npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 6.0.0 → 6.0.2 - Mend

jbrowse-plugin-graphgenomeviewer 6.0.0 → 6.0.2

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Files changed (67) hide show

package/dist/chunks/chunk-XYYKXQ73.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@mui/material/SvgIcon", "global-externals:mobx", "../../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@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-UMNCCYBN.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-Y3IOTZJA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ES2N6V56.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RX5CSWJW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZHCDYSA5.js", 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"../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CS3E4ETM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQ2AOHU4.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EJ5OZTCK.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CR7EGAFE.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CTSBC2O6.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-SMQ545MU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@6.0.4/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\"];", "'use client';\n\nexport { createSvgIcon as default } from '@mui/material/SvgIcon';", "// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  return packAbgr(\n    Math.min(255, Math.round(abgrRed(c) * factor)),\n    Math.min(255, Math.round(abgrGreen(c) * factor)),\n    Math.min(255, Math.round(abgrBlue(c) * factor)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "import {\n  bypassedPoints\n} from \"./chunk-4EMPBO7S.js\";\nimport {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-2CVHXFK7.js\";\n\n// src/util/edgeCurves.ts\nvar cache = /* @__PURE__ */ new WeakMap();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  const { scaleX, scaleY } = axis;\n  const cached = cache.get(nodePositions);\n  if (cached?.graph === graph && cached.scaleX === scaleX && cached.scaleY === scaleY && cached.deletions === deletions && cached.routes === routes && cached.stranded === stranded && cached.version === version) {\n    return cached.curves;\n  }\n  const curves = /* @__PURE__ */ new Map();\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const from = nodePositions[edge.from];\n    const to = nodePositions[edge.to];\n    if (from?.length && to?.length) {\n      const bypassed = deletions?.get(ei);\n      const route = bypassed && routes?.[ei];\n      curves.set(\n        ei,\n        route ? routedEdgeCurves(\n          from,\n          to,\n          route,\n          stranded ? strandSides(edge) : void 0\n        ) : computeEdgeCurves(\n          from,\n          to,\n          edgeJoinOf(edge, stranded),\n          0,\n          0,\n          axis,\n          bypassed ? bypassedPoints(nodePositions, bypassed) : []\n        )\n      );\n    }\n  }\n  cache.set(nodePositions, {\n    graph,\n    scaleX,\n    scaleY,\n    deletions,\n    routes,\n    stranded,\n    version,\n    curves\n  });\n  return curves;\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  function add(from, to) {\n    const list = neighbors.get(from);\n    if (list) {\n      list.push(to);\n    } else {\n      neighbors.set(from, [to]);\n    }\n  }\n  for (const edge of graph.edges) {\n    add(edge.from, edge.to);\n    add(edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-UMNCCYBN.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-Y3IOTZJA.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-X5L37W4J.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-ES2N6V56.js\";\nimport {\n  meanDepth,\n  nodeWidthPx\n} from \"./chunk-PBENCR5L.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-2CVHXFK7.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_WALK_LANE_PX = 4;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\nfunction polylinePx(segments, scale, yToX) {\n  let length = 0;\n  for (let i = 1; i < segments.length; i++) {\n    length += Math.hypot(\n      segments[i].x - segments[i - 1].x,\n      (segments[i].y - segments[i - 1].y) * yToX\n    );\n  }\n  return length * scale;\n}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  if (stranded) {\n    return strandSides(edge).from === \"start\";\n  }\n  const gap = (p) => Math.hypot(p.x - first.x0, (p.y - first.y0) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\n}\nfunction intoDirection(last, toSegments) {\n  if (toSegments.length < 2) {\n    return void 0;\n  }\n  const first = toSegments[0];\n  const final = toSegments[toSegments.length - 1];\n  const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);\n  return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };\n}\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  const pointNormals = [];\n  for (let i = 0; i < points.length; i++) {\n    let nx = 0;\n    let ny = 0;\n    if (i === 0) {\n      const dx = points[1].x - points[0].x;\n      const dy = points[1].y - points[0].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else if (i === points.length - 1) {\n      const dx = points[i].x - points[i - 1].x;\n      const dy = points[i].y - points[i - 1].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else {\n      const dx1 = points[i].x - points[i - 1].x;\n      const dy1 = points[i].y - points[i - 1].y;\n      const len1 = Math.hypot(dx1, dy1);\n      const dx2 = points[i + 1].x - points[i].x;\n      const dy2 = points[i + 1].y - points[i].y;\n      const len2 = Math.hypot(dx2, dy2);\n      if (len1 > 0 && len2 > 0) {\n        const nx1 = -dy1 / len1;\n        const ny1 = dx1 / len1;\n        const nx2 = -dy2 / len2;\n        const ny2 = dx2 / len2;\n        nx = (nx1 + nx2) / 2;\n        ny = (ny1 + ny2) / 2;\n        const dot = nx1 * nx + ny1 * ny;\n        if (dot > 0.1) {\n          nx /= dot;\n          ny /= dot;\n        }\n      } else if (len1 > 0) {\n        nx = -dy1 / len1;\n        ny = dx1 / len1;\n      } else if (len2 > 0) {\n        nx = -dy2 / len2;\n        ny = dx2 / len2;\n      }\n    }\n    pointNormals.push({ nx, ny });\n  }\n  return pointNormals;\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  return points.map((p, i) => ({\n    x: p.x + normals[i].nx * distance,\n    y: p.y + normals[i].ny * distance / yToX\n  }));\n}\nfunction packNorm(r, g, b, a) {\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nfunction hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  const [r, g, b] = hslToRgb(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS);\n  return packNorm(r, g, b, alpha);\n}\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state. A node with no reference position at\n    // all \u2014 nothing anchored, or an allele whose flanks fell outside the cut \u2014\n    // is grey rather than a hue it has not earned.\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      const mid = ramp?.midpoints.get(node.id);\n      if (ramp === void 0 || mid === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      if (node.stable !== void 0 && node.stable.rank > 0) {\n        return REFERENCE_RAMP_ALT_COLOR;\n      }\n      const frac = Math.max(0, Math.min(1, (mid - ramp.start) / ramp.span));\n      const [r, g, b] = hslToRgb(\n        frac * REFERENCE_RAMP_MAX_HUE,\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n      return packNorm(r, g, b, 1);\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      const [r, g, b] = hslToRgb(hue, 0.75, 0.5);\n      return packNorm(r, g, b, 1);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds) {\n  for (const c of curves) {\n    const cMinX = Math.min(c.x0, c.cx0, c.cx1, c.x1);\n    const cMaxX = Math.max(c.x0, c.cx0, c.cx1, c.x1);\n    const cMinY = Math.min(c.y0, c.cy0, c.cy1, c.y1);\n    const cMaxY = Math.max(c.y0, c.cy0, c.cy1, c.y1);\n    if (cMaxX >= bounds.minX && cMinX <= bounds.maxX && cMaxY >= bounds.minY && cMinY <= bounds.maxY) {\n      return true;\n    }\n  }\n  return false;\n}\nvar paletteCache = /* @__PURE__ */ new WeakMap();\nfunction pathPaletteOf(graph) {\n  let palette = paletteCache.get(graph);\n  if (!palette) {\n    const pathColorByIndex = [];\n    const pathIndexByName = /* @__PURE__ */ new Map();\n    const paths = graph.paths ?? [];\n    for (let i = 0; i < paths.length; i++) {\n      const [r, g, b] = hslToRgb(\n        pathHueAt(i, paths.length),\n        PATH_SATURATION,\n        PATH_LIGHTNESS\n      );\n      pathColorByIndex.push(packNorm(r, g, b, 0.85));\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        const visits = slots.get(nodeId);\n        if (visits) {\n          visits.push(pathIdx);\n        } else {\n          slots.set(nodeId, [pathIdx]);\n        }\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\nfunction buildGeometry(options) {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = \"uniform\",\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const depthNorm = nodeWidth === \"depth\" ? meanDepth(graph) : 0;\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = { ...computeColorSchemeRange(graph), referenceRamp };\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE);\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const fromSegments = nodePositions[edge.from];\n    const toSegments = nodePositions[edge.to];\n    const baseCurves = sharedCurves.get(ei);\n    if (!fromSegments?.length || !toSegments?.length || !baseCurves || hiddenEdges?.has(ei)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const bypassed = deletions?.get(ei);\n    const isDeletion = bypassed !== void 0;\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false;\n    const edgeThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\n    const ribbons = drawPaths && numPaths > 0;\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;\n    const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);\n    const toNode = nodeById.get(edge.to);\n    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;\n    const buildSingleEdge = (offsetX, offsetY, color, arrowColor) => {\n      const curves = offsetX === 0 && offsetY === 0 ? baseCurves : translateCurves(baseCurves, offsetX, offsetY);\n      if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n        return;\n      }\n      if (isDeletion) {\n        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {\n          edgeCurves.push({ curves: dash, thickness: edgeThickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness: edgeThickness, color });\n      }\n      const head = showArrows && arrowColor !== void 0 ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: arrowColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(fromSegments, yToX);\n      const { nx, ny } = (leavesStart(\n        edge,\n        fromSegments,\n        baseCurves[0],\n        stranded,\n        yToX\n      ) ? normals[0] : normals.at(-1)) ?? {\n        nx: 0,\n        ny: 0\n      };\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      laneWalks.forEach((walk, lane) => {\n        if (!walk.edgeIndexes.has(ei)) {\n          return;\n        }\n        const offset = (lane - (laneWalks.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        const curves = offset === 0 ? baseCurves : translateCurves(baseCurves, nx * offset, ny * offset / yToX);\n        if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n          return;\n        }\n        edgeCurves.push({\n          curves,\n          thickness: laneWidth / 2,\n          color: walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\n        });\n      });\n    } else if (!ribbons) {\n      buildSingleEdge(0, 0, edgeColor, edgeColor);\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const offset = offsets[pathIdx];\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        buildSingleEdge(\n          offset.x,\n          offset.y,\n          highlight && !highlight.names.has(edge.pathIds[pathIdx]) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor,\n          pathIdx === arrowRibbon ? edgeColor : void 0\n        );\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      lanes.forEach((walk, lane) => {\n        const laneColor = walk.colors.get(nodeId);\n        if (laneColor === void 0) {\n          return;\n        }\n        const offset = (lane - (lanes.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        nodeStrokes.push({\n          points: lanes.length === 1 ? segments : offsetPolyline(segments, normals, offset, yToX),\n          thickness: laneWidth / 2,\n          color: laneColor\n        });\n      });\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_MAX_HUE\n} from \"./chunk-RX5CSWJW.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-Y3IOTZJA.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-MREQ7GIA.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-YMSSF2RK.js\";\nimport {\n  nodeLabelBudget,\n  placeSizeLabels,\n  rowLabelBox,\n  sizeLabelCandidates\n} from \"./chunk-N62KBLFC.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.showDeletionEdges ? 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", "export function emptyTrackShapes() {\n    return {\n        rectangles: [],\n        curves: [],\n        corners: [],\n        verticalRectangles: [],\n        featureRectangles: [],\n    };\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; the passes below still share module state, but layoutTubeMap resets\n// all of it on entry and runs synchronously, so no two calls see each other's.\nimport { emptyTrackShapes } from './types.js';\nconst DEBUG = false;\nconst DEFAULT_TRACK_COLORS = [\n    '#1f77b4',\n    '#ff7f0e',\n    '#2ca02c',\n    '#d62728',\n    '#9467bd',\n    '#8c564b',\n    '#e377c2',\n    '#7f7f7f',\n];\nfunction configFrom(options) {\n    return {\n        mergeNodesFlag: options.mergeNodes ?? true,\n        showReads: options.showReads ?? true,\n        coarsenedReadView: options.coarsenedReadView ?? false,\n        ignoreStrand: options.ignoreStrand ?? false,\n        nodeWidthOption: options.nodeWidthOption ?? 'normal',\n        charWidth: options.charWidth ?? 8.401,\n        trackWidth: options.trackWidth ?? 15,\n        mappingQualityCutoff: options.mappingQualityCutoff ?? 0,\n        focusReadNames: options.focusReadNames ?? null,\n        showExonsFlag: options.showExons ?? false,\n        trackColor: options.trackColor ??\n            (track => DEFAULT_TRACK_COLORS[track.id % DEFAULT_TRACK_COLORS.length]),\n        trackAlpha: options.trackAlpha ?? (() => 1),\n    };\n}\nlet config = configFrom({});\nlet bed = null;\nlet nodes = [];\n// Each track has a `path`, which is an array of Segment objects describing pieces of the path that need to be drawn, in order along the path.\nlet tracks = [];\n// Each read also has a `path` list of Segments, but reads are organized vertically using a different system than non-read tracks.\nlet reads = [];\nlet nodeMap = new Map();\nlet nodesPerOrder = [];\n// Scratch array used only during generateNodeOrder. Indexed by node index;\n// undefined = \"not yet assigned.\" Copied into node.order at end of layout.\nlet nodeOrders = [];\n// Lane assignment info for tracks, in one list per horizontal \"order\" slot.\n// Duplicates info in tracks' `path` lists but is organized by order. Reads do not use this.\nlet assignments = [];\nlet extraLeft = [];\nlet extraRight = [];\nlet maxOrder = -1; // horizontal order of the rightmost node\nlet shapes = emptyTrackShapes();\nlet imageBounds = { minX: 0, maxX: 0, minY: 0, maxY: 0 };\nlet trackForRuler;\nlet coarsenedEdgeMeta = new Map();\n// Lay out `inputNodes` and `inputTracks` (and `inputReads`, when\n// `showReads`), or return undefined when nothing visible is left to draw.\n// Neither input is modified. Track 0 is the reference the layout straightens.\nexport function layoutTubeMap(inputNodes, inputTracks, inputReads = [], options = {}) {\n    config = configFrom(options);\n    bed = options.bed ?? null;\n    shapes = emptyTrackShapes();\n    assignments = [];\n    extraLeft = [];\n    extraRight = [];\n    nodesPerOrder = [];\n    imageBounds = { minX: 0, maxX: 0, minY: 0, maxY: 0 };\n    trackForRuler = undefined;\n    coarsenedEdgeMeta = new Map();\n    if (inputNodes.length === 0 || inputTracks.length === 0) {\n        return undefined;\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    const copies = deepCopy(inputNodes);\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    nodes = [];\n    copies.forEach((node, i) => {\n        nodes[i + 1] = node;\n    });\n    tracks = deepCopy(inputTracks);\n    // Whether any reads were loaded at all, distinct from `reads.length` below:\n    // a mapping-quality cutoff or focus-name filter can filter every read out,\n    // and that should not make the coarsened view fall back to bunching\n    // haplotypes instead \u2014 the graph does have reads, they're just all hidden.\n    const hadInputReads = inputReads.length > 0;\n    // Drop the reads we will never draw before cloning them \u2014 the deep copy of a\n    // large GAM is the single most expensive step in a redraw.\n    reads = deepCopy(filterReads(inputReads));\n    for (let i = tracks.length - 1; i >= 0; i -= 1) {\n        const t = tracks[i];\n        if (t.type === undefined) {\n            t.type = 'haplotype';\n        }\n        if (t.hidden === true) {\n            tracks.splice(i, 1);\n            continue;\n        }\n        if (t.indexOfFirstBase !== undefined) {\n            trackForRuler = t.name;\n        }\n    }\n    if (tracks.length === 0) {\n        return undefined;\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(0);\n    nodeMap = generateNodeMap();\n    generateTrackIndexSequences(tracks);\n    if (config.showReads && reads.length > 0)\n        generateTrackIndexSequences(reads);\n    generateNodeWidth();\n    if (config.mergeNodesFlag) {\n        generateNodeSuccessors();\n        generateNodeOrder();\n        if (config.showReads && reads.length > 0)\n            reverseReversedReads();\n        mergeNodes();\n        nodeMap = generateNodeMap();\n        generateNodeWidth();\n        generateTrackIndexSequences(tracks);\n        if (config.showReads && reads.length > 0)\n            generateTrackIndexSequences(reads);\n    }\n    generateNodeSuccessors();\n    generateNodeDegree();\n    if (DEBUG)\n        console.log(`${nodes.length} nodes.`);\n    generateNodeOrder();\n    maxOrder = getMaxOrder();\n    // can cause problems when there is a reversed single track node\n    // OTOH, can solve problems with complex inversion patterns\n    switchNodeOrientation();\n    generateNodeOrder();\n    maxOrder = getMaxOrder();\n    // Coarsened (Sankey) mode normally collapses the *read* list into synthetic\n    // per-edge bands (below). A haplotype-only graph has no reads to coarsen,\n    // so a coarsened request there instead coarsens every haplotype but the\n    // reference: that one keeps its normal per-track lane (so it still carries\n    // the ruler) while the rest are pulled out of `tracks` here, before\n    // calculateTrackWidth/generateLaneAssignment ever see them, and rejoin the\n    // layout below through the same reads-style overlay used for coarsened\n    // reads.\n    const coarsenHaplotypes = config.showReads && config.coarsenedReadView && !hadInputReads;\n    if (coarsenHaplotypes) {\n        const rulerIndex = trackForRuler === undefined\n            ? -1\n            : tracks.findIndex(t => t.name === trackForRuler);\n        const refIndex = rulerIndex === -1 ? 0 : rulerIndex;\n        const altHaplotypes = tracks.filter((_, i) => i !== refIndex);\n        if (altHaplotypes.length > 0) {\n            const bands = buildCoarsenedSyntheticBands(altHaplotypes, 'haplotype');\n            // A haplotype that only ever visits one node produces no edge, so an\n            // all-single-node set of alts would otherwise leave `reads` empty and\n            // fall through to the no-overlay branch below, which never gives their\n            // nodes a y/contentHeight. Keep them off to the side instead of\n            // dropping them silently.\n            if (bands.length > 0) {\n                tracks = [tracks[refIndex]];\n                reads = bands;\n            }\n        }\n    }\n    calculateTrackWidth();\n    generateLaneAssignment();\n    if (config.showExonsFlag && bed !== null)\n        addTrackFeatures();\n    // Coarsened (Sankey) mode: collapse the read list (or, when coarsening\n    // haplotypes, the alt haplotypes pulled out above) to one synthetic \"read\"\n    // per (srcSigned \u2192 dstSigned) edge BEFORE the normal read placement runs.\n    // Each synthetic read traverses exactly two nodes, so the rest of the\n    // pipeline (placeReads, generateSVGShapesFromPath, curve drawing) handles\n    // it like any normal read: it gets a lane, picks up the \"right-down-left-\n    // up-right\" topology for loops automatically, and uses the same elegant\n    // bezier. Node heights end up proportional to *edge* count (typically\n    // tens) rather than *read* or *haplotype* count (potentially thousands).\n    const drawCoarsenedReads = config.showReads &&\n        config.coarsenedReadView &&\n        reads.length > 0 &&\n        !coarsenHaplotypes;\n    if (config.showReads && reads.length > 0) {\n        generateReadOnlyNodeAttributes();\n        reverseReversedReads();\n        generateTrackIndexSequences(reads);\n        if (drawCoarsenedReads) {\n            reads = buildCoarsenedSyntheticBands(reads, 'read');\n            reverseReversedReads();\n            generateTrackIndexSequences(reads);\n        }\n        placeReads();\n        tracks = tracks.concat(reads);\n    }\n    else {\n        nodes.forEach(node => {\n            if (node) {\n                node.incomingReads = [];\n                node.outgoingReads = [];\n                node.internalReads = [];\n            }\n        });\n    }\n    generateNodeXCoords();\n    generateSVGShapesFromPath();\n    if (DEBUG) {\n        console.log('Tracks:');\n        console.log(tracks);\n        console.log('Nodes:');\n        console.log(nodes);\n        console.log('Lane assignment:');\n        console.log(assignments);\n    }\n    getImageDimensions();\n    return {\n        nodes,\n        tracks,\n        reads,\n        nodeMap,\n        shapes,\n        bounds: imageBounds,\n        maxOrder,\n        trackForRuler,\n        coarsenedEdgeMeta,\n    };\n}\nfunction generateTrackColor(track, highlight = 'plain') {\n    return config.trackColor(track, highlight);\n}\nfunction generateTrackAlpha(track) {\n    return config.trackAlpha(track);\n}\n// structuredClone preserves sparse-array holes; JSON round-trip would fill them with null.\nfunction deepCopy(val) {\n    return structuredClone(val);\n}\n// Return true if the given name names a reverse strand node, and false otherwise.\nexport function isReverse(nodeName) {\n    const s = String(nodeName);\n    return s.length >= 1 && s.startsWith('-');\n}\n// Get the forward version of a node name, which may be either forward or backward (negative)\nexport function forward(nodeName) {\n    return isReverse(nodeName) ? String(nodeName).substring(1) : nodeName;\n}\n// Get the reverse version of a node name, which may be either forward or backward (negative)\nexport function reverse(nodeName) {\n    return isReverse(nodeName) ? nodeName : `-${nodeName}`;\n}\n// Get the opposite orientation node name for the given node.\nexport function flip(nodeName) {\n    return isReverse(nodeName) ? forward(nodeName) : reverse(nodeName);\n}\n// Signed-index orientation test. Uses 1/n to distinguish -0 from +0 since\n// indexSequence entries can be negative-zero for reverse-strand visits of node 0.\nexport function isForwardIndex(n) {\n    return (n || 1 / n) >= 0;\n}\n// straighten track given by index by inverting inverted nodes\n// only keep them inverted if this single track runs through them in both directions\n// Operates on the per-render `nodes`/`tracks` copies; inputs are left untouched.\nfunction straightenTrack(index) {\n    const nodesToInvert = new Set();\n    // find out which nodes should be inverted\n    let currentSequence = tracks[index].sequence;\n    for (let i = 0; i < currentSequence.length; i += 1) {\n        const cur = currentSequence[i];\n        if (isReverse(cur)) {\n            const nodeName = forward(cur);\n            const firstForwardIndex = currentSequence.indexOf(nodeName);\n            if (firstForwardIndex === -1 || firstForwardIndex > i) {\n                // only if this inverted node is no repeat\n                nodesToInvert.add(nodeName);\n            }\n        }\n    }\n    // invert nodes in the tracks' sequence\n    for (const track of tracks) {\n        currentSequence = track.sequence;\n        for (let j = 0; j < currentSequence.length; j += 1) {\n            const cur = currentSequence[j];\n            if (!isReverse(cur)) {\n                if (nodesToInvert.has(cur)) {\n                    currentSequence[j] = reverse(cur);\n                }\n            }\n            else if (nodesToInvert.has(forward(cur))) {\n                currentSequence[j] = forward(cur);\n            }\n        }\n    }\n    // invert the sequence within the nodes\n    nodes.forEach(node => {\n        if (node && nodesToInvert.has(node.name)) {\n            node.seq = node.seq.split('').reverse().join('');\n        }\n    });\n}\n// generates attributes (node.y, node.contentHeight) for nodes without tracks, only reads\nfunction generateReadOnlyNodeAttributes() {\n    nodesPerOrder = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        nodesPerOrder[i] = [];\n    }\n    const orderY = new Map();\n    nodes.forEach(node => {\n        if (node.y !== undefined) {\n            setMapToMax(orderY, node.order, node.y + node.contentHeight);\n        }\n    });\n    // for order values where there is no node with haplotypes, orderY is calculated via tracks\n    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    nodes.forEach((node, i) => {\n        if (node.order >= 0 && node.y === undefined) {\n            node.y = (orderY.get(node.order) ?? 0) + 25;\n            node.contentHeight = 0;\n            nodesPerOrder[node.order].push(i);\n        }\n    });\n}\nfunction setMapToMax(map, key, value) {\n    const existing = map.get(key);\n    if (existing === undefined) {\n        map.set(key, value);\n    }\n    else {\n        map.set(key, Math.max(existing, value));\n    }\n}\nexport const READ_WIDTH = 7;\n// add info about reads to nodes (incoming, outgoing and internal reads)\nfunction assignReadsToNodes() {\n    nodes.forEach(node => {\n        if (node) {\n            node.incomingReads = [];\n            node.outgoingReads = [];\n            node.internalReads = [];\n        }\n    });\n    reads.forEach((read, idx) => {\n        // Honor a pre-set width (e.g. coarsened Sankey bands pre-size themselves\n        // by traversing-read count) \u2014 only fall back to the default for normal\n        // reads which leave width unset.\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                nodes[firstNode].internalReads.push(idx);\n            }\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                        nodes[firstNode].outgoingReads.push([idx, pathIdx]);\n                    }\n                }\n                else {\n                    const elemNode = element.node;\n                    if (elemNode !== null) {\n                        nodes[elemNode].incomingReads.push([idx, pathIdx]);\n                    }\n                }\n            });\n        }\n    });\n}\n// calculate paths (incl. correct y coordinate) for all reads\nfunction placeReads() {\n    generateBasicPathsForReads();\n    assignReadsToNodes();\n    // sort nodes by order, then by y-coordinate\n    const sortedNodes = nodes.slice();\n    sortedNodes.sort(compareNodesByOrder);\n    // Organize read IDs by source track\n    const readsBySource = new Map();\n    for (let i = 0; i < reads.length; i++) {\n        const source = reads[i].sourceTrackID;\n        const bucket = readsBySource.get(source);\n        if (bucket === undefined) {\n            readsBySource.set(source, [i]);\n        }\n        else {\n            bucket.push(i);\n        }\n    }\n    const allSources = Array.from(readsBySource.keys()).sort((a, b) => a - b);\n    // Space out read tracks if multiple exist\n    const topMargin = allSources.length > 1 ? READ_WIDTH : 0;\n    sortedNodes.forEach(node => {\n        if (!node)\n            return;\n        // For each node\n        for (const source of allSources) {\n            // Go through all source tracks in order\n            // Place the reads from this source in this node.\n            // Use a margin to separate multiple read tracks if we have them.\n            placeReadSet(readsBySource.get(source), node, topMargin);\n        }\n    });\n    // place read segments which are without node\n    const bottomY = calculateBottomY();\n    const elementsWithoutNode = [];\n    reads.forEach((read, idx) => {\n        const len = read.path.length;\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(len);\n        let lastValidPrev;\n        for (let i = 0; i < len; i++) {\n            if (i === 0) {\n                prevSegment[i] = undefined;\n            }\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        const nextSegment = new Array(len);\n        let firstValidNext;\n        for (let i = len - 1; i >= 0; i--) {\n            if (i === len - 1) {\n                nextSegment[i] = undefined;\n            }\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        read.path.forEach((element, pathIdx) => {\n            if (element.y === undefined) {\n                const previousVisitToNode = prevSegment[pathIdx];\n                const nextVisitToNode = nextSegment[pathIdx];\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                    nextVisitToNode.isForward !== undefined &&\n                    previousVisitToNode.isForward !== undefined &&\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                element.betweenCycleReverseTraversal = betweenCycleReverseTraversal;\n                elementsWithoutNode.push({\n                    readIndex: idx,\n                    pathIndex: pathIdx,\n                    previousY: previousVisitToNode?.y,\n                    previousNode: previousVisitToNode?.node,\n                });\n            }\n        });\n    });\n    elementsWithoutNode.sort(compareNoNodeReads);\n    elementsWithoutNode.forEach(element => {\n        const read = reads[element.readIndex];\n        const segment = read.path[element.pathIndex];\n        segment.y = bottomY[segment.order];\n        bottomY[segment.order] += read.width;\n    });\n    if (DEBUG) {\n        console.log('Reads:');\n        console.log(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(readIDs, node, topMargin) {\n    // Turn the read IDs into a set\n    const toPlace = new Set(readIDs);\n    // Get arrays of the read entry/exit/internal-ness records we want to work on\n    let incomingReads = node.incomingReads.filter(([readID]) => toPlace.has(readID));\n    const outgoingReads = node.outgoingReads.filter(([readID]) => toPlace.has(readID));\n    const internalReads = node.internalReads.filter(readID => toPlace.has(readID));\n    // Only actually use the top margin if we have any reads on the node.\n    if (incomingReads.length === 0 &&\n        outgoingReads.length === 0 &&\n        internalReads.length === 0) {\n        topMargin = 0;\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    // 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 = reads[readID].path;\n        let decisionStep = pathIdx + 1;\n        let foundY;\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    // place incoming reads\n    let currentY = startY;\n    const occupiedUntil = new Map();\n    incomingReads.forEach(readElement => {\n        const read = 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    // sort outgoing reads\n    outgoingReads.sort(compareReadOutgoingSegmentsByGoingTo);\n    // place outgoing reads\n    const occupiedFrom = new Map();\n    currentY = startY;\n    outgoingReads.forEach(readElement => {\n        const read = 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        }\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 = reads[incReadElementIndices[0]];\n                const incReadPathElement = incRead.path[incReadElementIndices[1]];\n                if (incReadPathElement.y !== undefined &&\n                    incReadPathElement.y >= currentY) {\n                    incReadPathElement.y += read.width;\n                    setOccupiedUntil(occupiedUntil, incRead, incReadElementIndices[1], incReadPathElement.y, node);\n                }\n            });\n            currentY += read.width;\n            maxY += read.width;\n        }\n    });\n    // sort internal reads\n    internalReads.sort(compareInternalReads);\n    // place internal reads\n    internalReads.forEach(readIdx => {\n        const currentRead = reads[readIdx];\n        const firstNodeOffset = currentRead.firstNodeOffset ?? 0;\n        const finalNodeCoverLength = currentRead.finalNodeCoverLength ?? 0;\n        currentY = startY;\n        while (firstNodeOffset < (occupiedUntil.get(currentY) ?? -Infinity) + 2 ||\n            finalNodeCoverLength > (occupiedFrom.get(currentY) ?? Infinity) - 3) {\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    // adjust node height and move other nodes vertically down\n    const heightIncrease = maxY - node.y - node.contentHeight;\n    node.contentHeight += heightIncrease;\n    adjustVertically3(node, heightIncrease);\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(a, b) {\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// keeps track of where reads end within nodes\nfunction setOccupiedUntil(map, read, pathIndex, y, node) {\n    if (pathIndex === read.path.length - 1) {\n        // last node of current read\n        map.set(y, read.finalNodeCoverLength ?? 0);\n    }\n    else {\n        // read covers the whole node\n        map.set(y, node.sequenceLength);\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(a, b) {\n    const readA = reads[a.readIndex];\n    const readB = 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 = nodes[a.previousNode];\n        const prevNodeB = nodes[b.previousNode];\n        if (prevNodeA && prevNodeB && prevNodeA.order !== prevNodeB.order) {\n            return prevNodeA.order - prevNodeB.order;\n        }\n    }\n    // We want to sort in reverse order when the segment is along the reverse-going part of a cycle.\n    // This ensures a loop that starts on the outside, stays on the outside,\n    // and rolls up in order with other loops.\n    const aPrev = a.previousY ?? 0;\n    const bPrev = b.previousY ?? 0;\n    if (segmentA.betweenCycleReverseTraversal &&\n        segmentB.betweenCycleReverseTraversal) {\n        return bPrev - aPrev;\n    }\n    else {\n        return aPrev - bPrev;\n    }\n}\n// compare read segments by where they are going to\nfunction compareReadOutgoingSegmentsByGoingTo([readIndexA, pathIndexA], [readIndexB, pathIndexB]) {\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    // 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 = reads[readIndexA];\n    const readB = reads[readIndexB];\n    let previousValidYA;\n    let previousValidYB;\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    if (previousValidYA && previousValidYB) {\n        return previousValidYA - previousValidYB;\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 = initialNodeA != null ? nodes[initialNodeA] : null;\n    let nodeB = initialNodeB != null ? 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 != null && nodeB != null && nodeA === nodeB) {\n        if (pathIndexA < readA.path.length - 1) {\n            pathIndexA += 1;\n            while (readA.path[pathIndexA]?.node === null)\n                pathIndexA += 1; // skip null nodes in path\n            const nextNodeIdx = readA.path[pathIndexA]?.node;\n            nodeA = nextNodeIdx != null ? nodes[nextNodeIdx] : null;\n        }\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; // skip null nodes in path\n            const nextNodeIdx = readB.path[pathIndexB]?.node;\n            nodeB = nextNodeIdx != null ? nodes[nextNodeIdx] : null;\n        }\n        else {\n            nodeB = null;\n        }\n    }\n    if (nodeA != null) {\n        if (nodeB != null)\n            return compareNodesByOrder(nodeA, nodeB);\n        return 1; // nodeB is null, nodeA not null\n    }\n    if (nodeB != null)\n        return -1; // 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    // break tie: both reads cover the same nodes and begin at the same position\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// Compare tracks based on ordering at their first convergence\nfunction compareTrackByInitialOrdering(trackA, trackB) {\n    // Find the first node where the two tracks converge, sort by layer.\n    // Tracks with no path sort first, and two of them tie.\n    if (trackA.path === undefined || trackB.path === undefined) {\n        return ((trackA.path === undefined ? 0 : 1) - (trackB.path === undefined ? 0 : 1));\n    }\n    const pathA = trackA.path;\n    const pathB = trackB.path;\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        }\n        else if (trackAOrder < trackBOrder) {\n            AIndex += 1;\n        }\n        else if (trackAOrder > trackBOrder) {\n            BIndex += 1;\n        }\n        else {\n            // Orders are equal but are traversing out of nodes\n            AIndex += 1;\n            BIndex += 1;\n        }\n    }\n    // Tracks do not converge, keep the same ordering\n    return 0;\n}\n// compare 2 reads which are completely within a single node\nfunction compareInternalReads(idxA, idxB) {\n    const a = reads[idxA];\n    const b = 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    // 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    return 0;\n}\n// determine biggest y-coordinate for each order-value\nfunction calculateBottomY() {\n    const bottomY = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        bottomY.push(0);\n    }\n    nodes.forEach(node => {\n        if (node.y !== undefined) {\n            bottomY[node.order] = Math.max(bottomY[node.order], node.y + node.contentHeight + 20);\n        }\n    });\n    tracks.forEach(track => {\n        track.path.forEach(element => {\n            bottomY[element.order] = Math.max(bottomY[element.order], (element.y ?? 0) + track.width);\n        });\n    });\n    return bottomY;\n}\n// generate path-info for each read\n// containing order, node and orientation, but no concrete coordinates\n// TODO: Duplicates a lot of the same work as generateLaneAssignment() does for non-read tracks.\nfunction generateBasicPathsForReads() {\n    reads.forEach(read => {\n        // add info for start of track\n        let currentNodeIndex = Math.abs(read.indexSequence[0]);\n        let currentNodeIsForward = isForwardIndex(read.indexSequence[0]);\n        let currentNode = nodes[currentNodeIndex];\n        let previousNode;\n        let previousNodeIsForward;\n        read.path = [];\n        read.path.push({\n            order: currentNode.order,\n            isForward: currentNodeIsForward,\n            node: currentNodeIndex,\n        });\n        for (let i = 1; i < read.sequence.length; i += 1) {\n            previousNode = currentNode;\n            previousNodeIsForward = currentNodeIsForward;\n            currentNodeIndex = Math.abs(read.indexSequence[i]);\n            currentNodeIsForward = isForwardIndex(read.indexSequence[i]);\n            currentNode = nodes[currentNodeIndex];\n            if (currentNode.order > previousNode.order) {\n                if (!previousNodeIsForward) {\n                    // backward to forward at previous node\n                    read.path.push({\n                        order: previousNode.order,\n                        isForward: true,\n                        node: null,\n                    });\n                }\n                for (let j = previousNode.order + 1; j < currentNode.order; j += 1) {\n                    // forward without nodes\n                    read.path.push({ order: j, isForward: true, node: null });\n                }\n                if (!currentNodeIsForward) {\n                    // forward to backward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    // current Node forward\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n            else if (currentNode.order < previousNode.order) {\n                if (previousNodeIsForward) {\n                    // turnaround from fw to bw at previous node\n                    read.path.push({\n                        order: previousNode.order,\n                        isForward: false,\n                        node: null,\n                    });\n                }\n                for (let j = previousNode.order - 1; j > currentNode.order; j -= 1) {\n                    // bachward without nodes\n                    read.path.push({ order: j, isForward: false, node: null });\n                }\n                if (currentNodeIsForward) {\n                    // backward to forward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    // backward at current node\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n            else {\n                if (currentNodeIsForward !== previousNodeIsForward) {\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                }\n                else {\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: !currentNodeIsForward,\n                        node: null,\n                    });\n                    read.path.push({\n                        order: currentNode.order,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                }\n            }\n        }\n    });\n}\n// reverse reads which are reversed\nfunction reverseReversedReads() {\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            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(entry.mismatches, nodeByName(entry.nodeName).sequenceLength);\n            }\n            // adjust firstNodeOffset and finalNodeCoverLength\n            const temp = read.firstNodeOffset ?? 0;\n            const firstLen = nodeByName(read.sequence[0]).sequenceLength;\n            read.firstNodeOffset = firstLen - (read.finalNodeCoverLength ?? 0);\n            const lastLen = nodeByName(read.sequence[read.sequence.length - 1]).sequenceLength;\n            read.finalNodeCoverLength = lastLen - temp;\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 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. Exported for testing.\nexport function reverseMismatches(mismatches, sequenceLength) {\n    mismatches.forEach(mm => {\n        if (mm.type === 'insertion') {\n            mm.pos = sequenceLength - mm.pos;\n        }\n        else if (mm.type === 'deletion') {\n            mm.pos = sequenceLength - mm.pos - (mm.length ?? 0);\n        }\n        else if (mm.type === 'substitution') {\n            mm.pos = sequenceLength - mm.pos - (mm.seq?.length ?? 0);\n        }\n        if (mm.seq !== undefined) {\n            // NOTE: reverse-complement followed by reverse is a plain complement.\n            // Preserved verbatim from the original code rather than \"fixed\" here.\n            mm.seq = getReverseComplement(mm.seq).split('').reverse().join('');\n        }\n    });\n}\nconst COMPLEMENT = { A: 'T', T: 'A', C: 'G', G: 'C' };\nfunction getReverseComplement(s) {\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// for each track: generate sequence of node indices from seq. of node names\nfunction generateTrackIndexSequences(tracksOrReads) {\n    tracksOrReads.forEach(track => {\n        track.indexSequence = [];\n        track.sequence.forEach(rawNodeName => {\n            let nodeName = rawNodeName;\n            // if node was switched, reverse it here\n            // Q? Is flipping the index enough? It looks like yes. Or should we also flip the node name in 'sequence'?\n            const fwdIdx = nodeMap.get(forward(nodeName));\n            const switched = nodes[fwdIdx]?.switched ?? false;\n            if (switched) {\n                nodeName = flip(nodeName);\n            }\n            // Get the index to visit the node. If the node is switched, this means\n            // visiting it reverse. Otherwise, this means visiting it forward.\n            const nodeIndex = nodeMap.get(forward(nodeName));\n            if (nodeIndex === 0) {\n                // If a node index is ever 0, we can't visit it in reverse, so we don't allow that to happen.\n                throw new Error('Node ' + forward(nodeName) + ' has prohibited index 0');\n            }\n            if (isReverse(nodeName) !== switched) {\n                // If we visit the node in reverse XOR the node is switched, go through\n                // it right to left as displayed.\n                track.indexSequence.push(-nodeIndex);\n            }\n            else {\n                // If either the node isn't switched and we go through it forward, or\n                // the node is switched *and* we go through it backward, go through it\n                // left to right as displayed.\n                track.indexSequence.push(nodeIndex);\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// get the minimum and maximum coordinates used in the image to calculate image dimensions\nfunction getImageDimensions() {\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 = { minX: 99, maxX: -99, minY: 99, maxY: -99 };\n    nodes.forEach(node => {\n        if (!node)\n            return;\n        if (node.x !== undefined) {\n            bounds.minX = Math.min(bounds.minX, node.x);\n            bounds.maxX = Math.max(bounds.maxX, node.x + NODE_HORIZONTAL_SLACK + node.pixelWidth);\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    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    imageBounds = bounds;\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(nodeName) {\n    const index = nodeMap.get(forward(nodeName));\n    const node = index === undefined ? undefined : nodes[index];\n    if (node === undefined) {\n        throw new Error(`Unknown node ${nodeName}`);\n    }\n    return node;\n}\n// map node names to node indices\nfunction generateNodeMap() {\n    nodeMap = new Map();\n    nodes.forEach((node, index) => {\n        if (node) {\n            nodeMap.set(node.name, index);\n        }\n    });\n    return nodeMap;\n}\n// adds a successor-array to each node containing the indices of the nodes coming directly after the current node\nfunction generateNodeSuccessors() {\n    const successorSets = nodes.map(() => new Set());\n    const predecessorSets = nodes.map(() => new Set());\n    const addEdges = (track) => {\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    tracks.forEach(addEdges);\n    if (config.showReads && reads.length > 0) {\n        reads.forEach(addEdges);\n    }\n    nodes.forEach((node, i) => {\n        if (node) {\n            node.successors = Array.from(successorSets[i]);\n            node.predecessors = Array.from(predecessorSets[i]);\n        }\n    });\n}\nfunction generateNodeOrderOfSingleTrack(sequence) {\n    let forwardOrder = 0;\n    let backwardOrder = 0;\n    let minOrder = 0;\n    sequence.forEach(nodeIndex => {\n        const idx = Math.abs(nodeIndex);\n        if (nodeIndex < 0) {\n            if (nodeOrders[idx] === undefined)\n                nodeOrders[idx] = backwardOrder;\n            const order = nodeOrders[idx];\n            if (order < minOrder)\n                minOrder = order;\n            forwardOrder = order;\n            backwardOrder = order - 1;\n        }\n        else {\n            if (nodeOrders[idx] === undefined)\n                nodeOrders[idx] = forwardOrder;\n            const order = nodeOrders[idx];\n            forwardOrder = order + 1;\n            backwardOrder = order;\n        }\n    });\n    if (minOrder < 0) {\n        increaseOrderForAllNodes(-minOrder);\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(sequence) {\n    let anchorIndex = 0;\n    let minOrder = 0;\n    while (anchorIndex < sequence.length &&\n        nodeOrders[Math.abs(sequence[anchorIndex])] === undefined) {\n        anchorIndex += 1; // anchor = first node in common with existing graph\n    }\n    if (anchorIndex >= sequence.length) {\n        return null;\n    }\n    const anchorSeqVal = sequence[anchorIndex];\n    let currentOrder;\n    let increment;\n    if (anchorSeqVal >= 0) {\n        // regular node\n        currentOrder = nodeOrders[anchorSeqVal] - 1;\n        increment = -1;\n    }\n    else {\n        // reverse node\n        currentOrder = nodeOrders[-anchorSeqVal] + 1;\n        increment = 1;\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 (nodeOrders[idx] === undefined) {\n            nodeOrders[idx] = currentOrder;\n            minOrder = Math.min(minOrder, currentOrder);\n            currentOrder += increment;\n        }\n    }\n    if (minOrder < 0) {\n        increaseOrderForAllNodes(-minOrder);\n    }\n    return anchorIndex;\n}\n// Sentinel order for nodes no track or read reaches.\nexport const UNREACHABLE_ORDER = -1;\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(orders) {\n    const filled = [];\n    for (const order of orders) {\n        filled.push(order ?? UNREACHABLE_ORDER);\n    }\n    return filled;\n}\n// generate global sequence of nodes from left to right, starting with first track and adding other tracks sequentially\nfunction generateNodeOrder() {\n    let modifiedSequence;\n    let currentOrder;\n    let rightIndex;\n    let leftIndex;\n    let minOrder = 0;\n    const tracksAndReads = config.showReads && reads.length > 0 ? tracks.concat(reads) : tracks;\n    const reachability = {\n        stamp: new Int32Array(nodes.length),\n        generation: 0,\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    nodeOrders = new Array(nodes.length).fill(undefined);\n    nodes.forEach(node => {\n        if (node) {\n            node.order = undefined;\n        }\n    });\n    generateNodeOrderOfSingleTrack(tracks[0].indexSequence);\n    for (let i = 1; i < tracksAndReads.length; i += 1) {\n        if (DEBUG)\n            console.log(`generating order for track ${i + 1}`);\n        rightIndex = generateNodeOrderTrackBeginning(tracksAndReads[i].indexSequence);\n        if (rightIndex === null) {\n            if (tracksAndReads[i].type === 'haplotype') {\n                generateNodeOrderOfSingleTrack(tracksAndReads[i].indexSequence);\n            }\n            else {\n                tracksAndReads.splice(i, 1);\n                reads.splice(i - tracks.length, 1);\n                i -= 1;\n            }\n            continue;\n        }\n        modifiedSequence = uninvert(tracksAndReads[i].indexSequence);\n        while (rightIndex < modifiedSequence.length) {\n            // move right until the end of the sequence\n            leftIndex = rightIndex;\n            rightIndex += 1;\n            while (rightIndex < modifiedSequence.length &&\n                nodeOrders[modifiedSequence[rightIndex]] === undefined) {\n                rightIndex += 1;\n            }\n            if (rightIndex < modifiedSequence.length) {\n                // middle segment between two anchors\n                currentOrder = nodeOrders[modifiedSequence[leftIndex]] + 1;\n                for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n                    nodeOrders[modifiedSequence[j]] = currentOrder;\n                    currentOrder += 1;\n                }\n                if (nodeOrders[modifiedSequence[rightIndex]] >\n                    nodeOrders[modifiedSequence[leftIndex]]) {\n                    if (nodeOrders[modifiedSequence[rightIndex]] < currentOrder) {\n                        increaseOrderForSuccessors(modifiedSequence[rightIndex], modifiedSequence[rightIndex - 1], currentOrder);\n                    }\n                }\n                else {\n                    if (tracksAndReads[i].indexSequence[rightIndex] >= 0 &&\n                        !isSuccessor(modifiedSequence[rightIndex], modifiedSequence[leftIndex], reachability)) {\n                        // no real reversal\n                        increaseOrderForSuccessors(modifiedSequence[rightIndex], modifiedSequence[rightIndex - 1], currentOrder);\n                    }\n                    else {\n                        // real reversal\n                        if (tracksAndReads[i].indexSequence[leftIndex] < 0 ||\n                            (nodes[modifiedSequence[leftIndex + 1]].degree < 2 &&\n                                nodeOrders[modifiedSequence[rightIndex]] <\n                                    nodeOrders[modifiedSequence[leftIndex]])) {\n                            currentOrder = nodeOrders[modifiedSequence[leftIndex]] - 1;\n                            for (let j = leftIndex + 1; j < rightIndex; j += 1) {\n                                nodeOrders[modifiedSequence[j]] = currentOrder;\n                                minOrder = Math.min(minOrder, currentOrder);\n                                currentOrder -= 1;\n                            }\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 = nodeOrders[modifiedSequence[leftIndex]] + 1;\n                    for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n                        const idx = modifiedSequence[j];\n                        if (nodeOrders[idx] === undefined) {\n                            nodeOrders[idx] = currentOrder;\n                            currentOrder += 1;\n                        }\n                    }\n                }\n                else {\n                    // elongate towards the left\n                    currentOrder = nodeOrders[modifiedSequence[leftIndex]] - 1;\n                    for (let j = leftIndex + 1; j < modifiedSequence.length; j += 1) {\n                        const idx = modifiedSequence[j];\n                        if (nodeOrders[idx] === undefined) {\n                            nodeOrders[idx] = currentOrder;\n                            minOrder = Math.min(minOrder, currentOrder);\n                            currentOrder -= 1;\n                        }\n                    }\n                }\n            }\n        }\n    }\n    if (minOrder < 0)\n        increaseOrderForAllNodes(-minOrder);\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(nodeOrders);\n    nodeOrders = finalOrders;\n    finalOrders.forEach((order, i) => {\n        const node = nodes[i];\n        if (node !== undefined) {\n            node.order = order;\n        }\n    });\n}\nfunction isSuccessor(first, second, scratch) {\n    scratch.generation += 1;\n    const { stamp, generation } = scratch;\n    const stack = [first];\n    stamp[first] = generation;\n    while (stack.length > 0) {\n        const current = stack.pop();\n        if (current === second)\n            return true;\n        for (const childIndex of nodes[current].successors) {\n            if (stamp[childIndex] !== generation) {\n                stamp[childIndex] = generation;\n                stack.push(childIndex);\n            }\n        }\n    }\n    return false;\n}\n// get order number of the rightmost node\nfunction getMaxOrder() {\n    let max = -1;\n    nodeOrders.forEach(order => {\n        if (order !== undefined && order > max)\n            max = order;\n    });\n    return max;\n}\n// generates sequence keeping the order but switching all reversed (negative) nodes to forward nodes\nfunction uninvert(sequence) {\n    return sequence.map(v => Math.abs(v));\n}\n// increases the order-value of all nodes by amount\nfunction increaseOrderForAllNodes(amount) {\n    nodeOrders.forEach((order, i) => {\n        if (order !== undefined)\n            nodeOrders[i] = order + amount;\n    });\n}\n// increases the order-value for currentNode and (if necessary) successor nodes recursively\nfunction increaseOrderForSuccessors(startingNode, tabuNode, newOrder) {\n    const increasedOrders = new Map();\n    // Walked with a head pointer rather than shift(), which is O(length) per pop.\n    const queue = [[startingNode, newOrder]];\n    let head = 0;\n    while (head < queue.length) {\n        const [currentNode, currentOrder] = queue[head];\n        head += 1;\n        const currentNodeOrder = nodeOrders[currentNode];\n        if (currentNodeOrder !== undefined && currentNodeOrder < currentOrder) {\n            if (!increasedOrders.has(currentNode) ||\n                increasedOrders.get(currentNode) < currentOrder) {\n                increasedOrders.set(currentNode, currentOrder);\n                nodes[currentNode].successors.forEach(successor => {\n                    if (nodeOrders[successor] > currentNodeOrder &&\n                        successor !== tabuNode) {\n                        // only increase order of successors to the right of currentNode\n                        queue.push([successor, currentOrder + 1]);\n                    }\n                });\n                if (currentNode !== startingNode) {\n                    nodes[currentNode].predecessors.forEach(predecessor => {\n                        if (nodeOrders[predecessor] > currentNodeOrder &&\n                            predecessor !== tabuNode) {\n                            // only increase order of predecessors to the right of currentNode\n                            queue.push([predecessor, currentOrder + 1]);\n                        }\n                    });\n                }\n            }\n        }\n    }\n    increasedOrders.forEach((value, key) => {\n        nodeOrders[key] = value;\n    });\n}\n// calculates the node degree: the number of tracks passing through the node / the node height\nfunction generateNodeDegree() {\n    nodes.forEach(node => {\n        node.tracks = [];\n    });\n    tracks.forEach(track => {\n        track.indexSequence.forEach(nodeIndex => {\n            nodes[Math.abs(nodeIndex)].tracks.push(track.id);\n        });\n    });\n    nodes.forEach(node => {\n        if (node.tracks !== undefined)\n            node.degree = node.tracks.length;\n    });\n}\n// Optimize the orientations for nodes in the global `nodes` for displaying the\n// paths in the global `tracks` and the read paths, if applicable, in the\n// global `reads`\nfunction switchNodeOrientation() {\n    const pivotPath = tracks[0];\n    let countPaths = tracks.slice(1, tracks.length);\n    if (config.showReads && reads.length > 0) {\n        countPaths = countPaths.concat(reads);\n    }\n    switchNodeOrientationForPaths(countPaths, pivotPath);\n    if (config.showReads && reads.length > 0) {\n        // Any changes should be committed back\n        for (let i = 0; i < reads.length; i++) {\n            if (reads[i] !== countPaths[i + tracks.length - 1]) {\n                throw new Error('Read inequality');\n            }\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. Processes all paths' nodes in\n// place, so if you want e.g. a first track with nodes fixed in that\n// orientation, pass it as pivotPath.\n// References and modifies the global nodes variable.\nfunction switchNodeOrientationForPaths(paths, pivotPath) {\n    const toSwitch = new Map();\n    const pivotNames = pivotPath ? new Set(pivotPath.sequence) : null;\n    for (const path of paths) {\n        const sequence = path.sequence;\n        for (let j = 0; j < sequence.length; j += 1) {\n            const nodeName = forward(sequence[j]);\n            const currentNode = nodeByName(nodeName);\n            if (pivotNames && !pivotNames.has(nodeName)) {\n                // do not change orientation for nodes which are part of the pivot path\n                const prevOrder = j > 0 ? nodeByName(sequence[j - 1]).order : undefined;\n                const nextOrder = j < sequence.length - 1\n                    ? nodeByName(sequence[j + 1]).order\n                    : undefined;\n                if ((prevOrder === undefined || prevOrder < currentNode.order) &&\n                    (nextOrder === undefined || currentNode.order < nextOrder)) {\n                    // Node is visited in increasing order along the path. Reverse\n                    // visits count towards switching, forward visits against it.\n                    addToSwitchScore(toSwitch, nodeName, isReverse(sequence[j]) ? 1 : -1);\n                }\n                if ((prevOrder === undefined || prevOrder > currentNode.order) &&\n                    (nextOrder === undefined || currentNode.order > nextOrder)) {\n                    // Node is visited in *decreasing* order along the path, so is already\n                    // backward: the votes are the other way round.\n                    addToSwitchScore(toSwitch, nodeName, isReverse(sequence[j]) ? -1 : 1);\n                }\n            }\n        }\n    }\n    for (const path of paths) {\n        path.sequence.forEach((node, nodeIndex) => {\n            const score = toSwitch.get(forward(node));\n            if (score !== undefined && score > 0) {\n                // This node is backward more so flip it around\n                path.sequence[nodeIndex] = flip(node);\n                path.indexSequence[nodeIndex] = -path.indexSequence[nodeIndex];\n            }\n        });\n    }\n    // invert the sequence within the nodes and mark them as \"switched\"\n    toSwitch.forEach((value, key) => {\n        if (value > 0) {\n            const node = nodeByName(key);\n            node.seq = getReverseComplement(node.seq);\n            node.switched = true;\n        }\n    });\n}\nfunction addToSwitchScore(scores, nodeName, delta) {\n    scores.set(nodeName, (scores.get(nodeName) ?? 0) + delta);\n}\n// calculates the concrete values for the nodes' x-coordinates\nfunction generateNodeXCoords() {\n    let currentX = 0;\n    let nextX = 20;\n    let currentOrder = -1;\n    const sortedNodes = nodes.slice();\n    sortedNodes.sort(compareNodesByOrder);\n    const extra = calculateExtraSpace();\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// 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() {\n    const leftSideEdges = [];\n    const rightSideEdges = [];\n    const fallAngleAdjustment = [];\n    const extra = [];\n    for (let i = 0; i <= maxOrder; i += 1) {\n        leftSideEdges.push(0);\n        rightSideEdges.push(0);\n        fallAngleAdjustment.push(0);\n    }\n    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                }\n                else {\n                    rightSideEdges[seg.order] = rightSideEdges[seg.order] + 1;\n                }\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(yDifference / 17.5, fallAngleAdjustment[seg.order]);\n            }\n        }\n    });\n    extra.push(Math.max(0, leftSideEdges[0] - 1));\n    for (let i = 1; i <= 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(Math.max(Math.max(0, leftSideEdges[i] - 1) +\n            Math.max(0, rightSideEdges[i - 1] - 1), fallAngleAdjustment[i]));\n    }\n    return extra;\n}\n// create and fill assignment-variable, which contains info about tracks and lanes for each order-value\nfunction generateLaneAssignment() {\n    let segmentNumber;\n    let currentNodeIndex;\n    let currentNodeIsForward;\n    let currentNode;\n    let previousNode;\n    let previousNodeIsForward;\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 = [];\n    // Index into assignments[order] by node, so addToAssignment can find an\n    // existing entry without scanning the whole order slot.\n    const assignmentByOrderAndNode = [];\n    // create empty variables\n    for (let i = 0; i <= maxOrder; i += 1) {\n        assignments[i] = [];\n        assignmentByOrderAndNode[i] = new Map();\n        prevSegmentPerOrderPerTrack[i] = [];\n        for (let j = 0; j < tracks.length; j += 1) {\n            prevSegmentPerOrderPerTrack[i][j] = null;\n        }\n    }\n    tracks.forEach((track, trackNo) => {\n        // Trace along each track and create Segment objects in the track's path\n        // field, and SegmentAssignment objects in NodeAssignment objects in all\n        // the order slots that are visited by the track. Set up all the\n        // cross-reverencing indexes and work out when we need segments to let\n        // tracks pass nodes and turn around, but leave all the assigned lane\n        // values empty for now.\n        // add info for start of track\n        currentNodeIndex = Math.abs(track.indexSequence[0]);\n        currentNodeIsForward = isForwardIndex(track.indexSequence[0]);\n        currentNode = nodes[currentNodeIndex];\n        track.path = [];\n        track.path.push({\n            order: currentNode.order,\n            lane: null,\n            isForward: currentNodeIsForward,\n            node: currentNodeIndex,\n        });\n        addToAssignment(currentNode.order, currentNodeIndex, trackNo, 0, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n        segmentNumber = 1;\n        for (let i = 1; i < track.sequence.length; i += 1) {\n            previousNode = currentNode;\n            previousNodeIsForward = currentNodeIsForward;\n            currentNodeIndex = Math.abs(track.indexSequence[i]);\n            currentNodeIsForward = isForwardIndex(track.indexSequence[i]);\n            currentNode = nodes[currentNodeIndex];\n            if (currentNode.order > previousNode.order) {\n                if (!previousNodeIsForward) {\n                    // backward to forward at previous node\n                    track.path.push({\n                        order: previousNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(previousNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                for (let j = previousNode.order + 1; j < currentNode.order; j += 1) {\n                    // forward without nodes\n                    track.path.push({\n                        order: j,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(j, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                if (!currentNodeIsForward) {\n                    // forward to backward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    // current Node forward\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n            }\n            else if (currentNode.order < previousNode.order) {\n                if (previousNodeIsForward) {\n                    // turnaround from fw to bw at previous node\n                    track.path.push({\n                        order: previousNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(previousNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                for (let j = previousNode.order - 1; j > currentNode.order; j -= 1) {\n                    // bachward without nodes\n                    track.path.push({\n                        order: j,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(j, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                if (currentNodeIsForward) {\n                    // backward to forward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: true,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    // backward at current node\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: false,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n            }\n            else {\n                if (currentNodeIsForward !== previousNodeIsForward) {\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                }\n                else {\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: !currentNodeIsForward,\n                        node: null,\n                    });\n                    addToAssignment(currentNode.order, null, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\n                    track.path.push({\n                        order: currentNode.order,\n                        lane: null,\n                        isForward: currentNodeIsForward,\n                        node: currentNodeIndex,\n                    });\n                    addToAssignment(currentNode.order, currentNodeIndex, trackNo, segmentNumber, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode);\n                    segmentNumber += 1;\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 <= maxOrder; i += 1) {\n        generateSingleLaneAssignment(assignments[i], i); // this is where the lanes get assigned\n    }\n}\nfunction addToAssignment(order, nodeIndex, trackNo, segmentID, prevSegmentPerOrderPerTrack, assignmentByOrderAndNode) {\n    const segment = {\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 = nodeIndex === null\n        ? undefined\n        : assignmentByOrderAndNode[order].get(nodeIndex);\n    if (existing === undefined) {\n        const assignment = {\n            type: 'single',\n            node: nodeIndex,\n            tracks: [segment],\n        };\n        assignments[order].push(assignment);\n        if (nodeIndex !== null) {\n            assignmentByOrderAndNode[order].set(nodeIndex, assignment);\n        }\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// looks at assignment and sets idealY and idealLane by looking at where the tracks come from\nfunction getIdealLanesAndCoords(assignment, order) {\n    let index;\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            }\n            else {\n                if (tracks[track.trackID].path[track.segmentID - 1].order ===\n                    order - 1) {\n                    track.idealLane =\n                        tracks[track.trackID].path[track.segmentID - 1].lane ?? undefined;\n                    track.idealY = tracks[track.trackID].path[track.segmentID - 1].y;\n                }\n                else if (track.segmentID < tracks[track.trackID].path.length - 1 &&\n                    tracks[track.trackID].path[track.segmentID + 1].order === order - 1) {\n                    track.idealLane =\n                        tracks[track.trackID].path[track.segmentID + 1].lane ?? undefined;\n                    track.idealY = tracks[track.trackID].path[track.segmentID + 1].y;\n                }\n                else {\n                    index = track.segmentID - 1;\n                    while (index >= 0 &&\n                        tracks[track.trackID].path[index].order !== order - 1) {\n                        index -= 1;\n                    }\n                    if (index < 0) {\n                        track.idealLane = track.trackID;\n                        track.idealY = null;\n                    }\n                    else {\n                        track.idealLane =\n                            tracks[track.trackID].path[index].lane ?? undefined;\n                        track.idealY = tracks[track.trackID].path[index].y;\n                    }\n                }\n            }\n            node.idealLane += track.idealLane;\n        });\n        node.idealLane /= node.tracks.length;\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(assignment, order) {\n    let currentLane = 0;\n    const potentialAdjustmentValues = new Set();\n    let currentY = 20;\n    let prevNameIsNull = false;\n    let prevTrack = -1;\n    getIdealLanesAndCoords(assignment, order);\n    assignment.sort(compareByIdealLane);\n    assignment.forEach(node => {\n        if (node.node !== null) {\n            nodes[node.node].topLane = currentLane;\n            if (prevNameIsNull)\n                currentY -= 10;\n            nodes[node.node].y = currentY;\n            nodes[node.node].contentHeight = 0;\n            prevNameIsNull = false;\n        }\n        else {\n            if (prevNameIsNull)\n                currentY -= 25;\n            else if (currentY > 20)\n                currentY -= 10;\n            prevNameIsNull = true;\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            tracks[track.trackID].path[track.segmentID].lane = currentLane;\n            tracks[track.trackID].path[track.segmentID].y = currentY;\n            if (track.idealY != null) {\n                potentialAdjustmentValues.add(track.idealY - currentY);\n            }\n            currentLane += 1;\n            currentY += tracks[track.trackID].width;\n            if (node.node !== null) {\n                nodes[node.node].contentHeight += tracks[track.trackID].width;\n            }\n            prevTrack = track.trackID;\n        });\n        currentY += 25;\n    });\n    adjustVertically(assignment, potentialAdjustmentValues);\n}\n// moves all tracks at a single horizontal location (=order) up/down to minimize lane changes\nfunction adjustVertically(assignment, potentialAdjustmentValues) {\n    let verticalAdjustment = 0;\n    let minAdjustmentCost = Number.MAX_SAFE_INTEGER;\n    potentialAdjustmentValues.forEach(moveBy => {\n        if (getVerticalAdjustmentCost(assignment, moveBy) < minAdjustmentCost) {\n            minAdjustmentCost = getVerticalAdjustmentCost(assignment, moveBy);\n            verticalAdjustment = moveBy;\n        }\n    });\n    assignment.forEach(node => {\n        if (node.node !== null) {\n            nodes[node.node].y += verticalAdjustment;\n        }\n        node.tracks.forEach(track => {\n            const seg = tracks[track.trackID].path[track.segmentID];\n            seg.y = seg.y + verticalAdjustment;\n        });\n    });\n}\n// Budge down all nodes and out-of-node tracks below this node by this amount\nfunction adjustVertically3(node, adjustBy) {\n    if (node.order < 0 || assignments[node.order] === undefined)\n        return;\n    assignments[node.order].forEach(assignmentNode => {\n        if (assignmentNode.node !== null) {\n            const aNode = nodes[assignmentNode.node];\n            if (aNode !== node && aNode.y > node.y) {\n                aNode.y += adjustBy;\n                assignmentNode.tracks.forEach(track => {\n                    const seg = tracks[track.trackID].path[track.segmentID];\n                    seg.y = seg.y + adjustBy;\n                });\n            }\n        }\n        else {\n            // track-segment not within a node\n            assignmentNode.tracks.forEach(track => {\n                const seg = tracks[track.trackID].path[track.segmentID];\n                if (seg.y >= node.y) {\n                    seg.y = seg.y + adjustBy;\n                }\n            });\n        }\n    });\n    if (nodesPerOrder[node.order].length > 0) {\n        nodesPerOrder[node.order].forEach(nodeIndex => {\n            if (nodes[nodeIndex] !== node && nodes[nodeIndex].y > node.y) {\n                nodes[nodeIndex].y += adjustBy;\n            }\n        });\n    }\n}\n// calculates cost of vertical adjustment as vertical distance * width of track\nfunction getVerticalAdjustmentCost(assignment, moveBy) {\n    let result = 0;\n    assignment.forEach(node => {\n        node.tracks.forEach(track => {\n            if (track.idealY != null && tracks[track.trackID].type !== 'read') {\n                result +=\n                    Math.abs(track.idealY -\n                        moveBy -\n                        tracks[track.trackID].path[track.segmentID].y) * tracks[track.trackID].width;\n            }\n        });\n    });\n    return result;\n}\nfunction compareByIdealLane(a, b) {\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            return 0;\n        }\n        return -1;\n    }\n    if (b.idealLane !== undefined) {\n        return 1;\n    }\n    return 0;\n}\nfunction compareNodesByOrder(a, b) {\n    if (!a) {\n        if (!b)\n            return 0;\n        return -1;\n    }\n    if (!b)\n        return 1;\n    if (a.order !== undefined) {\n        if (b.order !== undefined) {\n            if (a.order < b.order)\n                return -1;\n            else if (a.order > b.order)\n                return 1;\n            if (a.y !== undefined && b.y !== undefined) {\n                if (a.y < b.y)\n                    return -1;\n                else if (a.y > b.y)\n                    return 1;\n            }\n            return 0;\n        }\n        return -1;\n    }\n    if (b.order !== undefined)\n        return 1;\n    return 0;\n}\nfunction addTrackFeatures() {\n    let nodeStart;\n    let nodeEnd;\n    let feature = {};\n    bed.forEach(line => {\n        let i = 0;\n        while (i < tracks.length && tracks[i].name !== line.track)\n            i += 1;\n        if (i < tracks.length) {\n            nodeStart = 0;\n            tracks[i].path.forEach(node => {\n                if (node.node !== null) {\n                    feature = {};\n                    nodeEnd = nodeStart + nodes[node.node].sequenceLength - 1;\n                    if (nodeStart >= line.start && nodeStart <= line.end) {\n                        feature.start = 0;\n                    }\n                    if (nodeStart < line.start && nodeEnd >= line.start) {\n                        feature.start = line.start - nodeStart;\n                    }\n                    if (nodeEnd <= line.end && nodeEnd >= line.start) {\n                        feature.end = nodeEnd - nodeStart;\n                        if (nodeEnd < line.end)\n                            feature.continue = true;\n                    }\n                    if (nodeEnd > line.end && nodeStart <= line.end) {\n                        feature.end = line.end - nodeStart;\n                    }\n                    if (feature.start !== undefined) {\n                        feature.type = line.type;\n                        feature.name = line.name;\n                        if (node.features === undefined)\n                            node.features = [];\n                        node.features.push(feature);\n                    }\n                    nodeStart = nodeEnd + 1;\n                }\n            });\n        }\n    });\n}\nfunction calculateTrackWidth() {\n    // flag: if vg returns freq of 0 for all tracks, we will increase width manually\n    let allAreFour = true;\n    const NARROW_WIDTH = 4;\n    const WIDE_WIDTH = config.trackWidth;\n    tracks.forEach(track => {\n        if (track.freq !== undefined) {\n            // custom track width\n            track.width = Math.round((Math.log(track.freq) + 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    if (allAreFour) {\n        tracks.forEach(track => {\n            if (track.freq !== undefined) {\n                track.width = WIDE_WIDTH;\n            }\n        });\n    }\n}\nfunction getReadXStart(read) {\n    const seg = read.path[0];\n    const node = 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(node, seg.isForward ? offset : node.sequenceLength - offset);\n}\nfunction getReadXEnd(read) {\n    const seg = read.path[read.path.length - 1];\n    const node = 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(node, seg.isForward ? cover : node.sequenceLength - cover);\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(node, base) {\n    if (base > node.sequenceLength)\n        return null; // equality is allowed\n    return clampedXCoordinateOfBaseWithinNode(node, base);\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(node, base) {\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// transforms the info in the tracks' path attribute into actual coordinates\n// and saves them in shapes.rectangles and shapes.curves\nfunction generateSVGShapesFromPath() {\n    let xStart;\n    let xEnd;\n    let yStart;\n    let yEnd;\n    let trackColor;\n    let trackAlpha;\n    let highlight;\n    let dummy;\n    let reversalFlag;\n    for (let i = 0; i <= maxOrder; i += 1) {\n        extraLeft.push(0);\n        extraRight.push(0);\n    }\n    // generate x coords where each order starts and ends\n    const orderStartX = [];\n    const orderEndX = [];\n    nodes.forEach(node => {\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            }\n            else {\n                orderEndX[node.order] = Math.max(orderEndX[node.order], node.x + node.pixelWidth);\n            }\n        }\n    });\n    // Helps generation of verticalRectangles, correct increments of extraRight and extraLeft\n    tracks.sort(compareTrackByInitialOrdering);\n    tracks.forEach(track => {\n        highlight = 'plain';\n        // Both are pure functions of (track, highlight); alpha doesn't even look at\n        // highlight. Recomputing them per path segment was pure overhead.\n        trackColor = generateTrackColor(track, highlight);\n        trackAlpha = generateTrackAlpha(track);\n        let colorHighlight = highlight;\n        const colorForCurrentHighlight = () => {\n            if (colorHighlight !== highlight) {\n                colorHighlight = highlight;\n                trackColor = generateTrackColor(track, highlight);\n            }\n            return trackColor;\n        };\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            }\n            else {\n                // The track starts with a forward node\n                xStart = orderStartX[track.path[0].order] - 20;\n            }\n        }\n        else {\n            xStart = getReadXStart(track);\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].features !== undefined) {\n                    reversalFlag =\n                        i > 0 && track.path[i - 1].order === track.path[i].order;\n                    dummy = createFeatureRectangle(track.path[i], orderStartX[track.path[i].order], orderEndX[track.path[i].order], highlight, track, xStart, yStart, trackColor, reversalFlag);\n                    highlight = dummy.highlight;\n                    xStart = dummy.xStart;\n                }\n            }\n            else {\n                if (track.path[i - 1].isForward) {\n                    xEnd = orderEndX[track.path[i - 1].order];\n                }\n                else {\n                    xEnd = orderStartX[track.path[i - 1].order];\n                }\n                if (xEnd !== xStart) {\n                    trackColor = colorForCurrentHighlight();\n                    shapes.rectangles.push({\n                        xStart: Math.min(xStart, xEnd),\n                        yStart,\n                        xEnd: Math.max(xStart, xEnd),\n                        yEnd: yStart + track.width - 1,\n                        color: trackColor,\n                        alpha: trackAlpha,\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                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                    trackColor = colorForCurrentHighlight();\n                    shapes.curves.push({\n                        xStart,\n                        yStart,\n                        xEnd: xEnd + 1,\n                        yEnd,\n                        width: track.width,\n                        color: trackColor,\n                        alpha: trackAlpha,\n                        laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),\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                    });\n                    xStart = xEnd;\n                    yStart = yEnd;\n                }\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                    trackColor = colorForCurrentHighlight();\n                    shapes.curves.push({\n                        xStart: xStart + 1,\n                        yStart,\n                        xEnd,\n                        yEnd,\n                        width: track.width,\n                        color: trackColor,\n                        alpha: trackAlpha,\n                        laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),\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                    });\n                    xStart = xEnd;\n                    yStart = yEnd;\n                }\n                else {\n                    // change of direction\n                    if (track.path[i - 1].isForward) {\n                        yEnd = track.path[i].y;\n                        generateTurnaround(1, xEnd, yStart, yEnd, track.width, trackColor, track.id, track.path[i].order, track.type, track.name);\n                        xStart = orderEndX[track.path[i].order];\n                        yStart = track.path[i].y;\n                    }\n                    else {\n                        yEnd = track.path[i].y;\n                        generateTurnaround(-1, xEnd, yStart, yEnd, track.width, trackColor, track.id, track.path[i].order, track.type, track.name);\n                        xStart = orderStartX[track.path[i].order];\n                        yStart = track.path[i].y;\n                    }\n                }\n                if (track.path[i].features !== undefined) {\n                    reversalFlag = track.path[i - 1].order === track.path[i].order;\n                    dummy = createFeatureRectangle(track.path[i], orderStartX[track.path[i].order], orderEndX[track.path[i].order], highlight, track, xStart, yStart, trackColor, reversalFlag);\n                    highlight = dummy.highlight;\n                    xStart = dummy.xStart;\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            }\n            else {\n                // The track ends with a forward node\n                xEnd = orderEndX[track.path[track.path.length - 1].order] + 20;\n            }\n        }\n        else {\n            xEnd = getReadXEnd(track);\n        }\n        shapes.rectangles.push({\n            xStart: Math.min(xStart, xEnd),\n            yStart,\n            xEnd: Math.max(xStart, xEnd),\n            yEnd: yStart + track.width - 1,\n            color: trackColor,\n            alpha: trackAlpha,\n            id: track.id,\n            name: track.name,\n            type: track.type,\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, bezier shape, AND color\n// scheme as a real read \u2014 colors come from generateTrackColor's natural\n// `id % palette.length` rotation, no custom palette needed.\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) => id >= COARSENED_ID_BASE;\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(source, unit) {\n    coarsenedEdgeMeta = new Map();\n    const edges = new Map();\n    // When ignoring strand, (+A\u2192+B) and (-B\u2192-A) refer to the same underlying\n    // graph connection \u2014 collapse both into one canonical key. We pick the\n    // lexicographically smaller of the two orientations so a stable canonical\n    // form is chosen; whichever orientation is seen first determines the\n    // visual band direction.\n    const ignoreStrand = config.ignoreStrand;\n    for (const item of source) {\n        const seq = item.indexSequence;\n        if (!seq || seq.length < 2)\n            continue;\n        for (let i = 0; i < seq.length - 1; i += 1) {\n            const sSigned = seq[i];\n            const dSigned = seq[i + 1];\n            const sIdx = Math.abs(sSigned);\n            const dIdx = Math.abs(dSigned);\n            const srcNode = nodes[sIdx];\n            const dstNode = nodes[dIdx];\n            if (!srcNode || !dstNode)\n                continue;\n            let key;\n            if (ignoreStrand) {\n                const a = `${sSigned}>${dSigned}`;\n                const b = `${-dSigned}>${-sSigned}`;\n                key = a < b ? a : b;\n            }\n            else {\n                key = `${sSigned}>${dSigned}`;\n            }\n            const existing = edges.get(key);\n            if (existing === undefined) {\n                edges.set(key, {\n                    sSigned,\n                    dSigned,\n                    sName: sSigned < 0 ? `-${srcNode.name}` : srcNode.name,\n                    dName: dSigned < 0 ? `-${dstNode.name}` : dstNode.name,\n                    count: 1,\n                    sourceTrackID: item.sourceTrackID,\n                });\n            }\n            else {\n                existing.count += 1;\n            }\n        }\n    }\n    // Square-root scaling on count gives heavy edges visible weight without\n    // letting one massive edge dwarf everything else. Min stays near READ_WIDTH\n    // so single-read edges still look like a normal read; max is generous so\n    // hot edges read as obvious \"highways.\"\n    let maxEdgeCount = 0;\n    for (const e of edges.values()) {\n        if (e.count > maxEdgeCount)\n            maxEdgeCount = e.count;\n    }\n    const BAND_MIN_WIDTH = READ_WIDTH;\n    const BAND_MAX_WIDTH = 60;\n    const widthForCount = (c) => {\n        if (maxEdgeCount <= 1)\n            return BAND_MIN_WIDTH;\n        return (BAND_MIN_WIDTH +\n            (BAND_MAX_WIDTH - BAND_MIN_WIDTH) * Math.sqrt(c / maxEdgeCount));\n    };\n    const synthetic = [];\n    let i = 0;\n    for (const edge of edges.values()) {\n        const id = COARSENED_ID_BASE + i;\n        const label = `${edge.count.toLocaleString()} ${unit}${edge.count === 1 ? '' : 's'}: Node ${edge.sName} \u2192 Node ${edge.dName}`;\n        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 = nodes[Math.abs(edge.sSigned)]?.sequenceLength ?? 0; // node may be absent for a dangling edge\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.count),\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        });\n        i += 1;\n    }\n    // Single-line debug summary so the user can verify node sizing.\n    let tallestName = '?';\n    let tallestH = 0;\n    for (const n of nodes) {\n        if (!n)\n            continue;\n        const h = n.contentHeight;\n        if (h > tallestH) {\n            tallestH = h;\n            tallestName = n.name;\n        }\n    }\n    if (DEBUG) {\n        console.log(`[coarsened] ${unit}s_in=${source.length} edges_out=${synthetic.length} ` +\n            `tallestNodeBeforePlace=${tallestName}(${tallestH.toFixed(1)})`);\n    }\n    return synthetic;\n}\nfunction createFeatureRectangle(node, nodeXStart, nodeXEnd, highlight, track, rectXStart, yStart, trackColor, reversalFlag) {\n    let currentHighlight = highlight;\n    let c;\n    let co;\n    let featureXStart;\n    let featureXEnd;\n    nodeXStart -= 8;\n    nodeXEnd += 8;\n    const nodeWidth = nodes[node.node].sequenceLength;\n    node.features.sort((a, b) => a.start - b.start);\n    node.features.forEach(feature => {\n        if (currentHighlight !== feature.type) {\n            // finish incoming rectangle\n            c = generateTrackColor(track, currentHighlight);\n            if (node.isForward) {\n                featureXStart =\n                    nodeXStart +\n                        Math.round((feature.start * (nodeXEnd - nodeXStart + 1)) / nodeWidth);\n                // overwrite narrow post-inversion rectangle if highlight starts near beginning of node\n                if (reversalFlag && featureXStart < nodeXStart + 8) {\n                    featureXEnd =\n                        nodeXStart +\n                            Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                            1;\n                    co = generateTrackColor(track, feature.type);\n                    shapes.featureRectangles.push({\n                        xStart: featureXStart,\n                        yStart,\n                        xEnd: featureXEnd,\n                        yEnd: yStart + track.width - 1,\n                        color: co,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n                if (featureXStart > rectXStart + 1) {\n                    shapes.featureRectangles.push({\n                        xStart: rectXStart,\n                        yStart,\n                        xEnd: featureXStart - 1,\n                        yEnd: yStart + track.width - 1,\n                        color: c,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n            }\n            else {\n                featureXStart =\n                    nodeXEnd -\n                        Math.round((feature.start * (nodeXEnd - nodeXStart + 1)) / nodeWidth);\n                // overwrite narrow post-inversion rectangle if highlight starts near beginning of node\n                if (reversalFlag && featureXStart > nodeXEnd - 8) {\n                    featureXEnd =\n                        nodeXEnd -\n                            Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                            1;\n                    co = generateTrackColor(track, feature.type);\n                    shapes.featureRectangles.push({\n                        xStart: featureXEnd,\n                        yStart,\n                        xEnd: featureXStart,\n                        yEnd: yStart + track.width - 1,\n                        color: co,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n                if (rectXStart > featureXStart + 1) {\n                    shapes.featureRectangles.push({\n                        xStart: featureXStart + 1,\n                        yStart,\n                        xEnd: rectXStart,\n                        yEnd: yStart + track.width - 1,\n                        color: c,\n                        id: track.id,\n                        name: track.name,\n                        type: track.type,\n                    });\n                }\n            }\n            rectXStart = featureXStart;\n            currentHighlight = feature.type;\n        }\n        if (feature.end < nodeWidth - 1 || feature.continue === undefined) {\n            // finish internal rectangle\n            c = generateTrackColor(track, currentHighlight);\n            if (node.isForward) {\n                featureXEnd =\n                    nodeXStart +\n                        Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                        1;\n                shapes.featureRectangles.push({\n                    xStart: rectXStart,\n                    yStart,\n                    xEnd: featureXEnd,\n                    yEnd: yStart + track.width - 1,\n                    color: c,\n                    id: track.id,\n                    name: track.name,\n                    type: track.type,\n                });\n            }\n            else {\n                featureXEnd =\n                    nodeXEnd -\n                        Math.round(((feature.end + 1) * (nodeXEnd - nodeXStart + 1)) / nodeWidth) -\n                        1;\n                shapes.featureRectangles.push({\n                    xStart: featureXEnd,\n                    yStart,\n                    xEnd: rectXStart,\n                    yEnd: yStart + track.width - 1,\n                    color: c,\n                    id: track.id,\n                    name: track.name,\n                    type: track.type,\n                });\n            }\n            rectXStart = featureXEnd + 1;\n            currentHighlight = 'plain';\n        }\n    });\n    return { xStart: rectXStart, highlight: currentHighlight };\n}\nconst MIN_BEND_WIDTH = 7;\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(dir, x, yStart, yEnd, trackWidth, trackColor, trackID, order, type, trackName) {\n    const extra = dir === 1 ? extraRight : 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    const horizontal = (segTop) => {\n        shapes.verticalRectangles.push({\n            xStart: stubNear,\n            yStart: segTop,\n            xEnd: stubFar,\n            yEnd: segTop + trackWidth - 1,\n            color: trackColor,\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    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        color: trackColor,\n        id: trackID,\n        name: trackName,\n        type,\n    });\n    horizontal(yEnd);\n    const inner = apex + dir * radius;\n    const outer = apex + dir * (radius + stem);\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    shapes.corners.push({ path: d, color: trackColor, id: trackID, type });\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    shapes.corners.push({ path: d, color: trackColor, id: trackID, type });\n    extra[order] += 1;\n}\nexport function nodePixelCoordinatesInX(node) {\n    // Add and subtract 4 to account for stroke width - TODO: figure out what the 4 means\n    const nodeLeftX = node.x - 4;\n    const nodeRightX = node.x + node.pixelWidth + 4;\n    return [nodeLeftX, nodeRightX];\n}\n// calculate node widths depending on sequence lengths and chosen calculation method\nfunction generateNodeWidth() {\n    // Promote the input's optional sequenceLength; Node declares it required, so\n    // widen to InputNode to make the still-possibly-undefined read explicit.\n    nodes.forEach((node) => {\n        if (node.sequenceLength === undefined) {\n            node.sequenceLength = node.seq.length;\n        }\n    });\n    switch (config.nodeWidthOption) {\n        case 'compressed':\n            nodes.forEach(node => {\n                node.width = 1 + Math.log(node.sequenceLength) / Math.log(2);\n                node.pixelWidth = Math.round((node.width - 1) * 8.401);\n            });\n            break;\n        case 'small':\n            nodes.forEach(node => {\n                node.width = node.sequenceLength / 100;\n                node.pixelWidth = Math.round((node.width - 1) * 8.401);\n            });\n            break;\n        case 'fixed':\n            // when there's no reads in the node, it should be a little wider\n            nodes.forEach(node => {\n                node.width = 10;\n                node.pixelWidth = Math.round(node.width * 8.401);\n            });\n            break;\n        case 'normal': {\n            // The sequence is drawn in a monospace font, so one character's width,\n            // which the caller measures, sizes every node.\n            const charWidth = config.charWidth;\n            nodes.forEach(node => {\n                node.width = node.sequenceLength;\n                const len = node.seq?.length ?? 1;\n                node.pixelWidth = Math.round(charWidth * len);\n            });\n            break;\n        }\n        default:\n            throw new Error(`${config.nodeWidthOption} not implemented`);\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() {\n    let nodeName;\n    let nodeName2;\n    // One set per node index, including the hole at 0 (Array.from materializes\n    // holes, unlike forEach/map).\n    const predSets = Array.from(nodes, () => new Set());\n    const succSets = Array.from(nodes, () => new Set());\n    let tracksAndReads;\n    if (config.showReads && reads.length > 0)\n        tracksAndReads = tracks.concat(reads);\n    else\n        tracksAndReads = tracks;\n    tracksAndReads.forEach(track => {\n        for (let i = 0; i < track.sequence.length; i += 1) {\n            if (!isReverse(track.sequence[i])) {\n                // forward Node\n                if (i > 0) {\n                    nodeName = track.sequence[i - 1];\n                    predSets[nodeMap.get(track.sequence[i])].add(nodeName);\n                    if (isReverse(nodeName)) {\n                        // add 2 predecessors, to make sure there is no node merging in this case\n                        predSets[nodeMap.get(track.sequence[i])].add(forward(nodeName));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    predSets[nodeMap.get(track.sequence[i])].add('None');\n                }\n                if (i < track.sequence.length - 1) {\n                    nodeName = track.sequence[i + 1];\n                    succSets[nodeMap.get(track.sequence[i])].add(nodeName);\n                    if (isReverse(nodeName)) {\n                        // add 2 successors, to make sure there is no node merging in this case\n                        succSets[nodeMap.get(track.sequence[i])].add(forward(nodeName));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    succSets[nodeMap.get(track.sequence[i])].add('None');\n                }\n            }\n            else {\n                // reverse Node\n                nodeName = forward(track.sequence[i]);\n                if (i > 0) {\n                    nodeName2 = track.sequence[i - 1];\n                    if (isReverse(nodeName2)) {\n                        succSets[nodeMap.get(nodeName)].add(forward(nodeName2));\n                    }\n                    else {\n                        // add 2 successors, to make sure there is no node merging in this case\n                        succSets[nodeMap.get(nodeName)].add(nodeName2);\n                        succSets[nodeMap.get(nodeName)].add(reverse(nodeName2));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    succSets[nodeMap.get(nodeName)].add('None');\n                }\n                if (i < track.sequence.length - 1) {\n                    nodeName2 = track.sequence[i + 1];\n                    if (isReverse(nodeName2)) {\n                        predSets[nodeMap.get(nodeName)].add(forward(nodeName2));\n                    }\n                    else {\n                        predSets[nodeMap.get(nodeName)].add(nodeName2);\n                        predSets[nodeMap.get(nodeName)].add(reverse(nodeName2));\n                    }\n                }\n                else if (track.type === 'haplotype') {\n                    predSets[nodeMap.get(nodeName)].add('None');\n                }\n            }\n        }\n    });\n    // convert sets to arrays\n    const pred = predSets.map(s => Array.from(s));\n    const succ = succSets.map(s => Array.from(s));\n    // update reads which pass through merging nodes\n    if (config.showReads && reads.length > 0) {\n        // sort nodes by order, then by y-coordinate\n        const sortedNodes = nodes.slice();\n        sortedNodes.sort(compareNodesByOrder);\n        // iterate over all nodes and calculate their position within the new merged node\n        // Both maps carry an entry for each orientation of every node name (\"7\"\n        // and \"-7\"), because the read update below looks up whichever orientation\n        // the read happens to visit.\n        const mergeOffset = new Map();\n        // maps to leftmost node of a node's \"merging cascade\"\n        const mergeOrigin = new Map();\n        const offsetOf = (nodeName) => {\n            const offset = mergeOffset.get(nodeName);\n            if (offset === undefined) {\n                throw new Error(`No merge offset recorded for node ${nodeName}`);\n            }\n            return offset;\n        };\n        const originOf = (nodeName) => {\n            const origin = mergeOrigin.get(nodeName);\n            if (origin === undefined) {\n                throw new Error(`No merge origin recorded for node ${nodeName}`);\n            }\n            return origin;\n        };\n        sortedNodes.forEach(node => {\n            const predecessor = mergeableWithPred(nodeMap.get(node.name), pred, succ);\n            if (predecessor) {\n                // Nodes are visited in order, so the predecessor of a merge cascade is\n                // always recorded before the node that follows it.\n                const offset = offsetOf(predecessor) + nodeByName(predecessor).sequenceLength;\n                mergeOffset.set(node.name, offset);\n                mergeOffset.set(reverse(node.name), offset);\n                mergeOrigin.set(node.name, originOf(predecessor));\n                mergeOrigin.set(reverse(node.name), originOf(predecessor));\n            }\n            else {\n                mergeOffset.set(node.name, 0);\n                mergeOffset.set(reverse(node.name), 0);\n                mergeOrigin.set(node.name, node.name);\n                mergeOrigin.set(reverse(node.name), node.name);\n            }\n        });\n        reads.forEach(read => {\n            const sequenceNew = read.sequenceNew ?? [];\n            read.firstNodeOffset =\n                (read.firstNodeOffset ?? 0) + offsetOf(read.sequence[0]);\n            read.finalNodeCoverLength =\n                (read.finalNodeCoverLength ?? 0) +\n                    offsetOf(read.sequence[read.sequence.length - 1]);\n            for (let i = read.sequence.length - 1; i >= 0; i -= 1) {\n                const nodeName = forward(read.sequence[i]);\n                const predecessor = mergeableWithPred(nodeMap.get(nodeName), pred, succ);\n                if (predecessor &&\n                    mergeableWithSucc(nodeMap.get(predecessor), pred, succ)) {\n                    if (i > 0) {\n                        read.sequence.splice(i, 1);\n                        // adjust position of mismatches\n                        const predLength = nodeByName(predecessor).sequenceLength;\n                        sequenceNew[i].mismatches.forEach(mismatch => {\n                            mismatch.pos += predLength;\n                        });\n                        // append mismatches to previous entry's mismatches\n                        sequenceNew[i - 1].mismatches = sequenceNew[i - 1].mismatches.concat(sequenceNew[i].mismatches);\n                        sequenceNew.splice(i, 1);\n                    }\n                    else {\n                        read.sequence[0] = originOf(read.sequence[0]);\n                        const firstEntry = sequenceNew[0];\n                        const firstOffset = offsetOf(firstEntry.nodeName);\n                        firstEntry.mismatches.forEach(mismatch => {\n                            mismatch.pos += firstOffset;\n                        });\n                        firstEntry.nodeName = originOf(firstEntry.nodeName);\n                    }\n                }\n            }\n        });\n    }\n    // update node sequences + sequence lengths\n    for (let i = 0; i < nodes.length; i += 1) {\n        if (mergeableWithSucc(i, pred, succ) && !mergeableWithPred(i, pred, succ)) {\n            let donor = i;\n            while (mergeableWithSucc(donor, pred, succ)) {\n                donor = nodeMap.get(forward(succ[donor][0]));\n                nodes[i].sequenceLength += nodes[donor].sequenceLength;\n                nodes[i].seq += nodes[donor].seq;\n            }\n        }\n    }\n    // actually merge the nodes by removing the corresponding nodes from track data\n    tracks.forEach(track => {\n        for (let i = track.sequence.length - 1; i >= 0; i -= 1) {\n            nodeName = forward(track.sequence[i]);\n            const nodeIndex = nodeMap.get(nodeName);\n            if (mergeableWithPred(nodeIndex, pred, succ)) {\n                track.sequence.splice(i, 1);\n            }\n        }\n    });\n    // remove the nodes from node-array\n    for (let i = nodes.length - 1; i >= 0; i -= 1) {\n        if (mergeableWithPred(i, pred, succ)) {\n            nodes.splice(i, 1);\n        }\n    }\n}\nfunction mergeableWithPred(index, pred, succ) {\n    if (pred[index].length !== 1)\n        return false;\n    if (pred[index][0] === 'None')\n        return false;\n    const predecessor = forward(pred[index][0]);\n    const predecessorIndex = nodeMap.get(predecessor);\n    if (succ[predecessorIndex].length !== 1)\n        return false;\n    if (succ[predecessorIndex][0] === 'None')\n        return false;\n    return predecessor;\n}\nfunction mergeableWithSucc(index, pred, succ) {\n    if (succ[index].length !== 1)\n        return false;\n    if (succ[index][0] === 'None')\n        return false;\n    const successor = forward(succ[index][0]);\n    const successorIndex = nodeMap.get(successor);\n    if (pred[successorIndex].length !== 1)\n        return false;\n    if (pred[successorIndex][0] === 'None')\n        return false;\n    return true;\n}\nfunction filterReads(readList) {\n    const focusNames = config.focusReadNames\n        ? new Set(config.focusReadNames)\n        : null;\n    return readList.filter(read => read.is_secondary !== true &&\n        (read.mapping_quality ?? 0) >= config.mappingQualityCutoff &&\n        (focusNames === null ||\n            (read.name !== undefined && focusNames.has(read.name))));\n}\n", "function groupBy(items, key) {\n    const groups = new Map();\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        }\n        else {\n            group.push(item);\n        }\n    }\n    return groups;\n}\nfunction compareCurvesByXYStartValue(a, b) {\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    return 0;\n}\n// The curves of one track type in draw order, each with its `path` set. Curves\n// between the same pair of nodes form a group whose control points fan out, so\n// a bundle of tracks changing lanes together stays parallel rather than\n// crossing at one x.\nexport function curvePaths(curves, type) {\n    const groupedCurves = groupBy(curves.filter(curve => curve.type === type), curve => `${curve.nodeStart},${curve.nodeEnd}`);\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        // 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        curveGroup.sort(compareCurvesByXYStartValue);\n        curveGroup.forEach(curve => {\n            let xAdjusted;\n            // NextAdjusted is used to try to draw a parallel curve on the way back\n            let xNextAdjusted;\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            }\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} ${curve.yStart + curve.width} ${curve.xStart} ${curve.yStart + curve.width}`;\n            d += ' Z';\n            curve.path = d;\n        });\n    });\n    // One flat list ordered by group, then by the within-group sort\n    const groupKeys = Array.from(groupedCurves.keys());\n    groupKeys.sort(function (a, b) {\n        const aParts = a.split(',').map(Number);\n        const bParts = b.split(',').map(Number);\n        const a0 = aParts[0] ?? 0;\n        const a1 = aParts[1] ?? 0;\n        const b0 = bParts[0] ?? 0;\n        const b1 = bParts[1] ?? 0;\n        if (a0 < b0) {\n            return -1;\n        }\n        else if (a0 > b0) {\n            return 1;\n        }\n        else {\n            if (a1 < b1) {\n                return -1;\n            }\n            else if (a1 > b1) {\n                return 1;\n            }\n            else {\n                return 0;\n            }\n        }\n    });\n    const flattenedGroups = [];\n    for (const key of groupKeys) {\n        const group = groupedCurves.get(key);\n        if (group !== undefined) {\n            flattenedGroups.push(...group);\n        }\n    }\n    return flattenedGroups;\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) {\n    // top left arc\n    let d = `M ${node.x - 9} ${node.y} Q ${node.x - 9} ${node.y - 9} ${node.x} ${node.y - 9}`;\n    let x = node.x;\n    let y = node.y - 9;\n    // top straight\n    if (node.width > 1) {\n        x += node.pixelWidth;\n        d += ` L ${x} ${y}`;\n    }\n    // top right arc\n    d += ` Q ${x + 9} ${y} ${x + 9} ${y + 9}`;\n    x += 9;\n    y += 9;\n    // right straight\n    if (node.contentHeight > 0) {\n        y += node.contentHeight - 0;\n        d += ` L ${x} ${y}`;\n    }\n    // bottom right arc\n    d += ` Q ${x} ${y + 9} ${x - 9} ${y + 9}`;\n    x -= 9;\n    y += 9;\n    // bottom straight\n    if (node.width > 1) {\n        x -= node.pixelWidth;\n        d += ` L ${x} ${y}`;\n    }\n    // bottom left arc\n    d += ` Q ${x - 9} ${y} ${x - 9} ${y - 9}`;\n    x -= 9;\n    y -= 9;\n    // left straight\n    if (node.contentHeight > 0) {\n        y -= node.contentHeight - 0;\n        d += ` L ${x} ${y}`;\n    }\n    return d;\n}\n", "import {\n  canonicalStrand,\n  readColor,\n  stepName,\n  tubeMapReads\n} from \"./chunk-TEDQJPMI.js\";\nimport {\n  pathCssColor,\n  pathGreyCssColor\n} from \"./chunk-X5L37W4J.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/layout/tubeMapLayout.ts\nimport { layoutTubeMap } from \"@gmod/tubemap-core\";\nfunction visitStrands(graph) {\n  const strands = /* @__PURE__ */ new Map();\n  for (const [segment, visits] of graph.pathVisits ?? []) {\n    for (const visit of visits) {\n      const key = `${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    trackColor: (track) => track.type === \"read\" ? readColor(track) : pathColors[track.id]\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  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", "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) {\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 * READOUT_ROOM,\n    maxY: walks.rows.length * 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  walkRowLayout\n};\n", "import {\n  hasTubeMapPaths,\n  tubeMapLayout,\n  tubeMapReferenceLayout\n} from \"./chunk-R6ZUK4Y3.js\";\nimport {\n  sampleRowLayout\n} from \"./chunk-LOEA5IHZ.js\";\nimport {\n  anchoredLayout\n} from \"./chunk-L3O7AWLI.js\";\nimport {\n  orderedLayout\n} from \"./chunk-HNQPEMYE.js\";\nimport {\n  walkRowLayout\n} from \"./chunk-EZPBJPK6.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", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_MAX_HUE,\n  hslToRgb\n} from \"./chunk-RX5CSWJW.js\";\nimport {\n  packAbgr\n} from \"./chunk-UMNCCYBN.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"rainbow\", label: \"Rainbow\" }\n];\nvar FAMILIES = [\"blue\", \"red\", \"purple\", \"green\"];\nvar isField = (v) => WALK_FIELDS.some((f) => f.value === v);\nvar isScheme = (v) => WALK_SCHEMES.some((s) => s.value === v);\nfunction resolveEncoding(layer, reference, picked, alone = true) {\n  const { field: askedField, scheme: askedScheme } = layer.color ?? {};\n  const field = isField(askedField) ? askedField : alone ? \"progress\" : \"walk\";\n  const family = reference ? \"grey\" : FAMILIES[picked % FAMILIES.length];\n  const scheme = isScheme(askedScheme) ? askedScheme === \"rainbow\" && field !== \"reference\" ? family : askedScheme : family;\n  return { field, scheme };\n}\nvar BASE_T = 0.5;\nvar toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;\nvar toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;\nfunction oklab(hex) {\n  const [r, g, b] = [1, 3, 5].map(\n    (i) => toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255)\n  );\n  const l = Math.cbrt(0.4122214708 * r + 0.5363325363 * g + 0.0514459929 * b);\n  const m = Math.cbrt(0.2119034982 * r + 0.6806995451 * g + 0.1073969566 * b);\n  const s = Math.cbrt(0.0883024619 * r + 0.2817188376 * g + 0.6299787005 * b);\n  return [\n    0.2104542553 * l + 0.793617785 * m - 0.0040720468 * s,\n    1.9779984951 * l - 2.428592205 * m + 0.4505937099 * s,\n    0.0259040371 * l + 0.7827717662 * m - 0.808675766 * s\n  ];\n}\nfunction oklabToRgb([L, a, b]) {\n  const l = (L + 0.3963377774 * a + 0.2158037573 * b) ** 3;\n  const m = (L - 0.1055613458 * a - 0.0638541728 * b) ** 3;\n  const s = (L - 0.0894841775 * a - 1.291485548 * b) ** 3;\n  return [\n    4.0767416621 * l - 3.3077115913 * m + 0.2309699292 * s,\n    -1.2684380046 * l + 2.6097574011 * m - 0.3413193965 * s,\n    -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s\n  ].map((c) => toGamma(Math.max(0, Math.min(1, c))) * 255);\n}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const family = WALK_SCHEMES.find((s) => s.value === scheme);\n  if (!family || !(\"ends\" in family)) {\n    return hslToRgb(x * REFERENCE_RAMP_MAX_HUE, 0.7, 0.5).map((c) => c * 255);\n  }\n  const from = oklab(family.ends[0]);\n  const to = oklab(family.ends[1]);\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));\n}\nfunction schemeCss(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor({ field, scheme }, t) {\n  return field === \"walk\" ? schemeColor(scheme, BASE_T) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops({ field, scheme }) {\n  return field === \"walk\" ? [{ offset: 0, color: schemeCss(scheme, BASE_T) }] : Array.from({ length: 7 }, (_, i) => ({\n    offset: i / 6,\n    color: schemeCss(scheme, i / 6)\n  }));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\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}\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  facetSettingOf,\n  facetCells\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}, ${pathCount} alleles`\n  };\n}\nvar BUBBLE_KIND_COLORS = {\n  snp: \"#5b6b7a\",\n  substitution: \"#5b6b7a\",\n  insertion: \"#2f8fd6\",\n  deletion: \"#c94040\",\n  inversion: \"#e07b00\",\n  repeat: \"#8e3fbf\",\n  superbubble: \"#8e3fbf\",\n  complex: \"#8e3fbf\"\n};\nvar BUBBLE_KIND_NAMES = {\n  snp: \"SNP\",\n  substitution: \"substitution\",\n  insertion: \"insertion\",\n  deletion: \"deletion\",\n  inversion: \"inversion\",\n  repeat: \"repeat array\",\n  superbubble: \"superbubble\",\n  complex: \"site\"\n};\nfunction bubbleSegmentIds(b) {\n  return b.segments.split(\",\").filter(Boolean);\n}\n\nexport {\n  formatBp,\n  classifyBubble,\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds\n};\n", "import {\n  RAMP_GRADIENT_CSS,\n  RAMP_GRADIENT_STOPS,\n  rampHueCss,\n  rampStops\n} from \"./chunk-ZHCDYSA5.js\";\nimport {\n  REFERENCE_RAMP_ALT_CSS\n} from \"./chunk-RX5CSWJW.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  el\n} from \"./chunk-NNODIW4U.js\";\n\n// src/layout/walkRowDraw.ts\nvar ON_REFERENCE = \"#2f8fd6\";\nvar OFF_REFERENCE = \"#8e3fbf\";\nvar OUTSIDE_CUT = \"#bdbdbd\";\nvar GENE_INK = \"#1c1c22\";\nvar BAR_PX = 12;\nvar GAP_PX = 4;\nvar MIN_TILE_PX = 3;\nfunction kb(bp) {\n  return `${(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 ${rowsText(o.genes.unread)}`,\n        note: true\n      });\n    }\n  }\n  return entries;\n}\nvar CALL_TICK = \"#111\";\nvar UNBACKED_TICK = \"#9e9e9e\";\nvar DISAGREES = \"#c62828\";\nfunction walkRowsKeyTree(entries, x, y, idPrefix = \"walk-key\") {\n  let at = 0;\n  const parts = entries.flatMap((e, i) => {\n    const rampId = `${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 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 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 ? 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 - 3,\n        width: 2,\n        height: barPx + 6,\n        fill: call.spanningReads === 0 ? UNBACKED_TICK : CALL_TICK\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  kb,\n  walkRowReadout,\n  readoutPlacement,\n  unitTicks,\n  runPaint,\n  alongRow,\n  rowSpan,\n  genesOnRow,\n  placeRowGenes,\n  boxesGenes,\n  rowGeneBoxes,\n  walkRowsKey,\n  DISAGREES,\n  walkRowsKeyTree,\n  coalesceRuns,\n  walkRowsTree\n};\n", "import {\n  alongRow,\n  boxesGenes\n} from \"./chunk-PJESIRDU.js\";\nimport {\n  pathOrigin\n} from \"./chunk-ST2IBUAN.js\";\nimport {\n  LABEL_CHAR_PX\n} from \"./chunk-AB35TJST.js\";\nimport {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\nimport {\n  el\n} from \"./chunk-NNODIW4U.js\";\n\n// src/layout/walkStrip.ts\nvar PAD_PX = 6;\nvar WALK_STRIP_CEILING_PX = 260;\nvar LABEL_FONT_PX = 11;\nvar MIN_ROW_PX = 3;\nvar LABELLED_ROW_PX = 12;\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 = Math.max(\n    MIN_ROW_PX,\n    Math.min(ROW_HEIGHT_PX, Math.floor((maxHeight - 2 * PAD_PX) / count))\n  );\n  const labelled = rowPx >= LABELLED_ROW_PX;\n  const readouts = rowPx >= 14;\n  const barPx = Math.max(2, Math.round(rowPx * 0.6));\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  WALK_STRIP_CEILING_PX,\n  LABELLED_ROW_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-UMNCCYBN.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}:${weight}`;\n    const group = into.get(key);\n    if (group) {\n      group.items.push(item);\n    } else {\n      into.set(key, { color, items: [item] });\n    }\n  }\n  return [...groups.values(), ...deferred.values()];\n}\n\nexport {\n  Canvas2DRenderer,\n  arrowheadOutline\n};\n", "import {\n  formatBp,\n  groupDigits\n} from \"./chunk-N62KBLFC.js\";\n\n// src/walkKey.ts\nfunction rangeText(contig, start, end) {\n  const s = Math.round(start);\n  const e = Math.round(end);\n  return `${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-N62KBLFC.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 \"@gmod/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-EJ5OZTCK.js\";\n\n// src/tubeMap/draw.ts\nimport { curvePaths, nodeOutlinePath } from \"@gmod/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, alpha, track) {\n  const commands = parsePath(d);\n  return { commands, color, track, alpha, ...extentOf(commands) };\n}\nfunction layerOf(layout, type) {\n  const { shapes } = layout;\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: r.color,\n    track: trackOf(r),\n    alpha: r.alpha ?? 1,\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, c.color, c.alpha ?? 1, trackOf(c))\n  );\n  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, c.color, 1, trackOf(c)));\n  return { rects, shapes: [...curves, ...corners] };\n}\nfunction tubeMapPicture(layout) {\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: [layerOf(layout, \"haplotype\"), layerOf(layout, \"read\")],\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 key = `${colorOf(item)}|${item.alpha}`;\n      const list = byColor.get(key);\n      if (list) {\n        list.push(item);\n      } else {\n        byColor.set(key, [item]);\n      }\n    }\n  }\n  for (const list of byColor.values()) {\n    ctx.fillStyle = colorOf(list[0]);\n    ctx.globalAlpha = list[0].alpha;\n    ctx.beginPath();\n    for (const item of list) {\n      addTo(item);\n    }\n    ctx.fill();\n  }\n  ctx.globalAlpha = 1;\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  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  tubeMapPicture,\n  drawTubeMap,\n  mismatchesLegible,\n  mismatchOnScreen\n};\n", "import {\n  tubeSpan\n} from \"./chunk-CS3E4ETM.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-RX5CSWJW.js\";\nimport {\n  abgrToCssRgba\n} from \"./chunk-UMNCCYBN.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');"],
+  "mappings": 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"right", "top", "agrees", "walkBp", "callBp", "nearest", "walks", "calls", "W", "C", "cost", "paired", "j", "together", "dropWalk", "dropCall", "out", "byLength", "items", "bp", "item", "i", "a", "b", "backed", "call", "scored", "row", "pairSample", "rows", "taken", "c", "unphased", "ranked", "r", "stages", "pool", "group", "free", "open", "pick", "k", "withCalls", "bySample", "sample", "called", "import_jsx_runtime", "Settings_default", "_jsx"]
+}