jbrowse-plugin-graphgenomeviewer 7.3.2 → 7.4.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.3.2",
+  "version": "7.4.1",
   "description": "JBrowse 2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -32,7 +32,7 @@
     "@jbrowse/core": "5.0.0-beta.11",
     "@jbrowse/display-kit": "5.0.0-beta.11",
     "@jbrowse/display-ui": "5.0.0-beta.11",
-    "@jbrowse/graph-walks": "^3.1.0",
+    "@jbrowse/graph-walks": "^4.0.0",
     "@jbrowse/render-core": "5.0.0-beta.11",
     "@jbrowse/synteny-core": "5.0.0-beta.11"
   },
@@ -40,7 +40,7 @@
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
     "@eslint/js": "^10.0.1",
-    "@jbrowse/bandage-core": "^11.6.1",
+    "@jbrowse/bandage-core": "^11.7.0",
     "@jbrowse/cli": "^4.3.0",
     "@jbrowse/mobx-state-tree": "^6.9.0",
     "@jbrowse/plugin-linear-genome-view": "5.0.0-beta.11",

package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.test.ts

@@ -518,7 +518,10 @@ function cigarSpans(cigar: string) {
 }
 
 const largestGap = (cigar: string) =>
-  Math.max(0, ...[...cigar.matchAll(/(\d+)[ID]/g)].map(([, n]) => Number(n)))
+  [...cigar.matchAll(/(\d+)[ID]/g)].reduce(
+    (max, [, n]) => Math.max(max, Number(n)),
+    0,
+  )
 
 // HG01361#2 and HG02145#2 each carry a ~170 bp insertion against GRCh38 at
 // 31,498,602, which a band composed through GRCh38 draws as nothing
@@ -539,8 +542,8 @@ const anchoredAdapter = (conf: Record<string, unknown> = {}) =>
   })
 
 const spanOf = (intervals: { start: number; end: number }[]) => ({
-  start: Math.min(...intervals.map(i => i.start)),
-  end: Math.max(...intervals.map(i => i.end)),
+  start: intervals.reduce((min, i) => Math.min(min, i.start), Infinity),
+  end: intervals.reduce((max, i) => Math.max(max, i.end), -Infinity),
 })
 
 test('the adapter type declares that a window of its anchor answers any lane pair', () => {
@@ -683,7 +686,10 @@ test('sequence both lanes carry and GRCh38 lacks aligns inside the pair record',
     targetAssemblyName: 'HG01361#2',
   })
   expect(
-    Math.max(...againstReference.map(f => largestGap(cigarOf(f)))),
+    againstReference.reduce(
+      (max, f) => Math.max(max, largestGap(cigarOf(f))),
+      0,
+    ),
   ).toBeGreaterThan(150)
   const records = await feats(adapter, insertionWindow, pair)
   for (const f of records) {

package/src/GbzBaseSyntenyAdapter/companion.test.ts

@@ -10,10 +10,12 @@ vi.mock('@jbrowse/core/util/io', async importOriginal => {
   const io = await importOriginal<typeof IO>()
   return {
     ...io,
-    openLocation: (...args: Parameters<typeof io.openLocation>) => {
+    openLocation: (
+      ...[location, pluginManager]: Parameters<typeof io.openLocation>
+    ) => {
       const error = statError.current
       return error === undefined
-        ? io.openLocation(...args)
+        ? io.openLocation(location, pluginManager)
         : { stat: () => Promise.reject(error) }
     },
   }

package/src/GetSubgraph.ts

@@ -31,6 +31,8 @@ export interface SubgraphCutOptions {
   // a cut for walk rows: its runs come with the tables, and the
   // step budget, which guards a Graph of every step, does not apply
   walkRows?: boolean
+  // abridged walks, `sample#haplotype#contig`, a walk-file cut reads in full
+  expand?: string[]
 }
 
 // What an adapter's cut is handed: the payload, plus the call's own signal so

package/src/GraphGenomeView/components/ElTree.tsx

@@ -24,7 +24,7 @@ function toReact(node: El | string, key: number): ReactNode {
       props[propName(name)] = value
     }
   }
-  return createElement(node.tag, props, ...node.children.map(toReact))
+  return createElement(node.tag, props, node.children.map(toReact))
 }
 
 // A useId fit for an SVG id and for url(#…)

package/src/GraphGenomeView/components/FacetPanels.tsx

@@ -198,7 +198,10 @@ const FacetPanels = observer(function FacetPanels({
       <div
         style={{
           ...keyStyle,
-          gridRow: Math.floor(Math.max(...place.cells) / columns) + 2,
+          gridRow:
+            Math.floor(
+              place.cells.reduce((a, b) => Math.max(a, b), -Infinity) / columns,
+            ) + 2,
         }}
         data-testid="graph-facet-key"
       >

package/src/GraphGenomeView/components/PaneContextMenu.tsx

@@ -46,6 +46,10 @@ function nodeMenuItems(model: GraphPaneModel, nodeId: string): MenuItem[] {
   ]
 }
 
+function formatSteps(steps: number) {
+  return steps >= 1000 ? `${Math.round(steps / 1000)} k` : `${steps}`
+}
+
 // A walk row's bar stands for a span of its haplotype's own contig, so the
 // question a right-click asks is answered by a linear view on that assembly,
 // with its genes
@@ -80,6 +84,16 @@ function walkRowMenuItems(
             : 'This walk states no contig coordinates',
           onClick: () => {},
         },
+    ...(walk?.abridgedSteps
+      ? [
+          {
+            label: `Load the ${formatSteps(walk.abridgedSteps)} abridged steps`,
+            onClick: () => {
+              model.expandWalk(walk.name)
+            },
+          },
+        ]
+      : []),
     ...(walk && model.liftsWalks && model.modeDrawsNodes
       ? [
           {

package/src/GraphGenomeView/components/PaneSvg.tsx

@@ -143,7 +143,8 @@ function Keys({
   }
   const pad = 6
   const rows = sections.flat()
-  const boxWidth = Math.max(...rows.map(r => r.width)) + pad * 2
+  const boxWidth =
+    rows.reduce((max, r) => Math.max(max, r.width), -Infinity) + pad * 2
   const boxHeight =
     rows.reduce((sum, r) => sum + r.height, 0) + sections.length * pad
   const right = model.paneWidth - LEGEND_INSET_PX

package/src/GraphGenomeView/legendSections.ts

@@ -301,10 +301,10 @@ export function tubeMapRows(model: GraphPaneModel): LegendRow[] {
   if (values) {
     rows.push(
       tubeRow('value-reference', flat(PANEL_REFERENCE_TUBE), 'reference'),
-      ...values.map(({ value, color }) =>
-        tubeRow(`value-${value}`, flat(color), value),
-      ),
     )
+    for (const { value, color } of values) {
+      rows.push(tubeRow(`value-${value}`, flat(color), value))
+    }
   }
   if (roles) {
     rows.push(

package/src/GraphGenomeView/model.test.ts

@@ -50,6 +50,9 @@ import type { LayoutModeValue } from '@jbrowse/bandage-core/layoutModes'
 import type { Renderer } from '@jbrowse/bandage-core/renderer/types'
 import type { Graph } from '@jbrowse/bandage-core/types'
 
+const minOf = (v: number[]) => v.reduce((a, b) => Math.min(a, b))
+const maxOf = (v: number[]) => v.reduce((a, b) => Math.max(a, b))
+
 const mockRpcCall = vi.fn()
 // The canonical assembly a name or alias resolves to, which is what
 // assemblyManager.assemblyNameMap does: it is keyed by [name, ...aliases].
@@ -1575,8 +1578,8 @@ describe('canvas height follows the drawing', () => {
     const ys = points.map(p => p.y)
     const xs = points.map(p => p.x)
     return {
-      w: Math.max(...xs) - Math.min(...xs),
-      h: Math.max(...ys) - Math.min(...ys),
+      w: maxOf(xs) - minOf(xs),
+      h: maxOf(ys) - minOf(ys),
     }
   }
 
@@ -2498,8 +2501,7 @@ describe('bubbleSpread', () => {
   })
 
   test('compressing shrinks the drawn length range', () => {
-    const range = (lengths: number[]) =>
-      Math.max(...lengths) / Math.min(...lengths)
+    const range = (lengths: number[]) => maxOf(lengths) / minOf(lengths)
     // the rope: on the real cut the longest node draws tens of times the
     // shortest, so zoom-to-fit frames the long one and the alleles vanish
     expect(range(lengthsUnder('auto'))).toBeGreaterThan(20)
@@ -2608,7 +2610,7 @@ describe('layoutBounds on a reference axis', () => {
     const drawnX = Object.values(model.nodePositions!)
       .flat()
       .map(s => s.x)
-    expect(Math.min(...drawnX)).toBeLessThan(FAR_REGION.start)
+    expect(minOf(drawnX)).toBeLessThan(FAR_REGION.start)
 
     expect(model.layoutBounds!.minX).toBe(FAR_REGION.start)
     expect(model.layoutBounds!.w).toBe(FAR_REGION.end - FAR_REGION.start)
@@ -2639,9 +2641,7 @@ describe('layoutBounds on a reference axis', () => {
     const drawnY = Object.values(model.nodePositions!)
       .flat()
       .map(s => s.y)
-    expect(model.layoutBounds!.h).toBe(
-      Math.max(...drawnY) - Math.min(...drawnY),
-    )
+    expect(model.layoutBounds!.h).toBe(maxOf(drawnY) - minOf(drawnY))
   })
 
   test('a force layout keeps the extent it measured', async () => {
@@ -2659,10 +2659,8 @@ describe('layoutBounds on a reference axis', () => {
     const drawnX = Object.values(model.nodePositions!)
       .flat()
       .map(s => s.x)
-    expect(model.layoutBounds!.minX).toBe(Math.min(...drawnX))
-    expect(model.layoutBounds!.w).toBe(
-      Math.max(...drawnX) - Math.min(...drawnX),
-    )
+    expect(model.layoutBounds!.minX).toBe(minOf(drawnX))
+    expect(model.layoutBounds!.w).toBe(maxOf(drawnX) - minOf(drawnX))
   })
 })
 
@@ -2749,7 +2747,7 @@ describe('a row layout draws y in pixels', () => {
     const xs = Object.values(model.nodePositions!)
       .flat()
       .map(p => p.x * model.scaleX + model.translateX)
-    expect(Math.max(...xs) - Math.min(...xs)).toBeCloseTo(
+    expect(maxOf(xs) - minOf(xs)).toBeCloseTo(
       model.width - model.fitPadLeft - 40,
       5,
     )
@@ -2847,7 +2845,7 @@ describe('what the row axis draws, in pixels', () => {
     return model
   }
 
-  const spread = (v: number[]) => Math.max(...v) - Math.min(...v)
+  const spread = (v: number[]) => maxOf(v) - minOf(v)
 
   test('the rows are one pitch apart and the pane holds them', async () => {
     const model = await fitted()
@@ -2861,8 +2859,8 @@ describe('what the row axis draws, in pixels', () => {
 
     // three row gaps, and each tube half a thickness either side of its row
     expect(spread(rowYs)).toBeCloseTo(3 * ROW_HEIGHT_PX, 5)
-    expect(Math.min(...rowYs) - model.contigThickness / 2).toBeGreaterThan(0)
-    expect(Math.max(...rowYs) + model.contigThickness / 2).toBeLessThan(
+    expect(minOf(rowYs) - model.contigThickness / 2).toBeGreaterThan(0)
+    expect(maxOf(rowYs) + model.contigThickness / 2).toBeLessThan(
       model.canvasHeight,
     )
   })
@@ -2877,8 +2875,8 @@ describe('what the row axis draws, in pixels', () => {
     expect(model.deletions).toHaveLength(1)
     const points = render(model)
 
-    const top = Math.min(...points.map(p => p.y))
-    const bottom = Math.max(...points.map(p => p.y))
+    const top = minOf(points.map(p => p.y))
+    const bottom = maxOf(points.map(p => p.y))
     // it does bow past the rows — a flat arc would mean the bow was dropped,
     // not converted; the rows themselves span three pitches
     expect(bottom - top).toBeGreaterThanOrEqual(3 * ROW_HEIGHT_PX)
@@ -2917,11 +2915,11 @@ describe('what the row axis draws, in pixels', () => {
 
   test('the fit starts the drawing right of the row labels', async () => {
     const model = await fitted()
-    const labelsEnd = Math.max(
-      ...model.drawnRowLabels.map(r => rowLabelBox(r.label, 0).x1),
+    const labelsEnd = maxOf(
+      model.drawnRowLabels.map(r => rowLabelBox(r.label, 0).x1),
     )
     expect(labelsEnd).toBeGreaterThan(40)
-    expect(Math.min(...render(model).map(p => p.x))).toBeGreaterThan(labelsEnd)
+    expect(minOf(render(model).map(p => p.x))).toBeGreaterThan(labelsEnd)
   })
 
   // Zoom is an x-only gesture on this axis, so afterwards the rows are drawn in

package/src/GraphGenomeView/model.ts

@@ -67,6 +67,9 @@ export const GraphPane = withLaunchActions
         haplotypes: self.cutHaplotypes,
         ...(self.chosenLayoutMode === 'walkrows' ? { walkRows: true } : {}),
         ...(self.cutsWholeWalks ? { snarls: 'overlapping' as const } : {}),
+        ...(self.expandedWalks.length > 0
+          ? { expand: self.expandedWalks }
+          : {}),
       }
     },
   }))

package/src/GraphGenomeView/pane/fitViews.ts

@@ -155,9 +155,9 @@ export const withFitViews = withHostViews
     // The row labels are pinned to the pane's left edge, so the fit starts
     // the drawing past the widest one.
     get fitPadLeft() {
-      return Math.max(
+      return this.drawnRowLabels.reduce(
+        (pad, r) => Math.max(pad, rowLabelBox(r.label, 0).x1 + 6),
         FIT_PADDING,
-        ...this.drawnRowLabels.map(r => rowLabelBox(r.label, 0).x1 + 6),
       )
     },
     // Extent of the drawing in layout units, shared by the pane height and

package/src/GraphGenomeView/pane/paneBase.ts

@@ -332,6 +332,8 @@ export const paneBase = types
       // the haplotypes a GBZ or walk-indexed cut is for; unset is
       // trackHaplotypes
       subgraphHaplotypes: types.maybe(types.frozen<string[]>()),
+      // abridged walks the user asked to load in full
+      expandedWalks: types.optional(types.frozen<string[]>(), []),
     }),
   )
   .volatile(() => ({

package/src/GraphGenomeView/pane/renderingActions.ts

@@ -424,3 +424,12 @@ export const withRenderingActions = withLoadActions
         : self.switchLayout('force')
     },
   }))
+  .actions(self => ({
+    // reads the abridged walk `name` in full with the next cut
+    expandWalk(name: string) {
+      if (!self.expandedWalks.includes(name)) {
+        self.expandedWalks = self.expandedWalks.concat(name)
+        self.retryLoad()
+      }
+    },
+  }))

package/src/GraphGenomeView/repeats/walkCalls.test.ts

@@ -107,8 +107,8 @@ test('the threshold falls in a gap the ABCA7 cohort leaves empty', () => {
   const scored = rows.filter(r => r.call?.agrees !== undefined)
   const near = scored.filter(r => r.call!.agrees)
   const far = scored.filter(r => !r.call!.agrees)
-  expect(Math.max(...near.map(apart))).toBeLessThan(0.08)
-  expect(Math.min(...far.map(apart))).toBeGreaterThan(0.14)
+  expect(near.map(apart).reduce((a, b) => Math.max(a, b))).toBeLessThan(0.08)
+  expect(far.map(apart).reduce((a, b) => Math.min(a, b))).toBeGreaterThan(0.14)
   expect(CALL_TOLERANCE).toBeGreaterThan(0.08)
   expect(CALL_TOLERANCE).toBeLessThan(0.14)
   expect({

package/src/GraphGenomeView/subgraphLoad.test.ts

@@ -305,6 +305,20 @@ describe('canceling and retrying', () => {
     })
   })
 
+  test('expanding a walk cuts again with its name', async () => {
+    const model = await cut(ON_HG38)
+    mockRpcCall.mockClear()
+    model.expandWalk('HG002#1#chr1')
+    model.expandWalk('HG002#1#chr1')
+    expect(model.expandedWalks).toEqual(['HG002#1#chr1'])
+    await vi.waitFor(() => {
+      expect(mockRpcCall).toHaveBeenCalledTimes(1)
+    })
+    expect(mockRpcCall.mock.calls[0]?.[2]).toMatchObject({
+      opts: { expand: ['HG002#1#chr1'] },
+    })
+  })
+
   test('a newer cut aborts the one it replaces', () => {
     pendingCuts()
     const model = launchedView()
@@ -621,7 +635,8 @@ describe('reads', () => {
       [x((r.x0 + r.x1) / 2), y((r.y0 + r.y1) / 2)] as const
     const [haplotypes, reads] = picture.layers
 
-    model.setHoveredTube(model.tubeAt(...onScreen(reads!.rects[0]!)))
+    const [readX, readY] = onScreen(reads!.rects[0]!)
+    model.setHoveredTube(model.tubeAt(readX, readY))
     expect(model.hoveredTubeText).toEqual({
       label: 'r1',
       readout: 'MAPQ 60, forward strand',
@@ -636,7 +651,8 @@ describe('reads', () => {
     )
 
     const alt = haplotypes!.rects.find(r => r.id === 1)!
-    model.setHoveredTube(model.tubeAt(...onScreen(alt)))
+    const [altX, altY] = onScreen(alt)
+    model.setHoveredTube(model.tubeAt(altX, altY))
     expect(model.hoveredTubeText).toEqual({
       label: 'alt',
       readout: 'haplotype',

package/src/GraphGenomeView/tubeMapPanels.test.ts

@@ -93,8 +93,10 @@ test('panels stack down the pane, a title gap above each', () => {
   expect(a!.result.tubeMap.layout.tracks).toHaveLength(3)
   expect(b!.result.tubeMap.layout.tracks).toHaveLength(2)
   const ys = Object.values(split.nodePositions).flatMap(s => s.map(p => p.y))
-  expect(Math.min(...ys)).toBeGreaterThanOrEqual(PANEL_GAP)
-  expect(Math.max(...ys)).toBeLessThanOrEqual(split.extent!.maxY!)
+  expect(ys.reduce((a, b) => Math.min(a, b))).toBeGreaterThanOrEqual(PANEL_GAP)
+  expect(ys.reduce((a, b) => Math.max(a, b))).toBeLessThanOrEqual(
+    split.extent!.maxY!,
+  )
 })
 
 test('one group draws the whole map, unsplit', () => {

package/src/GraphGenomeView/tubeMapPanels.ts

@@ -198,8 +198,8 @@ export function memberAt(
   if (spans.length === 0) {
     return undefined
   }
-  const start = Math.min(...spans.map(s => s.start))
-  const end = Math.max(...spans.map(s => s.end))
+  const start = spans.reduce((min, s) => Math.min(min, s.start), Infinity)
+  const end = spans.reduce((max, s) => Math.max(max, s.end), -Infinity)
   const share = right > left ? (sx - left) / (right - left) : 0
   const bp = start + Math.min(1, Math.max(0, share)) * (end - start)
   const distance = (s: { start: number; end: number }) =>

package/src/RgfaTabixAdapter/configSchema.ts

@@ -48,7 +48,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'RgfaTabixAdapter',
- *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5.GRCh38',
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  *   defaultHaplotypes: ['HG002', 'HG00733', 'HG02257', 'NA19240'],
  * }

package/src/RgfaTabixAdapter/walkFiles.test.ts

@@ -7,6 +7,7 @@ import {
 } from '@jbrowse/bandage-core/gfa/graphTables'
 import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { readConfObject } from '@jbrowse/core/configuration'
+import { WalkReader } from '@jbrowse/graph-walks'
 import { firstValueFrom } from 'rxjs'
 import { toArray } from 'rxjs/operators'
 
@@ -17,9 +18,9 @@ import type { WalkCut } from './walkCut.ts'
 import type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'
 
 // chr22 of HPRC v2.1 at base level, one walk file per reference in walk
-// format 4, built under ~/work/scratch/walks-20261008/f4. Skipped where the
+// format 5, built under ~/work/scratch/walks-20261008/f5. Skipped where the
 // files are absent.
-const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f4/chr22'
+const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f5/chr22'
 const present = ['GRCh38', 'CHM13'].every(sample =>
   existsSync(`${chr22}.${sample}.walks.bed.gz`),
 )
@@ -201,6 +202,17 @@ test("the haplotypes a walk file's header names", async () => {
   expect(gfa).not.toMatch(/^S\t8\t/m)
 })
 
+test('a cut asked to expand walks hands the reader their names', async () => {
+  const cut = vi.spyOn(WalkReader.prototype, 'cut')
+  await makeAdapter(headerPrefix).getSubgraph(chr1(1000, 2600), {
+    expand: ['HG002#1#chr1'],
+  })
+  const expand = cut.mock.calls[0]?.[2]?.expand
+  expect(expand?.('HG002#1#chr1')).toBe(true)
+  expect(expand?.('HG002#2#chr1')).toBe(false)
+  cut.mockRestore()
+})
+
 test('a cut for some haplotypes keeps a reference walk named without a haplotype', async () => {
   const cut = (await makeAdapter(twoPartPrefix).getSubgraph(chr1(1000, 2600), {
     haplotypes: ['HG002#1'],
@@ -215,7 +227,7 @@ test('a cut for some haplotypes keeps a reference walk named without a haplotype
 
 test('a format 1 walk file is refused, with what to rebuild it with', async () => {
   const cut = makeAdapter(fixture('walks1_header')).getSubgraph(chr1(0, 600))
-  await expect(cut).rejects.toThrow(/rebuild it with gfa-to-tabix 1.2/)
+  await expect(cut).rejects.toThrow(/rebuild it with gfa-to-tabix 1.4/)
 })
 
 test('a cut over walkByteBudget reads no row', async () => {

package/src/RgfaTabixAdapter/walkReader.ts

@@ -57,7 +57,7 @@ export class WalkIndex {
   async subgraph(
     refName: string,
     region: { start: number; end: number },
-    { signal, haplotypes, walkRows }: SubgraphAdapterOptions,
+    { signal, haplotypes, walkRows, expand }: SubgraphAdapterOptions,
   ) {
     const budgets = this.budgets()
     const { graph, kept, fragments } = await this.reader.cut(refName, region, {
@@ -68,6 +68,9 @@ export class WalkIndex {
         haplotypes?.map(lane => resolvePanSNPrefix(this.adapter, lane)),
         refName,
       ),
+      ...(expand?.length
+        ? { expand: (name: string) => expand.includes(name) }
+        : {}),
     })
     return walkCutFor(graph.tables(kept, fragments), region, walkRows)
   }

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts

@@ -111,7 +111,10 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
   }
 
   // The window's walks for the haplotypes named and the reference, with no
-  // link read; a window past a budget fails as a zoom-in notice for lanes
+  // link read; a window past a budget fails as a zoom-in notice for lanes.
+  // Named lanes come back in full where format 5 abridged them: an abridged
+  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32
+  // lanes empty.
   private async laneWalks(
     refName: string,
     region: Region,
@@ -119,12 +122,14 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
     opts: LaneFeatureOptions,
     status: string,
   ) {
+    const keep = walksKept(prefixes, refName)
     return updateStatus(status, opts.statusCallback, () =>
       this.walks.reader
         .cut(refName, region, {
           ...this.walks.budgets(),
           signal: opts.signal,
-          keep: walksKept(prefixes, refName),
+          keep,
+          expand: keep,
           links: false,
         })
         .catch((error: unknown) => {

package/src/WalkTabixSyntenyAdapter/configSchema.ts

@@ -32,7 +32,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'WalkTabixSyntenyAdapter',
- *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f5.GRCh38',
  *   assemblyNames: ['hg38'],
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  * }

package/src/WalkTabixSyntenyAdapter/gbzParity.test.ts

@@ -12,10 +12,9 @@ import type { Feature } from '@jbrowse/core/util'
 import type { SyntenyMate } from '@jbrowse/synteny-core'
 
 // chr22 of HPRC v2.1 as a gbz-base database and as gfa-to-tabix's GRCh38
-// walk file in walk format 4, built 2026-10-08 and 2026-10-20. Skipped where
-// the files are absent.
+// walk file in walk format 5. Skipped where the files are absent.
 const dir = '/home/cdiesh/work/scratch/walks-20261008'
-const walkPrefix = `${dir}/f4/chr22.GRCh38`
+const walkPrefix = `${dir}/f5/chr22.GRCh38`
 const present =
   existsSync(`${walkPrefix}.walks.bed.gz`) && existsSync(`${dir}/chr22.gbz.db`)
 

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.3.2'
+export const version = '7.4.1'