jbrowse-plugin-graphgenomeviewer 7.6.0 → 8.0.0

package/dist/chunks/{WalkTabixSyntenyAdapter-JFNFX3JP.js → WalkTabixSyntenyAdapter-62PJZBRP.js}

@@ -1,2 +1,2 @@
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this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(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}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks 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G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends ${constructor(){super(...arguments);this.walks=new K(D(this,["walksLocation"],["walksIndex"]),this);this.refNames=new H(this.walks.file,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={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(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}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),h=c.filter(m=>m.name===e),d=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&d(m)>=0).sort((m,b)=>d(m)-d(b)).flatMap(m=>h.flatMap(b=>p(m,b).map(P=>C({chain:P,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(h=>f(N).flatMap(d=>u(d,h).map(y=>C({chain:y,target:h,query:d,assemblyName:c.queryAssemblyName,refName:W(h.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return q(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 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+//# sourceMappingURL=WalkTabixSyntenyAdapter-62PJZBRP.js.map

package/dist/chunks/chunk-26SCNTI3.js

@@ -0,0 +1,2 @@
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Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,h)=>p!==void 0&&p>0?[c[h]===void 0?{bp:p}:{bp:p,spanningReads:c[h]}]:[]),f=u.length>0||!t?u:K(N(a.GT)[0],t,n);f.length>0&&(o[s]=f)}return Object.keys(o).length>0?o:void 0}function Y(e,t){let n=d(e,"start"),r=d(e,"end"),o=m(d(e,"SVLEN"))[0];return t&&o!==void 0?{start:n+1,end:n+1+o}:{start:n,end:r}}function en(e){let t=[];for(let n of e){let r=W(n),{start:o,end:s}=Y(n,r!==void 0),a=V(n);if(!(s>o)||a===void 0)continue;let c=d(n,"refName"),u=y(n,M),f=y(n,j);t.push({key:`${c}:${o}-${s}`,name:(f&&!D.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(o+1).toLocaleString("en-US")}-${s.toLocaleString("en-US")}`),refName:c,start:o,end:s,unit:a,motif:u,calls:q(n,r,s-o)})}return t.sort((n,r)=>n.start-r.start)}function k(e){let t=[];for(let n of[...e].sort((r,o)=>r.start-o.start)){let r=t.at(-1);r&&n.start<=r.end?r.end=Math.max(r.end,n.end):t.push({...n})}return t}function E(e){let t=[],n=new Map;for(let r of[...e].sort((o,s)=>o.start-s.start)){let o=`${r.refName}	${r.strand}	${r.name}`,s=n.get(o);if(s&&r.start<s.end)s.end=Math.max(s.end,r.end),s.exons=k([...s.exons,...r.exons]);else{let a={...r,exons:k(r.exons)};t.push(a),n.set(o,a)}}return t}var J=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),z=/gene|refseq|gencode|ensembl|annotation/i,X=new Set(["BedTabixAdapter","BedAdapter"]);function mn(e,t){let n=t?T(e,t):void 0;if(n)return n;let r=e.filter(o=>J.has(o.adapterType)&&!R.test(g(o)));return r.find(o=>z.test(g(o)))??r.find(o=>!X.has(o.adapterType))}var Q=/\bTEs?\b|transpos/i;function ln(e){return e&&Q.test(g(e))?"TE":"gene"}function gn(e,t){let n=e.tracks?.find(r=>A(r.configuration,"trackId")===t)?.displays[0];return n?A(n.configuration,"filter")??[]:[]}var Z=new Set(["chromosome","region","contig","supercontig","scaffold"]),ee=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function $(e,t){let n=i(e,"type");typeof n=="string"&&ee.has(n)&&t.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let o of r??[])$(o,t)}function hn(e){let t=[];for(let n of e){let r=i(n,"gene_name")??i(n,"name")??i(n,"gene")??i(n,"gene_id"),o=i(n,"start"),s=i(n,"end");if(!r||!(s>o)||Z.has(i(n,"type")))continue;let a=[];$(n,a),t.push({name:r,refName:i(n,"refName"),start:o,end:s,strand:i(n,"strand")??0,exons:a.length?k(a):[{start:o,end:s}]})}return E(t)}var l=JBrowseExports["tss-react/mui"],ne=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var Tn=ne("makeStyles"),yn=l&&l.__esModule?l.default:l;export{oe as a,P as b,se as c,ie as d,ae as e,ce as f,ue as g,U as h,Ze as i,en as j,J as k,mn as l,ln as m,gn as n,hn as o,Tn as p};
+//# sourceMappingURL=chunk-26SCNTI3.js.map

package/dist/chunks/chunk-26SCNTI3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\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 '\" + \"tss-react/mui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
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+}

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+  "sourcesContent": ["// src/layout/rowSpacing.ts\nvar ROW_HEIGHT_PX = 20;\n\nexport {\n  ROW_HEIGHT_PX\n};\n", "import {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\n\n// src/util/geometry.ts\nfunction svgPath(points) {\n  const round = (v) => Math.round(v * 100) / 100;\n  return points.map((p, i) => `${i ? \"L\" : \"M\"}${round(p.x)},${round(p.y)}`).join(\"\");\n}\nfunction projectLine(x1, y1, x2, y2, distance) {\n  const d = Math.hypot(y2 - y1, x2 - x1);\n  if (d === 0) {\n    return [x2, y2];\n  }\n  const vx = (x2 - x1) / d;\n  const vy = (y2 - y1) / d;\n  return [x2 + distance * vx, y2 + distance * vy];\n}\nfunction curvePointAt(c, t) {\n  const u = 1 - t;\n  const a = u * u * u;\n  const b = 3 * u * u * t;\n  const d = 3 * u * t * t;\n  const e = t * t * t;\n  return {\n    x: a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1,\n    y: a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1\n  };\n}\nfunction curveMidpoint(curves) {\n  const mid = curves[Math.floor(curves.length / 2)];\n  return mid ? curvePointAt(mid, 0.5) : void 0;\n}\nfunction curveBounds(curves) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const c of curves) {\n    minX = Math.min(minX, c.x0, c.cx0, c.cx1, c.x1);\n    maxX = Math.max(maxX, c.x0, c.cx0, c.cx1, c.x1);\n    minY = Math.min(minY, c.y0, c.cy0, c.cy1, c.y1);\n    maxY = Math.max(maxY, c.y0, c.cy0, c.cy1, c.y1);\n  }\n  return { minX, minY, maxX, maxY };\n}\nfunction subCurve(c, t0, t1) {\n  const p0 = curvePointAt(c, t0);\n  const p1 = curvePointAt(c, t1);\n  const dt = (t1 - t0) / 3;\n  const d0 = curveTangentAt(c, t0);\n  const d1 = curveTangentAt(c, t1);\n  return {\n    x0: p0.x,\n    y0: p0.y,\n    cx0: p0.x + d0.x * dt,\n    cy0: p0.y + d0.y * dt,\n    cx1: p1.x - d1.x * dt,\n    cy1: p1.y - d1.y * dt,\n    x1: p1.x,\n    y1: p1.y\n  };\n}\nfunction curveTangentAt(c, t) {\n  const u = 1 - t;\n  const a = 3 * u * u;\n  const b = 6 * u * t;\n  const d = 3 * t * t;\n  return {\n    x: a * (c.cx0 - c.x0) + b * (c.cx1 - c.cx0) + d * (c.x1 - c.cx1),\n    y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)\n  };\n}\nvar VISIBLE_SAMPLES = 32;\nfunction visibleStretches(curves, lengths, bounds, yToX) {\n  const stretches = [];\n  let start = 0;\n  curves.forEach((c, k) => {\n    const length = lengths[k];\n    const pad = length / VISIBLE_SAMPLES;\n    let last = curvePointAt(c, 0);\n    for (let i = 1; i <= VISIBLE_SAMPLES; i++) {\n      const next = curvePointAt(c, i / VISIBLE_SAMPLES);\n      if (Math.max(last.x, next.x) + pad >= bounds.minX && Math.min(last.x, next.x) - pad <= bounds.maxX && Math.max(last.y, next.y) + pad / yToX >= bounds.minY && Math.min(last.y, next.y) - pad / yToX <= bounds.maxY) {\n        const from = start + length * (i - 1) / VISIBLE_SAMPLES;\n        const to = start + length * i / VISIBLE_SAMPLES;\n        const prev = stretches.at(-1);\n        if (prev && prev[1] >= from) {\n          prev[1] = to;\n        } else {\n          stretches.push([from, to]);\n        }\n      }\n      last = next;\n    }\n    start += length;\n  });\n  return stretches;\n}\nvar dashCurves = (curves, dashWorld, yToX = 1, bounds) => dashSpans(curves, dashWorld, yToX, bounds).map((d) => d.curves);\nfunction dashSpans(curves, dashWorld, yToX = 1, bounds) {\n  const lengths = curves.map(\n    (c) => Math.hypot(c.cx0 - c.x0, (c.cy0 - c.y0) * yToX) + Math.hypot(c.cx1 - c.cx0, (c.cy1 - c.cy0) * yToX) + Math.hypot(c.x1 - c.cx1, (c.y1 - c.cy1) * yToX)\n  );\n  const total = lengths.reduce((a, b) => a + b, 0);\n  const periods = Math.round(total / dashWorld);\n  const spans = Math.max(3, periods % 2 ? periods : periods + 1);\n  const stretches = bounds ? visibleStretches(curves, lengths, bounds, yToX) : void 0;\n  let seen = 0;\n  const out = [];\n  for (let i = 0; i < spans; i += 2) {\n    const from = i / spans * total;\n    const to = (i + 1) / spans * total;\n    if (stretches) {\n      while (seen < stretches.length && stretches[seen][1] < from) {\n        seen++;\n      }\n      if (seen === stretches.length) {\n        break;\n      }\n      if (stretches[seen][0] > to) {\n        continue;\n      }\n    }\n    const dash = [];\n    const along = [];\n    let start = 0;\n    curves.forEach((c, k) => {\n      const length = lengths[k];\n      const end = start + length;\n      if (length > 0 && end > from && start < to) {\n        const t0 = Math.max(0, (from - start) / length);\n        const t1 = Math.min(1, (to - start) / length);\n        dash.push(subCurve(c, t0, t1));\n        along.push((k + t0) / curves.length, (k + t1) / curves.length);\n      }\n      start = end;\n    });\n    if (dash.length) {\n      out.push({\n        curves: dash,\n        startAlong: along[0],\n        endAlong: along.at(-1)\n      });\n    }\n  }\n  return out;\n}\nvar slideAt = (from, to, along) => ({\n  dx: from.dx + (to.dx - from.dx) * along,\n  dy: from.dy + (to.dy - from.dy) * along\n});\nfunction slideCurves(curves, fromDx, fromDy, toDx, toDy) {\n  const n = curves.length;\n  const out = new Array(n);\n  for (let i = 0; i < n; i++) {\n    const c = curves[i];\n    const a = i / n;\n    const b = (i + 1) / n;\n    const adx = fromDx + (toDx - fromDx) * a;\n    const ady = fromDy + (toDy - fromDy) * a;\n    const bdx = fromDx + (toDx - fromDx) * b;\n    const bdy = fromDy + (toDy - fromDy) * b;\n    out[i] = {\n      x0: c.x0 + adx,\n      y0: c.y0 + ady,\n      cx0: c.cx0 + adx,\n      cy0: c.cy0 + ady,\n      cx1: c.cx1 + bdx,\n      cy1: c.cy1 + bdy,\n      x1: c.x1 + bdx,\n      y1: c.y1 + bdy\n    };\n  }\n  return out;\n}\nfunction translateCurves(curves, dx, dy) {\n  const out = new Array(curves.length);\n  for (let i = 0; i < curves.length; i++) {\n    const c = curves[i];\n    out[i] = {\n      x0: c.x0 + dx,\n      y0: c.y0 + dy,\n      cx0: c.cx0 + dx,\n      cy0: c.cy0 + dy,\n      cx1: c.cx1 + dx,\n      cy1: c.cy1 + dy,\n      x1: c.x1 + dx,\n      y1: c.y1 + dy\n    };\n  }\n  return out;\n}\nfunction attachment(segments, side) {\n  const last = segments.length - 1;\n  return side === \"end\" ? { at: segments[last], inward: segments[last - 1] } : { at: segments[0], inward: segments[1] };\n}\nvar TANGENT_SPAN_FACTOR = 0.5;\nvar MAX_TANGENT = 80;\nfunction ownStrand(id) {\n  return id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction strandSides(edge) {\n  const own = (id, strand) => (strand ?? ownStrand(id)) === ownStrand(id);\n  return {\n    from: own(edge.from, edge.fromStrand) ? \"end\" : \"start\",\n    to: own(edge.to, edge.toStrand) ? \"start\" : \"end\"\n  };\n}\nfunction spanOf(segments) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const s of segments) {\n    min = Math.min(min, s.x);\n    max = Math.max(max, s.x);\n  }\n  return { min, max };\n}\nfunction distanceToSpan(x, span) {\n  return Math.max(0, span.min - x, x - span.max);\n}\nfunction facingSide(segments, other, tieBreak) {\n  const startGap = distanceToSpan(segments[0].x, other);\n  const endGap = distanceToSpan(segments[segments.length - 1].x, other);\n  return startGap === endGap ? tieBreak : startGap < endGap ? \"start\" : \"end\";\n}\nfunction facingSides(fromSegments, toSegments) {\n  return {\n    from: facingSide(fromSegments, spanOf(toSegments), \"end\"),\n    to: facingSide(toSegments, spanOf(fromSegments), \"start\")\n  };\n}\nvar laidSides = /* @__PURE__ */ new WeakMap();\nfunction heldFacingSides(fromSegments, toSegments) {\n  let byTo = laidSides.get(fromSegments);\n  if (!byTo) {\n    byTo = /* @__PURE__ */ new WeakMap();\n    laidSides.set(fromSegments, byTo);\n  }\n  let sides = byTo.get(toSegments);\n  if (!sides) {\n    sides = facingSides(fromSegments, toSegments);\n    byTo.set(toSegments, sides);\n  }\n  return sides;\n}\nvar APEX_FRACTION = 0.75;\nvar BOW_CLEARANCE = 1.15;\nvar ALONG_FRACTION = 0.35;\nvar MAX_ROW_BOW_PX = 3 * ROW_HEIGHT_PX;\nfunction bowAround(p1x, p1y, p2x, p2y, toward, maxBow) {\n  const chord = Math.hypot(p2x - p1x, p2y - p1y);\n  const ux = chord === 0 ? 1 : (p2x - p1x) / chord;\n  const uy = chord === 0 ? 0 : (p2y - p1y) / chord;\n  let reach = 0;\n  let minAlong = Infinity;\n  let maxAlong = -Infinity;\n  for (const p of toward) {\n    const dx = p.x - p1x;\n    const dy = p.y - p1y;\n    const perp = dx * -uy + dy * ux;\n    if (Math.abs(perp) > Math.abs(reach)) {\n      reach = perp;\n    }\n    const along = dx * ux + dy * uy;\n    minAlong = Math.min(minAlong, along);\n    maxAlong = Math.max(maxAlong, along);\n  }\n  const span = toward.length ? maxAlong - minAlong : 0;\n  const uncapped = Math.max(\n    Math.abs(reach) * BOW_CLEARANCE / APEX_FRACTION,\n    span * ALONG_FRACTION\n  );\n  const size = maxBow === void 0 ? uncapped : Math.min(uncapped, maxBow);\n  return reach < 0 ? -size : size;\n}\nfunction yToXOf({ scaleX, scaleY }) {\n  return scaleY / scaleX;\n}\nvar PATH_RIBBON_SPACING_PX = 3;\nfunction drawnDirection(a, b, yToX) {\n  const dx = b.x - a.x;\n  const dy = (b.y - a.y) * yToX;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? void 0 : { x: dx / len, y: dy / len };\n}\nfunction pathRibbonOffsets(fromSegments, toSegments, count, axis) {\n  const yToX = yToXOf(axis);\n  const spacing = PATH_RIBBON_SPACING_PX / Math.max(axis.scaleX, 1e-6);\n  const dir = drawnDirection(\n    fromSegments[fromSegments.length - 1],\n    toSegments[0],\n    yToX\n  ) ?? drawnDirection(fromSegments[0], fromSegments.at(-1), yToX) ?? drawnDirection(toSegments[0], toSegments.at(-1), yToX) ?? { x: 1, y: 0 };\n  const offsets = [];\n  for (let i = 0; i < count; i++) {\n    const distance = (i - (count - 1) / 2) * spacing;\n    offsets.push({ x: -dir.y * distance, y: dir.x * distance / yToX });\n  }\n  return offsets;\n}\nfunction scaleYOf(points, yToX) {\n  return points.map((p) => ({ x: p.x, y: p.y * yToX }));\n}\nfunction unscaleYOf(curves, yToX) {\n  for (const c of curves) {\n    c.y0 /= yToX;\n    c.cy0 /= yToX;\n    c.cy1 /= yToX;\n    c.y1 /= yToX;\n  }\n  return curves;\n}\nfunction polylinePx(points, scaleX, scaleY) {\n  let total = 0;\n  for (let i = 1; i < points.length; i++) {\n    const a = points[i - 1];\n    const b = points[i];\n    total += Math.hypot((b.x - a.x) * scaleX, (b.y - a.y) * scaleY);\n  }\n  return total;\n}\nvar SELF_LOOP_MIN_PX = 12;\nvar SELF_LOOP_MAX_PX = 40;\nfunction selfLoopReach(segments, scale) {\n  const nodePx = polylinePx(segments, scale, scale);\n  const reachPx = Math.min(\n    SELF_LOOP_MAX_PX,\n    Math.max(SELF_LOOP_MIN_PX, nodePx / 2)\n  );\n  return reachPx / Math.max(scale, Number.EPSILON);\n}\nfunction selfLinkOf(edge) {\n  if (edge.from !== edge.to) {\n    return false;\n  }\n  return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand ? edge.fromStrand === \"+\" ? \"end\" : \"start\" : true;\n}\nfunction edgeJoinOf(edge, stranded = false) {\n  const self = selfLinkOf(edge);\n  if (!stranded) {\n    return self;\n  }\n  const sides = strandSides(edge);\n  return self === false ? sides : sides.from === sides.to ? sides.from : true;\n}\nfunction hairpinCurves(attach, reach) {\n  const { at, inward } = attach;\n  const dx = inward ? at.x - inward.x : 1;\n  const dy = inward ? at.y - inward.y : 0;\n  const len = Math.hypot(dx, dy) || 1;\n  const ux = dx / len;\n  const uy = dy / len;\n  const px = at.x;\n  const py = at.y;\n  const nearX = px + ux * reach / 3;\n  const nearY = py + uy * reach / 3;\n  const apexX = px + ux * reach;\n  const apexY = py + uy * reach;\n  const sideX = -uy * reach / 2;\n  const sideY = ux * reach / 2;\n  return [\n    {\n      x0: px,\n      y0: py,\n      cx0: nearX,\n      cy0: nearY,\n      cx1: apexX + sideX,\n      cy1: apexY + sideY,\n      x1: apexX,\n      y1: apexY\n    },\n    {\n      x0: apexX,\n      y0: apexY,\n      cx0: apexX - sideX,\n      cy0: apexY - sideY,\n      cx1: nearX,\n      cy1: nearY,\n      x1: px,\n      y1: py\n    }\n  ];\n}\nfunction computeEdgeCurves(fromSegments, toSegments, join, axis, bypassed = [], maxBowIn) {\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);\n  if (join === false) {\n    join = heldFacingSides(fromSegments, toSegments);\n  }\n  if (yToX !== 1) {\n    return unscaleYOf(\n      computeEdgeCurves(\n        scaleYOf(fromSegments, yToX),\n        scaleYOf(toSegments, yToX),\n        join,\n        { scaleX: scale, scaleY: scale },\n        scaleYOf(bypassed, yToX),\n        // the cap is a y measure and the body works in x units, so it converts\n        // with everything else that crosses this boundary\n        maxBow === void 0 ? void 0 : maxBow * yToX\n      ),\n      yToX\n    );\n  }\n  if (typeof join === \"string\") {\n    return hairpinCurves(\n      attachment(fromSegments, join),\n      selfLoopReach(fromSegments, scale)\n    );\n  }\n  const loop = join === true;\n  const sides = join === true ? { from: \"end\", to: \"start\" } : join;\n  const fromAttach = attachment(fromSegments, sides.from);\n  const toAttach = attachment(toSegments, sides.to);\n  const fromEnd = fromAttach.at;\n  const toStart = toAttach.at;\n  const p1x = fromEnd.x;\n  const p1y = fromEnd.y;\n  const p2x = toStart.x;\n  const p2y = toStart.y;\n  if (loop) {\n    let segDirX = 1;\n    let segDirY = 0;\n    if (fromAttach.inward) {\n      const dx = fromEnd.x - fromAttach.inward.x;\n      const dy = fromEnd.y - fromAttach.inward.y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        segDirX = dx / len;\n        segDirY = dy / len;\n      }\n    }\n    const ext = selfLoopReach(fromSegments, scale);\n    const perpX = -segDirY;\n    const perpY = segDirX;\n    const midX = (fromEnd.x + toStart.x) / 2 + perpX * ext;\n    const midY = (fromEnd.y + toStart.y) / 2 + perpY * ext;\n    const cp1x = p1x + segDirX * ext;\n    const cp1y = p1y + segDirY * ext;\n    const cp2x = p2x - segDirX * ext;\n    const cp2y = p2y - segDirY * ext;\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cp1x,\n        cy0: cp1y,\n        cx1: cp1x + perpX * ext,\n        cy1: cp1y + perpY * ext,\n        x1: midX,\n        y1: midY\n      },\n      {\n        x0: midX,\n        y0: midY,\n        cx0: cp2x + perpX * ext,\n        cy0: cp2y + perpY * ext,\n        cx1: cp2x,\n        cy1: cp2y,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  } else {\n    const fromPrev = fromAttach.inward ?? {\n      x: fromEnd.x - (toStart.x - fromEnd.x),\n      y: fromEnd.y - (toStart.y - fromEnd.y)\n    };\n    const toNext = toAttach.inward ?? {\n      x: toStart.x - (fromEnd.x - toStart.x),\n      y: toStart.y - (fromEnd.y - toStart.y)\n    };\n    const dist = Math.hypot(p2x - p1x, p2y - p1y);\n    const tangentProj = (prev, at, towardX, towardY) => {\n      const dx = at.x - prev.x;\n      const dy = at.y - prev.y;\n      const len = Math.hypot(dx, dy);\n      const along = len === 0 ? 0 : (towardX * dx + towardY * dy) / len;\n      return Math.max(\n        0,\n        Math.min(dist * TANGENT_SPAN_FACTOR, MAX_TANGENT, along * 0.5)\n      );\n    };\n    const towardToX = toStart.x - fromEnd.x;\n    const towardToY = toStart.y - fromEnd.y;\n    const [cx1, cy1] = projectLine(\n      fromPrev.x,\n      fromPrev.y,\n      fromEnd.x,\n      fromEnd.y,\n      tangentProj(fromPrev, fromEnd, towardToX, towardToY)\n    );\n    const [cx2, cy2] = projectLine(\n      toNext.x,\n      toNext.y,\n      toStart.x,\n      toStart.y,\n      tangentProj(toNext, toStart, -towardToX, -towardToY)\n    );\n    const bulge = bypassed.length ? bowAround(p1x, p1y, p2x, p2y, bypassed, maxBow) : 0;\n    const chordLen = dist === 0 ? 1 : dist;\n    const ux = (p2x - p1x) / chordLen;\n    const uy = (p2y - p1y) / chordLen;\n    const bulgeX = -uy * bulge;\n    const bulgeY = ux * bulge;\n    const spreadX = ux * Math.abs(bulge);\n    const spreadY = uy * Math.abs(bulge);\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cx1 + bulgeX - spreadX,\n        cy0: cy1 + bulgeY - spreadY,\n        cx1: cx2 + bulgeX + spreadX,\n        cy1: cy2 + bulgeY + spreadY,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  }\n}\nfunction nearerEnd(segments, to) {\n  const start = segments[0];\n  const end = segments.at(-1);\n  return Math.hypot(start.x - to.x, start.y - to.y) < Math.hypot(end.x - to.x, end.y - to.y) ? \"start\" : \"end\";\n}\nfunction routedEdgeCurves(fromSegments, toSegments, route, sides) {\n  const fromAttach = attachment(\n    fromSegments,\n    sides?.from ?? nearerEnd(fromSegments, route[0])\n  );\n  const toAttach = attachment(\n    toSegments,\n    sides?.to ?? nearerEnd(toSegments, route.at(-1))\n  );\n  const points = [fromAttach.at, ...route, toAttach.at];\n  const tangent = (i) => {\n    const p = points[i];\n    const span = (q) => Math.hypot(q.x - p.x, q.y - p.y);\n    const along = (inward, next) => {\n      const len = inward ? span(inward) : 0;\n      const reach = span(next);\n      return len === 0 ? { x: next.x - p.x, y: next.y - p.y } : {\n        x: (p.x - inward.x) / len * reach,\n        y: (p.y - inward.y) / len * reach\n      };\n    };\n    if (i === 0) {\n      return along(fromAttach.inward, points[1]);\n    }\n    if (i === points.length - 1) {\n      const out = along(toAttach.inward, points[i - 1]);\n      return { x: -out.x, y: -out.y };\n    }\n    return {\n      x: (points[i + 1].x - points[i - 1].x) / 2,\n      y: (points[i + 1].y - points[i - 1].y) / 2\n    };\n  };\n  const curves = [];\n  for (let i = 0; i < points.length - 1; i++) {\n    const a = points[i];\n    const b = points[i + 1];\n    const ta = tangent(i);\n    const tb = tangent(i + 1);\n    curves.push({\n      x0: a.x,\n      y0: a.y,\n      cx0: a.x + ta.x / 3,\n      cy0: a.y + ta.y / 3,\n      cx1: b.x - tb.x / 3,\n      cy1: b.y - tb.y / 3,\n      x1: b.x,\n      y1: b.y\n    });\n  }\n  return curves;\n}\n\nexport {\n  svgPath,\n  projectLine,\n  curvePointAt,\n  curveMidpoint,\n  curveBounds,\n  dashCurves,\n  dashSpans,\n  slideAt,\n  slideCurves,\n  translateCurves,\n  ownStrand,\n  strandSides,\n  bowAround,\n  yToXOf,\n  PATH_RIBBON_SPACING_PX,\n  pathRibbonOffsets,\n  polylinePx,\n  selfLinkOf,\n  edgeJoinOf,\n  computeEdgeCurves,\n  routedEdgeCurves\n};\n", "// src/util/weakMemo.ts\nfunction weakMemo() {\n  const cache = /* @__PURE__ */ new WeakMap();\n  return (key, deps, compute) => {\n    const hit = cache.get(key);\n    if (hit?.deps.length === deps.length && hit.deps.every((d, i) => Object.is(d, deps[i]))) {\n      return hit.value;\n    }\n    const value = compute();\n    cache.set(key, { deps, value });\n    return value;\n  };\n}\n\nexport {\n  weakMemo\n};\n", "// src/overlayLabels.ts\nvar LABEL_PX = 11;\nvar LABEL_CHAR_PX = 6.2;\nvar LABEL_PAD = 4;\nfunction labelWidth(text) {\n  return text.length * LABEL_CHAR_PX + LABEL_PAD * 2;\n}\nfunction overlaps(a, b) {\n  return a.x0 < b.x1 && a.x1 > b.x0 && a.y0 < b.y1 && a.y1 > b.y0;\n}\nfunction offFrame(box, frame) {\n  return box.x1 <= 0 || box.x0 >= frame.width || box.y1 <= 0 || box.y0 >= frame.height;\n}\nfunction insideFrame(box, frame) {\n  return box.x0 >= 0 && box.x1 <= frame.width && box.y0 >= 0 && box.y1 <= frame.height;\n}\nfunction occupancy(frame, reserved = []) {\n  const placed = [...reserved];\n  return (box) => {\n    if (offFrame(box, frame) || placed.some((p) => overlaps(p, box))) {\n      return false;\n    }\n    placed.push(box);\n    return true;\n  };\n}\nfunction placeLabels(candidates, frame, take) {\n  const out = [];\n  const row = LABEL_PX + LABEL_PAD * 2;\n  const place = (c, text) => {\n    const w = labelWidth(text);\n    const direction = c.y > frame.height / 2 ? -1 : 1;\n    for (let tries = 0; tries <= (c.stack ?? 0); tries++) {\n      const y = c.y + direction * tries * row;\n      const box = {\n        x0: c.x - w / 2,\n        x1: c.x + w / 2,\n        y0: y - LABEL_PX - LABEL_PAD,\n        y1: y + LABEL_PAD\n      };\n      if (offFrame(box, frame)) {\n        return void 0;\n      }\n      if (insideFrame(box, frame) && (c.fits?.(box) ?? true) && take(box)) {\n        return { ...c, text, y, w };\n      }\n    }\n    return void 0;\n  };\n  for (const c of candidates) {\n    const placed = place(c, c.text) ?? (c.fallback === void 0 ? void 0 : place(c, c.fallback));\n    if (placed) {\n      out.push(placed);\n    }\n  }\n  return out;\n}\n\nexport {\n  LABEL_PX,\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  labelWidth,\n  overlaps,\n  occupancy,\n  placeLabels\n};\n", "import {\n  ownStrand,\n  strandSides\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/mergeRuns.ts\nfunction flip(strand) {\n  return strand === \"+\" ? \"-\" : \"+\";\n}\nfunction mergeRuns(graph, alone = /* @__PURE__ */ new Set()) {\n  const sides = graph.edges.map(strandSides);\n  const at = /* @__PURE__ */ new Map();\n  const attach = (id, side, ei) => {\n    pushTo(at, `${id}|${side}`, ei);\n  };\n  graph.edges.forEach((edge, ei) => {\n    attach(edge.from, sides[ei].from, ei);\n    attach(edge.to, sides[ei].to, ei);\n  });\n  const joinAfter = (a) => {\n    const out = at.get(`${a}|end`);\n    if (out?.length !== 1) {\n      return void 0;\n    }\n    const ei = out[0];\n    const edge = graph.edges[ei];\n    return edge.from === a && edge.to !== a && !alone.has(a) && !alone.has(edge.to) && sides[ei].from === \"end\" && sides[ei].to === \"start\" && at.get(`${edge.to}|start`)?.length === 1 ? ei : void 0;\n  };\n  const joined = /* @__PURE__ */ new Set();\n  const runOf = /* @__PURE__ */ new Map();\n  const runs = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const into = at.get(`${node.id}|start`);\n    const pred = into?.length === 1 ? graph.edges[into[0]].from : void 0;\n    if (runOf.has(node.id) || pred !== void 0 && joinAfter(pred) === into[0]) {\n      continue;\n    }\n    const run = [node.id];\n    for (; ; ) {\n      const ei = joinAfter(run.at(-1));\n      const next = ei === void 0 ? void 0 : graph.edges[ei].to;\n      if (next === void 0 || runOf.has(next)) {\n        break;\n      }\n      joined.add(ei);\n      run.push(next);\n    }\n    for (const id of run) {\n      runOf.set(id, node.id);\n    }\n    if (run.length > 1) {\n      runs.set(node.id, run);\n    }\n  }\n  for (const node of graph.nodes) {\n    if (!runOf.has(node.id)) {\n      runOf.set(node.id, node.id);\n    }\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const nodes = [];\n  for (const node of graph.nodes) {\n    if (runOf.get(node.id) !== node.id) {\n      continue;\n    }\n    const run = runs.get(node.id);\n    if (!run) {\n      nodes.push(node);\n      continue;\n    }\n    const members = run.map((id) => byId.get(id));\n    const backbone = members.filter(isBackbone);\n    const first = backbone.length ? backbone.reduce((a, b) => a.stable.start <= b.stable.start ? a : b) : members[0];\n    nodes.push({\n      id: node.id,\n      name: node.name,\n      length: members.reduce((sum, n) => sum + n.length, 0),\n      depth: node.depth,\n      stable: first.stable\n    });\n  }\n  const seen = /* @__PURE__ */ new Set();\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const from = runOf.get(edge.from);\n    const to = runOf.get(edge.to);\n    const side = sides[ei];\n    const key = `${from}|${side.from}>${to}|${side.to}`;\n    if (joined.has(ei) || seen.has(key)) {\n      return;\n    }\n    seen.add(key);\n    edges.push({\n      from,\n      to,\n      ...side.from === \"start\" ? { fromStrand: flip(ownStrand(from)) } : {},\n      ...side.to === \"end\" ? { toStrand: flip(ownStrand(to)) } : {}\n    });\n  });\n  return {\n    graph: { ...graph, nodes, edges, paths: void 0, pathVisits: void 0 },\n    runs\n  };\n}\nfunction splitRuns(positions, runs, weightOf) {\n  const out = { ...positions };\n  for (const [id, members] of runs) {\n    const line = positions[id];\n    if (!line?.length) {\n      continue;\n    }\n    delete out[id];\n    const arc = arcPrefix(line);\n    const total = arc.at(-1);\n    const weights = members.map((m) => Math.max(weightOf(m), 0));\n    const weightSum = weights.reduce((a, b) => a + b, 0);\n    let from = 0;\n    members.forEach((member, k) => {\n      const share = weightSum ? weights[k] / weightSum * total : total / members.length;\n      const to = k === members.length - 1 ? total : from + share;\n      out[member] = slice(line, arc, from, to);\n      from = to;\n    });\n  }\n  return out;\n}\nfunction polylineSlice(line, from, to) {\n  if (line.length === 0) {\n    return [];\n  }\n  const arc = arcPrefix(line);\n  const total = arc.at(-1);\n  return slice(line, arc, from * total, to * total);\n}\nfunction polylineMidpoint(line) {\n  const arc = arcPrefix(line);\n  return pointAt(line, arc, arc.at(-1) / 2);\n}\nfunction arcPrefix(line) {\n  const arc = [0];\n  for (let i = 1; i < line.length; i++) {\n    arc.push(\n      arc[i - 1] + Math.hypot(line[i].x - line[i - 1].x, line[i].y - line[i - 1].y)\n    );\n  }\n  return arc;\n}\nfunction firstReaching(arc, s) {\n  let lo = 0;\n  let hi = arc.length;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (arc[mid] < s) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\nfunction pointAt(line, arc, s) {\n  if (s <= 0) {\n    return { ...line[0] };\n  }\n  const i = firstReaching(arc, s);\n  if (i >= arc.length) {\n    return { ...line.at(-1) };\n  }\n  const span = arc[i] - arc[i - 1];\n  const t = span > 0 ? (s - arc[i - 1]) / span : 0;\n  const a = line[i - 1];\n  const b = line[i];\n  return { x: a.x + (b.x - a.x) * t, y: a.y + (b.y - a.y) * t };\n}\nfunction slice(line, arc, from, to) {\n  const points = [pointAt(line, arc, from)];\n  for (let i = firstReaching(arc, from); i < line.length && arc[i] < to; i++) {\n    if (arc[i] > from) {\n      points.push({ ...line[i] });\n    }\n  }\n  points.push(pointAt(line, arc, to));\n  return points;\n}\n\nexport {\n  mergeRuns,\n  splitRuns,\n  polylineSlice,\n  polylineMidpoint\n};\n", "import {\n  pathOrigin,\n  trimOrigins\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  PathVisitsBuilder\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  isBackbone,\n  overlapsWindow\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/trimToWindow.ts\nfunction trimToWindow(graph, window) {\n  const inWindow = new Set(\n    graph.nodes.filter((n) => isBackbone(n) && overlapsWindow(n, window)).map((n) => n.id)\n  );\n  const paths = graph.paths ?? [];\n  if (inWindow.size === 0 || paths.length === 0) {\n    return graph;\n  }\n  const spans = paths.map((path) => {\n    let first = -1;\n    let last = -1;\n    path.nodeIds.forEach((id, i) => {\n      if (inWindow.has(id)) {\n        if (first < 0) {\n          first = i;\n        }\n        last = i;\n      }\n    });\n    return first < 0 ? void 0 : { first, last };\n  });\n  if (spans.every(\n    (span, i) => span?.first === 0 && span.last === paths[i].nodeIds.length - 1\n  )) {\n    return graph;\n  }\n  const kept = /* @__PURE__ */ new Set();\n  const trimmed = [];\n  const stretches = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    const span = spans[i];\n    if (span) {\n      const nodeIds = path.nodeIds.slice(span.first, span.last + 1);\n      for (const id of nodeIds) {\n        kept.add(id);\n      }\n      trimmed.push({ ...path, nodeIds });\n      stretches.set(path.name, { first: span.first, nodeIds });\n    }\n  });\n  return {\n    ...graph,\n    nodes: graph.nodes.filter((n) => kept.has(n.id)),\n    edges: graph.edges.filter((e) => kept.has(e.from) && kept.has(e.to)),\n    paths: trimmed,\n    pathVisits: graph.pathVisits && trimVisits(\n      graph.pathVisits,\n      paths,\n      spans,\n      new Map(graph.nodes.map((n) => [n.id, n.name]))\n    ),\n    anchorPaths: trimOrigins(graph, stretches)\n  };\n}\nfunction trimVisits(visits, paths, spans, nameOf) {\n  const next = visits.replay();\n  const out = new PathVisitsBuilder();\n  paths.forEach((path, p) => {\n    const origin = visits.pathIndex(pathOrigin(path.name).name);\n    const span = spans[p];\n    path.nodeIds.forEach((id, i) => {\n      const segment = nameOf.get(id) ?? id;\n      const at = next(visits.slot(segment), origin);\n      if (at >= 0 && span && i >= span.first && i <= span.last) {\n        out.add(\n          segment,\n          visits.paths[origin],\n          visits.samples[origin],\n          visits.start[at],\n          visits.reversed[at] === 1\n        );\n      }\n    });\n  });\n  return out.build();\n}\nfunction clipToWindow(graph, window, reachBp) {\n  const nodes = graph.nodes.map((node) => {\n    if (!isBackbone(node)) {\n      return node;\n    }\n    const from = node.stable.start;\n    const to = from + node.length;\n    const [start, end] = overlapsWindow(node, window) ? [Math.max(from, window.start), Math.min(to, window.end)] : to <= window.start ? [Math.max(from, to - reachBp), to] : [from, Math.min(to, from + reachBp)];\n    return start === from && end === to ? node : {\n      ...node,\n      length: end - start,\n      stable: { ...node.stable, start },\n      unclipped: { start: from, length: node.length }\n    };\n  });\n  return nodes.some((node, i) => node !== graph.nodes[i]) ? { ...graph, nodes } : graph;\n}\nfunction unclipped(graph) {\n  return graph.nodes.some((n) => n.unclipped) ? {\n    ...graph,\n    nodes: graph.nodes.map(\n      ({ unclipped: full, ...node }) => full && node.stable ? {\n        ...node,\n        length: full.length,\n        stable: { ...node.stable, start: full.start }\n      } : node\n    )\n  } : graph;\n}\n\nexport {\n  trimToWindow,\n  clipToWindow,\n  unclipped\n};\n", "import {\n  unclipped\n} from \"./chunk-TLWXLNLY.js\";\nimport {\n  referenceVisitStarts\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  firstNodeAtOrAfter,\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/deletionEdges.ts\nvar MIN_DELETION_BP = 1;\nvar deletionKey = (reference) => `skips ${reference ?? \"the reference\"} sequence (a deletion)`;\nfunction bypassedPoints(nodePositions, bypassed) {\n  return bypassed.flatMap((id) => nodePositions[id] ?? []);\n}\nfunction edgeCurvesOf(nodePositions, edge, axis, bypassed, route, stranded) {\n  const from = nodePositions[edge.from];\n  const to = nodePositions[edge.to];\n  if (!from?.length || !to?.length) {\n    return void 0;\n  }\n  return route ? routedEdgeCurves(\n    from,\n    to,\n    route,\n    stranded ? strandSides(edge) : void 0\n  ) : computeEdgeCurves(\n    from,\n    to,\n    edgeJoinOf(edge, stranded),\n    axis,\n    bypassed ? bypassedPoints(nodePositions, bypassed) : []\n  );\n}\nfunction backboneBySequence(graph) {\n  const bySequence = groupBy(\n    graph.nodes.filter(isBackbone),\n    (node) => node.stable.refName\n  );\n  for (const list of bySequence.values()) {\n    list.sort((a, b) => a.stable.start - b.stable.start);\n  }\n  return bySequence;\n}\nfunction bypassedNodes(nodes, start, end) {\n  const bypassed = [];\n  if (nodes) {\n    for (let i = firstNodeAtOrAfter(nodes, start); i < nodes.length; i++) {\n      const node = nodes[i];\n      if (node.stable.start >= end) {\n        break;\n      }\n      if (node.stable.start + node.length <= end) {\n        bypassed.push(node.id);\n      }\n    }\n  }\n  return bypassed;\n}\nfunction skipsBetween(edge, from, to, forwards) {\n  const { fromStrand, toStrand } = edge;\n  if (fromStrand === void 0 || toStrand === void 0) {\n    return true;\n  }\n  const leavesRight = fromStrand === (from.stable.strand ?? \"+\");\n  const arrivesLeft = toStrand === (to.stable.strand ?? \"+\");\n  return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft;\n}\nfunction skippedSpan(edge, from, to, startsOf) {\n  let best;\n  for (const a of startsOf(from)) {\n    for (const b of startsOf(to)) {\n      const forwards = a <= b;\n      const span = forwards ? { start: a + from.length, end: b } : { start: b + to.length, end: a };\n      if (skipsBetween(edge, from, to, forwards) && (!best || Math.abs(span.end - span.start) < Math.abs(best.end - best.start))) {\n        best = span;\n      }\n    }\n  }\n  return best;\n}\nvar COPY_SWITCH_SHARE = 0.01;\nfunction repeatCopies(backbone, startsOf) {\n  const bySequence = /* @__PURE__ */ new Map();\n  for (const [refName, nodes] of backbone) {\n    const copies = nodes.flatMap((node) => {\n      const starts = startsOf(node);\n      return starts.slice(1).map((next, i) => ({\n        at: starts[i],\n        copy: next - starts[i]\n      }));\n    });\n    if (copies.length) {\n      bySequence.set(\n        refName,\n        copies.sort((a, b) => a.at - b.at)\n      );\n    }\n  }\n  return bySequence;\n}\nfunction switchesCopy(copies, start, bp) {\n  if (!copies) {\n    return false;\n  }\n  const i = partitionPoint(copies.length, (k) => copies[k].at < start);\n  const near = [copies[i - 1], copies[i]].filter((c) => c !== void 0).sort((a, b) => Math.abs(a.at - start) - Math.abs(b.at - start))[0];\n  return near !== void 0 && Math.abs(near.at - start) <= near.copy && Math.abs(bp - near.copy) <= near.copy * COPY_SWITCH_SHARE;\n}\nfunction deletionEdges(cut) {\n  const graph = unclipped(cut);\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const backbone = backboneBySequence(graph);\n  const startsOf = referenceVisitStarts(graph);\n  const copies = repeatCopies(backbone, startsOf);\n  const found = [];\n  for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {\n    const edge = graph.edges[edgeIndex];\n    const from = byId.get(edge.from);\n    const to = byId.get(edge.to);\n    if (!edge.foldBridge && from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {\n      const span = skippedSpan(edge, from, to, startsOf);\n      const refName = from.stable.refName;\n      const bp = span ? span.end - span.start : 0;\n      if (span && bp >= MIN_DELETION_BP && !switchesCopy(copies.get(refName), span.start, bp)) {\n        const { start, end } = span;\n        found.push({\n          edgeIndex,\n          from: edge.from,\n          to: edge.to,\n          ...edge.fromStrand ? { fromStrand: edge.fromStrand } : {},\n          ...edge.toStrand ? { toStrand: edge.toStrand } : {},\n          refName,\n          start,\n          end,\n          bp,\n          bypassed: bypassedNodes(backbone.get(refName), start, end)\n        });\n      }\n    }\n  }\n  return found;\n}\nfunction closableDeletions(graph, deletions) {\n  const parent = /* @__PURE__ */ new Map();\n  const root = (id) => {\n    let r = id;\n    while (parent.has(r)) {\n      r = parent.get(r);\n    }\n    if (r !== id) {\n      parent.set(id, r);\n    }\n    return r;\n  };\n  const join = (a, b) => {\n    const [ra, rb] = [root(a), root(b)];\n    if (ra !== rb) {\n      parent.set(ra, rb);\n    }\n    return ra !== rb;\n  };\n  const candidates = new Set(deletions.map((d) => d.edgeIndex));\n  graph.edges.forEach((e, ei) => {\n    if (!candidates.has(ei)) {\n      join(e.from, e.to);\n    }\n  });\n  return new Set(\n    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)\n  );\n}\nvar drawings = /* @__PURE__ */ new WeakMap();\nfunction deletionDrawing(graph, deletions, show = true) {\n  let byShow = drawings.get(deletions);\n  if (!byShow) {\n    byShow = /* @__PURE__ */ new Map();\n    drawings.set(deletions, byShow);\n  }\n  let drawing = byShow.get(show);\n  if (!drawing) {\n    const hidden = show ? /* @__PURE__ */ new Set() : closableDeletions(graph, deletions);\n    drawing = {\n      shown: deletions.filter((d) => !hidden.has(d.edgeIndex)),\n      bypassed: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),\n      hidden\n    };\n    byShow.set(show, drawing);\n  }\n  return drawing;\n}\n\nexport {\n  deletionKey,\n  edgeCurvesOf,\n  deletionEdges,\n  closableDeletions,\n  deletionDrawing\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  labelWidth,\n  occupancy\n} from \"./chunk-AB35TJST.js\";\nimport {\n  polylineMidpoint\n} from \"./chunk-HNNP5QUN.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-OMQWCVOJ.js\";\nimport {\n  curveBounds,\n  curveMidpoint,\n  polylinePx\n} from \"./chunk-JJV2GT2Z.js\";\n\n// src/graphLabels.ts\nvar MIN_DELETION_LABEL_PX = 26;\nvar PX_PER_NODE_LABEL = 4e4;\nvar MIN_NODE_LABELS = 8;\nvar LEADER_GAP_PX = 8;\nvar LABEL_CHAR_PX = 5.7;\nvar LABEL_PAD_PX = 6;\nvar LABEL_HEIGHT_PX = 13;\nvar LABEL_GAP_PX = 3;\nvar MAX_LABEL_OVERHANG = 2;\nfunction labelHalfWidth(text) {\n  return (text.length * LABEL_CHAR_PX + LABEL_PAD_PX + LABEL_GAP_PX) / 2;\n}\nvar LABEL_HALF_HEIGHT = (LABEL_HEIGHT_PX + LABEL_GAP_PX) / 2;\nvar MIN_LABEL_HALF_WIDTH = labelHalfWidth(\"1 bp\");\nfunction boxAt(halfW, x, y) {\n  return {\n    x0: x - halfW,\n    x1: x + halfW,\n    y0: y - LABEL_HALF_HEIGHT,\n    y1: y + LABEL_HALF_HEIGHT\n  };\n}\nfunction rowLabelBox(text, screenY) {\n  return {\n    x0: 6,\n    x1: 6 + labelWidth(text) + LABEL_GAP_PX,\n    y0: screenY - 8 - LABEL_GAP_PX / 2,\n    y1: screenY + 8 + LABEL_GAP_PX / 2\n  };\n}\nfunction clamp(v, lo, hi) {\n  return hi < lo ? v : Math.min(Math.max(v, lo), hi);\n}\nfunction groupDigits(n) {\n  return String(n).replace(/\\B(?=(\\d{3})+$)/g, \",\");\n}\nfunction formatBp(bp) {\n  const [value, unit] = bp >= 999500 ? [bp / 1e6, \"Mb\"] : bp >= 1e3 ? [bp / 1e3, \"kb\"] : [];\n  if (value === void 0) {\n    return `${bp} bp`;\n  }\n  return `${+value.toFixed(value >= 100 ? 0 : 1)} ${unit}`;\n}\nfunction deletionText(bp) {\n  return `${formatBp(bp)} del`;\n}\nfunction arcOutward(curves, apex, scaleX, scaleY) {\n  const first = curves[0];\n  const last = curves[curves.length - 1];\n  const dx = (apex.x - (first.x0 + last.x1) / 2) * scaleX;\n  const dy = (apex.y - (first.y0 + last.y1) / 2) * scaleY;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? { x: 0, y: -1 } : { x: dx / len, y: dy / len };\n}\nfunction boxSupport(box, dir) {\n  return Math.abs(dir.x) * (box.x1 - box.x0) / 2 + Math.abs(dir.y) * (box.y1 - box.y0) / 2;\n}\nfunction boxRayCrossing(box, dir) {\n  const halfW = (box.x1 - box.x0) / 2;\n  const halfH = (box.y1 - box.y0) / 2;\n  return Math.min(\n    dir.x === 0 ? Infinity : halfW / Math.abs(dir.x),\n    dir.y === 0 ? Infinity : halfH / Math.abs(dir.y)\n  );\n}\nfunction runBounds(nodeIds, nodePositions) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const id of nodeIds) {\n    for (const p of nodePositions[id] ?? []) {\n      minX = Math.min(minX, p.x);\n      maxX = Math.max(maxX, p.x);\n      minY = Math.min(minY, p.y);\n      maxY = Math.max(maxY, p.y);\n    }\n  }\n  return minX === Infinity ? void 0 : { minX, minY, maxX, maxY };\n}\nvar nodeOrderCache = weakMemo();\nfunction labelOrder(nodePositions, nodeLengths) {\n  return nodeOrderCache(\n    nodePositions,\n    [nodeLengths],\n    () => Object.entries(nodePositions).filter(([id, segments]) => segments.length > 0 && nodeLengths.has(id)).sort(([a], [b]) => nodeLengths.get(b) - nodeLengths.get(a))\n  );\n}\nvar arcCache = weakMemo();\nfunction arcPlacements(nodePositions, deletions, axis, version, routes, stranded) {\n  const { scaleX, scaleY } = axis;\n  return arcCache(\n    nodePositions,\n    [deletions, routes, stranded, scaleX, scaleY, version],\n    () => {\n      const arcs = [];\n      for (const deletion of [...deletions].sort((a, b) => b.bp - a.bp)) {\n        const curves = edgeCurvesOf(\n          nodePositions,\n          deletion,\n          axis,\n          deletion.bypassed,\n          routes?.[deletion.edgeIndex],\n          stranded\n        );\n        const apex = curves ? curveMidpoint(curves) : void 0;\n        if (curves && apex) {\n          const { minX, minY, maxX, maxY } = curveBounds(curves);\n          arcs.push({\n            deletion,\n            curves,\n            apex,\n            // in screen px, so the two axes' units cannot be added by accident\n            extent: Math.max((maxX - minX) * scaleX, (maxY - minY) * scaleY)\n          });\n        }\n      }\n      return arcs;\n    }\n  );\n}\nfunction sizeLabelCandidates({\n  nodePositions,\n  nodeLengths,\n  deletions,\n  deletionRoutes,\n  stranded = false,\n  alleleDeletions,\n  axis,\n  translateX,\n  translateY,\n  width,\n  height,\n  version = 0\n}) {\n  const { scaleX, scaleY } = axis;\n  const deletionCandidates = [];\n  const nodeCandidates = [];\n  for (const { deletion, curves, apex, extent } of arcPlacements(\n    nodePositions,\n    deletions,\n    axis,\n    version,\n    deletionRoutes,\n    stranded\n  )) {\n    if (extent >= MIN_DELETION_LABEL_PX) {\n      const text = deletionText(deletion.bp);\n      const halfW = labelHalfWidth(text);\n      const box = boxAt(halfW, 0, 0);\n      const arcX = apex.x * scaleX + translateX;\n      const arcY = apex.y * scaleY + translateY;\n      if (arcX < 0 || arcX > width || arcY < 0 || arcY > height) {\n        continue;\n      }\n      const fits = extent >= halfW * 2 / MAX_LABEL_OVERHANG;\n      const bow = arcOutward(curves, apex, scaleX, scaleY);\n      const offset = boxSupport(box, bow) + LEADER_GAP_PX;\n      const x = fits ? arcX : clamp(arcX + bow.x * offset, halfW, width - halfW);\n      const y = fits ? arcY : clamp(\n        arcY + bow.y * offset,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      const away = Math.hypot(x - arcX, y - arcY);\n      let leader;\n      if (away > 0) {\n        const dir = { x: (x - arcX) / away, y: (y - arcY) / away };\n        const crossing = boxRayCrossing(box, dir);\n        leader = {\n          arcX,\n          arcY,\n          labelX: x - dir.x * crossing,\n          labelY: y - dir.y * crossing\n        };\n      }\n      deletionCandidates.push({\n        label: {\n          key: `del:${deletion.edgeIndex}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\",\n          leader\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  const labelledByDeletion = /* @__PURE__ */ new Set();\n  const alleleRuns = [...alleleDeletions ?? []].sort((a, b) => b.bp - a.bp);\n  for (const run of alleleRuns) {\n    const drawn = runBounds(run.nodeIds, nodePositions);\n    if (!drawn) {\n      continue;\n    }\n    const shownLeft = Math.max(drawn.minX * scaleX + translateX, 0);\n    const shownRight = Math.min(drawn.maxX * scaleX + translateX, width);\n    const shownTop = Math.max(drawn.minY * scaleY + translateY, 0);\n    const shownBottom = Math.min(drawn.maxY * scaleY + translateY, height);\n    if (shownRight < shownLeft || shownBottom < shownTop) {\n      continue;\n    }\n    const extent = Math.max(shownRight - shownLeft, shownBottom - shownTop);\n    const text = deletionText(run.bp);\n    const halfW = labelHalfWidth(text);\n    if (extent >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      for (const id of run.nodeIds) {\n        labelledByDeletion.add(id);\n      }\n      const x = clamp((shownLeft + shownRight) / 2, halfW, width - halfW);\n      const y = clamp(\n        (shownTop + shownBottom) / 2,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      deletionCandidates.push({\n        label: {\n          key: `alleledel:${run.nodeIds.join(\",\")}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\"\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  for (const [id, segments] of labelOrder(nodePositions, nodeLengths)) {\n    if (labelledByDeletion.has(id)) {\n      continue;\n    }\n    const { x, y } = polylineMidpoint(segments);\n    const screenY = y * scaleY + translateY;\n    if (screenY + LABEL_HALF_HEIGHT <= 0 || screenY - LABEL_HALF_HEIGHT >= height) {\n      continue;\n    }\n    const drawn = polylinePx(segments, scaleX, scaleY);\n    if (drawn < MIN_LABEL_HALF_WIDTH * 2 / MAX_LABEL_OVERHANG) {\n      continue;\n    }\n    const text = formatBp(nodeLengths.get(id));\n    const halfW = labelHalfWidth(text);\n    if (drawn >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      const screenX = x * scaleX + translateX;\n      nodeCandidates.push({\n        label: {\n          key: `node:${id}`,\n          text,\n          x: screenX,\n          y: screenY,\n          kind: \"node\"\n        },\n        box: boxAt(halfW, screenX, screenY)\n      });\n    }\n  }\n  return { deletions: deletionCandidates, nodes: nodeCandidates };\n}\nfunction nodeLabelBudget(width, height) {\n  return Math.max(\n    MIN_NODE_LABELS,\n    Math.floor(width * height / PX_PER_NODE_LABEL)\n  );\n}\nfunction placeSizeLabels(candidates, take, budget = Infinity) {\n  const labels = [];\n  for (const { label, box } of candidates) {\n    if (labels.length >= budget) {\n      break;\n    }\n    if (take(box)) {\n      labels.push(label);\n    }\n  }\n  return labels;\n}\nfunction graphLabels({\n  reserved,\n  take,\n  ...args\n}) {\n  take ??= occupancy(args, reserved);\n  const { deletions, nodes } = sizeLabelCandidates(args);\n  return [\n    ...placeSizeLabels(deletions, take),\n    ...placeSizeLabels(nodes, take, nodeLabelBudget(args.width, args.height))\n  ];\n}\n\nexport {\n  rowLabelBox,\n  groupDigits,\n  formatBp,\n  sizeLabelCandidates,\n  nodeLabelBudget,\n  placeSizeLabels,\n  graphLabels\n};\n", "import {\n  groupDigits\n} from \"./chunk-ENBFQH7Y.js\";\nimport {\n  pathOrigin\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  isGenericSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathColors.ts\nfunction nameHue(name) {\n  let hash = 0;\n  for (let i = 0; i < name.length; i++) {\n    hash = name.charCodeAt(i) + ((hash << 5) - hash);\n  }\n  return Math.abs(hash % 360);\n}\nfunction pathHueAt(index, count) {\n  return index * 360 / count;\n}\nvar PATH_SATURATION = 0.7;\nvar PATH_LIGHTNESS = 0.5;\nvar MAX_PATH_COLORS = 16;\nfunction pathColorsLegible(pathCount) {\n  return pathCount > 0 && pathCount <= MAX_PATH_COLORS;\n}\nfunction pathCssColor(index, count) {\n  return `hsl(${pathHueAt(index, count)}, ${PATH_SATURATION * 100}%, ${PATH_LIGHTNESS * 100}%)`;\n}\nfunction pathGreyCssColor(index, count) {\n  const lightness = count > 1 ? 25 + 45 * index / (count - 1) : 45;\n  return `hsl(0, 0%, ${lightness}%)`;\n}\nfunction labelTiers(name) {\n  const parts = pathOrigin(name).name.split(\"#\");\n  const full = parts.join(\"#\");\n  if (parts.length >= 3 && isGenericSample(parts[0])) {\n    const contig = parts.slice(2).join(\"#\");\n    return [contig, contig, full];\n  }\n  return [parts[0], parts.slice(0, 2).join(\"#\"), full];\n}\nfunction offsetTiers(name, tiers) {\n  const { start } = pathOrigin(name);\n  return tiers.map((t) => `${t} @${groupDigits(start)}`);\n}\nfunction pathLegend(paths, colors) {\n  const firstOf = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    if (!firstOf.has(path.name)) {\n      firstOf.set(path.name, i);\n    }\n  });\n  const entries = [...firstOf].map(([name2, i]) => ({ name: name2, i }));\n  const named = entries.map((e) => labelTiers(e.name));\n  const name = (t) => entries.map((_, k) => named[k][t]);\n  const offset = (t) => entries.map((e, k) => offsetTiers(e.name, named[k])[t]);\n  const candidates = [\n    name(0),\n    name(1),\n    offset(0),\n    name(2),\n    offset(1),\n    offset(2)\n  ];\n  const distinct = candidates.find(\n    (labels2) => new Set(labels2).size === entries.length\n  );\n  const labels = distinct ?? candidates.at(-1);\n  return entries.map(({ name: name2, i }, k) => ({\n    name: name2,\n    label: labels[k],\n    color: colors?.[i] ?? pathCssColor(i, paths.length)\n  }));\n}\nfunction walkLabelsOf(entries) {\n  const seen = /* @__PURE__ */ new Map();\n  return new Map(\n    [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {\n      const n = (seen.get(e.label) ?? 0) + 1;\n      seen.set(e.label, n);\n      return [e.name, n > 1 ? `${e.label} (${n})` : e.label];\n    })\n  );\n}\n\nexport {\n  nameHue,\n  pathHueAt,\n  PATH_SATURATION,\n  PATH_LIGHTNESS,\n  MAX_PATH_COLORS,\n  pathColorsLegible,\n  pathCssColor,\n  pathGreyCssColor,\n  pathLegend,\n  walkLabelsOf\n};\n", "import {\n  panSNHaplotype\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/nodeWidths.ts\nvar NODE_WIDTHS = [\n  {\n    value: \"depth\",\n    label: \"By depth\",\n    description: \"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform.\"\n  },\n  {\n    value: \"frequency\",\n    label: \"By frequency\",\n    description: \"As wide as the share of haplotypes that pass a node, or its AF tag: full width at 100%, half at 50%, and wider where a haplotype passes it more than once.\"\n  },\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every node the same thickness.\"\n  }\n];\nvar MIN_FACTOR = 0.3;\nvar MAX_FACTOR = 3;\nvar MIN_FREQUENCY_FACTOR = 0.05;\nfunction meanDepth(graph) {\n  let weighted = 0;\n  let length = 0;\n  for (const node of graph.nodes) {\n    weighted += node.depth * node.length;\n    length += node.length;\n  }\n  return length > 0 ? weighted / length : 0;\n}\nfunction haplotypeOf(path) {\n  return path.sample === void 0 ? panSNHaplotype(path.name) ?? path.name : `${path.sample}#${path.haplotype ?? 0}`;\n}\nfunction haplotypeCount(graph) {\n  return new Set((graph.paths ?? []).map(haplotypeOf)).size;\n}\nfunction nodeFrequency(node, haplotypes) {\n  return node.frequency ?? (haplotypes > 0 ? node.depth / haplotypes : void 0);\n}\nfunction withFrequencies(graph, frequencies) {\n  if (!frequencies) {\n    return graph;\n  }\n  const nodes = graph.nodes.map((node) => {\n    const frequency = frequencies[node.name];\n    return frequency === void 0 ? node : { ...node, frequency };\n  });\n  return { ...graph, nodes };\n}\nfunction widthNorm(graph, nodeWidth) {\n  return nodeWidth === \"depth\" ? meanDepth(graph) : nodeWidth === \"frequency\" ? haplotypeCount(graph) : 0;\n}\nfunction frequencyFactor(f) {\n  return Math.min(MAX_FACTOR, Math.max(MIN_FREQUENCY_FACTOR, f));\n}\nfunction frequencyWidthFactor(node, haplotypes) {\n  const f = nodeFrequency(node, haplotypes);\n  return f === void 0 ? 1 : frequencyFactor(f);\n}\nfunction frequencyKey(contigThickness) {\n  return [1, 0.5, 0.1].map((f) => ({\n    label: `${f * 100}%`,\n    widthPx: contigThickness * frequencyFactor(f)\n  }));\n}\nfunction depthWidthFactor(node, mean) {\n  if (!(mean > 0) || !(node.depth > 0)) {\n    return 1;\n  }\n  return Math.min(\n    MAX_FACTOR,\n    Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))\n  );\n}\nfunction nodeWidthPx(node, contigThickness, nodeWidth, norm) {\n  return contigThickness * (nodeWidth === \"depth\" ? depthWidthFactor(node, norm) : nodeWidth === \"frequency\" ? frequencyWidthFactor(node, norm) : 1);\n}\nfunction maxNodeWidthPx(contigThickness, nodeWidth) {\n  return contigThickness * (nodeWidth === \"uniform\" ? 1 : MAX_FACTOR);\n}\nvar MIN_WALK_LANE_PX = 4;\nfunction walkLaneWidthPx(width, lanes) {\n  return Math.max(width / lanes, MIN_WALK_LANE_PX);\n}\nfunction nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {\n  const norm = graph ? widthNorm(graph, nodeWidth) : 0;\n  const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;\n  return {\n    maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),\n    halfWidthPx: (id) => {\n      const node = nodeById?.get(id);\n      return reach(\n        node ? nodeWidthPx(node, contigThickness, nodeWidth, norm) : contigThickness\n      );\n    }\n  };\n}\n\nexport {\n  NODE_WIDTHS,\n  meanDepth,\n  haplotypeCount,\n  nodeFrequency,\n  withFrequencies,\n  widthNorm,\n  frequencyKey,\n  nodeWidthPx,\n  maxNodeWidthPx,\n  walkLaneWidthPx,\n  nodeInk\n};\n", "// src/edgeWidths.ts\nvar EDGE_WIDTHS = [\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every link the same thickness.\"\n  },\n  {\n    value: \"walks\",\n    label: \"By walks\",\n    description: \"Thicker the more walks take a link, on the square root of its count against the busiest link in the cut. A graph without walks draws uniform.\"\n  }\n];\nvar MIN_FACTOR = 0.5;\nvar MAX_FACTOR = 4;\nfunction busiestEdge(graph) {\n  let most = 0;\n  for (const edge of graph.edges) {\n    most = Math.max(most, edge.pathIds?.length ?? 0);\n  }\n  return most;\n}\nfunction edgeWidthFactor(walks, busiest, edgeWidth) {\n  if (edgeWidth === \"uniform\" || busiest === 0) {\n    return 1;\n  }\n  return MIN_FACTOR + (MAX_FACTOR - MIN_FACTOR) * Math.sqrt(walks / busiest);\n}\n\nexport {\n  EDGE_WIDTHS,\n  busiestEdge,\n  edgeWidthFactor\n};\n"],
+  "mappings": 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"isBackbone", "first", "b", "sum", "seen", "edges", "from", "to", "key", "ownStrand", "splitRuns", "positions", "weightOf", "line", "arc", "arcPrefix", "total", "weights", "m", "weightSum", "member", "k", "share", "slice", "polylineSlice", "polylineMidpoint", "pointAt", "i", "firstReaching", "s", "lo", "hi", "mid", "span", "t", "points", "trimToWindow", "graph", "window", "inWindow", "n", "isBackbone", "overlapsWindow", "paths", "spans", "path", "first", "last", "id", "i", "span", "kept", "trimmed", "stretches", "nodeIds", "e", "trimVisits", "trimOrigins", "visits", "nameOf", "next", "out", "PathVisitsBuilder", "p", "origin", "pathOrigin", "segment", "at", "clipToWindow", "reachBp", "nodes", "node", "from", "to", "start", "end", "unclipped", "full", "MIN_DELETION_BP", "deletionKey", "reference", "bypassedPoints", "nodePositions", "bypassed", "id", "edgeCurvesOf", "edge", "axis", "route", "stranded", "from", "to", "routedEdgeCurves", "strandSides", "computeEdgeCurves", "edgeJoinOf", "backboneBySequence", "graph", "bySequence", "groupBy", "isBackbone", "node", "list", "a", "b", "bypassedNodes", "nodes", "start", "end", "i", "firstNodeAtOrAfter", "skipsBetween", "forwards", "fromStrand", "toStrand", "leavesRight", "arrivesLeft", "skippedSpan", "startsOf", "best", "span", "COPY_SWITCH_SHARE", "repeatCopies", "backbone", "refName", "copies", "starts", "next", "switchesCopy", "bp", "partitionPoint", "k", "near", "c", "deletionEdges", "cut", "unclipped", "byId", "n", "referenceVisitStarts", "found", "edgeIndex", "closableDeletions", "deletions", "parent", "root", "r", "join", "ra", "rb", "candidates", "d", "e", "ei", "drawings", "deletionDrawing", "show", "byShow", "drawing", "hidden", "MIN_DELETION_LABEL_PX", "PX_PER_NODE_LABEL", "MIN_NODE_LABELS", "LEADER_GAP_PX", "LABEL_CHAR_PX", "LABEL_PAD_PX", "LABEL_HEIGHT_PX", "LABEL_GAP_PX", "MAX_LABEL_OVERHANG", "labelHalfWidth", "text", "LABEL_HALF_HEIGHT", "MIN_LABEL_HALF_WIDTH", "boxAt", "halfW", "x", "y", "rowLabelBox", "screenY", "labelWidth", "clamp", "v", "lo", "hi", "groupDigits", "n", "formatBp", "bp", "value", "unit", "deletionText", "arcOutward", "curves", "apex", "scaleX", "scaleY", "first", "last", "dx", "dy", "len", "boxSupport", "box", "dir", "boxRayCrossing", "halfH", "runBounds", "nodeIds", "nodePositions", "minX", "minY", "maxX", "maxY", "id", "p", "nodeOrderCache", "weakMemo", "labelOrder", "nodeLengths", "segments", "a", "b", "arcCache", "arcPlacements", "deletions", "axis", "version", "routes", "stranded", "arcs", "deletion", "edgeCurvesOf", "curveMidpoint", "curveBounds", "sizeLabelCandidates", "deletionRoutes", "alleleDeletions", "translateX", "translateY", "width", "height", "deletionCandidates", "nodeCandidates", "extent", "arcX", "arcY", "fits", "bow", "offset", "away", "leader", "crossing", "labelledByDeletion", "alleleRuns", "run", "drawn", "shownLeft", "shownRight", "shownTop", "shownBottom", "polylineMidpoint", "polylinePx", "screenX", "nodeLabelBudget", "placeSizeLabels", "candidates", "take", "budget", "labels", "label", "graphLabels", "reserved", "args", "occupancy", "nodes", "nameHue", "name", "hash", "i", "pathHueAt", "index", "count", "PATH_SATURATION", "PATH_LIGHTNESS", "MAX_PATH_COLORS", "pathColorsLegible", "pathCount", "pathCssColor", "pathGreyCssColor", "labelTiers", "parts", "pathOrigin", "full", "isGenericSample", "contig", "offsetTiers", "tiers", "start", "t", "groupDigits", "pathLegend", "paths", "colors", "firstOf", "path", "entries", "name2", "named", "e", "_", "k", "offset", "candidates", "labels", "labels2", "walkLabelsOf", "seen", "a", "b", "n", "NODE_WIDTHS", "MIN_FACTOR", "MAX_FACTOR", "MIN_FREQUENCY_FACTOR", "meanDepth", "graph", "weighted", "length", "node", "haplotypeOf", "path", "panSNHaplotype", "haplotypeCount", "nodeFrequency", "haplotypes", "widthNorm", "graph", "nodeWidth", "meanDepth", "haplotypeCount", "frequencyFactor", "f", "MAX_FACTOR", "MIN_FREQUENCY_FACTOR", "frequencyWidthFactor", "node", "haplotypes", "nodeFrequency", "depthWidthFactor", "node", "mean", "MAX_FACTOR", "MIN_FACTOR", "nodeWidthPx", "contigThickness", "nodeWidth", "norm", "frequencyWidthFactor", "maxNodeWidthPx", "MIN_WALK_LANE_PX", "walkLaneWidthPx", "width", "lanes", "nodeInk", "graph", "nodeById", "widthNorm", "reach", "id", "EDGE_WIDTHS", "MIN_FACTOR", "MAX_FACTOR", "busiestEdge", "graph", "most", "edge", "edgeWidthFactor", "walks", "busiest", "edgeWidth"]
+}

package/dist/chunks/chunk-3VGXCEMQ.js

@@ -0,0 +1,2 @@
+var e=JBrowseExports["@jbrowse/core/util/tracks"],t=o=>e!=null&&o in Object(e)?e[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tracks' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var s=t("getConfAssemblyNamesOrNone");var r=t("getTrackName");var n=t("makeIndexType");var a=t("toTrackConfigEntry");var c=e&&e.__esModule?e.default:e;export{s as a,r as b,n as c,a as d};
+//# sourceMappingURL=chunk-3VGXCEMQ.js.map

package/dist/chunks/{chunk-7WIBGKBU.js.map → chunk-3VGXCEMQ.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["host:@jbrowse/core/util/tracks"],
-  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tracks\"]\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/core/util/tracks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const UNKNOWN = /* @__PURE__ */ read(\"UNKNOWN\")\nexport const UNSUPPORTED = /* @__PURE__ */ read(\"UNSUPPORTED\")\nexport const addAdapterGuesser = /* @__PURE__ */ read(\"addAdapterGuesser\")\nexport const addTrackTypeGuesser = /* @__PURE__ */ read(\"addTrackTypeGuesser\")\nexport const allSessionTracks = /* @__PURE__ */ read(\"allSessionTracks\")\nexport const annotationTrackIds = /* @__PURE__ */ read(\"annotationTrackIds\")\nexport const canonicalAssemblyNames = /* @__PURE__ */ read(\"canonicalAssemblyNames\")\nexport const clearFileFromCache = /* @__PURE__ */ read(\"clearFileFromCache\")\nexport const ensureFileHandleReady = /* @__PURE__ */ read(\"ensureFileHandleReady\")\nexport const expandLooseTrackConfig = /* @__PURE__ */ read(\"expandLooseTrackConfig\")\nexport const filterTracks = /* @__PURE__ */ read(\"filterTracks\")\nexport const findFileHandleIds = /* @__PURE__ */ read(\"findFileHandleIds\")\nexport const generateUnknownTrackConf = /* @__PURE__ */ read(\"generateUnknownTrackConf\")\nexport const generateUnsupportedTrackConf = /* @__PURE__ */ read(\"generateUnsupportedTrackConf\")\nexport const getBlob = /* @__PURE__ */ read(\"getBlob\")\nexport const getBlobMap = /* @__PURE__ */ read(\"getBlobMap\")\nexport const getConfAssemblyNames = /* @__PURE__ */ read(\"getConfAssemblyNames\")\nexport const getConfAssemblyNamesOrNone = /* @__PURE__ */ read(\"getConfAssemblyNamesOrNone\")\nexport const getConfRpcSessionId = /* @__PURE__ */ read(\"getConfRpcSessionId\")\nexport const getFileFromCache = /* @__PURE__ */ read(\"getFileFromCache\")\nexport const getFileName = /* @__PURE__ */ read(\"getFileName\")\nexport const getRpcSessionId = /* @__PURE__ */ read(\"getRpcSessionId\")\nexport const getTrackAssemblyNames = /* @__PURE__ */ read(\"getTrackAssemblyNames\")\nexport const getTrackName = /* @__PURE__ */ read(\"getTrackName\")\nexport const guessAdapter = /* @__PURE__ */ read(\"guessAdapter\")\nexport const guessTabixIndex = /* @__PURE__ */ read(\"guessTabixIndex\")\nexport const guessTrackConf = /* @__PURE__ */ read(\"guessTrackConf\")\nexport const guessTrackConfForLocation = /* @__PURE__ */ read(\"guessTrackConfForLocation\")\nexport const guessTrackType = /* @__PURE__ */ read(\"guessTrackType\")\nexport const hasFileHandlesInCache = /* @__PURE__ */ read(\"hasFileHandlesInCache\")\nexport const hideTrackGeneric = /* @__PURE__ */ read(\"hideTrackGeneric\")\nexport const isLooseTrackConfig = /* @__PURE__ */ read(\"isLooseTrackConfig\")\nexport const isSameAssemblyName = /* @__PURE__ */ read(\"isSameAssemblyName\")\nexport const launchToggleTrackGeneric = /* @__PURE__ */ read(\"launchToggleTrackGeneric\")\nexport const launchTrackGeneric = /* @__PURE__ */ read(\"launchTrackGeneric\")\nexport const makeIndex = /* @__PURE__ */ read(\"makeIndex\")\nexport const makeIndexType = /* @__PURE__ */ read(\"makeIndexType\")\nexport const normalizeTrackInit = /* @__PURE__ */ read(\"normalizeTrackInit\")\nexport const offeredTracks = /* @__PURE__ */ read(\"offeredTracks\")\nexport const openAssemblyInLinearView = /* @__PURE__ */ read(\"openAssemblyInLinearView\")\nexport const openMateLabel = /* @__PURE__ */ read(\"openMateLabel\")\nexport const pickDisplayForView = /* @__PURE__ */ read(\"pickDisplayForView\")\nexport const restoreFileHandles = /* @__PURE__ */ read(\"restoreFileHandles\")\nexport const restoreFileHandlesFromSnapshot = /* @__PURE__ */ read(\"restoreFileHandlesFromSnapshot\")\nexport const setBlobMap = /* @__PURE__ */ read(\"setBlobMap\")\nexport const setFileInCache = /* @__PURE__ */ read(\"setFileInCache\")\nexport const showTrackGeneric = /* @__PURE__ */ read(\"showTrackGeneric\")\nexport const storeBlobLocation = /* @__PURE__ */ read(\"storeBlobLocation\")\nexport const storeFileHandleLocation = /* @__PURE__ */ read(\"storeFileHandleLocation\")\nexport const stripFileExtension = /* @__PURE__ */ read(\"stripFileExtension\")\nexport const stripTrackIds = /* @__PURE__ */ read(\"stripTrackIds\")\nexport const toggleTrackGeneric = /* @__PURE__ */ read(\"toggleTrackGeneric\")\nexport const viewCanDisplayTrack = /* @__PURE__ */ read(\"viewCanDisplayTrack\")\nexport const viewDisplayNames = /* @__PURE__ */ read(\"viewDisplayNames\")\nexport const warmTrackDisplayGeneric = /* @__PURE__ */ read(\"warmTrackDisplayGeneric\")\nexport default host && host.__esModule ? host.default : host"],
-  "mappings": "AAAA,IAAMA,EAAO,eAAe,2BAA2B,EACjDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,2IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAwBC,IAAMC,EAA+BC,EAAK,cAAc,EAaxD,IAAMC,EAAgCC,EAAK,eAAe,EAmBjE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
-  "names": ["host", "read", "name", "getTrackName", "read", "makeIndexType", "read", "tracks_default", "host"]
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tracks\"]\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/core/util/tracks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const UNKNOWN = /* @__PURE__ */ read(\"UNKNOWN\")\nexport const UNSUPPORTED = /* @__PURE__ */ read(\"UNSUPPORTED\")\nexport const addAdapterGuesser = /* @__PURE__ */ read(\"addAdapterGuesser\")\nexport const addTrackTypeGuesser = /* @__PURE__ */ read(\"addTrackTypeGuesser\")\nexport const allSessionTracks = /* @__PURE__ */ read(\"allSessionTracks\")\nexport const annotationTrackIds = /* @__PURE__ */ read(\"annotationTrackIds\")\nexport const canonicalAssemblyNames = /* @__PURE__ */ read(\"canonicalAssemblyNames\")\nexport const clearFileFromCache = /* @__PURE__ */ read(\"clearFileFromCache\")\nexport const ensureFileHandleReady = /* @__PURE__ */ read(\"ensureFileHandleReady\")\nexport const expandLooseTrackConfig = /* @__PURE__ */ read(\"expandLooseTrackConfig\")\nexport const filterTracks = /* @__PURE__ */ read(\"filterTracks\")\nexport const findFileHandleIds = /* @__PURE__ */ read(\"findFileHandleIds\")\nexport const generateUnknownTrackConf = /* @__PURE__ */ read(\"generateUnknownTrackConf\")\nexport const generateUnsupportedTrackConf = /* @__PURE__ */ read(\"generateUnsupportedTrackConf\")\nexport const getBlob = /* @__PURE__ */ read(\"getBlob\")\nexport const getBlobMap = /* @__PURE__ */ read(\"getBlobMap\")\nexport const getConfAssemblyNames = /* @__PURE__ */ read(\"getConfAssemblyNames\")\nexport const getConfAssemblyNamesOrNone = /* @__PURE__ */ read(\"getConfAssemblyNamesOrNone\")\nexport const getConfRpcSessionId = /* @__PURE__ */ read(\"getConfRpcSessionId\")\nexport const getFileFromCache = /* @__PURE__ */ read(\"getFileFromCache\")\nexport const getFileName = /* @__PURE__ */ read(\"getFileName\")\nexport const getRpcSessionId = /* @__PURE__ */ read(\"getRpcSessionId\")\nexport const getTrackAssemblyNames = /* @__PURE__ */ read(\"getTrackAssemblyNames\")\nexport const getTrackName = /* @__PURE__ */ read(\"getTrackName\")\nexport const guessAdapter = /* @__PURE__ */ read(\"guessAdapter\")\nexport const guessTabixIndex = /* @__PURE__ */ read(\"guessTabixIndex\")\nexport const guessTrackConf = /* @__PURE__ */ read(\"guessTrackConf\")\nexport const guessTrackConfForLocation = /* @__PURE__ */ read(\"guessTrackConfForLocation\")\nexport const guessTrackType = /* @__PURE__ */ read(\"guessTrackType\")\nexport const hasFileHandlesInCache = /* @__PURE__ */ read(\"hasFileHandlesInCache\")\nexport const hideTrackGeneric = /* @__PURE__ */ read(\"hideTrackGeneric\")\nexport const isLooseTrackConfig = /* @__PURE__ */ read(\"isLooseTrackConfig\")\nexport const isSameAssemblyName = /* @__PURE__ */ read(\"isSameAssemblyName\")\nexport const launchToggleTrackGeneric = /* @__PURE__ */ read(\"launchToggleTrackGeneric\")\nexport const launchTrackGeneric = /* @__PURE__ */ read(\"launchTrackGeneric\")\nexport const makeIndex = /* @__PURE__ */ read(\"makeIndex\")\nexport const makeIndexType = /* @__PURE__ */ read(\"makeIndexType\")\nexport const normalizeTrackInit = /* @__PURE__ */ read(\"normalizeTrackInit\")\nexport const offeredTracks = /* @__PURE__ */ read(\"offeredTracks\")\nexport const openAssemblyInLinearView = /* @__PURE__ */ read(\"openAssemblyInLinearView\")\nexport const openMateLabel = /* @__PURE__ */ read(\"openMateLabel\")\nexport const pickDisplayForView = /* @__PURE__ */ read(\"pickDisplayForView\")\nexport const restoreFileHandles = /* @__PURE__ */ read(\"restoreFileHandles\")\nexport const restoreFileHandlesFromSnapshot = /* @__PURE__ */ read(\"restoreFileHandlesFromSnapshot\")\nexport const setBlobMap = /* @__PURE__ */ read(\"setBlobMap\")\nexport const setFileInCache = /* @__PURE__ */ read(\"setFileInCache\")\nexport const showTrackGeneric = /* @__PURE__ */ read(\"showTrackGeneric\")\nexport const storeBlobLocation = /* @__PURE__ */ read(\"storeBlobLocation\")\nexport const storeFileHandleLocation = /* @__PURE__ */ read(\"storeFileHandleLocation\")\nexport const stripFileExtension = /* @__PURE__ */ read(\"stripFileExtension\")\nexport const stripTrackIds = /* @__PURE__ */ read(\"stripTrackIds\")\nexport const toTrackConfigEntry = /* @__PURE__ */ read(\"toTrackConfigEntry\")\nexport const toggleTrackGeneric = /* @__PURE__ */ read(\"toggleTrackGeneric\")\nexport const trackCatalog = /* @__PURE__ */ read(\"trackCatalog\")\nexport const trackCatalogEntry = /* @__PURE__ */ read(\"trackCatalogEntry\")\nexport const trackDisplayType = /* @__PURE__ */ read(\"trackDisplayType\")\nexport const viewCanDisplayTrack = /* @__PURE__ */ read(\"viewCanDisplayTrack\")\nexport const viewDisplayNames = /* @__PURE__ */ read(\"viewDisplayNames\")\nexport const warmTrackDisplayGeneric = /* @__PURE__ */ read(\"warmTrackDisplayGeneric\")\nexport default host && host.__esModule ? host.default : host"],
+  "mappings": "AAAA,IAAMA,EAAO,eAAe,2BAA2B,EACjDC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,2IAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAkBC,IAAMC,EAA6CC,EAAK,4BAA4B,EAMpF,IAAMC,EAA+BC,EAAK,cAAc,EAaxD,IAAMC,EAAgCC,EAAK,eAAe,EAe1D,IAAMC,EAAqCC,EAAK,oBAAoB,EAQ3E,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
+  "names": ["host", "read", "name", "getConfAssemblyNamesOrNone", "read", "getTrackName", "read", "makeIndexType", "read", "toTrackConfigEntry", "read", "tracks_default", "host"]
 }

package/dist/chunks/chunk-3WG3GF2A.js

@@ -0,0 +1,2 @@
+var e=JBrowseExports["mobx-state-tree"],t=o=>e!=null&&o in Object(e)?e[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from 'mobx-state-tree' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o}),n=t("addDisposer");var s=t("flow");var r=t("getEnv");var p=t("getRoot");var c=t("isAlive");var i=t("types");var a=e&&e.__esModule?e.default:e;export{n as a,s as b,r as c,p as d,c as e,i as f};
+//# sourceMappingURL=chunk-3WG3GF2A.js.map

package/dist/chunks/{chunk-NDRLCGPC.js.map → chunk-3WG3GF2A.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["host:@jbrowse/mobx-state-tree"],
-  "sourcesContent": ["const host = JBrowseExports[\"mobx-state-tree\"]\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 '\" + \"mobx-state-tree\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const addDisposer = /* @__PURE__ */ read(\"addDisposer\")\nexport const addMiddleware = /* @__PURE__ */ read(\"addMiddleware\")\nexport const applyAction = /* @__PURE__ */ read(\"applyAction\")\nexport const applyPatch = /* @__PURE__ */ read(\"applyPatch\")\nexport const applySnapshot = /* @__PURE__ */ read(\"applySnapshot\")\nexport const asArrayType = /* @__PURE__ */ read(\"asArrayType\")\nexport const asMapType = /* @__PURE__ */ read(\"asMapType\")\nexport const asModelType = /* @__PURE__ */ read(\"asModelType\")\nexport const cannotDetermineSubtype = /* @__PURE__ */ read(\"cannotDetermineSubtype\")\nexport const cast = /* @__PURE__ */ read(\"cast\")\nexport const castFlowReturn = /* @__PURE__ */ read(\"castFlowReturn\")\nexport const castToReferenceSnapshot = /* @__PURE__ */ read(\"castToReferenceSnapshot\")\nexport const castToSnapshot = /* @__PURE__ */ read(\"castToSnapshot\")\nexport const clone = /* @__PURE__ */ read(\"clone\")\nexport const createActionTrackingMiddleware = /* @__PURE__ */ read(\"createActionTrackingMiddleware\")\nexport const createActionTrackingMiddleware2 = /* @__PURE__ */ read(\"createActionTrackingMiddleware2\")\nexport const decorate = /* @__PURE__ */ read(\"decorate\")\nexport const destroy = /* @__PURE__ */ read(\"destroy\")\nexport const detach = /* @__PURE__ */ read(\"detach\")\nexport const escapeJsonPath = /* @__PURE__ */ read(\"escapeJsonPath\")\nexport const extendInstance = /* @__PURE__ */ read(\"extendInstance\")\nexport const flow = /* @__PURE__ */ read(\"flow\")\nexport const getChildType = /* @__PURE__ */ read(\"getChildType\")\nexport const getEnv = /* @__PURE__ */ read(\"getEnv\")\nexport const getIdentifier = /* @__PURE__ */ read(\"getIdentifier\")\nexport const getLivelinessChecking = /* @__PURE__ */ read(\"getLivelinessChecking\")\nexport const getMembers = /* @__PURE__ */ read(\"getMembers\")\nexport const getNodeId = /* @__PURE__ */ read(\"getNodeId\")\nexport const getParent = /* @__PURE__ */ read(\"getParent\")\nexport const getParentOfType = /* @__PURE__ */ read(\"getParentOfType\")\nexport const getPath = /* @__PURE__ */ read(\"getPath\")\nexport const getPathParts = /* @__PURE__ */ read(\"getPathParts\")\nexport const getPropertyMembers = /* @__PURE__ */ read(\"getPropertyMembers\")\nexport const getRelativePath = /* @__PURE__ */ read(\"getRelativePath\")\nexport const getRoot = /* @__PURE__ */ read(\"getRoot\")\nexport const getRunningActionContext = /* @__PURE__ */ read(\"getRunningActionContext\")\nexport const getSnapshot = /* @__PURE__ */ read(\"getSnapshot\")\nexport const getType = /* @__PURE__ */ read(\"getType\")\nexport const getUnionSubtypes = /* @__PURE__ */ read(\"getUnionSubtypes\")\nexport const getWrappedType = /* @__PURE__ */ read(\"getWrappedType\")\nexport const hasParent = /* @__PURE__ */ read(\"hasParent\")\nexport const hasParentOfType = /* @__PURE__ */ read(\"hasParentOfType\")\nexport const isActionContextChildOf = /* @__PURE__ */ read(\"isActionContextChildOf\")\nexport const isActionContextThisOrChildOf = /* @__PURE__ */ read(\"isActionContextThisOrChildOf\")\nexport const isAlive = /* @__PURE__ */ read(\"isAlive\")\nexport const isArrayType = /* @__PURE__ */ read(\"isArrayType\")\nexport const isFrozenType = /* @__PURE__ */ read(\"isFrozenType\")\nexport const isIdentifierType = /* @__PURE__ */ read(\"isIdentifierType\")\nexport const isLateType = /* @__PURE__ */ read(\"isLateType\")\nexport const isLiteralType = /* @__PURE__ */ read(\"isLiteralType\")\nexport const isMapType = /* @__PURE__ */ read(\"isMapType\")\nexport const isModelType = /* @__PURE__ */ read(\"isModelType\")\nexport const isOptionalType = /* @__PURE__ */ read(\"isOptionalType\")\nexport const isPrimitiveType = /* @__PURE__ */ read(\"isPrimitiveType\")\nexport const isProtected = /* @__PURE__ */ read(\"isProtected\")\nexport const isReferenceType = /* @__PURE__ */ read(\"isReferenceType\")\nexport const isRefinementType = /* @__PURE__ */ read(\"isRefinementType\")\nexport const isRoot = /* @__PURE__ */ read(\"isRoot\")\nexport const isStateTreeNode = /* @__PURE__ */ read(\"isStateTreeNode\")\nexport const isType = /* @__PURE__ */ read(\"isType\")\nexport const isUnionType = /* @__PURE__ */ read(\"isUnionType\")\nexport const isValidReference = /* @__PURE__ */ read(\"isValidReference\")\nexport const joinJsonPath = /* @__PURE__ */ read(\"joinJsonPath\")\nexport const onAction = /* @__PURE__ */ read(\"onAction\")\nexport const onPatch = /* @__PURE__ */ read(\"onPatch\")\nexport const onSnapshot = /* @__PURE__ */ read(\"onSnapshot\")\nexport const protect = /* @__PURE__ */ read(\"protect\")\nexport const recordActions = /* @__PURE__ */ read(\"recordActions\")\nexport const recordPatches = /* @__PURE__ */ read(\"recordPatches\")\nexport const resolveIdentifier = /* @__PURE__ */ read(\"resolveIdentifier\")\nexport const resolvePath = /* @__PURE__ */ read(\"resolvePath\")\nexport const setDevMode = /* @__PURE__ */ read(\"setDevMode\")\nexport const setLivelinessChecking = /* @__PURE__ */ read(\"setLivelinessChecking\")\nexport const setLivelynessChecking = /* @__PURE__ */ read(\"setLivelynessChecking\")\nexport const setTypeChecking = /* @__PURE__ */ read(\"setTypeChecking\")\nexport const splitJsonPath = /* @__PURE__ */ read(\"splitJsonPath\")\nexport const t = /* @__PURE__ */ read(\"t\")\nexport const toGenerator = /* @__PURE__ */ read(\"toGenerator\")\nexport const toGeneratorFunction = /* @__PURE__ */ read(\"toGeneratorFunction\")\nexport const tryReference = /* @__PURE__ */ read(\"tryReference\")\nexport const tryResolve = /* @__PURE__ */ read(\"tryResolve\")\nexport const typecheck = /* @__PURE__ */ read(\"typecheck\")\nexport const types = /* @__PURE__ */ read(\"types\")\nexport const unescapeJsonPath = /* @__PURE__ */ read(\"unescapeJsonPath\")\nexport const unprotect = /* @__PURE__ */ read(\"unprotect\")\nexport const unwrapType = /* @__PURE__ */ read(\"unwrapType\")\nexport const walk = /* @__PURE__ */ read(\"walk\")\nexport default host && host.__esModule ? host.default : host"],
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+  "sourcesContent": ["const host = JBrowseExports[\"mobx-state-tree\"]\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 '\" + \"mobx-state-tree\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const addDisposer = /* @__PURE__ */ read(\"addDisposer\")\nexport const addMiddleware = /* @__PURE__ */ read(\"addMiddleware\")\nexport const applyAction = /* @__PURE__ */ read(\"applyAction\")\nexport const applyPatch = /* @__PURE__ */ read(\"applyPatch\")\nexport const applySnapshot = /* @__PURE__ */ read(\"applySnapshot\")\nexport const asArrayType = /* @__PURE__ */ read(\"asArrayType\")\nexport const asMapType = /* @__PURE__ */ read(\"asMapType\")\nexport const asModelType = /* @__PURE__ */ read(\"asModelType\")\nexport const cannotDetermineSubtype = /* @__PURE__ */ read(\"cannotDetermineSubtype\")\nexport const cast = /* @__PURE__ */ read(\"cast\")\nexport const castFlowReturn = /* @__PURE__ */ read(\"castFlowReturn\")\nexport const castToReferenceSnapshot = /* @__PURE__ */ read(\"castToReferenceSnapshot\")\nexport const castToSnapshot = /* @__PURE__ */ read(\"castToSnapshot\")\nexport const clone = /* @__PURE__ */ read(\"clone\")\nexport const createActionTrackingMiddleware = /* @__PURE__ */ read(\"createActionTrackingMiddleware\")\nexport const createActionTrackingMiddleware2 = /* @__PURE__ */ read(\"createActionTrackingMiddleware2\")\nexport const decorate = /* @__PURE__ */ read(\"decorate\")\nexport const destroy = /* @__PURE__ */ read(\"destroy\")\nexport const detach = /* @__PURE__ */ read(\"detach\")\nexport const escapeJsonPath = /* @__PURE__ */ read(\"escapeJsonPath\")\nexport const extendInstance = /* @__PURE__ */ read(\"extendInstance\")\nexport const findParent = /* @__PURE__ */ read(\"findParent\")\nexport const flow = /* @__PURE__ */ read(\"flow\")\nexport const getChildType = /* @__PURE__ */ read(\"getChildType\")\nexport const getEnv = /* @__PURE__ */ read(\"getEnv\")\nexport const getIdentifier = /* @__PURE__ */ read(\"getIdentifier\")\nexport const getLivelinessChecking = /* @__PURE__ */ read(\"getLivelinessChecking\")\nexport const getMembers = /* @__PURE__ */ read(\"getMembers\")\nexport const getNodeId = /* @__PURE__ */ read(\"getNodeId\")\nexport const getParent = /* @__PURE__ */ read(\"getParent\")\nexport const getParentOfType = /* @__PURE__ */ read(\"getParentOfType\")\nexport const getPath = /* @__PURE__ */ read(\"getPath\")\nexport const getPathParts = /* @__PURE__ */ read(\"getPathParts\")\nexport const getPropertyMembers = /* @__PURE__ */ read(\"getPropertyMembers\")\nexport const getRelativePath = /* @__PURE__ */ read(\"getRelativePath\")\nexport const getRoot = /* @__PURE__ */ read(\"getRoot\")\nexport const getRunningActionContext = /* @__PURE__ */ read(\"getRunningActionContext\")\nexport const getSnapshot = /* @__PURE__ */ read(\"getSnapshot\")\nexport const getType = /* @__PURE__ */ read(\"getType\")\nexport const getUnionSubtypes = /* @__PURE__ */ read(\"getUnionSubtypes\")\nexport const getWrappedType = /* @__PURE__ */ read(\"getWrappedType\")\nexport const hasParent = /* @__PURE__ */ read(\"hasParent\")\nexport const hasParentOfType = /* @__PURE__ */ read(\"hasParentOfType\")\nexport const isActionContextChildOf = /* @__PURE__ */ read(\"isActionContextChildOf\")\nexport const isActionContextThisOrChildOf = /* @__PURE__ */ read(\"isActionContextThisOrChildOf\")\nexport const isAlive = /* @__PURE__ */ read(\"isAlive\")\nexport const isArrayType = /* @__PURE__ */ read(\"isArrayType\")\nexport const isFrozenType = /* @__PURE__ */ read(\"isFrozenType\")\nexport const isIdentifierType = /* @__PURE__ */ read(\"isIdentifierType\")\nexport const isLateType = /* @__PURE__ */ read(\"isLateType\")\nexport const isLiteralType = /* @__PURE__ */ read(\"isLiteralType\")\nexport const isMapType = /* @__PURE__ */ read(\"isMapType\")\nexport const isModelType = /* @__PURE__ */ read(\"isModelType\")\nexport const isOptionalType = /* @__PURE__ */ read(\"isOptionalType\")\nexport const isPrimitiveType = /* @__PURE__ */ read(\"isPrimitiveType\")\nexport const isProtected = /* @__PURE__ */ read(\"isProtected\")\nexport const isReferenceType = /* @__PURE__ */ read(\"isReferenceType\")\nexport const isRefinementType = /* @__PURE__ */ read(\"isRefinementType\")\nexport const isRoot = /* @__PURE__ */ read(\"isRoot\")\nexport const isStateTreeNode = /* @__PURE__ */ read(\"isStateTreeNode\")\nexport const isType = /* @__PURE__ */ read(\"isType\")\nexport const isUnionType = /* @__PURE__ */ read(\"isUnionType\")\nexport const isValidReference = /* @__PURE__ */ read(\"isValidReference\")\nexport const joinJsonPath = /* @__PURE__ */ read(\"joinJsonPath\")\nexport const onAction = /* @__PURE__ */ read(\"onAction\")\nexport const onPatch = /* @__PURE__ */ read(\"onPatch\")\nexport const onSnapshot = /* @__PURE__ */ read(\"onSnapshot\")\nexport const protect = /* @__PURE__ */ read(\"protect\")\nexport const recordActions = /* @__PURE__ */ read(\"recordActions\")\nexport const recordPatches = /* @__PURE__ */ read(\"recordPatches\")\nexport const resolveIdentifier = /* @__PURE__ */ read(\"resolveIdentifier\")\nexport const resolvePath = /* @__PURE__ */ read(\"resolvePath\")\nexport const setDevMode = /* @__PURE__ */ read(\"setDevMode\")\nexport const setLivelinessChecking = /* @__PURE__ */ read(\"setLivelinessChecking\")\nexport const setLivelynessChecking = /* @__PURE__ */ read(\"setLivelynessChecking\")\nexport const setTypeChecking = /* @__PURE__ */ read(\"setTypeChecking\")\nexport const splitJsonPath = /* @__PURE__ */ read(\"splitJsonPath\")\nexport const t = /* @__PURE__ */ read(\"t\")\nexport const toGenerator = /* @__PURE__ */ read(\"toGenerator\")\nexport const toGeneratorFunction = /* @__PURE__ */ read(\"toGeneratorFunction\")\nexport const tryReference = /* @__PURE__ */ read(\"tryReference\")\nexport const tryResolve = /* @__PURE__ */ read(\"tryResolve\")\nexport const typecheck = /* @__PURE__ */ read(\"typecheck\")\nexport const types = /* @__PURE__ */ read(\"types\")\nexport const unescapeJsonPath = /* @__PURE__ */ read(\"unescapeJsonPath\")\nexport const unprotect = /* @__PURE__ */ read(\"unprotect\")\nexport const unwrapType = /* @__PURE__ */ read(\"unwrapType\")\nexport const walk = /* @__PURE__ */ read(\"walk\")\nexport default host && host.__esModule ? host.default : host"],
+  "mappings": "AAAA,IAAMA,EAAO,eAAe,iBAAiB,EACvCC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,iIAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EACOC,EAA8BF,EAAK,aAAa,EAsBtD,IAAMG,EAAuBC,EAAK,MAAM,EAExC,IAAMC,EAAyBC,EAAK,QAAQ,EAW5C,IAAMC,EAA0BC,EAAK,SAAS,EAU9C,IAAMC,EAA0BC,EAAK,SAAS,EAsC9C,IAAMC,EAAwBC,EAAK,OAAO,EAKjD,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
+  "names": ["host", "read", "name", "addDisposer", "flow", "read", "getEnv", "read", "getRoot", "read", "isAlive", "read", "types", "read", "mobx_state_tree_default", "host"]
 }