npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.4.3 → 7.4.4 - Mend

jbrowse-plugin-graphgenomeviewer 7.4.3 → 7.4.4

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Files changed (121) hide show

package/dist/chunks/chunk-G53BI7VK.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{c as Wt,o as Ht,r as pt}from"./chunk-LE7FZM6Y.js";import{a as St,c as Dt,d as Vt,e as Zt}from"./chunk-6SWXMRAV.js";var fe="ws",ce="we",Xt=["elsewhere","break","end"],ke={missing:"not in the graph",elsewhere:"on nodes filed elsewhere",unknown:"gap, cause unknown",abridged:"abridged: steps not loaded"},ye="outside the extracted subgraph";function Kt(t,e,s){if(!e&&!s)return[{bp:t}];let n=Math.min(e?.trimmed??0,t),r=Math.min(s?.trimmed??0,t-n),i=t-n-r,h=e?.kind==="break"?Math.min(e.bp,i):0;i-=h;let c=s?.kind==="break"?Math.min(s.bp,i):0;i-=c;let o=[e,s].find(k=>k?.kind==="elsewhere");return[{bp:n},{bp:h,cause:"missing"},o?.kind==="elsewhere"?{bp:i,cause:"elsewhere",chunk:o.chunk}:{bp:i,cause:"unknown"},{bp:c,cause:"missing"},{bp:r}].filter(k=>k.bp>0)}function xt(t,e){let s=t.bp[e],n=t.chunkRefs[e];return qt(t.kindNames[t.kinds[e]],Number.isNaN(s)?void 0:s,t.trimmed[e],n<0?void 0:{refName:t.chunkRefNames[n],start:t.chunkStarts[e]})}function qt(t,e,s,n){let r=s>0?{trimmed:s}:{};return t==="elsewhere"&&n?{kind:t,chunk:n,...e===void 0?{}:{bp:e},...r}:t==="break"&&e!==void 0?{kind:t,bp:e,...n?{chunk:n}:{},...r}:t==="end"?{kind:t,...r}:void 0}function zt(t){let[e,...s]=t.split(","),n,r=0,i;for(let h of s)if(h.startsWith("bp="))n=+h.slice(3);else if(h.startsWith("trimmed="))r=+h.slice(8);else if(h.startsWith("chunk=")){let c=h.lastIndexOf(":");i={refName:h.slice(6,c),start:+h.slice(c+1)}}return qt(e,n,r,i)}function Ft(t,e){return{...t?{before:t}:{},...e?{after:e}:{}}}function Ae(t){let e=t[fe],s=t[ce];return Ft(typeof e=="string"?zt(e):void 0,typeof s=="string"?zt(s):void 0)}var we=class{constructor(){this.kinds=[],this.bp=[],this.trimmed=[],this.chunkRefs=[],this.chunkStarts=[],this.chunkRefNames=[],this.refIndex=new Map}push(t){this.kinds.push(Xt.indexOf(t.kind)),this.bp.push("bp"in t&&t.bp!==void 0?t.bp:NaN),this.trimmed.push(t.trimmed??0);let e="chunk"in t?t.chunk:void 0;if(e){let s=this.refIndex.get(e.refName);s===void 0&&(s=this.chunkRefNames.length,this.refIndex.set(e.refName,s),this.chunkRefNames.push(e.refName)),this.chunkRefs.push(s),this.chunkStarts.push(e.start)}else this.chunkRefs.push(-1),this.chunkStarts.push(NaN)}table(){return{kinds:Uint8Array.from(this.kinds),kindNames:[...Xt],bp:Float64Array.from(this.bp),trimmed:Float64Array.from(this.trimmed),chunkRefs:Int32Array.from(this.chunkRefs),chunkStarts:Float64Array.from(this.chunkStarts),chunkRefNames:this.chunkRefNames}}};function le(t,e,s){return e===0?t:`${t}:${e}-${s}`}function Mt(t,e){let s=t.names[e],n=Zt(s),r=t.starts[e],i=t.abridgedSteps?.[e]??Number.NaN,h=Number.isNaN(i)?{}:{abridged:{steps:i,bp:t.abridgedBp?.[e]??0}};return n?{name:`${n.sample}#${n.haplotype}#${n.contig}`,start:r,...n,...Ft(t.before&&xt(t.before,e),t.after&&xt(t.after,e)),...h}:{name:le(s,r,t.ends[e]),start:r}}function he(t,e,s,n){let r=new Int32Array(s+1);for(let o of t)r[o+1]++;for(let o=0;o<s;o++)r[o+1]+=r[o];let i=r.slice(0,s),h=new Int32Array(t.length);t.forEach((o,p)=>{h[i[o]++]=e[p]});let c=new Int32Array(n.length).fill(-1);return Array.from({length:s},(o,p)=>{let k=[];for(let R=r[p];R<r[p+1];R++){let j=h[R];c[j]!==p&&(c[j]=p,k.push(n[j]))}return k})}function Tt({nodes:t,links:e,walks:s},n){let r=new Uint8Array(t.names.length),i=(c,o)=>{r[c]===0&&(r[c]=o?2:1)};for(let c=0;c<e.from.length;c++)i(e.from[c],e.strands[c]&1),i(e.to[c],e.strands[c]&2);let h=s.offsets[s.names.length]??0;for(let c=0;c<h;c++){let o=s.steps[c];i(o,s.reversed[c]),n&&n[o]++}return t.names.map((c,o)=>`${c}${r[o]===2?"-":"+"}`)}function xe({nodes:t,links:e,walks:s},n="Imported GFA"){let r=t.names.length,i=t.lengths.length,h=[];for(let a=0;a<s.names.length;a++)s.offsets[a+1]>s.offsets[a]&&h.push(a);let c=new Int32Array(r),o=Tt({nodes:t,links:e,walks:s},c),p=[];for(let a=0;a<i;a++){let v=t.refs[a];p.push({id:o[a],name:t.names[a],length:t.lengths[a],depth:Math.max(c[a],1),stable:v<0?void 0:{refName:t.refNames[v],start:t.starts[a],rank:t.ranks[a]},samples:void 0})}let k=[],R=new Array(r),j=(a,v)=>{let u=R[a];if(u){for(let w=0;w<u.length;w+=2)if(u[w]===v)return u[w+1]}},W=(a,v,u)=>{let w=R[a];w?w.push(v,u):R[a]=[v,u]},at=[],tt=0;for(let a=0;a<e.from.length;a++){let v=e.from[a],u=e.to[a];k.push({from:o[v],to:o[u],fromStrand:e.strands[a]&1?"-":"+",toStrand:e.strands[a]&2?"-":"+"});let w=j(v,u);w===void 0&&(w=tt++,W(v,u,w),W(u,v,w)),at.push(w)}let M=new Int32Array(r+1);for(let a=0;a<r;a++)M[a+1]=M[a]+(R[a]?.length??0)/2;let it=new Int32Array(M[r]),ft=new Int32Array(M[r]);R.forEach((a,v)=>{for(let u=0;u<a.length;u+=2)it[M[v]+u/2]=a[u],ft[M[v]+u/2]=a[u+1]});let Rt=(a,v)=>{for(let u=M[a];u<M[a+1];u++)if(it[u]===v)return ft[u];return-1},O=new Map,B=[],V=new Int32Array(s.offsets[s.names.length]??0),ct=new Int32Array(V.length),et=0,x=new Int32Array(tt).fill(-1),gt=[],U=[],Z=s.offsets[s.names.length]??0,lt=new Int32Array(Z),Nt=new Float64Array(Z),H=new Uint8Array(Z),I=new Int32Array(r).fill(-1),T=[],G=[0],st=[],X=new Map,z=[];for(let a of h){let v=Mt(s,a),{start:u,name:w}=v,K=v.sample===void 0?s.names[a]:w,q=O.get(K);q===void 0&&(q=B.length,O.set(K,q),B.push(K),st.push(St(K)));let f=X.get(w);f===void 0&&(f=z.length,X.set(w,f),z.push(w));let g=st[q],$=s.offsets[a],L=new Array(s.offsets[a+1]-$),E=u,y=-1;for(let P=$;P<s.offsets[a+1];P++){let S=s.steps[P];L[P-$]=o[S],I[S]===-1&&(I[S]=G.at(-1),G.push(I[S]+c[S]),T.push(S));let J=I[S]++;if(lt[J]=q,Nt[J]=E,H[J]=s.reversed[P],E+=S<i?t.lengths[S]:0,y>=0){let D=Rt(y,S);D>=0&&x[D]!==a&&(x[D]=a,V[et]=D,ct[et++]=f)}y=S}gt.push({...v,nodeIds:L}),U.push({name:K,sample:g,start:u,length:E-u})}let bt=he(V.subarray(0,et),ct,tt,z);k.forEach((a,v)=>{let u=bt[at[v]];u.length>0&&(a.pathIds=u)});let ht=h.length>0;return{name:n,nodes:p,edges:k,paths:ht?gt:void 0,anchorPaths:ht?U:void 0,pathVisits:ht?new Ht({segments:T.map(a=>t.names[a]),offsets:Int32Array.from(G),path:lt.subarray(0,G.at(-1)),start:Nt.subarray(0,G.at(-1)),reversed:H.subarray(0,G.at(-1)),paths:B,samples:st}):void 0,anchoredBy:p.some(a=>a.stable)?"tags":void 0}}var Pt=1,Qt=2,It=4,Yt=[void 0,"missing","elsewhere","unknown","abridged"],te=3,ue=t=>Yt.indexOf(t)<<te;function ee(t,e,s){return e!==void 0&&t.includes(e)?e:t.find(n=>s.has(n))??t[0]}function de(t){return ee((t.paths??[]).map(e=>pt(e.name).name),t.referencePath,new Set(t.nodes.flatMap(e=>e.stable?.rank===0?[e.stable.refName]:[])))}function pe(t){let e=new Map,s=[],n=[],r=p=>{let k=e.get(p);return k===void 0&&(k=s.length,e.set(p,k),s.push(p),n.push(0)),k};for(let p of t.nodes)n[r(p.id)]=p.length;let i=t.paths??[],h=new Int32Array(i.length),c=new Int32Array(i.length),o=[];return i.forEach((p,k)=>{h[k]=o.length;for(let R of p.nodeIds)o.push(r(R));c[k]=o.length}),{heads:i,from:h,to:c,steps:Int32Array.from(o),lengths:Int32Array.from(n),names:s,reference:de(t)}}function me(t,e,s){let{nodes:n,walks:r}=t,i=[];for(let o=0;o<r.names.length;o++)r.offsets[o+1]>r.offsets[o]&&i.push(o);let h=i.map(o=>Mt(r,o)),c=new Set;for(let o=0;o<n.lengths.length;o++)n.refs[o]>=0&&n.ranks[o]===0&&c.add(n.refNames[n.refs[o]]);return{heads:h,from:Int32Array.from(i,o=>r.offsets[o]),to:Int32Array.from(i,o=>r.offsets[o+1]),steps:r.steps,lengths:n.lengths,names:s?Tt(t):n.names,reference:ee(h.map(o=>pt(o.name).name),e,c)}}function se(t){return t.sample??St(t.name)}function ge(t){return t.haplotype!==void 0&&t.sample!==void 0?`${t.sample}#${t.haplotype}`:se(t)}var Jt=class{constructor(t){this.offsets=[0],this.values=Array.from({length:t},()=>[])}get length(){return this.values[0].length}push(t,e,s,n,r){let i=this.values;i[0].push(t),i[1].push(e),i[2].push(s),i[3].push(n),r!==void 0&&i[4].push(r)}endRow(){this.offsets.push(this.length)}reorder(t,e){let s=new Uint32Array(t.length+1);t.forEach((r,i)=>{s[i+1]=s[i]+this.offsets[r+1]-this.offsets[r]});let n=e.map((r,i)=>{let h=this.values[i],c=r(this.length),o=0;for(let p of t)for(let k=this.offsets[p];k<this.offsets[p+1];k++)c[o++]=h[k];return c});return{offsets:s,columns:n}}},mt=t=>new Float64Array(t);function je(t,e,s={}){let{heads:n,from:r,to:i,steps:h,lengths:c,names:o,reference:p}="walks"in t?me(t,s.referencePath,s.visits):pe(t),k=c.length,R=f=>f<k?c[f]:0,j=f=>pt(n[f].name).name,W=f=>n[f].start,at=(f,g)=>(W(f)??0)-(W(g)??0),tt=n.map((f,g)=>g),M=tt.filter(f=>j(f)===p).sort(at),it=M[0],ft=tt.filter(f=>j(f)!==p);if(it===void 0\|\|ft.length===0)return;let Rt=Wt(ft,j),O=new Float64Array(o.length).fill(Number.NaN),B=new Float64Array(o.length),V=new Map,ct=!1,et=!1,x=e&&e.end>e.start?e:void 0;for(let f of M){let g=W(f)??0;for(let $=r[f],L=i[f];$<L;$++){let E=h[$],y=R(E);if(Number.isNaN(O[E]))O[E]=g,B[E]=g+y,x&&(ct\|\|=g+y<=x.start,et\|\|=g>=x.end);else{let P=V.get(E);P?P.push(g):V.set(E,[O[E],g])}g+=y}}let gt=x===void 0\|\|ct&&et,U=new Jt(5),Z=[],lt=new Map,Nt=f=>{if(!f)return-1;let g=`${f.refName}:${f.start}`,$=lt.get(g);return $===void 0&&($=Z.length,lt.set(g,$),Z.push(f)),$},H=s.visits?new Jt(4):void 0,I=new Int32Array(0),T=new Float64Array(0),G=f=>{let g=n[f[0]],$=[...f].sort(at),L=$.length-1,E=0;for(let l of $)L+=i[l]-r[l]+(n[l].abridged?1:0),E+=n[l].abridged?.steps??0;L>I.length&&(I=new Int32Array(L2),T=new Float64Array(L2));let y=0,P=!1,S,J,D=new Map;for(let l of $){let d=W(l);(d===void 0\|\|S!==void 0&&d<S)&&(P=!0),S!==void 0&&d!==void 0&&d>S&&(D.set(y,Kt(d-S,J===void 0?void 0:n[J].after,n[l].before)),I[y]=-(d-S),T[y++]=S);let b=d??0,A=n[l].abridged;for(let m=r[l],N=i[l];m<N;m++){let F=h[m],_=A?A.bp-(b-(d??0))-R(F):0;_>0&&m===N-1&&m>r[l]&&(D.set(y,[{bp:_,cause:"abridged"}]),I[y]=-_,T[y++]=b,b+=_),I[y]=F,T[y++]=b,b+=R(F)}S=d===void 0?void 0:b,J=l}let _t=l=>l>=0&&l<y&&I[l]>=0&&!Number.isNaN(O[I[l]]),$t=l=>{let d=I[l];return T[l]+(d<0?-d:R(d))},ne=(l,d)=>{let b=l>=0?l:d,A=-1;for(let Y=1;A<0&&Y<y;Y++)A=[b-Y,b+Y].find(_t)??-1;if(A<0)return;let 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z)f.label=Dt(f.name)??f.label;X.sort((f,g)=>Number(g.meta.complete)-Number(f.meta.complete)\|\|g.meta.bp-f.meta.bp\|\|f.meta.label.localeCompare(g.meta.label));let bt=[0,...X.map(f=>f.row)],{offsets:ht,columns:a}=U.reorder(bt,[mt,mt,mt,f=>new Uint8Array(f),f=>new Int32Array(f)]),[v,u,w,K,q]=a;return{origin:x?x.start:W(it)??0,rows:[st,...X.map(f=>f.meta)],offsets:ht,start:v,bp:u,referenceStart:w,flags:K,chunk:q,chunks:Z,visits:H&&Ne(H,bt,o)}}function Ne(t,e,s){let{offsets:n,columns:r}=t.reorder(e,[p=>new Int32Array(p),mt,mt,p=>new Uint8Array(p)]),[i,h,c,o]=r;return{offsets:n,node:i,start:h,bp:c,onReference:o,names:s}}function be(t,e){let s=t.flags[e],n={start:t.start[e],bp:t.bp[e],onReference:(s&Pt)!==0};if(s&It){n.gap=!0;let r=Yt[s>>te&7];r&&(n.cause=r);let i=t.chunks[t.chunk[e]];i&&(n.chunk=i)}else n.referenceStart=Number.isNaN(t.referenceStart[e])?void 0:t.referenceStart[e];return s&Qt&&(n.reversed=!0),n}function ve(t,e){let s=[];for(let n=t.offsets[e];n<t.offsets[e+1];n++)s.push({node:t.names[t.node[n]],start:t.start[n],bp:t.bp[n],onReference:t.onReference[n]===1});return s}function Be(t,e){let s=t.rows.map((n,r)=>{let i=[];for(let h=t.offsets[r];h<t.offsets[r+1];h++)i.push(be(t,h));return{...n,runs:i,visits:t.visits&&ve(t.visits,r)}});return{origin:t.origin,unit:e,reference:s[0],rows:s.slice(1)}}export{fe as a,ce as b,ke as c,ye as d,Kt as e,zt as f,Ae as g,we as h,Mt as i,xe as j,de as k,je as l,Be as m};
2	+ //# sourceMappingURL=chunk-G53BI7VK.js.map

package/dist/chunks/{chunk-6OXXT2YP.js.map → chunk-G53BI7VK.js.map} RENAMED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LG2UK4MB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-7L7MN2OM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G7SG4XMK.js"],
-  "sourcesContent": ["// src/gfa/walkStops.ts\nvar START_STOP_TAG = \"ws\";\nvar END_STOP_TAG = \"we\";\nvar STOP_KINDS = [\"elsewhere\", \"break\", \"end\"];\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  unknown: \"gap, cause unknown\",\n  abridged: \"abridged: steps not loaded\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(bp, after, before) {\n  if (!after && !before) {\n    return [{ bp }];\n  }\n  const left = Math.min(after?.trimmed ?? 0, bp);\n  const right = Math.min(before?.trimmed ?? 0, bp - left);\n  let rest = bp - left - right;\n  const lead = after?.kind === \"break\" ? Math.min(after.bp, rest) : 0;\n  rest -= lead;\n  const trail = before?.kind === \"break\" ? Math.min(before.bp, rest) : 0;\n  rest -= trail;\n  const elsewhere = [after, before].find((s) => s?.kind === \"elsewhere\");\n  const parts = [\n    { bp: left },\n    { bp: lead, cause: \"missing\" },\n    elsewhere?.kind === \"elsewhere\" ? { bp: rest, cause: \"elsewhere\", chunk: elsewhere.chunk } : { bp: rest, cause: \"unknown\" },\n    { bp: trail, cause: \"missing\" },\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\nfunction stopAt(table, i) {\n  const bp = table.bp[i];\n  const ref = table.chunkRefs[i];\n  return stopOf(\n    table.kindNames[table.kinds[i]],\n    Number.isNaN(bp) ? void 0 : bp,\n    table.trimmed[i],\n    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }\n  );\n}\nfunction stopOf(kind, bp, trimmed, chunk) {\n  const cut = trimmed > 0 ? { trimmed } : {};\n  if (kind === \"elsewhere\" && chunk) {\n    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };\n  }\n  if (kind === \"break\" && bp !== void 0) {\n    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };\n  }\n  return kind === \"end\" ? { kind, ...cut } : void 0;\n}\nfunction stopTag(stop) {\n  const parts = [stop.kind];\n  if (\"bp\" in stop && stop.bp !== void 0) {\n    parts.push(`bp=${stop.bp}`);\n  }\n  if (stop.trimmed) {\n    parts.push(`trimmed=${stop.trimmed}`);\n  }\n  if (\"chunk\" in stop && stop.chunk) {\n    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);\n  }\n  return parts.join(\",\");\n}\nfunction parseStopTag(value) {\n  const [kind, ...fields] = value.split(\",\");\n  let bp;\n  let trimmed = 0;\n  let chunk;\n  for (const field of fields) {\n    if (field.startsWith(\"bp=\")) {\n      bp = +field.slice(3);\n    } else if (field.startsWith(\"trimmed=\")) {\n      trimmed = +field.slice(8);\n    } else if (field.startsWith(\"chunk=\")) {\n      const at = field.lastIndexOf(\":\");\n      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };\n    }\n  }\n  return stopOf(kind, bp, trimmed, chunk);\n}\nfunction stopFields(before, after) {\n  return {\n    ...before ? { before } : {},\n    ...after ? { after } : {}\n  };\n}\nfunction walkStopFields(tags) {\n  const before = tags[START_STOP_TAG];\n  const after = tags[END_STOP_TAG];\n  return stopFields(\n    typeof before === \"string\" ? parseStopTag(before) : void 0,\n    typeof after === \"string\" ? parseStopTag(after) : void 0\n  );\n}\nfunction walkStopTags(walks, p) {\n  const tags = [];\n  for (const [tag, table] of [\n    [START_STOP_TAG, walks.before],\n    [END_STOP_TAG, walks.after]\n  ]) {\n    const stop = table && stopAt(table, p);\n    if (stop) {\n      tags.push(`\t${tag}:Z:${stopTag(stop)}`);\n    }\n  }\n  return tags.join(\"\");\n}\nvar StopColumns = class {\n  constructor() {\n    this.kinds = [];\n    this.bp = [];\n    this.trimmed = [];\n    this.chunkRefs = [];\n    this.chunkStarts = [];\n    this.chunkRefNames = [];\n    this.refIndex = /* @__PURE__ */ new Map();\n  }\n  push(stop) {\n    this.kinds.push(STOP_KINDS.indexOf(stop.kind));\n    this.bp.push(\"bp\" in stop && stop.bp !== void 0 ? stop.bp : NaN);\n    this.trimmed.push(stop.trimmed ?? 0);\n    const chunk = \"chunk\" in stop ? stop.chunk : void 0;\n    if (chunk) {\n      let ref = this.refIndex.get(chunk.refName);\n      if (ref === void 0) {\n        ref = this.chunkRefNames.length;\n        this.refIndex.set(chunk.refName, ref);\n        this.chunkRefNames.push(chunk.refName);\n      }\n      this.chunkRefs.push(ref);\n      this.chunkStarts.push(chunk.start);\n    } else {\n      this.chunkRefs.push(-1);\n      this.chunkStarts.push(NaN);\n    }\n  }\n  table() {\n    return {\n      kinds: Uint8Array.from(this.kinds),\n      kindNames: [...STOP_KINDS],\n      bp: Float64Array.from(this.bp),\n      trimmed: Float64Array.from(this.trimmed),\n      chunkRefs: Int32Array.from(this.chunkRefs),\n      chunkStarts: Float64Array.from(this.chunkStarts),\n      chunkRefNames: this.chunkRefNames\n    };\n  }\n};\n\nexport {\n  START_STOP_TAG,\n  END_STOP_TAG,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts,\n  stopAt,\n  stopTag,\n  parseStopTag,\n  stopFields,\n  walkStopFields,\n  walkStopTags,\n  StopColumns\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  PathVisits\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...stopFields(\n      w.before && stopAt(w.before, p),\n      w.after && stopAt(w.after, p)\n    ),\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-7L7MN2OM.js\";\nimport {\n  gapParts\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  pathOrigin\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"unknown\",\n  \"abridged\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  for (const node of graph.nodes) {\n    lengths[indexOf(node.id)] = node.length;\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference: referenceWalkName(graph)\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference: referenceOf(\n      heads.map((h) => pathOrigin(h.name).name),\n      referencePath,\n      rankZero\n    )\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  if (first === void 0 || others.length === 0) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let reachesBefore = false;\n  let reachesAfter = false;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        if (cut) {\n          reachesBefore ||= pos + len <= cut.start;\n          reachesAfter ||= pos >= cut.end;\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || reachesBefore && reachesAfter;\n  const runs = new Columns(5);\n  const chunks = [];\n  const chunkIndex = /* @__PURE__ */ new Map();\n  const chunkOf = (chunk2) => {\n    if (!chunk2) {\n      return -1;\n    }\n    const key = `${chunk2.refName}:${chunk2.start}`;\n    let i = chunkIndex.get(key);\n    if (i === void 0) {\n      i = chunks.length;\n      chunkIndex.set(key, i);\n      chunks.push(chunk2);\n    }\n    return i;\n  };\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const rowOf = (pieces) => {\n    const head = heads[pieces[0]];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      if (start2 === void 0 || end !== void 0 && start2 < end) {\n        unplaced = true;\n      }\n      if (end !== void 0 && start2 !== void 0 && start2 > end) {\n        partsAt.set(\n          length,\n          gapParts(\n            start2 - end,\n            previous === void 0 ? void 0 : heads[previous].after,\n            heads[piece].before\n          )\n        );\n        steps[length] = -(start2 - end);\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const partialSide = (i0, i1) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      let near = -1;\n      for (let d = 1; near < 0 && d < length; d++) {\n        near = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      if (near < 0) {\n        return void 0;\n      }\n      const forward = near > flank === spanStart[steps[near]] > spanStart[steps[flank]];\n      const after = forward === (flank === i0);\n      const last2 = after ? length - 1 : 0;\n      const contigEnds = onReference(last2);\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0\n      };\n      return {\n        stop: stop2,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward ? after ? stepEnd(flank) : stepStart[0] : after ? stepEnd(length - 1) : stepStart[flank]\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const id = steps[i];\n        if (id >= 0 && !Number.isNaN(spanStart[id])) {\n          if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {\n            bestEnd = spanEnd[id];\n            i0 = i;\n          }\n          if (spanStart[id] >= cut.end && spanStart[id] < bestStart) {\n            bestStart = spanStart[id];\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false;\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : void 0;\n        if (inside) {\n          ;\n          ({ lo, hi, backward, axisStart, stop } = inside);\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? { contig, start: stepEnd(flankFrom), reversed: false } : { contig, start: stepStart[flankFrom], reversed: true };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      if (id < 0) {\n        const parts = partsAt.get(index);\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            chunkOf(part.chunk)\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, -1);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    runs.endRow();\n    visits?.endRow();\n    return {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {}\n    };\n  };\n  const referenceRow = rowOf(referencePieces);\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces),\n    row: i + 1\n  }));\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    (n) => new Int32Array(n)\n  ]);\n  const [start, bp, referenceStart, flags, chunk] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    chunk,\n    chunks,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const chunk = t.chunks[t.chunk[k]];\n    if (chunk) {\n      run.chunk = chunk;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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-  "names": ["START_STOP_TAG", "END_STOP_TAG", "STOP_KINDS", "GAP_CAUSE_TEXT", "OUTSIDE_TEXT", "gapParts", "bp", "after", "before", "left", "right", "rest", "lead", "trail", "elsewhere", "s", "part", "stopAt", "table", "i", "ref", "stopOf", "kind", "trimmed", "chunk", "cut", "parseStopTag", "value", "kind", "fields", "bp", "trimmed", "chunk", "field", "at", "stopOf", "stopFields", "before", "after", "walkStopFields", "tags", "START_STOP_TAG", "END_STOP_TAG", "StopColumns", "stop", "STOP_KINDS", "chunk", "ref", "pLineName", "name", "start", "end", "tablePath", "w", "p", "walkName", "fields", "panSNFields", "steps", "abridged", "stopFields", "stopAt", "namesByList", "lists", "names", "listCount", "pathNames", "starts", "list", "i", "fill", "grouped", "listed", "_", "out", "k", "tableNodeIds", "n", "l", "traversals", "canonical", "claim", "node", "reversed", "stepCount", "s", "segment", "graphFromTables", "count", "declared", "drawnWalks", "ids", "nodes", "ref", "edges", "neighbours", "pairList", "b", "near", "j", "addPair", "edgeLists", "a", "adjacency", "adjacentNode", "adjacentList", "listOf", "nameIndex", "crossedList", "crossedName", "crossings", "lastWalk", "paths", "anchorPaths", "totalSteps", "visitPath", "visitStart", "visitReversed", "visitOrder", "blocks", "pathSamples", "edgeNameIndex", "edgeNames", "head", "pathName", "visitName", "named", "panSNSample", "edgeNamed", "visitSample", "first", "nodeIds", "pos", "prev", "at", "listNames", "edge", "walked", "PathVisits", "RUN_ON_REFERENCE", "RUN_REVERSED", "RUN_GAP", "GAP_CAUSES", "CAUSE_SHIFT", "causeFlags", "cause", "referenceOf", "names", "referencePath", "rankZero", "referenceWalkName", "graph", "p", "pathOrigin", "n", "graphPieces", "index", "lengths", "indexOf", "id", "i", "node", "heads", "from", "to", "steps", "path", "tablePieces", "tables", "visits", "w", "kept", "tablePath", "tableNodeIds", "h", "sampleOf", "panSNSample", "labelOf", "Columns", "width", "a", "b", "c", "d", "e", "v", "order", "make", "offsets", "row", "columns", "m", "out", "at", "float64", "walkRowRuns", "source", "region", "o", "all", "reference", "declared", "lengthOf", "nameOf", "startOf", "byStart", "pieceIds", "_", "referencePieces", "first", "others", "walks", "groupBy", "spanStart", "spanEnd", "revisits", "reachesBefore", "reachesAfter", "cut", "piece", "pos", "s", "stop", "len", "starts", "flanked", "runs", "chunks", "chunkIndex", "chunkOf", "chunk2", "key", "stepStart", "rowOf", "pieces", "head", "ordered", "count", "abridgedSteps", "length", "unplaced", "end", "previous", "partsAt", "start2", "gapParts", "abridged", "stop2", "bp3", "onReference", "stepEnd", "partialSide", "i0", "i1", "flank", "near", "forward", "after", "last2", "contigEnds", "lo", "hi", "backward", "complete", "flankFrom", "flankTo", "axisStart", "bestEnd", "bestStart", "inside", "contig", "panSNContig", "axis", "bp2", "offReferenceBp", "gapBp", "step", "last", "lastFlags", "lastRef", "cursor", "placeOf", "best", "bestGap", "gap", "runBp", "runRef", "runFlags", "k", "parts", "part", "on", "placed", "back", "referenceRow", "rows", "r", "start", "bp", "referenceStart", "flags", "chunk", "visitColumns", "runAt", "f", "run", "visitsOf", "walkRowsOf", "unit", "meta"]
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LG2UK4MB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-7L7MN2OM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LODKC7PJ.js"],
+  "sourcesContent": ["// src/gfa/walkStops.ts\nvar START_STOP_TAG = \"ws\";\nvar END_STOP_TAG = \"we\";\nvar STOP_KINDS = [\"elsewhere\", \"break\", \"end\"];\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  unknown: \"gap, cause unknown\",\n  abridged: \"abridged: steps not loaded\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(bp, after, before) {\n  if (!after && !before) {\n    return [{ bp }];\n  }\n  const left = Math.min(after?.trimmed ?? 0, bp);\n  const right = Math.min(before?.trimmed ?? 0, bp - left);\n  let rest = bp - left - right;\n  const lead = after?.kind === \"break\" ? Math.min(after.bp, rest) : 0;\n  rest -= lead;\n  const trail = before?.kind === \"break\" ? Math.min(before.bp, rest) : 0;\n  rest -= trail;\n  const elsewhere = [after, before].find((s) => s?.kind === \"elsewhere\");\n  const parts = [\n    { bp: left },\n    { bp: lead, cause: \"missing\" },\n    elsewhere?.kind === \"elsewhere\" ? { bp: rest, cause: \"elsewhere\", chunk: elsewhere.chunk } : { bp: rest, cause: \"unknown\" },\n    { bp: trail, cause: \"missing\" },\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\nfunction stopAt(table, i) {\n  const bp = table.bp[i];\n  const ref = table.chunkRefs[i];\n  return stopOf(\n    table.kindNames[table.kinds[i]],\n    Number.isNaN(bp) ? void 0 : bp,\n    table.trimmed[i],\n    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }\n  );\n}\nfunction stopOf(kind, bp, trimmed, chunk) {\n  const cut = trimmed > 0 ? { trimmed } : {};\n  if (kind === \"elsewhere\" && chunk) {\n    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };\n  }\n  if (kind === \"break\" && bp !== void 0) {\n    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };\n  }\n  return kind === \"end\" ? { kind, ...cut } : void 0;\n}\nfunction stopTag(stop) {\n  const parts = [stop.kind];\n  if (\"bp\" in stop && stop.bp !== void 0) {\n    parts.push(`bp=${stop.bp}`);\n  }\n  if (stop.trimmed) {\n    parts.push(`trimmed=${stop.trimmed}`);\n  }\n  if (\"chunk\" in stop && stop.chunk) {\n    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);\n  }\n  return parts.join(\",\");\n}\nfunction parseStopTag(value) {\n  const [kind, ...fields] = value.split(\",\");\n  let bp;\n  let trimmed = 0;\n  let chunk;\n  for (const field of fields) {\n    if (field.startsWith(\"bp=\")) {\n      bp = +field.slice(3);\n    } else if (field.startsWith(\"trimmed=\")) {\n      trimmed = +field.slice(8);\n    } else if (field.startsWith(\"chunk=\")) {\n      const at = field.lastIndexOf(\":\");\n      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };\n    }\n  }\n  return stopOf(kind, bp, trimmed, chunk);\n}\nfunction stopFields(before, after) {\n  return {\n    ...before ? { before } : {},\n    ...after ? { after } : {}\n  };\n}\nfunction walkStopFields(tags) {\n  const before = tags[START_STOP_TAG];\n  const after = tags[END_STOP_TAG];\n  return stopFields(\n    typeof before === \"string\" ? parseStopTag(before) : void 0,\n    typeof after === \"string\" ? parseStopTag(after) : void 0\n  );\n}\nfunction walkStopTags(walks, p) {\n  const tags = [];\n  for (const [tag, table] of [\n    [START_STOP_TAG, walks.before],\n    [END_STOP_TAG, walks.after]\n  ]) {\n    const stop = table && stopAt(table, p);\n    if (stop) {\n      tags.push(`\t${tag}:Z:${stopTag(stop)}`);\n    }\n  }\n  return tags.join(\"\");\n}\nvar StopColumns = class {\n  constructor() {\n    this.kinds = [];\n    this.bp = [];\n    this.trimmed = [];\n    this.chunkRefs = [];\n    this.chunkStarts = [];\n    this.chunkRefNames = [];\n    this.refIndex = /* @__PURE__ */ new Map();\n  }\n  push(stop) {\n    this.kinds.push(STOP_KINDS.indexOf(stop.kind));\n    this.bp.push(\"bp\" in stop && stop.bp !== void 0 ? stop.bp : NaN);\n    this.trimmed.push(stop.trimmed ?? 0);\n    const chunk = \"chunk\" in stop ? stop.chunk : void 0;\n    if (chunk) {\n      let ref = this.refIndex.get(chunk.refName);\n      if (ref === void 0) {\n        ref = this.chunkRefNames.length;\n        this.refIndex.set(chunk.refName, ref);\n        this.chunkRefNames.push(chunk.refName);\n      }\n      this.chunkRefs.push(ref);\n      this.chunkStarts.push(chunk.start);\n    } else {\n      this.chunkRefs.push(-1);\n      this.chunkStarts.push(NaN);\n    }\n  }\n  table() {\n    return {\n      kinds: Uint8Array.from(this.kinds),\n      kindNames: [...STOP_KINDS],\n      bp: Float64Array.from(this.bp),\n      trimmed: Float64Array.from(this.trimmed),\n      chunkRefs: Int32Array.from(this.chunkRefs),\n      chunkStarts: Float64Array.from(this.chunkStarts),\n      chunkRefNames: this.chunkRefNames\n    };\n  }\n};\n\nexport {\n  START_STOP_TAG,\n  END_STOP_TAG,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts,\n  stopAt,\n  stopTag,\n  parseStopTag,\n  stopFields,\n  walkStopFields,\n  walkStopTags,\n  StopColumns\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  PathVisits\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...stopFields(\n      w.before && stopAt(w.before, p),\n      w.after && stopAt(w.after, p)\n    ),\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-7L7MN2OM.js\";\nimport {\n  gapParts\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  pathOrigin\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"unknown\",\n  \"abridged\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  for (const node of graph.nodes) {\n    lengths[indexOf(node.id)] = node.length;\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference: referenceWalkName(graph)\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference: referenceOf(\n      heads.map((h) => pathOrigin(h.name).name),\n      referencePath,\n      rankZero\n    )\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  if (first === void 0 || others.length === 0) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let reachesBefore = false;\n  let reachesAfter = false;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        if (cut) {\n          reachesBefore ||= pos + len <= cut.start;\n          reachesAfter ||= pos >= cut.end;\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || reachesBefore && reachesAfter;\n  const runs = new Columns(5);\n  const chunks = [];\n  const chunkIndex = /* @__PURE__ */ new Map();\n  const chunkOf = (chunk2) => {\n    if (!chunk2) {\n      return -1;\n    }\n    const key = `${chunk2.refName}:${chunk2.start}`;\n    let i = chunkIndex.get(key);\n    if (i === void 0) {\n      i = chunks.length;\n      chunkIndex.set(key, i);\n      chunks.push(chunk2);\n    }\n    return i;\n  };\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const rowOf = (pieces) => {\n    const head = heads[pieces[0]];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      if (start2 === void 0 || end !== void 0 && start2 < end) {\n        unplaced = true;\n      }\n      if (end !== void 0 && start2 !== void 0 && start2 > end) {\n        partsAt.set(\n          length,\n          gapParts(\n            start2 - end,\n            previous === void 0 ? void 0 : heads[previous].after,\n            heads[piece].before\n          )\n        );\n        steps[length] = -(start2 - end);\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const partialSide = (i0, i1) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      let near = -1;\n      for (let d = 1; near < 0 && d < length; d++) {\n        near = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      if (near < 0) {\n        return void 0;\n      }\n      const forward = near > flank === spanStart[steps[near]] > spanStart[steps[flank]];\n      const after = forward === (flank === i0);\n      const last2 = after ? length - 1 : 0;\n      const contigEnds = onReference(last2);\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0\n      };\n      return {\n        stop: stop2,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward ? after ? stepEnd(flank) : stepStart[0] : after ? stepEnd(length - 1) : stepStart[flank]\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const id = steps[i];\n        if (id >= 0 && !Number.isNaN(spanStart[id])) {\n          if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {\n            bestEnd = spanEnd[id];\n            i0 = i;\n          }\n          if (spanStart[id] >= cut.end && spanStart[id] < bestStart) {\n            bestStart = spanStart[id];\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false;\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : void 0;\n        if (inside) {\n          ;\n          ({ lo, hi, backward, axisStart, stop } = inside);\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? { contig, start: stepEnd(flankFrom), reversed: false } : { contig, start: stepStart[flankFrom], reversed: true };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      if (id < 0) {\n        const parts = partsAt.get(index);\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            chunkOf(part.chunk)\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, -1);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    runs.endRow();\n    visits?.endRow();\n    return {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {}\n    };\n  };\n  const referenceRow = rowOf(referencePieces);\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces),\n    row: i + 1\n  }));\n  const metas = [referenceRow, ...rows.map((r) => r.meta)];\n  if (new Set(metas.map((m) => m.label)).size < metas.length) {\n    for (const meta of metas) {\n      meta.label = panSNHaplotype(meta.name) ?? meta.label;\n    }\n  }\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    (n) => new Int32Array(n)\n  ]);\n  const [start, bp, referenceStart, flags, chunk] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    chunk,\n    chunks,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const chunk = t.chunks[t.chunk[k]];\n    if (chunk) {\n      run.chunk = chunk;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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n)a(e.nodeStrokes,e.nodeStrokeRuns.get(r));t.forEach(({from:r,to:s},i)=>{(n.has(r)||n.has(s))&&(a(e.edgeCurves,e.edgeCurveRuns.get(i)),a(e.arrows,e.arrowRuns.get(i)))})}function ts(e){return e<.5?4*e*e*e:1-(-2*e+2)**3/2}function Hg(e,t,n,o){return!(e.referenceAxis||t.referenceAxis||e.pixelRows||t.pixelRows||t.tubeMap||o||n>za)}function Wg(){return typeof requestAnimationFrame<"u"&&!("matchMedia"in window&&window.matchMedia("(prefers-reduced-motion: reduce)").matches)}function Fg(e,t,n){let o={frame:0,finish:()=>{e(1)}},a=0,r=performance.now(),s=()=>{if(!t()){n();return}let i=performance.now();a+=Math.min(i-r,Ka),r=i;let c=Math.min(1,a/Ua);e(ts(c)),c<1?o.frame=requestAnimationFrame(s):n()};return o.frame=requestAnimationFrame(s),o}function Dg(e,t,n,o){for(let[a,r]of Object.entries(e)){let s=t[a],i=n[a];!s||!i||r.forEach((c,d)=>{c.x=o===1?i[d].x:s[d].x+(i[d].x-s[d].x)*o,c.y=o===1?i[d].y:s[d].y+(i[d].y-s[d].y)*o})}}var ns=8,os=19,Dr=Pe+os,rs=48;function as(e,t,n){if(!(!e||!t))return 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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 a=this.fitPadTopBase,r=this.fitRoom,s=m=>(e.paneWidth-this.fitPadLeft-m)/t.w,i=m=>e.pixelRows?t.h+m+B<=r?1/0:0:(r-m-B)/t.h,c=Math.min(s(n+2*ee),i(a));return Math.min(s(B),i(a+o+ee))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ee:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(B,e.legendSize.width+2*ee):B},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(Zn/o,(this.paneCeiling-this.fitPadTop-B)/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?nt(t.map(a=>a.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?et({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-Dr)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ee+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-rs?t+2*ee:ns},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(rt,o.total+Dr);let a=Math.max(rt,e.legendSize.height+2*ee+e.referenceStripZonePx),r=this.fitPads,s=r.top+r.bottom;if(e.pixelRows)return Math.min(n,Math.max(a,t.h+s));let i=e.paneWidth-r.left-r.right;return t.w>0&&i>0?Math.min(n,Math.max(a,t.h*Math.max(i/t.w,this.minFitScale)+s)):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:K,top:K,right:K,bottom:K}:{left:this.fitPadLeft,top:this.fitPadTop,right:this.fitPadRight,bottom:B}},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,a=this.fitPads;return t?Ae(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:a.left,padTop:a.top,padRight:a.right,padBottom:a.bottom}):void 0}})).views(e=>({viewportToBuild(){return Yn(oo(e),to)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,eo]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=Do();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]:qn)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:a,layoutResult:r,deletionDrawing:s}=e;if(!o||!a||!r||!s)return;Ge(e.viewportDirty,e.positionsVersion);let i=Pt(()=>e.viewportToBuild()),c=Ke({..._e(r,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:a,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:Pt(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Fr(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return Lo(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Ao(t,o.id,o.length)??"not on this walk":void 0},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${Y(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},figure(){let{graph:t,layoutResult:n}=e;return t&&n&&!this.figureUnavailable?nn(t,n,{width:e.paneWidth,height:e.paneCeiling,walks:e.walkLayers,facet:e.facetSpec,colorScheme:e.effectiveColorScheme,nodeWidth:e.nodeWidth,showDeletionEdges:e.showDeletionEdges,linearLayout:e.linearLayout,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,region:e.graphRegion,colorDomain:e.statedColorDomain,genes:e.showGenes?e.backboneGenes:void 0,walkRows:e.walkRowBars,walkRowPitch:e.walkRowPitch,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps,walkStrip:e.walkStripRows&&{rows:e.walkStripRows,rowGenes:e.walkRowGenes,rowGeneGaps:e.walkRowGeneGaps}}):void 0}})).views(e=>({get followsHostView(){let t=e.layoutResult;return!!e.host&&!e.hostPlacesX&&!!t&&!t.referenceAxis&&!t.pixelRows&&!t.tubeMap&&!e.facetGrid}}));var fn=W(D("path",{d:"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z"}),"LineStyle");var Xr=W(D("path",{d:"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z"}),"CompareArrows");var Vr=W(D("path",{d:"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2"}),"HighlightAlt");var ss="Linear genome view",is="Linear synteny view",cs="No synteny track in this session aligns these assemblies";function jr({label:e,icon:t,entries:n,entryLabel:o,onSelect:a,disabledHelpText:r,nameTheOnlyEntry:s=!0}){let[i]=n,c=r?[{label:e,icon:t,disabled:!0,disabledHelpText:r,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:s?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:a(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(d=>({label:o(d),onClick:a(d)}))}]}function vw({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:a}){let r=n[0]?.coverage??e.length;return[...jr({label:ss,icon:fn,entries:t,entryLabel:s=>`${s.sample} ${ne(s)}`,onSelect:s=>()=>{o({location:s,assembly:s.sample})}}),...e.length>=2?jr({label:`${is} (${r} assemblies)`,icon:Xr,entries:n,entryLabel:s=>s.coverage<r?`${s.name} (${s.coverage} of ${r})`:s.name,nameTheOnlyEntry:!1,disabledHelpText:cs,onSelect:s=>()=>{a(s.trackId)}}):[]]}function Mw({own:e,reference:t,highlight:n,onShowLinear:o,onHighlight:a}){let r=[e?{label:`Open in ${e.assembly} \u2014 ${ne(e.location)}`,target:e}:void 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