@molgenis/vip-report-template 2.7.3 → 3.0.0

package/src/mocks/GRCh37/decisionTree.json

@@ -0,0 +1,354 @@
+{
+  "rootNode": "filter",
+  "nodes": {
+    "filter": {
+      "type": "BOOL",
+      "description": "All filters passed",
+      "query": {
+        "field": "FILTER",
+        "operator": "==",
+        "value": [
+          "PASS"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "vkgl"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_lq"
+      },
+      "outcomeMissing": {
+        "nextNode": "vkgl"
+      }
+    },
+    "spliceAI": {
+      "type": "BOOL_MULTI",
+      "fields": [
+        "INFO/CSQ/SpliceAI_pred_DS_AG",
+        "INFO/CSQ/SpliceAI_pred_DS_AL",
+        "INFO/CSQ/SpliceAI_pred_DS_DG",
+        "INFO/CSQ/SpliceAI_pred_DS_DL"
+      ],
+      "outcomes": [
+        {
+          "operator": "OR",
+          "queries": [
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AG",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_AL",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DG",
+              "operator": ">",
+              "value": 0.42
+            },
+            {
+              "field": "INFO/CSQ/SpliceAI_pred_DS_DL",
+              "operator": ">",
+              "value": 0.42
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lp"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "annotSV"
+      },
+      "outcomeMissing": {
+        "nextNode": "annotSV"
+      }
+    },
+    "vkgl": {
+      "type": "CATEGORICAL",
+      "description": "VKGL classification",
+      "field": "INFO/CSQ/VKGL_CL",
+      "outcomeMap": {
+        "P": {
+          "nextNode": "exit_p"
+        },
+        "LP": {
+          "nextNode": "exit_lp"
+        },
+        "LB": {
+          "nextNode": "exit_lb"
+        },
+        "B": {
+          "nextNode": "exit_b"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "clinVar"
+      },
+      "outcomeDefault": {
+        "nextNode": "clinVar"
+      }
+    },
+    "annotSV": {
+      "type": "CATEGORICAL",
+      "description": "VKGL classification",
+      "field": "INFO/CSQ/ASV_ACMG_class",
+      "outcomeMap": {
+        "5": {
+          "nextNode": "exit_p"
+        },
+        "4": {
+          "nextNode": "exit_lp"
+        },
+        "2": {
+          "nextNode": "exit_lb"
+        },
+        "1": {
+          "nextNode": "exit_b"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "impact"
+      },
+      "outcomeDefault": {
+        "nextNode": "impact"
+      }
+    },
+    "gnomad": {
+      "type": "BOOL_MULTI",
+      "description": "gnomAD_AF < 0.02 && gnomAD_HN < 5",
+      "fields": [
+        "INFO/CSQ/gnomAD_AF",
+        "INFO/CSQ/gnomAD_HN"
+      ],
+      "outcomes": [
+        {
+          "operator": "OR",
+          "queries": [
+            {
+              "field": "INFO/CSQ/gnomAD_AF",
+              "operator": ">=",
+              "value": 0.02
+            },
+            {
+              "field": "INFO/CSQ/gnomAD_HN",
+              "operator": ">=",
+              "value": 5
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lb"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "effect"
+      },
+      "outcomeMissing": {
+        "nextNode": "effect"
+      }
+    },
+    "effect": {
+      "type": "BOOL",
+      "description": "Consequence contains 'missense'",
+      "query": {
+        "field": "INFO/CSQ/Consequence",
+        "operator": "contains",
+        "value": "missense_variant"
+      },
+      "outcomeTrue": {
+        "nextNode": "sift"
+      },
+      "outcomeFalse": {
+        "nextNode": "spliceAI"
+      },
+      "outcomeMissing": {
+        "nextNode": "spliceAI"
+      }
+    },
+    "clinVar": {
+      "type": "BOOL_MULTI",
+      "fields": [
+        "INFO/CSQ/CLIN_SIG"
+      ],
+      "outcomes": [
+        {
+          "queries": [
+            {
+              "field": "INFO/CSQ/CLIN_SIG",
+              "operator": "contains_any",
+              "value": [
+                "conflicting_interpretations_of_pathogenicity",
+                "conflicting_data_from_submitters",
+                "uncertain_significance"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "gnomad"
+          }
+        },
+        {
+          "queries": [
+            {
+              "field": "INFO/CSQ/CLIN_SIG",
+              "operator": "contains_any",
+              "value": [
+                "likely_benign",
+                "benign"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lb"
+          }
+        },
+        {
+          "queries": [
+            {
+              "field": "INFO/CSQ/CLIN_SIG",
+              "operator": "contains_any",
+              "value": [
+                "likely_pathogenic",
+                "pathogenic"
+              ]
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lp"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "gnomad"
+      },
+      "outcomeMissing": {
+        "nextNode": "gnomad"
+      }
+    },
+    "sift": {
+      "description": "SIFT qualitative prediction",
+      "type": "BOOL",
+      "query": {
+        "field": "INFO/CSQ/SIFT",
+        "operator": "<",
+        "value": 0.05
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_lp"
+      },
+      "outcomeFalse": {
+        "nextNode": "polyphen"
+      },
+      "outcomeMissing": {
+        "nextNode": "polyphen"
+      }
+    },
+    "polyphen": {
+      "description": "PolyPhen qualitative prediction",
+      "type": "BOOL_MULTI",
+      "fields": [
+        "INFO/CSQ/PolyPhen"
+      ],
+      "outcomes": [
+        {
+          "queries": [
+            {
+              "field": "INFO/CSQ/PolyPhen",
+              "operator": "<",
+              "value": 0.15
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lb"
+          }
+        },
+        {
+          "operator": "AND",
+          "queries": [
+            {
+              "field": "INFO/CSQ/PolyPhen",
+              "operator": ">",
+              "value": 0.15
+            },
+            {
+              "field": "INFO/CSQ/PolyPhen",
+              "operator": "<",
+              "value": 0.85
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_vus"
+          }
+        },
+        {
+          "queries": [
+            {
+              "field": "INFO/CSQ/PolyPhen",
+              "operator": ">",
+              "value": 0.85
+            }
+          ],
+          "outcomeTrue": {
+            "nextNode": "exit_lp"
+          }
+        }
+      ],
+      "outcomeDefault": {
+        "nextNode": "impact"
+      },
+      "outcomeMissing": {
+        "nextNode": "impact"
+      }
+    },
+    "impact": {
+      "type": "CATEGORICAL",
+      "description": "IMPACT rating",
+      "field": "INFO/CSQ/IMPACT",
+      "outcomeMap": {
+        "MODIFIER": {
+          "nextNode": "exit_lb"
+        },
+        "LOW": {
+          "nextNode": "exit_lb"
+        },
+        "MODERATE": {
+          "nextNode": "exit_vus"
+        },
+        "HIGH": {
+          "nextNode": "exit_lp"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_vus"
+      }
+    },
+    "exit_lq": {
+      "description": "Low quality variants.",
+      "type": "LEAF",
+      "class": "LQ"
+    },
+    "exit_b": {
+      "type": "LEAF",
+      "class": "B"
+    },
+    "exit_lb": {
+      "type": "LEAF",
+      "class": "LB"
+    },
+    "exit_vus": {
+      "type": "LEAF",
+      "class": "VUS"
+    },
+    "exit_lp": {
+      "type": "LEAF",
+      "class": "LP"
+    },
+    "exit_p": {
+      "type": "LEAF",
+      "class": "P"
+    }
+  }
+}

package/src/mocks/GRCh37/static.ts

@@ -0,0 +1,179 @@
+import bamUrl from "./alignment.bam.blob";
+import decisionTreeJson from "./decisionTree.json";
+import fastaUrl1_10042288_10042788 from "./fasta/1-10042288-10042788.fasta.gz.blob";
+import fastaUrl1_16375333_16375833 from "./fasta/1-16375333-16375833.fasta.gz.blob";
+import fastaUrl1_16376162_16376662 from "./fasta/1-16376162-16376662.fasta.gz.blob";
+import fastaUrl1_17348965_17349469 from "./fasta/1-17348965-17349469.fasta.gz.blob";
+import fastaUrl1_17348969_17349469 from "./fasta/1-17348969-17349469.fasta.gz.blob";
+import fastaUrl1_17354844_17355344 from "./fasta/1-17354844-17355344.fasta.gz.blob";
+import fastaUrl1_152520538_152521038 from "./fasta/1-152520538-152521038.fasta.gz.blob";
+import fastaUrl2_47635417_47635917 from "./fasta/2-47635417-47635917.fasta.gz.blob";
+import fastaUrl4_106320044_106320544 from "./fasta/4-106320044-106320544.fasta.gz.blob";
+import fastaUrl7_42017061_42017561 from "./fasta/7-42017061-42017561.fasta.gz.blob";
+import fastaUrl7_42064707_42065207 from "./fasta/7-42064707-42065207.fasta.gz.blob";
+import fastaUrl8_61764893_61765393 from "./fasta/8-61764893-61765393.fasta.gz.blob";
+import fastaUrl8_145140250_145140750 from "./fasta/8-145140250-145140750.fasta.gz.blob";
+import fastaUrl9_107546383_107546883 from "./fasta/9-107546383-107546883.fasta.gz.blob";
+import fastaUrl9_107584614_107585114 from "./fasta/9-107584614-107585114.fasta.gz.blob";
+import fastaUrl10_126091249_126091749 from "./fasta/10-126091249-126091749.fasta.gz.blob";
+import fastaUrl11_134013975_134014475 from "./fasta/11-134013975-134014475.fasta.gz.blob";
+import fastaUrl13_77569878_77570378 from "./fasta/13-77569878-77570378.fasta.gz.blob";
+import fastaUrl14_89307588_89308088 from "./fasta/14-89307588-89308088.fasta.gz.blob";
+import fastaUrl14_89309945_89310445 from "./fasta/14-89309945-89310445.fasta.gz.blob";
+import fastaUrl14_89336157_89336657 from "./fasta/14-89336157-89336657.fasta.gz.blob";
+import fastaUrl14_105167610_105168110 from "./fasta/14-105167610-105168110.fasta.gz.blob";
+import fastaUrl17_29555814_29556314 from "./fasta/17-29555814-29556314.fasta.gz.blob";
+import fastaUrl17_29585172_29585672 from "./fasta/17-29585172-29585672.fasta.gz.blob";
+import fastaUrl17_29663629_29664129 from "./fasta/17-29663629-29664129.fasta.gz.blob";
+import fastaUrl17_29675976_29676476 from "./fasta/17-29675976-29676476.fasta.gz.blob";
+import fastaUrl17_29683733_29684233 from "./fasta/17-29683733-29684233.fasta.gz.blob";
+import fastaUrl19_11215896_11216396 from "./fasta/19-11215896-11216396.fasta.gz.blob";
+import fastaUrl19_11223801_11224301 from "./fasta/19-11223801-11224301.fasta.gz.blob";
+import fastaUrl19_17449149_17449649 from "./fasta/19-17449149-17449649.fasta.gz.blob";
+import fastaUrl19_17451747_17452247 from "./fasta/19-17451747-17452247.fasta.gz.blob";
+import fastaUrl20_62326742_62327242 from "./fasta/20-62326742-62327242.fasta.gz.blob";
+import fastaUrl22_50627343_50627843 from "./fasta/22-50627343-50627843.fasta.gz.blob";
+import fastaUrl22_50721296_50721796 from "./fasta/22-50721296-50721796.fasta.gz.blob";
+import fastaUrlX_48932771_48933271 from "./fasta/X-48932771-48933271.fasta.gz.blob";
+import fastaUrlY_2655391_2655891 from "./fasta/Y-2655391-2655891.fasta.gz.blob";
+import fastaUrlMT_15076_15576 from "./fasta/MT-15076-15576.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 { 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 = {
+  "1:10042288-10042788": await fetchAsBytes(fastaUrl1_10042288_10042788 as string),
+  "1:16375333-16375833": await fetchAsBytes(fastaUrl1_16375333_16375833 as string),
+  "1:16376162-16376662": await fetchAsBytes(fastaUrl1_16376162_16376662 as string),
+  "1:17348965-17349469": await fetchAsBytes(fastaUrl1_17348965_17349469 as string),
+  "1:17348969-17349469": await fetchAsBytes(fastaUrl1_17348969_17349469 as string),
+  "1:17354844-17355344": await fetchAsBytes(fastaUrl1_17354844_17355344 as string),
+  "1:152520538-152521038": await fetchAsBytes(fastaUrl1_152520538_152521038 as string),
+  "2:47635417-47635917": await fetchAsBytes(fastaUrl2_47635417_47635917 as string),
+  "4:106320044-106320544": await fetchAsBytes(fastaUrl4_106320044_106320544 as string),
+  "7:42017061-42017561": await fetchAsBytes(fastaUrl7_42017061_42017561 as string),
+  "7:42064707-42065207": await fetchAsBytes(fastaUrl7_42064707_42065207 as string),
+  "8:61764893-61765393": await fetchAsBytes(fastaUrl8_61764893_61765393 as string),
+  "8:145140250-145140750": await fetchAsBytes(fastaUrl8_145140250_145140750 as string),
+  "9:107546383-107546883": await fetchAsBytes(fastaUrl9_107546383_107546883 as string),
+  "9:107584614-107585114": await fetchAsBytes(fastaUrl9_107584614_107585114 as string),
+  "10:126091249-126091749": await fetchAsBytes(fastaUrl10_126091249_126091749 as string),
+  "11:134013975-134014475": await fetchAsBytes(fastaUrl11_134013975_134014475 as string),
+  "13:77569878-77570378": await fetchAsBytes(fastaUrl13_77569878_77570378 as string),
+  "14:89307588-89308088": await fetchAsBytes(fastaUrl14_89307588_89308088 as string),
+  "14:89309945-89310445": await fetchAsBytes(fastaUrl14_89309945_89310445 as string),
+  "14:89336157-89336657": await fetchAsBytes(fastaUrl14_89336157_89336657 as string),
+  "14:105167610-105168110": await fetchAsBytes(fastaUrl14_105167610_105168110 as string),
+  "17:29555814-29556314": await fetchAsBytes(fastaUrl17_29555814_29556314 as string),
+  "17:29585172-29585672": await fetchAsBytes(fastaUrl17_29585172_29585672 as string),
+  "17:29663629-29664129": await fetchAsBytes(fastaUrl17_29663629_29664129 as string),
+  "17:29675976-29676476": await fetchAsBytes(fastaUrl17_29675976_29676476 as string),
+  "17:29683733-29684233": await fetchAsBytes(fastaUrl17_29683733_29684233 as string),
+  "19:11215896-11216396": await fetchAsBytes(fastaUrl19_11215896_11216396 as string),
+  "19:11223801-11224301": await fetchAsBytes(fastaUrl19_11223801_11224301 as string),
+  "19:17449149-17449649": await fetchAsBytes(fastaUrl19_17449149_17449649 as string),
+  "19:17451747-17452247": await fetchAsBytes(fastaUrl19_17451747_17452247 as string),
+  "20:62326742-62327242": await fetchAsBytes(fastaUrl20_62326742_62327242 as string),
+  "22:50627343-50627843": await fetchAsBytes(fastaUrl22_50627343_50627843 as string),
+  "22:50721296-50721796": await fetchAsBytes(fastaUrl22_50721296_50721796 as string),
+  "X:48932771-48933271": await fetchAsBytes(fastaUrlX_48932771_48933271 as string),
+  "Y:2655391-2655891": await fetchAsBytes(fastaUrlY_2655391_2655891 as string),
+  "MT:15076-15576": await fetchAsBytes(fastaUrlMT_15076_15576 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: 0,
+      proband: true,
+    },
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "MotherHasQuiteALongName",
+        paternalId: "0",
+        maternalId: "0",
+        sex: "FEMALE",
+        affectedStatus: "UNAFFECTED",
+      },
+      index: 2,
+      proband: false,
+    },
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "Father",
+        paternalId: "0",
+        maternalId: "0",
+        sex: "MALE",
+        affectedStatus: "UNAFFECTED",
+      },
+      index: 1,
+      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",
+      },
+    },
+  ],
+};