jbrowse-plugin-graphgenomeviewer 9.0.0 → 9.0.1

package/dist/chunks/{WalkTabixSyntenyAdapter-KI7ESKKP.js.map → WalkTabixSyntenyAdapter-AQ56UH4Y.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
-  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type {\n  WalkDeparture,\n  WalkFragment,\n  WalkNode,\n} from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n\n/**\n * Whether a walk's fragment steps on the reference inside the window: on a\n * node of `refName` overlapping it\n */\nexport function stepsInWindow(\n  fragment: WalkFragment,\n  nodes: Map<number, WalkNode>,\n  refName: string,\n  window: { start: number; end: number },\n) {\n  return Array.from(fragment.ids).some(id => {\n    const node = nodes.get(id)\n    return (\n      node?.rank === 0 &&\n      node.refName === refName &&\n      node.start < window.end &&\n      node.end > window.start\n    )\n  })\n}\n\n/** Whether the reference between a departure's ends covers the whole window */\nexport function departureSpans(\n  { leavePos, rejoinPos }: WalkDeparture,\n  window: { start: number; end: number },\n) {\n  return (\n    Math.min(leavePos, rejoinPos) <= window.start &&\n    Math.max(leavePos, rejoinPos) >= window.end\n  )\n}\n\n/**\n * A haplotype whose departure from the reference spans the whole window, as\n * the record a multi-way display lifts out as a deletion: `spansWindow`, the\n * reference between the departure's ends whole so its length heads the lane,\n * and the haplotype's own sequence between them as its mate, a point where\n * it has none. The record runs the way the walk rejoins the reference, and\n * carries no CIGAR and no identity, so no ramp or identity filter reads it\n * as an alignment.\n */\nexport function departureFeature({\n  departure,\n  refName,\n  assemblyName,\n  mateAssemblyName,\n}: {\n  departure: WalkDeparture\n  refName: string\n  assemblyName: string\n  mateAssemblyName: string\n}) {\n  const { name, hapStart, ownBp, leavePos, rejoinPos, rejoinReversed } =\n    departure\n  const id = `${name}:${hapStart}:${leavePos}:departure`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start: Math.min(leavePos, rejoinPos),\n    end: Math.max(leavePos, rejoinPos),\n    type: 'departure',\n    strand: rejoinReversed ? -1 : 1,\n    syntenyId: id,\n    spansWindow: true,\n    mate: {\n      refName: panSNContig(name),\n      start: hapStart,\n      end: hapStart + ownBp,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport {\n  anchorAligner,\n  chainFeature,\n  departureFeature,\n  departureSpans,\n  lanePairAligner,\n  stepsInWindow,\n} from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openWalkReader } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nconst haplotypeOf = ({ name }: { name: string }) => panSNHaplotype(name) ?? name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(openWalkReader(this), this)\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.source,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolveForCut(region, {\n      signal: opts.signal,\n    })\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with\n  // every departure from the reference over it and no link read; a window\n  // past a budget fails as a zoom-in notice for lanes. Named lanes come back\n  // in full where the walk file abridged them: an abridged walk is two\n  // reference steps, which drew 15 of the HPRC MHC launch's 32 lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate. A haplotype with no step\n   * on the reference inside the window whose departure spans it is one\n   * `spansWindow` record of the departure's stretch, its mate the haplotype's\n   * own sequence between the departure's ends, a point where it has none.\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const status = `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`\n    const { graph, fragments, departures } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      status,\n    )\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = ({ name }: { name: string }) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix => panSNMatchesPrefix(name, prefix))\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const laneOf = (walk: { name: string }) =>\n      laneAssemblyName(asmByPrefix, haplotypeOf(walk))\n    const references = fragments.filter(f => f.name === refName)\n    const walked = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .map(query => ({\n        rank: rank(query),\n        features: references.flatMap(reference =>\n          align(query, reference).map(chain =>\n            chainFeature({\n              chain,\n              target: reference,\n              query,\n              assemblyName: region.assemblyName,\n              refName: region.refName,\n              mateAssemblyName: laneOf(query),\n            }),\n          ),\n        ),\n      }))\n    // NA19036#1 skips the IGL locus on one contig and walks it on another\n    const walking = new Set(\n      fragments\n        .filter(fragment =>\n          stepsInWindow(fragment, graph.nodes, refName, region),\n        )\n        .map(haplotypeOf),\n    )\n    const spanning = departures\n      .filter(\n        departure =>\n          rank(departure) >= 0 &&\n          !walking.has(haplotypeOf(departure)) &&\n          departureSpans(departure, region),\n      )\n      .sort((a, b) => a.name.localeCompare(b.name))\n      .map(departure => ({\n        rank: rank(departure),\n        features: [\n          departureFeature({\n            departure,\n            refName: region.refName,\n            assemblyName: region.assemblyName,\n            mateAssemblyName: laneOf(departure),\n          }),\n        ],\n      }))\n    return [...walked, ...spanning]\n      .sort((a, b) => a.rank - b.rank)\n      .flatMap(lane => lane.features)\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
-  "mappings": 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-  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "singleVisits", "rev", "twice", "directionShares", "visits", "visitsOf", "found", "theirs", "opposite", "other", "lanePairAligner", "subsequence", "chained", "shares", "TURNED_MIN_BP", "anchorAligner", "records", "taken", "chain", "chainFeature", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "stepsInWindow", "window", "departureSpans", "leavePos", "rejoinPos", "departureFeature", "departure", "name", "hapStart", "ownBp", "rejoinReversed", "SyntenyFeature", "haplotypeOf", "name", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openWalkReader", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "keep", "walksKept", "updateStatus", "error", "laneZoomNotice", "wanted", "lane", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "departures", "rank", "align", "anchorAligner", "laneOf", "walk", "references", "f", "walked", "fragment", "query", "reference", "chain", "chainFeature", "walking", "stepsInWindow", "spanning", "departure", "departureSpans", "a", "b", "departureFeature", "pairs", "sides", "pair", "side", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
+  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type {\n  WalkDeparture,\n  WalkFragment,\n  WalkNode,\n} from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n\n/**\n * Whether a walk's fragment steps on the reference inside the window: on a\n * node of `refName` overlapping it\n */\nexport function stepsInWindow(\n  fragment: WalkFragment,\n  nodes: Map<number, WalkNode>,\n  refName: string,\n  window: { start: number; end: number },\n) {\n  return Array.from(fragment.ids).some(id => {\n    const node = nodes.get(id)\n    return (\n      node?.rank === 0 &&\n      node.refName === refName &&\n      node.start < window.end &&\n      node.end > window.start\n    )\n  })\n}\n\n/** Whether the reference between a departure's ends covers the whole window */\nexport function departureSpans(\n  { leavePos, rejoinPos }: WalkDeparture,\n  window: { start: number; end: number },\n) {\n  return (\n    Math.min(leavePos, rejoinPos) <= window.start &&\n    Math.max(leavePos, rejoinPos) >= window.end\n  )\n}\n\n/**\n * A haplotype whose departure from the reference spans the whole window, as\n * the record a multi-way display lifts out as a deletion: `spansWindow`, the\n * reference between the departure's ends whole so its length heads the lane,\n * and the haplotype's own sequence between them as its mate, a point where\n * it has none. The record runs the way the walk rejoins the reference, and\n * carries no CIGAR and no identity, so no ramp or identity filter reads it\n * as an alignment.\n */\nexport function departureFeature({\n  departure,\n  refName,\n  assemblyName,\n  mateAssemblyName,\n}: {\n  departure: WalkDeparture\n  refName: string\n  assemblyName: string\n  mateAssemblyName: string\n}) {\n  const { name, hapStart, ownBp, leavePos, rejoinPos, rejoinReversed } =\n    departure\n  const id = `${name}:${hapStart}:${leavePos}:departure`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start: Math.min(leavePos, rejoinPos),\n    end: Math.max(leavePos, rejoinPos),\n    type: 'departure',\n    strand: rejoinReversed ? -1 : 1,\n    syntenyId: id,\n    spansWindow: true,\n    mate: {\n      refName: panSNContig(name),\n      start: hapStart,\n      end: hapStart + ownBp,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport {\n  anchorAligner,\n  chainFeature,\n  departureFeature,\n  departureSpans,\n  lanePairAligner,\n  stepsInWindow,\n} from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openWalkReader } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nconst haplotypeOf = ({ name }: { name: string }) => panSNHaplotype(name) ?? name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(openWalkReader(this), this)\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.source,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolveForCut(region, {\n      signal: opts.signal,\n    })\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with\n  // every departure from the reference over it and no link read; a window\n  // past a budget fails as a zoom-in notice for lanes. Named lanes come back\n  // in full where the walk file abridged them: an abridged walk is two\n  // reference steps, which drew 15 of the HPRC MHC launch's 32 lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate. A haplotype with no step\n   * on the reference inside the window whose departure spans it is one\n   * `spansWindow` record of the departure's stretch, its mate the haplotype's\n   * own sequence between the departure's ends, a point where it has none.\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const status = `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`\n    const { graph, fragments, departures } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      status,\n    )\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = ({ name }: { name: string }) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix => panSNMatchesPrefix(name, prefix))\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const laneOf = (walk: { name: string }) =>\n      laneAssemblyName(asmByPrefix, haplotypeOf(walk))\n    const references = fragments.filter(f => f.name === refName)\n    const walked = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .map(query => ({\n        rank: rank(query),\n        features: references.flatMap(reference =>\n          align(query, reference).map(chain =>\n            chainFeature({\n              chain,\n              target: reference,\n              query,\n              assemblyName: region.assemblyName,\n              refName: region.refName,\n              mateAssemblyName: laneOf(query),\n            }),\n          ),\n        ),\n      }))\n    // NA19036#1 skips the IGL locus on one contig and walks it on another\n    const walking = new Set(\n      fragments\n        .filter(fragment =>\n          stepsInWindow(fragment, graph.nodes, refName, region),\n        )\n        .map(haplotypeOf),\n    )\n    const spanning = departures\n      .filter(\n        departure =>\n          rank(departure) >= 0 &&\n          !walking.has(haplotypeOf(departure)) &&\n          departureSpans(departure, region),\n      )\n      .sort((a, b) => a.name.localeCompare(b.name))\n      .map(departure => ({\n        rank: rank(departure),\n        features: [\n          departureFeature({\n            departure,\n            refName: region.refName,\n            assemblyName: region.assemblyName,\n            mateAssemblyName: laneOf(departure),\n          }),\n        ],\n      }))\n    return [...walked, ...spanning]\n      .sort((a, b) => a.rank - b.rank)\n      .flatMap(lane => lane.features)\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolveMapped(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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+  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "y", "x", "singleVisits", "rev", "twice", "directionShares", "visits", "visitsOf", "found", "theirs", "opposite", "other", "lanePairAligner", "subsequence", "chained", "shares", "TURNED_MIN_BP", "anchorAligner", "records", "taken", "chain", "chainFeature", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "stepsInWindow", "window", "departureSpans", "leavePos", "rejoinPos", "departureFeature", "departure", "name", "hapStart", "ownBp", "rejoinReversed", "SyntenyFeature", "haplotypeOf", "name", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openWalkReader", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "keep", "walksKept", "updateStatus", "error", "laneZoomNotice", "wanted", "lane", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "departures", "rank", "align", "anchorAligner", "laneOf", "walk", "references", "f", "walked", "fragment", "query", "reference", "chain", "chainFeature", "walking", "stepsInWindow", "spanning", "departure", "departureSpans", "a", "b", "departureFeature", "pairs", "sides", "pair", "side", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
 }

package/dist/chunks/{chunk-3HSJ7SAT.js → chunk-2CSE6SGH.js}

@@ -1,2 +1,2 @@
-import{a as O,l as M,o as W,s as F}from"./chunk-N4ZFGZDN.js";import{f as B}from"./chunk-MPUAUZSJ.js";import{K as f,Q as A,X as _}from"./chunk-LQSOJR7D.js";import{f as R}from"./chunk-J2PN6CG3.js";import{D as x,E,H as S,d as C,o as T,q as I,r as L,s as w,t as N,w as D,y as G,z as P}from"./chunk-WE7DQVXF.js";import{b as t,c as r,d as s}from"./chunk-DUU6T2I5.js";var k=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var U=s(function({label:n,value:e,options:o,testId:p,size:h,sx:a,disabled:m,title:u,shown:b,onChange:H}){let y=R();return r(w,{size:h,sx:a,disabled:m,title:u,children:[t(D,{id:y,shrink:!0,children:n}),t(x,{labelId:y,value:e,label:n,notched:!0,displayEmpty:!0,"data-testid":p,renderValue:i=>b??o.find(Y=>Y.value===i)?.label??i,onChange:i=>{H(i.target.value)},children:o.map(i=>t(P,{value:i.value,disabled:i.disabled,title:i.disabled?void 0:i.description,children:t(G,{primary:i.label,secondary:i.disabled?i.description:void 0})},i.value))})]})});var g=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}}),l=s(function({warn:n=!1,children:e}){return t(S,{variant:"caption",component:"div",color:n?"warning.main":"text.secondary",children:e})}),v=s(function({title:n,children:e}){let{classes:o}=g();return r("section",{className:o.group,children:[t(S,{variant:"subtitle1",className:o.heading,children:n}),e]})}),Q=s(function({label:n,checked:e,onChange:o,children:p}){let{classes:h}=g();return r("div",{className:h.section,children:[t(N,{control:t(E,{checked:e,onChange:a=>{o(a.target.checked)}}),label:n}),p]})}),d=s(function({children:n,...e}){let{classes:o}=g();return r("div",{className:o.section,children:[t(U,{sx:{minWidth:200},...e}),n]})}),$=[5e3,2e4,5e4,1e5];function q(c){return[...new Set([...$,c])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}var z=s(function({label:n,choices:e,stored:o,auto:p,testId:h,onChange:a,children:m}){return e.length>0?t(d,{label:n,value:e.some(u=>u.trackId===o)?o:"",options:[{value:"",label:`Automatic (${p?.name??"none"})`},...e.map(({trackId:u,name:b})=>({value:u,label:b}))],testId:h,onChange:a,children:m}):null}),K=s(function(n){let{model:e,onClose:o,children:p}=n,{classes:h}=g();return r(C,{open:!0,onClose:o,title:"Graph settings",children:[r(L,{children:[r(v,{title:"Subgraph",children:[p,t(d,{label:"Node limit",value:String(e.maxGraphNodes),options:q(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(l,{children:"The most nodes a layout draws; past it the graph is declined. 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-//# sourceMappingURL=chunk-3HSJ7SAT.js.map
+import{a as O,l as M,o as W,s as F}from"./chunk-ULWTJWXX.js";import{f as B}from"./chunk-P5SI66S3.js";import{K as f,Q as A,X as _}from"./chunk-I6NW3VGS.js";import{f as R}from"./chunk-J2PN6CG3.js";import{D as x,E,H as S,d as C,o as T,q as I,r as L,s as w,t as N,w as D,y as G,z as P}from"./chunk-WE7DQVXF.js";import{b as t,c as r,d as s}from"./chunk-DUU6T2I5.js";var k=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var U=s(function({label:n,value:e,options:o,testId:p,size:h,sx:a,disabled:m,title:u,shown:b,onChange:H}){let y=R();return r(w,{size:h,sx:a,disabled:m,title:u,children:[t(D,{id:y,shrink:!0,children:n}),t(x,{labelId:y,value:e,label:n,notched:!0,displayEmpty:!0,"data-testid":p,renderValue:i=>b??o.find(Y=>Y.value===i)?.label??i,onChange:i=>{H(i.target.value)},children:o.map(i=>t(P,{value:i.value,disabled:i.disabled,title:i.disabled?void 0:i.description,children:t(G,{primary:i.label,secondary:i.disabled?i.description:void 0})},i.value))})]})});var g=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}}),l=s(function({warn:n=!1,children:e}){return t(S,{variant:"caption",component:"div",color:n?"warning.main":"text.secondary",children:e})}),v=s(function({title:n,children:e}){let{classes:o}=g();return r("section",{className:o.group,children:[t(S,{variant:"subtitle1",className:o.heading,children:n}),e]})}),Q=s(function({label:n,checked:e,onChange:o,children:p}){let{classes:h}=g();return r("div",{className:h.section,children:[t(N,{control:t(E,{checked:e,onChange:a=>{o(a.target.checked)}}),label:n}),p]})}),d=s(function({children:n,...e}){let{classes:o}=g();return r("div",{className:o.section,children:[t(U,{sx:{minWidth:200},...e}),n]})}),$=[5e3,2e4,5e4,1e5];function q(c){return[...new Set([...$,c])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}var z=s(function({label:n,choices:e,stored:o,auto:p,testId:h,onChange:a,children:m}){return e.length>0?t(d,{label:n,value:e.some(u=>u.trackId===o)?o:"",options:[{value:"",label:`Automatic (${p?.name??"none"})`},...e.map(({trackId:u,name:b})=>({value:u,label:b}))],testId:h,onChange:a,children:m}):null}),K=s(function(n){let{model:e,onClose:o,children:p}=n,{classes:h}=g();return r(C,{open:!0,onClose:o,title:"Graph settings",children:[r(L,{children:[r(v,{title:"Subgraph",children:[p,t(d,{label:"Node limit",value:String(e.maxGraphNodes),options:q(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(l,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),r(v,{title:"Drawing",children:[e.anchorPaths.length>1?t(d,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(l,{children:"The path the anchored layouts place x along"})}):null,t(d,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(l,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),t(d,{label:"Link width",value:e.linkWidth,options:_,testId:"graph-link-width-select",onChange:a=>{e.setLinkWidth(a)},children:t(l,{children:"Walks as width, so a common route reads heavy and a private one thin."})}),r(Q,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(l,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(l,{warn:!0,children:e.pathCount>f?`Off: ${e.pathCount.toLocaleString()} paths is past the ${f} this can tell apart`:"Off: this graph states no paths"}):null]}),t(z,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:W(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(l,{children:"Where genes on the backbone come from"})}),t(z,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:M(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(l,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),r(v,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:h.section,children:t(l,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(d,{label:"Engine",value:e.chosenLayoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(l,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(d,{label:"Layout quality",value:String(e.layoutQuality),options:k.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(l,{children:"The engine's iteration budget; higher is slower"})}),t(d,{label:"Bubble spread",value:e.bubbleSpread,options:B,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(l,{children:"How far the layout opens a bubble"})}),e.chosenLayoutEngine==="stress"?null:t(Q,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(l,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:o,children:"Close"})})]})}),be=K;export{U as a,be as b};
+//# sourceMappingURL=chunk-2CSE6SGH.js.map

package/dist/chunks/{chunk-3HSJ7SAT.js.map → chunk-2CSE6SGH.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@13.1.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@13.3.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
   "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default observer(function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n})\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { EDGE_WIDTHS } from '@jbrowse/bandage-core/edgeWidths'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\n  },\n})\n\nconst Caption = observer(function Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n})\n\nconst Group = observer(function Group({\n  title,\n  children,\n}: {\n  title: string\n  children: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\n})\n\nconst SettingSwitch = observer(function SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n})\n\n// one dropdown setting, at the dialog's width, and its caption\nconst SettingSelect = observer(function SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n})\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nconst TrackPickSetting = observer(function TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n})\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            >\n              <Caption>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          >\n            <Caption>\n              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Link width\"\n            value={model.linkWidth}\n            options={EDGE_WIDTHS}\n            testId=\"graph-link-width-select\"\n            onChange={links => {\n              model.setLinkWidth(links)\n            }}\n          >\n            <Caption>\n              Walks as width, so a common route reads heavy and a private one\n              thin.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\n            </Caption>\n            {model.drawPaths && !model.effectiveDrawPaths ? (\n              <Caption warn>\n                {model.pathCount > MAX_PATH_COLORS\n                  ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                  : 'Off: this graph states no paths'}\n              </Caption>\n            ) : null}\n          </SettingSwitch>\n\n          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? 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