npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.4.2 → 7.4.3 - Mend

jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.3

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package/dist/chunks/{chunk-S75MFZDE.js.map → chunk-4I3K4RHE.js.map} RENAMED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-XTF2VWJN.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VX656OAZ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VB4IXIPM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-I5SGYTRM.js"],
-  "sourcesContent": ["// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  const t = Math.max(0, 1 - 1 / factor);\n  const lift = (v) => Math.round(v + (255 - v) * t);\n  return packAbgr(\n    lift(abgrRed(c)),\n    lift(abgrGreen(c)),\n    lift(abgrBlue(c)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "// src/referenceRampCss.ts\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nfunction rampHueCss(hue) {\n  return `hsl(${hue}, ${REFERENCE_RAMP_SATURATION * 100}%, ${REFERENCE_RAMP_LIGHTNESS * 100}%)`;\n}\nfunction rampHueAt(frac) {\n  return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;\n}\nfunction rampHue(bp, domain) {\n  return rampHueAt((bp - domain.start) / (domain.end - domain.start));\n}\nvar HUE_STOP_DEG = 30;\nfunction rampStops({ start, bp, reversed }, domain) {\n  const low = rampHue(start, domain);\n  const high = rampHue(start + bp, domain);\n  if (high - low < 1) {\n    return [(low + high) / 2];\n  }\n  const n = Math.ceil((high - low) / HUE_STOP_DEG);\n  return Array.from(\n    { length: n + 1 },\n    (_, i) => rampHue(start + bp * (reversed ? n - i : i) / n, domain)\n  );\n}\nvar RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({\n  offset: i / 6,\n  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)\n}));\nvar RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(\n  (s) => `${s.color} ${s.offset * 100}%`\n).join(\", \")})`;\n\nexport {\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_SATURATION,\n  REFERENCE_RAMP_LIGHTNESS,\n  rampHueCss,\n  rampHueAt,\n  rampHue,\n  rampStops,\n  RAMP_GRADIENT_STOPS,\n  RAMP_GRADIENT_CSS\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-5NZRT7GL.js\";\n\n// src/util/edgeCurves.ts\nvar cache = weakMemo();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  return cache(\n    nodePositions,\n    [graph, axis.scaleX, axis.scaleY, deletions, routes, stranded, version],\n    () => {\n      const curves = /* @__PURE__ */ new Map();\n      for (let ei = 0; ei < graph.edges.length; ei++) {\n        const bypassed = deletions?.get(ei);\n        const edgeCurves = edgeCurvesOf(\n          nodePositions,\n          graph.edges[ei],\n          axis,\n          bypassed,\n          bypassed && routes?.[ei],\n          stranded\n        );\n        if (edgeCurves) {\n          curves.set(ei, edgeCurves);\n        }\n      }\n      return curves;\n    }\n  );\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  for (const edge of graph.edges) {\n    pushTo(neighbors, edge.from, edge.to);\n    pushTo(neighbors, edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-XTF2VWJN.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-3UGWYQNY.js\";\nimport {\n  meanDepth,\n  nodeWidthPx,\n  walkLaneWidthPx\n} from \"./chunk-ZANALBSX.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  polylinePx,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-VACK24HF.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, scale * yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\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 normal(a, b) {\n  if (!a || !b) {\n    return void 0;\n  }\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  const len = Math.hypot(dx, dy);\n  return len > 0 ? { nx: -dy / len, ny: dx / len } : void 0;\n}\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  return points.map((p, i) => {\n    const before = normal(points[i - 1], p);\n    const after = normal(p, points[i + 1]);\n    if (before && after) {\n      const nx = (before.nx + after.nx) / 2;\n      const ny = (before.ny + after.ny) / 2;\n      const dot = before.nx * nx + before.ny * ny;\n      return dot > 0.1 ? { nx: nx / dot, ny: ny / dot } : { nx, ny };\n    }\n    return before ?? after ?? { nx: 0, ny: 0 };\n  });\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  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 hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nfunction packHsl(h, s, l, a = 1) {\n  const [r, g, b] = hslToRgb(h, s, l);\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  return packHsl(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS, alpha);\n}\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction rampFraction(node, ramp) {\n  const mid = ramp.midpoints.get(node.id);\n  return isBackbone(node) && mid !== void 0 ? (mid - ramp.start) / ramp.span : void 0;\n}\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph, referenceRamp) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length,\n    referenceRamp\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state, so only the backbone takes a hue\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      if (ramp === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      const t = rampFraction(node, ramp);\n      return t === void 0 ? REFERENCE_RAMP_ALT_COLOR : packHsl(\n        rampHueAt(t),\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      return packHsl(hue, 0.75, 0.5);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds) {\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      pathColorByIndex.push(\n        packHsl(\n          pathHueAt(i, paths.length),\n          PATH_SATURATION,\n          PATH_LIGHTNESS,\n          0.85\n        )\n      );\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        pushTo(slots, nodeId, pathIdx);\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\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 worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = computeColorSchemeRange(graph, referenceRamp);\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const 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 inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);\n    const stroke = (curves, thickness, color) => {\n      if (isDeletion) {\n        for (const dash of dashCurves(\n          curves,\n          DELETION_DASH_PX / scale,\n          yToX,\n          viewportBounds\n        )) {\n          edgeCurves.push({ curves: dash, thickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness, color });\n      }\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: edgeColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight?.walks.length && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = walkLaneWidthPx(width, laneWalks.length);\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      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 (inView(curves)) {\n          stroke(\n            curves,\n            laneWidth / 2,\n            walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\n          );\n        }\n      });\n      if (edgeCurves.length > edgeCurveStart) {\n        arrowOn(baseCurves);\n      }\n    } else if (!ribbons) {\n      if (inView(baseCurves)) {\n        stroke(baseCurves, edgeThickness, edgeColor);\n        arrowOn(baseCurves);\n      }\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const { x, y } = offsets[pathIdx];\n        const curves = x === 0 && y === 0 ? baseCurves : translateCurves(baseCurves, x, y);\n        if (!inView(curves)) {\n          continue;\n        }\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        stroke(\n          curves,\n          edgeThickness,\n          highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor\n        );\n        if (pathIdx === arrowRibbon) {\n          arrowOn(curves);\n        }\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = walkLaneWidthPx(width, lanes.length);\n      const normals = pointNormalsOf(segments, yToX);\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      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  rampFraction,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  hslToRgb\n} from \"./chunk-VB4IXIPM.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"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}\nvar endsCache = /* @__PURE__ */ new Map();\nfunction oklabEnds(scheme) {\n  if (!endsCache.has(scheme)) {\n    const family = WALK_SCHEMES.find((s) => s.value === scheme);\n    endsCache.set(\n      scheme,\n      family && \"ends\" in family ? family.ends.map(oklab) : void 0\n    );\n  }\n  return endsCache.get(scheme);\n}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const ends = oklabEnds(scheme);\n  if (!ends) {\n    return hslToRgb(\n      rampHueAt(x),\n      REFERENCE_RAMP_SATURATION,\n      REFERENCE_RAMP_LIGHTNESS\n    ).map((c) => c * 255);\n  }\n  const [from, to] = ends;\n  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  const stop = (offset, t) => ({\n    offset,\n    color: schemeCss(scheme, t),\n    abgr: schemeColor(scheme, t)\n  });\n  return field === \"walk\" ? [stop(0, BASE_T)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, i / 6));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-GQZVR5DW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-33KUO34R.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VX656OAZ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VXKL2ZLR.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-6RB5ZQ34.js"],
+  "sourcesContent": ["// src/renderer/colorBits.ts\nfunction packAbgr(r, g, b, a) {\n  return (a << 24 | b << 16 | g << 8 | r) >>> 0;\n}\nfunction abgrRed(c) {\n  return c & 255;\n}\nfunction abgrGreen(c) {\n  return c >>> 8 & 255;\n}\nfunction abgrBlue(c) {\n  return c >>> 16 & 255;\n}\nfunction abgrAlpha(c) {\n  return c >>> 24 & 255;\n}\nfunction abgrToCssRgba(c) {\n  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;\n}\nfunction normalizedRgbToCssRgba(c, alpha) {\n  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;\n}\nfunction fadeAbgr(c, alpha) {\n  return packAbgr(\n    abgrRed(c),\n    abgrGreen(c),\n    abgrBlue(c),\n    Math.round(abgrAlpha(c) * alpha)\n  );\n}\nfunction brightenAbgr(c, factor) {\n  const t = Math.max(0, 1 - 1 / factor);\n  const lift = (v) => Math.round(v + (255 - v) * t);\n  return packAbgr(\n    lift(abgrRed(c)),\n    lift(abgrGreen(c)),\n    lift(abgrBlue(c)),\n    abgrAlpha(c)\n  );\n}\n\nexport {\n  packAbgr,\n  abgrRed,\n  abgrGreen,\n  abgrBlue,\n  abgrAlpha,\n  abgrToCssRgba,\n  normalizedRgbToCssRgba,\n  fadeAbgr,\n  brightenAbgr\n};\n", "// src/referenceRampCss.ts\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nfunction rampHueCss(hue) {\n  return `hsl(${hue}, ${REFERENCE_RAMP_SATURATION * 100}%, ${REFERENCE_RAMP_LIGHTNESS * 100}%)`;\n}\nfunction rampHueAt(frac) {\n  return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;\n}\nfunction rampHue(bp, domain) {\n  return rampHueAt((bp - domain.start) / (domain.end - domain.start));\n}\nvar HUE_STOP_DEG = 30;\nfunction rampStops({ start, bp, reversed }, domain) {\n  const low = rampHue(start, domain);\n  const high = rampHue(start + bp, domain);\n  if (high - low < 1) {\n    return [(low + high) / 2];\n  }\n  const n = Math.ceil((high - low) / HUE_STOP_DEG);\n  return Array.from(\n    { length: n + 1 },\n    (_, i) => rampHue(start + bp * (reversed ? n - i : i) / n, domain)\n  );\n}\nvar RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({\n  offset: i / 6,\n  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)\n}));\nvar RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(\n  (s) => `${s.color} ${s.offset * 100}%`\n).join(\", \")})`;\n\nexport {\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_SATURATION,\n  REFERENCE_RAMP_LIGHTNESS,\n  rampHueCss,\n  rampHueAt,\n  rampHue,\n  rampStops,\n  RAMP_GRADIENT_STOPS,\n  RAMP_GRADIENT_CSS\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-P276TWPM.js\";\n\n// src/util/edgeCurves.ts\nvar cache = weakMemo();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  return cache(\n    nodePositions,\n    [graph, axis.scaleX, axis.scaleY, deletions, routes, stranded, version],\n    () => {\n      const curves = /* @__PURE__ */ new Map();\n      for (let ei = 0; ei < graph.edges.length; ei++) {\n        const bypassed = deletions?.get(ei);\n        const edgeCurves = edgeCurvesOf(\n          nodePositions,\n          graph.edges[ei],\n          axis,\n          bypassed,\n          bypassed && routes?.[ei],\n          stranded\n        );\n        if (edgeCurves) {\n          curves.set(ei, edgeCurves);\n        }\n      }\n      return curves;\n    }\n  );\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  for (const edge of graph.edges) {\n    pushTo(neighbors, edge.from, edge.to);\n    pushTo(neighbors, edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-33KUO34R.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-GD6RUZU5.js\";\nimport {\n  meanDepth,\n  nodeWidthPx,\n  walkLaneWidthPx\n} from \"./chunk-ZANALBSX.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-VX656OAZ.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  polylinePx,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-VACK24HF.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, scale * yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\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 normal(a, b) {\n  if (!a || !b) {\n    return void 0;\n  }\n  const dx = b.x - a.x;\n  const dy = b.y - a.y;\n  const len = Math.hypot(dx, dy);\n  return len > 0 ? { nx: -dy / len, ny: dx / len } : void 0;\n}\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  return points.map((p, i) => {\n    const before = normal(points[i - 1], p);\n    const after = normal(p, points[i + 1]);\n    if (before && after) {\n      const nx = (before.nx + after.nx) / 2;\n      const ny = (before.ny + after.ny) / 2;\n      const dot = before.nx * nx + before.ny * ny;\n      return dot > 0.1 ? { nx: nx / dot, ny: ny / dot } : { nx, ny };\n    }\n    return before ?? after ?? { nx: 0, ny: 0 };\n  });\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  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 hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nfunction packHsl(h, s, l, a = 1) {\n  const [r, g, b] = hslToRgb(h, s, l);\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  return packHsl(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS, alpha);\n}\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction rampFraction(node, ramp) {\n  const mid = ramp.midpoints.get(node.id);\n  return isBackbone(node) && mid !== void 0 ? (mid - ramp.start) / ramp.span : void 0;\n}\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph, referenceRamp) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length,\n    referenceRamp\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state, so only the backbone takes a hue\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      if (ramp === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      const t = rampFraction(node, ramp);\n      return t === void 0 ? REFERENCE_RAMP_ALT_COLOR : packHsl(\n        rampHueAt(t),\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      return packHsl(hue, 0.75, 0.5);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds) {\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      pathColorByIndex.push(\n        packHsl(\n          pathHueAt(i, paths.length),\n          PATH_SATURATION,\n          PATH_LIGHTNESS,\n          0.85\n        )\n      );\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        pushTo(slots, nodeId, pathIdx);\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\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 worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = computeColorSchemeRange(graph, referenceRamp);\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const 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 inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);\n    const stroke = (curves, thickness, color) => {\n      if (isDeletion) {\n        for (const dash of dashCurves(\n          curves,\n          DELETION_DASH_PX / scale,\n          yToX,\n          viewportBounds\n        )) {\n          edgeCurves.push({ curves: dash, thickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness, color });\n      }\n    };\n    const arrowOn = (curves) => {\n      const head = showArrows ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: edgeColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight?.walks.length && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = walkLaneWidthPx(width, laneWalks.length);\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      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 (inView(curves)) {\n          stroke(\n            curves,\n            laneWidth / 2,\n            walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\n          );\n        }\n      });\n      if (edgeCurves.length > edgeCurveStart) {\n        arrowOn(baseCurves);\n      }\n    } else if (!ribbons) {\n      if (inView(baseCurves)) {\n        stroke(baseCurves, edgeThickness, edgeColor);\n        arrowOn(baseCurves);\n      }\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const { x, y } = offsets[pathIdx];\n        const curves = x === 0 && y === 0 ? baseCurves : translateCurves(baseCurves, x, y);\n        if (!inView(curves)) {\n          continue;\n        }\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        stroke(\n          curves,\n          edgeThickness,\n          highlight && (highlight.walks.length ? !highlight.names.has(edge.pathIds[pathIdx]) : !onWalk) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor\n        );\n        if (pathIdx === arrowRibbon) {\n          arrowOn(curves);\n        }\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = walkLaneWidthPx(width, lanes.length);\n      const normals = pointNormalsOf(segments, yToX);\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      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  rampFraction,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  hslToRgb\n} from \"./chunk-VXKL2ZLR.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  REFERENCE_RAMP_LIGHTNESS,\n  REFERENCE_RAMP_SATURATION,\n  rampHueAt\n} from \"./chunk-GQZVR5DW.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"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}\nvar endsCache = /* @__PURE__ */ new Map();\nfunction oklabEnds(scheme) {\n  if (!endsCache.has(scheme)) {\n    const family = WALK_SCHEMES.find((s) => s.value === scheme);\n    endsCache.set(\n      scheme,\n      family && \"ends\" in family ? family.ends.map(oklab) : void 0\n    );\n  }\n  return endsCache.get(scheme);\n}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const ends = oklabEnds(scheme);\n  if (!ends) {\n    return hslToRgb(\n      rampHueAt(x),\n      REFERENCE_RAMP_SATURATION,\n      REFERENCE_RAMP_LIGHTNESS\n    ).map((c) => c * 255);\n  }\n  const [from, to] = ends;\n  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  const stop = (offset, t) => ({\n    offset,\n    color: schemeCss(scheme, t),\n    abgr: schemeColor(scheme, t)\n  });\n  return field === \"walk\" ? [stop(0, BASE_T)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, i / 6));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
   "mappings": 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package/dist/chunks/{chunk-MEMUEG5Z.js → chunk-6OXXT2YP.js} RENAMED Viewed

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+//# sourceMappingURL=chunk-6OXXT2YP.js.map

package/dist/chunks/{chunk-MEMUEG5Z.js.map → chunk-6OXXT2YP.js.map} RENAMED Viewed

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LG2UK4MB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-7L7MN2OM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G7SG4XMK.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LG2UK4MB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-7L7MN2OM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G7SG4XMK.js"],
   "sourcesContent": ["// src/gfa/walkStops.ts\nvar START_STOP_TAG = \"ws\";\nvar END_STOP_TAG = \"we\";\nvar STOP_KINDS = [\"elsewhere\", \"break\", \"end\"];\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  unknown: \"gap, cause unknown\",\n  abridged: \"abridged: steps not loaded\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(bp, after, before) {\n  if (!after && !before) {\n    return [{ bp }];\n  }\n  const left = Math.min(after?.trimmed ?? 0, bp);\n  const right = Math.min(before?.trimmed ?? 0, bp - left);\n  let rest = bp - left - right;\n  const lead = after?.kind === \"break\" ? Math.min(after.bp, rest) : 0;\n  rest -= lead;\n  const trail = before?.kind === \"break\" ? Math.min(before.bp, rest) : 0;\n  rest -= trail;\n  const elsewhere = [after, before].find((s) => s?.kind === \"elsewhere\");\n  const parts = [\n    { bp: left },\n    { bp: lead, cause: \"missing\" },\n    elsewhere?.kind === \"elsewhere\" ? { bp: rest, cause: \"elsewhere\", chunk: elsewhere.chunk } : { bp: rest, cause: \"unknown\" },\n    { bp: trail, cause: \"missing\" },\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\nfunction stopAt(table, i) {\n  const bp = table.bp[i];\n  const ref = table.chunkRefs[i];\n  return stopOf(\n    table.kindNames[table.kinds[i]],\n    Number.isNaN(bp) ? void 0 : bp,\n    table.trimmed[i],\n    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }\n  );\n}\nfunction stopOf(kind, bp, trimmed, chunk) {\n  const cut = trimmed > 0 ? { trimmed } : {};\n  if (kind === \"elsewhere\" && chunk) {\n    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };\n  }\n  if (kind === \"break\" && bp !== void 0) {\n    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };\n  }\n  return kind === \"end\" ? { kind, ...cut } : void 0;\n}\nfunction stopTag(stop) {\n  const parts = [stop.kind];\n  if (\"bp\" in stop && stop.bp !== void 0) {\n    parts.push(`bp=${stop.bp}`);\n  }\n  if (stop.trimmed) {\n    parts.push(`trimmed=${stop.trimmed}`);\n  }\n  if (\"chunk\" in stop && stop.chunk) {\n    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);\n  }\n  return parts.join(\",\");\n}\nfunction parseStopTag(value) {\n  const [kind, ...fields] = value.split(\",\");\n  let bp;\n  let trimmed = 0;\n  let chunk;\n  for (const field of fields) {\n    if (field.startsWith(\"bp=\")) {\n      bp = +field.slice(3);\n    } else if (field.startsWith(\"trimmed=\")) {\n      trimmed = +field.slice(8);\n    } else if (field.startsWith(\"chunk=\")) {\n      const at = field.lastIndexOf(\":\");\n      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };\n    }\n  }\n  return stopOf(kind, bp, trimmed, chunk);\n}\nfunction stopFields(before, after) {\n  return {\n    ...before ? { before } : {},\n    ...after ? { after } : {}\n  };\n}\nfunction walkStopFields(tags) {\n  const before = tags[START_STOP_TAG];\n  const after = tags[END_STOP_TAG];\n  return stopFields(\n    typeof before === \"string\" ? parseStopTag(before) : void 0,\n    typeof after === \"string\" ? parseStopTag(after) : void 0\n  );\n}\nfunction walkStopTags(walks, p) {\n  const tags = [];\n  for (const [tag, table] of [\n    [START_STOP_TAG, walks.before],\n    [END_STOP_TAG, walks.after]\n  ]) {\n    const stop = table && stopAt(table, p);\n    if (stop) {\n      tags.push(`\t${tag}:Z:${stopTag(stop)}`);\n    }\n  }\n  return tags.join(\"\");\n}\nvar StopColumns = class {\n  constructor() {\n    this.kinds = [];\n    this.bp = [];\n    this.trimmed = [];\n    this.chunkRefs = [];\n    this.chunkStarts = [];\n    this.chunkRefNames = [];\n    this.refIndex = /* @__PURE__ */ new Map();\n  }\n  push(stop) {\n    this.kinds.push(STOP_KINDS.indexOf(stop.kind));\n    this.bp.push(\"bp\" in stop && stop.bp !== void 0 ? stop.bp : NaN);\n    this.trimmed.push(stop.trimmed ?? 0);\n    const chunk = \"chunk\" in stop ? stop.chunk : void 0;\n    if (chunk) {\n      let ref = this.refIndex.get(chunk.refName);\n      if (ref === void 0) {\n        ref = this.chunkRefNames.length;\n        this.refIndex.set(chunk.refName, ref);\n        this.chunkRefNames.push(chunk.refName);\n      }\n      this.chunkRefs.push(ref);\n      this.chunkStarts.push(chunk.start);\n    } else {\n      this.chunkRefs.push(-1);\n      this.chunkStarts.push(NaN);\n    }\n  }\n  table() {\n    return {\n      kinds: Uint8Array.from(this.kinds),\n      kindNames: [...STOP_KINDS],\n      bp: Float64Array.from(this.bp),\n      trimmed: Float64Array.from(this.trimmed),\n      chunkRefs: Int32Array.from(this.chunkRefs),\n      chunkStarts: Float64Array.from(this.chunkStarts),\n      chunkRefNames: this.chunkRefNames\n    };\n  }\n};\n\nexport {\n  START_STOP_TAG,\n  END_STOP_TAG,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts,\n  stopAt,\n  stopTag,\n  parseStopTag,\n  stopFields,\n  walkStopFields,\n  walkStopTags,\n  StopColumns\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  PathVisits\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...stopFields(\n      w.before && stopAt(w.before, p),\n      w.after && stopAt(w.after, p)\n    ),\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-7L7MN2OM.js\";\nimport {\n  gapParts\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  pathOrigin\n} from \"./chunk-3YBP46PB.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"unknown\",\n  \"abridged\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  for (const node of graph.nodes) {\n    lengths[indexOf(node.id)] = node.length;\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference: referenceWalkName(graph)\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference: referenceOf(\n      heads.map((h) => pathOrigin(h.name).name),\n      referencePath,\n      rankZero\n    )\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  if (first === void 0 || others.length === 0) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let reachesBefore = false;\n  let reachesAfter = false;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        if (cut) {\n          reachesBefore ||= pos + len <= cut.start;\n          reachesAfter ||= pos >= cut.end;\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || reachesBefore && reachesAfter;\n  const runs = new Columns(5);\n  const chunks = [];\n  const chunkIndex = /* @__PURE__ */ new Map();\n  const chunkOf = (chunk2) => {\n    if (!chunk2) {\n      return -1;\n    }\n    const key = `${chunk2.refName}:${chunk2.start}`;\n    let i = chunkIndex.get(key);\n    if (i === void 0) {\n      i = chunks.length;\n      chunkIndex.set(key, i);\n      chunks.push(chunk2);\n    }\n    return i;\n  };\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const rowOf = (pieces) => {\n    const head = heads[pieces[0]];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      if (start2 === void 0 || end !== void 0 && start2 < end) {\n        unplaced = true;\n      }\n      if (end !== void 0 && start2 !== void 0 && start2 > end) {\n        partsAt.set(\n          length,\n          gapParts(\n            start2 - end,\n            previous === void 0 ? void 0 : heads[previous].after,\n            heads[piece].before\n          )\n        );\n        steps[length] = -(start2 - end);\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const partialSide = (i0, i1) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      let near = -1;\n      for (let d = 1; near < 0 && d < length; d++) {\n        near = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      if (near < 0) {\n        return void 0;\n      }\n      const forward = near > flank === spanStart[steps[near]] > spanStart[steps[flank]];\n      const after = forward === (flank === i0);\n      const last2 = after ? length - 1 : 0;\n      const contigEnds = onReference(last2);\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0\n      };\n      return {\n        stop: stop2,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward ? after ? stepEnd(flank) : stepStart[0] : after ? stepEnd(length - 1) : stepStart[flank]\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const id = steps[i];\n        if (id >= 0 && !Number.isNaN(spanStart[id])) {\n          if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {\n            bestEnd = spanEnd[id];\n            i0 = i;\n          }\n          if (spanStart[id] >= cut.end && spanStart[id] < bestStart) {\n            bestStart = spanStart[id];\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false;\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : void 0;\n        if (inside) {\n          ;\n          ({ lo, hi, backward, axisStart, stop } = inside);\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? { contig, start: stepEnd(flankFrom), reversed: false } : { contig, start: stepStart[flankFrom], reversed: true };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      if (id < 0) {\n        const parts = partsAt.get(index);\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            chunkOf(part.chunk)\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, -1);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    runs.endRow();\n    visits?.endRow();\n    return {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {}\n    };\n  };\n  const referenceRow = rowOf(referencePieces);\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces),\n    row: i + 1\n  }));\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    (n) => new Int32Array(n)\n  ]);\n  const [start, bp, referenceStart, flags, chunk] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    chunk,\n    chunks,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const chunk = t.chunks[t.chunk[k]];\n    if (chunk) {\n      run.chunk = chunk;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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package/dist/chunks/{chunk-U5PIXAF2.js.map → chunk-CNNZDE6I.js.map} RENAMED Viewed

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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZPZ7GNBT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-3YBP46PB.js"],
   "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n", "import {\n  PathVisitsBuilder\n} from \"./chunk-ZPZ7GNBT.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  REFERENCE_RANK\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathAnchoring.ts\nvar RANGE_SUFFIX = /:(\\d+)-\\d+$/;\nvar VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\\d+)(?:\\[(\\d+)-\\d+\\])?$/;\nvar VG_SUBRANGE = /\\[(\\d+)-\\d+\\]$/;\nfunction pathOrigin(pathName) {\n  const fragment = VG_FRAGMENT.exec(pathName);\n  if (fragment) {\n    return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };\n  }\n  const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);\n  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };\n}\nfunction surveyPaths(paths, lengthOf) {\n  const anchorPaths = [];\n  const visits = new PathVisitsBuilder();\n  for (const path of paths) {\n    const sample = panSNSample(path.name);\n    const p = visits.pathOf(path.name, sample);\n    let pos = path.start;\n    for (const step of path.steps) {\n      visits.addAt(visits.declare(step.id), p, pos, step.strand === \"-\");\n      pos += lengthOf(step.id);\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start\n    });\n  }\n  return { anchorPaths, pathVisits: visits.build() };\n}\nfunction chooseReferencePath(anchorPaths, preferred) {\n  const named = anchorPaths.find(\n    (p) => p.sample === preferred || p.name === preferred\n  );\n  return named ?? anchorPaths[0];\n}\nvar OFF_REFERENCE_RANK = 1;\nfunction anchorNode(node, visits, reference, samplesOf) {\n  const slot = visits.slot(node.name);\n  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {\n    return node;\n  }\n  const own = visits.firstBy(slot, reference);\n  const anchor = own >= 0 ? own : visits.offsets[slot];\n  return {\n    ...node,\n    stable: {\n      refName: visits.paths[visits.path[anchor]],\n      start: visits.start[anchor],\n      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n      strand: visits.strand(anchor)\n    },\n    samples: samplesOf(slot)\n  };\n}\nfunction sampleSorter(visits) {\n  const sorted = [...new Set(visits.samples)].sort();\n  const rank = new Map(sorted.map((sample, i) => [sample, i]));\n  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));\n  const seen = new Uint8Array(sorted.length);\n  const ranks = new Int32Array(sorted.length);\n  return (slot) => {\n    let n = 0;\n    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {\n      const r = pathRank[visits.path[i]];\n      if (seen[r] === 0) {\n        seen[r] = 1;\n        ranks[n++] = r;\n      }\n    }\n    let out;\n    if (n === sorted.length) {\n      out = sorted;\n      seen.fill(0);\n    } else if (n * 8 < sorted.length) {\n      const found = ranks.subarray(0, n);\n      found.forEach((r) => seen[r] = 0);\n      out = Array.from(found.sort(), (r) => sorted[r]);\n    } else {\n      out = [];\n      for (let r = 0; r < sorted.length; r++) {\n        if (seen[r] === 1) {\n          seen[r] = 0;\n          out.push(sorted[r]);\n        }\n      }\n    }\n    return out;\n  };\n}\nfunction anchorFromPaths(graph, preferred) {\n  const { anchorPaths, pathVisits } = graph;\n  const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;\n  if (!reference || !anchorPaths || !pathVisits) {\n    return graph;\n  }\n  const samplesOf = sampleSorter(pathVisits);\n  const referenceIndex = pathVisits.pathIndex(reference.name);\n  return {\n    ...graph,\n    nodes: graph.nodes.map(\n      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)\n    ),\n    anchoredBy: \"paths\",\n    referencePath: reference.name\n  };\n}\nfunction anchorGraph(graph, preferred) {\n  if (graph.anchoredBy !== \"tags\") {\n    return anchorFromPaths(graph, preferred);\n  }\n  const referencePath = taggedReferencePath(graph);\n  return referencePath ? { ...graph, referencePath } : graph;\n}\nfunction taggedReferencePath(graph) {\n  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;\n  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;\n}\nfunction trimOrigins(graph, kept) {\n  if (!graph.anchorPaths) {\n    return void 0;\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const bp = (ids, end = ids.length) => {\n    let sum = 0;\n    for (let i = 0; i < end; i++) {\n      sum += lengthOf.get(ids[i]) ?? 0;\n    }\n    return sum;\n  };\n  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);\n  return graph.anchorPaths.map((o) => {\n    const pieces = byOrigin.get(o.name);\n    const path = pieces?.length === 1 ? pieces[0] : void 0;\n    const stretch = path && kept.get(path.name);\n    return path && stretch ? {\n      ...o,\n      start: o.start + bp(path.nodeIds, stretch.first),\n      length: bp(stretch.nodeIds)\n    } : o;\n  });\n}\nfunction referenceVisitStarts(graph) {\n  const { pathVisits } = graph;\n  const cache = /* @__PURE__ */ new Map();\n  return (node) => {\n    let starts = cache.get(node.id);\n    if (!starts) {\n      starts = [];\n      const slot = pathVisits ? pathVisits.slot(node.name) : -1;\n      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;\n      if (p >= 0) {\n        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {\n          if (pathVisits.path[i] === p) {\n            starts.push(pathVisits.start[i]);\n          }\n        }\n      }\n      if (starts.length < 2) {\n        starts = [node.stable.start];\n      }\n      cache.set(node.id, starts);\n    }\n    return starts;\n  };\n}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins,\n  referenceVisitStarts\n};\n"],
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