@molgenis/vip-report-template 6.2.0 → 7.0.0

package/src/mocks/GRCh38/sampleTree.json

@@ -0,0 +1,175 @@
+{
+  "rootNode": "gt",
+  "nodes": {
+    "gt": {
+      "label": "Genotype",
+      "description": "Genotype",
+      "type": "CATEGORICAL",
+      "field": "FORMAT/GENOTYPE/TYPE",
+      "outcomeMap": {
+        "HET": {
+          "nextNode": "gq"
+        },
+        "HOM_REF": {
+          "nextNode": "exit_u3"
+        },
+        "HOM_VAR": {
+          "nextNode": "gq"
+        },
+        "MIXED": {
+          "nextNode": "gq"
+        },
+        "NO_CALL": {
+          "nextNode": "exit_u3"
+        },
+        "UNAVAILABLE": {
+          "nextNode": "exit_u3"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "gq"
+      },
+      "outcomeDefault": {
+        "nextNode": "gq"
+      }
+    },
+    "gq": {
+      "type": "BOOL",
+      "label": "Genotype quality",
+      "description": "Genotype quality",
+      "query": {
+        "field": "FORMAT/GQ",
+        "operator": ">=",
+        "value": 20
+      },
+      "outcomeTrue": {
+        "nextNode": "only_IP"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "only_IP"
+      }
+    },
+    "only_IP": {
+      "type": "BOOL",
+      "label": "Only if AD IP",
+      "description": "Only AD IP suitable for pedigree.",
+      "query": {
+        "field": "FORMAT/VI",
+        "operator": "contains_none",
+        "value": ["AR","AD","XLR","XLD","YL","MT","AR_C"]
+      },
+      "outcomeTrue": {
+        "nextNode": "vid_IP"
+      },
+      "outcomeFalse": {
+        "nextNode": "vim"
+      },
+      "outcomeMissing": {
+        "nextNode": "vim"
+      }
+    },
+    "vim": {
+      "type": "BOOL",
+      "label": "Inheritance match",
+      "description": "Inheritance match",
+      "query": {
+        "field": "FORMAT/VIG",
+        "operator": "contains",
+        "value": "field:INFO/CSQ/Gene"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "vid"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
+    "vim_IP": {
+      "type": "BOOL",
+      "label": "Inheritance match (IP)",
+      "description": "Inheritance match",
+      "query": {
+        "field": "FORMAT/VIG",
+        "operator": "contains",
+        "value": "field:INFO/CSQ/Gene"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u4"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u4"
+      }
+    },
+    "vid": {
+      "type": "BOOL",
+      "label": "Inheritance denovo",
+      "description": "Inheritance denovo",
+      "query": {
+        "field": "FORMAT/VID",
+        "operator": "==",
+        "value": 1
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
+    "vid_IP": {
+      "type": "BOOL",
+      "label": "Inheritance denovo (IP)",
+      "description": "Inheritance denovo",
+      "query": {
+        "field": "FORMAT/VID",
+        "operator": "==",
+        "value": 1
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "vim_IP"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
+    "exit_u1": {
+      "label": "Usable: probably",
+      "description": "Usable: probably",
+      "type": "LEAF",
+      "class": "U1"
+    },
+    "exit_u2": {
+      "label": "Usable: maybe",
+      "description": "Usable: maybe",
+      "type": "LEAF",
+      "class": "U2"
+    },
+    "exit_u3": {
+      "label": "Usable: probably not",
+      "description": "Usable: probably not",
+      "type": "LEAF",
+      "class": "U3"
+    },
+    "exit_u4": {
+      "label": "Usable: if IP",
+      "description": "Usable: in case of incomplete penetrance",
+      "type": "LEAF",
+      "class": "U4"
+    }
+  }
+}

package/src/mocks/GRCh38/static.ts

@@ -1,8 +1,13 @@
+/* eslint-disable */
+// @ts-nocheck
 import cramUrl from "./alignment.cram.blob";
 import craiUrl from "./alignment.cram.crai.blob";
+import strCramUrl from "./str.cram.blob";
+import strCraiUrl from "./str.cram.crai.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_149380406_149403321 from "./fasta/chr1_149380406-149403321.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";
@@ -27,65 +32,118 @@ 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.gff.gz.blob";
-import vcfMetaJson from "./field_metadata.json";
 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 vcfUrlStr from "./vcf/str.vcf.blob";
+/* eslint-enable */
 import decisionTreeJson from "./decisionTree.json";
-import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
-import { Metadata } from "@molgenis/vip-report-vcf/src/FieldMetadata";
+import decisionTreeStrJson from "./decisionTreeStr.json";
+import sampleTreeJson from "./sampleTree.json";
+import vcfMetaJson from "./field_metadata.json";
+import { fetchAsBytes } from "../utils";
+import { DecisionTree } from "@molgenis/vip-report-api";
+import { SupplementaryMetadata } from "@molgenis/vip-report-vcf";
+
+export async function fetchCram() {
+  return await fetchAsBytes(cramUrl as string);
+}
 
-export const cram = await fetchAsBytes(cramUrl as string);
-export const crai = await fetchAsBytes(craiUrl as string);
+export async function fetchCrai() {
+  return await fetchAsBytes(craiUrl as string);
+}
+
+export async function fetchStrCram() {
+  return await fetchAsBytes(strCramUrl as string);
+}
+
+export async function fetchStrCrai() {
+  return await fetchAsBytes(strCraiUrl as string);
+}
 
 export const decisionTree: DecisionTree = decisionTreeJson as unknown as DecisionTree;
+export const decisionTreeStr: DecisionTree = decisionTreeStrJson as unknown as DecisionTree;
+export const sampleTree: DecisionTree = sampleTreeJson as unknown 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 async function fetchFastaGz() {
+  return {
+    "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),
+    "chr1:149380406-149403321": await fetchAsBytes(fastaUrl_chr1_149380406_149403321 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 async function fetchGenesGz() {
+  return await fetchAsBytes(genesUrl as string);
+}
 
-export const vcfMeta = vcfMetaJson as unknown as Metadata;
+export const vcfMeta = vcfMetaJson as unknown as SupplementaryMetadata;
 
-export const vcfFamily = await fetchAsBytes(vcfUrlFamily as string);
+export async function fetchVcfFamily() {
+  return await fetchAsBytes(vcfUrlFamily as string);
+}
 
-export const vcfNoVep = await fetchAsBytes(vcfUrlNoVep as string);
+export async function fetchVcfNoVep() {
+  return await fetchAsBytes(vcfUrlNoVep as string);
+}
 
-export const vcfSamples0 = await fetchAsBytes(vcfUrlSamples0 as string);
+export async function fetchVcfSamples0() {
+  return await fetchAsBytes(vcfUrlSamples0 as string);
+}
 
-export const vcfSamples1 = await fetchAsBytes(vcfUrlSamples1 as string);
+export async function fetchVcfSamples1() {
+  return await fetchAsBytes(vcfUrlSamples1 as string);
+}
 
-export const vcfSamples100 = await fetchAsBytes(vcfUrlSamples100 as string);
+export async function fetchVcfSamples100() {
+  return await fetchAsBytes(vcfUrlSamples100 as string);
+}
+
+export async function fetchVcfStr() {
+  return await fetchAsBytes(vcfUrlStr as string);
+}
+
+export const samplesStr = {
+  samples: [
+    {
+      person: {
+        familyId: "FAM001",
+        individualId: "Patient",
+        sex: "FEMALE",
+        affectedStatus: "AFFECTED",
+      },
+      index: 0,
+      proband: true,
+    },
+  ],
+  phenotypes: [],
+};
 
 export const samplesFamily = {
   samples: [
@@ -100,6 +158,7 @@ export const samplesFamily = {
       },
       index: 3,
       proband: true,
+      filter_classes: ["U1", "U2"],
     },
     {
       person: {