jbrowse-plugin-graphgenomeviewer 7.1.13 → 7.2.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.1.13",
+  "version": "7.2.1",
   "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": "^2.0.0",
+    "@jbrowse/graph-walks": "^2.1.0",
     "@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": "^11.0.0",
+    "@jbrowse/bandage-core": "^11.4.0",
     "@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

@@ -12,6 +12,7 @@ import {
 } from '@jbrowse/bandage-core/gbzWindow'
 import { gfaTables } from '@jbrowse/bandage-core/gfa/gfaTables'
 import { graphTablesGFA } from '@jbrowse/bandage-core/gfa/graphTables'
+import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { walkRows } from '@jbrowse/bandage-core/layout/walkRows'
 import { loadGraph } from '@jbrowse/bandage-core/pipeline'
 import { numericCigarToString } from '@jbrowse/cigar-utils'
@@ -27,10 +28,9 @@ import Adapter, {
 } from './GbzBaseSyntenyAdapter.ts'
 import configSchema from './configSchema.ts'
 import GbzBaseSyntenyAdapterF from './index.ts'
-import { walkRowsOf } from '../RgfaTabixAdapter/walkRowRuns.ts'
 import { laneAssemblyName } from '../synteny/lanePairs.ts'
 
-import type { WalkCut } from '../RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from '../RgfaTabixAdapter/walkCut.ts'
 import type { GBZBase } from '@gmod/gbz-base'
 import type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'
 import type { SyntenyMate } from '@jbrowse/synteny-core'

package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts

@@ -20,7 +20,7 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 
 import { findCompanion } from './companion.ts'
-import { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'
+import { walkCutFor } from '../RgfaTabixAdapter/walkCut.ts'
 import { GafFile } from '../gaf/gafFile.ts'
 import { locationIsSet } from '../locationName.ts'
 import { openTabixSlot } from '../panSNTabix.ts'

package/src/GetSubgraph.ts

@@ -4,7 +4,7 @@ import { rpcResultWithArrayBuffers } from '@jbrowse/core/util/librpc'
 
 import { adapterImplementing } from './adapterImplementing'
 
-import type { WalkCut } from './RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from './RgfaTabixAdapter/walkCut.ts'
 import type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'
 import type { Region } from '@jbrowse/core/util'
 

package/src/GraphGenomeView/genes/genes.test.ts

@@ -232,8 +232,26 @@ test('exons land on the backbone stretch they cover, and the name at the midpoin
   const [pin] = genePins(graph, geneModelsFrom([gene]), positions)
   expect(pin!.exons).toBe('M20,0L60,0M100,20L100,80')
   expect(pin!.exonsByNode).toEqual([
-    { nodeId: 'v1+', d: 'M20,0L60,0' },
-    { nodeId: 'v2+', d: 'M100,20L100,80' },
+    {
+      nodeId: 'v1+',
+      d: 'M20,0L60,0',
+      stretches: [
+        [
+          { x: 20, y: 0 },
+          { x: 60, y: 0 },
+        ],
+      ],
+    },
+    {
+      nodeId: 'v2+',
+      d: 'M100,20L100,80',
+      stretches: [
+        [
+          { x: 100, y: 20 },
+          { x: 100, y: 80 },
+        ],
+      ],
+    },
   ])
   expect(pin!.at).toEqual({ x: 100, y: 0 })
   expect(pin!.covered).toBe(1)

package/src/GraphGenomeView/legendSections.test.ts

@@ -39,7 +39,7 @@ test("the ramp key's bp read the same in every locale", () => {
   const model = {
     walkLift: undefined,
     referenceRampDomain: { start: 999.5, end: 123_456.5 },
-    referenceRampOffKeys: { offReference: false, unplaced: false },
+    referenceRampDrawsOffReference: false,
     bubbleHalos: [],
     genePins: [],
     pathLegend: [],

package/src/GraphGenomeView/legendSections.ts

@@ -39,8 +39,6 @@ import type { LiftedWalk } from '@jbrowse/bandage-core/walkHighlight'
 export const SWATCH_PX = 18
 const BAR_PX = 48
 
-// getNodeColor's grey for a node the ramp cannot place
-const UNPLACED_SWATCH = 'rgb(160, 160, 160)'
 // LIFT_BACKDROP_CSS reads paler alone than faded strokes do where they
 // overlap, so the key samples it darker
 const FADED_SWATCH = 'rgba(160, 160, 160, 0.45)'
@@ -147,19 +145,15 @@ function rampRows(model: GraphPaneModel): LegendRow[] {
   // a measured domain runs between node midpoints, which can fall on a half bp
   const start = Math.round(domain.start)
   const end = Math.round(domain.end)
-  const { offReference, unplaced } = model.referenceRampOffKeys
   return [
     {
       key: 'ramp',
       label: `${start.toLocaleString('en-US')}-${end.toLocaleString('en-US')} (${formatBp(end - start)})`,
       swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },
     },
-    ...(offReference
+    ...(model.referenceRampDrawsOffReference
       ? [fillRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference', BAR_PX)]
       : []),
-    ...(unplaced
-      ? [fillRow('unplaced', UNPLACED_SWATCH, 'no reference position', BAR_PX)]
-      : []),
   ]
 }
 

package/src/GraphGenomeView/model.test.ts

@@ -40,7 +40,7 @@ import { EMPTY_BATCH, SELECT_BRIGHTEN } from './pane/paneBase'
 import { PANEL_REFERENCE_TUBE, PANEL_TUBES } from './tubeMapPanels'
 import stateModelFactory from './viewModel'
 import { SECTION_HEADER_PX, walkRowTrees } from './walkRowGroups'
-import { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'
+import { walkCutFor } from '../RgfaTabixAdapter/walkCut.ts'
 
 import type { GraphLayers } from './graphLayers'
 import type { SubgraphCutOptions } from '../GetSubgraph'
@@ -1903,7 +1903,6 @@ describe('zoomToFit on a tube map', () => {
     const { nodes } = model.tubeMapPicture!
     expect(nodes.length).toBeGreaterThan(0)
     expect(nodes.every(n => model.tubeMapNodeColors!.has(n.name))).toBe(true)
-    expect(model.referenceRampOffKeys.unplaced).toBe(false)
   })
 
   test('a fold change lays the tube map out again', async () => {

package/src/GraphGenomeView/pane/graphViews.ts

@@ -1,3 +1,4 @@
+import { isBackbone } from '@jbrowse/bandage-core/anchoredNodes'
 import { bubbleHalos } from '@jbrowse/bandage-core/bubbles/bubbleHalos'
 import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'
 import { bubbleSegmentIds } from '@jbrowse/bandage-core/bubbles/classifyBubble'
@@ -11,6 +12,10 @@ import {
 import { facetSettingOf } from '@jbrowse/bandage-core/facetGrid'
 import { genePins } from '@jbrowse/bandage-core/genes/genePins'
 import { formatBp } from '@jbrowse/bandage-core/graphLabels'
+import {
+  walkRowRuns,
+  walkRowsOf,
+} from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { filterSamples, walkRows } from '@jbrowse/bandage-core/layout/walkRows'
 import {
   layoutModeByValue,
@@ -51,7 +56,6 @@ import {
 import { computed } from 'mobx'
 
 import { TUBE_MAP_MODES, dependOn, geometryPainted, paneBase } from './paneBase'
-import { walkRowRuns, walkRowsOf } from '../../RgfaTabixAdapter/walkRowRuns.ts'
 import {
   canonicalAssemblyName,
   trackAssemblies,
@@ -82,7 +86,7 @@ import {
 import { groupByOf, groupWalkRows, metadataColumns } from '../walkRowGroups'
 
 import type { ScreenTransform } from './keepInView'
-import type { WalkCut } from '../../RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from '../../RgfaTabixAdapter/walkCut.ts'
 import type { GraphLayers } from '../graphLayers'
 import type { HoverHighlight } from '../hoverHighlight'
 import type { NodeColor } from '../nodeColor'
@@ -471,16 +475,11 @@ export const withGraphViews = paneBase
     // Whether a lifted lane paints a node charcoal, the colour a lane coloured
     // by reference position gives what is off the reference
     get liftPaintsOffReference() {
-      for (const w of this.walkLift?.walks ?? []) {
-        if (w.encoding.field !== 'walk') {
-          for (const color of w.colors.values()) {
-            if (color === NO_VALUE_COLOR) {
-              return true
-            }
-          }
-        }
-      }
-      return false
+      return !!this.walkLift?.walks.some(
+        w =>
+          w.encoding.field !== 'walk' &&
+          [...w.colors.values()].includes(NO_VALUE_COLOR),
+      )
     },
     // what the faded rest of the drawing is not on
     get liftedWalksLabel() {
@@ -1086,29 +1085,19 @@ export const withGraphViews = paneBase
         ? { start: ramp.start, end: ramp.start + ramp.span }
         : undefined
     },
-    // The ramp's two colours for nodes off it, as getNodeColor paints them:
-    // charcoal where an rGFA rank puts a node off the reference, grey where
-    // a node has no reference position at all. A tube map draws the window
-    // alone (trimToWindow), so there only the boxes it drew count.
-    get referenceRampOffKeys() {
-      const ramp = self.referenceRamp
-      const layout = self.layoutResult
-      const drawn = layout?.tubeMap ? layout.nodePositions : undefined
-      let offReference = false
-      let unplaced = false
-      if (ramp && self.drawnGraph) {
-        for (const node of self.drawnGraph.nodes) {
-          if (drawn && !drawn[node.id]) {
-            continue
-          }
-          if (!ramp.midpoints.has(node.id)) {
-            unplaced = true
-          } else if (node.stable && node.stable.rank > 0) {
-            offReference = true
-          }
-        }
-      }
-      return { offReference, unplaced }
+    // Whether nodes take their scheme's colour: the drawing's own, or a tube
+    // map's boxes. Walk rows draw bars with a key of their own.
+    get paintsNodeColors() {
+      return self.drawsNodes || !!self.layoutResult?.tubeMap
+    },
+    // Whether the ramp paints a drawn node charcoal, as getNodeColor does
+    // every node off the backbone
+    get referenceRampDrawsOffReference() {
+      return (
+        !!self.referenceRamp &&
+        this.paintsNodeColors &&
+        !!self.drawnGraph?.nodes.some(node => !isBackbone(node))
+      )
     },
     // Each tube map box in its node's colour, where the scheme paints one
     get tubeMapNodeColors() {

package/src/GraphGenomeView/pane/loadActions.ts

@@ -6,6 +6,8 @@ import {
   clipToWindow,
   trimToWindow,
 } from '@jbrowse/bandage-core/layout/trimToWindow'
+import { walkRowLayoutOf } from '@jbrowse/bandage-core/layout/walkRowLayout'
+import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { layoutModeByValue } from '@jbrowse/bandage-core/layoutModes'
 import {
   anchorFromPaths,
@@ -33,7 +35,6 @@ import {
 } from './paneBase'
 import { withSettingActions } from './settingActions'
 import { namesReads } from '../../GetGraphReads'
-import { walkRowsOf } from '../../RgfaTabixAdapter/walkRowRuns.ts'
 import { geneModelsFrom } from '../genes/geneFeatures'
 import { gfaText } from '../gfaText'
 import { repeatArraysFrom } from '../repeats/repeatFeatures'
@@ -43,10 +44,10 @@ import {
   withTubeMapPanels,
 } from '../tubeMapPanels'
 import { parseSamplesTsv } from '../walkRowGroups'
-import { walkRowLayoutOf, walkRowsGraph } from '../walkRowsCut.ts'
+import { walkRowsGraph } from '../walkRowsCut.ts'
 
 import type { SubgraphCutOptions, SubgraphRegion } from '../../GetSubgraph'
-import type { WalkCut } from '../../RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from '../../RgfaTabixAdapter/walkCut.ts'
 import type { GafReads } from '../../gaf/gafFile'
 import type { PaneLayout } from '../tubeMapPanels'
 import type { MinigraphBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'

package/src/GraphGenomeView/pane/paneBase.ts

@@ -12,7 +12,7 @@ import { lenientOptionalEnum } from '../lenientEnum'
 
 import type { MorphEntering } from './morph'
 import type { SubgraphRegion } from '../../GetSubgraph'
-import type { WalkCut } from '../../RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from '../../RgfaTabixAdapter/walkCut.ts'
 import type { RepeatArray } from '../repeats/repeatFeatures'
 import type { PaneLayout } from '../tubeMapPanels'
 import type { SampleRow } from '../walkRowGroups'

package/src/GraphGenomeView/pane/renderingActions.ts

@@ -107,12 +107,14 @@ export const withRenderingActions = withLoadActions
             { fireImmediately: true },
           ),
         )
-        // A host fits the rows once, when it takes the pane over, which is
-        // before the legend measures the room it needs above them
+        // A host fits the rows when it takes the pane over, which is before
+        // the legend measures the room it needs above them and before a split
+        // into panels changes how tall the drawing is
         addDisposer(
           self,
           reaction(
-            () => self.fitPadTop,
+            () =>
+              `${self.fitPadTop} ${self.layoutBounds?.h} ${self.usableHeight}`,
             () => {
               if (self.viewportOwner === 'host') {
                 self.zoomToFit()

package/src/GraphGenomeView/subgraphLoad.test.ts

@@ -494,9 +494,49 @@ describe('reads', () => {
     const drawn = model.tubeMapPicture!.nodes.map(n => n.name)
     const h0 = model.graph!.nodes.find(n => n.name === 'h0')!
     expect(drawn).not.toContain(h0.id)
-    expect(model.referenceRampOffKeys.offReference).toBe(false)
+    expect(model.referenceRampDrawsOffReference).toBe(false)
   })
 
+  // a chain of six alleles runs past the flanking walk's reach, which once
+  // keyed its middle as a second, lighter grey
+  const DEEP = [
+    'H\tVN:Z:1.0',
+    'S\ts0\t*\tLN:i:1000\tSN:Z:GRCh38#0#chr6\tSO:i:32000000\tSR:i:0',
+    'S\ts1\t*\tLN:i:1000\tSN:Z:GRCh38#0#chr6\tSO:i:32001000\tSR:i:0',
+    ...Array.from(
+      { length: 6 },
+      (_, i) =>
+        `S\th${i}\t*\tLN:i:50\tSN:Z:NA20809#2#CM094351.1\tSO:i:${i * 50}\tSR:i:1`,
+    ),
+    'L\ts0\t+\ts1\t+\t0M',
+    'L\ts0\t+\th0\t+\t0M',
+    ...Array.from({ length: 5 }, (_, i) => `L\th${i}\t+\th${i + 1}\t+\t0M`),
+    'L\th5\t+\ts1\t+\t0M',
+  ].join('\n')
+
+  test.each([
+    ['force', true],
+    ['walkrows', false],
+  ])(
+    'a %s layout keys deep alleles as off the reference: %s',
+    async (layoutMode, keyed) => {
+      mockRpcCall.mockImplementation((_sid: unknown, method: string) =>
+        method === 'GetSubgraph'
+          ? Promise.resolve(DEEP)
+          : Promise.reject(new Error(`Unexpected RPC: ${method}`)),
+      )
+      const model = createView({
+        layoutMode,
+        color: { field: 'position' },
+        loadedTrackId: TRACK.trackId,
+        loadedRegion: ON_HG38,
+      })
+      await model.load()
+
+      expect(model.referenceRampDrawsOffReference).toBe(keyed)
+    },
+  )
+
   // `flank` walks only s0, before the window, so the tube map draws no tube
   // for it, and the legend and a hover pair names with the tubes drawn
   test("a walk the window trims away takes no tube's colour", async () => {

package/src/GraphGenomeView/walkRowsCut.ts

@@ -1,20 +1,9 @@
-import {
-  backboneNodes,
-  backbonePositions,
-  overlapsWindow,
-} from '@jbrowse/bandage-core/anchoredNodes'
-import {
-  walkRowLabels,
-  walkRowsExtent,
-} from '@jbrowse/bandage-core/layout/walkRowLayout'
+import { tablePath } from '@jbrowse/bandage-core/gfa/graphTables'
 import { loadGraph } from '@jbrowse/bandage-core/pipeline'
 
-import { walkPath } from '../RgfaTabixAdapter/walkRowRuns.ts'
-
-import type { WalkCut } from '../RgfaTabixAdapter/walkRowRuns.ts'
+import type { WalkCut } from '../RgfaTabixAdapter/walkCut.ts'
 import type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'
-import type { WalkRows } from '@jbrowse/bandage-core/layout/walkRows'
-import type { Graph, LayoutResult } from '@jbrowse/bandage-core/types'
+import type { Graph } from '@jbrowse/bandage-core/types'
 
 /**
  * The Graph a walk-rows cut parses to: nodes with their depth over every
@@ -49,36 +38,13 @@ export function walkRowsGraph(
   graph.nodes.forEach((node, i) => {
     node.depth = Math.max(depth[i]!, 1)
   })
-  const stubs = w.names.slice(1).flatMap((walk, i) => {
-    if (w.offsets[i + 2]! <= w.offsets[i + 1]!) {
-      return []
-    }
-    return [{ ...walkPath(walk), nodeIds: [], start: w.starts[i + 1]! }]
-  })
+  const stubs = w.names
+    .slice(1)
+    .flatMap((_, i) =>
+      w.offsets[i + 2]! > w.offsets[i + 1]!
+        ? [{ ...tablePath(w, i + 1), nodeIds: [] }]
+        : [],
+    )
   graph.paths = [...(graph.paths ?? []), ...stubs]
   return graph
 }
-
-/** bandage-core's walkRowLayout, over rows already made */
-export function walkRowLayoutOf(
-  graph: Graph,
-  walks: WalkRows,
-  region?: { start: number; end: number },
-): LayoutResult | undefined {
-  const backbone = backboneNodes(graph)
-  if (backbone.length === 0) {
-    return undefined
-  }
-  const overWindow = region
-    ? backbone.filter(n => overlapsWindow(n, region))
-    : backbone
-  return {
-    nodePositions: backbonePositions(
-      overWindow.length > 0 ? overWindow : backbone,
-    ),
-    rowLabels: walkRowLabels(walks),
-    referenceAxis: true,
-    pixelRows: true,
-    extent: walkRowsExtent(walks),
-  }
-}

package/src/LinearGraphDisplay/LinearGraphDisplay.test.ts

@@ -1,3 +1,4 @@
+import { fittedTranslateY } from '@jbrowse/bandage-core/pipeline'
 import PluginManager from '@jbrowse/core/PluginManager'
 import {
   ConfigurationReference,
@@ -770,6 +771,20 @@ test('a tube map on its own axis ties each reference box to its bp in the linear
   expect(pane.tubeMapConnectors).toEqual([])
 })
 
+test('a hosted drawing whose height changes after the host took the pane is placed again', async () => {
+  const { pane } = await shownGraph({ paths: true })
+  await pane.switchLayout('tubemapref')
+  await wait(SETTLE_MS)
+  const expected = fittedTranslateY(
+    pane.layoutBounds!,
+    pane.usableHeight,
+    pane.scaleY,
+    pane.fitPads.top,
+  )
+  expect(pane.viewportOwner).toBe('host')
+  expect(pane.translateY).toBeCloseTo(expected, 6)
+})
+
 test("a folded tube map draws the cut's reference as merged nodes, and the rest as ticks or routes", async () => {
   const { pane } = await shownGraph({ paths: true })
   const labels = () =>

package/src/LinearGraphDisplay/configSchema.ts

@@ -38,6 +38,7 @@ export function configSchemaFactory() {
       color: {
         type: 'frozen',
         defaultValue: {},
+        plot: true,
       },
       /**
        * #slot
@@ -48,6 +49,7 @@ export function configSchemaFactory() {
       size: {
         type: 'frozen',
         defaultValue: { field: 'depth', value: 6 },
+        plot: true,
       },
       /**
        * #slot
@@ -61,6 +63,7 @@ export function configSchemaFactory() {
       layers: {
         type: 'frozen',
         defaultValue: {},
+        plot: true,
       },
       /**
        * #slot
@@ -71,6 +74,7 @@ export function configSchemaFactory() {
       facet: {
         type: 'frozen',
         defaultValue: {},
+        plot: true,
       },
       /**
        * #slot
@@ -79,6 +83,7 @@ export function configSchemaFactory() {
       rows: {
         type: 'frozen',
         defaultValue: {},
+        plot: true,
       },
       /**
        * #slot

package/src/RgfaTabixAdapter/RgfaTabixAdapter.test.ts

@@ -5,18 +5,24 @@ import { join } from 'node:path'
 import { gunzipSync } from 'node:zlib'
 
 import { TabixIndexedFile } from '@gmod/tabix'
+import { convertGFAToGraph } from '@jbrowse/bandage-core/gfa/gfaConverter'
 import { parseGFA } from '@jbrowse/bandage-core/gfa-core/index'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { readConfObject } from '@jbrowse/core/configuration'
+import {
+  formatSubgraph,
+  linkKey,
+  parseLinkLine,
+  parseSegmentLine,
+} from '@jbrowse/graph-walks'
 import { firstValueFrom } from 'rxjs'
 import { toArray } from 'rxjs/operators'
 
 import Adapter from './RgfaTabixAdapter.ts'
 import configSchema from './configSchema.ts'
 import RgfaTabixAdapterF from './index.ts'
-import { linkKey, parseLinkLine } from './rgfaBed.ts'
 
-import type { WalkCut } from './walkRowRuns.ts'
+import type { WalkCut } from './walkCut.ts'
 
 // Built by `gfa-to-tabix --layout contig` from the minigraph rGFA of four E. coli
 // strains at jbrowse.org/demos/ecoli_pangenome/ecoli_rgfa_slice.gfa (the
@@ -333,8 +339,7 @@ test('getFeatures carries SM:Z: onto the feature', async () => {
 })
 
 // The other half of the same fixture: the graph route reads the samples off the
-// synthesized S-line, and rgfaBed.test.ts asserts that from a hand-written row.
-// This is the same claim against a real indexed file.
+// synthesized S-line
 test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
   const gfa = gfaText(await makePggbAdapter().getSubgraph(is5))
   expect(gfa.split('\n')).toContain(
@@ -342,6 +347,20 @@ test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
   )
 })
 
+// An indexed cut has no P/W lines, so this tag is its only record of which
+// haplotypes visit a segment, and the node popup shows GraphNode.samples
+test('SM:Z: on a segs row reaches GraphNode.samples', () => {
+  const segment = parseSegmentLine(
+    'K12#1#chr\t1004477\t1004500\ts119690\t0\tSM:Z:K12.1,Sakai.1,NCTC86.1',
+  )
+  const gfa = formatSubgraph(new Map([[segment.id, segment]]), new Map())
+  expect(convertGFAToGraph(parseGFA(gfa)).nodes[0]!.samples).toEqual([
+    'K12.1',
+    'Sakai.1',
+    'NCTC86.1',
+  ])
+})
+
 // An rGFA has no sixth column, so the attribute is absent rather than 0: a
 // color expression reading `sampleCount` on such a track gets undefined, not a
 // count of zero.

package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts

@@ -1,6 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { SimpleFeature, updateStatus } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { parseSegmentRow, rgfaCut, segmentSamples } from '@jbrowse/graph-walks'
 
 import { locationIsSet } from '../locationName.ts'
 import {
@@ -9,13 +10,11 @@ import {
   unmappedRegionMessage,
 } from '../panSNTabix.ts'
 import { getLines } from '../tabixRange.ts'
-import { parseSegmentRow, segmentSamples } from './rgfaBed.ts'
-import { rgfaCut } from './rgfaCut.ts'
 import { WalkIndex } from './walkReader.ts'
 
 import type { RgfaTabixAdapterConfig } from './configSchema.ts'
 import type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'
-import type { WalkCut } from './walkRowRuns.ts'
+import type { WalkCut } from './walkCut.ts'
 import type { TabixIndexedFile } from '@gmod/tabix'
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
 import type { Feature } from '@jbrowse/core/util'

package/src/RgfaTabixAdapter/bubbleTier.test.ts

@@ -3,7 +3,7 @@ import { parseGFA } from '@jbrowse/bandage-core/gfa-core/index'
 import Adapter from './RgfaTabixAdapter.ts'
 import configSchema from './configSchema.ts'
 
-import type { WalkCut } from './walkRowRuns.ts'
+import type { WalkCut } from './walkCut.ts'
 
 // A level-of-detail tier: the same two files the adapter always reads, but one
 // node per bubble instead of one per GFA segment. Built by

package/src/RgfaTabixAdapter/walkCut.ts

@@ -0,0 +1,20 @@
+import { walkRowRuns } from '@jbrowse/bandage-core/layout/walkRowRuns'
+
+import type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'
+import type { WalkRowRuns } from '@jbrowse/bandage-core/layout/walkRowRuns'
+
+/**
+ * A cut for walk rows: the tables, and the rows' runs over the window, which
+ * the main thread draws without a Graph of the walks' steps
+ */
+export type WalkCut = GraphTables & { walkRowRuns?: WalkRowRuns }
+
+export function walkCutFor(
+  tables: GraphTables,
+  region: { start: number; end: number },
+  walkRows: boolean | undefined,
+): WalkCut {
+  return walkRows
+    ? { ...tables, walkRowRuns: walkRowRuns(tables, region) }
+    : tables
+}

package/src/RgfaTabixAdapter/walkFiles.test.ts

@@ -5,15 +5,15 @@ import {
   graphFromTables,
   graphTablesGFA,
 } from '@jbrowse/bandage-core/gfa/graphTables'
+import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { firstValueFrom } from 'rxjs'
 import { toArray } from 'rxjs/operators'
 
 import Adapter from './RgfaTabixAdapter.ts'
 import configSchema from './configSchema.ts'
-import { walkRowsOf } from './walkRowRuns.ts'
 
-import type { WalkCut } from './walkRowRuns.ts'
+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

package/src/RgfaTabixAdapter/walkReader.ts

@@ -2,7 +2,7 @@ import { resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'
 import { WalkReader, referenceNodes, walksKept } from '@jbrowse/graph-walks'
 
 import { getLines } from '../tabixRange.ts'
-import { walkCutFor } from './walkRowRuns.ts'
+import { walkCutFor } from './walkCut.ts'
 
 import type { SubgraphAdapterOptions } from '../GetSubgraph.ts'
 import type { TabixIndexedFile } from '@gmod/tabix'

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts

@@ -1,4 +1,5 @@
 import { graphTablesGFA } from '@jbrowse/bandage-core/gfa/graphTables'
+import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { walkRows } from '@jbrowse/bandage-core/layout/walkRows'
 import { loadGraph } from '@jbrowse/bandage-core/pipeline'
 import PluginManager from '@jbrowse/core/PluginManager'
@@ -14,7 +15,6 @@ import {
   referenceAligner,
   walkAligner,
 } from './walkLanes.ts'
-import { walkRowsOf } from '../RgfaTabixAdapter/walkRowRuns.ts'
 import { PairTargetError } from '../synteny/lanePairs.ts'
 
 import type { PairChain } from '@gmod/gbz-base/pairAlignment'