@molgenis/vip-report-template 8.2.1 → 8.3.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "8.2.1",
+  "version": "8.3.0",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "license": "LGPL-3.0",
   "devDependencies": {

package/scripts/validateConfig/schema.ts

@@ -106,6 +106,7 @@ const schemaConfigJsonField: JTDSchemaType<ConfigJsonField> = {
         name: {
           enum: [
             "clinVar",
+            "confidenceInterval",
             "gene",
             "genotype",
             "genotype_maternal",
@@ -114,6 +115,7 @@ const schemaConfigJsonField: JTDSchemaType<ConfigJsonField> = {
             "hpo",
             "inheritancePattern",
             "locus",
+            "spanningReads",
             "vipC",
             "vipCS",
             "vkgl",

package/src/components/field/composed/FieldComposed.tsx

@@ -5,11 +5,14 @@ import { FieldGenotype } from "./FieldGenotype";
 import { FieldGene } from "./FieldGene";
 import { ErrorNotification } from "../../ErrorNotification";
 import { FieldClinVar } from "./FieldClinVar";
+import { FieldConfidenceInterval } from "./FieldConfidenceInterval";
+import { FieldSpanningReads } from "./FieldSpanningReads";
 import { FieldGnomAd } from "./FieldGnomAd";
 import { FieldHpo } from "./FieldHpo";
 import { ConfigCellCustom } from "../../../types/configCells";
 import {
   CellValueClinVar,
+  CellValueConfidenceInterval,
   CellValueCustom,
   CellValueGene,
   CellValueGenotype,
@@ -17,6 +20,7 @@ import {
   CellValueHpo,
   CellValueInheritanceModes,
   CellValueLocus,
+  CellValueSpanningReads,
   CellValueVipC,
   CellValueVipCS,
   CellValueVkgl,
@@ -36,6 +40,9 @@ export const FieldComposed: Component<{
       <Match when={id() === "clinVar"}>
         <FieldClinVar value={props.value as CellValueClinVar} />
       </Match>
+      <Match when={id() === "confidenceInterval"}>
+        <FieldConfidenceInterval value={props.value as CellValueConfidenceInterval} />
+      </Match>
       <Match when={id() === "gene"}>
         <FieldGene value={props.value as CellValueGene} />
       </Match>
@@ -54,6 +61,9 @@ export const FieldComposed: Component<{
       <Match when={id() === "locus"}>
         <FieldLocus value={props.value as CellValueLocus} />
       </Match>
+      <Match when={id() === "spanningReads"}>
+        <FieldSpanningReads value={props.value as CellValueSpanningReads} />
+      </Match>
       <Match when={id() === "vipC"}>
         <FieldVipC value={props.value as CellValueVipC} />
       </Match>

package/src/components/field/composed/FieldConfidenceInterval.tsx

@@ -0,0 +1,14 @@
+import { Component } from "solid-js";
+import { CellValueConfidenceInterval } from "../../../types/configCellComposed";
+
+export const FieldConfidenceInterval: Component<{
+  value: CellValueConfidenceInterval;
+}> = (props) => {
+  return (
+    <span>
+      {props.value.genotype.a
+        .map((allele) => (allele !== null ? props.value.confidenceInterval[allele - 1] : "?"))
+        .join("/")}
+    </span>
+  );
+};

package/src/components/field/composed/FieldGenotypeStr.tsx

@@ -15,7 +15,9 @@ export const FieldGenotypeStr: Component<{
           <AlleleStr value={props.value.repeatUnitValue!} />
         </abbr>
       </Show>
-      <span class="ml-1">{`(n=${props.value.repeatCount!})`}</span>
+      <span class="ml-1">{`(n=${props.value.genotype.a
+        .map((allele) => (allele !== null ? props.value.repeatCount![allele - 1] : "?"))
+        .join("/")})`}</span>
       <Show when={props.value.repeatUnitMatch === false}>
         <abbr
           title={"the called repeat unit does not match the repeat unit in the loci bed file"}

package/src/components/field/composed/FieldHpo.tsx

@@ -4,7 +4,7 @@ import { FieldString } from "../typed/FieldString";
 import { CellValueHpo } from "../../../types/configCellComposed";
 
 type HpoTerm = {
-  id: string;
+  label: string;
   href: string;
 };
 
@@ -13,7 +13,7 @@ export const FieldHpo: Component<{
 }> = (props) => {
   const hpoTerms = (): HpoTerm[] =>
     props.value.hpos.map((category) => ({
-      id: category!.value!,
+      label: category!.label,
       href: `https://hpo.jax.org/app/browse/term/${encodeURI(category!.value!)}`,
     }));
 
@@ -26,7 +26,7 @@ export const FieldHpo: Component<{
           <>
             {i() !== 0 && <span>, </span>}
             <Anchor href={hpoTerm.href}>
-              <FieldString value={hpoTerm.id} />
+              <FieldString value={hpoTerm.label} />
             </Anchor>
           </>
         )}

package/src/components/field/composed/FieldSpanningReads.tsx

@@ -0,0 +1,14 @@
+import { Component } from "solid-js";
+import { CellValueSpanningReads } from "../../../types/configCellComposed";
+
+export const FieldSpanningReads: Component<{
+  value: CellValueSpanningReads;
+}> = (props) => {
+  return (
+    <span>
+      {props.value.genotype.a
+        .map((allele) => (allele !== null ? props.value.spanningReads[allele - 1] : "?"))
+        .join("/")}
+    </span>
+  );
+};

package/src/mocks/GRCh38/field_metadata.json

@@ -14,12 +14,11 @@
       "numberCount": 1,
       "type": "STRING"
     },
-    "ADSP": {
+    "RU_SPAN": {
       "label": "Spanning reads",
       "description": "Number of spanning reads consistent with the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
+      "numberType": "PER_ALT",
+      "type": "INTEGER"
     },
     "LC": {
       "label": "Coverage",
@@ -28,13 +27,6 @@
       "numberCount": 1,
       "type": "FLOAT"
     },
-    "REPCI": {
-      "label": "Repeat CI",
-      "description": "Confidence interval for the number of repeat units spanned by the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
     "REPCN": {
       "label": "Repeats",
       "description": "Number of repeat units spanned by the allele",
@@ -92,7 +84,7 @@
   },
   "info": {
     "n_object0": {
-      "nestedAttributes" : {
+      "nestedAttributes": {
         "separator": "|"
       },
       "nestedFields": {
@@ -115,7 +107,7 @@
       }
     },
     "CSQ": {
-      "nestedAttributes" : {
+      "nestedAttributes": {
         "prefix": "Consequence annotations from Ensembl VEP. Format: ",
         "separator": "|"
       },
@@ -822,6 +814,12 @@
       "numberCount": 1,
       "type": "STRING"
     },
+    "RU_CI": {
+      "label": "Repeat CI",
+      "description": "Confidence interval for the number of repeat units spanned by the allele",
+      "numberType": "PER_ALT",
+      "type": "STRING"
+    },
     "VIPC_S": {
       "label": "VIP sample classification",
       "numberType": "OTHER",