jbrowse-plugin-graphgenomeviewer 7.2.0 → 7.3.0

package/dist/chunks/chunk-PA4HKAUJ.js

@@ -1,2 +0,0 @@
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-  "sourcesContent": ["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-4XWZNPQ2.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}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins\n};\n", "// src/util/weakMemo.ts\nfunction weakMemo() {\n  const cache = /* @__PURE__ */ new WeakMap();\n  return (key, deps, compute) => {\n    const hit = cache.get(key);\n    if (hit?.deps.length === deps.length && hit.deps.every((d, i) => Object.is(d, deps[i]))) {\n      return hit.value;\n    }\n    const value = compute();\n    cache.set(key, { deps, value });\n    return value;\n  };\n}\n\nexport {\n  weakMemo\n};\n", "// src/overlayLabels.ts\nvar LABEL_PX = 11;\nvar LABEL_CHAR_PX = 6.2;\nvar LABEL_PAD = 4;\nfunction labelWidth(text) {\n  return text.length * LABEL_CHAR_PX + LABEL_PAD * 2;\n}\nfunction overlaps(a, b) {\n  return a.x0 < b.x1 && a.x1 > b.x0 && a.y0 < b.y1 && a.y1 > b.y0;\n}\nfunction offFrame(box, frame) {\n  return box.x1 <= 0 || box.x0 >= frame.width || box.y1 <= 0 || box.y0 >= frame.height;\n}\nfunction insideFrame(box, frame) {\n  return box.x0 >= 0 && box.x1 <= frame.width && box.y0 >= 0 && box.y1 <= frame.height;\n}\nfunction occupancy(frame, reserved = []) {\n  const placed = [...reserved];\n  return (box) => {\n    if (offFrame(box, frame) || placed.some((p) => overlaps(p, box))) {\n      return false;\n    }\n    placed.push(box);\n    return true;\n  };\n}\nfunction placeLabels(candidates, frame, take) {\n  const out = [];\n  const row = LABEL_PX + LABEL_PAD * 2;\n  const place = (c, text) => {\n    const w = labelWidth(text);\n    const direction = c.y > frame.height / 2 ? -1 : 1;\n    for (let tries = 0; tries <= (c.stack ?? 0); tries++) {\n      const y = c.y + direction * tries * row;\n      const box = {\n        x0: c.x - w / 2,\n        x1: c.x + w / 2,\n        y0: y - LABEL_PX - LABEL_PAD,\n        y1: y + LABEL_PAD\n      };\n      if (offFrame(box, frame)) {\n        return void 0;\n      }\n      if (insideFrame(box, frame) && (c.fits?.(box) ?? true) && take(box)) {\n        return { ...c, text, y, w };\n      }\n    }\n    return void 0;\n  };\n  for (const c of candidates) {\n    const placed = place(c, c.text) ?? (c.fallback === void 0 ? void 0 : place(c, c.fallback));\n    if (placed) {\n      out.push(placed);\n    }\n  }\n  return out;\n}\n\nexport {\n  LABEL_PX,\n  LABEL_CHAR_PX,\n  LABEL_PAD,\n  labelWidth,\n  overlaps,\n  occupancy,\n  placeLabels\n};\n", "// src/layout/rowSpacing.ts\nvar ROW_HEIGHT_PX = 20;\n\nexport {\n  ROW_HEIGHT_PX\n};\n", "import {\n  ROW_HEIGHT_PX\n} from \"./chunk-CPMHA4W5.js\";\n\n// src/util/geometry.ts\nfunction svgPath(points) {\n  const round = (v) => Math.round(v * 100) / 100;\n  return points.map((p, i) => `${i ? \"L\" : \"M\"}${round(p.x)},${round(p.y)}`).join(\"\");\n}\nfunction projectLine(x1, y1, x2, y2, distance) {\n  const d = Math.hypot(y2 - y1, x2 - x1);\n  if (d === 0) {\n    return [x2, y2];\n  }\n  const vx = (x2 - x1) / d;\n  const vy = (y2 - y1) / d;\n  return [x2 + distance * vx, y2 + distance * vy];\n}\nfunction curvePointAt(c, t) {\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  return {\n    x: a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1,\n    y: a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1\n  };\n}\nfunction curveMidpoint(curves) {\n  const mid = curves[Math.floor(curves.length / 2)];\n  return mid ? curvePointAt(mid, 0.5) : void 0;\n}\nfunction curveBounds(curves) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const c of curves) {\n    minX = Math.min(minX, c.x0, c.cx0, c.cx1, c.x1);\n    maxX = Math.max(maxX, c.x0, c.cx0, c.cx1, c.x1);\n    minY = Math.min(minY, c.y0, c.cy0, c.cy1, c.y1);\n    maxY = Math.max(maxY, c.y0, c.cy0, c.cy1, c.y1);\n  }\n  return { minX, minY, maxX, maxY };\n}\nfunction subCurve(c, t0, t1) {\n  const p0 = curvePointAt(c, t0);\n  const p1 = curvePointAt(c, t1);\n  const dt = (t1 - t0) / 3;\n  const d0 = curveTangentAt(c, t0);\n  const d1 = curveTangentAt(c, t1);\n  return {\n    x0: p0.x,\n    y0: p0.y,\n    cx0: p0.x + d0.x * dt,\n    cy0: p0.y + d0.y * dt,\n    cx1: p1.x - d1.x * dt,\n    cy1: p1.y - d1.y * dt,\n    x1: p1.x,\n    y1: p1.y\n  };\n}\nfunction curveTangentAt(c, t) {\n  const u = 1 - t;\n  const a = 3 * u * u;\n  const b = 6 * u * t;\n  const d = 3 * t * t;\n  return {\n    x: a * (c.cx0 - c.x0) + b * (c.cx1 - c.cx0) + d * (c.x1 - c.cx1),\n    y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)\n  };\n}\nfunction dashCurves(curves, dashWorld) {\n  const lengths = curves.map(\n    (c) => Math.hypot(c.cx0 - c.x0, c.cy0 - c.y0) + Math.hypot(c.cx1 - c.cx0, c.cy1 - c.cy0) + Math.hypot(c.x1 - c.cx1, c.y1 - c.cy1)\n  );\n  const total = lengths.reduce((a, b) => a + b, 0);\n  const spans = Math.max(3, Math.round(total / dashWorld) | 1);\n  const out = [];\n  for (let i = 0; i < spans; i += 2) {\n    const from = i / spans * total;\n    const to = (i + 1) / spans * total;\n    const dash = [];\n    let start = 0;\n    curves.forEach((c, k) => {\n      const length = lengths[k];\n      const end = start + length;\n      if (length > 0 && end > from && start < to) {\n        dash.push(\n          subCurve(\n            c,\n            Math.max(0, (from - start) / length),\n            Math.min(1, (to - start) / length)\n          )\n        );\n      }\n      start = end;\n    });\n    if (dash.length) {\n      out.push(dash);\n    }\n  }\n  return out;\n}\nfunction translateCurves(curves, dx, dy) {\n  const out = new Array(curves.length);\n  for (let i = 0; i < curves.length; i++) {\n    const c = curves[i];\n    out[i] = {\n      x0: c.x0 + dx,\n      y0: c.y0 + dy,\n      cx0: c.cx0 + dx,\n      cy0: c.cy0 + dy,\n      cx1: c.cx1 + dx,\n      cy1: c.cy1 + dy,\n      x1: c.x1 + dx,\n      y1: c.y1 + dy\n    };\n  }\n  return out;\n}\nfunction attachment(segments, side) {\n  const last = segments.length - 1;\n  return side === \"end\" ? { at: segments[last], inward: segments[last - 1] } : { at: segments[0], inward: segments[1] };\n}\nvar TANGENT_SPAN_FACTOR = 0.5;\nvar MAX_TANGENT = 80;\nfunction ownStrand(id) {\n  return id.endsWith(\"-\") ? \"-\" : \"+\";\n}\nfunction strandSides(edge) {\n  const own = (id, strand) => (strand ?? ownStrand(id)) === ownStrand(id);\n  return {\n    from: own(edge.from, edge.fromStrand) ? \"end\" : \"start\",\n    to: own(edge.to, edge.toStrand) ? \"start\" : \"end\"\n  };\n}\nfunction spanOf(segments) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const s of segments) {\n    min = Math.min(min, s.x);\n    max = Math.max(max, s.x);\n  }\n  return { min, max };\n}\nfunction distanceToSpan(x, span) {\n  return Math.max(0, span.min - x, x - span.max);\n}\nfunction facingSide(segments, other, tieBreak) {\n  const startGap = distanceToSpan(segments[0].x, other);\n  const endGap = distanceToSpan(segments[segments.length - 1].x, other);\n  return startGap === endGap ? tieBreak : startGap < endGap ? \"start\" : \"end\";\n}\nfunction facingSides(fromSegments, toSegments) {\n  return {\n    from: facingSide(fromSegments, spanOf(toSegments), \"end\"),\n    to: facingSide(toSegments, spanOf(fromSegments), \"start\")\n  };\n}\nvar laidSides = /* @__PURE__ */ new WeakMap();\nfunction heldFacingSides(fromSegments, toSegments) {\n  let byTo = laidSides.get(fromSegments);\n  if (!byTo) {\n    byTo = /* @__PURE__ */ new WeakMap();\n    laidSides.set(fromSegments, byTo);\n  }\n  let sides = byTo.get(toSegments);\n  if (!sides) {\n    sides = facingSides(fromSegments, toSegments);\n    byTo.set(toSegments, sides);\n  }\n  return sides;\n}\nvar APEX_FRACTION = 0.75;\nvar BOW_CLEARANCE = 1.15;\nvar ALONG_FRACTION = 0.35;\nvar MAX_ROW_BOW_PX = 3 * ROW_HEIGHT_PX;\nfunction bowAround(p1x, p1y, p2x, p2y, toward, maxBow) {\n  const chord = Math.hypot(p2x - p1x, p2y - p1y);\n  const ux = chord === 0 ? 1 : (p2x - p1x) / chord;\n  const uy = chord === 0 ? 0 : (p2y - p1y) / chord;\n  let reach = 0;\n  let minAlong = Infinity;\n  let maxAlong = -Infinity;\n  for (const p of toward) {\n    const dx = p.x - p1x;\n    const dy = p.y - p1y;\n    const perp = dx * -uy + dy * ux;\n    if (Math.abs(perp) > Math.abs(reach)) {\n      reach = perp;\n    }\n    const along = dx * ux + dy * uy;\n    minAlong = Math.min(minAlong, along);\n    maxAlong = Math.max(maxAlong, along);\n  }\n  const span = toward.length ? maxAlong - minAlong : 0;\n  const uncapped = Math.max(\n    Math.abs(reach) * BOW_CLEARANCE / APEX_FRACTION,\n    span * ALONG_FRACTION\n  );\n  const size = maxBow === void 0 ? uncapped : Math.min(uncapped, maxBow);\n  return reach < 0 ? -size : size;\n}\nfunction yToXOf({ scaleX, scaleY }) {\n  return scaleY / scaleX;\n}\nvar PATH_RIBBON_SPACING_PX = 3;\nfunction drawnDirection(a, b, yToX) {\n  const dx = b.x - a.x;\n  const dy = (b.y - a.y) * yToX;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? void 0 : { x: dx / len, y: dy / len };\n}\nfunction pathRibbonOffsets(fromSegments, toSegments, count, axis) {\n  const yToX = yToXOf(axis);\n  const spacing = PATH_RIBBON_SPACING_PX / Math.max(axis.scaleX, 1e-6);\n  const dir = drawnDirection(\n    fromSegments[fromSegments.length - 1],\n    toSegments[0],\n    yToX\n  ) ?? drawnDirection(fromSegments[0], fromSegments.at(-1), yToX) ?? drawnDirection(toSegments[0], toSegments.at(-1), yToX) ?? { x: 1, y: 0 };\n  const offsets = [];\n  for (let i = 0; i < count; i++) {\n    const distance = (i - (count - 1) / 2) * spacing;\n    offsets.push({ x: -dir.y * distance, y: dir.x * distance / yToX });\n  }\n  return offsets;\n}\nfunction scaleYOf(points, yToX) {\n  return points.map((p) => ({ x: p.x, y: p.y * yToX }));\n}\nfunction unscaleYOf(curves, yToX) {\n  for (const c of curves) {\n    c.y0 /= yToX;\n    c.cy0 /= yToX;\n    c.cy1 /= yToX;\n    c.y1 /= yToX;\n  }\n  return curves;\n}\nfunction polylinePx(points, scaleX, scaleY) {\n  let total = 0;\n  for (let i = 1; i < points.length; i++) {\n    const a = points[i - 1];\n    const b = points[i];\n    total += Math.hypot((b.x - a.x) * scaleX, (b.y - a.y) * scaleY);\n  }\n  return total;\n}\nvar SELF_LOOP_MIN_PX = 12;\nvar SELF_LOOP_MAX_PX = 40;\nfunction selfLoopReach(segments, scale) {\n  const nodePx = polylinePx(segments, scale, scale);\n  const reachPx = Math.min(\n    SELF_LOOP_MAX_PX,\n    Math.max(SELF_LOOP_MIN_PX, nodePx / 2)\n  );\n  return reachPx / Math.max(scale, Number.EPSILON);\n}\nfunction selfLinkOf(edge) {\n  if (edge.from !== edge.to) {\n    return false;\n  }\n  return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand ? edge.fromStrand === \"+\" ? \"end\" : \"start\" : true;\n}\nfunction edgeJoinOf(edge, stranded = false) {\n  const self = selfLinkOf(edge);\n  if (!stranded) {\n    return self;\n  }\n  const sides = strandSides(edge);\n  return self === false ? sides : sides.from === sides.to ? sides.from : true;\n}\nfunction hairpinCurves(attach, reach) {\n  const { at, inward } = attach;\n  const dx = inward ? at.x - inward.x : 1;\n  const dy = inward ? at.y - inward.y : 0;\n  const len = Math.hypot(dx, dy) || 1;\n  const ux = dx / len;\n  const uy = dy / len;\n  const px = at.x;\n  const py = at.y;\n  const nearX = px + ux * reach / 3;\n  const nearY = py + uy * reach / 3;\n  const apexX = px + ux * reach;\n  const apexY = py + uy * reach;\n  const sideX = -uy * reach / 2;\n  const sideY = ux * reach / 2;\n  return [\n    {\n      x0: px,\n      y0: py,\n      cx0: nearX,\n      cy0: nearY,\n      cx1: apexX + sideX,\n      cy1: apexY + sideY,\n      x1: apexX,\n      y1: apexY\n    },\n    {\n      x0: apexX,\n      y0: apexY,\n      cx0: apexX - sideX,\n      cy0: apexY - sideY,\n      cx1: nearX,\n      cy1: nearY,\n      x1: px,\n      y1: py\n    }\n  ];\n}\nfunction computeEdgeCurves(fromSegments, toSegments, join, axis, bypassed = [], maxBowIn) {\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);\n  if (join === false) {\n    join = heldFacingSides(fromSegments, toSegments);\n  }\n  if (yToX !== 1) {\n    return unscaleYOf(\n      computeEdgeCurves(\n        scaleYOf(fromSegments, yToX),\n        scaleYOf(toSegments, yToX),\n        join,\n        { scaleX: scale, scaleY: scale },\n        scaleYOf(bypassed, yToX),\n        // the cap is a y measure and the body works in x units, so it converts\n        // with everything else that crosses this boundary\n        maxBow === void 0 ? void 0 : maxBow * yToX\n      ),\n      yToX\n    );\n  }\n  if (typeof join === \"string\") {\n    return hairpinCurves(\n      attachment(fromSegments, join),\n      selfLoopReach(fromSegments, scale)\n    );\n  }\n  const loop = join === true;\n  const sides = join === true ? { from: \"end\", to: \"start\" } : join;\n  const fromAttach = attachment(fromSegments, sides.from);\n  const toAttach = attachment(toSegments, sides.to);\n  const fromEnd = fromAttach.at;\n  const toStart = toAttach.at;\n  const p1x = fromEnd.x;\n  const p1y = fromEnd.y;\n  const p2x = toStart.x;\n  const p2y = toStart.y;\n  if (loop) {\n    let segDirX = 1;\n    let segDirY = 0;\n    if (fromAttach.inward) {\n      const dx = fromEnd.x - fromAttach.inward.x;\n      const dy = fromEnd.y - fromAttach.inward.y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        segDirX = dx / len;\n        segDirY = dy / len;\n      }\n    }\n    const ext = selfLoopReach(fromSegments, scale);\n    const perpX = -segDirY;\n    const perpY = segDirX;\n    const midX = (fromEnd.x + toStart.x) / 2 + perpX * ext;\n    const midY = (fromEnd.y + toStart.y) / 2 + perpY * ext;\n    const cp1x = p1x + segDirX * ext;\n    const cp1y = p1y + segDirY * ext;\n    const cp2x = p2x - segDirX * ext;\n    const cp2y = p2y - segDirY * ext;\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cp1x,\n        cy0: cp1y,\n        cx1: cp1x + perpX * ext,\n        cy1: cp1y + perpY * ext,\n        x1: midX,\n        y1: midY\n      },\n      {\n        x0: midX,\n        y0: midY,\n        cx0: cp2x + perpX * ext,\n        cy0: cp2y + perpY * ext,\n        cx1: cp2x,\n        cy1: cp2y,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  } else {\n    const fromPrev = fromAttach.inward ?? {\n      x: fromEnd.x - (toStart.x - fromEnd.x),\n      y: fromEnd.y - (toStart.y - fromEnd.y)\n    };\n    const toNext = toAttach.inward ?? {\n      x: toStart.x - (fromEnd.x - toStart.x),\n      y: toStart.y - (fromEnd.y - toStart.y)\n    };\n    const dist = Math.hypot(p2x - p1x, p2y - p1y);\n    const tangentProj = (prev, at, towardX, towardY) => {\n      const dx = at.x - prev.x;\n      const dy = at.y - prev.y;\n      const len = Math.hypot(dx, dy);\n      const along = len === 0 ? 0 : (towardX * dx + towardY * dy) / len;\n      return Math.max(\n        0,\n        Math.min(dist * TANGENT_SPAN_FACTOR, MAX_TANGENT, along * 0.5)\n      );\n    };\n    const towardToX = toStart.x - fromEnd.x;\n    const towardToY = toStart.y - fromEnd.y;\n    const [cx1, cy1] = projectLine(\n      fromPrev.x,\n      fromPrev.y,\n      fromEnd.x,\n      fromEnd.y,\n      tangentProj(fromPrev, fromEnd, towardToX, towardToY)\n    );\n    const [cx2, cy2] = projectLine(\n      toNext.x,\n      toNext.y,\n      toStart.x,\n      toStart.y,\n      tangentProj(toNext, toStart, -towardToX, -towardToY)\n    );\n    const bulge = bypassed.length ? bowAround(p1x, p1y, p2x, p2y, bypassed, maxBow) : 0;\n    const chordLen = dist === 0 ? 1 : dist;\n    const ux = (p2x - p1x) / chordLen;\n    const uy = (p2y - p1y) / chordLen;\n    const bulgeX = -uy * bulge;\n    const bulgeY = ux * bulge;\n    const spreadX = ux * Math.abs(bulge);\n    const spreadY = uy * Math.abs(bulge);\n    return [\n      {\n        x0: p1x,\n        y0: p1y,\n        cx0: cx1 + bulgeX - spreadX,\n        cy0: cy1 + bulgeY - spreadY,\n        cx1: cx2 + bulgeX + spreadX,\n        cy1: cy2 + bulgeY + spreadY,\n        x1: p2x,\n        y1: p2y\n      }\n    ];\n  }\n}\nfunction nearerEnd(segments, to) {\n  const start = segments[0];\n  const end = segments.at(-1);\n  return Math.hypot(start.x - to.x, start.y - to.y) < Math.hypot(end.x - to.x, end.y - to.y) ? \"start\" : \"end\";\n}\nfunction routedEdgeCurves(fromSegments, toSegments, route, sides) {\n  const fromAttach = attachment(\n    fromSegments,\n    sides?.from ?? nearerEnd(fromSegments, route[0])\n  );\n  const toAttach = attachment(\n    toSegments,\n    sides?.to ?? nearerEnd(toSegments, route.at(-1))\n  );\n  const points = [fromAttach.at, ...route, toAttach.at];\n  const tangent = (i) => {\n    const p = points[i];\n    const span = (q) => Math.hypot(q.x - p.x, q.y - p.y);\n    const along = (inward, next) => {\n      const len = inward ? span(inward) : 0;\n      const reach = span(next);\n      return len === 0 ? { x: next.x - p.x, y: next.y - p.y } : {\n        x: (p.x - inward.x) / len * reach,\n        y: (p.y - inward.y) / len * reach\n      };\n    };\n    if (i === 0) {\n      return along(fromAttach.inward, points[1]);\n    }\n    if (i === points.length - 1) {\n      const out = along(toAttach.inward, points[i - 1]);\n      return { x: -out.x, y: -out.y };\n    }\n    return {\n      x: (points[i + 1].x - points[i - 1].x) / 2,\n      y: (points[i + 1].y - points[i - 1].y) / 2\n    };\n  };\n  const curves = [];\n  for (let i = 0; i < points.length - 1; i++) {\n    const a = points[i];\n    const b = points[i + 1];\n    const ta = tangent(i);\n    const tb = tangent(i + 1);\n    curves.push({\n      x0: a.x,\n      y0: a.y,\n      cx0: a.x + ta.x / 3,\n      cy0: a.y + ta.y / 3,\n      cx1: b.x - tb.x / 3,\n      cy1: b.y - tb.y / 3,\n      x1: b.x,\n      y1: b.y\n    });\n  }\n  return curves;\n}\n\nexport {\n  svgPath,\n  projectLine,\n  curvePointAt,\n  curveMidpoint,\n  curveBounds,\n  dashCurves,\n  translateCurves,\n  ownStrand,\n  strandSides,\n  bowAround,\n  yToXOf,\n  PATH_RIBBON_SPACING_PX,\n  pathRibbonOffsets,\n  polylinePx,\n  selfLinkOf,\n  edgeJoinOf,\n  computeEdgeCurves,\n  routedEdgeCurves\n};\n", "import {\n  ownStrand,\n  strandSides\n} from \"./chunk-UBQSRCWR.js\";\nimport {\n  pushTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/layout/mergeRuns.ts\nfunction flip(strand) {\n  return strand === \"+\" ? \"-\" : \"+\";\n}\nfunction mergeRuns(graph, alone = /* @__PURE__ */ new Set()) {\n  const sides = graph.edges.map(strandSides);\n  const at = /* @__PURE__ */ new Map();\n  const attach = (id, side, ei) => {\n    pushTo(at, `${id}|${side}`, ei);\n  };\n  graph.edges.forEach((edge, ei) => {\n    attach(edge.from, sides[ei].from, ei);\n    attach(edge.to, sides[ei].to, ei);\n  });\n  const joinAfter = (a) => {\n    const out = at.get(`${a}|end`);\n    if (out?.length !== 1) {\n      return void 0;\n    }\n    const ei = out[0];\n    const edge = graph.edges[ei];\n    return edge.from === a && edge.to !== a && !alone.has(a) && !alone.has(edge.to) && sides[ei].from === \"end\" && sides[ei].to === \"start\" && at.get(`${edge.to}|start`)?.length === 1 ? ei : void 0;\n  };\n  const joined = /* @__PURE__ */ new Set();\n  const runOf = /* @__PURE__ */ new Map();\n  const runs = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const into = at.get(`${node.id}|start`);\n    const pred = into?.length === 1 ? graph.edges[into[0]].from : void 0;\n    if (runOf.has(node.id) || pred !== void 0 && joinAfter(pred) === into[0]) {\n      continue;\n    }\n    const run = [node.id];\n    for (; ; ) {\n      const ei = joinAfter(run.at(-1));\n      const next = ei === void 0 ? void 0 : graph.edges[ei].to;\n      if (next === void 0 || runOf.has(next)) {\n        break;\n      }\n      joined.add(ei);\n      run.push(next);\n    }\n    for (const id of run) {\n      runOf.set(id, node.id);\n    }\n    if (run.length > 1) {\n      runs.set(node.id, run);\n    }\n  }\n  for (const node of graph.nodes) {\n    if (!runOf.has(node.id)) {\n      runOf.set(node.id, node.id);\n    }\n  }\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const nodes = [];\n  for (const node of graph.nodes) {\n    if (runOf.get(node.id) !== node.id) {\n      continue;\n    }\n    const run = runs.get(node.id);\n    if (!run) {\n      nodes.push(node);\n      continue;\n    }\n    const members = run.map((id) => byId.get(id));\n    const backbone = members.filter(isBackbone);\n    const first = backbone.length ? backbone.reduce((a, b) => a.stable.start <= b.stable.start ? a : b) : members[0];\n    nodes.push({\n      id: node.id,\n      name: node.name,\n      length: members.reduce((sum, n) => sum + n.length, 0),\n      depth: node.depth,\n      stable: first.stable\n    });\n  }\n  const seen = /* @__PURE__ */ new Set();\n  const edges = [];\n  graph.edges.forEach((edge, ei) => {\n    const from = runOf.get(edge.from);\n    const to = runOf.get(edge.to);\n    const side = sides[ei];\n    const key = `${from}|${side.from}>${to}|${side.to}`;\n    if (joined.has(ei) || seen.has(key)) {\n      return;\n    }\n    seen.add(key);\n    edges.push({\n      from,\n      to,\n      ...side.from === \"start\" ? { fromStrand: flip(ownStrand(from)) } : {},\n      ...side.to === \"end\" ? { toStrand: flip(ownStrand(to)) } : {}\n    });\n  });\n  return {\n    graph: { ...graph, nodes, edges, paths: void 0, pathVisits: void 0 },\n    runs\n  };\n}\nfunction splitRuns(positions, runs, weightOf) {\n  const out = { ...positions };\n  for (const [id, members] of runs) {\n    const line = positions[id];\n    if (!line?.length) {\n      continue;\n    }\n    delete out[id];\n    const arc = arcPrefix(line);\n    const total = arc.at(-1);\n    const weights = members.map((m) => Math.max(weightOf(m), 0));\n    const weightSum = weights.reduce((a, b) => a + b, 0);\n    let from = 0;\n    members.forEach((member, k) => {\n      const share = weightSum ? weights[k] / weightSum * total : total / members.length;\n      const to = k === members.length - 1 ? total : from + share;\n      out[member] = slice(line, arc, from, to);\n      from = to;\n    });\n  }\n  return out;\n}\nfunction polylineSlice(line, from, to) {\n  if (line.length === 0) {\n    return [];\n  }\n  const arc = arcPrefix(line);\n  const total = arc.at(-1);\n  return slice(line, arc, from * total, to * total);\n}\nfunction polylineMidpoint(line) {\n  const arc = arcPrefix(line);\n  return pointAt(line, arc, arc.at(-1) / 2);\n}\nfunction arcPrefix(line) {\n  const arc = [0];\n  for (let i = 1; i < line.length; i++) {\n    arc.push(\n      arc[i - 1] + Math.hypot(line[i].x - line[i - 1].x, line[i].y - line[i - 1].y)\n    );\n  }\n  return arc;\n}\nfunction pointAt(line, arc, s) {\n  if (s <= 0) {\n    return { ...line[0] };\n  }\n  let i = 1;\n  while (i < arc.length && arc[i] < s) {\n    i++;\n  }\n  if (i >= arc.length) {\n    return { ...line.at(-1) };\n  }\n  const span = arc[i] - arc[i - 1];\n  const t = span > 0 ? (s - arc[i - 1]) / span : 0;\n  const a = line[i - 1];\n  const b = line[i];\n  return { x: a.x + (b.x - a.x) * t, y: a.y + (b.y - a.y) * t };\n}\nfunction slice(line, arc, from, to) {\n  const points = [pointAt(line, arc, from)];\n  for (let i = 0; i < line.length; i++) {\n    if (arc[i] > from && arc[i] < to) {\n      points.push({ ...line[i] });\n    }\n  }\n  points.push(pointAt(line, arc, to));\n  return points;\n}\n\nexport {\n  mergeRuns,\n  splitRuns,\n  polylineSlice,\n  polylineMidpoint\n};\n", "import {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-UBQSRCWR.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  firstNodeAtOrAfter,\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\n\n// src/deletionEdges.ts\nvar MIN_DELETION_BP = 1;\nfunction bypassedPoints(nodePositions, bypassed) {\n  return bypassed.flatMap((id) => nodePositions[id] ?? []);\n}\nfunction edgeCurvesOf(nodePositions, edge, axis, bypassed, route, stranded) {\n  const from = nodePositions[edge.from];\n  const to = nodePositions[edge.to];\n  if (!from?.length || !to?.length) {\n    return void 0;\n  }\n  return route ? routedEdgeCurves(\n    from,\n    to,\n    route,\n    stranded ? strandSides(edge) : void 0\n  ) : computeEdgeCurves(\n    from,\n    to,\n    edgeJoinOf(edge, stranded),\n    axis,\n    bypassed ? bypassedPoints(nodePositions, bypassed) : []\n  );\n}\nfunction backboneBySequence(graph) {\n  const bySequence = groupBy(\n    graph.nodes.filter(isBackbone),\n    (node) => node.stable.refName\n  );\n  for (const list of bySequence.values()) {\n    list.sort((a, b) => a.stable.start - b.stable.start);\n  }\n  return bySequence;\n}\nfunction bypassedNodes(nodes, start, end) {\n  const bypassed = [];\n  if (nodes) {\n    for (let i = firstNodeAtOrAfter(nodes, start); i < nodes.length; i++) {\n      const node = nodes[i];\n      if (node.stable.start >= end) {\n        break;\n      }\n      if (node.stable.start + node.length <= end) {\n        bypassed.push(node.id);\n      }\n    }\n  }\n  return bypassed;\n}\nfunction skipsBetween(edge, from, to, forwards) {\n  const { fromStrand, toStrand } = edge;\n  if (fromStrand === void 0 || toStrand === void 0) {\n    return true;\n  }\n  const leavesRight = fromStrand === (from.stable.strand ?? \"+\");\n  const arrivesLeft = toStrand === (to.stable.strand ?? \"+\");\n  return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft;\n}\nfunction deletionEdges(graph) {\n  const byId = new Map(graph.nodes.map((n) => [n.id, n]));\n  const backbone = backboneBySequence(graph);\n  const found = [];\n  for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {\n    const edge = graph.edges[edgeIndex];\n    const from = byId.get(edge.from);\n    const to = byId.get(edge.to);\n    if (from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {\n      const forwards = from.stable.start <= to.stable.start;\n      const [left, right] = forwards ? [from, to] : [to, from];\n      const start = left.stable.start + left.length;\n      const end = right.stable.start;\n      const bp = end - start;\n      if (bp >= MIN_DELETION_BP && skipsBetween(edge, from, to, forwards)) {\n        const refName = left.stable.refName;\n        found.push({\n          edgeIndex,\n          from: edge.from,\n          to: edge.to,\n          ...edge.fromStrand ? { fromStrand: edge.fromStrand } : {},\n          ...edge.toStrand ? { toStrand: edge.toStrand } : {},\n          refName,\n          start,\n          end,\n          bp,\n          bypassed: bypassedNodes(backbone.get(refName), start, end)\n        });\n      }\n    }\n  }\n  return found;\n}\nfunction closableDeletions(graph, deletions) {\n  const parent = /* @__PURE__ */ new Map();\n  const root = (id) => {\n    let r = id;\n    while (parent.has(r)) {\n      r = parent.get(r);\n    }\n    if (r !== id) {\n      parent.set(id, r);\n    }\n    return r;\n  };\n  const join = (a, b) => {\n    const [ra, rb] = [root(a), root(b)];\n    if (ra !== rb) {\n      parent.set(ra, rb);\n    }\n    return ra !== rb;\n  };\n  const candidates = new Set(deletions.map((d) => d.edgeIndex));\n  graph.edges.forEach((e, ei) => {\n    if (!candidates.has(ei)) {\n      join(e.from, e.to);\n    }\n  });\n  return new Set(\n    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)\n  );\n}\nvar drawings = /* @__PURE__ */ new WeakMap();\nfunction deletionDrawing(graph, deletions, show = true) {\n  let byShow = drawings.get(deletions);\n  if (!byShow) {\n    byShow = /* @__PURE__ */ new Map();\n    drawings.set(deletions, byShow);\n  }\n  let drawing = byShow.get(show);\n  if (!drawing) {\n    const hidden = show ? /* @__PURE__ */ new Set() : closableDeletions(graph, deletions);\n    drawing = {\n      shown: deletions.filter((d) => !hidden.has(d.edgeIndex)),\n      bypassed: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),\n      hidden\n    };\n    byShow.set(show, drawing);\n  }\n  return drawing;\n}\n\nexport {\n  edgeCurvesOf,\n  deletionEdges,\n  closableDeletions,\n  deletionDrawing\n};\n", "import {\n  weakMemo\n} from \"./chunk-HMXCN6PG.js\";\nimport {\n  labelWidth,\n  occupancy\n} from \"./chunk-AB35TJST.js\";\nimport {\n  polylineMidpoint\n} from \"./chunk-BZFOFC4D.js\";\nimport {\n  edgeCurvesOf\n} from \"./chunk-CGMSKIEO.js\";\nimport {\n  curveBounds,\n  curveMidpoint,\n  polylinePx\n} from \"./chunk-UBQSRCWR.js\";\n\n// src/graphLabels.ts\nvar MIN_DELETION_LABEL_PX = 26;\nvar PX_PER_NODE_LABEL = 4e4;\nvar MIN_NODE_LABELS = 8;\nvar LEADER_GAP_PX = 8;\nvar LABEL_CHAR_PX = 5.7;\nvar LABEL_PAD_PX = 6;\nvar LABEL_HEIGHT_PX = 13;\nvar LABEL_GAP_PX = 3;\nvar MAX_LABEL_OVERHANG = 2;\nfunction labelHalfWidth(text) {\n  return (text.length * LABEL_CHAR_PX + LABEL_PAD_PX + LABEL_GAP_PX) / 2;\n}\nvar LABEL_HALF_HEIGHT = (LABEL_HEIGHT_PX + LABEL_GAP_PX) / 2;\nvar MIN_LABEL_HALF_WIDTH = labelHalfWidth(\"1 bp\");\nfunction boxAt(halfW, x, y) {\n  return {\n    x0: x - halfW,\n    x1: x + halfW,\n    y0: y - LABEL_HALF_HEIGHT,\n    y1: y + LABEL_HALF_HEIGHT\n  };\n}\nfunction rowLabelBox(text, screenY) {\n  return {\n    x0: 6,\n    x1: 6 + labelWidth(text) + LABEL_GAP_PX,\n    y0: screenY - 8 - LABEL_GAP_PX / 2,\n    y1: screenY + 8 + LABEL_GAP_PX / 2\n  };\n}\nfunction clamp(v, lo, hi) {\n  return hi < lo ? v : Math.min(Math.max(v, lo), hi);\n}\nfunction groupDigits(n) {\n  return String(n).replace(/\\B(?=(\\d{3})+$)/g, \",\");\n}\nfunction formatBp(bp) {\n  const [value, unit] = bp >= 1e6 ? [bp / 1e6, \"Mb\"] : bp >= 1e3 ? [bp / 1e3, \"kb\"] : [];\n  if (value === void 0) {\n    return `${bp} bp`;\n  }\n  return `${+value.toFixed(value >= 100 ? 0 : 1)} ${unit}`;\n}\nfunction deletionText(bp) {\n  return `${formatBp(bp)} del`;\n}\nfunction arcOutward(curves, apex, scaleX, scaleY) {\n  const first = curves[0];\n  const last = curves[curves.length - 1];\n  const dx = (apex.x - (first.x0 + last.x1) / 2) * scaleX;\n  const dy = (apex.y - (first.y0 + last.y1) / 2) * scaleY;\n  const len = Math.hypot(dx, dy);\n  return len === 0 ? { x: 0, y: -1 } : { x: dx / len, y: dy / len };\n}\nfunction boxSupport(box, dir) {\n  return Math.abs(dir.x) * (box.x1 - box.x0) / 2 + Math.abs(dir.y) * (box.y1 - box.y0) / 2;\n}\nfunction boxRayCrossing(box, dir) {\n  const halfW = (box.x1 - box.x0) / 2;\n  const halfH = (box.y1 - box.y0) / 2;\n  return Math.min(\n    dir.x === 0 ? Infinity : halfW / Math.abs(dir.x),\n    dir.y === 0 ? Infinity : halfH / Math.abs(dir.y)\n  );\n}\nfunction runBounds(nodeIds, nodePositions) {\n  let minX = Infinity;\n  let minY = Infinity;\n  let maxX = -Infinity;\n  let maxY = -Infinity;\n  for (const id of nodeIds) {\n    for (const p of nodePositions[id] ?? []) {\n      minX = Math.min(minX, p.x);\n      maxX = Math.max(maxX, p.x);\n      minY = Math.min(minY, p.y);\n      maxY = Math.max(maxY, p.y);\n    }\n  }\n  return minX === Infinity ? void 0 : { minX, minY, maxX, maxY };\n}\nvar nodeOrderCache = weakMemo();\nfunction labelOrder(nodePositions, nodeLengths) {\n  return nodeOrderCache(\n    nodePositions,\n    [nodeLengths],\n    () => Object.entries(nodePositions).filter(([id, segments]) => segments.length > 0 && nodeLengths.has(id)).sort(([a], [b]) => nodeLengths.get(b) - nodeLengths.get(a))\n  );\n}\nvar arcCache = weakMemo();\nfunction arcPlacements(nodePositions, deletions, axis, version, routes, stranded) {\n  const { scaleX, scaleY } = axis;\n  return arcCache(\n    nodePositions,\n    [deletions, routes, stranded, scaleX, scaleY, version],\n    () => {\n      const arcs = [];\n      for (const deletion of [...deletions].sort((a, b) => b.bp - a.bp)) {\n        const curves = edgeCurvesOf(\n          nodePositions,\n          deletion,\n          axis,\n          deletion.bypassed,\n          routes?.[deletion.edgeIndex],\n          stranded\n        );\n        const apex = curves ? curveMidpoint(curves) : void 0;\n        if (curves && apex) {\n          const { minX, minY, maxX, maxY } = curveBounds(curves);\n          arcs.push({\n            deletion,\n            curves,\n            apex,\n            // in screen px, so the two axes' units cannot be added by accident\n            extent: Math.max((maxX - minX) * scaleX, (maxY - minY) * scaleY)\n          });\n        }\n      }\n      return arcs;\n    }\n  );\n}\nfunction sizeLabelCandidates({\n  nodePositions,\n  nodeLengths,\n  deletions,\n  deletionRoutes,\n  stranded = false,\n  alleleDeletions,\n  axis,\n  translateX,\n  translateY,\n  width,\n  height,\n  version = 0\n}) {\n  const { scaleX, scaleY } = axis;\n  const deletionCandidates = [];\n  const nodeCandidates = [];\n  for (const { deletion, curves, apex, extent } of arcPlacements(\n    nodePositions,\n    deletions,\n    axis,\n    version,\n    deletionRoutes,\n    stranded\n  )) {\n    if (extent >= MIN_DELETION_LABEL_PX) {\n      const text = deletionText(deletion.bp);\n      const halfW = labelHalfWidth(text);\n      const box = boxAt(halfW, 0, 0);\n      const arcX = apex.x * scaleX + translateX;\n      const arcY = apex.y * scaleY + translateY;\n      if (arcX < 0 || arcX > width || arcY < 0 || arcY > height) {\n        continue;\n      }\n      const fits = extent >= halfW * 2 / MAX_LABEL_OVERHANG;\n      const bow = arcOutward(curves, apex, scaleX, scaleY);\n      const offset = boxSupport(box, bow) + LEADER_GAP_PX;\n      const x = fits ? arcX : clamp(arcX + bow.x * offset, halfW, width - halfW);\n      const y = fits ? arcY : clamp(\n        arcY + bow.y * offset,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      const away = Math.hypot(x - arcX, y - arcY);\n      let leader;\n      if (away > 0) {\n        const dir = { x: (x - arcX) / away, y: (y - arcY) / away };\n        const crossing = boxRayCrossing(box, dir);\n        leader = {\n          arcX,\n          arcY,\n          labelX: x - dir.x * crossing,\n          labelY: y - dir.y * crossing\n        };\n      }\n      deletionCandidates.push({\n        label: {\n          key: `del:${deletion.edgeIndex}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\",\n          leader\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  const labelledByDeletion = /* @__PURE__ */ new Set();\n  const alleleRuns = [...alleleDeletions ?? []].sort((a, b) => b.bp - a.bp);\n  for (const run of alleleRuns) {\n    const drawn = runBounds(run.nodeIds, nodePositions);\n    if (!drawn) {\n      continue;\n    }\n    const shownLeft = Math.max(drawn.minX * scaleX + translateX, 0);\n    const shownRight = Math.min(drawn.maxX * scaleX + translateX, width);\n    const shownTop = Math.max(drawn.minY * scaleY + translateY, 0);\n    const shownBottom = Math.min(drawn.maxY * scaleY + translateY, height);\n    if (shownRight < shownLeft || shownBottom < shownTop) {\n      continue;\n    }\n    const extent = Math.max(shownRight - shownLeft, shownBottom - shownTop);\n    const text = deletionText(run.bp);\n    const halfW = labelHalfWidth(text);\n    if (extent >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      for (const id of run.nodeIds) {\n        labelledByDeletion.add(id);\n      }\n      const x = clamp((shownLeft + shownRight) / 2, halfW, width - halfW);\n      const y = clamp(\n        (shownTop + shownBottom) / 2,\n        LABEL_HALF_HEIGHT,\n        height - LABEL_HALF_HEIGHT\n      );\n      deletionCandidates.push({\n        label: {\n          key: `alleledel:${run.nodeIds.join(\",\")}`,\n          text,\n          x,\n          y,\n          kind: \"deletion\"\n        },\n        box: boxAt(halfW, x, y)\n      });\n    }\n  }\n  for (const [id, segments] of labelOrder(nodePositions, nodeLengths)) {\n    if (labelledByDeletion.has(id)) {\n      continue;\n    }\n    const { x, y } = polylineMidpoint(segments);\n    const screenY = y * scaleY + translateY;\n    if (screenY + LABEL_HALF_HEIGHT <= 0 || screenY - LABEL_HALF_HEIGHT >= height) {\n      continue;\n    }\n    const drawn = polylinePx(segments, scaleX, scaleY);\n    if (drawn < MIN_LABEL_HALF_WIDTH * 2 / MAX_LABEL_OVERHANG) {\n      continue;\n    }\n    const text = formatBp(nodeLengths.get(id));\n    const halfW = labelHalfWidth(text);\n    if (drawn >= halfW * 2 / MAX_LABEL_OVERHANG) {\n      const screenX = x * scaleX + translateX;\n      nodeCandidates.push({\n        label: {\n          key: `node:${id}`,\n          text,\n          x: screenX,\n          y: screenY,\n          kind: \"node\"\n        },\n        box: boxAt(halfW, screenX, screenY)\n      });\n    }\n  }\n  return { deletions: deletionCandidates, nodes: nodeCandidates };\n}\nfunction nodeLabelBudget(width, height) {\n  return Math.max(\n    MIN_NODE_LABELS,\n    Math.floor(width * height / PX_PER_NODE_LABEL)\n  );\n}\nfunction placeSizeLabels(candidates, take, budget = Infinity) {\n  const labels = [];\n  for (const { label, box } of candidates) {\n    if (labels.length >= budget) {\n      break;\n    }\n    if (take(box)) {\n      labels.push(label);\n    }\n  }\n  return labels;\n}\nfunction graphLabels({\n  reserved,\n  take,\n  ...args\n}) {\n  take ??= occupancy(args, reserved);\n  const { deletions, nodes } = sizeLabelCandidates(args);\n  return [\n    ...placeSizeLabels(deletions, take),\n    ...placeSizeLabels(nodes, take, nodeLabelBudget(args.width, args.height))\n  ];\n}\n\nexport {\n  rowLabelBox,\n  groupDigits,\n  formatBp,\n  sizeLabelCandidates,\n  nodeLabelBudget,\n  placeSizeLabels,\n  graphLabels\n};\n", "import {\n  pathOrigin\n} from \"./chunk-B5X2RLJG.js\";\nimport {\n  groupDigits\n} from \"./chunk-PFRQBCGC.js\";\nimport {\n  isGenericSample\n} from \"./chunk-4XWZNPQ2.js\";\n\n// src/pathColors.ts\nfunction nameHue(name) {\n  let hash = 0;\n  for (let i = 0; i < name.length; i++) {\n    hash = name.charCodeAt(i) + ((hash << 5) - hash);\n  }\n  return Math.abs(hash % 360);\n}\nfunction pathHueAt(index, count) {\n  return index * 360 / count;\n}\nvar PATH_SATURATION = 0.7;\nvar PATH_LIGHTNESS = 0.5;\nvar MAX_PATH_COLORS = 16;\nfunction pathColorsLegible(pathCount) {\n  return pathCount > 0 && pathCount <= MAX_PATH_COLORS;\n}\nfunction pathCssColor(index, count) {\n  return `hsl(${pathHueAt(index, count)}, ${PATH_SATURATION * 100}%, ${PATH_LIGHTNESS * 100}%)`;\n}\nfunction pathGreyCssColor(index, count) {\n  const lightness = count > 1 ? 25 + 45 * index / (count - 1) : 45;\n  return `hsl(0, 0%, ${lightness}%)`;\n}\nfunction labelTiers(name) {\n  const parts = pathOrigin(name).name.split(\"#\");\n  const full = parts.join(\"#\");\n  if (parts.length >= 3 && isGenericSample(parts[0])) {\n    const contig = parts.slice(2).join(\"#\");\n    return [contig, contig, full];\n  }\n  return [parts[0], parts.slice(0, 2).join(\"#\"), full];\n}\nfunction offsetTiers(name, tiers) {\n  const { start } = pathOrigin(name);\n  return tiers.map((t) => `${t} @${groupDigits(start)}`);\n}\nfunction pathLegend(paths, colors) {\n  const firstOf = /* @__PURE__ */ new Map();\n  paths.forEach((path, i) => {\n    if (!firstOf.has(path.name)) {\n      firstOf.set(path.name, i);\n    }\n  });\n  const entries = [...firstOf].map(([name, i]) => ({ name, i }));\n  const named = entries.map((e) => labelTiers(e.name));\n  const candidates = [0, 1, 2].flatMap((t) => [\n    entries.map((_, k) => named[k][t]),\n    entries.map((e, k) => offsetTiers(e.name, named[k])[t])\n  ]);\n  const distinct = candidates.find(\n    (labels2) => new Set(labels2).size === entries.length\n  );\n  const labels = distinct ?? candidates.at(-1);\n  return entries.map(({ name, i }, k) => ({\n    name,\n    label: labels[k],\n    color: colors?.[i] ?? pathCssColor(i, paths.length)\n  }));\n}\nfunction walkLabelsOf(entries) {\n  const seen = /* @__PURE__ */ new Map();\n  return new Map(\n    [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {\n      const n = (seen.get(e.label) ?? 0) + 1;\n      seen.set(e.label, n);\n      return [e.name, n > 1 ? `${e.label} (${n})` : e.label];\n    })\n  );\n}\n\nexport {\n  nameHue,\n  pathHueAt,\n  PATH_SATURATION,\n  PATH_LIGHTNESS,\n  MAX_PATH_COLORS,\n  pathColorsLegible,\n  pathCssColor,\n  pathGreyCssColor,\n  pathLegend,\n  walkLabelsOf\n};\n", "// src/nodeWidths.ts\nvar NODE_WIDTHS = [\n  {\n    value: \"depth\",\n    label: \"By depth\",\n    description: \"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform.\"\n  },\n  {\n    value: \"uniform\",\n    label: \"Uniform\",\n    description: \"Every node the same thickness.\"\n  }\n];\nvar MIN_FACTOR = 0.3;\nvar MAX_FACTOR = 3;\nfunction meanDepth(graph) {\n  let weighted = 0;\n  let length = 0;\n  for (const node of graph.nodes) {\n    weighted += node.depth * node.length;\n    length += node.length;\n  }\n  return length > 0 ? weighted / length : 0;\n}\nfunction depthWidthFactor(node, mean) {\n  if (!(mean > 0) || !(node.depth > 0)) {\n    return 1;\n  }\n  return Math.min(\n    MAX_FACTOR,\n    Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))\n  );\n}\nfunction nodeWidthPx(node, contigThickness, nodeWidth, mean) {\n  return contigThickness * (nodeWidth === \"depth\" ? depthWidthFactor(node, mean) : 1);\n}\nfunction maxNodeWidthPx(contigThickness, nodeWidth) {\n  return contigThickness * (nodeWidth === \"depth\" ? MAX_FACTOR : 1);\n}\nfunction nodeInk(graph, nodeById, contigThickness, nodeWidth) {\n  const mean = graph ? meanDepth(graph) : 0;\n  return {\n    maxHalfWidthPx: maxNodeWidthPx(contigThickness, nodeWidth) / 2,\n    halfWidthPx: (id) => {\n      const node = nodeById?.get(id);\n      return node ? nodeWidthPx(node, contigThickness, nodeWidth, mean) / 2 : contigThickness / 2;\n    }\n  };\n}\n\nexport {\n  NODE_WIDTHS,\n  meanDepth,\n  nodeWidthPx,\n  maxNodeWidthPx,\n  nodeInk\n};\n"],
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-}

package/dist/chunks/chunk-PFAHNHMM.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=chunk-PFAHNHMM.js.map

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

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/walkRowRuns.ts"],
-  "sourcesContent": ["import { gapParts, stopAt } from '@jbrowse/bandage-core/gfa/walkStops'\nimport {\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from '@jbrowse/bandage-core/pansn'\n\nimport type { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'\nimport type { GapCause, GapPart } from '@jbrowse/bandage-core/gfa/walkStops'\nimport type {\n  WalkAxis,\n  WalkRow,\n  WalkRows,\n  WalkRun,\n  WalkStop,\n} from '@jbrowse/bandage-core/layout/walkRows'\nimport type { PathStop, StopChunk } from '@jbrowse/bandage-core/types'\n\nconst RUN_ON_REFERENCE = 1\nconst RUN_REVERSED = 2\nconst RUN_GAP = 4\n// a gap's cause, by index from bit 3\nconst GAP_CAUSES = [undefined, 'missing', 'elsewhere', 'unknown'] as const\nconst CAUSE_SHIFT = 3\n\nconst causeFlags = (cause: GapCause | undefined) =>\n  GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT\n\ntype WalkRowMeta = Omit<WalkRow, 'runs'>\n\n/**\n * A cut for walk rows: the tables, and the rows' runs over the window, which\n * the main thread draws without a Graph of the walks' steps\n */\nexport type WalkCut = GraphTables & { walkRowRuns?: WalkRowRuns }\n\nexport function walkCutFor(\n  tables: GraphTables,\n  region: { start: number; end: number },\n  walkRows: boolean | undefined,\n): WalkCut {\n  return walkRows\n    ? { ...tables, walkRowRuns: walkRowRuns(tables, region) }\n    : tables\n}\n\n/**\n * bandage-core's `walkRows` over a cut's tables, each row's runs as typed\n * arrays that cross from the worker beside the tables. Row 0 is the\n * reference.\n */\nexport interface WalkRowRuns {\n  origin: number\n  rows: WalkRowMeta[]\n  offsets: Uint32Array\n  start: Float64Array\n  bp: Float64Array\n  referenceStart: Float64Array\n  flags: Uint8Array\n  // a gap's chunk elsewhere, as an index into `chunks`, -1 for none\n  chunk: Int32Array\n  chunks: StopChunk[]\n}\n\n/**\n * A walk's PanSN fields: `HG002#1#chr1`, or a pggb P-line's `chm13#chr1`,\n * which has no haplotype\n */\nexport function walkPath(name: string) {\n  const sample = panSNSample(name)\n  const haplotype = panSNHaplotype(name)\n  return {\n    name,\n    sample,\n    haplotype:\n      haplotype === undefined ? undefined : +haplotype.slice(sample.length + 1),\n    contig: panSNContig(name),\n  }\n}\n\ntype Path = ReturnType<typeof walkPath> & {\n  start: number\n  from: number\n  to: number\n  before?: PathStop\n  after?: PathStop\n}\n\nclass RunWriter {\n  start: number[] = []\n  bp: number[] = []\n  referenceStart: number[] = []\n  flags: number[] = []\n  chunk: number[] = []\n  chunks: StopChunk[] = []\n  offsets = [0]\n  private chunkIndex = new Map<string, number>()\n\n  get length() {\n    return this.bp.length\n  }\n\n  push(\n    start: number,\n    bp: number,\n    flags: number,\n    referenceStart: number,\n    chunk?: StopChunk,\n  ) {\n    this.start.push(start)\n    this.bp.push(bp)\n    this.flags.push(flags)\n    this.referenceStart.push(referenceStart)\n    this.chunk.push(chunk ? this.chunkOf(chunk) : -1)\n  }\n\n  private chunkOf(chunk: StopChunk) {\n    const key = `${chunk.refName}:${chunk.start}`\n    let i = this.chunkIndex.get(key)\n    if (i === undefined) {\n      i = this.chunks.length\n      this.chunkIndex.set(key, i)\n      this.chunks.push(chunk)\n    }\n    return i\n  }\n\n  endRow() {\n    this.offsets.push(this.bp.length)\n  }\n}\n\n/**\n * `walkRows(graphFromTables(tables), region)` for a cut whose first walk is\n * the reference, which every walk-file and GBZ cut is, in as many pieces as\n * the cut breaks it into; a step is a node index. A gap between two pieces of\n * one haplotype is a step of `-bp`, split into its parts by the pieces' stops\n * as walkRows splits it. One difference: a walk reaching only one\n * of the region's flanks measures from that flank, where walkRows takes the\n * whole walk the cut holds, so its length is a lower bound that no longer\n * grows with the cut's context.\n */\nexport function walkRowRuns(\n  { nodes: n, walks: w }: GraphTables,\n  region?: { start: number; end: number },\n): WalkRowRuns | undefined {\n  const declared = n.lengths.length\n  const lengthOf = (node: number) => (node < declared ? n.lengths[node]! : 0)\n  const paths: Path[] = []\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1]! > w.offsets[p]!) {\n      const before = w.before && stopAt(w.before, p)\n      const after = w.after && stopAt(w.after, p)\n      paths.push({\n        ...walkPath(w.names[p]!),\n        start: w.starts[p]!,\n        from: w.offsets[p]!,\n        to: w.offsets[p + 1]!,\n        ...(before ? { before } : {}),\n        ...(after ? { after } : {}),\n      })\n    }\n  }\n  const referencePieces = paths\n    .filter(p => p.name === paths[0]?.name)\n    .sort((a, b) => a.start - b.start)\n  const first = referencePieces[0]\n  const others = paths.filter(p => p.name !== first?.name)\n  if (!first || others.length === 0) {\n    return undefined\n  }\n  const walks = new Map<string, Path[]>()\n  for (const path of others) {\n    const list = walks.get(path.name)\n    if (list) {\n      list.push(path)\n    } else {\n      walks.set(path.name, [path])\n    }\n  }\n\n  const spanStart = new Float64Array(n.names.length).fill(Number.NaN)\n  const spanEnd = new Float64Array(n.names.length)\n  let flankedBefore = false\n  let flankedAfter = false\n  const cut = region && region.end > region.start ? region : undefined\n  for (const piece of referencePieces) {\n    let pos = piece.start\n    for (let s = piece.from; s < piece.to; s++) {\n      const node = w.steps[s]!\n      const len = lengthOf(node)\n      if (Number.isNaN(spanStart[node]!)) {\n        spanStart[node] = pos\n        spanEnd[node] = pos + len\n        if (cut) {\n          flankedBefore ||= pos + len <= cut.start\n          flankedAfter ||= pos >= cut.end\n        }\n      }\n      pos += len\n    }\n  }\n  const flanked = cut === undefined || (flankedBefore && flankedAfter)\n\n  const out = new RunWriter()\n  let steps = new Int32Array(0)\n  let stepStart = new Float64Array(0)\n  const rowOf = (pieces: Path[]): WalkRowMeta => {\n    const path = pieces[0]!\n    const ordered = [...pieces].sort((a, b) => a.start - b.start)\n    // the walk's steps, each piece's gap from the last as a step of -bp\n    let count = ordered.length - 1\n    for (const piece of ordered) {\n      count += piece.to - piece.from\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 overlaps = false\n    let end: number | undefined\n    let previous: Path | undefined\n    // each gap step's parts, by step index\n    const partsAt = new Map<number, GapPart[]>()\n    for (const piece of ordered) {\n      if (end !== undefined && piece.start < end) {\n        overlaps = true\n      }\n      if (end !== undefined && piece.start > end) {\n        partsAt.set(\n          length,\n          gapParts(piece.start - end, previous?.after, piece.before),\n        )\n        steps[length] = -(piece.start - end)\n        stepStart[length++] = end\n      }\n      let pos = piece.start\n      for (let s = piece.from; s < piece.to; s++) {\n        const node = w.steps[s]!\n        steps[length] = node\n        stepStart[length++] = pos\n        pos += node < declared ? n.lengths[node]! : 0\n      }\n      end = pos\n      previous = piece\n    }\n    // A walk with one flank, whose contig ends inside the window: the steps\n    // past that flank, read in the reference's direction. Which side is\n    // inside follows the walk's direction along the reference at the\n    // flank, from the nearest other step on it.\n    const partialSide = (i0: number, i1: number) => {\n      const flank = i0 >= 0 ? i0 : i1\n      let near = -1\n      for (let d = 1; near < 0 && d < length; d++) {\n        for (const j of [flank - d, flank + d]) {\n          const id = j >= 0 && j < length ? steps[j]! : -1\n          if (near < 0 && id >= 0 && !Number.isNaN(spanStart[id]!)) {\n            near = j\n          }\n        }\n      }\n      if (near < 0) {\n        return undefined\n      }\n      const forward =\n        near > flank === spanStart[steps[near]!]! > spanStart[steps[flank]!]!\n      const after = forward === (flank === i0)\n      const end = after ? length - 1 : 0\n      const endId = steps[end]!\n      const contigEnds = endId >= 0 && !Number.isNaN(spanStart[endId]!)\n      const stop: WalkStop = {\n        contigEnds,\n        shortBp: contigEnds\n          ? Math.max(\n              0,\n              cut!.start - spanEnd[endId]!,\n              spanStart[endId]! - cut!.end,\n            )\n          : 0,\n      }\n      return {\n        stop,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward\n          ? after\n            ? stepEnd(flank)\n            : stepStart[0]!\n          : after\n            ? stepEnd(length - 1)\n            : stepStart[flank]!,\n      }\n    }\n    const stepEnd = (i: number) => {\n      const id = steps[i]!\n      return stepStart[i]! + (id < 0 ? -id : lengthOf(id))\n    }\n\n    let lo = 0\n    let hi = length\n    let backward = false\n    let complete = true\n    let from = -1\n    let to = -1\n    let axisStart: number | undefined\n    let stop: WalkStop | undefined\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) : undefined\n        if (inside) {\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        from = i0\n        to = i1\n      }\n    }\n    const axis: WalkAxis | undefined =\n      overlaps || length === 0\n        ? undefined\n        : axisStart !== undefined\n          ? { contig: path.contig, start: axisStart, reversed: backward }\n          : from < 0\n            ? { contig: path.contig, start: stepStart[0]!, reversed: false }\n            : from < to\n              ? { contig: path.contig, start: stepEnd(from), reversed: false }\n              : { contig: path.contig, start: stepStart[from]!, reversed: true }\n\n    let bp = 0\n    let offReferenceBp = 0\n    let gapBp = 0\n    let step = 0\n    let lastAt = -1\n    let lastFlags = 0\n    let lastRef = Number.NaN\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) ?? [{ bp: -id }]\n        // a row read backwards meets a gap's parts last first\n        for (const part of backward ? [...parts].reverse() : parts) {\n          out.push(\n            bp,\n            part.bp,\n            RUN_GAP | causeFlags(part.cause),\n            Number.NaN,\n            part.chunk,\n          )\n          bp += part.bp\n        }\n        lastAt = out.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 sStart = spanStart[id]!\n      const onRef = !Number.isNaN(sStart)\n      const at = lastRef\n      const hasAt = lastAt >= 0 && !Number.isNaN(at)\n      const forward =\n        onRef && hasAt && step >= 0 && at + (out.bp[lastAt] ?? 0) === sStart\n      const back = onRef && hasAt && step <= 0 && spanEnd[id] === at\n      if (\n        !onRef &&\n        lastAt >= 0 &&\n        !(lastFlags & RUN_ON_REFERENCE) &&\n        !(lastFlags & RUN_GAP)\n      ) {\n        out.bp[lastAt]! += len\n      } else if (forward || back) {\n        out.bp[lastAt]! += len\n        if (!forward) {\n          lastRef = sStart\n          out.referenceStart[lastAt] = sStart\n          lastFlags |= RUN_REVERSED\n          out.flags[lastAt] = lastFlags\n        }\n        step = forward ? 1 : -1\n      } else {\n        lastFlags = onRef ? RUN_ON_REFERENCE : 0\n        lastRef = onRef ? sStart : Number.NaN\n        out.push(bp, len, lastFlags, lastRef)\n        lastAt = out.length - 1\n        step = 0\n      }\n      bp += len\n      if (!onRef) {\n        offReferenceBp += len\n      }\n    }\n    out.endRow()\n    return {\n      name: path.name,\n      label:\n        path.haplotype === undefined\n          ? path.sample\n          : `${path.sample}#${path.haplotype}`,\n      sample: path.sample,\n      haplotype: path.haplotype,\n      bp,\n      offReferenceBp,\n      gapBp,\n      complete,\n      ...(stop ? { stop } : {}),\n      axis,\n    }\n  }\n\n  const reference = rowOf(referencePieces)\n  const rowList = [...walks.values()].map(pieces => ({\n    meta: rowOf(pieces),\n    row: out.offsets.length - 2,\n  }))\n  rowList.sort(\n    (a, b) =>\n      Number(b.meta.complete) - Number(a.meta.complete) ||\n      b.meta.bp - a.meta.bp ||\n      a.meta.label.localeCompare(b.meta.label),\n  )\n  // rows in drawn order: the reference, then the sorted walks\n  const order = [0, ...rowList.map(r => r.row)]\n  const total = out.length\n  const offsets = new Uint32Array(order.length + 1)\n  const start = new Float64Array(total)\n  const bpOut = new Float64Array(total)\n  const referenceStart = new Float64Array(total)\n  const flags = new Uint8Array(total)\n  const chunk = new Int32Array(total)\n  let at = 0\n  order.forEach((row, i) => {\n    const a = out.offsets[row]!\n    const b = out.offsets[row + 1]!\n    for (let k = a; k < b; k++, at++) {\n      start[at] = out.start[k]!\n      bpOut[at] = out.bp[k]!\n      referenceStart[at] = out.referenceStart[k]!\n      flags[at] = out.flags[k]!\n      chunk[at] = out.chunk[k]!\n    }\n    offsets[i + 1] = at\n  })\n  return {\n    origin: cut ? cut.start : first.start,\n    rows: [reference, ...rowList.map(r => r.meta)],\n    offsets,\n    start,\n    bp: bpOut,\n    referenceStart,\n    flags,\n    chunk,\n    chunks: out.chunks,\n  }\n}\n\nfunction runAt(t: WalkRowRuns, k: number): WalkRun {\n  const f = t.flags[k]!\n  const run: WalkRun = {\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) & 3]\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]!)\n      ? undefined\n      : t.referenceStart[k]\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true\n  }\n  return run\n}\n\n/** The rows as bandage-core's `WalkRows`, a run object per run */\nexport function walkRowsOf(t: WalkRowRuns, unit?: number): WalkRows {\n  const rows = t.rows.map((meta, i) => {\n    const runs: WalkRun[] = []\n    for (let k = t.offsets[i]!; k < t.offsets[i + 1]!; k++) {\n      runs.push(runAt(t, k))\n    }\n    return { ...meta, runs }\n  })\n  return { origin: t.origin, unit, reference: rows[0]!, rows: rows.slice(1) }\n}\n"],
-  "mappings": 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