jbrowse-plugin-graphgenomeviewer 4.1.0 → 4.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "4.1.0",
+  "version": "4.2.0",
   "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": {
@@ -76,7 +76,7 @@
     "typescript-eslint": "^8.70.1",
     "typescript7": "npm:typescript@^7.0.2",
     "vitest": "^5.0.2",
-    "@jbrowse/bandage-core": "4.1.0"
+    "@jbrowse/bandage-core": "4.2.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",

package/src/GraphGenomeView/components/WalkRowsOverlay.tsx

@@ -20,8 +20,8 @@ import type { KeySwatch } from '@jbrowse/bandage-core/layout/walkRowDraw'
 
 // The walk-rows layout's bars: one per haplotype walk under the reference
 // row, each on its own bp axis from the window's left edge, drawn from core's
-// walkRowsTree: runs coloured by how the graph aligned the walk to the
-// reference, unit separators, each row's genes from its own assembly's
+// walkRowsTree: runs coloured by whether they are on the reference walk's
+// path, unit separators, each row's genes from its own assembly's
 // annotation, the allele a repeat genotype called and a readout. Under the
 // reference-position ramp an aligned run takes the hue of the reference it is
 // threaded through. In a tandem array that is the aligner's pick among

package/src/GraphGenomeView/model.test.ts

@@ -2672,7 +2672,7 @@ describe('walk rows', () => {
     const svg = model.figure()!
     expect(svg).toContain('>B#1</text>')
     expect(svg).not.toContain('>A#1</text>')
-    expect(svg).toContain('aligned to')
+    expect(svg).toContain("'s path")
   })
 
   test('walks lift together, each keeping the colour it was given', async () => {

package/src/GraphGenomeView/model.ts

@@ -2658,12 +2658,10 @@ export function GraphPaneMixin() {
                   // the assembly to load to open this node on its own
                   // coordinates
                   contributingHaplotype: nodeOwnLocation(node)?.haplotype,
-                  // Every assembly that traverses it, which is a different
-                  // question and one only a path GFA can answer. Absent on an
-                  // rGFA rather than approximated, so the two are never
-                  // confused: there `contributingAssembly` is first-seen, not
-                  // carriage.
-                  carriedBy: node.samples?.join(', '),
+                  // Every haplotype whose path visits it, which only a path
+                  // GFA records. Absent on an rGFA, where
+                  // `contributingAssembly` is the first-seen assembly alone.
+                  samples: node.samples?.join(', '),
                   ...(region && span
                     ? {
                         refName: region.refName,

package/src/RgfaTabixAdapter/RgfaTabixAdapter.test.ts

@@ -203,7 +203,7 @@ test('getFeatures carries SM:Z: onto the feature', async () => {
   const private1199 = features.find(f => f.get('name') === '196827')!
   expect(private1199.get('end') - private1199.get('start')).toBe(1199)
   expect(private1199.get('samples')).toEqual(['K12.1'])
-  expect(private1199.get('carriers')).toBe(1)
+  expect(private1199.get('sampleCount')).toBe(1)
 
   const core = features.find(f => f.get('name') === '196843')!
   expect(core.get('samples')).toEqual([
@@ -213,10 +213,10 @@ test('getFeatures carries SM:Z: onto the feature', async () => {
     'NCTC86.1',
     'IAI39.1',
   ])
-  expect(core.get('carriers')).toBe(5)
+  expect(core.get('sampleCount')).toBe(5)
 })
 
-// The other half of the same fixture: the graph route reads carriage off the
+// 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.
 test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
@@ -226,16 +226,16 @@ test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
   )
 })
 
-// An rGFA has no sixth column, so the attribute is absent rather than 0 — a
-// color expression reading `carriers` on such a track gets undefined, not a
-// claim that nothing carries the segment.
-test('getFeatures omits carriage on a graph that states none', async () => {
+// 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.
+test('getFeatures omits samples on a graph that records none', async () => {
   const features = await firstValueFrom(
     makeAdapter().getFeatures(k12).pipe(toArray()),
   )
   expect(features.length).toBeGreaterThan(0)
   expect(features.every(f => f.get('samples') === undefined)).toBe(true)
-  expect(features.every(f => f.get('carriers') === undefined)).toBe(true)
+  expect(features.every(f => f.get('sampleCount') === undefined)).toBe(true)
 })
 
 // Minigraph-Cactus writes PanSN stable names, so HPRC release 2 calls the

package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts

@@ -124,11 +124,10 @@ export default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAd
             signal,
             lineCallback: line => {
               const segment = parseSegmentLine(line)
-              // `samples` is who, `carriers` is how many, and the second is not
-              // just a convenience: a lane colored by carriage is a jexl
-              // expression in a config, where counting a list means relying on
-              // jexl resolving `.length` through a member access on an array.
-              // The count is the axis the color reads, so the index states it.
+              // `samples` lists the haplotypes whose paths visit the segment and
+              // `sampleCount` counts them. A lane's color reads the count, and
+              // a count in jexl would otherwise rely on `.length` resolving
+              // through a member access on an array.
               const samples = segmentSamples(segment)
               observer.next(
                 new SimpleFeature({
@@ -140,7 +139,7 @@ export default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAd
                   type: 'segment',
                   rank: segment.rank,
                   stableName: segment.refName,
-                  ...(samples && { samples, carriers: samples.length }),
+                  ...(samples && { samples, sampleCount: samples.length }),
                 }),
               )
             },

package/src/RgfaTabixAdapter/rgfaBed.test.ts

@@ -119,15 +119,15 @@ test('a valid tag beside a malformed one keeps only the valid one', () => {
   )
 })
 
-test('segmentSamples reads the carriers off the tag column', () => {
+test('segmentSamples reads the samples off the tag column', () => {
   const segment = parseSegmentLine(
     'K12#1#chr\t1004477\t1004500\ts119690\t0\tSM:Z:K12.1,Sakai.1,NCTC86.1',
   )
   expect(segmentSamples(segment)).toEqual(['K12.1', 'Sakai.1', 'NCTC86.1'])
 })
 
-// Undefined, not [], so a lane can tell a graph that states nothing about
-// carriage apart from a segment nothing carries.
+// Undefined, not [], so a lane can tell a graph that records no samples from a
+// segment no path visits.
 test('segmentSamples is undefined when the column says nothing', () => {
   expect(segmentSamples(parseSegmentLine(RGFA_SEG))).toBeUndefined()
   expect(segmentSamples(parseSegmentLine(TAGGED_SEG))).toBeUndefined()
@@ -148,11 +148,11 @@ test('segmentSamples finds the tag beside other tags', () => {
   expect(segmentSamples(segment)).toEqual(['HG002.1', 'HG002.2'])
 })
 
-// The whole carriage chain in one test, because it spans three files and each
+// The whole samples chain in one test, because it spans three files and each
 // half is covered on its own: a segs.bed SM:Z: column -> the synthesized S-line
-// -> the GFA parser -> GraphNode.samples, which is what model.ts renders as
-// `carriedBy` in the node popup. An indexed cut has no P/W lines, so this tag is
-// the only statement of carriage it can carry, and nothing else asserts that it
+// -> the GFA parser -> GraphNode.samples, which model.ts renders as `samples`
+// in the node popup. An indexed cut has no P/W lines, so this tag is its only
+// record of which haplotypes visit a segment, and nothing else asserts that it
 // survives the round trip.
 test('SM:Z: on a segs row reaches GraphNode.samples', async () => {
   const { parseGFA } = await import('@jbrowse/bandage-core/gfa-core/index')

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.1.0'
+export const version = '4.2.0'