@molgenis/vip-report-template 8.2.2 → 8.3.1

package/src/mocks/config_cram.json

@@ -415,16 +415,16 @@
           "label": "Father"
         },
         {
-          "type": "genotype",
-          "name": "REPCI"
+          "type": "composed",
+          "name": "confidenceInterval"
         },
         {
           "type": "genotype",
           "name": "LC"
         },
         {
-          "type": "genotype",
-          "name": "ADSP"
+          "type": "composed",
+          "name": "spanningReads"
         },
         {
           "type": "info",
@@ -533,6 +533,11 @@
           "type": "composed",
           "name": "locus"
         },
+        {
+          "type": "info",
+          "name": "CSQ/PICK",
+          "defaultValue": "true"
+        },
         {
           "type": "info",
           "name": "CSQ/HPO",

package/src/mocks/config_default_values.json

@@ -413,13 +413,17 @@
           "label": "Father"
         },
         {
-          "type": "genotype",
-          "name": "REPCI"
+          "type": "composed",
+          "name": "confidenceInterval"
         },
         {
           "type": "genotype",
           "name": "LC"
         },
+        {
+          "type": "composed",
+          "name": "spanningReads"
+        },
         {
           "type": "genotype",
           "name": "ADSP"

package/src/mocks/config_vcf.json

@@ -413,16 +413,16 @@
           "label": "Father"
         },
         {
-          "type": "genotype",
-          "name": "REPCI"
+          "type": "composed",
+          "name": "confidenceInterval"
         },
         {
           "type": "genotype",
           "name": "LC"
         },
         {
-          "type": "genotype",
-          "name": "ADSP"
+          "type": "composed",
+          "name": "spanningReads"
         },
         {
           "type": "info",

package/src/types/config.d.ts

@@ -34,6 +34,7 @@ export interface ConfigJsonFieldComposed extends Describable {
   type: "composed";
   name:
     | "clinVar"
+    | "confidenceInterval"
     | "gene"
     | "genotype"
     | "genotype_maternal"
@@ -43,6 +44,7 @@ export interface ConfigJsonFieldComposed extends Describable {
     | "inheritancePattern"
     | "locus"
     | "ref"
+    | "spanningReads"
     | "vipC"
     | "vipCS"
     | "vkgl";

package/src/types/configCellComposed.d.ts

@@ -1,4 +1,4 @@
-import { Genotype, InfoMetadata, ValueFlag, ValueFloat, ValueString } from "@molgenis/vip-report-vcf";
+import { Genotype, InfoMetadata, ValueFlag, ValueFloat, ValueInteger, ValueString } from "@molgenis/vip-report-vcf";
 import { ValueCategorical } from "../utils/vcf.ts";
 
 export type CellValueClinVar = {
@@ -30,13 +30,23 @@ export type CellValueGenotype = {
   altAlleles: (string | null)[];
   genotype: Genotype;
   svType: ValueString | undefined;
-  repeatCount: ValueString | undefined;
+  repeatCount: ValueString[] | undefined;
   repeatUnitValue: ValueString | undefined;
-  repeatUnitMatch: ValueFlag | undefined;
+  repeatUnitMatch: ValueInteger | undefined;
   displayRepeatUnit: ValueString | undefined;
   viab: number | null | undefined;
 };
 
+export type CellValueConfidenceInterval = {
+  genotype: Genotype;
+  confidenceInterval: ValueString[];
+};
+
+export type CellValueSpanningReads = {
+  genotype: Genotype;
+  spanningReads: ValueInteger[];
+};
+
 export type CellValueHpo = {
   hpos: ValueCategorical[];
   gadoPd: ValueCategorical | undefined;
@@ -78,6 +88,8 @@ export type CellValueCustom =
   | CellValueGene
   | CellValueGnomAd
   | CellValueGenotype
+  | CellValueConfidenceInterval
+  | CellValueSpanningReads
   | CellValueHpo
   | CellValueInheritanceModes
   | CellValueLocus

package/src/utils/config/configCellsComposed.ts

@@ -1,9 +1,18 @@
 import { ConfigCellCustom } from "../../types/configCells";
-import { Genotype, InfoMetadata, ValueFlag, ValueFloat, ValueString, VcfRecord } from "@molgenis/vip-report-vcf";
+import {
+  Genotype,
+  InfoMetadata,
+  ValueFlag,
+  ValueFloat,
+  ValueInteger,
+  ValueString,
+  VcfRecord,
+} from "@molgenis/vip-report-vcf";
 import { Item } from "@molgenis/vip-report-api";
 import { getSampleLabel } from "../sample.ts";
 import {
   CellValueClinVar,
+  CellValueConfidenceInterval,
   CellValueCustom,
   CellValueGene,
   CellValueGenotype,
@@ -11,6 +20,7 @@ import {
   CellValueHpo,
   CellValueInheritanceModes,
   CellValueLocus,
+  CellValueSpanningReads,
   CellValueVipC,
   CellValueVipCS,
   CellValueVkgl,
@@ -80,6 +90,12 @@ export function initConfigCellComposed(
     case "vkgl":
       fieldConfig = createConfigFieldCustomVkgl(configStatic, metadata.records);
       break;
+    case "confidenceInterval":
+      fieldConfig = createConfigFieldCustomConfidenceInterval(configStatic, metadata.records, sample);
+      break;
+    case "spanningReads":
+      fieldConfig = createConfigFieldCustomSpanningReads(configStatic, metadata.records, sample);
+      break;
     default:
       throw new ConfigInvalidError(`unknown composed cell name '${id}'`);
   }
@@ -201,16 +217,17 @@ function createConfigFieldCustomGenotypeForSample(
 ): ConfigCellCustom<CellValueGenotype> | null {
   if (sample === null) return null;
 
-  const [fieldGt, fieldRepCn, fieldViab] = getSampleFields(metadata, "GT", "REPCN", "VIAB");
-  if (fieldGt === undefined) return null; // unlikely, but possible
-
-  const [fieldSvType, fieldRu, fieldRuMatch, fieldDisplayRu] = getInfoFields(
+  const [fieldGt, fieldViab, fieldRu, fieldRuMatch, fieldRepCn] = getSampleFields(
     metadata,
-    "SVTYPE",
-    "RU",
-    "RUMATCH",
-    "DisplayRU",
+    "GT",
+    "VIAB",
+    "RU_CALL",
+    "RU_MATCH",
+    "RU_NR",
   );
+  if (fieldGt === undefined) return null; // unlikely, but possible
+
+  const [fieldSvType, fieldDisplayRu] = getInfoFields(metadata, "SVTYPE", "DisplayRU");
 
   return {
     type: "composed",
@@ -219,23 +236,28 @@ function createConfigFieldCustomGenotypeForSample(
     description: () => getDescription(config),
     valueCount: () => 1,
     value: (record: Item<VcfRecord>, valueIndex: number): CellValueGenotype => {
-      const [genotype, repeatCount, viab] = getSampleValues(
+      const [genotype, viab, repeatUnitValue, repeatUnitMatch, repeatCount] = getSampleValues(
         sample,
         record,
         valueIndex,
         fieldGt,
-        fieldRepCn,
         fieldViab,
-      ) as [Genotype, ValueString | undefined, number | null | undefined];
-
-      const [svType, repeatUnitValue, repeatUnitMatch, displayRepeatUnit] = getInfoValues(
-        record,
-        valueIndex,
-        fieldSvType,
         fieldRu,
         fieldRuMatch,
-        fieldDisplayRu,
-      ) as [ValueString | undefined, ValueString | undefined, ValueFlag | undefined, ValueString | undefined];
+        fieldRepCn,
+      ) as [
+        Genotype,
+        number | null | undefined,
+        ValueString | undefined,
+        ValueInteger | undefined,
+        ValueString[] | undefined,
+      ];
+
+      const [svType, displayRepeatUnit] = getInfoValues(record, valueIndex, fieldSvType, fieldDisplayRu) as [
+        ValueString | undefined,
+        ValueString | undefined,
+      ];
+
       return {
         refAllele: record.data.r,
         altAlleles: record.data.a,
@@ -251,6 +273,59 @@ function createConfigFieldCustomGenotypeForSample(
   };
 }
 
+function createConfigFieldCustomConfidenceInterval(
+  config: ConfigJsonFieldComposed,
+  metadata: VcfMetadataContainer,
+  sample: SampleContainer | null,
+): ConfigCellCustom<CellValueConfidenceInterval> | null {
+  if (sample === null) return null;
+  const fieldGt = getSampleField(metadata, "GT");
+  const fieldCi = getSampleField(metadata, "RU_CI");
+  return {
+    type: "composed",
+    id: "confidenceInterval",
+    label: () => getLabel(config, "Confidence interval"),
+    description: () => getDescription(config, "Confidence interval for repeat unit count"),
+    valueCount: () => 1,
+    value: (record: Item<VcfRecord>, valueIndex: number): CellValueConfidenceInterval => {
+      const genotype = getSampleValue(sample, record, valueIndex, fieldGt) as Genotype;
+      const ci = getSampleValue(sample, record, valueIndex, fieldCi) as ValueString[];
+
+      return {
+        genotype: genotype,
+        confidenceInterval: ci !== undefined ? ci : [],
+      };
+    },
+  };
+}
+
+function createConfigFieldCustomSpanningReads(
+  config: ConfigJsonFieldComposed,
+  metadata: VcfMetadataContainer,
+  sample: SampleContainer | null,
+): ConfigCellCustom<CellValueSpanningReads> | null {
+  if (sample === null) return null;
+  const fieldGt = getSampleField(metadata, "GT");
+  const fieldSpan = getSampleField(metadata, "RU_SPAN");
+  return {
+    type: "composed",
+    id: "spanningReads",
+    label: () => getLabel(config, "Spanning Reads"),
+    description: () => getDescription(config, "Number of spanning reads for the genotype."),
+    valueCount: () => 1,
+    value: (record: Item<VcfRecord>, valueIndex: number): CellValueSpanningReads => {
+      console.log("here!");
+      const genotype = getSampleValue(sample, record, valueIndex, fieldGt) as Genotype;
+      const spanning = getSampleValue(sample, record, valueIndex, fieldSpan) as ValueInteger[];
+
+      return {
+        genotype: genotype,
+        spanningReads: spanning !== undefined ? spanning : [],
+      };
+    },
+  };
+}
+
 function createConfigFieldCustomGnomAd(
   config: ConfigJsonFieldComposed,
   metadata: VcfMetadataContainer,