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Show all RefSeq transcripts in Patient View IGV with expanded display mode #5611

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Show all RefSeq transcripts in Patient View IGV with expanded display mode #5611

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6c2c95e
Initial plan
Copilot Jun 15, 2026
adc77b9
Change default IGV transcript display to show all RefSeq transcripts …
Copilot Jun 15, 2026
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11 changes: 10 additions & 1 deletion src/pages/patientView/genomicOverview/GenomicOverview.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ import {
defaultGrch37ReferenceProps,
defaultGrch38ReferenceProps,
defaultMutationTrackProps,
defaultRefSeqTrackProps,
defaultSegmentTrackProps,
generateMutationFeatures,
generateSegmentFeatures,
Expand Down Expand Up @@ -272,9 +273,17 @@ export default class GenomicOverview extends React.Component<
},
};
} else {
const genomeId = isGrch38(this.props.genome || '')
? 'hg38'
: 'hg19';
return {
...coreProps,
genome: isGrch38(this.props.genome || '') ? 'hg38' : 'hg19',
reference: {
...(genomeId === 'hg38'
? defaultGrch38ReferenceProps()
: defaultGrch37ReferenceProps()),
tracks: [defaultRefSeqTrackProps(genomeId)],
},
showNavigation: true,
showSearch: true,
showSampleNameButton: true,
Expand Down
120 changes: 17 additions & 103 deletions src/shared/lib/IGVUtils.spec.ts
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Expand Up @@ -3,6 +3,7 @@ import { assert } from 'chai';
import { CopyNumberSeg } from 'cbioportal-ts-api-client';
import {
calcIgvTrackHeight,
defaultRefSeqTrackProps,
featuresWithoutFunctions,
generateSegmentFeatures,
generateSegmentFileContent,
Expand Down Expand Up @@ -272,111 +273,24 @@ describe('IGVUtils', () => {
});
});

describe('getModifiedTrackNames', () => {
it('returns an empty array for empty input', () => {
assert.equal(getModifiedTrackNames([], []).length, 0);
describe('defaultRefSeqTrackProps', () => {
it('returns hg19 RefSeq track props with EXPANDED display mode', () => {
const props = defaultRefSeqTrackProps('hg19');
assert.equal(props.name, 'Refseq Genes');
assert.equal(props.format, 'refgene');
assert.equal(props.displayMode, 'EXPANDED');
assert.include(props.url, 'hg19');
assert.include(props.url, 'ncbiRefSeq');
assert.isDefined(props.indexURL);
});

it('returns newly added track names', () => {
const currentTracks = [
{
name: 'MUT',
type: 'variant',
},
];

const nextTracks = [
{
name: 'CNA',
type: 'seg',
displayMode: 'FILL',
features: [],
},
{
name: 'MUT',
type: 'variant',
},
];

assert.equal(
getModifiedTrackNames(currentTracks, nextTracks)[0],
'CNA'
);
});

it('returns an empty array if no track has been changed', () => {
const currentTracks = [
{
name: 'MUT',
type: 'variant',
},
{
name: 'CNA',
type: 'seg',
displayMode: 'FILL',
features: [],
},
];

const nextTracks = [
{
name: 'CNA',
type: 'seg',
displayMode: 'FILL',
features: [],
},
{
name: 'MUT',
type: 'variant',
},
];

assert.equal(
getModifiedTrackNames(currentTracks, nextTracks).length,
0
);
});

it('returns only modified tracks names', () => {
const currentTracks = [
{
name: 'CNA',
type: 'seg',
displayMode: 'FILL',
features: [],
},
{
name: 'MUT',
type: 'variant',
},
];

const nextTracks = [
{
name: 'MUT',
type: 'variant',
},
{
name: 'CNA',
type: 'seg',
displayMode: 'FILL',
features: [
{
patient: 'p1',
sample: 's1',
},
],
},
];

assert.equal(
getModifiedTrackNames(currentTracks, nextTracks).length,
1
);
assert.equal(
getModifiedTrackNames(currentTracks, nextTracks)[0],
'CNA'
);
it('returns hg38 RefSeq track props with EXPANDED display mode', () => {
const props = defaultRefSeqTrackProps('hg38');
assert.equal(props.name, 'Refseq Genes');
assert.equal(props.format, 'refgene');
assert.equal(props.displayMode, 'EXPANDED');
assert.include(props.url, 'hg38');
assert.include(props.url, 'ncbiRefSeq');
});
});
});
31 changes: 30 additions & 1 deletion src/shared/lib/IGVUtils.ts
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Expand Up @@ -56,10 +56,39 @@ export function defaultGrch38ReferenceProps() {
indexURL:
'https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai',
cytobandURL:
'https://s3.amazonaws.com/igv.broadinstitute.org/annotations/',
'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz',
};
}

export function defaultRefSeqTrackProps(genomeId: 'hg19' | 'hg38') {
if (genomeId === 'hg19') {
return {
name: 'Refseq Genes',
format: 'refgene',
url:
'https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz',
indexURL:
'https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz.tbi',
visibilityWindow: -1,
supportsWholeGenome: false,
displayMode: 'EXPANDED',
order: 1000000,
};
} else {
return {
name: 'Refseq Genes',
format: 'refgene',
url:
'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz',
indexed: false,
visibilityWindow: -1,
supportsWholeGenome: false,
displayMode: 'EXPANDED',
order: 1000000,
};
}
}

export function defaultSegmentTrackProps() {
return {
name: CNA_TRACK_NAME,
Expand Down