jbrowse-plugin-graphgenomeviewer 6.24.0 → 6.25.0

package/README.md

@@ -2,6 +2,62 @@
 
 Pangenome graphs in JBrowse 2.
 
+## Do it yourself
+
+Tutorials in the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/tutorials/), each
+with commands you can run:
+
+- **[Hosting your own graph](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph)**
+  — start here. One script turns an rGFA or GFA into indexed files and a track
+  config; later sections add haplotype walks and gbz-base
+- [pggb](https://jbrowse.org/jb2/docs/tutorials/pangenome_ecoli) — five _E.
+  coli_ strains from FASTA to graph, index, synteny and variants
+- [Minigraph-Cactus](https://jbrowse.org/jb2/docs/tutorials/pangenome_cactus) —
+  the same from `cactus-pangenome`
+- [Cattle](https://jbrowse.org/jb2/docs/tutorials/pangenome_cattle) and
+  [mouse](https://jbrowse.org/jb2/docs/tutorials/pangenome_mouse) — published
+  graphs: `vg deconstruct` one, rank the bubbles of another
+- HPRC release 2:
+  [graph alleles](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc),
+  [haplotypes against each other](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_haplotypes),
+  [repeat lengths](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats)
+- [Graph genome view user guide](https://jbrowse.org/jb2/docs/user_guides/graph_genome_view)
+
+## What data to use
+
+The plugin reads a graph as tabix files or a gbz-base database, one window at a
+time. A GFA small enough to load whole opens with **Add → Graph genome view**.
+
+Build the graph with [minigraph](https://github.com/lh3/minigraph) (rGFA),
+[pggb](https://github.com/pangenome/pggb) or
+[Minigraph-Cactus](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md)
+(GFA and GBZ), then index what you have:
+
+- **rGFA** — `gfa-to-tabix build graph.rgfa.gz -o out` (0.11.0+). It calls
+  [gfatools](https://github.com/lh3/gfatools) for the bubbles and writes
+  `.segs.bed.gz`, `.links.bed.gz`, `.bubbles.bed.gz`, `.alleles.bed.gz`, a
+  coarse tier, a `.graph.json` manifest and a track config. Opening
+  `out.segs.bed.gz` in **Add pangenome graph track** reads the manifest.
+  Adapter: `RgfaTabixAdapter`
+- **Plain GFA** (pggb, odgi, vg, base-level Minigraph-Cactus) — the same
+  command, with `--reference`, `--assembly` and `--snarls`, a VCF from
+  `vg deconstruct -a` or `pggb -V`
+- **Alleles, with a CIGAR each** — `build` writes `.alleles.bed.gz`, which an
+  alignments track draws; `gfa-to-tabix alleles <prefix>` makes one from a
+  `--layout contig` index
+- **Haplotype walks, as tabix files** — `vg convert -f graph.gbz`, then
+  `gfa-to-tabix --walks`. Adapter: `WalkTabixSyntenyAdapter`, or
+  `RgfaTabixAdapter` with `walksUri`
+- **Haplotype walks, as one database** — `vg chains`, `gbz-base construct`,
+  `gbz-haplotype-index` make `.gbz.db` and `.haplotype-index.db`. Adapter:
+  `GbzBaseSyntenyAdapter`
+- **Reads** — `vg giraffe -o gaf`, `vg gamsort -G`, `bgzip`, `tabix` make a
+  `.gaf.gz` for a gbz-base adapter's `reads`
+- **Minigraph paths per assembly** — `minigraph -cxasm --call` per sample, then
+  `gfa-to-tabix paths` (0.9.0+) writes one row per bubble and sample
+
+[vg](https://github.com/vgteam/vg) 1.69.0 or later covers the GBZ steps.
+
 ## As a track of a linear view
 
 A `GraphTrack` cuts the graph for the view's window and redraws it as you pan. A
@@ -26,13 +82,6 @@ above it.
 
 ![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)
 
-- **Variants at their bp.** A tube map on the reference axis puts each of MICB's
-  variant columns under its exon. HPRC's multiple alignment, cut to the same
-  eight haplotypes, marks a mismatch in a row wherever its tube leaves GRCh38's
-  route.
-
-![MICB's exons 2–4 as a tube map on the reference axis under the RefSeq genes and the eight haplotypes' alignment rows](img/tube_map_micb_ref.png)
-
 - **Allele frequency as a tube map.** A tube per route, as wide as the
   haplotypes taking it, coloured by superpopulation. Over C4's RCCX module, 35
   of 60 haplotypes skip the 6.4 kb HERV-K in C4B, so their C4B is short; thin
@@ -88,6 +137,10 @@ Needs JBrowse 5.0.0-beta.11 or later.
   (`.gbz.db`) as a `GraphTrack`. It finds the links and indexes beside the url,
   which a presigned url's signature doesn't cover; spell out each location in a
   config instead
+- Open track's **Add pangenome graph track** workflow also reads
+  `<prefix>.graph.json` beside a `<prefix>.segs.bed.gz` (written by
+  `gfa-to-tabix build`) for the coarse tier and the reference's PanSN sample;
+  without one, the track has no coarse tier
 - A hand-written track needs only the adapter:
 
 ```json
@@ -100,8 +153,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
     "type": "RgfaTabixAdapter",
     "uri": "https://example.com/hprc",
     "coarse": {
-      "uri": "https://example.com/hprc.tier10000",
-      "aboveBpPerPx": 1000
+      "uri": "https://example.com/hprc.fold10000",
+      "foldBelowBp": 10000
     }
   }
 }
@@ -110,8 +163,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
 - The track menu picks layout, colour and highlighted haplotypes, and switches
   to the segments lane or, for gbz-base and walk-indexed graphs, the haplotype
   lanes
-- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
-  `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)
+- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`
+  (default `foldBelowBp / 10`), the `coarse` tier (`gfa-to-tabix fold`)
 - Past the cut (5 Mb, or a gbz-base adapter's `nodeLimit`) the track asks you to
   zoom in. For a population view of a wide window, add the graph's VCF as a
   variant track (`vg deconstruct` makes one from a GBZ)
@@ -131,6 +184,39 @@ Needs JBrowse 5.0.0-beta.11 or later.
 - [docs/layouts.md](docs/layouts.md) — layouts, bubbles, walks, genes, loci
 - [docs/developing.md](docs/developing.md) — building, testing, `host-compat`
 
+## See also
+
+Apps and figures
+
+- [BandageJS](https://github.com/cmdcolin/BandageJS) - standalone page with the
+  same layouts, outside JBrowse
+- [ggbandage](https://github.com/GMOD/ggbandage) - R port of the Bandage layout,
+  as ggplot2 layers
+- [ggtubemap](https://github.com/GMOD/ggtubemap) - R port of the tube map, as
+  ggplot2 layers
+- [sequenceTubeMap, MemPanG26 edition](https://github.com/cmdcolin/sequenceTubeMap) -
+  our fork of the tube map app
+
+Libraries
+
+- [@jbrowse/bandage-core](https://github.com/GMOD/bandage-core) - the layout and
+  drawing engine behind this plugin
+- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout) -
+  stress layout that straightens the reference
+- [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) - tube map
+  layout
+- [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) - range-request reader
+  for `.gbz.db` databases
+
+Preparing data
+
+- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) - indexes a GFA for the
+  graph track
+- [gbz-haplotype-index](https://github.com/GMOD/gbz-haplotype-index) - names
+  every walk in a gbz-base cut
+- [gfa-to-pairwise-paf](https://github.com/cmdcolin/gfa-to-pairwise-paf-rs) -
+  graph to PAF, for synteny views
+
 ## License
 
 GPL-3.0-or-later (this module is based on work from Bandage and ODGF graph

package/dist/chunks/AddTrackWorkflow-ZKAN5JYJ.js

@@ -0,0 +1,2 @@
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package/dist/chunks/AddTrackWorkflow-ZKAN5JYJ.js.map

@@ -0,0 +1,7 @@
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+}

package/dist/chunks/GbzBaseSyntenyAdapter-RLEI3RDF.js

@@ -0,0 +1,2 @@
+import{a as H,b as ae,c as fe,d as re}from"./chunk-W7UGHWWS.js";import{b as G,c as V,d as te,e as ne}from"./chunk-AHE4Y2TX.js";import{a as E,b as O}from"./chunk-ANYQG5I7.js";import{h as W,i as Z,j as de,k as U,l as u,m as B,n as M,o as F,p as k,q as z,s as X,t as ee}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{e as R,f as P,g as C}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import{b as Y,c as J,d as K}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import{e as j,o as $}from"./chunk-TENPGIPX.js";function A(t){let s=/\.gbz\.db$/i;return s.test(t)?t.replace(s,".haplotype-index.db"):void 0}function he(t){return J(t)&&A(Y(t))?K(t,s=>A(s)):void 0}function ue(t){return t instanceof Error&&(/\bHTTP 40[34]\b/.test(t.message)||t.code==="ENOENT")}async function oe(t,s){let n=he(t);if(!n)return{};try{return await N(n,s).stat(),{location:n}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,q=class extends Error{constructor(n){super(`this GAF is ${(n/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(t,s){if(t.length<=s)return t;let n=t.length/s;return Array.from({length:s},(e,a)=>t[Math.floor(a*n)])}var se=(t,s)=>t.path.some(n=>s.has(n.name)),I=class{constructor(s,n){this.file=s;this.tabix=n;this.whole=G({setup:async({signal:s})=>{let{size:n}=await this.file.stat();if(n>ye)throw new q(n);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await te(e):e);return O(a)}})}async readIndexed(s,n,e){let a=1/0,r=-1/0;for(let c of n){let i=Number(c);Number.isInteger(i)&&(a=Math.min(a,i),r=Math.max(r,i))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let i=E(c);i&&se(i,n)&&o.push(i)}}),o}async readsOver(s,{signal:n}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,n):(await this.whole({signal:n})).filter(a=>se(a,s));return{records:be(e,ge),total:e.length}}};var v=class extends Error{constructor(n){super(n===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${n}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=class extends Error{constructor(n,e){super(`the graph is cut on its reference, ${e}; a window on ${n} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function ie(t,s){let n=u(s);return t[n]??t[s.sample]??n}function we(t,s){return`${u(t)}#${t.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:t,assemblyName:s,refName:n,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=t;if(!(!t.resolved||r<=a)){let{name:i,hapStart:p,hapEnd:d}=t,f=we(i,t),g={uniqueId:f,assemblyName:s,refName:n,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:i.contig,start:p,end:d,assemblyName:e}};return new H(g)}}function Se({pair:t,lane:s,mateLane:n}){let e=`${u(t.target)}#${t.target.contig}:${t.targetStart}-${t.targetEnd}|${u(t.query)}#${t.query.contig}:${t.queryStart}-${t.queryEnd}`;return new H({uniqueId:e,assemblyName:s,refName:t.target.contig,start:t.targetStart,end:t.targetEnd,type:"match",strand:t.strand==="-"?-1:1,CIGAR:t.cigar,syntenyId:e,identity:t.matches/Math.max(t.columns,1),numMatches:t.matches,blockLen:t.columns,mate:{refName:t.query.contig,start:t.queryStart,end:t.queryEnd,assemblyName:n}})}var Pe=12e4;function Ne(t,s){let n=new Map;for(let a of t)for(let{name:r,start:o,end:c}of a.walkSpans()){let i=u(r);if(s.has(i)){let p=`${i}#${r.contig}`;n.set(p,[...n.get(p)??[],[o,c]])}}let e=0;for(let a of n.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(t,s){return t instanceof U&&(t.message=`Zoom in to about ${j(t.fitsBp)} to see ${s}`),t}var ce=t=>({...t,start:Math.floor(t.start),end:Math.ceil(t.end)}),_=t=>!("uri"in t)||t.uri!=="",D=class extends ae{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let n=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=_(e)?{location:e}:await oe(n,this.pluginManager),r=a.location,o=await Z.open({source:N(n,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 i=await M(o),p=F({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:i});return{db:o,anchor:c,referenceSample:p,referenceSamples:i,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let n=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return _(n)?new I(N(n,this.pluginManager),_(e)?ne(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(n,e){let{db:a,referenceSample:r}=await this.graph(e);return k(a,r,n)}async getHaplotypes(n={}){let{db:e,referenceSamples:a}=await 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this.graph(e),{assemblyName:r,refName:o,start:c,end:i}=n,p=P(this,e.targetAssemblyName),d=C(this),f=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${i.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:i,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(l=>{throw T(z(l,y,i-c)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?xe({alignment:l,assemblyName:r,refName:o,lane:ie(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(n,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:i}=n,d=(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),f=new Set(d.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await 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+//# sourceMappingURL=GbzBaseSyntenyAdapter-RLEI3RDF.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-RLEI3RDF.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FLFBYSJO.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      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  return { refName: m[1], start: n(m[2]), end: n(m[3]) };\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${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 { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { 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 {\n  NoReferenceSampleError,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\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 */\nexport interface 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'\nexport type GbzFeatureOptions = LaneFeatureOptions\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 ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix. The fallback stays at\n * haplotype depth, unlike the multi-genome PAF adapters', because a diploid\n * sample's two walks are two lanes here.\n */\nexport function laneAssemblyName(\n  asmByPrefix: Record<string, string>,\n  name: Pick<PathName, 'sample' | 'haplotype'>,\n) {\n  const prefix = haplotypePrefix(name)\n  return asmByPrefix[prefix] ?? asmByPrefix[name.sample] ?? prefix\n}\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: HaplotypeAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: HaplotypeAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (!alignment.resolved || refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${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        byPath.set(key, [...(byPath.get(key) ?? []), [start, end]])\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\nconst isSet = (location: FileLocation) =>\n  !('uri' in location) || location.uri !== ''\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 = isSet(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),\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 isSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            isSet(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: GbzFeatureOptions) {\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(asmByPrefix, alignment.name),\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: GbzFeatureOptions,\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: GbzFeatureOptions = {}) {\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", "laneAssemblyName", "asmByPrefix", "name", "prefix", "haplotypePrefix", "fragmentId", "alignment", "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", "key", "widest", "spans", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "wholeBp", "region", "isSet", "location", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "assemblyByPanSNPrefix", "lanes", "haplotype", "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/{GraphGenomeView-MKMBVOOJ.js → GraphGenomeView-NFC2XO4Z.js}

@@ -1,4 +1,4 @@
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package/dist/chunks/{GraphGenomeView-MKMBVOOJ.js.map → GraphGenomeView-NFC2XO4Z.js.map}

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   "sources": ["../../src/GraphGenomeView/components/GraphLoadStatus.tsx", "../../src/GraphGenomeView/components/ImportForm.tsx", "../../src/GraphGenomeView/components/GraphGenomeView.tsx"],
   "sourcesContent": ["import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs, and after a\n// load of a source it can retry was canceled or failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (model.isLoading) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses variant=\"h6\" message={model.statusMessage} />\n          <Button\n            size=\"small\"\n            data-testid=\"graph-genome-cancel\"\n            onClick={() => {\n              model.cancelLoad()\n            }}\n          >\n            Cancel\n          </Button>\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    const uri = url.trim()\n    if (uri) {\n      void model.loadGFAFromLocation({ uri, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    // or picking the same file again fires no change\n    event.target.value = ''\n    if (file) {\n      file\n        .text()\n        .then(text => model.loadGFA(text, file.name))\n        .catch((err: unknown) => {\n          model.setError(err)\n        })\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleUrlLoad()\n            }}\n            disabled={!url.trim()}\n          >\n            Open\n          </Button>\n        </div>\n      </div>\n\n      <div className={classes.footer}>\n        <Button\n          size=\"small\"\n          onClick={() => {\n            void model.loadGFA(EXAMPLE_GFA, 'Example graph')\n          }}\n        >\n          Load 4-node example\n        </Button>\n      </div>\n\n      {model.error ? <ErrorBanner error={model.error} /> : null}\n    </Paper>\n  )\n})\n\nexport default ImportForm\n", "import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphPaneModel } from '../model'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it when that source fails\n  if (model.canRetryLoad && (model.error || model.loadCanceled)) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n"],
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 }

package/dist/chunks/{GraphTrackSettingsDialog-ZDCUPUUR.js → GraphTrackSettingsDialog-TTF52EZ2.js}

@@ -1,6 +1,6 @@
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 `)||(e.setSubgraphHaplotypes(p),e.cut())};return a(f,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:t,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:p=>{o(p.target.value)},onBlur:()=>{r()},onKeyDown:p=>{p.key==="Enter"&&r()}})}),P=i(function({model:e,names:t}){let[o,r]=c(e.chosenHaplotypes??[]),[p,d]=c(!1),y=l=>{l.join(`
 `)!==(e.chosenHaplotypes??[]).join(`
 `)&&(e.setSubgraphHaplotypes(l),e.cut())};return a(g,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:t,value:o,open:p,onOpen:()=>{d(!0)},onClose:()=>{d(!1),y(o)},onChange:(l,m)=>{r(m),p||y(m)},renderInput:l=>a(f,{...l,label:"Haplotypes",placeholder:o.length===0?"every haplotype":void 0,slotProps:{...l.slotProps,htmlInput:{...l.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),I=i(function({model:e}){let{classes:t}=F(),o=e.haplotypeNames,r=e.chosenHaplotypes?.join(",")??"";return H(e.adapterConfig)?s("div",{className:t.section,children:[o?a(P,{model:e,names:o},r):a(N,{model:e},r),s(h,{variant:"caption",color:"text.secondary",children:[o?`The haplotypes the cut is for, of the graph's ${o.length.toLocaleString()}, or a PanSN prefix typed and entered (HG002 for both of its haplotypes).`:"The haplotypes the cut is for, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both), separated by commas."," ","The cut keeps their walks and the nodes those walks visit, with the reference. Empty is every haplotype."]})]}):null}),k=I;function D({model:n,open:e,onClose:t}){return s(x,{model:n,open:e,onClose:t,children:[a(G,{model:n}),a(k,{model:n})]})}export{D as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-ZDCUPUUR.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-TTF52EZ2.js.map

package/dist/chunks/{HighlightColorDialog-OYQBBJW5.js → HighlightColorDialog-6B3HM5K5.js}

@@ -1,2 +1,2 @@
-import{o as v,p as C}from"./chunk-IJAG73UX.js";import"./chunk-M6QFGGKW.js";import"./chunk-6RG24DCP.js";import"./chunk-NSPHIJRY.js";import{E as g,G as t,c as u,n as y,p as c,q as d,y as s}from"./chunk-ECD5B2ZM.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
-//# sourceMappingURL=HighlightColorDialog-OYQBBJW5.js.map
+import{o as v,p as C}from"./chunk-RDMX5TUB.js";import"./chunk-BHWFRHIB.js";import"./chunk-D257CI4F.js";import"./chunk-E2GK6JEL.js";import{E as g,G as t,c as u,n as y,p as c,q as d,y as s}from"./chunk-ECD5B2ZM.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
+//# sourceMappingURL=HighlightColorDialog-6B3HM5K5.js.map

package/dist/chunks/LinearGraphDisplay-77UBGSWR.js

@@ -0,0 +1,2 @@
+import{a as g}from"./chunk-P7JWWI3F.js";import"./chunk-LLAHUPEG.js";import"./chunk-Y3C2W4GA.js";import"./chunk-EJSTB4U6.js";import"./chunk-KRND5VBT.js";import"./chunk-KYNMYJME.js";import"./chunk-RDMX5TUB.js";import"./chunk-BHWFRHIB.js";import"./chunk-7ANVPYX5.js";import"./chunk-ANYQG5I7.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import"./chunk-E2GK6JEL.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{g as T}from"./chunk-6OPB7FOJ.js";import"./chunk-ECD5B2ZM.js";import{b as e,c as l,d as y}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var v=s&&s.__esModule?s.default:s;var a=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var h=a&&a.__esModule?a.default:a;var i=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=i&&i.__esModule?i.default:i;var n=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var f=n&&n.__esModule?n.default:n;var t=JBrowseExports["@jbrowse/display-ui"],p=r=>t!=null&&r in Object(t)?t[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=p("BottomRightCornerContext");var c=p("TrackOverlayPortal");var L=p("useChromeOverlayOverride");var j=t&&t.__esModule?t.default:t;var D={TooLarge:f,ErrorBar:h,Loading:O,BackgroundProgress:v};function d({model:r,phase:o,drawn:u,testid:_,style:C,children:E,...B}){let{TooLarge:G,ErrorBar:S,Loading:m,BackgroundProgress:P}=L()??D,[b,A]=T(null),{displayId:x}=r.configuration;return o==="tooLarge"?e("div",{style:{display:"contents"},"data-display-id":x,"data-display-phase":o,children:e(c,{children:e("div",{style:{pointerEvents:"auto"},children:e(G,{model:r})})})}):l("div",{...B,style:{position:"relative",height:r.height,...C},"data-testid":_,"data-display-id":x,"data-display-drawn":u,"data-display-phase":o,children:[e(w,{value:b,children:E}),l(c,{children:[e(S,{model:r,visible:o==="error"}),e(m,{model:r,visible:o==="loading"||o==="canceled",immediate:!u}),e("div",{ref:A,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:e(P,{model:r,visible:o==="ready"})})]})]})}var I=y(function({model:o}){return e(d,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(g,{model:o,ownChrome:!1})})}),Q=I;export{Q as default};
+//# sourceMappingURL=LinearGraphDisplay-77UBGSWR.js.map

package/dist/chunks/{LinearGraphDisplay-4UOSXTZS.js.map → LinearGraphDisplay-77UBGSWR.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["host:@jbrowse/display-kit/DisplayBackgroundProgress", "host:@jbrowse/display-kit/DisplayErrorBar", "host:@jbrowse/display-kit/DisplayLoadingOverlay", "host:@jbrowse/display-kit/TooLargeMessage", "host:@jbrowse/display-ui", "../../src/LinearGraphDisplay/components/GraphStatusChrome.tsx", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
   "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/DisplayBackgroundProgress\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayBackgroundProgress\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayErrorBar\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayErrorBar\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayLoadingOverlay\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayLoadingOverlay\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/TooLargeMessage\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/TooLargeMessage\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-ui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-ui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const AXIS_GUTTER_WIDTH_PX = /* @__PURE__ */ read(\"AXIS_GUTTER_WIDTH_PX\")\nexport const AXIS_RIGHT_INSET_PX = /* @__PURE__ */ read(\"AXIS_RIGHT_INSET_PX\")\nexport const AxisCaption = /* @__PURE__ */ read(\"AxisCaption\")\nexport const AxisCaptionOverlay = /* @__PURE__ */ read(\"AxisCaptionOverlay\")\nexport const AxisGutter = /* @__PURE__ */ read(\"AxisGutter\")\nexport const BOTTOM_RIGHT_CONTROLS_ORDER = /* @__PURE__ */ read(\"BOTTOM_RIGHT_CONTROLS_ORDER\")\nexport const BottomRightCornerContext = /* @__PURE__ */ read(\"BottomRightCornerContext\")\nexport const COMPACT_AXIS_HEIGHT = /* @__PURE__ */ read(\"COMPACT_AXIS_HEIGHT\")\nexport const CrossHatchLines = /* @__PURE__ */ read(\"CrossHatchLines\")\nexport const CrossHatches = /* @__PURE__ */ read(\"CrossHatches\")\nexport const DEFAULT_RULE_COLOR = /* @__PURE__ */ read(\"DEFAULT_RULE_COLOR\")\nexport const DisplayChromeOverlayProvider = /* @__PURE__ */ read(\"DisplayChromeOverlayProvider\")\nexport const DisplayUIProvider = /* @__PURE__ */ read(\"DisplayUIProvider\")\nexport const FLOATING_LEGEND_RIGHT_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_RIGHT_PX\")\nexport const FLOATING_LEGEND_TOP_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_TOP_PX\")\nexport const FloatingLegend = /* @__PURE__ */ read(\"FloatingLegend\")\nexport const FloatingSvgOverlay = /* @__PURE__ */ read(\"FloatingSvgOverlay\")\nexport const FloatingText = /* @__PURE__ */ read(\"FloatingText\")\nexport const PointerLayer = /* @__PURE__ */ read(\"PointerLayer\")\nexport const SCORE_CAPTION_HEIGHT = /* @__PURE__ */ read(\"SCORE_CAPTION_HEIGHT\")\nexport const ScoreDomainCaption = /* @__PURE__ */ read(\"ScoreDomainCaption\")\nexport const ScoreRuleLines = /* @__PURE__ */ read(\"ScoreRuleLines\")\nexport const ScoreRules = /* @__PURE__ */ read(\"ScoreRules\")\nexport const SvgHaloText = /* @__PURE__ */ read(\"SvgHaloText\")\nexport const TEXT_BASELINE_RATIO = /* @__PURE__ */ read(\"TEXT_BASELINE_RATIO\")\nexport const Tooltip = /* @__PURE__ */ read(\"Tooltip\")\nexport const TrackControlProvider = /* @__PURE__ */ read(\"TrackControlProvider\")\nexport const TrackOverlayContext = /* @__PURE__ */ read(\"TrackOverlayContext\")\nexport const TrackOverlayPortal = /* @__PURE__ */ read(\"TrackOverlayPortal\")\nexport const TrackOverlaySlot = /* @__PURE__ */ read(\"TrackOverlaySlot\")\nexport const YSCALEBAR_LABEL_OFFSET = /* @__PURE__ */ read(\"YSCALEBAR_LABEL_OFFSET\")\nexport const YScaleBar = /* @__PURE__ */ read(\"YScaleBar\")\nexport const YScaleBarOverlay = /* @__PURE__ */ read(\"YScaleBarOverlay\")\nexport const axisDrawn = /* @__PURE__ */ read(\"axisDrawn\")\nexport const axisGutterLeft = /* @__PURE__ */ read(\"axisGutterLeft\")\nexport const axisGutterWidth = /* @__PURE__ */ read(\"axisGutterWidth\")\nexport const axisPlotBox = /* @__PURE__ */ read(\"axisPlotBox\")\nexport const clampStrokeInsideAxis = /* @__PURE__ */ read(\"clampStrokeInsideAxis\")\nexport const cullOverlappingLabels = /* @__PURE__ */ read(\"cullOverlappingLabels\")\nexport const formatScore = /* @__PURE__ */ read(\"formatScore\")\nexport const isLiveModel = /* @__PURE__ */ read(\"isLiveModel\")\nexport const leftAxisGutterWidth = /* @__PURE__ */ read(\"leftAxisGutterWidth\")\nexport const plainChromeOverlays = /* @__PURE__ */ read(\"plainChromeOverlays\")\nexport const plainTrackControl = /* @__PURE__ */ read(\"plainTrackControl\")\nexport const resolveOverlays = /* @__PURE__ */ read(\"resolveOverlays\")\nexport const scoreToAxisY = /* @__PURE__ */ read(\"scoreToAxisY\")\nexport const textHalo = /* @__PURE__ */ read(\"textHalo\")\nexport const tooLargeBannerText = /* @__PURE__ */ read(\"tooLargeBannerText\")\nexport const useChromeOverlayOverride = /* @__PURE__ */ read(\"useChromeOverlayOverride\")\nexport const useTooltip = /* @__PURE__ */ read(\"useTooltip\")\nexport const useTrackControlMenu = /* @__PURE__ */ read(\"useTrackControlMenu\")\nexport const useTrackControlOverride = /* @__PURE__ */ read(\"useTrackControlOverride\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\nimport type { CSSProperties, ReactNode } from 'react'\n\nimport DisplayBackgroundProgress from '@jbrowse/display-kit/DisplayBackgroundProgress'\nimport DisplayErrorBar from '@jbrowse/display-kit/DisplayErrorBar'\nimport DisplayLoadingOverlay from '@jbrowse/display-kit/DisplayLoadingOverlay'\nimport TooLargeMessage from '@jbrowse/display-kit/TooLargeMessage'\nimport {\n  BottomRightCornerContext,\n  TrackOverlayPortal,\n  useChromeOverlayOverride,\n} from '@jbrowse/display-ui'\n\nimport type { LinearGraphDisplayModel } from '../model'\nimport type { DisplayStatusPhase } from '@jbrowse/render-core/displayPhase'\n\nconst muiOverlays = {\n  TooLarge: TooLargeMessage,\n  ErrorBar: DisplayErrorBar,\n  Loading: DisplayLoadingOverlay,\n  BackgroundProgress: DisplayBackgroundProgress,\n}\n\n/**\n * The status chrome of a display that owns its canvas: the zoom-in notice in\n * place of the display, and the error bar, loading overlay and progress chip\n * over it in the track's overlay layer. Core's `DisplayStatusChrome` drew this\n * until jbrowse-web main removed it on 2026-10-08 (d8db736896), and its named\n * import came back undefined there, failing the track with React error #130.\n * Built here from the overlays every host from 5.0.0-beta.11 serves.\n */\nexport default function GraphStatusChrome({\n  model,\n  phase,\n  drawn,\n  testid,\n  style,\n  children,\n  ...dataProps\n}: {\n  model: LinearGraphDisplayModel\n  phase: DisplayStatusPhase\n  drawn: boolean\n  testid: string\n  style?: CSSProperties\n  children: ReactNode\n} & Record<`data-${string}`, unknown>) {\n  const { TooLarge, ErrorBar, Loading, BackgroundProgress } =\n    useChromeOverlayOverride() ?? muiOverlays\n  const [corner, setCorner] = useState<HTMLDivElement | null>(null)\n  const { displayId } = model.configuration\n  if (phase === 'tooLarge') {\n    return (\n      <div\n        style={{ display: 'contents' }}\n        data-display-id={displayId}\n        data-display-phase={phase}\n      >\n        <TrackOverlayPortal>\n          <div style={{ pointerEvents: 'auto' }}>\n            <TooLarge model={model} />\n          </div>\n        </TrackOverlayPortal>\n      </div>\n    )\n  }\n  return (\n    <div\n      {...dataProps}\n      style={{ position: 'relative', height: model.height, ...style }}\n      data-testid={testid}\n      data-display-id={displayId}\n      data-display-drawn={drawn}\n      data-display-phase={phase}\n    >\n      <BottomRightCornerContext value={corner}>\n        {children}\n      </BottomRightCornerContext>\n      <TrackOverlayPortal>\n        <ErrorBar model={model} visible={phase === 'error'} />\n        <Loading\n          model={model}\n          visible={phase === 'loading' || phase === 'canceled'}\n          immediate={!drawn}\n        />\n        <div\n          ref={setCorner}\n          style={{\n            position: 'absolute',\n            bottom: 2,\n            right: 2,\n            display: 'flex',\n            flexDirection: 'column',\n            alignItems: 'flex-end',\n            gap: 4,\n            pointerEvents: 'none',\n          }}\n        >\n          <BackgroundProgress model={model} visible={phase === 'ready'} />\n        </div>\n      </TrackOverlayPortal>\n    </div>\n  )\n}\n", "import { observer } from 'mobx-react'\n\nimport GraphStatusChrome from './GraphStatusChrome'\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <GraphStatusChrome\n      model={model}\n      phase={model.displayPhase}\n      drawn={model.painted && model.geometryPainted}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      <GraphCanvas model={model} ownChrome={false} />\n    </GraphStatusChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
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+import{a as u,b as P,c as O}from"./chunk-O5GO45MS.js";import{a as B,c as I,e as R,f as v}from"./chunk-AHE4Y2TX.js";import{t as T}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{c as F,f as M}from"./chunk-E2GK6JEL.js";import"./chunk-OGQ6OQDN.js";import{a as $,o as A}from"./chunk-TENPGIPX.js";function y(i){let e=i.split("	"),a=e.length>=8,r=a?5:0;return{anchored:a,segment:{refName:e[r],start:+e[r+1],end:+e[r+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function G(i){let e=i.tags.split(" ").find(r=>r.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(r=>r.trim()).filter(Boolean);return a.length>0?a:void 0}function W(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function w(i){let e=i.split("	"),a=W(e[3]),r=W(e[4]);return{source:a.id,sourceStrand:a.strand,target:r.id,targetStrand:r.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:r.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let r=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),s=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||r(n.sourceSegment)*r(n.targetSegment)===-1){s.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&s.set(S(n),n);return{segments:t,links:s}}function H(i,e,a){let r=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...j(i.filter(t=>t.rank>0),e,a.end-a.start),...j(i.filter(t=>t.rank===0&&r(t)),new Set(i.map(t=>t.id)),0)]}function j(i,e,a){let r=[...i].sort((s,n)=>b(s.refName,n.refName)||s.start-n.start),t=[];for(let s of r){let n=t.at(-1);n?.refName===s.refName&&s.start-n.end<=a?(n.needed||=s.start>n.end||e.has(s.id),n.end=Math.max(n.end,s.end)):t.push({refName:s.refName,start:s.start,end:s.end,needed:e.has(s.id)})}return t.filter(s=>s.needed).map(({refName:s,start:n,end:o})=>({refName:s,start:n,end:o}))}function _(i,e,a){let r=t=>e.has(t.id)||a.some(s=>s.refName===t.refName&&t.start>=s.start&&t.end<=s.end);return i.filter(t=>r(t.sourceSegment)&&r(t.targetSegment))}var K=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function z(i){let{id:e,refName:a,start:r,end:t,rank:s,tags:n}=i,o=n.split(" ").filter(f=>K.test(f)),c=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-r}	SN:Z:${a}	SO:i:${r}	SR:i:${s}${c}`}function J(i){let{source:e,sourceStrand:a,target:r,targetStrand:t}=i;return`L	${e}	${a}	${r}	${t}	0M`}function b(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,s)=>b(t.refName,s.refName)||t.start-s.start||b(t.id,s.id)),r=[...e.keys()].sort((t,s)=>b(t,s));return["H	VN:Z:1.0",...a.map(t=>z(t)),...r.map(t=>J(e.get(t)))].join(`
+`)}function D(i){return i.filter(e=>e.rank>0)}var V=1e3,C=class extends B{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,a,r){super(e,a,r),this.fine=this.openIndex([])}openIndex(e){let a=R(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),r=this.getConf("walksLocation"),t=e.length===0&&(!("uri"in r)||r.uri!==""),s=R(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:s,walks:t?new O({walks:R(this,["walksLocation"],["walksIndex"]),nodes:a,links:s},this.getConf("walkChunk")):void 0,refNames:new v(a,this)}}async getHaplotypeNames(e={}){let a=await this.fine.walks?.header(e);return a?.haplotypes.length?a.haplotypes:void 0}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,a={}){let{signal:r,statusCallback:t}=a;return I(async s=>{let n=await this.fine.refNames.resolve(e,a);if(n!==void 0){let o=this.fine.walks?await this.fine.walks.queryStart(e.start,a):e.start;await A("Downloading segments",t,()=>u(this.fine.segments,n,o,e.end,{signal:r,lineCallback:c=>{let{segment:f,anchored:h}=y(c);if(h&&f.refName!==n)return;let l=G(f);s.next(new $({uniqueId:f.id,refName:e.refName,start:f.start,end:f.end,name:f.id,type:"segment",rank:f.rank,stableName:f.refName,...l&&{samples:l,sampleCount:l.length}}))}}))}s.complete()},r)}async getSubgraph(e,a={}){let{hops:r=0,signal:t,tier:s}=a,n=this.index(s),o=new Map,c=new Map,f=await n.refNames.resolve(e,{signal:t}),h=async(p,m,g)=>{let d=[];return await u(n.links,p,m,g,{signal:t,lineCallback:E=>{let k=w(E);c.set(S(k),k);for(let N of[k.sourceSegment,k.targetSegment])o.has(N.id)||(o.set(N.id,N),d.push(N))}}),d};if(f===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);if(n.walks)return this.walkSubgraph(n.walks,f,e,a);let l={anchored:!1};if(await u(n.segments,f,e.start,e.end,{signal:t,lineCallback:p=>{let m=y(p);l.anchored||=m.anchored,o.set(m.segment.id,m.segment)}}),l.anchored){let p=[];await u(n.links,f,e.start,e.end,{signal:t,lineCallback:g=>{p.push(w(g))}});let m=Z(o,p,{refName:f,start:e.start,end:e.end});return L(m.segments,m.links)}let x=D(await h(f,e.start,e.end));for(let p=0;p<r;p++){let m=await Promise.all(x.map(g=>h(g.refName,g.start,g.end)));x=D(m.flat())}if(r>0){let p=H([...o.values()],new Set(x.map(g=>g.id)),{refName:f,start:e.start,end:e.end}),m=[];await Promise.all(p.map(g=>u(n.links,g.refName,g.start,g.end,{signal:t,lineCallback:d=>{m.push(w(d))}})));for(let g of _(m,o,p)){c.set(S(g),g);for(let d of[g.sourceSegment,g.targetSegment])o.has(d.id)||o.set(d.id,d)}}return L(o,c)}async walkSubgraph(e,a,r,t){let{graph:s,kept:n,fragments:o}=await e.cut(a,r,{signal:t.signal,keep:P(t.haplotypes?.map(c=>M(this,c)),F(a)),stepBudget:t.walkRows?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:V});return T(s.tables(n,o),r,t.walkRows)}};export{C as default};
+//# sourceMappingURL=RgfaTabixAdapter-Q2URYHKT.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-RXTCCCDB.js

@@ -0,0 +1,2 @@
+import{b as O,c as D}from"./chunk-O5GO45MS.js";import{a as _,b as q,d as j}from"./chunk-W7UGHWWS.js";import{c as v,e as x,f as T}from"./chunk-AHE4Y2TX.js";import{f as C,g as L,k as $,t as I}from"./chunk-BPN3IL3K.js";import"./chunk-WAGGHKBL.js";import"./chunk-D257CI4F.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-E2GK6JEL.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import{o as R}from"./chunk-TENPGIPX.js";var Y=50;function Z(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=Y&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function ee(i){return i.map(([e,t])=>`${t}${e}`).join("")}function H(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>L({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var te=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function X(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,g]=C(o,n,e),[f,l]=C(o.map(b=>b^1).reverse(),n,e),u=l>g,c=u?f:p,d=Math.max(g,l);if(d<te)return[];let h=t(n),m=t(o),y=b=>u?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[U,J]=[y(k-1),y(k)].sort((Q,V)=>Q-V);E(w,"I",m[J]-m[U+1]),E(w,"D",h[b]-h[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[z,K]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[z],queryEnd:m[K+1],targetStart:h[c[0][1]],targetEnd:h[c.at(-1)[1]+1],strand:u?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,g=t.hapStart+i.queryEnd,f=Z(i.edits),l=f.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=f.reduce((d,[,h])=>d+h,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${g}`;return new _({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:ee(f),syntenyId:c,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:F(t.name),start:p,end:g,assemblyName:a}})}var ae=1e3;function G(i,e){return i[e]??i[S(e)]??e}var ne=i=>P(i.name)??i.name,B=class extends q{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new D({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new T(s,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:G(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(e){return{stepBudget:e?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:ae}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:a}=t,n=await this.refNames.resolve(e,{signal:r});if(n===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:o,kept:p,fragments:g}=await this.reader.cut(n,e,{...this.budgets(a),signal:r,keep:O(s?.map(f=>N(this,f)),P(n))});return I(o.tables(p,g),e,a)}async laneWalks(e,t,r,s,a){return R(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:O(r,P(e)),links:!1}).catch(n=>{throw n instanceof $&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:g,fragments:f}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=X(g.nodes),u=W(this),c=f.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return f.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:G(u,ne(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),g=H(o.nodes),f=l=>p.filter(u=>A(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:c})=>f(u).flatMap(d=>f(c).flatMap(h=>g(h,d).map(m=>M({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=j(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,G as laneOf};
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