jbrowse-plugin-graphgenomeviewer 7.2.0 → 7.3.0

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

@@ -1,7 +0,0 @@
-{
-  "version": 3,
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-  "sourcesContent": ["import {\n  panSNFields\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/facetGrid.ts\nvar FACET_GAP_PX = 8;\nvar FACET_TITLE_PX = 34;\nvar FACET_PAD_PX = 12;\nvar MIN_FACET_PANEL_PX = 60;\nfunction facetGrid({\n  count,\n  bounds,\n  pixelRows,\n  width,\n  room,\n  columns\n}) {\n  function tile(across) {\n    const rows = Math.ceil(count / across);\n    const panelWidth = Math.floor(\n      (width - (across - 1) * FACET_GAP_PX) / across\n    );\n    const panelRoom = (room - rows * FACET_TITLE_PX - (rows - 1) * FACET_GAP_PX) / rows;\n    const fitX = (panelWidth - 2 * FACET_PAD_PX) / bounds.w;\n    const fitY = bounds.h > 0 ? (panelRoom - 2 * FACET_PAD_PX) / bounds.h : Infinity;\n    const scale = pixelRows ? fitX : Math.min(fitX, fitY);\n    const drawn = pixelRows ? bounds.h : bounds.h * scale;\n    const height = Math.floor(\n      Math.max(\n        MIN_FACET_PANEL_PX,\n        Math.min(drawn + 2 * FACET_PAD_PX, panelRoom)\n      )\n    );\n    return {\n      columns: across,\n      width: panelWidth,\n      height,\n      scale,\n      total: rows * (height + FACET_TITLE_PX) + (rows - 1) * FACET_GAP_PX\n    };\n  }\n  if (columns !== void 0) {\n    return tile(Math.max(1, Math.min(count, Math.round(columns))));\n  }\n  let best = tile(1);\n  for (let across = 2; across <= count; across++) {\n    const grid = tile(across);\n    if (grid.scale > best.scale) {\n      best = grid;\n    }\n  }\n  return best;\n}\nvar FACET_FIELDS = [\n  { value: \"\", label: \"None\", description: \"Every lifted walk in one drawing\" },\n  {\n    value: \"walk\",\n    label: \"A panel per walk\",\n    description: \"One panel per lifted walk, side by side\"\n  },\n  {\n    value: \"sample\",\n    label: \"A row per sample\",\n    description: \"A row per sample, a column per haplotype\"\n  }\n];\nfunction facetSettingOf(facet) {\n  const raw = typeof facet === \"string\" ? { field: facet } : facet ?? {};\n  const field = raw.field === \"walk\" || raw.field === \"sample\" ? raw.field : \"\";\n  return {\n    field,\n    domain: [...raw.domain ?? []],\n    ...raw.columns === void 0 ? {} : { columns: raw.columns }\n  };\n}\nfunction domainFirst(names, domain) {\n  const rank = new Map(domain.map((name, i) => [name, i]));\n  const listed = (name) => rank.get(name) ?? domain.length;\n  return names.map((name, i) => ({ name, i })).sort((a, b) => listed(a.name) - listed(b.name) || a.i - b.i).map(({ name }) => name);\n}\nfunction facetCells(names, by, domain = []) {\n  const wrapOrder = domainFirst(names, domain);\n  const wrap = {\n    columns: void 0,\n    count: names.length,\n    cells: names.map((name) => wrapOrder.indexOf(name))\n  };\n  if (by === \"walk\") {\n    return wrap;\n  }\n  const places = names.map((name) => {\n    const fields = panSNFields(name);\n    return fields && Number.isInteger(fields.haplotype) && fields.haplotype >= 0 ? { sample: fields.sample, column: Math.max(0, fields.haplotype - 1) } : void 0;\n  });\n  const rows = domainFirst(\n    [...new Set(places.flatMap((p) => p ? [p.sample] : []))],\n    domain\n  );\n  const columns = Math.max(1, ...places.map((p) => p ? p.column + 1 : 1));\n  const cells = places.map(\n    (p) => p ? rows.indexOf(p.sample) * columns + p.column : -1\n  );\n  return cells.includes(-1) || new Set(cells).size < cells.length ? wrap : { columns, count: rows.length * columns, cells };\n}\n\nexport {\n  FACET_GAP_PX,\n  FACET_TITLE_PX,\n  FACET_PAD_PX,\n  facetGrid,\n  FACET_FIELDS,\n  facetSettingOf,\n  facetCells\n};\n", "import {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/orientToReference.ts\nfunction orientToReference(graph, positions) {\n  const backbone = graph.nodes.filter(\n    (node) => isBackbone(node) && (positions[node.id]?.length ?? 0) > 0\n  );\n  if (backbone.length < 2) {\n    return positions;\n  }\n  const points = backbone.map((node) => {\n    const segments = positions[node.id];\n    const mid = segments[Math.floor(segments.length / 2)];\n    return {\n      x: mid.x,\n      y: mid.y,\n      r: node.stable.start + node.length / 2,\n      w: node.length\n    };\n  });\n  const weight = points.reduce((sum, p) => sum + p.w, 0);\n  if (weight === 0) {\n    return positions;\n  }\n  const cx = points.reduce((sum, p) => sum + p.x * p.w, 0) / weight;\n  const cy = points.reduce((sum, p) => sum + p.y * p.w, 0) / weight;\n  const cr = points.reduce((sum, p) => sum + p.r * p.w, 0) / weight;\n  let sxr = 0;\n  let syr = 0;\n  for (const p of points) {\n    sxr += p.w * (p.x - cx) * (p.r - cr);\n    syr += p.w * (p.y - cy) * (p.r - cr);\n  }\n  const angle = -Math.atan2(syr, sxr);\n  const c = Math.cos(angle);\n  const s = Math.sin(angle);\n  const out = {};\n  for (const [id, segments] of Object.entries(positions)) {\n    out[id] = segments.map((p) => {\n      const x = p.x - cx;\n      const y = p.y - cy;\n      return { x: cx + c * x - s * y, y: cy + s * x + c * y };\n    });\n  }\n  let below = 0;\n  let above = 0;\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      continue;\n    }\n    for (const p of out[node.id] ?? []) {\n      if (p.y > cy) {\n        below++;\n      } else {\n        above++;\n      }\n    }\n  }\n  if (above > below) {\n    for (const segments of Object.values(out)) {\n      for (const p of segments) {\n        p.y = 2 * cy - p.y;\n      }\n    }\n  }\n  return out;\n}\n\nexport {\n  orientToReference\n};\n", "import {\n  buildNeighbors\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  drawnNodeLength\n} from \"./chunk-34BOZKIE.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/referenceSeeds.ts\nvar LANE_GAP = 30;\nfunction referenceSeeds(graph, scaling) {\n  const { opts } = scaling;\n  const drawn = new Map(\n    scaling.nodes.map((node) => [node.id, drawnNodeLength(opts, node.length)])\n  );\n  const drawnOf = (id) => drawn.get(id) ?? opts.minimumNodeLength;\n  const backbone = graph.nodes.filter(isBackbone).sort((a, b) => a.stable.start - b.stable.start);\n  const seeds = /* @__PURE__ */ new Map();\n  let x = 0;\n  for (const node of backbone) {\n    seeds.set(node.id, { x, y: 0 });\n    x += drawnOf(node.id) + opts.edgeLength;\n  }\n  const adjacent = buildNeighbors(graph);\n  const depth = new Map(backbone.map((node) => [node.id, 0]));\n  const queue = backbone.map((node) => node.id);\n  for (const id of queue) {\n    const at = seeds.get(id);\n    const next = depth.get(id) + 1;\n    for (const neighbour of adjacent.get(id) ?? []) {\n      if (depth.has(neighbour)) {\n        continue;\n      }\n      depth.set(neighbour, next);\n      seeds.set(neighbour, { x: at.x + drawnOf(id) / 2, y: LANE_GAP * next });\n      queue.push(neighbour);\n    }\n  }\n  let unreached = 0;\n  for (const node of graph.nodes) {\n    if (!seeds.has(node.id)) {\n      seeds.set(node.id, {\n        x: unreached++ * x / graph.nodes.length,\n        y: LANE_GAP * 3\n      });\n    }\n  }\n  return seeds;\n}\nfunction seededNodes(graph, scaling) {\n  const seeds = referenceSeeds(graph, scaling);\n  return scaling.nodes.map((node) => ({ ...node, ...seeds.get(node.id) }));\n}\n\nexport {\n  referenceSeeds,\n  seededNodes\n};\n", "// src/layout/smoothChains.ts\nvar STEP_TURN = Math.PI / 24;\nfunction turnAt(line, i) {\n  const a = line[i - 1];\n  const b = line[i];\n  const c = line[i + 1];\n  if (!a || !c) {\n    return 0;\n  }\n  const t = Math.abs(\n    Math.atan2(c.y - b.y, c.x - b.x) - Math.atan2(b.y - a.y, b.x - a.x)\n  );\n  return t > Math.PI ? 2 * Math.PI - t : t;\n}\nfunction centripetal(p0, p1, p2, p3, u) {\n  const knot = (a, b) => Math.max(Math.hypot(b.x - a.x, b.y - a.y) ** 0.5, 1e-9);\n  const t1 = knot(p0, p1);\n  const t2 = t1 + knot(p1, p2);\n  const t3 = t2 + knot(p2, p3);\n  const t = t1 + u * (t2 - t1);\n  const lerp = (a, b, ta, tb) => {\n    const f = (t - ta) / (tb - ta);\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n  };\n  const a1 = lerp(p0, p1, 0, t1);\n  const a2 = lerp(p1, p2, t1, t2);\n  const a3 = lerp(p2, p3, t2, t3);\n  return lerp(lerp(a1, a2, 0, t2), lerp(a2, a3, t1, t3), t1, t2);\n}\nvar reflect = (p, about) => ({\n  x: 2 * about.x - p.x,\n  y: 2 * about.y - p.y\n});\nfunction smoothChain(line) {\n  if (line.length < 3) {\n    return line;\n  }\n  const out = [line[0]];\n  for (let i = 0; i + 1 < line.length; i++) {\n    const p1 = line[i];\n    const p2 = line[i + 1];\n    const steps = Math.ceil(\n      Math.max(turnAt(line, i), turnAt(line, i + 1)) / STEP_TURN\n    );\n    const p0 = line[i - 1] ?? reflect(p2, p1);\n    const p3 = line[i + 2] ?? reflect(p1, p2);\n    for (let s = 1; s < steps; s++) {\n      out.push(centripetal(p0, p1, p2, p3, s / steps));\n    }\n    out.push(p2);\n  }\n  return out;\n}\n\nexport {\n  smoothChain\n};\n", "// src/layout/deletionRoutes.ts\nimport { ROUTE_ID } from \"@jbrowse/graph-stress-layout\";\nvar ROUTE_FRACTION = 0.5;\nfunction withDeletionRoutes(graph, deletions, dropped = /* @__PURE__ */ new Set()) {\n  const routes = new Map(\n    deletions.map((d) => [d.edgeIndex, `${ROUTE_ID}${d.edgeIndex}`])\n  );\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const id = routes.get(ei);\n    if (dropped.has(ei)) {\n      return;\n    }\n    if (id === void 0) {\n      edges.push(edge);\n    } else {\n      const { fromStrand, toStrand } = edge;\n      edges.push(\n        { from: edge.from, to: id, ...fromStrand ? { fromStrand } : {} },\n        { from: id, to: edge.to, ...toStrand ? { toStrand } : {} }\n      );\n    }\n  });\n  return {\n    graph: {\n      ...graph,\n      nodes: [\n        ...graph.nodes,\n        ...[...routes.values()].map((id) => ({\n          id,\n          name: id,\n          length: 0,\n          depth: 0\n        }))\n      ],\n      edges\n    },\n    routes,\n    ids: new Set(routes.values())\n  };\n}\nfunction routeNodes(graph, deletions, routes, drawnOf, opts) {\n  const lengths = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  return deletions.map((d) => {\n    const skipped = d.bypassed.reduce(\n      (sum, id2) => sum + (lengths.get(id2) ?? 0),\n      0\n    );\n    const drawn = Math.max(\n      opts.minimumNodeLength,\n      drawnOf(skipped) * ROUTE_FRACTION\n    );\n    const id = routes.get(d.edgeIndex);\n    return {\n      id,\n      name: id,\n      length: Math.round(drawn * 1e6 / opts.nodeLengthPerMegabase),\n      depth: 0\n    };\n  });\n}\nfunction takeRoutes(positions, routes) {\n  const nodePositions = { ...positions };\n  const deletionRoutes = {};\n  for (const [edgeIndex, id] of routes) {\n    const route = nodePositions[id];\n    delete nodePositions[id];\n    if (route?.length) {\n      deletionRoutes[edgeIndex] = route;\n    }\n  }\n  return { nodePositions, deletionRoutes };\n}\n\nexport {\n  withDeletionRoutes,\n  routeNodes,\n  takeRoutes\n};\n", "// src/gfa-core/gfaParser.ts\nfunction parseTag(tag, tags) {\n  const nameEnd = tag.indexOf(\":\");\n  const typeEnd = tag.indexOf(\":\", nameEnd + 1);\n  if (nameEnd !== -1 && typeEnd !== -1) {\n    const name = tag.slice(0, nameEnd);\n    const type = tag.slice(nameEnd + 1, typeEnd);\n    const val = tag.slice(typeEnd + 1);\n    if (type === \"i\" || type === \"f\") {\n      tags[name] = +val;\n    } else if (type === \"Z\") {\n      tags[name] = val;\n    }\n  }\n}\nfunction parseTags(fields) {\n  const tags = {};\n  for (const field of fields) {\n    parseTag(field, tags);\n  }\n  return tags;\n}\nfunction stableCoordinate(node) {\n  const { SN, SO, SR } = node.tags;\n  return typeof SN === \"string\" && typeof SO === \"number\" && typeof SR === \"number\" ? { refName: SN, start: SO, rank: SR } : void 0;\n}\nvar GT = 62;\nvar LT = 60;\nfunction parseWalkBody(body) {\n  const segments = [];\n  let strand = \"+\";\n  let start = 0;\n  function push(end) {\n    if (end > start) {\n      segments.push({ id: body.slice(start, end), strand });\n    }\n  }\n  for (let i = 0; i < body.length; i++) {\n    const ch = body.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      push(i);\n      strand = ch === GT ? \"+\" : \"-\";\n      start = i + 1;\n    }\n  }\n  push(body.length);\n  return segments;\n}\nfunction parseGFA(file) {\n  const graph = {\n    nodes: [],\n    links: [],\n    paths: [],\n    walks: [],\n    header: [],\n    id: \"\"\n  };\n  for (const rawLine of file.split(\"\\n\")) {\n    const line = rawLine.endsWith(\"\\r\") ? rawLine.slice(0, -1) : rawLine;\n    const type = line.split(\"\t\", 1)[0];\n    if (type === \"H\") {\n      const [, ...rest] = line.split(\"\t\");\n      graph.header.push(parseTags(rest));\n    } else if (type === \"S\") {\n      const [, name, ...rest] = line.split(\"\t\");\n      let len;\n      let seq;\n      let tagfields;\n      let gfa1 = false;\n      const first = rest[0] ?? \"*\";\n      if (/^\\d+$/.test(first)) {\n        len = +first;\n        seq = rest[1] ?? \"*\";\n        tagfields = rest.slice(2);\n      } else {\n        gfa1 = true;\n        seq = first;\n        len = seq === \"*\" ? 0 : seq.length;\n        tagfields = rest.slice(1);\n      }\n      const tags = parseTags(tagfields);\n      if (gfa1 && \"LN\" in tags) {\n        len = +tags.LN;\n      }\n      graph.nodes.push({ id: name, length: len, sequence: seq, tags });\n    } else if (type === \"E\") {\n      const [, , source, target, , , , , cigar, ...rest] = line.split(\"\t\");\n      if (source && target) {\n        graph.links.push({\n          source: source.slice(0, -1),\n          target: target.slice(0, -1),\n          strand1: source.at(-1),\n          strand2: target.at(-1),\n          cigar: cigar ?? \"*\",\n          tags: parseTags(rest)\n        });\n      }\n    } else if (type === \"L\") {\n      const [, source, strand1, target, strand2, cigar, ...rest] = line.split(\"\t\");\n      if (source && target && strand2) {\n        graph.links.push({\n          source,\n          target,\n          strand1,\n          strand2,\n          cigar: cigar ?? \"*\",\n          tags: parseTags(rest)\n        });\n      }\n    } else if (type === \"W\") {\n      const [, sample, hap, contig, start, end, body, ...rest] = line.split(\"\t\");\n      if (sample && hap && contig && start && end && body) {\n        graph.walks.push({\n          sample,\n          haplotype: +hap,\n          contig,\n          start: start === \"*\" ? -1 : +start,\n          end: end === \"*\" ? -1 : +end,\n          segments: parseWalkBody(body),\n          tags: parseTags(rest)\n        });\n      }\n    } else if (type === \"P\") {\n      const [, name, path, ...rest] = line.split(\"\t\");\n      if (name && path) {\n        graph.paths.push({ name, path, rest });\n      }\n    }\n  }\n  return graph;\n}\n\nexport {\n  stableCoordinate,\n  parseGFA\n};\n", "import {\n  stableCoordinate\n} from \"./chunk-5I3K4R2G.js\";\nimport {\n  pathOrigin,\n  surveyPaths\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  walkStopFields\n} from \"./chunk-EIY2SKD3.js\";\n\n// src/gfa/gfaConverter.ts\nfunction surveySegments(gfaGraph, pathSteps) {\n  const canonical = /* @__PURE__ */ new Map();\n  const traversals = /* @__PURE__ */ new Map();\n  function claim(id, strand) {\n    if (!canonical.has(id)) {\n      canonical.set(id, strand);\n    }\n  }\n  function traverse(id, strand) {\n    const seen = traversals.get(id);\n    if (seen === void 0) {\n      claim(id, strand);\n    }\n    traversals.set(id, (seen ?? 0) + 1);\n  }\n  for (const link of gfaGraph.links) {\n    claim(link.source, link.strand1 === \"-\" ? \"-\" : \"+\");\n    claim(link.target, link.strand2 === \"-\" ? \"-\" : \"+\");\n  }\n  for (const { steps } of pathSteps) {\n    for (const step of steps) {\n      traverse(step.id, step.strand);\n    }\n  }\n  for (const walk of gfaGraph.walks) {\n    for (const step of walk.segments) {\n      traverse(step.id, step.strand);\n    }\n  }\n  return { canonical, traversals };\n}\nvar walkStart = (w) => w.start === -1 ? 0 : w.start;\nfunction stepsOfPath(p) {\n  return {\n    ...pathOrigin(p.name),\n    steps: p.path.split(\",\").map((segment) => ({\n      id: segment.slice(0, -1),\n      strand: segment.endsWith(\"-\") ? \"-\" : \"+\"\n    }))\n  };\n}\nfunction anchorablePaths(gfaGraph, pathSteps) {\n  return [\n    ...pathSteps,\n    ...gfaGraph.walks.map((w) => ({\n      name: `${w.sample}#${w.haplotype}#${w.contig}`,\n      start: walkStart(w),\n      steps: w.segments\n    }))\n  ];\n}\nfunction carriedSamples(gfaNode) {\n  const sm = gfaNode.tags.SM;\n  if (typeof sm !== \"string\") {\n    return void 0;\n  }\n  const samples = sm.split(\",\").map((s) => s.trim()).filter(Boolean);\n  return samples.length > 0 ? samples : void 0;\n}\nvar positive = (v) => typeof v === \"number\" && v > 0 ? v : void 0;\nfunction statedDepth({ tags, length }) {\n  const count = positive(tags.RC) ?? positive(tags.FC) ?? positive(tags.KC);\n  return positive(tags.dp) ?? positive(tags.DP) ?? (count !== void 0 && length > 0 ? count / length : void 0);\n}\nfunction makeNode(gfaNode, strand, depth) {\n  return {\n    id: `${gfaNode.id}${strand}`,\n    name: gfaNode.id,\n    length: gfaNode.length,\n    depth,\n    stable: stableCoordinate(gfaNode),\n    samples: carriedSamples(gfaNode)\n  };\n}\nfunction convertGFAToGraph(gfaGraph, name = \"Imported GFA\") {\n  const nodes = [];\n  const edges = [];\n  const pathSteps = gfaGraph.paths.map(stepsOfPath);\n  const { canonical, traversals } = surveySegments(gfaGraph, pathSteps);\n  const nodeIds = /* @__PURE__ */ new Map();\n  const nodeId = (segmentId) => {\n    let id = nodeIds.get(segmentId);\n    if (id === void 0) {\n      id = `${segmentId}${canonical.get(segmentId) ?? \"+\"}`;\n      nodeIds.set(segmentId, id);\n    }\n    return id;\n  };\n  const lengths = /* @__PURE__ */ new Map();\n  for (const gfaNode of gfaGraph.nodes) {\n    if (lengths.has(gfaNode.id)) {\n      continue;\n    }\n    lengths.set(gfaNode.id, gfaNode.length);\n    const depth = statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1);\n    nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? \"+\", depth));\n  }\n  for (const link of gfaGraph.links) {\n    edges.push({\n      from: nodeId(link.source),\n      to: nodeId(link.target),\n      fromStrand: link.strand1 === \"-\" ? \"-\" : \"+\",\n      toStrand: link.strand2 === \"-\" ? \"-\" : \"+\"\n    });\n  }\n  const paths = [];\n  const pathsByPair = /* @__PURE__ */ new Map();\n  const pairPaths = (a, b) => pathsByPair.get(a)?.get(b);\n  function addPair(a, b, set) {\n    let to = pathsByPair.get(a);\n    if (!to) {\n      to = /* @__PURE__ */ new Map();\n      pathsByPair.set(a, to);\n    }\n    to.set(b, set);\n  }\n  const edgePaths = edges.map((edge) => {\n    let set = pairPaths(edge.from, edge.to);\n    if (!set) {\n      set = /* @__PURE__ */ new Set();\n      addPair(edge.from, edge.to, set);\n      addPair(edge.to, edge.from, set);\n    }\n    return set;\n  });\n  function recordPathEdges(nodeIds2, name2) {\n    for (let i = 0; i < nodeIds2.length - 1; i++) {\n      pairPaths(nodeIds2[i], nodeIds2[i + 1])?.add(name2);\n    }\n  }\n  gfaGraph.paths.forEach(({ name: name2 }, i) => {\n    const { start, steps } = pathSteps[i];\n    const nodeIds2 = steps.map((step) => nodeId(step.id));\n    paths.push({ name: name2, nodeIds: nodeIds2, start });\n    recordPathEdges(nodeIds2, name2);\n  });\n  for (const walk of gfaGraph.walks) {\n    const nodeIds2 = walk.segments.map((seg) => nodeId(seg.id));\n    const name2 = `${walk.sample}#${walk.haplotype}#${walk.contig}`;\n    paths.push({\n      name: name2,\n      nodeIds: nodeIds2,\n      start: walkStart(walk),\n      sample: walk.sample,\n      haplotype: walk.haplotype,\n      contig: walk.contig,\n      ...walkStopFields(walk.tags)\n    });\n    recordPathEdges(nodeIds2, name2);\n  }\n  edges.forEach((edge, i) => {\n    const pathIds = edgePaths[i];\n    if (pathIds.size > 0) {\n      edge.pathIds = [...pathIds];\n    }\n  });\n  const anchoring = gfaGraph.paths.length > 0 || gfaGraph.walks.length > 0 ? surveyPaths(\n    anchorablePaths(gfaGraph, pathSteps),\n    (id) => lengths.get(id) ?? 0\n  ) : void 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: paths.length > 0 ? paths : void 0,\n    anchorPaths: anchoring?.anchorPaths,\n    pathVisits: anchoring?.pathVisits,\n    // rGFA's own tags win wherever they are present; pathAnchoring only ever\n    // fills in for a graph that carries none.\n    anchoredBy: nodes.some((n) => n.stable) ? \"tags\" : void 0\n  };\n}\n\nexport {\n  convertGFAToGraph\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  PathVisits\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const canonical = new Uint8Array(count);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  for (const p of drawnWalks) {\n    for (let s = w.offsets[p]; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      if (traversals[node] === 0) {\n        claim(node, w.reversed[s]);\n      }\n      traversals[node]++;\n    }\n  }\n  const ids = n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const walkName = w.names[p];\n    const fields = panSNFields(walkName);\n    const start = w.starts[p];\n    const visitName = fields ? `${fields.sample}#${fields.haplotype}#${fields.contig}` : walkName;\n    const pathName = fields ? visitName : pLineName(walkName, start, w.ends[p]);\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({\n      name: pathName,\n      nodeIds,\n      start,\n      ...fields,\n      ...fields ? stopFields(\n        w.before && stopAt(w.before, p),\n        w.after && stopAt(w.after, p)\n      ) : {}\n    });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  orientToReference\n} from \"./chunk-3PZSBNLI.js\";\nimport {\n  seededNodes\n} from \"./chunk-CKUVEHSS.js\";\nimport {\n  smoothChain\n} from \"./chunk-OPPVSPEF.js\";\nimport {\n  routeNodes,\n  takeRoutes,\n  withDeletionRoutes\n} from \"./chunk-VPE4AYP7.js\";\nimport {\n  convertGFAToGraph\n} from \"./chunk-FFHJGWDK.js\";\nimport {\n  parseGFA\n} from \"./chunk-5I3K4R2G.js\";\nimport {\n  graphFromTables\n} from \"./chunk-3XSRT7RQ.js\";\nimport {\n  anchorGraph\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  gfaTables\n} from \"./chunk-DZR37KXT.js\";\nimport {\n  mergeRuns,\n  splitRuns\n} from \"./chunk-BZFOFC4D.js\";\nimport {\n  spreadFor\n} from \"./chunk-HKYXWZQS.js\";\nimport {\n  drawnLengthOf,\n  drawnNodeLength,\n  layoutScaling\n} from \"./chunk-34BOZKIE.js\";\nimport {\n  deletionDrawing,\n  deletionEdges\n} from \"./chunk-CGMSKIEO.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/pipeline.ts\nfunction graphOf(source, name) {\n  if (typeof source !== \"string\") {\n    return graphFromTables(source, name);\n  }\n  const tables = gfaTables(source);\n  return tables ? graphFromTables(tables, name) : convertGFAToGraph(parseGFA(source), name);\n}\nfunction loadGraph(source, name, opts = {}) {\n  const graph = anchorGraph(graphOf(source, name), opts.referencePath);\n  if (graph.nodes.length === 0) {\n    throw new Error(`No graph segments in ${name}`);\n  }\n  if (opts.maxNodes !== void 0 && graph.nodes.length > opts.maxNodes) {\n    throw new Error(\n      `Graph too large to draw: ${graph.nodes.length.toLocaleString()} nodes (limit ${opts.maxNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`\n    );\n  }\n  return graph;\n}\nvar ENGINE_DEFAULTS = {\n  engine: \"fmmm\",\n  quality: 2,\n  linearLayout: false,\n  bubbleSpread: \"auto\",\n  spacing: 1,\n  componentSeparation: 1,\n  showDeletionEdges: true\n};\nfunction engineSettingsOf(s = {}) {\n  return {\n    engine: s.engine ?? ENGINE_DEFAULTS.engine,\n    quality: s.quality ?? ENGINE_DEFAULTS.quality,\n    linearLayout: s.linearLayout ?? ENGINE_DEFAULTS.linearLayout,\n    bubbleSpread: s.bubbleSpread ?? ENGINE_DEFAULTS.bubbleSpread,\n    spacing: s.spacing ?? ENGINE_DEFAULTS.spacing,\n    componentSeparation: s.componentSeparation ?? ENGINE_DEFAULTS.componentSeparation,\n    showDeletionEdges: s.showDeletionEdges ?? ENGINE_DEFAULTS.showDeletionEdges\n  };\n}\nvar COMPONENT_SEPARATION = 15;\nfunction engineRequest(graph, scaling, settings) {\n  const anchored = graph.nodes.some(isBackbone);\n  const s = engineSettingsOf(settings);\n  const spaced = {\n    ...scaling,\n    opts: {\n      ...scaling.opts,\n      edgeLength: scaling.opts.edgeLength * s.spacing\n    }\n  };\n  return {\n    graph: {\n      nodes: anchored ? seededNodes(graph, spaced) : spaced.nodes,\n      edges: graph.edges\n    },\n    options: {\n      quality: s.quality,\n      linearLayout: s.linearLayout,\n      ...spaced.opts,\n      componentSeparation: COMPONENT_SEPARATION * s.componentSeparation,\n      ...anchored ? { rotateComponents: false } : {},\n      engine: s.engine\n    }\n  };\n}\nfunction engineKey(graph, settings) {\n  const anchored = graph.nodes.some(isBackbone);\n  return [\n    ...Object.values(engineSettingsOf(settings)),\n    anchored,\n    graph.referencePath ?? \"\"\n  ].join(\"|\");\n}\nasync function forceLayout(graph, settings, engine) {\n  const spread = spreadFor(settings.bubbleSpread);\n  const { shown: deletions, hidden: dropped } = deletionDrawing(\n    graph,\n    deletionEdges(graph),\n    settings.showDeletionEdges !== false\n  );\n  const routed = withDeletionRoutes(graph, deletions, dropped);\n  const merged = mergeRuns(routed.graph, routed.ids);\n  const runs = {\n    ...merged.graph,\n    nodes: merged.graph.nodes.filter((n) => !routed.ids.has(n.id))\n  };\n  const engineScaling = layoutScaling(runs, spread);\n  const { result, duration } = await engine(\n    engineRequest(\n      merged.graph,\n      {\n        ...engineScaling,\n        nodes: [\n          ...engineScaling.nodes,\n          ...routeNodes(\n            graph,\n            deletions,\n            routed.routes,\n            drawnLengthOf(runs, spread),\n            engineScaling.opts\n          )\n        ]\n      },\n      settings\n    )\n  );\n  const scaling = layoutScaling(graph, spread);\n  const drawn = new Map(\n    scaling.nodes.map((n) => [n.id, drawnNodeLength(scaling.opts, n.length)])\n  );\n  const smoothed = Object.fromEntries(\n    Object.entries(result.nodePositions).map(([id, line]) => [\n      id,\n      smoothChain(line)\n    ])\n  );\n  const positions = splitRuns(smoothed, merged.runs, (id) => drawn.get(id) ?? 0);\n  const { nodePositions, deletionRoutes } = takeRoutes(\n    graph.nodes.some(isBackbone) ? orientToReference(graph, positions) : positions,\n    routed.routes\n  );\n  return {\n    result: {\n      ...result,\n      nodePositions,\n      stranded: true,\n      ...deletions.length ? { deletionRoutes, extent: layoutExtent(deletionRoutes) } : {}\n    },\n    duration\n  };\n}\nfunction layoutExtent(nodePositions) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const segments of Object.values(nodePositions)) {\n    for (const seg of segments) {\n      minX = Math.min(minX, seg.x);\n      minY = Math.min(minY, seg.y);\n      maxX = Math.max(maxX, seg.x);\n      maxY = Math.max(maxY, seg.y);\n    }\n  }\n  return { minX, minY, maxX, maxY };\n}\nvar FIT_PADDING = 40;\nvar MIN_ZOOM = 1e-6;\nvar MAX_ZOOM = 100;\nfunction clampZoom(zoom) {\n  return Math.max(MIN_ZOOM, Math.min(MAX_ZOOM, zoom));\n}\nfunction fittedTranslateY(bounds, usableHeight, yScale, padTop = FIT_PADDING) {\n  const leftoverY = usableHeight - bounds.h * yScale;\n  return padTop - bounds.minY * yScale + Math.max(0, leftoverY) / 2;\n}\nfunction fitTransform(bounds, paneWidth, paneHeight, pixelRows, {\n  minScale = 0,\n  padLeft = FIT_PADDING,\n  padTop = FIT_PADDING,\n  padRight = FIT_PADDING,\n  padBottom = FIT_PADDING\n} = {}) {\n  const usableWidth = paneWidth - padLeft - padRight;\n  const usableHeight = paneHeight - padTop - padBottom;\n  if (usableWidth <= 0 || usableHeight <= 0 || !(bounds.w > 0 || !pixelRows && bounds.h > 0)) {\n    return void 0;\n  }\n  const fitX = bounds.w > 0 ? usableWidth / bounds.w : Infinity;\n  const fitY = bounds.h > 0 ? usableHeight / bounds.h : Infinity;\n  const scale = clampZoom(\n    Math.max(minScale, pixelRows ? fitX : Math.min(fitX, fitY))\n  );\n  const leftoverX = usableWidth - bounds.w * scale;\n  return {\n    scale,\n    translateX: padLeft - bounds.minX * scale + Math.max(0, leftoverX) / 2,\n    translateY: fittedTranslateY(\n      bounds,\n      usableHeight,\n      pixelRows ? 1 : scale,\n      padTop\n    )\n  };\n}\nfunction drawingBounds(layout, opts = {}) {\n  let { minX, minY, maxX, maxY } = layoutExtent(layout.nodePositions);\n  const { region } = opts;\n  if (layout.referenceAxis && region && region.end > region.start) {\n    minX = region.start;\n    maxX = region.end;\n  }\n  const extent = opts.extent ?? layout.extent;\n  if (extent) {\n    minX = Math.min(minX, extent.minX ?? minX);\n    minY = Math.min(minY, extent.minY ?? minY);\n    maxX = Math.max(maxX, extent.maxX ?? maxX);\n    maxY = Math.max(maxY, extent.maxY ?? maxY);\n  }\n  return { minX, minY, w: maxX - minX, h: maxY - minY };\n}\n\nexport {\n  loadGraph,\n  ENGINE_DEFAULTS,\n  engineSettingsOf,\n  engineRequest,\n  engineKey,\n  forceLayout,\n  layoutExtent,\n  FIT_PADDING,\n  clampZoom,\n  fittedTranslateY,\n  fitTransform,\n  drawingBounds\n};\n", "import {\n  engineKey,\n  forceLayout\n} from \"./chunk-KDU4EF66.js\";\n\n// src/layout/forceCache.ts\nvar DEFAULT_SIZE = 4;\nfunction createForceLayoutCache(size = DEFAULT_SIZE) {\n  const caches = /* @__PURE__ */ new WeakMap();\n  const cacheOf = (graph) => {\n    let cache = caches.get(graph);\n    if (!cache) {\n      cache = /* @__PURE__ */ new Map();\n      caches.set(graph, cache);\n    }\n    return cache;\n  };\n  return {\n    layout(graph, settings, engine) {\n      const cache = cacheOf(graph);\n      const key = engineKey(graph, settings);\n      const hit = cache.get(key);\n      if (hit) {\n        return hit.run;\n      }\n      if (cache.size >= size) {\n        cache.delete(cache.keys().next().value);\n      }\n      const started = performance.now();\n      const entry = {\n        run: forceLayout(graph, settings, engine).then((r) => {\n          entry.done = r.result;\n          return { ...r, duration: r.duration || performance.now() - started };\n        })\n      };\n      entry.run.catch(() => {\n        if (cache.get(key) === entry) {\n          cache.delete(key);\n        }\n      });\n      cache.set(key, entry);\n      return entry.run;\n    },\n    ready(graph, settings) {\n      return caches.get(graph)?.get(engineKey(graph, settings))?.done;\n    },\n    inherit(from, to) {\n      const cache = caches.get(from);\n      if (cache && from !== to) {\n        caches.set(to, cache);\n      }\n    }\n  };\n}\n\nexport {\n  createForceLayoutCache\n};\n", "import {\n  clampZoom\n} from \"./chunk-KDU4EF66.js\";\n\n// src/viewport.ts\nfunction axisScaleOf(scale, pixelRows) {\n  return { scaleX: scale, scaleY: pixelRows ? 1 : scale, pixelRows };\n}\nfunction viewportOf(t, axis, width, height) {\n  return {\n    minX: -t.translateX / axis.scaleX,\n    minY: -t.translateY / axis.scaleY,\n    maxX: (width - t.translateX) / axis.scaleX,\n    maxY: (height - t.translateY) / axis.scaleY\n  };\n}\nfunction padded(v, panes) {\n  const w = (v.maxX - v.minX) * panes;\n  const h = (v.maxY - v.minY) * panes;\n  return {\n    minX: v.minX - w,\n    minY: v.minY - h,\n    maxX: v.maxX + w,\n    maxY: v.maxY + h\n  };\n}\nfunction contains(outer, inner) {\n  return inner.minX >= outer.minX && inner.maxX <= outer.maxX && inner.minY >= outer.minY && inner.maxY <= outer.maxY;\n}\nfunction zoomAbout(t, factor, centerX, centerY, pixelRows) {\n  const scale = clampZoom(t.scale * factor);\n  const ratio = scale / t.scale;\n  return {\n    scale,\n    translateX: centerX - (centerX - t.translateX) * ratio,\n    translateY: pixelRows ? t.translateY : centerY - (centerY - t.translateY) * ratio\n  };\n}\nfunction screenToLayout(x, y, t, axis) {\n  return {\n    x: (x - t.translateX) / axis.scaleX,\n    y: (y - t.translateY) / axis.scaleY\n  };\n}\n\nexport {\n  axisScaleOf,\n  viewportOf,\n  padded,\n  contains,\n  zoomAbout,\n  screenToLayout\n};\n", "const host = JBrowseExports[\"@jbrowse/render-core/RenderLifecycleMixin\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/render-core/RenderLifecycleMixin\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const RenderLifecycleMixin = /* @__PURE__ */ read(\"RenderLifecycleMixin\")\nexport default host && host.__esModule ? host.default : host", "import { types } from '@jbrowse/mobx-state-tree'\n\n// Persisted choices that read a value outside `values` as unset. A plain\n// `types.enumeration` throws on one, so a session saved by a build that had an\n// option this one dropped failed to load at all; here it opens on the default.\nfunction knownOrUnset<T extends string>(values: readonly T[]) {\n  return (value: string | undefined) =>\n    values.includes(value as T) ? (value as T) : undefined\n}\n\nexport function lenientMaybeEnum<T extends string>(values: T[]) {\n  return types.snapshotProcessor(types.maybe(types.enumeration(values)), {\n    preProcessor: knownOrUnset(values),\n  })\n}\n\nexport function lenientOptionalEnum<T extends string>(\n  values: T[],\n  fallback: T,\n) {\n  return types.snapshotProcessor(\n    types.optional(types.enumeration(values), fallback),\n    { preProcessor: knownOrUnset(values) },\n  )\n}\n", "import { lazy } from 'react'\n\nimport { BUBBLE_SPREAD_VALUES } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { createForceLayoutCache } from '@jbrowse/bandage-core/layout/forceCache'\nimport { LAYOUT_ENGINE_VALUES } from '@jbrowse/bandage-core/layoutEngines'\nimport { viewportOf } from '@jbrowse/bandage-core/viewport'\nimport { types } from '@jbrowse/mobx-state-tree'\nimport { RenderLifecycleMixin } from '@jbrowse/render-core/RenderLifecycleMixin'\n\nimport { SEGMENTS_SUFFIX } from '../../locationName.ts'\nimport { lenientOptionalEnum } from '../lenientEnum'\n\nimport type { MorphEntering } from './morph'\nimport type { SubgraphRegion } from '../../GetSubgraph'\nimport type { WalkCut } from '../../RgfaTabixAdapter/walkRowRuns.ts'\nimport type { RepeatArray } from '../repeats/repeatFeatures'\nimport type { PaneLayout } from '../tubeMapPanels'\nimport type { SampleRow } from '../walkRowGroups'\nimport type { MinigraphBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { LayoutModeValue } from '@jbrowse/bandage-core/layoutModes'\nimport type { Bounds } from '@jbrowse/bandage-core/pipeline'\nimport type { RenderBatch } from '@jbrowse/bandage-core/renderer/types'\nimport type { TubeMapMismatch } from '@jbrowse/bandage-core/tubeMap/mismatches'\nimport type { Graph } from '@jbrowse/bandage-core/types'\nimport type { AxisScale } from '@jbrowse/bandage-core/util/geometry'\nimport type { WalkLayer } from '@jbrowse/bandage-core/walkEncoding'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\n// Ceiling on the pane, and what it falls back to before there is a layout to\n// size against. A roughly square drawing (FMMM) hits this and keeps the\n// scrollable pane it has always had.\nexport const MAX_CANVAS_HEIGHT = 600\n// Floor, so a window holding only backbone \u2014 one row, no height at all \u2014 still\n// leaves room to hover a node and read its tooltip.\nexport const MIN_CANVAS_HEIGHT = 160\n// The pane's background, as the renderer clears to it and as CSS. It stays\n// white under a dark theme, because Bandage's deletion edges, the deletion\n// labels and the gene ink are near-black.\nexport const PAPER: [number, number, number, number] = [1, 1, 1, 1]\nexport const PAPER_CSS = 'rgb(255, 255, 255)'\n// The thinnest a fit draws a tube map's tubes\nexport const MIN_FIT_TUBE_PX = 5\n\nexport const TUBE_MAP_MODES = new Set<string>(['tubemap', 'tubemapref'])\n\n// the tube the pointer is on, by track id, and the mismatch mark under it\nexport interface HoveredTube {\n  track: number\n  mismatch?: TubeMapMismatch\n}\n\nexport const ChooseSamplesDialog = lazy(\n  () => import('../components/ChooseSamplesDialog'),\n)\nexport const ChooseWalksDialog = lazy(\n  () => import('../components/ChooseWalksDialog'),\n)\nexport const HighlightColorDialog = lazy(\n  () => import('../components/HighlightColorDialog'),\n)\n\n// Past this many walks the Haplotypes menu lists only the lifted ones and offers a\n// searchable picker\nexport const WALK_MENU_ITEMS = 12\n\n// The sizes a tube map folds variants under. MICB's 22 kb cut draws 475\n// columns whole, 34 under 3 bp and one under 50, where only its structural\n// variants would stand: human windows are mostly SNPs.\nexport const TUBE_MAP_FOLDS = [\n  { bp: 0, label: 'None' },\n  { bp: 3, label: 'Under 3 bp' },\n  { bp: 10, label: 'Under 10 bp' },\n  { bp: 50, label: 'Under 50 bp, leaving structural variants' },\n  { bp: 1000, label: 'Under 1 kb' },\n]\n\n// The rGFA index prefix an adapter config names, from either spelling the\n// config schema accepts: the `uri` shorthand or an explicit segments location.\nexport function bubblePrefix(adapterConfig: Record<string, unknown>) {\n  if (typeof adapterConfig.uri === 'string') {\n    return adapterConfig.uri\n  }\n  const segments = adapterConfig.segmentsLocation as\n    { uri?: string } | undefined\n  const uri = segments?.uri\n  return typeof uri === 'string' && uri.endsWith(SEGMENTS_SUFFIX)\n    ? uri.slice(0, -SEGMENTS_SUFFIX.length)\n    : undefined\n}\nexport const HOVER_BRIGHTEN = 1.15\nexport const SELECT_BRIGHTEN = 1.6\nexport const VIEWPORT_DEBOUNCE_MS = 150\nexport const VIEWPORT_PANES_BUILT = 1\n// How many walk rows read their haplotype's genes, the first rows down\nexport const WALK_GENE_ROWS = 40\n\n// What the canvas draws under the tube map, whose ink is all TubeMapOverlay's\nexport type TubeMapRoutes = 'each' | 'grouped' | 'bundled'\n\nexport const TUBE_MAP_ROUTES: { value: TubeMapRoutes; label: string }[] = [\n  { value: 'each', label: 'A tube per haplotype' },\n  { value: 'grouped', label: 'A tube per haplotype, grouped by route' },\n  { value: 'bundled', label: 'A tube per route' },\n]\n\nexport const EMPTY_BATCH: RenderBatch = {\n  nodeStrokes: [],\n  nodeStrokeRuns: new Map(),\n  arrows: [],\n  arrowRuns: new Map(),\n  edgeCurves: [],\n  edgeCurveRuns: new Map(),\n}\n\n// MobX tracks every observable read while a computed or autorun runs, so\n// passing values here registers them as dependencies without otherwise using\n// them.\nexport function dependOn(..._values: unknown[]) {}\n\n// Hard size cap for the single-mode graph view. Past it the view declines with a\n// \"zoom in\" message rather than switching to a degraded rendering mode \u2014 one mode\n// only, since the large-region case is a linear synteny view, not a graph.\n//\n// This bounds the *fetch*, and it is the only cap that can be applied before one\n// happens. It is a poor proxy for cost, because cost tracks node count, so the\n// number is chosen against the density of the graphs it can actually guard: a\n// region is fetched through `getSubgraph`, and the rGFA cut is what this number\n// was chosen against (the GBZ cut is base-level and has its own `nodeLimit`,\n// which trips long before 5 Mb). Both measured rGFAs are sparse, and at 5 Mb\n// both land at or under the ~2k nodes that redraw in under 10 ms (see agent-docs/reference/GRAPH_SCALE_AND_LOD.md):\n//\n//   HPRC MC GRCh38   ~7,000 bp/segment   whole 4.9 Mb MHC   1,173 nodes\n//   ecoli minigraph   3,078 bp/segment   whole 4.6 Mb genome 2,415 nodes\n//\n// Fetch cost does not scale with the window either: against the hosted HPRC\n// index a 4.9 Mb links query and a 100 kb one both cost ~1.3 s, being dominated\n// by HTTP setup. FMMM is the slowest consumer at this size and stays tolerable,\n// ~0.1-3 s for ~1k nodes depending on layout quality (bandage-layout-js), and it\n// runs off the main thread.\n//\n// A dense graph is what this cannot protect against, because bp per node varies\n// by orders of magnitude between graph types \u2014 a base-level pggb graph runs ~17\n// bp/node, where 5 Mb would be hundreds of thousands. Such a graph has no region\n// query to reach this check with today, and the node budget below is the cap that\n// catches it if one ever does.\nexport const MAX_GRAPH_REGION_BP = 5_000_000\n\n// The cap in a message, in the unit that reads: `5 Mb`, not `5000 kb`.\nexport function formatSpanBp(bp: number) {\n  return bp >= 1_000_000\n    ? `${+(bp / 1_000_000).toFixed(1)} Mb`\n    : `${Math.round(bp / 1000)} kb`\n}\n\n// What the view will actually draw, checked once the graph is parsed and so\n// applying to a whole-file import as much as to a subgraph fetch. Measured on\n// bubble-chain graphs: ~1-2k nodes redraws in under 10 ms, 10k takes ~43 ms of\n// geometry and ~125k canvas draw calls per frame (single-digit fps while\n// panning), and 100k needs 632 ms and 75 MB of vertex buffers. So this is set\n// where the tab stops being usable rather than where it stops being smooth, and\n// it is a view prop rather than a constant so a session can raise it \u2014 the same\n// escape hatch strangepg gives with `-T N`.\nexport const DEFAULT_MAX_GRAPH_NODES = 20_000\n\n// the last segment of a file's path, its query dropped, or a blob's own name\nexport function fileName(location: FileLocation) {\n  const path =\n    'uri' in location\n      ? location.uri.split(/[?#]/)[0]!\n      : 'localPath' in location\n        ? location.localPath\n        : 'name' in location\n          ? location.name\n          : ''\n  return path.split(/[\\\\/]/).at(-1) ?? ''\n}\n\n// A url bandage-figure can read again, or undefined for a local file\nexport function uriOf(location: FileLocation | undefined) {\n  return location && 'uri' in location && location.uri\n    ? new URL(location.uri, location.baseUri ?? window.location.href).href\n    : undefined\n}\n\ntype ViewportOwner = 'fit' | 'user' | 'host'\n\ninterface BuiltViewport {\n  scale: number\n  bounds: Bounds\n  viewportDirty: number\n}\n\nexport function geometryPainted(model: {\n  viewportRebuildPending: boolean\n  viewportDirty: number\n  builtViewport?: BuiltViewport\n  paintedViewport?: BuiltViewport\n}) {\n  return (\n    model.builtViewport !== undefined &&\n    model.paintedViewport === model.builtViewport &&\n    model.builtViewport.viewportDirty === model.viewportDirty &&\n    !model.viewportRebuildPending\n  )\n}\n\n// What the pane shows, in layout units: what each panel shows while faceted\nexport function paneViewportOf(model: {\n  translateX: number\n  translateY: number\n  axisScale: AxisScale\n  viewBox: { width: number; height: number }\n}): Bounds {\n  const { width, height } = model.viewBox\n  return viewportOf(model, model.axisScale, width, height)\n}\n\n// Force layouts already computed for a graph, keyed by the view props the\n// engine reads. Every layout mode is local and costs a millisecond except this\n// one, which is seconds: measured on the committed engine, a 1,201-node bubble\n// chain is 0.6 s proportional, 4.3 s at 'Wide bubbles' and 3.4 s at the highest\n// quality.\n//\n// Worth keeping because a session revisits the same layout. The two drawings\n// answer different questions and the README's own figure is one subgraph in\n// both, so Anchored <-> Force is a round trip a reader makes repeatedly \u2014 and\n// picking a reference path calls `recomputeLayout` whether or not the current\n// mode reads it, which in force mode was a multi-second re-run of an identical\n// layout.\n// Both are hits. The cache itself is core's, which BandageJS keeps too.\nexport const forceLayouts = createForceLayoutCache()\n\nexport const paneBase = types\n  .compose(\n    'GraphPane',\n    RenderLifecycleMixin(),\n    types.model({\n      // FMMM's iteration budget, 0-4, the same scale Bandage's own settings\n      // dialog exposes: 3+1 iterations at 0, 15+10 at 1, 30+20 at 2, 60+40 at\n      // 3, 120+60 at 4 (BandageNG layout/graphlayoutworker.cpp).\n      //\n      // 2 because that is what the engine we vendor ships as its default\n      // (`graphLayoutQuality = IntSetting(2, 0, 4)`, program/settings.cpp).\n      // Cost at the sizes this view draws is milliseconds, and the header\n      // states the layout time.\n      layoutQuality: types.optional(types.number, 2),\n      // Which engine draws the force layout: Bandage's FMMM, or the stress\n      // layout, which reads the reference straight. See LAYOUT_ENGINES.\n      layoutEngine: lenientOptionalEnum(LAYOUT_ENGINE_VALUES, 'fmmm'),\n      linearLayout: types.optional(types.boolean, false),\n      // How far the force layout opens a bubble, which on a variation graph is\n      // the difference between a legible drawing and a rope. See\n      // BUBBLE_SPREADS; no effect on the reference-anchored layouts, which\n      // place a node from its coordinates rather than from a force sim.\n      bubbleSpread: lenientOptionalEnum(BUBBLE_SPREAD_VALUES, 'auto'),\n      // Variants under this many bp fold into the reference before a tube map\n      // is laid out, each kept as a tick on its walk's tube (coarsen.ts); 0\n      // draws every one\n      tubeMapFold: types.optional(types.number, 0),\n      // A tube per haplotype, or a tube per route the haplotypes take, as\n      // wide as how many take it (bundleRoutes)\n      tubeMapRoutes: lenientOptionalEnum<TubeMapRoutes>(\n        ['each', 'grouped', 'bundled'],\n        'each',\n      ),\n      // A sample table column whose values colour the tubes, the reference\n      // charcoal; empty colours them by role\n      tubeMapColorBy: types.optional(types.string, ''),\n      // Which track the genes come from; empty picks the assembly's\n      // annotation track (pickGeneTrack).\n      geneTrackId: types.optional(types.string, ''),\n      // Which track the walk rows read tandem repeat arrays from; empty\n      // picks a track whose name says repeats (pickRepeatTrack).\n      repeatTrackId: types.optional(types.string, ''),\n      // The array the walk rows measure between and tile by, as\n      // RepeatArray.key; empty measures the whole window untiled.\n      repeatKey: types.optional(types.string, ''),\n      // Walks lifted out of the drawing, each a layer with a lane of its own\n      // and the rest fading, coloured by the encoding it states or by the\n      // default one. See walkEncoding.ts. Empty lifts none.\n      walkLayers: types.optional(types.frozen<WalkLayer[]>(), []),\n      // Which of a general GFA's paths the anchored layouts put on x. A path\n      // GFA's names are arbitrary and none of them is marked as the\n      // reference, so this is a choice; empty means \"infer\", which is the\n      // assembly a subgraph was cut against, and the first path in the file\n      // for a whole-file import. No effect on an rGFA, whose segments carry\n      // their own coordinates. See pathAnchoring.ts.\n      referencePath: types.optional(types.string, ''),\n      // Whether the toolbar spells out `fetch 12371ms \u00B7 layout 4ms \u00B7 geom 9ms`.\n      // Off by default because it was in the toolbar of every published graph\n      // figure, where a machine's fetch time is noise a reader has to skip\n      // past. The numbers themselves are always on the element as `data-*`\n      // attributes, which is what browser tests assert against, so hiding the\n      // text costs no coverage.\n      showPerf: types.optional(types.boolean, false),\n      connectorThickness: types.optional(types.number, 2),\n      scale: types.optional(types.number, 1),\n      translateX: types.optional(types.number, 0),\n      translateY: types.optional(types.number, 0),\n      // Ceiling on the drawing pane, in css px, for a session or a figure that\n      // wants a shorter one than the drawing asks for. Unset means the built-in\n      // MAX_CANVAS_HEIGHT, which is what every existing session gets.\n      //\n      // Why this is a knob rather than a smaller default: the pane is as tall\n      // as the drawing's own aspect ratio (see canvasHeight), which is right \u2014\n      // a graph that is twice as tall as it is wide should not be squeezed\n      // into a strip. But one very long node in a cut of short ones makes that\n      // aspect ratio all arc: the HPRC CHM13 figure draws a 142 kb allele\n      // among sub-kb backbone segments, pins the 600 px ceiling and spends\n      // most of it on the loop, with the chain squashed along the bottom edge.\n      // Lowering the ceiling there scales the whole drawing down, which is\n      // exactly the trade that figure wants and the wrong default for a graph\n      // whose height is carrying information.\n      paneHeight: types.maybe(types.number),\n      // Raise to draw a bigger graph than the default budget allows; see\n      // DEFAULT_MAX_GRAPH_NODES for what the numbers cost.\n      maxGraphNodes: types.optional(types.number, DEFAULT_MAX_GRAPH_NODES),\n      // the linear view a graph of its own is paired with for the hover sync\n      connectedViewId: types.maybe(types.string),\n      // The bp ceiling on a fine cut, a proxy for node count that only\n      // holds at fine granularity; `maxGraphNodes` counts what came back.\n      maxRegionBp: types.optional(types.number, MAX_GRAPH_REGION_BP),\n      // How far the cut follows links past the region's own segments. At\n      // 0 a detour that leaves the backbone before the window and rejoins\n      // after it arrives as a fragment, since its interior is indexed only\n      // under its own sequence, so one bubble draws as two unrelated\n      // insertions. A hop follows alleles only, so it never walks the\n      // backbone out of the window.\n      subgraphContext: types.optional(types.number, 1),\n      // the haplotypes a GBZ or walk-indexed cut is for; unset is\n      // trackHaplotypes\n      subgraphHaplotypes: types.maybe(types.frozen<string[]>()),\n    }),\n  )\n  .volatile(() => ({\n    graph: undefined as Graph | undefined,\n    // a walk-rows cut's tables and runs, which draw the rows in place of the\n    // graph's walks\n    walkCut: undefined as WalkCut | undefined,\n    // the reference window the graph on screen was cut for, set with it\n    graphRegion: undefined as SubgraphRegion | undefined,\n    // The walk the track's graph lies on for the region's assembly, which\n    // the track's config declares; x starts along it unless the user chose\n    // another. Undefined for an rGFA, whose backbone is fixed, and for a\n    // graph with no region.\n    loadedReferencePath: undefined as string | undefined,\n    layoutResult: undefined as PaneLayout | undefined,\n    // the mode that drew layoutResult: force where the chosen one could not\n    drawnLayoutMode: undefined as LayoutModeValue | undefined,\n    // what the legends in the pane's top-right corner measure, so no label\n    // is placed under them\n    legendSize: { width: 0, height: 0 },\n    // The bubble index rows over the cut window, when the source track has\n    // one beside its segments. Undefined for a graph with no index, whose\n    // bubbles are `derivedBubbles` instead.\n    indexBubbles: undefined as MinigraphBubble[] | undefined,\n    // the size under which the graph on screen has variants folded into the\n    // reference, by this cut or by the tier it was cut from\n    foldedBelowBp: undefined as number | undefined,\n    // the gene track's features over the cut window, read once per cut\n    geneTrackFeatures: undefined as Feature[] | undefined,\n    // each walk row's genes, read from its haplotype's own assembly, by walk\n    // name\n    walkGeneFeatures: undefined as Map<string, GeneModel[]> | undefined,\n    // the source track's samples TSV, which walk rows group by\n    walkRowSampleTable: undefined as SampleRow[] | undefined,\n    // the tandem repeat arrays over the cut window, from the repeat track\n    repeatArrays: undefined as RepeatArray[] | undefined,\n    // the layout mode the drawing was last laid out for, so a change from the\n    // menu is not laid out a second time by the reaction that catches the rest\n    handledLayoutMode: undefined as LayoutModeValue | undefined,\n    // The bubbles opened in place, outermost first, each inside the one before\n    // it. The drawing keeps the innermost in colour and greys the rest.\n    openBubbles: [] as MinigraphBubble[],\n\n    // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n    error: undefined as unknown,\n    isLoading: false,\n    loadCanceled: false,\n    statusMessage: '',\n    hoveredNode: null as string | null,\n    // where on the pane the pointer hovered it, when the canvas set it\n    hoveredAt: null as { x: number; y: number } | null,\n    hoveredTube: null as HoveredTube | null,\n    // the tube map panel the pointer is over, while the map is split\n    hoveredPanel: null as number | null,\n    // the walks of the per-sample lane row the linear view's pointer is on\n    hoveredRowWalks: [] as string[],\n    // the bubble whose label the pointer is on\n    hoveredBubble: null as MinigraphBubble | null,\n    // whether the pointer is over this pane, whose own hit test then says\n    // what it is on\n    pointerInPane: false,\n    // the strip point the pointer is over, which lights its node above\n    stripHover: null as { row: string; offset: number } | null,\n    // the walk row the pointer is on, by walk name\n    hoveredWalkRow: null as string | null,\n    hoveredEdge: null as number | null,\n    selectedNode: null as string | null,\n    viewportDirty: 0,\n    // Bumped when the layout's positions are mutated IN PLACE, which only a\n    // node drag does. Separate from `viewportDirty` because that one also\n    // fires on pan and zoom, and the things keyed off this \u2014 the two hit\n    // indexes and the label placement's per-layout caches \u2014 do not depend on\n    // the transform at all. Rebuilding a 12k-edge hit index because the user\n    // panned cost ~14 ms of the first mousemove after every gesture.\n    positionsVersion: 0,\n    // what a morph under way is fading in\n    morphEntering: undefined as MorphEntering | undefined,\n    // The batch the canvas holds, which the hover layer lights over it\n    drawnBatch: EMPTY_BATCH,\n    // The zoom and the window the current batch was built for; a pan that\n    // stays inside it needs no rebuild.\n    builtViewport: undefined as BuiltViewport | undefined,\n    // The builtViewport whose batch is on the canvas\n    paintedViewport: undefined as BuiltViewport | undefined,\n    draggingNode: null as string | null,\n    // Dragging the background rather than a node. Lives here beside\n    // draggingNode instead of in a component ref+state pair, so the two\n    // mutually exclusive drag modes are one piece of state read from one place.\n    isPanning: false,\n    // Who places the view. 'fit' refits it to every new layout, 'user' leaves\n    // it where a gesture or a restored session put it, and 'host' takes x\n    // from the linear view the pane sits in. Not derived from\n    // `isDefaultViewport`, which zoomToFit itself invalidates on its first\n    // run \u2014 that made the fit fire once against not-yet-measured dimensions\n    // and then never re-fit.\n    // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n    viewportOwner: 'fit' as ViewportOwner,\n    viewportDirtyTimer: undefined as ReturnType<typeof setTimeout> | undefined,\n    // 0 is never a live rAF handle, so it doubles as \"nothing pending\"\n    positionsDirtyFrame: 0,\n    // Performance instrumentation, surfaced in GraphStats for browser tests\n    // to assert against budgets. `fetchMs` is the GetSubgraph RPC round-trip,\n    // `layoutMs` the last layout's compute time in any mode (near zero on a\n    // cache hit), `geometryMs` the main-thread buildGeometry pass and\n    // `geometryStrokeCount` the node strokes it produced.\n    lastFetchMs: undefined as number | undefined,\n    // how many of the cut's reads the tube map was handed, of how many\n    readsShown: undefined as { shown: number; total: number } | undefined,\n    lastLayoutMs: undefined as number | undefined,\n    lastGeometryMs: undefined as number | undefined,\n    lastGeometryStrokeCount: undefined as number | undefined,\n    viewportRebuildPending: false,\n  }))\n", "// src/renderer/svgCanvas.ts\nvar n = (v) => +v.toFixed(1);\nvar alpha = (v) => +v.toFixed(3);\nfunction paint(css) {\n  const m = /^rgba?\\(([^,]+),([^,]+),([^,)]+)(?:,([^)]+))?\\)$/.exec(\n    css.replaceAll(\" \", \"\")\n  );\n  if (!m) {\n    return { color: css, opacity: 1 };\n  }\n  const opacity = m[4] === void 0 ? 1 : Number(m[4]);\n  return { color: `rgb(${m[1]},${m[2]},${m[3]})`, opacity };\n}\nfunction paintAttrs(kind, css) {\n  const { color, opacity } = paint(css);\n  return `${kind}=\"${color}\"${opacity < 1 ? ` ${kind}-opacity=\"${alpha(opacity)}\"` : \"\"}`;\n}\nvar DOT_PX = 0.5;\nvar DOT_CELL_PX = 0.25;\nfunction svgCanvas(width, height) {\n  const out = [];\n  let subpaths = [];\n  const start = (x, y) => {\n    const s = { d: `M${n(x)} ${n(y)}`, segments: 0, x0: x, x1: x, y0: y, y1: y };\n    subpaths.push(s);\n    return s;\n  };\n  const reach = (points) => {\n    const s = subpaths.at(-1) ?? start(points[0], points[1]);\n    for (let i = 0; i < points.length; i += 2) {\n      s.x0 = Math.min(s.x0, points[i]);\n      s.x1 = Math.max(s.x1, points[i]);\n      s.y0 = Math.min(s.y0, points[i + 1]);\n      s.y1 = Math.max(s.y1, points[i + 1]);\n    }\n    s.segments++;\n    return s;\n  };\n  const pathData = (dots) => {\n    const seen = /* @__PURE__ */ new Set();\n    return subpaths.map((s) => {\n      if (!dots || s.x1 - s.x0 >= DOT_PX || s.y1 - s.y0 >= DOT_PX) {\n        return s.d;\n      }\n      const x = (s.x0 + s.x1) / 2;\n      const y = (s.y0 + s.y1) / 2;\n      const cell = `${Math.round(x / DOT_CELL_PX)} ${Math.round(y / DOT_CELL_PX)}`;\n      if (s.segments === 0 || seen.has(cell)) {\n        return \"\";\n      }\n      seen.add(cell);\n      return `M${n(x)} ${n(y)}h0`;\n    }).join(\"\");\n  };\n  const ctx = {\n    canvas: void 0,\n    fillStyle: \"#000\",\n    strokeStyle: \"#000\",\n    lineWidth: 1,\n    lineCap: \"butt\",\n    lineJoin: \"miter\",\n    beginPath() {\n      subpaths = [];\n    },\n    moveTo(x, y) {\n      start(x, y);\n    },\n    lineTo(x, y) {\n      reach([x, y]).d += `L${n(x)} ${n(y)}`;\n    },\n    bezierCurveTo(cx0, cy0, cx1, cy1, x, y) {\n      reach([cx0, cy0, cx1, cy1, x, y]).d += `C${n(cx0)} ${n(cy0)} ${n(cx1)} ${n(cy1)} ${n(x)} ${n(y)}`;\n    },\n    closePath() {\n      const s = subpaths.at(-1);\n      if (s) {\n        s.d += \"Z\";\n      }\n    },\n    stroke() {\n      const d = pathData(ctx.lineCap !== \"butt\");\n      if (d) {\n        out.push(\n          `<path d=\"${d}\" fill=\"none\" ${paintAttrs(\"stroke\", ctx.strokeStyle)} stroke-width=\"${n(ctx.lineWidth)}\" stroke-linecap=\"${ctx.lineCap}\" stroke-linejoin=\"${ctx.lineJoin}\"/>`\n        );\n      }\n    },\n    fill() {\n      const d = pathData(false);\n      if (d) {\n        out.push(`<path d=\"${d}\" ${paintAttrs(\"fill\", ctx.fillStyle)}/>`);\n      }\n    },\n    // the renderer only ever clears the whole canvas\n    clearRect() {\n      out.length = 0;\n    },\n    fillRect(x, y, w, h) {\n      out.push(\n        `<rect x=\"${n(x)}\" y=\"${n(y)}\" width=\"${n(w)}\" height=\"${n(h)}\" ${paintAttrs(\"fill\", ctx.fillStyle)}/>`\n      );\n    }\n  };\n  const canvas = {\n    width,\n    height,\n    style: {},\n    getContext: () => ctx\n  };\n  ctx.canvas = canvas;\n  return {\n    canvas,\n    // the drawing so far, as SVG elements in canvas pixels\n    markup: () => out.join(\"\")\n  };\n}\n\nexport {\n  svgCanvas\n};\n", "// src/renderer/canvas.ts\nvar MAX_DPR = 2;\nvar MAX_CANVAS_DIM_PX = 8192;\nfunction getDpr(width = 0, height = 0) {\n  const dpr = typeof devicePixelRatio === \"undefined\" ? 1 : Math.min(devicePixelRatio, MAX_DPR);\n  return Math.min(dpr, MAX_CANVAS_DIM_PX / Math.max(width, height, 1));\n}\nfunction syncCanvasSize(canvas, width, height) {\n  const dpr = getDpr(width, height);\n  const pw = Math.round(width * dpr);\n  const ph = Math.round(height * dpr);\n  if (canvas.width !== pw || canvas.height !== ph) {\n    canvas.width = pw;\n    canvas.height = ph;\n  }\n  const cssWidth = `${width}px`;\n  const cssHeight = `${height}px`;\n  if (canvas.style.width !== cssWidth) {\n    canvas.style.width = cssWidth;\n  }\n  if (canvas.style.height !== cssHeight) {\n    canvas.style.height = cssHeight;\n  }\n  return dpr;\n}\n\nexport {\n  MAX_DPR,\n  MAX_CANVAS_DIM_PX,\n  getDpr,\n  syncCanvasSize\n};\n", "import {\n  getDpr,\n  syncCanvasSize\n} from \"./chunk-RBCE2OQH.js\";\nimport {\n  abgrToCssRgba,\n  brightenAbgr,\n  normalizedRgbToCssRgba\n} from \"./chunk-G2FD7S3C.js\";\n\n// src/renderer/Canvas2DRenderer.ts\nvar Canvas2DRenderer = class {\n  constructor(canvas) {\n    this.transform = null;\n    this.batch = null;\n    this.nodeHighlights = /* @__PURE__ */ new Map();\n    this.highlightedEdge = null;\n    this.highlightFactor = 1;\n    this.fit = 1;\n    const ctx = canvas.getContext(\"2d\");\n    if (!ctx) {\n      throw new Error(\"Canvas 2D context not available\");\n    }\n    this.canvas = canvas;\n    this.ctx = ctx;\n  }\n  setErrorHandler(_handler) {\n  }\n  releaseOffscreenTargets() {\n  }\n  // A host builds its transform at `getDpr()`. Where syncCanvasSize had to\n  // shrink the ratio to stay under MAX_CANVAS_DIM_PX, `fit` shrinks the\n  // transform to match, so the picture still fills the css box.\n  resize(width, height) {\n    this.fit = syncCanvasSize(this.canvas, width, height) / getDpr();\n  }\n  uploadGeometry(batch) {\n    this.batch = batch;\n    this.highlightedEdge = null;\n  }\n  setNodeHighlights(factors) {\n    this.nodeHighlights = factors;\n  }\n  setEdgeHighlight(edgeIndex, factor) {\n    this.highlightedEdge = edgeIndex;\n    this.highlightFactor = factor;\n  }\n  updateTransform(transform) {\n    this.transform = transform;\n  }\n  fitted() {\n    const t = this.transform;\n    const k = this.fit;\n    return !t || k === 1 ? t : {\n      ...t,\n      scaleX: t.scaleX * k,\n      scaleY: t.scaleY * k,\n      translateX: t.translateX * k,\n      translateY: t.translateY * k,\n      dpr: t.dpr * k\n    };\n  }\n  render(clearColor) {\n    const t = this.fitted();\n    if (!t) {\n      return;\n    }\n    const ctx = this.ctx;\n    const { width, height } = ctx.canvas;\n    if (clearColor[3] < 1) {\n      ctx.clearRect(0, 0, width, height);\n    }\n    ctx.fillStyle = normalizedRgbToCssRgba(\n      [clearColor[0], clearColor[1], clearColor[2]],\n      clearColor[3]\n    );\n    ctx.fillRect(0, 0, width, height);\n    const batch = this.batch;\n    if (!batch) {\n      return;\n    }\n    ctx.lineCap = \"round\";\n    ctx.lineJoin = \"round\";\n    const factor = this.highlightFactor;\n    const edgeRun = this.edgeRun(batch.edgeCurveRuns);\n    for (const { color, items } of groupByPaint(batch.edgeCurves, (e, i) => ({\n      color: inRun(edgeRun, i) ? brightenAbgr(e.color, factor) : e.color,\n      weight: e.thickness,\n      last: inRun(edgeRun, i)\n    }))) {\n      this.strokeCurves(items, color, t);\n    }\n    const lifted = this.liftedStrokes(batch);\n    for (const { color, items } of groupByPaint(batch.nodeStrokes, (s, i) => {\n      const f = lifted.get(i);\n      return {\n        color: f === void 0 ? s.color : brightenAbgr(s.color, f),\n        weight: s.thickness,\n        last: f !== void 0\n      };\n    })) {\n      this.strokeNodes(items, color, t);\n    }\n    const arrowRun = this.edgeRun(batch.arrowRuns);\n    for (const { color, items } of groupByPaint(batch.arrows, (a, i) => ({\n      color: inRun(arrowRun, i) ? brightenAbgr(a.color, factor) : a.color,\n      weight: 0,\n      last: inRun(arrowRun, i)\n    }))) {\n      this.fillArrows(items, color, t);\n    }\n  }\n  // Only what the highlights lift, over a transparent clear, for a hover layer\n  // stacked on a canvas that drew the batch without them: a pointer move then\n  // repaints one node or edge rather than the whole drawing\n  renderHighlights() {\n    const ctx = this.ctx;\n    ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);\n    const batch = this.batch;\n    const t = this.fitted();\n    if (!t || !batch) {\n      return;\n    }\n    ctx.lineCap = \"round\";\n    ctx.lineJoin = \"round\";\n    const factor = this.highlightFactor;\n    const curves = runItems(batch.edgeCurves, this.edgeRun(batch.edgeCurveRuns));\n    for (const { color, items } of groupByPaint(curves, (e) => ({\n      color: brightenAbgr(e.color, factor),\n      weight: e.thickness,\n      last: false\n    }))) {\n      this.strokeCurves(items, color, t);\n    }\n    const lifted = [...this.liftedStrokes(batch)];\n    for (const { color, items } of groupByPaint(lifted, ([i, f]) => ({\n      color: brightenAbgr(batch.nodeStrokes[i].color, f),\n      weight: batch.nodeStrokes[i].thickness,\n      last: false\n    }))) {\n      this.strokeNodes(\n        items.map(([i]) => batch.nodeStrokes[i]),\n        color,\n        t\n      );\n    }\n    const arrows = runItems(batch.arrows, this.edgeRun(batch.arrowRuns));\n    for (const { color, items } of groupByPaint(arrows, (a) => ({\n      color: brightenAbgr(a.color, factor),\n      weight: 0,\n      last: false\n    }))) {\n      this.fillArrows(items, color, t);\n    }\n  }\n  edgeRun(runs) {\n    return this.highlightedEdge === null ? void 0 : runs.get(this.highlightedEdge);\n  }\n  // stroke index -> brighten factor, for the nodes the model lifted\n  liftedStrokes(batch) {\n    const lifted = /* @__PURE__ */ new Map();\n    for (const [nodeId, factor] of this.nodeHighlights) {\n      const run = batch.nodeStrokeRuns.get(nodeId);\n      if (run) {\n        for (let i = run.start; i < run.start + run.count; i++) {\n          lifted.set(i, factor);\n        }\n      }\n    }\n    return lifted;\n  }\n  strokeCurves(items, color, t) {\n    const ctx = this.ctx;\n    ctx.strokeStyle = abgrToCssRgba(color);\n    ctx.lineWidth = items[0].thickness * 2 * t.dpr;\n    ctx.beginPath();\n    for (const e of items) {\n      const first = e.curves[0];\n      ctx.moveTo(\n        first.x0 * t.scaleX + t.translateX,\n        first.y0 * t.scaleY + t.translateY\n      );\n      for (const c of e.curves) {\n        ctx.bezierCurveTo(\n          c.cx0 * t.scaleX + t.translateX,\n          c.cy0 * t.scaleY + t.translateY,\n          c.cx1 * t.scaleX + t.translateX,\n          c.cy1 * t.scaleY + t.translateY,\n          c.x1 * t.scaleX + t.translateX,\n          c.y1 * t.scaleY + t.translateY\n        );\n      }\n    }\n    ctx.stroke();\n  }\n  strokeNodes(items, color, t) {\n    const ctx = this.ctx;\n    ctx.strokeStyle = abgrToCssRgba(color);\n    ctx.lineWidth = items[0].thickness * 2 * t.dpr;\n    ctx.beginPath();\n    for (const s of items) {\n      const p0 = s.points[0];\n      ctx.moveTo(p0.x * t.scaleX + t.translateX, p0.y * t.scaleY + t.translateY);\n      for (let i = 1, l = s.points.length; i < l; i++) {\n        const p = s.points[i];\n        ctx.lineTo(p.x * t.scaleX + t.translateX, p.y * t.scaleY + t.translateY);\n      }\n    }\n    ctx.stroke();\n  }\n  fillArrows(items, color, t) {\n    const ctx = this.ctx;\n    ctx.fillStyle = abgrToCssRgba(color);\n    ctx.beginPath();\n    for (const a of items) {\n      const [tip, left, notch, right] = arrowheadOutline(a, t);\n      ctx.moveTo(tip.x, tip.y);\n      ctx.lineTo(left.x, left.y);\n      ctx.lineTo(notch.x, notch.y);\n      ctx.lineTo(right.x, right.y);\n      ctx.closePath();\n    }\n    ctx.fill();\n  }\n  dispose() {\n    this.batch = null;\n    this.nodeHighlights = /* @__PURE__ */ new Map();\n    this.highlightedEdge = null;\n  }\n};\nvar ARROW_NOTCH = 0.25;\nfunction arrowheadOutline(a, t) {\n  const ux = Math.cos(a.angle);\n  const uy = Math.sin(a.angle);\n  const tipX = a.x * t.scaleX + t.translateX;\n  const tipY = a.y * t.scaleY + t.translateY;\n  const length = a.length * t.dpr;\n  const halfWidth = a.halfWidth * t.dpr;\n  const backX = tipX - ux * length;\n  const backY = tipY - uy * length;\n  const notchBack = length * (1 - ARROW_NOTCH);\n  return [\n    { x: tipX, y: tipY },\n    { x: backX - uy * halfWidth, y: backY + ux * halfWidth },\n    { x: tipX - ux * notchBack, y: tipY - uy * notchBack },\n    { x: backX + uy * halfWidth, y: backY - ux * halfWidth }\n  ];\n}\nfunction runItems(items, run) {\n  return run ? items.slice(run.start, run.start + run.count) : [];\n}\nfunction inRun(run, i) {\n  return run !== void 0 && i >= run.start && i < run.start + run.count;\n}\nfunction groupByPaint(items, paintOf) {\n  const groups = /* @__PURE__ */ new Map();\n  const deferred = /* @__PURE__ */ new Map();\n  for (let i = 0, l = items.length; i < l; i++) {\n    const item = items[i];\n    const { color, weight, last } = paintOf(item, i);\n    const into = last ? deferred : groups;\n    const key = `${color}:${weight}`;\n    const group = into.get(key);\n    if (group) {\n      group.items.push(item);\n    } else {\n      into.set(key, { color, items: [item] });\n    }\n  }\n  return [...groups.values(), ...deferred.values()];\n}\n\nexport {\n  Canvas2DRenderer,\n  arrowheadOutline\n};\n", "import {\n  baseEdgeCurves\n} from \"./chunk-WA5WNP6V.js\";\nimport {\n  curveBounds,\n  pathRibbonOffsets\n} from \"./chunk-UBQSRCWR.js\";\n\n// src/util/SpatialIndex.ts\nvar FALLBACK_CELL_SIZE = 50;\nfunction meanExtentCellSize(extentTotal, count) {\n  return count > 0 ? Math.max(1, extentTotal / count) : FALLBACK_CELL_SIZE;\n}\nfunction rowPitchOf(boxes) {\n  const distinct = /* @__PURE__ */ new Set();\n  let min = Infinity;\n  let max = -Infinity;\n  for (const box of boxes) {\n    distinct.add(box.minY);\n    min = Math.min(min, box.minY);\n    max = Math.max(max, box.minY);\n  }\n  return distinct.size > 1 ? (max - min) / (distinct.size - 1) : void 0;\n}\nfunction cellSizeFrom(boxes, extentX, extentY) {\n  const x = meanExtentCellSize(extentX, boxes.length);\n  return {\n    x,\n    y: extentY > 0 ? meanExtentCellSize(extentY, boxes.length) : rowPitchOf(boxes) ?? x\n  };\n}\nfunction resolveCellSize(given, boxes, extentX, extentY) {\n  return given === void 0 ? cellSizeFrom(boxes, extentX, extentY) : typeof given === \"number\" ? { x: given, y: given } : given;\n}\nfunction getOrCreateCell(cells, cx, cy) {\n  let row = cells.get(cx);\n  if (!row) {\n    row = /* @__PURE__ */ new Map();\n    cells.set(cx, row);\n  }\n  let cell = row.get(cy);\n  if (!cell) {\n    cell = [];\n    row.set(cy, cell);\n  }\n  return cell;\n}\nfunction addToGrid(cells, cellSize, minX, minY, maxX, maxY, entry) {\n  const cx0 = Math.floor(minX / cellSize.x);\n  const cx1 = Math.floor(maxX / cellSize.x);\n  const cy0 = Math.floor(minY / cellSize.y);\n  const cy1 = Math.floor(maxY / cellSize.y);\n  for (let cx = cx0; cx <= cx1; cx++) {\n    for (let cy = cy0; cy <= cy1; cy++) {\n      getOrCreateCell(cells, cx, cy).push(entry);\n    }\n  }\n}\nfunction queryGrid(cells, cellSize, x, y, radiusX, radiusY) {\n  const cx0 = Math.floor((x - radiusX) / cellSize.x);\n  const cx1 = Math.floor((x + radiusX) / cellSize.x);\n  const cy0 = Math.floor((y - radiusY) / cellSize.y);\n  const cy1 = Math.floor((y + radiusY) / cellSize.y);\n  const results = [];\n  const seen = /* @__PURE__ */ new Set();\n  for (let cx = cx0; cx <= cx1; cx++) {\n    const row = cells.get(cx);\n    if (row) {\n      for (let cy = cy0; cy <= cy1; cy++) {\n        const cell = row.get(cy);\n        if (cell) {\n          for (const entry of cell) {\n            if (!seen.has(entry)) {\n              seen.add(entry);\n              results.push(entry);\n            }\n          }\n        }\n      }\n    }\n  }\n  return results;\n}\nvar SpatialIndex = class {\n  constructor(nodePositions, cellSize) {\n    this.cells = /* @__PURE__ */ new Map();\n    const boxes = [];\n    let extentX = 0;\n    let extentY = 0;\n    for (const [nodeId, segments] of Object.entries(nodePositions)) {\n      for (let i = 0; i < segments.length - 1; i++) {\n        const seg = segments[i];\n        const next = segments[i + 1];\n        const minX = Math.min(seg.x, next.x);\n        const minY = Math.min(seg.y, next.y);\n        const maxX = Math.max(seg.x, next.x);\n        const maxY = Math.max(seg.y, next.y);\n        extentX += maxX - minX;\n        extentY += maxY - minY;\n        boxes.push({ entry: { nodeId, segmentIdx: i }, minX, minY, maxX, maxY });\n      }\n    }\n    this.cellSize = resolveCellSize(cellSize, boxes, extentX, extentY);\n    for (const b of boxes) {\n      addToGrid(\n        this.cells,\n        this.cellSize,\n        b.minX,\n        b.minY,\n        b.maxX,\n        b.maxY,\n        b.entry\n      );\n    }\n  }\n  query(x, y, radiusX, radiusY = radiusX) {\n    return queryGrid(this.cells, this.cellSize, x, y, radiusX, radiusY);\n  }\n};\nvar EdgeSpatialIndex = class {\n  constructor(nodePositions, graph, drawPaths, axis, deletions, version = 0, routes, stranded = false) {\n    this.cells = /* @__PURE__ */ new Map();\n    this.edgeCurves = baseEdgeCurves(\n      nodePositions,\n      graph,\n      axis,\n      deletions,\n      version,\n      routes,\n      stranded\n    );\n    const boxes = [];\n    let extentX = 0;\n    let extentY = 0;\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 curves = this.edgeCurves.get(ei);\n      if (fromSegments?.length && toSegments?.length && curves) {\n        let { minX, minY, maxX, maxY } = curveBounds(curves);\n        const numPaths = edge.pathIds?.length ?? 0;\n        if (drawPaths && numPaths > 0) {\n          let padX = 0;\n          let padY = 0;\n          for (const o of pathRibbonOffsets(\n            fromSegments,\n            toSegments,\n            numPaths,\n            axis\n          )) {\n            padX = Math.max(padX, Math.abs(o.x));\n            padY = Math.max(padY, Math.abs(o.y));\n          }\n          minX -= padX;\n          minY -= padY;\n          maxX += padX;\n          maxY += padY;\n        }\n        extentX += maxX - minX;\n        extentY += maxY - minY;\n        boxes.push({ ei, minX, minY, maxX, maxY });\n      }\n    }\n    this.cellSize = cellSizeFrom(boxes, extentX, extentY);\n    for (const b of boxes) {\n      addToGrid(this.cells, this.cellSize, b.minX, b.minY, b.maxX, b.maxY, b.ei);\n    }\n  }\n  getCurves(ei) {\n    return this.edgeCurves.get(ei);\n  }\n  query(x, y, radiusX, radiusY = radiusX) {\n    return queryGrid(this.cells, this.cellSize, x, y, radiusX, radiusY);\n  }\n};\n\nexport {\n  SpatialIndex,\n  EdgeSpatialIndex\n};\n", "import {\n  EdgeSpatialIndex,\n  SpatialIndex\n} from \"./chunk-3VCKBSML.js\";\nimport {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  pathRibbonOffsets,\n  translateCurves,\n  yToXOf\n} from \"./chunk-UBQSRCWR.js\";\n\n// src/util/hitDetection.ts\nfunction distanceToSegment(px, py, x1, y1, x2, y2) {\n  const dx = x2 - x1;\n  const dy = y2 - y1;\n  const lenSq = dx * dx + dy * dy;\n  if (lenSq === 0) {\n    return Math.hypot(px - x1, py - y1);\n  }\n  const t = Math.max(0, Math.min(1, ((px - x1) * dx + (py - y1) * dy) / lenSq));\n  return Math.hypot(px - (x1 + t * dx), py - (y1 + t * dy));\n}\nfunction distanceToCubicBezier(px, py, c) {\n  let minDist = Infinity;\n  const samples = 20;\n  let lastX = c.x0;\n  let lastY = c.y0;\n  for (let i = 1; i <= samples; i++) {\n    const t = i / samples;\n    const u = 1 - t;\n    const bx = u * u * u * c.x0 + 3 * u * u * t * c.cx0 + 3 * u * t * t * c.cx1 + t * t * t * c.x1;\n    const by = u * u * u * c.y0 + 3 * u * u * t * c.cy0 + 3 * u * t * t * c.cy1 + t * t * t * c.y1;\n    minDist = Math.min(minDist, distanceToSegment(px, py, lastX, lastY, bx, by));\n    lastX = bx;\n    lastY = by;\n  }\n  return minDist;\n}\nfunction distanceToEdgeCurves(px, py, curves, yToX = 1) {\n  let minDist = Infinity;\n  for (const c of curves) {\n    const d = distanceToCubicBezier(\n      px,\n      py,\n      yToX === 1 ? c : {\n        x0: c.x0,\n        y0: c.y0 * yToX,\n        cx0: c.cx0,\n        cy0: c.cy0 * yToX,\n        cx1: c.cx1,\n        cy1: c.cy1 * yToX,\n        x1: c.x1,\n        y1: c.y1 * yToX\n      }\n    );\n    if (d < minDist) {\n      minDist = d;\n    }\n  }\n  return minDist;\n}\nvar nodeCache = weakMemo();\nfunction getSpatialIndex(nodePositions, version) {\n  return nodeCache(\n    nodePositions,\n    [version],\n    () => new SpatialIndex(nodePositions)\n  );\n}\nvar edgeCache = weakMemo();\nfunction getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version, deletions, routes, stranded = false) {\n  return edgeCache(\n    nodePositions,\n    [\n      graph,\n      drawPaths,\n      axis.scaleX,\n      axis.scaleY,\n      version,\n      deletions,\n      routes,\n      stranded\n    ],\n    () => new EdgeSpatialIndex(\n      nodePositions,\n      graph,\n      drawPaths,\n      axis,\n      deletions,\n      version,\n      routes,\n      stranded\n    )\n  );\n}\nvar MIN_NODE_REACH_PX = 5;\nfunction findHoveredNode(nodePositions, graphX, graphY, axis, version = 0, ink) {\n  const yToX = yToXOf(axis);\n  const index = getSpatialIndex(nodePositions, version);\n  const reach = (px) => Math.max(MIN_NODE_REACH_PX, px) / axis.scaleX;\n  const queryReach = reach(ink?.maxHalfWidthPx ?? 0);\n  const candidates = index.query(graphX, graphY, queryReach, queryReach / yToX);\n  let hovered = null;\n  let best = Infinity;\n  for (const { nodeId, segmentIdx } of candidates) {\n    const segments = nodePositions[nodeId];\n    const dist = distanceToSegment(\n      graphX,\n      graphY * yToX,\n      segments[segmentIdx].x,\n      segments[segmentIdx].y * yToX,\n      segments[segmentIdx + 1].x,\n      segments[segmentIdx + 1].y * yToX\n    );\n    if (dist < best && dist < reach(ink?.halfWidthPx(nodeId) ?? 0)) {\n      best = dist;\n      hovered = nodeId;\n    }\n  }\n  return hovered;\n}\nfunction segmentMeetsBox(a, b, box) {\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  let t0 = 0;\n  let t1 = 1;\n  for (const [p, q] of [\n    [-dx, a.x - box.x0],\n    [dx, box.x1 - a.x],\n    [-dy, a.y - box.y0],\n    [dy, box.y1 - a.y]\n  ]) {\n    if (p === 0) {\n      if (q < 0) {\n        return false;\n      }\n    } else if (p < 0) {\n      t0 = Math.max(t0, q / p);\n    } else {\n      t1 = Math.min(t1, q / p);\n    }\n  }\n  return t0 <= t1;\n}\nfunction nodesUnderBox(nodePositions, t, version = 0) {\n  const index = getSpatialIndex(nodePositions, version);\n  const screen = (p) => ({\n    x: p.x * t.scaleX + t.translateX,\n    y: p.y * t.scaleY + t.translateY\n  });\n  return (box) => {\n    const hits = /* @__PURE__ */ new Set();\n    const candidates = index.query(\n      ((box.x0 + box.x1) / 2 - t.translateX) / t.scaleX,\n      ((box.y0 + box.y1) / 2 - t.translateY) / t.scaleY,\n      Math.abs((box.x1 - box.x0) / 2 / t.scaleX),\n      Math.abs((box.y1 - box.y0) / 2 / t.scaleY)\n    );\n    for (const { nodeId, segmentIdx } of candidates) {\n      const line = nodePositions[nodeId];\n      if (!hits.has(nodeId) && segmentMeetsBox(\n        screen(line[segmentIdx]),\n        screen(line[segmentIdx + 1]),\n        box\n      )) {\n        hits.add(nodeId);\n      }\n    }\n    return hits;\n  };\n}\nfunction findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version = 0, deletions, hiddenEdges, deletionRoutes, stranded = false) {\n  const yToX = yToXOf(axis);\n  const edgeThreshold = 10 / axis.scaleX;\n  const edgeIndex = getEdgeSpatialIndex(\n    nodePositions,\n    graph,\n    drawPaths,\n    axis,\n    version,\n    deletions,\n    deletionRoutes,\n    stranded\n  );\n  const candidates = edgeIndex.query(\n    graphX,\n    graphY,\n    edgeThreshold,\n    edgeThreshold / yToX\n  );\n  let hovered = null;\n  let best = edgeThreshold;\n  for (const edgeIdx of candidates) {\n    const edge = graph.edges[edgeIdx];\n    const fromSegments = nodePositions[edge.from];\n    const toSegments = nodePositions[edge.to];\n    if (!fromSegments?.length || !toSegments?.length || hiddenEdges?.has(edgeIdx)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const baseCurves = edgeIndex.getCurves(edgeIdx);\n    if (!baseCurves) {\n      continue;\n    }\n    let dist;\n    if (!drawPaths || numPaths === 0) {\n      dist = distanceToEdgeCurves(graphX, graphY * yToX, baseCurves, yToX);\n    } else {\n      let minDist = Infinity;\n      for (const offset of pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      )) {\n        const curves = offset.x === 0 && offset.y === 0 ? baseCurves : translateCurves(baseCurves, offset.x, offset.y);\n        const d = distanceToEdgeCurves(graphX, graphY * yToX, curves, yToX);\n        if (d < minDist) {\n          minDist = d;\n        }\n      }\n      dist = minDist;\n    }\n    if (dist < best) {\n      best = dist;\n      hovered = edgeIdx;\n    }\n  }\n  return hovered;\n}\n\nexport {\n  distanceToSegment,\n  distanceToCubicBezier,\n  findHoveredNode,\n  nodesUnderBox,\n  findHoveredEdge\n};\n", "import {\n  nodesUnderBox\n} from \"./chunk-OMUPUB4J.js\";\nimport {\n  graphLabels,\n  rowLabelBox\n} from \"./chunk-PFRQBCGC.js\";\nimport {\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  LABEL_PX,\n  occupancy,\n  placeLabels\n} from \"./chunk-AB35TJST.js\";\n\n// src/labelLayout.ts\nvar HALO_FACTOR = 3.4;\nvar LEGEND_INSET_PX = 6;\nvar GENE_PIN_DROP_PX = 18;\nvar GENE_STACK = 2;\nvar BUBBLE_STACK = 3;\nvar TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;\nfunction geneCoverageNote(pin) {\n  const length = pin.gene.end - pin.gene.start;\n  if (pin.covered >= 0.98) {\n    return void 0;\n  }\n  const [per, unit] = length >= 1e6 ? [1e6, \"Mb\"] : length >= 1e3 ? [1e3, \"kb\"] : [1, \"bp\"];\n  const amount = (bp) => +(bp / per).toFixed(per === 1 ? 0 : 1);\n  return `${amount(pin.covered * length)} of ${amount(length)} ${unit}`;\n}\nfunction geneLabelCandidates(pins, screen, contigThickness, nodesUnder) {\n  const ink = contigThickness / 2;\n  return byExtent(pins, (pin) => pin.gene.end - pin.gene.start).map((pin) => {\n    const { x, y } = screen(pin.at);\n    const note = geneCoverageNote(pin);\n    return {\n      item: pin,\n      x,\n      y: y + contigThickness + GENE_PIN_DROP_PX,\n      text: note ? `${pin.gene.name} \\xB7 ${note}` : pin.gene.name,\n      fallback: note ? `${pin.gene.name} \\u2026` : void 0,\n      stack: GENE_STACK,\n      fits: (box) => [\n        ...nodesUnder({\n          x0: box.x0 - ink,\n          x1: box.x1 + ink,\n          y0: box.y0 - ink,\n          y1: box.y1 + ink\n        })\n      ].every((id) => pin.nodeIds.has(id))\n    };\n  });\n}\nfunction byExtent(items, extent) {\n  return [...items].sort((a, b) => extent(b) - extent(a));\n}\nfunction layoutLabels(m) {\n  const { paneWidth: width, canvasHeight: height, translateX, translateY } = m;\n  const { scaleX, scaleY } = m.axisScale;\n  const frame = { width, height };\n  const screen = (p) => ({\n    x: p.x * scaleX + translateX,\n    y: p.y * scaleY + translateY\n  });\n  const reserved = m.drawnRowLabels.map(\n    ({ label, y }) => rowLabelBox(label, y * scaleY + translateY)\n  );\n  const stripPx = m.referenceStripZonePx ?? 0;\n  if (stripPx > 0) {\n    reserved.push({ x0: 0, x1: width, y0: 0, y1: stripPx });\n  }\n  if (m.legendSize.width > 0) {\n    reserved.push({\n      x0: width - LEGEND_INSET_PX - m.legendSize.width,\n      x1: width,\n      y0: 0,\n      y1: stripPx + LEGEND_INSET_PX + m.legendSize.height\n    });\n  }\n  if (m.poppedFrom) {\n    reserved.push({\n      x0: 0,\n      x1: 60 + m.poppedFrom.label.length * LABEL_CHAR_PX * 1.2,\n      y0: 0,\n      y1: 44\n    });\n  }\n  const take = occupancy(frame, reserved);\n  const onRows = m.drawnRowLabels.length > 0;\n  const rowsTop = onRows ? Math.min(...m.drawnRowLabels.map((r) => r.y)) : Infinity;\n  const halo = m.contigThickness * HALO_FACTOR;\n  const above = (h, gap) => {\n    const { x, y } = screen({\n      x: h.labelAt.x,\n      y: Math.min(h.labelAt.y, rowsTop)\n    });\n    const baseline = y - halo / 2 - gap;\n    return { x, y: onRows ? Math.max(baseline, TOPMOST_BASELINE) : baseline };\n  };\n  const byBubble = byExtent(\n    m.bubbleHalos.filter((h) => !h.tick),\n    (h) => h.whole ? -1 : h.members\n  );\n  const bubbles = placeLabels(\n    byBubble.map((h) => ({\n      item: h,\n      ...above(h, 6),\n      text: h.label,\n      // `0 bp\u201311 kb superbubble` where `\u2026, 1198 segments, 5 routes` does not fit\n      fallback: h.label.includes(\",\") ? h.label.split(\",\")[0] : void 0,\n      stack: BUBBLE_STACK\n    })),\n    frame,\n    take\n  );\n  const ticks = m.bubbleHalos.filter((h) => h.tick && !h.whole).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);\n  const genes = placeLabels(\n    geneLabelCandidates(\n      m.genePins,\n      screen,\n      m.contigThickness,\n      nodesUnderBox(\n        m.nodePositions ?? {},\n        { scaleX, scaleY, translateX, translateY },\n        m.positionsVersion\n      )\n    ),\n    frame,\n    take\n  );\n  const sizes = m.nodePositions && m.labelsNodeSizes ? graphLabels({\n    nodePositions: m.nodePositions,\n    nodeLengths: m.nodeLengths,\n    deletions: m.deletions,\n    deletionRoutes: m.deletionRoutes,\n    stranded: m.stranded,\n    alleleDeletions: m.alleleDeletions,\n    axis: m.axisScale,\n    translateX,\n    translateY,\n    width,\n    height,\n    version: m.positionsVersion,\n    take\n  }) : [];\n  return {\n    bubbles,\n    ticks,\n    genes,\n    sizes\n  };\n}\n\nexport {\n  HALO_FACTOR,\n  LEGEND_INSET_PX,\n  geneCoverageNote,\n  geneLabelCandidates,\n  layoutLabels\n};\n", "const host = JBrowseExports[\"mobx\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"mobx\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const $mobx = /* @__PURE__ */ read(\"$mobx\")\nexport const FlowCancellationError = /* @__PURE__ */ read(\"FlowCancellationError\")\nexport const ObservableMap = /* @__PURE__ */ read(\"ObservableMap\")\nexport const ObservableSet = /* @__PURE__ */ read(\"ObservableSet\")\nexport const Reaction = /* @__PURE__ */ read(\"Reaction\")\nexport const _allowStateChanges = /* @__PURE__ */ read(\"_allowStateChanges\")\nexport const _allowStateChangesInsideComputed = /* @__PURE__ */ read(\"_allowStateChangesInsideComputed\")\nexport const _allowStateReadsEnd = /* @__PURE__ */ read(\"_allowStateReadsEnd\")\nexport const _allowStateReadsStart = /* @__PURE__ */ read(\"_allowStateReadsStart\")\nexport const _autoAction = /* @__PURE__ */ read(\"_autoAction\")\nexport const _autoActionBound = /* @__PURE__ */ read(\"_autoActionBound\")\nexport const _endAction = /* @__PURE__ */ read(\"_endAction\")\nexport const _getAdministration = /* @__PURE__ */ read(\"_getAdministration\")\nexport const _getGlobalState = /* @__PURE__ */ read(\"_getGlobalState\")\nexport const _interceptReads = /* @__PURE__ */ read(\"_interceptReads\")\nexport const _isComputingDerivation = /* @__PURE__ */ read(\"_isComputingDerivation\")\nexport const _resetGlobalState = /* @__PURE__ */ read(\"_resetGlobalState\")\nexport const _startAction = /* @__PURE__ */ read(\"_startAction\")\nexport const action = /* @__PURE__ */ read(\"action\")\nexport const actionBound = /* @__PURE__ */ read(\"actionBound\")\nexport const autorun = /* @__PURE__ */ read(\"autorun\")\nexport const compareDefault = /* @__PURE__ */ read(\"compareDefault\")\nexport const compareIdentity = /* @__PURE__ */ read(\"compareIdentity\")\nexport const compareShallow = /* @__PURE__ */ read(\"compareShallow\")\nexport const compareStructural = /* @__PURE__ */ read(\"compareStructural\")\nexport const computed = /* @__PURE__ */ read(\"computed\")\nexport const computedStruct = /* @__PURE__ */ read(\"computedStruct\")\nexport const configure = /* @__PURE__ */ read(\"configure\")\nexport const createAtom = /* @__PURE__ */ read(\"createAtom\")\nexport const defineProperty = /* @__PURE__ */ read(\"defineProperty\")\nexport const entries = /* @__PURE__ */ read(\"entries\")\nexport const extendObservable = /* @__PURE__ */ read(\"extendObservable\")\nexport const flow = /* @__PURE__ */ read(\"flow\")\nexport const flowBound = /* @__PURE__ */ read(\"flowBound\")\nexport const flowResult = /* @__PURE__ */ read(\"flowResult\")\nexport const get = /* @__PURE__ */ read(\"get\")\nexport const getAtom = /* @__PURE__ */ read(\"getAtom\")\nexport const getDebugName = /* @__PURE__ */ read(\"getDebugName\")\nexport const getDependencyTree = /* @__PURE__ */ read(\"getDependencyTree\")\nexport const getObserverTree = /* @__PURE__ */ read(\"getObserverTree\")\nexport const has = /* @__PURE__ */ read(\"has\")\nexport const intercept = /* @__PURE__ */ read(\"intercept\")\nexport const isAction = /* @__PURE__ */ read(\"isAction\")\nexport const isBoxedObservable = /* @__PURE__ */ read(\"isBoxedObservable\")\nexport const isComputed = /* @__PURE__ */ read(\"isComputed\")\nexport const isComputedProp = /* @__PURE__ */ read(\"isComputedProp\")\nexport const isFlow = /* @__PURE__ */ read(\"isFlow\")\nexport const isFlowCancellationError = /* @__PURE__ */ read(\"isFlowCancellationError\")\nexport const isObservable = /* @__PURE__ */ read(\"isObservable\")\nexport const isObservableArray = /* @__PURE__ */ read(\"isObservableArray\")\nexport const isObservableMap = /* @__PURE__ */ read(\"isObservableMap\")\nexport const isObservableObject = /* @__PURE__ */ read(\"isObservableObject\")\nexport const isObservableProp = /* @__PURE__ */ read(\"isObservableProp\")\nexport const isObservableSet = /* @__PURE__ */ read(\"isObservableSet\")\nexport const keys = /* @__PURE__ */ read(\"keys\")\nexport const makeAutoObservable = /* @__PURE__ */ read(\"makeAutoObservable\")\nexport const makeObservable = /* @__PURE__ */ read(\"makeObservable\")\nexport const observable = /* @__PURE__ */ read(\"observable\")\nexport const observableDeep = /* @__PURE__ */ read(\"observableDeep\")\nexport const observableRef = /* @__PURE__ */ read(\"observableRef\")\nexport const observableShallow = /* @__PURE__ */ read(\"observableShallow\")\nexport const observableStruct = /* @__PURE__ */ read(\"observableStruct\")\nexport const observe = /* @__PURE__ */ read(\"observe\")\nexport const onBecomeObserved = /* @__PURE__ */ read(\"onBecomeObserved\")\nexport const onBecomeUnobserved = /* @__PURE__ */ read(\"onBecomeUnobserved\")\nexport const onReactionError = /* @__PURE__ */ read(\"onReactionError\")\nexport const override = /* @__PURE__ */ read(\"override\")\nexport const ownKeys = /* @__PURE__ */ read(\"ownKeys\")\nexport const reaction = /* @__PURE__ */ read(\"reaction\")\nexport const remove = /* @__PURE__ */ read(\"remove\")\nexport const runInAction = /* @__PURE__ */ read(\"runInAction\")\nexport const set = /* @__PURE__ */ read(\"set\")\nexport const spy = /* @__PURE__ */ read(\"spy\")\nexport const toJS = /* @__PURE__ */ read(\"toJS\")\nexport const transaction = /* @__PURE__ */ read(\"transaction\")\nexport const untracked = /* @__PURE__ */ read(\"untracked\")\nexport const values = /* @__PURE__ */ read(\"values\")\nexport const when = /* @__PURE__ */ read(\"when\")\nexport default host && host.__esModule ? host.default : host", "import {\n  parseCs\n} from \"./chunk-C44YRP5F.js\";\n\n// src/tubeMap/reads.ts\nfunction canonicalStrand(node) {\n  return node.id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction stepName(node, strand) {\n  return strand === canonicalStrand(node) ? node.id : `-${node.id}`;\n}\nfunction stepStarts(lengths, total) {\n  const starts = lengths.map(() => void 0);\n  let head = 0;\n  let i = 0;\n  for (; i < lengths.length && lengths[i] !== void 0; i++) {\n    starts[i] = head;\n    head += lengths[i];\n  }\n  let tail = total;\n  for (let j = lengths.length - 1; j > i && lengths[j] !== void 0; j--) {\n    tail -= lengths[j];\n    starts[j] = tail;\n  }\n  return starts;\n}\nfunction mismatchesByStep(record, lengths) {\n  const byStep = record.path.map(() => []);\n  if (record.cs === void 0) {\n    return byStep;\n  }\n  const starts = stepStarts(lengths, record.pathLength);\n  const known = starts.flatMap((start, s) => start === void 0 ? [] : [s]);\n  const startOf = (k) => starts[known[k]];\n  const endOf = (k) => startOf(k) + lengths[known[k]];\n  let first = 0;\n  const stepAt = (pos2) => {\n    while (first < known.length && endOf(first) < pos2) {\n      first++;\n    }\n    for (let k = first; k < known.length && startOf(k) <= pos2; k++) {\n      const end = endOf(k);\n      if (pos2 < end) {\n        return { s: known[k], local: pos2 - startOf(k), room: end - pos2 };\n      }\n    }\n    return void 0;\n  };\n  const unplacedFrom = (pos2) => {\n    for (let k = first; k < known.length; k++) {\n      if (startOf(k) > pos2) {\n        return startOf(k) - pos2;\n      }\n    }\n    return Infinity;\n  };\n  const add = (s, mismatch) => {\n    const list = byStep[s];\n    const last = list.at(-1);\n    if (mismatch.type === \"substitution\" && last?.type === \"substitution\" && last.pos + last.seq.length === mismatch.pos) {\n      last.seq += mismatch.seq;\n    } else {\n      list.push(mismatch);\n    }\n  };\n  let pos = record.pathStart;\n  for (const op of parseCs(record.cs)) {\n    if (op.op === \"match\") {\n      pos += op.length;\n    } else if (op.op === \"substitution\") {\n      const at = stepAt(pos);\n      if (at) {\n        add(at.s, { type: \"substitution\", pos: at.local, seq: op.seq });\n      }\n      pos += 1;\n    } else if (op.op === \"insertion\") {\n      const at = pos > record.pathStart && pos < record.pathEnd ? stepAt(pos) : void 0;\n      if (at) {\n        add(at.s, { type: \"insertion\", pos: at.local, seq: op.seq });\n      }\n    } else {\n      let left = op.length;\n      while (left > 0) {\n        const at = stepAt(pos);\n        const take = Math.min(left, at ? at.room : unplacedFrom(pos));\n        if (at) {\n          add(at.s, { type: \"deletion\", pos: at.local, length: take });\n        }\n        pos += take;\n        left -= take;\n      }\n    }\n  }\n  return byStep;\n}\nfunction tubeMapReads(graph, records, firstId) {\n  const nodeByName = new Map(graph.nodes.map((n) => [n.name, n]));\n  const reads = [];\n  for (const record of records) {\n    const nodes = record.path.map((step) => nodeByName.get(step.name));\n    const kept = nodes.flatMap((node, i) => node ? [i] : []);\n    const first = kept[0];\n    const last = kept.at(-1);\n    if (first !== void 0 && last !== void 0) {\n      const mismatches = mismatchesByStep(\n        record,\n        nodes.map((n) => n?.length)\n      );\n      const names = kept.map((i) => stepName(nodes[i], record.path[i].strand));\n      const lastLength = nodes[last].length;\n      reads.push({\n        id: firstId + reads.length,\n        name: record.name,\n        type: \"read\",\n        sourceTrackID: 1,\n        sequence: names,\n        sequenceNew: kept.map((i, k) => ({\n          nodeName: names[k],\n          mismatches: mismatches[i]\n        })),\n        firstNodeOffset: first === 0 ? record.pathStart : 0,\n        finalNodeCoverLength: last === record.path.length - 1 ? lastLength - (record.pathLength - record.pathEnd) : lastLength,\n        // 255 is GAF's missing MAPQ\n        mapping_quality: record.mappingQuality === 255 ? void 0 : record.mappingQuality,\n        is_secondary: record.secondary,\n        is_reverse: record.strand === \"-\"\n      });\n    }\n  }\n  return reads;\n}\nvar FORWARD_READ_COLORS = [\"#6baed6\", \"#4292c6\", \"#2171b5\", \"#08519c\"];\nvar REVERSE_READ_COLORS = [\"#fb6a4a\", \"#ef3b2c\", \"#cb181d\", \"#a50f15\"];\nfunction readColor(read) {\n  const colors = read.is_reverse ? REVERSE_READ_COLORS : FORWARD_READ_COLORS;\n  return colors[read.id % colors.length];\n}\n\nexport {\n  canonicalStrand,\n  stepName,\n  tubeMapReads,\n  FORWARD_READ_COLORS,\n  REVERSE_READ_COLORS,\n  readColor\n};\n", "// src/el.ts\nfunction el(tag, attrs = {}, ...children) {\n  return {\n    tag,\n    attrs,\n    children: children.filter((c) => !!c || c === \"\")\n  };\n}\nfunction escapeText(s) {\n  return s.replaceAll(\"&\", \"&amp;\").replaceAll(\"<\", \"&lt;\").replaceAll(\">\", \"&gt;\");\n}\nfunction escapeAttr(s) {\n  return escapeText(s).replaceAll('\"', \"&quot;\");\n}\nfunction serializeEl(node) {\n  if (typeof node === \"string\") {\n    return escapeText(node);\n  }\n  const attrs = Object.entries(node.attrs).filter(([, v]) => v !== void 0).map(([k, v]) => ` ${k}=\"${escapeAttr(String(v))}\"`).join(\"\");\n  return `<${node.tag}${attrs}>${node.children.map(serializeEl).join(\"\")}</${node.tag}>`;\n}\n\nexport {\n  el,\n  escapeAttr,\n  serializeEl\n};\n", "import {\n  el\n} from \"./chunk-H2H4Y3TV.js\";\nimport {\n  REFERENCE_RAMP_ALT_CSS\n} from \"./chunk-SWCULW6S.js\";\nimport {\n  RAMP_GRADIENT_CSS,\n  RAMP_GRADIENT_STOPS,\n  rampHueCss,\n  rampStops\n} from \"./chunk-GQZVR5DW.js\";\nimport {\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  panSNContig\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/layout/walkRowDraw.ts\nvar ON_REFERENCE = \"#2f8fd6\";\nvar OFF_REFERENCE = \"#8e3fbf\";\nvar OUTSIDE_CUT = \"#bdbdbd\";\nvar MISSING_INK = \"#8a8a8a\";\nvar UNKNOWN_GAP = \"#e2e2e2\";\nvar GENE_INK = \"#1c1c22\";\nvar BAR_PX = 12;\nvar GAP_PX = 4;\nvar MISSING_PX = 1;\nvar LABELLED_ROW_PX = 12;\nvar MIN_TILED_BAR_PX = 6;\nvar MIN_TILE_PX = 3;\nfunction kb(bp) {\n  return `${(bp / 1e3).toFixed(bp < 1e4 ? 1 : 0)} kb`;\n}\nfunction signedLength(delta) {\n  const size = Math.abs(delta);\n  return `${delta > 0 ? \"+\" : \"\\u2212\"}${size < 1e3 ? `${size} bp` : kb(size)}`;\n}\nfunction units(bp, unit) {\n  return unit ? ` \\u2248 ${Math.round(bp / unit)} units` : \"\";\n}\nvar near = ({ refName, start }) => `${panSNContig(refName)}:${start < 1e6 ? `${Math.round(start / 1e3)} kb` : `${(start / 1e6).toFixed(1)} Mb`}`;\nfunction gapsText(gapBp, runs) {\n  const gaps = (runs ?? []).filter((r) => r.gap);\n  if (gapBp <= 0) {\n    return \"\";\n  }\n  if (!gaps.some((g) => g.cause)) {\n    return ` \\xB7 ${kb(gapBp)} ${OUTSIDE_TEXT}`;\n  }\n  const bpOf = (cause) => gaps.filter((g) => g.cause === cause).reduce((sum, g) => sum + g.bp, 0);\n  const places = [\n    ...new Set(gaps.flatMap((g) => g.chunk ? [near(g.chunk)] : []))\n  ];\n  const parts = [\n    [bpOf(\"missing\"), GAP_CAUSE_TEXT.missing],\n    [\n      bpOf(\"elsewhere\"),\n      `on nodes filed near ${places[0]}${places.length > 1 ? ` and ${places.length - 1} more place${places.length > 2 ? \"s\" : \"\"}` : \"\"}`\n    ],\n    [bpOf(\"unknown\"), GAP_CAUSE_TEXT.unknown],\n    [bpOf(void 0), OUTSIDE_TEXT]\n  ];\n  return parts.filter(([bp]) => bp > 0).map(([bp, text]) => ` \\xB7 ${kb(bp)} ${text}`).join(\"\");\n}\nfunction walkRowReadout(row, reference, unit, call) {\n  const { bp, gapBp, complete, stop } = row;\n  if (!reference) {\n    return `${kb(bp)}${units(bp, unit)}`;\n  }\n  const outside = gapsText(gapBp, row.runs);\n  const called = call ? ` \\xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? \" \\xB7 no spanning read\" : \"\"}` : \"\";\n  if (complete) {\n    const delta = bp - reference.bp;\n    const against = delta === 0 ? \"\" : ` (${signedLength(delta)})`;\n    return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;\n  }\n  const region = unit ? \"repeat\" : \"window\";\n  if (stop?.contigEnds && bp === 0) {\n    const where = stop.shortBp > 0 ? `${kb(stop.shortBp)} before` : \"at\";\n    return `contig ends ${where} the ${region}${called}`;\n  }\n  const why = !stop ? \"partial walk\" : stop.contigEnds ? `contig ends inside the ${region}` : \"does not rejoin the reference within the extracted subgraph\";\n  return `\\u2265 ${kb(bp)}${units(bp, unit)} \\xB7 ${why}${outside}${called}`;\n}\nfunction readoutPlacement(text, endX, width) {\n  const x = endX + 6;\n  const fits = x + text.length * LABEL_CHAR_PX < width;\n  return fits ? { x, anchor: \"start\", halo: false } : { x: endX - 6, anchor: \"end\", halo: true };\n}\nfunction unitTicks(bp, unit, pxPerBp) {\n  if (unit * pxPerBp < MIN_TILE_PX) {\n    return [];\n  }\n  const ticks = [];\n  for (let k = unit; k < bp; k += unit) {\n    ticks.push(k);\n  }\n  return ticks;\n}\nfunction gapStyle(cause) {\n  return cause === \"missing\" ? { fill: MISSING_INK, px: MISSING_PX, label: GAP_CAUSE_TEXT.missing } : cause === \"unknown\" ? { fill: UNKNOWN_GAP, px: GAP_PX, label: GAP_CAUSE_TEXT.unknown } : { fill: OUTSIDE_CUT, px: GAP_PX, label: OUTSIDE_TEXT };\n}\nfunction runPaint(run, ramp) {\n  if (run.gap) {\n    return { fill: gapStyle(run.cause).fill };\n  }\n  if (!ramp) {\n    return { fill: run.onReference ? ON_REFERENCE : OFF_REFERENCE };\n  }\n  if (run.referenceStart === void 0) {\n    return { fill: REFERENCE_RAMP_ALT_CSS };\n  }\n  const stops = rampStops({ ...run, start: run.referenceStart }, ramp);\n  return stops.length === 1 ? { fill: rampHueCss(stops[0]) } : { stops: stops.map(rampHueCss) };\n}\nfunction alongRow(axis, start, end) {\n  return axis.reversed ? { start: axis.start - end, end: axis.start - start } : { start: start - axis.start, end: end - axis.start };\n}\nfunction rowSpan(axis, bp) {\n  return axis.reversed ? { start: axis.start - bp, end: axis.start } : { start: axis.start, end: axis.start + bp };\n}\nfunction genesOnRow(row, genes) {\n  const contig = row.axis?.contig;\n  return genes.filter(\n    (g) => g.refName === contig || g.refName.endsWith(`#${contig}`)\n  );\n}\nfunction placeRowGenes(rows, byRow) {\n  const placed = /* @__PURE__ */ new Map();\n  for (const row of rows) {\n    const genes = byRow.get(row.name);\n    if (!row.axis || !genes) {\n      continue;\n    }\n    const axis = row.axis;\n    const clip = ({ start, end }) => ({\n      start: Math.max(0, start),\n      end: Math.min(row.bp, end)\n    });\n    placed.set(\n      row.name,\n      genes.map((g) => ({\n        name: g.name,\n        ...clip(alongRow(axis, g.start, g.end)),\n        exons: g.exons.map((e) => clip(alongRow(axis, e.start, e.end))).filter((e) => e.end > e.start)\n      })).filter((g) => g.end > g.start).sort((a, b) => a.start - b.start)\n    );\n  }\n  return placed;\n}\nvar GENE_FONT_PX = 9;\nvar GENE_CHAR_PX = 5.2;\nvar MIN_LETTERED_BAR_PX = 8;\nvar genePad = (rowPx, barPx) => Math.min(2, (rowPx - barPx) / 2 - 1);\nfunction boxesGenes(rowPx, barPx) {\n  return genePad(rowPx, barPx) >= 1;\n}\nfunction rowGeneBoxes(genes, X, y, { rowPx = ROW_HEIGHT_PX, barPx = BAR_PX } = {}) {\n  if (!boxesGenes(rowPx, barPx)) {\n    return [];\n  }\n  const pad = genePad(rowPx, barPx);\n  const boxes = genes.map((g) => {\n    const x = X(g.start);\n    return {\n      g,\n      x,\n      w: Math.max(2, X(g.end) - x)\n    };\n  });\n  const taken = [];\n  const named = new Set(\n    (barPx >= MIN_LETTERED_BAR_PX ? [...boxes] : []).sort((a, b) => a.w - b.w).filter(({ g, x, w }) => {\n      const half = g.name.length * GENE_CHAR_PX / 2;\n      const at = [x + w / 2 - half, x + w / 2 + half];\n      if (2 * half > w + 6 || taken.some(([a, b]) => at[0] < b + 2 && at[1] > a - 2)) {\n        return false;\n      }\n      taken.push(at);\n      return true;\n    })\n  );\n  return boxes.map((box) => ({\n    name: box.g.name,\n    x: box.x,\n    y: y - barPx / 2 - pad,\n    w: box.w,\n    h: barPx + 2 * pad,\n    exons: box.g.exons.map((e) => ({\n      x: X(e.start),\n      w: Math.max(1, X(e.end) - X(e.start))\n    })),\n    label: named.has(box) ? { x: box.x + box.w / 2, y: y + 3, size: GENE_FONT_PX } : void 0\n  }));\n}\nvar rowsText = (n) => `${n} row${n === 1 ? \"\" : \"s\"}`;\nfunction walkRowsKey(bars, o = {}) {\n  const entries = [\n    {\n      swatch: o.ramp ? { kind: \"bar\", fill: o.rampCss ?? RAMP_GRADIENT_CSS, ramp: true } : { kind: \"bar\", fill: ON_REFERENCE },\n      label: `on ${bars.reference.label}'s path`\n    },\n    {\n      swatch: {\n        kind: \"bar\",\n        fill: o.ramp ? REFERENCE_RAMP_ALT_CSS : OFF_REFERENCE\n      },\n      label: `off ${bars.reference.label}'s path`\n    }\n  ];\n  const gaps = [bars.reference, ...bars.rows].flatMap(\n    (row) => row.runs.filter((run) => run.gap)\n  );\n  const labels = new Set(gaps.map((run) => gapStyle(run.cause).label));\n  for (const cause of [void 0, \"missing\", \"unknown\"]) {\n    const { fill, px, label } = gapStyle(cause);\n    if (labels.has(label)) {\n      entries.push({ swatch: { kind: \"gap\", fill, px }, label });\n    }\n  }\n  if (o.genes?.crowded) {\n    entries.push({\n      swatch: { kind: \"gene\" },\n      label: \"genes left out: too many rows to box them in\",\n      note: true\n    });\n  } else if (o.genes) {\n    entries.push({\n      swatch: { kind: \"gene\" },\n      label: \"gene\"\n    });\n    if (o.genes.untracked) {\n      entries.push({\n        swatch: { kind: \"gene\" },\n        label: `no gene track for ${rowsText(o.genes.untracked)}`,\n        note: true\n      });\n    }\n    if (o.genes.unplaced) {\n      entries.push({\n        swatch: { kind: \"gene\" },\n        label: `no contig coordinates for ${rowsText(o.genes.unplaced)}`,\n        note: true\n      });\n    }\n    if (o.genes.unread) {\n      entries.push({\n        swatch: { kind: \"gene\" },\n        label: `genes not read for the last ${rowsText(o.genes.unread)}`,\n        note: true\n      });\n    }\n  }\n  return entries;\n}\nvar CALL_TICK = \"#111\";\nvar UNBACKED_TICK = \"#9e9e9e\";\nvar DISAGREES = \"#c62828\";\nfunction callTickInk(call) {\n  return call.agrees === false ? DISAGREES : call.spanningReads === 0 ? UNBACKED_TICK : CALL_TICK;\n}\nfunction walkRowsKeyTree(entries, x, y, idPrefix = \"walk-key\") {\n  let at = 0;\n  const parts = entries.flatMap((e, i) => {\n    const rampId = `${idPrefix}-ramp-${i}`;\n    const ramp = !e.note && e.swatch.kind === \"bar\" && e.swatch.ramp ? el(\n      \"linearGradient\",\n      { id: rampId },\n      ...RAMP_GRADIENT_STOPS.map(\n        (s) => el(\"stop\", { offset: s.offset, \"stop-color\": s.color })\n      )\n    ) : void 0;\n    const swatch = e.note ? void 0 : e.swatch.kind === \"gene\" ? el(\"rect\", {\n      x: at,\n      y: 5,\n      width: 18,\n      height: 8,\n      fill: \"none\",\n      stroke: GENE_INK,\n      \"stroke-width\": 1.5\n    }) : el(\"rect\", {\n      x: at,\n      y: e.swatch.kind === \"gap\" ? 9 - e.swatch.px / 2 : 5,\n      width: 18,\n      height: e.swatch.kind === \"gap\" ? e.swatch.px : 8,\n      rx: 2,\n      fill: ramp ? `url(#${rampId})` : e.swatch.fill\n    });\n    const text = el(\n      \"text\",\n      {\n        x: e.note ? at : at + 23,\n        y: 13,\n        \"font-style\": e.note ? \"italic\" : void 0,\n        fill: e.note ? \"#666\" : void 0\n      },\n      e.label\n    );\n    at += (e.note ? 0 : 23) + e.label.length * LABEL_CHAR_PX + 16;\n    return [ramp, swatch, text].filter((p) => p !== void 0);\n  });\n  return {\n    width: at,\n    tree: el(\n      \"g\",\n      {\n        transform: `translate(${x} ${y})`,\n        \"font-family\": \"Helvetica, Arial, sans-serif\",\n        \"font-size\": 11\n      },\n      ...parts\n    )\n  };\n}\nfunction rowPitch(count, room, minRowPx = 0) {\n  const fit = room / Math.max(1, count);\n  const rowPx = Math.max(\n    minRowPx,\n    Math.min(ROW_HEIGHT_PX, fit >= 1 ? Math.floor(fit) : fit)\n  );\n  return {\n    rowPx,\n    barPx: rowPx <= 3 ? rowPx : Math.max(3, Math.round(rowPx * 0.6)),\n    labelled: rowPx >= LABELLED_ROW_PX,\n    readouts: rowPx >= LABELLED_ROW_PX\n  };\n}\nfunction coalesceRuns(runs, pxPerBp) {\n  const minBp = 1 / pxPerBp;\n  const out = [];\n  let bucket = [];\n  const flush = () => {\n    if (bucket.length === 0) {\n      return;\n    }\n    if (bucket.length === 1) {\n      out.push(bucket[0]);\n    } else {\n      let on = 0;\n      let off = 0;\n      for (const r of bucket) {\n        if (r.onReference) {\n          on += r.bp;\n        } else {\n          off += r.bp;\n        }\n      }\n      const onReference = on >= off;\n      const lead = bucket.find((r) => r.onReference === onReference);\n      out.push({\n        start: bucket[0].start,\n        bp: on + off,\n        onReference,\n        referenceStart: onReference ? lead.referenceStart : void 0,\n        ...lead.reversed ? { reversed: true } : {}\n      });\n    }\n    bucket = [];\n  };\n  let held = 0;\n  for (const run of runs) {\n    if (run.gap || run.bp >= minBp) {\n      flush();\n      held = 0;\n      out.push(run);\n      continue;\n    }\n    bucket.push(run);\n    held += run.bp;\n    if (held >= minBp) {\n      flush();\n      held = 0;\n    }\n  }\n  flush();\n  return out;\n}\nfunction geneTree(box, y, barPx) {\n  return el(\n    \"g\",\n    { class: \"row-gene\", \"data-testid\": \"graph-walk-gene\" },\n    el(\"title\", {}, box.name),\n    ...box.exons.map(\n      (e) => el(\"rect\", {\n        x: e.x,\n        y: y - barPx / 2,\n        width: e.w,\n        height: barPx,\n        fill: GENE_INK,\n        opacity: 0.35\n      })\n    ),\n    el(\"rect\", {\n      x: box.x,\n      y: box.y,\n      width: box.w,\n      height: box.h,\n      fill: \"none\",\n      stroke: GENE_INK,\n      \"stroke-width\": 1.5\n    }),\n    box.label && el(\n      \"text\",\n      {\n        x: box.label.x,\n        y: box.label.y,\n        \"font-family\": \"sans-serif\",\n        \"font-size\": box.label.size,\n        \"font-weight\": 600,\n        \"text-anchor\": \"middle\",\n        fill: GENE_INK,\n        stroke: \"white\",\n        \"stroke-width\": 2.5,\n        \"paint-order\": \"stroke\"\n      },\n      box.name\n    )\n  );\n}\nfunction walkRowsTree(bars, frame, o = {}) {\n  const X = (bp) => bp * frame.scaleX + frame.translateX;\n  const rowPx = frame.rowPx ?? ROW_HEIGHT_PX;\n  const barPx = frame.barPx ?? BAR_PX;\n  const overhang = Math.min(3, Math.max(0, (rowPx - barPx) / 2));\n  const Y = (row) => row * rowPx * frame.scaleY + frame.translateY;\n  const { origin, unit, reference, rows } = bars;\n  const along = (offset) => X(origin + offset);\n  const prefix = o.idPrefix ?? \"walkrow\";\n  const rowTree = (row, i) => {\n    const y = Y(i);\n    if (y < -barPx || y > frame.height + barPx) {\n      return void 0;\n    }\n    const drawn = frame.bars === false ? [] : row.runs;\n    const runs = coalesceRuns(drawn, frame.scaleX).flatMap((run) => {\n      const paint = runPaint(run, o.ramp);\n      const h = run.gap ? Math.min(gapStyle(run.cause).px, barPx) : barPx;\n      const id = `${prefix}-${i}-${run.start}`;\n      const rect = el(\"rect\", {\n        x: along(run.start),\n        y: y - h / 2,\n        width: Math.max(1, run.bp * frame.scaleX),\n        height: h,\n        fill: \"stops\" in paint ? `url(#${id})` : paint.fill\n      });\n      return \"stops\" in paint ? [\n        el(\n          \"linearGradient\",\n          { id },\n          ...paint.stops.map(\n            (color, k) => el(\"stop\", {\n              offset: k / (paint.stops.length - 1),\n              \"stop-color\": color\n            })\n          )\n        ),\n        rect\n      ] : [rect];\n    });\n    const ticks = unit && barPx >= MIN_TILED_BAR_PX ? unitTicks(row.bp, unit, frame.scaleX).map(\n      (k) => el(\"line\", {\n        x1: along(k),\n        x2: along(k),\n        y1: y - barPx / 2,\n        y2: y + barPx / 2,\n        stroke: \"white\",\n        \"stroke-width\": 1\n      })\n    ) : [];\n    const { call } = row;\n    const text = walkRowReadout(\n      row,\n      i === 0 ? void 0 : reference,\n      unit,\n      call\n    );\n    const at = readoutPlacement(text, along(row.bp), frame.width);\n    const readouts = frame.readouts ?? true;\n    return el(\n      \"g\",\n      {\n        \"data-testid\": i === 0 ? \"graph-walk-reference\" : \"graph-walk-row\"\n      },\n      ...runs,\n      ...ticks,\n      ...rowGeneBoxes(o.rowGenes?.get(row.name) ?? [], along, y, {\n        rowPx,\n        barPx\n      }).map((box) => geneTree(box, y, barPx)),\n      call && el(\"rect\", {\n        \"data-testid\": \"graph-walk-call\",\n        x: along(call.bp) - 1,\n        y: y - barPx / 2 - overhang,\n        width: 2,\n        height: barPx + 2 * overhang,\n        fill: callTickInk(call)\n      }),\n      readouts && el(\n        \"text\",\n        {\n          x: at.x,\n          y: y + 4,\n          \"font-family\": \"sans-serif\",\n          \"font-size\": 11,\n          fill: call?.agrees === false ? DISAGREES : \"#333\",\n          stroke: at.halo ? \"white\" : void 0,\n          \"stroke-width\": at.halo ? 3 : void 0,\n          \"paint-order\": \"stroke\",\n          \"text-anchor\": at.anchor\n        },\n        text\n      )\n    );\n  };\n  return el(\"g\", {}, ...[reference, ...rows].map(rowTree));\n}\n\nexport {\n  ON_REFERENCE,\n  OFF_REFERENCE,\n  OUTSIDE_CUT,\n  MISSING_INK,\n  UNKNOWN_GAP,\n  GENE_INK,\n  BAR_PX,\n  GAP_PX,\n  MISSING_PX,\n  LABELLED_ROW_PX,\n  walkRowReadout,\n  readoutPlacement,\n  unitTicks,\n  gapStyle,\n  runPaint,\n  alongRow,\n  rowSpan,\n  genesOnRow,\n  placeRowGenes,\n  boxesGenes,\n  rowGeneBoxes,\n  walkRowsKey,\n  CALL_TICK,\n  UNBACKED_TICK,\n  DISAGREES,\n  callTickInk,\n  walkRowsKeyTree,\n  rowPitch,\n  coalesceRuns,\n  walkRowsTree\n};\n", "import {\n  SATURATED_PATH_COUNT\n} from \"./chunk-FX4RDMDN.js\";\nimport {\n  formatBp\n} from \"./chunk-PFRQBCGC.js\";\n\n// src/bubbles/classifyBubble.ts\nvar REPEAT_GROWTH = 10;\nfunction coveringRepeat(b, repeats) {\n  const span = b.end - b.start;\n  const growth = b.longestAlleleLength - b.shortestAlleleLength;\n  return repeats.find(\n    (r) => growth <= REPEAT_GROWTH * (r.end - r.start) && (span === 0 ? r.start <= b.start && b.start <= r.end : Math.min(b.end, r.end) - Math.max(b.start, r.start) >= span / 2)\n  );\n}\nvar SUPERBUBBLE_SEGMENTS = 40;\nfunction formatBpRange(shortest, longest) {\n  const low = formatBp(shortest);\n  const high = formatBp(longest);\n  const unit = high.slice(high.indexOf(\" \"));\n  return low.endsWith(unit) ? `${low.slice(0, -unit.length)}\\u2013${high}` : `${low}\\u2013${high}`;\n}\nfunction routes(count) {\n  if (count >= SATURATED_PATH_COUNT) {\n    return \"\\u22652.1B routes\";\n  }\n  if (count >= 1e5) {\n    return `${(count / 1e3).toFixed(0)}k routes`;\n  }\n  return `${count} routes`;\n}\nfunction classifyBubble(b, repeats = []) {\n  const c = classifyShape(b, repeats);\n  return b.partial ? { ...c, label: `${c.label}, partial` } : c;\n}\nfunction classifyShape(b, repeats) {\n  const refSpan = b.end - b.start;\n  const {\n    shortestAlleleLength: shortest,\n    longestAlleleLength: longest,\n    pathCount,\n    segmentCount,\n    inversion\n  } = b;\n  const range = formatBpRange(shortest, longest);\n  if (segmentCount >= SUPERBUBBLE_SEGMENTS) {\n    return {\n      kind: \"superbubble\",\n      label: `${range} superbubble, ${segmentCount} segments, ${routes(pathCount)}${inversion ? \", inv\" : \"\"}`\n    };\n  }\n  if (inversion) {\n    return { kind: \"inversion\", label: `${formatBp(longest)} inv` };\n  }\n  if (b.offReference) {\n    return shortest === longest ? sameLength(shortest) : { kind: \"complex\", label: `${range}, ${routes(pathCount)}` };\n  }\n  const repeat = longest !== shortest ? coveringRepeat(b, repeats) : void 0;\n  if (repeat) {\n    const name = repeat.name ? ` (${repeat.name})` : \"\";\n    return {\n      kind: \"repeat\",\n      label: `${range} repeat array${name}, ${routes(pathCount)}`\n    };\n  }\n  const alleles = pathCount > 2 ? `, ${pathCount} alleles` : \"\";\n  if (shortest === longest && shortest === refSpan) {\n    return sameLength(refSpan);\n  }\n  if (refSpan === 0 || shortest === refSpan) {\n    return {\n      kind: \"insertion\",\n      label: `\\u2264${formatBp(longest - refSpan)} ins${alleles}`\n    };\n  }\n  if (longest === refSpan) {\n    return {\n      kind: \"deletion\",\n      label: `${formatBp(refSpan - shortest)} del${alleles}`\n    };\n  }\n  return {\n    kind: \"complex\",\n    label: `${formatBp(refSpan)} ref \\u2192 ${range}, ${pathCount} alleles`\n  };\n}\nfunction sameLength(bp) {\n  return bp <= 1 ? { kind: \"snp\", label: \"SNP\" } : { kind: \"substitution\", label: `${formatBp(bp)} sub` };\n}\nvar BUBBLE_KIND_COLORS = {\n  snp: \"#5b6b7a\",\n  substitution: \"#5b6b7a\",\n  insertion: \"#2f8fd6\",\n  deletion: \"#c94040\",\n  inversion: \"#e07b00\",\n  repeat: \"#8e3fbf\",\n  superbubble: \"#8e3fbf\",\n  complex: \"#8e3fbf\"\n};\nvar BUBBLE_KIND_NAMES = {\n  snp: \"SNP\",\n  substitution: \"substitution\",\n  insertion: \"insertion\",\n  deletion: \"deletion\",\n  inversion: \"inversion\",\n  repeat: \"repeat array\",\n  superbubble: \"superbubble\",\n  complex: \"site\"\n};\nfunction bubbleSegmentIds(b) {\n  return b.segments.split(\",\").filter(Boolean);\n}\n\nexport {\n  classifyBubble,\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds\n};\n", "import {\n  formatBp\n} from \"./chunk-PFRQBCGC.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/tubeMap/axis.ts\nfunction referenceBoxes({\n  graph,\n  layout\n}) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const byRefName = /* @__PURE__ */ new Map();\n  layout.nodes.forEach((node, index) => {\n    const graphNode = nodeById.get(node.name);\n    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {\n      const { refName, start } = graphNode.stable;\n      pushTo(byRefName, refName, {\n        name: node.name,\n        index,\n        bp0: start,\n        bp1: start + graphNode.length,\n        x0: node.x,\n        x1: node.x + node.pixelWidth\n      });\n    }\n  });\n  for (const boxes of byRefName.values()) {\n    boxes.sort((a, b) => a.bp0 - b.bp0);\n  }\n  return byRefName;\n}\nfunction tubeX(boxes, bp, isEnd = false) {\n  const i = partitionPoint(\n    boxes.length - 1,\n    (j) => isEnd ? boxes[j].bp1 < bp : boxes[j].bp1 <= bp\n  );\n  return boxX(boxes[i], bp);\n}\nfunction boxX(box, bp) {\n  const span = box.bp1 - box.bp0;\n  return bp <= box.bp0 || span <= 0 ? box.x0 : box.x0 + (Math.min(bp, box.bp1) - box.bp0) / span * (box.x1 - box.x0);\n}\nfunction tubeSpan(boxes, start, end) {\n  const a = tubeX(boxes, start);\n  const b = tubeX(boxes, end, true);\n  return { x0: Math.min(a, b), x1: Math.max(a, b) };\n}\nfunction rulerBoxes(byRefName) {\n  let best;\n  for (const boxes of byRefName.values()) {\n    if (!best || boxes.length > best.length) {\n      best = boxes;\n    }\n  }\n  return best;\n}\nvar TICK_PX = 5;\nvar LABEL_GAP_PX = 10;\nvar TARGET_TICK_PX = 110;\nvar MIN_BRACKET_PX = 3;\nfunction rulerInk(darkMode) {\n  return darkMode ? \"#b0b0b8\" : \"#55555c\";\n}\nfunction niceStep(raw) {\n  const pow = 10 ** Math.floor(Math.log10(raw));\n  const m = raw / pow;\n  return (m <= 1 ? 1 : m <= 2 ? 2 : m <= 5 ? 5 : 10) * pow;\n}\nfunction placeLabels(candidates) {\n  const placed = [];\n  for (const a of candidates) {\n    if (placed.every(\n      (b) => Math.abs(a.at - b.at) >= (a.width + b.width) / 2 + LABEL_GAP_PX\n    )) {\n      placed.push(a);\n    }\n  }\n  return placed.map(({ text, at }) => ({ text, at }));\n}\nfunction scaleMarks(boxes, x, width, measure) {\n  const first = boxes[0];\n  const last = boxes.at(-1);\n  if (!first || !last) {\n    return void 0;\n  }\n  const from = x(first.x0);\n  const to = x(last.x1);\n  const bpSpan = last.bp1 - first.bp0;\n  if (to <= from || bpSpan <= 0) {\n    return void 0;\n  }\n  const step = niceStep(bpSpan / (to - from) * TARGET_TICK_PX);\n  const ticks = [];\n  const positions = [];\n  for (let bp = Math.ceil(first.bp0 / step) * step; bp <= last.bp1; bp += step) {\n    const sx = Math.round(x(tubeX(boxes, bp))) + 0.5;\n    if (sx >= 0 && sx <= width) {\n      ticks.push(sx);\n      const text = bp.toLocaleString(\"en-US\");\n      positions.push({ text, at: sx, width: measure(text) });\n    }\n  }\n  return {\n    spans: [{ x0: from, x1: to }],\n    ticks,\n    labels: placeLabels(positions)\n  };\n}\nfunction boxMarks(boxes, x, width, measure) {\n  const shown = boxes.map((box) => ({ box, s0: x(box.x0), s1: x(box.x1) })).filter(({ s0, s1 }) => s1 >= 0 && s0 <= width);\n  const first = shown[0];\n  const last = shown.at(-1);\n  if (!first || !last) {\n    return void 0;\n  }\n  const label = (text, at) => ({\n    text,\n    at,\n    width: measure(text)\n  });\n  const position = (bp, at) => label(bp.toLocaleString(\"en-US\"), at);\n  const spans = [];\n  const ticks = [];\n  const lengths = [];\n  const boundaries = [];\n  for (const { box, s0, s1 } of shown) {\n    spans.push({ x0: s0, x1: s1 });\n    ticks.push(Math.round(s0) + 0.5);\n    if (s1 - s0 >= MIN_BRACKET_PX) {\n      ticks.push(Math.round(s1) + 0.5);\n    }\n    const length = label(formatBp(box.bp1 - box.bp0), (s0 + s1) / 2);\n    if (length.width <= s1 - s0) {\n      lengths.push(length);\n    }\n    if (box !== first.box) {\n      boundaries.push(position(box.bp0, s0));\n    }\n  }\n  const ends = [\n    position(first.box.bp0, first.s0),\n    position(last.box.bp1, last.s1)\n  ];\n  return {\n    spans,\n    ticks,\n    labels: placeLabels([...ends, ...lengths, ...boundaries])\n  };\n}\nfunction rulerMarks(boxes, x, width, measure, referenceAxis = false) {\n  return (referenceAxis ? scaleMarks : boxMarks)(boxes, x, width, measure);\n}\nfunction drawTubeMapRuler(ctx, boxes, frame, top, referenceAxis = false) {\n  const { x, width, darkMode } = frame;\n  ctx.font = \"10px sans-serif\";\n  const marks = rulerMarks(\n    boxes,\n    x,\n    width,\n    (text) => ctx.measureText(text).width,\n    referenceAxis\n  );\n  if (!marks) {\n    return;\n  }\n  const ink = rulerInk(darkMode);\n  const y = top + 0.5;\n  ctx.strokeStyle = ink;\n  ctx.fillStyle = ink;\n  ctx.lineWidth = 1;\n  ctx.textAlign = \"center\";\n  ctx.textBaseline = \"top\";\n  ctx.beginPath();\n  for (const { x0, x1 } of marks.spans) {\n    ctx.moveTo(Math.max(0, x0), y);\n    ctx.lineTo(Math.min(width, x1), y);\n  }\n  for (const sx of marks.ticks) {\n    ctx.moveTo(sx, top);\n    ctx.lineTo(sx, top + TICK_PX);\n  }\n  ctx.stroke();\n  for (const { text, at } of marks.labels) {\n    ctx.fillText(text, at, top + TICK_PX + 2);\n  }\n}\n\nexport {\n  referenceBoxes,\n  tubeX,\n  boxX,\n  tubeSpan,\n  rulerBoxes,\n  rulerInk,\n  rulerMarks,\n  drawTubeMapRuler\n};\n", "// src/tubeMap/connectors.ts\nfunction tubeMapConnectors(boxes, bpToScreen, tubeToScreen, width) {\n  const out = [];\n  for (const box of boxes) {\n    const bottom0 = tubeToScreen(box.x0);\n    const bottom1 = tubeToScreen(box.x1);\n    if (bottom1 >= 0 && bottom0 <= width) {\n      out.push({\n        node: box.name,\n        top0: bpToScreen(box.bp0),\n        top1: bpToScreen(box.bp1),\n        bottom0,\n        bottom1\n      });\n    }\n  }\n  return out;\n}\nvar HIT_SLOP_PX = 3;\nfunction connectorAt(connectors, zoneBottom, sx, sy) {\n  if (zoneBottom <= 0 || sy < 0 || sy > zoneBottom) {\n    return void 0;\n  }\n  const t = sy / zoneBottom;\n  let hit;\n  let best = HIT_SLOP_PX;\n  for (const c of connectors) {\n    const a = c.top0 + (c.bottom0 - c.top0) * t;\n    const b = c.top1 + (c.bottom1 - c.top1) * t;\n    const dist = Math.max(0, Math.min(a, b) - sx, sx - Math.max(a, b));\n    if (dist < best) {\n      best = dist;\n      hit = c.node;\n    }\n  }\n  return hit;\n}\nfunction band(ctx, c, bottom) {\n  ctx.moveTo(c.top0, 0);\n  ctx.lineTo(c.top1, 0);\n  ctx.lineTo(c.bottom1, bottom);\n  ctx.lineTo(c.bottom0, bottom);\n  ctx.closePath();\n}\nfunction sides(ctx, c, bottom) {\n  ctx.moveTo(c.top0, 0);\n  ctx.lineTo(c.bottom0, bottom);\n  ctx.moveTo(c.top1, 0);\n  ctx.lineTo(c.bottom1, bottom);\n}\nfunction drawTubeMapConnectors(ctx, connectors, bottom, {\n  highlightNode,\n  darkMode\n}) {\n  if (bottom <= 0 || connectors.length === 0) {\n    return;\n  }\n  const ink = darkMode ? \"255,255,255\" : \"0,0,0\";\n  ctx.beginPath();\n  for (const c of connectors) {\n    band(ctx, c, bottom);\n  }\n  ctx.fillStyle = `rgba(${ink},0.07)`;\n  ctx.fill();\n  ctx.beginPath();\n  for (const c of connectors) {\n    sides(ctx, c, bottom);\n  }\n  ctx.strokeStyle = `rgba(${ink},0.35)`;\n  ctx.lineWidth = 0.5;\n  ctx.stroke();\n  drawLitConnector(ctx, connectors, bottom, highlightNode);\n}\nfunction drawLitConnector(ctx, connectors, bottom, node) {\n  const lit = bottom > 0 && node ? connectors.find((c) => c.node === node) : void 0;\n  if (lit) {\n    ctx.beginPath();\n    band(ctx, lit, bottom);\n    ctx.fillStyle = \"rgba(255,192,203,0.5)\";\n    ctx.fill();\n    ctx.beginPath();\n    sides(ctx, lit, bottom);\n    ctx.strokeStyle = \"#ff0000\";\n    ctx.lineWidth = 1;\n    ctx.stroke();\n  }\n}\n\nexport {\n  tubeMapConnectors,\n  connectorAt,\n  drawTubeMapConnectors,\n  drawLitConnector\n};\n", "import {\n  pathOrigin\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  gapParts\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNSample\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/layout/walkRows.ts\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar NodeTable = class {\n  constructor(graph) {\n    this.index = /* @__PURE__ */ new Map();\n    this.lengths = [];\n    this.onReference = new Uint8Array(0);\n    this.referenceStart = new Float64Array(0);\n    this.referenceEnd = new Float64Array(0);\n    for (const node of graph.nodes) {\n      this.lengths[this.indexOf(node.id)] = node.length;\n    }\n  }\n  indexOf(id) {\n    let i = this.index.get(id);\n    if (i === void 0) {\n      i = this.lengths.length;\n      this.index.set(id, i);\n      this.lengths.push(0);\n    }\n    return i;\n  }\n  nodesOf(path) {\n    const nodes = new Int32Array(path.nodeIds.length);\n    path.nodeIds.forEach((id, k) => {\n      nodes[k] = this.indexOf(id);\n    });\n    return nodes;\n  }\n  spanAt(steps, k) {\n    const node = k >= 0 && k < steps.length ? steps[k] : -1;\n    return node >= 0 && this.onReference[node] ? { start: this.referenceStart[node], end: this.referenceEnd[node] } : void 0;\n  }\n};\nfunction stepsOf(pieces, table) {\n  const out = [];\n  const gaps = [];\n  let end;\n  let previous;\n  for (const piece of pieces) {\n    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {\n      gaps.push(gapParts(piece.start - end, previous?.after, piece.before));\n      out.push(-gaps.length);\n    }\n    let bp = 0;\n    for (const node of piece.nodes) {\n      out.push(node);\n      bp += table.lengths[node];\n    }\n    end = piece.start === void 0 ? void 0 : piece.start + bp;\n    previous = piece;\n  }\n  return { steps: Float64Array.from(out), gaps };\n}\nfunction stepSpan(pieces, table, k) {\n  let end;\n  let at = 0;\n  let found;\n  for (const piece of pieces) {\n    if (piece.start === void 0 || end !== void 0 && piece.start < end) {\n      return void 0;\n    }\n    if (end !== void 0 && piece.start > end) {\n      if (at++ === k) {\n        found = { start: end, end: piece.start };\n      }\n    }\n    let pos = piece.start;\n    for (const node of piece.nodes) {\n      const len = table.lengths[node];\n      if (at++ === k) {\n        found = { start: pos, end: pos + len };\n      }\n      pos += len;\n    }\n    end = pos;\n  }\n  return found;\n}\nfunction sliceBetween(steps, table, region, flanked = true) {\n  if (!region || !flanked) {\n    return { ids: steps, complete: true, from: -1, to: -1 };\n  }\n  const { onReference, referenceStart, referenceEnd } = table;\n  let i0 = -1;\n  let i1 = -1;\n  let bestEnd = -Infinity;\n  let bestStart = Infinity;\n  for (let i = 0; i < steps.length; i++) {\n    const node = steps[i];\n    if (node >= 0 && onReference[node]) {\n      const end2 = referenceEnd[node];\n      const start = referenceStart[node];\n      if (end2 <= region.start && end2 > bestEnd) {\n        bestEnd = end2;\n        i0 = i;\n      }\n      if (start >= region.end && start < bestStart) {\n        bestStart = start;\n        i1 = i;\n      }\n    }\n  }\n  if (i0 >= 0 && i1 >= 0) {\n    const ids2 = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));\n    return {\n      ids: i0 < i1 ? ids2 : ids2.reverse(),\n      complete: true,\n      from: i0,\n      to: i1\n    };\n  }\n  const spanAt = (k) => table.spanAt(steps, k);\n  const flank = i0 >= 0 ? i0 : i1;\n  let near = -1;\n  for (let d = 1; flank >= 0 && near < 0 && d < steps.length; d++) {\n    near = [flank - d, flank + d].find((j) => spanAt(j) !== void 0) ?? -1;\n  }\n  if (near < 0) {\n    return { ids: steps, complete: false, from: -1, to: -1 };\n  }\n  const forward = near > flank === spanAt(near).start > spanAt(flank).start;\n  const after = forward === (flank === i0);\n  const ids = after ? steps.slice(flank + 1) : steps.slice(0, flank).reverse();\n  const last = ids.length > 0 ? ids.length - 1 : -1;\n  const end = last < 0 ? spanAt(flank) : spanAt(after ? flank + 1 + last : 0);\n  const stop = {\n    contigEnds: end !== void 0,\n    shortBp: !end ? 0 : Math.max(0, region.start - end.end, end.start - region.end)\n  };\n  return {\n    ids,\n    complete: false,\n    from: flank,\n    to: after ? steps.length : -1,\n    stop\n  };\n}\nfunction filterSamples(rows, samples) {\n  return samples ? rows.filter((r) => samples.includes(r.sample)).sort(\n    (a, b) => samples.indexOf(a.sample) - samples.indexOf(b.sample) || a.label.localeCompare(b.label)\n  ) : rows;\n}\nfunction referenceWalkName(graph) {\n  const names = (graph.paths ?? []).map((p) => pathOrigin(p.name).name);\n  if (graph.referencePath !== void 0 && names.includes(graph.referencePath)) {\n    return graph.referencePath;\n  }\n  const rankZero = new Set(\n    graph.nodes.flatMap((n) => n.stable?.rank === 0 ? [n.stable.refName] : [])\n  );\n  return names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction walkRows(graph, region, unit) {\n  const paths = graph.paths ?? [];\n  const nameOf = (p) => pathOrigin(p.name).name;\n  const referenceName = referenceWalkName(graph);\n  const referencePieces = paths.filter((p) => nameOf(p) === referenceName).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));\n  const first = referencePieces[0];\n  const others = paths.filter((p) => !referencePieces.includes(p));\n  if (!first || others.length === 0) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const table = new NodeTable(graph);\n  const referenceStart = first.start ?? 0;\n  const cut = region && region.end > region.start ? region : void 0;\n  const referenceNodes = referencePieces.map((piece) => table.nodesOf(piece));\n  const nodeCount = table.lengths.length;\n  table.onReference = new Uint8Array(nodeCount);\n  table.referenceStart = new Float64Array(nodeCount);\n  table.referenceEnd = new Float64Array(nodeCount);\n  let reachesBefore = false;\n  let reachesAfter = false;\n  for (const [p, piece] of referencePieces.entries()) {\n    let pos = piece.start ?? 0;\n    for (const node of referenceNodes[p]) {\n      const len = table.lengths[node];\n      if (!table.onReference[node]) {\n        table.onReference[node] = 1;\n        table.referenceStart[node] = pos;\n        table.referenceEnd[node] = pos + len;\n        reachesBefore ||= cut !== void 0 && pos + len <= cut.start;\n        reachesAfter ||= cut !== void 0 && pos >= cut.end;\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || reachesBefore && reachesAfter;\n  const rowOf = (paths2, nodes) => {\n    const path = paths2[0];\n    const pieces = paths2.map((piece, p) => ({\n      start: piece.start,\n      nodes: nodes?.[p] ?? table.nodesOf(piece),\n      before: piece.before,\n      after: piece.after\n    })).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));\n    const { steps, gaps } = stepsOf(pieces, table);\n    const { ids, complete, from, to, stop } = sliceBetween(\n      steps,\n      table,\n      cut,\n      flanked\n    );\n    const contig = path.contig ?? panSNContig(pathOrigin(path.name).name);\n    const axisSpan = stepSpan(pieces, table, from < 0 ? 0 : from);\n    const axis = !axisSpan ? void 0 : from < 0 ? { contig, start: axisSpan.start, reversed: false } : from < to ? { contig, start: axisSpan.end, reversed: false } : { contig, start: axisSpan.start, reversed: true };\n    const { lengths, onReference, referenceStart: referenceStart2, referenceEnd } = table;\n    const runs = [];\n    let last;\n    let bp = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    const backwards = from >= 0 && from > to;\n    for (const node of ids) {\n      if (node < 0) {\n        const parts = gaps[-node - 1];\n        for (const { bp: partBp, ...why } of backwards ? [...parts].reverse() : parts) {\n          last = {\n            start: bp,\n            bp: partBp,\n            onReference: false,\n            gap: true,\n            ...why\n          };\n          runs.push(last);\n          bp += partBp;\n          gapBp += partBp;\n        }\n        step = 0;\n        continue;\n      }\n      const len = lengths[node];\n      const on = onReference[node] === 1;\n      const at = last?.referenceStart;\n      const forward = on && at !== void 0 && step >= 0 && at + last.bp === referenceStart2[node];\n      const backward = on && at !== void 0 && step <= 0 && referenceEnd[node] === at;\n      if (!on && last && !last.onReference && !last.gap) {\n        last.bp += len;\n      } else if (forward || backward) {\n        last.bp += len;\n        if (!forward) {\n          last.referenceStart = referenceStart2[node];\n          last.reversed = true;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        last = {\n          start: bp,\n          bp: len,\n          onReference: on,\n          referenceStart: on ? referenceStart2[node] : void 0\n        };\n        runs.push(last);\n        step = 0;\n      }\n      bp += len;\n      if (!on) {\n        offReferenceBp += len;\n      }\n    }\n    return {\n      name: path.name,\n      label: labelOf(path),\n      sample: sampleOf(path),\n      haplotype: path.haplotype,\n      bp,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      runs,\n      axis\n    };\n  };\n  const origin = cut ? cut.start : referenceStart;\n  return {\n    origin,\n    unit,\n    reference: rowOf(referencePieces, referenceNodes),\n    rows: [...walks.values()].map((paths2) => rowOf(paths2)).sort(\n      (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)\n    )\n  };\n}\n\nexport {\n  filterSamples,\n  referenceWalkName,\n  walkRows\n};\n", "export function groupBy<T, K>(\n  items: readonly T[],\n  key: (item: T) => K,\n): Map<K, T[]> {\n  const groups = new Map<K, T[]>()\n  for (const item of items) {\n    const k = key(item)\n    const group = groups.get(k)\n    if (group === undefined) {\n      groups.set(k, [item])\n    } else {\n      group.push(item)\n    }\n  }\n  return groups\n}\n", "// A PanSN path name: sample#haplotype#contig, sometimes with further\n// #-separated fields such as a fragment offset after the contig.\n// https://github.com/pangenome/PanSN-spec\nexport interface PanSNName {\n  sample: string\n  haplotype: number\n  contig: string\n}\n\n// gbz-base names a generic reference `_gbwt_ref#0#contig` and a haplotype the\n// GBWT kept no metadata for `unknown#N#contig`; neither names a sample.\nconst NOT_SAMPLES = new Set(['_gbwt_ref', 'unknown'])\n\n// The sample, haplotype and contig of a PanSN name, or undefined for any other\n// name: fewer than three fields, an empty sample or contig, a haplotype that\n// isn't a whole number, or a placeholder sample.\nexport function parsePanSN(name: string | undefined): PanSNName | undefined {\n  const [sample, haplotype, contig] = name?.split('#') ?? []\n  if (\n    sample === undefined ||\n    sample === '' ||\n    NOT_SAMPLES.has(sample) ||\n    haplotype === undefined ||\n    !/^\\d+$/.test(haplotype) ||\n    contig === undefined ||\n    contig === ''\n  ) {\n    return undefined\n  }\n  return { sample, haplotype: Number(haplotype), contig }\n}\n", "// The tube map layout, from input nodes and tracks to drawable shapes. Ported\n// from the original sequenceTubeMap JS, where it shared one module with the d3\n// drawing. It runs in two phases, each on a fresh LayoutState: layoutTopology\n// merges, orders, orients and sizes the nodes and fixes their x, and\n// placeTubeMap stacks a chosen set of tracks and reads on that topology.\nimport { groupBy } from './groupBy.ts'\nimport { parsePanSN } from './panSN.ts'\n\nimport type {\n  HaplotypeShare,\n  ImageBounds,\n  InputNode,\n  InputTrack,\n  LayoutNode,\n  Mismatch,\n  Node,\n  ReadSequenceEntry,\n  Segment,\n  Track,\n  TrackShapes,\n  TrackType,\n} from './types.ts'\n\n// Node and Track declare some fields that not every entry gets: layout places\n// only the nodes a track or read reaches, and a normal read has no width until\n// assignReadsToNodes.\ntype MaybeUnset<T, K extends keyof T> = Omit<T, K> & Partial<Pick<T, K>>\ntype MaybeUnplacedNode = MaybeUnset<LayoutNode, 'x' | 'y'>\n\nexport type NodeWidthOption = 'normal' | 'compressed' | 'small' | 'fixed'\n\n// The fields of a placed track a renderer colors it by. Shapes carry only the\n// track's id, so a renderer can recolor without laying out again.\nexport interface ColorableTrack {\n  id: number\n  sourceTrackID: number\n  type?: TrackType\n  name?: string\n  mapping_quality?: number\n  is_reverse?: boolean\n  haplotypeShare?: HaplotypeShare\n}\n\nexport type LayerData = 'haplotypes' | 'reads'\n\n// A track set placement draws, and the stat it runs first. `coarsen` turns\n// the set into one band per edge; banded haplotypes keep the reference's lane.\nexport interface Layer {\n  data: LayerData\n  stat?: 'coarsen'\n}\n\n// The options a topology fixes. trackWidth, the layers and ignoreStrand leave\n// node order alone, but the topology measures x from placing every track and\n// read under them.\nexport interface TopologyOptions {\n  mergeNodes?: boolean\n  showReads?: boolean\n  // Shorthand for `layers` when those are unset: band the reads, or the\n  // haplotypes when no reads were loaded\n  coarsenedReadView?: boolean\n  // The haplotypes draw first and the reads stack under them, each data under\n  // the stat of its first layer here\n  layers?: readonly Layer[]\n  ignoreStrand?: boolean\n  // normal: width is sequence length, at `charWidth` per base\n  // compressed: log2 of sequence length\n  // small: 1% of sequence length\n  // fixed: every node one width\n  nodeWidthOption?: NodeWidthOption\n  charWidth?: number\n  // a haplotype tube's width in layout px, where no `freq` scales it\n  trackWidth?: number\n  // how `freq` widens a tube: log grows slowly, as sequenceTubeMap draws vg's\n  // frequencies; linear makes a walk standing for n haplotypes n tubes wide,\n  // so widths compare as counts\n  freqWidth?: 'log' | 'linear'\n}\n\nexport const READ_FACET_FIELDS = ['read_group', 'sample_name'] as const\nexport type ReadFacetBy = (typeof READ_FACET_FIELDS)[number]\n// A read field, or the sample in the haplotypes' PanSN names\nexport const FACET_FIELDS = [...READ_FACET_FIELDS, 'haplotype_sample'] as const\nexport type FacetBy = (typeof FACET_FIELDS)[number]\n\n// One panel's subset. A read facet keeps every haplotype and the reads whose\n// `by` field is `key`, or that lack one when `key` is null. A haplotype facet\n// keeps the reference and no reads, plus the haplotypes of sample `key`, or\n// those with no PanSN sample when `key` is null; its `reads` panel keeps the\n// reference and the reads.\nexport interface ReadFacet {\n  by: ReadFacetBy\n  key: string | null\n}\nexport type HaplotypeFacet =\n  | { by: 'haplotype_sample'; key: string | null }\n  | { by: 'haplotype_sample'; reads: true }\nexport type Facet = ReadFacet | HaplotypeFacet\n\n// Which of a topology's tracks and reads a placement draws\nexport interface PlacementOptions {\n  mappingQualityCutoff?: number\n  focusReadNames?: string[] | null\n  facet?: Facet | undefined\n}\n\nexport interface FacetOptions extends PlacementOptions {\n  // One panel per value of this field\n  facetBy?: FacetBy | null\n}\n\nexport interface LayoutOptions extends TopologyOptions, PlacementOptions {}\n\nexport type CoarsenedUnit = 'read' | 'haplotype'\n\n// A coarsened band's count of contributing reads or haplotypes and its label,\n// keyed by the band's synthetic track id, unique across layers\nexport interface CoarsenedEdgeMeta {\n  count: number\n  label: string\n}\n\n// What a layer's coarsening drew as bands, how many reads or haplotypes it\n// banded (counting a deduplicated walk `freq` times), and whether any band\n// runs reverse-strand\nexport interface Coarsening {\n  unit: CoarsenedUnit\n  total: number\n  reverse: boolean\n}\n\n// Each layer that drew bands, by its data\nexport type Coarsenings = Partial<Record<LayerData, Coarsening>>\n\nexport interface TubeMapLayout {\n  // 1-indexed with a hole at 0: a signed index\n  // is an oriented visit, and 0 has no sign\n  nodes: LayoutNode[]\n  // the haplotype tracks and placed reads together, sorted by where each\n  // first meets the others, which is the order their shapes were made in\n  tracks: Track[]\n  // the placed reads alone\n  reads: Track[]\n  nodeMap: ReadonlyMap<string, number>\n  shapes: TrackShapes\n  bounds: ImageBounds\n  maxOrder: number\n  // the name of the track that carries a coordinate for the ruler\n  trackForRuler: string | undefined\n  coarsenedEdgeMeta: Map<number, CoarsenedEdgeMeta>\n  coarsened: Coarsenings\n}\n\n// A node before placement gives it a y and the reads through it\nexport type TopologyNode = Omit<\n  LayoutNode,\n  'y' | 'contentHeight' | 'incomingReads' | 'outgoingReads' | 'internalReads'\n>\n\n// A haplotype or read before placement gives it a width and lanes\nexport type TopologyTrack = Omit<Track, 'path' | 'width'>\n\n// What every placement of one input shares: the merged, ordered and oriented\n// nodes with their widths and x positions, and the oriented haplotypes and\n// reads. A placement reads it and never changes it.\nexport interface TubeMapTopology {\n  options: Required<TopologyOptions>\n  // 1-indexed with a hole at 0, like TubeMapLayout.nodes. A node no track or\n  // read reaches has order UNREACHABLE_ORDER and no x.\n  nodes: readonly TopologyNode[]\n  // the visible haplotypes, track 0 read left to right\n  tracks: readonly TopologyTrack[]\n  // every primary alignment that shares a node with a track, unfiltered\n  reads: readonly TopologyTrack[]\n  nodeMap: ReadonlyMap<string, number>\n  maxOrder: number\n  trackForRuler: string | undefined\n}\n\ntype LayoutConfig = Required<TopologyOptions>\n\n// sequenceTubeMap's character width. The compressed, small and fixed node\n// widths always scale by it and ignore `charWidth`.\nconst DEFAULT_CHAR_WIDTH = 8.401\n\n// The coarsened view bands haplotypes only when no reads were loaded, not when\n// a filter hides them all\nfunction layersFrom(\n  { layers, coarsenedReadView = false, showReads = true }: TopologyOptions,\n  hasReads: boolean,\n): readonly Layer[] {\n  if (layers !== undefined) {\n    return layers\n  }\n  const coarsen = coarsenedReadView && showReads\n  const stat = (banded: boolean): Pick<Layer, 'stat'> =>\n    banded ? { stat: 'coarsen' } : {}\n  return [\n    { data: 'haplotypes', ...stat(coarsen && !hasReads) },\n    { data: 'reads', ...stat(coarsen && hasReads) },\n  ]\n}\n\nfunction statOf(layers: readonly Layer[], data: LayerData) {\n  return layers.find(layer => layer.data === data)?.stat\n}\n\nfunction configFrom(options: TopologyOptions, hasReads: boolean): LayoutConfig {\n  return {\n    mergeNodes: options.mergeNodes ?? true,\n    showReads: options.showReads ?? true,\n    coarsenedReadView: options.coarsenedReadView ?? false,\n    layers: layersFrom(options, hasReads),\n    ignoreStrand: options.ignoreStrand ?? false,\n    nodeWidthOption: options.nodeWidthOption ?? 'normal',\n    charWidth: options.charWidth ?? DEFAULT_CHAR_WIDTH,\n    trackWidth: options.trackWidth ?? 15,\n    freqWidth: options.freqWidth ?? 'log',\n  }\n}\n\n// One track's segment in an order slot, and where its lane would ideally go\ninterface SegmentAssignment {\n  trackID: number\n  segmentID: number\n  idealLane?: number | undefined\n  idealY?: number | null | undefined\n}\n\n// The segments of one order slot that visit one node, or a single segment\n// passing or turning in a gap when `node` is null\ninterface NodeAssignment {\n  node: number | null\n  tracks: SegmentAssignment[]\n  idealLane?: number | undefined\n}\n\nfunction emptyTrackShapes(): TrackShapes {\n  return {\n    rectangles: [],\n    curves: [],\n    corners: [],\n    verticalRectangles: [],\n  }\n}\n\n// The working state of one topology or placement, shared by its passes.\ninterface LayoutState {\n  config: LayoutConfig\n  // Sparse like TubeMapLayout.nodes, but forEach, map and sort skip the hole\n  // and noUncheckedIndexedAccess already types indexed reads as possibly\n  // undefined, so only for...of would ever see it.\n  nodes: LayoutNode[]\n  // Each track's `path` lists the Segments to draw, in order along the path.\n  tracks: Track[]\n  // Reads have a `path` too, but stack vertically by a different system.\n  reads: Track[]\n  nodeMap: ReadonlyMap<string, number>\n  nodesPerOrder: number[][]\n  // generateNodeOrder's scratch, by node index; undefined until assigned.\n  nodeOrders: (number | undefined)[]\n  // Lane assignments for tracks (not reads), one list per order slot.\n  assignments: NodeAssignment[][]\n  extraLeft: number[]\n  extraRight: number[]\n  // horizontal order of the rightmost node\n  maxOrder: number\n  shapes: TrackShapes\n  trackForRuler: string | undefined\n  coarsenedEdgeMeta: Map<number, CoarsenedEdgeMeta>\n}\n\nfunction emptyState(config: LayoutConfig): LayoutState {\n  return {\n    config,\n    nodes: [],\n    tracks: [],\n    reads: [],\n    nodeMap: new Map(),\n    nodesPerOrder: [],\n    nodeOrders: [],\n    assignments: [],\n    extraLeft: [],\n    extraRight: [],\n    maxOrder: -1,\n    shapes: emptyTrackShapes(),\n    trackForRuler: undefined,\n    coarsenedEdgeMeta: new Map(),\n  }\n}\n\n// placeTubeMap(layoutTopology(...), options). Undefined when nothing visible\n// is left to draw.\nexport function layoutTubeMap(\n  inputNodes: readonly InputNode[],\n  inputTracks: readonly InputTrack[],\n  inputReads: readonly InputTrack[] = [],\n  options: LayoutOptions = {},\n): TubeMapLayout | undefined {\n  const topology = layoutTopology(inputNodes, inputTracks, inputReads, options)\n  return topology && placeTubeMap(topology, options)\n}\n\n// Each topology's placement of every track and read, which fixed its x\nconst measurements = new WeakMap<TubeMapTopology, TubeMapLayout>()\n\n// Merge, order and orient the nodes under the visible `inputTracks` and, when\n// `showReads`, every primary alignment in `inputReads`, then size them and\n// fix their x positions. Undefined when nothing visible is left to draw.\n// Neither input is modified. Track 0 is the reference the layout straightens.\n// The x gaps between order slots make room for the tracks' turns and slopes,\n// so the topology takes its x positions from placing every track and read.\nexport function layoutTopology(\n  inputNodes: readonly InputNode[],\n  inputTracks: readonly InputTrack[],\n  inputReads: readonly InputTrack[] = [],\n  options: TopologyOptions = {},\n): TubeMapTopology | undefined {\n  const topology = arrangeTopology(inputNodes, inputTracks, inputReads, options)\n  if (topology === undefined) {\n    return undefined\n  }\n  const everything = place(topology, topology.tracks, topology.reads, 'measure')\n  everything.nodes.forEach((node, i) => {\n    if (node.order >= 0) {\n      topology.nodes[i]!.x = node.x\n    }\n  })\n  measurements.set(topology, everything)\n  return topology\n}\n\n// Lay out the haplotypes and reads `options` keep at the topology's x\n// positions, stacking each read under the nodes it visits. When they keep\n// everything, this returns the placement layoutTopology measured x from, the\n// same object on every such call.\nexport function placeTubeMap(\n  topology: TubeMapTopology,\n  options: PlacementOptions = {},\n): TubeMapLayout {\n  return placeSubset(\n    topology,\n    selectTracks(topology, options.facet),\n    selectReads(topology, options),\n  )\n}\n\nfunction placeSubset(\n  topology: TubeMapTopology,\n  tracks: readonly TopologyTrack[],\n  reads: readonly TopologyTrack[],\n  bandIdBase?: BandIdBase,\n): TubeMapLayout {\n  const measured = measurements.get(topology)\n  return measured !== undefined &&\n    tracks.length === topology.tracks.length &&\n    reads.length === topology.reads.length\n    ? measured\n    : place(topology, tracks, reads, 'topology', bandIdBase)\n}\n\nfunction arrangeTopology(\n  inputNodes: readonly InputNode[],\n  inputTracks: readonly InputTrack[],\n  inputReads: readonly InputTrack[],\n  options: TopologyOptions,\n): TubeMapTopology | undefined {\n  const state = emptyState(configFrom(options, inputReads.length > 0))\n\n  if (inputNodes.length === 0 || inputTracks.length === 0) {\n    return undefined\n  }\n\n  // Boundary promotion: layout passes below populate the Node/Track fields\n  // (width, order, x/y, path, indexSequence, etc.) before any reader runs.\n  //\n  // Nodes are referenced in inputs by internal `name` attribute and not by\n  // index. Internally in e.g. a path's indexSequence we need to reference\n  // nodes by *signed* index, so index 0 can never be used: budge everything\n  // down and leave a hole (rather than an `undefined` entry) at 0, which we\n  // won't iterate over. Made after the copy, because not every structuredClone\n  // keeps a hole.\n  structuredClone(inputNodes).forEach((node, i) => {\n    node.seq ??= ''\n    node.sequenceLength ??= node.seq.length\n    state.nodes[i + 1] = node as LayoutNode\n  })\n  state.tracks = structuredClone(inputTracks) as Track[]\n  // Secondary alignments never draw, so drop them before the deep copy, the\n  // most expensive step in a redraw.\n  state.reads = state.config.showReads\n    ? (structuredClone(\n        inputReads.filter(read => read.is_secondary !== true),\n      ) as Track[])\n    : []\n\n  for (let i = state.tracks.length - 1; i >= 0; i -= 1) {\n    const t = state.tracks[i]!\n    t.type ??= 'haplotype'\n    if (t.hidden === true) {\n      state.tracks.splice(i, 1)\n      continue\n    }\n    if (t.indexOfFirstBase !== undefined) {\n      state.trackForRuler = t.name\n    }\n  }\n  if (state.tracks.length === 0) {\n    return undefined\n  }\n\n  // Run against the visible tracks only, so hiding the reference doesn't leave\n  // the layout straightened around a track that is no longer drawn.\n  straightenTrack(state, 0)\n\n  state.nodeMap = generateNodeMap(state)\n  generateTrackIndexSequences(state, state.tracks)\n  generateTrackIndexSequences(state, state.reads)\n  generateNodeWidth(state)\n\n  if (state.config.mergeNodes) {\n    generateNodeSuccessors(state)\n    generateNodeOrder(state)\n    reverseReversedReads(state)\n    mergeNodes(state)\n    state.nodeMap = generateNodeMap(state)\n    generateNodeWidth(state)\n    generateTrackIndexSequences(state, state.tracks)\n    generateTrackIndexSequences(state, state.reads)\n  }\n\n  generateNodeSuccessors(state)\n  generateNodeDegree(state)\n  generateNodeOrder(state)\n\n  // can cause problems when there is a reversed single track node\n  // OTOH, can solve problems with complex inversion patterns\n  switchNodeOrientation(state)\n  generateNodeOrder(state)\n  reverseReversedReads(state)\n  generateTrackIndexSequences(state, state.reads)\n\n  return {\n    options: state.config,\n    nodes: state.nodes,\n    tracks: state.tracks,\n    reads: state.reads,\n    nodeMap: state.nodeMap,\n    maxOrder: getMaxOrder(state),\n    trackForRuler: state.trackForRuler,\n  }\n}\n\nfunction selectReads(\n  topology: TubeMapTopology,\n  { mappingQualityCutoff = 0, focusReadNames = null, facet }: PlacementOptions,\n): readonly TopologyTrack[] {\n  const focus = focusReadNames ? new Set(focusReadNames) : null\n  return topology.reads.filter(\n    read =>\n      (read.mapping_quality ?? 0) >= mappingQualityCutoff &&\n      (focus === null || (read.name !== undefined && focus.has(read.name))) &&\n      (facet === undefined || facetHoldsRead(facet, read)),\n  )\n}\n\n// Whether a panel of `facet` draws this read when the read filters keep it\nexport function facetHoldsRead(\n  facet: Facet,\n  read: Pick<TopologyTrack, ReadFacetBy>,\n): boolean {\n  return facet.by === 'haplotype_sample'\n    ? 'reads' in facet\n    : (read[facet.by] ?? null) === facet.key\n}\n\n// What every haplotype panel keeps: track 0, which the topology straightened,\n// and the track carrying the ruler's coordinates, when that is another\nfunction references(topology: TubeMapTopology): Set<TopologyTrack> {\n  return new Set(\n    topology.tracks.filter(\n      (track, i) => i === 0 || track.name === topology.trackForRuler,\n    ),\n  )\n}\n\nfunction selectTracks(\n  topology: TubeMapTopology,\n  facet: Facet | undefined,\n): readonly TopologyTrack[] {\n  if (facet?.by !== 'haplotype_sample') {\n    return topology.tracks\n  }\n  const kept = references(topology)\n  return topology.tracks.filter(\n    track =>\n      kept.has(track) || (!('reads' in facet) && sampleOf(track) === facet.key),\n  )\n}\n\nfunction sampleOf(track: TopologyTrack): string | null {\n  return parsePanSN(track.name)?.sample ?? null\n}\n\n// The haplotypes among `tracks` beside the reference, a PanSN haplotype\n// counted once however many walks it makes through the window\nfunction haplotypeCount(\n  topology: TubeMapTopology,\n  tracks: readonly TopologyTrack[],\n): number {\n  const skip = references(topology)\n  return new Set(\n    tracks.flatMap(track => {\n      if (skip.has(track)) {\n        return []\n      }\n      const name = parsePanSN(track.name)\n      return [name ? `${name.sample}#${name.haplotype}` : track]\n    }),\n  ).size\n}\n\n// A facet and the haplotypes and reads it draws\nexport interface FacetSubset<F extends Facet = Facet> {\n  facet: F\n  tracks: readonly TopologyTrack[]\n  reads: readonly TopologyTrack[]\n}\n\n// Group `items` by key: in sort order, the null key last\nfunction sortedGroups<T>(\n  items: readonly T[],\n  keyOf: (item: T) => string | null,\n): [string | null, T[]][] {\n  return [...groupBy(items, keyOf)].sort(([a], [b]) =>\n    a === null || b === null\n      ? Number(a === null) - Number(b === null)\n      : a.localeCompare(b, undefined, { numeric: true }),\n  )\n}\n\n// Split the reads `options` keep by their `by` field: one subset per value,\n// in sort order with the reads lacking one last, and none left empty. Every\n// subset keeps every haplotype.\nexport function facetReads(\n  topology: TubeMapTopology,\n  by: ReadFacetBy,\n  options: PlacementOptions = {},\n): FacetSubset<ReadFacet>[] {\n  return sortedGroups(\n    selectReads(topology, { ...options, facet: undefined }),\n    read => read[by] ?? null,\n  ).map(([key, reads]) => ({\n    facet: { by, key },\n    tracks: topology.tracks,\n    reads,\n  }))\n}\n\n// Split the haplotypes beside the reference by the sample in their PanSN\n// names: one subset per sample, in sort order, then one for the haplotypes\n// with no PanSN name, each holding the reference too and no reads. The reads\n// `options` keep, when any, go in a last subset with the reference alone. No\n// haplotype beside the reference leaves nothing to split.\nexport function facetHaplotypes(\n  topology: TubeMapTopology,\n  options: PlacementOptions = {},\n): FacetSubset<HaplotypeFacet>[] {\n  const kept = references(topology)\n  const samples = sortedGroups(\n    topology.tracks.filter(track => !kept.has(track)),\n    sampleOf,\n  )\n  if (samples.length === 0) {\n    return []\n  }\n  const ofSample = samples.map(([key]) => {\n    const facet: HaplotypeFacet = { by: 'haplotype_sample', key }\n    return { facet, tracks: selectTracks(topology, facet), reads: [] }\n  })\n  const facet: HaplotypeFacet = { by: 'haplotype_sample', reads: true }\n  const reads = selectReads(topology, { ...options, facet })\n  return reads.length === 0\n    ? ofSample\n    : [...ofSample, { facet, tracks: selectTracks(topology, facet), reads }]\n}\n\n// One placement in a stack of them. Its layout keeps its own coordinates;\n// `offsetY` moves it into the stack.\nexport interface FacetPanel {\n  // undefined for the one panel of an unfaceted view\n  facet?: Facet\n  readCount: number\n  // beside the reference, a PanSN haplotype counted once\n  haplotypeCount: number\n  layout: TubeMapLayout\n  offsetY: number\n}\n\nexport interface FacetedLayout {\n  panels: FacetPanel[]\n  // every panel and its label, in stack coordinates\n  bounds: ImageBounds\n}\n\n// Room above each faceted panel for its label, and between one panel and the\n// next label\nexport const FACET_LABEL_HEIGHT = 30\nexport const FACET_GAP = 40\n\n// Place the topology once per facet and stack the placements top to bottom,\n// the first where an unfaceted placement would draw. Every panel takes the\n// topology's x, so the panels line up in x. Band ids run on from one panel to\n// the next where panels band different tracks: the reads under a read facet,\n// the haplotypes under a haplotype facet, whose bands then take their share\n// of the panel's haplotypes. Without `facetBy`, or with nothing to split, this\n// is one panel of placeTubeMap's layout.\nexport function placeFacets(\n  topology: TubeMapTopology,\n  options: FacetOptions = {},\n): FacetedLayout {\n  const { facetBy, ...placement } = options\n  const subsets =\n    facetBy === undefined || facetBy === null\n      ? []\n      : facetBy === 'haplotype_sample'\n        ? facetHaplotypes(topology, placement)\n        : facetReads(topology, facetBy, placement)\n  if (subsets.length === 0) {\n    const layout = placeTubeMap(topology, placement)\n    return {\n      panels: [\n        {\n          layout,\n          readCount: layout.reads.length,\n          haplotypeCount: haplotypeCount(topology, topology.tracks),\n          offsetY: 0,\n        },\n      ],\n      bounds: layout.bounds,\n    }\n  }\n  const banded: LayerData =\n    facetBy === 'haplotype_sample' ? 'haplotypes' : 'reads'\n  let nextBandId: number | undefined\n  let bottom = 0\n  const panels = subsets.map(({ facet, tracks, reads }, i) => {\n    const layout = placeSubset(\n      topology,\n      tracks,\n      reads,\n      nextBandId === undefined ? undefined : { [banded]: nextBandId },\n    )\n    for (const id of layout.coarsenedEdgeMeta.keys()) {\n      if (nextBandId === undefined || id >= nextBandId) {\n        nextBandId = id + 1\n      }\n    }\n    const offsetY =\n      i === 0 ? 0 : bottom + FACET_GAP + FACET_LABEL_HEIGHT - layout.bounds.minY\n    bottom = offsetY + layout.bounds.maxY\n    return {\n      facet,\n      readCount: reads.length,\n      haplotypeCount: haplotypeCount(topology, tracks),\n      layout,\n      offsetY,\n    }\n  })\n  return {\n    panels,\n    bounds: {\n      minX: Math.min(...panels.map(p => p.layout.bounds.minX)),\n      maxX: Math.max(...panels.map(p => p.layout.bounds.maxX)),\n      minY: panels[0]!.layout.bounds.minY - FACET_LABEL_HEIGHT,\n      maxY: bottom,\n    },\n  }\n}\n\n// The first id each layer's bands take\ntype BandIdBase = Partial<Record<LayerData, number>>\n\n// Place copies of the topology's nodes and the given tracks and reads,\n// measuring x from them or taking the topology's. Haplotype bands take ids\n// from COARSENED_ID_BASE and read bands straight after, unless `bandIdBase`\n// says otherwise.\nfunction place(\n  topology: TubeMapTopology,\n  tracks: readonly TopologyTrack[],\n  reads: readonly TopologyTrack[],\n  x: 'measure' | 'topology',\n  bandIdBase: BandIdBase = {},\n): TubeMapLayout {\n  const state = emptyState(topology.options)\n  topology.nodes.forEach((node, i) => {\n    state.nodes[i] = { ...node } as LayoutNode\n  })\n  state.tracks = tracks.map(track => ({ ...track }) as Track)\n  state.reads = reads.map(read => ({ ...read }) as Track)\n  state.nodeMap = topology.nodeMap\n  state.maxOrder = topology.maxOrder\n  state.trackForRuler = topology.trackForRuler\n\n  // Banded haplotypes leave the reference its lane and join the reads'\n  // overlay, above the reads, before calculateTrackWidth and\n  // generateLaneAssignment see the tracks.\n  const { layers, ignoreStrand } = state.config\n  const haplotypeBandIdBase = bandIdBase.haplotypes ?? COARSENED_ID_BASE\n  const haplotypeBands =\n    statOf(layers, 'haplotypes') === 'coarsen'\n      ? bandHaplotypes(state, haplotypeBandIdBase)\n      : undefined\n  if (haplotypeBands !== undefined) {\n    state.tracks = [haplotypeBands.ref]\n  }\n\n  calculateTrackWidth(state)\n  generateLaneAssignment(state)\n  // also places the nodes that only filtered-out reads visit\n  generateReadOnlyNodeAttributes(state)\n\n  // A band crosses exactly two nodes, so placeReads and the shapes handle it\n  // like any read, and node heights grow with the edge count rather than the\n  // read or haplotype count.\n  const readBands =\n    statOf(layers, 'reads') === 'coarsen' && state.reads.length > 0\n      ? buildCoarsenedSyntheticBands(\n          state,\n          state.reads,\n          'read',\n          bandIdBase.reads ??\n            haplotypeBandIdBase + (haplotypeBands?.bands.length ?? 0),\n        )\n      : undefined\n  if (readBands !== undefined) {\n    state.reads = readBands.bands\n  }\n  const coarsened: Coarsenings = {}\n  for (const [data, unit, banding] of [\n    ['haplotypes', 'haplotype', haplotypeBands],\n    ['reads', 'read', readBands],\n  ] as const) {\n    if (banding !== undefined) {\n      reverseReversedReads(state, banding.bands)\n      generateTrackIndexSequences(state, banding.bands)\n      coarsened[data] = {\n        unit,\n        total: banding.total,\n        reverse: !ignoreStrand && banding.bands.some(b => b.is_reverse),\n      }\n    }\n  }\n  if (haplotypeBands !== undefined) {\n    state.reads = haplotypeBands.bands.concat(state.reads)\n  }\n\n  placeReads(state)\n  state.tracks = state.tracks.concat(state.reads)\n\n  if (x === 'measure') {\n    generateNodeXCoords(state)\n  }\n\n  generateSVGShapesFromPath(state)\n  return {\n    nodes: state.nodes,\n    tracks: state.tracks,\n    reads: state.reads,\n    nodeMap: state.nodeMap,\n    shapes: state.shapes,\n    bounds: getImageDimensions(state),\n    maxOrder: state.maxOrder,\n    trackForRuler: state.trackForRuler,\n    coarsenedEdgeMeta: state.coarsenedEdgeMeta,\n    coarsened,\n  }\n}\n\n// Return true if the given name names a reverse strand node, and false otherwise.\nexport function isReverse(nodeName: string): boolean {\n  return nodeName.startsWith('-')\n}\n\n// Get the forward version of a node name, which may be either forward or backward (negative)\nexport function forward(nodeName: string): string {\n  return isReverse(nodeName) ? nodeName.substring(1) : nodeName\n}\n\n// Get the reverse version of a node name, which may be either forward or backward (negative)\nexport function reverse(nodeName: string): string {\n  return isReverse(nodeName) ? nodeName : `-${nodeName}`\n}\n\n// Get the opposite orientation node name for the given node.\nexport function flip(nodeName: string): string {\n  return isReverse(nodeName) ? forward(nodeName) : reverse(nodeName)\n}\n\n// Whether a signed node index visits its node forward. Index 0 is never a\n// node, so no visit is -0.\nexport function isForwardIndex(n: number): boolean {\n  return n > 0\n}\n\n// Turn around every node the given track visits in reverse before it visits\n// it forward, so that track reads left to right, and flip every track's and\n// read's visits to those nodes to match, as switchNodeOrientationForPaths\n// does for the nodes it switches.\nfunction straightenTrack(state: LayoutState, index: number): void {\n  const nodesToInvert = new Set<string>()\n  const visitedForward = new Set<string>()\n  for (const visit of state.tracks[index]!.sequence) {\n    if (!isReverse(visit)) {\n      visitedForward.add(visit)\n    } else if (!visitedForward.has(forward(visit))) {\n      nodesToInvert.add(forward(visit))\n    }\n  }\n  if (nodesToInvert.size === 0) {\n    return\n  }\n\n  for (const { sequence } of [...state.tracks, ...state.reads]) {\n    for (let j = 0; j < sequence.length; j += 1) {\n      if (nodesToInvert.has(forward(sequence[j]!))) {\n        sequence[j] = flip(sequence[j]!)\n      }\n    }\n  }\n\n  state.nodes.forEach(node => {\n    if (nodesToInvert.has(node.name)) {\n      node.seq = getReverseComplement(node.seq)\n    }\n  })\n}\n\n// generates attributes (node.y, node.contentHeight) for nodes without tracks, only reads\nfunction generateReadOnlyNodeAttributes(state: LayoutState): void {\n  state.nodesPerOrder = Array.from({ length: state.maxOrder + 1 }, () => [])\n\n  const orderY = new Map<number, number>()\n  state.nodes.forEach((node: MaybeUnplacedNode) => {\n    if (node.y !== undefined) {\n      setMapToMax(orderY, node.order, node.y + node.contentHeight)\n    }\n  })\n\n  // for order values where there is no node with haplotypes, orderY is calculated via tracks\n  state.tracks.forEach(track => {\n    if (track.type === 'haplotype') {\n      track.path.forEach(step => {\n        setMapToMax(orderY, step.order, (step.y ?? 0) + track.width)\n      })\n    }\n  })\n\n  state.nodes.forEach((node: MaybeUnplacedNode, i) => {\n    if (node.order >= 0 && node.y === undefined) {\n      node.y = (orderY.get(node.order) ?? 0) + 25\n      node.contentHeight = 0\n      state.nodesPerOrder[node.order]!.push(i)\n    }\n  })\n}\n\nfunction setMapToMax<K>(map: Map<K, number>, key: K, value: number): void {\n  const existing = map.get(key)\n  if (existing === undefined) {\n    map.set(key, value)\n  } else {\n    map.set(key, Math.max(existing, value))\n  }\n}\n\nexport const READ_WIDTH = 7\n\n// add info about reads to nodes (incoming, outgoing and internal reads)\nfunction assignReadsToNodes(state: LayoutState): void {\n  state.nodes.forEach(node => {\n    node.incomingReads = []\n    node.outgoingReads = []\n    node.internalReads = []\n  })\n  state.reads.forEach((read: MaybeUnset<Track, 'width'>, idx) => {\n    // coarsened bands arrive sized by their crossing count\n    if (read.width === undefined || read.width === 0) {\n      read.width = READ_WIDTH\n    }\n    read.path.forEach((segment, pathIdx) => {\n      if (segment.node === null) {\n        return\n      }\n      const node = state.nodes[segment.node]!\n      if (read.path.length === 1) {\n        node.internalReads.push(idx)\n      } else if (pathIdx === 0) {\n        node.outgoingReads.push([idx, pathIdx])\n      } else {\n        node.incomingReads.push([idx, pathIdx])\n      }\n    })\n  })\n}\n\n// calculate paths (incl. correct y coordinate) for all reads\nfunction placeReads(state: LayoutState): void {\n  state.reads.forEach(read => {\n    read.path = basicPath(state, read)\n  })\n  assignReadsToNodes(state)\n\n  // placed nodes by order, then by y-coordinate\n  const sortedNodes = state.nodes.filter(node => node.order >= 0)\n  sortedNodes.sort(compareNodesByOrder)\n\n  // One set per layer and source track: haplotype bands, then each read file\n  const sets = new Map<\n    string,\n    { layer: number; source: number; reads: Set<number> }\n  >()\n  for (let i = 0; i < state.reads.length; i++) {\n    const read = state.reads[i]!\n    const layer = read.haplotypeShare === undefined ? 1 : 0\n    const source = read.sourceTrackID\n    const key = `${layer}:${source}`\n    const set = sets.get(key)\n    if (set === undefined) {\n      sets.set(key, { layer, source, reads: new Set([i]) })\n    } else {\n      set.reads.add(i)\n    }\n  }\n  const orderedSets = [...sets.values()].sort(\n    (a, b) => a.layer - b.layer || a.source - b.source,\n  )\n\n  // A margin sets each set apart from the one above it\n  const topMargin = orderedSets.length > 1 ? READ_WIDTH : 0\n  sortedNodes.forEach(node => {\n    for (const { reads } of orderedSets) {\n      placeReadSet(state, reads, node, topMargin)\n    }\n  })\n\n  // place read segments which are without node\n  const bottomY = calculateBottomY(state)\n  const elementsWithoutNode: ElementWithoutNode[] = []\n  state.reads.forEach((read, idx) => {\n    // The nearest node visit before and after each segment. A read starts and\n    // ends on a node, so only its first and last segments lack one.\n    const prevSegment: (Segment | undefined)[] = []\n    const nextSegment: (Segment | undefined)[] = []\n    let visit: Segment | undefined\n    read.path.forEach((seg, i) => {\n      prevSegment[i] = visit\n      if (seg.node !== null) {\n        visit = seg\n      }\n    })\n    visit = undefined\n    for (let i = read.path.length - 1; i >= 0; i -= 1) {\n      nextSegment[i] = visit\n      if (read.path[i]!.node !== null) {\n        visit = read.path[i]\n      }\n    }\n\n    read.path.forEach((element, pathIdx) => {\n      if (element.y === undefined) {\n        const previousVisitToNode = prevSegment[pathIdx]\n        const nextVisitToNode = nextSegment[pathIdx]\n\n        // Specifically referring to segments between a cycle that's traversing from right to left\n        const betweenCycleReverseTraversal = Boolean(\n          // A segment can be between a cycle if it there are nodes on both sides\n          nextVisitToNode &&\n          previousVisitToNode &&\n          // A segment is between a cycle if the next node it visits is behind the previous node it visited\n          (previousVisitToNode.order > nextVisitToNode.order ||\n            // A segment can also be between a cycle if it's visiting the same node it just visited in the same direction\n            (nextVisitToNode.order === previousVisitToNode.order &&\n              nextVisitToNode.isForward === previousVisitToNode.isForward)),\n        )\n\n        element.betweenCycleReverseTraversal = betweenCycleReverseTraversal\n\n        elementsWithoutNode.push({\n          readIndex: idx,\n          pathIndex: pathIdx,\n          previousY: previousVisitToNode?.y,\n          previousNode: previousVisitToNode?.node,\n        })\n      }\n    })\n  })\n\n  elementsWithoutNode.sort((a, b) => compareNoNodeReads(state, a, b))\n  elementsWithoutNode.forEach(element => {\n    const read = state.reads[element.readIndex]!\n    const segment = read.path[element.pathIndex]!\n    segment.y = bottomY[segment.order]!\n    bottomY[segment.order]! += read.width\n  })\n}\n\n// Place a particular collection of reads, identified by a list of read\n// numbers, into the given node at the right Y coordinates. All reads in all\n// nodes above it, and no reads in any nodes below it, are already placed.\n// Makes the given node bigger if needed and moves other nodes down if needed.\n// If topMargin is set, applies that amount of spacing down from whatever is above the reads.\nfunction placeReadSet(\n  state: LayoutState,\n  toPlace: Set<number>,\n  node: LayoutNode,\n  topMargin: number,\n): void {\n  // Get arrays of the read entry/exit/internal-ness records we want to work on\n  let incomingReads = node.incomingReads.filter(([readID]) =>\n    toPlace.has(readID),\n  )\n  const outgoingReads = node.outgoingReads.filter(([readID]) =>\n    toPlace.has(readID),\n  )\n  const internalReads = node.internalReads.filter(readID => toPlace.has(readID))\n\n  // Only actually use the top margin if we have any reads on the node.\n  if (\n    incomingReads.length === 0 &&\n    outgoingReads.length === 0 &&\n    internalReads.length === 0\n  ) {\n    topMargin = 0\n  }\n\n  // twice the margin, as sequenceTubeMap spaces them, keeps reads out of the\n  // lanes beside them\n  const startY = node.y + node.contentHeight + topMargin * 2\n\n  // Sort incoming reads by how far back along each path its last placed\n  // segment is (decisionStep: the smallest k >= 1 where path[pathIdx - k].y\n  // is set, or pathIdx + 1 when none is) and then by that segment's y\n  const incomingKeys = incomingReads.map(entry => {\n    const [readID, pathIdx] = entry\n    const path = state.reads[readID]!.path\n    let decisionStep = pathIdx + 1\n    let foundY: number | undefined\n    for (let k = 1; k <= pathIdx; k++) {\n      const y = path[pathIdx - k]?.y\n      if (y !== undefined) {\n        decisionStep = k\n        foundY = y\n        break\n      }\n    }\n    return { entry, decisionStep, y: foundY }\n  })\n  incomingKeys.sort(compareIncomingReadKeys)\n  incomingReads = incomingKeys.map(k => k.entry)\n\n  let currentY = startY\n  const occupiedUntil = new Map<number, number>()\n  incomingReads.forEach(readElement => {\n    const read = state.reads[readElement[0]]!\n    read.path[readElement[1]]!.y = currentY\n    setOccupiedUntil(occupiedUntil, read, readElement[1], currentY, node)\n    currentY += read.width\n  })\n  let maxY = currentY\n\n  outgoingReads.sort((a, b) =>\n    compareReadOutgoingSegmentsByGoingTo(state, a, b),\n  )\n\n  const occupiedFrom = new Map<number, number>()\n  currentY = startY\n  outgoingReads.forEach(readElement => {\n    const read = state.reads[readElement[0]]!\n    const firstNodeOffset = read.firstNodeOffset ?? 0\n    read.path[readElement[1]]!.y = currentY\n    occupiedFrom.set(currentY, firstNodeOffset)\n    // a read that starts the base after an incoming one ends shares its lane,\n    // which lets coarsened bands through a 1 bp node share one\n    const occUntil = occupiedUntil.get(currentY)\n    if (occUntil === undefined || occUntil + 1 <= firstNodeOffset) {\n      currentY += read.width\n      maxY = Math.max(maxY, currentY)\n    } else {\n      // otherwise push down incoming reads to make place for outgoing Read\n      occupiedUntil.set(currentY, 0)\n      incomingReads.forEach(incReadElementIndices => {\n        const incRead = state.reads[incReadElementIndices[0]]!\n        const incReadPathElement = incRead.path[incReadElementIndices[1]]!\n        if (\n          incReadPathElement.y !== undefined &&\n          incReadPathElement.y >= currentY\n        ) {\n          incReadPathElement.y += read.width\n          setOccupiedUntil(\n            occupiedUntil,\n            incRead,\n            incReadElementIndices[1],\n            incReadPathElement.y,\n            node,\n          )\n        }\n      })\n      currentY += read.width\n      maxY += read.width\n    }\n  })\n\n  internalReads.sort((a, b) => compareInternalReads(state, a, b))\n\n  internalReads.forEach(readIdx => {\n    const currentRead = state.reads[readIdx]!\n    const firstNodeOffset = currentRead.firstNodeOffset ?? 0\n    const finalNodeCoverLength = currentRead.finalNodeCoverLength ?? 0\n    currentY = startY\n    while (\n      firstNodeOffset < (occupiedUntil.get(currentY) ?? -Infinity) + 2 ||\n      finalNodeCoverLength > (occupiedFrom.get(currentY) ?? Infinity) - 3\n    ) {\n      currentY += currentRead.width\n    }\n    currentRead.path[0]!.y = currentY\n    occupiedUntil.set(currentY, finalNodeCoverLength)\n    maxY = Math.max(maxY, currentY)\n  })\n\n  // adjust node height and move other nodes vertically down\n  const heightIncrease = maxY - node.y - node.contentHeight\n  node.contentHeight += heightIncrease\n  adjustVertically3(state, node, heightIncrease)\n}\n\n// The decorated sort key for one incoming read segment; see the comment in\n// placeReadSet for how it is derived\ninterface IncomingReadKey {\n  decisionStep: number\n  y: number | undefined\n}\n\n// Smaller decisionStep wins. On a tie, entries that walked off the front of the\n// path (no defined y) sort first and tie with each other; otherwise compare y.\nfunction compareIncomingReadKeys(\n  a: IncomingReadKey,\n  b: IncomingReadKey,\n): number {\n  if (a.decisionStep !== b.decisionStep) {\n    return a.decisionStep - b.decisionStep\n  }\n  if (a.y === undefined || b.y === undefined) {\n    return (a.y === undefined ? 0 : 1) - (b.y === undefined ? 0 : 1)\n  }\n  return a.y - b.y\n}\n\n// keeps track of where reads end within nodes\nfunction setOccupiedUntil(\n  map: Map<number, number>,\n  read: Track,\n  pathIndex: number,\n  y: number,\n  node: Node,\n): void {\n  map.set(\n    y,\n    pathIndex === read.path.length - 1\n      ? (read.finalNodeCoverLength ?? 0)\n      : node.sequenceLength,\n  )\n}\n\ninterface ElementWithoutNode {\n  readIndex: number\n  pathIndex: number\n  previousY: number | undefined\n  previousNode: number | null | undefined\n}\n\n// compare read segments which are outside of nodes to sort them in a good horizontal\n// and then vertical display order.\nfunction compareNoNodeReads(\n  state: LayoutState,\n  a: ElementWithoutNode,\n  b: ElementWithoutNode,\n): number {\n  const readA = state.reads[a.readIndex]!\n  const readB = state.reads[b.readIndex]!\n  const segmentA = readA.path[a.pathIndex]!\n  const segmentB = readB.path[b.pathIndex]!\n  // Sort by order by segments\n  if (segmentA.order !== segmentB.order) {\n    return segmentA.order - segmentB.order\n  }\n  // Sort by reads' source track\n  if (readA.sourceTrackID !== readB.sourceTrackID) {\n    return readA.sourceTrackID - readB.sourceTrackID\n  }\n  // Sort by order of previous node\n  if (a.previousNode && b.previousNode) {\n    const prevNodeA = state.nodes[a.previousNode]\n    const prevNodeB = state.nodes[b.previousNode]\n    if (prevNodeA && prevNodeB && prevNodeA.order !== prevNodeB.order) {\n      return prevNodeA.order - prevNodeB.order\n    }\n  }\n  // Segments on the reverse-going part of a cycle go below the rest, in\n  // reverse order, so a loop that starts on the outside stays there and rolls\n  // up in order with the other loops.\n  const aPrev = a.previousY ?? 0\n  const bPrev = b.previousY ?? 0\n  const aReverse = segmentA.betweenCycleReverseTraversal === true\n  const bReverse = segmentB.betweenCycleReverseTraversal === true\n  if (aReverse !== bReverse) {\n    return aReverse ? 1 : -1\n  }\n  return aReverse ? bPrev - aPrev : aPrev - bPrev\n}\n\n// Order reads leaving a node by the y of each one's last placed segment, else\n// by the node where their paths part, else by where each starts and ends\nfunction compareReadOutgoingSegmentsByGoingTo(\n  state: LayoutState,\n  [readIndexA, pathIndexA]: [number, number],\n  [readIndexB, pathIndexB]: [number, number],\n): number {\n  const readA = state.reads[readIndexA]!\n  const readB = state.reads[readIndexB]!\n  const lastYA = readA.path.findLast(seg => seg.y !== undefined)?.y\n  const lastYB = readB.path.findLast(seg => seg.y !== undefined)?.y\n  if (lastYA !== undefined && lastYB !== undefined) {\n    return lastYA - lastYB\n  }\n\n  const nodeAt = (read: Track, i: number) => {\n    const node = read.path[i]?.node\n    return node === null || node === undefined\n      ? null\n      : (state.nodes[node] ?? null)\n  }\n  const nextVisit = (read: Track, i: number) => {\n    let next = i + 1\n    while (read.path[next]?.node === null) {\n      next += 1\n    }\n    return next\n  }\n  let nodeA = nodeAt(readA, pathIndexA)\n  let nodeB = nodeAt(readB, pathIndexB)\n  while (nodeA !== null && nodeA === nodeB) {\n    pathIndexA = nextVisit(readA, pathIndexA)\n    pathIndexB = nextVisit(readB, pathIndexB)\n    nodeA = nodeAt(readA, pathIndexA)\n    nodeB = nodeAt(readB, pathIndexB)\n  }\n  if (nodeA !== null && nodeB !== null) {\n    return compareNodesByOrder(nodeA, nodeB)\n  }\n  if (nodeA !== null || nodeB !== null) {\n    return nodeA === null ? -1 : 1\n  }\n  return (\n    (readA.firstNodeOffset ?? 0) - (readB.firstNodeOffset ?? 0) ||\n    (readA.finalNodeCoverLength ?? 0) - (readB.finalNodeCoverLength ?? 0)\n  )\n}\n\n// Compare tracks based on ordering at their first convergence\nfunction compareTrackByInitialOrdering(trackA: Track, trackB: Track): number {\n  // Find the first node where the two tracks converge, sort by layer.\n  const pathA = trackA.path\n  const pathB = trackB.path\n\n  let AIndex = 0\n  let BIndex = 0\n  while (AIndex < pathA.length && BIndex < pathB.length) {\n    const a = pathA[AIndex]!\n    const b = pathB[BIndex]!\n    const trackAOrder = a.order\n    const trackBOrder = b.order\n    if (trackAOrder === trackBOrder && a.node && b.node) {\n      return (b.y ?? 0) - (a.y ?? 0)\n    } else if (trackAOrder < trackBOrder) {\n      AIndex += 1\n    } else if (trackAOrder > trackBOrder) {\n      BIndex += 1\n    } else {\n      // Orders are equal but are traversing out of nodes\n      AIndex += 1\n      BIndex += 1\n    }\n  }\n\n  // Tracks do not converge, keep the same ordering\n  return 0\n}\n\n// compare 2 reads which are completely within a single node\nfunction compareInternalReads(\n  state: LayoutState,\n  idxA: number,\n  idxB: number,\n): number {\n  const a = state.reads[idxA]!\n  const b = state.reads[idxB]!\n  return (\n    (a.firstNodeOffset ?? 0) - (b.firstNodeOffset ?? 0) ||\n    (a.finalNodeCoverLength ?? 0) - (b.finalNodeCoverLength ?? 0)\n  )\n}\n\n// determine biggest y-coordinate for each order-value\nfunction calculateBottomY(state: LayoutState): number[] {\n  const bottomY = new Array<number>(state.maxOrder + 1).fill(0)\n\n  state.nodes.forEach((node: MaybeUnplacedNode) => {\n    if (node.y !== undefined) {\n      bottomY[node.order] = Math.max(\n        bottomY[node.order]!,\n        node.y + node.contentHeight + 20,\n      )\n    }\n  })\n\n  state.tracks.forEach(track => {\n    track.path.forEach(element => {\n      bottomY[element.order] = Math.max(\n        bottomY[element.order]!,\n        (element.y ?? 0) + track.width,\n      )\n    })\n  })\n  return bottomY\n}\n\n// The segments a track draws, in order: one per node visit, plus one per\n// order slot it passes or turns around in without visiting a node. They carry\n// no lanes or coordinates yet.\nfunction basicPath(state: LayoutState, track: Track): Segment[] {\n  const path: Segment[] = []\n  const pass = (order: number, isForward: boolean): void => {\n    path.push({ order, isForward, node: null })\n  }\n  const visit = (order: number, isForward: boolean, node: number): void => {\n    path.push({ order, isForward, node })\n  }\n\n  let currentNodeIndex = Math.abs(track.indexSequence[0]!)\n  let currentNodeIsForward = isForwardIndex(track.indexSequence[0]!)\n  let currentNode = state.nodes[currentNodeIndex]!\n  visit(currentNode.order, currentNodeIsForward, currentNodeIndex)\n\n  for (let i = 1; i < track.sequence.length; i += 1) {\n    const previousNode = currentNode\n    const previousNodeIsForward = currentNodeIsForward\n    currentNodeIndex = Math.abs(track.indexSequence[i]!)\n    currentNodeIsForward = isForwardIndex(track.indexSequence[i]!)\n    currentNode = state.nodes[currentNodeIndex]!\n    const { order } = currentNode\n\n    if (order > previousNode.order) {\n      if (!previousNodeIsForward) {\n        pass(previousNode.order, true)\n      }\n      for (let j = previousNode.order + 1; j < order; j += 1) {\n        pass(j, true)\n      }\n      if (!currentNodeIsForward) {\n        pass(order, true)\n      }\n    } else if (order < previousNode.order) {\n      if (previousNodeIsForward) {\n        pass(previousNode.order, false)\n      }\n      for (let j = previousNode.order - 1; j > order; j -= 1) {\n        pass(j, false)\n      }\n      if (currentNodeIsForward) {\n        pass(order, false)\n      }\n    } else if (currentNodeIsForward === previousNodeIsForward) {\n      pass(order, !currentNodeIsForward)\n    }\n    visit(order, currentNodeIsForward, currentNodeIndex)\n  }\n  return path\n}\n\n// Turn each read that visits only reverse nodes around to visit them forward\nfunction reverseReversedReads(\n  state: LayoutState,\n  reads: readonly Track[] = state.reads,\n): void {\n  reads.forEach(read => {\n    if (!read.sequence.every(isReverse)) {\n      return\n    }\n    // each turn flips the strand, since a later node switch can turn a read\n    // back and a read can arrive already flagged reverse\n    read.is_reverse = read.is_reverse !== true\n    read.sequence = read.sequence.toReversed().map(forward)\n    if (read.sequenceNew !== undefined) {\n      read.sequenceNew = read.sequenceNew.toReversed()\n    }\n    for (const entry of read.sequenceNew ?? []) {\n      entry.nodeName = forward(entry.nodeName)\n      const { sequenceLength } = nodeByName(state, entry.nodeName)\n      entry.mismatches = entry.mismatches.map(mm =>\n        mirroredMismatch(mm, sequenceLength),\n      )\n    }\n\n    const firstOffset = read.firstNodeOffset ?? 0\n    const firstLen = nodeByName(state, read.sequence[0]!).sequenceLength\n    const lastLen = nodeByName(state, read.sequence.at(-1)!).sequenceLength\n    read.firstNodeOffset = firstLen - (read.finalNodeCoverLength ?? 0)\n    read.finalNodeCoverLength = lastLen - firstOffset\n  })\n}\n\n// A mismatch on the opposite strand: its position counted from the node's\n// other end and its bases reverse-complemented. The pivot is sequenceLength,\n// not node.width, because positions count bases.\nexport function mirroredMismatch(\n  mm: Mismatch,\n  sequenceLength: number,\n): Mismatch {\n  const span =\n    mm.type === 'insertion'\n      ? 0\n      : mm.type === 'deletion'\n        ? (mm.length ?? 0)\n        : (mm.seq?.length ?? 0)\n  return {\n    ...mm,\n    pos: sequenceLength - mm.pos - span,\n    ...(mm.seq !== undefined && { seq: getReverseComplement(mm.seq) }),\n  }\n}\n\nconst COMPLEMENT: Record<string, string> = { A: 'T', T: 'A', C: 'G', G: 'C' }\n\nfunction getReverseComplement(s: string): string {\n  let result = ''\n  for (let i = s.length - 1; i >= 0; i -= 1) {\n    result += COMPLEMENT[s.charAt(i)] ?? 'N'\n  }\n  return result\n}\n\n// for each track: generate sequence of node indices from seq. of node names.\n// Tracks revisit the same names, so each name resolves once per call.\nfunction generateTrackIndexSequences(\n  state: LayoutState,\n  tracksOrReads: Track[],\n): void {\n  const signedIndexOf = new Map<string, number>()\n  tracksOrReads.forEach(track => {\n    track.indexSequence = track.sequence.map(nodeName => {\n      let signed = signedIndexOf.get(nodeName)\n      if (signed === undefined) {\n        const index = state.nodeMap.get(forward(nodeName))\n        if (index === undefined) {\n          throw new Error(\n            `Track ${track.name ?? track.id} visits unknown node ${nodeName}`,\n          )\n        }\n        signed = isReverse(nodeName) ? -index : index\n        signedIndexOf.set(nodeName, signed)\n      }\n      return signed\n    })\n  })\n}\n\n// Tracks enter and leave a node this far outside it horizontally\nconst NODE_HORIZONTAL_SLACK = 20\n\n// The box around every node outline and track shape. A turnaround's corners\n// reach no further out than its vertical rectangles, so the rectangles and\n// curves stand in for them.\nfunction getImageDimensions(state: LayoutState): ImageBounds {\n  const bounds: ImageBounds = {\n    minX: Infinity,\n    maxX: -Infinity,\n    minY: Infinity,\n    maxY: -Infinity,\n  }\n\n  const { rectangles, verticalRectangles, curves } = state.shapes\n  for (const shapes of [rectangles, verticalRectangles, curves]) {\n    for (const { xStart, xEnd } of shapes) {\n      bounds.minX = Math.min(bounds.minX, xStart, xEnd)\n      bounds.maxX = Math.max(bounds.maxX, xStart, xEnd)\n    }\n  }\n\n  state.nodes.forEach((node: MaybeUnplacedNode) => {\n    if (node.x !== undefined) {\n      bounds.minX = Math.min(bounds.minX, node.x - 9)\n      bounds.maxX = Math.max(\n        bounds.maxX,\n        node.x + NODE_HORIZONTAL_SLACK + node.pixelWidth,\n      )\n    }\n    if (node.y !== undefined) {\n      bounds.minY = Math.min(bounds.minY, node.y - 10)\n      bounds.maxY = Math.max(bounds.maxY, node.y + node.contentHeight + 10)\n    }\n  })\n\n  state.tracks.forEach(track => {\n    track.path.forEach(segment => {\n      const y = segment.y ?? 0\n      bounds.maxY = Math.max(bounds.maxY, y + track.width)\n      bounds.minY = Math.min(bounds.minY, y)\n    })\n  })\n\n  return bounds\n}\n\n// Resolve a (possibly reverse-oriented) node name to its layout node. Every\n// caller runs after generateNodeMap, so a miss is a programming error.\nfunction nodeByName(state: LayoutState, nodeName: string): LayoutNode {\n  const index = state.nodeMap.get(forward(nodeName))\n  const node = index === undefined ? undefined : state.nodes[index]\n  if (node === undefined) {\n    throw new Error(`Unknown node ${nodeName}`)\n  }\n  return node\n}\n\n// map node names to node indices\nfunction generateNodeMap(state: LayoutState): Map<string, number> {\n  const nodeMap = new Map<string, number>()\n  state.nodes.forEach((node, index) => {\n    nodeMap.set(node.name, index)\n  })\n  return nodeMap\n}\n\n// adds a successor-array to each node containing the indices of the nodes coming directly after the current node\nfunction generateNodeSuccessors(state: LayoutState): void {\n  const successorSets: Set<number>[] = state.nodes.map(() => new Set())\n  const predecessorSets: Set<number>[] = state.nodes.map(() => new Set())\n\n  const addEdges = (track: Track): void => {\n    for (let i = 0; i < track.indexSequence.length - 1; i += 1) {\n      const current = Math.abs(track.indexSequence[i]!)\n      const follower = Math.abs(track.indexSequence[i + 1]!)\n      successorSets[current]!.add(follower)\n      predecessorSets[follower]!.add(current)\n    }\n  }\n\n  state.tracks.forEach(addEdges)\n  state.reads.forEach(addEdges)\n\n  state.nodes.forEach((node, i) => {\n    node.successors = Array.from(successorSets[i]!)\n    node.predecessors = Array.from(predecessorSets[i]!)\n  })\n}\n\nfunction generateNodeOrderOfSingleTrack(\n  state: LayoutState,\n  sequence: number[],\n): void {\n  let forwardOrder = 0\n  let backwardOrder = 0\n  let minOrder = 0\n\n  sequence.forEach(nodeIndex => {\n    const idx = Math.abs(nodeIndex)\n    if (nodeIndex < 0) {\n      const order = (state.nodeOrders[idx] ??= backwardOrder)\n      if (order < minOrder) {\n        minOrder = order\n      }\n      forwardOrder = order\n      backwardOrder = order - 1\n    } else {\n      const order = (state.nodeOrders[idx] ??= forwardOrder)\n      forwardOrder = order + 1\n      backwardOrder = order\n    }\n  })\n  if (minOrder < 0) {\n    increaseOrderForAllNodes(state, -minOrder)\n  }\n}\n\n// calculate the order-value of nodes contained in sequence which are to the left of the first node which already has an order-value\nfunction generateNodeOrderTrackBeginning(\n  state: LayoutState,\n  sequence: number[],\n): number | null {\n  let anchorIndex = 0\n  let minOrder = 0\n\n  while (\n    anchorIndex < sequence.length &&\n    state.nodeOrders[Math.abs(sequence[anchorIndex]!)] === undefined\n  ) {\n    anchorIndex += 1 // anchor = first node in common with existing graph\n  }\n  if (anchorIndex >= sequence.length) {\n    return null\n  }\n\n  const anchorSeqVal = sequence[anchorIndex]!\n  let currentOrder: number\n  let increment: number\n  if (anchorSeqVal >= 0) {\n    currentOrder = state.nodeOrders[anchorSeqVal]! - 1\n    increment = -1\n  } else {\n    currentOrder = state.nodeOrders[-anchorSeqVal]! + 1\n    increment = 1\n  }\n\n  for (let j = anchorIndex - 1; j >= 0; j -= 1) {\n    // assign order to nodes which are left of anchor node\n    const idx = Math.abs(sequence[j]!)\n    if (state.nodeOrders[idx] === undefined) {\n      state.nodeOrders[idx] = currentOrder\n      minOrder = Math.min(minOrder, currentOrder)\n      currentOrder += increment\n    }\n  }\n\n  if (minOrder < 0) {\n    increaseOrderForAllNodes(state, -minOrder)\n  }\n  return anchorIndex\n}\n\n// Sentinel order for nodes no track or read reaches.\nexport const UNREACHABLE_ORDER = -1\n\n// Replace every unassigned entry, holes included, with UNREACHABLE_ORDER\nfunction fillUnassignedOrders(\n  orders: readonly (number | undefined)[],\n): number[] {\n  return Array.from(orders, order => order ?? UNREACHABLE_ORDER)\n}\n\n// increaseOrderForSuccessors can move every node off an order, and\n// generateSVGShapesFromPath has no x for a lane change at an empty order, so\n// the used orders are renumbered 0, 1, 2, ...\nfunction compactOrders(orders: readonly number[]): number[] {\n  const used = [...new Set(orders.filter(order => order >= 0))].sort(\n    (a, b) => a - b,\n  )\n  const rank = new Map(used.map((order, i) => [order, i]))\n  return orders.map(order => rank.get(order) ?? order)\n}\n\n// generate global sequence of nodes from left to right, starting with first track and adding other tracks sequentially\nfunction generateNodeOrder(state: LayoutState): void {\n  let modifiedSequence: number[]\n  let currentOrder: number\n  let rightIndex: number | null\n  let leftIndex: number\n  let minOrder = 0\n  const tracksAndReads = state.tracks.concat(state.reads)\n  const reachability: ReachabilityScratch = {\n    stamp: new Int32Array(state.nodes.length),\n    generation: 0,\n  }\n\n  // fill() makes the array dense: `new Array(n)` alone is all holes, which\n  // forEach skips, so neither the sentinel pass nor the copy-back below ran.\n  state.nodeOrders = new Array<number | undefined>(state.nodes.length).fill(\n    undefined,\n  )\n  // Widened to Node, whose order is optional, to clear the previous run's orders\n  state.nodes.forEach((node: Node) => {\n    node.order = undefined\n  })\n\n  generateNodeOrderOfSingleTrack(state, state.tracks[0]!.indexSequence)\n\n  for (let i = 1; i < tracksAndReads.length; i += 1) {\n    rightIndex = generateNodeOrderTrackBeginning(\n      state,\n      tracksAndReads[i]!.indexSequence,\n    )\n    if (rightIndex === null) {\n      if (i < state.tracks.length) {\n        generateNodeOrderOfSingleTrack(state, tracksAndReads[i]!.indexSequence)\n      } else {\n        tracksAndReads.splice(i, 1)\n        state.reads.splice(i - state.tracks.length, 1)\n        i -= 1\n      }\n      continue\n    }\n    modifiedSequence = uninvert(tracksAndReads[i]!.indexSequence)\n\n    while (rightIndex < modifiedSequence.length) {\n      // move right until the end of the sequence\n      leftIndex = rightIndex\n      rightIndex += 1\n      while (\n        rightIndex < modifiedSequence.length &&\n        state.nodeOrders[modifiedSequence[rightIndex]!] === undefined\n      ) {\n        rightIndex += 1\n      }\n\n      if (rightIndex < modifiedSequence.length) {\n        // middle segment between two anchors\n        currentOrder = state.nodeOrders[modifiedSequence[leftIndex]!]! + 1\n        for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n          state.nodeOrders[modifiedSequence[j]!] = currentOrder\n          currentOrder += 1\n        }\n\n        if (\n          state.nodeOrders[modifiedSequence[rightIndex]!]! >\n          state.nodeOrders[modifiedSequence[leftIndex]!]!\n        ) {\n          if (state.nodeOrders[modifiedSequence[rightIndex]!]! < currentOrder) {\n            increaseOrderForSuccessors(\n              state,\n              modifiedSequence[rightIndex]!,\n              modifiedSequence[rightIndex - 1]!,\n              currentOrder,\n            )\n          }\n        } else {\n          if (\n            tracksAndReads[i]!.indexSequence[rightIndex]! >= 0 &&\n            !isSuccessor(\n              state,\n              modifiedSequence[rightIndex]!,\n              modifiedSequence[leftIndex]!,\n              reachability,\n            )\n          ) {\n            // no real reversal\n            increaseOrderForSuccessors(\n              state,\n              modifiedSequence[rightIndex]!,\n              modifiedSequence[rightIndex - 1]!,\n              currentOrder,\n            )\n          } else {\n            // real reversal\n            if (\n              tracksAndReads[i]!.indexSequence[leftIndex]! < 0 ||\n              (state.nodes[modifiedSequence[leftIndex + 1]!]!.degree < 2 &&\n                state.nodeOrders[modifiedSequence[rightIndex]!]! <\n                  state.nodeOrders[modifiedSequence[leftIndex]!]!)\n            ) {\n              currentOrder = state.nodeOrders[modifiedSequence[leftIndex]!]! - 1\n              for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n                state.nodeOrders[modifiedSequence[j]!] = currentOrder\n                minOrder = Math.min(minOrder, currentOrder)\n                currentOrder -= 1\n              }\n            }\n          }\n        }\n      } else {\n        // right segment to the right of last anchor\n        if (tracksAndReads[i]!.indexSequence[leftIndex]! >= 0) {\n          // elongate towards the right\n          currentOrder = state.nodeOrders[modifiedSequence[leftIndex]!]! + 1\n          for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n            const idx = modifiedSequence[j]!\n            if (state.nodeOrders[idx] === undefined) {\n              state.nodeOrders[idx] = currentOrder\n              currentOrder += 1\n            }\n          }\n        } else {\n          // elongate towards the left\n          currentOrder = state.nodeOrders[modifiedSequence[leftIndex]!]! - 1\n          for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n            const idx = modifiedSequence[j]!\n            if (state.nodeOrders[idx] === undefined) {\n              state.nodeOrders[idx] = currentOrder\n              minOrder = Math.min(minOrder, currentOrder)\n              currentOrder -= 1\n            }\n          }\n        }\n      }\n    }\n  }\n\n  if (minOrder < 0) {\n    increaseOrderForAllNodes(state, -minOrder)\n  }\n\n  // Nodes unreachable from any track get UNREACHABLE_ORDER so every node ends\n  // up with a defined order; downstream code uses `order >= 0` to skip them.\n  state.nodeOrders = compactOrders(fillUnassignedOrders(state.nodeOrders))\n  state.nodes.forEach((node, i) => {\n    node.order = state.nodeOrders[i]!\n  })\n}\n\n// Reusable visited-set for the reachability searches in generateNodeOrder.\n// Stamping with a generation counter avoids reallocating (and re-zeroing) an\n// array of nodes.length booleans on every call.\ninterface ReachabilityScratch {\n  stamp: Int32Array\n  generation: number\n}\n\nfunction isSuccessor(\n  state: LayoutState,\n  first: number,\n  second: number,\n  scratch: ReachabilityScratch,\n): boolean {\n  scratch.generation += 1\n  const { stamp, generation } = scratch\n  const stack: number[] = [first]\n  stamp[first] = generation\n  while (stack.length > 0) {\n    const current = stack.pop()!\n    if (current === second) {\n      return true\n    }\n    for (const childIndex of state.nodes[current]!.successors) {\n      if (stamp[childIndex] !== generation) {\n        stamp[childIndex] = generation\n        stack.push(childIndex)\n      }\n    }\n  }\n  return false\n}\n\n// get order number of the rightmost node\nfunction getMaxOrder(state: LayoutState): number {\n  let max = -1\n  state.nodeOrders.forEach(order => {\n    if (order !== undefined && order > max) {\n      max = order\n    }\n  })\n  return max\n}\n\n// generates sequence keeping the order but switching all reversed (negative) nodes to forward nodes\nfunction uninvert(sequence: number[]): number[] {\n  return sequence.map(v => Math.abs(v))\n}\n\n// increases the order-value of all nodes by amount\nfunction increaseOrderForAllNodes(state: LayoutState, amount: number): void {\n  state.nodeOrders.forEach((order, i) => {\n    if (order !== undefined) {\n      state.nodeOrders[i] = order + amount\n    }\n  })\n}\n\n// increases the order-value for currentNode and (if necessary) successor nodes recursively\nfunction increaseOrderForSuccessors(\n  state: LayoutState,\n  startingNode: number,\n  tabuNode: number,\n  newOrder: number,\n): void {\n  const increasedOrders = new Map<number, number>()\n  // Walked with a head pointer rather than shift(), which is O(length) per pop.\n  const queue: [number, number][] = [[startingNode, newOrder]]\n  let head = 0\n\n  while (head < queue.length) {\n    const [currentNode, currentOrder] = queue[head]!\n    head += 1\n    const currentNodeOrder = state.nodeOrders[currentNode]\n\n    if (currentNodeOrder !== undefined && currentNodeOrder < currentOrder) {\n      if ((increasedOrders.get(currentNode) ?? -Infinity) < currentOrder) {\n        increasedOrders.set(currentNode, currentOrder)\n        state.nodes[currentNode]!.successors.forEach(successor => {\n          if (\n            state.nodeOrders[successor]! > currentNodeOrder &&\n            successor !== tabuNode\n          ) {\n            // only increase order of successors to the right of currentNode\n            queue.push([successor, currentOrder + 1])\n          }\n        })\n        if (currentNode !== startingNode) {\n          state.nodes[currentNode]!.predecessors.forEach(predecessor => {\n            if (\n              state.nodeOrders[predecessor]! > currentNodeOrder &&\n              predecessor !== tabuNode\n            ) {\n              // only increase order of predecessors to the right of currentNode\n              queue.push([predecessor, currentOrder + 1])\n            }\n          })\n        }\n      }\n    }\n  }\n\n  increasedOrders.forEach((value, key) => {\n    state.nodeOrders[key] = value\n  })\n}\n\n// calculates the node degree: the number of tracks passing through the node / the node height\nfunction generateNodeDegree(state: LayoutState): void {\n  state.nodes.forEach(node => {\n    node.tracks = []\n  })\n\n  state.tracks.forEach(track => {\n    track.indexSequence.forEach(nodeIndex => {\n      state.nodes[Math.abs(nodeIndex)]!.tracks.push(track.id)\n    })\n  })\n\n  state.nodes.forEach(node => {\n    node.degree = node.tracks.length\n  })\n}\n\n// Orient the nodes to suit the tracks and reads\nfunction switchNodeOrientation(state: LayoutState): void {\n  switchNodeOrientationForPaths(\n    state,\n    [...state.tracks.slice(1), ...state.reads],\n    state.tracks[0]!,\n  )\n}\n\n// If more of the given paths pass through a specific node in reverse direction than in\n// regular direction, switch its orientation. Nodes the pivot path visits\n// forward keep theirs. Processes all paths' nodes in place, reading each\n// visit's node from its indexSequence, which must match its sequence.\nfunction switchNodeOrientationForPaths(\n  state: LayoutState,\n  paths: Track[],\n  pivotPath: Track,\n): void {\n  const scores = new Int32Array(state.nodes.length)\n  const onPivot = new Uint8Array(state.nodes.length)\n  for (const nodeName of pivotPath.sequence) {\n    const index = isReverse(nodeName) ? undefined : state.nodeMap.get(nodeName)\n    if (index !== undefined) {\n      onPivot[index] = 1\n    }\n  }\n\n  for (const path of paths) {\n    const { sequence, indexSequence } = path\n    const last = indexSequence.length - 1\n    for (let j = 0; j <= last; j += 1) {\n      const index = Math.abs(indexSequence[j]!)\n      if (onPivot[index] === 1) {\n        continue\n      }\n      const order = state.nodes[index]!.order\n      const prevOrder =\n        j > 0 ? state.nodes[Math.abs(indexSequence[j - 1]!)]!.order : undefined\n      const nextOrder =\n        j < last\n          ? state.nodes[Math.abs(indexSequence[j + 1]!)]!.order\n          : undefined\n      // A reverse visit votes for switching when the path runs left to right\n      // through the node, and against when it runs right to left.\n      const vote = isReverse(sequence[j]!) ? 1 : -1\n      if (\n        (prevOrder === undefined || prevOrder < order) &&\n        (nextOrder === undefined || order < nextOrder)\n      ) {\n        scores[index]! += vote\n      }\n      if (\n        (prevOrder === undefined || prevOrder > order) &&\n        (nextOrder === undefined || order > nextOrder)\n      ) {\n        scores[index]! -= vote\n      }\n    }\n  }\n\n  for (const path of paths) {\n    const { sequence, indexSequence } = path\n    for (let j = 0; j < indexSequence.length; j += 1) {\n      if (scores[Math.abs(indexSequence[j]!)]! > 0) {\n        sequence[j] = flip(sequence[j]!)\n        indexSequence[j] = -indexSequence[j]!\n      }\n    }\n  }\n\n  state.nodes.forEach((node, index) => {\n    if (scores[index]! > 0) {\n      node.seq = getReverseComplement(node.seq)\n      node.switched = true\n    }\n  })\n}\n\n// calculates the concrete values for the nodes' x-coordinates\nfunction generateNodeXCoords(state: LayoutState): void {\n  let currentX = 0\n  let nextX = 20\n  let currentOrder = -1\n  const sortedNodes = state.nodes.slice()\n  sortedNodes.sort(compareNodesByOrder)\n  const extra = calculateExtraSpace(state)\n\n  sortedNodes.forEach(node => {\n    if (node.order >= 0) {\n      if (node.order > currentOrder) {\n        currentOrder = node.order\n        currentX = nextX + 10 * extra[node.order]!\n      }\n      node.x = currentX\n      nextX = Math.max(nextX, currentX + 40 + node.pixelWidth)\n    }\n  })\n}\n\n// A lane change rising or falling this many px or less keeps sequenceTubeMap's\n// slope; one rising further turns steeper\nconst RISE_KNEE = 35\n\n// The extra space, in units of 10 px, that a gap takes for a track rising or\n// falling `rise` px across it. Past RISE_KNEE it grows with the square root of\n// the rise, so a long jump steepens its curve more than it widens the column.\nfunction riseExtra(rise: number): number {\n  return rise <= RISE_KNEE\n    ? rise / 17.5\n    : (RISE_KNEE / 17.5) * Math.sqrt(rise / RISE_KNEE)\n}\n\n// calculates additional horizontal space needed between two nodes\n// two neighboring nodes have to be moved further apart if there is a lot going on in between them\n// -> edges turning to vertical orientation should not overlap\nfunction calculateExtraSpace(state: LayoutState): number[] {\n  const slots = state.maxOrder + 1\n  const leftSideEdges = new Array<number>(slots).fill(0)\n  const rightSideEdges = new Array<number>(slots).fill(0)\n  const fallAngleAdjustment = new Array<number>(slots).fill(0)\n  const extra: number[] = []\n\n  state.tracks.forEach(track => {\n    for (let i = 1; i < track.path.length; i += 1) {\n      const seg = track.path[i]!\n      const prevSeg = track.path[i - 1]!\n      // Track is going to the same node, account for space taken up by edges looping around\n      if (seg.order === prevSeg.order) {\n        // repeat or translocation\n        if (seg.isForward) {\n          leftSideEdges[seg.order]! += 1\n        } else {\n          rightSideEdges[seg.order]! += 1\n        }\n      } else {\n        // TODO: Extra space should also be accounted when there are too many tracks curving at the nodes\n        fallAngleAdjustment[seg.order] = Math.max(\n          riseExtra(Math.abs((seg.y ?? 0) - (prevSeg.y ?? 0))),\n          fallAngleAdjustment[seg.order]!,\n        )\n      }\n    }\n  })\n\n  extra.push(Math.max(0, leftSideEdges[0]! - 1))\n  for (let i = 1; i <= state.maxOrder; i += 1) {\n    // Extra space uses space needed for edges(tracks looping), or space needed to limit rise/fall angle, whichever is larger\n    extra.push(\n      Math.max(\n        Math.max(0, leftSideEdges[i]! - 1) +\n          Math.max(0, rightSideEdges[i - 1]! - 1),\n        fallAngleAdjustment[i]!,\n      ),\n    )\n  }\n  return extra\n}\n\n// Gather each order slot's segments, those visiting one node together, then\n// sweep left to right giving every segment a lane\nfunction generateLaneAssignment(state: LayoutState): void {\n  state.assignments = Array.from({ length: state.maxOrder + 1 }, () => [])\n  const byNode = new Map<number, NodeAssignment>()\n  state.tracks.forEach((track, trackID) => {\n    track.path = basicPath(state, track)\n    track.path.forEach(({ order, node }, segmentID) => {\n      const segment: SegmentAssignment = { trackID, segmentID }\n      const existing = node === null ? undefined : byNode.get(node)\n      if (existing === undefined) {\n        const assignment: NodeAssignment = { node, tracks: [segment] }\n        state.assignments[order]!.push(assignment)\n        if (node !== null) {\n          byNode.set(node, assignment)\n        }\n      } else {\n        existing.tracks.push(segment)\n      }\n    })\n  })\n\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    generateSingleLaneAssignment(state, state.assignments[i]!, i)\n  }\n}\n\n// looks at assignment and sets idealY and idealLane by looking at where the tracks come from\nfunction getIdealLanesAndCoords(\n  state: LayoutState,\n  assignment: NodeAssignment[],\n  order: number,\n): void {\n  assignment.forEach(node => {\n    let laneSum = 0\n    node.tracks.forEach(track => {\n      const from = segmentToTheLeft(\n        state.tracks[track.trackID]!.path,\n        track.segmentID,\n        order - 1,\n      )\n      track.idealLane = from === undefined ? track.trackID : from.lane\n      track.idealY = from === undefined ? null : from.y\n      laneSum += track.idealLane!\n    })\n    node.idealLane = laneSum / node.tracks.length\n  })\n}\n\n// The segment a track's lane follows in from order slot `leftOrder`: its\n// neighbor on either side there, else its last earlier visit to it\nfunction segmentToTheLeft(\n  path: readonly Segment[],\n  segmentID: number,\n  leftOrder: number,\n): Segment | undefined {\n  if (segmentID === 0) {\n    return undefined\n  }\n  if (path[segmentID - 1]!.order === leftOrder) {\n    return path[segmentID - 1]\n  }\n  if (path[segmentID + 1]?.order === leftOrder) {\n    return path[segmentID + 1]\n  }\n  return path.slice(0, segmentID).findLast(seg => seg.order === leftOrder)\n}\n\n// assigns the optimal lanes for a single horizontal position (=order)\n// first an ideal lane is calculated for each track (which is ~ the lane of its predecessor)\n// then the nodes are sorted by their average ideal lane\n// and the whole construct is then moved up or down if necessary\nfunction generateSingleLaneAssignment(\n  state: LayoutState,\n  assignment: NodeAssignment[],\n  order: number,\n): void {\n  let currentLane = 0\n  const potentialAdjustmentValues = new Set<number>()\n  let currentY = 20\n  let prevNameIsNull = false\n  let prevTrack = -1\n\n  getIdealLanesAndCoords(state, assignment, order)\n  assignment.sort(compareByIdealLane)\n\n  assignment.forEach(node => {\n    const placed = node.node === null ? undefined : state.nodes[node.node]!\n    if (placed !== undefined) {\n      if (prevNameIsNull) {\n        currentY -= 10\n      }\n      placed.y = currentY\n      placed.contentHeight = 0\n      prevNameIsNull = false\n    } else {\n      if (prevNameIsNull) {\n        currentY -= 25\n      } else if (currentY > 20) {\n        currentY -= 10\n      }\n      prevNameIsNull = true\n    }\n\n    node.tracks.sort(compareByIdealLane)\n    node.tracks.forEach(track => {\n      const { path, width } = state.tracks[track.trackID]!\n      if (\n        track.trackID === prevTrack &&\n        placed === undefined &&\n        prevNameIsNull\n      ) {\n        currentY += 10\n      }\n      path[track.segmentID]!.lane = currentLane\n      path[track.segmentID]!.y = currentY\n      if (typeof track.idealY === 'number') {\n        potentialAdjustmentValues.add(track.idealY - currentY)\n      }\n      currentLane += 1\n      currentY += width\n      if (placed !== undefined) {\n        placed.contentHeight += width\n      }\n      prevTrack = track.trackID\n    })\n    currentY += 25\n  })\n\n  adjustVertically(state, assignment, potentialAdjustmentValues)\n}\n\n// moves all tracks at a single horizontal location (=order) up/down to minimize lane changes\nfunction adjustVertically(\n  state: LayoutState,\n  assignment: NodeAssignment[],\n  potentialAdjustmentValues: Set<number>,\n): void {\n  let verticalAdjustment = 0\n  let minAdjustmentCost = Number.MAX_SAFE_INTEGER\n\n  potentialAdjustmentValues.forEach(moveBy => {\n    const cost = getVerticalAdjustmentCost(state, assignment, moveBy)\n    if (cost < minAdjustmentCost) {\n      minAdjustmentCost = cost\n      verticalAdjustment = moveBy\n    }\n  })\n\n  assignment.forEach(node => {\n    if (node.node !== null) {\n      state.nodes[node.node]!.y += verticalAdjustment\n    }\n    node.tracks.forEach(track => {\n      const seg = state.tracks[track.trackID]!.path[track.segmentID]!\n      seg.y = seg.y! + verticalAdjustment\n    })\n  })\n}\n\n// Budge down all nodes and out-of-node tracks below this node by this amount\nfunction adjustVertically3(\n  state: LayoutState,\n  node: LayoutNode,\n  adjustBy: number,\n): void {\n  if (node.order < 0 || state.assignments[node.order] === undefined) {\n    return\n  }\n  state.assignments[node.order]!.forEach(assignmentNode => {\n    if (assignmentNode.node !== null) {\n      const aNode = state.nodes[assignmentNode.node]!\n      if (aNode !== node && aNode.y > node.y) {\n        aNode.y += adjustBy\n        assignmentNode.tracks.forEach(track => {\n          const seg = state.tracks[track.trackID]!.path[track.segmentID]!\n          seg.y = seg.y! + adjustBy\n        })\n      }\n    } else {\n      // track-segment not within a node\n      assignmentNode.tracks.forEach(track => {\n        const seg = state.tracks[track.trackID]!.path[track.segmentID]!\n        if (seg.y! >= node.y) {\n          seg.y = seg.y! + adjustBy\n        }\n      })\n    }\n  })\n  state.nodesPerOrder[node.order]!.forEach(nodeIndex => {\n    const other = state.nodes[nodeIndex]!\n    if (other !== node && other.y > node.y) {\n      other.y += adjustBy\n    }\n  })\n}\n\n// calculates cost of vertical adjustment as vertical distance * width of track\nfunction getVerticalAdjustmentCost(\n  state: LayoutState,\n  assignment: NodeAssignment[],\n  moveBy: number,\n): number {\n  let result = 0\n  assignment.forEach(node => {\n    node.tracks.forEach(track => {\n      const { type, path, width } = state.tracks[track.trackID]!\n      if (typeof track.idealY === 'number' && type !== 'read') {\n        result +=\n          Math.abs(track.idealY - moveBy - path[track.segmentID]!.y!) * width\n      }\n    })\n  })\n  return result\n}\n\nfunction compareByIdealLane(\n  a: { idealLane?: number | undefined },\n  b: { idealLane?: number | undefined },\n): number {\n  if (a.idealLane === undefined || b.idealLane === undefined) {\n    return Number(a.idealLane === undefined) - Number(b.idealLane === undefined)\n  }\n  return a.idealLane - b.idealLane\n}\n\nfunction compareNodesByOrder(\n  a: MaybeUnplacedNode,\n  b: MaybeUnplacedNode,\n): number {\n  if (a.order !== b.order) {\n    return a.order - b.order\n  }\n  if (a.y !== undefined && b.y !== undefined) {\n    return a.y - b.y\n  }\n  return 0\n}\n\nfunction calculateTrackWidth(state: LayoutState): void {\n  const NARROW_WIDTH = 4\n  const WIDE_WIDTH = state.config.trackWidth\n\n  if (state.config.freqWidth === 'linear') {\n    for (const track of state.tracks) {\n      track.width =\n        track.type === 'read'\n          ? NARROW_WIDTH\n          : Math.max(1, Math.round(track.freq ?? 1)) * WIDE_WIDTH\n    }\n    return\n  }\n\n  for (const track of state.tracks) {\n    track.width =\n      track.freq !== undefined\n        ? Math.round((Math.log(Math.max(track.freq, 1)) + 1) * NARROW_WIDTH)\n        : track.type === 'read'\n          ? NARROW_WIDTH\n          : WIDE_WIDTH\n  }\n\n  // freqs of 0 and 1 all draw narrow, which means vg gave no real frequencies\n  if (state.tracks.every(track => track.width === NARROW_WIDTH)) {\n    state.tracks.forEach(track => {\n      if (track.freq !== undefined) {\n        track.width = WIDE_WIDTH\n      }\n    })\n  }\n}\n\n// The x of base `base` of a read's visit, counted from the node's left end\n// on a forward visit and from its right end on a reverse one\nfunction readBaseX(state: LayoutState, seg: Segment, base: number): number {\n  const node = state.nodes[seg.node!]!\n  return clampedXCoordinateOfBaseWithinNode(\n    node,\n    seg.isForward ? base : node.sequenceLength - base,\n  )\n}\n\n// returns the x coordinate (in pixels) of (the left side) of the given base\n// position within the given node, or null if the position is past its end\nexport function getXCoordinateOfBaseWithinNode(\n  node: Node,\n  base: number,\n): number | null {\n  if (base > node.sequenceLength) {\n    return null\n  } // equality is allowed\n  return clampedXCoordinateOfBaseWithinNode(node, base)\n}\n\n// Same, but a base outside the node maps to the nearest node edge. Callers that\n// have to produce a coordinate no matter what use this: falling back to 0 would\n// put the shape at the far left of the whole image instead.\nexport function clampedXCoordinateOfBaseWithinNode(\n  node: Node,\n  base: number,\n): number {\n  const [nodeLeftX, nodeRightX] = nodePixelCoordinatesInX(node)\n  if (node.sequenceLength === 0) {\n    return nodeLeftX\n  }\n  const clamped = Math.min(Math.max(base, 0), node.sequenceLength)\n  return nodeLeftX + (clamped / node.sequenceLength) * (nodeRightX - nodeLeftX)\n}\n\n// transforms the info in the tracks' path attribute into actual coordinates\n// and saves them in shapes.rectangles and shapes.curves\nfunction generateSVGShapesFromPath(state: LayoutState): void {\n  state.extraLeft = new Array<number>(state.maxOrder + 1).fill(0)\n  state.extraRight = new Array<number>(state.maxOrder + 1).fill(0)\n\n  // generate x coords where each order starts and ends\n  const orderStartX: number[] = []\n  const orderEndX: number[] = []\n  state.nodes.forEach((node: MaybeUnplacedNode) => {\n    if (node.x !== undefined) {\n      orderStartX[node.order] = node.x\n      orderEndX[node.order] = Math.max(\n        orderEndX[node.order] ?? -Infinity,\n        node.x + node.pixelWidth,\n      )\n    }\n  })\n\n  const reference = state.tracks[0]\n\n  // Helps generation of verticalRectangles, correct increments of extraRight and extraLeft\n  state.tracks.sort(compareTrackByInitialOrdering)\n\n  state.tracks.forEach(track => {\n    const { id, name, type, width, path } = track\n    const rectangle = (xStart: number, xEnd: number, yStart: number): void => {\n      state.shapes.rectangles.push({\n        xStart: Math.min(xStart, xEnd),\n        yStart,\n        xEnd: Math.max(xStart, xEnd),\n        yEnd: yStart + width - 1,\n        id,\n        name,\n        type,\n      })\n    }\n    const exitX = (seg: Segment) =>\n      seg.isForward ? orderEndX[seg.order]! : orderStartX[seg.order]!\n\n    const first = path[0]!\n    let yStart = first.y!\n    let xStart =\n      type === 'read'\n        ? readBaseX(state, first, track.firstNodeOffset ?? 0)\n        : first.isForward\n          ? orderStartX[first.order]! - 20\n          : orderEndX[first.order]! + 20\n\n    for (let i = 1; i < path.length; i += 1) {\n      const prev = path[i - 1]!\n      const seg = path[i]!\n      if (seg.y === yStart) {\n        continue\n      }\n      const xEnd = exitX(prev)\n      if (xEnd !== xStart) {\n        rectangle(xStart, xEnd, yStart)\n      }\n      const yEnd = seg.y!\n      const step = seg.order - prev.order\n      if (step === 1 || step === -1) {\n        const xNext =\n          step === 1 ? orderStartX[seg.order]! : orderEndX[seg.order]!\n        state.shapes.curves.push({\n          xStart: step === 1 ? xEnd : xEnd + 1,\n          yStart,\n          xEnd: step === 1 ? xNext + 1 : xNext,\n          yEnd,\n          width,\n          id,\n          name,\n          type,\n          nodeStart: prev.node,\n          nodeEnd: seg.node,\n          orderStart: prev.order,\n          orderEnd: seg.order,\n          ...(track === reference ? { reference: true } : {}),\n        })\n        xStart = xNext\n      } else {\n        generateTurnaround(\n          state,\n          track,\n          prev.isForward ? 1 : -1,\n          xEnd,\n          yStart,\n          yEnd,\n          seg.order,\n        )\n        xStart = xEnd\n      }\n      yStart = yEnd\n    }\n\n    const last = path[path.length - 1]!\n    const xEnd =\n      type === 'read'\n        ? readBaseX(state, last, track.finalNodeCoverLength ?? 0)\n        : exitX(last) + (last.isForward ? 20 : -20)\n    rectangle(xStart, xEnd, yStart)\n  })\n}\n\n// Sankey-mode synthesis: one synthetic \"read\" per (srcSigned \u2192 dstSigned) edge,\n// fed through the normal placeReads/generateSVGShapesFromPath pipeline so the\n// band gets the same lane assignment, loop topology and bezier shape as a real\n// read. A read band takes its source's palette; a haplotype band carries its\n// share of the haplotypes for the colorer to shade by.\n//\n// Synthetic-track ids live above this base so they don't collide with real\n// track ids and so click/hover handlers can show count info instead of the\n// per-read info dialog.\nconst COARSENED_ID_BASE = 1_000_000_000\nexport const isCoarsenedId = (id: number) => id >= COARSENED_ID_BASE\n\n// Build one synthetic read per (srcSigned \u2192 dstSigned) edge in `source`\n// (real reads, or the alt haplotype tracks). The synthetic reads replace the\n// real ones BEFORE placeReads runs, so:\n//   \u2022 placeReads sees N_edges reads instead of N_reads (huge node-height win),\n//   \u2022 each band gets a lane and an \"right-down-left-up-right\" loop topology\n//     for free (placeReads handles reversals and out-of-order jumps),\n//   \u2022 generateSVGShapesFromPath emits exactly one TrackCurve per band using\n//     the same bezier as a real read \u2014 no special draw path needed.\n//\n// The synthetic track's `sequence` is just the two signed node names. After\n// generateTrackIndexSequences runs, indexSequence is set and the rest of the\n// layout follows.\nfunction buildCoarsenedSyntheticBands(\n  state: LayoutState,\n  source: Track[],\n  unit: CoarsenedUnit,\n  firstId: number,\n): { bands: Track[]; total: number } {\n  // Aggregate by signed-edge key. Preserve orientation so e.g. (+A\u2192+B) and\n  // (-B\u2192-A) stack as separate bands \u2014 they're different visual flows.\n  interface EdgeAgg {\n    sSigned: number\n    dSigned: number\n    sName: string\n    dName: string\n    // distinct walks, so a walk that loops back over an edge, or crosses it\n    // both ways under ignoreStrand, counts once\n    count: number\n    // every crossing, loops included, which is what sizes the band\n    crossings: number\n    sourceTrackID: number\n    lastSource: number\n  }\n  const edges = new Map<number, EdgeAgg>()\n  let total = 0\n  // One number per signed edge: signed indices run from -span to span.\n  const span = state.nodes.length\n  const edgeKey = (s: number, d: number): number =>\n    (s + span) * (2 * span + 1) + d + span\n  // When ignoring strand, (+A\u2192+B) and (-B\u2192-A) refer to the same underlying\n  // graph connection, so both collapse into the smaller of their two keys;\n  // whichever orientation is seen first determines the visual band direction.\n  const ignoreStrand = state.config.ignoreStrand\n  for (const [sourceIndex, item] of source.entries()) {\n    // a deduplicated walk stands for `freq` identical haplotypes\n    const weight = Math.max(item.freq ?? 1, 1)\n    total += weight\n    const seq = item.indexSequence\n    if (seq.length < 2) {\n      continue\n    }\n    for (let i = 0; i < seq.length - 1; i += 1) {\n      const sSigned = seq[i]!\n      const dSigned = seq[i + 1]!\n      const srcNode = state.nodes[Math.abs(sSigned)]!\n      const dstNode = state.nodes[Math.abs(dSigned)]!\n      const key = ignoreStrand\n        ? Math.min(edgeKey(sSigned, dSigned), edgeKey(-dSigned, -sSigned))\n        : edgeKey(sSigned, dSigned)\n      const existing = edges.get(key)\n      if (existing === undefined) {\n        edges.set(key, {\n          sSigned,\n          dSigned,\n          sName: sSigned < 0 ? `-${srcNode.name}` : srcNode.name,\n          dName: dSigned < 0 ? `-${dstNode.name}` : dstNode.name,\n          count: weight,\n          crossings: weight,\n          sourceTrackID: item.sourceTrackID,\n          lastSource: sourceIndex,\n        })\n      } else {\n        existing.crossings += weight\n        if (existing.lastSource !== sourceIndex) {\n          existing.count += weight\n          existing.lastSource = sourceIndex\n        }\n      }\n    }\n  }\n\n  // Square-root scaling on crossings gives heavy edges visible weight without\n  // letting one massive edge dwarf everything else. Min stays near READ_WIDTH\n  // so single-read edges still look like a normal read; max is generous so\n  // hot edges read as obvious \"highways.\"\n  let maxEdgeCount = 0\n  for (const e of edges.values()) {\n    if (e.crossings > maxEdgeCount) {\n      maxEdgeCount = e.crossings\n    }\n  }\n  const BAND_MIN_WIDTH = READ_WIDTH\n  const BAND_MAX_WIDTH = 60\n  const widthForCount = (c: number): number => {\n    if (maxEdgeCount <= 1) {\n      return BAND_MIN_WIDTH\n    }\n    return (\n      BAND_MIN_WIDTH +\n      (BAND_MAX_WIDTH - BAND_MIN_WIDTH) * Math.sqrt(c / maxEdgeCount)\n    )\n  }\n\n  const synthetic: Track[] = []\n  let i = 0\n  for (const edge of edges.values()) {\n    const id = firstId + i\n    const share =\n      unit === 'haplotype' ? { count: edge.count, total } : undefined\n    const shareText = share === undefined ? '' : ` (${formatShare(share)})`\n    const crossingsText =\n      edge.crossings === edge.count\n        ? ''\n        : `, ${edge.crossings.toLocaleString()} crossings`\n    const label = `${edge.count.toLocaleString()} ${unit}${edge.count === 1 ? '' : 's'}${shareText}${crossingsText}: Node ${edge.sName} \u2192 Node ${edge.dName}`\n    state.coarsenedEdgeMeta.set(id, { count: edge.count, label })\n    // Place each synthetic band so it touches *only* its endpoint nodes' edges:\n    //   \u2022 firstNodeOffset = src.sequenceLength \u2192 curve exits at src's right\n    //     pixel edge, no rectangle drawn inside src.\n    //   \u2022 finalNodeCoverLength = 0 \u2192 curve enters at dst's left pixel edge,\n    //     no rectangle drawn inside dst.\n    // The crucial side effect is in placeReadSet's conflict check: at any\n    // node B with an incoming edge (A\u2192B) and an outgoing edge (B\u2192C), the\n    // incoming's finalNodeCoverLength=0 and the outgoing's firstNodeOffset=\n    // B.length leave them with no horizontal overlap, so they share a single\n    // lane. Node heights collapse from ~(N_in + N_out) lanes down to\n    // ~max(N_in, N_out) lanes.\n    //\n    // Note: reverseReversedReads will swap firstNodeOffset/finalNodeCoverLength\n    // for fully-reverse synthetics. The math works out: pre-flip values of\n    // (srcLen, 0) become post-flip (newSrcLen, 0), which is the same pattern\n    // \u2014 bands stay edge-only regardless of orientation.\n    const srcLen = state.nodes[Math.abs(edge.sSigned)]!.sequenceLength\n    synthetic.push({\n      id,\n      sourceTrackID: edge.sourceTrackID,\n      type: 'read',\n      // Human-readable so the name surfaces sensibly in any UI that uses it\n      // (right-click \u2192 add to group, etc.) \u2014 and so trackTooltipText fallback\n      // shows something meaningful.\n      name: label,\n      sequence: [edge.sName, edge.dName],\n      indexSequence: [],\n      path: [],\n      // assignReadsToNodes keeps a width already set\n      width: widthForCount(edge.crossings),\n      firstNodeOffset: srcLen,\n      finalNodeCoverLength: 0,\n      sequenceNew: [\n        { nodeName: edge.sName, mismatches: [] },\n        { nodeName: edge.dName, mismatches: [] },\n      ],\n      mapping_quality: 0,\n      is_secondary: false,\n      sample_name: null,\n      read_group: null,\n      score: edge.count,\n      haplotypeShare: share,\n    })\n    i += 1\n  }\n\n  return { bands: synthetic, total }\n}\n\n// Band every haplotype but the reference, which keeps its lane and the ruler.\n// Undefined when no alternate crosses an edge: a haplotype that stays on one\n// node makes no band, and its node would get no y from the read overlay.\nfunction bandHaplotypes(\n  state: LayoutState,\n  firstId: number,\n): { ref: Track; bands: Track[]; total: number } | undefined {\n  const rulerIndex =\n    state.trackForRuler === undefined\n      ? -1\n      : state.tracks.findIndex(t => t.name === state.trackForRuler)\n  const refIndex = rulerIndex === -1 ? 0 : rulerIndex\n  const ref = state.tracks[refIndex]!\n  // A deduplicated reference walk also stands for the haplotypes identical to\n  // it through the window; those belong in the bands, not the reference lane.\n  const refDuplicates = (ref.freq ?? 1) - 1\n  const refSigns = firstVisitSigns(state, ref)\n  const altHaplotypes = state.tracks\n    .filter((_, i) => i !== refIndex)\n    .map(walk => orientedLike(refSigns, walk))\n  if (refDuplicates > 0) {\n    altHaplotypes.push({ ...ref, freq: refDuplicates })\n  }\n  if (altHaplotypes.length === 0) {\n    return undefined\n  }\n  const { bands, total } = buildCoarsenedSyntheticBands(\n    state,\n    altHaplotypes,\n    'haplotype',\n    firstId,\n  )\n  return bands.length > 0 ? { ref, bands, total } : undefined\n}\n\n// A graph can store a walk in either orientation, so a haplotype can arrive\n// back to front relative to the reference. Banded that way, one allele splits\n// into a forward and a reverse band. Turn a walk around when it runs against\n// the reference on most of the nodes they share.\nfunction orientedLike(refSigns: Int8Array, walk: Track): Track {\n  let agreement = 0\n  for (const visit of walk.indexSequence) {\n    const sign = refSigns[Math.abs(visit)]\n    if (sign !== undefined && sign !== 0) {\n      agreement += sign === Math.sign(visit) ? 1 : -1\n    }\n  }\n  return agreement >= 0\n    ? walk\n    : {\n        ...walk,\n        sequence: walk.sequence.map(flip).reverse(),\n        indexSequence: walk.indexSequence.map(visit => -visit).reverse(),\n      }\n}\n\n// The sign of `ref`'s first visit to each node index, 0 where it never visits.\nfunction firstVisitSigns(state: LayoutState, ref: Track): Int8Array {\n  const signs = new Int8Array(state.nodes.length)\n  for (const visit of ref.indexSequence) {\n    const node = Math.abs(visit)\n    if (signs[node] === 0) {\n      signs[node] = Math.sign(visit)\n    }\n  }\n  return signs\n}\n\nfunction formatShare({ count, total }: HaplotypeShare): string {\n  const share = count / total\n  if (share < 0.01) {\n    return '<1%'\n  }\n  if (share > 0.99 && count < total) {\n    return '>99%'\n  }\n  return `${Math.round(share * 100)}%`\n}\n\nconst MIN_BEND_WIDTH = 7\n\n// Emit the vertical rectangles + rounded corners for a track turning around at\n// one end of an order slot. The two directions are mirror images of each other:\n// a forward-to-reverse turn bulges out to the right of the node and consumes an\n// `extraRight` slot, a reverse-to-forward turn bulges out to the left and\n// consumes an `extraLeft` slot. `dir` is +1 for right, -1 for left.\nfunction generateTurnaround(\n  state: LayoutState,\n  { width: trackWidth, id: trackID, name: trackName, type }: Track,\n  dir: 1 | -1,\n  x: number,\n  yStart: number,\n  yEnd: number,\n  order: number,\n): void {\n  const extra = dir === 1 ? state.extraRight : state.extraLeft\n  const offset = 10 * extra[order]!\n  // The turn's apex, and the outward direction from it.\n  const apex = x + dir * (offset + 5)\n  const radius = MIN_BEND_WIDTH\n  const stem = Math.min(MIN_BEND_WIDTH, trackWidth)\n  const yTop = Math.min(yStart, yEnd)\n  const yBottom = Math.max(yStart, yEnd)\n  // The incoming/outgoing stubs run from the node's edge out to the apex. The\n  // one-pixel asymmetry between the two directions is carried over verbatim\n  // from the original pair of functions.\n  const stubNear = dir === 1 ? x : apex - 1\n  const stubFar = dir === 1 ? apex : x\n\n  const horizontal = (segTop: number): void => {\n    state.shapes.verticalRectangles.push({\n      xStart: stubNear,\n      yStart: segTop,\n      xEnd: stubFar,\n      yEnd: segTop + trackWidth - 1,\n      id: trackID,\n      name: trackName,\n      type,\n    })\n  }\n  // elongate the incoming and outgoing rectangles a bit past the node\n  horizontal(yStart)\n  state.shapes.verticalRectangles.push({\n    xStart: dir === 1 ? apex + radius : apex - radius - stem,\n    yStart: yTop + trackWidth + radius - 1,\n    xEnd: dir === 1 ? apex + radius + stem - 1 : apex - radius - 1,\n    yEnd: yBottom - radius + 1,\n    id: trackID,\n    name: trackName,\n    type,\n  })\n  horizontal(yEnd)\n\n  const inner = apex + dir * radius\n  const outer = apex + dir * (radius + stem)\n\n  // bottom 90 degree bend\n  let d = `M ${apex} ${yBottom}`\n  d += ` Q ${inner} ${yBottom} ${inner} ${yBottom - radius}`\n  d += ` H ${outer}`\n  d += ` Q ${outer} ${yBottom + trackWidth} ${apex} ${yBottom + trackWidth}`\n  d += ' Z '\n  state.shapes.corners.push({ path: d, id: trackID, name: trackName, type })\n\n  // top 90 degree bend\n  d = `M ${apex} ${yTop}`\n  d += ` Q ${outer} ${yTop} ${outer} ${yTop + trackWidth + radius}`\n  d += ` H ${inner}`\n  d += ` Q ${inner} ${yTop + trackWidth} ${apex} ${yTop + trackWidth}`\n  d += ' Z '\n  state.shapes.corners.push({ path: d, id: trackID, name: trackName, type })\n  extra[order]! += 1\n}\n\n// The x extent of a node's bases: pixelWidth, plus about half a character\n// each side under nodeWidthOption 'normal'\nexport function nodePixelCoordinatesInX(node: Node): [number, number] {\n  const nodeLeftX = node.x - 4\n  const nodeRightX = node.x + node.pixelWidth + 4\n  return [nodeLeftX, nodeRightX]\n}\n\n// calculate node widths depending on sequence lengths and chosen calculation method\nfunction generateNodeWidth(state: LayoutState): void {\n  switch (state.config.nodeWidthOption) {\n    case 'compressed':\n      state.nodes.forEach(node => {\n        node.width = 1 + Math.log2(Math.max(node.sequenceLength, 1))\n        node.pixelWidth = Math.round((node.width - 1) * DEFAULT_CHAR_WIDTH)\n      })\n      break\n    case 'small':\n      state.nodes.forEach(node => {\n        node.width = node.sequenceLength / 100\n        node.pixelWidth = Math.max(\n          Math.round((node.width - 1) * DEFAULT_CHAR_WIDTH),\n          0,\n        )\n      })\n      break\n    case 'fixed':\n      state.nodes.forEach(node => {\n        node.width = 10\n        node.pixelWidth = Math.round(node.width * DEFAULT_CHAR_WIDTH)\n      })\n      break\n    case 'normal': {\n      // The label draws a base per character from x - 4, in a monospace font\n      // whose character width the caller measures. pixelWidth runs from the\n      // first character to the last, so the outline, 9 px wider each side,\n      // holds the whole label, and nodePixelCoordinatesInX's half character\n      // each side puts base i under letter i.\n      const charWidth = state.config.charWidth\n      state.nodes.forEach(node => {\n        node.width = node.sequenceLength\n        node.pixelWidth = Math.round(\n          charWidth * Math.max(node.sequenceLength - 1, 0),\n        )\n      })\n      break\n    }\n    default:\n      throw new Error(`${state.config.nodeWidthOption} not implemented`)\n  }\n}\n\n// A node's distinct neighbors on one side, kept only as far as mergeNodes\n// needs them: none, exactly one, or several. A neighbor is a signed node index,\n// or TRACK_END where a haplotype starts or stops.\ninterface Neighbors {\n  first: Int32Array\n  count: Uint8Array\n}\n\nconst TRACK_END = 0\n\nfunction noNeighbors(nodeCount: number): Neighbors {\n  return { first: new Int32Array(nodeCount), count: new Uint8Array(nodeCount) }\n}\n\nfunction addNeighbor(\n  neighbors: Neighbors,\n  index: number,\n  neighbor: number,\n): void {\n  const count = neighbors.count[index]!\n  if (count === 0) {\n    neighbors.first[index] = neighbor\n    neighbors.count[index] = 1\n  } else if (count === 1 && neighbors.first[index] !== neighbor) {\n    neighbors.count[index] = 2\n  }\n}\n\n// The index of a node's one neighbor on this side, or 0 when it has none,\n// several, or a track end.\nfunction soleNeighbor(neighbors: Neighbors, index: number): number {\n  return neighbors.count[index] === 1 ? Math.abs(neighbors.first[index]!) : 0\n}\n\n// remove redundant nodes\n// two nodes A and B can be merged if all tracks leaving A go directly into B\n// and all tracks entering B come directly from A\n// (plus no inversions involved)\nfunction mergeNodes(state: LayoutState): void {\n  const pred = noNeighbors(state.nodes.length)\n  const succ = noNeighbors(state.nodes.length)\n  const signedIndexOf = new Map<string, number>()\n  const visit = (nodeName: string): number => {\n    let signed = signedIndexOf.get(nodeName)\n    if (signed === undefined) {\n      const index = state.nodeMap.get(forward(nodeName))!\n      signed = isReverse(nodeName) ? -index : index\n      signedIndexOf.set(nodeName, signed)\n    }\n    return signed\n  }\n\n  const tracksAndReads = state.tracks.concat(state.reads)\n\n  // A reverse visit on either side adds both orientations of the neighbor, so\n  // no merge happens across an inversion.\n  tracksAndReads.forEach(track => {\n    const { sequence } = track\n    const isHaplotype = track.type === 'haplotype'\n    const last = sequence.length - 1\n    let previous = TRACK_END\n    let current = last >= 0 ? visit(sequence[0]!) : TRACK_END\n    for (let i = 0; i <= last; i += 1) {\n      const next = i < last ? visit(sequence[i + 1]!) : TRACK_END\n      if (current > 0) {\n        if (i > 0) {\n          addNeighbor(pred, current, previous)\n          if (previous < 0) {\n            addNeighbor(pred, current, -previous)\n          }\n        } else if (isHaplotype) {\n          addNeighbor(pred, current, TRACK_END)\n        }\n        if (i < last) {\n          addNeighbor(succ, current, next)\n          if (next < 0) {\n            addNeighbor(succ, current, -next)\n          }\n        } else if (isHaplotype) {\n          addNeighbor(succ, current, TRACK_END)\n        }\n      } else {\n        const index = -current\n        if (i > 0) {\n          addNeighbor(succ, index, -previous)\n          if (previous > 0) {\n            addNeighbor(succ, index, previous)\n          }\n        } else if (isHaplotype) {\n          addNeighbor(succ, index, TRACK_END)\n        }\n        if (i < last) {\n          addNeighbor(pred, index, -next)\n          if (next > 0) {\n            addNeighbor(pred, index, next)\n          }\n        } else if (isHaplotype) {\n          addNeighbor(pred, index, TRACK_END)\n        }\n      }\n      previous = current\n      current = next\n    }\n  })\n\n  const absorbed = new Uint8Array(state.nodes.length)\n  state.nodes.forEach((_, i) => {\n    if (mergeableWithPred(i, pred, succ)) {\n      absorbed[i] = 1\n    }\n  })\n\n  // Merge each run into its first node, noting the node every run member\n  // merges into and where the member's bases start and end within it.\n  const origin = new Int32Array(state.nodes.length)\n  const start = new Float64Array(state.nodes.length)\n  const end = new Float64Array(state.nodes.length)\n  state.nodes.forEach((node, head) => {\n    if (absorbed[head] === 1) {\n      return\n    }\n    origin[head] = head\n    end[head] = node.sequenceLength\n    for (let donor = head; mergeableWithSucc(donor, pred, succ);) {\n      donor = soleNeighbor(succ, donor)\n      origin[donor] = head\n      start[donor] = node.sequenceLength\n      node.sequenceLength += state.nodes[donor]!.sequenceLength\n      node.seq += state.nodes[donor]!.seq\n      end[donor] = node.sequenceLength\n    }\n  })\n\n  // A read's offsets and mismatch positions count along the strand it visits\n  // a node on: from the left end of a forward visit, the right end of a\n  // reverse one. A forward visit to an absorbed node folds into the visit\n  // before it, a reverse one into the visit after it.\n  state.reads.forEach(read => {\n    const { sequence } = read\n    const entries =\n      read.sequenceNew ??\n      sequence.map(nodeName => ({ nodeName, mismatches: [] as Mismatch[] }))\n    const shift = (nodeName: string): number => {\n      const index = Math.abs(visit(nodeName))\n      return isReverse(nodeName)\n        ? state.nodes[origin[index]!]!.sequenceLength - end[index]!\n        : start[index]!\n    }\n    const last = sequence.length - 1\n    read.firstNodeOffset = (read.firstNodeOffset ?? 0) + shift(sequence[0]!)\n    read.finalNodeCoverLength =\n      (read.finalNodeCoverLength ?? 0) + shift(sequence[last]!)\n\n    const mergedSequence: string[] = []\n    const mergedEntries: ReadSequenceEntry[] = []\n    let carried: Mismatch[] = []\n    sequence.forEach((nodeName, i) => {\n      const index = Math.abs(visit(nodeName))\n      const { mismatches } = entries[i]!\n      const by = shift(nodeName)\n      mismatches.forEach(mismatch => {\n        mismatch.pos += by\n      })\n      if (absorbed[index] === 1 && !isReverse(nodeName) && i > 0) {\n        mergedEntries.at(-1)!.mismatches.push(...mismatches)\n      } else if (absorbed[index] === 1 && isReverse(nodeName) && i < last) {\n        carried.push(...mismatches)\n      } else {\n        const name = state.nodes[origin[index]!]!.name\n        const merged = isReverse(nodeName) ? reverse(name) : name\n        mergedSequence.push(merged)\n        mergedEntries.push({\n          nodeName: merged,\n          mismatches: carried.concat(mismatches),\n        })\n        carried = []\n      }\n    })\n    read.sequence = mergedSequence\n    if (read.sequenceNew !== undefined) {\n      read.sequenceNew = mergedEntries\n    }\n  })\n\n  state.tracks.forEach(track => {\n    const { sequence } = track\n    let kept = 0\n    for (const nodeName of sequence) {\n      if (absorbed[Math.abs(visit(nodeName))] === 0) {\n        sequence[kept] = nodeName\n        kept += 1\n      }\n    }\n    sequence.length = kept\n  })\n\n  let kept = 1\n  for (let i = 1; i < state.nodes.length; i += 1) {\n    if (absorbed[i] === 0) {\n      state.nodes[kept] = state.nodes[i]!\n      kept += 1\n    }\n  }\n  state.nodes.length = kept\n}\n\nfunction mergeableWithPred(\n  index: number,\n  pred: Neighbors,\n  succ: Neighbors,\n): boolean {\n  const predecessor = soleNeighbor(pred, index)\n  return predecessor !== 0 && soleNeighbor(succ, predecessor) !== 0\n}\n\nfunction mergeableWithSucc(\n  index: number,\n  pred: Neighbors,\n  succ: Neighbors,\n): boolean {\n  const successor = soleNeighbor(succ, index)\n  return successor !== 0 && soleNeighbor(pred, successor) !== 0\n}\n", "// SVG path data for the shapes a layout leaves as coordinates: a curve's\n// ribbon and a node's rounded outline. Both are strings so the same geometry\n// draws as an SVG `d` attribute or, through Path2D, on a canvas, and\n// flattenPath turns either into points for a renderer that fills polygons.\nimport { groupBy } from './groupBy.ts'\n\nimport type { Node, TrackCurve, TrackType } from './types.ts'\n\nfunction compareCurvesByXYStartValue(a: TrackCurve, b: TrackCurve): number {\n  return b.xStart - a.xStart || a.yStart - b.yStart\n}\n\n// Where a curve leaves and enters: a node, or a gap at an order slot\nfunction curveEnds(curve: TrackCurve): [number, number, number, number] {\n  return [\n    curve.nodeStart ?? -1,\n    curve.nodeEnd ?? -1,\n    curve.nodeStart === null ? curve.orderStart : -1,\n    curve.nodeEnd === null ? curve.orderEnd : -1,\n  ]\n}\n\nfunction compareTuples(a: readonly number[], b: readonly number[]): number {\n  for (let i = 0; i < a.length; i += 1) {\n    const d = a[i]! - b[i]!\n    if (d !== 0) {\n      return d\n    }\n  }\n  return 0\n}\n\n// Where a cubic with both control points at one x is steepest, it is 3/4 of\n// the way from the ends' mean x to that control x\nconst STEEP_SHARE = 0.75\n// The most of a gap a group's steep stretch may spread over, so its edges keep\n// some of the turn\nconst MAX_SPREAD = 0.8\n\n// How far apart, as shares of the gap, each curve of a group puts its top and\n// bottom edges' control points. A ribbon whose edges turn at one x is only as\n// thick across as its width times the cosine of its slope, which on a steep\n// lane change is a hairline; with its outer edge turning late and its inner\n// edge early, its steep stretch keeps its width, or as much as the gap allows.\n// A shallow curve needs none. The reference takes what it needs first, so its\n// line stays legible where a wide tube shares its gap. Groups of more than five\n// keep at least sequenceTubeMap's 0.4 in all, which stops their curves\n// crossing at one x.\nfunction spreads(group: readonly TrackCurve[], gapWidth: number) {\n  const first = group[0]!\n  const span = Math.min(Math.abs(first.xEnd - first.xStart), gapWidth)\n  if (span === 0) {\n    return group.map(() => 0)\n  }\n  const floor = group.length > 5 ? 0.4 / group.length : 0\n  const wanted = group.map(c => {\n    const rise = Math.abs(c.yEnd - c.yStart)\n    const across =\n      (rise / Math.hypot(rise, span)) *\n      Math.min(c.width, MAX_SPREAD * STEEP_SHARE * span)\n    return Math.max(floor, across / (STEEP_SHARE * span))\n  })\n  const sum = (pick: (c: TrackCurve) => boolean) =>\n    wanted.reduce((total, w, i) => total + (pick(group[i]!) ? w : 0), 0)\n  const reference = sum(c => c.reference === true)\n  const others = sum(c => c.reference !== true)\n  const referenceScale = reference > MAX_SPREAD ? MAX_SPREAD / reference : 1\n  const room = MAX_SPREAD - reference * referenceScale\n  const othersScale = others > room ? room / others : 1\n  return wanted.map(\n    (w, i) => w * (group[i]!.reference ? referenceScale : othersScale),\n  )\n}\n\nexport interface CurvePathOptions {\n  // The most px a gap between columns draws across, where the drawing squeezes\n  // the layout's x, as a reference axis does; a curve's steepness is judged at\n  // that width\n  gapWidth?: number\n}\n\n// The curves of one track type in draw order, each with its `path` set. Curves\n// between the same pair of nodes, or gaps, form a group whose control points\n// fan out top to bottom, so a bundle of tracks changing lanes together stays\n// parallel rather than crossing at one x, and each curve's bottom edge is the\n// next one's top edge.\nexport function curvePaths(\n  curves: readonly TrackCurve[],\n  type: TrackType | undefined,\n  { gapWidth = Infinity }: CurvePathOptions = {},\n): TrackCurve[] {\n  const groupedCurves = groupBy(\n    curves.filter(curve => curve.type === type),\n    curve => curveEnds(curve).join(','),\n  )\n\n  groupedCurves.forEach(curveGroup => {\n    curveGroup.sort(compareCurvesByXYStartValue)\n    const spread = spreads(curveGroup, gapWidth)\n    // share of the gap at which a boundary between the group's tubes turns,\n    // for a curve that rises; one that falls turns at its complement\n    let adjustValue = 0.5 - spread.reduce((sum, s) => sum + s, 0) / 2\n\n    curveGroup.forEach((curve, i) => {\n      const at = (share: number) =>\n        curve.xStart +\n        (curve.xEnd - curve.xStart) *\n          (curve.yStart < curve.yEnd ? 1 - share : share)\n      const xAdjusted = at(adjustValue)\n      adjustValue += spread[i]!\n      // the bottom edge, on the way back, parallel to the next curve's top\n      const xNextAdjusted = at(adjustValue)\n      let d = `M ${curve.xStart} ${curve.yStart}`\n      d += ` C ${xAdjusted} ${curve.yStart} ${xAdjusted} ${curve.yEnd} ${curve.xEnd} ${curve.yEnd}`\n      d += ` V ${curve.yEnd + curve.width}`\n      d += ` C ${xNextAdjusted} ${curve.yEnd + curve.width} ${xNextAdjusted} ${\n        curve.yStart + curve.width\n      } ${curve.xStart} ${curve.yStart + curve.width}`\n      d += ' Z'\n      curve.path = d\n    })\n  })\n\n  // One flat list ordered by group, then by the within-group sort\n  return [...groupedCurves.values()]\n    .sort((a, b) => compareTuples(curveEnds(a[0]!), curveEnds(b[0]!)))\n    .flat()\n}\n\n// The outline that path data from curvePaths, nodeOutlinePath or a corner\n// traces, as points, for a renderer that fills polygons rather than paths.\n// Each B\u00E9zier becomes `steps` straight pieces; the closing Z adds no point.\nexport function flattenPath(d: string, steps = 16): [number, number][] {\n  const tokens = d.match(/[A-Za-z]|-?(?:\\d+\\.?\\d*|\\.\\d+)(?:e[-+]?\\d+)?/g) ?? []\n  const points: [number, number][] = []\n  let x = 0\n  let y = 0\n  let i = 0\n  const num = () => Number(tokens[i++])\n  while (i < tokens.length) {\n    const command = tokens[i++]\n    if (command === 'M' || command === 'L') {\n      x = num()\n      y = num()\n      points.push([x, y])\n    } else if (command === 'H') {\n      x = num()\n      points.push([x, y])\n    } else if (command === 'V') {\n      y = num()\n      points.push([x, y])\n    } else if (command === 'C') {\n      const [x1, y1, x2, y2, x3, y3] = [\n        num(),\n        num(),\n        num(),\n        num(),\n        num(),\n        num(),\n      ]\n      for (let s = 1; s <= steps; s += 1) {\n        const t = s / steps\n        const u = 1 - t\n        const a = u * u * u\n        const b = 3 * u * u * t\n        const c = 3 * u * t * t\n        const e = t * t * t\n        points.push([\n          a * x + b * x1 + c * x2 + e * x3,\n          a * y + b * y1 + c * y2 + e * y3,\n        ])\n      }\n      x = x3\n      y = y3\n    } else if (command === 'Q') {\n      const [x1, y1, x2, y2] = [num(), num(), num(), num()]\n      for (let s = 1; s <= steps; s += 1) {\n        const t = s / steps\n        const u = 1 - t\n        points.push([\n          u * u * x + 2 * u * t * x1 + t * t * x2,\n          u * u * y + 2 * u * t * y1 + t * t * y2,\n        ])\n      }\n      x = x2\n      y = y2\n    } else if (command !== 'Z') {\n      throw new Error(`flattenPath: unsupported path command ${command}`)\n    }\n  }\n  return points\n}\n\n// A node's outline: a rounded box 9 units outside the node's x extent and its\n// content height, the tracks through it inside.\nexport function nodeOutlinePath(node: Node): string {\n  // top left arc\n  let d = `M ${node.x - 9} ${node.y} Q ${node.x - 9} ${node.y - 9} ${\n    node.x\n  } ${node.y - 9}`\n  let x = node.x\n  let y = node.y - 9\n\n  // top straight\n  if (node.width > 1) {\n    x += node.pixelWidth\n    d += ` L ${x} ${y}`\n  }\n\n  // top right arc\n  d += ` Q ${x + 9} ${y} ${x + 9} ${y + 9}`\n  x += 9\n  y += 9\n\n  // right straight\n  if (node.contentHeight > 0) {\n    y += node.contentHeight\n    d += ` L ${x} ${y}`\n  }\n\n  // bottom right arc\n  d += ` Q ${x} ${y + 9} ${x - 9} ${y + 9}`\n  x -= 9\n  y += 9\n\n  // bottom straight\n  if (node.width > 1) {\n    x -= node.pixelWidth\n    d += ` L ${x} ${y}`\n  }\n\n  // bottom left arc\n  d += ` Q ${x - 9} ${y} ${x - 9} ${y - 9}`\n  x -= 9\n  y -= 9\n\n  // left straight\n  if (node.contentHeight > 0) {\n    y -= node.contentHeight\n    d += ` L ${x} ${y}`\n  }\n  return d\n}\n", "import {\n  canonicalStrand,\n  stepName,\n  tubeMapReads\n} from \"./chunk-A7H753BA.js\";\nimport {\n  referenceWalkName\n} from \"./chunk-CIDSF47D.js\";\nimport {\n  pathCssColor,\n  pathGreyCssColor\n} from \"./chunk-3GP3KT5L.js\";\nimport {\n  pathOrigin\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  ownStrand,\n  strandSides\n} from \"./chunk-UBQSRCWR.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/tubeMapLayout.ts\nimport { forward, isReverse, layoutTubeMap } from \"@jbrowse/tubemap-core\";\nfunction pathSteps(graph) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const visits = graph.pathVisits;\n  const next = visits?.replay();\n  return (graph.paths ?? []).map((path) => {\n    const walk = visits?.pathIndex(pathOrigin(path.name).name) ?? -1;\n    return path.nodeIds.flatMap((id) => {\n      const node = nodeById.get(id);\n      if (!node) {\n        return [];\n      }\n      const at = visits && next ? next(visits.slot(node.name), walk) : -1;\n      return [\n        { node, strand: at >= 0 ? visits.strand(at) : canonicalStrand(node) }\n      ];\n    });\n  });\n}\nfunction tubeMapTracks(graph) {\n  const steps = pathSteps(graph);\n  const tracks = (graph.paths ?? []).flatMap((path, index) => {\n    const sequence = steps[index].map((s) => stepName(s.node, s.strand));\n    return sequence.length > 0 ? [\n      {\n        id: index,\n        name: path.name,\n        sequence,\n        sourceTrackID: 0,\n        type: \"haplotype\",\n        ...path.members ? { freq: path.members.length } : {}\n      }\n    ] : [];\n  });\n  const name = referenceWalkName(graph);\n  const reference = tracks.findIndex((t) => pathOrigin(t.name).name === name);\n  if (reference > 0) {\n    tracks.unshift(...tracks.splice(reference, 1));\n  }\n  return tracks;\n}\nfunction tubeMapNodes(graph) {\n  return graph.nodes.map((n) => ({\n    name: n.id,\n    seq: \"\",\n    sequenceLength: Math.max(1, n.length)\n  }));\n}\nfunction hasTubeMapPaths(graph) {\n  return (graph.paths?.length ?? 0) > 0;\n}\nvar STACK_PX = 600;\nvar MIN_TUBE_PX = 3;\nvar MAX_TUBE_PX = 15;\nfunction tubeWidth(trackCount) {\n  return Math.max(\n    MIN_TUBE_PX,\n    Math.min(MAX_TUBE_PX, Math.floor(STACK_PX / Math.max(1, trackCount)))\n  );\n}\nfunction straightened(first) {\n  const flipped = /* @__PURE__ */ new Set();\n  const forwards = /* @__PURE__ */ new Set();\n  for (const step of first?.sequence ?? []) {\n    if (!isReverse(step)) {\n      forwards.add(step);\n    } else if (!forwards.has(forward(step))) {\n      flipped.add(forward(step));\n    }\n  }\n  return flipped;\n}\nfunction mergedRuns(graph, layout, walks) {\n  const flipped = straightened(walks[0]);\n  const before = /* @__PURE__ */ new Map();\n  for (const { sequence, is_secondary } of walks) {\n    if (!is_secondary) {\n      sequence.forEach((step, i) => {\n        const id = forward(step);\n        const against = isReverse(step) !== flipped.has(id);\n        const neighbour = against ? sequence[i + 1] : sequence[i - 1];\n        if (!layout.nodeMap.has(id) && neighbour !== void 0) {\n          before.set(id, forward(neighbour));\n        }\n      });\n    }\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, Math.max(1, n.length)]));\n  const after = new Map([...before].map(([node, prev]) => [prev, node]));\n  const members = /* @__PURE__ */ new Map();\n  for (const head of after.keys()) {\n    const index = layout.nodeMap.get(head);\n    if (index !== void 0) {\n      const run = [head];\n      for (let n = after.get(head); n !== void 0; n = after.get(n)) {\n        run.push(n);\n      }\n      const bp = run.reduce((sum, id) => sum + (lengthOf.get(id) ?? 0), 0);\n      if (bp === layout.nodes[index].sequenceLength) {\n        members.set(head, run);\n      }\n    }\n  }\n  return { members, flipped };\n}\nvar opposite = { start: \"end\", end: \"start\" };\nvar otherStrand = { \"+\": \"-\", \"-\": \"+\" };\nfunction boxGraph(graph, { members, flipped }) {\n  if (members.size === 0) {\n    return graph;\n  }\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const boxOf = /* @__PURE__ */ new Map();\n  const inner = /* @__PURE__ */ new Set();\n  const drawn = (id, side) => flipped.has(id) ? opposite[side] : side;\n  for (const [box, run] of members) {\n    run.forEach((id, i) => {\n      boxOf.set(id, box);\n      const next = run[i + 1];\n      if (next !== void 0) {\n        inner.add(`${id}:${drawn(id, \"end\")}\t${next}:${drawn(next, \"start\")}`);\n      }\n    });\n  }\n  const absorbed = new Set(\n    [...boxOf].filter(([id, box]) => id !== box).map(([id]) => id)\n  );\n  const nodes = graph.nodes.flatMap((node) => {\n    const run = members.get(node.id);\n    if (!run) {\n      return absorbed.has(node.id) ? [] : [node];\n    }\n    const parts = run.map((id) => nodeById.get(id));\n    const starts = parts.flatMap((p) => p.stable ? [p.stable.start] : []);\n    return [\n      {\n        ...node,\n        length: parts.reduce((sum, p) => sum + p.length, 0),\n        stable: node.stable && { ...node.stable, start: Math.min(...starts) }\n      }\n    ];\n  });\n  const leaving = (id, box, side) => drawn(box, drawn(id, side)) === \"end\" ? ownStrand(box) : otherStrand[ownStrand(box)];\n  const edges = graph.edges.flatMap((edge) => {\n    const sides = strandSides(edge);\n    const from = `${edge.from}:${sides.from}`;\n    const to = `${edge.to}:${sides.to}`;\n    if (inner.has(`${from}\t${to}`) || inner.has(`${to}\t${from}`)) {\n      return [];\n    }\n    const fromBox = boxOf.get(edge.from);\n    const toBox = boxOf.get(edge.to);\n    return [\n      {\n        ...edge,\n        ...fromBox === void 0 ? {} : {\n          from: fromBox,\n          fromStrand: leaving(edge.from, fromBox, sides.from)\n        },\n        ...toBox === void 0 ? {} : {\n          to: toBox,\n          toStrand: otherStrand[leaving(edge.to, toBox, sides.to)]\n        }\n      }\n    ];\n  });\n  const absorbedNames = new Set(\n    [...absorbed].map((id) => nodeById.get(id)?.name ?? id)\n  );\n  return {\n    ...graph,\n    nodes,\n    edges,\n    paths: graph.paths?.map((path) => ({\n      ...path,\n      nodeIds: path.nodeIds.filter((id) => !absorbed.has(id))\n    })),\n    pathVisits: graph.pathVisits?.filter(\n      () => true,\n      (segment) => !absorbedNames.has(segment)\n    )\n  };\n}\nfunction runTubeMap(graph) {\n  const paths = graph.paths ?? [];\n  const tracks = tubeMapTracks(graph);\n  const reads = graph.reads ? tubeMapReads(graph, graph.reads, paths.length) : [];\n  const tubeColor = reads.length > 0 ? pathGreyCssColor : pathCssColor;\n  const pathColors = paths.map((_, i) => tubeColor(i, paths.length));\n  const bundled = paths.some((p) => p.members);\n  const walks = paths.reduce((n, p) => n + (p.members?.length ?? 1), 0);\n  const layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {\n    nodeWidthOption: \"compressed\",\n    trackWidth: tubeWidth(bundled ? walks : tracks.length),\n    ...bundled ? { freqWidth: \"linear\" } : {}\n  });\n  if (!layout) {\n    return void 0;\n  }\n  const runs = mergedRuns(graph, layout, [...tracks, ...reads]);\n  return {\n    layout,\n    pathColors,\n    members: runs.members,\n    graph: boxGraph(graph, runs)\n  };\n}\nfunction drawnNodes(layout) {\n  const nodes = [];\n  layout.nodes.forEach((node) => {\n    if (node.order >= 0) {\n      nodes.push(node);\n    }\n  });\n  return nodes;\n}\nfunction centreline(node, yOffset, x0, x1) {\n  const y = node.y + node.contentHeight / 2 - yOffset;\n  return [\n    { x: x0, y },\n    { x: x1, y }\n  ];\n}\nfunction extentOf(layout, yOffset) {\n  return {\n    minY: layout.bounds.minY - yOffset,\n    maxY: layout.bounds.maxY - yOffset\n  };\n}\nfunction tubeMapLayout(graph) {\n  const run = hasTubeMapPaths(graph) ? runTubeMap(graph) : void 0;\n  if (!run) {\n    return void 0;\n  }\n  const { layout, ...drawing } = run;\n  const yOffset = layout.bounds.minY;\n  const nodePositions = {};\n  for (const node of drawnNodes(layout)) {\n    nodePositions[node.name] = centreline(\n      node,\n      yOffset,\n      node.x,\n      node.x + node.pixelWidth\n    );\n  }\n  const { minY, maxY } = extentOf(layout, yOffset);\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, ...drawing },\n    extent: {\n      minX: layout.bounds.minX,\n      maxX: layout.bounds.maxX,\n      minY,\n      maxY\n    }\n  };\n}\nfunction tubeMapColumns(graph, layout) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const byOrder = groupBy(drawnNodes(layout), (node) => node.order);\n  const columns = [];\n  let end = -Infinity;\n  for (const order of [...byOrder.keys()].sort((a, b) => a - b)) {\n    const nodes = byOrder.get(order);\n    let bp0 = Infinity;\n    let bp1 = -Infinity;\n    for (const node of nodes) {\n      const graphNode = nodeById.get(node.name);\n      if (graphNode && isBackbone(graphNode)) {\n        bp0 = Math.min(bp0, graphNode.stable.start);\n        bp1 = Math.max(bp1, graphNode.stable.start + graphNode.length);\n      }\n    }\n    if (bp0 === Infinity) {\n      bp0 = bp1 = end;\n    }\n    if (bp0 < end) {\n      bp0 = end;\n      bp1 = Math.max(end, bp1);\n    }\n    end = Math.max(end, bp1);\n    columns.push({\n      order,\n      x0: Math.min(...nodes.map((n) => n.x)),\n      x1: Math.max(...nodes.map((n) => n.x + n.pixelWidth)),\n      bp0,\n      bp1\n    });\n  }\n  const first = columns.find((c) => c.bp0 !== -Infinity);\n  for (const column of columns) {\n    if (column.bp0 === -Infinity) {\n      column.bp0 = column.bp1 = first?.bp0 ?? 0;\n    }\n  }\n  return columns;\n}\nfunction hasTubeMapBackbone(graph) {\n  return hasTubeMapPaths(graph) && graph.nodes.some(isBackbone);\n}\nfunction tubeMapReferenceLayout(graph) {\n  const run = hasTubeMapBackbone(graph) ? runTubeMap(graph) : void 0;\n  if (!run) {\n    return void 0;\n  }\n  const { layout, ...drawing } = run;\n  const columns = tubeMapColumns(drawing.graph, layout);\n  const byOrder = new Map(columns.map((c) => [c.order, c]));\n  const yOffset = layout.bounds.minY;\n  const nodePositions = {};\n  for (const node of drawnNodes(layout)) {\n    const column = byOrder.get(node.order);\n    nodePositions[node.name] = centreline(node, yOffset, column.bp0, column.bp1);\n  }\n  return {\n    nodePositions,\n    tubeMap: { layout, yOffset, columns, ...drawing },\n    referenceAxis: true,\n    pixelRows: true,\n    extent: extentOf(layout, yOffset)\n  };\n}\n\nexport {\n  pathSteps,\n  tubeMapTracks,\n  hasTubeMapPaths,\n  tubeMapLayout,\n  hasTubeMapBackbone,\n  tubeMapReferenceLayout\n};\n", "import {\n  pathSteps\n} from \"./chunk-PK5QQOMN.js\";\nimport {\n  pathOrigin\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  PathVisitsBuilder\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/tubeMap/coarsen.ts\nfunction readWalk(path, steps) {\n  const runs = [];\n  const open = () => ({ a: -Infinity, b: Infinity, detour: [], bp: 0 });\n  const gaps = [open()];\n  for (const { node, strand } of steps) {\n    const gap = gaps.at(-1);\n    const last = runs.at(-1);\n    if (isBackbone(node)) {\n      const start = node.stable.start;\n      const end = start + node.length;\n      const inverted = strand !== (node.stable.strand ?? \"+\");\n      const joins = last !== void 0 && gap.detour.length === 0;\n      if (joins && !last.inverted && !inverted && last.end === start) {\n        last.end = end;\n      } else if (joins && last.inverted && inverted && last.start === end) {\n        last.start = start;\n      } else {\n        runs.push({ start, end, inverted });\n        gaps.push(open());\n      }\n    } else {\n      gap.detour.push({ node, strand });\n      gap.bp += node.length;\n    }\n  }\n  runs.forEach((run, i) => {\n    gaps[i].b = run.start;\n    gaps[i + 1].a = run.end;\n  });\n  return { path, runs, gaps };\n}\nfunction isSmall(gap, sigma) {\n  return Number.isFinite(gap.a) && Number.isFinite(gap.b) && gap.b >= gap.a && Math.max(gap.b - gap.a, gap.bp) < sigma;\n}\nfunction strictlyInside(cuts, a, b) {\n  const i = partitionPoint(cuts.length, (j) => cuts[j] <= a);\n  return i < cuts.length && cuts[i] < b;\n}\nfunction referenceGaps(backbone) {\n  const cuts = /* @__PURE__ */ new Map();\n  for (let i = 1; i < backbone.length; i++) {\n    const prev = backbone[i - 1];\n    const node = backbone[i];\n    const end = prev.stable.start + prev.length;\n    if (end !== node.stable.start) {\n      cuts.set(end, \"reference-gap\");\n      cuts.set(node.stable.start, \"reference-gap\");\n    }\n  }\n  return cuts;\n}\nfunction findCuts(walks, sigma, cuts) {\n  const cut = (bp, cause) => {\n    if (Number.isFinite(bp) && !cuts.has(bp)) {\n      cuts.set(bp, cause);\n    }\n  };\n  for (const { runs, gaps } of walks) {\n    const first = runs[0];\n    const last = runs.at(-1);\n    if (first && last) {\n      cut(first.start, \"walk-end\");\n      cut(last.end, \"walk-end\");\n    }\n    for (const run of runs) {\n      if (run.inverted && run.end - run.start >= sigma) {\n        cut(run.start, \"inversion\");\n        cut(run.end, \"inversion\");\n      }\n    }\n    for (const gap of gaps) {\n      if (gap.b < gap.a) {\n        cut(gap.a, \"backward\");\n        cut(gap.b, \"backward\");\n      } else if (!isSmall(gap, sigma)) {\n        cut(gap.a, \"variant\");\n        cut(gap.b, \"variant\");\n      }\n    }\n  }\n  const spans = walks.flatMap(({ runs, gaps }) => [\n    ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),\n    ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])\n  ]);\n  for (let changed = true; changed; ) {\n    changed = false;\n    const sorted = [...cuts.keys()].sort((x, y) => x - y);\n    for (const [a, b] of spans) {\n      if (strictlyInside(sorted, a, b)) {\n        changed ||= !cuts.has(a) || !cuts.has(b);\n        cut(a, \"overlap\");\n        cut(b, \"overlap\");\n      }\n    }\n  }\n  return cuts;\n}\nfunction mergeReference(backbone, cuts) {\n  const merged = [];\n  let group = [];\n  const close = () => {\n    const first = group[0];\n    const last = group.at(-1);\n    if (first && last) {\n      const bp0 = first.stable.start;\n      const bp1 = last.stable.start + last.length;\n      const name = `${bp0}-${bp1}`;\n      merged.push({\n        node: {\n          id: `${name}+`,\n          name,\n          length: bp1 - bp0,\n          depth: 0,\n          stable: {\n            refName: first.stable.refName,\n            start: bp0,\n            rank: 0,\n            strand: \"+\"\n          }\n        },\n        members: group\n      });\n    }\n    group = [];\n  };\n  for (const node of backbone) {\n    if (cuts.has(node.stable.start)) {\n      close();\n    }\n    group.push(node);\n  }\n  close();\n  return merged;\n}\nfunction lastAtMost(items, key, x) {\n  return Math.max(0, partitionPoint(items.length, (i) => key(items[i]) <= x) - 1);\n}\nfunction coarsenTubeMap(graph, sigma) {\n  const backbone = graph.nodes.filter(isBackbone).sort((a, b) => a.stable.start - b.stable.start);\n  const paths = graph.paths ?? [];\n  if (backbone.length === 0 || paths.length === 0) {\n    return void 0;\n  }\n  const stepsOf = pathSteps(graph);\n  const walks = paths.map((p, i) => readWalk(p, stepsOf[i]));\n  const cuts = findCuts(walks, sigma, referenceGaps(backbone));\n  const sortedCuts = [...cuts.keys()].sort((x, y) => x - y);\n  const merged = mergeReference(backbone, cuts);\n  const mergedAt = (bp) => lastAtMost(merged, (m) => m.node.stable.start, bp);\n  const members = /* @__PURE__ */ new Map();\n  const coarseOf = /* @__PURE__ */ new Map();\n  for (const m of merged) {\n    members.set(\n      m.node.id,\n      m.members.map((n) => n.id)\n    );\n    for (const n of m.members) {\n      coarseOf.set(n.id, m.node.id);\n    }\n  }\n  const routes = /* @__PURE__ */ new Map();\n  const routeFor = (gap) => {\n    const key = `${gap.a}\t${gap.b}\t${gap.detour.map((s) => s.node.id + s.strand).join(\",\")}`;\n    let node = routes.get(key);\n    if (!node) {\n      const name = `r${routes.size}`;\n      node = {\n        id: `${name}+`,\n        name,\n        length: gap.bp,\n        depth: 0,\n        stable: {\n          refName: backbone[0].stable.refName,\n          start: Number.isFinite(gap.a) ? gap.a : gap.b,\n          rank: 1,\n          strand: \"+\"\n        }\n      };\n      routes.set(key, node);\n      members.set(\n        node.id,\n        gap.detour.map((s) => s.node.id)\n      );\n      for (const s of gap.detour) {\n        if (!coarseOf.has(s.node.id)) {\n          coarseOf.set(s.node.id, node.id);\n        }\n      }\n    }\n    return node;\n  };\n  const deviations = /* @__PURE__ */ new Map();\n  const coarsePaths = [];\n  const pathVisits = new PathVisitsBuilder();\n  const edges = /* @__PURE__ */ new Map();\n  const depth = /* @__PURE__ */ new Map();\n  for (const { path, runs, gaps } of walks) {\n    const steps = [];\n    const devs = [];\n    let continuing = false;\n    const append = (node, strand) => {\n      const last = steps.at(-1);\n      if (!(continuing && last?.node === node && last.strand === strand)) {\n        steps.push({ node, strand });\n      }\n      continuing = true;\n    };\n    const structural = (gap) => {\n      continuing = false;\n      if (gap.detour.length > 0) {\n        append(routeFor(gap), \"+\");\n        continuing = false;\n      }\n    };\n    const fold = (gap) => {\n      if (gap.bp > 0 || gap.b > gap.a) {\n        devs.push({ start: gap.a, end: gap.b, bp: gap.bp });\n      }\n      const home = merged[mergedAt(gap.b > gap.a ? gap.a : gap.a - 1)];\n      for (const s of gap.detour) {\n        if (!coarseOf.has(s.node.id)) {\n          coarseOf.set(s.node.id, home.node.id);\n          members.get(home.node.id).push(s.node.id);\n        }\n      }\n    };\n    runs.forEach((run, i) => {\n      const gap = gaps[i];\n      if (isSmall(gap, sigma) && !strictlyInside(sortedCuts, gap.a, gap.b)) {\n        fold(gap);\n      } else {\n        structural(gap);\n      }\n      const i0 = mergedAt(run.start);\n      const i1 = mergedAt(run.end - 1);\n      const small = run.end - run.start < sigma;\n      if (run.inverted && !small) {\n        continuing = false;\n        for (let j = i1; j >= i0; j--) {\n          append(merged[j].node, \"-\");\n        }\n        continuing = false;\n      } else {\n        if (run.inverted) {\n          devs.push({\n            start: run.start,\n            end: run.end,\n            bp: run.end - run.start,\n            inverted: true\n          });\n        }\n        for (let j = i0; j <= i1; j++) {\n          append(merged[j].node, \"+\");\n        }\n      }\n    });\n    structural(gaps.at(-1));\n    const visitName = pathOrigin(path.name).name;\n    let pos = 0;\n    steps.forEach(({ node, strand }, i) => {\n      depth.set(node.id, (depth.get(node.id) ?? 0) + 1);\n      pathVisits.add(\n        node.name,\n        visitName,\n        path.sample ?? visitName,\n        pos,\n        strand === \"-\"\n      );\n      pos += node.length;\n      const next = steps[i + 1];\n      if (next) {\n        const key = `${node.id}${strand}\t${next.node.id}${next.strand}`;\n        const edge = edges.get(key);\n        if (edge) {\n          edge.pathIds.push(path.name);\n        } else {\n          edges.set(key, {\n            from: node.id,\n            to: next.node.id,\n            fromStrand: strand,\n            toStrand: next.strand,\n            pathIds: [path.name]\n          });\n        }\n      }\n    });\n    coarsePaths.push({ ...path, nodeIds: steps.map((s) => s.node.id) });\n    deviations.set(path.name, devs);\n  }\n  const nodes = [...merged.map((m) => m.node), ...routes.values()].filter((n) => depth.has(n.id)).map((n) => ({ ...n, depth: depth.get(n.id) }));\n  return {\n    graph: {\n      ...graph,\n      nodes,\n      edges: [...edges.values()],\n      paths: coarsePaths,\n      pathVisits: pathVisits.build(),\n      reads: void 0\n    },\n    members,\n    coarseOf,\n    deviations,\n    cuts\n  };\n}\n\nexport {\n  lastAtMost,\n  coarsenTubeMap\n};\n", "import {\n  lastAtMost\n} from \"../chunks/chunk-EY2ZGSCP.js\";\nimport {\n  boxX,\n  referenceBoxes\n} from \"../chunks/chunk-HSVFCA2J.js\";\nimport \"../chunks/chunk-PK5QQOMN.js\";\nimport \"../chunks/chunk-A7H753BA.js\";\nimport \"../chunks/chunk-C44YRP5F.js\";\nimport \"../chunks/chunk-CIDSF47D.js\";\nimport \"../chunks/chunk-3GP3KT5L.js\";\nimport {\n  pathOrigin\n} from \"../chunks/chunk-B5X2RLJG.js\";\nimport \"../chunks/chunk-EIY2SKD3.js\";\nimport \"../chunks/chunk-ZPZ7GNBT.js\";\nimport \"../chunks/chunk-PFRQBCGC.js\";\nimport \"../chunks/chunk-HMXCN6PG.js\";\nimport \"../chunks/chunk-AB35TJST.js\";\nimport \"../chunks/chunk-BZFOFC4D.js\";\nimport \"../chunks/chunk-CGMSKIEO.js\";\nimport \"../chunks/chunk-UBQSRCWR.js\";\nimport \"../chunks/chunk-CPMHA4W5.js\";\nimport {\n  pushTo\n} from \"../chunks/chunk-BSOZW3FC.js\";\nimport \"../chunks/chunk-RJWPJCIB.js\";\nimport \"../chunks/chunk-HOAIOEI7.js\";\nimport \"../chunks/chunk-4XWZNPQ2.js\";\n\n// src/tubeMap/deviations.ts\nfunction boxAt(boxes, bp, visited) {\n  const lo = lastAtMost(boxes, (box) => box.bp0, bp);\n  return [boxes[lo], boxes[lo - 1]].find(\n    (box) => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1\n  );\n}\nfunction deviationsByPath(graph, deviations) {\n  const byWalk = /* @__PURE__ */ new Map();\n  for (const [name, devs] of deviations) {\n    for (const d of devs) {\n      pushTo(byWalk, pathOrigin(name).name, d);\n    }\n  }\n  const byPath = /* @__PURE__ */ new Map();\n  for (const path of graph.paths ?? []) {\n    if (path.members) {\n      const union = /* @__PURE__ */ new Map();\n      for (const d of path.members.flatMap((m) => byWalk.get(m) ?? [])) {\n        union.set(`${d.start}-${d.end}`, d);\n      }\n      byPath.set(path.name, [...union.values()]);\n    } else {\n      byPath.set(path.name, deviations.get(path.name) ?? []);\n    }\n  }\n  return byPath;\n}\nfunction deviationMarks(drawing, deviations) {\n  const { graph, layout } = drawing;\n  const boxes = [...referenceBoxes(drawing).values()].flat().sort((a, b) => a.bp0 - b.bp0);\n  const byPath = deviationsByPath(graph, deviations);\n  const marks = [];\n  for (const track of layout.tracks) {\n    const devs = track.name ? byPath.get(track.name) : void 0;\n    if (devs?.length) {\n      const visited = /* @__PURE__ */ new Map();\n      for (const segment of track.path) {\n        if (segment.node !== null && segment.y !== void 0 && !visited.has(segment.node)) {\n          visited.set(segment.node, segment.y);\n        }\n      }\n      for (const d of devs) {\n        const box = boxAt(boxes, d.start, visited);\n        if (box) {\n          marks.push({\n            x0: boxX(box, d.start),\n            x1: boxX(box, d.end),\n            y: visited.get(box.index),\n            height: track.width\n          });\n        }\n      }\n    }\n  }\n  return marks;\n}\nfunction deviationInk(darkMode) {\n  return darkMode ? \"rgba(255,255,255,0.9)\" : \"rgba(0,0,0,0.8)\";\n}\nfunction drawDeviationMarks(ctx, marks, { x, y, width, darkMode }) {\n  if (marks.length === 0) {\n    return;\n  }\n  ctx.fillStyle = deviationInk(darkMode);\n  ctx.beginPath();\n  for (const m of marks) {\n    const left = x(m.x0);\n    const right = Math.max(x(m.x1), left + 1);\n    if (right >= 0 && left <= width) {\n      const top = y(m.y);\n      ctx.rect(left, top, right - left, y(m.y + m.height) - top);\n    }\n  }\n  ctx.fill();\n}\nexport {\n  deviationInk,\n  deviationMarks,\n  drawDeviationMarks\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/tubeMap/warp.ts\nvar MAX_GAP_PX = 24;\nvar MAX_GAP_SHARE = 0.5;\nvar isReal = (c) => c.bp1 > c.bp0;\nfunction referenceKnots(columns, bpToScreen) {\n  const real = columns.filter(isReal);\n  if (real.length === 0) {\n    const first = columns[0];\n    return first ? [{ tx: first.x0, sx: bpToScreen(first.bp0) }] : [];\n  }\n  const tx = [];\n  const target = [];\n  const gap = [];\n  real.forEach((c, i) => {\n    tx.push(c.x0, c.x1);\n    target.push(bpToScreen(c.bp0), bpToScreen(c.bp1));\n    gap.push(i === 0 ? 0 : Math.min(c.x0 - real[i - 1].x1, MAX_GAP_PX), 0);\n  });\n  const span = target.at(-1) - target[0];\n  const demand = gap.reduce((a, b) => a + b, 0);\n  const scale = demand > 0 ? Math.min(1, MAX_GAP_SHARE * span / demand) : 1;\n  return spread(target, gap, scale).map((sx, k) => ({ tx: tx[k], sx }));\n}\nfunction spread(target, gap, scale) {\n  const offset = [];\n  let sum = 0;\n  for (const g of gap) {\n    sum += g * scale;\n    offset.push(sum);\n  }\n  const blocks = [];\n  target.forEach((t, k) => {\n    let block = { mean: t - offset[k], n: 1 };\n    let last = blocks.at(-1);\n    while (last && last.mean >= block.mean) {\n      blocks.pop();\n      const n = last.n + block.n;\n      block = { mean: (last.mean * last.n + block.mean * block.n) / n, n };\n      last = blocks.at(-1);\n    }\n    blocks.push(block);\n  });\n  return blocks.flatMap((b) => Array(b.n).fill(b.mean)).map((q, k) => q + offset[k]);\n}\nfunction warpX(knots, tx) {\n  const n = knots.length;\n  if (n === 0) {\n    return tx;\n  }\n  const first = knots[0];\n  const last = knots[n - 1];\n  if (tx <= first.tx) {\n    return first.sx + (tx - first.tx);\n  }\n  if (tx >= last.tx) {\n    return last.sx + (tx - last.tx);\n  }\n  const hi = 1 + partitionPoint(n - 2, (i) => knots[i + 1].tx <= tx);\n  const a = knots[hi - 1];\n  const b = knots[hi];\n  const span = b.tx - a.tx;\n  return span > 0 ? a.sx + (tx - a.tx) / span * (b.sx - a.sx) : a.sx;\n}\n\nexport {\n  MAX_GAP_PX,\n  referenceKnots,\n  warpX\n};\n", "// src/tubeMap/mismatches.ts\nimport {\n  forward,\n  getXCoordinateOfBaseWithinNode,\n  mirroredMismatch\n} from \"@jbrowse/tubemap-core\";\nfunction readMismatches(read, layout) {\n  const marks = [];\n  const entries = read.sequenceNew ?? [];\n  const visits = read.path.filter((segment) => segment.node !== null);\n  entries.forEach((entry, i) => {\n    const nodeIndex = layout.nodeMap.get(forward(entry.nodeName));\n    const node = nodeIndex === void 0 ? void 0 : layout.nodes[nodeIndex];\n    const visit = visits[i];\n    if (node && visit?.y !== void 0) {\n      const base = { readId: read.id, y: visit.y, height: read.width };\n      const at = (pos) => getXCoordinateOfBaseWithinNode(node, pos);\n      for (const edit of entry.mismatches) {\n        const mm = visit.isForward ? edit : mirroredMismatch(edit, node.sequenceLength);\n        const x0 = at(mm.pos);\n        if (x0 !== null) {\n          if (mm.type === \"insertion\") {\n            marks.push({ ...base, kind: \"insertion\", x: x0, seq: mm.seq });\n          } else if (mm.type === \"deletion\" && mm.length !== void 0) {\n            const x1 = at(mm.pos + mm.length);\n            if (x1 !== null) {\n              marks.push({\n                ...base,\n                kind: \"deletion\",\n                x0,\n                x1,\n                length: mm.length\n              });\n            }\n          } else if (mm.type === \"substitution\" && mm.seq !== void 0) {\n            const x1 = at(mm.pos + mm.seq.length);\n            if (x1 !== null) {\n              marks.push({ ...base, kind: \"substitution\", x0, x1, seq: mm.seq });\n            }\n          }\n        }\n      }\n    }\n  });\n  return marks;\n}\nfunction tubeMapMismatches(layout) {\n  return layout.reads.flatMap((read) => readMismatches(read, layout));\n}\n\nexport {\n  tubeMapMismatches\n};\n", "import {\n  MAX_GAP_PX\n} from \"./chunk-MYDHU2UV.js\";\nimport {\n  tubeMapMismatches\n} from \"./chunk-BX4AUMZE.js\";\nimport {\n  readColor\n} from \"./chunk-A7H753BA.js\";\nimport {\n  referenceWalkName\n} from \"./chunk-CIDSF47D.js\";\nimport {\n  pathOrigin\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\n\n// src/tubeMap/draw.ts\nimport { curvePaths, flattenPath, nodeOutlinePath } from \"@jbrowse/tubemap-core\";\nfunction parsePath(d) {\n  const tokens = d.trim().split(/[\\s,]+/);\n  const commands = [];\n  let i = 0;\n  const num = () => Number(tokens[i++]);\n  while (i < tokens.length) {\n    const op = tokens[i++];\n    if (op === \"M\" || op === \"L\") {\n      commands.push({ op, x: num(), y: num() });\n    } else if (op === \"H\") {\n      commands.push({ op, x: num() });\n    } else if (op === \"V\") {\n      commands.push({ op, y: num() });\n    } else if (op === \"Q\") {\n      commands.push({ op, x1: num(), y1: num(), x: num(), y: num() });\n    } else if (op === \"C\") {\n      commands.push({\n        op,\n        x1: num(),\n        y1: num(),\n        x2: num(),\n        y2: num(),\n        x: num(),\n        y: num()\n      });\n    } else if (op === \"Z\") {\n      commands.push({ op });\n    }\n  }\n  return commands;\n}\nfunction extentOf(commands) {\n  let x0 = Infinity;\n  let x1 = -Infinity;\n  for (const c of commands) {\n    if (\"x\" in c) {\n      x0 = Math.min(x0, c.x);\n      x1 = Math.max(x1, c.x);\n    }\n    if (\"x1\" in c) {\n      x0 = Math.min(x0, c.x1);\n      x1 = Math.max(x1, c.x1);\n    }\n  }\n  return { x0, x1 };\n}\nfunction shapeOf(d, color, id, haplotype, reference) {\n  const commands = parsePath(d);\n  return {\n    commands,\n    outline: flattenPath(d, 12),\n    color,\n    id,\n    haplotype,\n    reference,\n    ...extentOf(commands)\n  };\n}\nfunction trackColors(layout, pathColors) {\n  return new Map(\n    layout.tracks.map((track) => [\n      track.id,\n      track.type === \"read\" ? readColor(track) : pathColors[track.id]\n    ])\n  );\n}\nfunction layerOf(layout, type, colors, referenceIds, gapWidth) {\n  const { shapes } = layout;\n  const haplotype = type === \"haplotype\";\n  const colorOf = (s) => colors.get(s.id);\n  const isReference = (s) => haplotype && referenceIds.has(s.id);\n  const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({\n    color: colorOf(r),\n    id: r.id,\n    haplotype,\n    reference: isReference(r),\n    x0: r.xStart,\n    x1: r.xEnd + 1,\n    y0: r.yStart,\n    y1: r.yEnd + 1\n  }));\n  const curves = curvePaths(shapes.curves, type, { gapWidth }).map(\n    (c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c))\n  );\n  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c)));\n  return { rects, shapes: [...curves, ...corners] };\n}\nfunction referenceTrackIds(graph) {\n  const ids = /* @__PURE__ */ new Set();\n  const name = graph && referenceWalkName(graph);\n  graph?.paths?.forEach((path, i) => {\n    if (pathOrigin(path.name).name === name) {\n      ids.add(i);\n    }\n  });\n  return ids;\n}\nfunction tubeMapPicture({\n  layout,\n  pathColors,\n  graph,\n  columns\n}) {\n  const colors = trackColors(layout, pathColors);\n  const referenceIds = referenceTrackIds(graph);\n  const gapWidth = columns ? MAX_GAP_PX : void 0;\n  const nodes = [];\n  layout.nodes.forEach((node) => {\n    if (node.order >= 0) {\n      const commands = parsePath(nodeOutlinePath(node));\n      nodes.push({ name: node.name, commands, ...extentOf(commands) });\n    }\n  });\n  return {\n    bounds: layout.bounds,\n    layers: [\n      layerOf(layout, \"haplotype\", colors, referenceIds, gapWidth),\n      layerOf(layout, \"read\", colors, referenceIds, gapWidth)\n    ],\n    nodes,\n    mismatches: tubeMapMismatches(layout)\n  };\n}\nfunction trace(ctx, commands, x, y) {\n  let cx = 0;\n  let cy = 0;\n  for (const c of commands) {\n    switch (c.op) {\n      case \"M\":\n        cx = c.x;\n        cy = c.y;\n        ctx.moveTo(x(cx), y(cy));\n        break;\n      case \"L\":\n        cx = c.x;\n        cy = c.y;\n        ctx.lineTo(x(cx), y(cy));\n        break;\n      case \"H\":\n        cx = c.x;\n        ctx.lineTo(x(cx), y(cy));\n        break;\n      case \"V\":\n        cy = c.y;\n        ctx.lineTo(x(cx), y(cy));\n        break;\n      case \"Q\":\n        cx = c.x;\n        cy = c.y;\n        ctx.quadraticCurveTo(x(c.x1), y(c.y1), x(cx), y(cy));\n        break;\n      case \"C\":\n        cx = c.x;\n        cy = c.y;\n        ctx.bezierCurveTo(x(c.x1), y(c.y1), x(c.x2), y(c.y2), x(cx), y(cy));\n        break;\n      case \"Z\":\n        ctx.closePath();\n        break;\n    }\n  }\n}\nfunction fillByColor(ctx, items, visible, colorOf, addTo) {\n  const byColor = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    if (visible(item)) {\n      pushTo(byColor, colorOf(item), item);\n    }\n  }\n  for (const list of byColor.values()) {\n    ctx.fillStyle = colorOf(list[0]);\n    ctx.beginPath();\n    for (const item of list) {\n      addTo(item);\n    }\n    ctx.fill();\n  }\n}\nvar FULL_OUTLINE_PX = 12;\nvar MIN_OUTLINE_ALPHA = 0.15;\nfunction outlineAlpha(screenWidth) {\n  return Math.max(MIN_OUTLINE_ALPHA, Math.min(1, screenWidth / FULL_OUTLINE_PX));\n}\nvar NODE_TINT_ALPHA = 0.55;\nfunction drawTubeMap(ctx, picture, frame) {\n  const { x, y, width } = frame;\n  const visible = (item) => x(item.x1) >= 0 && x(item.x0) <= width;\n  const colorOf = (item) => item.haplotype && frame.tubeColors?.[item.id] || item.color;\n  ctx.globalAlpha = 1;\n  for (const layer of picture.layers) {\n    for (const reference of [false, true]) {\n      const inPass = (item) => item.reference === reference;\n      fillByColor(\n        ctx,\n        layer.rects,\n        (r) => inPass(r) && visible(r),\n        colorOf,\n        (r) => {\n          const left = x(r.x0);\n          const top = y(r.y0);\n          ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);\n        }\n      );\n      fillByColor(\n        ctx,\n        layer.shapes,\n        (s) => inPass(s) && visible(s),\n        colorOf,\n        (s) => {\n          trace(ctx, s.commands, x, y);\n        }\n      );\n    }\n  }\n  const stroke = frame.darkMode ? \"#d0d0d0\" : \"#000000\";\n  const fill = frame.darkMode ? \"rgba(40,40,40,0.4)\" : \"rgba(255,255,255,0.4)\";\n  ctx.lineWidth = outlineWidth(frame);\n  for (const node of picture.nodes) {\n    if (visible(node) && node.name !== frame.highlightNode) {\n      ctx.beginPath();\n      trace(ctx, node.commands, x, y);\n      const tint = frame.nodeColors?.get(node.name);\n      ctx.fillStyle = tint ?? fill;\n      ctx.strokeStyle = stroke;\n      ctx.globalAlpha = tint ? NODE_TINT_ALPHA : 1;\n      ctx.fill();\n      ctx.globalAlpha = outlineAlpha(x(node.x1) - x(node.x0));\n      ctx.stroke();\n      ctx.globalAlpha = 1;\n    }\n  }\n  drawTubeMapHighlight(ctx, picture, frame);\n  drawMismatches(ctx, picture.mismatches, frame);\n}\nfunction outlineWidth(frame) {\n  return 2 * Math.max(0.25, Math.min(1, frame.yScale));\n}\nfunction drawTubeMapHighlight(ctx, picture, frame) {\n  const node = frame.highlightNode ? picture.nodes.find((n) => n.name === frame.highlightNode) : void 0;\n  if (node) {\n    ctx.beginPath();\n    trace(ctx, node.commands, frame.x, frame.y);\n    ctx.globalAlpha = 1;\n    ctx.lineWidth = outlineWidth(frame);\n    ctx.fillStyle = \"rgba(255,192,203,0.5)\";\n    ctx.strokeStyle = \"#ff0000\";\n    ctx.fill();\n    ctx.stroke();\n  }\n}\nvar MISMATCH_FONT_PX = 12;\nvar MIN_MISMATCH_FONT_PX = 6;\nfunction mismatchesLegible(yScale) {\n  return MISMATCH_FONT_PX * yScale >= MIN_MISMATCH_FONT_PX;\n}\nfunction mismatchOnScreen(m, { x, width }) {\n  const [x0, x1] = m.kind === \"insertion\" ? [m.x, m.x] : [m.x0, m.x1];\n  return x(x1) >= 0 && x(x0) <= width;\n}\nfunction drawMismatches(ctx, marks, frame) {\n  const { x, y, yScale, darkMode } = frame;\n  if (!mismatchesLegible(yScale) || marks.length === 0) {\n    return;\n  }\n  const fontPx = MISMATCH_FONT_PX * yScale;\n  ctx.fillStyle = \"grey\";\n  ctx.beginPath();\n  for (const m of marks) {\n    if (m.kind === \"deletion\" && mismatchOnScreen(m, frame)) {\n      const left = x(m.x0);\n      const top = y(m.y);\n      ctx.rect(left, top, x(m.x1) - left, y(m.y + m.height) - top);\n    }\n  }\n  ctx.fill();\n  ctx.font = `${fontPx}px monospace`;\n  ctx.textAlign = \"left\";\n  ctx.textBaseline = \"alphabetic\";\n  ctx.fillStyle = darkMode ? \"#ffffff\" : \"#000000\";\n  for (const m of marks) {\n    if (!mismatchOnScreen(m, frame)) {\n      continue;\n    }\n    if (m.kind === \"substitution\") {\n      ctx.fillText(m.seq, x(m.x0) + 1, y(m.y + m.height));\n    } else if (m.kind === \"insertion\") {\n      ctx.fillText(\"*\", x(m.x) - 3, y(m.y + m.height));\n    }\n  }\n}\nfunction inside(points, sx, sy) {\n  let hit = false;\n  for (let i = 0, j = points.length - 1; i < points.length; j = i++) {\n    const [xi, yi] = points[i];\n    const [xj, yj] = points[j];\n    if (yi > sy !== yj > sy && sx < (xj - xi) * (sy - yi) / (yj - yi) + xi) {\n      hit = !hit;\n    }\n  }\n  return hit;\n}\nfunction tubeMapTrackAt(picture, { x, y }, sx, sy) {\n  for (let l = picture.layers.length - 1; l >= 0; l--) {\n    const { rects, shapes } = picture.layers[l];\n    for (const reference of [true, false]) {\n      for (const r of rects) {\n        if (r.reference === reference && x(r.x0) <= sx && sx <= x(r.x1) && y(r.y0) <= sy && sy <= y(r.y1)) {\n          return r.id;\n        }\n      }\n      for (const s of shapes) {\n        if (s.reference === reference && x(s.x0) <= sx && sx <= x(s.x1) && inside(\n          s.outline.map(([px, py]) => [x(px), y(py)]),\n          sx,\n          sy\n        )) {\n          return s.id;\n        }\n      }\n    }\n  }\n  return void 0;\n}\nvar INSERTION_SLOP_PX = 4;\nfunction tubeMapMismatchAt(picture, frame, sx, sy) {\n  const { x, y, yScale } = frame;\n  return mismatchesLegible(yScale) ? picture.mismatches.find(\n    (m) => y(m.y) <= sy && sy <= y(m.y + m.height) && (m.kind === \"insertion\" ? Math.abs(x(m.x) - sx) <= INSERTION_SLOP_PX : x(m.x0) <= sx && sx <= x(m.x1))\n  ) : void 0;\n}\n\nexport {\n  parsePath,\n  trackColors,\n  tubeMapPicture,\n  drawTubeMap,\n  drawTubeMapHighlight,\n  mismatchesLegible,\n  mismatchOnScreen,\n  tubeMapTrackAt,\n  tubeMapMismatchAt\n};\n", "const host = JBrowseExports[\"@jbrowse/core/util/groupKeys\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/groupKeys\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const MAX_GROUPS = /* @__PURE__ */ read(\"MAX_GROUPS\")\nexport const OVERFLOW_GROUP_KEY = /* @__PURE__ */ read(\"OVERFLOW_GROUP_KEY\")\nexport const capGroupKeys = /* @__PURE__ */ read(\"capGroupKeys\")\nexport const carryGroupDomain = /* @__PURE__ */ read(\"carryGroupDomain\")\nexport const compareGroupKeys = /* @__PURE__ */ read(\"compareGroupKeys\")\nexport const groupKeyComparator = /* @__PURE__ */ read(\"groupKeyComparator\")\nexport const groupKeySpaceOf = /* @__PURE__ */ read(\"groupKeySpaceOf\")\nexport const overflowLabel = /* @__PURE__ */ read(\"overflowLabel\")\nexport const valueText = /* @__PURE__ */ read(\"valueText\")\nexport default host && host.__esModule ? host.default : host", "import { walkRowsTree } from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { groupKeyComparator } from '@jbrowse/core/util/groupKeys'\n\nimport type { El } from '@jbrowse/bandage-core/el'\nimport type {\n  WalkRowsFrame,\n  WalkRowsWithCalls,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\n\n// Walk rows stacked into one section per value of a sample table's column,\n// as jbrowse-plugin-tandem-repeat's \"Group by\u2026\" stacks its alleles. Placement\n// here, not in bandage-core's walkRowsTree, which puts row i at i * rowPx.\n\n// One row of a samples TSV: the sample's name and a value per column\nexport type SampleRow = { name: string } & Record<string, string>\n\nexport interface WalkRowGroupBy {\n  field: string\n  domain?: string[]\n}\n\nexport interface WalkRowSection {\n  // '' for the rows with no value\n  key: string\n  title: string\n  // index of the section's first row among the reference row and the rows\n  first: number\n  count: number\n}\n\nexport const SECTION_HEADER_PX = 16\n\n// A samples TSV as core's samplesTsv reads one: a header row, the sample's\n// name in the first column, the first row of a repeated name kept. Hosts\n// re-export that module only from v5.0.0-beta.11, so it is read here.\nexport function parseSamplesTsv(text: string): SampleRow[] {\n  const [head = '', ...lines] = text.split(/\\r\\n|\\r|\\n/)\n  const columns = head.split('\\t').slice(1)\n  const rows = new Map<string, SampleRow>()\n  for (const line of lines) {\n    if (!line) {\n      continue\n    }\n    const [name = '', ...values] = line.split('\\t')\n    if (name && !rows.has(name)) {\n      rows.set(name, {\n        ...Object.fromEntries(columns.map((c, i) => [c, values[i] ?? ''])),\n        name,\n      })\n    }\n  }\n  return [...rows.values()]\n}\n\nexport function metadataColumns(rows: SampleRow[] | undefined) {\n  const columns = new Set<string>()\n  for (const row of rows ?? []) {\n    for (const key of Object.keys(row)) {\n      if (key !== 'name') {\n        columns.add(key)\n      }\n    }\n  }\n  return [...columns]\n}\n\n// The setting as a snapshot may hold it: a bare field name, or the object\nexport function groupByOf(value: unknown): WalkRowGroupBy | undefined {\n  if (typeof value === 'string') {\n    return value ? { field: value } : undefined\n  }\n  const { field, domain } = (value ?? {}) as Record<string, unknown>\n  if (typeof field !== 'string' || !field) {\n    return undefined\n  }\n  return Array.isArray(domain)\n    ? { field, domain: domain.filter(d => typeof d === 'string') }\n    : { field }\n}\n\nexport function plural(n: number, noun: string) {\n  return `${n} ${noun}${n === 1 ? '' : 's'}`\n}\n\n// A walk's value in a column: its haplotype's row (`HG00097#1`), else its\n// sample's (`HG00097`), else ''\nexport function columnValueOf(field: string, table: SampleRow[]) {\n  const valueOf = new Map(table.map(row => [row.name, row[field] ?? '']))\n  return (haplotype: string, sample: string) =>\n    valueOf.get(haplotype) || valueOf.get(sample) || ''\n}\n\n// Items grouped by their value in a column, each group in the order its items\n// came in, the groups in the order a JBrowse Group by sorts them, and each\n// titled with its value and how many distinct `noun`s its items are\nexport function groupsByColumn<T>(\n  items: readonly T[],\n  valueOf: (item: T) => string,\n  { field, domain }: { field: string; domain?: readonly string[] },\n  noun: string,\n  nounOf: (item: T) => string,\n) {\n  const groups = new Map<string, T[]>()\n  for (const item of items) {\n    const key = valueOf(item)\n    const group = groups.get(key)\n    if (group) {\n      group.push(item)\n    } else {\n      groups.set(key, [item])\n    }\n  }\n  return [...groups.keys()].sort(groupKeyComparator(domain)).map(key => {\n    const members = groups.get(key)!\n    const n = new Set(members.map(nounOf)).size\n    return {\n      key,\n      members,\n      title: `${key || `${field}: none`} \u00B7 ${plural(n, noun)}`,\n    }\n  })\n}\n\n// The rows reordered section by section; rows with no value stack last\nexport function groupWalkRows<R extends { sample: string; label: string }>(\n  rows: R[],\n  table: SampleRow[],\n  groupBy: WalkRowGroupBy,\n) {\n  const valueOf = columnValueOf(groupBy.field, table)\n  const groups = groupsByColumn(\n    rows,\n    row => valueOf(row.label, row.sample),\n    groupBy,\n    'haplotype',\n    row => row.label,\n  )\n  let first = 1\n  const sections: WalkRowSection[] = groups.map(({ key, members, title }) => {\n    const section = { key, title, first, count: members.length }\n    first += members.length\n    return section\n  })\n  return {\n    rows: groups.flatMap(g => g.members),\n    sections,\n  }\n}\n\n// Where rows and section headers sit, in px down from the reference row's\n// centre, at one row pitch shared by every section: a header strip above\n// each section's first row pushes every row after it down\nexport function sectionPlacement(sections: WalkRowSection[], rowPx: number) {\n  const sectionOf = (i: number) => {\n    let k = -1\n    while (k + 1 < sections.length && sections[k + 1]!.first <= i) {\n      k++\n    }\n    return k\n  }\n  const rowY = (i: number) => i * rowPx + (sectionOf(i) + 1) * SECTION_HEADER_PX\n  return {\n    rowY,\n    headers: sections.map((s, k) => ({\n      ...s,\n      top: (s.first - 0.5) * rowPx + k * SECTION_HEADER_PX,\n    })),\n    headersPx: sections.length * SECTION_HEADER_PX,\n    // the row whose centre is nearest y\n    rowAt(y: number, rows: number) {\n      let best = 0\n      for (let k = -1; k < sections.length; k++) {\n        const lo = k < 0 ? 0 : sections[k]!.first\n        const hi =\n          k < 0\n            ? Math.min(rows, sections[0]?.first ?? rows)\n            : lo + sections[k]!.count\n        const shift = (k + 1) * SECTION_HEADER_PX\n        const i = Math.min(\n          hi - 1,\n          Math.max(lo, Math.round((y - shift) / rowPx)),\n        )\n        if (Math.abs(rowY(i) - y) < Math.abs(rowY(best) - y)) {\n          best = i\n        }\n      }\n      return best\n    },\n  }\n}\n\n// The rows' trees, a section at a time while grouped. walkRowsTree puts its\n// i-th row at i * rowPx below its reference row and draws that row too, so\n// each section is drawn shifted down to its place with its reference row\n// dropped.\nexport function walkRowTrees(\n  bars: WalkRowsWithCalls,\n  sections: WalkRowSection[],\n  rowY: (i: number) => number,\n  frame: WalkRowsFrame & { rowPx: number },\n  o: Parameters<typeof walkRowsTree>[2] & { idPrefix: string },\n): El[] {\n  if (sections.length === 0) {\n    return [walkRowsTree(bars, frame, o)]\n  }\n  return [\n    walkRowsTree({ ...bars, rows: [] }, frame, o),\n    ...sections.flatMap((section, k) => {\n      const tree = walkRowsTree(\n        {\n          ...bars,\n          rows: bars.rows.slice(\n            section.first - 1,\n            section.first - 1 + section.count,\n          ),\n        },\n        {\n          ...frame,\n          translateY:\n            frame.translateY +\n            (rowY(section.first) - frame.rowPx) * frame.scaleY,\n        },\n        { ...o, idPrefix: `${o.idPrefix}-s${k}` },\n      )\n      return tree.children.filter(\n        (c): c is El =>\n          typeof c !== 'string' &&\n          c.attrs['data-testid'] !== 'graph-walk-reference',\n      )\n    }),\n  ]\n}\n", "import {\n  buildNeighbors\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  REFERENCE_RANK,\n  isAnchored\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/alleleProjection/projectAlleles.ts\nfunction collectRun(seed, byId, adj, claimed) {\n  const members = [];\n  const anchors = [];\n  const queue = [seed];\n  claimed.add(seed);\n  while (queue.length > 0) {\n    const id = queue.pop();\n    const node = byId.get(id);\n    if (node) {\n      members.push(node);\n      for (const neighborId of adj.get(id) ?? []) {\n        const neighbor = byId.get(neighborId);\n        if (neighbor) {\n          if (neighbor.stable.rank === REFERENCE_RANK) {\n            anchors.push(neighbor);\n          } else if (!claimed.has(neighborId)) {\n            claimed.add(neighborId);\n            queue.push(neighborId);\n          }\n        }\n      }\n    }\n  }\n  return { members, anchors };\n}\nfunction anchorSpan(anchors) {\n  const refNames = new Set(anchors.map((a) => a.stable.refName));\n  if (refNames.size !== 1 || anchors.length < 2) {\n    return void 0;\n  }\n  const sorted = [...anchors].sort((a, b) => a.stable.start - b.stable.start);\n  const first = sorted[0];\n  const last = sorted.at(-1);\n  const start = first.stable.start + first.length;\n  const end = last.stable.start;\n  return end >= start ? { start, end, entry: first } : void 0;\n}\nfunction runDistances(members, entry, adj) {\n  const byId = new Map(members.map((m) => [m.id, m]));\n  const dist = /* @__PURE__ */ new Map();\n  const queue = [];\n  for (const neighborId of adj.get(entry.id) ?? []) {\n    if (byId.has(neighborId)) {\n      dist.set(neighborId, 0);\n      queue.push(neighborId);\n    }\n  }\n  if (queue.length === 0) {\n    for (const member of members) {\n      dist.set(member.id, 0);\n      queue.push(member.id);\n    }\n  }\n  for (const id of queue) {\n    const reach = dist.get(id) + byId.get(id).length;\n    for (const neighborId of adj.get(id) ?? []) {\n      if (byId.has(neighborId)) {\n        const known = dist.get(neighborId);\n        if (known === void 0 || reach < known) {\n          dist.set(neighborId, reach);\n          queue.push(neighborId);\n        }\n      }\n    }\n  }\n  return dist;\n}\nfunction runOffsets(members, entry, adj) {\n  const dist = runDistances(members, entry, adj);\n  const ordered = [...members].sort((a, b) => dist.get(a.id) - dist.get(b.id));\n  const rank = new Map(ordered.map((m, i) => [m.id, i]));\n  const byId = new Map(members.map((m) => [m.id, m]));\n  const offsets = /* @__PURE__ */ new Map();\n  for (const [i, member] of ordered.entries()) {\n    let offset = 0;\n    for (const neighborId of adj.get(member.id) ?? []) {\n      const neighbor = byId.get(neighborId);\n      if (neighbor && rank.get(neighborId) < i) {\n        offset = Math.max(offset, offsets.get(neighborId) + neighbor.length);\n      }\n    }\n    offsets.set(member.id, offset);\n  }\n  return { offsets, ordered };\n}\nfunction projectAlleles(graph) {\n  const byId = new Map(\n    graph.nodes.filter(isAnchored).map((n) => [n.id, n])\n  );\n  const adj = buildNeighbors(graph);\n  const claimed = /* @__PURE__ */ new Set();\n  const alleles = [];\n  for (const node of byId.values()) {\n    if (node.stable.rank !== REFERENCE_RANK && !claimed.has(node.id)) {\n      const { members, anchors } = collectRun(node.id, byId, adj, claimed);\n      const span = anchorSpan(anchors);\n      if (span) {\n        const { offsets, ordered } = runOffsets(members, span.entry, adj);\n        alleles.push({\n          start: span.start,\n          refSpan: span.end - span.start,\n          nodeIds: ordered.map((m) => m.id),\n          nodeOffsets: ordered.map((m) => offsets.get(m.id)),\n          pathLength: ordered.reduce(\n            (max, m) => Math.max(max, offsets.get(m.id) + m.length),\n            0\n          )\n        });\n      }\n    }\n  }\n  return alleles.sort((a, b) => a.start - b.start);\n}\n\nexport {\n  projectAlleles\n};\n", "import { parsePanSN } from '@jbrowse/bandage-core/alleleProjection/projectAlleles'\nimport { formatBp } from '@jbrowse/bandage-core/graphLabels'\nimport { pathOrigin } from '@jbrowse/bandage-core/pathAnchoring'\nimport { drawTubeMapHighlight } from '@jbrowse/bandage-core/tubeMap/draw'\nimport { groupKeyComparator } from '@jbrowse/core/util/groupKeys'\n\nimport { columnValueOf, groupsByColumn, plural } from './walkRowGroups'\n\nimport type { SampleRow } from './walkRowGroups'\nimport type { FacetBy } from '@jbrowse/bandage-core/facetGrid'\nimport type { TubeMapDrawing } from '@jbrowse/bandage-core/layout/tubeMapLayout'\nimport type { TubeMapPicture } from '@jbrowse/bandage-core/tubeMap/draw'\nimport type { TubeMapTransform } from '@jbrowse/bandage-core/tubeMap/frame'\nimport type { Graph, LayoutResult } from '@jbrowse/bandage-core/types'\n\n// A tube map split into small multiples: a panel per sample, or per walk, each\n// the reference and that group's walks laid out alone, stacked down the pane.\n// On the reference axis every panel's columns sit at their bp, so a box lines\n// up across the panels and with the linear view's tracks.\n\n// px above each panel, which its title takes\nexport const PANEL_GAP = 28\nexport const PANEL_REFERENCE_TUBE = '#4d4d4d'\nexport const PANEL_TUBE = '#5b8cc4'\nexport const PANEL_TUBES = [PANEL_TUBE, '#82abd9']\n// greys beside boxes tinted by the node scheme, so no tube shares a box's hue\nexport const TINTED_TUBES = ['#8c8c8c', '#adadad']\nexport const PANEL_TITLE_FONT = '12px sans-serif'\n\nexport const TUBE_MAP_PANELS: { field: '' | FacetBy; label: string }[] = [\n  { field: '', label: 'None' },\n  { field: 'sample', label: 'A panel per sample' },\n  { field: 'walk', label: 'A panel per haplotype' },\n]\n\n// How the walks split: by sample or walk, the groups the domain names first\n// and the rest in the graph's order, or by a sample table column, its values\n// in the order a JBrowse Group by sorts them\nexport type TubeMapPanelSplit =\n  | { by: FacetBy; domain?: readonly string[] }\n  | { by: 'column'; field: string; table: SampleRow[]; domain?: string[] }\n\nexport interface TubeMapPanelGroup {\n  key: string\n  // the graph's own path names, pieces of one walk included\n  paths: string[]\n  // a column's value names a group of samples, and says how many\n  label?: string\n}\n\nexport interface TubeMapPanel extends TubeMapPanelGroup {\n  result: LayoutResult & { tubeMap: TubeMapDrawing }\n  // where the panel's drawing starts down the stack, in tube px\n  top: number\n  height: number\n}\n\n// a pane's layout: a tube map split into panels carries them, and the stack's\n// extent and node positions in place of the whole map's\nexport type PaneLayout = LayoutResult & { tubeMapPanels?: TubeMapPanel[] }\n\nconst walkOf = (name: string) => pathOrigin(name).name\n\n// A tube coloured by its role where no key could name a hue per walk: the\n// reference charcoal and the haplotypes blue, or grey beside tinted boxes,\n// neighbours alternating two shades so each stays countable in a bundle\nexport function roleTubeColors(\n  paths: readonly { name: string }[],\n  reference: string | undefined,\n  tubes = PANEL_TUBES,\n) {\n  let haplotype = 0\n  return paths.map(p =>\n    walkOf(p.name) === reference\n      ? PANEL_REFERENCE_TUBE\n      : tubes[haplotype++ % tubes.length]!,\n  )\n}\n\n// a categorical palette for a column's values, a hue each in sorted order\nconst VALUE_TUBES = [\n  '#4e79a7',\n  '#f28e2b',\n  '#59a14f',\n  '#e15759',\n  '#b07aa1',\n  '#76b7b2',\n  '#edc948',\n  '#9c755f',\n  '#ff9da7',\n  '#bab0ac',\n]\nexport const NO_VALUE_TUBE = '#c8c8c8'\n\n// Each of a column's values its hue, in the order a JBrowse Group by sorts\n// them; a value past the palette, or none, is grey\nexport function valueTubePalette(values: Iterable<string>) {\n  const sorted = [...new Set(values)]\n    .filter(v => v !== '')\n    .sort(groupKeyComparator())\n  return new Map(sorted.map((v, i) => [v, VALUE_TUBES[i] ?? NO_VALUE_TUBE]))\n}\n\n// The reference charcoal and each walk, or the bundle it stands for, in its\n// value's hue\nexport function valueTubeColors(\n  paths: readonly { name: string; members?: string[] }[],\n  reference: string | undefined,\n  valueOf: (walk: string) => string,\n  palette: ReadonlyMap<string, string>,\n) {\n  return paths.map(p => {\n    const walk = walkOf(p.name)\n    return walk === reference\n      ? PANEL_REFERENCE_TUBE\n      : (palette.get(valueOf(p.members?.[0] ?? walk)) ?? NO_VALUE_TUBE)\n  })\n}\n\n// A PanSN walk's value in a column\nexport function columnKeyOf(field: string, table: SampleRow[]) {\n  const valueOf = columnValueOf(field, table)\n  return (walk: string) => {\n    const { sample, haplotype } = parsePanSN(walk)\n    return valueOf(`${sample}#${haplotype}`, sample)\n  }\n}\n\n// Each non-reference walk's group\nexport function tubeMapPanelGroups(\n  graph: Graph,\n  split: TubeMapPanelSplit,\n): TubeMapPanelGroup[] {\n  const names = (graph.paths ?? [])\n    .map(p => p.name)\n    .filter(name => walkOf(name) !== graph.referencePath)\n  if (split.by === 'column') {\n    const keyOf = columnKeyOf(split.field, split.table)\n    return groupsByColumn(\n      names,\n      name => keyOf(walkOf(name)),\n      split,\n      'sample',\n      name => parsePanSN(walkOf(name)).sample,\n    ).map(({ key, members, title }) => ({ key, paths: members, label: title }))\n  }\n  const keyOf =\n    split.by === 'sample'\n      ? (walk: string) => parsePanSN(walk).sample\n      : (walk: string) => walk\n  const groups = new Map<string, string[]>()\n  for (const name of names) {\n    const key = keyOf(walkOf(name))\n    const list = groups.get(key)\n    if (list) {\n      list.push(name)\n    } else {\n      groups.set(key, [name])\n    }\n  }\n  const domain = split.domain ?? []\n  const rank = new Map(domain.map((key, i) => [key, i]))\n  const listed = (key: string) => rank.get(key) ?? domain.length\n  return [...groups]\n    .map(([key, paths], i) => ({ key, paths, i }))\n    .sort((a, b) => listed(a.key) - listed(b.key) || a.i - b.i)\n    .map(({ key, paths }) => ({ key, paths }))\n}\n\n// The box a panel draws a node of the laid graph in: the node itself, or the\n// merged run holding it\nexport function boxOf(drawing: TubeMapDrawing, node: string) {\n  if (drawing.graph.nodes.some(n => n.id === node)) {\n    return node\n  }\n  for (const [box, members] of drawing.members) {\n    if (members.includes(node)) {\n      return box\n    }\n  }\n  return undefined\n}\n\n// The member of a merged run under pane x `sx`, a run drawn from `left` to\n// `right` across its members' bp, so a panel's count is of the bp the pointer\n// is on, not of the whole run. Undefined when no member has a span.\nexport function memberAt(\n  members: readonly string[],\n  spanOf: (id: string) => { start: number; end: number } | undefined,\n  left: number,\n  right: number,\n  sx: number,\n) {\n  const spans = members.flatMap(id => {\n    const span = spanOf(id)\n    return span ? [{ id, ...span }] : []\n  })\n  if (spans.length === 0) {\n    return undefined\n  }\n  const start = Math.min(...spans.map(s => s.start))\n  const end = Math.max(...spans.map(s => s.end))\n  const share = right > left ? (sx - left) / (right - left) : 0\n  const bp = start + Math.min(1, Math.max(0, share)) * (end - start)\n  const distance = (s: { start: number; end: number }) =>\n    bp < s.start ? s.start - bp : bp >= s.end ? bp - s.end + 1 : 0\n  return spans.reduce((a, b) => (distance(b) < distance(a) ? b : a)).id\n}\n\n// How many of a panel's walks pass through `box`, of how many it holds, a\n// bundle counting each walk it stands for\nexport function walksThrough(graph: Graph, box: string) {\n  const all = new Set<string>()\n  const here = new Set<string>()\n  for (const p of graph.paths ?? []) {\n    const walk = walkOf(p.name)\n    if (walk !== graph.referencePath) {\n      for (const member of p.members ?? [walk]) {\n        all.add(member)\n        if (p.nodeIds.includes(box)) {\n          here.add(member)\n        }\n      }\n    }\n  }\n  return { here: here.size, of: all.size }\n}\n\nconst COUNT_FONT = 'bold 11px sans-serif'\nconst MIN_COUNT_RUN_PX = 80\nconst MIN_COUNT_TUBE_PX = 9\n\n// Each bundle's count on its tube, along every straight run wide and tall\n// enough to hold it, so the count stands where its route parts from others\nexport function drawBundleCounts(\n  ctx: CanvasRenderingContext2D,\n  picture: TubeMapPicture,\n  graph: Graph,\n  { x, y, width }: TubeMapTransform & { width: number },\n) {\n  const paths = graph.paths ?? []\n  if (!paths.some(p => p.members)) {\n    return\n  }\n  const counts = new Map<number, number>()\n  paths.forEach((p, i) => {\n    if (walkOf(p.name) !== graph.referencePath) {\n      counts.set(i, p.members?.length ?? 1)\n    }\n  })\n  ctx.font = COUNT_FONT\n  ctx.textAlign = 'left'\n  ctx.textBaseline = 'middle'\n  ctx.fillStyle = '#0b1f3a'\n  for (const r of picture.layers[0]?.rects ?? []) {\n    const n = counts.get(r.id)\n    const left = Math.max(0, x(r.x0))\n    const right = Math.min(width, x(r.x1))\n    const top = y(r.y0)\n    const bottom = y(r.y1)\n    if (\n      n !== undefined &&\n      right - left >= MIN_COUNT_RUN_PX &&\n      bottom - top >= MIN_COUNT_TUBE_PX\n    ) {\n      ctx.fillText(`\u00D7${n}`, left + 4, (top + bottom) / 2)\n    }\n  }\n}\n\nconst LENGTH_FONT = '10px sans-serif'\nconst MIN_LENGTH_LABEL_BP = 1000\n\n// Each box of a reference-axis map whose sequence the axis squeezes narrower\n// than its length's label, labelled beside it: off the reference a 33 kb\n// module draws a few px wide, as a SNP's box does. Boxes of one length\n// stacked in a column share a label, \"each\", at the lowest, where the stack\n// has room; a label that would overlap one already drawn is left out.\nexport function drawSqueezedLengths(\n  ctx: CanvasRenderingContext2D,\n  drawing: TubeMapDrawing,\n  { x, y, width }: TubeMapTransform & { width: number },\n) {\n  if (!drawing.columns) {\n    return\n  }\n  const lengthOf = new Map(drawing.graph.nodes.map(n => [n.id, n.length]))\n  ctx.font = LENGTH_FONT\n  const stacks = new Map<\n    string,\n    { text: string; right: number; mid: number; count: number }\n  >()\n  // sparse, so forEach, which skips its holes\n  drawing.layout.nodes.forEach(node => {\n    const bp = lengthOf.get(node.name) ?? 0\n    const left = x(node.x)\n    const right = x(node.x + node.pixelWidth)\n    const text = formatBp(bp)\n    if (\n      node.order >= 0 &&\n      bp >= MIN_LENGTH_LABEL_BP &&\n      right - left < ctx.measureText(text).width\n    ) {\n      const mid = (y(node.y) + y(node.y + node.contentHeight)) / 2\n      const key = `${Math.round(right)}:${text}`\n      const stack = stacks.get(key)\n      if (stack) {\n        stack.count++\n        stack.mid = Math.max(stack.mid, mid)\n      } else {\n        stacks.set(key, { text, right, mid, count: 1 })\n      }\n    }\n  })\n  ctx.textAlign = 'left'\n  ctx.textBaseline = 'middle'\n  ctx.lineJoin = 'round'\n  ctx.lineWidth = 3\n  ctx.strokeStyle = 'rgba(255,255,255,0.9)'\n  ctx.fillStyle = 'rgba(0,0,0,0.75)'\n  const drawn: { x0: number; x1: number; y0: number; y1: number }[] = []\n  for (const { text, right, mid, count } of stacks.values()) {\n    const label = count > 1 ? `${text} each` : text\n    const box = {\n      x0: right + 3,\n      x1: right + 3 + ctx.measureText(label).width,\n      y0: mid - 6,\n      y1: mid + 6,\n    }\n    if (\n      box.x1 <= width &&\n      !drawn.some(\n        d => d.x0 < box.x1 && box.x0 < d.x1 && d.y0 < box.y1 && box.y0 < d.y1,\n      )\n    ) {\n      drawn.push(box)\n      ctx.strokeText(label, box.x0, mid)\n      ctx.fillText(label, box.x0, mid)\n    }\n  }\n}\n\ninterface PanelOnScreen {\n  picture: TubeMapPicture\n  frame: TubeMapTransform\n  label: string\n  titleTop: number\n  top: number\n}\n\n// The hovered box in each panel that draws it, and beside each title how many\n// of that panel's haplotypes pass through it. On the hover layer, so a hover\n// repaints no tube.\nexport function paintPanelHover(\n  ctx: CanvasRenderingContext2D,\n  panels: PanelOnScreen[],\n  hover: ({ box: string; here: number; of: number } | undefined)[] | undefined,\n  { width, lit }: { width: number; lit: boolean },\n) {\n  panels.forEach((p, i) => {\n    const hit = hover?.[i]\n    if (!hit) {\n      return\n    }\n    if (lit) {\n      drawTubeMapHighlight(ctx, p.picture, {\n        ...p.frame,\n        width,\n        highlightNode: hit.box,\n      })\n    }\n    ctx.font = PANEL_TITLE_FONT\n    ctx.textAlign = 'left'\n    ctx.textBaseline = 'top'\n    ctx.fillStyle = '#c00000'\n    ctx.fillText(\n      ` \u00B7 ${hit.here} of ${plural(hit.of, 'haplotype')} here`,\n      6 + ctx.measureText(p.label).width,\n      p.titleTop + 4,\n    )\n  })\n}\n\n// The reference and `paths` alone: the nodes they visit and the links between\n// them, without reads, which name no sample\nexport function graphOfPaths(graph: Graph, paths: readonly string[]): Graph {\n  const kept = new Set(paths)\n  const keptPaths = (graph.paths ?? []).filter(\n    p => kept.has(p.name) || walkOf(p.name) === graph.referencePath,\n  )\n  const walks = new Set(keptPaths.map(p => walkOf(p.name)))\n  const nodeIds = new Set(keptPaths.flatMap(p => p.nodeIds))\n  const nodes = graph.nodes.filter(n => nodeIds.has(n.id))\n  const names = new Set(nodes.map(n => n.name))\n  const pathVisits = graph.pathVisits?.filter(\n    path => walks.has(path),\n    segment => names.has(segment),\n  )\n  return {\n    ...graph,\n    nodes,\n    edges: graph.edges.filter(e => nodeIds.has(e.from) && nodeIds.has(e.to)),\n    paths: keptPaths,\n    anchorPaths: graph.anchorPaths?.filter(p => walks.has(p.name)),\n    pathVisits,\n    reads: undefined,\n  }\n}\n\n// `whole` with each group's own tube map stacked in its place, a title's gap\n// above each, or `whole` alone when fewer than two groups draw\nexport function withTubeMapPanels(\n  whole: LayoutResult,\n  laidOut: (TubeMapPanelGroup & { result: LayoutResult | undefined })[],\n): PaneLayout {\n  const panels: TubeMapPanel[] = []\n  const nodePositions: LayoutResult['nodePositions'] = {}\n  let y = 0\n  let minX = Infinity\n  let maxX = -Infinity\n  for (const { key, paths, label, result } of laidOut) {\n    const tubeMap = result?.tubeMap\n    const extent = result?.extent\n    if (tubeMap && extent) {\n      const top = y + PANEL_GAP\n      const height = (extent.maxY ?? 0) - (extent.minY ?? 0)\n      panels.push({\n        key,\n        paths,\n        label,\n        result: { ...result, tubeMap },\n        top,\n        height,\n      })\n      const dy = top - (extent.minY ?? 0)\n      for (const [id, segments] of Object.entries(result.nodePositions)) {\n        nodePositions[id] = segments.map(s => ({ x: s.x, y: s.y + dy }))\n      }\n      y = top + height\n      minX = Math.min(minX, extent.minX ?? minX)\n      maxX = Math.max(maxX, extent.maxX ?? maxX)\n    }\n  }\n  return panels.length > 1\n    ? {\n        ...whole,\n        nodePositions,\n        extent: {\n          ...(minX <= maxX ? { minX, maxX } : {}),\n          minY: 0,\n          maxY: y,\n        },\n        tubeMapPanels: panels,\n      }\n    : whole\n}\n", "import {\n  el\n} from \"./chunk-H2H4Y3TV.js\";\n\n// src/genes/exonOutline.ts\nvar EXON_COLOR = \"#daa520\";\nvar EXON_GAP_PX = 1;\nvar EXON_LINE_PX = 2;\nvar MIN_LANE_PX = 4;\nfunction exonStretches(pins, halfWidthPx, lift, pathOf = (d) => d) {\n  const inkPx = (nodeId) => {\n    const own = halfWidthPx(nodeId) * 2;\n    return lift?.nodeIds.has(nodeId) ? Math.max(own, lift.walks.length * MIN_LANE_PX) : own;\n  };\n  return pins.flatMap(\n    (pin) => pin.exonsByNode.map(({ nodeId, d }) => ({\n      key: `${pin.gene.name}-${pin.gene.start}-${nodeId}`,\n      d: pathOf(d),\n      inner: inkPx(nodeId) + 2 * EXON_GAP_PX\n    }))\n  );\n}\nfunction exonOutlineTree(stretches, o) {\n  if (stretches.length === 0) {\n    return void 0;\n  }\n  const stroke = (s, color, width) => el(\"path\", {\n    d: s.d,\n    fill: \"none\",\n    stroke: color,\n    \"stroke-width\": width,\n    \"stroke-linecap\": \"round\",\n    \"stroke-linejoin\": \"round\",\n    \"vector-effect\": o.transform ? \"non-scaling-stroke\" : void 0\n  });\n  return el(\n    \"g\",\n    {},\n    el(\n      \"mask\",\n      {\n        id: o.id,\n        maskUnits: \"userSpaceOnUse\",\n        x: 0,\n        y: 0,\n        width: o.width,\n        height: o.height\n      },\n      el(\n        \"g\",\n        { transform: o.transform },\n        ...stretches.map((s) => stroke(s, \"#fff\", s.inner + 2 * EXON_LINE_PX)),\n        ...stretches.map((s) => stroke(s, \"#000\", s.inner))\n      )\n    ),\n    el(\"rect\", {\n      width: o.width,\n      height: o.height,\n      fill: EXON_COLOR,\n      mask: `url(#${o.id})`\n    })\n  );\n}\n\nexport {\n  EXON_COLOR,\n  exonStretches,\n  exonOutlineTree\n};\n", "import {\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  formatBp,\n  groupDigits\n} from \"./chunk-PFRQBCGC.js\";\n\n// src/walkKey.ts\nfunction rangeText(contig, start, end) {\n  const s = Math.round(start);\n  const e = Math.round(end);\n  return `${contig ? `${contig}:` : \"\"}${groupDigits(s)}-${groupDigits(e)} (${formatBp(e - s)})`;\n}\nfunction walkKey(walk, reference) {\n  const { field } = walk.encoding;\n  const own = walk.range ? rangeText(walk.range.contig, walk.range.start, walk.range.end) : void 0;\n  const scale = field === \"progress\" ? own : field === \"reference\" && reference ? rangeText(reference.name, reference.start, reference.end) : void 0;\n  const spanned = walk.range ? walk.range.end - walk.range.start : walk.bp;\n  const outside = spanned - walk.bp - walk.missingBp - walk.unknownBp;\n  const gaps = [\n    [walk.missingBp, GAP_CAUSE_TEXT.missing],\n    [walk.unknownBp, GAP_CAUSE_TEXT.unknown],\n    [outside, OUTSIDE_TEXT]\n  ];\n  return {\n    delta: walk.referenceBp === void 0 || spanned === walk.referenceBp ? \"\" : ` ${spanned > walk.referenceBp ? \"+\" : \"\\u2212\"}${formatBp(Math.abs(spanned - walk.referenceBp))}`,\n    gaps: gaps.filter(([bp]) => bp > 0).map(([bp, text]) => `, ${formatBp(bp)} ${text}`).join(\"\"),\n    reversed: walk.reversedBp > 0 ? `, ${formatBp(walk.reversedBp)} reversed` : \"\",\n    shades: field !== \"walk\",\n    scale,\n    hover: scale === own ? void 0 : own\n  };\n}\nfunction walkPosition(walk, nodeId, length) {\n  const progress = walk.progress.get(nodeId);\n  const range = walk.range;\n  if (progress === void 0 || !range) {\n    return void 0;\n  }\n  const start = Math.round(\n    range.start + progress * (range.end - range.start) - length / 2\n  );\n  return `${range.contig}:${groupDigits(start)}-${groupDigits(start + length)}`;\n}\n\nexport {\n  rangeText,\n  walkKey,\n  walkPosition\n};\n", "import {\n  tubeSpan\n} from \"./chunk-HSVFCA2J.js\";\n\n// src/tubeMap/genes.ts\nfunction tubeMapGenes(byRefName, genes) {\n  const out = [];\n  for (const gene of genes) {\n    const boxes = byRefName.get(gene.refName);\n    const first = boxes?.[0];\n    const last = boxes?.at(-1);\n    if (!boxes || !first || !last) {\n      continue;\n    }\n    const start = Math.max(gene.start, first.bp0);\n    const end = Math.min(gene.end, last.bp1);\n    if (end <= start) {\n      continue;\n    }\n    out.push({\n      gene,\n      ...tubeSpan(boxes, start, end),\n      exons: gene.exons.filter((e) => e.end > start && e.start < end).map(\n        (e) => tubeSpan(boxes, Math.max(e.start, start), Math.min(e.end, end))\n      )\n    });\n  }\n  return out;\n}\nvar GENE_ROW_PX = 22;\nvar MAX_GENE_ROWS = 4;\nvar EXON_PX = 8;\nvar NAME_FONT = \"11px sans-serif\";\nvar NAME_GAP_PX = 8;\nfunction tubeMapGeneRows(genes) {\n  const edges = genes.flatMap((g) => [\n    { x: g.x0, step: 1 },\n    { x: g.x1, step: -1 }\n  ]).sort((a, b) => a.x - b.x || a.step - b.step);\n  let depth = 0;\n  let most = 0;\n  for (const { step } of edges) {\n    depth += step;\n    most = Math.max(most, depth);\n  }\n  return Math.min(MAX_GENE_ROWS, most);\n}\nfunction drawTubeMapGenes(ctx, genes, frame, bottom, top = 0) {\n  const { x, width, darkMode } = frame;\n  const rows = Math.max(1, Math.floor((bottom - top) / GENE_ROW_PX));\n  const rowEnds = [];\n  const ink = darkMode ? \"#e0e0e6\" : \"#1c1c22\";\n  ctx.font = NAME_FONT;\n  ctx.textAlign = \"center\";\n  ctx.textBaseline = \"alphabetic\";\n  ctx.fillStyle = ink;\n  ctx.strokeStyle = ink;\n  ctx.lineWidth = 1;\n  const placed = genes.map((g) => ({ g, s0: x(g.x0), s1: x(g.x1) })).filter(({ s0, s1 }) => s1 >= 0 && s0 <= width).sort((a, b) => a.s0 - b.s0);\n  for (const { g, s0, s1 } of placed) {\n    const arrow = g.gene.strand > 0 ? \" \\u2192\" : g.gene.strand < 0 ? \"\\u2190 \" : \"\";\n    const label = g.gene.strand < 0 ? `${arrow}${g.gene.name}` : `${g.gene.name}${arrow}`;\n    const mid = (Math.max(s0, 0) + Math.min(s1, width)) / 2;\n    const half = ctx.measureText(label).width / 2;\n    const left = Math.min(s0, mid - half);\n    const right = Math.max(s1, mid + half);\n    let row = rowEnds.findIndex((end) => end + NAME_GAP_PX <= left);\n    if (row === -1) {\n      row = Math.min(rowEnds.length, rows - 1);\n    }\n    rowEnds[row] = Math.max(rowEnds[row] ?? -Infinity, right);\n    const glyphY = bottom - row * GENE_ROW_PX - EXON_PX / 2;\n    ctx.beginPath();\n    ctx.moveTo(s0, glyphY + 0.5);\n    ctx.lineTo(s1, glyphY + 0.5);\n    ctx.stroke();\n    for (const e of g.exons) {\n      const e0 = x(e.x0);\n      ctx.fillRect(e0, glyphY - EXON_PX / 2, Math.max(1, x(e.x1) - e0), EXON_PX);\n    }\n    ctx.fillText(label, mid, glyphY - EXON_PX / 2 - 2);\n  }\n}\n\nexport {\n  tubeMapGenes,\n  GENE_ROW_PX,\n  tubeMapGeneRows,\n  drawTubeMapGenes\n};\n", "import {\n  LIFT_BACKDROP_CSS,\n  computeColorSchemeRange,\n  getNodeColor\n} from \"./chunk-SWCULW6S.js\";\nimport {\n  abgrToCssRgba\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/referenceStrip.ts\nvar REFERENCE_STRIP_PX = 12;\nvar REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8;\nvar OVERHANG_PX = 8;\nvar OVERHANG_CAP_PX = OVERHANG_PX + 3;\nvar MIN_STAGGER_PX = 12;\nfunction referenceStripBlocks(graph, {\n  colorScheme,\n  referenceRamp,\n  walks\n}) {\n  const range = computeColorSchemeRange(graph, referenceRamp);\n  const out = [];\n  graph.nodes.forEach((node, index) => {\n    if (isBackbone(node)) {\n      const colors = walks ? walks.map((w) => {\n        const lane = w.colors.get(node.id);\n        return lane === void 0 ? LIFT_BACKDROP_CSS : abgrToCssRgba(lane);\n      }) : [abgrToCssRgba(getNodeColor(node, index, colorScheme, range))];\n      out.push({\n        node: node.id,\n        bp0: node.stable.start,\n        bp1: node.stable.start + node.length,\n        colors,\n        faded: colors.includes(LIFT_BACKDROP_CSS)\n      });\n    }\n  });\n  return out.sort((a, b) => a.bp0 - b.bp0);\n}\nfunction span(frame, bp0, bp1) {\n  const a = bp0 * frame.scale + frame.translateX;\n  const b = bp1 * frame.scale + frame.translateX;\n  return a < b ? [a, b] : [b, a];\n}\nvar HIT_SLOP_PX = 2;\nfunction stripOverhang(blocks, frame, width) {\n  const a = -frame.translateX / frame.scale;\n  const b = (width - frame.translateX) / frame.scale;\n  const lo = Math.min(a, b);\n  const hi = Math.max(a, b);\n  let below = 0;\n  let above = 0;\n  for (const block of blocks) {\n    below += Math.max(0, Math.min(block.bp1, lo) - block.bp0);\n    above += Math.max(0, block.bp1 - Math.max(block.bp0, hi));\n  }\n  return frame.scale >= 0 ? { left: Math.round(below), right: Math.round(above) } : { left: Math.round(above), right: Math.round(below) };\n}\nfunction stripBlockAt(blocks, frame, sx, sy) {\n  if (sy < 0 || sy > REFERENCE_STRIP_PX + HIT_SLOP_PX) {\n    return void 0;\n  }\n  let hit;\n  let best = HIT_SLOP_PX;\n  for (const b of blocks) {\n    const [x0, x1] = span(frame, b.bp0, b.bp1);\n    const dist = Math.max(0, x0 - sx, sx - x1);\n    if (dist <= best) {\n      best = dist;\n      hit = b.node;\n    }\n  }\n  return hit;\n}\nfunction nodeAnchor(segments, toScreen) {\n  const p = segments?.[Math.floor(segments.length / 2)];\n  return p ? toScreen(p) : void 0;\n}\nfunction stripPixels(blocks, frame, width, dpr) {\n  const placed = blocks.map((b) => {\n    const [x0, x1] = span(frame, b.bp0, b.bp1);\n    const px0 = Math.round(x0 * dpr);\n    return {\n      colors: b.colors,\n      x0,\n      px0,\n      px1: Math.max(Math.round(x1 * dpr), px0 + 1)\n    };\n  }).filter((b) => b.px1 > 0 && b.px0 < width * dpr).sort((a, b) => a.x0 - b.x0);\n  const out = [];\n  let claimed = -Infinity;\n  const tierEnds = [-Infinity, -Infinity];\n  for (const { colors, px0, px1 } of placed) {\n    const start = Math.max(px0, claimed);\n    if (px1 > start) {\n      const tier = tierEnds[0] < start ? 0 : 1;\n      tierEnds[tier] = px1;\n      out.push({ colors, x0: start / dpr, x1: px1 / dpr, tier });\n      claimed = px1;\n    }\n  }\n  const covered = out.length > 0 ? out.at(-1).x1 - out[0].x0 : 0;\n  return covered >= out.length * MIN_STAGGER_PX ? out : out.map(({ tier: _, ...b }) => b);\n}\nfunction drawOverhang(ctx, edgeX, inward, ink) {\n  const capX = inward > 0 ? edgeX : edgeX - OVERHANG_CAP_PX;\n  ctx.clearRect(capX, 0, OVERHANG_CAP_PX, REFERENCE_STRIP_PX);\n  const tipX = edgeX + inward;\n  const baseX = tipX + inward * OVERHANG_PX;\n  ctx.beginPath();\n  ctx.moveTo(tipX, REFERENCE_STRIP_PX / 2);\n  ctx.lineTo(baseX, 0);\n  ctx.lineTo(baseX, REFERENCE_STRIP_PX);\n  ctx.closePath();\n  ctx.fillStyle = ink;\n  ctx.fill();\n}\nfunction rowEdge(row, rows, dpr) {\n  return Math.round(row * REFERENCE_STRIP_PX * dpr / rows) / dpr;\n}\nfunction drawReferenceStrip(ctx, blocks, frame, {\n  width,\n  lit,\n  darkMode,\n  dpr = 1\n}) {\n  const ink = darkMode ? \"#ffffff\" : \"#18181c\";\n  ctx.clearRect(0, 0, width, REFERENCE_STRIP_ZONE_PX);\n  for (const b of stripPixels(blocks, frame, width, dpr)) {\n    const { tier } = b;\n    const staggered = tier !== void 0 && b.colors.length === 1;\n    const rows = staggered ? 2 : b.colors.length;\n    b.colors.forEach((color, i) => {\n      const row = staggered ? tier : i;\n      const y0 = rowEdge(row, rows, dpr);\n      ctx.fillStyle = color;\n      ctx.fillRect(b.x0, y0, b.x1 - b.x0, rowEdge(row + 1, rows, dpr) - y0);\n    });\n  }\n  const overhang = stripOverhang(blocks, frame, width);\n  if (overhang.left > 0) {\n    drawOverhang(ctx, 0, 1, ink);\n  }\n  if (overhang.right > 0) {\n    drawOverhang(ctx, width, -1, ink);\n  }\n  if (lit) {\n    const [x0, x1] = span(frame, lit.start, lit.end);\n    const w = Math.max(x1 - x0, 3);\n    const left = (x0 + x1) / 2 - w / 2;\n    ctx.strokeStyle = ink;\n    ctx.lineWidth = 1.5;\n    ctx.strokeRect(left, 0.75, w, REFERENCE_STRIP_PX - 1.5);\n    if (lit.anchor) {\n      ctx.beginPath();\n      ctx.moveTo(left + w / 2, REFERENCE_STRIP_PX);\n      ctx.lineTo(lit.anchor.x, lit.anchor.y);\n      ctx.lineWidth = 1;\n      ctx.stroke();\n    }\n  }\n}\n\nexport {\n  REFERENCE_STRIP_PX,\n  REFERENCE_STRIP_ZONE_PX,\n  referenceStripBlocks,\n  stripOverhang,\n  stripBlockAt,\n  nodeAnchor,\n  stripPixels,\n  drawReferenceStrip\n};\n", "import type { RepeatCall } from './repeatFeatures'\n\n// Which genotyped allele belongs to which haplotype walk. A VCF states a\n// sample's alleles in genotype order, which is the genotyper's own order and\n// carries no correspondence to the assembly's haplotype numbering \u2014 TRGTdb's\n// ABCA7 record, for one, lists them shortest first. So the walks and the\n// alleles are paired by length instead: the pairing whose total difference is\n// smallest, which for lengths on a line is the non-crossing one.\n//\n// A walk that does not reach both flanking reference nodes is measured whole\n// rather than across the array, and an allele no read spanned is a copy of the\n// one that was called. Neither states a length for this array, so they pair\n// last and take no verdict \u2014 pairing them first let a walk that stops inside\n// the array take the allele that fit one spanning it, and the spanning walk\n// then read as a disagreement.\n\ninterface WalkCall extends RepeatCall {\n  // undefined where the walk and the allele are not both measurements\n  agrees?: boolean\n}\n\n// Every walk/call pair over the 94 HPRC samples TRGT genotyped at the ABCA7\n// VNTR is either within 8% of its allele or more than 14% from it, so any\n// threshold across that gap separates them the same way.\nexport const CALL_TOLERANCE = 0.1\n\nfunction agrees(walkBp: number, callBp: number) {\n  return Math.abs(callBp - walkBp) <= CALL_TOLERANCE * Math.max(walkBp, callBp)\n}\n\n// Pair two ascending lists of lengths, leaving out the surplus of whichever is\n// longer. `out[i]` is the index in `calls` that `walks[i]` took.\nfunction nearest(walks: number[], calls: number[]) {\n  const W = walks.length\n  const C = calls.length\n  const cost = Array.from({ length: W + 1 }, () => new Array(C + 1).fill(0))\n  const paired = Array.from({ length: W + 1 }, () =>\n    new Array<boolean>(C + 1).fill(false),\n  )\n  for (let i = W - 1; i >= 0; i--) {\n    for (let j = C - 1; j >= 0; j--) {\n      const together = Math.abs(walks[i]! - calls[j]!) + cost[i + 1]![j + 1]!\n      const dropWalk = W - i > C - j ? cost[i + 1]![j]! : Infinity\n      const dropCall = C - j > W - i ? cost[i]![j + 1]! : Infinity\n      cost[i]![j] = Math.min(together, dropWalk, dropCall)\n      paired[i]![j] = cost[i]![j] === together\n    }\n  }\n  const out = new Array<number | undefined>(W).fill(undefined)\n  for (let i = 0, j = 0; i < W && j < C;) {\n    if (paired[i]![j]) {\n      out[i++] = j++\n    } else if (W - i > C - j) {\n      i++\n    } else {\n      j++\n    }\n  }\n  return out\n}\n\nfunction byLength<T>(items: T[], bp: (item: T) => number) {\n  return items\n    .map((item, i) => ({ item, i }))\n    .sort((a, b) => bp(a.item) - bp(b.item))\n}\n\nconst backed = (call: RepeatCall) => call.spanningReads !== 0\n\nfunction scored(row: { bp: number; complete: boolean }, call: RepeatCall) {\n  return {\n    ...call,\n    agrees: row.complete && backed(call) ? agrees(row.bp, call.bp) : undefined,\n  }\n}\n\n// A phased genotype names its walk's haplotype outright, though a contig\n// break can give that haplotype two walks. Within a haplotype, and among the\n// unphased alleles, pairing goes by length: the walks that span the array\n// against the alleles reads spanned, then everything else against what those\n// two left. That decides the ambiguous cases on merit: which walk takes the\n// one allele a lone spanning read supports, and which allele a walk that stops\n// inside the array is drawn against.\nfunction pairSample<\n  R extends { bp: number; complete: boolean; haplotype?: number },\n>(rows: R[], calls: RepeatCall[]) {\n  const out = new Map<number, WalkCall>()\n  const taken = new Set<RepeatCall>()\n  const ranked = byLength(rows, r => r.bp)\n  const pair = (pool: typeof ranked, group: RepeatCall[]) => {\n    const stages = [\n      [pool.filter(r => r.item.complete), group.filter(backed)],\n      [pool, group],\n    ] as const\n    for (const [walks, alleles] of stages) {\n      const free = walks.filter(r => !out.has(r.i))\n      const open = byLength(\n        alleles.filter(call => !taken.has(call)),\n        call => call.bp,\n      )\n      nearest(\n        free.map(r => r.item.bp),\n        open.map(c => c.item.bp),\n      ).forEach((pick, k) => {\n        if (pick !== undefined) {\n          const row = free[k]!\n          const call = open[pick]!.item\n          taken.add(call)\n          out.set(row.i, scored(row.item, call))\n        }\n      })\n    }\n  }\n  for (const haplotype of new Set(calls.flatMap(c => c.haplotype ?? []))) {\n    pair(\n      ranked.filter(r => r.item.haplotype === haplotype),\n      calls.filter(c => c.haplotype === haplotype),\n    )\n  }\n  pair(\n    ranked,\n    calls.filter(c => c.haplotype === undefined),\n  )\n  return out\n}\n\nexport function withCalls<\n  R extends {\n    sample: string\n    bp: number\n    complete: boolean\n    haplotype?: number\n  },\n>(rows: R[], calls: Record<string, RepeatCall[]> | undefined) {\n  if (!calls) {\n    return rows as (R & { call?: WalkCall })[]\n  }\n  const paired = new Map<R, WalkCall>()\n  const bySample = new Map<string, R[]>()\n  for (const row of rows) {\n    const group = bySample.get(row.sample)\n    if (group) {\n      group.push(row)\n    } else {\n      bySample.set(row.sample, [row])\n    }\n  }\n  for (const [sample, group] of bySample) {\n    const called = calls[sample]\n    if (called) {\n      for (const [i, call] of pairSample(group, called)) {\n        paired.set(group[i]!, call)\n      }\n    }\n  }\n  return rows.map(row => ({ ...row, call: paired.get(row) }))\n}\n", "import { getDpr } from '@jbrowse/bandage-core/renderer/canvas'\nimport { observable, runInAction } from 'mobx'\n\nconst ratio = observable.box(\n  typeof devicePixelRatio === 'undefined' ? 1 : devicePixelRatio,\n)\n\n// A resolution query matches one ratio, so each change re-arms it for the next\nfunction watch() {\n  matchMedia(`(resolution: ${devicePixelRatio}dppx)`).addEventListener(\n    'change',\n    () => {\n      runInAction(() => {\n        ratio.set(devicePixelRatio)\n      })\n      watch()\n    },\n    { once: true },\n  )\n}\n\nif (typeof matchMedia === 'function') {\n  watch()\n}\n\n// getDpr() that an autorun or computed re-runs on: a browser zoom or a move to\n// another monitor changes the ratio with no event MobX would otherwise see.\n// Code painting a 2D context directly passes the canvas size, as\n// syncCanvasSize does; a Renderer's transform omits it and the renderer fits.\nexport function trackedDpr(width = 0, height = 0) {\n  ratio.get()\n  return getDpr(width, height)\n}\n"],
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-}