jbrowse-plugin-graphgenomeviewer 7.4.3 → 7.5.0

package/dist/chunks/{chunk-DUPBXBYE.js → chunk-POUV7OPY.js}

@@ -1,4 +1,4 @@
-import{a as I,b as L,f as S,h as w}from"./chunk-6OXXT2YP.js";import{p as T}from"./chunk-CNNZDE6I.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=e=>e.endsWith("\r")?e.slice(0,-1):e;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(e){return this.byName.has(e)}add(e){let s=this.names.length;this.byName.set(e,s),this.names.push(e);let t=+e;return Number.isSafeInteger(t)&&String(t)===e&&this.byNumber.set(t,s),s}of(e){return this.byName.get(e)??this.add(e)}ofNumber(e){return this.byNumber.get(e)}};function U(e){let[,s,t="*",...r]=e.split("	");if(!s||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,f,o;for(let c of r){if(!_.test(c))return;let a=c.slice(5),p=c.slice(0,2);p==="LN"?i=+a:p==="SN"?n=a:p==="SO"?f=+a:o=+a}return{name:s,length:i,stable:n!==void 0&&f!==void 0&&o!==void 0?{refName:n,start:f,rank:o}:void 0}}function $(e,s,t,r){let i=0,n=-1,f=0,o=!0,d=a=>{if(n>=0&&a>n){let p=o&&a-n<16&&(a-n===1||e.charCodeAt(n)!==k)?t.ofNumber(f):void 0;r.nodes.push(p??t.of(e.slice(n,a))),r.reversed.push(i)}},c=s;for(;c<e.length;c++){let a=e.charCodeAt(c);if(a===O||a===Z)d(c),i=a===Z?1:0,n=c+1,f=0,o=!0;else{if(a===G)break;o&&a>=k&&a<=z?f=f*10+a-k:o=!1}}return d(c),c}function x(e){let s=[],t=0;for(;s.length<6;){let d=e.indexOf("	",t);if(d===-1)return;s.push(e.slice(t,d)),t=d+1}let[,r,i,n,f,o]=s;return r&&i&&n&&f&&o&&t<e.length?{sample:r,haplotype:i,contig:n,start:f,end:o,body:t}:void 0}function K(e){let s=e.split(`
+import{a as I,b as L,f as S,h as w}from"./chunk-DEWZOJSC.js";import{p as T}from"./chunk-SPL3UO2D.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=e=>e.endsWith("\r")?e.slice(0,-1):e;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(e){return this.byName.has(e)}add(e){let s=this.names.length;this.byName.set(e,s),this.names.push(e);let t=+e;return Number.isSafeInteger(t)&&String(t)===e&&this.byNumber.set(t,s),s}of(e){return this.byName.get(e)??this.add(e)}ofNumber(e){return this.byNumber.get(e)}};function U(e){let[,s,t="*",...r]=e.split("	");if(!s||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,f,o;for(let c of r){if(!_.test(c))return;let a=c.slice(5),p=c.slice(0,2);p==="LN"?i=+a:p==="SN"?n=a:p==="SO"?f=+a:o=+a}return{name:s,length:i,stable:n!==void 0&&f!==void 0&&o!==void 0?{refName:n,start:f,rank:o}:void 0}}function $(e,s,t,r){let i=0,n=-1,f=0,o=!0,d=a=>{if(n>=0&&a>n){let p=o&&a-n<16&&(a-n===1||e.charCodeAt(n)!==k)?t.ofNumber(f):void 0;r.nodes.push(p??t.of(e.slice(n,a))),r.reversed.push(i)}},c=s;for(;c<e.length;c++){let a=e.charCodeAt(c);if(a===O||a===Z)d(c),i=a===Z?1:0,n=c+1,f=0,o=!0;else{if(a===G)break;o&&a>=k&&a<=z?f=f*10+a-k:o=!1}}return d(c),c}function x(e){let s=[],t=0;for(;s.length<6;){let d=e.indexOf("	",t);if(d===-1)return;s.push(e.slice(t,d)),t=d+1}let[,r,i,n,f,o]=s;return r&&i&&n&&f&&o&&t<e.length?{sample:r,haplotype:i,contig:n,start:f,end:o,body:t}:void 0}function K(e){let s=e.split(`
 `),t=new R,r=[],i=[],n=[],f=[],o=[],d=new Map;for(let u of s){if(q.test(u))return;if(u.startsWith("S	")){let l=U(C(u));if(!l||t.has(l.name))return;t.add(l.name),r.push(l.length);let h=-1;l.stable&&(h=d.get(l.stable.refName)??o.length,h===o.length&&(o.push(l.stable.refName),d.set(l.stable.refName,h))),i.push(h),n.push(l.stable?.start??0),f.push(l.stable?.rank??0)}}let c=[],a=[],p=[],v=[],E=[],W=[],y=[0],g=P(),A=new w,N=new w;for(let u of s)if(u.startsWith("L	")){let[,l,h,b,m]=C(u).split("	");l&&b&&m&&(c.push(t.of(l)),a.push(t.of(b)),p.push((h==="-"?1:0)|(m==="-"?2:0)))}else if(u.startsWith("W	")){let l=C(u),h=x(l);if(h){v.push(`${h.sample}#${h.haplotype}#${h.contig}`),E.push(h.start==="*"?0:+h.start),W.push(h.end==="*"?-1:+h.end);let b=$(l,h.body,t,g),m=F(l,b);if(m===void 0||(m.before&&A.push(m.before),m.after&&N.push(m.after),g.nodes.length===y.at(-1)))return;y.push(g.nodes.length)}}if(![A.kinds.length,N.kinds.length].some(u=>u>0&&u<v.length))return{nodes:{names:t.names,lengths:Int32Array.from(r),refs:Int32Array.from(i),starts:Float64Array.from(n),ranks:Int32Array.from(f),refNames:o},links:{from:Int32Array.from(c),to:Int32Array.from(a),strands:Uint8Array.from(p)},walks:{names:v,starts:Float64Array.from(E),ends:Float64Array.from(W),offsets:Int32Array.from(y),steps:g.nodes.data.slice(0,g.nodes.length),reversed:g.reversed.data.slice(0,g.reversed.length),...B(v.length,A,N)}}}function F(e,s){let t={};for(let r of s<e.length?e.slice(s+1).split("	"):[]){let i=r.slice(5);if(r.startsWith(`${I}:Z:`)){if(t.before=S(i),!t.before)return}else if(r.startsWith(`${L}:Z:`)&&(t.after=S(i),!t.after))return}return t}function B(e,s,t){return{...s.kinds.length===e&&e>0?{before:s.table()}:{},...t.kinds.length===e&&e>0?{after:t.table()}:{}}}var D=/([><])([^><]+)/g;function M(e){if(!e.startsWith(">")&&!e.startsWith("<"))return;let s=[];for(let[,t,r]of e.matchAll(D))s.push({name:r,strand:t===">"?"+":"-"});return s}function Q(e){let s=e.trimEnd(),t=s.split("	");if(t.length<12||s.startsWith("#"))return;let r=M(t[5]);if(!r)return;let i,n=!1;for(let f=12;f<t.length;f++){let o=t[f];o.startsWith("cs:Z:")?i=o.slice(5):o==="tp:A:S"&&(n=!0)}return{name:t[0],queryLength:+t[1],queryStart:+t[2],queryEnd:+t[3],strand:t[4]==="-"?"-":"+",path:r,pathLength:+t[6],pathStart:+t[7],pathEnd:+t[8],matches:+t[9],blockLength:+t[10],mappingQuality:+t[11],secondary:n,...i===void 0?{}:{cs:i}}}function Y(e){let s=[];for(let t of e.split(`
 `)){let r=Q(t);r&&s.push(r)}return s}var j=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function tt(e){let s=[];for(let t of e.matchAll(j))t[1]!==void 0?s.push({op:"match",length:+t[1]}):t[2]!==void 0?s.push({op:"match",length:t[2].length}):t[3]!==void 0?s.push({op:"substitution",seq:t[3].toUpperCase()}):t[4]!==void 0?s.push({op:"insertion",seq:t[4].toUpperCase()}):t[5]!==void 0?s.push({op:"deletion",length:t[5].length}):t[6]!==void 0&&s.push({op:"match",length:+t[6]});return s}export{K as a,Q as b,Y as c,tt as d};
-//# sourceMappingURL=chunk-DUPBXBYE.js.map
+//# sourceMappingURL=chunk-POUV7OPY.js.map

package/dist/chunks/{chunk-DUPBXBYE.js.map → chunk-POUV7OPY.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VSSIYQYF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VSSIYQYF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
   "sourcesContent": ["import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  Column\n} from \"./chunk-ZPZ7GNBT.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(text) {\n  const line = text.trimEnd();\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line);\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
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package/dist/chunks/{chunk-CNNZDE6I.js.map → chunk-SPL3UO2D.js.map}

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   "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n", "import {\n  PathVisitsBuilder\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  REFERENCE_RANK\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathAnchoring.ts\nvar RANGE_SUFFIX = /:(\\d+)-\\d+$/;\nvar VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\\d+)(?:\\[(\\d+)-\\d+\\])?$/;\nvar VG_SUBRANGE = /\\[(\\d+)-\\d+\\]$/;\nfunction pathOrigin(pathName) {\n  const fragment = VG_FRAGMENT.exec(pathName);\n  if (fragment) {\n    return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };\n  }\n  const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);\n  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };\n}\nfunction surveyPaths(paths, lengthOf) {\n  const anchorPaths = [];\n  const visits = new PathVisitsBuilder();\n  for (const path of paths) {\n    const sample = panSNSample(path.name);\n    const p = visits.pathOf(path.name, sample);\n    let pos = path.start;\n    for (const step of path.steps) {\n      visits.addAt(visits.declare(step.id), p, pos, step.strand === \"-\");\n      pos += lengthOf(step.id);\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start\n    });\n  }\n  return { anchorPaths, pathVisits: visits.build() };\n}\nfunction chooseReferencePath(anchorPaths, preferred) {\n  const named = anchorPaths.find(\n    (p) => p.sample === preferred || p.name === preferred\n  );\n  return named ?? anchorPaths[0];\n}\nvar OFF_REFERENCE_RANK = 1;\nfunction anchorNode(node, visits, reference, samplesOf) {\n  const slot = visits.slot(node.name);\n  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {\n    return node;\n  }\n  const own = visits.firstBy(slot, reference);\n  const anchor = own >= 0 ? own : visits.offsets[slot];\n  return {\n    ...node,\n    stable: {\n      refName: visits.paths[visits.path[anchor]],\n      start: visits.start[anchor],\n      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n      strand: visits.strand(anchor)\n    },\n    samples: samplesOf(slot)\n  };\n}\nfunction sampleSorter(visits) {\n  const sorted = [...new Set(visits.samples)].sort();\n  const rank = new Map(sorted.map((sample, i) => [sample, i]));\n  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));\n  const seen = new Uint8Array(sorted.length);\n  const ranks = new Int32Array(sorted.length);\n  return (slot) => {\n    let n = 0;\n    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {\n      const r = pathRank[visits.path[i]];\n      if (seen[r] === 0) {\n        seen[r] = 1;\n        ranks[n++] = r;\n      }\n    }\n    let out;\n    if (n === sorted.length) {\n      out = sorted;\n      seen.fill(0);\n    } else if (n * 8 < sorted.length) {\n      const found = ranks.subarray(0, n);\n      found.forEach((r) => seen[r] = 0);\n      out = Array.from(found.sort(), (r) => sorted[r]);\n    } else {\n      out = [];\n      for (let r = 0; r < sorted.length; r++) {\n        if (seen[r] === 1) {\n          seen[r] = 0;\n          out.push(sorted[r]);\n        }\n      }\n    }\n    return out;\n  };\n}\nfunction anchorFromPaths(graph, preferred) {\n  const { anchorPaths, pathVisits } = graph;\n  const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;\n  if (!reference || !anchorPaths || !pathVisits) {\n    return graph;\n  }\n  const samplesOf = sampleSorter(pathVisits);\n  const referenceIndex = pathVisits.pathIndex(reference.name);\n  return {\n    ...graph,\n    nodes: graph.nodes.map(\n      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)\n    ),\n    anchoredBy: \"paths\",\n    referencePath: reference.name\n  };\n}\nfunction anchorGraph(graph, preferred) {\n  if (graph.anchoredBy !== \"tags\") {\n    return anchorFromPaths(graph, preferred);\n  }\n  const referencePath = taggedReferencePath(graph);\n  return referencePath ? { ...graph, referencePath } : graph;\n}\nfunction taggedReferencePath(graph) {\n  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;\n  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;\n}\nfunction trimOrigins(graph, kept) {\n  if (!graph.anchorPaths) {\n    return void 0;\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const bp = (ids, end = ids.length) => {\n    let sum = 0;\n    for (let i = 0; i < end; i++) {\n      sum += lengthOf.get(ids[i]) ?? 0;\n    }\n    return sum;\n  };\n  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);\n  return graph.anchorPaths.map((o) => {\n    const pieces = byOrigin.get(o.name);\n    const path = pieces?.length === 1 ? pieces[0] : void 0;\n    const stretch = path && kept.get(path.name);\n    return path && stretch ? {\n      ...o,\n      start: o.start + bp(path.nodeIds, stretch.first),\n      length: bp(stretch.nodeIds)\n    } : o;\n  });\n}\nfunction referenceVisitStarts(graph) {\n  const { pathVisits } = graph;\n  const cache = /* @__PURE__ */ new Map();\n  return (node) => {\n    let starts = cache.get(node.id);\n    if (!starts) {\n      starts = [];\n      const slot = pathVisits ? pathVisits.slot(node.name) : -1;\n      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;\n      if (p >= 0) {\n        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {\n          if (pathVisits.path[i] === p) {\n            starts.push(pathVisits.start[i]);\n          }\n        }\n      }\n      if (starts.length < 2) {\n        starts = [node.stable.start];\n      }\n      cache.set(node.id, starts);\n    }\n    return starts;\n  };\n}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins,\n  referenceVisitStarts\n};\n"],
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package/dist/chunks/chunk-VTMJQFN5.js

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package/dist/chunks/chunk-VTMJQFN5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-4KBZ7WPP.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-P2GJBFNA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VX656OAZ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GXCMBPC6.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EB4Q35QD.js"],
+  "sourcesContent": ["import {\n  slideAt\n} from \"./chunk-JJV2GT2Z.js\";\n\n// src/renderer/walkLanes.ts\nvar THREAD_PX = 2;\nvar THREAD_GAP_PX = 1.5;\nvar SLOT_GAP_PX = 4;\nvar LANE_SMOOTHING_PX = 12;\nvar THREAD_REACH_PX = 64;\nvar THREAD_TAPER_PX = 24;\nvar MAX_BAND_PX = 48;\nvar PASSES_KEY = \"a thread per pass through a node\";\nvar threadsPasses = (walks) => walks.length > 1 && walks.some((w) => w.mostPasses > 1);\nvar threadsWidth = (threads) => threads * THREAD_PX + Math.max(0, threads - 1) * THREAD_GAP_PX;\nvar sum = (values) => values.reduce((a, b) => a + b, 0);\nfunction slotLayout(spans, mostPasses, laneWidth) {\n  const widths = spans.map(\n    (m, i) => mostPasses[i] > 1 ? threadsWidth(m) : laneWidth * Math.min(1, m)\n  );\n  let seen = 0;\n  const gaps = spans.map((m) => {\n    const share = Math.min(1, m);\n    const gap = SLOT_GAP_PX * share * seen;\n    seen = Math.max(seen, share);\n    return gap;\n  });\n  return { widths, gaps, band: sum(widths) + sum(gaps) };\n}\nvar THREAD_PITCH_PX = THREAD_PX + THREAD_GAP_PX;\nfunction slotCentres(spans, mostPasses, held = spans) {\n  const { widths, gaps, band } = slotLayout(spans, mostPasses, THREAD_PX);\n  let at = -band / 2;\n  return widths.map((width, i) => {\n    at += gaps[i];\n    const slack = mostPasses[i] > 1 ? Math.max(0, width - threadsWidth(held[i])) : 0;\n    const centre = at + slack / 2 + THREAD_PX / 2;\n    at += width;\n    return centre;\n  });\n}\nvar bandWidthPx = (mostPasses) => slotLayout(mostPasses, mostPasses, THREAD_PX).band;\nvar bandScale = (mostPasses) => Math.min(1, MAX_BAND_PX / (bandWidthPx(mostPasses) || 1));\nvar passesKey = (walks) => bandScale(walks.map((w) => w.mostPasses)) < 1 ? `${PASSES_KEY}, thinned to fit` : PASSES_KEY;\nfunction laneSlideAt(start, end, along) {\n  const vector = ({ normal, offsetX: offsetX2 }) => ({\n    dx: normal.nx * offsetX2,\n    dy: normal.ny * offsetX2\n  });\n  const { dx, dy } = slideAt(vector(start), vector(end), along);\n  const offsetX = Math.hypot(dx, dy);\n  return offsetX > 0 ? { normal: { nx: dx / offsetX, ny: dy / offsetX }, offsetX } : { normal: { nx: 0, ny: 0 }, offsetX: 0 };\n}\nvar gapOf = (a, b) => Math.hypot(b.x - a.x, b.y - a.y);\nfunction arcOf(run) {\n  const s = new Float64Array(run.length);\n  for (let i = 1; i < run.length; i++) {\n    s[i] = s[i - 1] + gapOf(run[i - 1], run[i]);\n  }\n  return s;\n}\nfunction laneRuns(routes, nodePositions, yToX, jump) {\n  const seen = /* @__PURE__ */ new Set();\n  const owns = routes.map(\n    (route) => route.map((id) => {\n      if (seen.has(id)) {\n        return false;\n      }\n      seen.add(id);\n      return !!nodePositions[id]?.length;\n    })\n  );\n  const gap = (a, b) => Math.hypot(b.x - a.x, b.y * yToX - a.y);\n  const runs = [];\n  const owned = [];\n  let run = [];\n  let mine = [];\n  const breakRun = () => {\n    if (run.length) {\n      runs.push(run);\n      owned.push(mine);\n    }\n    run = [];\n    mine = [];\n  };\n  routes.forEach((route, r) => {\n    if (!owns[r].includes(true)) {\n      return;\n    }\n    route.forEach((id, step) => {\n      const segments = nodePositions[id];\n      if (!segments?.length) {\n        breakRun();\n        return;\n      }\n      const first = segments[0];\n      const last = segments.at(-1);\n      const prev = run.at(-1);\n      const next = nodePositions[route[step + 1] ?? \"\"];\n      const toNext = (p) => {\n        const at = { x: p.x, y: p.y * yToX };\n        return next?.length ? Math.min(gap(at, next[0]), gap(at, next.at(-1))) : 0;\n      };\n      const forward = prev ? gap(prev, first) <= gap(prev, last) : toNext(last) <= toNext(first);\n      if (prev && gap(prev, forward ? first : last) > jump) {\n        breakRun();\n      }\n      const middle = Math.floor(segments.length / 2);\n      for (let k = 0; k < segments.length; k++) {\n        const index = forward ? k : segments.length - 1 - k;\n        const p = segments[index];\n        run.push({\n          x: p.x,\n          y: p.y * yToX,\n          id,\n          index,\n          middle: index === middle,\n          forward\n        });\n        mine.push(owns[r][step]);\n      }\n    });\n    breakRun();\n  });\n  return { runs, owned };\n}\nfunction ownedWindows(s, owned, margin) {\n  const windows = [];\n  for (let i = 0; i < owned.length; i++) {\n    if (!owned[i]) {\n      continue;\n    }\n    let j = i;\n    while (j + 1 < owned.length && owned[j + 1]) {\n      j++;\n    }\n    const last = windows.at(-1);\n    const floor = last ? last[1] : 0;\n    let lo = i;\n    while (lo > floor && s[i] - s[lo - 1] <= margin) {\n      lo--;\n    }\n    let hi = j;\n    while (hi + 1 < s.length && s[hi + 1] - s[j] <= margin) {\n      hi++;\n    }\n    if (last && lo <= last[1] + 1) {\n      last[1] = hi;\n    } else {\n      windows.push([lo, hi]);\n    }\n    i = j;\n  }\n  return windows;\n}\nfunction smoothedNormals(run, reach) {\n  const s = arcOf(run);\n  const end = s.at(-1);\n  const pointAt = (at, j) => {\n    const a = run[j];\n    const b = run[Math.min(j + 1, run.length - 1)];\n    const span = s[Math.min(j + 1, run.length - 1)] - s[j];\n    const f = span > 0 ? (at - s[j]) / span : 0;\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n  };\n  let lo = 0;\n  let hi = 0;\n  return run.map((_, i) => {\n    const back = Math.max(0, s[i] - reach / 2);\n    const ahead = Math.min(end, s[i] + reach / 2);\n    while (lo < run.length - 1 && s[lo + 1] <= back) {\n      lo++;\n    }\n    while (hi < run.length - 1 && s[hi + 1] <= ahead) {\n      hi++;\n    }\n    const a = pointAt(back, lo);\n    const b = pointAt(ahead, hi);\n    const len = gapOf(a, b);\n    return len > 0 ? { nx: -(b.y - a.y) / len, ny: (b.x - a.x) / len } : void 0;\n  });\n}\nfunction cutCurls(run, close, length) {\n  const s = arcOf(run);\n  const out = run.slice();\n  const picks = [];\n  s.forEach((at, k) => {\n    const last = picks.at(-1);\n    if (last === void 0 || at - s[last] >= close / 4) {\n      picks.push(k);\n    }\n  });\n  if (picks.at(-1) !== run.length - 1) {\n    picks.push(run.length - 1);\n  }\n  let a = 0;\n  while (a < picks.length) {\n    const i = picks[a];\n    let to = -1;\n    for (let b = a + 1; b < picks.length && s[picks[b]] - s[i] <= length; b++) {\n      const j2 = picks[b];\n      if (s[j2] - s[i] > Math.PI * close && gapOf(run[i], run[j2]) <= close) {\n        to = b;\n      }\n    }\n    if (to < 0) {\n      a++;\n      continue;\n    }\n    const j = picks[to];\n    const p = run[i];\n    const q = run[j];\n    for (let k = i + 1; k < j; k++) {\n      const f = (s[k] - s[i]) / (s[j] - s[i]);\n      out[k] = {\n        ...run[k],\n        x: p.x + (q.x - p.x) * f,\n        y: p.y + (q.y - p.y) * f\n      };\n    }\n    a = to;\n  }\n  return out;\n}\nfunction rounded(run, half) {\n  const n = run.length;\n  const s = arcOf(run);\n  const end = s[n - 1];\n  const sumW = new Float64Array(n + 1);\n  const sumX = new Float64Array(n + 1);\n  const sumY = new Float64Array(n + 1);\n  for (let i = 0; i < n; i++) {\n    const p = run[i];\n    const w = (s[Math.min(i + 1, n - 1)] - s[Math.max(i - 1, 0)]) / 2;\n    sumW[i + 1] = sumW[i] + w;\n    sumX[i + 1] = sumX[i] + w * p.x;\n    sumY[i + 1] = sumY[i] + w * p.y;\n  }\n  const out = new Array(n);\n  let lo = 0;\n  let hi = 0;\n  for (let i = 0; i < n; i++) {\n    const p = run[i];\n    const reach = Math.min(half, s[i], end - s[i]);\n    const from = s[i] - reach;\n    const to = s[i] + reach + 1e-9 * (1 + end);\n    while (lo < n && s[lo] < from) {\n      lo++;\n    }\n    while (hi < n && s[hi] < to) {\n      hi++;\n    }\n    const w = sumW[hi] - sumW[lo];\n    out[i] = w > 0 ? { x: (sumX[hi] - sumX[lo]) / w, y: (sumY[hi] - sumY[lo]) / w } : { x: p.x, y: p.y };\n  }\n  return out;\n}\nfunction fieldSetter(field, nodePositions) {\n  return ({ id, index }, value) => {\n    let own = field.get(id);\n    if (!own) {\n      own = new Array(nodePositions[id].length);\n      field.set(id, own);\n    }\n    own[index] = value;\n  };\n}\nfunction laneLines(lanes, nodePositions, yToX, reach, band, smooth = true) {\n  const turn = Math.max(reach, 2 * band);\n  const curl = Math.PI * band;\n  const margin = smooth ? curl + band / 2 + turn / 2 : turn / 2;\n  const normals = /* @__PURE__ */ new Map();\n  const shifts = /* @__PURE__ */ new Map();\n  const setNormal = fieldSetter(normals, nodePositions);\n  const setShift = fieldSetter(shifts, nodePositions);\n  lanes.runs.forEach((run, r) => {\n    const owned = lanes.owned[r];\n    const pieces = ownedWindows(arcOf(run), owned, margin).map(([lo, hi]) => {\n      const points = run.slice(lo, hi + 1);\n      const line = smooth ? rounded(cutCurls(points, band / 2, curl), band / 2) : points;\n      return { lo, points, line, normals: smoothedNormals(line, turn) };\n    });\n    let agree = 0;\n    let along = 0;\n    for (const piece of pieces) {\n      piece.points.forEach((p, i) => {\n        const theirs = normals.get(p.id)?.[p.index];\n        const mine = piece.normals[i];\n        if (theirs && mine) {\n          agree += theirs.nx * mine.nx + theirs.ny * mine.ny;\n        }\n        along += p.forward ? 1 : -1;\n      });\n    }\n    const sign = (agree === 0 ? along : agree) < 0 ? -1 : 1;\n    for (const { lo, points, line, normals: own } of pieces) {\n      points.forEach((p, i) => {\n        if (!owned[lo + i]) {\n          return;\n        }\n        const n = own[i];\n        if (n) {\n          setNormal(p, sign > 0 ? n : { nx: -n.nx, ny: -n.ny });\n        }\n        if (smooth) {\n          setShift(p, {\n            dx: line[i].x - p.x,\n            dy: (line[i].y - p.y) / yToX\n          });\n        }\n      });\n    }\n  });\n  return { normals, shifts };\n}\nfunction windowed(s, v, half, sign) {\n  const out = new Array(v.length);\n  const deque = [];\n  let head = 0;\n  let next = 0;\n  for (let i = 0; i < v.length; i++) {\n    while (next < v.length && s[next] - s[i] <= half) {\n      while (deque.length > head && sign * v[deque.at(-1)] <= sign * v[next]) {\n        deque.pop();\n      }\n      deque.push(next++);\n    }\n    while (s[i] - s[deque[head]] > half) {\n      head++;\n    }\n    out[i] = v[deque[head]];\n  }\n  return out;\n}\nfunction windowMean(s, v, half, counted = () => true) {\n  const n = v.length;\n  const weight = s.map(\n    (_, i) => !counted(v[i]) ? 0 : n > 1 ? (s[Math.min(i + 1, n - 1)] - s[Math.max(i - 1, 0)]) / 2 : 1\n  );\n  const sumW = [0];\n  const sumWV = [0];\n  for (let i = 0; i < n; i++) {\n    sumW.push(sumW[i] + weight[i]);\n    sumWV.push(sumWV[i] + weight[i] * v[i]);\n  }\n  let lo = 0;\n  let hi = 0;\n  return v.map((value, i) => {\n    while (s[i] - s[lo] > half) {\n      lo++;\n    }\n    while (hi < n && s[hi] - s[i] <= half) {\n      hi++;\n    }\n    const w = sumW[hi] - sumW[lo];\n    return w > 0 ? (sumWV[hi] - sumWV[lo]) / w : value;\n  });\n}\nvar ONE_THREAD = [0];\nfunction repeats(passes) {\n  for (const p of passes.values()) {\n    if (p > 1) {\n      return true;\n    }\n  }\n  return false;\n}\nfunction walkThreads(route, passes, nodePositions, yToX, reach) {\n  if (!repeats(passes)) {\n    return {\n      span: passes,\n      nodeThreads: /* @__PURE__ */ new Map(),\n      threadPasses: /* @__PURE__ */ new Map(),\n      linkThreads: /* @__PURE__ */ new Map()\n    };\n  }\n  const index = /* @__PURE__ */ new Map();\n  const ids = [];\n  const widths = [];\n  const visits = [];\n  const steps = [];\n  const stepVisits = [];\n  const stepWants = [];\n  for (const piece of route) {\n    const points = [];\n    const nodes = [];\n    for (const id of piece) {\n      let k = index.get(id);\n      if (k === void 0) {\n        k = ids.length;\n        index.set(id, k);\n        ids.push(id);\n        widths.push(0);\n        visits.push(0);\n      }\n      nodes.push(k);\n      const segments = nodePositions[id];\n      const mid = segments?.[Math.floor(segments.length / 2)];\n      points.push(\n        mid ? { x: mid.x, y: mid.y * yToX } : points.at(-1) ?? { x: 0, y: 0 }\n      );\n    }\n    const s = arcOf(points);\n    const p = piece.map((id) => passes.get(id) ?? 1);\n    const most = windowed(s, p, reach / 2, 1);\n    const copy = nodes.map((k) => ++visits[k]);\n    const n = piece.length;\n    const before = new Int32Array(n);\n    let last = -1;\n    for (let i = 0; i < n; i++) {\n      last = p[i] === most[i] ? i : last;\n      before[i] = last;\n    }\n    const after = new Int32Array(n);\n    last = -1;\n    for (let i = n - 1; i >= 0; i--) {\n      last = p[i] === most[i] ? i : last;\n      after[i] = last;\n    }\n    const wants = new Array(n);\n    for (let i = 0; i < n; i++) {\n      const b = before[i];\n      const a = after[i];\n      const nearest = b < 0 ? a : a < 0 ? b : s[i] - s[b] <= s[a] - s[i] ? b : a;\n      wants[i] = Math.min(copy[nearest], most[i]) - 1;\n      widths[nodes[i]] = Math.max(widths[nodes[i]], most[i]);\n    }\n    steps.push(nodes);\n    stepVisits.push(copy);\n    stepWants.push(wants);\n  }\n  const taken = [];\n  const threadOf = [];\n  const free = (k, want) => {\n    const width = widths[k];\n    const own = taken[k] ??= /* @__PURE__ */ new Set();\n    for (let d = 0; d < width; d++) {\n      for (const c of [want - d, want + d]) {\n        if (c >= 0 && c < width && !own.has(c)) {\n          return c;\n        }\n      }\n    }\n    return want;\n  };\n  steps.forEach((nodes, piece) => {\n    nodes.forEach((k, i) => {\n      if (widths[k] > 1) {\n        const t = free(k, stepWants[piece][i]);\n        taken[k].add(t);\n        (threadOf[k] ??= [])[stepVisits[piece][i]] = t;\n      }\n    });\n  });\n  const span = /* @__PURE__ */ new Map();\n  const nodeThreads = /* @__PURE__ */ new Map();\n  const threadPasses = /* @__PURE__ */ new Map();\n  ids.forEach((id, k) => {\n    span.set(id, widths[k]);\n    nodeThreads.set(\n      id,\n      taken[k] ? [...taken[k]].sort((a, b) => a - b) : ONE_THREAD\n    );\n    const passOf = [];\n    threadOf[k]?.forEach((thread, visit) => {\n      passOf[thread] = visit - 1;\n    });\n    threadPasses.set(id, passOf);\n  });\n  const linkThreads = /* @__PURE__ */ new Map();\n  steps.forEach((nodes, piece) => {\n    const visit = stepVisits[piece];\n    for (let i = 1; i < nodes.length; i++) {\n      const from = nodes[i - 1];\n      const to = nodes[i];\n      const pair = [\n        threadOf[from]?.[visit[i - 1]] ?? 0,\n        threadOf[to]?.[visit[i]] ?? 0\n      ];\n      let ahead = linkThreads.get(ids[from]);\n      if (!ahead) {\n        ahead = /* @__PURE__ */ new Map();\n        linkThreads.set(ids[from], ahead);\n      }\n      const list = ahead.get(ids[to]);\n      if (!list) {\n        ahead.set(ids[to], [pair]);\n      } else if (!list.some(([a, b]) => a === pair[0] && b === pair[1])) {\n        list.push(pair);\n      }\n    }\n  });\n  return { span, nodeThreads, threadPasses, linkThreads };\n}\nfunction bandSpans(lanes, spans, { reach, taper }) {\n  const out = /* @__PURE__ */ new Map();\n  lanes.runs.forEach((run, r) => {\n    const s = arcOf(run);\n    const mids = run.flatMap((p, i) => p.middle ? [i] : []);\n    const along = mids.map((i) => s[i]);\n    const owned = mids.map((i) => lanes.owned[r][i]);\n    for (const [lo, hi] of ownedWindows(along, owned, reach / 2 + taper / 2)) {\n      const at = along.slice(lo, hi + 1);\n      const ids = mids.slice(lo, hi + 1).map((i) => run[i].id);\n      const eased = spans.map((own) => {\n        const raw = ids.map((id) => own.get(id) ?? 0);\n        return raw.every((v) => v === raw[0]) ? { slot: raw, held: raw } : {\n          slot: windowMean(at, windowed(at, raw, reach / 2, 1), taper / 2),\n          held: windowMean(at, raw, taper / 2, (v) => v > 0)\n        };\n      });\n      ids.forEach((id, i) => {\n        if (owned[lo + i]) {\n          out.set(id, {\n            slot: eased.map((e) => e.slot[i]),\n            held: eased.map((e) => e.held[i])\n          });\n        }\n      });\n    }\n  });\n  return out;\n}\nfunction liftLanes(walks, nodePositions, yToX, worldPerScreenPx) {\n  const threaded = threadsPasses(walks);\n  const passes = walks.map((w) => w.mostPasses);\n  const reach = THREAD_REACH_PX * worldPerScreenPx;\n  const runs = laneRuns(\n    walks.flatMap((w) => w.route),\n    nodePositions,\n    yToX,\n    LANE_SMOOTHING_PX * worldPerScreenPx\n  );\n  const lines = laneLines(\n    runs,\n    nodePositions,\n    yToX,\n    LANE_SMOOTHING_PX * worldPerScreenPx,\n    bandWidthPx(passes) * (threaded ? bandScale(passes) : 1) * worldPerScreenPx,\n    threaded\n  );\n  const threads = threaded ? walks.map((w) => walkThreads(w.route, w.passes, nodePositions, yToX, reach)) : void 0;\n  const spans = threads ? bandSpans(\n    runs,\n    threads.map((t) => t.span),\n    { reach, taper: THREAD_TAPER_PX * worldPerScreenPx }\n  ) : void 0;\n  const furthestShift = { dx: 0, dy: 0 };\n  for (const own of lines.shifts.values()) {\n    for (const shift of own) {\n      furthestShift.dx = Math.max(furthestShift.dx, Math.abs(shift?.dx ?? 0));\n      furthestShift.dy = Math.max(furthestShift.dy, Math.abs(shift?.dy ?? 0));\n    }\n  }\n  return { lines, threads, spans, furthestShift };\n}\n\nexport {\n  THREAD_PX,\n  THREAD_GAP_PX,\n  SLOT_GAP_PX,\n  LANE_SMOOTHING_PX,\n  THREAD_REACH_PX,\n  THREAD_TAPER_PX,\n  MAX_BAND_PX,\n  PASSES_KEY,\n  threadsPasses,\n  THREAD_PITCH_PX,\n  slotCentres,\n  bandWidthPx,\n  bandScale,\n  passesKey,\n  laneSlideAt,\n  laneRuns,\n  laneLines,\n  walkThreads,\n  bandSpans,\n  liftLanes\n};\n", "// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  const t = Math.max(0, 1 - 1 / factor);\n  const lift = (v) => Math.round(v + (255 - v) * t);\n  return packAbgr(\n    lift(abgrRed(c)),\n    lift(abgrGreen(c)),\n    lift(abgrBlue(c)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "// src/referenceRampCss.ts\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nfunction rampHueCss(hue) {\n  return `hsl(${hue}, ${REFERENCE_RAMP_SATURATION * 100}%, ${REFERENCE_RAMP_LIGHTNESS * 100}%)`;\n}\nfunction rampHueAt(frac) {\n  return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;\n}\nfunction rampHue(bp, domain) {\n  return rampHueAt((bp - domain.start) / (domain.end - domain.start));\n}\nvar HUE_STOP_DEG = 30;\nfunction rampStops({ start, bp, reversed }, domain) {\n  const low = rampHue(start, domain);\n  const high = rampHue(start + bp, domain);\n  if (high - low < 1) {\n    return [(low + high) / 2];\n  }\n  const n = Math.ceil((high - low) / HUE_STOP_DEG);\n  return Array.from(\n    { length: n + 1 },\n    (_, i) => rampHue(start + bp * (reversed ? n - i : i) / n, domain)\n  );\n}\nvar RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({\n  offset: i / 6,\n  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)\n}));\nvar RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(\n  (s) => `${s.color} ${s.offset * 100}%`\n).join(\", \")})`;\n\nexport {\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_SATURATION,\n  REFERENCE_RAMP_LIGHTNESS,\n  rampHueCss,\n  rampHueAt,\n  rampHue,\n  rampStops,\n  RAMP_GRADIENT_STOPS,\n  RAMP_GRADIENT_CSS\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-3GORESBG.js\";\n\n// src/util/edgeCurves.ts\nvar cache = weakMemo();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  return cache(\n    nodePositions,\n    [graph, axis.scaleX, axis.scaleY, deletions, routes, stranded, version],\n    () => {\n      const curves = /* @__PURE__ */ new Map();\n      for (let ei = 0; ei < graph.edges.length; ei++) {\n        const bypassed = deletions?.get(ei);\n        const edgeCurves = edgeCurvesOf(\n          nodePositions,\n          graph.edges[ei],\n          axis,\n          bypassed,\n          bypassed && routes?.[ei],\n          stranded\n        );\n        if (edgeCurves) {\n          curves.set(ei, edgeCurves);\n        }\n      }\n      return curves;\n    }\n  );\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  for (const edge of graph.edges) {\n    pushTo(neighbors, edge.from, edge.to);\n    pushTo(neighbors, edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  THREAD_PITCH_PX,\n  THREAD_PX,\n  bandScale,\n  bandWidthPx,\n  laneSlideAt,\n  liftLanes,\n  slotCentres,\n  threadsPasses\n} from \"./chunk-4KBZ7WPP.js\";\nimport {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-P2GJBFNA.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-VQ353UDK.js\";\nimport {\n  meanDepth,\n  nodeWidthPx,\n  walkLaneWidthPx\n} from \"./chunk-ZANALBSX.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  dashSpans,\n  pathRibbonOffsets,\n  polylinePx,\n  slideCurves,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-JJV2GT2Z.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  busiestEdge,\n  edgeWidthFactor\n} from \"./chunk-DAEEMZ74.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, scale * yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\nvar FIRST_THREADS = [[0, 0]];\nvar ONE_PASS = [0];\nvar NO_SHIFT = { dx: 0, dy: 0 };\nfunction nearerStart(at, segments, yToX) {\n  const gap = (p) => Math.hypot(p.x - at.x, (p.y - at.y) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\n}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  return stranded ? strandSides(edge).from === \"start\" : nearerStart({ x: first.x0, y: first.y0 }, segments, yToX);\n}\nfunction intoDirection(last, toSegments) {\n  if (toSegments.length < 2) {\n    return void 0;\n  }\n  const first = toSegments[0];\n  const final = toSegments[toSegments.length - 1];\n  const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);\n  return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };\n}\nfunction normal(a, b) {\n  if (!a || !b) {\n    return void 0;\n  }\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  const len = Math.hypot(dx, dy);\n  return len > 0 ? { nx: -dy / len, ny: dx / len } : void 0;\n}\nvar MITRE_LIMIT = 0.1;\nvar LONGEST_NORMAL = 1 / Math.sqrt(MITRE_LIMIT);\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  return points.map((p, i) => {\n    const before = normal(points[i - 1], p);\n    const after = normal(p, points[i + 1]);\n    if (before && after) {\n      const nx = (before.nx + after.nx) / 2;\n      const ny = (before.ny + after.ny) / 2;\n      const dot = before.nx * nx + before.ny * ny;\n      return dot > MITRE_LIMIT ? { nx: nx / dot, ny: ny / dot } : { nx, ny };\n    }\n    return before ?? after ?? { nx: 0, ny: 0 };\n  });\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  const out = new Array(points.length);\n  for (let i = 0; i < points.length; i++) {\n    out[i] = {\n      x: points[i].x + normals[i].nx * distance,\n      y: points[i].y + normals[i].ny * distance / yToX\n    };\n  }\n  return out;\n}\nfunction hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nfunction packHsl(h, s, l, a = 1) {\n  const [r, g, b] = hslToRgb(h, s, l);\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  return packHsl(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS, alpha);\n}\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction rampFraction(node, ramp) {\n  const mid = ramp.midpoints.get(node.id);\n  return isBackbone(node) && mid !== void 0 ? (mid - ramp.start) / ramp.span : void 0;\n}\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph, referenceRamp) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length,\n    referenceRamp\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state, so only the backbone takes a hue\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      if (ramp === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      const t = rampFraction(node, ramp);\n      return t === void 0 ? REFERENCE_RAMP_ALT_COLOR : packHsl(\n        rampHueAt(t),\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      return packHsl(hue, 0.75, 0.5);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds, growX = 0, growY = 0) {\n  for (const c of curves) {\n    const cMinX = Math.min(c.x0, c.cx0, c.cx1, c.x1);\n    const cMaxX = Math.max(c.x0, c.cx0, c.cx1, c.x1);\n    const cMinY = Math.min(c.y0, c.cy0, c.cy1, c.y1);\n    const cMaxY = Math.max(c.y0, c.cy0, c.cy1, c.y1);\n    if (cMaxX >= bounds.minX - growX && cMinX <= bounds.maxX + growX && cMaxY >= bounds.minY - growY && cMinY <= bounds.maxY + growY) {\n      return true;\n    }\n  }\n  return false;\n}\nvar paletteCache = /* @__PURE__ */ new WeakMap();\nfunction pathPaletteOf(graph) {\n  let palette = paletteCache.get(graph);\n  if (!palette) {\n    const pathColorByIndex = [];\n    const pathIndexByName = /* @__PURE__ */ new Map();\n    const paths = graph.paths ?? [];\n    for (let i = 0; i < paths.length; i++) {\n      pathColorByIndex.push(\n        packHsl(\n          pathHueAt(i, paths.length),\n          PATH_SATURATION,\n          PATH_LIGHTNESS,\n          0.85\n        )\n      );\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        pushTo(slots, nodeId, pathIdx);\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\nvar lanesCache = weakMemo();\nvar linksCache = /* @__PURE__ */ new WeakMap();\nfunction linksOf(graph) {\n  let links = linksCache.get(graph);\n  if (!links) {\n    links = /* @__PURE__ */ new Map();\n    for (const { from, to } of graph.edges) {\n      let out = links.get(from);\n      if (!out) {\n        out = /* @__PURE__ */ new Set();\n        links.set(from, out);\n      }\n      out.add(to);\n    }\n    linksCache.set(graph, links);\n  }\n  return links;\n}\nfunction buildGeometry(options) {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = \"uniform\",\n    edgeWidth = \"uniform\",\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const depthNorm = nodeWidth === \"depth\" ? meanDepth(graph) : 0;\n  const busiest = edgeWidth === \"walks\" ? busiestEdge(graph) : 0;\n  const scale = axis.scaleX;\n  const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = computeColorSchemeRange(graph, referenceRamp);\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const liftedWalks = highlight?.walks ?? [];\n  const threaded = threadsPasses(liftedWalks);\n  const lanePasses = liftedWalks.map((w) => w.mostPasses);\n  const thinned = threaded ? bandScale(lanePasses) : 1;\n  const fields = highlight && liftedWalks.length > 1 ? lanesCache(\n    highlight,\n    [nodePositions, version, axis.scaleX, axis.scaleY],\n    () => liftLanes(liftedWalks, nodePositions, yToX, worldPerScreenPx)\n  ) : void 0;\n  const lines = fields?.lines;\n  const threads = fields?.threads;\n  const spanField = fields?.spans;\n  const plainCentres = threaded ? slotCentres(lanePasses, lanePasses) : [];\n  const centresByNode = /* @__PURE__ */ new Map();\n  const centresOf = (nodeId) => {\n    let centres = centresByNode.get(nodeId);\n    if (!centres) {\n      const spans = spanField?.get(nodeId);\n      centres = spans ? slotCentres(spans.slot, lanePasses, spans.held) : plainCentres;\n      centresByNode.set(nodeId, centres);\n    }\n    return centres;\n  };\n  const laneOffset = (nodeId, laneWidth, lane, pass) => threaded ? (centresOf(nodeId)[lane] + pass * THREAD_PITCH_PX) * thinned : (lane - (liftedWalks.length - 1) / 2) * laneWidth;\n  const laneHalfWidth = (laneWidth) => threaded ? THREAD_PX / 2 * thinned : laneWidth / 2;\n  const laneNormals = /* @__PURE__ */ new Map();\n  const laneNormalsOf = (nodeId, segments) => {\n    let normals = laneNormals.get(nodeId);\n    if (!normals) {\n      const smoothed = lines?.normals.get(nodeId);\n      normals = smoothed ? pointNormalsOf(segments, yToX).map((n, i) => smoothed[i] ?? n) : pointNormalsOf(segments, yToX);\n      laneNormals.set(nodeId, normals);\n    }\n    return normals;\n  };\n  const laneWidths = /* @__PURE__ */ new Map();\n  const laneWidthOf = (id) => {\n    let width = laneWidths.get(id);\n    if (width === void 0) {\n      const node = nodeById.get(id);\n      width = walkLaneWidthPx(\n        node ? nodeWidthPx(node, contigThickness, nodeWidth, depthNorm) : contigThickness,\n        liftedWalks.length\n      );\n      laneWidths.set(id, width);\n    }\n    return width;\n  };\n  const laneShiftOf = (nodeId, index) => lines?.shifts.get(nodeId)?.[index] ?? NO_SHIFT;\n  const laneEndOf = (id, segments, atStart) => {\n    const at = atStart ? 0 : segments.length - 1;\n    return {\n      id,\n      laneWidth: laneWidthOf(id),\n      normal: laneNormalsOf(id, segments)[at] ?? { nx: 0, ny: 0 },\n      shift: laneShiftOf(id, at)\n    };\n  };\n  const lanesMayShow = (curves, fromId) => {\n    if (!viewportBounds) {\n      return true;\n    }\n    const offset = threaded ? bandWidthPx(lanePasses) * thinned : (liftedWalks.length - 1) / 2 * laneWidthOf(fromId);\n    const reach = LONGEST_NORMAL * offset * worldPerScreenPx;\n    return isBezierInBounds(\n      curves,\n      viewportBounds,\n      reach + (fields?.furthestShift.dx ?? 0),\n      reach / yToX + (fields?.furthestShift.dy ?? 0)\n    );\n  };\n  const threadPairs = (lane, from, to) => {\n    const own = threads?.[lane]?.linkThreads;\n    if (!own?.size) {\n      return FIRST_THREADS;\n    }\n    const ahead = own.get(from)?.get(to);\n    const back = linksOf(graph).get(to)?.has(from) ? void 0 : own.get(to)?.get(from);\n    if (!back) {\n      return ahead ?? FIRST_THREADS;\n    }\n    const turned = back.map(([a, b]) => [b, a]);\n    return ahead ? [...ahead, ...turned] : turned;\n  };\n  const threadColor = (lane, nodeId, thread) => liftedWalks[lane]?.passColors.get(nodeId)?.[threads?.[lane]?.threadPasses.get(nodeId)?.[thread] ?? 0];\n  const lanePointsOf = (nodeId, segments) => lines?.shifts.has(nodeId) ? segments.map((p, i) => {\n    const { dx, dy } = laneShiftOf(nodeId, i);\n    return { ...p, x: p.x + dx, y: p.y + dy };\n  }) : segments;\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE);\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const fromSegments = nodePositions[edge.from];\n    const toSegments = nodePositions[edge.to];\n    const baseCurves = sharedCurves.get(ei);\n    if (!fromSegments?.length || !toSegments?.length || !baseCurves || hiddenEdges?.has(ei)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const bypassed = deletions?.get(ei);\n    const isDeletion = bypassed !== void 0;\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false;\n    const ribbonThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\n    const edgeThickness = isDeletion ? ribbonThickness : connectorThickness / 2 * edgeWidthFactor(numPaths, busiest, edgeWidth);\n    const ribbons = drawPaths && numPaths > 0;\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;\n    const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);\n    const toNode = nodeById.get(edge.to);\n    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;\n    const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);\n    const dashesOf = (curves) => dashSpans(curves, DELETION_DASH_PX / scale, yToX, viewportBounds);\n    const stroke = (curves, thickness, color) => {\n      if (!isDeletion) {\n        edgeCurves.push({ curves, thickness, color });\n        return;\n      }\n      for (const dash of dashesOf(curves)) {\n        edgeCurves.push({ curves: dash.curves, thickness, color });\n      }\n    };\n    const laneStroke = (curves, thickness, color, walk, pass, normal2, offsetX, endNormal, endOffsetX) => {\n      if (!isDeletion) {\n        edgeCurves.push({\n          curves,\n          thickness,\n          color,\n          walk,\n          pass,\n          normal: normal2,\n          offsetX,\n          endNormal,\n          endOffsetX\n        });\n        return;\n      }\n      const start = { normal: normal2, offsetX };\n      const end = { normal: endNormal, offsetX: endOffsetX };\n      for (const dash of dashesOf(curves)) {\n        const a = dash.startAlong === 0 ? start : laneSlideAt(start, end, dash.startAlong);\n        const b = dash.endAlong === 1 ? end : laneSlideAt(start, end, dash.endAlong);\n        edgeCurves.push({\n          curves: dash.curves,\n          thickness,\n          color,\n          walk,\n          pass,\n          normal: a.normal,\n          offsetX: a.offsetX,\n          endNormal: b.normal,\n          endOffsetX: b.offsetX\n        });\n      }\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: isDeletion || ribbons ? connectorThickness / 2 : edgeThickness,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: edgeColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight?.walks.length && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks && !lanesMayShow(baseCurves, edge.from)) {\n      continue;\n    }\n    if (laneWalks) {\n      const from = laneEndOf(\n        edge.from,\n        fromSegments,\n        leavesStart(edge, fromSegments, baseCurves[0], stranded, yToX)\n      );\n      const last = baseCurves.at(-1);\n      const to = threaded ? laneEndOf(\n        edge.to,\n        toSegments,\n        nearerStart({ x: last.x1, y: last.y1 }, toSegments, yToX)\n      ) : from;\n      const single = laneWalks.length === 1;\n      const thickness = laneHalfWidth(from.laneWidth);\n      for (let lane = 0; lane < laneWalks.length; lane++) {\n        const walk = laneWalks[lane];\n        if (!walk.edgeIndexes.has(ei)) {\n          continue;\n        }\n        for (const [pass, toPass] of threadPairs(lane, edge.from, edge.to)) {\n          const offsetX = single ? 0 : laneOffset(from.id, from.laneWidth, lane, pass) * worldPerScreenPx;\n          const endOffsetX = threaded ? laneOffset(to.id, to.laneWidth, lane, toPass) * worldPerScreenPx : offsetX;\n          const curves = threaded ? slideCurves(\n            baseCurves,\n            from.shift.dx + from.normal.nx * offsetX,\n            from.shift.dy + from.normal.ny * offsetX / yToX,\n            to.shift.dx + to.normal.nx * endOffsetX,\n            to.shift.dy + to.normal.ny * endOffsetX / yToX\n          ) : offsetX === 0 ? baseCurves : translateCurves(\n            baseCurves,\n            from.normal.nx * offsetX,\n            from.normal.ny * offsetX / yToX\n          );\n          if (inView(curves)) {\n            laneStroke(\n              curves,\n              thickness,\n              threadColor(lane, edge.from, pass) ?? threadColor(lane, edge.to, toPass) ?? plainEdgeColor,\n              lane,\n              pass,\n              from.normal,\n              offsetX,\n              to.normal,\n              endOffsetX\n            );\n          }\n        }\n      }\n      if (edgeCurves.length > edgeCurveStart) {\n        arrowOn(baseCurves);\n      }\n    } else if (!ribbons) {\n      if (inView(baseCurves)) {\n        stroke(baseCurves, edgeThickness, edgeColor);\n        arrowOn(baseCurves);\n      }\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const { x, y } = offsets[pathIdx];\n        const curves = x === 0 && y === 0 ? baseCurves : translateCurves(baseCurves, x, y);\n        if (!inView(curves)) {\n          continue;\n        }\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        stroke(\n          curves,\n          ribbonThickness,\n          highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor\n        );\n        if (pathIdx === arrowRibbon) {\n          arrowOn(curves);\n        }\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = walkLaneWidthPx(width, lanes.length);\n      const normals = lanes.length > 1 ? laneNormalsOf(nodeId, segments) : [];\n      const points = lanes.length > 1 ? lanePointsOf(nodeId, segments) : segments;\n      const thickness = laneHalfWidth(laneWidth);\n      for (let lane = 0; lane < lanes.length; lane++) {\n        const laneColor = lanes[lane].colors.get(nodeId);\n        if (laneColor === void 0) {\n          continue;\n        }\n        const onThreads = threads?.[lane]?.nodeThreads.get(nodeId) ?? ONE_PASS;\n        for (const pass of onThreads) {\n          const color2 = threadColor(lane, nodeId, pass) ?? laneColor;\n          if (lanes.length === 1) {\n            nodeStrokes.push({\n              points: segments,\n              thickness,\n              color: color2,\n              walk: lane,\n              pass\n            });\n            continue;\n          }\n          const offsetX = laneOffset(nodeId, laneWidth, lane, pass) * worldPerScreenPx;\n          nodeStrokes.push({\n            points: offsetPolyline(points, normals, offsetX, yToX),\n            thickness,\n            color: color2,\n            walk: lane,\n            pass,\n            normals,\n            offsetX\n          });\n        }\n      }\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  rampFraction,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  hslToRgb\n} from \"./chunk-GXCMBPC6.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"orange\", label: \"Peach to rust\", ends: [\"#ffc285\", \"#8f3a00\"] },\n  { value: \"rainbow\", label: \"Rainbow\" }\n];\nvar FAMILIES = [\"blue\", \"red\", \"purple\", \"green\"];\nvar isField = (v) => WALK_FIELDS.some((f) => f.value === v);\nvar isScheme = (v) => WALK_SCHEMES.some((s) => s.value === v);\nfunction resolveEncoding(layer, reference, picked, alone = true) {\n  const { field: askedField, scheme: askedScheme } = layer.color ?? {};\n  const field = isField(askedField) ? askedField : alone ? \"progress\" : \"walk\";\n  const family = reference ? \"grey\" : FAMILIES[picked % FAMILIES.length];\n  const scheme = isScheme(askedScheme) ? askedScheme === \"rainbow\" && field !== \"reference\" ? family : askedScheme : family;\n  const round = Math.floor(picked / FAMILIES.length) % SHADES.length;\n  return field === \"walk\" && scheme === family && round > 0 ? { field, scheme, shade: SHADES[round] } : alone || field === \"walk\" ? { field, scheme } : { field, scheme, darkest: TOGETHER_DARKEST };\n}\nvar TOGETHER_DARKEST = 0.55;\nvar BASE_T = 0.5;\nvar SHADES = [BASE_T, 0.85, 0.2];\nvar STRETCH_GAP = 0.08;\nvar rampsOn = ({ field, scheme }) => field !== \"walk\" && scheme !== \"rainbow\";\nfunction splitFamilies(encodings) {\n  const counts = /* @__PURE__ */ new Map();\n  for (const e of encodings) {\n    if (rampsOn(e)) {\n      counts.set(e.scheme, (counts.get(e.scheme) ?? 0) + 1);\n    }\n  }\n  const seen = /* @__PURE__ */ new Map();\n  return encodings.map((e) => {\n    const k = rampsOn(e) ? counts.get(e.scheme) : 1;\n    if (k < 2) {\n      return e;\n    }\n    const j = seen.get(e.scheme) ?? 0;\n    seen.set(e.scheme, j + 1);\n    const half = STRETCH_GAP / 2;\n    return {\n      ...e,\n      stretch: [\n        j / k + (j > 0 ? half : 0),\n        (j + 1) / k - (j < k - 1 ? half : 0)\n      ]\n    };\n  });\n}\nvar along = ({ stretch }, t) => stretch ? stretch[0] + (stretch[1] - stretch[0]) * t : t;\nvar toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;\nvar toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;\nfunction oklab(hex) {\n  const [r, g, b] = [1, 3, 5].map(\n    (i) => toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255)\n  );\n  const l = Math.cbrt(0.4122214708 * r + 0.5363325363 * g + 0.0514459929 * b);\n  const m = Math.cbrt(0.2119034982 * r + 0.6806995451 * g + 0.1073969566 * b);\n  const s = Math.cbrt(0.0883024619 * r + 0.2817188376 * g + 0.6299787005 * b);\n  return [\n    0.2104542553 * l + 0.793617785 * m - 0.0040720468 * s,\n    1.9779984951 * l - 2.428592205 * m + 0.4505937099 * s,\n    0.0259040371 * l + 0.7827717662 * m - 0.808675766 * s\n  ];\n}\nfunction oklabToRgb([L, a, b]) {\n  const l = (L + 0.3963377774 * a + 0.2158037573 * b) ** 3;\n  const m = (L - 0.1055613458 * a - 0.0638541728 * b) ** 3;\n  const s = (L - 0.0894841775 * a - 1.291485548 * b) ** 3;\n  return [\n    4.0767416621 * l - 3.3077115913 * m + 0.2309699292 * s,\n    -1.2684380046 * l + 2.6097574011 * m - 0.3413193965 * s,\n    -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s\n  ].map((c) => toGamma(Math.max(0, Math.min(1, c))) * 255);\n}\nvar endsCache = /* @__PURE__ */ new Map();\nfunction oklabEnds(scheme) {\n  if (!endsCache.has(scheme)) {\n    const family = WALK_SCHEMES.find((s) => s.value === scheme);\n    endsCache.set(\n      scheme,\n      family && \"ends\" in family ? family.ends.map(oklab) : void 0\n    );\n  }\n  return endsCache.get(scheme);\n}\nfunction schemeRgb(scheme, t, darkest = 0) {\n  const x = Math.max(0, Math.min(1, t));\n  const ends = oklabEnds(scheme);\n  if (!ends) {\n    return hslToRgb(\n      rampHueAt(x),\n      REFERENCE_RAMP_SATURATION,\n      REFERENCE_RAMP_LIGHTNESS\n    ).map((c) => c * 255);\n  }\n  const [from, to] = ends;\n  const light = from[0];\n  const dark = to[0];\n  const reach = dark < darkest && light > darkest ? (light - darkest) / (light - dark) : 1;\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x * reach));\n}\nfunction schemeCss(scheme, t, darkest) {\n  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t, darkest) {\n  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor(encoding, t) {\n  const { field, scheme, darkest, shade = BASE_T } = encoding;\n  return field === \"walk\" ? schemeColor(scheme, shade) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, along(encoding, t), darkest);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops(encoding) {\n  const { field, scheme, darkest, shade = BASE_T } = encoding;\n  const stop = (offset, t) => ({\n    offset,\n    color: schemeCss(scheme, t, darkest),\n    abgr: schemeColor(scheme, t, darkest)\n  });\n  return field === \"walk\" ? [stop(0, shade)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, along(encoding, i / 6)));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  splitFamilies,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
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+  "names": ["THREAD_PX", "THREAD_GAP_PX", "SLOT_GAP_PX", "LANE_SMOOTHING_PX", "THREAD_REACH_PX", "THREAD_TAPER_PX", "MAX_BAND_PX", "PASSES_KEY", "threadsPasses", "walks", "w", "threadsWidth", "threads", "sum", "values", "a", "b", "slotLayout", "spans", "mostPasses", "laneWidth", "widths", "m", "i", "seen", "gaps", "share", "gap", "THREAD_PITCH_PX", "slotCentres", "held", "band", "at", "width", "slack", "centre", "bandWidthPx", "bandScale", "passesKey", "laneSlideAt", "start", "end", "along", "vector", "normal", "offsetX2", "dx", "dy", "slideAt", "offsetX", "gapOf", "arcOf", "run", "s", "laneRuns", "routes", "nodePositions", "yToX", "jump", "owns", "route", "id", "runs", "owned", "mine", "breakRun", "r", "step", "segments", "first", "last", "prev", "next", "toNext", "p", "forward", "middle", "k", "index", "ownedWindows", "margin", "windows", "j", "floor", "lo", "hi", "smoothedNormals", "reach", "pointAt", "span", "f", "_", "back", "ahead", "len", "cutCurls", "close", "length", "out", 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+}