npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.2.0 → 6.3.1 - Mend

jbrowse-plugin-graphgenomeviewer 6.2.0 → 6.3.1

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package/dist/chunks/chunk-B7KMMGFB.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@mui/material/SvgIcon", "global-externals:mobx", "global-externals:@jbrowse/core/util/groupKeys", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/utils/createSvgIcon.mjs", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-6ZNQJ5ZD.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-NNODIW4U.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-3S3YVOJ7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-MLSWIMZO.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FP4H7SFT.js", 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"../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-KCRL5JB2.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-OWFPAIJI.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-W253V6RR.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/tubeMap/deviations.js", "../../src/GraphGenomeView/repeats/walkCalls.ts", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/Settings.mjs"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@mui/material/SvgIcon\"];", "module.exports = JBrowseExports[\"mobx\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/groupKeys\"];", "'use client';\n\nexport { createSvgIcon as default } from '@mui/material/SvgIcon';", "import {\n  REFERENCE_RAMP_MAX_HUE\n} from \"./chunk-HBEKUQO4.js\";\n\n// src/referenceRampCss.ts\nfunction rampHueCss(hue) {\n  return `hsl(${hue}, 70%, 50%)`;\n}\nfunction rampHue(bp, domain) {\n  const frac = (bp - domain.start) / (domain.end - domain.start);\n  return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;\n}\nvar HUE_STOP_DEG = 30;\nfunction rampStops({ start, bp, reversed }, domain) {\n  const low = rampHue(start, domain);\n  const high = rampHue(start + bp, domain);\n  if (high - low < 1) {\n    return [(low + high) / 2];\n  }\n  const n = Math.ceil((high - low) / HUE_STOP_DEG);\n  return Array.from(\n    { length: n + 1 },\n    (_, i) => rampHue(start + bp * (reversed ? n - i : i) / n, domain)\n  );\n}\nvar RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({\n  offset: i / 6,\n  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)\n}));\nvar RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(\n  (s) => `${s.color} ${s.offset * 100}%`\n).join(\", \")})`;\n\nexport {\n  rampHueCss,\n  rampHue,\n  rampStops,\n  RAMP_GRADIENT_STOPS,\n  RAMP_GRADIENT_CSS\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  serializeEl\n};\n", "import {\n  el\n} from \"./chunk-NNODIW4U.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  baseEdgeCurves\n} from \"./chunk-WFB5TXRA.js\";\nimport {\n  curveBounds,\n  pathRibbonOffsets\n} from \"./chunk-2CVHXFK7.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, cellSize, 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 = resolveCellSize(cellSize, 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-MLSWIMZO.js\";\nimport {\n  pathRibbonOffsets,\n  translateCurves,\n  yToXOf\n} from \"./chunk-2CVHXFK7.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, x1, y1, cx1, cy1, cx2, cy2, x2, y2) {\n  let minDist = Infinity;\n  const samples = 20;\n  let lastX = x1;\n  let lastY = y1;\n  for (let i = 1; i <= samples; i++) {\n    const t = i / samples;\n    const u = 1 - t;\n    const bx = u * u * u * x1 + 3 * u * u * t * cx1 + 3 * u * t * t * cx2 + t * t * t * x2;\n    const by = u * u * u * y1 + 3 * u * u * t * cy1 + 3 * u * t * t * cy2 + t * t * t * y2;\n    minDist = Math.min(minDist, distanceToSegment(px, py, lastX, lastY, bx, by));\n    lastX = bx;\n    lastY = by;\n  }\n  return minDist;\n}\nfunction distanceToBezierCurve(px, py, c) {\n  return distanceToCubicBezier(\n    px,\n    py,\n    c.x0,\n    c.y0,\n    c.cx0,\n    c.cy0,\n    c.cx1,\n    c.cy1,\n    c.x1,\n    c.y1\n  );\n}\nfunction distanceToEdgeCurves(px, py, curves, yToX = 1) {\n  let minDist = Infinity;\n  for (const c of curves) {\n    const d = distanceToBezierCurve(\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 = /* @__PURE__ */ new WeakMap();\nfunction getSpatialIndex(nodePositions, version) {\n  const cached = nodeCache.get(nodePositions);\n  if (cached?.version === version) {\n    return cached.index;\n  }\n  const index = new SpatialIndex(nodePositions);\n  nodeCache.set(nodePositions, { version, index });\n  return index;\n}\nvar edgeCache = /* @__PURE__ */ new WeakMap();\nfunction getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version, deletions, routes, stranded = false) {\n  const cached = edgeCache.get(nodePositions);\n  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version && cached.deletions === deletions && cached.routes === routes && cached.stranded === stranded) {\n    return cached.index;\n  }\n  const index = new EdgeSpatialIndex(\n    nodePositions,\n    graph,\n    drawPaths,\n    axis,\n    void 0,\n    deletions,\n    version,\n    routes,\n    stranded\n  );\n  edgeCache.set(nodePositions, {\n    graph,\n    drawPaths,\n    scaleX: axis.scaleX,\n    scaleY: axis.scaleY,\n    version,\n    index,\n    deletions,\n    routes,\n    stranded\n  });\n  return index;\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-FP4H7SFT.js\";\nimport {\n  nodeLabelBudget,\n  placeSizeLabels,\n  rowLabelBox,\n  sizeLabelCandidates\n} from \"./chunk-3ZZSX5HN.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 ROUTE_STACK = 8;\nvar GENE_PIN_DROP_PX = 18;\nvar GENE_STACK = 2;\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 byBubble = byExtent(m.bubbleHalos, (h) => h.members);\n  const bubbles = placeLabels(\n    byBubble.map((h) => {\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 - 6;\n      return {\n        item: h,\n        x,\n        y: onRows ? Math.max(baseline, TOPMOST_BASELINE) : baseline,\n        text: h.label\n      };\n    }),\n    frame,\n    take\n  );\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 sizeCandidates = m.nodePositions && m.labelsNodeSizes ? sizeLabelCandidates({\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  }) : { deletions: [], nodes: [] };\n  const deletionLabels = placeSizeLabels(sizeCandidates.deletions, take);\n  const routes = placeLabels(\n    byBubble.flatMap(\n      (h) => h.routes.map((route) => {\n        const { x, y } = screen(route.at);\n        return {\n          item: { halo: h, route },\n          x,\n          y: y + 4,\n          text: route.text,\n          stack: ROUTE_STACK\n        };\n      })\n    ),\n    frame,\n    take\n  );\n  const nodeLabels = placeSizeLabels(\n    sizeCandidates.nodes,\n    take,\n    nodeLabelBudget(width, height)\n  );\n  return {\n    bubbles,\n    genes,\n    routes,\n    sizes: [...deletionLabels, ...nodeLabels]\n  };\n}\n\nexport {\n  HALO_FACTOR,\n  LEGEND_INSET_PX,\n  geneCoverageNote,\n  geneLabelCandidates,\n  layoutLabels\n};\n", "import { isAnchored } from '@jbrowse/bandage-core/anchoredNodes'\nimport {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from '@jbrowse/bandage-core/pansn'\n\nimport type { AnchoredNode } from '@jbrowse/bandage-core/anchoredNodes'\nimport type { Graph, GraphNode } from '@jbrowse/bandage-core/types'\n\nexport interface GraphLocation {\n  // PanSN sample name off the node's own stable sequence. The assembly that\n  // contributed the sequence, which is a *name*, not a resolved assembly \u2014 see\n  // resolveContributors.\n  sample: string\n  // `sample#hap` where the stable name states a haplotype (HPRC release 2.1\n  // names every node `NA20809#2#CM094351.1`), so a sample loaded as two\n  // assemblies opens the right one; undefined where it states none\n  haplotype: string | undefined\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a node's own sequence lives, in the coordinates of the assembly that\n// contributed it. rGFA states this on every segment: SN names the stable\n// sequence and SO the offset on it, so this is exact at every rank.\n//\n// It is the other question from nodeReferenceSpan, which asks where a node sits\n// on the *reference* axis and can only approximate that off the backbone. A\n// rank>0 node has an exact coordinate of its own; what it has no coordinate for\n// is the reference.\nexport function nodeOwnLocation(node: GraphNode): GraphLocation | undefined {\n  return isAnchored(node) ? anchoredNodeLocation(node) : undefined\n}\n\nfunction anchoredNodeLocation(node: AnchoredNode): GraphLocation {\n  return {\n    sample: panSNSample(node.stable.refName),\n    haplotype: panSNHaplotype(node.stable.refName),\n    refName: panSNContig(node.stable.refName),\n    start: node.stable.start,\n    end: node.stable.start + node.length,\n  }\n}\n\nexport interface Contributor extends GraphLocation {\n  // lowest rank this assembly holds here: 0 means it is the reference backbone\n  rank: number\n  nodeCount: number\n}\n\ninterface Span {\n  start: number\n  end: number\n}\n\n// The widest run of spans with no gap larger than `maxGap`, which is the locus\n// this assembly contributes *here*. A bare union of every span would be wrong\n// on a graph where a sample also contributes sequence from a distant\n// duplication: the union then reads as a multi-megabase locus, and a linear view\n// launched at it shows neither end.\nfunction widestCluster(spans: Span[], maxGap: number) {\n  const sorted = [...spans].sort((a, b) => a.start - b.start)\n  let best: Span | undefined\n  let current: Span | undefined\n  for (const span of sorted) {\n    current =\n      current && span.start - current.end <= maxGap\n        ? { start: current.start, end: Math.max(current.end, span.end) }\n        : { start: span.start, end: span.end }\n    if (!best || current.end - current.start > best.end - best.start) {\n      best = current\n    }\n  }\n  return best\n}\n\ninterface Group {\n  sample: string\n  haplotype: string | undefined\n  refName: string\n  rank: number\n  spans: Span[]\n}\n\nfunction groupKey(loc: GraphLocation) {\n  return `${loc.haplotype ?? loc.sample}\\u0000${loc.refName}`\n}\n\n// Every assembly with a segment in this graph, and the locus each one covers on\n// its own coordinates.\n//\n// This is what makes a launch out of the graph possible at all: the graph names\n// its contributors in the data (rGFA's SN tag), so a node, a row and the graph\n// as a whole can each say which assembly they belong to without consulting an\n// alignment.\n//\n// Ordered reference-first, then by name, so the row order matches\n// sampleRowLayout's and neither reshuffles as the window moves.\nexport function contributingAssemblies(\n  graph: Graph,\n  { maxGap = Infinity }: { maxGap?: number } = {},\n): Contributor[] {\n  const groups = new Map<string, Group>()\n  for (const node of graph.nodes) {\n    if (isAnchored(node)) {\n      const loc = anchoredNodeLocation(node)\n      const key = groupKey(loc)\n      const group = groups.get(key)\n      if (group) {\n        group.spans.push({ start: loc.start, end: loc.end })\n        group.rank = Math.min(group.rank, node.stable.rank)\n      } else {\n        groups.set(key, {\n          sample: loc.sample,\n          haplotype: loc.haplotype,\n          refName: loc.refName,\n          rank: node.stable.rank,\n          spans: [{ start: loc.start, end: loc.end }],\n        })\n      }\n    }\n  }\n\n  // One entry per assembly (a haplotype where the names state one, else the\n  // sample): an assembly contributing on several contigs is launched at the\n  // contig it contributes most of, since a linear view opens on one region.\n  const bySample = new Map<string, Contributor>()\n  for (const group of groups.values()) {\n    const span = widestCluster(group.spans, maxGap)\n    if (span) {\n      const candidate = {\n        sample: group.sample,\n        haplotype: group.haplotype,\n        refName: group.refName,\n        start: span.start,\n        end: span.end,\n        rank: group.rank,\n        nodeCount: group.spans.length,\n      }\n      const key = group.haplotype ?? group.sample\n      const existing = bySample.get(key)\n      if (!existing || candidate.nodeCount > existing.nodeCount) {\n        bySample.set(key, candidate)\n      }\n    }\n  }\n\n  // Reference first, then by name: the same order sampleRowLayout gives its\n  // rows, so the menu lists the assemblies in the order they are stacked on\n  // screen. Sorting by rank instead would order them by minigraph's build\n  // order, which is not what the labels beside the drawing say.\n  return [...bySample.values()].sort(\n    (a, b) =>\n      Number(a.rank !== 0) - Number(b.rank !== 0) ||\n      a.sample.localeCompare(b.sample) ||\n      (a.haplotype ?? '').localeCompare(b.haplotype ?? ''),\n  )\n}\n\n// The assembly a location opens on: its haplotype's where the name states one\n// and the session holds it, else its sample's. A session holding both\n// haplotypes of a sample opens the right one; one holding a haplotype under\n// the bare sample name still opens it.\nexport function resolveLocationAssembly(\n  resolve: (sample: string) => string | undefined,\n  loc: Pick<GraphLocation, 'sample' | 'haplotype'>,\n) {\n  const byHaplotype =\n    loc.haplotype === undefined ? undefined : resolve(loc.haplotype)\n  return byHaplotype ?? resolve(loc.sample)\n}\n\n// Contributors that name an assembly this session has loaded, which are the\n// only ones a linear or synteny view can open on.\n//\n// The two cases this filters apart are both normal. An E. coli pangenome demo\n// loads every strain as its own assembly, so every contributor resolves and the\n// whole graph is navigable. An HPRC graph names hundreds of haplotypes that no\n// session would ever load as assemblies, so only the reference resolves \u2014\n// there the reference projection (nodeReferenceSpan) is the way back to a\n// coordinate, not this.\n//\n// `resolve` is a name lookup rather than a list of names, because a PanSN sample\n// is the *graph's* spelling and need not be the assembly's. HPRC's graph writes\n// `CHM13`, and the assembly holding that sequence is UCSC's `hs1`, with CHM13\n// among its aliases; matching on names alone leaves that donor unopenable unless\n// the reader renames their assembly after the graph. The resolved (canonical)\n// name replaces the sample, so a launch opens the assembly the session knows.\nexport function resolveContributors(\n  contributors: Contributor[],\n  resolve: (sample: string) => string | undefined,\n) {\n  return contributors.flatMap(c => {\n    const sample = resolveLocationAssembly(resolve, c)\n    return sample === undefined ? [] : [{ ...c, sample }]\n  })\n}\n\n// 1-based inclusive, which is what a locstring means. Unformatted digits: this\n// is parsed, not read. locLabel is the one people read.\nexport function locString(loc: GraphLocation) {\n  return `${loc.refName}:${loc.start + 1}-${loc.end}`\n}\n\nexport function locLabel(loc: { refName: string; start: number; end: number }) {\n  return `${loc.refName}:${(loc.start + 1).toLocaleString()}-${loc.end.toLocaleString()}`\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M9.01 14H2v2h7.01v3L13 15l-3.99-4zm5.98-1v-3H22V8h-7.01V5L11 9z\"\n}), 'CompareArrows');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M17 5h-2V3h2zm-2 16h2v-2.59L19.59 21 21 19.59 18.41 17H21v-2h-6zm4-12h2V7h-2zm0 4h2v-2h-2zm-8 8h2v-2h-2zM7 5h2V3H7zM3 17h2v-2H3zm2 4v-2H3c0 1.1.9 2 2 2M19 3v2h2c0-1.1-.9-2-2-2m-8 2h2V3h-2zM3 9h2V7H3zm4 12h2v-2H7zm-4-8h2v-2H3zm0-8h2V3c-1.1 0-2 .9-2 2\"\n}), 'HighlightAlt');", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M3 16h5v-2H3zm6.5 0h5v-2h-5zm6.5 0h5v-2h-5zM3 20h2v-2H3zm4 0h2v-2H7zm4 0h2v-2h-2zm4 0h2v-2h-2zm4 0h2v-2h-2zM3 12h8v-2H3zm10 0h8v-2h-8zM3 4v4h18V4z\"\n}), 'LineStyle');", "import CompareArrowsIcon from '@mui/icons-material/CompareArrows'\nimport HighlightAltIcon from '@mui/icons-material/HighlightAlt'\nimport LineStyleIcon from '@mui/icons-material/LineStyle'\n\nimport { locLabel } from './contributors'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { LaunchableSyntenyTrack } from './syntenyTracks'\nimport type { MenuItem } from '@jbrowse/core/ui'\n\nconst LINEAR_LABEL = 'Linear genome view'\nconst SYNTENY_LABEL = 'Linear synteny view'\nconst NO_SYNTENY_TRACK =\n  'No synteny track in this session aligns these assemblies'\n\nexport interface LinearTarget {\n  location: GraphLocation\n  assembly: string\n}\n\n// One flat item when there is one thing to open, a submenu when there is a\n// choice. Same shape as subgraphMenuItems uses in the other direction, so the\n// two ends of the graph <-> linear trip read the same way.\nfunction oneOrMany<T>({\n  label,\n  icon,\n  entries,\n  entryLabel,\n  onSelect,\n  disabledHelpText,\n  nameTheOnlyEntry = true,\n}: {\n  label: string\n  icon: React.ElementType\n  entries: T[]\n  entryLabel: (entry: T) => string\n  onSelect: (entry: T) => () => void\n  disabledHelpText?: string\n  // Whether a lone entry's name is worth appending to the item. It is when the\n  // entry is where you land (`GRCh38 chr6:31,980,000-32,050,000`) and not when\n  // it is the ingredient used to get there \u2014 a synteny track's name says\n  // nothing the item does not already say, and reading it costs the width of\n  // `pggb graph: all-vs-all synteny (wfmash)`.\n  nameTheOnlyEntry?: boolean\n}): MenuItem[] {\n  const [first] = entries\n  // Nothing to open: a *disabled* item with the reason in its tooltip, when\n  // there is a reason worth reading. An item that vanishes teaches nobody that\n  // the session is one synteny track short of a multi-genome view.\n  const empty: MenuItem[] = disabledHelpText\n    ? [{ label, icon, disabled: true, disabledHelpText, onClick: () => {} }]\n    : []\n  return entries.length === 0\n    ? empty\n    : entries.length === 1 && first\n      ? [\n          {\n            label: nameTheOnlyEntry ? `${label} \u2014 ${entryLabel(first)}` : label,\n            icon,\n            onClick: onSelect(first),\n          },\n        ]\n      : [\n          {\n            label,\n            icon,\n            type: 'subMenu',\n            subMenu: entries.map(entry => ({\n              label: entryLabel(entry),\n              onClick: onSelect(entry),\n            })),\n          },\n        ]\n}\n\n// The graph's way out: a linear view of any assembly the graph names here, and a\n// synteny view of all of them at once. Until this existed the triangle had two\n// edges \u2014 a linear view could open a graph or a synteny view of a locus, and the\n// graph could open nothing at all.\n//\n// `contributors` are already resolved against the session's assemblies. On an\n// E. coli pangenome every strain is its own assembly, so all of them appear and\n// the synteny item is the interesting one; on an HPRC graph the 400-odd\n// contributing haplotypes are not loaded assemblies and only the reference\n// appears, which is the honest answer rather than a missing feature.\nexport function graphLaunchMenuItems({\n  contributors,\n  syntenyTracks,\n  onShowLinear,\n  onShowSynteny,\n}: {\n  contributors: Contributor[]\n  syntenyTracks: LaunchableSyntenyTrack[]\n  onShowLinear: (target: LinearTarget) => void\n  onShowSynteny: (trackId: string) => void\n}): MenuItem[] {\n  // sorted widest first\n  const widest = syntenyTracks[0]?.coverage ?? contributors.length\n  return [\n    ...oneOrMany({\n      label: LINEAR_LABEL,\n      icon: LineStyleIcon,\n      entries: contributors,\n      entryLabel: c => `${c.sample} ${locLabel(c)}`,\n      onSelect: c => () => {\n        onShowLinear({ location: c, assembly: c.sample })\n      },\n    }),\n    ...(contributors.length >= 2\n      ? oneOrMany({\n          // the count the launch opens, which is what the widest track aligns\n          // and not always every contributor; see launchSyntenyView\n          label: `${SYNTENY_LABEL} (${widest} assemblies)`,\n          icon: CompareArrowsIcon,\n          entries: syntenyTracks,\n          entryLabel: track =>\n            track.coverage < widest\n              ? `${track.name} (${track.coverage} of ${widest})`\n              : track.name,\n          nameTheOnlyEntry: false,\n          disabledHelpText: NO_SYNTENY_TRACK,\n          onSelect: track => () => {\n            onShowSynteny(track.trackId)\n          },\n        })\n      : []),\n  ]\n}\n\n// A single node's way out, for the node context menu. Two different questions,\n// both worth offering:\n//\n//   - the node's own coordinates, on the assembly that contributed it. Exact,\n//     from the node's SN/SO, and available at every rank \u2014 but only openable\n//     when that assembly is loaded, which for an HPRC haplotype it is not.\n//   - where the node sits on the reference the graph was cut against. Always\n//     openable, and off the backbone it is the flanking projection rather than\n//     an exact span (see nodeReferenceSpan), so it is labelled as the region\n//     around the node rather than as the node.\n//\n// Labels are verbs. Review: \"the lineargenomeview menu item should say launch\n// if that is what it does\" \u2014 a bare `Linear genome view \u2014 hg38 chr6:\u2026` names a\n// place and leaves the reader to guess whether clicking scrolls the view beside\n// the graph or opens a new one. It does the first when there is one to scroll\n// (see showInLinearView), so \"Open in\" covers both without claiming a launch.\n//\n// Verb, assembly, and where \u2014 nothing else. Every word here is read inside a\n// menu opened on a node, so \"this node in the hg38 view\" and \"in linear view\"\n// restate the context they are already in; what a coordinate opens in is not in\n// question, and the assembly name is.\n//\n// Flat, not under a \"Launch view\" submenu: this menu is a handful of items and\n// every one is contextual to the node just clicked.\nexport function nodeLaunchMenuItems({\n  own,\n  reference,\n  highlight,\n  onShowLinear,\n  onHighlight,\n}: {\n  own: LinearTarget | undefined\n  reference: LinearTarget | undefined\n  // the node's exact reference span, where `reference` is padded to open on\n  highlight: LinearTarget | undefined\n  onShowLinear: (target: LinearTarget) => void\n  // absent when no linear view in the session is this graph's to mark\n  onHighlight?: (target: LinearTarget) => void\n}): MenuItem[] {\n  const entries = [\n    own\n      ? {\n          label: `Open in ${own.assembly} \u2014 ${locLabel(own.location)}`,\n          target: own,\n        }\n      : undefined,\n    // Only when it says something the item above doesn't. A backbone segment on\n    // a loaded reference answers both questions with the same assembly and\n    // nearly the same span, and offering that twice reads as two different\n    // places to go.\n    reference && reference.assembly !== own?.assembly\n      ? {\n          label: `Open in ${reference.assembly} \u2014 around this node`,\n          target: reference,\n        }\n      : undefined,\n  ].filter(entry => entry !== undefined)\n\n  // The reference projection, not the node's own coordinates: a highlight is\n  // drawn in the linear view already on screen, and that view is on the\n  // reference the subgraph was cut from.\n  return [\n    ...(onHighlight && highlight\n      ? [\n          {\n            label: `Highlight in ${highlight.assembly}`,\n            icon: HighlightAltIcon,\n            onClick: () => {\n              onHighlight(highlight)\n            },\n          },\n        ]\n      : []),\n    ...entries.map(({ label, target }) => ({\n      label,\n      icon: LineStyleIcon,\n      onClick: () => {\n        onShowLinear(target)\n      },\n    })),\n  ]\n}\n", "import {\n  parseCs\n} from \"./chunk-C44YRP5F.js\";\n\n// src/tubeMap/reads.ts\nfunction canonicalStrand(node) {\n  return node.id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction stepName(node, strand) {\n  return strand === canonicalStrand(node) ? node.id : `-${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 stepAt = (pos2, atEnd = false) => {\n    for (let s = 0; s < starts.length; s++) {\n      const start = starts[s];\n      const length = lengths[s];\n      if (start !== void 0 && length !== void 0 && start <= pos2 && (pos2 < start + length || atEnd && pos2 === start + length)) {\n        return { s, local: pos2 - start, room: start + length - pos2 };\n      }\n    }\n    return void 0;\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 = stepAt(pos, pos === record.pathEnd);\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 = at ? Math.min(left, at.room) : left;\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        mapping_quality: record.mappingQuality === 255 ? 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", "import {\n  buildNeighbors\n} from \"./chunk-ES2N6V56.js\";\nimport {\n  REFERENCE_RANK,\n  isAnchored\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/alleleProjection/projectAlleles.ts\nfunction parsePanSN(refName) {\n  const parts = refName.split(\"#\");\n  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN;\n  return {\n    sample: parts[0] ?? refName,\n    haplotype: Number.isFinite(haplotype) ? haplotype : void 0\n  };\n}\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  parsePanSN,\n  projectAlleles\n};\n", "import {\n  projectAlleles\n} from \"./chunk-RVS2QCOX.js\";\nimport {\n  buildNeighbors\n} from \"./chunk-ES2N6V56.js\";\n\n// src/layout/placeOffReference.ts\nvar MIN_DELETION_BP = 1;\nvar MIN_ALLELE_SPAN_FRACTION = 0.015;\nfunction placeOffReference({\n  graph,\n  span,\n  rowY,\n  positions\n}) {\n  const minSpan = span * MIN_ALLELE_SPAN_FRACTION;\n  const alleles = projectAlleles(graph);\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const alleleDeletions = [];\n  for (const allele of alleles) {\n    const skipped = allele.refSpan - allele.pathLength;\n    if (skipped >= MIN_DELETION_BP) {\n      alleleDeletions.push({ nodeIds: allele.nodeIds, bp: skipped });\n    }\n    const drawn = Math.max(allele.refSpan, minSpan);\n    const scale = allele.pathLength > 0 ? drawn / allele.pathLength : 0;\n    allele.nodeIds.forEach((nodeId, i) => {\n      const node = byId.get(nodeId);\n      if (node) {\n        const offset = allele.nodeOffsets[i];\n        const even = drawn / allele.nodeIds.length;\n        const at = (bp) => allele.start + bp * scale;\n        const y = rowY(node);\n        positions[nodeId] = scale ? [\n          { x: at(offset), y },\n          { x: at(offset + node.length), y }\n        ] : [\n          { x: allele.start + i * even, y },\n          { x: allele.start + (i + 1) * even, y }\n        ];\n      }\n    });\n  }\n  const neighbors = buildNeighbors(graph);\n  const queue = Object.keys(positions);\n  for (const fromId of queue) {\n    const fromEnd = positions[fromId].at(-1).x;\n    for (const nextId of neighbors.get(fromId) ?? []) {\n      const next = byId.get(nextId);\n      if (next && !(nextId in positions)) {\n        const y = rowY(next);\n        positions[nextId] = [\n          { x: fromEnd, y },\n          { x: fromEnd + minSpan, y }\n        ];\n        queue.push(nextId);\n      }\n    }\n  }\n  return alleleDeletions;\n}\n\nexport {\n  placeOffReference\n};\n", "import {\n  placeOffReference\n} from \"./chunk-TZFWUT2C.js\";\nimport {\n  parsePanSN\n} from \"./chunk-RVS2QCOX.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  isOffReference,\n  referenceSpan\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/sampleRowLayout.ts\nfunction contributingSamples(graph, keep) {\n  const carried = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isOffReference(node)) {\n      const { sample } = parsePanSN(node.stable.refName);\n      carried.set(sample, (carried.get(sample) ?? 0) + node.length);\n    }\n  }\n  const held = new Map(keep.map((sample, row) => [sample, row]));\n  return [...carried.keys()].sort(\n    (a, b) => (held.get(a) ?? Infinity) - (held.get(b) ?? Infinity) || carried.get(b) - carried.get(a) || a.localeCompare(b)\n  );\n}\nfunction sampleRowLayout(graph, region, keep = []) {\n  const backbone = backboneNodes(graph);\n  const samples = contributingSamples(graph, keep);\n  if (backbone.length === 0 || samples.length === 0) {\n    return void 0;\n  }\n  const span = referenceSpan(backbone, region);\n  const rowOf = new Map(samples.map((s, i) => [s, i + 1]));\n  const nodePositions = backbonePositions(backbone);\n  const spareRow = samples.length + 1;\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: (node) => {\n      const stable = node.stable;\n      const row = stable ? rowOf.get(parsePanSN(stable.refName).sample) : void 0;\n      return (row ?? spareRow) * ROW_HEIGHT_PX;\n    },\n    positions: nodePositions\n  });\n  const referenceSample = parsePanSN(backbone[0].stable.refName).sample;\n  const rowLabels = [\n    { label: referenceSample, y: 0 },\n    ...samples.map((sample) => ({\n      label: sample,\n      y: rowOf.get(sample) * ROW_HEIGHT_PX\n    }))\n  ];\n  return {\n    nodePositions,\n    rowLabels,\n    sampleRows: samples,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions\n  };\n}\n\nexport {\n  sampleRowLayout\n};\n", "export type MismatchType = 'insertion' | 'deletion' | 'substitution'\n\nexport interface Mismatch {\n  type: MismatchType\n  pos: number\n  seq?: string\n  length?: number\n}\n\nexport interface ReadSequenceEntry {\n  nodeName: string\n  mismatches: Mismatch[]\n}\n\nexport type TrackType = 'haplotype' | 'read'\n\nexport interface TrackRectangle {\n  xStart: number\n  yStart: number\n  xEnd: number\n  yEnd: number\n  id: number\n  name?: string | undefined\n  type?: TrackType | undefined\n}\n\nexport interface TrackCurve {\n  xStart: number\n  yStart: number\n  xEnd: number\n  yEnd: number\n  width: number\n  id: number\n  name?: string | undefined\n  type?: TrackType | undefined\n  // the nodes the curve leaves and enters, null at a gap in a track's path\n  nodeStart: number | null\n  nodeEnd: number | null\n  // the order slots it leaves and enters\n  orderStart: number\n  orderEnd: number\n  path?: string\n}\n\nexport interface TrackCorner {\n  path: string\n  id: number\n  name?: string | undefined\n  type?: TrackType | undefined\n}\n\nexport interface Segment {\n  order: number\n  lane?: number\n  isForward: boolean\n  node: number | null\n  y?: number\n  betweenCycleReverseTraversal?: boolean\n}\n\n// Loose input shape: just the basics produced by vgExtractTracks /\n// vgExtractReads. Layout passes accrete indexSequence / path / width.\nexport interface InputTrack {\n  id: number\n  name?: string\n  sequence: string[]\n  type?: TrackType\n  freq?: number\n  hidden?: boolean\n  sourceTrackID: number\n  indexOfFirstBase?: number\n  isCompletelyReverse?: boolean\n  // Read-specific fields populated by vgExtractReads.\n  sequenceNew?: ReadSequenceEntry[]\n  firstNodeOffset?: number\n  finalNodeCoverLength?: number\n  mapping_quality?: number\n  is_secondary?: boolean\n  is_reverse?: boolean\n  sample_name?: string | null\n  read_group?: string | null\n  cigar_string?: string\n  score?: number\n}\n\n// How many of the banded haplotypes take a coarsened band\nexport interface HaplotypeShare {\n  count: number\n  total: number\n}\n\n// Layout-complete track shape, as layoutTubeMap returns it.\nexport interface Track extends InputTrack {\n  indexSequence: number[]\n  path: Segment[]\n  width: number\n  haplotypeShare?: HaplotypeShare | undefined\n}\n\n// Loose input shape passed to layoutTubeMap. Its passes (generateNodeWidth \u2192\n// generateNodeOrder \u2192 generateLaneAssignment \u2192 generateNodeXCoords) accrete\n// more fields, producing the full `Node` below. A graph fetched with\n// removeSequences has no seq, and sequenceLength defaults to seq's length.\nexport interface InputNode {\n  name: string\n  seq?: string\n  sequenceLength?: number\n}\n\n// Layout-complete node \u2014 fields used by drawing code after the pipeline.\n// (Marked optional only for the genuinely conditional fields like switched/d.)\n// layoutTubeMap fills in seq, as '' when the input had none, and\n// sequenceLength.\nexport interface Node extends InputNode {\n  seq: string\n  sequenceLength: number\n  width: number\n  pixelWidth: number\n  order?: number | undefined\n  y: number\n  contentHeight: number\n  x: number\n  topLane: number\n  successors: number[]\n  predecessors: number[]\n  tracks: number[]\n  degree: number\n  switched?: boolean\n  incomingReads: [number, number][]\n  outgoingReads: [number, number][]\n  internalReads: number[]\n  d?: string\n}\n\n// Node after generateNodeOrder() has run \u2014 order is guaranteed to be set.\nexport interface LayoutNode extends Node {\n  order: number\n}\n\nexport interface SegmentAssignment {\n  trackID: number\n  segmentID: number\n  compareToFromSame: SegmentAssignment | null\n  idealLane?: number | undefined\n  idealY?: number | null | undefined\n  lane?: number\n}\n\nexport interface NodeAssignment {\n  type: 'single' | 'multiple'\n  node: number | null\n  tracks: SegmentAssignment[]\n  idealLane?: number | undefined\n}\n\n// Drawing instructions from one layout, in layout coordinates.\nexport interface TrackShapes {\n  rectangles: TrackRectangle[]\n  curves: TrackCurve[]\n  corners: TrackCorner[]\n  // drawn separately so they don't overlap the horizontal rectangles\n  verticalRectangles: TrackRectangle[]\n}\n\nexport function emptyTrackShapes(): TrackShapes {\n  return {\n    rectangles: [],\n    curves: [],\n    corners: [],\n    verticalRectangles: [],\n  }\n}\n\n// The extent of the drawn content, in layout coordinates.\nexport interface ImageBounds {\n  minX: number\n  maxX: number\n  minY: number\n  maxY: number\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 { parsePanSN } from './panSN.ts'\nimport { emptyTrackShapes } from './types.ts'\n\nimport type {\n  HaplotypeShare,\n  ImageBounds,\n  InputNode,\n  InputTrack,\n  LayoutNode,\n  Mismatch,\n  Node,\n  NodeAssignment,\n  ReadSequenceEntry,\n  Segment,\n  SegmentAssignment,\n  Track,\n  TrackShapes,\n  TrackType,\n} from './types.ts'\n\nconst DEBUG = false as boolean\n\nfunction debugLog(...args: unknown[]): void {\n  if (DEBUG) {\n    // eslint-disable-next-line no-console\n    console.log(...args)\n  }\n}\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}\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'\n  | 'contentHeight'\n  | 'topLane'\n  | 'incomingReads'\n  | 'outgoingReads'\n  | '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// 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 ?? 8.401,\n    trackWidth: options.trackWidth ?? 15,\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  imageBounds: ImageBounds\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    imageBounds: { minX: 0, maxX: 0, minY: 0, maxY: 0 },\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 groupBy<T>(\n  items: readonly T[],\n  keyOf: (item: T) => string | null,\n): [string | null, T[]][] {\n  const groups = new Map<string | null, T[]>()\n  for (const item of items) {\n    const key = keyOf(item)\n    const group = groups.get(key)\n    if (group === undefined) {\n      groups.set(key, [item])\n    } else {\n      group.push(item)\n    }\n  }\n  return [...groups].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 groupBy(\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 = groupBy(\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    const bandIds = [...layout.coarsenedEdgeMeta.keys()]\n    if (bandIds.length > 0) {\n      nextBandId = Math.max(...bandIds) + 1\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  if (state.reads.length > 0) {\n    placeReads(state)\n    state.tracks = state.tracks.concat(state.reads)\n  } else {\n    state.nodes.forEach(node => {\n      node.incomingReads = []\n      node.outgoingReads = []\n      node.internalReads = []\n    })\n  }\n\n  if (x === 'measure') {\n    generateNodeXCoords(state)\n  }\n\n  generateSVGShapesFromPath(state)\n  debugLog('Tracks:', state.tracks)\n  debugLog('Nodes:', state.nodes)\n  debugLog('Lane assignment:', state.assignments)\n  getImageDimensions(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: state.imageBounds,\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 = []\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    state.nodesPerOrder[i] = []\n  }\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    if (read.path.length === 1) {\n      const firstNode = read.path[0]!.node\n      if (firstNode !== null) {\n        state.nodes[firstNode]!.internalReads.push(idx)\n      }\n    } else {\n      read.path.forEach((element, pathIdx) => {\n        if (pathIdx === 0) {\n          const firstNode = read.path[0]!.node\n          if (firstNode !== null) {\n            state.nodes[firstNode]!.outgoingReads.push([idx, pathIdx])\n          }\n        } else {\n          const elemNode = element.node\n          if (elemNode !== null) {\n            state.nodes[elemNode]!.incomingReads.push([idx, pathIdx])\n          }\n        }\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    const len = read.path.length\n\n    // For each path index, precompute the nearest preceding/following segment\n    // whose node is non-null and truthy. Falls back to the boundary segment when\n    // none qualifies, matching the original walking-loop semantics.\n    const prevSegment = new Array<Segment | undefined>(len)\n    let lastValidPrev: Segment | undefined\n    for (let i = 0; i < len; i++) {\n      if (i === 0) {\n        prevSegment[i] = undefined\n      } else {\n        prevSegment[i] = lastValidPrev ?? read.path[0]\n      }\n      const seg = read.path[i]!\n      if (seg.node !== null && seg.node) {\n        lastValidPrev = seg\n      }\n    }\n    const nextSegment = new Array<Segment | undefined>(len)\n    let firstValidNext: Segment | undefined\n    for (let i = len - 1; i >= 0; i--) {\n      if (i === len - 1) {\n        nextSegment[i] = undefined\n      } else {\n        nextSegment[i] = firstValidNext ?? read.path[len - 1]\n      }\n      const seg = read.path[i]!\n      if (seg.node !== null && seg.node) {\n        firstValidNext = seg\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  debugLog('Reads:', state.reads)\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  // Determine where we start vertically in the node.\n  // TODO: Why do we have to double this to keep reads out of adjacent lanes???\n  const startY = node.y + node.contentHeight + topMargin * 2\n\n  // sort incoming reads \u2014 decorate with a precomputed key so each compare is O(1).\n  // The original comparator walks pathIdx backwards in lockstep on both sides, picking\n  // the first step where either has a defined y (or reaches index 0). The walk's outcome\n  // for a single entry is fully captured by:\n  //   decisionStep: the smallest k>=1 where path[pathIdx-k].y is defined, or pathIdx+1\n  //                 if no preceding segment has a defined y (the \"reached 0\" case).\n  //   y:            the defined y at decisionStep, or undefined for \"reached 0\".\n  // Smaller decisionStep wins; ties put the \"reached 0\" entries first;\n  // otherwise compare y's.\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  // place incoming reads\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  // sort outgoing reads\n  outgoingReads.sort((a, b) =>\n    compareReadOutgoingSegmentsByGoingTo(state, a, b),\n  )\n\n  // place outgoing reads\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    // place in next lane\n    read.path[readElement[1]]!.y = currentY\n    occupiedFrom.set(currentY, firstNodeOffset)\n    // if no conflicts. The original predicate was strict-less-than, which\n    // treats two reads that exactly touch (incoming ends at base K, outgoing\n    // starts at base K+1) as conflicting. They don't overlap, so they can\n    // share a lane \u2014 relax to <=. This also matters for coarsened Sankey\n    // bands at single-base nodes (e.g. a 1bp \"G\" node): with edge-only offsets\n    // the math becomes 0+1 < 1 (conflict, wrong) vs. 0+1 <= 1 (no conflict).\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  // sort internal reads\n  internalReads.sort((a, b) => compareInternalReads(state, a, b))\n\n  // place internal reads\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 || READ_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. Exported for testing.\nexport interface 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.\nexport function 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  if (pathIndex === read.path.length - 1) {\n    // last node of current read\n    map.set(y, read.finalNodeCoverLength ?? 0)\n  } else {\n    // read covers the whole node\n    map.set(y, 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// compare read segments by where they are going to\nfunction compareReadOutgoingSegmentsByGoingTo(\n  state: LayoutState,\n  [readIndexA, pathIndexA]: [number, number],\n  [readIndexB, pathIndexB]: [number, number],\n): number {\n  // Expect two arrays both containing 2 integers.\n  // The first index of each array contains the read index\n  // The second index of each array contains the path index\n\n  // Segments are first sorted by the y value of their last node,\n  // then by the node they end on,\n  // then by length in final node\n  const readA = state.reads[readIndexA]!\n  const readB = state.reads[readIndexB]!\n  let previousValidYA: number | undefined\n  let previousValidYB: number | undefined\n  let lastPathIndexA = readA.path.length - 1\n  let lastPathIndexB = readB.path.length - 1\n  while (!previousValidYA && lastPathIndexA >= 0) {\n    previousValidYA = readA.path[lastPathIndexA]?.y\n    lastPathIndexA -= 1\n  }\n  while (!previousValidYB && lastPathIndexB >= 0) {\n    previousValidYB = readB.path[lastPathIndexB]?.y\n    lastPathIndexB -= 1\n  }\n\n  if (previousValidYA && previousValidYB) {\n    return previousValidYA - previousValidYB\n  }\n\n  // Couldn't find a valid y value for at least one of the reads, sort by which node reads end on\n  const initialNodeA = readA.path[pathIndexA]?.node\n  const initialNodeB = readB.path[pathIndexB]?.node\n  let nodeA: LayoutNode | null | undefined =\n    typeof initialNodeA === 'number' ? state.nodes[initialNodeA] : null\n  let nodeB: LayoutNode | null | undefined =\n    typeof initialNodeB === 'number' ? state.nodes[initialNodeB] : null\n  // Follow the reads' paths until we find the node they diverge at\n  // Or, they go through all the same nodes and we do a tiebreaker at the end\n  while (nodeA && nodeB && nodeA === nodeB) {\n    if (pathIndexA < readA.path.length - 1) {\n      pathIndexA += 1\n      while (readA.path[pathIndexA]?.node === null) {\n        pathIndexA += 1\n      } // skip null nodes in path\n      const nextNodeIdx = readA.path[pathIndexA]?.node\n      nodeA = typeof nextNodeIdx === 'number' ? state.nodes[nextNodeIdx] : null\n    } else {\n      nodeA = null\n    }\n    if (pathIndexB < readB.path.length - 1) {\n      pathIndexB += 1\n      while (readB.path[pathIndexB]?.node === null) {\n        pathIndexB += 1\n      } // skip null nodes in path\n      const nextNodeIdx = readB.path[pathIndexB]?.node\n      nodeB = typeof nextNodeIdx === 'number' ? state.nodes[nextNodeIdx] : null\n    } else {\n      nodeB = null\n    }\n  }\n  if (nodeA) {\n    if (nodeB) {\n      return compareNodesByOrder(nodeA, nodeB)\n    }\n    return 1 // nodeB is null, nodeA not null\n  }\n  if (nodeB) {\n    return -1\n  } // nodeB not null, nodeA null\n  // both nodes are null -> both end in the same node\n  const beginDiff = (readA.firstNodeOffset ?? 0) - (readB.firstNodeOffset ?? 0)\n  if (beginDiff !== 0) {\n    return beginDiff\n  }\n\n  // break tie: both reads cover the same nodes and begin at the same position\n\n  // One or both reads didn't have a previously valid Y value, compare by the endPosition of the read\n  return (readA.finalNodeCoverLength ?? 0) - (readB.finalNodeCoverLength ?? 0)\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  // compare by first base within first node\n  const aFirst = a.firstNodeOffset ?? 0\n  const bFirst = b.firstNodeOffset ?? 0\n  if (aFirst < bFirst) {\n    return -1\n  } else if (aFirst > bFirst) {\n    return 1\n  }\n\n  // compare by last base within last node\n  const aLast = a.finalNodeCoverLength ?? 0\n  const bLast = b.finalNodeCoverLength ?? 0\n  if (aLast < bLast) {\n    return -1\n  } else if (aLast > bLast) {\n    return 1\n  }\n\n  return 0\n}\n\n// determine biggest y-coordinate for each order-value\nfunction calculateBottomY(state: LayoutState): number[] {\n  const bottomY: number[] = []\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    bottomY.push(0)\n  }\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    let pos = 0\n    while (pos < read.sequence.length && read.sequence[pos]!.startsWith('-')) {\n      pos += 1\n    }\n    if (pos === read.sequence.length) {\n      // completely reversed read\n      read.is_reverse = true\n      read.sequence = read.sequence.reverse() // invert sequence\n      for (let i = 0; i < read.sequence.length; i += 1) {\n        read.sequence[i] = forward(read.sequence[i]!) // visit nodes forward\n        // TODO: Do we really want to visit all the nodes forward here? Are we\n        // sure we aren't in mixed orientation?\n      }\n\n      const sequenceNew = read.sequenceNew ?? []\n      sequenceNew.reverse() // invert sequence\n      read.sequenceNew = sequenceNew\n      for (const entry of sequenceNew) {\n        entry.nodeName = forward(entry.nodeName) // visit nodes forward\n        reverseMismatches(\n          entry.mismatches,\n          nodeByName(state, entry.nodeName).sequenceLength,\n        )\n      }\n\n      // adjust firstNodeOffset and finalNodeCoverLength\n      const temp = read.firstNodeOffset ?? 0\n      const firstLen = nodeByName(state, read.sequence[0]!).sequenceLength\n      read.firstNodeOffset = firstLen - (read.finalNodeCoverLength ?? 0)\n      const lastLen = nodeByName(\n        state,\n        read.sequence[read.sequence.length - 1]!,\n      ).sequenceLength\n      read.finalNodeCoverLength = lastLen - temp\n    }\n  })\n}\n\n// Flip a node's mismatches onto the opposite strand: positions are measured\n// from the other end of the node, and sequences are reverse-complemented.\n// sequenceLength (not node.width, which is only equal to it in 'normal'\n// node-width mode) is the right pivot because mismatch positions are base\n// offsets.\nexport function reverseMismatches(\n  mismatches: Mismatch[],\n  sequenceLength: number,\n): void {\n  mismatches.forEach(mm => {\n    Object.assign(mm, mirroredMismatch(mm, sequenceLength))\n  })\n}\n\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. Note that\n// getImageDimensions() below only adds it on the right: the pannable area\n// understates the left edge of the drawing by this much.\nconst NODE_HORIZONTAL_SLACK = 20\n\n// get the minimum and maximum coordinates used in the image to calculate image dimensions\nfunction getImageDimensions(state: LayoutState): void {\n  // Sentinels, deliberately crossed: if nothing below runs, minZoom() and\n  // alignSVG() detect the empty content rather than computing a negative scale.\n  const bounds: ImageBounds = { minX: 99, maxX: -99, minY: 99, maxY: -99 }\n\n  state.nodes.forEach((node: MaybeUnplacedNode) => {\n    if (node.x !== undefined) {\n      bounds.minX = Math.min(bounds.minX, node.x)\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  state.imageBounds = 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    // regular node\n    currentOrder = state.nodeOrders[anchorSeqVal]! - 1\n    increment = -1\n  } else {\n    // reverse node\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 with UNREACHABLE_ORDER, producing a dense\n// array. Holes matter here: `new Array(n)` is all holes and forEach/map skip\n// them, so an in-place forEach would leave the sentinel unset.\nexport function fillUnassignedOrders(\n  orders: readonly (number | undefined)[],\n): number[] {\n  const filled: number[] = []\n  for (const order of orders) {\n    filled.push(order ?? UNREACHABLE_ORDER)\n  }\n  return filled\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    debugLog(`generating order for track ${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  const finalOrders = fillUnassignedOrders(state.nodeOrders)\n  state.nodeOrders = finalOrders\n  finalOrders.forEach((order, i) => {\n    const node = state.nodes[i]\n    if (node !== undefined) {\n      node.order = order\n    }\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 (\n        !increasedOrders.has(currentNode) ||\n        increasedOrders.get(currentNode)! < currentOrder\n      ) {\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// 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 leftSideEdges: number[] = []\n  const rightSideEdges: number[] = []\n  const fallAngleAdjustment: number[] = []\n  const extra: number[] = []\n\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    leftSideEdges.push(0)\n    rightSideEdges.push(0)\n    fallAngleAdjustment.push(0)\n  }\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] = leftSideEdges[seg.order]! + 1\n        } else {\n          rightSideEdges[seg.order] = rightSideEdges[seg.order]! + 1\n        }\n      } else {\n        // Track is going to a different node; account for space needed to limit rise/fall angle\n        const yDifference = Math.abs((seg.y ?? 0) - (prevSeg.y ?? 0))\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          yDifference / 17.5,\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// create and fill assignment-variable, which contains info about tracks and lanes for each order-value\nfunction generateLaneAssignment(state: LayoutState): void {\n  // For each horizontal order slot, for each track number, holds the\n  // SegmentAssignment object for the visit of that track to that order slot.\n  // When an order slot is visited multiple times, holds whatever\n  // SegmentAssignment was created most recently.\n  const prevSegmentPerOrderPerTrack: SegmentAssignment[][] = []\n  // Index into assignments[order] by node, so addToAssignment can find an\n  // existing entry without scanning the whole order slot.\n  const assignmentByOrderAndNode: Map<number, NodeAssignment>[] = []\n\n  // create empty variables\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    state.assignments[i] = []\n    assignmentByOrderAndNode[i] = new Map()\n    prevSegmentPerOrderPerTrack[i] = []\n  }\n\n  // Record each track's segments in the order slots they cross, leaving the\n  // lanes for the sweep below.\n  state.tracks.forEach((track, trackNo) => {\n    track.path = basicPath(state, track)\n    track.path.forEach((segment, segmentNumber) => {\n      addToAssignment(\n        state,\n        segment.order,\n        segment.node,\n        trackNo,\n        segmentNumber,\n        prevSegmentPerOrderPerTrack,\n        assignmentByOrderAndNode,\n      )\n    })\n  })\n\n  // Now sweep left to right across order slots and assign vertical lanes to all the segments.\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    generateSingleLaneAssignment(state, state.assignments[i]!, i) // this is where the lanes get assigned\n  }\n}\n\nfunction addToAssignment(\n  state: LayoutState,\n  order: number,\n  nodeIndex: number | null,\n  trackNo: number,\n  segmentID: number,\n  prevSegmentPerOrderPerTrack: SegmentAssignment[][],\n  assignmentByOrderAndNode: Map<number, NodeAssignment>[],\n): void {\n  const segment: SegmentAssignment = {\n    trackID: trackNo,\n    segmentID,\n    compareToFromSame: prevSegmentPerOrderPerTrack[order]![trackNo] ?? null,\n  }\n  // A null node means the track is passing through / turning around here rather\n  // than visiting a node, so such segments never share a NodeAssignment.\n  const existing =\n    nodeIndex === null\n      ? undefined\n      : assignmentByOrderAndNode[order]!.get(nodeIndex)\n\n  if (existing === undefined) {\n    const assignment: NodeAssignment = {\n      type: 'single',\n      node: nodeIndex,\n      tracks: [segment],\n    }\n    state.assignments[order]!.push(assignment)\n    if (nodeIndex !== null) {\n      assignmentByOrderAndNode[order]!.set(nodeIndex, assignment)\n    }\n  } else {\n    // add to existing node in assignment\n    existing.type = 'multiple'\n    existing.tracks.push(segment)\n  }\n  prevSegmentPerOrderPerTrack[order]![trackNo] = segment\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  let index: number\n\n  assignment.forEach(node => {\n    node.idealLane = 0\n    node.tracks.forEach(track => {\n      if (track.segmentID === 0) {\n        track.idealLane = track.trackID\n        track.idealY = null\n      } else {\n        if (\n          state.tracks[track.trackID]!.path[track.segmentID - 1]!.order ===\n          order - 1\n        ) {\n          track.idealLane =\n            state.tracks[track.trackID]!.path[track.segmentID - 1]!.lane ??\n            undefined\n          track.idealY =\n            state.tracks[track.trackID]!.path[track.segmentID - 1]!.y\n        } else if (\n          track.segmentID < state.tracks[track.trackID]!.path.length - 1 &&\n          state.tracks[track.trackID]!.path[track.segmentID + 1]!.order ===\n            order - 1\n        ) {\n          track.idealLane =\n            state.tracks[track.trackID]!.path[track.segmentID + 1]!.lane ??\n            undefined\n          track.idealY =\n            state.tracks[track.trackID]!.path[track.segmentID + 1]!.y\n        } else {\n          index = track.segmentID - 1\n          while (\n            index >= 0 &&\n            state.tracks[track.trackID]!.path[index]!.order !== order - 1\n          ) {\n            index -= 1\n          }\n          if (index < 0) {\n            track.idealLane = track.trackID\n            track.idealY = null\n          } else {\n            track.idealLane = state.tracks[track.trackID]!.path[index]!.lane\n            track.idealY = state.tracks[track.trackID]!.path[index]!.y\n          }\n        }\n      }\n      node.idealLane! += track.idealLane!\n    })\n    node.idealLane /= node.tracks.length\n  })\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    if (node.node !== null) {\n      state.nodes[node.node]!.topLane = currentLane\n      if (prevNameIsNull) {\n        currentY -= 10\n      }\n      state.nodes[node.node]!.y = currentY\n      state.nodes[node.node]!.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      track.lane = currentLane\n      if (track.trackID === prevTrack && node.node === null && prevNameIsNull) {\n        currentY += 10\n      }\n      state.tracks[track.trackID]!.path[track.segmentID]!.lane = currentLane\n      state.tracks[track.trackID]!.path[track.segmentID]!.y = currentY\n      if (typeof track.idealY === 'number') {\n        potentialAdjustmentValues.add(track.idealY - currentY)\n      }\n      currentLane += 1\n      currentY += state.tracks[track.trackID]!.width\n      if (node.node !== null) {\n        state.nodes[node.node]!.contentHeight +=\n          state.tracks[track.trackID]!.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  if (state.nodesPerOrder[node.order]!.length > 0) {\n    state.nodesPerOrder[node.order]!.forEach(nodeIndex => {\n      if (\n        state.nodes[nodeIndex] !== node &&\n        state.nodes[nodeIndex]!.y > node.y\n      ) {\n        state.nodes[nodeIndex]!.y += adjustBy\n      }\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      if (\n        typeof track.idealY === 'number' &&\n        state.tracks[track.trackID]!.type !== 'read'\n      ) {\n        result +=\n          Math.abs(\n            track.idealY -\n              moveBy -\n              state.tracks[track.trackID]!.path[track.segmentID]!.y!,\n          ) * state.tracks[track.trackID]!.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) {\n    if (b.idealLane !== undefined) {\n      if (a.idealLane < b.idealLane) {\n        return -1\n      } else if (a.idealLane > b.idealLane) {\n        return 1\n      }\n      return 0\n    }\n    return -1\n  }\n  if (b.idealLane !== undefined) {\n    return 1\n  }\n  return 0\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  // flag: if vg returns freq of 0 for all tracks, we will increase width manually\n  let allAreFour = true\n\n  const NARROW_WIDTH = 4\n  const WIDE_WIDTH = state.config.trackWidth\n\n  for (const track of state.tracks) {\n    if (track.freq !== undefined) {\n      track.width = Math.round(\n        (Math.log(Math.max(track.freq, 1)) + 1) * NARROW_WIDTH,\n      )\n    } else {\n      // default track width\n      track.width = WIDE_WIDTH\n      if (track.type !== undefined && track.type === 'read') {\n        track.width = NARROW_WIDTH\n      }\n    }\n    if (track.width !== NARROW_WIDTH) {\n      allAreFour = false\n    }\n  }\n\n  if (allAreFour) {\n    state.tracks.forEach(track => {\n      if (track.freq !== undefined) {\n        track.width = WIDE_WIDTH\n      }\n    })\n  }\n}\n\nfunction getReadXStart(state: LayoutState, read: Track): number {\n  const seg = read.path[0]!\n  const node = state.nodes[seg.node!]!\n  const offset = read.firstNodeOffset ?? 0\n  // read starts in forward direction, or backward from the node's far end\n  return clampedXCoordinateOfBaseWithinNode(\n    node,\n    seg.isForward ? offset : node.sequenceLength - offset,\n  )\n}\n\nfunction getReadXEnd(state: LayoutState, read: Track): number {\n  const seg = read.path[read.path.length - 1]!\n  const node = state.nodes[seg.node!]!\n  const cover = read.finalNodeCoverLength ?? 0\n  // read ends in forward direction, or backward from the node's far end\n  return clampedXCoordinateOfBaseWithinNode(\n    node,\n    seg.isForward ? cover : node.sequenceLength - cover,\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  let xStart: number\n  let xEnd: number\n  let yStart: number\n  let yEnd: number\n\n  for (let i = 0; i <= state.maxOrder; i += 1) {\n    state.extraLeft.push(0)\n    state.extraRight.push(0)\n  }\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      if (orderEndX[node.order] === undefined) {\n        orderEndX[node.order] = node.x + node.pixelWidth\n      } else {\n        orderEndX[node.order] = Math.max(\n          orderEndX[node.order]!,\n          node.x + node.pixelWidth,\n        )\n      }\n    }\n  })\n\n  // Helps generation of verticalRectangles, correct increments of extraRight and extraLeft\n  state.tracks.sort(compareTrackByInitialOrdering)\n\n  state.tracks.forEach(track => {\n    // start of path\n    yStart = track.path[0]!.y!\n    if (track.type !== 'read') {\n      if (track.sequence[0]!.startsWith('-')) {\n        // The track starts with an inversed node\n        xStart = orderEndX[track.path[0]!.order]! + 20\n      } else {\n        // The track starts with a forward node\n        xStart = orderStartX[track.path[0]!.order]! - 20\n      }\n    } else {\n      xStart = getReadXStart(state, track)\n    }\n\n    // middle of path\n    for (let i = 0; i < track.path.length; i += 1) {\n      if (track.path[i]!.y !== yStart) {\n        if (track.path[i - 1]!.isForward) {\n          xEnd = orderEndX[track.path[i - 1]!.order]!\n        } else {\n          xEnd = orderStartX[track.path[i - 1]!.order]!\n        }\n        if (xEnd !== xStart) {\n          state.shapes.rectangles.push({\n            xStart: Math.min(xStart, xEnd),\n            yStart,\n            xEnd: Math.max(xStart, xEnd),\n            yEnd: yStart + track.width - 1,\n            // TODO: This is not actually the index of the track!\n            id: track.id,\n            name: track.name,\n            type: track.type,\n          })\n        }\n\n        if (track.path[i]!.order - 1 === track.path[i - 1]!.order) {\n          // regular forward connection\n          xStart = xEnd\n          xEnd = orderStartX[track.path[i]!.order]!\n          yEnd = track.path[i]!.y!\n          state.shapes.curves.push({\n            xStart,\n            yStart,\n            xEnd: xEnd + 1,\n            yEnd,\n            width: track.width,\n            id: track.id,\n            name: track.name,\n            type: track.type,\n            nodeStart: track.path[i - 1]!.node,\n            nodeEnd: track.path[i]!.node,\n            orderStart: track.path[i - 1]!.order,\n            orderEnd: track.path[i]!.order,\n          })\n          xStart = xEnd\n          yStart = yEnd\n        } else if (track.path[i]!.order + 1 === track.path[i - 1]!.order) {\n          // regular backward connection\n          xStart = xEnd\n          xEnd = orderEndX[track.path[i]!.order]!\n          yEnd = track.path[i]!.y!\n          state.shapes.curves.push({\n            xStart: xStart + 1,\n            yStart,\n            xEnd,\n            yEnd,\n            width: track.width,\n            id: track.id,\n            name: track.name,\n            type: track.type,\n            nodeStart: track.path[i - 1]!.node,\n            nodeEnd: track.path[i]!.node,\n            orderStart: track.path[i - 1]!.order,\n            orderEnd: track.path[i]!.order,\n          })\n          xStart = xEnd\n          yStart = yEnd\n        } else {\n          // change of direction\n          if (track.path[i - 1]!.isForward) {\n            yEnd = track.path[i]!.y!\n            generateTurnaround(\n              state,\n              1,\n              xEnd,\n              yStart,\n              yEnd,\n              track.width,\n              track.id,\n              track.path[i]!.order,\n              track.type,\n              track.name,\n            )\n            xStart = orderEndX[track.path[i]!.order]!\n            yStart = track.path[i]!.y!\n          } else {\n            yEnd = track.path[i]!.y!\n            generateTurnaround(\n              state,\n              -1,\n              xEnd,\n              yStart,\n              yEnd,\n              track.width,\n              track.id,\n              track.path[i]!.order,\n              track.type,\n              track.name,\n            )\n            xStart = orderStartX[track.path[i]!.order]!\n            yStart = track.path[i]!.y!\n          }\n        }\n      }\n    }\n\n    // ending edges\n    if (track.type !== 'read') {\n      if (!track.path[track.path.length - 1]!.isForward) {\n        // The track ends with an inversed node\n        xEnd = orderStartX[track.path[track.path.length - 1]!.order]! - 20\n      } else {\n        // The track ends with a forward node\n        xEnd = orderEndX[track.path[track.path.length - 1]!.order]! + 20\n      }\n    } else {\n      xEnd = getReadXEnd(state, track)\n    }\n    state.shapes.rectangles.push({\n      xStart: Math.min(xStart, xEnd),\n      yStart,\n      xEnd: Math.max(xStart, xEnd),\n      yEnd: yStart + track.width - 1,\n      id: track.id,\n      name: track.name,\n      type: track.type,\n    })\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 = COARSENED_ID_BASE,\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      // Pre-set width so placeReads / placeReadSet allocate the right vertical\n      // space and assignReadsToNodes (patched to honor pre-set widths) leaves\n      // it alone.\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  if (DEBUG) {\n    let tallestName = '?'\n    let tallestH = 0\n    state.nodes.forEach(n => {\n      if (n.contentHeight > tallestH) {\n        tallestH = n.contentHeight\n        tallestName = n.name\n      }\n    })\n    debugLog(\n      `[coarsened] ${unit}s_in=${source.length} edges_out=${synthetic.length} ` +\n        `tallestNodeBeforePlace=${tallestName}(${tallestH.toFixed(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  dir: 1 | -1,\n  x: number,\n  yStart: number,\n  yEnd: number,\n  trackWidth: number,\n  trackID: number,\n  order: number,\n  type: TrackType | undefined,\n  trackName: string | undefined,\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, 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} ${yTop + trackWidth}`\n  d += ' Z '\n  state.shapes.corners.push({ path: d, id: trackID, type })\n  extra[order]! += 1\n}\n\n// The x extent of a node's bases: pixelWidth, plus about half a character\n// each side under nodeWidthOption 'normal'\nexport function nodePixelCoordinatesInX(node: Node): [number, number] {\n  const nodeLeftX = node.x - 4\n  const nodeRightX = node.x + node.pixelWidth + 4\n  return [nodeLeftX, nodeRightX]\n}\n\n// calculate node widths depending on sequence lengths and chosen calculation method\nfunction generateNodeWidth(state: LayoutState): void {\n  switch (state.config.nodeWidthOption) {\n    case 'compressed':\n      state.nodes.forEach(node => {\n        node.width = 1 + Math.log2(Math.max(node.sequenceLength, 1))\n        node.pixelWidth = Math.round((node.width - 1) * 8.401)\n      })\n      break\n    case 'small':\n      state.nodes.forEach(node => {\n        node.width = node.sequenceLength / 100\n        node.pixelWidth = Math.max(Math.round((node.width - 1) * 8.401), 0)\n      })\n      break\n    case 'fixed':\n      state.nodes.forEach(node => {\n        node.width = 10\n        node.pixelWidth = Math.round(node.width * 8.401)\n      })\n      break\n    case 'normal': {\n      // The label draws a base per character from x - 4, in a monospace font\n      // whose character width the caller measures. pixelWidth runs from the\n      // first character to the last, so the outline, 9 px wider each side,\n      // holds the whole label, and nodePixelCoordinatesInX's half character\n      // each side puts base i under letter i.\n      const charWidth = state.config.charWidth\n      state.nodes.forEach(node => {\n        node.width = node.sequenceLength\n        node.pixelWidth = Math.round(\n          charWidth * Math.max(node.sequenceLength - 1, 0),\n        )\n      })\n      break\n    }\n    default:\n      throw new Error(`${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) !== 0) {\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\n// The index of the node `index` merges into, or 0 when it merges into none.\nfunction mergeableWithPred(\n  index: number,\n  pred: Neighbors,\n  succ: Neighbors,\n): number {\n  const predecessor = soleNeighbor(pred, index)\n  return predecessor !== 0 && soleNeighbor(succ, predecessor) !== 0\n    ? predecessor\n    : 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.\nimport type { Node, TrackCurve, TrackType } from './types.ts'\n\nfunction groupBy<T, K>(items: readonly T[], key: (item: T) => K): 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\nfunction compareCurvesByXYStartValue(a: TrackCurve, b: TrackCurve): number {\n  if (a.xStart < b.xStart) {\n    return 1\n  } else if (a.xStart > b.xStart) {\n    return -1\n  } else if (a.yStart > b.yStart) {\n    return 1\n  } else if (a.yStart < b.yStart) {\n    return -1\n  }\n  return 0\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// 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, so a bundle of tracks changing lanes together stays parallel rather\n// than crossing at one x.\nexport function curvePaths(\n  curves: readonly TrackCurve[],\n  type: TrackType | undefined,\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    // Control point adjustment range: 30% to 70% of the original x values\n    let adjustValue = 0.3\n    let adjustIncrement = 0.4 / curveGroup.length\n\n    // Ignore Beziar Curve skewing when a group is not too big\n    if (curveGroup.length <= 5) {\n      adjustValue = 0.5\n      adjustIncrement = 0\n    }\n\n    curveGroup.sort(compareCurvesByXYStartValue)\n\n    curveGroup.forEach(curve => {\n      let xAdjusted: number\n      // NextAdjusted is used to try to draw a parallel curve on the way back\n      let xNextAdjusted: number\n      if (curve.yStart < curve.yEnd) {\n        xAdjusted =\n          curve.xStart + (curve.xEnd - curve.xStart) * (1 - adjustValue)\n        adjustValue += adjustIncrement\n        xNextAdjusted =\n          curve.xStart + (curve.xEnd - curve.xStart) * (1 - adjustValue)\n      } else {\n        xAdjusted = curve.xStart + (curve.xEnd - curve.xStart) * adjustValue\n        adjustValue += adjustIncrement\n        xNextAdjusted = curve.xStart + (curve.xEnd - curve.xStart) * adjustValue\n      }\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// 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} ${y}`\n  }\n  return d\n}\n", "import {\n  canonicalStrand,\n  stepName,\n  tubeMapReads\n} from \"./chunk-TEDQJPMI.js\";\nimport {\n  pathCssColor,\n  pathGreyCssColor\n} from \"./chunk-7GBL7SJY.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/tubeMapLayout.ts\nimport { layoutTubeMap } from \"@jbrowse/tubemap-core\";\nfunction visitStrands(graph) {\n  const strands = /* @__PURE__ */ new Map();\n  for (const [segment, visits] of graph.pathVisits ?? []) {\n    for (const visit of visits) {\n      const key = `${visit.path}\t${segment}`;\n      const list = strands.get(key);\n      if (list) {\n        list.push(visit.strand);\n      } else {\n        strands.set(key, [visit.strand]);\n      }\n    }\n  }\n  return strands;\n}\nfunction tubeMapTracks(graph) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const strands = visitStrands(graph);\n  const paths = (graph.paths ?? []).map((path, index) => ({ path, index }));\n  const reference = paths.findIndex(\n    (p) => pathOrigin(p.path.name).name === graph.referencePath\n  );\n  if (reference > 0) {\n    paths.unshift(...paths.splice(reference, 1));\n  }\n  return paths.flatMap(({ path, index }) => {\n    const visitName = pathOrigin(path.name).name;\n    const seen = /* @__PURE__ */ new Map();\n    const sequence = path.nodeIds.flatMap((id) => {\n      const node = nodeById.get(id);\n      if (!node) {\n        return [];\n      }\n      const k = seen.get(node.name) ?? 0;\n      seen.set(node.name, k + 1);\n      const strand = strands.get(`${visitName}\t${node.name}`)?.[k] ?? canonicalStrand(node);\n      return [stepName(node, strand)];\n    });\n    return sequence.length > 0 ? [\n      {\n        id: index,\n        name: path.name,\n        sequence,\n        sourceTrackID: 0,\n        type: \"haplotype\"\n      }\n    ] : [];\n  });\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 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 layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {\n    nodeWidthOption: \"compressed\",\n    trackWidth: tubeWidth(tracks.length)\n  });\n  return layout ? { layout, pathColors } : void 0;\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, pathColors } = 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, pathColors },\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 = /* @__PURE__ */ new Map();\n  for (const node of drawnNodes(layout)) {\n    const list = byOrder.get(node.order);\n    if (list) {\n      list.push(node);\n    } else {\n      byOrder.set(node.order, [node]);\n    }\n  }\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 + node.sequenceLength);\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 pathsReachBackbone(graph) {\n  return graph.nodes.some(isBackbone) && hasTubeMapPaths(graph);\n}\nfunction tubeMapReferenceLayout(graph) {\n  const run = pathsReachBackbone(graph) ? runTubeMap(graph) : void 0;\n  if (!run) {\n    return void 0;\n  }\n  const { layout, pathColors } = run;\n  const columns = tubeMapColumns(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, pathColors },\n    referenceAxis: true,\n    pixelRows: true,\n    extent: extentOf(layout, yOffset)\n  };\n}\n\nexport {\n  visitStrands,\n  tubeMapTracks,\n  hasTubeMapPaths,\n  tubeWidth,\n  tubeMapLayout,\n  tubeMapReferenceLayout\n};\n", "import {\n  placeOffReference\n} from \"./chunk-TZFWUT2C.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  referenceSpan\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/anchoredLayout.ts\nfunction rankRows(graph) {\n  const present = /* @__PURE__ */ new Set();\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      present.add(node.stable.rank);\n    }\n  }\n  return new Map([...present].sort((a, b) => a - b).map((r, i) => [r, i]));\n}\nfunction anchoredLayout(graph, region) {\n  const backbone = backboneNodes(graph);\n  if (backbone.length === 0) {\n    return void 0;\n  }\n  const span = referenceSpan(backbone, region);\n  const rows = rankRows(graph);\n  const nodePositions = backbonePositions(backbone);\n  const alleleDeletions = placeOffReference({\n    graph,\n    span,\n    rowY: (node) => (node.stable ? rows.get(node.stable.rank) ?? rows.size : rows.size) * ROW_HEIGHT_PX,\n    positions: nodePositions\n  });\n  const rowLabels = [...rows].map(([rank, row]) => ({\n    label: rank === 0 ? \"Reference (rank 0)\" : `Rank ${rank}`,\n    y: row * ROW_HEIGHT_PX\n  }));\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    alleleDeletions\n  };\n}\n\nexport {\n  anchoredLayout\n};\n", "import {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/orderedLayout.ts\nvar GUTTER = 12;\nvar LANE_PX = ROW_HEIGHT_PX;\nfunction nodeWidth(node) {\n  return 10 + 8 * Math.log2(1 + node.length);\n}\nfunction compare(a, b) {\n  return a < b ? -1 : a > b ? 1 : 0;\n}\nfunction compareKeys(a, b) {\n  return compare(a.at, b.at) || compare(a.side, b.side) || compare(a.hops, b.hops);\n}\nvar UNREACHED = { at: Infinity, side: 0, hops: 0 };\nfunction referenceOrder(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const key = orderKeys(graph);\n  return graph.nodes.map((n) => n.id).sort(\n    (a, b) => compareKeys(key.get(a) ?? UNREACHED, key.get(b) ?? UNREACHED) || compare(byId.get(a).name, byId.get(b).name) || compare(a, b)\n  );\n}\nfunction placeByWalks(graph, backbone) {\n  const isNode = new Set(graph.nodes.map((n) => n.id));\n  const startOf = new Map(backbone.map((n) => [n.id, n.stable.start]));\n  const next = /* @__PURE__ */ new Map();\n  const prev = /* @__PURE__ */ new Map();\n  backbone.forEach((n, i) => {\n    prev.set(n.id, backbone[i - 1]?.id);\n    next.set(n.id, backbone[i + 1]?.id);\n  });\n  let head = backbone[0]?.id;\n  const insertAfter = (at, id) => {\n    const after = next.get(at);\n    next.set(at, id);\n    prev.set(id, at);\n    next.set(id, after);\n    if (after !== void 0) {\n      prev.set(after, id);\n    }\n  };\n  const insertBefore = (at, id) => {\n    const before = prev.get(at);\n    if (before === void 0) {\n      head = id;\n      prev.set(id, void 0);\n      next.set(id, at);\n      prev.set(at, id);\n    } else {\n      insertAfter(before, id);\n    }\n  };\n  for (const path of graph.paths ?? []) {\n    let rising = 0;\n    let falling = 0;\n    let last;\n    for (const id of path.nodeIds) {\n      const start = startOf.get(id);\n      if (start !== void 0) {\n        if (last !== void 0 && start !== last) {\n          if (start > last) {\n            rising++;\n          } else {\n            falling++;\n          }\n        }\n        last = start;\n      }\n    }\n    const ids = falling > rising ? [...path.nodeIds].reverse() : path.nodeIds;\n    let from;\n    const leading = /* @__PURE__ */ new Set();\n    for (const id of ids) {\n      if (next.has(id)) {\n        if (from === void 0) {\n          for (const lead of leading) {\n            insertBefore(id, lead);\n          }\n        }\n        from = id;\n      } else if (isNode.has(id)) {\n        if (from === void 0) {\n          leading.add(id);\n        } else {\n          insertAfter(from, id);\n          from = id;\n        }\n      }\n    }\n  }\n  const placed = [];\n  for (let id = head; id !== void 0; id = next.get(id)) {\n    placed.push(id);\n  }\n  return placed;\n}\nfunction placeBySearch(adjacent, key) {\n  const queue = [...key.entries()].sort(([a, ka], [b, kb]) => compareKeys(ka, kb) || compare(a, b)).map(([id]) => id);\n  const placed = queue.length;\n  for (const id of queue) {\n    const from = key.get(id);\n    for (const nb of adjacent.get(id) ?? []) {\n      if (!key.has(nb)) {\n        key.set(nb, { at: from.at, side: 1, hops: from.hops + 1 });\n        queue.push(nb);\n      }\n    }\n  }\n  const searched = new Set(queue.slice(placed));\n  const sided = /* @__PURE__ */ new Set();\n  for (const seed of searched) {\n    if (sided.has(seed)) {\n      continue;\n    }\n    const { at } = key.get(seed);\n    const run = [seed];\n    sided.add(seed);\n    let farHalf = true;\n    for (const id of run) {\n      const { hops } = key.get(id);\n      let deadEnd = true;\n      let touchesLeft = false;\n      for (const nb of adjacent.get(id) ?? []) {\n        const other = key.get(nb);\n        if (other.at === at && searched.has(nb)) {\n          deadEnd &&= other.hops <= hops;\n          if (!sided.has(nb)) {\n            sided.add(nb);\n            run.push(nb);\n          }\n        } else if (other.at !== at) {\n          touchesLeft ||= other.at < at;\n          farHalf &&= other.at < at;\n        }\n      }\n      farHalf &&= !deadEnd || touchesLeft;\n    }\n    if (farHalf) {\n      for (const id of run) {\n        const k = key.get(id);\n        key.set(id, { ...k, side: -1, hops: -k.hops });\n      }\n    }\n  }\n}\nfunction orderKeys(graph) {\n  const ids = new Set(graph.nodes.map((n) => n.id));\n  const adjacent = /* @__PURE__ */ new Map();\n  for (const e of graph.edges) {\n    if (!ids.has(e.from) || !ids.has(e.to)) {\n      continue;\n    }\n    ;\n    (adjacent.get(e.from) ?? adjacent.set(e.from, []).get(e.from)).push(e.to);\n    (adjacent.get(e.to) ?? adjacent.set(e.to, []).get(e.to)).push(e.from);\n  }\n  const backbone = graph.nodes.filter(isBackbone).sort(\n    (a, b) => compare(a.stable.start, b.stable.start) || compare(a.name, b.name)\n  );\n  const key = /* @__PURE__ */ new Map();\n  placeByWalks(graph, backbone).forEach((id, rank) => {\n    key.set(id, { at: rank, side: 0, hops: 0 });\n  });\n  placeBySearch(adjacent, key);\n  return key;\n}\nfunction layerGraph(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const order = referenceOrder(graph);\n  const key = new Map(order.map((id, i) => [id, i]));\n  const isRef = (id) => isBackbone(byId.get(id));\n  const preds = new Map(order.map((id) => [id, []]));\n  const succs = new Map(order.map((id) => [id, []]));\n  const link = (a, b) => {\n    preds.get(b).push(a);\n    succs.get(a).push(b);\n  };\n  for (const e of graph.edges) {\n    if (e.from === e.to || !key.has(e.from) || !key.has(e.to)) {\n      continue;\n    }\n    if (key.get(e.from) < key.get(e.to)) {\n      link(e.from, e.to);\n    } else {\n      link(e.to, e.from);\n    }\n  }\n  const backbone = order.filter(isRef);\n  for (let i = 1; i < backbone.length; i++) {\n    link(backbone[i - 1], backbone[i]);\n  }\n  const layerOf = /* @__PURE__ */ new Map();\n  for (const id of order) {\n    let l = 0;\n    for (const p of preds.get(id)) {\n      l = Math.max(l, layerOf.get(p) + 1);\n    }\n    layerOf.set(id, l);\n  }\n  for (let i = order.length - 1; i >= 0; i--) {\n    const id = order[i];\n    const s = succs.get(id);\n    if (isRef(id) || s.length === 0) {\n      continue;\n    }\n    let minSucc = Infinity;\n    for (const t of s) {\n      minSucc = Math.min(minSucc, layerOf.get(t));\n    }\n    const lo = layerOf.get(id);\n    const hi = Math.max(lo, minSucc - 1);\n    layerOf.set(id, Math.floor((lo + hi) / 2));\n  }\n  const layers = [];\n  for (const id of order) {\n    ;\n    (layers[layerOf.get(id)] ??= []).push(id);\n  }\n  return { layers, layerOf, preds };\n}\nfunction orderedLayout(graph) {\n  if (!graph.nodes.some(isBackbone)) {\n    return void 0;\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const isRef = (id) => isBackbone(byId.get(id));\n  const { layers, layerOf: layer, preds } = layerGraph(graph);\n  const layerWidth = layers.map((ids) => {\n    let w = 0;\n    for (const id of ids) {\n      w = Math.max(w, nodeWidth(byId.get(id)));\n    }\n    return w;\n  });\n  const layerX = [];\n  let x = 0;\n  for (let l = 0; l < layers.length; l++) {\n    layerX[l] = x;\n    x += layerWidth[l] + GUTTER;\n  }\n  const y = /* @__PURE__ */ new Map();\n  for (const ids of layers) {\n    const free = [];\n    for (const id of ids) {\n      if (isRef(id)) {\n        y.set(id, 0);\n        continue;\n      }\n      const placed = preds.get(id).filter((p) => y.has(p));\n      let ideal = 0;\n      for (const p of placed) {\n        ideal += y.get(p) / placed.length;\n      }\n      free.push({ id, ideal: ideal === 0 ? LANE_PX : ideal });\n    }\n    free.sort((a, b) => a.ideal - b.ideal);\n    const taken = /* @__PURE__ */ new Set([0]);\n    for (const { id, ideal } of free) {\n      let lane = Math.round(ideal / LANE_PX);\n      if (lane === 0) {\n        lane = ideal >= 0 ? 1 : -1;\n      }\n      for (let d = 1; taken.has(lane); d++) {\n        if (!taken.has(lane + d)) {\n          lane += d;\n        } else if (!taken.has(lane - d)) {\n          lane -= d;\n        }\n      }\n      taken.add(lane);\n      y.set(id, lane * LANE_PX);\n    }\n  }\n  const nodePositions = {};\n  for (const n of graph.nodes) {\n    const l = layer.get(n.id);\n    const w = nodeWidth(n);\n    const cx = layerX[l] + layerWidth[l] / 2;\n    const ny = y.get(n.id);\n    nodePositions[n.id] = [\n      { x: cx - w / 2, y: ny },\n      { x: cx + w / 2, y: ny }\n    ];\n  }\n  return { nodePositions, referenceAxis: false, pixelRows: true };\n}\n\nexport {\n  referenceOrder,\n  layerGraph,\n  orderedLayout\n};\n", "import {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  panSNContig,\n  panSNSample\n} from \"./chunk-BPLIXMH7.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}\nfunction stepsOf(pieces, lengthOf) {\n  const steps = [];\n  let end;\n  for (const piece of pieces) {\n    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {\n      steps.push(piece.start - end);\n    }\n    steps.push(...piece.nodeIds);\n    const bp = piece.nodeIds.reduce(\n      (sum, id) => sum + (lengthOf.get(id) ?? 0),\n      0\n    );\n    end = piece.start === void 0 ? void 0 : piece.start + bp;\n  }\n  return steps;\n}\nfunction stepSpans(pieces, lengthOf) {\n  const spans = [];\n  let end;\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      spans.push({ start: end, end: piece.start });\n    }\n    let pos = piece.start;\n    for (const id of piece.nodeIds) {\n      const len = lengthOf.get(id) ?? 0;\n      spans.push({ start: pos, end: pos + len });\n      pos += len;\n    }\n    end = pos;\n  }\n  return spans;\n}\nfunction sliceBetween(steps, span, region, flanked = true) {\n  if (!region || !flanked) {\n    return { ids: steps, complete: true, from: -1, to: -1 };\n  }\n  let i0 = -1;\n  let i1 = -1;\n  let bestEnd = -Infinity;\n  let bestStart = Infinity;\n  steps.forEach((id, i) => {\n    const s = typeof id === \"string\" ? span.get(id) : void 0;\n    if (s) {\n      if (s.end <= region.start && s.end > bestEnd) {\n        bestEnd = s.end;\n        i0 = i;\n      }\n      if (s.start >= region.end && s.start < bestStart) {\n        bestStart = s.start;\n        i1 = i;\n      }\n    }\n  });\n  if (i0 < 0 || i1 < 0) {\n    return { ids: steps, complete: false, from: -1, to: -1 };\n  }\n  const ids = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));\n  return {\n    ids: i0 < i1 ? ids : ids.reverse(),\n    complete: true,\n    from: i0,\n    to: i1\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 walkRows(graph, region, unit) {\n  const paths = graph.paths ?? [];\n  const isReference = (p) => pathOrigin(p.name).name === graph.referencePath;\n  const referencePieces = paths.some(isReference) ? paths.filter(isReference).sort((a, b) => (a.start ?? 0) - (b.start ?? 0)) : paths.slice(0, 1);\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 = /* @__PURE__ */ new Map();\n  for (const path of others) {\n    walks.set(path.name, [...walks.get(path.name) ?? [], path]);\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const referenceStart = first.start ?? 0;\n  const cut = region && region.end > region.start ? region : void 0;\n  const span = /* @__PURE__ */ new Map();\n  for (const piece of referencePieces) {\n    let pos = piece.start ?? 0;\n    for (const id of piece.nodeIds) {\n      const len = lengthOf.get(id) ?? 0;\n      if (!span.has(id)) {\n        span.set(id, { start: pos, end: pos + len });\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || [...span.values()].some((s) => s.end <= cut.start) && [...span.values()].some((s) => s.start >= cut.end);\n  const rowOf = (pieces) => {\n    const path = pieces[0];\n    const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));\n    const { ids, complete, from, to } = sliceBetween(\n      stepsOf(ordered, lengthOf),\n      span,\n      cut,\n      flanked\n    );\n    const spans = stepSpans(ordered, lengthOf);\n    const contig = path.contig ?? panSNContig(pathOrigin(path.name).name);\n    const axis = !spans?.length ? void 0 : from < 0 ? { contig, start: spans[0].start, reversed: false } : from < to ? { contig, start: spans[from].end, reversed: false } : { contig, start: spans[from].start, reversed: true };\n    const runs = [];\n    let bp = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    for (const id of ids) {\n      if (typeof id === \"number\") {\n        runs.push({ start: bp, bp: id, onReference: false, gap: true });\n        bp += id;\n        gapBp += id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf.get(id) ?? 0;\n      const s = span.get(id);\n      const last = runs.at(-1);\n      const at = last?.referenceStart;\n      const forward = s && at !== void 0 && step >= 0 && at + last.bp === s.start;\n      const backward = s && at !== void 0 && step <= 0 && s.end === at;\n      if (!s && last && !last.onReference && !last.gap) {\n        last.bp += len;\n      } else if (forward || backward) {\n        last.bp += len;\n        if (!forward) {\n          last.referenceStart = s.start;\n          last.reversed = true;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        runs.push({\n          start: bp,\n          bp: len,\n          onReference: s !== void 0,\n          referenceStart: s?.start\n        });\n        step = 0;\n      }\n      bp += len;\n      if (!s) {\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      runs,\n      axis\n    };\n  };\n  const origin = cut ? cut.start : referenceStart;\n  return {\n    origin,\n    unit,\n    reference: rowOf(referencePieces),\n    rows: [...walks.values()].map(rowOf).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  walkRows\n};\n", "import {\n  walkRows\n} from \"./chunk-SZNZ2T6D.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  backboneNodes,\n  backbonePositions,\n  overlapsWindow\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/walkRowLayout.ts\nvar READOUT_ROOM = 1.3;\nfunction walkRowsExtent(walks, pitch = {\n  rowPx: ROW_HEIGHT_PX,\n  readouts: true\n}) {\n  let longest = walks.reference.bp;\n  for (const row of walks.rows) {\n    longest = Math.max(longest, row.bp);\n  }\n  return {\n    maxX: walks.origin + longest * (pitch.readouts ? READOUT_ROOM : 1),\n    maxY: walks.rows.length * pitch.rowPx\n  };\n}\nfunction walkRowLabels(rows, layout, pitch) {\n  if (!rows) {\n    return layout?.rowLabels ?? [];\n  }\n  if (pitch && !pitch.labelled) {\n    return [];\n  }\n  return [rows.reference, ...rows.rows].map((row, i) => ({\n    label: row.label,\n    y: i * (pitch?.rowPx ?? ROW_HEIGHT_PX)\n  }));\n}\nfunction walkRowLayout(graph, region) {\n  const backbone = backboneNodes(graph);\n  const walks = walkRows(graph, region);\n  if (backbone.length === 0 || !walks) {\n    return void 0;\n  }\n  const overWindow = region ? backbone.filter((n) => overlapsWindow(n, region)) : backbone;\n  const nodePositions = backbonePositions(\n    overWindow.length > 0 ? overWindow : backbone\n  );\n  const rowLabels = [\n    { label: walks.reference.label, y: 0 },\n    ...walks.rows.map((row, i) => ({\n      label: row.label,\n      y: (i + 1) * ROW_HEIGHT_PX\n    }))\n  ];\n  return {\n    nodePositions,\n    rowLabels,\n    referenceAxis: true,\n    pixelRows: true,\n    extent: walkRowsExtent(walks)\n  };\n}\n\nexport {\n  walkRowsExtent,\n  walkRowLabels,\n  walkRowLayout\n};\n", "import {\n  sampleRowLayout\n} from \"./chunk-LOEA5IHZ.js\";\nimport {\n  hasTubeMapPaths,\n  tubeMapLayout,\n  tubeMapReferenceLayout\n} from \"./chunk-W2I4DOL4.js\";\nimport {\n  anchoredLayout\n} from \"./chunk-L3O7AWLI.js\";\nimport {\n  orderedLayout\n} from \"./chunk-HNQPEMYE.js\";\nimport {\n  walkRowLayout\n} from \"./chunk-MP7LXLWV.js\";\nimport {\n  isBackbone,\n  isOffReference\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layoutModes.ts\nvar FORCE_LAYOUT_LABEL = \"Force-directed layout\";\nvar hasBackbone = (graph) => graph.nodes.some(isBackbone);\nvar hasWalks = (graph) => hasBackbone(graph) && (graph.paths?.length ?? 0) > 1;\nvar hasTubeMapBackbone = (graph) => hasBackbone(graph) && hasTubeMapPaths(graph);\nvar hasAlleles = (graph) => hasBackbone(graph) && graph.nodes.some(isOffReference);\nvar LAYOUT_MODES = [\n  {\n    value: \"auto\",\n    label: \"Anchored\",\n    description: \"x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.\",\n    run: anchoredLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n    drawsNodes: true\n  },\n  {\n    value: \"samplerows\",\n    label: \"Sample rows\",\n    description: \"x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.\",\n    run: sampleRowLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasAlleles,\n    drawsLocally: hasAlleles,\n    drawsNodes: true\n  },\n  {\n    value: \"walkrows\",\n    label: \"Walk rows\",\n    description: \"x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs W or P lines.\",\n    run: walkRowLayout,\n    cutMargins: false,\n    wholeWalks: true,\n    available: hasWalks,\n    drawsLocally: hasWalks,\n    drawsNodes: false\n  },\n  {\n    value: \"ordered\",\n    label: \"Ordered\",\n    description: \"x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.\",\n    run: orderedLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasBackbone,\n    drawsLocally: hasBackbone,\n    drawsNodes: true\n  },\n  {\n    value: \"tubemap\",\n    label: \"Tube map\",\n    description: \"sequenceTubeMap: every path a coloured tube through boxed nodes, columns in node order and node widths log-scaled. Needs P or W lines.\",\n    run: tubeMapLayout,\n    cutMargins: false,\n    wholeWalks: false,\n    available: hasTubeMapPaths,\n    drawsLocally: hasTubeMapPaths,\n    drawsNodes: false\n  },\n  {\n    value: \"tubemapref\",\n    label: \"Tube map on reference\",\n    description: \"The tube map with each column at the reference bp it covers, so the tubes line up with the tracks around them. Needs P or W lines and a reference path.\",\n    run: tubeMapReferenceLayout,\n    cutMargins: true,\n    wholeWalks: false,\n    available: hasTubeMapBackbone,\n    drawsLocally: hasTubeMapBackbone,\n    drawsNodes: false\n  },\n  {\n    value: \"force\",\n    label: FORCE_LAYOUT_LABEL,\n    description: \"OGDF FMMM, via the external Bandage engine.\",\n    run: () => void 0,\n    cutMargins: false,\n    wholeWalks: false,\n    available: () => true,\n    drawsLocally: () => false,\n    drawsNodes: true\n  }\n];\nvar LAYOUT_MODE_VALUES = LAYOUT_MODES.map((m) => m.value);\nfunction modeUsesLayoutEngine(value, graph) {\n  return !layoutModeByValue(value).drawsLocally(graph);\n}\nfunction layoutModeByValue(value) {\n  return LAYOUT_MODES.find((m) => m.value === value) ?? LAYOUT_MODES[0];\n}\n\nexport {\n  FORCE_LAYOUT_LABEL,\n  LAYOUT_MODES,\n  LAYOUT_MODE_VALUES,\n  modeUsesLayoutEngine,\n  layoutModeByValue\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 [sample, haplotype, contig] = name.split(\"#\");\n    const n = Number(haplotype);\n    return contig !== void 0 && Number.isInteger(n) && n >= 0 ? { sample, column: Math.max(0, n - 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 { groupKeyComparator } from '@jbrowse/core/util/groupKeys'\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\nfunction haplotypes(rows: { label: string }[]) {\n  const n = new Set(rows.map(r => r.label)).size\n  return `${n} haplotype${n === 1 ? '' : 's'}`\n}\n\n// The rows reordered section by section, each keeping the order it came in.\n// A row's value is its table row's, looked up by haplotype (`HG00097#1`)\n// and then by sample (`HG00097`); rows with none stack last.\nexport function groupWalkRows<R extends { sample: string; label: string }>(\n  rows: R[],\n  table: SampleRow[],\n  { field, domain }: WalkRowGroupBy,\n) {\n  const valueOf = new Map(table.map(row => [row.name, row[field] ?? '']))\n  const groups = new Map<string, R[]>()\n  for (const row of rows) {\n    const key = valueOf.get(row.label) || valueOf.get(row.sample) || ''\n    const group = groups.get(key)\n    if (group) {\n      group.push(row)\n    } else {\n      groups.set(key, [row])\n    }\n  }\n  let first = 1\n  const sections: WalkRowSection[] = [...groups.keys()]\n    .sort(groupKeyComparator(domain))\n    .map(key => {\n      const members = groups.get(key)!\n      const section = {\n        key,\n        title: `${key || `${field}: none`} \u00B7 ${haplotypes(members)}`,\n        first,\n        count: members.length,\n      }\n      first += members.length\n      return section\n    })\n  return {\n    rows: sections.flatMap(s => groups.get(s.key)!),\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", "import {\n  SATURATED_PATH_COUNT\n} from \"./chunk-MFKORG3F.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 formatBp(bp) {\n  if (bp >= 1e4) {\n    return `${(bp / 1e3).toFixed(0)} kb`;\n  }\n  if (bp >= 1e3) {\n    return `${(bp / 1e3).toFixed(1)} kb`;\n  }\n  return `${bp} bp`;\n}\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: `${formatBp(longest)} inv` };\n  }\n  const repeat = longest !== shortest ? coveringRepeat(b, repeats) : void 0;\n  if (repeat) {\n    const name = repeat.name ? ` (${repeat.name})` : \"\";\n    return {\n      kind: \"repeat\",\n      label: `${range} repeat array${name}, ${routes(pathCount)}`\n    };\n  }\n  const alleles = pathCount > 2 ? `, ${pathCount} alleles` : \"\";\n  if (shortest === longest && shortest === refSpan) {\n    return refSpan <= 1 ? { kind: \"snp\", label: \"SNP\" } : { kind: \"substitution\", label: `${formatBp(refSpan)} sub` };\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}, ${pathCount} alleles`\n  };\n}\nvar BUBBLE_KIND_COLORS = {\n  snp: \"#5b6b7a\",\n  substitution: \"#5b6b7a\",\n  insertion: \"#2f8fd6\",\n  deletion: \"#c94040\",\n  inversion: \"#e07b00\",\n  repeat: \"#8e3fbf\",\n  superbubble: \"#8e3fbf\",\n  complex: \"#8e3fbf\"\n};\nvar BUBBLE_KIND_NAMES = {\n  snp: \"SNP\",\n  substitution: \"substitution\",\n  insertion: \"insertion\",\n  deletion: \"deletion\",\n  inversion: \"inversion\",\n  repeat: \"repeat array\",\n  superbubble: \"superbubble\",\n  complex: \"site\"\n};\nfunction bubbleSegmentIds(b) {\n  return b.segments.split(\",\").filter(Boolean);\n}\n\nexport {\n  formatBp,\n  classifyBubble,\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds\n};\n", "import {\n  RAMP_GRADIENT_CSS,\n  RAMP_GRADIENT_STOPS,\n  rampHueCss,\n  rampStops\n} from \"./chunk-6ZNQJ5ZD.js\";\nimport {\n  REFERENCE_RAMP_ALT_CSS\n} from \"./chunk-HBEKUQO4.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  el\n} from \"./chunk-NNODIW4U.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\n\n// src/layout/walkRowDraw.ts\nvar ON_REFERENCE = \"#2f8fd6\";\nvar OFF_REFERENCE = \"#8e3fbf\";\nvar OUTSIDE_CUT = \"#bdbdbd\";\nvar GENE_INK = \"#1c1c22\";\nvar BAR_PX = 12;\nvar GAP_PX = 4;\nvar LABELLED_ROW_PX = 12;\nvar MIN_TILED_BAR_PX = 6;\nvar MIN_TILE_PX = 3;\nfunction kb(bp) {\n  return `${(bp / 1e3).toFixed(bp < 1e4 ? 1 : 0)} kb`;\n}\nfunction units(bp, unit) {\n  return unit ? ` \\u2248 ${Math.round(bp / unit)} units` : \"\";\n}\nfunction walkRowReadout(row, reference, unit, call) {\n  const { bp, gapBp, complete } = row;\n  if (!reference) {\n    return `${kb(bp)}${units(bp, unit)}`;\n  }\n  const delta = bp - reference.bp;\n  const against = delta === 0 ? \"\" : ` (${delta > 0 ? \"+\" : \"\\u2212\"}${kb(Math.abs(delta))})`;\n  const outside = gapBp > 0 ? ` \\xB7 ${kb(gapBp)} outside the cut` : \"\";\n  const called = call ? ` \\xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? \" \\xB7 no spanning read\" : \"\"}` : \"\";\n  return `${kb(bp)}${units(bp, unit)}${against}${outside}${complete ? \"\" : \" \\xB7 partial walk\"}${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 runPaint(run, ramp) {\n  if (run.gap) {\n    return { fill: OUTSIDE_CUT };\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  if ([bars.reference, ...bars.rows].some((row) => row.gapBp > 0)) {\n    entries.push({\n      swatch: { kind: \"gap\", fill: OUTSIDE_CUT },\n      label: \"walked outside the cut\"\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: \"genes, each row's own annotation\"\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-${i}`;\n    const ramp = !e.note && e.swatch.kind === \"bar\" && e.swatch.ramp ? el(\n      \"linearGradient\",\n      { id: rampId },\n      ...RAMP_GRADIENT_STOPS.map(\n        (s) => el(\"stop\", { offset: s.offset, \"stop-color\": s.color })\n      )\n    ) : void 0;\n    const swatch = e.note ? void 0 : e.swatch.kind === \"gene\" ? el(\"rect\", {\n      x: at,\n      y: 5,\n      width: 18,\n      height: 8,\n      fill: \"none\",\n      stroke: GENE_INK,\n      \"stroke-width\": 1.5\n    }) : el(\"rect\", {\n      x: at,\n      y: e.swatch.kind === \"gap\" ? 7 : 5,\n      width: 18,\n      height: e.swatch.kind === \"gap\" ? GAP_PX : 8,\n      rx: 2,\n      fill: ramp ? `url(#${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 runs = coalesceRuns(row.runs, frame.scaleX).flatMap((run) => {\n      const paint = runPaint(run, o.ramp);\n      const h = run.gap ? Math.min(GAP_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  GENE_INK,\n  BAR_PX,\n  GAP_PX,\n  LABELLED_ROW_PX,\n  kb,\n  walkRowReadout,\n  readoutPlacement,\n  unitTicks,\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  alongRow,\n  boxesGenes,\n  rowPitch\n} from \"./chunk-V3MD3IZB.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  el\n} from \"./chunk-NNODIW4U.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\n\n// src/layout/walkStrip.ts\nfunction walkStripApplies(o) {\n  return o.walkStrip && o.mode.drawsNodes && !o.drawsPicture && !o.popped && !o.host && o.walks > 1;\n}\nfunction cutsWholeWalks(mode, o) {\n  return mode.wholeWalks || o.walkStrip && !o.host;\n}\nvar PAD_PX = 6;\nvar WALK_STRIP_CEILING_PX = 260;\nvar LABEL_FONT_PX = 11;\nvar MIN_ROW_PX = 3;\nvar READOUT_ROOM = 1.3;\nvar MARK_INK = \"#111\";\nvar TICK_PX = 3;\nfunction stripMarks(graph, rows, node) {\n  const visits = graph.pathVisits?.get(node.name) ?? [];\n  const marks = [];\n  for (const row of rows) {\n    const axis = row.axis;\n    if (!axis) {\n      continue;\n    }\n    const path = pathOrigin(row.name).name;\n    for (const v of visits) {\n      if (v.path !== path) {\n        continue;\n      }\n      const { start, end } = alongRow(axis, v.start, v.start + node.length);\n      if (end > 0 && start < row.bp) {\n        marks.push({ row: row.name, start, bp: end - start });\n      }\n    }\n  }\n  return marks;\n}\nvar spanCache = /* @__PURE__ */ new WeakMap();\nfunction spansOf(graph, name) {\n  let byName = spanCache.get(graph);\n  if (!byName) {\n    byName = /* @__PURE__ */ new Map();\n    spanCache.set(graph, byName);\n  }\n  if (byName.has(name)) {\n    return byName.get(name);\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const pieces = (graph.paths ?? []).filter((p) => p.name === name);\n  let spans;\n  if (pieces.every((p) => p.start !== void 0)) {\n    spans = { ids: [], starts: [], ends: [] };\n    for (const piece of [...pieces].sort((a, b) => a.start - b.start)) {\n      let pos = piece.start;\n      for (const id of piece.nodeIds) {\n        const len = lengthOf.get(id) ?? 0;\n        spans.ids.push(id);\n        spans.starts.push(pos);\n        spans.ends.push(pos + len);\n        pos += len;\n      }\n    }\n  }\n  byName.set(name, spans);\n  return spans;\n}\nfunction segmentAt(graph, row, offset, pxPerBp) {\n  const axis = row.axis;\n  const spans = axis && spansOf(graph, row.name);\n  if (!axis || !spans || offset < 0 || offset > row.bp) {\n    return void 0;\n  }\n  const at = axis.reversed ? axis.start - offset : axis.start + offset;\n  const tol = 0.5 / pxPerBp;\n  const bar = axis.reversed ? { start: axis.start - row.bp, end: axis.start } : { start: axis.start, end: axis.start + row.bp };\n  const from = Math.max(at - tol, bar.start);\n  const to = Math.min(at + tol, bar.end);\n  let lo = 0;\n  let hi = spans.starts.length;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (spans.ends[mid] <= from) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  let best;\n  let bestLen = -1;\n  let bestHolds = false;\n  for (let i = lo; i < spans.starts.length && spans.starts[i] < to; i++) {\n    const len = spans.ends[i] - spans.starts[i];\n    const holds = spans.starts[i] <= at && at < spans.ends[i];\n    if (len > bestLen || len === bestLen && holds && !bestHolds) {\n      bestLen = len;\n      best = spans.ids[i];\n      bestHolds = holds;\n    }\n  }\n  return best;\n}\nfunction walkStripFrame(bars, o) {\n  const maxHeight = o.maxHeight ?? WALK_STRIP_CEILING_PX;\n  const labelPx = o.labelPx ?? Math.max(...[bars.reference, ...bars.rows].map((r) => r.label.length)) * LABEL_CHAR_PX + 16;\n  const count = bars.rows.length + 1;\n  const { rowPx, barPx, labelled, readouts } = rowPitch(\n    count,\n    maxHeight - 2 * PAD_PX,\n    MIN_ROW_PX\n  );\n  const longest = Math.max(bars.reference.bp, ...bars.rows.map((r) => r.bp), 1);\n  const left = labelled ? labelPx : PAD_PX;\n  const usable = Math.max(1, o.width - left - PAD_PX);\n  const scaleX = usable / (longest * (readouts ? READOUT_ROOM : 1));\n  return {\n    scaleX,\n    scaleY: 1,\n    translateX: left - bars.origin * scaleX,\n    translateY: PAD_PX + rowPx / 2,\n    width: o.width,\n    height: count * rowPx + 2 * PAD_PX,\n    rowPx,\n    barPx,\n    readouts,\n    labelled,\n    boxesGenes: boxesGenes(rowPx, barPx)\n  };\n}\nfunction stripRowAt(bars, frame, x, y) {\n  const i = Math.round((y - frame.translateY) / frame.rowPx);\n  const row = [bars.reference, ...bars.rows][i];\n  const offset = (x - frame.translateX) / frame.scaleX - bars.origin;\n  return row && i >= 0 && offset >= 0 && offset <= row.bp ? { index: i, row, offset } : void 0;\n}\nfunction walkMarksTree(bars, frame, marks) {\n  const index = new Map(\n    [bars.reference, ...bars.rows].map((row, i) => [row.name, i])\n  );\n  const X = (offset) => (bars.origin + offset) * frame.scaleX + frame.translateX;\n  return el(\n    \"g\",\n    { \"data-testid\": \"graph-walk-marks\" },\n    ...marks.flatMap((m) => {\n      const i = index.get(m.row);\n      if (i === void 0) {\n        return [];\n      }\n      const y = i * frame.rowPx + frame.translateY;\n      const x = X(m.start);\n      const w = Math.max(2, m.bp * frame.scaleX);\n      const tick = (top) => el(\"rect\", { x, y: top, width: w, height: TICK_PX, fill: MARK_INK });\n      return [\n        tick(y - frame.barPx / 2 - TICK_PX - 1),\n        tick(y + frame.barPx / 2 + 1)\n      ];\n    })\n  );\n}\nfunction walkStripLabelsTree(bars, frame, bold = /* @__PURE__ */ new Set()) {\n  return el(\n    \"g\",\n    { \"font-family\": \"sans-serif\", \"font-size\": LABEL_FONT_PX, fill: \"#333\" },\n    ...(frame.labelled ? [bars.reference, ...bars.rows] : []).map(\n      (row, i) => el(\n        \"text\",\n        {\n          x: 6,\n          y: i * frame.rowPx + frame.translateY + 4,\n          \"font-weight\": bold.has(row.name) ? 600 : void 0\n        },\n        row.label\n      )\n    )\n  );\n}\nfunction stripGeneGaps(frame, rowGenes, gaps) {\n  if (!rowGenes?.size) {\n    return void 0;\n  }\n  return frame.boxesGenes ? gaps : { untracked: 0, unread: 0, ...gaps, crowded: true };\n}\n\nexport {\n  walkStripApplies,\n  cutsWholeWalks,\n  WALK_STRIP_CEILING_PX,\n  stripMarks,\n  segmentAt,\n  walkStripFrame,\n  stripRowAt,\n  walkMarksTree,\n  walkStripLabelsTree,\n  stripGeneGaps\n};\n", "// src/renderer/canvas.ts\nvar MAX_DPR = 2;\nvar MAX_CANVAS_DIM_PX = 8192;\nfunction getDpr() {\n  return typeof devicePixelRatio === \"undefined\" ? 1 : Math.min(devicePixelRatio, MAX_DPR);\n}\nvar warnedCanvasClamp = false;\nfunction backingPx(cssSize, dpr, axis) {\n  const value = Math.round(cssSize * dpr);\n  if (value > MAX_CANVAS_DIM_PX) {\n    if (!warnedCanvasClamp) {\n      warnedCanvasClamp = true;\n      console.warn(\n        `Canvas ${axis} ${value}px exceeds the safe limit ${MAX_CANVAS_DIM_PX}px and was clamped`\n      );\n    }\n    return MAX_CANVAS_DIM_PX;\n  }\n  return value;\n}\nfunction syncCanvasSize(canvas, width, height) {\n  const dpr = getDpr();\n  const pw = backingPx(width, dpr, \"width\");\n  const ph = backingPx(height, dpr, \"height\");\n  if (canvas.width !== pw || canvas.height !== ph) {\n    canvas.width = pw;\n    canvas.height = ph;\n  }\n  const cssWidth = `${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}\n\nexport {\n  MAX_DPR,\n  MAX_CANVAS_DIM_PX,\n  getDpr,\n  syncCanvasSize\n};\n", "import {\n  syncCanvasSize\n} from \"./chunk-4BYTEJGW.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    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  // Not a local `width * devicePixelRatio`: syncCanvasSize clamps the backing\n  // store at MAX_CANVAS_DIM_PX, reads the ratio through `getDpr()` so this\n  // agrees with the transform the model builds, and writes the css size\n  // independently of the backing size.\n  resize(width, height) {\n    syncCanvasSize(this.canvas, width, height);\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  render(clearColor) {\n    const t = this.transform;\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    this.renderEdges(batch);\n    this.renderNodes(batch);\n    this.renderArrows(batch);\n  }\n  renderEdges(batch) {\n    const t = this.transform;\n    const ctx = this.ctx;\n    const hl = this.highlightedEdge === null ? void 0 : batch.edgeCurveRuns.get(this.highlightedEdge);\n    for (const { color, items } of groupByPaint(batch.edgeCurves, (e, i) => ({\n      color: inRun(hl, i) ? brightenAbgr(e.color, this.highlightFactor) : e.color,\n      weight: e.thickness,\n      last: inRun(hl, i)\n    }))) {\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  }\n  renderNodes(batch) {\n    const t = this.transform;\n    const ctx = this.ctx;\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    for (const { color, items } of groupByPaint(batch.nodeStrokes, (s, i) => {\n      const factor = lifted.get(i);\n      return {\n        color: factor === void 0 ? s.color : brightenAbgr(s.color, factor),\n        weight: s.thickness,\n        last: factor !== void 0\n      };\n    })) {\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(\n          p0.x * t.scaleX + t.translateX,\n          p0.y * t.scaleY + t.translateY\n        );\n        for (let i = 1, l = s.points.length; i < l; i++) {\n          const p = s.points[i];\n          ctx.lineTo(\n            p.x * t.scaleX + t.translateX,\n            p.y * t.scaleY + t.translateY\n          );\n        }\n      }\n      ctx.stroke();\n    }\n  }\n  renderArrows(batch) {\n    const t = this.transform;\n    const ctx = this.ctx;\n    const hl = this.highlightedEdge === null ? void 0 : batch.arrowRuns.get(this.highlightedEdge);\n    for (const { color, items } of groupByPaint(batch.arrows, (a, i) => ({\n      color: inRun(hl, i) ? brightenAbgr(a.color, this.highlightFactor) : a.color,\n      weight: 0,\n      last: inRun(hl, i)\n    }))) {\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  }\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 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}:${weight}`;\n    const group = into.get(key);\n    if (group) {\n      group.items.push(item);\n    } else {\n      into.set(key, { color, items: [item] });\n    }\n  }\n  return [...groups.values(), ...deferred.values()];\n}\n\nexport {\n  Canvas2DRenderer,\n  arrowheadOutline\n};\n", "import {\n  formatBp,\n  groupDigits\n} from \"./chunk-3ZZSX5HN.js\";\n\n// src/walkKey.ts\nfunction rangeText(contig, start, end) {\n  const s = Math.round(start);\n  const e = Math.round(end);\n  return `${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;\n  return {\n    delta: walk.referenceBp === void 0 || spanned === walk.referenceBp ? \"\" : ` ${spanned > walk.referenceBp ? \"+\" : \"\\u2212\"}${formatBp(Math.abs(spanned - walk.referenceBp))}`,\n    outside: outside > 0 ? `, ${formatBp(outside)} outside the cut` : \"\",\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  formatBp\n} from \"./chunk-3ZZSX5HN.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/tubeMap/axis.ts\nfunction referenceBoxes(graph, layout) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const byRefName = /* @__PURE__ */ new Map();\n  layout.nodes.forEach((node) => {\n    const graphNode = nodeById.get(node.name);\n    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {\n      const { refName, start } = graphNode.stable;\n      const boxes = byRefName.get(refName) ?? byRefName.set(refName, []).get(refName);\n      boxes.push({\n        bp0: start,\n        bp1: start + node.sequenceLength,\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  let lo = 0;\n  let hi = boxes.length - 1;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    const bp1 = boxes[mid].bp1;\n    if (isEnd ? bp1 < bp : bp1 <= bp) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  const box = boxes[lo];\n  if (bp <= box.bp0) {\n    return box.x0;\n  }\n  const span = box.bp1 - box.bp0;\n  return span > 0 ? box.x0 + (Math.min(bp, box.bp1) - box.bp0) / span * (box.x1 - box.x0) : 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  tubeSpan,\n  rulerBoxes,\n  rulerInk,\n  rulerMarks,\n  drawTubeMapRuler\n};\n", "import {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/tubeMap/connectors.ts\nfunction referenceNodes(graph, layout) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const out = [];\n  layout.nodes.forEach((node) => {\n    const graphNode = nodeById.get(node.name);\n    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {\n      out.push({\n        node: node.name,\n        bp0: graphNode.stable.start,\n        bp1: graphNode.stable.start + node.sequenceLength,\n        x0: node.x,\n        x1: node.x + node.pixelWidth\n      });\n    }\n  });\n  return out;\n}\nfunction tubeMapConnectors(nodes, bpToScreen, tubeToScreen, width) {\n  const out = [];\n  for (const n of nodes) {\n    const bottom0 = tubeToScreen(n.x0);\n    const bottom1 = tubeToScreen(n.x1);\n    if (bottom1 >= 0 && bottom0 <= width) {\n      out.push({\n        node: n.node,\n        top0: bpToScreen(n.bp0),\n        top1: bpToScreen(n.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  const lit = connectors.find((c) => c.node === highlightNode);\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  referenceNodes,\n  tubeMapConnectors,\n  connectorAt,\n  drawTubeMapConnectors\n};\n", "// src/tubeMap/mismatches.ts\nimport { forward, getXCoordinateOfBaseWithinNode } from \"@jbrowse/tubemap-core\";\nfunction readMismatches(read, layout) {\n  const marks = [];\n  const entries = read.sequenceNew ?? [];\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    let pathIndex = i;\n    while (pathIndex < read.path.length && read.path[pathIndex].node !== nodeIndex) {\n      pathIndex += 1;\n    }\n    const y = read.path[pathIndex]?.y;\n    if (node && y !== void 0) {\n      const base = { readId: read.id, y, height: read.width, nodeY: node.y };\n      const at = (pos) => getXCoordinateOfBaseWithinNode(node, pos);\n      for (const mm of entry.mismatches) {\n        const x0 = at(mm.pos);\n        if (x0 !== null) {\n          if (mm.type === \"insertion\") {\n            const softClip = i === 0 && mm.pos === read.firstNodeOffset || i === entries.length - 1 && mm.pos === read.finalNodeCoverLength;\n            marks.push({\n              ...base,\n              kind: \"insertion\",\n              x: x0,\n              seq: mm.seq,\n              softClip\n            });\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({ ...base, kind: \"deletion\", x0, x1 });\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  tubeMapMismatches\n} from \"./chunk-733L2TS6.js\";\nimport {\n  readColor\n} from \"./chunk-TEDQJPMI.js\";\n\n// src/tubeMap/draw.ts\nimport { curvePaths, 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, track) {\n  const commands = parsePath(d);\n  return { commands, color, track, ...extentOf(commands) };\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) {\n  const { shapes } = layout;\n  const colorOf = (s) => colors.get(s.id);\n  const trackOf = (s) => type === \"haplotype\" ? s.id : void 0;\n  const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({\n    color: colorOf(r),\n    track: trackOf(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).map(\n    (c) => shapeOf(c.path, colorOf(c), trackOf(c))\n  );\n  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), trackOf(c)));\n  return { rects, shapes: [...curves, ...corners] };\n}\nfunction tubeMapPicture({\n  layout,\n  pathColors\n}) {\n  const colors = trackColors(layout, pathColors);\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),\n      layerOf(layout, \"read\", colors)\n    ],\n    nodes,\n    mismatches: tubeMapMismatches(layout).filter(\n      (m) => m.kind !== \"insertion\" || !m.softClip\n    )\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      const color = colorOf(item);\n      const list = byColor.get(color);\n      if (list) {\n        list.push(item);\n      } else {\n        byColor.set(color, [item]);\n      }\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.track !== void 0 && frame.tubeColors?.[item.track] || item.color;\n  ctx.globalAlpha = 1;\n  for (const layer of picture.layers) {\n    fillByColor(ctx, layer.rects, visible, colorOf, (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    fillByColor(ctx, layer.shapes, visible, colorOf, (s) => {\n      trace(ctx, s.commands, x, y);\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 = 2 * Math.max(0.25, Math.min(1, frame.yScale));\n  for (const node of picture.nodes) {\n    if (visible(node)) {\n      const lit = node.name === frame.highlightNode;\n      ctx.beginPath();\n      trace(ctx, node.commands, x, y);\n      const tint = lit ? void 0 : frame.nodeColors?.get(node.name);\n      ctx.fillStyle = lit ? \"rgba(255,192,203,0.5)\" : tint ?? fill;\n      ctx.strokeStyle = lit ? \"#ff0000\" : stroke;\n      ctx.globalAlpha = tint ? NODE_TINT_ALPHA : 1;\n      ctx.fill();\n      ctx.globalAlpha = lit ? 1 : outlineAlpha(x(node.x1) - x(node.x0));\n      ctx.stroke();\n      ctx.globalAlpha = 1;\n    }\n  }\n  drawMismatches(ctx, picture.mismatches, frame);\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.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}\n\nexport {\n  parsePath,\n  trackColors,\n  tubeMapPicture,\n  drawTubeMap,\n  mismatchesLegible,\n  mismatchOnScreen\n};\n", "import {\n  tubeSpan\n} from \"./chunk-DRA7733Q.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-HBEKUQO4.js\";\nimport {\n  abgrToCssRgba\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.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 {\n  isBackbone\n} from \"../chunks/chunk-FYQWPEEY.js\";\n\n// src/tubeMap/deviations.ts\nfunction boxesOf(graph, layout) {\n  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));\n  const boxes = [];\n  layout.nodes.forEach((node, index) => {\n    const g = nodeById.get(node.name);\n    if (node.order >= 0 && g && isBackbone(g)) {\n      const bp0 = g.stable.start;\n      boxes.push({ bp0, bp1: bp0 + node.sequenceLength, index, node });\n    }\n  });\n  return boxes.sort((a, b) => a.bp0 - b.bp0);\n}\nfunction boxAt(boxes, bp, visited) {\n  let lo = 0;\n  let hi = boxes.length - 1;\n  while (lo < hi) {\n    const mid = lo + hi + 1 >> 1;\n    if (boxes[mid].bp0 <= bp) {\n      lo = mid;\n    } else {\n      hi = mid - 1;\n    }\n  }\n  return [boxes[lo], boxes[lo - 1]].find(\n    (box) => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1\n  );\n}\nfunction deviationMarks(graph, layout, deviations) {\n  const boxes = boxesOf(graph, layout);\n  const marks = [];\n  for (const track of layout.tracks) {\n    const devs = track.name ? deviations.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          const { node, bp0, bp1 } = box;\n          const at = (bp) => node.x + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * node.pixelWidth;\n          marks.push({\n            x0: at(d.start),\n            x1: at(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 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\nexport interface 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. The rest go by\n// length: the walks that span the array against the alleles reads spanned,\n// then everything else against what those two left. That decides the\n// ambiguous cases on merit: which walk carries the one allele a lone spanning\n// read supports, and which allele a walk that stops inside the array is drawn\n// 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  rows.forEach((row, i) => {\n    const call = calls.find(\n      c => c.haplotype !== undefined && c.haplotype === row.haplotype,\n    )\n    if (call) {\n      taken.add(call)\n      out.set(i, scored(row, call))\n    }\n  })\n  const unphased = calls.filter(call => call.haplotype === undefined)\n  const ranked = byLength(rows, r => r.bp)\n  const stages = [\n    [ranked.filter(r => r.item.complete), unphased.filter(backed)],\n    [ranked, unphased],\n  ] as const\n  for (const [pool, group] of stages) {\n    const free = pool.filter(r => !out.has(r.i))\n    const open = byLength(\n      group.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  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    bySample.set(row.sample, [...(bySample.get(row.sample) ?? []), row])\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", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6\"\n}), 'Settings');"],
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+}