jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2

package/src/launchFromGraph/launchFromGraph.ts

@@ -1,13 +1,16 @@
+import { regionLabel } from '@jbrowse/bandage-core/hoverText'
 import { readConfObject } from '@jbrowse/core/configuration'
 
-import { locLabel, locString } from './contributors'
+import { locString } from './contributors'
 import { linearViewTarget } from './linearViewTarget'
 
 import type { Contributor, GraphLocation } from './contributors'
+import type { SubgraphRegion } from '../GetSubgraph'
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
 export interface TrackScanSession {
   tracks: AnyConfigurationModel[]
+  // core's getTrackName reads these
   assemblies: AnyConfigurationModel[]
   // optional, as a hand-built session in a test has none
   assemblyManager?: {
@@ -46,17 +49,11 @@ export interface GraphLaunchSession extends TrackScanSession {
     type: string,
     snapshot?: Record<string, unknown>,
   ) => Promise<{ id: string }>
-  assemblyNames: string[]
   views: unknown[]
   // optional, as a hand-built session in a test has none
   notifyError?: (message: string, error?: unknown) => void
   // a highlight every linear view on its assembly draws
-  addHighlight?: (highlight: {
-    refName: string
-    start: number
-    end: number
-    assemblyName: string
-  }) => void
+  addHighlight?: (highlight: SubgraphRegion) => void
 }
 
 // A launch is a promise nothing waits on. Let go, a refusal moved nothing and
@@ -107,9 +104,7 @@ export function paddedLocation(
 // assemblies, or the reference is filtered out by the name this replaces.
 export function withReferenceRegion(
   contributors: Contributor[],
-  region:
-    | { refName: string; assemblyName: string; start: number; end: number }
-    | undefined,
+  region: SubgraphRegion | undefined,
 ): Contributor[] {
   return region
     ? contributors.map(c =>
@@ -160,13 +155,13 @@ export function showInLinearView({
   if (existing) {
     reportFailure(
       session,
-      `Could not show ${assembly} ${locLabel(location)}`,
+      `Could not show ${assembly} ${regionLabel(location)}`,
       Promise.resolve(existing.navToLocString(locString(location), assembly)),
     )
     viewId = existing.id
   } else {
     viewId = session.addView('LinearGenomeView', {
-      displayName: `${assembly} — ${locLabel(location)}`,
+      displayName: `${assembly} — ${regionLabel(location)}`,
       init: { assembly, loc: locString(location), tracks },
     }).id
   }

package/src/panSNTabix.test.ts

@@ -1,29 +1,4 @@
-import {
-  PanSNRefNames,
-  buildRefNameLookup,
-  resolveRefName,
-} from './panSNTabix.ts'
-
-// The reason both tabix graph adapters need this at all: a graph's stable
-// sequences are usually PanSN while the assembly asking for them uses the bare
-// contig, and a session may hold the same sample as one assembly or as two.
-test('a PanSN stable name resolves under its sample and under its haplotype', () => {
-  const lookup = buildRefNameLookup([
-    'GRCh38#0#chr6',
-    'NA20809#2#CM094351.1',
-    'chrM',
-  ])
-  expect(resolveRefName(lookup, 'GRCh38', 'chr6')).toBe('GRCh38#0#chr6')
-  expect(resolveRefName(lookup, 'GRCh38#0', 'chr6')).toBe('GRCh38#0#chr6')
-  expect(resolveRefName(lookup, 'NA20809#2', 'CM094351.1')).toBe(
-    'NA20809#2#CM094351.1',
-  )
-  expect(resolveRefName(lookup, 'NA20809', 'CM094351.1')).toBe(
-    'NA20809#2#CM094351.1',
-  )
-  expect(resolveRefName(lookup, 'hg38', 'chrM')).toBe('chrM')
-  expect(resolveRefName(lookup, 'NA20809#1', 'CM094351.1')).toBeUndefined()
-})
+import { PanSNRefNames } from './panSNTabix.ts'
 
 // The index's names are read once and every query awaits that one read. It is
 // shared, so it cannot take on one caller's signal: a track fetch the user

package/src/panSNTabix.ts

@@ -1,16 +1,17 @@
 import { TabixIndexedFile } from '@gmod/tabix'
 import {
   panSNContig,
-  panSNHaplotype,
   panSNMatchesPrefix,
-  panSNSample,
   resolvePanSNPrefix,
 } from '@jbrowse/bandage-core/pansn'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { openLocation, openTabixIndexFilehandle } from '@jbrowse/core/util/io'
+import { refNameLookup, resolveRefName } from '@jbrowse/graph-walks'
 import { types } from '@jbrowse/mobx-state-tree'
 
+import { bytesForRegions } from './tabixRange.ts'
+
 import type {
   BaseFeatureDataAdapter,
   BaseOptions,
@@ -19,16 +20,12 @@ import type { Region } from '@jbrowse/core/util/types'
 
 // What a tabix-indexed graph track answers about its own reference names, for
 // the two adapters that read one: `RgfaTabixAdapter` over segments and links,
-// and `MinigraphBubbleAdapter` over bubbles.
-//
-// The two carried this verbatim — the opener, the cached lookup, `getRefNames`,
-// `resolve` — and the bubble adapter reached across into
-// `RgfaTabixAdapter/rgfaBed.ts` for the lookup half, which is a BED row grammar
-// and not this. Same reason `ComparativeAdapterBase` exists: the answers that do
-// not depend on which config slot names the file belong in one place.
+// and `MinigraphBubbleAdapter` over bubbles. @jbrowse/graph-walks builds the
+// name lookup.
 //
-// A class rather than a base class, for the reason that file records: a base
-// generic over the config cannot prove a slot name to `getConf`, so the adapter
+// A class rather than a base class, for the reason ComparativeAdapterBase.ts
+// records: a base generic over the config cannot prove a slot name to
+// `getConf`, so the adapter
 // keeps the two lines that read its own slots and hands over the file. Reading
 // `assemblyNameToPanSN` IS hoistable, because every schema here declares it and
 // `resolvePanSNPrefix` is already generic over the base adapter type.
@@ -38,6 +35,12 @@ import type { Region } from '@jbrowse/core/util/types'
 // kB of compressed blocks, and re-fetching them per pan is the cost this avoids.
 const CHUNK_CACHE_SIZE = 50 * 2 ** 20
 
+// A file slot whose default is a url, '' for none
+export const fileLocationSlot = (uri: string) => ({
+  type: 'fileLocation' as const,
+  defaultValue: { uri, locationType: 'UriLocation' },
+})
+
 /**
  * The index slot `openTabixSlot` reads: its own `location` and `indexType`
  */
@@ -54,10 +57,7 @@ export const tabixIndexSchema = (name: string, defaultUri = '') =>
     /**
      * #slot
      */
-    location: {
-      type: 'fileLocation',
-      defaultValue: { uri: defaultUri, locationType: 'UriLocation' },
-    },
+    location: fileLocationSlot(defaultUri),
   })
 
 // The index slot's snapshot for a file whose `.tbi`, or `.csi`, sits beside it
@@ -68,6 +68,20 @@ export function tbiBeside(uri: string, baseUri: unknown, csi: unknown) {
   }
 }
 
+// The `walksUri` shorthand: `<walksUri>.walks.bed.gz` and its index
+export function walksLocations(snap: Record<string, unknown>) {
+  const { walksUri, baseUri, csi } = snap
+  if (typeof walksUri !== 'string') {
+    return snap
+  }
+  const walks = `${walksUri}.walks.bed.gz`
+  return {
+    ...snap,
+    walksLocation: { uri: walks, baseUri },
+    walksIndex: tbiBeside(walks, baseUri, csi),
+  }
+}
+
 // One indexed file from the pair of slots that names it: the data location, and
 // an index slot holding its own `location` and `indexType`. Paths, so the pair
 // can sit in a sub-schema.
@@ -88,41 +102,6 @@ export function openTabixSlot(
   })
 }
 
-// A tab can occur in neither half — both come out of BED columns.
-function qualifiedKey(assemblyName: string, refName: string) {
-  return `${assemblyName}\t${refName}`
-}
-
-// The stable sequences in these files are usually PanSN (`K12#1#chr`) while the
-// assembly asking for them uses the bare contig (`chr` in assembly `K12`). One
-// map answers both spellings: the raw tabix name, plus a sample+contig key for
-// PanSN names.
-export function buildRefNameLookup(tabixRefNames: string[]) {
-  const lookup = new Map<string, string>()
-  for (const name of tabixRefNames) {
-    lookup.set(name, name)
-    const sample = panSNSample(name)
-    if (sample !== name) {
-      const contig = panSNContig(name)
-      lookup.set(qualifiedKey(sample, contig), name)
-      const haplotype = panSNHaplotype(name)
-      if (haplotype !== undefined) {
-        lookup.set(qualifiedKey(haplotype, contig), name)
-      }
-    }
-  }
-  return lookup
-}
-
-export function resolveRefName(
-  lookup: Map<string, string>,
-  assemblyName: string,
-  refName: string,
-) {
-  const qualified = lookup.get(qualifiedKey(assemblyName, refName))
-  return qualified === undefined ? lookup.get(refName) : qualified
-}
-
 /**
  * The reference-name half of a tabix graph track, against one indexed file.
  *
@@ -136,7 +115,7 @@ export class PanSNRefNames {
   // read going for the rest, and retries a failed read.
   private lookup = cachedSetup({
     setup: async opts =>
-      buildRefNameLookup(await this.file.getReferenceSequenceNames(opts)),
+      refNameLookup(await this.file.getReferenceSequenceNames(opts)),
   })
 
   constructor(
@@ -179,4 +158,28 @@ export class PanSNRefNames {
       region.refName,
     )
   }
+
+  /**
+   * The compressed bytes a read of `regions` fetches from the file, as its
+   * index estimates them, for the display's byte gate. `queryStart` moves a
+   * region's start to where the read begins.
+   */
+  async regionBytes(
+    regions: Region[],
+    opts: BaseOptions = {},
+    queryStart = async (start: number) => start,
+  ) {
+    const spans = []
+    for (const region of regions) {
+      const refName = await this.resolve(region, opts)
+      if (refName !== undefined) {
+        spans.push({
+          refName,
+          start: await queryStart(region.start),
+          end: region.end,
+        })
+      }
+    }
+    return bytesForRegions(this.file, spans, opts)
+  }
 }

package/src/synteny/lanePairs.ts

@@ -49,6 +49,14 @@ export function requestedPairs(opts: LaneFeatureOptions): LanePair[] {
   }
 }
 
+// The status a fetch of lane pairs shows while it reads
+export function lanePairsStatus(pairs: LanePair[]) {
+  const [first] = pairs
+  return pairs.length === 1 && first
+    ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`
+    : `Reading ${pairs.length} lane pairs`
+}
+
 /**
  * The lane a haplotype draws on: the JBrowse assembly the config maps to its
  * `sample#haplotype` prefix, else to its sample, else the prefix itself. The

package/src/synteny/matchFeature.ts

@@ -0,0 +1,52 @@
+import SyntenyFeature from './SyntenyFeature.ts'
+
+export interface MatchSide {
+  name: string
+  assemblyName: string
+  refName: string
+  start: number
+  end: number
+}
+
+/**
+ * One record of a walk aligned to another, on the target walk's contig with
+ * the query walk as its mate and the CIGAR read along the target, a `D` being
+ * target bases the query lacks. Each side's walk name and extent make the id.
+ */
+export function matchFeature({
+  target,
+  query,
+  strand,
+  cigar,
+  matches,
+  columns,
+}: {
+  target: MatchSide
+  query: MatchSide
+  strand: string
+  cigar: string
+  matches: number
+  columns: number
+}) {
+  const id = `${target.name}:${target.start}-${target.end}|${query.name}:${query.start}-${query.end}`
+  return new SyntenyFeature({
+    uniqueId: id,
+    assemblyName: target.assemblyName,
+    refName: target.refName,
+    start: target.start,
+    end: target.end,
+    type: 'match',
+    strand: strand === '-' ? -1 : 1,
+    CIGAR: cigar,
+    syntenyId: id,
+    identity: matches / Math.max(columns, 1),
+    numMatches: matches,
+    blockLen: columns,
+    mate: {
+      refName: query.refName,
+      start: query.start,
+      end: query.end,
+      assemblyName: query.assemblyName,
+    },
+  })
+}

package/src/tabixRange.ts

@@ -1,14 +1,6 @@
-import type { TabixIndexedFile } from '@gmod/tabix'
+import { checkRange } from '@jbrowse/graph-walks'
 
-// tabix-js loops forever on a NaN end and reads nothing for a NaN start
-// (GMOD/tabix-js#157), so every query refuses a range that is not finite first
-export function checkRange(refName: string, start: number, end: number) {
-  if (!Number.isFinite(start) || !Number.isFinite(end)) {
-    throw new Error(
-      `${refName}:${start}-${end} is not a finite range to query the graph's index for`,
-    )
-  }
-}
+import type { TabixIndexedFile } from '@gmod/tabix'
 
 export async function getLines(
   file: TabixIndexedFile,
@@ -23,3 +15,14 @@ export async function getLines(
   checkRange(refName, start, end)
   return file.getLines(refName, start, end, opts)
 }
+
+export async function bytesForRegions(
+  file: TabixIndexedFile,
+  regions: { refName: string; start: number; end: number }[],
+  opts: { signal?: AbortSignal },
+) {
+  for (const { refName, start, end } of regions) {
+    checkRange(refName, start, end)
+  }
+  return file.bytesForRegions(regions, opts)
+}

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.1.0'
+export const version = '7.1.2'

package/dist/chunks/AddTrackWorkflow-Q6RY23LF.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=AddTrackWorkflow-Q6RY23LF.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-TIXR4Y3J.js

@@ -1,2 +0,0 @@
-import{a as q,b as re,c as de,d as oe,e as T}from"./chunk-SAMJE6GH.js";import{a as ne}from"./chunk-KOB7YIMR.js";import{a as Z,b as U,c as X,d as g,e as C,f as M,g as k,h as E,i as z,k as Y}from"./chunk-YJHYBDYF.js";import"./chunk-EWFJBQDV.js";import{a as O,b as H}from"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-IXQK7JAW.js";import{a as ae}from"./chunk-TXI43PEN.js";import{a as ee,c as L,f as te}from"./chunk-AMFIBQVR.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as A,f as P,g as B}from"./chunk-446RWIA3.js";import"./chunk-E7J6SB5P.js";import{b as G,e as J,f as K,g as V}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function F(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function fe(n){return K(n)&&F(J(n))?V(n,i=>F(i)):void 0}function he(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function se(n,i){let t=fe(n);if(!t)return{};try{return await N(t,i).stat(),{location:t}}catch(e){return he(e)?{}:{unreadable:String(e)}}}var ge=5e3,ue=50*2**20,_=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ye(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var ie=(n,i)=>n.path.some(t=>i.has(t.name)),v=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=L({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new _(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&ie(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>ie(a,i));return{records:ye(e,ge),total:e.length}}};var I=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. 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q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var Se=12e4;function Pe(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=g(r);if(i.has(s)){let p=`${s}#${r.contig}`,l=t.get(p);l?l.push([o,c]):t.set(p,[[o,c]])}}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<=Se&&(e=Math.max(e,o))}}return e}function Q(n,i){return n instanceof X&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var ce=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),j=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 se(t,this.pluginManager),r=a.location,o=await U.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await M(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,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)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(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 c=g(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,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,referenceSamples:r}=await this.graph(t),o=B(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:T(o,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:P(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:A(g(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}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=>C(r,a)&&(e===void 0||A(g(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:u}=ce(t);if(p!==o)throw new D(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${l} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new I(s);let m=await Y(r,y,f,u,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw Q(b,"the graph")});return typeof m=="string"?m:ae(m,{start:f,end:u},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=>A(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=P(this,e.targetAssemblyName),l=B(this),f=this.keepPredicate(e.haplotypes,p),u=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(u?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:u,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(m=>{throw Q(z(m,y,s-c)??m,"lanes")})):[]).flatMap(m=>{let b=m.resolved?we({alignment:m,assemblyName:r,refName:o,lane:T(l,g(m.name))}):void 0;return b===void 0?[]:[b]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,l=(await Promise.all(e.map(async d=>({pair:d,featureSide:await this.laneHaplotypes(d.queryAssemblyName,a),mateSide:await this.laneHaplotypes(d.targetAssemblyName,a)})))).filter(({featureSide:d,mateSide:h})=>d.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:d,mateSide:h})=>[...d,...h].map(g))),u=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[m]=e,b=(d,h)=>r.getSubgraphs({path:d,start:c,end:s,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(g(S))}),pe=async d=>{let h=await b(d,x).catch(w=>{throw Q(z(w,y,s-c)??w,"lanes")}),S=Pe(h,f),R=Math.ceil(S/2)+2e3;return S>0&&R>x?b(d,R).catch(w=>{if(w instanceof Z)return h;throw w}):h};return(u&&m&&l.length>0?await $(e.length===1?`Reading ${m.queryAssemblyName} against ${m.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(u)):[]).flatMap(d=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(w=>R.flatMap(le=>d.pairAlignments({target:w,query:le,bases:!1}).map(me=>xe({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=ce(t);return ne(async r=>{let{db:o,anchor:c,unreadableIndex:s}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new I(s);if(a.assemblyName===c){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of l)r.next(f)}r.complete()},e.signal)}};export{D as HaplotypeWindowError,I as NoHaplotypeIndexError,de as PairTargetError,j as default,we as fragmentFeature,xe as pairFeature,Pe as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-TIXR4Y3J.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-TIXR4Y3J.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VQWHMWLF.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
-  "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample\n} from \"./chunk-Q7LYHGGQ.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 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  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\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  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 { laneAssemblyName, requestedPairs } from '../synteny/lanePairs.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\nexport interface 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'\nexport type { LanePair } from '../synteny/lanePairs.ts'\n\nexport class 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}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${haplotypePrefix(pair.target)}#${pair.target.contig}:${pair.targetStart}-${pair.targetEnd}|${haplotypePrefix(pair.query)}#${pair.query.contig}:${pair.queryStart}-${pair.queryEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName: lane,\n    refName: pair.target.contig,\n    start: pair.targetStart,\n    end: pair.targetEnd,\n    type: 'match',\n    strand: pair.strand === '-' ? -1 : 1,\n    CIGAR: pair.cigar,\n    syntenyId: id,\n    identity: pair.matches / Math.max(pair.columns, 1),\n    numMatches: pair.matches,\n    blockLen: pair.columns,\n    mate: {\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n      assemblyName: mateLane,\n    },\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${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, referenceSamples } = 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      referenceSample,\n      referenceSamples,\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 [first] = pairs\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 && first && answerable.length > 0\n        ? await updateStatus(\n            pairs.length === 1\n              ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n              : `Reading ${pairs.length} lane pairs`,\n            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", "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", "first", "context", "bridged", "SubgraphLimitError", "target", "mate", "asked", "ObservableCreate", "observer", "requestedPairs", "features"]
-}

package/dist/chunks/GraphTrackSettingsDialog-TAM6PMXD.js

@@ -1,6 +0,0 @@
-import{b as G}from"./chunk-J6NZIAZF.js";import{b as H,c as x}from"./chunk-E2QPSDQL.js";import{k as h}from"./chunk-YSTMDXXX.js";import"./chunk-MHPJB22Z.js";import"./chunk-AU73K7LX.js";import"./chunk-MVVXRZXV.js";import"./chunk-446RWIA3.js";import"./chunk-5OI6LO4I.js";import{g as u}from"./chunk-6OPB7FOJ.js";import{D as v,F as f,H as c,n as g,s as b,w as S,z as C}from"./chunk-E3WYW7Z6.js";import{b as a,c as l,d as i}from"./chunk-JMBDTNUR.js";var F=h()({section:{marginBottom:24},formControl:{minWidth:200}}),M=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],I=i(function({model:t}){let{classes:e}=F();return t.adapterConfig.type==="RgfaTabixAdapter"&&!H(t.adapterConfig)?l("div",{className:e.section,children:[l(b,{className:e.formControl,children:[a(S,{children:"Graph context"}),a(v,{value:t.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:o=>{t.setSubgraphContext(o.target.value),t.cut()},children:M.map(({value:o,label:p})=>a(C,{value:o,children:p},o))})]}),a(c,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),L=I;var N=h()({section:{marginBottom:24}});function P(n){let t=n.split(/[\s,]+/).map(e=>e.trim()).filter(e=>e!=="");return t.length===0?void 0:t}var T=i(function({model:t}){let[e,o]=u(t.cutHaplotypes?.join(", ")??""),p=()=>{let r=P(e)??[];r.join(`
-`)===(t.cutHaplotypes??[]).join(`
-`)||(t.setSubgraphHaplotypes(r),t.cut())};return a(f,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:e,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:r=>{o(r.target.value)},onBlur:()=>{p()},onKeyDown:r=>{r.key==="Enter"&&p()}})}),w=i(function({model:t,names:e}){let[o,p]=u(t.cutHaplotypes??[]),[r,d]=u(!1),m=s=>{s.join(`
-`)!==(t.cutHaplotypes??[]).join(`
-`)&&(t.setSubgraphHaplotypes(s),t.cut())};return a(g,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:e,value:o,open:r,onOpen:()=>{d(!0)},onClose:()=>{d(!1),m(o)},onChange:(s,y)=>{p(y),r||m(y)},renderInput:s=>a(f,{...s,label:"Haplotypes",placeholder:o.length===0?"every haplotype":void 0,slotProps:{...s.slotProps,htmlInput:{...s.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),D=i(function({model:t}){let{classes:e}=N(),o=t.haplotypeNames,p=t.cutHaplotypes?.join(",")??"";return x(t.adapterConfig)?l("div",{className:e.section,children:[o?a(w,{model:t,names:o},p):a(T,{model:t},p),l(c,{variant:"caption",component:"div",color:"text.secondary",children:[o?`Which of the graph's ${o.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),k=D;function B({model:n,open:t,onClose:e}){return l(G,{model:n,open:t,onClose:e,children:[a(L,{model:n}),a(k,{model:n})]})}export{B as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-TAM6PMXD.js.map

package/dist/chunks/GraphTrackSettingsDialog-TAM6PMXD.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
-  "sourcesContent": ["import {\n  FormControl,\n  InputLabel,\n  MenuItem,\n  Select,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: 0, label: 'None' },\n  { value: 1, label: '1 hop' },\n  { value: 2, label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  return model.adapterConfig.type === 'RgfaTabixAdapter' &&\n    !walkIndexed(model.adapterConfig) ? (\n    <div className={classes.section}>\n      <FormControl className={classes.formControl}>\n        <InputLabel>Graph context</InputLabel>\n        <Select\n          value={model.subgraphContext}\n          label=\"Graph context\"\n          data-testid=\"graph-context-select\"\n          onChange={e => {\n            model.setSubgraphContext(e.target.value)\n            void model.cut()\n          }}\n        >\n          {SUBGRAPH_CONTEXTS.map(({ value, label }) => (\n            <MenuItem key={value} value={value}>\n              {label}\n            </MenuItem>\n          ))}\n        </Select>\n      </FormControl>\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nexport function parseHaplotypeList(text: string) {\n  const names = text\n    .split(/[\\s,]+/)\n    .map(name => name.trim())\n    .filter(name => name !== '')\n  return names.length === 0 ? undefined : names\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft) ?? []\n    const unchanged =\n      parsed.join('\\n') === (model.cutHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      void model.cut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too. The\n// set applies when the list closes or, with the list closed, as it changes.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const [open, setOpen] = useState(false)\n  const apply = (haplotypes: string[]) => {\n    if (haplotypes.join('\\n') !== (model.cutHaplotypes ?? []).join('\\n')) {\n      model.setSubgraphHaplotypes(haplotypes)\n      void model.cut()\n    }\n  }\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onClose={() => {\n        setOpen(false)\n        apply(draft)\n      }}\n      onChange={(_, value) => {\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set. The inner field is\n// keyed on it so an outside change (a restored session, a launch) resets the\n// draft rather than fighting it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const key = model.cutHaplotypes?.join(',') ?? ''\n  return cutsByHaplotype(model.adapterConfig) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField key={key} model={model} names={names} />\n      ) : (\n        <HaplotypeListField key={key} model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  open,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  open: boolean\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} open={open} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
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-}

package/dist/chunks/MinigraphBubbleAdapter-AGI2UYQR.js

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-//# sourceMappingURL=MinigraphBubbleAdapter-AGI2UYQR.js.map

package/dist/chunks/MinigraphBubbleAdapter-AGI2UYQR.js.map

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-{
-  "version": 3,
-  "sources": ["../../src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts"],
-  "sourcesContent": ["import {\n  bubbleDescription,\n  bubbleLabel,\n  parseBubbleLine,\n} from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\n\nimport type { MinigraphBubbleAdapterConfig } from './configSchema.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nexport default class MinigraphBubbleAdapter extends BaseFeatureDataAdapter<MinigraphBubbleAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly bubbles\n  // `gfatools bubble` names each row after the graph's stable sequence, so a\n  // Minigraph-Cactus graph produces PanSN rows (`GRCh38#0#chr6`) where a plain\n  // minigraph graph produces bare ones (`chr6`). Same resolution the segment\n  // adapter does, through the same `assemblyNameToPanSN` slot.\n  private readonly refNames\n\n  public constructor(\n    config: MinigraphBubbleAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.bubbles = openTabixSlot(this, ['bubblesLocation'], ['index'])\n    this.refNames = new PanSNRefNames(this.bubbles, this)\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading bubbles', statusCallback, () =>\n          getLines(this.bubbles, tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: (line, fileOffset) => {\n              const bubble = parseBubbleLine(line)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: `bubble-${fileOffset}`,\n                  refName: query.refName,\n                  start: bubble.start,\n                  end: bubble.end,\n                  // How variable this spot is, in two words, since that is the\n                  // whole point of the track.\n                  name: bubbleLabel(bubble),\n                  description: bubbleDescription(bubble),\n                  type: 'bubble',\n                  score: bubble.segmentCount,\n                  segmentCount: bubble.segmentCount,\n                  pathCount: bubble.pathCount,\n                  inversion: bubble.inversion,\n                  shortestAlleleLength: bubble.shortestAlleleLength,\n                  longestAlleleLength: bubble.longestAlleleLength,\n                  segments: bubble.segments,\n                  shortestAllele: bubble.shortestAllele,\n                  longestAllele: bubble.longestAllele,\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n}\n"],
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-}

package/dist/chunks/RgfaTabixAdapter-2OL5X3HF.js

@@ -1,3 +0,0 @@
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