as string),
+  "chr22:50188914-50189414": await fetchAsBytes(fastaUrl_chr22_50188914_50189414 as string),
+  "chr22:50282867-50283367": await fetchAsBytes(fastaUrl_chr22_50282867_50283367 as string),
+  "chrX:49075112-49075612": await fetchAsBytes(fastaUrl_chrX_49075112_49075612 as string),
+  "chrY:2787350-2787850": await fetchAsBytes(fastaUrl_chrY_2787350_2787850 as string),
+  "chrM:15075-15575": await fetchAsBytes(fastaUrl_chrM_15075_15575 as string),
+};
+
+export const genesGz = await fetchAsBytes(genesUrl as string);
+
+export const vcfFamily = await fetchAsBytes(vcfUrlFamily as string);
+
+export const vcfNoVep = await fetchAsBytes(vcfUrlNoVep as string);
+
+export const vcfSamples0 = await fetchAsBytes(vcfUrlSamples0 as string);
+
+export const vcfSamples1 = await fetchAsBytes(vcfUrlSamples1 as string);
+
+export const vcfSamples100 = await fetchAsBytes(vcfUrlSamples100 as string);
+
+export const samplesFamily = {
+  samples: [
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "Patient",
+        paternalId: "Father",
+        maternalId: "MotherHasQuiteALongName",
+        sex: "MALE",
+        affectedStatus: "AFFECTED",
+      },
+      index: 3,
+      proband: true,
+    },
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "MotherHasQuiteALongName",
+        paternalId: "0",
+        maternalId: "0",
+        sex: "FEMALE",
+        affectedStatus: "UNAFFECTED",
+      },
+      index: 1,
+      proband: false,
+    },
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "Father",
+        paternalId: "0",
+        maternalId: "0",
+        sex: "MALE",
+        affectedStatus: "AFFECTED",
+      },
+      index: 0,
+      proband: false,
+    },
+  ],
+  phenotypes: [
+    {
+      phenotypicFeaturesList: [
+        {
+          type: {
+            id: "HP:0000951",
+            label: "HP:0000951",
+          },
+        },
+        {
+          type: {
+            id: "HP:0003124",
+            label: "HP:0003124",
+          },
+        },
+      ],
+      subject: {
+        id: "Patient",
+      },
+    },
+    {
+      phenotypicFeaturesList: [
+        {
+          type: {
+            id: "HP:0000951",
+            label: "HP:0000951",
+          },
+        },
+      ],
+      subject: {
+        id: "MotherHasQuiteALongName",
+      },
+    },
+    {
+      phenotypicFeaturesList: [
+        {
+          type: {
+            id: "HP:0000951",
+            label: "HP:0000951",
+          },
+        },
+      ],
+      subject: {
+        id: "Father",
+      },
+    },
+  ],
+};