Show all RefSeq transcripts in Patient View IGV with expanded display mode#5611
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…in expanded mode Switch expanded IGV view from using `genome` shorthand to explicit `reference` with RefSeq annotation track configured with `displayMode: 'EXPANDED'`. This shows all transcripts with a scrollbar instead of only the first two. Also fixes the incomplete hg38 cytobandURL.
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[WIP] Change default transcript of IGV in patient view
Show all RefSeq transcripts in Patient View IGV with expanded display mode
Jun 15, 2026
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The IGV component in Patient View only displayed 2 RefSeq transcripts without a scrollbar, causing mutations (e.g. TP53 x125_splice) to fall outside the visible annotation. This happened because the
genome: 'hg19'shorthand loads IGV's default collapsed annotation track.Changes
src/shared/lib/IGVUtils.ts: AddeddefaultRefSeqTrackProps(genomeId)returning ncbiRefSeq track config withdisplayMode: 'EXPANDED'; fixed broken hg38cytobandURLsrc/pages/patientView/genomicOverview/GenomicOverview.tsx: Expanded view now uses explicitreferencewith RefSeq track instead ofgenomeshorthand, matching the pattern already used by compact viewsrc/shared/lib/IGVUtils.spec.ts: Tests for new helperApproach
Instead of relying on IGV's opaque genome definition (which controls track display internally), we now provide the reference and annotation track explicitly:
This ensures all RefSeq transcripts render with a scrollbar, making splice-site mutations visible in the annotation context.