jbrowse-plugin-graphgenomeviewer 8.7.0 → 8.7.2

package/dist/chunks/chunk-5TT5TG4Q.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-D7ZTAGDM.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-IDPBN2BP.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-O6SLIY74.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 has no step on the reference\n  // across the window, which says nothing of what it carries instead\n  deleted: \"no step on the reference\"\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-D7ZTAGDM.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, skips }, 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    ...skips?.names.length ? { skips } : {}\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-IDPBN2BP.js\";\nimport {\n  gapParts\n} from \"./chunk-D7ZTAGDM.js\";\nimport {\n  pathOrigin\n} from \"./chunk-QBI6SC74.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}\nvar namesReference = (reference) => {\n  const contig = reference && panSNContig(reference);\n  return (name) => name !== void 0 && (name === reference || name === contig);\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  const reference = referenceWalkName(graph);\n  const onReferenceContig = namesReference(reference);\n  const stable = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    const i = indexOf(node.id);\n    lengths[i] = node.length;\n    if (node.stable?.rank === 0 && onReferenceContig(node.stable.refName)) {\n      stable.set(i, node.stable.start);\n    }\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,\n    stableStart: (node) => stable.get(node) ?? Number.NaN\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  const reference = referenceOf(\n    heads.map((h) => pathOrigin(h.name).name),\n    referencePath,\n    rankZero\n  );\n  const onReferenceContig = namesReference(reference);\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,\n    stableStart: (node) => node < n.lengths.length && n.ranks[node] === 0 && onReferenceContig(n.refNames[n.refs[node]]) ? n.starts[node] : Number.NaN\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    stableStart\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 } = source;\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    const abridgedAt = (i) => partsAt.get(i)?.[0]?.cause === \"abridged\";\n    const placeStart = (i) => {\n      const id = steps[i];\n      if (id < 0 || partsAt.has(i)) {\n        return Number.NaN;\n      }\n      return Number.isNaN(spanStart[id]) && (abridgedAt(i - 1) || abridgedAt(i + 1)) ? stableStart(id) : spanStart[id];\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 start2 = placeStart(i);\n        if (!Number.isNaN(start2)) {\n          const end2 = start2 + lengthOf(steps[i]);\n          if (end2 <= cut.start && end2 > bestEnd) {\n            bestEnd = end2;\n            i0 = i;\n          }\n          if (start2 >= cut.end && start2 < bestStart) {\n            bestStart = start2;\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 - bestEnd);\n        rightTrim = trimAbridged(i1 - inward, bestStart - flankStart);\n      }\n    }\n    const contig = head.contig ?? panSNContig(pathOrigin(head.name).name);\n    const axis2 = 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: axis2,\n      ...abridgedSteps > 0 ? { abridgedSteps } : {},\n      ...leftTrim + rightTrim > 0 ? { estimated: true } : {}\n    };\n  };\n  const skipRowOf = (name, start2, end, bar2) => {\n    const from2 = bar2 ? Math.max(start2, bar2.start) : start2;\n    const bp2 = Math.max((bar2 ? Math.min(end, bar2.end) : end) - from2, 0);\n    runs.push(\n      from2 - (bar2 ? bar2.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      deletionBp: end - start2\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  const { axis } = referenceRow;\n  const bar = axis ? {\n    start: axis.start,\n    end: axis.start + referenceRow.bp + referenceRow.gapBp\n  } : cut;\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], bar),\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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 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "jbrowse-host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "jbrowse-host:tss-react/mui"],
   "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
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package/dist/chunks/chunk-7BKSSU2R.js

@@ -0,0 +1,4 @@
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e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?Rt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>Rt(He(t,me(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(me(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return 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t&&n?Ao(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowList(){let t=this.walkRowBars;return t?[t.reference,...t.rows]:[]},get walkRowRibbons(){let t=this.walkRowGroups?.sections??[];return e.walkRibbons&&e.rowVisitsNeeded&&this.walkRowBars?Rn(this.walkRowList).filter(({row:n})=>jt(t,n)===jt(t,n+1)):void 0},get sharedBlocks(){return e.layerSet.has("walkBlocks")&&e.rowVisitsNeeded&&this.walkRowBars?xn(this.walkRowList):void 0},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ie(e.graph,n,t):[]},get bubbleHalos(){Te(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:ln(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return at(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Xe(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return 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