jbrowse-plugin-graphgenomeviewer 7.1.2 → 7.1.3

package/dist/chunks/{GraphGenomeView-NJ5XCREB.js → GraphGenomeView-LX7GDEDM.js}

@@ -1,4 +1,4 @@
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+import{a as C}from"./chunk-BHSELHTZ.js";import"./chunk-BUY2PV7D.js";import"./chunk-LVQUQSAH.js";import"./chunk-6PC7WKLS.js";import{k as d}from"./chunk-VJ3SO4CH.js";import"./chunk-LBY7U6OJ.js";import"./chunk-FITPB5X6.js";import"./chunk-WAMBI7OX.js";import"./chunk-W6EQLQ6H.js";import"./chunk-5O6YRJHL.js";import"./chunk-N6PQZSAX.js";import"./chunk-TUKJRVBS.js";import"./chunk-FVK2THE4.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-ZMOMFU2B.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as x}from"./chunk-YU7T5WOQ.js";import{A as l,F as L,H as p,e as s,j as v,o as n,x as G}from"./chunk-UGCNPRKC.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,S=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),T=i(function({model:e}){let{classes:t}=S(),[m,M]=x("");function u(){let o=m.trim();o&&e.loadGFAFromLocation({uri:o,locationType:"UriLocation"})}function N(o){let c=o.target.files?.[0];o.target.value="",c&&c.text().then(f=>e.loadGFA(f,c.name)).catch(f=>{e.setError(f)})}return r(l,{className:t.paper,children:[a("div",{className:t.header,children:a(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",a("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:o=>{N(o)}})]}),a(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[a(L,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{M(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),a(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),a("div",{className:t.footer,children:a(n,{size:"small",onClick:()=>{e.loadGFA(F,"Example graph")},children:"Load 4-node example"})}),e.error?a(s,{error:e.error}):null]})}),P=T;var A=i(function({model:e}){return e.hasGraph?a(C,{model:e}):e.canRetryLoad&&(e.error||e.loadCanceled)?a(g,{model:e}):r(y,{children:[e.isLoading?a(g,{model:e}):null,a("div",{hidden:e.isLoading,children:a(P,{model:e})})]})}),J=A;export{J as default};
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package/dist/chunks/{LinearGraphDisplay-TXTKAACH.js → LinearGraphDisplay-QLPIRKPR.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{WalkTabixSyntenyAdapter-U53JLYVU.js → WalkTabixSyntenyAdapter-GH6NYQTF.js}

@@ -1,2 +1,2 @@
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the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(s,e,t)}async laneWalks(e,t,s,n,a){return C(a,n.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:n.signal,keep:q(s,e),links:!1}).catch(r=>{throw z(r)&&r instanceof Error&&(r.message=r.message.replace("to see the graph","to see lanes")),r}))}async anchorFeatures(e,t,s){let n=s.haplotypes?.length?s.haplotypes.map(m=>k(this,m)):void 0,a=k(this,s.targetAssemblyName),r=a===void 0?n:n===void 0||n.some(m=>P(a,m)||P(m,a))?[a]:[];if(r?.length===0)return[];let{start:f,end:g}=t,{graph:y,fragments:l}=await this.laneWalks(e,t,r,s,`Reading walks ${t.refName}:${f.toLocaleString()}-${g.toLocaleString()}`),p=J(y.nodes),N=x(this),h=l.filter(m=>m.name===e),c=m=>r===void 0?0:r.findIndex(d=>P(m.name,d));return l.filter(m=>m.name!==e&&c(m)>=0).sort((m,d)=>c(m)-c(d)).flatMap(m=>h.flatMap(d=>p(m,d).map(A=>B({chain:A,target:d,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:E(N,ne(m))}))))}async pairFeatures(e,t,s,n){let a=s.map(l=>({pair:l,featurePrefix:k(this,l.queryAssemblyName),matePrefix:k(this,l.targetAssemblyName)})),{graph:r,fragments:f}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),n,D(s)),g=U(r.nodes),y=l=>f.filter(p=>P(p.name,l));return a.flatMap(({pair:l,featurePrefix:p,matePrefix:N})=>y(p).flatMap(h=>y(N).flatMap(c=>g(c,h).map(b=>B({chain:b,target:h,query:c,assemblyName:l.queryAssemblyName,refName:S(h.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return $(async s=>{let n=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(n!==void 0){let a=H(t),r=a.length>0?await this.pairFeatures(n,e,a,t):await this.anchorFeatures(n,e,t);for(let f of r)s.next(f)}s.complete()},t.signal)}};export{L as default};
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+import{a as G}from"./chunk-MND7GAOG.js";import{a as z}from"./chunk-PJ43KEV6.js";import{b as j,d as H,e as D,f as E,g as X}from"./chunk-EGDLEQ47.js";import{a as $}from"./chunk-KOB7YIMR.js";import{p as W,q as R,r as I}from"./chunk-T4HOC6O3.js";import"./chunk-FVK2THE4.js";import{e as q,m as T,n as _}from"./chunk-FHZXW7IG.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as F,c as v,d as S,e as P,f as k,g as x}from"./chunk-ZMOMFU2B.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as C}from"./chunk-TENPGIPX.js";var ee=50;function te(i){let o=[];for(let e=0;e<i.length;e++){let[t,s]=i[e],[n,a]=i[e+1]??[];s===a&&s<=ee&&(t==="I"&&n==="D"||t==="D"&&n==="I")?(o.push(["X",s]),e++):o.push([t,s])}return o}function M(i){return Array.from(i.ids,(o,e)=>2*o+i.rev[e])}function K(i,o){let e=i.get(o);return e===void 0?0:e.end-e.start}function U(i){let o=new Map,e=n=>{let a=K(i,n),r=o.get(a);return r===void 0&&(r="N".repeat(a),o.set(a,r)),r},t=new Map,s=n=>{let a=t.get(n);return a===void 0&&(a=M(n),t.set(n,a)),a};return(n,a)=>R({query:s(n),target:s(a),sequenceOf:e,bases:!1})}var ae=100;function O(i,o,e){let t=i.at(-1);e>0&&(t?.[0]===o?t[1]+=e:i.push([o,e]))}function J(i){let o=t=>K(i,t>>1),e=t=>{let s=new Float64Array(t.length+1);return t.forEach((n,a)=>{s[a+1]=s[a]+o(n)}),s};return(t,s)=>{let n=M(s),a=M(t),[r,f]=W(a,n,o),[g,y]=W(a.map(u=>u^1).reverse(),n,o),l=y>f,p=l?g:r,N=Math.max(f,y);if(N<ae)return[];let h=e(n),c=e(a),b=u=>l?a.length-1-p[u][0]:p[u][0],m=[];p.forEach(([,u],w)=>{if(w>0){let[Q,V]=[b(w-1),b(w)].sort((Y,Z)=>Y-Z);O(m,"I",c[V]-c[Q+1]),O(m,"D",h[u]-h[p[w-1][1]+1])}O(m,"=",o(n[u]))});let[d,A]=[b(0),b(p.length-1)].sort((u,w)=>u-w);return[{queryStart:c[d],queryEnd:c[A+1],targetStart:h[p[0][1]],targetEnd:h[p.at(-1)[1]+1],strand:l?"-":"+",edits:m,sharedBases:N}]}}function B({chain:i,target:o,query:e,assemblyName:t,refName:s,mateAssemblyName:n}){let a=te(i.edits);return X({target:{name:o.name,assemblyName:t,refName:s,start:o.hapStart+i.targetStart,end:o.hapStart+i.targetEnd},query:{name:e.name,assemblyName:n,refName:S(e.name),start:e.hapStart+i.queryStart,end:e.hapStart+i.queryEnd},strand:i.strand,cigar:I(a),matches:a.reduce((r,[f,g])=>r+(f==="="?g:0),0),columns:a.reduce((r,[,f])=>r+f,0)})}var ne=i=>v(i.name)??i.name,L=class extends j{constructor(){super(...arguments);this.walks=new G(T(this,["walksLocation"],["walksIndex"]),this);this.refNames=new _(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:s}=this,n=k(this,s),a=x(this);return{hasCoarseTier:!1,anchorAssemblyName:s,lanes:t.filter(r=>r!==n&&F(r)!==n).map(r=>({name:E(a,r),label:r,group:F(r)}))}}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 s=await this.refNames.resolve(e,{signal:t.signal});if(s===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(s,e,t)}async laneWalks(e,t,s,n,a){return C(a,n.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:n.signal,keep:q(s,e),links:!1}).catch(r=>{throw z(r)&&r instanceof Error&&(r.message=r.message.replace("to see the graph","to see lanes")),r}))}async anchorFeatures(e,t,s){let n=s.haplotypes?.length?s.haplotypes.map(m=>k(this,m)):void 0,a=k(this,s.targetAssemblyName),r=a===void 0?n:n===void 0||n.some(m=>P(a,m)||P(m,a))?[a]:[];if(r?.length===0)return[];let{start:f,end:g}=t,{graph:y,fragments:l}=await this.laneWalks(e,t,r,s,`Reading walks ${t.refName}:${f.toLocaleString()}-${g.toLocaleString()}`),p=J(y.nodes),N=x(this),h=l.filter(m=>m.name===e),c=m=>r===void 0?0:r.findIndex(d=>P(m.name,d));return l.filter(m=>m.name!==e&&c(m)>=0).sort((m,d)=>c(m)-c(d)).flatMap(m=>h.flatMap(d=>p(m,d).map(A=>B({chain:A,target:d,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:E(N,ne(m))}))))}async pairFeatures(e,t,s,n){let a=s.map(l=>({pair:l,featurePrefix:k(this,l.queryAssemblyName),matePrefix:k(this,l.targetAssemblyName)})),{graph:r,fragments:f}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),n,D(s)),g=U(r.nodes),y=l=>f.filter(p=>P(p.name,l));return a.flatMap(({pair:l,featurePrefix:p,matePrefix:N})=>y(p).flatMap(h=>y(N).flatMap(c=>g(c,h).map(b=>B({chain:b,target:h,query:c,assemblyName:l.queryAssemblyName,refName:S(h.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return $(async s=>{let n=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(n!==void 0){let a=H(t),r=a.length>0?await this.pairFeatures(n,e,a,t):await this.anchorFeatures(n,e,t);for(let f of r)s.next(f)}s.complete()},t.signal)}};export{L as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-GH6NYQTF.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-U53JLYVU.js.map → WalkTabixSyntenyAdapter-GH6NYQTF.js.map}

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

package/dist/chunks/{chunk-NWJYLP6Z.js → chunk-6PC7WKLS.js}

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t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?Vt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>Vt(dt(t,xe(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(xe(t)),s=new Set(n.nodes.filter(a=>o.has(a.name)).map(a=>a.id)),r=new Set;return n.edges.forEach((a,i)=>{s.has(a.from)&&s.has(a.to)&&r.add(i)}),{walks:[],nodeIds:s,edgeIndexes:r,names:new Set}},bubbleIsOpen(t){return e.openBubbles.some(n=>Et(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,s=this.openBubbleFocus;return o?!n.some(r=>o.nodeIds.has(r)):!!s&&!this.bubbleIsOpen(t)&&!n.every(r=>s.nodeIds.has(r))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(It));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(It(o))&&n.add(It(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Io(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get 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t?cn(t):e.graph?Ie(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=ne(e),o=n.has(t)?n.get(t):void 0,s=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(a=>s[a]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t=e.containingView;if(!t)return;let n=Js(t,e.geneTrack?.trackId);return n.length?new Xs({filters:n,jexl:po(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Qs(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,s=e.drawsLoadedReference||n!==void 0&&rn(t,[n])!==void 0;return t&&o&&s?sn(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?pe(e.drawnGraph):void 0},get nodeInk(){return xt(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?we(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?uc(n,t,t.unit):Ie(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[s,...r]=Nr([o.reference,...o.rows],t?.calls);return{...o,reference:s,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&fo(t)?t:void 0},get walkRowGroupFields(){return nr(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=dr(t,n),s=(e.graph?.paths??[]).map(r=>W(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:ir(s.map(o)),unvalued:s.some(r=>o(r)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,domain:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows;return t&&Qe(t.rows,e.walkRowSamples)},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?rr(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get drawsNodes(){return Q(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Je(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?ot(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){Je(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:Xn(e.graph,e.bubbles,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return qe(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?ye(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,o=n?.tubeMap?n.nodePositions:void 0,s=!1,r=!1;if(t&&e.drawnGraph)for(let a of e.drawnGraph.nodes)o&&!o[a.id]||(t.midpoints.has(a.id)?a.stable&&a.stable.rank>0&&(s=!0):r=!0);return{offReference:s,unplaced:r}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?Kn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!yt(n.length)||n.some(s=>s.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],s=this.tubeColorKind,r=e.tubeMapColoring;return s==="value"&&r?cr(o,t.referencePath,r.valueOf,r.palette):s==="tinted"?kn(o,t.referencePath,ar):s==="role"?kn(o,t.referencePath):n},fadeUnhovered(t,n,o){let s=new Set(e.hoveredRowWalks);return s.size>0?t.map((r,a)=>{let i=n[a]?.name??"";return s.has(i)||o!==void 0&&W(i).name===o?r:St}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return ia(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&aa(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&pe(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&yt(t.length)&&!t.some(o=>o.members)?We(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?ia(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var da=ca.views(e=>({get host(){let t=e.containingView;return Ms(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?de(t):[];return t?Rs(t,{maxGap:n.length>0?tn(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=ne(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([r,a])=>[a,r])),s=r=>r!==void 0&&t.has(r)?t.get(r)?.name??r:void 0;return r=>s(o.get(r))??s(r)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(mt.has(n.adapterType))for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let s=zt(o,"");return s?[[n,s]]:[]}))}})).views(e=>({get launchableAssemblies(){return vs(Ys(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&pt({views:[...ne(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?xs(n):void 0,s=o?nt(e.assemblyResolver,o):void 0,r=e.graphRegion,a=r?e.nodeSpan(t):void 0,i=r&&a?{sample:r.assemblyName,haplotype:void 0,refName:r.refName,...a}:void 0;return{own:o&&s?{location:Zn(o),assembly:s}:void 0,reference:r&&i?{location:Zn(i),assembly:r.assemblyName}:void 0,highlight:r&&i?{location:i,assembly:r.assemblyName}:void 0}}}));var pa=da.views(e=>({get walkStripShown(){return On({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:Qe(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return tt(t,{width:e.paneWidth})},get cutsWholeWalks(){return Bn(Q(e.chosenLayoutMode),{walkStrip:e.walkStrip,host:!!e.host})},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?Cn(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:nt(e.assemblyResolver,o),span:{refName:n.contig,...Ho(n,t.bp)}}},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:Gt(e.nodePositions?.[t],e.toScreen)}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,s=0;for(let r of t.rows){if(!r.axis){s++;continue}let{assembly:a,span:i}=e.rowLocation(r,r.axis),c=a?e.geneTracksByAssembly.get(a):void 0;if(!a||!c){o++;continue}n.push({row:r.name,trackId:c.trackId,region:{assemblyName:a,...i}})}return{reads:n.slice(0,An),gaps:{untracked:o,unplaced:s,unread:Math.max(0,n.length-An)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 0;if(!o?.axis)return;let{sample:s,haplotype:r,assembly:a,span:i}=e.rowLocation(o,o.axis);return{label:o.label,assembly:t===0?e.graphRegion?.assemblyName:a,location:{sample:s,haplotype:r,...i}}},get walkRowGenes(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=new Map(e.walkGeneFeatures??[]);return e.geneFeatures&&n.set(t.reference.name,e.geneFeatures),n.size?Xo([t.reference,...t.rows],n):void 0}}));var la=pa.views(e=>({get xIsReferenceBp(){return e.layoutResult?.referenceAxis===!0&&Q(e.drawnLayoutMode??e.chosenLayoutMode).cutMargins}})).views(e=>({get hostPlacesX(){let{host:t,graphRegion:n}=e;return t!==void 0&&t.initialized&&n!==void 0&&e.xIsReferenceBp&&!t.dynamicBlocks.contentBlocks.some(o=>o.refName===n.refName&&o.reversed)}})).views(e=>({get hostBpFrame(){let{host:t,graphRegion:n}=e;return t?.initialized&&n?Ns(t,n):void 0}})).views(e=>({get hostFrame(){return e.hostPlacesX?e.hostBpFrame:void 0},get tubeMapPicture(){let t=e.layoutResult?.tubeMap;return t?er(t):void 0},get tubeMapReference(){let t=e.layoutResult?.tubeMap;return t?Zo(t):void 0},get tubeMapDeviations(){let t=e.layoutResult?.tubeMap;return t?.coarse?Qo(t,t.coarse.deviations):[]},get tubeMapConnectedBoxes(){let t=this.tubeMapReference,{layoutResult:n}=e;return t&&!n?.referenceAxis&&!n?.tubeMapPanels?[...t.values()].flat():void 0}})).views(e=>({get tubeMapGenes(){let t=e.tubeMapReference;return e.showGenes&&!e.host&&t&&e.backboneGenes&&!e.layoutResult?.tubeMapPanels?kr(t,e.backboneGenes):[]},get referenceStripApplies(){return!!e.host?.initialized&&!!e.layoutResult&&e.drawsNodes&&!e.hostPlacesX&&!e.facetPanels}})).views(e=>({get referenceStripBlocks(){let{graph:t}=e;if(!e.showReferenceStrip||!e.referenceStripApplies||!t)return[];let n=vr(t,{colorScheme:e.effectiveColorScheme,referenceRamp:e.referenceRamp,walks:e.walkLift?.walks}),o=e.walkLift?void 0:e.openBubbleFocus;return o?n.map(s=>o.nodeIds.has(s.node)?s:{...s,colors:[St],faded:!0}):n}})).views(e=>({get referenceStripShown(){return e.referenceStripBlocks.length>0&&e.hostBpFrame!==void 0},get referenceStripOverhangs(){let t=e.hostBpFrame;if(!t||e.referenceStripBlocks.length===0)return!1;let{left:n,right:o}=Mr(e.referenceStripBlocks,t,e.paneWidth);return n>0||o>0},get referenceStripFaded(){return e.referenceStripBlocks.some(t=>t.faded)}})).views(e=>({get referenceStripLit(){if(!e.referenceStripShown)return;let t=e.hoveredNode===null?e.hoveredBubble:null;if(t&&!t.offReference){let s=e.bubbleHalos.find(r=>Et(r.bubble,t));return{start:t.start,end:t.end,anchor:s?e.toScreen(s.labelAt):void 0}}let n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeSpan(n);return o&&n!==null?{...o,anchor:Gt(e.nodePositions?.[n],e.toScreen)}:void 0},referenceStripNodeAt(t,n){let o=e.hostBpFrame;return e.referenceStripShown&&o?Lr(e.referenceStripBlocks,o,t,n):void 0},get referenceStripZonePx(){return e.referenceStripShown?Rr:0}}));var Qy=3e3,ek=350,tk=34;function mc(e){let t=[0];for(let n=1;n<e.length;n++)t.push(t[n-1]+Math.hypot(e[n].x-e[n-1].x,e[n].y-e[n-1].y));return t}function fc(e,t){if(e.length===1||t===1)return Array.from({length:t},()=>({...e[0]}));let n=mc(e),o=n.at(-1),s=[],r=1;for(let a=0;a<t;a++){let i=o*a/(t-1);for(;r<e.length-1&&n[r]<i;)r++;let c=n[r]-n[r-1],p=c>0?(i-n[r-1])/c:0,u=e[r-1],l=e[r];s.push({x:u.x+(l.x-u.x)*p,y:u.y+(l.y-u.y)*p})}return s}var hc=400,ua=1.8,gc=.1;function nk(e,t,n,o,s){let r=b=>({x:(b.x*t.scaleX+t.translateX-o.translateX)/o.scaleX,y:(b.y*t.scaleY+t.translateY-o.translateY)/o.scaleY}),a={};for(let[b,S]of Object.entries(n)){let x=e[b];x?.length&&S.length&&(a[b]=fc(x.map(r),S.length))}let i=new Map,c=(b,S)=>{let x=i.get(b);x?x.push(S):i.set(b,[S])};for(let b of s){let{from:S,to:x}=b;if(S!==x&&n[S]?.length&&n[x]?.length){let M=be(b);c(S,{id:x,side:M.to}),c(x,{id:S,side:M.from})}}let p=new Map,u=b=>p.get(b.id)??(b.side==="start"?a[b.id][0]:a[b.id].at(-1)),l=Object.keys(a),d=[];for(let b of l)for(let S of i.get(b)??[]){if(a[S.id]||p.has(S.id))continue;let x=i.get(S.id).find(M=>M.id===b);p.set(S.id,{...u(x)}),l.push(S.id),d.push(S.id)}let f=new Map(d.map((b,S)=>[b,S])),h=new Float64Array(d.map(b=>p.get(b).x)),w=new Float64Array(d.map(b=>p.get(b).y)),g=new Float64Array(d.length),m=new Float64Array(d.length),y=d.map((b,S)=>i.get(b).flatMap(x=>{let M=f.get(x.id);if(M===void 0){let P=u(x);return g[S]+=P.x,m[S]+=P.y,[]}return[M]})),k=d.map(b=>i.get(b).length);for(let b=0;b<hc;b++){let S=0;for(let x=0;x<d.length;x++){let M=g[x],P=m[x];for(let C of y[x])M+=h[C],P+=w[C];let F=ua*(M/k[x]-h[x]),B=ua*(P/k[x]-w[x]);S=Math.max(S,Math.abs(F*o.scaleX)+Math.abs(B*o.scaleY)),h[x]+=F,w[x]+=B}if(S<gc)break}d.forEach((b,S)=>{a[b]=n[b].map(()=>({x:h[S],y:w[S]}))});for(let[b,S]of Object.entries(n))a[b]??=S.map(x=>({...x}));return a}function bc(e,t){let n=0,o=1/0;return e.forEach((s,r)=>{let a=(s.x-t.x)**2+(s.y-t.y)**2;a<o&&(o=a,n=r)}),n}function ok(e,t,n,o){let s=(r,a)=>{let i=n[r],c=o[r];if(!i||!c||c.length===0)return{x:0,y:0};let p=bc(c,a);return{x:i[p].x-c[p].x,y:i[p].y-c[p].y}};return Object.fromEntries(Object.entries(e).map(([r,a])=>{let i=t[Number(r)],c=s(i?.from??"",a[0]),p=s(i?.to??"",a.at(-1));return[r,a.map((u,l)=>{let d=a.length>1?l/(a.length-1):0;return{x:u.x+c.x+(p.x-c.x)*d,y:u.y+c.y+(p.y-c.y)*d}})]}))}function ma(e,t,{ids:n,alpha:o}){let s=(r,a)=>{for(let i=0;a&&i<a.count;i++){let c=r[a.start+i];c.color=_o(c.color,o)}};for(let r of n)s(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:a},i)=>{(n.has(r)||n.has(a))&&(s(e.edgeCurves,e.edgeCurveRuns.get(i)),s(e.arrows,e.arrowRuns.get(i)))})}function rk(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function sk(e,t,n,o){for(let[s,r]of Object.entries(e)){let a=t[s],i=n[s];!a||!i||r.forEach((c,p)=>{c.x=o===1?i[p].x:a[p].x+(i[p].x-a[p].x)*o,c.y=o===1?i[p].y:a[p].y+(i[p].y-a[p].y)*o})}}var wc=8,yc=19,fa=je+yc,kc=48;function xc(e,t,n){if(!(!e||!t))return vt(e.rowPx,e.barPx)?n:{untracked:0,unread:0,...n,crowded:!0}}var Pk=la.views(e=>({get paneCeiling(){return Math.max(_t,e.paneHeight??Yr)},get fitRoom(){return e.host?this.canvasHeight:this.paneCeiling},get walkRowPitch(){let t=e.walkRowBars;if(!t)return;let n=this.fitRoom,o=(e.walkRowGroups?.sections.length??0)*tr;return Mt(t.rows.length+1,n-this.fitPadTopBase-H-o)},get walkRowPlacement(){let t=this.walkRowPitch;return t?sr(e.walkRowGroups?.sections??[],t.rowPx):void 0},get walkRowGeneKey(){return xc(this.walkRowPitch,!!e.walkRowGenes?.size,e.walkRowGeneGaps)},get drawnRowLabels(){let t=this.walkRowPlacement,n=Oe(e.walkRowBars,e.layoutResult,this.walkRowPitch);return e.walkRowBars&&t?n.map((o,s)=>({...o,y:t.rowY(s)})):n},get visibleRowLabels(){return this.drawnRowLabels.flatMap(({label:t,y:n})=>{let o=e.toScreen({x:0,y:n}).y;return o>=0&&o<=this.canvasHeight?[{label:t,y:n,top:o}]:[]})},get fitPadLeft(){return Math.max(H,...this.drawnRowLabels.map(t=>Eo(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?Ge(n,this.walkRowPitch):void 0;return t?Ke(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,s=o?t.reference:t.rows.find(r=>r.name===n);return s?{label:s.label,readout:Do(s,o?void 0:t.reference,t.unit,s.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,s=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!s||!r)return;let a=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][a],c=r.rowY(a)*e.scaleY+e.translateY,p=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=s.barPx/2+2&&p>=0&&p<=i.bp?a:void 0},get fitPadTopBase(){let t=Sr(e.tubeMapGenes);return H+Math.max(0,t-1)*xr+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let s=this.fitPadTopBase,r=this.fitRoom,a=u=>(e.paneWidth-this.fitPadLeft-u)/t.w,i=u=>e.pixelRows?t.h+u+H<=r?1/0:0:(r-u-H)/t.h,c=Math.min(a(n+2*ue),i(s));return Math.min(a(H),i(s+o+ue))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ue:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(H,e.legendSize.width+2*ue):H},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(zr/o,(this.paneCeiling-this.fitPadTop-H)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?Pt(t.map(s=>s.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?Nt({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-fa)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ue+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-kc?t+2*ue:wc},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(_t,o.total+fa);let s=Math.max(_t,e.legendSize.height+2*ue+e.referenceStripZonePx),r=this.fitPads,a=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(s,t.h+a));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(s,t.h*Math.max(i/t.w,this.minFitScale)+a)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:ae,top:ae,right:ae,bottom:ae}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:H}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,s=this.fitPads;return t?ze(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:s.left,padTop:s.top,padRight:s.right,padBottom:s.bottom}):void 0}})).views(e=>({viewportToBuild(){return Nn(Qr(e),Jr)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,qr]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=Jo();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:Ur)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:s,layoutResult:r,deletionDrawing:a}=e;if(!o||!s||!r||!a)return;Je(e.viewportDirty,e.positionsVersion);let i=dn(()=>e.viewportToBuild()),c=Rt({...rt(r,a,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:s,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:dn(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),p=e.morphEntering;return p?.layout===r&&ma(c,o.edges,p),{batch:c,viewportBounds:i}},get overlayLabels(){return gr(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?yr(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,s=t&&`${t.refName}:${t.start}-${t.end}`,r=Ee(e.sourceGfaLocation),a=n?.type==="GbzBaseSyntenyAdapter"?Ee(n.gbzDbLocation):void 0,i=r?{gfa:r,region:s}:a&&t&&s?{gbz:{db:a,index:Ee(n.haplotypeIndexLocation),region:s,haplotypes:e.cutHaplotypes?.map(d=>o?.[d]??d),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!i)return;let c=e.showGenes?e.geneTrack:void 0,p=c?ne(e).tracks.find(d=>d.trackId===c.trackId):void 0,u=p?mo(q(p,"adapter"),"gffGzLocation"):void 0,l=u?.type==="Gff3TabixAdapter"?{file:Ee(u.gffGzLocation),index:Ee(u.index?.location),format:"gff3"}:void 0;return 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