jbrowse-plugin-graphgenomeviewer 8.3.0 → 8.3.2

package/dist/chunks/chunk-CZI7IP5S.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VA5U4F23.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-4FPEQQFT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.1.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BIYQIWDO.js"],
-  "sourcesContent": ["// src/gfa/walkStops.ts\nvar START_STOP_TAG = \"ws\";\nvar END_STOP_TAG = \"we\";\nvar STOP_KINDS = [\"elsewhere\", \"break\", \"end\"];\nvar GAP_CAUSE_TEXT = {\n  missing: \"not in the graph\",\n  elsewhere: \"on nodes filed elsewhere\",\n  unknown: \"gap, cause unknown\",\n  abridged: \"abridged: steps not loaded\",\n  // a walk file's skip row: the haplotype jumps over the window\n  deleted: \"deleted in this haplotype\"\n};\nvar OUTSIDE_TEXT = \"outside the extracted subgraph\";\nfunction gapParts(bp, after, before) {\n  if (!after && !before) {\n    return [{ bp }];\n  }\n  const left = Math.min(after?.trimmed ?? 0, bp);\n  const right = Math.min(before?.trimmed ?? 0, bp - left);\n  let rest = bp - left - right;\n  const lead = after?.kind === \"break\" ? Math.min(after.bp, rest) : 0;\n  rest -= lead;\n  const trail = before?.kind === \"break\" ? Math.min(before.bp, rest) : 0;\n  rest -= trail;\n  const elsewhere = [after, before].find((s) => s?.kind === \"elsewhere\");\n  const parts = [\n    { bp: left },\n    { bp: lead, cause: \"missing\" },\n    elsewhere?.kind === \"elsewhere\" ? { bp: rest, cause: \"elsewhere\", chunk: elsewhere.chunk } : { bp: rest, cause: \"unknown\" },\n    { bp: trail, cause: \"missing\" },\n    { bp: right }\n  ];\n  return parts.filter((part) => part.bp > 0);\n}\nfunction stopAt(table, i) {\n  const bp = table.bp[i];\n  const ref = table.chunkRefs[i];\n  return stopOf(\n    table.kindNames[table.kinds[i]],\n    Number.isNaN(bp) ? void 0 : bp,\n    table.trimmed[i],\n    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }\n  );\n}\nfunction stopOf(kind, bp, trimmed, chunk) {\n  const cut = trimmed > 0 ? { trimmed } : {};\n  if (kind === \"elsewhere\" && chunk) {\n    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };\n  }\n  if (kind === \"break\" && bp !== void 0) {\n    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };\n  }\n  return kind === \"end\" ? { kind, ...cut } : void 0;\n}\nfunction stopTag(stop) {\n  const parts = [stop.kind];\n  if (\"bp\" in stop && stop.bp !== void 0) {\n    parts.push(`bp=${stop.bp}`);\n  }\n  if (stop.trimmed) {\n    parts.push(`trimmed=${stop.trimmed}`);\n  }\n  if (\"chunk\" in stop && stop.chunk) {\n    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);\n  }\n  return parts.join(\",\");\n}\nfunction parseStopTag(value) {\n  const [kind, ...fields] = value.split(\",\");\n  let bp;\n  let trimmed = 0;\n  let chunk;\n  for (const field of fields) {\n    if (field.startsWith(\"bp=\")) {\n      bp = +field.slice(3);\n    } else if (field.startsWith(\"trimmed=\")) {\n      trimmed = +field.slice(8);\n    } else if (field.startsWith(\"chunk=\")) {\n      const at = field.lastIndexOf(\":\");\n      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };\n    }\n  }\n  return stopOf(kind, bp, trimmed, chunk);\n}\nfunction stopFields(before, after) {\n  return {\n    ...before ? { before } : {},\n    ...after ? { after } : {}\n  };\n}\nfunction walkStopFields(tags) {\n  const before = tags[START_STOP_TAG];\n  const after = tags[END_STOP_TAG];\n  return stopFields(\n    typeof before === \"string\" ? parseStopTag(before) : void 0,\n    typeof after === \"string\" ? parseStopTag(after) : void 0\n  );\n}\nfunction walkStopTags(walks, p) {\n  const tags = [];\n  for (const [tag, table] of [\n    [START_STOP_TAG, walks.before],\n    [END_STOP_TAG, walks.after]\n  ]) {\n    const stop = table && stopAt(table, p);\n    if (stop) {\n      tags.push(`\t${tag}:Z:${stopTag(stop)}`);\n    }\n  }\n  return tags.join(\"\");\n}\nvar StopColumns = class {\n  constructor() {\n    this.kinds = [];\n    this.bp = [];\n    this.trimmed = [];\n    this.chunkRefs = [];\n    this.chunkStarts = [];\n    this.chunkRefNames = [];\n    this.refIndex = /* @__PURE__ */ new Map();\n  }\n  push(stop) {\n    this.kinds.push(STOP_KINDS.indexOf(stop.kind));\n    this.bp.push(\"bp\" in stop && stop.bp !== void 0 ? stop.bp : NaN);\n    this.trimmed.push(stop.trimmed ?? 0);\n    const chunk = \"chunk\" in stop ? stop.chunk : void 0;\n    if (chunk) {\n      let ref = this.refIndex.get(chunk.refName);\n      if (ref === void 0) {\n        ref = this.chunkRefNames.length;\n        this.refIndex.set(chunk.refName, ref);\n        this.chunkRefNames.push(chunk.refName);\n      }\n      this.chunkRefs.push(ref);\n      this.chunkStarts.push(chunk.start);\n    } else {\n      this.chunkRefs.push(-1);\n      this.chunkStarts.push(NaN);\n    }\n  }\n  table() {\n    return {\n      kinds: Uint8Array.from(this.kinds),\n      kindNames: [...STOP_KINDS],\n      bp: Float64Array.from(this.bp),\n      trimmed: Float64Array.from(this.trimmed),\n      chunkRefs: Int32Array.from(this.chunkRefs),\n      chunkStarts: Float64Array.from(this.chunkStarts),\n      chunkRefNames: this.chunkRefNames\n    };\n  }\n};\n\nexport {\n  START_STOP_TAG,\n  END_STOP_TAG,\n  GAP_CAUSE_TEXT,\n  OUTSIDE_TEXT,\n  gapParts,\n  stopAt,\n  stopTag,\n  parseStopTag,\n  stopFields,\n  walkStopFields,\n  walkStopTags,\n  StopColumns\n};\n", "import {\n  stopAt,\n  stopFields,\n  walkStopTags\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  PathVisits\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  panSNFields,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gfa/graphTables.ts\nfunction pLineName(name, start, end) {\n  return start === 0 ? name : `${name}:${start}-${end}`;\n}\nfunction tablePath(w, p) {\n  const walkName = w.names[p];\n  const fields = panSNFields(walkName);\n  const start = w.starts[p];\n  const steps = w.abridgedSteps?.[p] ?? Number.NaN;\n  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };\n  return fields ? {\n    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,\n    start,\n    ...fields,\n    ...stopFields(\n      w.before && stopAt(w.before, p),\n      w.after && stopAt(w.after, p)\n    ),\n    ...abridged\n  } : { name: pLineName(walkName, start, w.ends[p]), start };\n}\nfunction namesByList(lists, names, listCount, pathNames) {\n  const starts = new Int32Array(listCount + 1);\n  for (const list of lists) {\n    starts[list + 1]++;\n  }\n  for (let i = 0; i < listCount; i++) {\n    starts[i + 1] += starts[i];\n  }\n  const fill = starts.slice(0, listCount);\n  const grouped = new Int32Array(lists.length);\n  lists.forEach((list, i) => {\n    grouped[fill[list]++] = names[i];\n  });\n  const listed = new Int32Array(pathNames.length).fill(-1);\n  return Array.from({ length: listCount }, (_, list) => {\n    const out = [];\n    for (let i = starts[list]; i < starts[list + 1]; i++) {\n      const k = grouped[i];\n      if (listed[k] !== list) {\n        listed[k] = list;\n        out.push(pathNames[k]);\n      }\n    }\n    return out;\n  });\n}\nfunction tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {\n  const canonical = new Uint8Array(n.names.length);\n  const claim = (node, reversed) => {\n    if (canonical[node] === 0) {\n      canonical[node] = reversed ? 2 : 1;\n    }\n  };\n  for (let i = 0; i < l.from.length; i++) {\n    claim(l.from[i], l.strands[i] & 1);\n    claim(l.to[i], l.strands[i] & 2);\n  }\n  const stepCount = w.offsets[w.names.length] ?? 0;\n  for (let s = 0; s < stepCount; s++) {\n    const node = w.steps[s];\n    claim(node, w.reversed[s]);\n    if (traversals) {\n      traversals[node]++;\n    }\n  }\n  return n.names.map(\n    (segment, i) => `${segment}${canonical[i] === 2 ? \"-\" : \"+\"}`\n  );\n}\nfunction graphFromTables({ nodes: n, links: l, walks: w }, name = \"Imported GFA\") {\n  const count = n.names.length;\n  const declared = n.lengths.length;\n  const drawnWalks = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      drawnWalks.push(p);\n    }\n  }\n  const traversals = new Int32Array(count);\n  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);\n  const nodes = [];\n  for (let i = 0; i < declared; i++) {\n    const ref = n.refs[i];\n    nodes.push({\n      id: ids[i],\n      name: n.names[i],\n      length: n.lengths[i],\n      depth: Math.max(traversals[i], 1),\n      stable: ref < 0 ? void 0 : {\n        refName: n.refNames[ref],\n        start: n.starts[i],\n        rank: n.ranks[i]\n      },\n      samples: void 0\n    });\n  }\n  const edges = [];\n  const neighbours = new Array(count);\n  const pairList = (a, b) => {\n    const near = neighbours[a];\n    if (near) {\n      for (let j = 0; j < near.length; j += 2) {\n        if (near[j] === b) {\n          return near[j + 1];\n        }\n      }\n    }\n    return void 0;\n  };\n  const addPair = (a, b, list) => {\n    const near = neighbours[a];\n    if (near) {\n      near.push(b, list);\n    } else {\n      neighbours[a] = [b, list];\n    }\n  };\n  const edgeLists = [];\n  let lists = 0;\n  for (let i = 0; i < l.from.length; i++) {\n    const a = l.from[i];\n    const b = l.to[i];\n    edges.push({\n      from: ids[a],\n      to: ids[b],\n      fromStrand: l.strands[i] & 1 ? \"-\" : \"+\",\n      toStrand: l.strands[i] & 2 ? \"-\" : \"+\"\n    });\n    let list = pairList(a, b);\n    if (list === void 0) {\n      list = lists++;\n      addPair(a, b, list);\n      addPair(b, a, list);\n    }\n    edgeLists.push(list);\n  }\n  const adjacency = new Int32Array(count + 1);\n  for (let a = 0; a < count; a++) {\n    adjacency[a + 1] = adjacency[a] + (neighbours[a]?.length ?? 0) / 2;\n  }\n  const adjacentNode = new Int32Array(adjacency[count]);\n  const adjacentList = new Int32Array(adjacency[count]);\n  neighbours.forEach((near, a) => {\n    for (let j = 0; j < near.length; j += 2) {\n      adjacentNode[adjacency[a] + j / 2] = near[j];\n      adjacentList[adjacency[a] + j / 2] = near[j + 1];\n    }\n  });\n  const listOf = (a, b) => {\n    for (let j = adjacency[a]; j < adjacency[a + 1]; j++) {\n      if (adjacentNode[j] === b) {\n        return adjacentList[j];\n      }\n    }\n    return -1;\n  };\n  const nameIndex = /* @__PURE__ */ new Map();\n  const pathNames = [];\n  const crossedList = new Int32Array(w.offsets[w.names.length] ?? 0);\n  const crossedName = new Int32Array(crossedList.length);\n  let crossings = 0;\n  const lastWalk = new Int32Array(lists).fill(-1);\n  const paths = [];\n  const anchorPaths = [];\n  const totalSteps = w.offsets[w.names.length] ?? 0;\n  const visitPath = new Int32Array(totalSteps);\n  const visitStart = new Float64Array(totalSteps);\n  const visitReversed = new Uint8Array(totalSteps);\n  const fill = new Int32Array(count).fill(-1);\n  const visitOrder = [];\n  const blocks = [0];\n  const pathSamples = [];\n  const edgeNameIndex = /* @__PURE__ */ new Map();\n  const edgeNames = [];\n  for (const p of drawnWalks) {\n    const head = tablePath(w, p);\n    const { start, name: pathName } = head;\n    const visitName = head.sample === void 0 ? w.names[p] : pathName;\n    let named = nameIndex.get(visitName);\n    if (named === void 0) {\n      named = pathNames.length;\n      nameIndex.set(visitName, named);\n      pathNames.push(visitName);\n      pathSamples.push(panSNSample(visitName));\n    }\n    let edgeNamed = edgeNameIndex.get(pathName);\n    if (edgeNamed === void 0) {\n      edgeNamed = edgeNames.length;\n      edgeNameIndex.set(pathName, edgeNamed);\n      edgeNames.push(pathName);\n    }\n    const visitSample = pathSamples[named];\n    const first = w.offsets[p];\n    const nodeIds = new Array(w.offsets[p + 1] - first);\n    let pos = start;\n    let prev = -1;\n    for (let s = first; s < w.offsets[p + 1]; s++) {\n      const node = w.steps[s];\n      nodeIds[s - first] = ids[node];\n      if (fill[node] === -1) {\n        fill[node] = blocks.at(-1);\n        blocks.push(fill[node] + traversals[node]);\n        visitOrder.push(node);\n      }\n      const at = fill[node]++;\n      visitPath[at] = named;\n      visitStart[at] = pos;\n      visitReversed[at] = w.reversed[s];\n      pos += node < declared ? n.lengths[node] : 0;\n      if (prev >= 0) {\n        const list = listOf(prev, node);\n        if (list >= 0 && lastWalk[list] !== p) {\n          lastWalk[list] = p;\n          crossedList[crossings] = list;\n          crossedName[crossings++] = edgeNamed;\n        }\n      }\n      prev = node;\n    }\n    paths.push({ ...head, nodeIds });\n    anchorPaths.push({\n      name: visitName,\n      sample: visitSample,\n      start,\n      length: pos - start\n    });\n  }\n  const listNames = namesByList(\n    crossedList.subarray(0, crossings),\n    crossedName,\n    lists,\n    edgeNames\n  );\n  edges.forEach((edge, i) => {\n    const names = listNames[edgeLists[i]];\n    if (names.length > 0) {\n      edge.pathIds = names;\n    }\n  });\n  const walked = drawnWalks.length > 0;\n  return {\n    name,\n    nodes,\n    edges,\n    paths: walked ? paths : void 0,\n    anchorPaths: walked ? anchorPaths : void 0,\n    pathVisits: walked ? new PathVisits({\n      segments: visitOrder.map((node) => n.names[node]),\n      offsets: Int32Array.from(blocks),\n      path: visitPath.subarray(0, blocks.at(-1)),\n      start: visitStart.subarray(0, blocks.at(-1)),\n      reversed: visitReversed.subarray(0, blocks.at(-1)),\n      paths: pathNames,\n      samples: pathSamples\n    }) : void 0,\n    anchoredBy: nodes.some((node) => node.stable) ? \"tags\" : void 0\n  };\n}\nfunction graphTablesGFA({ nodes, links, walks }) {\n  const { names } = nodes;\n  const lines = [\"H\tVN:Z:1.1\"];\n  for (let i = 0; i < nodes.lengths.length; i++) {\n    const ref = nodes.refs[i];\n    const stable = ref < 0 ? \"\" : `\tSN:Z:${nodes.refNames[ref]}\tSO:i:${nodes.starts[i]}\tSR:i:${nodes.ranks[i]}`;\n    lines.push(`S\t${names[i]}\t*\tLN:i:${nodes.lengths[i]}${stable}`);\n  }\n  for (let i = 0; i < links.from.length; i++) {\n    const strands = links.strands[i];\n    lines.push(\n      `L\t${names[links.from[i]]}\t${strands & 1 ? \"-\" : \"+\"}\t${names[links.to[i]]}\t${strands & 2 ? \"-\" : \"+\"}\t0M`\n    );\n  }\n  for (let p = 0; p < walks.names.length; p++) {\n    const name = walks.names[p];\n    const fields = panSNFields(name);\n    const start = walks.starts[p];\n    const end = walks.ends[p];\n    const steps = [];\n    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {\n      steps.push([names[walks.steps[s]], walks.reversed[s]]);\n    }\n    lines.push(\n      fields ? `W\t${fields.sample}\t${fields.haplotype}\t${fields.contig}\t${start}\t${end}\t${steps.map(([id, rev]) => (rev ? \"<\" : \">\") + id).join(\"\")}${walkStopTags(walks, p)}` : `P\t${pLineName(name, start, end)}\t${steps.map(([id, rev]) => id + (rev ? \"-\" : \"+\")).join(\",\")}\t*`\n    );\n  }\n  return lines.join(\"\\n\");\n}\n\nexport {\n  tablePath,\n  tableNodeIds,\n  graphFromTables,\n  graphTablesGFA\n};\n", "import {\n  tableNodeIds,\n  tablePath\n} from \"./chunk-4FPEQQFT.js\";\nimport {\n  gapParts\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  pathOrigin\n} from \"./chunk-BRH73RCH.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  panSNContig,\n  panSNFields,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/layout/walkRowRuns.ts\nvar RUN_ON_REFERENCE = 1;\nvar RUN_REVERSED = 2;\nvar RUN_GAP = 4;\nvar GAP_CAUSES = [\n  void 0,\n  \"missing\",\n  \"elsewhere\",\n  \"unknown\",\n  \"abridged\",\n  \"deleted\"\n];\nvar CAUSE_SHIFT = 3;\nvar causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;\nfunction referenceOf(names, referencePath, rankZero) {\n  return referencePath !== void 0 && names.includes(referencePath) ? referencePath : names.find((n) => rankZero.has(n)) ?? names[0];\n}\nfunction referenceWalkName(graph) {\n  return referenceOf(\n    (graph.paths ?? []).map((p) => pathOrigin(p.name).name),\n    graph.referencePath,\n    new Set(\n      graph.nodes.flatMap(\n        (n) => n.stable?.rank === 0 ? [n.stable.refName] : []\n      )\n    )\n  );\n}\nfunction graphPieces(graph) {\n  const index = /* @__PURE__ */ new Map();\n  const names = [];\n  const lengths = [];\n  const indexOf = (id) => {\n    let i = index.get(id);\n    if (i === void 0) {\n      i = names.length;\n      index.set(id, i);\n      names.push(id);\n      lengths.push(0);\n    }\n    return i;\n  };\n  for (const node of graph.nodes) {\n    lengths[indexOf(node.id)] = node.length;\n  }\n  const heads = graph.paths ?? [];\n  const from = new Int32Array(heads.length);\n  const to = new Int32Array(heads.length);\n  const steps = [];\n  heads.forEach((path, p) => {\n    from[p] = steps.length;\n    for (const id of path.nodeIds) {\n      steps.push(indexOf(id));\n    }\n    to[p] = steps.length;\n  });\n  return {\n    heads,\n    from,\n    to,\n    steps: Int32Array.from(steps),\n    lengths: Int32Array.from(lengths),\n    names,\n    reference: referenceWalkName(graph)\n  };\n}\nfunction tablePieces(tables, referencePath, visits) {\n  const { nodes: n, walks: w } = tables;\n  const kept = [];\n  for (let p = 0; p < w.names.length; p++) {\n    if (w.offsets[p + 1] > w.offsets[p]) {\n      kept.push(p);\n    }\n  }\n  const heads = kept.map((p) => tablePath(w, p));\n  const rankZero = /* @__PURE__ */ new Set();\n  for (let i = 0; i < n.lengths.length; i++) {\n    if (n.refs[i] >= 0 && n.ranks[i] === 0) {\n      rankZero.add(n.refNames[n.refs[i]]);\n    }\n  }\n  return {\n    heads,\n    from: Int32Array.from(kept, (p) => w.offsets[p]),\n    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),\n    steps: w.steps,\n    lengths: n.lengths,\n    // a visit names its node as the Graph does, which costs a pass over the\n    // steps\n    names: visits ? tableNodeIds(tables) : n.names,\n    reference: referenceOf(\n      heads.map((h) => pathOrigin(h.name).name),\n      referencePath,\n      rankZero\n    )\n  };\n}\nfunction sampleOf(path) {\n  return path.sample ?? panSNSample(path.name);\n}\nfunction labelOf(path) {\n  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);\n}\nvar Columns = class {\n  constructor(width) {\n    this.offsets = [0];\n    this.values = Array.from({ length: width }, () => []);\n  }\n  get length() {\n    return this.values[0].length;\n  }\n  push(a, b, c, d, e) {\n    const v = this.values;\n    v[0].push(a);\n    v[1].push(b);\n    v[2].push(c);\n    v[3].push(d);\n    if (e !== void 0) {\n      v[4].push(e);\n    }\n  }\n  endRow() {\n    this.offsets.push(this.length);\n  }\n  // the rows in `order`, column i in the array `make[i]` makes\n  reorder(order, make) {\n    const offsets = new Uint32Array(order.length + 1);\n    order.forEach((row, i) => {\n      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];\n    });\n    const columns = make.map((m, c) => {\n      const from = this.values[c];\n      const out = m(this.length);\n      let at = 0;\n      for (const row of order) {\n        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {\n          out[at++] = from[k];\n        }\n      }\n      return out;\n    });\n    return { offsets, columns };\n  }\n};\nvar float64 = (n) => new Float64Array(n);\nfunction walkRowRuns(source, region, o = {}) {\n  const {\n    heads,\n    from,\n    to,\n    steps: all,\n    lengths,\n    names,\n    reference\n  } = \"walks\" in source ? tablePieces(source, o.referencePath, o.visits) : graphPieces(source);\n  const declared = lengths.length;\n  const lengthOf = (node) => node < declared ? lengths[node] : 0;\n  const nameOf = (p) => pathOrigin(heads[p].name).name;\n  const startOf = (p) => heads[p].start;\n  const byStart = (a, b) => (startOf(a) ?? 0) - (startOf(b) ?? 0);\n  const pieceIds = heads.map((_, p) => p);\n  const referencePieces = pieceIds.filter((p) => nameOf(p) === reference).sort(byStart);\n  const first = referencePieces[0];\n  const others = pieceIds.filter((p) => nameOf(p) !== reference);\n  const skips = \"walks\" in source ? source.skips : void 0;\n  if (first === void 0 || others.length === 0 && !skips?.names.length) {\n    return void 0;\n  }\n  const walks = groupBy(others, nameOf);\n  const spanStart = new Float64Array(names.length).fill(Number.NaN);\n  const spanEnd = new Float64Array(names.length);\n  const revisits = /* @__PURE__ */ new Map();\n  let flankEnd = -Infinity;\n  let flankStart = Infinity;\n  const cut = region && region.end > region.start ? region : void 0;\n  for (const piece of referencePieces) {\n    let pos = startOf(piece) ?? 0;\n    for (let s = from[piece], stop = to[piece]; s < stop; s++) {\n      const node = all[s];\n      const len = lengthOf(node);\n      if (!Number.isNaN(spanStart[node])) {\n        const starts = revisits.get(node);\n        if (starts) {\n          starts.push(pos);\n        } else {\n          revisits.set(node, [spanStart[node], pos]);\n        }\n      } else {\n        spanStart[node] = pos;\n        spanEnd[node] = pos + len;\n        if (cut) {\n          if (pos + len <= cut.start) {\n            flankEnd = Math.max(flankEnd, pos + len);\n          }\n          if (pos >= cut.end) {\n            flankStart = Math.min(flankStart, pos);\n          }\n        }\n      }\n      pos += len;\n    }\n  }\n  const flanked = cut === void 0 || flankEnd > -Infinity && flankStart < Infinity;\n  const runs = new Columns(5);\n  const chunks = [];\n  const chunkIndex = /* @__PURE__ */ new Map();\n  const chunkOf = (chunk2) => {\n    if (!chunk2) {\n      return -1;\n    }\n    const key = `${chunk2.refName}:${chunk2.start}`;\n    let i = chunkIndex.get(key);\n    if (i === void 0) {\n      i = chunks.length;\n      chunkIndex.set(key, i);\n      chunks.push(chunk2);\n    }\n    return i;\n  };\n  const visits = o.visits ? new Columns(4) : void 0;\n  let steps = new Int32Array(0);\n  let stepStart = new Float64Array(0);\n  const rowOf = (pieces) => {\n    const head = heads[pieces[0]];\n    const ordered = [...pieces].sort(byStart);\n    let count = ordered.length - 1;\n    let abridgedSteps = 0;\n    for (const piece of ordered) {\n      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);\n      abridgedSteps += heads[piece].abridged?.steps ?? 0;\n    }\n    if (count > steps.length) {\n      steps = new Int32Array(count * 2);\n      stepStart = new Float64Array(count * 2);\n    }\n    let length = 0;\n    let unplaced = false;\n    let end;\n    let previous;\n    const partsAt = /* @__PURE__ */ new Map();\n    let owed = 0;\n    for (const piece of ordered) {\n      const start2 = startOf(piece);\n      const jump = start2 === void 0 || end === void 0 ? 0 : start2 - end;\n      if (start2 === void 0 || jump < 0) {\n        unplaced = true;\n      }\n      if (jump < 0 && heads[previous].abridged) {\n        owed -= jump;\n      }\n      const covered = Math.min(owed, Math.max(jump, 0));\n      owed -= covered;\n      const gap = jump - covered;\n      if (gap > 0) {\n        partsAt.set(\n          length,\n          gapParts(\n            gap,\n            previous === void 0 ? void 0 : heads[previous].after,\n            heads[piece].before\n          )\n        );\n        steps[length] = -gap;\n        stepStart[length++] = end;\n      }\n      let pos = start2 ?? 0;\n      const abridged = heads[piece].abridged;\n      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {\n        const node = all[s];\n        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;\n        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {\n          partsAt.set(length, [{ bp: bp3, cause: \"abridged\" }]);\n          steps[length] = -bp3;\n          stepStart[length++] = pos;\n          pos += bp3;\n        }\n        steps[length] = node;\n        stepStart[length++] = pos;\n        pos += lengthOf(node);\n      }\n      end = start2 === void 0 ? void 0 : pos;\n      previous = piece;\n    }\n    const onReference = (i) => i >= 0 && i < length && steps[i] >= 0 && !Number.isNaN(spanStart[steps[i]]);\n    const stepEnd = (i) => {\n      const id = steps[i];\n      return stepStart[i] + (id < 0 ? -id : lengthOf(id));\n    };\n    const partialSide = (i0, i1) => {\n      const flank = i0 >= 0 ? i0 : i1;\n      let near = -1;\n      for (let d = 1; near < 0 && d < length; d++) {\n        near = [flank - d, flank + d].find(onReference) ?? -1;\n      }\n      if (near < 0) {\n        return void 0;\n      }\n      const forward = near > flank === spanStart[steps[near]] > spanStart[steps[flank]];\n      const after = forward === (flank === i0);\n      const last2 = after ? length - 1 : 0;\n      const contigEnds = onReference(last2);\n      const stop2 = {\n        contigEnds,\n        shortBp: contigEnds ? Math.max(\n          0,\n          cut.start - spanEnd[steps[last2]],\n          spanStart[steps[last2]] - cut.end\n        ) : 0\n      };\n      return {\n        stop: stop2,\n        lo: after ? flank + 1 : 0,\n        hi: after ? length : flank,\n        backward: !forward,\n        axisStart: forward ? after ? stepEnd(flank) : stepStart[0] : after ? stepEnd(length - 1) : stepStart[flank]\n      };\n    };\n    let lo = 0;\n    let hi = length;\n    let backward = false;\n    let complete = true;\n    let flankFrom = -1;\n    let flankTo = -1;\n    let axisStart;\n    let stop;\n    const trimAbridged = (inner, bp3) => {\n      const parts = partsAt.get(inner);\n      const gap = parts?.[0];\n      if (bp3 <= 0 || gap?.cause !== \"abridged\") {\n        return 0;\n      }\n      const trimmed = Math.min(bp3, gap.bp);\n      partsAt.set(\n        inner,\n        gap.bp > trimmed ? [{ ...gap, bp: gap.bp - trimmed }] : []\n      );\n      steps[inner] += trimmed;\n      return trimmed;\n    };\n    let leftTrim = 0;\n    let rightTrim = 0;\n    if (cut && flanked) {\n      let i0 = -1;\n      let i1 = -1;\n      let bestEnd = -Infinity;\n      let bestStart = Infinity;\n      for (let i = 0; i < length; i++) {\n        const id = steps[i];\n        if (id >= 0 && !Number.isNaN(spanStart[id])) {\n          if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {\n            bestEnd = spanEnd[id];\n            i0 = i;\n          }\n          if (spanStart[id] >= cut.end && spanStart[id] < bestStart) {\n            bestStart = spanStart[id];\n            i1 = i;\n          }\n        }\n      }\n      if (i0 < 0 || i1 < 0) {\n        complete = false;\n        const inside = i0 >= 0 || i1 >= 0 ? partialSide(i0, i1) : void 0;\n        if (inside) {\n          ;\n          ({ lo, hi, backward, axisStart, stop } = inside);\n        }\n      } else {\n        lo = Math.min(i0, i1) + 1;\n        hi = Math.max(i0, i1);\n        backward = i0 > i1;\n        flankFrom = i0;\n        flankTo = i1;\n        const inward = backward ? -1 : 1;\n        leftTrim = trimAbridged(i0 + inward, flankEnd - spanEnd[steps[i0]]);\n        rightTrim = trimAbridged(\n          i1 - inward,\n          spanStart[steps[i1]] - flankStart\n        );\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis = unplaced || length === 0 ? void 0 : axisStart !== void 0 ? { contig, start: axisStart, reversed: backward } : flankFrom < 0 ? { contig, start: stepStart[0], reversed: false } : flankFrom < flankTo ? {\n      contig,\n      start: stepEnd(flankFrom) + leftTrim,\n      reversed: false\n    } : {\n      contig,\n      start: stepStart[flankFrom] - leftTrim,\n      reversed: true\n    };\n    let bp2 = 0;\n    let offReferenceBp = 0;\n    let gapBp = 0;\n    let step = 0;\n    let last = -1;\n    let lastFlags = 0;\n    let lastRef = Number.NaN;\n    let cursor = Number.NaN;\n    const placeOf = (id) => {\n      const starts = revisits.get(id);\n      if (!starts || Number.isNaN(cursor)) {\n        return spanStart[id];\n      }\n      const len = lengthOf(id);\n      let best = starts[0];\n      let bestGap = Infinity;\n      for (const start2 of starts) {\n        const gap = Math.min(\n          Math.abs(start2 - cursor),\n          Math.abs(start2 + len - cursor)\n        );\n        if (gap < bestGap) {\n          best = start2;\n          bestGap = gap;\n        }\n      }\n      return best;\n    };\n    const [, runBp, runRef, runFlags] = runs.values;\n    for (let k = lo; k < hi; k++) {\n      const index = backward ? hi - 1 - (k - lo) : k;\n      const id = steps[index];\n      const parts = partsAt.get(index);\n      if (parts) {\n        for (const part of backward ? [...parts].reverse() : parts) {\n          runs.push(\n            bp2,\n            part.bp,\n            Number.NaN,\n            RUN_GAP | causeFlags(part.cause),\n            chunkOf(part.chunk)\n          );\n          bp2 += part.bp;\n        }\n        last = runs.length - 1;\n        lastFlags = RUN_GAP;\n        lastRef = Number.NaN;\n        gapBp += -id;\n        step = 0;\n        continue;\n      }\n      const len = lengthOf(id);\n      const at = placeOf(id);\n      const on = !Number.isNaN(at);\n      visits?.push(id, bp2, len, on ? 1 : 0);\n      const placed = last >= 0 && !Number.isNaN(lastRef);\n      const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;\n      const back = on && placed && step <= 0 && at + len === lastRef;\n      if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {\n        runBp[last] += len;\n      } else if (forward || back) {\n        runBp[last] += len;\n        if (!forward) {\n          lastRef = at;\n          runRef[last] = at;\n          lastFlags |= RUN_REVERSED;\n          runFlags[last] = lastFlags;\n        }\n        step = forward ? 1 : -1;\n      } else {\n        lastFlags = on ? RUN_ON_REFERENCE : 0;\n        lastRef = on ? at : Number.NaN;\n        runs.push(bp2, len, lastRef, lastFlags, -1);\n        last = runs.length - 1;\n        step = 0;\n      }\n      bp2 += len;\n      if (on) {\n        cursor = step < 0 ? at : at + len;\n      } else {\n        offReferenceBp += len;\n      }\n    }\n    runs.endRow();\n    visits?.endRow();\n    return {\n      name: head.name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: bp2,\n      offReferenceBp,\n      gapBp,\n      complete,\n      stop,\n      axis,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {},\n      ...leftTrim + rightTrim > 0 ? { estimated: true } : {}\n    };\n  };\n  const skipRowOf = (name, start2, end) => {\n    const from2 = cut ? Math.max(start2, cut.start) : start2;\n    const bp2 = (cut ? Math.min(end, cut.end) : end) - from2;\n    runs.push(\n      from2 - (cut ? cut.start : start2),\n      bp2,\n      Number.NaN,\n      RUN_GAP | causeFlags(\"deleted\"),\n      -1\n    );\n    runs.endRow();\n    visits?.endRow();\n    const head = { name, ...panSNFields(name) };\n    return {\n      name,\n      label: labelOf(head),\n      sample: sampleOf(head),\n      haplotype: head.haplotype,\n      bp: 0,\n      offReferenceBp: 0,\n      gapBp: bp2,\n      complete: true,\n      stop: void 0,\n      axis: void 0\n    };\n  };\n  const referenceRow = rowOf(referencePieces);\n  const rows = [...walks.values()].map((pieces, i) => ({\n    meta: rowOf(pieces),\n    row: i + 1\n  }));\n  const drawn = new Set(walks.keys());\n  skips?.names.forEach((name, k) => {\n    const contig = pathOrigin(name).name;\n    if (!drawn.has(contig)) {\n      drawn.add(contig);\n      rows.push({\n        meta: skipRowOf(contig, skips.starts[k], skips.ends[k]),\n        row: rows.length + 1\n      });\n    }\n  });\n  const metas = [referenceRow, ...rows.map((r) => r.meta)];\n  if (new Set(metas.map((m) => m.label)).size < metas.length) {\n    for (const meta of metas) {\n      meta.label = panSNHaplotype(meta.name) ?? meta.label;\n    }\n  }\n  rows.sort(\n    (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)\n  );\n  const order = [0, ...rows.map((r) => r.row)];\n  const { offsets, columns } = runs.reorder(order, [\n    float64,\n    float64,\n    float64,\n    (n) => new Uint8Array(n),\n    (n) => new Int32Array(n)\n  ]);\n  const [start, bp, referenceStart, flags, chunk] = columns;\n  return {\n    origin: cut ? cut.start : startOf(first) ?? 0,\n    rows: [referenceRow, ...rows.map((r) => r.meta)],\n    offsets,\n    start,\n    bp,\n    referenceStart,\n    flags,\n    chunk,\n    chunks,\n    visits: visits && visitColumns(visits, order, names)\n  };\n}\nfunction visitColumns(visits, order, names) {\n  const { offsets, columns } = visits.reorder(order, [\n    (n) => new Int32Array(n),\n    float64,\n    float64,\n    (n) => new Uint8Array(n)\n  ]);\n  const [node, start, bp, onReference] = columns;\n  return { offsets, node, start, bp, onReference, names };\n}\nfunction runAt(t, k) {\n  const f = t.flags[k];\n  const run = {\n    start: t.start[k],\n    bp: t.bp[k],\n    onReference: (f & RUN_ON_REFERENCE) !== 0\n  };\n  if (f & RUN_GAP) {\n    run.gap = true;\n    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];\n    if (cause) {\n      run.cause = cause;\n    }\n    const chunk = t.chunks[t.chunk[k]];\n    if (chunk) {\n      run.chunk = chunk;\n    }\n  } else {\n    run.referenceStart = Number.isNaN(t.referenceStart[k]) ? void 0 : t.referenceStart[k];\n  }\n  if (f & RUN_REVERSED) {\n    run.reversed = true;\n  }\n  return run;\n}\nfunction visitsOf(v, row) {\n  const out = [];\n  for (let k = v.offsets[row]; k < v.offsets[row + 1]; k++) {\n    out.push({\n      node: v.names[v.node[k]],\n      start: v.start[k],\n      bp: v.bp[k],\n      onReference: v.onReference[k] === 1\n    });\n  }\n  return out;\n}\nfunction walkRowsOf(t, unit) {\n  const rows = t.rows.map((meta, i) => {\n    const runs = [];\n    for (let k = t.offsets[i]; k < t.offsets[i + 1]; k++) {\n      runs.push(runAt(t, k));\n    }\n    return {\n      ...meta,\n      runs,\n      visits: t.visits && visitsOf(t.visits, i)\n    };\n  });\n  return { origin: t.origin, unit, reference: rows[0], rows: rows.slice(1) };\n}\n\nexport {\n  referenceWalkName,\n  walkRowRuns,\n  runAt,\n  walkRowsOf\n};\n"],
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package/dist/chunks/chunk-MCBYBZZJ.js

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-${s.bubble.segmentCount} segments${s.bubble.covering?"":h(s)?" \xB7 click to close":" \xB7 click to open"}`,testId:"graph-bubble-halo-label",onClick:s.bubble.covering?void 0:()=>{t.toggleBubble(s.bubble)},onHover:x=>{K(t)&&t.setHoveredBubble(x?s.bubble:null)}},W(s.bubble))),c?u($,{x:c.x,y:c.y-Re-4,w:te(c.item.label),text:c.item.label,color:S[c.item.kind],testId:"graph-bubble-tick-label"}):null]})}),Lo=on;function an(e,t,{lit:n,dpr:o}){let r=t.hostBpFrame;r&&nt(e,t.referenceStripBlocks,r,{width:t.paneWidth,lit:n,dpr:o})}var sn=m(function({model:t}){let n=M((o,r)=>{an(o,t,{lit:t.referenceStripLit,dpr:r})},[t]);return u(_,{model:t,zIndex:5,shown:t.referenceStripShown,testId:"graph-reference-strip",paint:n})}),vo=sn;var ln=.45;function cn(e,t,{highlightNode:n}){let o=t.tubeMapPicture,r=t.tubeMapFrame;if(!o||!r)return;let a=t.paneWidth,l=t.tubeMapPanelViews;if(l){pn(e,t,l,n);return}let i={...r,width:a,highlightNode:n,tubeColors:t.tubeMapTubeColors,nodeColors:t.tubeMapNodeColors};ce(e,o,i);let d=t.layoutResult?.tubeMap;d&&(ue(e,o,d.graph,i),de(e,d,i)),le(e,t.tubeMapDeviations,i),Ye(e,t.tubeMapConnectors,t.connectorZoneBottom,i);let{bounds:c}=o;tt(e,t.tubeMapGenes,i,r.y(c.minY)-2);let p=t.tubeMapRulerBoxes;p&&ie(e,p,i,r.y(c.maxY)+4,t.layoutResult?.referenceAxis)}function pn(e,t,n,o){let r=t.paneWidth;for(let i of n){if(i.bottom<0||i.titleTop>t.canvasHeight)continue;let d={...i.frame,width:r,highlightNode:o,tubeColors:i.tubeColors,nodeColors:i.nodeColors};ce(e,i.picture,d),ue(e,i.picture,i.panel.result.tubeMap.graph,d),de(e,i.panel.result.tubeMap,d),e.globalAlpha=ln,le(e,i.deviations,d),e.globalAlpha=1,e.strokeStyle="rgba(0,0,0,0.15)",e.lineWidth=1,e.beginPath(),e.moveTo(0,Math.round(i.titleTop)+.5),e.lineTo(r,Math.round(i.titleTop)+.5),e.stroke(),e.font=je,e.textAlign="left",e.textBaseline="top",e.fillStyle="rgba(0,0,0,0.85)",e.fillText(i.label,6,i.titleTop+4)}let a=n.at(-1),l=t.tubeMapPanelRulerBoxes;a&&l&&ie(e,l,{...a.frame,width:r},a.bottom+4,!0)}var un=m(function({model:t}){let n=M(o=>{cn(o,t,{highlightNode:t.selectedNode})},[t]);return u(_,{model:t,zIndex:1,shown:!!t.tubeMapPicture,testId:"graph-tube-map",paint:n})}),Uo=un;var v=JBrowseExports["@jbrowse/render-core/marks"],dn=e=>v!=null&&e in Object(v)?v[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/marks' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var kt=dn("spanMark");var zo=v&&v.__esModule?v.default:v;function xt(e){if(e.startsWith("#")){let r=Number.parseInt(e.slice(1),16);return[r>>16&255,r>>8&255,r&255]}let[t=0,n=0,o=0]=e.match(/[\d.]+/g).map(Number);return e.startsWith("hsl")?Te(t,n/100,o/100).map(r=>r*255):[t,n,o]}var yt=([e,t,n])=>Ee(Math.round(e),Math.round(t),Math.round(n),255),Rt=new Map;function bn(e){let t=Rt.get(e);return t===void 0&&(t=yt(xt(e)),Rt.set(e,t)),t}function fn(e,t,n){let o=e.start+e.bp,r=De(e,t);if("fill"in r)return[[e.start,o,bn(r.fill)]];let a=r.stops.map(xt),l=r.stops.map(p=>Number(/[\d.]+/.exec(p)[0])),i=Math.abs(l.at(-1)-l[0]),d=Math.max(1,Math.min(Math.ceil(e.bp*n),Math.ceil(i),e.bp)),c=[];for(let p=0;p<d;p++){let b=(p+.5)/d*(a.length-1),h=Math.min(Math.floor(b),a.length-2),s=a[h],f=a[h+1],g=b-h;c.push([Math.round(e.start+e.bp*p/d),Math.round(e.start+e.bp*(p+1)/d),yt([0,1,2].map(w=>s[w]+(f[w]-s[w])*g))])}return c}function ye(e){return{x:new Uint32Array(e),x2:new Uint32Array(e),row:new Uint32Array(e),color:new Uint32Array(e),count:0}}function J(e,t,n){return{x:e.x.subarray(t,n),x2:e.x2.subarray(t,n),row:e.row.subarray(t,n),color:e.color.subarray(t,n),count:n-t}}function St(e,t,n){let o=e.map(h=>Ue(h.runs,t).map(s=>({gap:s.gap,hairline:s.gap&&Ge(s.cause).px===se,pieces:fn(s,n,t)}))),r=0;for(let h of o)for(let s of h)r+=s.pieces.length;let a=ye(r),l=ye(r),i=ye(r),d=new Uint32Array(e.length+1),c=new Uint32Array(e.length+1),p=new Uint32Array(e.length+1),b=1;return o.forEach((h,s)=>{for(let f of h){let g=f.hairline?i:f.gap?l:a;for(let[w,P,x]of f.pieces){let L=g.count++;g.x[L]=w,g.x2[L]=P,g.row[L]=s,g.color[L]=x,b=Math.max(b,g.x2[L])}}d[s+1]=a.count,c[s+1]=l.count,p[s+1]=i.count}),{bars:J(a,0,a.count),gaps:J(l,0,l.count),hairlines:J(i,0,i.count),barRows:d,gapRows:c,hairlineRows:p,longest:b}}function Pt(e,t,n){let{longest:o}=t,r={start:0,end:o,screenStartPx:n.origin*n.scaleX+n.translateX,screenEndPx:(n.origin+o)*n.scaleX+n.translateX,reversed:!1,displayedRegionIndex:0},a={canvasWidth:n.width,canvasHeight:n.height},l=n.rowPx*n.scaleY;for(let{first:i,count:d,rowY:c}of n.blocks){let p=l/2-n.translateY-(c-i*n.rowPx)*n.scaleY,b=(c-n.rowPx/2)*n.scaleY+n.translateY;if(!(b>n.height||b+d*l<0))for(let[h,s,f]of[[t.bars,t.barRows,n.barPx],[t.gaps,t.gapRows,Math.min(We,n.barPx)],[t.hairlines,t.hairlineRows,Math.min(se,n.barPx)]])kt.paintBlock(e,J(h,s[i],s[i+d]),r,a,{rowHeight:l,rowProportion:f/l,minWidthPx:1,seamPx:0,scrollTop:p})}}function hn({model:e}){let t=U(()=>X(()=>{let o=e.walkRowBars;return o?St([o.reference,...o.rows],e.scaleX,e.referenceRampDomain):void 0}),[e]),n=M(o=>{let r=e.walkRowBars,a=e.walkRowPlacement,l=e.walkRowPitch,i=t.get();if(!r||!a||!l||!i)return;let d=e.walkRowGroups?.sections,c=d?.length?[{first:0,count:1,rowY:a.rowY(0)},...d.map(p=>({first:p.first,count:p.count,rowY:a.rowY(p.first)}))]:[{first:0,count:r.rows.length+1,rowY:a.rowY(0)}];Pt(o,i,{...e.screenTransform,width:e.paneWidth,height:e.canvasHeight,rowPx:l.rowPx,barPx:l.barPx,origin:r.origin,blocks:c})},[e,t]);return u(_,{model:e,zIndex:3,testId:"graph-walk-rows-spans",paint:n})}var gn="rgba(160, 196, 232, 0.55)",wn="rgba(160, 140, 220, 0.55)";function mn({model:e}){let t=M(n=>{let o=e.walkRowRibbons,r=e.walkRowBars,a=e.walkRowPlacement,l=e.walkRowPitch;if(!o||!r||!a||!l)return;let{scaleX:i,scaleY:d,translateX:c,translateY:p}=e.screenTransform,b=s=>(r.origin+s)*i+c,h=l.barPx/2;for(let{row:s,a0:f,a1:g,b0:w,b1:P}of o){let x=a.rowY(s)*d+p+h,L=a.rowY(s+1)*d+p-h;n.fillStyle=w>P?wn:gn,n.beginPath(),n.moveTo(b(f),x),n.lineTo(b(g),x),n.lineTo(b(P),L),n.lineTo(b(w),L),n.closePath(),n.fill()}},[e]);return u(_,{model:e,zIndex:2,testId:"graph-walk-rows-ribbons",paint:t})}function kn({model:e}){let t=M(n=>{let o=e.sharedBlocks,r=e.walkRowBars,a=e.walkRowPlacement,l=e.walkRowPitch;if(!o||!r||!a||!l)return;let{scaleX:i,scaleY:d,translateX:c,translateY:p}=e.screenTransform;it(n,o,{x:b=>(r.origin+b)*i+c,rowCentre:b=>a.rowY(b)*d+p,barPx:l.barPx})},[e]);return u(_,{model:e,zIndex:3,testId:"graph-walk-rows-blocks",paint:t})}var Rn=m(function({model:t}){let n=t.walkRowBars,o=t.walkRowPlacement,r=t.walkRowPitch;if(!n||!o||!r||!t.hoveredWalkRowText)return null;let a=[n.reference,...n.rows],l=a.findIndex(c=>c.name===t.hoveredWalkRow),i=a[l];if(!i)return null;let d=t.toScreen({x:n.origin,y:o.rowY(l)});return u("rect",{"data-testid":"graph-walk-row-hovered",x:d.x-2,y:d.y-r.rowPx/2-1,width:i.bp*t.scaleX+4,height:r.rowPx+2,fill:"none",stroke:"#111",strokeWidth:1})}),xn=m(function({model:t,vector:n=!1}){let o=A(),r=t.walkRowBars,a=t.walkRowPlacement,l=t.walkRowPitch;if(!r||!a||!l)return null;let{paneWidth:i,canvasHeight:d}=t,c={...t.screenTransform,width:i,height:d,...l,bars:n};return k(T,{children:[n||!t.walkRowRibbons?null:u(mn,{model:t}),n?null:u(hn,{model:t}),n||!t.sharedBlocks?null:u(kn,{model:t}),k(C,{model:t,zIndex:3,overflow:"visible",testId:"graph-walk-rows",children:[qe(r,t.walkRowGroups?.sections??[],a.rowY,c,{ramp:t.referenceRampDomain,rowGenes:t.walkRowGenes,idPrefix:o}).map((p,b)=>u(H,{el:p},b)),a.headers.map(p=>u("text",{x:10,y:t.toScreen({x:0,y:p.top}).y+Ve-4,fontFamily:"sans-serif",fontSize:11,fontWeight:"bold",fill:"#333","data-testid":"graph-walk-section",children:p.title},p.key)),u(Rn,{model:t})]})]})}),la=xn;export{Lt as a,ot as b,C as c,In as d,A as e,H as f,j as g,Nr as h,vr as i,Vt as j,Jt as k,Tr as l,Ar as m,tn as n,$r as o,Ur as p,Fr as q,Yr as r,nn as s,zr as t,Vr as u,no as v,Po as w,Lo as x,an as y,vo as z,cn as A,Uo as B,la as C};
-//# sourceMappingURL=chunk-MCBYBZZJ.js.map

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

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/GraphGenomeView/components/PaneLayer.tsx", "../../src/GraphGenomeView/components/BubbleHalos.tsx", "../../src/GraphGenomeView/walkRowBlocks.ts", "../../src/GraphGenomeView/legendSections.ts", "../../src/GraphGenomeView/components/ElTree.tsx", "../../src/GraphGenomeView/components/LegendSwatch.tsx", "../../src/GraphGenomeView/components/legendStyles.ts", "../../src/GraphGenomeView/components/GenePins.tsx", "../../src/GraphGenomeView/components/LabelChip.tsx", "../../src/GraphGenomeView/components/LabelLayer.tsx", "../../src/GraphGenomeView/components/ReferenceStripOverlay.tsx", "../../src/GraphGenomeView/components/TubeMapOverlay.tsx", "host:@jbrowse/render-core/marks", "../../src/GraphGenomeView/walkRowSpans.ts", "../../src/GraphGenomeView/components/WalkRowsOverlay.tsx"],
-  "sourcesContent": ["import { useEffect, useRef } from 'react'\nimport type { ReactNode } from 'react'\n\nimport { syncCanvasSize } from '@jbrowse/bandage-core/renderer/canvas'\nimport { autorun } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport { dependOn } from '../pane/paneBase'\nimport { trackedDpr } from '../trackedDpr'\n\nimport type { GraphPaneModel } from '../model'\n\n// marks an overlay whose labels move with the drawing, so a press on one pans\nexport const PANS_WITH_DRAWING = 'data-pans-with-drawing'\n\n// A layer over the pane's canvas that leaves the pointer to it\nexport function paneLayerStyle(\n  zIndex: number,\n  overflow?: 'hidden' | 'visible',\n) {\n  return {\n    position: 'absolute' as const,\n    left: 0,\n    top: 0,\n    pointerEvents: 'none' as const,\n    overflow,\n    zIndex,\n  }\n}\n\n// An SVG the pane's size, over the canvas or inside PaneSvg's export\nexport const PaneSvgLayer = observer(function PaneSvgLayer({\n  model,\n  zIndex,\n  overflow = 'hidden',\n  testId,\n  pansWithDrawing,\n  children,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  overflow?: 'hidden' | 'visible'\n  testId?: string\n  pansWithDrawing?: boolean\n  children: ReactNode\n}) {\n  return (\n    <svg\n      style={{\n        ...paneLayerStyle(zIndex, overflow),\n        userSelect: pansWithDrawing ? 'none' : undefined,\n      }}\n      width={model.paneWidth}\n      height={model.canvasHeight}\n      data-testid={testId}\n      {...(pansWithDrawing ? { [PANS_WITH_DRAWING]: '' } : {})}\n    >\n      {children}\n    </svg>\n  )\n})\n\n// Layout units onto the screen. Its own observer, so a pan frame re-renders\n// this group's transform and not the children a parent built.\nexport const PaneTransformGroup = observer(function PaneTransformGroup({\n  model,\n  children,\n}: {\n  model: GraphPaneModel\n  children: ReactNode\n}) {\n  const { scaleX, scaleY, translateX, translateY } = model\n  return (\n    <g\n      transform={`translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`}\n    >\n      {children}\n    </g>\n  )\n})\n\n// A canvas the pane's size that an autorun repaints, so a pan moves its ink in\n// the same frame as the drawing. `paint` draws in css px.\nexport function PaneOverlayCanvas({\n  model,\n  zIndex,\n  shown = true,\n  testId,\n  paint,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  shown?: boolean\n  testId: string\n  paint: (ctx: CanvasRenderingContext2D, dpr: number) => void\n}) {\n  const ref = useRef<HTMLCanvasElement>(null)\n  useEffect(() => {\n    if (!shown) {\n      return undefined\n    }\n    return autorun(() => {\n      const canvas = ref.current\n      const ctx = canvas?.getContext('2d')\n      if (canvas && ctx) {\n        const width = model.paneWidth\n        const height = model.canvasHeight\n        dependOn(trackedDpr())\n        const dpr = syncCanvasSize(canvas, width, height)\n        ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n        ctx.clearRect(0, 0, width, height)\n        paint(ctx, dpr)\n      }\n    })\n  }, [model, shown, paint])\n  return (\n    <canvas\n      ref={ref}\n      data-testid={shown ? testId : undefined}\n      style={{ ...paneLayerStyle(zIndex), display: shown ? 'block' : 'none' }}\n    />\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { HALO_FACTOR } from '@jbrowse/bandage-core/labelLayout'\nimport { observer } from 'mobx-react'\n\nimport { PaneSvgLayer, PaneTransformGroup } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The bubbles over a node drawing: each a translucent halo along its nodes,\n// drawn once in layout units and moved with the canvas by one transform. The\n// halo takes no pointer events, so the nodes under it still hover and drag;\n// its name and its routes' chips are LabelLayer's. A small variant is\n// LabelLayer's tick, and shows its halo only while hovered.\n\nconst BubbleHalos = observer(function BubbleHalos({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbleHalos, hoveredBubble } = model\n  if (bubbleHalos.length === 0) {\n    return null\n  }\n  const halo = model.contigThickness * HALO_FACTOR\n  return (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-bubble-halos\">\n      <PaneTransformGroup model={model}>\n        {bubbleHalos\n          .filter(\n            h =>\n              !h.whole &&\n              (!h.tick ||\n                (hoveredBubble && sameBubble(h.bubble, hoveredBubble))),\n          )\n          .map(h => (\n            <path\n              key={bubbleKey(h.bubble)}\n              d={h.path}\n              fill=\"none\"\n              stroke={BUBBLE_KIND_COLORS[h.kind]}\n              strokeOpacity={\n                hoveredBubble && sameBubble(h.bubble, hoveredBubble)\n                  ? 0.45\n                  : model.bubbleFaded(h)\n                    ? 0.06\n                    : 0.22\n              }\n              strokeWidth={halo}\n              strokeLinecap=\"round\"\n              strokeLinejoin=\"round\"\n              vectorEffect=\"non-scaling-stroke\"\n            />\n          ))}\n      </PaneTransformGroup>\n    </PaneSvgLayer>\n  )\n})\n\nexport default BubbleHalos\n", "import type { WalkRowBlock } from '@jbrowse/bandage-core/layout/walkRowLinks'\n\n// ggbandage's: the three biggest blocks in colour, the rest a pale grey that\n// still carries its letter\nconst BLOCK_COLORS = ['#d4735e', '#d8a94a', '#c98aa4']\nconst OTHER_BLOCK = '#e6e6e6'\nconst BLOCK_EDGE = '#555'\nconst LETTER_FONT = 'bold 11px sans-serif'\nconst MIN_LETTER_PX = 12\nconst MIN_LETTER_BAR_PX = 9\n\nexport const blockFill = (block: number) => BLOCK_COLORS[block] ?? OTHER_BLOCK\n\n// A, B, ... Z, then AA, AB, ...\nexport function blockLetter(block: number): string {\n  const letter = String.fromCharCode(65 + (block % 26))\n  return block < 26 ? letter : blockLetter(Math.floor(block / 26) - 1) + letter\n}\n\n// How many blocks get a colour of their own, for the key\nexport const COLORED_BLOCKS = BLOCK_COLORS.length\n\n// Each stretch as a box over its row's bar, lettered where it is wide enough\nexport function paintWalkRowBlocks(\n  ctx: CanvasRenderingContext2D,\n  blocks: WalkRowBlock[],\n  f: {\n    x: (offset: number) => number\n    rowCentre: (row: number) => number\n    barPx: number\n  },\n) {\n  ctx.font = LETTER_FONT\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'middle'\n  for (const { row, start, bp, block } of blocks) {\n    const left = f.x(start)\n    const width = f.x(start + bp) - left\n    const top = f.rowCentre(row) - f.barPx / 2\n    ctx.fillStyle = blockFill(block)\n    ctx.fillRect(left, top, width, f.barPx)\n    ctx.strokeStyle = BLOCK_EDGE\n    ctx.lineWidth = 1\n    ctx.strokeRect(left + 0.5, top + 0.5, width - 1, f.barPx - 1)\n    if (width >= MIN_LETTER_PX && f.barPx >= MIN_LETTER_BAR_PX) {\n      ctx.fillStyle = '#111'\n      ctx.fillText(blockLetter(block), left + width / 2, f.rowCentre(row))\n    }\n  }\n}\n", "import { sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport {\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n} from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { deletionKey } from '@jbrowse/bandage-core/deletionEdges'\nimport { edgeWidthFactor } from '@jbrowse/bandage-core/edgeWidths'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { formatBp } from '@jbrowse/bandage-core/graphLabels'\nimport {\n  BAR_PX as WALK_ROW_BAR_PX,\n  CALL_TICK,\n  DISAGREES,\n  GENE_INK,\n  UNBACKED_TICK,\n  walkRowsKey,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { frequencyKey, nodeWidthPx } from '@jbrowse/bandage-core/nodeWidths'\nimport { referenceLabel } from '@jbrowse/bandage-core/reference'\nimport { RAMP_GRADIENT_STOPS } from '@jbrowse/bandage-core/referenceRampCss'\nimport {\n  LIFT_BACKDROP_CSS,\n  REFERENCE_RAMP_ALT_CSS,\n} from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { deviationInk } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport {\n  FORWARD_READ_COLORS,\n  REVERSE_READ_COLORS,\n} from '@jbrowse/bandage-core/tubeMap/reads'\nimport { encodingStops } from '@jbrowse/bandage-core/walkEncoding'\nimport { fadedKey } from '@jbrowse/bandage-core/walkHighlight'\nimport { walkKey } from '@jbrowse/bandage-core/walkKey'\n\nimport { CALL_TOLERANCE } from './repeats/walkCalls'\nimport { PANEL_REFERENCE_TUBE } from './tubeMapPanels'\nimport { COLORED_BLOCKS, blockFill, blockLetter } from './walkRowBlocks'\n\nimport type { GraphPaneModel } from './model'\nimport type { KeySwatch } from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport type { GraphNode } from '@jbrowse/bandage-core/types'\nimport type { LiftedWalk } from '@jbrowse/bandage-core/walkHighlight'\n\n// The legend as data, so the screen's panel and the exported figure's key\n// draw the same rows from one place\n\nexport const SWATCH_PX = 18\nconst BAR_PX = 32\n\n// LIFT_BACKDROP_CSS reads paler alone than faded strokes do where they\n// overlap, so the key samples it darker\nconst FADED_SWATCH = 'rgba(160, 160, 160, 0.45)'\nconst DELETION_INK = '#18181c'\n\nconst STRIP_SAMPLES = 6\nconst TUBE_SWATCH_PX = 7\nconst FOLD_TICK_BACKING = '#b8b8c0'\nconst WALK_ROW_SWATCH_PX = WALK_ROW_BAR_PX - 4\nconst LINK_INK = 'rgba(119, 119, 119, 0.85)'\nconst LINE_PX = 15\nconst CHIP_PX = 10\n\nexport interface Stop {\n  offset: number\n  color: string\n}\n\nexport type LegendSwatch =\n  | {\n      kind: 'fill'\n      stops: Stop[]\n      width?: number\n      height?: number\n      square?: boolean\n      // a hairline edge, so a pale colour still shows on the white key\n      edged?: true\n    }\n  // the reference strip, a band per lifted walk\n  | { kind: 'bands'; bands: Stop[][] }\n  | { kind: 'line'; color: string; dashed?: true }\n  | { kind: 'halo'; color: string }\n  | {\n      kind: 'outline'\n      color: string\n      stroke: number\n      radius: number\n      height: number\n    }\n  | { kind: 'overhang' }\n  | { kind: 'glyph'; char: string }\n  | { kind: 'tick'; color: string; height: number; backing?: string }\n  | { kind: 'bracket' }\n  | { kind: 'blank' }\n\n// A row with no swatch is a note on the drawing\nexport interface LegendRow {\n  key: string\n  label: string\n  swatch?: LegendSwatch\n  strong?: string\n  under?: string\n  title?: string\n  walk?: LiftedWalk\n  closesBubble?: true\n}\n\ninterface LegendSection {\n  testid: string\n  rows: LegendRow[]\n  group?: string\n  // the group's name, over the first of its sections\n  heading?: string\n  // set apart from the group above by a heading's gap, though it has none\n  spaced?: true\n}\n\nexport function swatchWidth(swatch: LegendSwatch) {\n  return swatch.kind === 'fill' ? (swatch.width ?? SWATCH_PX) : SWATCH_PX\n}\n\nexport const bandPx = (bands: readonly unknown[]) => (bands.length > 1 ? 3 : 4)\n\nexport function swatchHeight(swatch: LegendSwatch) {\n  switch (swatch.kind) {\n    case 'fill':\n      return swatch.height ?? 8\n    case 'bands':\n      return bandPx(swatch.bands) * swatch.bands.length\n    case 'line':\n      return 3\n    case 'halo':\n    case 'overhang':\n      return 10\n    case 'outline':\n    case 'tick':\n      return swatch.height\n    case 'glyph':\n      return 15\n    case 'bracket':\n      return 7\n    case 'blank':\n      return 0\n  }\n}\n\n// One column every swatch of a key sits in, so the words after them line up\nexport function swatchColumn(rows: readonly LegendRow[]) {\n  return rows.reduce(\n    (px, row) => (row.swatch ? Math.max(px, swatchWidth(row.swatch)) : px),\n    0,\n  )\n}\n\n// One pitch for every line of a key, roomy enough for its tallest swatch, so\n// rows sit evenly however their swatches differ\nexport function rowPitch(rows: readonly LegendRow[]) {\n  return rows.reduce(\n    (px, row) =>\n      row.swatch ? Math.max(px, Math.ceil(swatchHeight(row.swatch)) + 3) : px,\n    LINE_PX,\n  )\n}\n\nconst flat = (color: string): Stop[] => [{ offset: 0, color }]\n\n// A colour's key is a square chip, so it never reads as a thickness bar\nfunction fillRow(key: string, color: string, label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: {\n      kind: 'fill',\n      stops: flat(color),\n      width: CHIP_PX,\n      height: CHIP_PX,\n      edged: true,\n    },\n  }\n}\n\n// hard-edged bands, a read taking one shade of its strand's palette\nfunction bandStops(colors: readonly string[]) {\n  return colors.flatMap((color, i) => [\n    { offset: i / colors.length, color },\n    { offset: (i + 1) / colors.length, color },\n  ])\n}\n\nfunction openBubbleRows(model: GraphPaneModel): LegendRow[] {\n  const open = model.openBubble\n  if (!open) {\n    return []\n  }\n  const halo = model.bubbleHalos.find(h => sameBubble(h.bubble, open))\n  return [\n    {\n      key: 'open',\n      label: `open: ${halo?.label ?? 'bubble'}`,\n      swatch: halo\n        ? { kind: 'halo', color: BUBBLE_KIND_COLORS[halo.kind] }\n        : { kind: 'blank' },\n      closesBubble: true,\n    },\n  ]\n}\n\n// Under lifted walks each lane states its own scale, and the rest is grey\nfunction rampRows(model: GraphPaneModel): LegendRow[] {\n  const domain = model.walkLift ? undefined : model.referenceRampDomain\n  if (!domain) {\n    return []\n  }\n  // a measured domain runs between node midpoints, which can fall on a half bp\n  const start = Math.round(domain.start)\n  const end = Math.round(domain.end)\n  const reference = model.graph ? referenceLabel(model.graph) : 'reference'\n  return [\n    {\n      key: 'ramp',\n      label: `position on ${reference}`,\n      swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },\n      under: `${start.toLocaleString('en-US')}-${end.toLocaleString('en-US')} (${formatBp(end - start)})`,\n    },\n    ...(model.referenceRampDrawsOffReference\n      ? [fillRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference')]\n      : []),\n  ]\n}\n\n// The strip's own colours: a band per lifted walk in its lane's, else the\n// node scheme's, a few of its blocks in bp order rather than a rainbow it\n// does not draw\nfunction stripBands(model: GraphPaneModel): Stop[][] {\n  const lift = model.walkLift\n  if (lift) {\n    return lift.walks.map(w => encodingStops(w.encoding))\n  }\n  if (model.effectiveColorScheme === 'reference-position') {\n    return [RAMP_GRADIENT_STOPS]\n  }\n  const colors = model.referenceStripBlocks\n    .map(b => b.colors[0]!)\n    .filter((c, i, all) => c !== all[i - 1])\n  const n = Math.min(STRIP_SAMPLES, colors.length)\n  return [\n    n === 0\n      ? flat(LIFT_BACKDROP_CSS)\n      : Array.from({ length: n }, (_, i) => ({\n          offset: n > 1 ? i / (n - 1) : 0,\n          color:\n            colors[\n              n > 1 ? Math.round((i * (colors.length - 1)) / (n - 1)) : 0\n            ]!,\n        })),\n  ]\n}\n\nfunction stripRows(model: GraphPaneModel): LegendRow[] {\n  if (!model.referenceStripShown) {\n    return []\n  }\n  const rowPerWalk = (model.walkLift?.walks.length ?? 0) > 1\n  return [\n    {\n      key: 'strip',\n      label: `reference${rowPerWalk ? ', a row per walk' : ''}`,\n      swatch: { kind: 'bands', bands: stripBands(model) },\n    },\n    ...(model.referenceStripFaded\n      ? [\n          fillRow(\n            'strip-faded',\n            LIFT_BACKDROP_CSS,\n            model.walkLift\n              ? `reference not on ${rowPerWalk ? \"that row's walk\" : model.liftedWalksLabel}`\n              : 'reference outside the open bubble',\n          ),\n        ]\n      : []),\n    ...(model.referenceStripOverhangs\n      ? [\n          {\n            key: 'overhang',\n            label: 'graph runs past this edge',\n            swatch: { kind: 'overhang' } as const,\n          },\n        ]\n      : []),\n  ]\n}\n\n// One row per halo colour drawn, naming the kinds it stands for\nfunction haloRows(model: GraphPaneModel): LegendRow[] {\n  const kindsByColor = new Map<string, Set<string>>()\n  for (const h of model.bubbleHalos) {\n    if (!h.whole) {\n      const color = BUBBLE_KIND_COLORS[h.kind]\n      const kinds = kindsByColor.get(color) ?? new Set<string>()\n      kinds.add(BUBBLE_KIND_NAMES[h.kind])\n      kindsByColor.set(color, kinds)\n    }\n  }\n  return [...kindsByColor].map(([color, kinds]) => {\n    const names = [...kinds].join(' or ')\n    return {\n      key: `halo-${color}`,\n      label:\n        names === BUBBLE_KIND_NAMES.superbubble ? names : `${names} bubble`,\n      swatch: { kind: 'halo', color },\n    }\n  })\n}\n\nfunction deletionRows(model: GraphPaneModel): LegendRow[] {\n  const { graph } = model\n  return graph && model.deletions.length > 0\n    ? [\n        {\n          key: 'deletion',\n          label: deletionKey(referenceLabel(graph)),\n          swatch: {\n            kind: 'line',\n            color: model.walkLift ? FADED_SWATCH : DELETION_INK,\n            dashed: true,\n          },\n        },\n      ]\n    : []\n}\n\nfunction thicknessRow(\n  key: string,\n  label: string,\n  px: number,\n  color: string,\n): LegendRow {\n  return {\n    key,\n    label,\n    swatch: { kind: 'fill', stops: flat(color), width: BAR_PX, height: px },\n  }\n}\n\nconst roundDepth = (depth: number) =>\n  depth >= 10 ? Math.round(depth) : Math.round(depth * 10) / 10\n\n// What a node's thickness counts, with bars as thick as the drawing makes\n// the thinnest, the mean and the thickest node\nfunction nodeWidthRows(model: GraphPaneModel): LegendRow[] {\n  const { graph, contigThickness: px, depthRange: range } = model\n  if (!graph || !model.drawsNodes || model.walkRowBars) {\n    return []\n  }\n  if (model.nodeWidth === 'frequency') {\n    const tagged = graph.nodes.some(n => n.frequency !== undefined)\n    return frequencyKey(px).map(({ label, widthPx }) =>\n      thicknessRow(\n        `width-${label}`,\n        tagged ? `AF ${label}` : `${label} of haplotypes`,\n        widthPx,\n        REFERENCE_RAMP_ALT_CSS,\n      ),\n    )\n  }\n  if (model.nodeWidth !== 'depth' || !range || range.min === range.max) {\n    return []\n  }\n  const walkCount = graph.paths?.length ?? 0\n  const walks = walkCount > 0\n  const depths = [\n    ...new Set(\n      [range.max, range.mean, range.min].map(walks ? Math.round : roundDepth),\n    ),\n  ]\n  // a walk looping through a repeat passes its nodes more than once, and\n  // each pass counts\n  const passes = depths[0]! > walkCount\n  const counted = (n: number) =>\n    passes\n      ? `${n.toLocaleString('en-US')} walk pass${n === 1 ? '' : 'es'}`\n      : `${n.toLocaleString('en-US')} walk${n === 1 ? '' : 's'}`\n  return depths.map(depth =>\n    thicknessRow(\n      `width-${depth}`,\n      walks ? counted(depth) : `depth ${depth.toLocaleString('en-US')}`,\n      nodeWidthPx({ depth } as GraphNode, px, 'depth', range.mean),\n      REFERENCE_RAMP_ALT_CSS,\n    ),\n  )\n}\n\nfunction linkWidthRows(model: GraphPaneModel): LegendRow[] {\n  const busiest = model.busiestLink\n  if (\n    !model.drawsNodes ||\n    model.walkRowBars ||\n    model.linkWidth !== 'walks' ||\n    busiest === 0\n  ) {\n    return []\n  }\n  const counts = busiest > 1 ? [busiest, 1] : [1]\n  return counts.map(n =>\n    thicknessRow(\n      `link-width-${n}`,\n      `${n.toLocaleString('en-US')} walk${n === 1 ? '' : 's'}`,\n      model.connectorThickness * edgeWidthFactor(n, busiest, 'walks'),\n      LINK_INK,\n    ),\n  )\n}\n\nfunction geneRows(model: GraphPaneModel): LegendRow[] {\n  return model.genePins.some(pin => pin.exonsByNode.length > 0)\n    ? [\n        {\n          key: 'exon',\n          label: 'exon',\n          swatch: {\n            kind: 'outline',\n            color: EXON_COLOR,\n            stroke: 2,\n            radius: 5,\n            height: 8,\n          },\n        },\n      ]\n    : []\n}\n\nfunction foldRows(model: GraphPaneModel): LegendRow[] {\n  const note = model.foldNote\n  return note ? [{ key: 'fold', label: note }] : []\n}\n\nfunction pathRows(model: GraphPaneModel): LegendRow[] {\n  return model.pathLegend.map(({ name, label, color }) => ({\n    key: `path-${name}`,\n    label,\n    swatch: { kind: 'line', color },\n  }))\n}\n\nfunction tubeRow(key: string, stops: Stop[], label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: { kind: 'fill', stops, height: TUBE_SWATCH_PX, square: true },\n  }\n}\n\n// What a tube map draws that nothing else on screen explains, each listed\n// only while it applies\nexport function tubeMapRows(model: GraphPaneModel): LegendRow[] {\n  const {\n    roles,\n    haplotypeTube,\n    bundled,\n    values,\n    logWidths,\n    foldBp,\n    forwardReads,\n    reverseReads,\n    substitution,\n    insertion,\n    deletion,\n  } = model.tubeMapKeys\n  const reads = model.readsShown\n  const rows: LegendRow[] = []\n  if (values) {\n    rows.push(\n      tubeRow('value-reference', flat(PANEL_REFERENCE_TUBE), 'reference'),\n    )\n    for (const { value, color } of values) {\n      rows.push(tubeRow(`value-${value}`, flat(color), value))\n    }\n  }\n  if (roles) {\n    rows.push(\n      tubeRow('ref', flat(PANEL_REFERENCE_TUBE), 'reference'),\n      tubeRow(\n        'hap',\n        flat(haplotypeTube),\n        bundled ? 'shared route, \u00D7n haplotypes' : 'haplotype',\n      ),\n    )\n  }\n  if (forwardReads) {\n    rows.push(\n      tubeRow(\n        'fwd',\n        bandStops(FORWARD_READ_COLORS),\n        'read on the forward strand',\n      ),\n    )\n  }\n  if (reverseReads) {\n    rows.push(\n      tubeRow(\n        'rev',\n        bandStops(REVERSE_READ_COLORS),\n        'read on the reverse strand',\n      ),\n    )\n  }\n  if (reads && reads.shown < reads.total) {\n    rows.push({\n      key: 'sampled',\n      label: `${reads.shown.toLocaleString('en-US')} of ${reads.total.toLocaleString('en-US')} reads shown`,\n      swatch: { kind: 'blank' },\n    })\n  }\n  if (substitution) {\n    rows.push({\n      key: 'sub',\n      label: 'read mismatch',\n      swatch: { kind: 'glyph', char: 'A' },\n    })\n  }\n  if (insertion) {\n    rows.push({\n      key: 'ins',\n      label: 'read insertion',\n      swatch: { kind: 'glyph', char: '*' },\n    })\n  }\n  if (deletion) {\n    rows.push(tubeRow('del', flat('grey'), 'read deletion'))\n  }\n  if (foldBp !== undefined) {\n    rows.push({\n      key: 'tube-fold',\n      label: `haplotype variant < ${formatBp(foldBp)}`,\n      swatch: {\n        kind: 'tick',\n        color: deviationInk(),\n        height: TUBE_SWATCH_PX,\n        backing: FOLD_TICK_BACKING,\n      },\n    })\n  }\n  if (logWidths) {\n    rows.push({\n      key: 'log',\n      label: 'width grows with log of length',\n      swatch: { kind: 'bracket' },\n    })\n  }\n  return rows\n}\n\nexport function walkRowSwatch(swatch: KeySwatch): LegendSwatch {\n  return swatch.kind === 'gene'\n    ? {\n        kind: 'outline',\n        color: GENE_INK,\n        stroke: 1.5,\n        radius: 0,\n        height: WALK_ROW_SWATCH_PX,\n      }\n    : {\n        kind: 'fill',\n        stops:\n          swatch.kind === 'bar' && swatch.ramp\n            ? RAMP_GRADIENT_STOPS\n            : flat(swatch.fill),\n        height: swatch.kind === 'gap' ? swatch.px : WALK_ROW_SWATCH_PX,\n      }\n}\n\n// The shared blocks the rows draw: each coloured one by its letter, then one\n// row for the grey rest\nfunction blockRows(model: GraphPaneModel): LegendRow[] {\n  const present = new Set(model.sharedBlocks?.map(b => b.block))\n  const swatch = (block: number) => ({\n    kind: 'fill' as const,\n    stops: flat(blockFill(block)),\n    height: WALK_ROW_SWATCH_PX,\n  })\n  return [\n    ...[...present]\n      .filter(block => block < COLORED_BLOCKS)\n      .sort((a, b) => a - b)\n      .map(block => ({\n        key: `block-${block}`,\n        label: `${blockLetter(block)}: off the reference, walked by several rows`,\n        swatch: swatch(block),\n      })),\n    ...([...present].some(block => block >= COLORED_BLOCKS)\n      ? [\n          {\n            key: 'block-more',\n            label: 'more shared blocks',\n            swatch: swatch(COLORED_BLOCKS),\n          },\n        ]\n      : []),\n  ]\n}\n\n// The walk rows' bar colours, genes and ticks; each tick row appears once\n// the rows hold one, so a catalogue with no genotypes keeps the plain key\nfunction walkRowsRows(model: GraphPaneModel): LegendRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  const calls = [bars.reference, ...bars.rows].flatMap(row => row.call ?? [])\n  const tick = (key: string, color: string, label: string): LegendRow => ({\n    key,\n    label,\n    swatch: { kind: 'tick', color, height: WALK_ROW_SWATCH_PX },\n  })\n  return [\n    ...walkRowsKey(bars, {\n      ramp: model.referenceRampDomain,\n      genes: model.walkRowGeneKey,\n      annotation: model.walkRowAnnotation,\n    }).map(entry => ({\n      key: `rows-${entry.label}`,\n      label: entry.label,\n      swatch: entry.note ? undefined : walkRowSwatch(entry.swatch),\n    })),\n    ...blockRows(model),\n    ...(calls.some(call => call.spanningReads !== 0)\n      ? [tick('call', CALL_TICK, 'allele length called for this walk')]\n      : []),\n    ...(calls.some(call => call.spanningReads === 0)\n      ? [tick('unbacked', UNBACKED_TICK, 'called with no read spanning it')]\n      : []),\n    ...(calls.some(call => call.agrees === false)\n      ? [\n          tick(\n            'disagrees',\n            DISAGREES,\n            `walk and call over ${Math.round(CALL_TOLERANCE * 100)}% apart`,\n          ),\n        ]\n      : []),\n  ]\n}\n\n// One lifted walk's key: a swatch, or a short bar of the scale its lane\n// shades by, then its name, with the scale's stretch under it\nexport function walkKeyRow(model: GraphPaneModel, walk: LiftedWalk): LegendRow {\n  const key = walkKey(walk, model.walkReference)\n  return {\n    key: `walk-${walk.name}`,\n    strong: model.walkLabel(walk.name),\n    label: key.delta + key.gaps + key.reversed,\n    swatch: {\n      kind: 'fill',\n      stops: encodingStops(walk.encoding),\n      width: key.shades ? BAR_PX : SWATCH_PX,\n    },\n    under: key.scale,\n    title: key.hover,\n    walk,\n  }\n}\n\n// The off-reference colour, where the lift paints it, and the faded rest.\n// rampRows draws no key while walks are lifted, so these rows name both.\nfunction fadedRows(model: GraphPaneModel, faded: string): LegendRow[] {\n  return [\n    ...(model.liftPaintsOffReference\n      ? [fillRow('lift-off', REFERENCE_RAMP_ALT_CSS, 'off the reference')]\n      : []),\n    fillRow('faded', FADED_SWATCH, faded),\n  ]\n}\n\n// Each lifted walk's key, then what the faded rest is\nfunction walkReadoutRows(model: GraphPaneModel): LegendRow[] {\n  const lift = model.walkLift\n  if (!lift || model.facetPanels) {\n    return []\n  }\n  const rows = lift.walks.map(w => walkKeyRow(model, w))\n  const faded = model.graph\n    ? fadedKey(model.graph, lift, model.liftedWalksLabel)\n    : `not on ${model.liftedWalksLabel}`\n  return [...rows, ...fadedRows(model, faded)]\n}\n\n// The faceted pane's one key line under its panels: each panel's title keys\n// its walk, so this keys only what every panel greys\nexport function facetKeyRows(model: GraphPaneModel): LegendRow[] {\n  const { graph, facetPanels } = model\n  if (!graph || !facetPanels) {\n    return []\n  }\n  const keys = new Set(\n    facetPanels.map(panel => fadedKey(graph, panel, \"the panel's walk\")),\n  )\n  return [\n    ...fadedRows(\n      model,\n      keys.size === 1 ? [...keys][0]! : \"not on the panel's walk\",\n    ),\n    ...deletionRows(model),\n  ]\n}\n\n// The keys in the order the panel stacks them, top first, each under its\n// group's heading once the key holds more than one group\nexport function legendSections(model: GraphPaneModel): LegendSection[] {\n  const sections: LegendSection[] = [\n    { testid: 'graph-open-bubble-legend', rows: openBubbleRows(model) },\n    { testid: 'graph-ramp-legend', rows: rampRows(model), group: 'Color' },\n    {\n      testid: 'graph-walk-readout',\n      rows: walkReadoutRows(model),\n      group: 'Walks',\n    },\n    {\n      testid: 'graph-width-legend',\n      rows: nodeWidthRows(model),\n      group: 'Node thickness',\n    },\n    {\n      testid: 'graph-link-width-legend',\n      rows: linkWidthRows(model),\n      group: 'Link thickness',\n    },\n    { testid: 'graph-halo-legend', rows: haloRows(model), group: 'Marks' },\n    {\n      testid: 'graph-deletion-legend',\n      rows: deletionRows(model),\n      group: 'Marks',\n    },\n    { testid: 'graph-gene-legend', rows: geneRows(model), group: 'Marks' },\n    { testid: 'graph-path-legend', rows: pathRows(model), group: 'Paths' },\n    {\n      testid: 'graph-tube-map-legend',\n      rows: tubeMapRows(model),\n      group: 'Tube map',\n    },\n    {\n      testid: 'graph-walk-rows-legend',\n      rows: walkRowsRows(model),\n      group: 'Walk rows',\n    },\n    {\n      testid: 'graph-reference-strip-legend',\n      rows: stripRows(model),\n      group: 'Top strip',\n    },\n    { testid: 'graph-fold-legend', rows: foldRows(model) },\n  ].filter(section => section.rows.length > 0)\n  const groups = new Set(sections.flatMap(section => section.group ?? []))\n  if (groups.size < 2) {\n    return sections\n  }\n  const headed = new Set<string>()\n  return sections.map((section, i) => {\n    const { group } = section\n    if (!group) {\n      return i === 0 ? section : { ...section, spaced: true as const }\n    }\n    if (headed.has(group)) {\n      return section\n    }\n    headed.add(group)\n    return { ...section, heading: group }\n  })\n}\n", "import { createElement, useId } from 'react'\nimport type { ReactNode } from 'react'\n\nimport type { El } from '@jbrowse/bandage-core/el'\n\n// SVG's attribute names as React's props: `class` is className, `data-` and\n// `aria-` keep their dashes, the rest are camel-cased (`stroke-width` is\n// strokeWidth)\nfunction propName(name: string) {\n  return name === 'class'\n    ? 'className'\n    : /^(data|aria)-/.test(name)\n      ? name\n      : name.replace(/-([a-z])/g, (_, c: string) => c.toUpperCase())\n}\n\nfunction toReact(node: El | string, key: number): ReactNode {\n  if (typeof node === 'string') {\n    return node\n  }\n  const props: Record<string, unknown> = { key }\n  for (const [name, value] of Object.entries(node.attrs)) {\n    if (value !== undefined) {\n      props[propName(name)] = value\n    }\n  }\n  return createElement(node.tag, props, node.children.map(toReact))\n}\n\n// A useId fit for an SVG id and for url(#\u2026)\nexport function useSvgId() {\n  return useId().replaceAll(/[^\\w-]/g, '')\n}\n\n// A core element tree as React elements\nexport default function ElTree({ el }: { el: El }) {\n  return toReact(el, 0)\n}\n", "import { rulerInk } from '@jbrowse/bandage-core/tubeMap/axis'\n\nimport { useSvgId } from './ElTree'\nimport { SWATCH_PX, bandPx, swatchHeight, swatchWidth } from '../legendSections'\n\nimport type { LegendSwatch, Stop } from '../legendSections'\n\nconst EDGE_INK = 'rgba(0, 0, 0, 0.28)'\n\nfunction Gradient({\n  id,\n  x,\n  y,\n  stops,\n  width,\n  height,\n  square,\n  edged,\n}: {\n  id: string\n  x: number\n  y: number\n  stops: readonly Stop[]\n  width: number\n  height: number\n  square?: boolean\n  edged?: boolean\n}) {\n  // an edge's stroke sits half inside, so the chip keeps its size\n  const inset = edged ? 0.5 : 0\n  const rect = (fill: string) => (\n    <rect\n      x={x + inset}\n      y={y + inset}\n      width={width - inset * 2}\n      height={height - inset * 2}\n      rx={square ? 0 : 2}\n      fill={fill}\n      stroke={edged ? EDGE_INK : undefined}\n    />\n  )\n  return stops.length > 1 ? (\n    <>\n      <defs>\n        <linearGradient id={id}>\n          {stops.map((s, i) => (\n            <stop key={i} offset={s.offset} stopColor={s.color} />\n          ))}\n        </linearGradient>\n      </defs>\n      {rect(`url(#${id})`)}\n    </>\n  ) : (\n    rect(stops[0]!.color)\n  )\n}\n\n// A row's swatch with its left edge at x, centred on the row's text 5 px\n// above the baseline\nexport function SvgSwatch({\n  swatch,\n  x,\n  id,\n}: {\n  swatch: LegendSwatch\n  x: number\n  id: string\n}) {\n  const mid = -5\n  switch (swatch.kind) {\n    case 'fill': {\n      const height = swatchHeight(swatch)\n      return (\n        <Gradient\n          id={id}\n          x={x}\n          y={mid - height / 2}\n          stops={swatch.stops}\n          width={swatchWidth(swatch)}\n          height={height}\n          square={swatch.square}\n          edged={swatch.edged}\n        />\n      )\n    }\n    case 'bands': {\n      const band = bandPx(swatch.bands)\n      const top = mid - swatchHeight(swatch) / 2\n      return (\n        <>\n          {swatch.bands.map((stops, i) => (\n            <Gradient\n              key={i}\n              id={`${id}-${i}`}\n              x={x}\n              y={top + i * band}\n              stops={stops}\n              width={SWATCH_PX}\n              height={band}\n              square\n            />\n          ))}\n        </>\n      )\n    }\n    case 'line':\n      return swatch.dashed ? (\n        <line\n          x1={x + 1}\n          x2={x + SWATCH_PX}\n          y1={mid}\n          y2={mid}\n          stroke={swatch.color}\n          strokeWidth={3}\n          strokeDasharray=\"4 3\"\n        />\n      ) : (\n        <rect\n          x={x}\n          y={mid - 1.5}\n          width={SWATCH_PX}\n          height={3}\n          rx={2}\n          fill={swatch.color}\n        />\n      )\n    case 'halo':\n      return (\n        <line\n          x1={x + 5}\n          x2={x + 13}\n          y1={mid}\n          y2={mid}\n          stroke={swatch.color}\n          strokeOpacity={0.35}\n          strokeWidth={8}\n          strokeLinecap=\"round\"\n        />\n      )\n    case 'outline': {\n      const inset = swatch.stroke / 2\n      return (\n        <rect\n          x={x + inset}\n          y={mid - swatch.height / 2 + inset}\n          width={SWATCH_PX - swatch.stroke}\n          height={swatch.height - swatch.stroke}\n          rx={Math.max(0, swatch.radius - inset)}\n          fill=\"none\"\n          stroke={swatch.color}\n          strokeWidth={swatch.stroke}\n        />\n      )\n    }\n    case 'overhang':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 5})`}\n          d=\"M0,5 L8,0 L8,10 Z M18,5 L10,0 L10,10 Z\"\n          fill=\"#18181c\"\n        />\n      )\n    case 'glyph':\n      return (\n        <text\n          x={x + SWATCH_PX / 2}\n          y={mid + 4}\n          textAnchor=\"middle\"\n          fontFamily=\"monospace\"\n          fontSize={12}\n          fill=\"currentColor\"\n        >\n          {swatch.char}\n        </text>\n      )\n    case 'tick': {\n      const y = mid - swatch.height / 2\n      return (\n        <>\n          {swatch.backing ? (\n            <rect\n              x={x}\n              y={y}\n              width={SWATCH_PX}\n              height={swatch.height}\n              fill={swatch.backing}\n            />\n          ) : null}\n          <rect\n            x={x + SWATCH_PX / 2 - 1}\n            y={y}\n            width={2}\n            height={swatch.height}\n            fill={swatch.color}\n          />\n        </>\n      )\n    }\n    case 'bracket':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 3.5})`}\n          d={`M0.5,6 V1.5 H5.5 V6 M8.5,6 V1.5 H${SWATCH_PX - 0.5} V6`}\n          fill=\"none\"\n          stroke={rulerInk()}\n        />\n      )\n    case 'blank':\n      return null\n  }\n}\n\n// The same swatch on screen, in a box as tall as the swatch so the row\n// centres it on its words\nexport function LegendSwatchView({ swatch }: { swatch: LegendSwatch }) {\n  const id = useSvgId()\n  const height = swatchHeight(swatch)\n  return (\n    <svg\n      width={swatchWidth(swatch)}\n      height={height}\n      overflow=\"visible\"\n      style={{ flex: 'none' }}\n    >\n      <g transform={`translate(0 ${height / 2 + 5})`}>\n        <SvgSwatch swatch={swatch} x={0} id={id} />\n      </g>\n    </svg>\n  )\n}\n", "// A key's section of the legend panel, and one row in it: a swatch beside its\n// words\nexport const legendBoxStyle = {\n  background: '#fff',\n  padding: '3px 6px',\n  fontSize: 11,\n  lineHeight: '15px',\n  whiteSpace: 'nowrap' as const,\n}\n\nexport const legendRowStyle = { display: 'flex', alignItems: 'center', gap: 5 }\n\n// A line with no swatch, such as what the drawing folded away\nexport const legendNoteStyle = { color: '#666' }\n\nexport const HEADING_INK = '#6b7479'\nexport const HEADING_GAP_PX = 4\n\n// A group's name over its rows, set apart by a gap unless it opens the key\nexport const legendHeadingStyle = {\n  color: HEADING_INK,\n  fontSize: 9.5,\n  fontWeight: 600,\n  letterSpacing: '0.06em',\n  textTransform: 'uppercase' as const,\n}\n", "import { useMemo } from 'react'\n\nimport {\n  exonOutlineTree,\n  exonStretches,\n} from '@jbrowse/bandage-core/genes/exonOutline'\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The session's genes drawn onto the graph: each exon outlined round its\n// stretch of node, as core's exonOutlineTree draws it for every host, moved by\n// the same transform the halos use. Their names are LabelLayer's.\n\nconst GenePins = observer(function GenePins({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const id = `exon-outline-${useSvgId()}`\n  // in layout units, so a pan frame reuses them and only moves the transform\n  const stretches = useMemo(\n    () =>\n      computed(() => {\n        const { genePins, walkLift } = model\n        // an open bubble rings only its own exons\n        const focus = walkLift ? undefined : model.openBubbleFocus\n        const pins = focus\n          ? genePins.map(pin => ({\n              ...pin,\n              exonsByNode: pin.exonsByNode.filter(e =>\n                focus.nodeIds.has(e.nodeId),\n              ),\n            }))\n          : genePins\n        return exonStretches(pins, model.nodeInk.halfWidthPx, walkLift)\n      }),\n    [model],\n  )\n  const { scaleX, scaleY, translateX, translateY, paneWidth, canvasHeight } =\n    model\n  const tree = exonOutlineTree(stretches.get(), {\n    id,\n    width: paneWidth,\n    height: canvasHeight,\n    transform: `translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`,\n  })\n  return tree ? (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-gene-pins\">\n      <ElTree el={tree} />\n    </PaneSvgLayer>\n  ) : null\n})\n\nexport default GenePins\n", "import { LABEL_PAD, LABEL_PX } from '@jbrowse/bandage-core/overlayLabels'\n\n// A chip's box, its text's baseline at y and centred on x\nfunction chipBox(x: number, y: number, w: number) {\n  return {\n    x: x - w / 2,\n    y: y - LABEL_PX - LABEL_PAD + 2,\n    width: w,\n    height: LABEL_PX + LABEL_PAD * 2 - 2,\n  }\n}\n\nexport function inChip(\n  chip: { x: number; y: number; w: number },\n  px: number,\n  py: number,\n) {\n  const box = chipBox(chip.x, chip.y, chip.w)\n  return (\n    px >= box.x &&\n    px <= box.x + box.width &&\n    py >= box.y &&\n    py <= box.y + box.height\n  )\n}\n\n// One label on an overlay: a white chip with a coloured edge and text. A note\n// follows the text in plain type. A chip takes the pointer only with a\n// handler, so its title shows only then.\nexport default function LabelChip({\n  x,\n  y,\n  w,\n  text,\n  note,\n  color,\n  edge = color,\n  italic,\n  dimmed,\n  title,\n  testId,\n  onClick,\n  onHover,\n}: {\n  x: number\n  y: number\n  w: number\n  text: string\n  note?: string\n  color: string\n  edge?: string\n  italic?: boolean\n  dimmed?: boolean\n  title?: string\n  testId?: string\n  onClick?: () => void\n  onHover?: (hovered: boolean) => void\n}) {\n  return (\n    <g\n      style={{\n        pointerEvents: onClick || onHover ? 'auto' : 'none',\n        cursor: onClick ? 'pointer' : undefined,\n        opacity: dimmed ? 0.35 : 1,\n      }}\n      data-testid={testId}\n      onClick={onClick}\n      onMouseEnter={() => {\n        onHover?.(true)\n      }}\n      onMouseLeave={() => {\n        onHover?.(false)\n      }}\n      // a clickable chip is a button to the keyboard too\n      {...(onClick && {\n        role: 'button',\n        tabIndex: 0,\n        'aria-label': (title ?? text).replaceAll('\\n', ', '),\n        onKeyDown: (e: React.KeyboardEvent) => {\n          if (e.key === 'Enter' || e.key === ' ') {\n            e.preventDefault()\n            onClick()\n          }\n        },\n        onFocus: () => {\n          onHover?.(true)\n        },\n        onBlur: () => {\n          onHover?.(false)\n        },\n      })}\n    >\n      {title ? <title>{title}</title> : null}\n      <rect\n        {...chipBox(x, y, w)}\n        rx={3}\n        fill=\"rgba(255,255,255,0.85)\"\n        stroke={edge}\n        strokeWidth={1}\n      />\n      <text\n        x={x}\n        y={y}\n        fontSize={LABEL_PX}\n        fontFamily=\"sans-serif\"\n        fontStyle={italic ? 'italic' : undefined}\n        fontWeight={italic ? 600 : undefined}\n        fill={color}\n        textAnchor=\"middle\"\n      >\n        {text}\n        {note ? (\n          <tspan fontStyle=\"normal\" fontWeight=\"normal\">\n            {note}\n          </tspan>\n        ) : null}\n      </text>\n    </g>\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { geneCoverageNote } from '@jbrowse/bandage-core/labelLayout'\nimport { LABEL_PX, labelWidth } from '@jbrowse/bandage-core/overlayLabels'\nimport { isAlive } from '@jbrowse/mobx-state-tree'\nimport { observer } from 'mobx-react'\n\nimport LabelChip, { inChip } from './LabelChip'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\nimport type { BubbleHalo } from '@jbrowse/bandage-core/bubbles/bubbleHalos'\nimport type { LabelLayout } from '@jbrowse/bandage-core/labelLayout'\n\n// Every chip drawn over the graph, above all of its ink: bubble names and gene\n// names on their pins. `overlayLabels` has placed\n// them against each other and against the row labels already.\n\nconst GENE_INK = '#1c1c22'\nconst TICK_PX = 9\nconst TICK_WIDTH = 3\n\n// What the gene chip under a point reads out, for the hover tooltip: those\n// chips leave the pointer to the canvas, so a drag can start on one\nexport function chipReadoutAt(\n  { genes }: Pick<LabelLayout, 'genes'>,\n  px: number,\n  py: number,\n) {\n  const pin = genes.find(chip => inChip(chip, px, py))?.item\n  if (!pin) {\n    return undefined\n  }\n  const { gene } = pin\n  const note = geneCoverageNote(pin)\n  return {\n    label: gene.name,\n    readout: `${gene.refName}:${gene.start.toLocaleString()}-${gene.end.toLocaleString()}${note ? `, ${note} in the cut` : ''}`,\n  }\n}\n\nconst LabelLayer = observer(function LabelLayer({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbles, genes, ticks } = model.overlayLabels\n  if (bubbles.length + genes.length + ticks.length === 0) {\n    return null\n  }\n  const { scaleY, translateY, contigThickness, hoveredBubble } = model\n  const hoveredTick = hoveredBubble\n    ? ticks.find(t => sameBubble(t.item.bubble, hoveredBubble))\n    : undefined\n  const tickAt = (target: EventTarget) =>\n    ticks[Number((target as Element).getAttribute('data-tick'))]\n  const dimmedBubble = (h: BubbleHalo) => model.bubbleFaded(h)\n  const isOpen = (h: BubbleHalo) => model.bubbleIsOpen(h.bubble)\n\n  return (\n    <PaneSvgLayer\n      model={model}\n      zIndex={3}\n      testId=\"graph-label-layer\"\n      pansWithDrawing\n    >\n      <g\n        data-testid=\"graph-bubble-ticks\"\n        onClick={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n        onMouseOver={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        // a leave also fires as the view closing it unmounts the tick\n        onMouseOut={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onFocus={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        onBlur={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onKeyDown={e => {\n          const tick = tickAt(e.target)\n          if (tick && (e.key === 'Enter' || e.key === ' ')) {\n            e.preventDefault()\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n      >\n        {ticks.map(({ item: h, x, y }, i) => (\n          <rect\n            key={bubbleKey(h.bubble)}\n            data-tick={i}\n            role=\"button\"\n            tabIndex={0}\n            aria-label={`${h.label}, ${isOpen(h) ? 'close' : 'open'} bubble`}\n            x={x - TICK_WIDTH / 2}\n            y={y - TICK_PX}\n            width={TICK_WIDTH}\n            height={TICK_PX}\n            rx={TICK_WIDTH / 2}\n            fill={BUBBLE_KIND_COLORS[h.kind]}\n            opacity={dimmedBubble(h) ? 0.35 : 1}\n            style={{ pointerEvents: 'all', cursor: 'pointer' }}\n          />\n        ))}\n      </g>\n      {genes.map(({ item: pin, x, y, w, text }) => {\n        const { gene } = pin\n        return (\n          <g key={`${gene.name}-${gene.start}`}>\n            <line\n              x1={x}\n              x2={x}\n              y1={y - LABEL_PX - 2}\n              y2={pin.at.y * scaleY + translateY + contigThickness / 2}\n              stroke={GENE_INK}\n              strokeWidth={0.8}\n              strokeOpacity={0.6}\n            />\n            <LabelChip\n              x={x}\n              y={y}\n              w={w}\n              text={gene.name}\n              note={text.slice(gene.name.length) || undefined}\n              color={GENE_INK}\n              edge={EXON_COLOR}\n              italic\n              testId=\"graph-gene-pin-label\"\n            />\n          </g>\n        )\n      })}\n      {bubbles.map(({ item: h, x, y, w, text }) => (\n        <LabelChip\n          key={bubbleKey(h.bubble)}\n          x={x}\n          y={y}\n          w={w}\n          text={text}\n          color={BUBBLE_KIND_COLORS[h.kind]}\n          dimmed={dimmedBubble(h)}\n          title={`${h.label}\\n${h.bubble.segmentCount} segments${h.bubble.covering ? '' : isOpen(h) ? ' \u00B7 click to close' : ' \u00B7 click to open'}`}\n          testId=\"graph-bubble-halo-label\"\n          // the bubble the drawing is would open into this same drawing\n          onClick={\n            h.bubble.covering\n              ? undefined\n              : () => {\n                  model.toggleBubble(h.bubble)\n                }\n          }\n          // a leave also fires as the view closing it unmounts the chip\n          onHover={hovered => {\n            if (isAlive(model)) {\n              model.setHoveredBubble(hovered ? h.bubble : null)\n            }\n          }}\n        />\n      ))}\n      {hoveredTick ? (\n        <LabelChip\n          x={hoveredTick.x}\n          y={hoveredTick.y - TICK_PX - 4}\n          w={labelWidth(hoveredTick.item.label)}\n          text={hoveredTick.item.label}\n          color={BUBBLE_KIND_COLORS[hoveredTick.item.kind]}\n          testId=\"graph-bubble-tick-label\"\n        />\n      ) : null}\n    </PaneSvgLayer>\n  )\n})\n\nexport default LabelLayer\n", "import { useCallback } from 'react'\n\nimport { drawReferenceStrip } from '@jbrowse/bandage-core/referenceStrip'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// Each reference segment at its bp in the linear view, onto the pane's\n// canvas or the linear view's SVG export\nexport function paintReferenceStrip(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  {\n    lit,\n    dpr,\n  }: { lit: GraphPaneModel['referenceStripLit'] | undefined; dpr: number },\n) {\n  const frame = model.hostBpFrame\n  if (frame) {\n    drawReferenceStrip(ctx, model.referenceStripBlocks, frame, {\n      width: model.paneWidth,\n      lit,\n      dpr,\n    })\n  }\n}\n\n// Each reference segment at its bp in the linear view, over a drawing that\n// has no bp axis of its own. Repainted by an autorun, so a pan in the linear\n// view moves the strip in the same frame as its other tracks.\nconst ReferenceStripOverlay = observer(function ReferenceStripOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D, dpr: number) => {\n      paintReferenceStrip(ctx, model, { lit: model.referenceStripLit, dpr })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={5}\n      shown={model.referenceStripShown}\n      testId=\"graph-reference-strip\"\n      paint={paint}\n    />\n  )\n})\n\nexport default ReferenceStripOverlay\n", "import { useCallback } from 'react'\n\nimport { drawTubeMapRuler } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { drawTubeMapConnectors } from '@jbrowse/bandage-core/tubeMap/connectors'\nimport { drawDeviationMarks } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport { drawTubeMap } from '@jbrowse/bandage-core/tubeMap/draw'\nimport { drawTubeMapGenes } from '@jbrowse/bandage-core/tubeMap/genes'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\nimport {\n  PANEL_TITLE_FONT,\n  drawBundleCounts,\n  drawSqueezedLengths,\n} from '../tubeMapPanels'\n\n// variants folded into a box mark texture under a panel's routes\nconst PANEL_TICK_ALPHA = 0.45\n\nimport type { GraphPaneModel } from '../model'\n\n// The tubes, their connectors, genes and ruler, onto a canvas sized to the\n// pane or onto the linear view's SVG export\nexport function paintTubeMap(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  { highlightNode }: { highlightNode: string | null },\n) {\n  const picture = model.tubeMapPicture\n  const frame = model.tubeMapFrame\n  if (!picture || !frame) {\n    return\n  }\n  const width = model.paneWidth\n  const panels = model.tubeMapPanelViews\n  if (panels) {\n    paintPanels(ctx, model, panels, highlightNode)\n    return\n  }\n  const tubeFrame = {\n    ...frame,\n    width,\n    highlightNode,\n    tubeColors: model.tubeMapTubeColors,\n    nodeColors: model.tubeMapNodeColors,\n  }\n  drawTubeMap(ctx, picture, tubeFrame)\n  const drawn = model.layoutResult?.tubeMap\n  if (drawn) {\n    drawBundleCounts(ctx, picture, drawn.graph, tubeFrame)\n    drawSqueezedLengths(ctx, drawn, tubeFrame)\n  }\n  drawDeviationMarks(ctx, model.tubeMapDeviations, tubeFrame)\n  drawTubeMapConnectors(\n    ctx,\n    model.tubeMapConnectors,\n    model.connectorZoneBottom,\n    tubeFrame,\n  )\n  const { bounds } = picture\n  drawTubeMapGenes(ctx, model.tubeMapGenes, tubeFrame, frame.y(bounds.minY) - 2)\n  const boxes = model.tubeMapRulerBoxes\n  if (boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      tubeFrame,\n      frame.y(bounds.maxY) + 4,\n      model.layoutResult?.referenceAxis,\n    )\n  }\n}\n\n// Each panel of a split tube map under a rule and its title, which the canvas\n// draws so a figure's SVG carries them\nfunction paintPanels(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  panels: NonNullable<GraphPaneModel['tubeMapPanelViews']>,\n  highlightNode: string | null,\n) {\n  const width = model.paneWidth\n  for (const p of panels) {\n    if (p.bottom < 0 || p.titleTop > model.canvasHeight) {\n      continue\n    }\n    const tubeFrame = {\n      ...p.frame,\n      width,\n      highlightNode,\n      tubeColors: p.tubeColors,\n      nodeColors: p.nodeColors,\n    }\n    drawTubeMap(ctx, p.picture, tubeFrame)\n    drawBundleCounts(ctx, p.picture, p.panel.result.tubeMap.graph, tubeFrame)\n    drawSqueezedLengths(ctx, p.panel.result.tubeMap, tubeFrame)\n    ctx.globalAlpha = PANEL_TICK_ALPHA\n    drawDeviationMarks(ctx, p.deviations, tubeFrame)\n    ctx.globalAlpha = 1\n    ctx.strokeStyle = 'rgba(0,0,0,0.15)'\n    ctx.lineWidth = 1\n    ctx.beginPath()\n    ctx.moveTo(0, Math.round(p.titleTop) + 0.5)\n    ctx.lineTo(width, Math.round(p.titleTop) + 0.5)\n    ctx.stroke()\n    ctx.font = PANEL_TITLE_FONT\n    ctx.textAlign = 'left'\n    ctx.textBaseline = 'top'\n    ctx.fillStyle = 'rgba(0,0,0,0.85)'\n    ctx.fillText(p.label, 6, p.titleTop + 4)\n  }\n  const last = panels.at(-1)\n  const boxes = model.tubeMapPanelRulerBoxes\n  if (last && boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      { ...last.frame, width },\n      last.bottom + 4,\n      true,\n    )\n  }\n}\n\n// The tube map's ink, over the canvas, which draws nothing under a tube map\n// layout. Above the tubes go the session's genes in a view of its own, or in\n// a linear view the bands tying each reference box to its bp there; under\n// them a reference ruler, unless the linear view's is already the axis.\n// Repainted by an autorun on every change of transform, so a pan in the linear\n// view above moves the tubes in the same frame as its other tracks.\nconst TubeMapOverlay = observer(function TubeMapOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      paintTubeMap(ctx, model, { highlightNode: model.selectedNode })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={1}\n      shown={!!model.tubeMapPicture}\n      testId=\"graph-tube-map\"\n      paint={paint}\n    />\n  )\n})\n\nexport default TubeMapOverlay\n", "const host = JBrowseExports[\"@jbrowse/render-core/marks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/render-core/marks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const BandPen = /* @__PURE__ */ read(\"BandPen\")\nexport const CONNECTOR_ARROW = /* @__PURE__ */ read(\"CONNECTOR_ARROW\")\nexport const CONNECTOR_BOW = /* @__PURE__ */ read(\"CONNECTOR_BOW\")\nexport const CONNECTOR_DASHED = /* @__PURE__ */ read(\"CONNECTOR_DASHED\")\nexport const CONNECTOR_LEADING_2 = /* @__PURE__ */ read(\"CONNECTOR_LEADING_2\")\nexport const CONNECTOR_MAX_REACH_PX = /* @__PURE__ */ read(\"CONNECTOR_MAX_REACH_PX\")\nexport const CONNECTOR_MINUS_1 = /* @__PURE__ */ read(\"CONNECTOR_MINUS_1\")\nexport const CONNECTOR_MINUS_2 = /* @__PURE__ */ read(\"CONNECTOR_MINUS_2\")\nexport const CONNECTOR_STRAIGHT = /* @__PURE__ */ read(\"CONNECTOR_STRAIGHT\")\nexport const HIDDEN_ROW = /* @__PURE__ */ read(\"HIDDEN_ROW\")\nexport const LINK_ELSEWHERE = /* @__PURE__ */ read(\"LINK_ELSEWHERE\")\nexport const LINK_NO_REGION = /* @__PURE__ */ read(\"LINK_NO_REGION\")\nexport const NO_ROW_COLOR = /* @__PURE__ */ read(\"NO_ROW_COLOR\")\nexport const RAMP_LINE_BANDS = /* @__PURE__ */ read(\"RAMP_LINE_BANDS\")\nexport const RAMP_NOT_A_NUMBER_COLOR = /* @__PURE__ */ read(\"RAMP_NOT_A_NUMBER_COLOR\")\nexport const RAMP_NO_VALUE_BITS = /* @__PURE__ */ read(\"RAMP_NO_VALUE_BITS\")\nexport const RAMP_NO_VALUE_COLOR = /* @__PURE__ */ read(\"RAMP_NO_VALUE_COLOR\")\nexport const RowKeys = /* @__PURE__ */ read(\"RowKeys\")\nexport const abgrToCssRgba = /* @__PURE__ */ read(\"abgrToCssRgba\")\nexport const appendGlyph = /* @__PURE__ */ read(\"appendGlyph\")\nexport const backToFront = /* @__PURE__ */ read(\"backToFront\")\nexport const barMark = /* @__PURE__ */ read(\"barMark\")\nexport const buildRowTable = /* @__PURE__ */ read(\"buildRowTable\")\nexport const connectorEnds = /* @__PURE__ */ read(\"connectorEnds\")\nexport const connectorMark = /* @__PURE__ */ read(\"connectorMark\")\nexport const defineMark = /* @__PURE__ */ read(\"defineMark\")\nexport const ellipseDistance = /* @__PURE__ */ read(\"ellipseDistance\")\nexport const ellipseNearest = /* @__PURE__ */ read(\"ellipseNearest\")\nexport const inkOfInstances = /* @__PURE__ */ read(\"inkOfInstances\")\nexport const instanceColor = /* @__PURE__ */ read(\"instanceColor\")\nexport const isThreshold = /* @__PURE__ */ read(\"isThreshold\")\nexport const keepRampValues = /* @__PURE__ */ read(\"keepRampValues\")\nexport const keySlot = /* @__PURE__ */ read(\"keySlot\")\nexport const lineCenterMark = /* @__PURE__ */ read(\"lineCenterMark\")\nexport const lineMarkOf = /* @__PURE__ */ read(\"lineMarkOf\")\nexport const lineStepMark = /* @__PURE__ */ read(\"lineStepMark\")\nexport const linkApex = /* @__PURE__ */ read(\"linkApex\")\nexport const linkFeet = /* @__PURE__ */ read(\"linkFeet\")\nexport const linkInstance = /* @__PURE__ */ read(\"linkInstance\")\nexport const linkLabelAnchor = /* @__PURE__ */ read(\"linkLabelAnchor\")\nexport const linkMark = /* @__PURE__ */ read(\"linkMark\")\nexport const makeAbgrFill = /* @__PURE__ */ read(\"makeAbgrFill\")\nexport const nearestMarkHit = /* @__PURE__ */ read(\"nearestMarkHit\")\nexport const paintColors = /* @__PURE__ */ read(\"paintColors\")\nexport const paintMarkBlocks = /* @__PURE__ */ read(\"paintMarkBlocks\")\nexport const planMarks = /* @__PURE__ */ read(\"planMarks\")\nexport const pointInsetPx = /* @__PURE__ */ read(\"pointInsetPx\")\nexport const pointInstance = /* @__PURE__ */ read(\"pointInstance\")\nexport const pointMark = /* @__PURE__ */ read(\"pointMark\")\nexport const rampAsThreshold = /* @__PURE__ */ read(\"rampAsThreshold\")\nexport const rampUniforms = /* @__PURE__ */ read(\"rampUniforms\")\nexport const rampValueBits = /* @__PURE__ */ read(\"rampValueBits\")\nexport const recordPath = /* @__PURE__ */ read(\"recordPath\")\nexport const rowColor = /* @__PURE__ */ read(\"rowColor\")\nexport const rowSlot = /* @__PURE__ */ read(\"rowSlot\")\nexport const rowSpanIndex = /* @__PURE__ */ read(\"rowSpanIndex\")\nexport const rowTableKeys = /* @__PURE__ */ read(\"rowTableKeys\")\nexport const rowTableTextures = /* @__PURE__ */ read(\"rowTableTextures\")\nexport const ruleMark = /* @__PURE__ */ read(\"ruleMark\")\nexport const shiftInk = /* @__PURE__ */ read(\"shiftInk\")\nexport const spanMark = /* @__PURE__ */ read(\"spanMark\")\nexport const spansInRow = /* @__PURE__ */ read(\"spansInRow\")\nexport const thresholdBandOf = /* @__PURE__ */ read(\"thresholdBandOf\")\nexport const valueWindow = /* @__PURE__ */ read(\"valueWindow\")\nexport const withPassId = /* @__PURE__ */ read(\"withPassId\")\nexport default host && host.__esModule ? host.default : host", "import {\n  GAP_PX,\n  MISSING_PX,\n  coalesceRuns,\n  gapStyle,\n  runPaint,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { hslToRgb } from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { packAbgr } from '@jbrowse/bandage-core/renderer/colorBits'\nimport { spanMark } from '@jbrowse/render-core/marks'\n\nimport type { WalkRow, WalkRun } from '@jbrowse/bandage-core/layout/walkRows'\nimport type { MarkContext2D, SpanChannels } from '@jbrowse/render-core/marks'\n\ntype Rgb = [number, number, number]\n\n// The colours runPaint writes: `#rrggbb`, `rgb(r, g, b)` and\n// `hsl(h, s%, l%)`\nexport function cssRgb(css: string): Rgb {\n  if (css.startsWith('#')) {\n    const v = Number.parseInt(css.slice(1), 16)\n    return [(v >> 16) & 0xff, (v >> 8) & 0xff, v & 0xff]\n  }\n  const [a = 0, b = 0, c = 0] = css.match(/[\\d.]+/g)!.map(Number)\n  return css.startsWith('hsl')\n    ? (hslToRgb(a, b / 100, c / 100).map(v => v * 255) as Rgb)\n    : [a, b, c]\n}\n\nconst abgr = ([r, g, b]: Rgb) =>\n  packAbgr(Math.round(r), Math.round(g), Math.round(b), 255)\n\nconst cssAbgr = new Map<string, number>()\nfunction packCss(css: string) {\n  let v = cssAbgr.get(css)\n  if (v === undefined) {\n    v = abgr(cssRgb(css))\n    cssAbgr.set(css, v)\n  }\n  return v\n}\n\n/**\n * A run as the pieces it paints in, each `[start, end, abgr]` in bp along\n * the row: one for a solid fill, and for a gradient one per pixel or per\n * degree of hue, whichever is fewer, coloured as the SVG gradient through\n * the same stops colours its middle\n */\nexport function runPieces(\n  run: WalkRun,\n  ramp: { start: number; end: number } | undefined,\n  pxPerBp: number,\n): [number, number, number][] {\n  const end = run.start + run.bp\n  const paint = runPaint(run, ramp)\n  if ('fill' in paint) {\n    return [[run.start, end, packCss(paint.fill)]]\n  }\n  const stops = paint.stops.map(cssRgb)\n  const hues = paint.stops.map(css => Number(/[\\d.]+/.exec(css)![0]))\n  const hueSpan = Math.abs(hues.at(-1)! - hues[0]!)\n  const n = Math.max(\n    1,\n    Math.min(Math.ceil(run.bp * pxPerBp), Math.ceil(hueSpan), run.bp),\n  )\n  const pieces: [number, number, number][] = []\n  for (let k = 0; k < n; k++) {\n    const t = ((k + 0.5) / n) * (stops.length - 1)\n    const i = Math.min(Math.floor(t), stops.length - 2)\n    const a = stops[i]!\n    const b = stops[i + 1]!\n    const f = t - i\n    pieces.push([\n      Math.round(run.start + (run.bp * k) / n),\n      Math.round(run.start + (run.bp * (k + 1)) / n),\n      abgr([0, 1, 2].map(j => a[j]! + (b[j]! - a[j]!) * f) as Rgb),\n    ])\n  }\n  return pieces\n}\n\nexport interface WalkRowSpans {\n  bars: SpanChannels & { color: Uint32Array }\n  gaps: SpanChannels & { color: Uint32Array }\n  // gaps of bases the graph lacks, which draw as a hairline\n  hairlines: SpanChannels & { color: Uint32Array }\n  // where each drawn row's spans start in `bars`, `gaps` and `hairlines`\n  barRows: Uint32Array\n  gapRows: Uint32Array\n  hairlineRows: Uint32Array\n  // the furthest any span reaches along its row, in bp, and at least 1\n  longest: number\n}\n\nfunction channels(capacity: number) {\n  return {\n    x: new Uint32Array(capacity),\n    x2: new Uint32Array(capacity),\n    row: new Uint32Array(capacity),\n    color: new Uint32Array(capacity),\n    count: 0,\n  }\n}\n\nfunction slice<T extends SpanChannels & { color: Uint32Array }>(\n  c: T,\n  a: number,\n  b: number,\n) {\n  return {\n    x: c.x.subarray(a, b),\n    x2: c.x2.subarray(a, b),\n    row: c.row.subarray(a, b),\n    color: c.color.subarray(a, b),\n    count: b - a,\n  }\n}\n\n/**\n * Each row's runs as `walkRowsTree` coalesces and colours them at\n * `pxPerBp`, as span channels: `x`/`x2` in bp along the row, `row` its index\n * among `rows`. Gaps go apart, since they draw thinner, and gaps of bases the\n * graph lacks apart again, as a hairline.\n */\nexport function walkRowSpans(\n  rows: WalkRow[],\n  pxPerBp: number,\n  ramp?: { start: number; end: number },\n): WalkRowSpans {\n  const pieces = rows.map(r =>\n    coalesceRuns(r.runs, pxPerBp).map(run => ({\n      gap: run.gap,\n      hairline: run.gap && gapStyle(run.cause).px === MISSING_PX,\n      pieces: runPieces(run, ramp, pxPerBp),\n    })),\n  )\n  let total = 0\n  for (const runs of pieces) {\n    for (const run of runs) {\n      total += run.pieces.length\n    }\n  }\n  const bars = channels(total)\n  const gaps = channels(total)\n  const hairlines = channels(total)\n  const barRows = new Uint32Array(rows.length + 1)\n  const gapRows = new Uint32Array(rows.length + 1)\n  const hairlineRows = new Uint32Array(rows.length + 1)\n  let longest = 1\n  pieces.forEach((runs, row) => {\n    for (const run of runs) {\n      const c = run.hairline ? hairlines : run.gap ? gaps : bars\n      for (const [x, x2, color] of run.pieces) {\n        const i = c.count++\n        c.x[i] = x\n        c.x2[i] = x2\n        c.row[i] = row\n        c.color[i] = color\n        longest = Math.max(longest, c.x2[i])\n      }\n    }\n    barRows[row + 1] = bars.count\n    gapRows[row + 1] = gaps.count\n    hairlineRows[row + 1] = hairlines.count\n  })\n  return {\n    bars: slice(bars, 0, bars.count),\n    gaps: slice(gaps, 0, gaps.count),\n    hairlines: slice(hairlines, 0, hairlines.count),\n    barRows,\n    gapRows,\n    hairlineRows,\n    longest,\n  }\n}\n\nexport interface WalkRowSpanFrame {\n  scaleX: number\n  scaleY: number\n  translateX: number\n  translateY: number\n  width: number\n  height: number\n  rowPx: number\n  barPx: number\n  origin: number\n  // runs of rows whose y is `rowY(first)` plus a row pitch each, as the\n  // reference row and each grouped section are\n  blocks: { first: number; count: number; rowY: number }[]\n}\n\n/**\n * Paints the spans through render-core's span mark, a block of rows at a\n * time: row i's bar centred where `walkRowsTree` centres it, `barPx` tall,\n * its x at `origin + bp` through the pane's transform.\n */\nexport function paintWalkRowSpans(\n  ctx: MarkContext2D,\n  spans: WalkRowSpans,\n  f: WalkRowSpanFrame,\n) {\n  const { longest } = spans\n  const block = {\n    start: 0,\n    end: longest,\n    screenStartPx: f.origin * f.scaleX + f.translateX,\n    screenEndPx: (f.origin + longest) * f.scaleX + f.translateX,\n    reversed: false,\n    displayedRegionIndex: 0,\n  }\n  const frame = { canvasWidth: f.width, canvasHeight: f.height }\n  const rowHeight = f.rowPx * f.scaleY\n  for (const { first, count, rowY } of f.blocks) {\n    // slot `row` centres at (rowY + (row - first) * rowPx) * scaleY + translateY\n    const scrollTop =\n      rowHeight / 2 - f.translateY - (rowY - first * f.rowPx) * f.scaleY\n    const top = (rowY - f.rowPx / 2) * f.scaleY + f.translateY\n    if (top > f.height || top + count * rowHeight < 0) {\n      continue\n    }\n    for (const [c, starts, barPx] of [\n      [spans.bars, spans.barRows, f.barPx],\n      [spans.gaps, spans.gapRows, Math.min(GAP_PX, f.barPx)],\n      [spans.hairlines, spans.hairlineRows, Math.min(MISSING_PX, f.barPx)],\n    ] as const) {\n      spanMark.paintBlock(\n        ctx,\n        slice(c, starts[first]!, starts[first + count]!),\n        block,\n        frame,\n        {\n          rowHeight,\n          rowProportion: barPx / rowHeight,\n          minWidthPx: 1,\n          seamPx: 0,\n          scrollTop,\n        },\n      )\n    }\n  }\n}\n", "import { useCallback, useMemo } from 'react'\n\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneOverlayCanvas, PaneSvgLayer } from './PaneLayer'\nimport { paintWalkRowBlocks } from '../walkRowBlocks'\nimport { SECTION_HEADER_PX, walkRowTrees } from '../walkRowGroups'\nimport { paintWalkRowSpans, walkRowSpans } from '../walkRowSpans'\n\nimport type { GraphPaneModel } from '../model'\n\n// The walk-rows layout's bars: one per haplotype walk under the reference\n// row, each on its own bp axis from the window's left edge. The runs paint as\n// spans on a canvas, coloured by whether they are on the reference walk's\n// path, and core's walkRowsTree draws the rest: unit separators, each row's\n// genes from its own assembly's annotation, the allele a repeat genotype\n// called and a readout. Under the\n// reference-position ramp an aligned run takes the hue of the reference it is\n// threaded through. In a tandem array that is the aligner's pick among\n// near-identical copies, so the hue says which reference copy the graph used,\n// not which one a copy resembles.\n//\n// The walk rows pair a repeat record's allele with each walk \u2014 see\n// repeats/walkCalls.ts, which also holds the threshold a red readout is read\n// off. Colouring each copy by its unit is jbrowse-plugin-tandem-repeat's.\n\n// The spans are recut only when the rows, the zoom or the ramp change\nfunction WalkRowSpansCanvas({ model }: { model: GraphPaneModel }) {\n  const spans = useMemo(\n    () =>\n      computed(() => {\n        const bars = model.walkRowBars\n        return bars\n          ? walkRowSpans(\n              [bars.reference, ...bars.rows],\n              model.scaleX,\n              model.referenceRampDomain,\n            )\n          : undefined\n      }),\n    [model],\n  )\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      const painted = spans.get()\n      if (!bars || !place || !pitch || !painted) {\n        return\n      }\n      const sections = model.walkRowGroups?.sections\n      const blocks = sections?.length\n        ? [\n            { first: 0, count: 1, rowY: place.rowY(0) },\n            ...sections.map(s => ({\n              first: s.first,\n              count: s.count,\n              rowY: place.rowY(s.first),\n            })),\n          ]\n        : [{ first: 0, count: bars.rows.length + 1, rowY: place.rowY(0) }]\n      paintWalkRowSpans(ctx, painted, {\n        ...model.screenTransform,\n        width: model.paneWidth,\n        height: model.canvasHeight,\n        rowPx: pitch.rowPx,\n        barPx: pitch.barPx,\n        origin: bars.origin,\n        blocks,\n      })\n    },\n    [model, spans],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={3}\n      testId=\"graph-walk-rows-spans\"\n      paint={paint}\n    />\n  )\n}\n\nconst RIBBON_FORWARD = 'rgba(160, 196, 232, 0.55)'\nconst RIBBON_REVERSED = 'rgba(160, 140, 220, 0.55)'\n\n// Under the bars, a ribbon from each stretch of a row to where the row below\n// walks the same nodes, lavender where it walks them backwards, as ggbandage\n// draws them: neighbours that share a copy, an inversion or a duplication\n// read off the ribbons' shape\nfunction WalkRowRibbonsCanvas({ model }: { model: GraphPaneModel }) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const links = model.walkRowRibbons\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      if (!links || !bars || !place || !pitch) {\n        return\n      }\n      const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n      const x = (offset: number) => (bars.origin + offset) * scaleX + translateX\n      const half = pitch.barPx / 2\n      for (const { row, a0, a1, b0, b1 } of links) {\n        const top = place.rowY(row) * scaleY + translateY + half\n        const bottom = place.rowY(row + 1) * scaleY + translateY - half\n        ctx.fillStyle = b0 > b1 ? RIBBON_REVERSED : RIBBON_FORWARD\n        ctx.beginPath()\n        ctx.moveTo(x(a0), top)\n        ctx.lineTo(x(a1), top)\n        ctx.lineTo(x(b1), bottom)\n        ctx.lineTo(x(b0), bottom)\n        ctx.closePath()\n        ctx.fill()\n      }\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={2}\n      testId=\"graph-walk-rows-ribbons\"\n      paint={paint}\n    />\n  )\n}\n\n// Over the bars, the lettered blocks: copy A on two rows, and C where another\n// row has A, read at a glance\nfunction WalkRowBlocksCanvas({ model }: { model: GraphPaneModel }) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const blocks = model.sharedBlocks\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      if (!blocks || !bars || !place || !pitch) {\n        return\n      }\n      const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n      paintWalkRowBlocks(ctx, blocks, {\n        x: offset => (bars.origin + offset) * scaleX + translateX,\n        rowCentre: row => place.rowY(row) * scaleY + translateY,\n        barPx: pitch.barPx,\n      })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={3}\n      testId=\"graph-walk-rows-blocks\"\n      paint={paint}\n    />\n  )\n}\n\n// Its own observer, so moving between rows redraws this rect and not every row\nconst HoveredWalkRow = observer(function HoveredWalkRow({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch || !model.hoveredWalkRowText) {\n    return null\n  }\n  const rows = [bars.reference, ...bars.rows]\n  const index = rows.findIndex(r => r.name === model.hoveredWalkRow)\n  const row = rows[index]\n  if (!row) {\n    return null\n  }\n  const start = model.toScreen({ x: bars.origin, y: place.rowY(index) })\n  return (\n    <rect\n      data-testid=\"graph-walk-row-hovered\"\n      x={start.x - 2}\n      y={start.y - pitch.rowPx / 2 - 1}\n      width={row.bp * model.scaleX + 4}\n      height={pitch.rowPx + 2}\n      fill=\"none\"\n      stroke=\"#111\"\n      strokeWidth={1}\n    />\n  )\n})\n\n// `vector` for an SVG export, which draws the bars as walkRowsTree's rects\nconst WalkRowsOverlay = observer(function WalkRowsOverlay({\n  model,\n  vector = false,\n}: {\n  model: GraphPaneModel\n  vector?: boolean\n}) {\n  const idPrefix = useSvgId()\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch) {\n    return null\n  }\n  const { paneWidth: width, canvasHeight } = model\n  // the canvas paints the bars, except in a vector export\n  const frame = {\n    ...model.screenTransform,\n    width,\n    height: canvasHeight,\n    ...pitch,\n    bars: vector,\n  }\n  return (\n    <>\n      {vector || !model.walkRowRibbons ? null : (\n        <WalkRowRibbonsCanvas model={model} />\n      )}\n      {vector ? null : <WalkRowSpansCanvas model={model} />}\n      {vector || !model.sharedBlocks ? null : (\n        <WalkRowBlocksCanvas model={model} />\n      )}\n      <PaneSvgLayer\n        model={model}\n        zIndex={3}\n        overflow=\"visible\"\n        testId=\"graph-walk-rows\"\n      >\n        {walkRowTrees(\n          bars,\n          model.walkRowGroups?.sections ?? [],\n          place.rowY,\n          frame,\n          {\n            ramp: model.referenceRampDomain,\n            rowGenes: model.walkRowGenes,\n            idPrefix,\n          },\n        ).map((tree, i) => (\n          <ElTree key={i} el={tree} />\n        ))}\n        {place.headers.map(header => (\n          <text\n            key={header.key}\n            x={10}\n            y={\n              model.toScreen({ x: 0, y: header.top }).y + SECTION_HEADER_PX - 4\n            }\n            fontFamily=\"sans-serif\"\n            fontSize={11}\n            fontWeight=\"bold\"\n            fill=\"#333\"\n            data-testid=\"graph-walk-section\"\n          >\n            {header.title}\n          </text>\n        ))}\n        <HoveredWalkRow model={model} />\n      </PaneSvgLayer>\n    </>\n  )\n})\n\nexport default WalkRowsOverlay\n"],
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"a", "b", "c", "hslToRgb", "abgr", "r", "g", "packAbgr", "cssAbgr", "packCss", "runPieces", "run", "ramp", "pxPerBp", "end", "paint", "runPaint", "stops", "hues", "hueSpan", "n", "pieces", "k", "t", "i", "f", "j", "channels", "capacity", "slice", "walkRowSpans", "rows", "coalesceRuns", "gapStyle", "MISSING_PX", "total", "runs", "bars", "gaps", "hairlines", "barRows", "gapRows", "hairlineRows", "longest", "row", "x", "x2", "color", "paintWalkRowSpans", "ctx", "spans", "block", "frame", "rowHeight", "first", "count", "rowY", "scrollTop", "top", "starts", "barPx", "GAP_PX", "spanMark", "WalkRowSpansCanvas", "model", "spans", "useMemo", "computed", "bars", "walkRowSpans", "paint", "useCallback", "ctx", "place", "pitch", "painted", "sections", "blocks", "s", "paintWalkRowSpans", "jsx", "PaneOverlayCanvas", "RIBBON_FORWARD", "RIBBON_REVERSED", "WalkRowRibbonsCanvas", "links", "scaleX", "scaleY", "translateX", "translateY", "x", "offset", "half", "row", "a0", "a1", "b0", "b1", "top", "bottom", "WalkRowBlocksCanvas", "paintWalkRowBlocks", "HoveredWalkRow", "observer", "rows", "index", "r", "start", "WalkRowsOverlay", "vector", "idPrefix", "useSvgId", "width", "canvasHeight", "frame", "jsxs", "Fragment", "PaneSvgLayer", "walkRowTrees", "tree", "i", "ElTree", "header", "SECTION_HEADER_PX", "WalkRowsOverlay_default"]
-}

package/dist/chunks/chunk-NOXHIOIM.js

@@ -1,2 +0,0 @@
-import{a as f}from"./chunk-HAAABGE7.js";import{h as l,i as c,k as m,z as b}from"./chunk-CZXJXNZN.js";import{h as g}from"./chunk-VKZALU57.js";var S={steps:"walkStepBudget",bytes:"walkByteBudget"},x=64,h=class{constructor(t,e){this.file=t;this.adapter=e;this.reader=new m(t)}async haplotypeNames(t={}){let{haplotypes:e}=await this.reader.header(t);return e.length>0?e:void 0}budgets(){return{stepBudget:this.adapter.getConf("walkStepBudget"),byteBudget:this.adapter.getConf("walkByteBudget"),budgetNames:S}}async subgraph(t,e,{signal:i,haplotypes:n,walkRows:a,expand:r}){let d=this.budgets(),p=c(n?.map(s=>g(this.adapter,s)),t),u=a&&p&&(n?.length??0)<=x?p:void 0,o=r?.length?s=>r.includes(s):void 0,{graph:B,kept:y,fragments:k,skips:w}=await this.reader.cut(t,e,{...d,stepBudget:a?1/0:d.stepBudget,signal:i,keep:p,...u||o?{expand:s=>!!u?.(s)||!!o?.(s)}:{}});return f(B.tables(y,k,w),e,a)}async referenceNodes(t,e,i){let n=[];await b(this.file,t,await this.reader.queryStart(e.start,{...i,refName:t,end:e.end}),e.end,{signal:i.signal,lineCallback:r=>{let d=r.split("	");d[3]==="ref"&&n.push(d)}});let a=new Set;return l(n).filter(r=>r.refName!==t||r.end<=e.start||r.start>=e.end||a.has(r.id)?!1:(a.add(r.id),!0))}};export{h as a};
-//# sourceMappingURL=chunk-NOXHIOIM.js.map

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

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/walkReader.ts"],
-  "sourcesContent": ["import { resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { WalkReader, referenceNodes, walksKept } from '@jbrowse/graph-walks'\n\nimport { getLines } from '../tabixRange.ts'\nimport { walkCutFor } from './walkCut.ts'\n\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// The zoom-in notices name the config slots that set the budgets\nexport const BUDGET_SLOTS = {\n  steps: 'walkStepBudget',\n  bytes: 'walkByteBudget',\n}\n\n// Walk rows read a list this long or shorter in full where format 5 abridged\n// it; a longer list, or every haplotype, keeps the abridged rows\nexport const EXPAND_NAMED_MAX = 64\n\n/**\n * A walk file and the answers both walk-indexed adapters give from it,\n * RgfaTabixAdapter and WalkTabixSyntenyAdapter, whose schemas declare the\n * budget slots. @jbrowse/graph-walks reads and cuts the file.\n */\nexport class WalkIndex {\n  readonly reader: WalkReader\n\n  constructor(\n    readonly file: TabixIndexedFile,\n    private adapter: BaseFeatureDataAdapter,\n  ) {\n    this.reader = new WalkReader(file)\n  }\n\n  /**\n   * The haplotypes the header names, `sample#haplotype` in byte order, or\n   * undefined when it names none\n   */\n  async haplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  budgets() {\n    return {\n      stepBudget: this.adapter.getConf('walkStepBudget') as number,\n      byteBudget: this.adapter.getConf('walkByteBudget') as number,\n      budgetNames: BUDGET_SLOTS,\n    }\n  }\n\n  /**\n   * The graph display's cut of a window: the reference walk, the walks of\n   * `haplotypes` (every walk when unset), and the nodes and links they visit,\n   * with the haplotypes whose deletion spans the window as `skips`, which walk\n   * rows draw. Walk rows draw runs, so the step budget spares them, and read a\n   * short list of named walks in full where format 5 abridged them.\n   */\n  async subgraph(\n    refName: string,\n    region: { start: number; end: number },\n    { signal, haplotypes, walkRows, expand }: SubgraphAdapterOptions,\n  ) {\n    const budgets = this.budgets()\n    const keep = walksKept(\n      haplotypes?.map(lane => resolvePanSNPrefix(this.adapter, lane)),\n      refName,\n    )\n    const named =\n      walkRows && keep && (haplotypes?.length ?? 0) <= EXPAND_NAMED_MAX\n        ? keep\n        : undefined\n    const asked = expand?.length\n      ? (name: string) => expand.includes(name)\n      : undefined\n    const { graph, kept, fragments, skips } = await this.reader.cut(\n      refName,\n      region,\n      {\n        ...budgets,\n        stepBudget: walkRows ? Infinity : budgets.stepBudget,\n        signal,\n        keep,\n        ...(named || asked\n          ? {\n              expand: (name: string) => !!named?.(name) || !!asked?.(name),\n            }\n          : {}),\n      },\n    )\n    return walkCutFor(graph.tables(kept, fragments, skips), region, walkRows)\n  }\n\n  /**\n   * The reference nodes overlapping a window, from the ref rows of its\n   * chunks. A row's tabix interval is its chunk's first base, and gfa-to-tabix\n   * files a node crossing in from a chunk before under that chunk, so the read\n   * starts at queryStart.\n   */\n  async referenceNodes(\n    refName: string,\n    region: { start: number; end: number },\n    opts: BaseOptions,\n  ) {\n    const refRows: string[][] = []\n    await getLines(\n      this.file,\n      refName,\n      await this.reader.queryStart(region.start, {\n        ...opts,\n        refName,\n        end: region.end,\n      }),\n      region.end,\n      {\n        signal: opts.signal,\n        lineCallback: line => {\n          const cols = line.split('\\t')\n          if (cols[3] === 'ref') {\n            refRows.push(cols)\n          }\n        },\n      },\n    )\n    const seen = new Set<number>()\n    return referenceNodes(refRows).filter(node => {\n      if (\n        node.refName !== refName ||\n        node.end <= region.start ||\n        node.start >= region.end ||\n        seen.has(node.id)\n      ) {\n        return false\n      }\n      seen.add(node.id)\n      return true\n    })\n  }\n}\n"],
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-  "names": ["BUDGET_SLOTS", "EXPAND_NAMED_MAX", "WalkIndex", "file", "adapter", "WalkReader", "opts", "haplotypes", "refName", "region", "signal", "walkRows", "expand", "budgets", "keep", "walksKept", "lane", "resolvePanSNPrefix", "named", "asked", "name", "graph", "kept", "fragments", "skips", "walkCutFor", "refRows", "getLines", "line", "cols", "seen", "referenceNodes", "node"]
-}