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PoC original straglr #325

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PoC original straglr #325

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db5af38
PoC for specific STR info
bartcharbon Jul 26, 2024
0fcf0e5
PoC for specific STR info
bartcharbon Aug 27, 2024
fb48fce
multiple fixes
bartcharbon Aug 27, 2024
b9cadb0
fix build
bartcharbon Aug 27, 2024
d5293dc
Fixes
bartcharbon Aug 27, 2024
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ script:
- pnpm run test
before_deploy:
- pnpm run build
- mv dist/index.html dist/vip-report-template.html
- mv dist/vip-template-6.2.0-str-poc.html dist/vip-report-template.html
deploy:
- provider: npm
api_token:
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6 changes: 3 additions & 3 deletions package.json
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@@ -1,6 +1,6 @@
{
"name": "@molgenis/vip-report-template",
"version": "6.2.0",
"version": "6.2.0-str-poc",
"description": "Report Template for Variant Call Format (VCF) Report Generator",
"scripts": {
"build": "vite build",
Expand Down Expand Up @@ -36,8 +36,8 @@
"dependencies": {
"@fortawesome/fontawesome-svg-core": "^6.5.2",
"@fortawesome/free-solid-svg-icons": "^6.5.2",
"@molgenis/vip-report-api": "^5.0.4",
"@molgenis/vip-report-vcf": "^2.0.2",
"@molgenis/vip-report-api": "link:C:/Users/bartc/WebstormProjects/vip-report-api/",
"@molgenis/vip-report-vcf": "link:C:/Users/bartc/WebstormProjects/vip-report-vcf/",
"@solidjs/router": "^0.13.5",
"base64-js": "^1.5.1",
"igv": "^2.15.11",
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18 changes: 4 additions & 14 deletions pnpm-lock.yaml
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5 changes: 4 additions & 1 deletion src/assets/sass/main.scss
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Expand Up @@ -85,4 +85,7 @@ table.is-borderless td,
margin-top: 8px;
overflow-y: auto;
max-height: calc(100vh - 78px) !important;
}
}

table.alternating tr:nth-child(even) {background-color: #DCDCDC;}
table.not_alternating tr {background-color: transparent;}
4 changes: 3 additions & 1 deletion src/components/InfoCollapsablePane.tsx
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Expand Up @@ -7,14 +7,15 @@ import { Info } from "./record/Info";
import { FieldValue } from "./record/field/Field";
import { isCsqInfo } from "../utils/csqUtils";
import { useLocation, A } from "@solidjs/router";
import { FieldHeader } from "./FieldHeader";

export const InfoCollapsablePane: Component<{
fields: FieldMetadata[];
record: Item<Record>;
htsFileMeta: HtsFileMetadata;
isPossibleCompound?: boolean;
}> = (props) => {
const [collapsed, setCollapsed]: Signal<boolean> = createSignal(false);
const [collapsed, setCollapsed]: Signal<boolean> = createSignal(true);

function toggleCollapse() {
setCollapsed(!collapsed());
Expand Down Expand Up @@ -53,6 +54,7 @@ export const InfoCollapsablePane: Component<{
<For each={props.fields}>
{(field, i) => (
<td>
<FieldHeader field={field} />
<For each={values()[i()]}>
{(value, j) => (
<>
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141 changes: 114 additions & 27 deletions src/components/VariantsSampleTable.tsx
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Expand Up @@ -5,10 +5,9 @@ import { Pos } from "./record/Pos";
import { HtsFileMetadata, Item, Sample } from "@molgenis/vip-report-api/src/Api";
import { GenotypeField } from "./record/format/GenotypeField";
import { InfoCollapsablePane } from "./InfoCollapsablePane";
import { Component, createMemo, createSignal, For, onMount, Show } from "solid-js";
import { Component, createMemo, createSignal, For, Match, onMount, Show, Switch } from "solid-js";
import { A } from "@solidjs/router";
import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
import { FieldHeader } from "./FieldHeader";
import { Abbr } from "./Abbr";
import { abbreviateHeader } from "../utils/field";
import {
Expand All @@ -19,6 +18,8 @@ import {
getSampleMother,
getSampleSexLabel,
} from "../utils/sample";
import { Info } from "./record/Info";
import { Format } from "./record/Format";

export const VariantsSampleTable: Component<{
item: Item<Sample>;
Expand Down Expand Up @@ -50,7 +51,7 @@ export const VariantsSampleTable: Component<{
<div style={{ display: "grid" }}>
{/* workaround for https://github.com/jgthms/bulma/issues/2572#issuecomment-523099776 */}
<div class="table-container">
<table class="table is-narrow">
<table class="table is-narrow alternating">
<thead>
<tr>
<th>Position</th>
Expand Down Expand Up @@ -83,9 +84,7 @@ export const VariantsSampleTable: Component<{
</th>
)}
</For>
{/* column containing collapse/expand icon */}
<th />
<For each={props.nestedFields}>{(field) => <FieldHeader field={field} />}</For>
<th colSpan={props.nestedFields.length + 1}>Information</th>
</tr>
</thead>
<tbody>
Expand All @@ -105,14 +104,39 @@ export const VariantsSampleTable: Component<{
<Show when={proband()} keyed>
{(proband) => (
<td>
<GenotypeField
genotype={record.data.s[proband.index]["GT"] as Genotype}
refAllele={record.data.r}
altAlleles={record.data.a}
isAbbreviate={true}
allelicBalance={record.data.s[proband.index]["VIAB"] as number | undefined | null}
readDepth={record.data.s[proband.index]["DP"] as number | undefined}
/>
<Switch fallback={<td>Huh?</td>}>
<Match when={record.data.n["SVTYPE"] !== "STR"}>
<GenotypeField
genotype={record.data.s[proband.index]["GT"] as Genotype}
refAllele={record.data.r}
altAlleles={record.data.a}
isAbbreviate={true}
allelicBalance={record.data.s[proband.index]["VIAB"] as number | undefined | null}
readDepth={record.data.s[proband.index]["DP"] as number | undefined}
/>
</Match>
<Match when={record.data.n["SVTYPE"] === "STR"}>
<Format
format={record.data.s[proband.index]["AC"]}
formatMetadata={props.recordsMetadata.format["AC"]}
record={record}
isAbbreviate={false}
allelicBalance={record.data.s[proband.index]["VIAB"] as number | undefined | null}
readDepth={record.data.s[proband.index]["DP"] as number | undefined}
/>
<br />
(
<Format
format={record.data.s[proband.index]["ACR"]}
formatMetadata={props.recordsMetadata.format["ACR"]}
record={record}
isAbbreviate={false}
allelicBalance={record.data.s[proband.index]["VIAB"] as number | undefined | null}
readDepth={record.data.s[proband.index]["DP"] as number | undefined}
/>
)
</Match>
</Switch>
</td>
)}
</Show>
Expand Down Expand Up @@ -160,19 +184,82 @@ export const VariantsSampleTable: Component<{
</>
)}
</For>
<Show when={proband()} keyed>
{(proband) => (
<InfoCollapsablePane
fields={props.nestedFields}
record={record}
htsFileMeta={props.htsFileMeta}
isPossibleCompound={
record.data.s[proband.index]["VIC"] !== null &&
record.data.s[proband.index]["VIC"] !== undefined
}
/>
)}
</Show>
<Switch fallback={<td>Huh?</td>}>
<Match when={record.data.n["SVTYPE"] !== "STR"}>
<Show when={proband()} keyed>
{(proband) => (
<td>
<InfoCollapsablePane
fields={props.nestedFields}
record={record}
htsFileMeta={props.htsFileMeta}
isPossibleCompound={
record.data.s[proband.index]["VIC"] !== null &&
record.data.s[proband.index]["VIC"] !== undefined
}
/>
</td>
)}
</Show>
</Match>
<Match when={record.data.n["SVTYPE"] === "STR"}>
<td>
<div class="columns">
<div class="column is-one-third">
<b>Gene ID: </b>
<Info
info={{ value: record.data.n["Gene_id"], record: record }}
infoMeta={props.recordsMetadata.info["Gene_id"]}
context={{}}
/>
<br />
<b>Normal maximum: </b>
<Info
info={{ value: record.data.n["NormalMax"], record: record }}
infoMeta={props.recordsMetadata.info["NormalMax"]}
context={{}}
/>
</div>
<div class="column is-one-third">
<b>Locus ID: </b>
<Info
info={{ value: record.data.n["Repeat_id"], record: record }}
infoMeta={props.recordsMetadata.info["Repeat_id"]}
context={{}}
/>
<br />
<b>Pathogenic minimum: </b>
<Info
info={{ value: record.data.n["PathogenicMin"], record: record }}
infoMeta={props.recordsMetadata.info["PathogenicMin"]}
context={{}}
/>
</div>
<div class="column is-one-third">
<b>Disease: </b>
<Info
info={{ value: record.data.n["Disease"], record: record }}
infoMeta={props.recordsMetadata.info["Disease"]}
context={{}}
/>
<br />
<b>Called repeat / catalog repeat: </b>
<Info
info={{ value: record.data.n["RU"], record: record }}
infoMeta={props.recordsMetadata.info["RU"]}
context={{}}
/>{" "}
/{" "}
<Info
info={{ value: record.data.n["repeat_unit"], record: record }}
infoMeta={props.recordsMetadata.info["repeat_unit"]}
context={{}}
/>
</div>
</div>
</td>
</Match>
</Switch>
</tr>
)}
</For>
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2 changes: 1 addition & 1 deletion src/components/record/field/FieldSingleValue.tsx
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Expand Up @@ -15,7 +15,7 @@ export const FieldSingleValue: Component<{
const type = () => props.infoMetadata.type;
return (
<Switch fallback={<Error error={`invalid info type ${type()}`} />}>
<Match when={type() === "CATEGORICAL" || type() === "STRING"}>
<Match when={type() === "CATEGORICAL" || type() === "STRING" || type() === "RANGE"}>
<FieldValueString value={props.info as string} />
</Match>
<Match when={type() === "CHARACTER"}>
Expand Down
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