jbrowse-plugin-graphgenomeviewer 7.2.1 → 7.3.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.2.1",
+  "version": "7.3.1",
   "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": "^2.1.0",
+    "@jbrowse/graph-walks": "^3.0.0",
     "@jbrowse/render-core": "5.0.0-beta.11",
     "@jbrowse/synteny-core": "5.0.0-beta.11"
   },

package/src/RgfaTabixAdapter/configSchema.ts

@@ -30,8 +30,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * `walksUri` takes the prefix of a walk file in place of `uri`, and resolves
  * `<walksUri>.walks.bed.gz` and its `.tbi`. `gfa-to-tabix --walks -o <prefix>`
  * writes one per reference sample, so a track names one as
- * `<prefix>.<sample>`. The adapter reads walk format 3, which gfa-to-tabix
- * writes from 1.1, through @jbrowse/graph-walks. Such a graph's cut carries
+ * `<prefix>.<sample>`. The adapter reads walk format 4, which gfa-to-tabix
+ * writes from 1.2, through @jbrowse/graph-walks. Such a graph's cut carries
  * the haplotypes' walks, and `defaultHaplotypes` names the ones it is cut for
  * until the user picks others.
  *
@@ -48,7 +48,7 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  * ```js
  * {
  *   type: 'RgfaTabixAdapter',
- *   walksUri: 'https://example.org/hprc-v2.1-mc-grch38.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  *   defaultHaplotypes: ['HG002', 'HG00733', 'HG02257', 'NA19240'],
  * }
@@ -152,7 +152,7 @@ const RgfaTabixAdapter = ConfigurationSchema(
     ),
     /**
      * #slot
-     * a `gfa-to-tabix --walks` file in walk format 3: per reference chunk,
+     * a `gfa-to-tabix --walks` file in walk format 4: per reference chunk,
      * the reference's path, the ways haplotypes leave it and each haplotype's
      * piece. Unset means the graph has no walks.
      */

package/src/RgfaTabixAdapter/walkFiles.test.ts

@@ -17,9 +17,9 @@ 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 3, built under ~/work/scratch/walks-20261008/f3. Skipped where the
+// format 4, built under ~/work/scratch/walks-20261008/f4. Skipped where the
 // files are absent.
-const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f3/chr22'
+const chr22 = '/home/cdiesh/work/scratch/walks-20261008/f4/chr22'
 const present = ['GRCh38', 'CHM13'].every(sample =>
   existsSync(`${chr22}.${sample}.walks.bed.gz`),
 )
@@ -34,27 +34,27 @@ const fixture = (name: string) =>
 //   W HG002   1 chr1 >1>2>7>4>5>6   7 replaces 3
 //   W HG002   2 chr1 >1>2>3>4>8>6   8 replaces 5
 //   W HG00097 1 chr1 >1>2>3>4>5>6
-const headerPrefix = fixture('walks3_header')
+const headerPrefix = fixture('walks4_header')
 
-// walks3_header's walks with the reference named as pggb names a P-line,
+// walks4_header's walks with the reference named as pggb names a P-line,
 // GRCh38#chr1
-const twoPartPrefix = fixture('walks3_twopart')
+const twoPartPrefix = fixture('walks4_twopart')
 
 // An unchopped graph, node 1 spanning 0-2600 and filed under chunk 0 alone:
 //   W GRCh38 0 chr1 >1>2>4
 //   W HG002  1 chr1 >1>3>4   3 replaces 2
-const maxNodePrefix = fixture('walks3_maxnode')
+const maxNodePrefix = fixture('walks4_maxnode')
 
 // Twelve 500 bp reference nodes over chr1:0-6000 in one 10 kb chunk:
 //   W GRCh38  0 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG002   1 chr1 >1>2>3>20>21>9>10>11>12   20 and 21, 2 kb each, replace 4-8
 //   W HG002   2 chr1 >1>2>3>4>5>6>7>8>9>10>11>12
 //   W HG003   1 chr1 >1>2>3>22                 the contig ends on 22, 300 bp
-const rejoinPrefix = fixture('walks3_rejoin')
+const rejoinPrefix = fixture('walks4_rejoin')
 
 // The same graph in 1 kb chunks, whose rows name the chunks their path goes on
 // in: HG002#1 leaves chunk 1000 for 20 and 21 and rejoins at 9, in chunk 4000
-const followPrefix = fixture('walks3_follow')
+const followPrefix = fixture('walks4_follow')
 
 function makeAdapter(prefix: string, slots = {}) {
   const local = (path: string) => ({
@@ -215,7 +215,7 @@ 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 1.1/)
+  await expect(cut).rejects.toThrow(/rebuild it with gfa-to-tabix 1.2/)
 })
 
 test('a cut over walkByteBudget reads no row', async () => {

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts

@@ -11,6 +11,7 @@ import Adapter from './WalkTabixSyntenyAdapter.ts'
 import configSchema from './configSchema.ts'
 import WalkTabixSyntenyAdapterF from './index.ts'
 import {
+  anchorAligner,
   bubblesAsMismatches,
   referenceAligner,
   walkAligner,
@@ -33,7 +34,7 @@ const fixture = (name: string) =>
 
 function makeAdapter(
   slots: Record<string, unknown> = {},
-  name = 'walks3_header',
+  name = 'walks4_header',
 ) {
   const local = (path: string) => ({
     localPath: path,
@@ -110,7 +111,7 @@ test('a fetch for some haplotypes answers those lanes in the order asked, named
 })
 
 test('a fetch for some haplotypes reads them against a reference walk named without a haplotype', async () => {
-  const found = await feats(makeAdapter({}, 'walks3_twopart'), {
+  const found = await feats(makeAdapter({}, 'walks4_twopart'), {
     haplotypes: ['HG002#1'],
   })
   expect(found.map(summary)).toEqual([
@@ -171,7 +172,7 @@ test('a batch of lane pairs answers each pair what it answers alone', async () =
   expect(batch).toHaveLength(2)
 })
 
-// walks3_lanepairs, a 5.5 kb reference of 2 kb flanks around three 500 bp
+// walks4_lanepairs, a 5.5 kb reference of 2 kb flanks around three 500 bp
 // nodes, in 1 kb chunks:
 //   W GRCh38  0 chr1 >1>2>3>4>5
 //   W HG002   1 chr1 >1>2>3>4>5
@@ -179,7 +180,7 @@ test('a batch of lane pairs answers each pair what it answers alone', async () =
 //   W HG00097 1 chr1 >1>2>6>2>6>2>3>4>5   2 three times, 6 a 30 bp spacer
 test('a lane pair matches through a copy-number array, and draws an inversion between the lanes as a reverse-strand record', async () => {
   const found = await firstValueFrom(
-    makeAdapter({}, 'walks3_lanepairs')
+    makeAdapter({}, 'walks4_lanepairs')
       .getFeatures(
         { ...window, end: 5500 },
         {
@@ -512,6 +513,81 @@ test('an inversion between two lanes is a reverse-strand record of its own when
   ])
 })
 
+// The same shape at a size the multi-way display names: 20 kb flanks around
+// a 15 kb stretch the haplotype runs backwards
+const largeInversionNodes = new Map(
+  [1, 2, 3, 4, 5].map(id => [
+    id,
+    {
+      refName: 'ref',
+      start: id * 100_000,
+      end: id * 100_000 + (id === 1 || id === 5 ? 20_000 : 5000),
+      rank: 0,
+      onWindow: true,
+    },
+  ]),
+)
+
+test('a walk turned against the reference for 10 kb or more gains a reverse-strand record of the turned stretch beside its own', () => {
+  expect(
+    drawn(anchorAligner(largeInversionNodes)(invertedLane, upperLane)),
+  ).toEqual([
+    {
+      query: '0-55000',
+      target: '0-55000',
+      strand: '+',
+      cigar: '20000=15000I15000D20000=',
+    },
+    {
+      query: '20000-35000',
+      target: '20000-35000',
+      strand: '-',
+      cigar: '15000=',
+    },
+  ])
+})
+
+// gfa-to-tabix --walks --refs GRCh38 --chunk 10000 over 20 kb flanks and three
+// 5 kb nodes:
+//   W GRCh38  0 chr1 >1>2>3>4>5
+//   W HG002   1 chr1 >1<4<3<2>5
+//   W HG00097 1 chr1 >1>2>3>4>5
+test('the anchor window answers a haplotype turned against the reference with a reverse-strand record of the turned stretch', async () => {
+  const records = await firstValueFrom(
+    makeAdapter({}, 'walks4_inversion')
+      .getFeatures({ ...window, end: 55_000 }, {})
+      .pipe(toArray()),
+  )
+  expect(
+    records
+      .filter(f => mateOf(f).assemblyName !== 'HG00097#1')
+      .map(f => ({
+        strand: f.get('strand'),
+        start: f.get('start'),
+        end: f.get('end'),
+      })),
+  ).toEqual([
+    { strand: 1, start: 0, end: 55_000 },
+    { strand: -1, start: 20_000, end: 35_000 },
+  ])
+})
+
+test('a walk turned for under 10 kb, or reversed whole, keeps its one record', () => {
+  expect(drawn(anchorAligner(inversionNodes)(invertedLane, upperLane))).toEqual(
+    drawn(referenceAligner(inversionNodes)(invertedLane, upperLane)),
+  )
+  const reversed = fragment('HG002#3#chr1', [
+    [5, 1],
+    [4, 1],
+    [3, 1],
+    [2, 1],
+    [1, 1],
+  ])
+  expect(
+    drawn(anchorAligner(largeInversionNodes)(reversed, upperLane)),
+  ).toEqual(drawn(referenceAligner(largeInversionNodes)(reversed, upperLane)))
+})
+
 test.each([
   ['the whole reference', window],
   ['a window inside it', { ...window, start: 1300, end: 2300 }],

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts

@@ -10,7 +10,7 @@ import { updateStatus } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { walksKept } from '@jbrowse/graph-walks'
 
-import { chainFeature, lanePairAligner, referenceAligner } from './walkLanes.ts'
+import { anchorAligner, chainFeature, lanePairAligner } from './walkLanes.ts'
 import { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'
 import { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'
 import { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'
@@ -168,7 +168,7 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
       opts,
       `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,
     )
-    const align = referenceAligner(graph.nodes)
+    const align = anchorAligner(graph.nodes)
     const asmByPrefix = assemblyByPanSNPrefix(this)
     const references = fragments.filter(f => f.name === refName)
     // lanes come back in the order the fetch names them, which is the order

package/src/WalkTabixSyntenyAdapter/configSchema.ts

@@ -25,14 +25,14 @@ import type { Instance } from '@jbrowse/mobx-state-tree'
  *
  * `walksUri` takes the prefix of one reference's walk file, `<prefix>.<sample>`,
  * and resolves `<walksUri>.walks.bed.gz` and its `.tbi`. The adapter reads walk
- * format 3, which gfa-to-tabix writes from 1.1, through @jbrowse/graph-walks.
+ * format 4, which gfa-to-tabix writes from 1.2, through @jbrowse/graph-walks.
  * Only a window on the anchor is answered.
  *
  * #example
  * ```js
  * {
  *   type: 'WalkTabixSyntenyAdapter',
- *   walksUri: 'https://example.org/hprc-v2.1-mc-grch38.GRCh38',
+ *   walksUri: 'https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38-f4.GRCh38',
  *   assemblyNames: ['hg38'],
  *   assemblyNameToPanSN: { hg38: 'GRCh38' },
  * }
@@ -56,7 +56,7 @@ const WalkTabixSyntenyAdapter = ConfigurationSchema(
     },
     /**
      * #slot
-     * a `gfa-to-tabix --walks` file in walk format 3
+     * a `gfa-to-tabix --walks` file in walk format 4
      */
     walksLocation: fileLocationSlot('/path/to/graph.walks.bed.gz'),
     /**

package/src/WalkTabixSyntenyAdapter/gbzParity.test.ts

@@ -12,10 +12,10 @@ 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 3, built 2026-10-08 and 2026-10-16. Skipped where
+// walk file in walk format 4, built 2026-10-08 and 2026-10-20. Skipped where
 // the files are absent.
 const dir = '/home/cdiesh/work/scratch/walks-20261008'
-const walkPrefix = `${dir}/f3/chr22.GRCh38`
+const walkPrefix = `${dir}/f4/chr22.GRCh38`
 const present =
   existsSync(`${walkPrefix}.walks.bed.gz`) && existsSync(`${dir}/chr22.gbz.db`)
 

package/src/WalkTabixSyntenyAdapter/walkLanes.ts

@@ -173,20 +173,9 @@ function singleVisits(fragment: WalkFragment) {
   return rev
 }
 
-/**
- * Aligns one lane's walk fragment to another's. The weighted subsequence
- * (`referenceAligner`) is the fast route and matches through copy-number
- * arrays, but it reads one direction per pair, so an inversion between the
- * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp
- * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to
- * pair chaining (`walkAligner`) instead, which answers the inverted stretch as
- * a reverse-strand record of its own. Chaining leaves out every node a walk
- * passes twice, so counting singly visited nodes misses no inversion it could
- * draw.
- */
-export function lanePairAligner(nodes: Map<number, WalkNode>) {
-  const subsequence = referenceAligner(nodes)
-  const chained = walkAligner(nodes)
+// The bases on singly visited nodes two walks pass the same way and the
+// opposite way
+function directionShares(nodes: Map<number, WalkNode>) {
   const visits = new Map<WalkFragment, Map<number, number>>()
   const visitsOf = (fragment: WalkFragment) => {
     let found = visits.get(fragment)
@@ -196,7 +185,7 @@ export function lanePairAligner(nodes: Map<number, WalkNode>) {
     }
     return found
   }
-  const inverted = (query: WalkFragment, target: WalkFragment) => {
+  return (query: WalkFragment, target: WalkFragment) => {
     const theirs = visitsOf(target)
     let same = 0
     let opposite = 0
@@ -208,12 +197,60 @@ export function lanePairAligner(nodes: Map<number, WalkNode>) {
         opposite += nodeLength(nodes, id)
       }
     }
-    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP
+    return { same, opposite }
   }
-  return (query: WalkFragment, target: WalkFragment) =>
-    inverted(query, target)
+}
+
+/**
+ * Aligns one lane's walk fragment to another's. The weighted subsequence
+ * (`referenceAligner`) is the fast route and matches through copy-number
+ * arrays, but it reads one direction per pair, so an inversion between the
+ * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp
+ * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to
+ * pair chaining (`walkAligner`) instead, which answers the inverted stretch as
+ * a reverse-strand record of its own. Chaining leaves out every node a walk
+ * passes twice, so counting singly visited nodes misses no inversion it could
+ * draw.
+ */
+export function lanePairAligner(nodes: Map<number, WalkNode>) {
+  const subsequence = referenceAligner(nodes)
+  const chained = walkAligner(nodes)
+  const shares = directionShares(nodes)
+  return (query: WalkFragment, target: WalkFragment) => {
+    const { same, opposite } = shares(query, target)
+    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP
       ? chained(query, target)
       : subsequence(query, target)
+  }
+}
+
+// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names
+// no inversion there
+const TURNED_MIN_BP = 10_000
+
+/**
+ * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`
+ * does, then adds the stretches it reads the other way. A walk sharing
+ * TURNED_MIN_BP or more of singly visited nodes in each direction is chained
+ * too, and the chained records on the strand the subsequence did not take are
+ * its turned stretches. The subsequence record stays, so a copy-number array,
+ * which chaining leaves out, still matches one pass alike in every lane.
+ */
+export function anchorAligner(nodes: Map<number, WalkNode>) {
+  const subsequence = referenceAligner(nodes)
+  const chained = walkAligner(nodes)
+  const shares = directionShares(nodes)
+  return (query: WalkFragment, target: WalkFragment) => {
+    const records = subsequence(query, target)
+    const taken = records[0]?.strand
+    const { same, opposite } = shares(query, target)
+    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP
+      ? records
+      : [
+          ...records,
+          ...chained(query, target).filter(chain => chain.strand !== taken),
+        ]
+  }
 }
 
 /**

package/src/panSNAliases/panSNAliases.test.ts

@@ -123,11 +123,11 @@ describe("a lanes track anchored on an alias of the window's assembly", () => {
           {
             type: 'WalkTabixSyntenyAdapter',
             walksLocation: local(
-              '../RgfaTabixAdapter/test_data/walks3_header.GRCh38.walks.bed.gz',
+              '../RgfaTabixAdapter/test_data/walks4_header.GRCh38.walks.bed.gz',
             ),
             walksIndex: {
               location: local(
-                '../RgfaTabixAdapter/test_data/walks3_header.GRCh38.walks.bed.gz.tbi',
+                '../RgfaTabixAdapter/test_data/walks4_header.GRCh38.walks.bed.gz.tbi',
               ),
             },
             assemblyNames: ['GRCh38'],

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.2.1'
+export const version = '7.3.1'

package/dist/chunks/WalkTabixSyntenyAdapter-I3PY6HJ2.js

@@ -1,2 +0,0 @@
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the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(n,e,t)}async laneWalks(e,t,n,r,a){return I(a,r.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:r.signal,keep:j(n,e),links:!1}).catch(s=>{throw K(s,t.end-t.start)}))}async anchorFeatures(e,t,n){let r=n.haplotypes?.length?n.haplotypes.map(l=>w(this,l)):void 0,a=w(this,n.targetAssemblyName),s=a===void 0?r:r===void 0||r.some(l=>F(a,l)||F(l,a))?[a]:[];if(s?.length===0)return[];let{start:c,end:u}=t,{graph:h,fragments:m}=await this.laneWalks(e,t,s,n,`Reading walks ${t.refName}:${c.toLocaleString()}-${u.toLocaleString()}`),p=C(h.nodes),g=x(this),d=m.filter(l=>l.name===e),f=l=>s===void 0?0:s.findIndex(y=>F(l.name,y));return m.filter(l=>l.name!==e&&f(l)>=0).sort((l,y)=>f(l)-f(y)).flatMap(l=>d.flatMap(y=>p(l,y).map(S=>L({chain:S,target:y,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(g,re(l))}))))}async pairFeatures(e,t,n,r){let a=n.map(m=>({pair:m,featurePrefix:w(this,m.queryAssemblyName),matePrefix:w(this,m.targetAssemblyName)})),{graph:s,fragments:c}=await this.laneWalks(e,t,a.flatMap(m=>[m.featurePrefix,m.matePrefix]),r,G(n)),u=Z(s.nodes),h=m=>c.filter(p=>F(p.name,m));return a.flatMap(({pair:m,featurePrefix:p,matePrefix:g})=>h(p).flatMap(d=>h(g).flatMap(f=>u(f,d).map(N=>L({chain:N,target:d,query:f,assemblyName:m.queryAssemblyName,refName:P(d.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return D(async n=>{let r=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(r!==void 0){let a=z(t),s=a.length>0?await this.pairFeatures(r,e,a,t):await this.anchorFeatures(r,e,t);for(let c of s)n.next(c)}n.complete()},t.signal)}};export{R as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-I3PY6HJ2.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-I3PY6HJ2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
-  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  const inverted = (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    inverted(query, target)\n      ? chained(query, target)\n      : subsequence(query, target)\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport { chainFeature, lanePairAligner, referenceAligner } from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolve(region, { signal: opts.signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep: walksKept(prefixes, refName),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = referenceAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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-  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "singleVisits", "rev", "twice", "lanePairAligner", "subsequence", "chained", "visits", "visitsOf", "found", "inverted", "theirs", "opposite", "other", "chainFeature", "chain", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openTabixSlot", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "updateStatus", "walksKept", "error", "laneZoomNotice", "wanted", "lane", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "align", "referenceAligner", "references", "f", "rank", "a", "b", "query", "reference", "chain", "chainFeature", "pairs", "sides", "pair", "side", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
-}