jbrowse-plugin-graphgenomeviewer 6.2.0 → 6.3.1

package/dist/chunks/{chunk-X24J6VF4.js → chunk-DILFGQIL.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-X24J6VF4.js.map → chunk-DILFGQIL.js.map}

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package/dist/chunks/{chunk-7MWOPEIC.js → chunk-EHV7EUMI.js}

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package/dist/chunks/{chunk-7MWOPEIC.js.map → chunk-EHV7EUMI.js.map}

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package/dist/chunks/chunk-GMSOU6VO.js

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package/dist/chunks/chunk-GMSOU6VO.js.map

@@ -0,0 +1,7 @@
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+  "sources": ["global-externals:tss-react/mui", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JKJWSY4V.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-6JEWNXCQ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-UVBGRJQX.js"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"tss-react/mui\"];", "// src/colorSchemes.ts\nvar COLOR_SCHEMES = [\n  // Mirrors `layoutModes`' 'auto': a value the model resolves rather than a\n  // colour of its own. It exists because 'uniform' was the default, so a\n  // launched graph opened flat grey and both tutorials spent a step saying \"now\n  // pick a colour\" \u2014 one figure literally drives that click. A graph with\n  // reference coordinates resolves to 'reference-position', which is the one\n  // ramp a linear track beside it can be painted with too; a graph with none\n  // keeps 'uniform', because there the ramp would be a hue nothing earned.\n  //\n  // Resolve through `effectiveColorScheme`; the dropdown reads the raw prop, so\n  // \"Auto\" stays selectable and visible as what it is.\n  { value: \"auto\", label: \"Auto\" },\n  { value: \"uniform\", label: \"Uniform\" },\n  { value: \"random\", label: \"Random\" },\n  { value: \"rainbow\", label: \"Rainbow\" },\n  { value: \"depth\", label: \"Depth\" },\n  { value: \"node-length\", label: \"Node length\" },\n  { value: \"stable-rank\", label: \"Stable rank\" },\n  { value: \"reference-position\", label: \"Reference position\" },\n  { value: \"grey\", label: \"Grey\" }\n];\nvar COLOR_SCHEME_VALUES = COLOR_SCHEMES.map((s) => s.value);\nfunction resolveColorScheme(scheme, graph) {\n  return scheme !== \"auto\" ? scheme : graph?.anchoredBy ? \"reference-position\" : \"uniform\";\n}\n\nexport {\n  COLOR_SCHEMES,\n  COLOR_SCHEME_VALUES,\n  resolveColorScheme\n};\n", "// src/layout/drawnScale.ts\nvar MEAN_NODE_LENGTH = 40;\nvar MIN_TOTAL_GRAPH_LENGTH = 500;\nvar BANDAGE_MINIMUM_NODE_LENGTH = 5;\nfunction drawnNodeLength(opts, length) {\n  return Math.max(\n    opts.nodeLengthPerMegabase * length / 1e6,\n    opts.minimumNodeLength\n  );\n}\nfunction bandageAutoScale(graph, minNodeLength = BANDAGE_MINIMUM_NODE_LENGTH) {\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const megabases = totalLength / 1e6;\n  const target = Math.max(\n    graph.nodes.length * MEAN_NODE_LENGTH,\n    MIN_TOTAL_GRAPH_LENGTH\n  );\n  return {\n    nodeLengthPerMegabase: megabases > 0 ? target / megabases : 1e4,\n    minimumNodeLength: Math.max(BANDAGE_MINIMUM_NODE_LENGTH, minNodeLength),\n    edgeLength: 5,\n    nodeSegmentLength: 20\n  };\n}\nvar PROPORTIONAL_LENGTH = { power: 1, effect: 1 };\nfunction isProportional(law) {\n  return law.power === 1 && law.effect === 1;\n}\nfunction drawnLengthFor(graph, law) {\n  const count = graph.nodes.length;\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const meanBp = count > 0 ? totalLength / count : 0;\n  const meanDrawn = count > 0 ? 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+}

package/dist/chunks/{chunk-EKMGHBWM.js → chunk-KRXALLQG.js}

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 function o(t){return t===void 0||t==="*"?void 0:t}function r(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],segmentCount:+e[3],pathCount:+e[4],inversion:e[5]==="1",shortestAlleleLength:+e[6],longestAlleleLength:+e[7],segments:e[11],shortestAllele:o(e[12]),longestAllele:o(e[13])}}function i(t,e){return t.refName===e.refName&&t.start===e.start&&t.end===e.end}function u(t){let{shortestAlleleLength:e,longestAlleleLength:n}=t;return e===n?`${n.toLocaleString()} bp`:`${e.toLocaleString()}-${n.toLocaleString()} bp`}var s=2147483647;function a(t){let{pathCount:e,segmentCount:n,inversion:l}=t;return[`${n} segments`,e===s?"more paths than gfatools counts":`up to ${e.toLocaleString()} paths`,...l?["inversion"]:[]].join(", ")}export{r as a,i as b,u as c,s as d,a as e};
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package/dist/chunks/chunk-WTOQRUK2.js.map

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+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-G2FD7S3C.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WFB5TXRA.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ES2N6V56.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HBEKUQO4.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DPV2CUIE.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", "import {\n  bypassedPoints\n} from \"./chunk-N6FECAXP.js\";\nimport {\n  computeEdgeCurves,\n  edgeJoinOf,\n  routedEdgeCurves,\n  strandSides\n} from \"./chunk-2CVHXFK7.js\";\n\n// src/util/edgeCurves.ts\nvar cache = /* @__PURE__ */ new WeakMap();\nfunction baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {\n  const { scaleX, scaleY } = axis;\n  const cached = cache.get(nodePositions);\n  if (cached?.graph === graph && cached.scaleX === scaleX && cached.scaleY === scaleY && cached.deletions === deletions && cached.routes === routes && cached.stranded === stranded && cached.version === version) {\n    return cached.curves;\n  }\n  const curves = /* @__PURE__ */ new Map();\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const from = nodePositions[edge.from];\n    const to = nodePositions[edge.to];\n    if (from?.length && to?.length) {\n      const bypassed = deletions?.get(ei);\n      const route = bypassed && routes?.[ei];\n      curves.set(\n        ei,\n        route ? routedEdgeCurves(\n          from,\n          to,\n          route,\n          stranded ? strandSides(edge) : void 0\n        ) : computeEdgeCurves(\n          from,\n          to,\n          edgeJoinOf(edge, stranded),\n          0,\n          0,\n          axis,\n          bypassed ? bypassedPoints(nodePositions, bypassed) : []\n        )\n      );\n    }\n  }\n  cache.set(nodePositions, {\n    graph,\n    scaleX,\n    scaleY,\n    deletions,\n    routes,\n    stranded,\n    version,\n    curves\n  });\n  return curves;\n}\n\nexport {\n  baseEdgeCurves\n};\n", "import {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/referenceSpan.ts\nvar MAX_BACKBONE_HOPS = 4;\nfunction buildNeighbors(graph) {\n  const neighbors = /* @__PURE__ */ new Map();\n  function add(from, to) {\n    const list = neighbors.get(from);\n    if (list) {\n      list.push(to);\n    } else {\n      neighbors.set(from, [to]);\n    }\n  }\n  for (const edge of graph.edges) {\n    add(edge.from, edge.to);\n    add(edge.to, edge.from);\n  }\n  return neighbors;\n}\nfunction flankingSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const seen = /* @__PURE__ */ new Set([nodeId]);\n  let frontier = [nodeId];\n  let minEnd = Infinity;\n  let maxStart = -Infinity;\n  for (let hop = 0; hop < MAX_BACKBONE_HOPS && frontier.length > 0; hop++) {\n    const next = [];\n    for (const id of frontier) {\n      const adjacent = neighbors.get(id);\n      if (adjacent) {\n        for (const neighborId of adjacent) {\n          if (!seen.has(neighborId)) {\n            seen.add(neighborId);\n            const neighbor = nodeById.get(neighborId);\n            if (neighbor && isBackbone(neighbor)) {\n              minEnd = Math.min(minEnd, neighbor.stable.start + neighbor.length);\n              maxStart = Math.max(maxStart, neighbor.stable.start);\n            } else {\n              next.push(neighborId);\n            }\n          }\n        }\n      }\n    }\n    frontier = next;\n  }\n  return minEnd === Infinity ? void 0 : {\n    start: Math.min(minEnd, maxStart),\n    end: Math.max(minEnd, maxStart)\n  };\n}\nfunction nodeReferenceSpan({\n  nodeId,\n  nodeById,\n  neighbors\n}) {\n  const node = nodeById.get(nodeId);\n  return node === void 0 ? void 0 : isBackbone(node) ? { start: node.stable.start, end: node.stable.start + node.length } : flankingSpan({ nodeId, nodeById, neighbors });\n}\nfunction referenceMidpoints(graph) {\n  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));\n  const neighbors = buildNeighbors(graph);\n  const midpoints = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const span = nodeReferenceSpan({ nodeId: node.id, nodeById, neighbors });\n    if (span) {\n      midpoints.set(node.id, (span.start + span.end) / 2);\n    }\n  }\n  return midpoints;\n}\n\nexport {\n  buildNeighbors,\n  nodeReferenceSpan,\n  referenceMidpoints\n};\n", "import {\n  abgrToCssRgba,\n  fadeAbgr,\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\nimport {\n  meanDepth,\n  nodeWidthPx\n} from \"./chunk-PBENCR5L.js\";\nimport {\n  PATH_LIGHTNESS,\n  PATH_SATURATION,\n  nameHue,\n  pathHueAt\n} from \"./chunk-7GBL7SJY.js\";\nimport {\n  baseEdgeCurves\n} from \"./chunk-WFB5TXRA.js\";\nimport {\n  referenceMidpoints\n} from \"./chunk-ES2N6V56.js\";\nimport {\n  dashCurves,\n  pathRibbonOffsets,\n  strandSides,\n  translateCurves,\n  yToXOf\n} from \"./chunk-2CVHXFK7.js\";\n\n// src/renderer/GeometryBuilder.ts\nvar EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);\nvar EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);\nvar EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);\nvar DELETION_THICKNESS_FACTOR = 2.2;\nvar LIFT_BACKDROP_COLOR = packAbgr(160, 160, 160, 255);\nvar FADED_ALPHA = 0.18;\nvar LIFT_BACKDROP_CSS = abgrToCssRgba(\n  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)\n);\nvar DELETION_DASH_PX = 11;\nvar MIN_PATH_STRIPE_PX = 1.2;\nvar MIN_WALK_LANE_PX = 4;\nvar MIN_SCALE_FOR_OFFSET = 1e-6;\nvar ARROW_LENGTH_BASE_PX = 7;\nvar ARROW_LENGTH_PER_EDGE_PX = 3;\nvar ARROW_HALF_WIDTH_BASE_PX = 3;\nvar ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;\nvar MIN_LINK_HEADS = 3;\nvar MIN_ARROW_FIT = 0.5;\nvar MIN_ARROW_SCALE = 0.45;\nvar ARROW_CURVE_STEPS = 12;\nvar ABUTTING_PX = 1e-6;\nvar walkX = new Float64Array(64);\nvar walkY = new Float64Array(64);\nvar walkPx = new Float64Array(64);\nfunction backFromEnd(curves, scale, yToX, untilPx) {\n  const most = curves.length * ARROW_CURVE_STEPS + 1;\n  if (walkX.length < most) {\n    walkX = new Float64Array(most);\n    walkY = new Float64Array(most);\n    walkPx = new Float64Array(most);\n  }\n  const last = curves[curves.length - 1];\n  walkX[0] = last.x1;\n  walkY[0] = last.y1;\n  walkPx[0] = 0;\n  let n = 1;\n  let px = 0;\n  for (let ci = curves.length - 1; ci >= 0 && px < untilPx; ci--) {\n    const c = curves[ci];\n    for (let k = 1; k <= ARROW_CURVE_STEPS && px < untilPx; k++) {\n      const t = 1 - (k / ARROW_CURVE_STEPS) ** 2;\n      const u = 1 - t;\n      const a = u * u * u;\n      const b = 3 * u * u * t;\n      const d = 3 * u * t * t;\n      const e = t * t * t;\n      const x = a * c.x0 + b * c.cx0 + d * c.cx1 + e * c.x1;\n      const y = a * c.y0 + b * c.cy0 + d * c.cy1 + e * c.y1;\n      px += Math.hypot(x - walkX[n - 1], (y - walkY[n - 1]) * yToX) * scale;\n      walkX[n] = x;\n      walkY[n] = y;\n      walkPx[n] = px;\n      n++;\n    }\n  }\n  return n;\n}\nfunction walkPointAt(n, px) {\n  let i = 1;\n  while (i < n - 1 && walkPx[i] < px) {\n    i++;\n  }\n  const from = walkPx[i - 1];\n  const to = walkPx[i];\n  const f = to > from ? Math.min(1, Math.max(0, (px - from) / (to - from))) : 0;\n  return {\n    x: walkX[i - 1] + (walkX[i] - walkX[i - 1]) * f,\n    y: walkY[i - 1] + (walkY[i] - walkY[i - 1]) * f\n  };\n}\nfunction arrowheadFor({\n  curves,\n  edgeHalfWidth,\n  nodeHalfWidth,\n  scale,\n  yToX,\n  color,\n  fromSegments,\n  toSegments\n}) {\n  const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;\n  const n = backFromEnd(\n    curves,\n    scale,\n    yToX,\n    nodeHalfWidth + MIN_LINK_HEADS * length\n  );\n  const lengthPx = walkPx[n - 1];\n  const abutting = lengthPx < ABUTTING_PX;\n  const inset = Math.min(nodeHalfWidth, lengthPx);\n  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, yToX) / length) : 1;\n  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {\n    return void 0;\n  }\n  const tip = walkPointAt(n, inset);\n  const base = walkPointAt(n, inset + length * fit);\n  const dx = tip.x - base.x;\n  const dy = (tip.y - base.y) * yToX;\n  const last = curves[curves.length - 1];\n  return {\n    x: tip.x,\n    y: tip.y,\n    angle: Math.hypot(dx, dy) > 0 ? Math.atan2(dy, dx) : endTangent(last, yToX, intoDirection(last, toSegments)),\n    length: length * fit,\n    halfWidth: (ARROW_HALF_WIDTH_BASE_PX + ARROW_HALF_WIDTH_PER_EDGE_PX * edgeHalfWidth) * fit,\n    color\n  };\n}\nfunction polylinePx(segments, scale, yToX) {\n  let length = 0;\n  for (let i = 1; i < segments.length; i++) {\n    length += Math.hypot(\n      segments[i].x - segments[i - 1].x,\n      (segments[i].y - segments[i - 1].y) * yToX\n    );\n  }\n  return length * scale;\n}\nfunction leavesStart(edge, segments, first, stranded, yToX) {\n  if (stranded) {\n    return strandSides(edge).from === \"start\";\n  }\n  const gap = (p) => Math.hypot(p.x - first.x0, (p.y - first.y0) * yToX);\n  return gap(segments[0]) < gap(segments.at(-1));\n}\nfunction intoDirection(last, toSegments) {\n  if (toSegments.length < 2) {\n    return void 0;\n  }\n  const first = toSegments[0];\n  const final = toSegments[toSegments.length - 1];\n  const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);\n  return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };\n}\nfunction pointNormalsOf(rawPoints, yToX = 1) {\n  const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));\n  const pointNormals = [];\n  for (let i = 0; i < points.length; i++) {\n    let nx = 0;\n    let ny = 0;\n    if (i === 0) {\n      const dx = points[1].x - points[0].x;\n      const dy = points[1].y - points[0].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else if (i === points.length - 1) {\n      const dx = points[i].x - points[i - 1].x;\n      const dy = points[i].y - points[i - 1].y;\n      const len = Math.hypot(dx, dy);\n      if (len > 0) {\n        nx = -dy / len;\n        ny = dx / len;\n      }\n    } else {\n      const dx1 = points[i].x - points[i - 1].x;\n      const dy1 = points[i].y - points[i - 1].y;\n      const len1 = Math.hypot(dx1, dy1);\n      const dx2 = points[i + 1].x - points[i].x;\n      const dy2 = points[i + 1].y - points[i].y;\n      const len2 = Math.hypot(dx2, dy2);\n      if (len1 > 0 && len2 > 0) {\n        const nx1 = -dy1 / len1;\n        const ny1 = dx1 / len1;\n        const nx2 = -dy2 / len2;\n        const ny2 = dx2 / len2;\n        nx = (nx1 + nx2) / 2;\n        ny = (ny1 + ny2) / 2;\n        const dot = nx1 * nx + ny1 * ny;\n        if (dot > 0.1) {\n          nx /= dot;\n          ny /= dot;\n        }\n      } else if (len1 > 0) {\n        nx = -dy1 / len1;\n        ny = dx1 / len1;\n      } else if (len2 > 0) {\n        nx = -dy2 / len2;\n        ny = dx2 / len2;\n      }\n    }\n    pointNormals.push({ nx, ny });\n  }\n  return pointNormals;\n}\nfunction offsetPolyline(points, normals, distance, yToX = 1) {\n  return points.map((p, i) => ({\n    x: p.x + normals[i].nx * distance,\n    y: p.y + normals[i].ny * distance / yToX\n  }));\n}\nfunction packNorm(r, g, b, a) {\n  return packAbgr(\n    Math.round(r * 255),\n    Math.round(g * 255),\n    Math.round(b * 255),\n    Math.round(a * 255)\n  );\n}\nfunction hslToRgb(h, s, l) {\n  const c = (1 - Math.abs(2 * l - 1)) * s;\n  const x = c * (1 - Math.abs(h / 60 % 2 - 1));\n  const m = l - c / 2;\n  let r = 0;\n  let g = 0;\n  let b = 0;\n  if (h < 60) {\n    r = c;\n    g = x;\n  } else if (h < 120) {\n    r = x;\n    g = c;\n  } else if (h < 180) {\n    g = c;\n    b = x;\n  } else if (h < 240) {\n    g = x;\n    b = c;\n  } else if (h < 300) {\n    r = x;\n    b = c;\n  } else {\n    r = c;\n    b = x;\n  }\n  return [r + m, g + m, b + m];\n}\nvar DEPTH_GRADIENT = [\n  [68, 1, 84],\n  [59, 82, 139],\n  [33, 145, 140],\n  [94, 201, 98],\n  [253, 231, 37]\n];\nvar STABLE_RANK_GRADIENT = [\n  [237, 137, 44],\n  [158, 42, 122]\n];\nvar NODE_LENGTH_GRADIENT = [\n  [220, 50, 50],\n  [50, 120, 220]\n];\nfunction sampleGradient(stops, t) {\n  const pos = Math.max(0, Math.min(1, t)) * (stops.length - 1);\n  const i = Math.min(stops.length - 2, Math.floor(pos));\n  const f = pos - i;\n  const a = stops[i];\n  const b = stops[i + 1];\n  return packAbgr(\n    Math.round(a[0] + (b[0] - a[0]) * f),\n    Math.round(a[1] + (b[1] - a[1]) * f),\n    Math.round(a[2] + (b[2] - a[2]) * f),\n    255\n  );\n}\nfunction hashColor(str, alpha) {\n  const [r, g, b] = hslToRgb(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS);\n  return packNorm(r, g, b, alpha);\n}\nvar REFERENCE_RAMP_MAX_HUE = 300;\nvar REFERENCE_RAMP_SATURATION = 0.7;\nvar REFERENCE_RAMP_LIGHTNESS = 0.5;\nvar REFERENCE_RAMP_ALT_RGB = [60, 65, 72];\nvar REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);\nvar REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(\", \")})`;\nfunction computeReferenceRamp(graph, domain) {\n  const midpoints = referenceMidpoints(graph);\n  if (domain && domain.end > domain.start) {\n    return {\n      start: domain.start,\n      span: domain.end - domain.start,\n      midpoints\n    };\n  }\n  let min = Infinity;\n  let max = -Infinity;\n  for (const mid of midpoints.values()) {\n    min = Math.min(min, mid);\n    max = Math.max(max, mid);\n  }\n  return {\n    start: min === Infinity ? 0 : min,\n    span: max > min ? max - min : 1,\n    midpoints\n  };\n}\nfunction computeColorSchemeRange(graph) {\n  let minDepth = Infinity;\n  let maxDepth = -Infinity;\n  let minLength = Infinity;\n  let maxLength = -Infinity;\n  let maxRank = 0;\n  for (const n of graph.nodes) {\n    if (n.stable !== void 0 && n.stable.rank > maxRank) {\n      maxRank = n.stable.rank;\n    }\n    if (n.depth < minDepth) {\n      minDepth = n.depth;\n    }\n    if (n.depth > maxDepth) {\n      maxDepth = n.depth;\n    }\n    if (n.length < minLength) {\n      minLength = n.length;\n    }\n    if (n.length > maxLength) {\n      maxLength = n.length;\n    }\n  }\n  return {\n    minDepth,\n    maxDepth,\n    minLength,\n    maxLength,\n    maxRank,\n    nodeCount: graph.nodes.length\n  };\n}\nfunction getNodeColor(node, nodeIndex, colorScheme, range) {\n  switch (colorScheme) {\n    case \"random\":\n      return hashColor(node.id, 1);\n    case \"depth\":\n      return sampleGradient(\n        DEPTH_GRADIENT,\n        range.maxDepth > range.minDepth ? (node.depth - range.minDepth) / (range.maxDepth - range.minDepth) : 0.5\n      );\n    case \"node-length\":\n      return sampleGradient(\n        NODE_LENGTH_GRADIENT,\n        range.maxLength > range.minLength ? (node.length - range.minLength) / (range.maxLength - range.minLength) : 0.5\n      );\n    // rGFA states the backbone rather than leaving it to be inferred: rank 0 is\n    // the reference, higher ranks are the sequence that diverges from it. A\n    // graph with no SR tags draws every node as unranked.\n    case \"stable-rank\":\n      return node.stable === void 0 ? packAbgr(160, 160, 160, 255) : node.stable.rank === 0 ? packAbgr(52, 152, 219, 255) : sampleGradient(\n        STABLE_RANK_GRADIENT,\n        range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0\n      );\n    // Position on the reference, the one quantity both panels of a\n    // graph-over-linear figure can state. A node with no reference position at\n    // all \u2014 nothing anchored, or an allele whose flanks fell outside the cut \u2014\n    // is grey rather than a hue it has not earned.\n    case \"reference-position\": {\n      const ramp = range.referenceRamp;\n      const mid = ramp?.midpoints.get(node.id);\n      if (ramp === void 0 || mid === void 0) {\n        return packAbgr(160, 160, 160, 255);\n      }\n      if (node.stable !== void 0 && node.stable.rank > 0) {\n        return REFERENCE_RAMP_ALT_COLOR;\n      }\n      const frac = Math.max(0, Math.min(1, (mid - ramp.start) / ramp.span));\n      const [r, g, b] = hslToRgb(\n        frac * REFERENCE_RAMP_MAX_HUE,\n        REFERENCE_RAMP_SATURATION,\n        REFERENCE_RAMP_LIGHTNESS\n      );\n      return packNorm(r, g, b, 1);\n    }\n    case \"grey\":\n      return packAbgr(160, 160, 160, 255);\n    case \"rainbow\": {\n      const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;\n      const [r, g, b] = hslToRgb(hue, 0.75, 0.5);\n      return packNorm(r, g, b, 1);\n    }\n    default:\n      return packAbgr(52, 152, 219, 255);\n  }\n}\nfunction endTangent(c, yToX = 1, into) {\n  const candidates = [\n    [c.cx1, c.cy1],\n    [c.cx0, c.cy0],\n    [c.x0, c.y0]\n  ];\n  for (const [x, y] of candidates) {\n    const dx = c.x1 - x;\n    const dy = (c.y1 - y) * yToX;\n    if (Math.hypot(dx, dy) > 0) {\n      return Math.atan2(dy, dx);\n    }\n  }\n  return into ? Math.atan2((into.to.y - into.from.y) * yToX, into.to.x - into.from.x) : 0;\n}\nfunction isPolylineInBounds(segments, bounds) {\n  let hit = false;\n  for (let i = 0; i < segments.length - 1 && !hit; i++) {\n    const a = segments[i];\n    const b = segments[i + 1];\n    hit = Math.max(a.x, b.x) >= bounds.minX && Math.min(a.x, b.x) <= bounds.maxX && Math.max(a.y, b.y) >= bounds.minY && Math.min(a.y, b.y) <= bounds.maxY;\n  }\n  return hit;\n}\nfunction isBezierInBounds(curves, bounds) {\n  for (const c of curves) {\n    const cMinX = Math.min(c.x0, c.cx0, c.cx1, c.x1);\n    const cMaxX = Math.max(c.x0, c.cx0, c.cx1, c.x1);\n    const cMinY = Math.min(c.y0, c.cy0, c.cy1, c.y1);\n    const cMaxY = Math.max(c.y0, c.cy0, c.cy1, c.y1);\n    if (cMaxX >= bounds.minX && cMinX <= bounds.maxX && cMaxY >= bounds.minY && cMinY <= bounds.maxY) {\n      return true;\n    }\n  }\n  return false;\n}\nvar paletteCache = /* @__PURE__ */ new WeakMap();\nfunction pathPaletteOf(graph) {\n  let palette = paletteCache.get(graph);\n  if (!palette) {\n    const pathColorByIndex = [];\n    const pathIndexByName = /* @__PURE__ */ new Map();\n    const paths = graph.paths ?? [];\n    for (let i = 0; i < paths.length; i++) {\n      const [r, g, b] = hslToRgb(\n        pathHueAt(i, paths.length),\n        PATH_SATURATION,\n        PATH_LIGHTNESS\n      );\n      pathColorByIndex.push(packNorm(r, g, b, 0.85));\n      if (!pathIndexByName.has(paths[i].name)) {\n        pathIndexByName.set(paths[i].name, i);\n      }\n    }\n    palette = { pathColorByIndex, pathIndexByName };\n    paletteCache.set(graph, palette);\n  }\n  return palette;\n}\nvar slotsCache = /* @__PURE__ */ new WeakMap();\nvar NO_SLOTS = /* @__PURE__ */ new Map();\nfunction pathSlotsOf(graph) {\n  let slots = slotsCache.get(graph);\n  if (!slots) {\n    slots = /* @__PURE__ */ new Map();\n    for (const [pathIdx, path] of (graph.paths ?? []).entries()) {\n      for (const nodeId of new Set(path.nodeIds)) {\n        const visits = slots.get(nodeId);\n        if (visits) {\n          visits.push(pathIdx);\n        } else {\n          slots.set(nodeId, [pathIdx]);\n        }\n      }\n    }\n    slotsCache.set(graph, slots);\n  }\n  return slots;\n}\nfunction buildGeometry(options) {\n  const {\n    nodePositions,\n    graph,\n    nodeById,\n    colorScheme,\n    contigThickness,\n    connectorThickness,\n    drawPaths,\n    nodeWidth = \"uniform\",\n    highlight,\n    axis,\n    linearLayout,\n    viewportBounds,\n    referenceRamp,\n    deletions,\n    deletionRoutes,\n    stranded,\n    hiddenEdges,\n    version = 0\n  } = options;\n  const depthNorm = nodeWidth === \"depth\" ? meanDepth(graph) : 0;\n  const scale = axis.scaleX;\n  const yToX = yToXOf(axis);\n  const sharedCurves = baseEdgeCurves(\n    nodePositions,\n    graph,\n    axis,\n    deletions,\n    version,\n    deletionRoutes,\n    stranded\n  );\n  const nodeStrokes = [];\n  const nodeStrokeRuns = /* @__PURE__ */ new Map();\n  const arrows = [];\n  const arrowRuns = /* @__PURE__ */ new Map();\n  const edgeCurves = [];\n  const edgeCurveRuns = /* @__PURE__ */ new Map();\n  const colorRange = { ...computeColorSchemeRange(graph), referenceRamp };\n  const nodeIndexMap = /* @__PURE__ */ new Map();\n  if (colorScheme === \"rainbow\") {\n    for (let i = 0; i < graph.nodes.length; i++) {\n      nodeIndexMap.set(graph.nodes[i].id, i);\n    }\n  }\n  const pathCount = graph.paths?.length ?? 0;\n  const { pathColorByIndex, pathIndexByName } = pathPaletteOf(graph);\n  const pathColorByName = (name) => pathColorByIndex[pathIndexByName.get(name) ?? -1] ?? EDGE_PATH_FALLBACK_COLOR;\n  const nodePathSlots = drawPaths && pathCount > 1 ? pathSlotsOf(graph) : NO_SLOTS;\n  const showArrows = scale > (linearLayout ? 1 : MIN_ARROW_SCALE);\n  for (let ei = 0; ei < graph.edges.length; ei++) {\n    const edge = graph.edges[ei];\n    const fromSegments = nodePositions[edge.from];\n    const toSegments = nodePositions[edge.to];\n    const baseCurves = sharedCurves.get(ei);\n    if (!fromSegments?.length || !toSegments?.length || !baseCurves || hiddenEdges?.has(ei)) {\n      continue;\n    }\n    const numPaths = edge.pathIds?.length ?? 0;\n    const bypassed = deletions?.get(ei);\n    const isDeletion = bypassed !== void 0;\n    const onWalk = highlight?.edgeIndexes.has(ei) ?? false;\n    const edgeThickness = connectorThickness / 2 * (isDeletion ? DELETION_THICKNESS_FACTOR : 1);\n    const ribbons = drawPaths && numPaths > 0;\n    const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;\n    const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);\n    const toNode = nodeById.get(edge.to);\n    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;\n    const buildSingleEdge = (offsetX, offsetY, color, arrowColor) => {\n      const curves = offsetX === 0 && offsetY === 0 ? baseCurves : translateCurves(baseCurves, offsetX, offsetY);\n      if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n        return;\n      }\n      if (isDeletion) {\n        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {\n          edgeCurves.push({ curves: dash, thickness: edgeThickness, color });\n        }\n      } else {\n        edgeCurves.push({ curves, thickness: edgeThickness, color });\n      }\n      const head = showArrows && arrowColor !== void 0 ? arrowheadFor({\n        curves,\n        edgeHalfWidth: connectorThickness / 2,\n        nodeHalfWidth: intoHalfWidth,\n        scale,\n        yToX,\n        color: arrowColor,\n        fromSegments,\n        toSegments\n      }) : void 0;\n      if (head) {\n        arrows.push(head);\n      }\n    };\n    const edgeCurveStart = edgeCurves.length;\n    const arrowStart = arrows.length;\n    const laneWalks = highlight && onWalk && !ribbons ? highlight.walks : void 0;\n    if (laneWalks) {\n      const fromNode = nodeById.get(edge.from);\n      const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;\n      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(fromSegments, yToX);\n      const { nx, ny } = (leavesStart(\n        edge,\n        fromSegments,\n        baseCurves[0],\n        stranded,\n        yToX\n      ) ? normals[0] : normals.at(-1)) ?? {\n        nx: 0,\n        ny: 0\n      };\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      laneWalks.forEach((walk, lane) => {\n        if (!walk.edgeIndexes.has(ei)) {\n          return;\n        }\n        const offset = (lane - (laneWalks.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        const curves = offset === 0 ? baseCurves : translateCurves(baseCurves, nx * offset, ny * offset / yToX);\n        if (viewportBounds && !isBezierInBounds(curves, viewportBounds)) {\n          return;\n        }\n        edgeCurves.push({\n          curves,\n          thickness: laneWidth / 2,\n          color: walk.colors.get(edge.from) ?? walk.colors.get(edge.to) ?? plainEdgeColor\n        });\n      });\n    } else if (!ribbons) {\n      buildSingleEdge(0, 0, edgeColor, edgeColor);\n    } else {\n      const offsets = pathRibbonOffsets(\n        fromSegments,\n        toSegments,\n        numPaths,\n        axis\n      );\n      const arrowRibbon = Math.floor((numPaths - 1) / 2);\n      for (let pathIdx = 0; pathIdx < numPaths; pathIdx++) {\n        const offset = offsets[pathIdx];\n        const ribbonColor = pathColorByName(edge.pathIds[pathIdx]);\n        buildSingleEdge(\n          offset.x,\n          offset.y,\n          highlight && !highlight.names.has(edge.pathIds[pathIdx]) ? fadeAbgr(ribbonColor, FADED_ALPHA) : ribbonColor,\n          pathIdx === arrowRibbon ? edgeColor : void 0\n        );\n      }\n    }\n    const edgeCurveCount = edgeCurves.length - edgeCurveStart;\n    if (edgeCurveCount > 0) {\n      edgeCurveRuns.set(ei, { start: edgeCurveStart, count: edgeCurveCount });\n    }\n    const arrowCount = arrows.length - arrowStart;\n    if (arrowCount > 0) {\n      arrowRuns.set(ei, { start: arrowStart, count: arrowCount });\n    }\n  }\n  for (const [nodeId, segments] of Object.entries(nodePositions)) {\n    const node = nodeById.get(nodeId);\n    if (!node) {\n      continue;\n    }\n    if (viewportBounds && !isPolylineInBounds(segments, viewportBounds)) {\n      continue;\n    }\n    const faded = highlight !== void 0 && !highlight.nodeIds.has(nodeId);\n    const own = faded ? LIFT_BACKDROP_COLOR : getNodeColor(\n      node,\n      nodeIndexMap.get(nodeId) ?? 0,\n      colorScheme,\n      colorRange\n    );\n    const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;\n    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);\n    const nodeThickness = width / 2;\n    const start = nodeStrokes.length;\n    const slots = nodePathSlots.get(nodeId);\n    const slotWidth = width / pathCount;\n    const drawable = segments.length >= 2;\n    const lanes = highlight && !faded && !slots?.length ? highlight.walks : void 0;\n    if (drawable && lanes) {\n      const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX);\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      lanes.forEach((walk, lane) => {\n        const laneColor = walk.colors.get(nodeId);\n        if (laneColor === void 0) {\n          return;\n        }\n        const offset = (lane - (lanes.length - 1) / 2) * laneWidth * worldPerScreenPx;\n        nodeStrokes.push({\n          points: lanes.length === 1 ? segments : offsetPolyline(segments, normals, offset, yToX),\n          thickness: laneWidth / 2,\n          color: laneColor\n        });\n      });\n    } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {\n      const normals = pointNormalsOf(segments, yToX);\n      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);\n      for (const slot of slots) {\n        const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;\n        const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;\n        nodeStrokes.push({\n          points: offsetPolyline(segments, normals, offset, yToX),\n          thickness: slotWidth / 2,\n          // a node off the lifted walk fades whichever way it is painted\n          color: faded ? fadeAbgr(stripe, FADED_ALPHA) : stripe\n        });\n      }\n    } else if (drawable) {\n      nodeStrokes.push({ points: segments, thickness: nodeThickness, color });\n    }\n    const count = nodeStrokes.length - start;\n    if (count > 0) {\n      nodeStrokeRuns.set(nodeId, { start, count });\n    }\n  }\n  return {\n    nodeStrokes,\n    nodeStrokeRuns,\n    arrows,\n    arrowRuns,\n    edgeCurves,\n    edgeCurveRuns\n  };\n}\n\nexport {\n  LIFT_BACKDROP_COLOR,\n  FADED_ALPHA,\n  LIFT_BACKDROP_CSS,\n  hslToRgb,\n  REFERENCE_RAMP_MAX_HUE,\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_ALT_CSS,\n  computeReferenceRamp,\n  computeColorSchemeRange,\n  getNodeColor,\n  endTangent,\n  buildGeometry\n};\n", "import {\n  REFERENCE_RAMP_ALT_COLOR,\n  REFERENCE_RAMP_MAX_HUE,\n  hslToRgb\n} from \"./chunk-HBEKUQO4.js\";\nimport {\n  packAbgr\n} from \"./chunk-G2FD7S3C.js\";\n\n// src/walkEncoding.ts\nvar WALK_FIELDS = [\n  { value: \"progress\", label: \"Progress along the walk\" },\n  { value: \"walk\", label: \"One colour for the walk\" },\n  { value: \"reference\", label: \"Reference position\" }\n];\nvar WALK_SCHEMES = [\n  { value: \"grey\", label: \"Grey to black\", ends: [\"#a3a3a3\", \"#151515\"] },\n  { value: \"blue\", label: \"Cyan to navy\", ends: [\"#6ee0f0\", \"#0b2c7a\"] },\n  { value: \"red\", label: \"Yellow to red\", ends: [\"#ffd24a\", \"#b3121b\"] },\n  { value: \"purple\", label: \"Pink to plum\", ends: [\"#f5a3d8\", \"#5e1a6e\"] },\n  { value: \"green\", label: \"Lime to forest\", ends: [\"#b6e36c\", \"#0b5d3b\"] },\n  { value: \"rainbow\", label: \"Rainbow\" }\n];\nvar FAMILIES = [\"blue\", \"red\", \"purple\", \"green\"];\nvar isField = (v) => WALK_FIELDS.some((f) => f.value === v);\nvar isScheme = (v) => WALK_SCHEMES.some((s) => s.value === v);\nfunction resolveEncoding(layer, reference, picked, alone = true) {\n  const { field: askedField, scheme: askedScheme } = layer.color ?? {};\n  const field = isField(askedField) ? askedField : alone ? \"progress\" : \"walk\";\n  const family = reference ? \"grey\" : FAMILIES[picked % FAMILIES.length];\n  const scheme = isScheme(askedScheme) ? askedScheme === \"rainbow\" && field !== \"reference\" ? family : askedScheme : family;\n  return { field, scheme };\n}\nvar BASE_T = 0.5;\nvar toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;\nvar toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;\nfunction oklab(hex) {\n  const [r, g, b] = [1, 3, 5].map(\n    (i) => toLinear(Number.parseInt(hex.slice(i, i + 2), 16) / 255)\n  );\n  const l = Math.cbrt(0.4122214708 * r + 0.5363325363 * g + 0.0514459929 * b);\n  const m = Math.cbrt(0.2119034982 * r + 0.6806995451 * g + 0.1073969566 * b);\n  const s = Math.cbrt(0.0883024619 * r + 0.2817188376 * g + 0.6299787005 * b);\n  return [\n    0.2104542553 * l + 0.793617785 * m - 0.0040720468 * s,\n    1.9779984951 * l - 2.428592205 * m + 0.4505937099 * s,\n    0.0259040371 * l + 0.7827717662 * m - 0.808675766 * s\n  ];\n}\nfunction oklabToRgb([L, a, b]) {\n  const l = (L + 0.3963377774 * a + 0.2158037573 * b) ** 3;\n  const m = (L - 0.1055613458 * a - 0.0638541728 * b) ** 3;\n  const s = (L - 0.0894841775 * a - 1.291485548 * b) ** 3;\n  return [\n    4.0767416621 * l - 3.3077115913 * m + 0.2309699292 * s,\n    -1.2684380046 * l + 2.6097574011 * m - 0.3413193965 * s,\n    -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s\n  ].map((c) => toGamma(Math.max(0, Math.min(1, c))) * 255);\n}\nfunction schemeRgb(scheme, t) {\n  const x = Math.max(0, Math.min(1, t));\n  const family = WALK_SCHEMES.find((s) => s.value === scheme);\n  if (!family || !(\"ends\" in family)) {\n    return hslToRgb(x * REFERENCE_RAMP_MAX_HUE, 0.7, 0.5).map((c) => c * 255);\n  }\n  const from = oklab(family.ends[0]);\n  const to = oklab(family.ends[1]);\n  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));\n}\nfunction schemeCss(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return `rgb(${r}, ${g}, ${b})`;\n}\nfunction schemeColor(scheme, t) {\n  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);\n  return packAbgr(r, g, b, 255);\n}\nfunction encodedColor({ field, scheme }, t) {\n  return field === \"walk\" ? schemeColor(scheme, BASE_T) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t);\n}\nvar NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;\nfunction encodingStops({ field, scheme }) {\n  return field === \"walk\" ? [{ offset: 0, color: schemeCss(scheme, BASE_T) }] : Array.from({ length: 7 }, (_, i) => ({\n    offset: i / 6,\n    color: schemeCss(scheme, i / 6)\n  }));\n}\nfunction encodingSwatchCss(encoding) {\n  const stops = encodingStops(encoding);\n  return stops.length === 1 ? stops[0].color : `linear-gradient(to right, ${stops.map((s) => `${s.color} ${s.offset * 100}%`).join(\", \")})`;\n}\n\nexport {\n  WALK_FIELDS,\n  WALK_SCHEMES,\n  resolveEncoding,\n  schemeRgb,\n  schemeCss,\n  schemeColor,\n  encodedColor,\n  NO_VALUE_COLOR,\n  encodingStops,\n  encodingSwatchCss\n};\n"],
+  "mappings": 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+}

package/dist/chunks/{chunk-JYZAMHIP.js → chunk-WUGRVNUJ.js}

@@ -1,5 +1,5 @@
-import{c as y}from"./chunk-F7V6ZPKD.js";import{a as m,b as L,c as S,d as u,e as N}from"./chunk-X24J6VF4.js";var O="unknown";function T(e){let t=e.split("	");return{fields:t,name:t.slice(1,4).join("	"),start:+t[4],end:+t[5]}}var b=e=>e.fields[6].match(/[<>][^<>]+/g)??[];function A(e){let t=new Map;for(let o of e)if(o.startsWith("S	")){let[,n,s,...a]=o.split("	"),i=a.find(r=>r.startsWith("LN:i:"));t.set(n,s==="*"&&i?+i.slice(5):s.length)}return t}function G(e,t,o){if(t.end<=e.end)return e;let n=b(t),s=t.start;for(let[a,i]of n.entries()){if(s===e.end){let f=[...e.fields];return f[5]=String(t.end),f[6]=e.fields[6]+n.slice(a).join(""),{...e,fields:f,end:t.end}}let r=o.get(i.slice(1));if(s>e.end||r===void 0)return;s+=r}}function B(e,t,o){let n=[];for(let s of e.sort((a,i)=>a.start-i.start)){let a=n.at(-1),[,i,r,f]=s.fields,d=a!==void 0&&(s.start<a.end||s.start===a.end&&!o(i,+r,f,s.start))?G(a,s,t):void 0;d?n[n.length-1]=d:n.push(s)}return n}var M=e=>e==="+"?"-":"+";function*R(e){let t=b(e).map(o=>({id:o.slice(1),sign:o.startsWith(">")?"+":"-"}));for(let o=1;o<t.length;o++){let n=t[o-1],s=t[o];yield{forward:`L	${n.id}	${n.sign}	${s.id}	${s.sign}	0M`,reverse:`L	${s.id}	${M(s.sign)}	${n.id}	${M(n.sign)}	0M`}}}function x(e,t){if(e.length<=1)return e[0]??"";let o=e.map(c=>c.split(`
+import{c as y}from"./chunk-MYJYGSOH.js";import{a as m,b as L,c as S,d as u,e as N}from"./chunk-DILFGQIL.js";var O="unknown";function T(e){let t=e.split("	");return{fields:t,name:t.slice(1,4).join("	"),start:+t[4],end:+t[5]}}var b=e=>e.fields[6].match(/[<>][^<>]+/g)??[];function A(e){let t=new Map;for(let o of e)if(o.startsWith("S	")){let[,n,s,...a]=o.split("	"),i=a.find(r=>r.startsWith("LN:i:"));t.set(n,s==="*"&&i?+i.slice(5):s.length)}return t}function G(e,t,o){if(t.end<=e.end)return e;let n=b(t),s=t.start;for(let[a,i]of n.entries()){if(s===e.end){let f=[...e.fields];return f[5]=String(t.end),f[6]=e.fields[6]+n.slice(a).join(""),{...e,fields:f,end:t.end}}let r=o.get(i.slice(1));if(s>e.end||r===void 0)return;s+=r}}function B(e,t,o){let n=[];for(let s of e.sort((a,i)=>a.start-i.start)){let a=n.at(-1),[,i,r,f]=s.fields,d=a!==void 0&&(s.start<a.end||s.start===a.end&&!o(i,+r,f,s.start))?G(a,s,t):void 0;d?n[n.length-1]=d:n.push(s)}return n}var M=e=>e==="+"?"-":"+";function*R(e){let t=b(e).map(o=>({id:o.slice(1),sign:o.startsWith(">")?"+":"-"}));for(let o=1;o<t.length;o++){let n=t[o-1],s=t[o];yield{forward:`L	${n.id}	${n.sign}	${s.id}	${s.sign}	0M`,reverse:`L	${s.id}	${M(s.sign)}	${n.id}	${M(n.sign)}	0M`}}}function x(e,t){if(e.length<=1)return e[0]??"";let o=e.map(c=>c.split(`
 `).filter(l=>l!=="")),n=(c,l)=>c.filter(w=>w.startsWith(`${l}	`)),s=A(o.flat()),a=0,i=o.map(c=>{let l=n(c,"W").map(T),w=a;for(let h of l.filter(g=>g.fields[1]===O)){let g=+h.fields[2]+w;h.fields[2]=String(g),h.name=h.fields.slice(1,4).join("	"),a=Math.max(a,g)}return l}),r=new Map;for(let c of[...i.flatMap(l=>l.slice(0,1)),...i.flatMap(l=>l.slice(1))]){let l=r.get(c.name);l?l.push(c):r.set(c.name,[c])}let f=[...r.values()].flatMap(c=>B(c,s,t)),p=new Set(o.flatMap(c=>n(c,"L")));for(let c of f)for(let l of R(c))!p.has(l.forward)&&!p.has(l.reverse)&&p.add(l.forward);return`${[...new Set([...n(o[0],"H"),...o.flatMap(c=>n(c,"S")),...p,...f.map(c=>c.fields.join("	"))])].join(`
 `)}
 `}var F=new Map([["hg38","GRCh38"],["hg19","GRCh37"],["hs1","CHM13"],["t2t-chm13","CHM13"],["chm13v2","CHM13"]]);function v(e){return F.get(e.toLowerCase())}function $(e){let t=e.includes("#")?m(e):void 0;return t===void 0||L(t)?void 0:t}function C(e){return S(e)??m(e)}function E(e){let t=new Set((e.anchorPaths??[]).map(n=>n.name));for(let n of e.nodes)n.stable&&t.add(n.stable.refName);let o=new Map;for(let n of t){let s=$(n);s!==void 0&&(o.get(s)??o.set(s,new Set).get(s)).add(C(n))}return o}function k(e,t){let o=new Set(e.map(f=>$(f.refName))),[n]=o;if(o.size!==1||n===void 0)return{contigs:e,prefixes:[],named:!1};let s=new Set(e.map(f=>C(f.refName))),a=[...t.get(n)??[]].every(f=>s.has(f)),i=new Set(e.map(f=>S(f.refName))),[r]=i;return{contigs:e,prefixes:[...a?[n]:[],...i.size===1&&r?[r]:[]],named:!0}}function H(e){let t=new Map;for(let n of e.nodes)if(y(n)){let{refName:s,start:a}=n.stable,i=a+n.length,r=t.get(s);r?(r.start=Math.min(r.start,a),r.end=Math.max(r.end,i)):t.set(s,{refName:s,contig:u(s),start:a,end:i})}let o=[...t.values()];return o.length?k(o,E(e)):void 0}function te(e,t){let o=H(e),n=t?u(t.refName):o?.contigs.length===1?o.contigs[0].contig:void 0,s=o?.named?m(o.contigs[0].refName):void 0;return n&&(s?`${s} ${n}`:n)}function U(e,t){let o=i=>[i.name,...i.aliases??[]],n=i=>r=>o(r).some(f=>f.toLowerCase()===i.toLowerCase()),s=[...e?.prefixes??[]].reverse(),a=e?.prefixes.find(i=>!i.includes("#"))?.toLowerCase();for(let i of s){let r=t.find(n(i));if(r)return r}return a===void 0?void 0:t.find(i=>o(i).some(r=>v(r)?.toLowerCase()===a))}function ne(e,t){let o=E(e);return e.anchorPaths?.find(n=>U(k([{refName:n.name,contig:u(n.name),start:n.start,end:n.start+n.length}],o),[t]))}function z(e){let t=e.replace(/^chr/i,""),o=t?/^(M|MT)$/i.test(t)?["M","MT"]:[t]:[];return[...new Set([e,...o.flatMap(n=>[n,`chr${n}`])])]}function K(e,t={}){let o=new Set(e),n=new Map;for(let s of o){let a=u(s),i=t[a];for(let r of new Set([...z(a),...i?[i]:[]]))n.set(r,n.has(r)?void 0:s)}return s=>o.has(s)?s:n.get(s)}function oe(e,t,o){let n=K(t.contigs.map(s=>s.refName),o);return e.flatMap(s=>{let a=n(s.refName);return a===void 0?[]:[a===s.refName?s:{...s,refName:a}]})}var W=class extends Error{constructor(e,t){super(t.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${e}" maps to none; set referenceSample`:`the anchor "${e}" is none of the graph's reference samples (${t.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`),this.name="NoReferenceSampleError"}},j=class extends Error{constructor(e,t,o){super(`this ${t.toLocaleString()} bp window reads more than nodeLimit (${e.toLocaleString()}) graph nodes; zoom in to about ${o.toLocaleString()} bp or raise nodeLimit`),this.fitsBp=o,this.name="NodeLimitError",this.regionTooLarge=!0}};function P(e){return`${e.sample}#${e.haplotype}`}function D(e,t){let o=P(e);return t===void 0||t.some(n=>N(o,n))}async function Q(e){return(await e.tag("gbwt_reference_samples")??"").split(/\s+/).filter(t=>t!=="")}function Z(e,t){let o=e.toLowerCase(),n=v(e)?.toLowerCase();return t.find(s=>s===e)??t.find(s=>s.toLowerCase()===o)??t.find(s=>s.toLowerCase()===n)}function q({configured:e,anchorPrefix:t,referenceSamples:o}){if(e!=="")return e;let n=Z(m(t),o)??(o.length===1?o[0]:void 0);if(n===void 0)throw new W(t,o);return n}async function I(e,t,o){let n=(await e.paths()).find(s=>s.isIndexed&&s.name.sample===t&&s.name.contig===o);return n?{sample:n.name.sample,contig:o,haplotype:n.name.haplotype}:void 0}function _(e,t,o){if(e instanceof Error&&(e.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(e.message))){let s=e.walkedBp,a=typeof s=="number"&&s>0?Math.floor(s*.8):Math.floor(o/2);return new j(t,o,Math.max(a,1))}else return}var J={context:1e3,snarls:"contained",limit:1e5};async function V(e,t,o,n,s){if(!t)return"";let a=await e.getSubgraphs({...s,path:t,start:o,end:n,haplotypes:"all"}).catch(r=>{throw _(r,s.limit,n-o)??r}),i=await e.paths();return x(await Promise.all(a.map(r=>r.toGFA())),(r,f,p,d)=>i.some(({name:c})=>c.sample===r&&c.haplotype===f&&c.contig===p&&c.fragment===d))}export{H as a,te as b,U as c,ne as d,oe as e,W as f,j as g,P as h,D as i,Q as j,q as k,I as l,_ as m,J as n,V as o};
-//# sourceMappingURL=chunk-JYZAMHIP.js.map
+//# sourceMappingURL=chunk-WUGRVNUJ.js.map

package/dist/chunks/{chunk-JYZAMHIP.js.map → chunk-WUGRVNUJ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@7.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WSIFAZU7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@7.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RAKOB6IV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@7.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LTUWJKHD.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-WSIFAZU7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RAKOB6IV.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-LTUWJKHD.js"],
   "sourcesContent": ["// src/gbzJoin.ts\nvar UNKNOWN_SAMPLE = \"unknown\";\nfunction parseWalk(line) {\n  const fields = line.split(\"\t\");\n  return {\n    fields,\n    name: fields.slice(1, 4).join(\"\t\"),\n    start: +fields[4],\n    end: +fields[5]\n  };\n}\nvar stepsOf = (walk) => walk.fields[6].match(/[<>][^<>]+/g) ?? [];\nfunction segmentLengths(lines) {\n  const lengths = /* @__PURE__ */ new Map();\n  for (const line of lines) {\n    if (line.startsWith(\"S\t\")) {\n      const [, id, sequence, ...tags] = line.split(\"\t\");\n      const ln = tags.find((tag) => tag.startsWith(\"LN:i:\"));\n      lengths.set(\n        id,\n        sequence === \"*\" && ln ? +ln.slice(\"LN:i:\".length) : sequence.length\n      );\n    }\n  }\n  return lengths;\n}\nfunction extend(a, b, lengths) {\n  if (b.end <= a.end) {\n    return a;\n  }\n  const steps = stepsOf(b);\n  let pos = b.start;\n  for (const [i, step] of steps.entries()) {\n    if (pos === a.end) {\n      const fields = [...a.fields];\n      fields[5] = String(b.end);\n      fields[6] = a.fields[6] + steps.slice(i).join(\"\");\n      return { ...a, fields, end: b.end };\n    }\n    const length = lengths.get(step.slice(1));\n    if (pos > a.end || length === void 0) {\n      return void 0;\n    }\n    pos += length;\n  }\n  return void 0;\n}\nfunction joinPieces(pieces, lengths, startsPath) {\n  const joined = [];\n  for (const piece of pieces.sort((a, b) => a.start - b.start)) {\n    const last = joined.at(-1);\n    const [, sample, haplotype, contig] = piece.fields;\n    const joins = last !== void 0 && (piece.start < last.end || piece.start === last.end && !startsPath(sample, +haplotype, contig, piece.start));\n    const extended = joins ? extend(last, piece, lengths) : void 0;\n    if (extended) {\n      joined[joined.length - 1] = extended;\n    } else {\n      joined.push(piece);\n    }\n  }\n  return joined;\n}\nvar flip = (sign) => sign === \"+\" ? \"-\" : \"+\";\nfunction* stepLinks(walk) {\n  const steps = stepsOf(walk).map((step) => ({\n    id: step.slice(1),\n    sign: step.startsWith(\">\") ? \"+\" : \"-\"\n  }));\n  for (let i = 1; i < steps.length; i++) {\n    const a = steps[i - 1];\n    const b = steps[i];\n    yield {\n      forward: `L\t${a.id}\t${a.sign}\t${b.id}\t${b.sign}\t0M`,\n      reverse: `L\t${b.id}\t${flip(b.sign)}\t${a.id}\t${flip(a.sign)}\t0M`\n    };\n  }\n}\nfunction joinCuts(gfas, startsPath) {\n  if (gfas.length <= 1) {\n    return gfas[0] ?? \"\";\n  }\n  const cuts = gfas.map((gfa) => gfa.split(\"\\n\").filter((line) => line !== \"\"));\n  const ofType = (cut, type) => cut.filter((line) => line.startsWith(`${type}\t`));\n  const lengths = segmentLengths(cuts.flat());\n  let unknownOffset = 0;\n  const walksByCut = cuts.map((cut) => {\n    const walks2 = ofType(cut, \"W\").map(parseWalk);\n    const offset = unknownOffset;\n    for (const walk of walks2.filter((w) => w.fields[1] === UNKNOWN_SAMPLE)) {\n      const haplotype = +walk.fields[2] + offset;\n      walk.fields[2] = String(haplotype);\n      walk.name = walk.fields.slice(1, 4).join(\"\t\");\n      unknownOffset = Math.max(unknownOffset, haplotype);\n    }\n    return walks2;\n  });\n  const byName = /* @__PURE__ */ new Map();\n  for (const walk of [\n    ...walksByCut.flatMap((walks2) => walks2.slice(0, 1)),\n    ...walksByCut.flatMap((walks2) => walks2.slice(1))\n  ]) {\n    const pieces = byName.get(walk.name);\n    if (pieces) {\n      pieces.push(walk);\n    } else {\n      byName.set(walk.name, [walk]);\n    }\n  }\n  const walks = [...byName.values()].flatMap(\n    (pieces) => joinPieces(pieces, lengths, startsPath)\n  );\n  const links = new Set(cuts.flatMap((cut) => ofType(cut, \"L\")));\n  for (const walk of walks) {\n    for (const link of stepLinks(walk)) {\n      if (!links.has(link.forward) && !links.has(link.reverse)) {\n        links.add(link.forward);\n      }\n    }\n  }\n  const lines = /* @__PURE__ */ new Set([\n    ...ofType(cuts[0], \"H\"),\n    ...cuts.flatMap((cut) => ofType(cut, \"S\")),\n    ...links,\n    ...walks.map((walk) => walk.fields.join(\"\t\"))\n  ]);\n  return `${[...lines].join(\"\\n\")}\n`;\n}\n\nexport {\n  joinCuts\n};\n", "import {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\nimport {\n  isBackbone\n} from \"./chunk-FYQWPEEY.js\";\n\n// src/reference.ts\nvar WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([\n  [\"hg38\", \"GRCh38\"],\n  [\"hg19\", \"GRCh37\"],\n  [\"hs1\", \"CHM13\"],\n  [\"t2t-chm13\", \"CHM13\"],\n  [\"chm13v2\", \"CHM13\"]\n]);\nfunction wellKnownSample(assemblyName) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());\n}\nfunction sampleOf(refName) {\n  const sample = refName.includes(\"#\") ? panSNSample(refName) : void 0;\n  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;\n}\nfunction haplotypeOf(refName) {\n  return panSNHaplotype(refName) ?? panSNSample(refName);\n}\nfunction graphHaplotypes(graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName);\n    }\n  }\n  const bySample = /* @__PURE__ */ new Map();\n  for (const refName of refNames) {\n    const sample = sampleOf(refName);\n    if (sample !== void 0) {\n      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);\n      haplotypes.add(haplotypeOf(refName));\n    }\n  }\n  return bySample;\n}\nfunction backboneFrom(contigs, haplotypes) {\n  const samples = new Set(contigs.map((c) => sampleOf(c.refName)));\n  const [sample] = samples;\n  if (samples.size !== 1 || sample === void 0) {\n    return { contigs, prefixes: [], named: false };\n  }\n  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));\n  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));\n  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));\n  const [haplotype] = shared;\n  return {\n    contigs,\n    prefixes: [\n      ...unique ? [sample] : [],\n      ...shared.size === 1 && haplotype ? [haplotype] : []\n    ],\n    named: true\n  };\n}\nfunction graphBackbone(graph) {\n  const spans = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable;\n      const end = start + node.length;\n      const span = spans.get(refName);\n      if (span) {\n        span.start = Math.min(span.start, start);\n        span.end = Math.max(span.end, end);\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end\n        });\n      }\n    }\n  }\n  const contigs = [...spans.values()];\n  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;\n}\nfunction referenceLabel(graph, region) {\n  const backbone = graphBackbone(graph);\n  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;\n  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;\n  return contig && (sample ? `${sample} ${contig}` : contig);\n}\nfunction backboneAssembly(backbone, assemblies) {\n  const names = (a) => [a.name, ...a.aliases ?? []];\n  const naming = (prefix) => (a) => names(a).some((n) => n.toLowerCase() === prefix.toLowerCase());\n  const prefixes = [...backbone?.prefixes ?? []].reverse();\n  const sample = backbone?.prefixes.find((p) => !p.includes(\"#\"))?.toLowerCase();\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix));\n    if (assembly) {\n      return assembly;\n    }\n  }\n  return sample === void 0 ? void 0 : assemblies.find(\n    (a) => names(a).some((n) => wellKnownSample(n)?.toLowerCase() === sample)\n  );\n}\nfunction assemblyWalk(graph, assembly) {\n  const haplotypes = graphHaplotypes(graph);\n  return graph.anchorPaths?.find(\n    (walk) => backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length\n          }\n        ],\n        haplotypes\n      ),\n      [assembly]\n    )\n  );\n}\nfunction contigNames(contig) {\n  const bare = contig.replace(/^chr/i, \"\");\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? [\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\n};\n", "import {\n  joinCuts\n} from \"./chunk-WSIFAZU7.js\";\nimport {\n  wellKnownSample\n} from \"./chunk-RAKOB6IV.js\";\nimport {\n  panSNMatchesPrefix,\n  panSNSample\n} from \"./chunk-BPLIXMH7.js\";\n\n// src/gbzWindow.ts\nvar NoReferenceSampleError = class extends Error {\n  constructor(anchor, referenceSamples) {\n    super(\n      referenceSamples.length === 0 ? `the graph names no reference sample (gbwt_reference_samples) and the anchor \"${anchor}\" maps to none; set referenceSample` : `the anchor \"${anchor}\" is none of the graph's reference samples (${referenceSamples.join(\", \")}); set referenceSample or map it through assemblyNameToPanSN`\n    );\n    this.name = \"NoReferenceSampleError\";\n  }\n};\nvar NodeLimitError = class extends Error {\n  constructor(limit, windowBp, fitsBp) {\n    super(\n      `this ${windowBp.toLocaleString()} bp window reads more than nodeLimit (${limit.toLocaleString()}) graph nodes; zoom in to about ${fitsBp.toLocaleString()} bp or raise nodeLimit`\n    );\n    this.fitsBp = fitsBp;\n    this.name = \"NodeLimitError\";\n    this.regionTooLarge = true;\n  }\n};\nfunction haplotypePrefix(name) {\n  return `${name.sample}#${name.haplotype}`;\n}\nfunction haplotypeWanted(name, wanted) {\n  const prefix = haplotypePrefix(name);\n  return wanted === void 0 || wanted.some((candidate) => panSNMatchesPrefix(prefix, candidate));\n}\nasync function referenceSamplesOf(db) {\n  return (await db.tag(\"gbwt_reference_samples\") ?? \"\").split(/\\s+/).filter((sample) => sample !== \"\");\n}\nfunction aliasedSample(anchorSample, referenceSamples) {\n  const lower = anchorSample.toLowerCase();\n  const alias = wellKnownSample(anchorSample)?.toLowerCase();\n  return referenceSamples.find((s) => s === anchorSample) ?? referenceSamples.find((s) => s.toLowerCase() === lower) ?? referenceSamples.find((s) => s.toLowerCase() === alias);\n}\nfunction resolveReferenceSample({\n  configured,\n  anchorPrefix,\n  referenceSamples\n}) {\n  if (configured !== \"\") {\n    return configured;\n  }\n  const sample = aliasedSample(panSNSample(anchorPrefix), referenceSamples) ?? (referenceSamples.length === 1 ? referenceSamples[0] : void 0);\n  if (sample === void 0) {\n    throw new NoReferenceSampleError(anchorPrefix, referenceSamples);\n  }\n  return sample;\n}\nasync function referencePathQuery(db, referenceSample, refName) {\n  const path = (await db.paths()).find(\n    (p) => p.isIndexed && p.name.sample === referenceSample && p.name.contig === refName\n  );\n  return path ? {\n    sample: path.name.sample,\n    contig: refName,\n    haplotype: path.name.haplotype\n  } : void 0;\n}\nfunction nodeLimitError(error, limit, windowBp) {\n  const isLimit = error instanceof Error && (error.name === \"SubgraphLimitError\" || /^Subgraph size limit of \\d+ nodes exceeded/.test(error.message));\n  if (!isLimit) {\n    return void 0;\n  } else {\n    const walked = error.walkedBp;\n    const fits = typeof walked === \"number\" && walked > 0 ? Math.floor(walked * 0.8) : Math.floor(windowBp / 2);\n    return new NodeLimitError(limit, windowBp, Math.max(fits, 1));\n  }\n}\nvar GBZ_CUT_DEFAULTS = {\n  context: 1e3,\n  snarls: \"contained\",\n  limit: 1e5\n};\nasync function cutWindowGFA(db, query, start, end, opts) {\n  if (!query) {\n    return \"\";\n  }\n  const subgraphs = await db.getSubgraphs({ ...opts, path: query, start, end, haplotypes: \"all\" }).catch((error) => {\n    throw nodeLimitError(error, opts.limit, end - start) ?? error;\n  });\n  const paths = await db.paths();\n  return joinCuts(\n    await Promise.all(subgraphs.map((subgraph) => subgraph.toGFA())),\n    (sample, haplotype, contig, at) => paths.some(\n      ({ name }) => name.sample === sample && name.haplotype === haplotype && name.contig === contig && name.fragment === at\n    )\n  );\n}\n\nexport {\n  NoReferenceSampleError,\n  NodeLimitError,\n  haplotypePrefix,\n  haplotypeWanted,\n  referenceSamplesOf,\n  resolveReferenceSample,\n  referencePathQuery,\n  nodeLimitError,\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA\n};\n"],
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