jbrowse-plugin-graphgenomeviewer 7.1.11 → 7.1.13

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "7.1.11",
+  "version": "7.1.13",
   "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": {

package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.test.ts

@@ -366,15 +366,13 @@ test('the graph lists its haplotypes with their contigs, and a fetch can be narr
   )
 })
 
-test('the node limit fails lanes and a graph cut as a zoom-in notice naming a span that fits', async () => {
+test('the node limit fails lanes as a zoom-in notice naming how far to zoom, and a graph cut naming a span that fits', async () => {
   const adapter = makeAdapter({ nodeLimit: 2 })
   const lanes: unknown = await feats(adapter, window).catch((e: unknown) => e)
   expect(lanes).toMatchObject({
     name: 'NodeLimitError',
     regionTooLarge: true,
-    message: expect.stringMatching(
-      /^Zoom in to about [\d.]+[KM]?bp to see lanes$/,
-    ),
+    message: expect.stringMatching(/^Zoom in about [\d.]+× to see lanes$/),
   })
   const graph: unknown = await adapter
     .getSubgraph(window)

package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts

@@ -31,6 +31,7 @@ import {
   lanePairsStatus,
   requestedPairs,
 } from '../synteny/lanePairs.ts'
+import { laneZoomNotice } from '../synteny/laneZoomNotice.ts'
 import { matchFeature } from '../synteny/matchFeature.ts'
 
 import type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'
@@ -223,6 +224,12 @@ function zoomInNotice(error: unknown, what: string) {
   return error
 }
 
+const laneLimitNotice = (error: unknown, nodeLimit: number, windowBp: number) =>
+  laneZoomNotice(
+    zoomInNotice(nodeLimitError(error, nodeLimit, windowBp) ?? error, 'lanes'),
+    windowBp,
+  )
+
 // gbz-base reads whole bp; a view asks at fractional ones
 const wholeBp = (region: Region) => ({
   ...region,
@@ -489,10 +496,7 @@ export default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBas
                 keep,
               })
               .catch((error: unknown) => {
-                throw zoomInNotice(
-                  nodeLimitError(error, nodeLimit, end - start) ?? error,
-                  'lanes',
-                )
+                throw laneLimitNotice(error, nodeLimit, end - start)
               }),
         )
       : []
@@ -562,10 +566,7 @@ export default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBas
     // a cut past the node limit for the wider context keeps the first one
     const bridged = async (path: PathQuery) => {
       const subgraphs = await cut(path, baseContext).catch((error: unknown) => {
-        throw zoomInNotice(
-          nodeLimitError(error, nodeLimit, end - start) ?? error,
-          'lanes',
-        )
+        throw laneLimitNotice(error, nodeLimit, end - start)
       })
       const gap = widestWalkGap(subgraphs, kept)
       const context = Math.ceil(gap / 2) + 2000

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts

@@ -9,10 +9,15 @@ import { toArray } from 'rxjs/operators'
 import Adapter from './WalkTabixSyntenyAdapter.ts'
 import configSchema from './configSchema.ts'
 import WalkTabixSyntenyAdapterF from './index.ts'
-import { bubblesAsMismatches, referenceAligner } from './walkLanes.ts'
+import {
+  bubblesAsMismatches,
+  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'
 import type { SyntenyMate } from '@jbrowse/synteny-core'
 
 // Four walks over a 3.6 kb reference of six 600 bp nodes, in 1 kb chunks
@@ -166,6 +171,66 @@ 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
+// nodes, in 1 kb chunks:
+//   W GRCh38  0 chr1 >1>2>3>4>5
+//   W HG002   1 chr1 >1>2>3>4>5
+//   W HG002   2 chr1 >1<4<3<2>5           the middle three inverted
+//   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')
+      .getFeatures(
+        { ...window, end: 5500 },
+        {
+          lanePairs: [
+            { queryAssemblyName: 'HG002#1', targetAssemblyName: 'HG002#2' },
+            { queryAssemblyName: 'HG002#1', targetAssemblyName: 'HG00097#1' },
+          ],
+        },
+      )
+      .pipe(toArray()),
+  )
+  expect(
+    found.map(f => ({
+      ...summary(f),
+      strand: f.get('strand'),
+      matches: f.get('numMatches'),
+    })),
+  ).toEqual([
+    {
+      lane: 'HG002#2',
+      refName: 'chr1',
+      start: 0,
+      end: 5500,
+      mate: 'chr1:0-5500',
+      cigar: '2000=1500I1500D2000=',
+      strand: 1,
+      matches: 4000,
+    },
+    {
+      lane: 'HG002#2',
+      refName: 'chr1',
+      start: 2000,
+      end: 3500,
+      mate: 'chr1:2000-3500',
+      cigar: '1500=',
+      strand: -1,
+      matches: 1500,
+    },
+    {
+      lane: 'HG00097#1',
+      refName: 'chr1',
+      start: 0,
+      end: 5500,
+      mate: 'chr1:0-6560',
+      cigar: '2500=1060I3000=',
+      strand: 1,
+      matches: 5500,
+    },
+  ])
+})
+
 test('a lane pair without its target lane is refused', async () => {
   await expect(
     feats(makeAdapter(), { queryAssemblyName: 'HG002#1' }),
@@ -228,12 +293,12 @@ test('getSubgraph cuts the window with the reference walk first', async () => {
   expect(walks).toEqual(['GRCh38#0#chr1', 'HG002#1#chr1'])
 })
 
-test('a window past the step budget fails as a zoom-in notice for lanes', async () => {
+test('a window past the step budget fails as a zoom-in notice for lanes naming how far to zoom', async () => {
   await expect(
     feats(makeAdapter({ walkStepBudget: 20 })),
   ).rejects.toMatchObject({
     name: 'NodeLimitError',
-    message: expect.stringMatching(/to see lanes$/),
+    message: expect.stringMatching(/^Zoom in about [\d.]+×.* to see lanes$/),
   })
 })
 
@@ -387,6 +452,66 @@ test('a haplotype running against the reference is a reverse-strand record', ()
   expect(cigar(chain!.edits)).toBe('1000=30I500=')
 })
 
+// Two lanes over 2 kb flanks and three 500 bp nodes, the second lane running
+// the middle three backwards: >1>2>3>4>5 against >1<4<3<2>5
+const inversionNodes = new Map(
+  [1, 2, 3, 4, 5].map(id => [
+    id,
+    {
+      refName: 'ref',
+      start: id * 10_000,
+      end: id * 10_000 + (id === 1 || id === 5 ? 2000 : 500),
+      rank: 0,
+      onWindow: true,
+    },
+  ]),
+)
+const upperLane = fragment('HG002#1#chr1', [
+  [1, 0],
+  [2, 0],
+  [3, 0],
+  [4, 0],
+  [5, 0],
+])
+const invertedLane = fragment('HG002#2#chr1', [
+  [1, 0],
+  [4, 1],
+  [3, 1],
+  [2, 1],
+  [5, 0],
+])
+const drawn = (chains: PairChain[]) =>
+  chains.map(
+    ({ queryStart, queryEnd, targetStart, targetEnd, strand, edits }) => ({
+      query: `${queryStart}-${queryEnd}`,
+      target: `${targetStart}-${targetEnd}`,
+      strand,
+      cigar: cigar(edits),
+    }),
+  )
+
+test('an inversion between two lanes is a reverse-strand record of its own when chained, and an insertion beside a deletion in the subsequence', () => {
+  expect(drawn(walkAligner(inversionNodes)(invertedLane, upperLane))).toEqual([
+    {
+      query: '0-5500',
+      target: '0-5500',
+      strand: '+',
+      cigar: '2000=1500I1500D2000=',
+    },
+    { query: '2000-3500', target: '2000-3500', strand: '-', cigar: '1500=' },
+  ])
+  expect(
+    drawn(referenceAligner(inversionNodes)(invertedLane, upperLane)),
+  ).toEqual([
+    {
+      query: '0-5500',
+      target: '0-5500',
+      strand: '+',
+      cigar: '2000=1500I1500D2000=',
+    },
+  ])
+})
+
 test.each([
   ['the whole reference', window],
   ['a window inside it', { ...window, start: 1300, end: 2300 }],

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts

@@ -10,9 +10,8 @@ import { updateStatus } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { walksKept } from '@jbrowse/graph-walks'
 
-import { chainFeature, referenceAligner, walkAligner } from './walkLanes.ts'
+import { chainFeature, lanePairAligner, referenceAligner } from './walkLanes.ts'
 import { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'
-import { isNodeLimitError } from '../nodeLimitError.ts'
 import { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'
 import { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'
 import {
@@ -20,6 +19,7 @@ import {
   lanePairsStatus,
   requestedPairs,
 } from '../synteny/lanePairs.ts'
+import { laneZoomNotice } from '../synteny/laneZoomNotice.ts'
 
 import type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'
 import type { SubgraphAdapterOptions } from '../GetSubgraph.ts'
@@ -128,13 +128,7 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
           links: false,
         })
         .catch((error: unknown) => {
-          if (isNodeLimitError(error) && error instanceof Error) {
-            error.message = error.message.replace(
-              'to see the graph',
-              'to see lanes',
-            )
-          }
-          throw error
+          throw laneZoomNotice(error, region.end - region.start)
         }),
     )
   }
@@ -228,7 +222,7 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
       opts,
       lanePairsStatus(pairs),
     )
-    const align = walkAligner(graph.nodes)
+    const align = lanePairAligner(graph.nodes)
     const walksOf = (prefix: string) =>
       fragments.filter(f => panSNMatchesPrefix(f.name, prefix))
     return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>

package/src/WalkTabixSyntenyAdapter/walkLanes.ts

@@ -156,6 +156,66 @@ export function referenceAligner(nodes: Map<number, WalkNode>) {
   }
 }
 
+// Each node a walk visits once, with the direction it passes it
+function singleVisits(fragment: WalkFragment) {
+  const rev = new Map<number, number>()
+  const twice = new Set<number>()
+  fragment.ids.forEach((id, i) => {
+    if (rev.has(id)) {
+      twice.add(id)
+    } else {
+      rev.set(id, fragment.rev[i]!)
+    }
+  })
+  for (const id of twice) {
+    rev.delete(id)
+  }
+  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)
+  const visits = new Map<WalkFragment, Map<number, number>>()
+  const visitsOf = (fragment: WalkFragment) => {
+    let found = visits.get(fragment)
+    if (found === undefined) {
+      found = singleVisits(fragment)
+      visits.set(fragment, found)
+    }
+    return found
+  }
+  const inverted = (query: WalkFragment, target: WalkFragment) => {
+    const theirs = visitsOf(target)
+    let same = 0
+    let opposite = 0
+    for (const [id, rev] of visitsOf(query)) {
+      const other = theirs.get(id)
+      if (other === rev) {
+        same += nodeLength(nodes, id)
+      } else if (other !== undefined) {
+        opposite += nodeLength(nodes, id)
+      }
+    }
+    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP
+  }
+  return (query: WalkFragment, target: WalkFragment) =>
+    inverted(query, target)
+      ? chained(query, target)
+      : subsequence(query, target)
+}
+
 /**
  * One record of a walk aligned to another, with its short balanced bubbles as
  * mismatches

package/src/synteny/clipFeatureToRegion.test.ts

@@ -366,3 +366,26 @@ test('the two regions are fetched at once and emitted in region order', async ()
   expect(adapter.completed).toEqual([1, 0])
   expect(features.map(f => f.id())).toEqual(['region0', 'region1'])
 })
+
+test('the runs of one record share its recordId, and two records do not', () => {
+  const runs = clipFeatureToRegion(
+    record({ CIGAR: '100M50D100M50I150M' }),
+    { start: 1000, end: 1400 },
+    40,
+  )
+  expect(runs.length).toBeGreaterThan(1)
+  expect(new Set(runs.map(r => r.get('recordId')))).toEqual(new Set(['r1']))
+  const other = clipFeatureToRegion(record({ uniqueId: 'r2', CIGAR }), {
+    start: 1000,
+    end: 1400,
+  })[0]!
+  expect(other.get('recordId')).toBe('r2')
+})
+
+test('a recordId the source already carries stays', () => {
+  const [piece] = clipFeatureToRegion(record({ recordId: 919 }), {
+    start: 1000,
+    end: 1400,
+  })
+  expect(piece!.get('recordId')).toBe(919)
+})

package/src/synteny/clipFeatureToRegion.ts

@@ -125,6 +125,7 @@ function clippedFeature(
   const data: SimpleFeatureSerialized = {
     ...source,
     uniqueId: `${feature.id()}${suffix}`,
+    recordId: source.recordId ?? feature.id(),
     start: clipped.start,
     end: clipped.end,
     mate: { ...mate, start: clipped.mateStart, end: clipped.mateEnd },
@@ -146,7 +147,9 @@ function clippedFeature(
  * the record misses the window, one otherwise, and with `splitAtGapBp` one per
  * gap-free run of its alignment, numbered after the window suffix so each run
  * is its own feature and its own `syntenyId` group. A piece keeps every field
- * of the record except the alignment strings; `keepAlignment` hands back its
+ * of the record except the alignment strings, and a `recordId` that names the
+ * record the piece was cut from, so a display can tell two runs of one record
+ * from two records; `keepAlignment` hands back its
  * own stretch of them as packed ops in `alignmentOps`. A feature with no
  * `mate` is not a pairwise record and passes through whole.
  *

package/src/synteny/laneZoomNotice.test.ts

@@ -0,0 +1,55 @@
+import { keptStepsError } from '@jbrowse/graph-walks'
+
+import { laneZoomFold, laneZoomNotice } from './laneZoomNotice.ts'
+
+const BUDGET = 4_000_000
+
+// A lane fetch over `fetchBp` keeping steps at a density whose fitting span
+// is `fitsBp`, refused as @jbrowse/graph-walks refuses it
+function refusal(fetchBp: number, fitsBp: number) {
+  const kept = Math.round((BUDGET * fetchBp) / fitsBp)
+  const fragment = { ids: new Int32Array(kept) }
+  return keptStepsError(
+    [fragment] as never,
+    BUDGET,
+    { start: 0, end: fetchBp },
+    false,
+  )
+}
+
+// On a 1,000 px canvas the display fetches the 800 px blocks the view touches:
+// a 5 Mb view three 4 Mb blocks, a 500 kb view three 400 kb ones
+test.each([
+  ['5 Mb', 12_000_000, 7_290_000, '7.29Mbp', '1.7'],
+  ['500 kb', 1_200_000, 762_000, '762Kbp', '1.6'],
+])(
+  'a %s view over the step budget is told how far to zoom in, not a span wider than it',
+  (_, fetchBp, fitsBp, span, fold) => {
+    const error = refusal(fetchBp, fitsBp)!
+    expect(error.message).toBe(
+      `Zoom in to about ${span}, or choose fewer haplotypes, to see the graph`,
+    )
+    expect(laneZoomNotice(error, fetchBp)).toMatchObject({
+      name: 'NodeLimitError',
+      message: `Zoom in about ${fold}×, or choose fewer haplotypes, to see lanes`,
+    })
+  },
+)
+
+test('the fold rounds up, to a tenth below 10 and a whole number above, and asks for at least 1.1', () => {
+  expect(laneZoomFold(1_010, 1_000)).toBe(1.1)
+  expect(laneZoomFold(1_100, 1_000)).toBe(1.1)
+  expect(laneZoomFold(9_910, 1_000)).toBe(10)
+  expect(laneZoomFold(32_100, 1_000)).toBe(33)
+  expect(laneZoomFold(1_000, 1_200)).toBe(1.1)
+})
+
+test('a refusal naming no span keeps its message', () => {
+  const error = Object.assign(new Error('Too many haplotype steps here'), {
+    name: 'NodeLimitError',
+    fitsBp: 1,
+  })
+  expect(laneZoomNotice(error, 1000)).toMatchObject({
+    message: 'Too many haplotype steps here',
+  })
+})

package/src/synteny/laneZoomNotice.ts

@@ -0,0 +1,34 @@
+import { isNodeLimitError } from '../nodeLimitError.ts'
+
+/**
+ * How many times over the view must zoom in for a lane fetch of `windowBp`
+ * to fit, where `fitsBp` is the widest fetch that would: rounded up to a
+ * tenth, to a whole number past 10, and never under 1.1.
+ */
+export function laneZoomFold(windowBp: number, fitsBp: number) {
+  const fits = Math.max(1, fitsBp)
+  return windowBp >= 10 * fits
+    ? Math.ceil(windowBp / fits)
+    : Math.max(11, Math.ceil((10 * windowBp) / fits)) / 10
+}
+
+/**
+ * A budget refusal for lanes, naming how far to zoom rather than a span. The
+ * display fetches lanes over the 800 px static blocks its view touches, up to
+ * a block past each edge, and never tells the adapter the view, so a span that
+ * fits the fetch can be wider than the view. The fetch narrows with the view,
+ * so a fold holds for both.
+ */
+export function laneZoomNotice(error: unknown, windowBp: number) {
+  if (isNodeLimitError(error) && error instanceof Error) {
+    const { fitsBp } = error as { fitsBp?: unknown }
+    error.message = error.message.replace('to see the graph', 'to see lanes')
+    if (typeof fitsBp === 'number') {
+      error.message = error.message.replace(
+        /^Zoom in to about [\d.,]*\d[KM]?bp/,
+        `Zoom in about ${laneZoomFold(windowBp, fitsBp)}×`,
+      )
+    }
+  }
+  return error
+}

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.1.11'
+export const version = '7.1.13'

package/dist/chunks/GbzBaseSyntenyAdapter-2MA3I6BM.js

@@ -1,2 +0,0 @@
-import{a as ae,b as re,c as de,d as oe,e as ie,f as H,g as se}from"./chunk-U4U5ZOCH.js";import{a as te}from"./chunk-KOB7YIMR.js";import{a as j,b as W,c as Z,d as u,e as M,f as $,g as U,h as k,i as z,k as X}from"./chunk-OBQFV4NL.js";import"./chunk-O7Y7LYN6.js";import{b as E,c as O}from"./chunk-N4WBX2OS.js";import"./chunk-BWP3XYKD.js";import"./chunk-T4HOC6O3.js";import{a as ne}from"./chunk-PFAHNHMM.js";import"./chunk-VDHDEEMF.js";import{a as V,c as L,m as ee}from"./chunk-EDSIYH4H.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{g as F,h as P,i as C}from"./chunk-GUXZESDR.js";import"./chunk-T4R3ZVEM.js";import{d as G,g as Y,h as J,i as K}from"./chunk-IKJZPPOA.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as D,o as I}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function he(n){return J(n)&&A(Y(n))?K(n,i=>A(i)):void 0}function ue(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let t=he(n);if(!t)return{};try{return await N(t,i).stat(),{location:t}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var pe=(n,i)=>n.path.some(t=>i.has(t.name)),v=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=L({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ye)throw new q(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await V(e):e);return O(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let s of t){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:s=>{let c=E(s);c&&pe(c,t)&&o.push(c)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>pe(a,i));return{records:be(e,ge),total:e.length}}};var B=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},_=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function we(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function xe({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,d=we(c,n),g={uniqueId:d,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:d,mate:{refName:c.contig,start:p,end:l,assemblyName:e}};return new ae(g)}}function Se({pair:n,lane:i,mateLane:t}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:t,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Pe=12e4;function Ne(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=t.get(p);l?l.push([o,s]):t.set(p,[[o,s]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Pe&&(e=Math.max(e,o))}}return e}function T(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${D(n.fitsBp)} to see ${i}`),n}var le=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),Q=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await ce(t,this.pluginManager),r=a.location,o=await W.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await $(o),p=U({configured:this.getConf("referenceSample"),anchorPrefix:P(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?ee(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a}=await this.graph(t),r=C(this),o=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&o.push({name:H(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,lanes:o}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,s=o===a?void 0:P(this,o),c=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>M(r,a)&&(e===void 0||F(u(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:d,end:g}=le(t);if(p!==o)throw new _(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let w=this.keepPredicate(e.haplotypes);if(w!==void 0&&!r.hasHaplotypeIndex)throw new B(c);let f=await X(r,y,d,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:w}).catch(x=>{throw T(x,"the graph")});return typeof f=="string"?f:ne(f,{start:d,end:g},e.walkRows)}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=P(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:s,end:c}=t,p=P(this,e.targetAssemblyName),l=C(this),d=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await I(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:d}).catch(f=>{throw T(z(f,y,c-s)??f,"lanes")})):[]).flatMap(f=>{let x=f.resolved?xe({alignment:f,assemblyName:r,refName:o,lane:H(l,u(f.name))}):void 0;return x===void 0?[]:[x]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=t,l=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),d=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),w=this.getConf("context"),f=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>d.has(u(S))}),x=async m=>{let h=await f(m,w).catch(b=>{throw T(z(b,y,c-s)??b,"lanes")}),S=Ne(h,d),R=Math.ceil(S/2)+2e3;return S>0&&R>w?f(m,R).catch(b=>{if(b instanceof j)return h;throw b}):h};return(g&&l.length>0?await I(ie(e),a.statusCallback,()=>x(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(b=>R.flatMap(me=>m.pairAlignments({target:b,query:me,bases:!1}).map(fe=>Se({pair:fe,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=le(t);return te(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new B(c);if(a.assemblyName===s){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let d of l)r.next(d)}r.complete()},e.signal)}};export{B as NoHaplotypeIndexError,de as PairTargetError,Q as default,Ne as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-2MA3I6BM.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-2MA3I6BM.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-TUQKGAK3.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
-  "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  NoReferenceSampleError,\n  aliasedSample,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf\n} from \"./chunk-NMWQUFPF.js\";\nimport {\n  panSNSample\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction gbzLocations({ db, index }) {\n  return db === \"hprc\" ? { db: HPRC_GBZ.db, index: index ?? HPRC_GBZ.index } : { db, index };\n}\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  if (ref) {\n    return aliasedSample(panSNSample(ref), samples) ?? ref;\n  }\n  const first = samples[0];\n  if (first === void 0) {\n    throw new NoReferenceSampleError(\"\", samples);\n  }\n  return first;\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  gbzLocations,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\ninterface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\n\nclass HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nfunction fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n// gbz-base writes the CIGAR along the target, which is the side a JBrowse\n// feature is, so it passes through unchanged\nfunction pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  return matchFeature({\n    target: {\n      name: `${haplotypePrefix(pair.target)}#${pair.target.contig}`,\n      assemblyName: lane,\n      refName: pair.target.contig,\n      start: pair.targetStart,\n      end: pair.targetEnd,\n    },\n    query: {\n      name: `${haplotypePrefix(pair.query)}#${pair.query.contig}`,\n      assemblyName: mateLane,\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n    },\n    strand: pair.strand,\n    cigar: pair.cigar,\n    matches: pair.matches,\n    columns: pair.columns,\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw zoomInNotice(\n                  nodeLimitError(error, nodeLimit, end - start) ?? error,\n                  'lanes',\n                )\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw zoomInNotice(\n          nodeLimitError(error, nodeLimit, end - start) ?? error,\n          'lanes',\n        )\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && answerable.length > 0\n        ? await updateStatus(lanePairsStatus(pairs), opts.statusCallback, () =>\n            bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(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": ["haplotypeIndexBeside", "db", "GBZ_DB", "siblingCompanion", "gbzDb", "readsSiblings", "haplotypeIndexBeside", "locationName", "renamed", "name", "isMissing", "error", "findCompanion", "pluginManager", "candidate", "openLocation", "MAX_READS", "MAX_UNINDEXED_BYTES", "UnindexedGafTooLargeError", "size", "sample", "records", "max", "stride", "_", "k", "touches", "record", "names", "step", "GafFile", "file", "tabix", "cachedSetup", "signal", "bytes", "text", "unzip", "parseGaf", "lo", "hi", "name", "id", "line", "parseGafLine", "r", "NoHaplotypeIndexError", "unreadable", "HaplotypeWindowError", "assemblyName", "anchor", "fragmentId", "name", "alignment", "haplotypePrefix", "fragmentFeature", "refName", "lane", "refStart", "refEnd", "strand", "cigar", "hapStart", "hapEnd", "id", "data", "SyntenyFeature", "pairFeature", "pair", "mateLane", "matchFeature", "BRIDGE_MAX_BP", "widestWalkGap", "subgraphs", "kept", "byPath", "subgraph", "start", "end", "prefix", "key", "spans", "widest", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "wholeBp", "region", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "locationIsSet", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "location", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "asmByPrefix", "assemblyByPanSNPrefix", "lanes", "haplotype", "laneAssemblyName", "contigs", "panSNMatchesPrefix", "haplotypes", "targetPrefix", "wantedPrefixes", "haplotypeWanted", "signal", "unreadableIndex", "query", "keep", "cut", "cutWindowTables", "walkCutFor", "nodeNames", "gaf", "nodeLimit", "updateStatus", "nodeLimitError", "feature", "pairs", "answerable", "featureSide", "mateSide", "baseContext", "context", "bridged", "SubgraphLimitError", "lanePairsStatus", "target", "mate", "asked", "ObservableCreate", "observer", "requestedPairs", "features"]
-}

package/dist/chunks/WalkTabixSyntenyAdapter-AIC3W7FL.js

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