From 6f0da321f6ddbf5ce842403aea820eedff960ff7 Mon Sep 17 00:00:00 2001
From: Dennis Hendriksen <d.hendriksen@umcg.nl>
Date: Fri, 1 Jul 2022 08:08:12 +0200
Subject: [PATCH] feat:replace incomplete penetrance column with gene indicator

---
 src/components/record/info/Gene.tsx | 31 ++++++++++++++++++++---------
 src/views/SampleVariants.tsx        |  1 -
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/src/components/record/info/Gene.tsx b/src/components/record/info/Gene.tsx
index c096ab3b..49e9e6e2 100644
--- a/src/components/record/info/Gene.tsx
+++ b/src/components/record/info/Gene.tsx
@@ -1,24 +1,25 @@
 import { Component, createMemo, Show } from "solid-js";
 import { Anchor } from "../../Anchor";
 import { FieldProps } from "../field/Field";
-import { ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
+import { ValueFlag, ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
 import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
+import { Abbr } from "../../Abbr";
 
 export const Gene: Component<FieldProps> = (props) => {
-  const symbol = (): string | null => props.info.value as ValueString;
+  const symbol = (): ValueString => props.info.value as ValueString;
 
-  const symbolSource = createMemo((): string | undefined => {
+  const symbolSource = createMemo((): ValueString | undefined => {
     if (symbol() === null) return undefined;
 
     const symbolSourceFieldIndex = getCsqInfoIndex(props.infoMeta, "SYMBOL_SOURCE");
-    return symbolSourceFieldIndex !== -1 ? (getCsqInfo(props.info, symbolSourceFieldIndex) as string) : undefined;
+    return symbolSourceFieldIndex !== -1 ? (getCsqInfo(props.info, symbolSourceFieldIndex) as ValueString) : undefined;
   });
 
-  const geneId = createMemo((): string | undefined => {
+  const geneId = createMemo((): ValueString | undefined => {
     if (symbol() === null) return undefined;
 
     const geneFieldIndex = getCsqInfoIndex(props.infoMeta, "Gene");
-    return geneFieldIndex !== -1 ? (getCsqInfo(props.info, geneFieldIndex) as string) : undefined;
+    return geneFieldIndex !== -1 ? (getCsqInfo(props.info, geneFieldIndex) as ValueString) : undefined;
   });
 
   const href = (): string | undefined => {
@@ -31,12 +32,24 @@ export const Gene: Component<FieldProps> = (props) => {
     return `https://www.genenames.org/tools/search/#!/?${queryString}`;
   };
 
+  const incompletePenetrance = (): ValueFlag | undefined => {
+    const ipFieldIndex = getCsqInfoIndex(props.infoMeta, "IncompletePenetrance");
+    return ipFieldIndex !== -1 ? (getCsqInfo(props.info, ipFieldIndex) as ValueFlag) : undefined;
+  };
+
   return (
     <Show when={symbol()}>
       {(symbol) => (
-        <Anchor href={href()}>
-          <span>{symbol}</span>
-        </Anchor>
+        <>
+          <Anchor href={href()}>
+            <span>{symbol}</span>
+          </Anchor>
+          {incompletePenetrance() && (
+            <sup class="ml-1">
+              <Abbr title="gene is known for incomplete penetrance" value="IP" />
+            </sup>
+          )}
+        </>
       )}
     </Show>
   );
diff --git a/src/views/SampleVariants.tsx b/src/views/SampleVariants.tsx
index 315032bb..f14d827e 100644
--- a/src/views/SampleVariants.tsx
+++ b/src/views/SampleVariants.tsx
@@ -122,7 +122,6 @@ export const SampleVariants: Component<{
       "Consequence",
       "SYMBOL",
       "InheritanceModesGene",
-      "IncompletePenetrance",
       "HPO",
       "HGVSc",
       "HGVSp",