jbrowse-plugin-graphgenomeviewer 7.1.11 → 7.1.13

package/dist/chunks/{chunk-T4HOC6O3.js.map → chunk-M2D7NUOY.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/gbwt/node.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/gbwt/sequence.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/lcs.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/pairAlignment.ts"],
-  "sourcesContent": ["export const ENDMARKER = 0\n\nexport type Orientation = 'forward' | 'reverse'\n\nexport function encodeNode(id: number, orientation: Orientation) {\n  return 2 * id + (orientation === 'reverse' ? 1 : 0)\n}\n\nexport function nodeId(handle: number) {\n  return Math.floor(handle / 2)\n}\n\nexport function nodeOrientation(handle: number): Orientation {\n  return handle % 2 === 0 ? 'forward' : 'reverse'\n}\n\nexport function isReverse(handle: number) {\n  return handle % 2 === 1\n}\n\nexport function flipNode(handle: number) {\n  return handle % 2 === 0 ? handle + 1 : handle - 1\n}\n\nexport type NodeSide = 'left' | 'right'\n\nexport function flipSide(side: NodeSide): NodeSide {\n  return side === 'left' ? 'right' : 'left'\n}\n\nexport function entrySide(orientation: Orientation): NodeSide {\n  return orientation === 'forward' ? 'left' : 'right'\n}\n\nexport function exitSide(orientation: Orientation): NodeSide {\n  return orientation === 'forward' ? 'right' : 'left'\n}\n\nexport function entryOrientation(side: NodeSide): Orientation {\n  return side === 'left' ? 'forward' : 'reverse'\n}\n\nexport function exitOrientation(side: NodeSide): Orientation {\n  return side === 'right' ? 'forward' : 'reverse'\n}\n\nexport function edgeIsCanonical(from: number, to: number) {\n  const fromId = nodeId(from)\n  const toId = nodeId(to)\n  return isReverse(from)\n    ? toId > fromId || (toId === fromId && !isReverse(to))\n    : toId >= fromId\n}\n\nexport function pathIsCanonical(path: number[]) {\n  return pathEndsAreCanonical(path[0], path[path.length - 1])\n}\n\nexport function pathEndsAreCanonical(\n  first: number | undefined,\n  last: number | undefined,\n) {\n  if (first === undefined || last === undefined) {\n    return true\n  }\n  return isReverse(first) === isReverse(last)\n    ? !isReverse(first)\n    : edgeIsCanonical(first, last)\n}\n", "const DECODE = ['', 'A', 'C', 'G', 'T', 'N']\n\nexport function encodedSequenceLength(encoded: Uint8Array) {\n  const last = encoded[encoded.length - 1]\n  if (last === undefined) {\n    return 0\n  }\n  let value = last\n  let inLast = 0\n  for (let i = 0; i < 3; i++) {\n    if (value % 6 === 0) {\n      break\n    }\n    value = Math.floor(value / 6)\n    inLast += 1\n  }\n  return 3 * (encoded.length - 1) + inLast\n}\n\nexport function decodeSequence(encoded: Uint8Array) {\n  let result = ''\n  for (const byte of encoded) {\n    let value = byte\n    for (let i = 0; i < 3; i++) {\n      const base = DECODE[value % 6]!\n      if (base === '') {\n        return result\n      }\n      value = Math.floor(value / 6)\n      result += base\n    }\n  }\n  return result\n}\n\nconst COMPLEMENT: Record<string, string> = {\n  A: 'T',\n  C: 'G',\n  G: 'C',\n  T: 'A',\n  N: 'N',\n}\n\nexport function reverseComplement(sequence: string) {\n  let result = ''\n  for (let i = sequence.length - 1; i >= 0; i--) {\n    result += COMPLEMENT[sequence[i]!] ?? 'N'\n  }\n  return result\n}\n", "type Weight = (x: number) => number\n\nfunction lowerBound(ascending: number[], value: number) {\n  let lo = 0\n  let hi = ascending.length\n  while (lo < hi) {\n    const mid = (lo + hi) >> 1\n    if (ascending[mid]! < value) {\n      lo = mid + 1\n    } else {\n      hi = mid\n    }\n  }\n  return lo\n}\n\nclass ColumnMax {\n  readonly ending: Float64Array\n  private readonly tree: Int32Array\n\n  constructor(columns: number) {\n    this.ending = new Float64Array(columns)\n    this.tree = new Int32Array(columns + 1).fill(-1)\n  }\n\n  bestBefore(column: number) {\n    let best = -1\n    for (let p = column; p > 0; p -= p & -p) {\n      const candidate = this.tree[p]!\n      if (\n        candidate !== -1 &&\n        (best === -1 || this.ending[candidate]! > this.ending[best]!)\n      ) {\n        best = candidate\n      }\n    }\n    return best\n  }\n\n  raise(column: number, value: number) {\n    this.ending[column] = value\n    for (let p = column + 1; p < this.tree.length; p += p & -p) {\n      const holder = this.tree[p]!\n      if (holder === -1 || value > this.ending[holder]!) {\n        this.tree[p] = column\n      }\n    }\n  }\n}\n\ninterface Trace {\n  row: Int32Array\n  column: Int32Array\n  previous: Int32Array\n  endingMatch: Int32Array\n  count: number\n}\n\nclass SparseLcs {\n  readonly pairs: [number, number][] = []\n  total = 0\n  private readonly a: number[]\n  private readonly b: number[]\n  private readonly weight: Weight\n  private readonly occurrences = new Map<number, number[]>()\n\n  constructor(a: number[], b: number[], weight: Weight) {\n    this.a = a\n    this.b = b\n    this.weight = weight\n    b.forEach((x, j) => {\n      const list = this.occurrences.get(x)\n      if (list) {\n        list.push(j)\n      } else {\n        this.occurrences.set(x, [j])\n      }\n    })\n  }\n\n  solve(a0: number, a1: number, b0: number, b1: number) {\n    let prefix = 0\n    while (\n      a0 + prefix < a1 &&\n      b0 + prefix < b1 &&\n      this.a[a0 + prefix] === this.b[b0 + prefix]\n    ) {\n      this.match(a0 + prefix, b0 + prefix)\n      prefix += 1\n    }\n    let suffix = 0\n    while (\n      a1 - suffix > a0 + prefix &&\n      b1 - suffix > b0 + prefix &&\n      this.a[a1 - suffix - 1] === this.b[b1 - suffix - 1]\n    ) {\n      suffix += 1\n    }\n    this.solveMiddle(a0 + prefix, a1 - suffix, b0 + prefix, b1 - suffix)\n    for (let k = suffix; k > 0; k--) {\n      this.match(a1 - k, b1 - k)\n    }\n  }\n\n  private match(i: number, j: number) {\n    this.pairs.push([i, j])\n    this.total += this.weight(this.a[i]!)\n  }\n\n  private solveMiddle(a0: number, a1: number, b0: number, b1: number) {\n    if (a0 === a1 || b0 === b1) {\n      return\n    }\n    const matches = this.matchCount(a0, a1, b0, b1)\n    if (matches === 0) {\n      return\n    }\n    if (matches <= a1 - a0 + (b1 - b0)) {\n      this.chain(a0, a1, b0, b1, matches)\n      return\n    }\n    const mid = (a0 + a1) >> 1\n    const split = this.split(a0, mid, a1, b0, b1)\n    this.solve(a0, mid, b0, split)\n    this.solve(mid, a1, split, b1)\n  }\n\n  private matchCount(a0: number, a1: number, b0: number, b1: number) {\n    let count = 0\n    for (let i = a0; i < a1; i++) {\n      const list = this.occurrences.get(this.a[i]!)\n      if (list) {\n        count += lowerBound(list, b1) - lowerBound(list, b0)\n      }\n    }\n    return count\n  }\n\n  private sweep(\n    from: number,\n    to: number,\n    step: 1 | -1,\n    b0: number,\n    b1: number,\n    columns: ColumnMax,\n    trace?: Trace,\n  ) {\n    for (let i = from; i !== to; i += step) {\n      const list = this.occurrences.get(this.a[i]!)\n      if (!list) {\n        continue\n      }\n      const w = this.weight(this.a[i]!)\n      const lo = lowerBound(list, b0)\n      const hi = lowerBound(list, b1)\n      for (let k = 0; k < hi - lo; k++) {\n        const column =\n          step === 1 ? list[hi - 1 - k]! - b0 : b1 - 1 - list[lo + k]!\n        const before = columns.bestBefore(column)\n        const value = (before === -1 ? 0 : columns.ending[before]!) + w\n        if (value > columns.ending[column]!) {\n          columns.raise(column, value)\n          if (trace) {\n            const match = trace.count++\n            trace.row[match] = i\n            trace.column[match] = column\n            trace.previous[match] =\n              before === -1 ? -1 : trace.endingMatch[before]!\n            trace.endingMatch[column] = match\n          }\n        }\n      }\n    }\n  }\n\n  private chain(\n    a0: number,\n    a1: number,\n    b0: number,\n    b1: number,\n    matches: number,\n  ) {\n    const columns = new ColumnMax(b1 - b0)\n    const trace: Trace = {\n      row: new Int32Array(matches),\n      column: new Int32Array(matches),\n      previous: new Int32Array(matches),\n      endingMatch: new Int32Array(b1 - b0),\n      count: 0,\n    }\n    this.sweep(a0, a1, 1, b0, b1, columns, trace)\n    const last = columns.bestBefore(b1 - b0)\n    if (last === -1) {\n      return\n    }\n    this.total += columns.ending[last]!\n    const chained: [number, number][] = []\n    for (\n      let match = trace.endingMatch[last]!;\n      match !== -1;\n      match = trace.previous[match]!\n    ) {\n      chained.push([trace.row[match]!, b0 + trace.column[match]!])\n    }\n    for (let k = chained.length - 1; k >= 0; k--) {\n      this.pairs.push(chained[k]!)\n    }\n  }\n\n  private frontier(\n    from: number,\n    to: number,\n    step: 1 | -1,\n    b0: number,\n    b1: number,\n  ) {\n    const columns = new ColumnMax(b1 - b0)\n    this.sweep(from, to, step, b0, b1, columns)\n    const best = new Float64Array(b1 - b0 + 1)\n    for (let column = 0; column < b1 - b0; column++) {\n      best[column + 1] = Math.max(best[column]!, columns.ending[column]!)\n    }\n    return best\n  }\n\n  private split(a0: number, mid: number, a1: number, b0: number, b1: number) {\n    const width = b1 - b0\n    const before = this.frontier(a0, mid, 1, b0, b1)\n    const after = this.frontier(a1 - 1, mid - 1, -1, b0, b1)\n    let split = 0\n    let best = -1\n    for (let s = 0; s <= width; s++) {\n      const combined = before[s]! + after[width - s]!\n      if (combined > best) {\n        best = combined\n        split = s\n      }\n    }\n    return b0 + split\n  }\n}\n\nexport function weightedLcs(\n  a: number[],\n  b: number[],\n  weight: Weight,\n): [pairs: [number, number][], weight: number] {\n  const lcs = new SparseLcs(a, b, weight)\n  lcs.solve(0, a.length, 0, b.length)\n  return [lcs.pairs, lcs.total]\n}\n", "import { isReverse, nodeId } from './gbwt/node.ts'\nimport { reverseComplement } from './gbwt/sequence.ts'\n\nexport type PairOp = '=' | 'X' | 'I' | 'D'\nexport type PairEdit = [PairOp, number]\n\nexport interface PairChain {\n  queryStart: number\n  queryEnd: number\n  targetStart: number\n  targetEnd: number\n  strand: '+' | '-'\n  edits: PairEdit[]\n  // bases on nodes both walks visit; the other `=` came from comparing bases\n  sharedBases: number\n}\n\nexport interface PairOptions {\n  query: number[]\n  target: number[]\n  sequenceOf: (id: number) => string\n  maxGap?: number | undefined\n  minMatch?: number | undefined\n  bases?: boolean | undefined\n}\n\n// An exact match: query [qs, qe) against target [ts, te), the target read\n// backwards when flipped.\ninterface Run {\n  qs: number\n  qe: number\n  ts: number\n  te: number\n  flipped: boolean\n}\n\nconst DEFAULT_MIN_MATCH = 100\nconst MAX_ALIGNED_CELLS = 4_000_000\nconst CHAIN_LOOKBACK = 5000\nconst KMER = 15\nconst MAX_KMER_OCCURRENCES = 64\n// each level's gaps lie strictly inside the last, so this only bounds the work\nconst MAX_FILL_DEPTH = 8\n\n// vg's scoring, the model the reference CIGARs in subgraph.ts are scored by\nconst MATCH = 1\nconst MISMATCH = -4\nconst GAP_OPEN = -6\nconst GAP_EXTEND = -1\nconst UNREACHABLE = -(2 ** 30)\n\nconst DIAGONAL = 0\nconst INSERTION = 1\nconst DELETION = 2\n\nfunction appendEdit(edits: PairEdit[], op: PairOp, 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\nfunction best(diagonal: number, insertion: number, deletion: number) {\n  return diagonal >= deletion && diagonal >= insertion\n    ? DIAGONAL\n    : deletion >= insertion\n      ? DELETION\n      : INSERTION\n}\n\n// The highest-scoring global alignment of a on b under affine gaps. Each cell\n// of `trace` packs, two bits apiece, the state each of the three states came\n// from. A tie goes to the diagonal, then to the deletion, so two stretches\n// with nothing in common read as an insertion followed by a deletion.\nfunction affineAlignment(a: string, b: string, edits: PairEdit[]) {\n  const la = a.length\n  const lb = b.length\n  const width = lb + 1\n  const trace = new Uint8Array((la + 1) * width)\n  let diagonal = new Int32Array(width).fill(UNREACHABLE)\n  let insertion = new Int32Array(width).fill(UNREACHABLE)\n  let deletion = new Int32Array(width).fill(UNREACHABLE)\n  diagonal[0] = 0\n  for (let j = 1; j <= lb; j++) {\n    deletion[j] = GAP_OPEN + (j - 1) * GAP_EXTEND\n    trace[j] = (j === 1 ? DIAGONAL : DELETION) << 4\n  }\n  for (let i = 1; i <= la; i++) {\n    const nextDiagonal = new Int32Array(width).fill(UNREACHABLE)\n    const nextInsertion = new Int32Array(width).fill(UNREACHABLE)\n    const nextDeletion = new Int32Array(width).fill(UNREACHABLE)\n    nextInsertion[0] = GAP_OPEN + (i - 1) * GAP_EXTEND\n    trace[i * width] = (i === 1 ? DIAGONAL : INSERTION) << 2\n    const ai = a.charCodeAt(i - 1)\n    for (let j = 1; j <= lb; j++) {\n      const fromDiagonal = best(\n        diagonal[j - 1]!,\n        insertion[j - 1]!,\n        deletion[j - 1]!,\n      )\n      nextDiagonal[j] =\n        Math.max(diagonal[j - 1]!, insertion[j - 1]!, deletion[j - 1]!) +\n        (ai === b.charCodeAt(j - 1) ? MATCH : MISMATCH)\n      const fromInsertion = best(\n        diagonal[j]! + GAP_OPEN,\n        insertion[j]! + GAP_EXTEND,\n        deletion[j]! + GAP_OPEN,\n      )\n      nextInsertion[j] = Math.max(\n        diagonal[j]! + GAP_OPEN,\n        insertion[j]! + GAP_EXTEND,\n        deletion[j]! + GAP_OPEN,\n      )\n      const fromDeletion = best(\n        nextDiagonal[j - 1]! + GAP_OPEN,\n        nextInsertion[j - 1]! + GAP_OPEN,\n        nextDeletion[j - 1]! + GAP_EXTEND,\n      )\n      nextDeletion[j] = Math.max(\n        nextDiagonal[j - 1]! + GAP_OPEN,\n        nextInsertion[j - 1]! + GAP_OPEN,\n        nextDeletion[j - 1]! + GAP_EXTEND,\n      )\n      trace[i * width + j] =\n        fromDiagonal | (fromInsertion << 2) | (fromDeletion << 4)\n    }\n    diagonal = nextDiagonal\n    insertion = nextInsertion\n    deletion = nextDeletion\n  }\n  const ops: PairOp[] = []\n  let i = la\n  let j = lb\n  let state = best(diagonal[lb]!, insertion[lb]!, deletion[lb]!)\n  while (i > 0 || j > 0) {\n    const from = (trace[i * width + j]! >> (2 * state)) & 3\n    if (state === DIAGONAL) {\n      ops.push(a[i - 1] === b[j - 1] ? '=' : 'X')\n      i -= 1\n      j -= 1\n    } else if (state === INSERTION) {\n      ops.push('I')\n      i -= 1\n    } else {\n      ops.push('D')\n      j -= 1\n    }\n    state = from\n  }\n  for (const op of ops.reverse()) {\n    appendEdit(edits, op, 1)\n  }\n}\n\n// What a chain of walk steps pays to go from one run to the next over dq\n// private query bases and dt target ones. Those runs lie outside both walks'\n// repeats, so each has one place to go and the cost only has to let a chain\n// hold through a structural variant of any size: vg's charge for a short\n// indel, growing with the logarithm past it.\nfunction stepJumpCost(dq: number, dt: number) {\n  const indel = Math.abs(dq - dt)\n  const indelCost =\n    indel === 0\n      ? 0\n      : Math.min(\n          -GAP_OPEN - (indel - 1) * GAP_EXTEND,\n          -GAP_OPEN + 10 * Math.log2(indel),\n        )\n  return indelCost + (Math.min(dq, dt) > 0 ? -MISMATCH : 0)\n}\n\n// What a chain of k-mer matches pays, which is minimap2's gap cost. Inside a\n// tandem array every copy offers a match, and the term that grows with the\n// indel is what keeps a chain in one register instead of hopping between\n// copies for a slightly longer match.\nfunction kmerJumpCost(dq: number, dt: number) {\n  const indel = Math.abs(dq - dt)\n  return indel === 0 ? 0 : 0.01 * KMER * indel + 0.5 * Math.log2(indel)\n}\n\ntype JumpCost = (dq: number, dt: number) => number\n\ninterface Link {\n  run: Run\n  trim: number\n}\n\ntype Interval = [number, number]\n\n// The stretch of a run from offset `from` to `to` along it\nfunction sliceRun(run: Run, from: number, to: number): Run {\n  return {\n    qs: run.qs + from,\n    qe: run.qs + to,\n    ts: run.flipped ? run.te - to : run.ts + from,\n    te: run.flipped ? run.te - from : run.ts + to,\n    flipped: run.flipped,\n  }\n}\n\n// What is left of a run once taken bases are cut out of it, as the pieces a\n// k-mer long or more. An exact match divides at any base, so a flank that runs\n// one base into an inversion by chance costs the inversion one base, not all\n// of it.\nfunction untakenPieces(run: Run, query: Interval[], target: Interval[]) {\n  const len = run.qe - run.qs\n  const blocked: Interval[] = []\n  for (const [s, e] of query) {\n    const lo = Math.max(0, s - run.qs)\n    const hi = Math.min(len, e - run.qs)\n    if (lo < hi) {\n      blocked.push([lo, hi])\n    }\n  }\n  for (const [s, e] of target) {\n    const lo = Math.max(0, run.flipped ? run.te - e : s - run.ts)\n    const hi = Math.min(len, run.flipped ? run.te - s : e - run.ts)\n    if (lo < hi) {\n      blocked.push([lo, hi])\n    }\n  }\n  if (blocked.length === 0) {\n    return [run]\n  }\n  blocked.sort((x, y) => x[0] - y[0])\n  const pieces: Run[] = []\n  let from = 0\n  for (const [lo, hi] of blocked) {\n    if (lo - from >= KMER) {\n      pieces.push(sliceRun(run, from, lo))\n    }\n    from = Math.max(from, hi)\n  }\n  if (len - from >= KMER) {\n    pieces.push(sliceRun(run, from, len))\n  }\n  return pieces\n}\n\n// The best-scoring collinear chain of runs matching minMatch bases or more,\n// then the best over the runs that overlap no accepted run on either sequence,\n// and so on: a second copy of a repeat finds its target taken and an inversion\n// finds its target free. A run that overlaps its predecessor is trimmed from\n// the front, which an exact match allows at any base.\nfunction chainRuns(\n  runs: Run[],\n  maxGap: number,\n  minMatch: number,\n  jumpCost: JumpCost,\n  maxChains = Infinity,\n) {\n  const chains: Link[][] = []\n  const basesTaken = { query: [] as Interval[], target: [] as Interval[] }\n  const spanTaken = {\n    forward: { query: [] as Interval[], target: [] as Interval[] },\n    flipped: { query: [] as Interval[], target: [] as Interval[] },\n  }\n  let pool = [...runs].sort((a, b) => a.qs - b.qs || a.ts - b.ts)\n  while (pool.length > 0 && chains.length < maxChains) {\n    const score = pool.map(run => run.qe - run.qs)\n    const back = new Int32Array(pool.length).fill(-1)\n    const trims = new Int32Array(pool.length)\n    for (let j = 0; j < pool.length; j++) {\n      const b = pool[j]!\n      const len = b.qe - b.qs\n      for (let i = j - 1; i >= Math.max(0, j - CHAIN_LOOKBACK); i--) {\n        if (score[i]! + len <= score[j]!) {\n          continue\n        }\n        const a = pool[i]!\n        const advances =\n          a.flipped === b.flipped &&\n          a.qs < b.qs &&\n          (b.flipped ? b.te < a.te : a.ts < b.ts)\n        if (advances) {\n          const trim = Math.max(\n            0,\n            a.qe - b.qs,\n            b.flipped ? b.te - a.ts : a.te - b.ts,\n          )\n          const dq = b.qs + trim - a.qe\n          const dt = b.flipped ? a.ts - (b.te - trim) : b.ts + trim - a.te\n          if (trim < len && dq <= maxGap && dt <= maxGap) {\n            const candidate = score[i]! + len - trim - jumpCost(dq, dt)\n            if (candidate > score[j]!) {\n              score[j] = candidate\n              back[j] = i\n              trims[j] = trim\n            }\n          }\n        }\n      }\n    }\n    const matched = new Int32Array(pool.length)\n    let end = -1\n    for (let j = 0; j < pool.length; j++) {\n      const run = pool[j]!\n      matched[j] = (matched[back[j]!] ?? 0) + run.qe - run.qs - trims[j]!\n      if (matched[j]! >= minMatch && (end < 0 || score[j]! > score[end]!)) {\n        end = j\n      }\n    }\n    if (end < 0) {\n      break\n    }\n    const chain: Link[] = []\n    for (let j = end; j >= 0; j = back[j]!) {\n      chain.push({ run: pool[j]!, trim: trims[j]! })\n    }\n    chain.reverse()\n    chains.push(chain)\n    // A record's CIGAR accounts for every base between its ends in its own\n    // orientation, so a later chain of that orientation may not nest in its\n    // gaps: taking only the runs let one re-claim an earlier record's bases on\n    // a paralog. An inversion is what a forward CIGAR cannot account for, so\n    // across orientations only the bases themselves are taken.\n    const first = chain[0]!\n    const last = chain.at(-1)!\n    const { flipped } = first.run\n    const spans = flipped ? spanTaken.flipped : spanTaken.forward\n    spans.query.push([first.run.qs + first.trim, last.run.qe])\n    spans.target.push(\n      flipped\n        ? [last.run.ts, first.run.te - first.trim]\n        : [first.run.ts + first.trim, last.run.te],\n    )\n    for (const { run, trim } of chain) {\n      basesTaken.query.push([run.qs + trim, run.qe])\n      basesTaken.target.push(\n        run.flipped ? [run.ts, run.te - trim] : [run.ts + trim, run.te],\n      )\n    }\n    pool = pool\n      .flatMap(run => {\n        const same = run.flipped ? spanTaken.flipped : spanTaken.forward\n        return untakenPieces(\n          run,\n          [...basesTaken.query, ...same.query],\n          [...basesTaken.target, ...same.target],\n        )\n      })\n      .sort((x, y) => x.qs - y.qs || x.ts - y.ts)\n  }\n  return chains\n}\n\n// Exact matches of KMER bases or more between a and b, as runs along a\n// diagonal. A k-mer the target holds many times over seeds nothing.\nfunction forwardKmerRuns(a: string, b: string) {\n  const index = new Map<string, number[]>()\n  for (let p = 0; p + KMER <= b.length; p++) {\n    const kmer = b.slice(p, p + KMER)\n    const seen = index.get(kmer)\n    if (seen) {\n      seen.push(p)\n    } else {\n      index.set(kmer, [p])\n    }\n  }\n  const runs: Run[] = []\n  const open = new Map<number, Run>()\n  for (let i = 0; i + KMER <= a.length; i++) {\n    const hits = index.get(a.slice(i, i + KMER))\n    if (hits && hits.length <= MAX_KMER_OCCURRENCES) {\n      for (const p of hits) {\n        const diagonal = p - i\n        const run = open.get(diagonal)\n        if (run && i <= run.qe) {\n          run.qe = i + KMER\n          run.te = p + KMER\n        } else {\n          const started = {\n            qs: i,\n            qe: i + KMER,\n            ts: p,\n            te: p + KMER,\n            flipped: false,\n          }\n          open.set(diagonal, started)\n          runs.push(started)\n        }\n      }\n    }\n  }\n  return runs\n}\n\nfunction kmerRuns(a: string, b: string) {\n  return [\n    ...forwardKmerRuns(a, b),\n    ...forwardKmerRuns(a, reverseComplement(b)).map(run => ({\n      ...run,\n      ts: b.length - run.te,\n      te: b.length - run.ts,\n      flipped: true,\n    })),\n  ]\n}\n\ntype GapFill = (\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  queryFrom: number,\n  targetFrom: number,\n) => void\n\n// The edits of one chain: each run is a run of `=`, and what lies between two\n// runs goes to `between`. Edits read along the query; the caller reverses a\n// flipped chain's so they read along the target.\nfunction chainEdits(\n  chain: Link[],\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  between: GapFill,\n) {\n  let previous: Run | undefined\n  for (const { run, trim } of chain) {\n    const qs = run.qs + trim\n    if (previous) {\n      const targetFrom = run.flipped ? run.te - trim : previous.te\n      const targetTo = run.flipped ? previous.ts : run.ts + trim\n      const target = b.slice(targetFrom, targetTo)\n      between(\n        a.slice(previous.qe, qs),\n        run.flipped ? reverseComplement(target) : target,\n        edits,\n        previous.qe,\n        targetFrom,\n      )\n    }\n    appendEdit(edits, '=', run.qe - qs)\n    previous = run\n  }\n}\n\n// An insertion and a deletion, which claims no homology\nfunction unaligned(a: string, b: string, edits: PairEdit[]) {\n  appendEdit(edits, 'I', a.length)\n  appendEdit(edits, 'D', b.length)\n}\n\nfunction alignExact(a: string, b: string, edits: PairEdit[]) {\n  if (a.length * b.length <= MAX_ALIGNED_CELLS) {\n    affineAlignment(a, b, edits)\n  } else {\n    unaligned(a, b, edits)\n  }\n}\n\n// The private bases between two runs of one chain, whose orientation the chain\n// has already fixed. Past the cell budget they are seeded on forward k-mers and\n// chained again, recursing into the gaps that chain leaves. It finds no\n// inversions, since the stretch has an orientation already.\nfunction fillGap(a: string, b: string, edits: PairEdit[], depth = 0) {\n  const [chain] =\n    a.length * b.length > MAX_ALIGNED_CELLS && depth < MAX_FILL_DEPTH\n      ? chainRuns(forwardKmerRuns(a, b), Infinity, KMER, kmerJumpCost, 1)\n      : []\n  if (!chain) {\n    alignExact(a, b, edits)\n    return\n  }\n  const deeper = (qa: string, tb: string, into: PairEdit[]) => {\n    fillGap(qa, tb, into, depth + 1)\n  }\n  const first = chain[0]!.run\n  const last = chain.at(-1)!.run\n  deeper(a.slice(0, first.qs), b.slice(0, first.ts), edits)\n  chainEdits(chain, a, b, edits, deeper)\n  deeper(a.slice(last.qe), b.slice(last.te), edits)\n}\n\nfunction fill(a: string, b: string, edits: PairEdit[]) {\n  fillGap(a, b, edits)\n}\n\n// A chain as a record in the coordinates of the two strings it was made on\nfunction recordOf(chain: Link[], a: string, b: string): PairChain {\n  const edits: PairEdit[] = []\n  chainEdits(chain, a, b, edits, fill)\n  const first = chain[0]!\n  const last = chain.at(-1)!\n  const { flipped } = first.run\n  return {\n    queryStart: first.run.qs + first.trim,\n    queryEnd: last.run.qe,\n    targetStart: flipped ? last.run.ts : first.run.ts + first.trim,\n    targetEnd: flipped ? first.run.te - first.trim : last.run.te,\n    strand: flipped ? '-' : '+',\n    edits: flipped ? edits.reverse() : edits,\n    sharedBases: 0,\n  }\n}\n\n// The private bases between two shared nodes. A pair too large for the exact\n// alignment is seeded on shared k-mers in both orientations and chained the\n// way the walks are, which aligns two long copies of one sequence the graph\n// left apart. The best forward chain becomes edits. A flipped chain is an\n// inversion, which no CIGAR holds, so it comes back as a record of its own in\n// the coordinates of a and b. What no chain reaches is an insertion and a\n// deletion, which claims no homology.\nfunction alignPrivate(\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  minMatch: number,\n): PairChain[] {\n  let inversions: PairChain[] = []\n  if (a.length * b.length <= MAX_ALIGNED_CELLS) {\n    affineAlignment(a, b, edits)\n  } else {\n    const chains = chainRuns(\n      kmerRuns(a, b),\n      Infinity,\n      Math.max(minMatch, KMER),\n      kmerJumpCost,\n    )\n    const forward = chains.find(chain => !chain[0]!.run.flipped)\n    inversions = chains\n      .filter(chain => chain[0]!.run.flipped)\n      .map(chain => recordOf(chain, a, b))\n    if (forward) {\n      // The forward record holds no inversion, so an inversion's bases stay\n      // unaligned in it. A gap that hides one is not seeded again: at a tandem\n      // array that finds only a neighbouring copy, matched forward over bases\n      // the inversion's own record already claims.\n      const forwardFill: GapFill = (qa, tb, into, queryFrom, targetFrom) => {\n        const hidesInversion = inversions.some(\n          inversion =>\n            (queryFrom < inversion.queryEnd &&\n              inversion.queryStart < queryFrom + qa.length) ||\n            (targetFrom < inversion.targetEnd &&\n              inversion.targetStart < targetFrom + tb.length),\n        )\n        if (hidesInversion) {\n          alignExact(qa, tb, into)\n        } else {\n          fillGap(qa, tb, into)\n        }\n      }\n      const first = forward[0]!.run\n      const last = forward.at(-1)!.run\n      forwardFill(a.slice(0, first.qs), b.slice(0, first.ts), edits, 0, 0)\n      chainEdits(forward, a, b, edits, forwardFill)\n      forwardFill(a.slice(last.qe), b.slice(last.te), edits, last.qe, last.te)\n    } else {\n      unaligned(a, b, edits)\n    }\n  }\n  return inversions\n}\n\ninterface Claimed extends PairChain {\n  // query stretches on nodes both walks visit\n  shared: Interval[]\n}\n\ntype Side = 'query' | 'target'\n\n// Each edit of a record with the query and target position it sits at. A `-`\n// record's edits read along the target, so its query runs down from queryEnd.\nfunction forEachEdit(\n  r: PairChain,\n  visit: (op: PairOp, len: number, query: number, target: number) => void,\n) {\n  const flipped = r.strand === '-'\n  let qi = 0\n  let ti = 0\n  for (const [op, len] of r.edits) {\n    visit(\n      op,\n      len,\n      flipped ? r.queryEnd - 1 - qi : r.queryStart + qi,\n      r.targetStart + ti,\n    )\n    if (op !== 'D') {\n      qi += len\n    }\n    if (op !== 'I') {\n      ti += len\n    }\n  }\n}\n\n// A record's score under vg's model over [lo, hi) on one side: a column counts\n// where its base on that side does, and a gap where it opens on that side.\nfunction scoreOver(r: PairChain, side: Side, lo: number, hi: number) {\n  const step = side === 'query' && r.strand === '-' ? -1 : 1\n  let score = 0\n  forEachEdit(r, (op, len, query, target) => {\n    const from = side === 'query' ? query : target\n    const inside = (k: number) => {\n      const at = from + step * k\n      return at >= lo && at < hi\n    }\n    if (op === '=' || op === 'X') {\n      for (let k = 0; k < len; k++) {\n        if (inside(k)) {\n          score += op === '=' ? MATCH : MISMATCH\n        }\n      }\n    } else if ((op === 'I') === (side === 'query')) {\n      for (let k = 0; k < len; k++) {\n        if (inside(k)) {\n          score += k === 0 ? GAP_OPEN : GAP_EXTEND\n        }\n      }\n    } else if (inside(0)) {\n      score += GAP_OPEN + (len - 1) * GAP_EXTEND\n    }\n  })\n  return score\n}\n\nfunction spanOf(r: PairChain, side: Side): Interval {\n  return side === 'query'\n    ? [r.queryStart, r.queryEnd]\n    : [r.targetStart, r.targetEnd]\n}\n\n// A record's edits with the aligned columns `lost` marks turned into an\n// insertion and a deletion, and its ends trimmed to the columns it keeps.\nfunction withoutColumns(r: Claimed, lost: Uint8Array): Claimed | undefined {\n  const flipped = r.strand === '-'\n  const edits: PairEdit[] = []\n  let pendingQuery = 0\n  let pendingTarget = 0\n  let column = 0\n  let sharedLost = 0\n  const sharedMask = new Uint8Array(r.queryEnd - r.queryStart)\n  for (const [s, e] of r.shared) {\n    sharedMask.fill(1, s - r.queryStart, e - r.queryStart)\n  }\n  const inShared = (at: number) => sharedMask[at - r.queryStart] === 1\n  const flush = () => {\n    appendEdit(edits, 'I', pendingQuery)\n    appendEdit(edits, 'D', pendingTarget)\n    pendingQuery = 0\n    pendingTarget = 0\n  }\n  forEachEdit(r, (op, len, query) => {\n    if (op === 'I') {\n      pendingQuery += len\n    } else if (op === 'D') {\n      pendingTarget += len\n    } else {\n      for (let k = 0; k < len; k++) {\n        if (lost[column + k]) {\n          pendingQuery += 1\n          pendingTarget += 1\n          if (inShared(flipped ? query - k : query + k)) {\n            sharedLost += 1\n          }\n        } else {\n          if (pendingQuery > 0 || pendingTarget > 0) {\n            flush()\n          }\n          appendEdit(edits, op, 1)\n        }\n      }\n      column += len\n    }\n  })\n  flush()\n  const lead = { I: 0, D: 0 }\n  while (edits[0]?.[0] === 'I' || edits[0]?.[0] === 'D') {\n    const [op, len] = edits.shift()!\n    lead[op as 'I' | 'D'] += len\n  }\n  const tail = { I: 0, D: 0 }\n  while (edits.at(-1)?.[0] === 'I' || edits.at(-1)?.[0] === 'D') {\n    const [op, len] = edits.pop()!\n    tail[op as 'I' | 'D'] += len\n  }\n  return edits.length === 0\n    ? undefined\n    : {\n        ...r,\n        queryStart: r.queryStart + (flipped ? tail.I : lead.I),\n        queryEnd: r.queryEnd - (flipped ? lead.I : tail.I),\n        targetStart: r.targetStart + lead.D,\n        targetEnd: r.targetEnd - tail.D,\n        edits,\n        sharedBases: r.sharedBases - sharedLost,\n      }\n}\n\n// A base aligns in one record at most. Where two records align the same bases\n// on either walk, the one scoring higher over the stretch their spans share\n// keeps them, and the other gives them up as an insertion and a deletion. In a\n// tandem array whose copies run both ways, one query copy aligns forward to one\n// target copy and inverted to another, and both are homology; the scoring\n// decides which one the pair's picture shows. A tie goes to the record with\n// more bases on shared nodes: alignPrivate finds an inversion a walk takes\n// through shared nodes again, base for base, in the gap of the forward record\n// spanning it.\nfunction claimOnce(\n  records: Claimed[],\n  queryLength: number,\n  targetLength: number,\n  minMatch: number,\n) {\n  const claims = {\n    query: new Uint8Array(queryLength),\n    target: new Uint8Array(targetLength),\n  }\n  const columnsOf = records.map(r => {\n    const columns: [number, number][] = []\n    forEachEdit(r, (op, len, query, target) => {\n      if (op === '=' || op === 'X') {\n        for (let k = 0; k < len; k++) {\n          columns.push([r.strand === '-' ? query - k : query + k, target + k])\n        }\n      }\n    })\n    for (const [query, target] of columns) {\n      claims.query[query] = Math.min(255, claims.query[query]! + 1)\n      claims.target[target] = Math.min(255, claims.target[target]! + 1)\n    }\n    return columns\n  })\n  const holders = {\n    query: new Map<number, number[]>(),\n    target: new Map<number, number[]>(),\n  }\n  columnsOf.forEach((columns, i) => {\n    for (const [query, target] of columns) {\n      for (const [side, at] of [\n        ['query', query],\n        ['target', target],\n      ] as const) {\n        if (claims[side][at]! > 1) {\n          const held = holders[side].get(at)\n          if (!held) {\n            holders[side].set(at, [i])\n          } else if (held.at(-1) !== i) {\n            held.push(i)\n          }\n        }\n      }\n    }\n  })\n  const beaten = new Map<string, boolean>()\n  const losesTo = (i: number, j: number, side: Side) => {\n    const key = `${side}:${i}:${j}`\n    let loses = beaten.get(key)\n    if (loses === undefined) {\n      const [si, ei] = spanOf(records[i]!, side)\n      const [sj, ej] = spanOf(records[j]!, side)\n      const lo = Math.max(si, sj)\n      const hi = Math.min(ei, ej)\n      const [mine, theirs] = [records[i]!, records[j]!]\n      const margins = [\n        scoreOver(theirs, side, lo, hi) - scoreOver(mine, side, lo, hi),\n        theirs.sharedBases - mine.sharedBases,\n        i - j,\n      ]\n      loses = margins.find(margin => margin !== 0)! > 0\n      beaten.set(key, loses)\n    }\n    return loses\n  }\n  return records.flatMap((r, i) => {\n    const columns = columnsOf[i]!\n    const lost = new Uint8Array(columns.length)\n    columns.forEach(([query, target], c) => {\n      for (const [side, at] of [\n        ['query', query],\n        ['target', target],\n      ] as const) {\n        if (\n          !lost[c] &&\n          holders[side].get(at)?.some(j => j !== i && losesTo(i, j, side))\n        ) {\n          lost[c] = 1\n        }\n      }\n    })\n    if (!lost.includes(1)) {\n      return [r]\n    }\n    const kept = withoutColumns(r, lost)\n    const matched =\n      kept?.edits.reduce((sum, [op, len]) => sum + (op === '=' ? len : 0), 0) ??\n      0\n    return kept && matched >= minMatch ? [kept] : []\n  })\n}\n\nfunction walkSequence(walk: number[], sequenceOf: (id: number) => string) {\n  return walk\n    .map(handle => {\n      const sequence = sequenceOf(nodeId(handle))\n      return isReverse(handle) ? reverseComplement(sequence) : sequence\n    })\n    .join('')\n}\n\nfunction walkOffsets(walk: number[], sequenceOf: (id: number) => string) {\n  const offsets = [0]\n  for (const handle of walk) {\n    offsets.push(offsets.at(-1)! + sequenceOf(nodeId(handle)).length)\n  }\n  return offsets\n}\n\n// The steps between a walk's first and last visit to any node it visits more\n// than once. Copies of a repeat folded onto one node say nothing about which\n// copy of one haplotype pairs with which copy of the other, and a graph can\n// pair them out of register, so there the bases decide.\nfunction repeatSteps(walk: number[]) {\n  const first = new Map<number, number>()\n  const last = new Map<number, number>()\n  walk.forEach((handle, i) => {\n    const id = nodeId(handle)\n    if (first.has(id)) {\n      last.set(id, i)\n    } else {\n      first.set(id, i)\n    }\n  })\n  const change = new Int32Array(walk.length + 1)\n  for (const [id, end] of last) {\n    change[first.get(id)!]! += 1\n    change[end + 1]! -= 1\n  }\n  const inside = new Uint8Array(walk.length)\n  let depth = 0\n  for (let i = 0; i < walk.length; i++) {\n    depth += change[i]!\n    inside[i] = depth > 0 ? 1 : 0\n  }\n  return inside\n}\n\n// Every stretch of steps the two walks take through the same nodes, in the\n// same order or the opposite one, outside both walks' repeats.\nfunction sharedRuns(\n  query: number[],\n  target: number[],\n  queryOffsets: number[],\n  targetOffsets: number[],\n) {\n  const queryRepeat = repeatSteps(query)\n  const targetRepeat = repeatSteps(target)\n  const visits = new Map<number, number[]>()\n  target.forEach((handle, rank) => {\n    if (!targetRepeat[rank]) {\n      visits.set(nodeId(handle), [rank])\n    }\n  })\n  const width = 2 * target.length\n  const key = (i: number, rank: number, flipped: boolean) =>\n    i * width + 2 * rank + (flipped ? 1 : 0)\n  const seeds = new Set<number>()\n  query.forEach((handle, i) => {\n    for (const rank of queryRepeat[i]\n      ? []\n      : (visits.get(nodeId(handle)) ?? [])) {\n      seeds.add(key(i, rank, isReverse(handle) !== isReverse(target[rank]!)))\n    }\n  })\n  const runs: Run[] = []\n  query.forEach((handle, i) => {\n    for (const rank of queryRepeat[i]\n      ? []\n      : (visits.get(nodeId(handle)) ?? [])) {\n      const flipped = isReverse(handle) !== isReverse(target[rank]!)\n      const step = flipped ? -1 : 1\n      const previous = rank - step\n      const continues =\n        i > 0 &&\n        previous >= 0 &&\n        previous < target.length &&\n        seeds.has(key(i - 1, previous, flipped))\n      if (!continues) {\n        let j = i\n        let r = rank\n        while (\n          j < query.length &&\n          r >= 0 &&\n          r < target.length &&\n          seeds.has(key(j, r, flipped))\n        ) {\n          j += 1\n          r += step\n        }\n        const lastRank = r - step\n        runs.push({\n          qs: queryOffsets[i]!,\n          qe: queryOffsets[j]!,\n          ts: targetOffsets[Math.min(rank, lastRank)]!,\n          te: targetOffsets[Math.max(rank, lastRank) + 1]!,\n          flipped,\n        })\n      }\n    }\n  })\n  return runs\n}\n\n// A query walk's alignments to a target walk. A stretch of nodes both walks\n// visit is a run of `=`, a record is the best collinear chain of those\n// stretches, and what lies between two of them is aligned base by base under\n// vg's scoring, an inversion there coming back as a record of its own. With\n// bases false it is an insertion and a deletion instead. A chain pays for the\n// gap it spans, so by default nothing bounds how far it reaches but the window;\n// maxGap caps that to bound the work. A record matching under minMatch bases is\n// dropped. Coordinates count from each walk's first base; a `-` record's edits\n// read along the target, the way minimap2 writes a reverse-strand row.\nexport function pairAlignments(opts: PairOptions): PairChain[] {\n  const { query, target, sequenceOf } = opts\n  const a = walkSequence(query, sequenceOf)\n  const b = walkSequence(target, sequenceOf)\n  const runs = sharedRuns(\n    query,\n    target,\n    walkOffsets(query, sequenceOf),\n    walkOffsets(target, sequenceOf),\n  )\n  const minMatch = opts.minMatch ?? DEFAULT_MIN_MATCH\n  const bases = opts.bases ?? true\n  const records: Claimed[] = []\n  for (const chain of chainRuns(\n    runs,\n    opts.maxGap ?? Infinity,\n    minMatch,\n    stepJumpCost,\n  )) {\n    const edits: PairEdit[] = []\n    const first = chain[0]!\n    const last = chain.at(-1)!\n    const { flipped } = first.run\n    const alignBetween: GapFill = (qa, tb, into, queryFrom, targetFrom) => {\n      for (const inversion of alignPrivate(qa, tb, into, minMatch)) {\n        const targetTo = targetFrom + tb.length\n        records.push({\n          ...inversion,\n          queryStart: queryFrom + inversion.queryStart,\n          queryEnd: queryFrom + inversion.queryEnd,\n          targetStart: flipped\n            ? targetTo - inversion.targetEnd\n            : targetFrom + inversion.targetStart,\n          targetEnd: flipped\n            ? targetTo - inversion.targetStart\n            : targetFrom + inversion.targetEnd,\n          strand: flipped ? '+' : '-',\n          edits: flipped ? inversion.edits.reverse() : inversion.edits,\n          shared: [],\n        })\n      }\n    }\n    chainEdits(chain, a, b, edits, bases ? alignBetween : unaligned)\n    records.push({\n      queryStart: first.run.qs + first.trim,\n      queryEnd: last.run.qe,\n      targetStart: flipped ? last.run.ts : first.run.ts + first.trim,\n      targetEnd: flipped ? first.run.te - first.trim : last.run.te,\n      strand: flipped ? '-' : '+',\n      edits: flipped ? edits.reverse() : edits,\n      sharedBases: chain.reduce(\n        (sum, { run, trim }) => sum + run.qe - run.qs - trim,\n        0,\n      ),\n      shared: chain.map(({ run, trim }) => [run.qs + trim, run.qe]),\n    })\n  }\n  return claimOnce(records, a.length, b.length, minMatch)\n    .map(({ shared: _, ...record }) => record)\n    .sort((x, y) => x.queryStart - y.queryStart)\n}\n\nexport function pairCigar(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n"],
-  "mappings": 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-  "names": ["encodeNode", "id", "orientation", "nodeId", "handle", "nodeOrientation", "isReverse", "flipNode", "flipSide", "side", "entrySide", "exitSide", "entryOrientation", "exitOrientation", "edgeIsCanonical", "from", "to", "fromId", "toId", "pathIsCanonical", "path", "pathEndsAreCanonical", "first", "last", "DECODE", "encodedSequenceLength", "encoded", "last", "value", "inLast", "i", "decodeSequence", "result", "byte", "base", "COMPLEMENT", "reverseComplement", "sequence", "lowerBound", "ascending", "value", "lo", "hi", "mid", "ColumnMax", "columns", "column", "best", "p", "candidate", "holder", "SparseLcs", "a", "b", "weight", "x", "j", "list", "a0", "a1", "b0", "b1", "prefix", "suffix", "k", "i", "matches", "split", "count", "from", "to", "step", "trace", "w", "before", "match", "last", "chained", "width", "after", "s", "combined", "weightedLcs", "lcs", "DEFAULT_MIN_MATCH", "MAX_ALIGNED_CELLS", "CHAIN_LOOKBACK", "KMER", "MAX_KMER_OCCURRENCES", "MAX_FILL_DEPTH", "MATCH", "MISMATCH", "GAP_OPEN", "GAP_EXTEND", "UNREACHABLE", "DIAGONAL", "INSERTION", "DELETION", "appendEdit", "edits", "op", "len", "last", "best", "diagonal", "insertion", "deletion", "affineAlignment", "a", "b", "la", "lb", "width", "trace", "j", "i", "nextDiagonal", "nextInsertion", "nextDeletion", "ai", "fromDiagonal", "fromInsertion", "fromDeletion", "ops", "state", "from", "stepJumpCost", "dq", "dt", "indel", "kmerJumpCost", "sliceRun", "run", "to", "untakenPieces", "query", "target", "blocked", "s", "e", "lo", "hi", "x", "y", "pieces", "chainRuns", "runs", "maxGap", "minMatch", "jumpCost", "maxChains", "chains", "basesTaken", "spanTaken", "pool", "score", "back", "trims", "trim", "candidate", "matched", "end", "chain", "first", "flipped", "spans", "same", "forwardKmerRuns", "index", "p", "kmer", "seen", "open", "hits", "started", "kmerRuns", "reverseComplement", "chainEdits", "between", "previous", "qs", "targetFrom", "targetTo", "unaligned", "alignExact", "fillGap", "depth", "deeper", "qa", "tb", "into", "fill", "recordOf", "alignPrivate", "inversions", "forward", "forwardFill", "queryFrom", "inversion", "forEachEdit", "r", "visit", "qi", "ti", "scoreOver", "side", "step", "inside", "k", "at", "spanOf", "withoutColumns", "lost", "pendingQuery", "pendingTarget", "column", "sharedLost", "sharedMask", "inShared", "flush", "lead", "tail", "claimOnce", "records", "queryLength", "targetLength", "claims", "columnsOf", "columns", "holders", "held", "beaten", "losesTo", "key", "loses", "si", "ei", "sj", "ej", "mine", "theirs", "margin", "c", "kept", "sum", "walkSequence", "walk", "sequenceOf", "handle", "sequence", "nodeId", "isReverse", "walkOffsets", "offsets", "repeatSteps", "id", "change", "sharedRuns", "queryOffsets", "targetOffsets", "queryRepeat", "targetRepeat", "visits", "rank", "seeds", "lastRank", "pairAlignments", "opts", "bases", "_", "record", "pairCigar"]
+  "sources": ["../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/gbwt/node.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/gbwt/sequence.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/lcs.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.4.1/node_modules/@gmod/gbz-base/src/pairAlignment.ts", "../../src/nodeLimitError.ts"],
+  "sourcesContent": ["export const ENDMARKER = 0\n\nexport type Orientation = 'forward' | 'reverse'\n\nexport function encodeNode(id: number, orientation: Orientation) {\n  return 2 * id + (orientation === 'reverse' ? 1 : 0)\n}\n\nexport function nodeId(handle: number) {\n  return Math.floor(handle / 2)\n}\n\nexport function nodeOrientation(handle: number): Orientation {\n  return handle % 2 === 0 ? 'forward' : 'reverse'\n}\n\nexport function isReverse(handle: number) {\n  return handle % 2 === 1\n}\n\nexport function flipNode(handle: number) {\n  return handle % 2 === 0 ? handle + 1 : handle - 1\n}\n\nexport type NodeSide = 'left' | 'right'\n\nexport function flipSide(side: NodeSide): NodeSide {\n  return side === 'left' ? 'right' : 'left'\n}\n\nexport function entrySide(orientation: Orientation): NodeSide {\n  return orientation === 'forward' ? 'left' : 'right'\n}\n\nexport function exitSide(orientation: Orientation): NodeSide {\n  return orientation === 'forward' ? 'right' : 'left'\n}\n\nexport function entryOrientation(side: NodeSide): Orientation {\n  return side === 'left' ? 'forward' : 'reverse'\n}\n\nexport function exitOrientation(side: NodeSide): Orientation {\n  return side === 'right' ? 'forward' : 'reverse'\n}\n\nexport function edgeIsCanonical(from: number, to: number) {\n  const fromId = nodeId(from)\n  const toId = nodeId(to)\n  return isReverse(from)\n    ? toId > fromId || (toId === fromId && !isReverse(to))\n    : toId >= fromId\n}\n\nexport function pathIsCanonical(path: number[]) {\n  return pathEndsAreCanonical(path[0], path[path.length - 1])\n}\n\nexport function pathEndsAreCanonical(\n  first: number | undefined,\n  last: number | undefined,\n) {\n  if (first === undefined || last === undefined) {\n    return true\n  }\n  return isReverse(first) === isReverse(last)\n    ? !isReverse(first)\n    : edgeIsCanonical(first, last)\n}\n", "const DECODE = ['', 'A', 'C', 'G', 'T', 'N']\n\nexport function encodedSequenceLength(encoded: Uint8Array) {\n  const last = encoded[encoded.length - 1]\n  if (last === undefined) {\n    return 0\n  }\n  let value = last\n  let inLast = 0\n  for (let i = 0; i < 3; i++) {\n    if (value % 6 === 0) {\n      break\n    }\n    value = Math.floor(value / 6)\n    inLast += 1\n  }\n  return 3 * (encoded.length - 1) + inLast\n}\n\nexport function decodeSequence(encoded: Uint8Array) {\n  let result = ''\n  for (const byte of encoded) {\n    let value = byte\n    for (let i = 0; i < 3; i++) {\n      const base = DECODE[value % 6]!\n      if (base === '') {\n        return result\n      }\n      value = Math.floor(value / 6)\n      result += base\n    }\n  }\n  return result\n}\n\nconst COMPLEMENT: Record<string, string> = {\n  A: 'T',\n  C: 'G',\n  G: 'C',\n  T: 'A',\n  N: 'N',\n}\n\nexport function reverseComplement(sequence: string) {\n  let result = ''\n  for (let i = sequence.length - 1; i >= 0; i--) {\n    result += COMPLEMENT[sequence[i]!] ?? 'N'\n  }\n  return result\n}\n", "type Weight = (x: number) => number\n\nfunction lowerBound(ascending: number[], value: number) {\n  let lo = 0\n  let hi = ascending.length\n  while (lo < hi) {\n    const mid = (lo + hi) >> 1\n    if (ascending[mid]! < value) {\n      lo = mid + 1\n    } else {\n      hi = mid\n    }\n  }\n  return lo\n}\n\nclass ColumnMax {\n  readonly ending: Float64Array\n  private readonly tree: Int32Array\n\n  constructor(columns: number) {\n    this.ending = new Float64Array(columns)\n    this.tree = new Int32Array(columns + 1).fill(-1)\n  }\n\n  bestBefore(column: number) {\n    let best = -1\n    for (let p = column; p > 0; p -= p & -p) {\n      const candidate = this.tree[p]!\n      if (\n        candidate !== -1 &&\n        (best === -1 || this.ending[candidate]! > this.ending[best]!)\n      ) {\n        best = candidate\n      }\n    }\n    return best\n  }\n\n  raise(column: number, value: number) {\n    this.ending[column] = value\n    for (let p = column + 1; p < this.tree.length; p += p & -p) {\n      const holder = this.tree[p]!\n      if (holder === -1 || value > this.ending[holder]!) {\n        this.tree[p] = column\n      }\n    }\n  }\n}\n\ninterface Trace {\n  row: Int32Array\n  column: Int32Array\n  previous: Int32Array\n  endingMatch: Int32Array\n  count: number\n}\n\nclass SparseLcs {\n  readonly pairs: [number, number][] = []\n  total = 0\n  private readonly a: number[]\n  private readonly b: number[]\n  private readonly weight: Weight\n  private readonly occurrences = new Map<number, number[]>()\n\n  constructor(a: number[], b: number[], weight: Weight) {\n    this.a = a\n    this.b = b\n    this.weight = weight\n    b.forEach((x, j) => {\n      const list = this.occurrences.get(x)\n      if (list) {\n        list.push(j)\n      } else {\n        this.occurrences.set(x, [j])\n      }\n    })\n  }\n\n  solve(a0: number, a1: number, b0: number, b1: number) {\n    let prefix = 0\n    while (\n      a0 + prefix < a1 &&\n      b0 + prefix < b1 &&\n      this.a[a0 + prefix] === this.b[b0 + prefix]\n    ) {\n      this.match(a0 + prefix, b0 + prefix)\n      prefix += 1\n    }\n    let suffix = 0\n    while (\n      a1 - suffix > a0 + prefix &&\n      b1 - suffix > b0 + prefix &&\n      this.a[a1 - suffix - 1] === this.b[b1 - suffix - 1]\n    ) {\n      suffix += 1\n    }\n    this.solveMiddle(a0 + prefix, a1 - suffix, b0 + prefix, b1 - suffix)\n    for (let k = suffix; k > 0; k--) {\n      this.match(a1 - k, b1 - k)\n    }\n  }\n\n  private match(i: number, j: number) {\n    this.pairs.push([i, j])\n    this.total += this.weight(this.a[i]!)\n  }\n\n  private solveMiddle(a0: number, a1: number, b0: number, b1: number) {\n    if (a0 === a1 || b0 === b1) {\n      return\n    }\n    const matches = this.matchCount(a0, a1, b0, b1)\n    if (matches === 0) {\n      return\n    }\n    if (matches <= a1 - a0 + (b1 - b0)) {\n      this.chain(a0, a1, b0, b1, matches)\n      return\n    }\n    const mid = (a0 + a1) >> 1\n    const split = this.split(a0, mid, a1, b0, b1)\n    this.solve(a0, mid, b0, split)\n    this.solve(mid, a1, split, b1)\n  }\n\n  private matchCount(a0: number, a1: number, b0: number, b1: number) {\n    let count = 0\n    for (let i = a0; i < a1; i++) {\n      const list = this.occurrences.get(this.a[i]!)\n      if (list) {\n        count += lowerBound(list, b1) - lowerBound(list, b0)\n      }\n    }\n    return count\n  }\n\n  private sweep(\n    from: number,\n    to: number,\n    step: 1 | -1,\n    b0: number,\n    b1: number,\n    columns: ColumnMax,\n    trace?: Trace,\n  ) {\n    for (let i = from; i !== to; i += step) {\n      const list = this.occurrences.get(this.a[i]!)\n      if (!list) {\n        continue\n      }\n      const w = this.weight(this.a[i]!)\n      const lo = lowerBound(list, b0)\n      const hi = lowerBound(list, b1)\n      for (let k = 0; k < hi - lo; k++) {\n        const column =\n          step === 1 ? list[hi - 1 - k]! - b0 : b1 - 1 - list[lo + k]!\n        const before = columns.bestBefore(column)\n        const value = (before === -1 ? 0 : columns.ending[before]!) + w\n        if (value > columns.ending[column]!) {\n          columns.raise(column, value)\n          if (trace) {\n            const match = trace.count++\n            trace.row[match] = i\n            trace.column[match] = column\n            trace.previous[match] =\n              before === -1 ? -1 : trace.endingMatch[before]!\n            trace.endingMatch[column] = match\n          }\n        }\n      }\n    }\n  }\n\n  private chain(\n    a0: number,\n    a1: number,\n    b0: number,\n    b1: number,\n    matches: number,\n  ) {\n    const columns = new ColumnMax(b1 - b0)\n    const trace: Trace = {\n      row: new Int32Array(matches),\n      column: new Int32Array(matches),\n      previous: new Int32Array(matches),\n      endingMatch: new Int32Array(b1 - b0),\n      count: 0,\n    }\n    this.sweep(a0, a1, 1, b0, b1, columns, trace)\n    const last = columns.bestBefore(b1 - b0)\n    if (last === -1) {\n      return\n    }\n    this.total += columns.ending[last]!\n    const chained: [number, number][] = []\n    for (\n      let match = trace.endingMatch[last]!;\n      match !== -1;\n      match = trace.previous[match]!\n    ) {\n      chained.push([trace.row[match]!, b0 + trace.column[match]!])\n    }\n    for (let k = chained.length - 1; k >= 0; k--) {\n      this.pairs.push(chained[k]!)\n    }\n  }\n\n  private frontier(\n    from: number,\n    to: number,\n    step: 1 | -1,\n    b0: number,\n    b1: number,\n  ) {\n    const columns = new ColumnMax(b1 - b0)\n    this.sweep(from, to, step, b0, b1, columns)\n    const best = new Float64Array(b1 - b0 + 1)\n    for (let column = 0; column < b1 - b0; column++) {\n      best[column + 1] = Math.max(best[column]!, columns.ending[column]!)\n    }\n    return best\n  }\n\n  private split(a0: number, mid: number, a1: number, b0: number, b1: number) {\n    const width = b1 - b0\n    const before = this.frontier(a0, mid, 1, b0, b1)\n    const after = this.frontier(a1 - 1, mid - 1, -1, b0, b1)\n    let split = 0\n    let best = -1\n    for (let s = 0; s <= width; s++) {\n      const combined = before[s]! + after[width - s]!\n      if (combined > best) {\n        best = combined\n        split = s\n      }\n    }\n    return b0 + split\n  }\n}\n\nexport function weightedLcs(\n  a: number[],\n  b: number[],\n  weight: Weight,\n): [pairs: [number, number][], weight: number] {\n  const lcs = new SparseLcs(a, b, weight)\n  lcs.solve(0, a.length, 0, b.length)\n  return [lcs.pairs, lcs.total]\n}\n", "import { isReverse, nodeId } from './gbwt/node.ts'\nimport { reverseComplement } from './gbwt/sequence.ts'\n\nexport type PairOp = '=' | 'X' | 'I' | 'D'\nexport type PairEdit = [PairOp, number]\n\nexport interface PairChain {\n  queryStart: number\n  queryEnd: number\n  targetStart: number\n  targetEnd: number\n  strand: '+' | '-'\n  edits: PairEdit[]\n  // bases on nodes both walks visit; the other `=` came from comparing bases\n  sharedBases: number\n}\n\nexport interface PairOptions {\n  query: number[]\n  target: number[]\n  sequenceOf: (id: number) => string\n  maxGap?: number | undefined\n  minMatch?: number | undefined\n  bases?: boolean | undefined\n}\n\n// An exact match: query [qs, qe) against target [ts, te), the target read\n// backwards when flipped.\ninterface Run {\n  qs: number\n  qe: number\n  ts: number\n  te: number\n  flipped: boolean\n}\n\nconst DEFAULT_MIN_MATCH = 100\nconst MAX_ALIGNED_CELLS = 4_000_000\nconst CHAIN_LOOKBACK = 5000\nconst KMER = 15\nconst MAX_KMER_OCCURRENCES = 64\n// each level's gaps lie strictly inside the last, so this only bounds the work\nconst MAX_FILL_DEPTH = 8\n\n// vg's scoring, the model the reference CIGARs in subgraph.ts are scored by\nconst MATCH = 1\nconst MISMATCH = -4\nconst GAP_OPEN = -6\nconst GAP_EXTEND = -1\nconst UNREACHABLE = -(2 ** 30)\n\nconst DIAGONAL = 0\nconst INSERTION = 1\nconst DELETION = 2\n\nfunction appendEdit(edits: PairEdit[], op: PairOp, 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\nfunction best(diagonal: number, insertion: number, deletion: number) {\n  return diagonal >= deletion && diagonal >= insertion\n    ? DIAGONAL\n    : deletion >= insertion\n      ? DELETION\n      : INSERTION\n}\n\n// The highest-scoring global alignment of a on b under affine gaps. Each cell\n// of `trace` packs, two bits apiece, the state each of the three states came\n// from. A tie goes to the diagonal, then to the deletion, so two stretches\n// with nothing in common read as an insertion followed by a deletion.\nfunction affineAlignment(a: string, b: string, edits: PairEdit[]) {\n  const la = a.length\n  const lb = b.length\n  const width = lb + 1\n  const trace = new Uint8Array((la + 1) * width)\n  let diagonal = new Int32Array(width).fill(UNREACHABLE)\n  let insertion = new Int32Array(width).fill(UNREACHABLE)\n  let deletion = new Int32Array(width).fill(UNREACHABLE)\n  diagonal[0] = 0\n  for (let j = 1; j <= lb; j++) {\n    deletion[j] = GAP_OPEN + (j - 1) * GAP_EXTEND\n    trace[j] = (j === 1 ? DIAGONAL : DELETION) << 4\n  }\n  for (let i = 1; i <= la; i++) {\n    const nextDiagonal = new Int32Array(width).fill(UNREACHABLE)\n    const nextInsertion = new Int32Array(width).fill(UNREACHABLE)\n    const nextDeletion = new Int32Array(width).fill(UNREACHABLE)\n    nextInsertion[0] = GAP_OPEN + (i - 1) * GAP_EXTEND\n    trace[i * width] = (i === 1 ? DIAGONAL : INSERTION) << 2\n    const ai = a.charCodeAt(i - 1)\n    for (let j = 1; j <= lb; j++) {\n      const fromDiagonal = best(\n        diagonal[j - 1]!,\n        insertion[j - 1]!,\n        deletion[j - 1]!,\n      )\n      nextDiagonal[j] =\n        Math.max(diagonal[j - 1]!, insertion[j - 1]!, deletion[j - 1]!) +\n        (ai === b.charCodeAt(j - 1) ? MATCH : MISMATCH)\n      const fromInsertion = best(\n        diagonal[j]! + GAP_OPEN,\n        insertion[j]! + GAP_EXTEND,\n        deletion[j]! + GAP_OPEN,\n      )\n      nextInsertion[j] = Math.max(\n        diagonal[j]! + GAP_OPEN,\n        insertion[j]! + GAP_EXTEND,\n        deletion[j]! + GAP_OPEN,\n      )\n      const fromDeletion = best(\n        nextDiagonal[j - 1]! + GAP_OPEN,\n        nextInsertion[j - 1]! + GAP_OPEN,\n        nextDeletion[j - 1]! + GAP_EXTEND,\n      )\n      nextDeletion[j] = Math.max(\n        nextDiagonal[j - 1]! + GAP_OPEN,\n        nextInsertion[j - 1]! + GAP_OPEN,\n        nextDeletion[j - 1]! + GAP_EXTEND,\n      )\n      trace[i * width + j] =\n        fromDiagonal | (fromInsertion << 2) | (fromDeletion << 4)\n    }\n    diagonal = nextDiagonal\n    insertion = nextInsertion\n    deletion = nextDeletion\n  }\n  const ops: PairOp[] = []\n  let i = la\n  let j = lb\n  let state = best(diagonal[lb]!, insertion[lb]!, deletion[lb]!)\n  while (i > 0 || j > 0) {\n    const from = (trace[i * width + j]! >> (2 * state)) & 3\n    if (state === DIAGONAL) {\n      ops.push(a[i - 1] === b[j - 1] ? '=' : 'X')\n      i -= 1\n      j -= 1\n    } else if (state === INSERTION) {\n      ops.push('I')\n      i -= 1\n    } else {\n      ops.push('D')\n      j -= 1\n    }\n    state = from\n  }\n  for (const op of ops.reverse()) {\n    appendEdit(edits, op, 1)\n  }\n}\n\n// What a chain of walk steps pays to go from one run to the next over dq\n// private query bases and dt target ones. Those runs lie outside both walks'\n// repeats, so each has one place to go and the cost only has to let a chain\n// hold through a structural variant of any size: vg's charge for a short\n// indel, growing with the logarithm past it.\nfunction stepJumpCost(dq: number, dt: number) {\n  const indel = Math.abs(dq - dt)\n  const indelCost =\n    indel === 0\n      ? 0\n      : Math.min(\n          -GAP_OPEN - (indel - 1) * GAP_EXTEND,\n          -GAP_OPEN + 10 * Math.log2(indel),\n        )\n  return indelCost + (Math.min(dq, dt) > 0 ? -MISMATCH : 0)\n}\n\n// What a chain of k-mer matches pays, which is minimap2's gap cost. Inside a\n// tandem array every copy offers a match, and the term that grows with the\n// indel is what keeps a chain in one register instead of hopping between\n// copies for a slightly longer match.\nfunction kmerJumpCost(dq: number, dt: number) {\n  const indel = Math.abs(dq - dt)\n  return indel === 0 ? 0 : 0.01 * KMER * indel + 0.5 * Math.log2(indel)\n}\n\ntype JumpCost = (dq: number, dt: number) => number\n\ninterface Link {\n  run: Run\n  trim: number\n}\n\ntype Interval = [number, number]\n\n// The stretch of a run from offset `from` to `to` along it\nfunction sliceRun(run: Run, from: number, to: number): Run {\n  return {\n    qs: run.qs + from,\n    qe: run.qs + to,\n    ts: run.flipped ? run.te - to : run.ts + from,\n    te: run.flipped ? run.te - from : run.ts + to,\n    flipped: run.flipped,\n  }\n}\n\n// What is left of a run once taken bases are cut out of it, as the pieces a\n// k-mer long or more. An exact match divides at any base, so a flank that runs\n// one base into an inversion by chance costs the inversion one base, not all\n// of it.\nfunction untakenPieces(run: Run, query: Interval[], target: Interval[]) {\n  const len = run.qe - run.qs\n  const blocked: Interval[] = []\n  for (const [s, e] of query) {\n    const lo = Math.max(0, s - run.qs)\n    const hi = Math.min(len, e - run.qs)\n    if (lo < hi) {\n      blocked.push([lo, hi])\n    }\n  }\n  for (const [s, e] of target) {\n    const lo = Math.max(0, run.flipped ? run.te - e : s - run.ts)\n    const hi = Math.min(len, run.flipped ? run.te - s : e - run.ts)\n    if (lo < hi) {\n      blocked.push([lo, hi])\n    }\n  }\n  if (blocked.length === 0) {\n    return [run]\n  }\n  blocked.sort((x, y) => x[0] - y[0])\n  const pieces: Run[] = []\n  let from = 0\n  for (const [lo, hi] of blocked) {\n    if (lo - from >= KMER) {\n      pieces.push(sliceRun(run, from, lo))\n    }\n    from = Math.max(from, hi)\n  }\n  if (len - from >= KMER) {\n    pieces.push(sliceRun(run, from, len))\n  }\n  return pieces\n}\n\n// The best-scoring collinear chain of runs matching minMatch bases or more,\n// then the best over the runs that overlap no accepted run on either sequence,\n// and so on: a second copy of a repeat finds its target taken and an inversion\n// finds its target free. A run that overlaps its predecessor is trimmed from\n// the front, which an exact match allows at any base.\nfunction chainRuns(\n  runs: Run[],\n  maxGap: number,\n  minMatch: number,\n  jumpCost: JumpCost,\n  maxChains = Infinity,\n) {\n  const chains: Link[][] = []\n  const basesTaken = { query: [] as Interval[], target: [] as Interval[] }\n  const spanTaken = {\n    forward: { query: [] as Interval[], target: [] as Interval[] },\n    flipped: { query: [] as Interval[], target: [] as Interval[] },\n  }\n  let pool = [...runs].sort((a, b) => a.qs - b.qs || a.ts - b.ts)\n  while (pool.length > 0 && chains.length < maxChains) {\n    const score = pool.map(run => run.qe - run.qs)\n    const back = new Int32Array(pool.length).fill(-1)\n    const trims = new Int32Array(pool.length)\n    for (let j = 0; j < pool.length; j++) {\n      const b = pool[j]!\n      const len = b.qe - b.qs\n      for (let i = j - 1; i >= Math.max(0, j - CHAIN_LOOKBACK); i--) {\n        if (score[i]! + len <= score[j]!) {\n          continue\n        }\n        const a = pool[i]!\n        const advances =\n          a.flipped === b.flipped &&\n          a.qs < b.qs &&\n          (b.flipped ? b.te < a.te : a.ts < b.ts)\n        if (advances) {\n          const trim = Math.max(\n            0,\n            a.qe - b.qs,\n            b.flipped ? b.te - a.ts : a.te - b.ts,\n          )\n          const dq = b.qs + trim - a.qe\n          const dt = b.flipped ? a.ts - (b.te - trim) : b.ts + trim - a.te\n          if (trim < len && dq <= maxGap && dt <= maxGap) {\n            const candidate = score[i]! + len - trim - jumpCost(dq, dt)\n            if (candidate > score[j]!) {\n              score[j] = candidate\n              back[j] = i\n              trims[j] = trim\n            }\n          }\n        }\n      }\n    }\n    const matched = new Int32Array(pool.length)\n    let end = -1\n    for (let j = 0; j < pool.length; j++) {\n      const run = pool[j]!\n      matched[j] = (matched[back[j]!] ?? 0) + run.qe - run.qs - trims[j]!\n      if (matched[j]! >= minMatch && (end < 0 || score[j]! > score[end]!)) {\n        end = j\n      }\n    }\n    if (end < 0) {\n      break\n    }\n    const chain: Link[] = []\n    for (let j = end; j >= 0; j = back[j]!) {\n      chain.push({ run: pool[j]!, trim: trims[j]! })\n    }\n    chain.reverse()\n    chains.push(chain)\n    // A record's CIGAR accounts for every base between its ends in its own\n    // orientation, so a later chain of that orientation may not nest in its\n    // gaps: taking only the runs let one re-claim an earlier record's bases on\n    // a paralog. An inversion is what a forward CIGAR cannot account for, so\n    // across orientations only the bases themselves are taken.\n    const first = chain[0]!\n    const last = chain.at(-1)!\n    const { flipped } = first.run\n    const spans = flipped ? spanTaken.flipped : spanTaken.forward\n    spans.query.push([first.run.qs + first.trim, last.run.qe])\n    spans.target.push(\n      flipped\n        ? [last.run.ts, first.run.te - first.trim]\n        : [first.run.ts + first.trim, last.run.te],\n    )\n    for (const { run, trim } of chain) {\n      basesTaken.query.push([run.qs + trim, run.qe])\n      basesTaken.target.push(\n        run.flipped ? [run.ts, run.te - trim] : [run.ts + trim, run.te],\n      )\n    }\n    pool = pool\n      .flatMap(run => {\n        const same = run.flipped ? spanTaken.flipped : spanTaken.forward\n        return untakenPieces(\n          run,\n          [...basesTaken.query, ...same.query],\n          [...basesTaken.target, ...same.target],\n        )\n      })\n      .sort((x, y) => x.qs - y.qs || x.ts - y.ts)\n  }\n  return chains\n}\n\n// Exact matches of KMER bases or more between a and b, as runs along a\n// diagonal. A k-mer the target holds many times over seeds nothing.\nfunction forwardKmerRuns(a: string, b: string) {\n  const index = new Map<string, number[]>()\n  for (let p = 0; p + KMER <= b.length; p++) {\n    const kmer = b.slice(p, p + KMER)\n    const seen = index.get(kmer)\n    if (seen) {\n      seen.push(p)\n    } else {\n      index.set(kmer, [p])\n    }\n  }\n  const runs: Run[] = []\n  const open = new Map<number, Run>()\n  for (let i = 0; i + KMER <= a.length; i++) {\n    const hits = index.get(a.slice(i, i + KMER))\n    if (hits && hits.length <= MAX_KMER_OCCURRENCES) {\n      for (const p of hits) {\n        const diagonal = p - i\n        const run = open.get(diagonal)\n        if (run && i <= run.qe) {\n          run.qe = i + KMER\n          run.te = p + KMER\n        } else {\n          const started = {\n            qs: i,\n            qe: i + KMER,\n            ts: p,\n            te: p + KMER,\n            flipped: false,\n          }\n          open.set(diagonal, started)\n          runs.push(started)\n        }\n      }\n    }\n  }\n  return runs\n}\n\nfunction kmerRuns(a: string, b: string) {\n  return [\n    ...forwardKmerRuns(a, b),\n    ...forwardKmerRuns(a, reverseComplement(b)).map(run => ({\n      ...run,\n      ts: b.length - run.te,\n      te: b.length - run.ts,\n      flipped: true,\n    })),\n  ]\n}\n\ntype GapFill = (\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  queryFrom: number,\n  targetFrom: number,\n) => void\n\n// The edits of one chain: each run is a run of `=`, and what lies between two\n// runs goes to `between`. Edits read along the query; the caller reverses a\n// flipped chain's so they read along the target.\nfunction chainEdits(\n  chain: Link[],\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  between: GapFill,\n) {\n  let previous: Run | undefined\n  for (const { run, trim } of chain) {\n    const qs = run.qs + trim\n    if (previous) {\n      const targetFrom = run.flipped ? run.te - trim : previous.te\n      const targetTo = run.flipped ? previous.ts : run.ts + trim\n      const target = b.slice(targetFrom, targetTo)\n      between(\n        a.slice(previous.qe, qs),\n        run.flipped ? reverseComplement(target) : target,\n        edits,\n        previous.qe,\n        targetFrom,\n      )\n    }\n    appendEdit(edits, '=', run.qe - qs)\n    previous = run\n  }\n}\n\n// An insertion and a deletion, which claims no homology\nfunction unaligned(a: string, b: string, edits: PairEdit[]) {\n  appendEdit(edits, 'I', a.length)\n  appendEdit(edits, 'D', b.length)\n}\n\nfunction alignExact(a: string, b: string, edits: PairEdit[]) {\n  if (a.length * b.length <= MAX_ALIGNED_CELLS) {\n    affineAlignment(a, b, edits)\n  } else {\n    unaligned(a, b, edits)\n  }\n}\n\n// The private bases between two runs of one chain, whose orientation the chain\n// has already fixed. Past the cell budget they are seeded on forward k-mers and\n// chained again, recursing into the gaps that chain leaves. It finds no\n// inversions, since the stretch has an orientation already.\nfunction fillGap(a: string, b: string, edits: PairEdit[], depth = 0) {\n  const [chain] =\n    a.length * b.length > MAX_ALIGNED_CELLS && depth < MAX_FILL_DEPTH\n      ? chainRuns(forwardKmerRuns(a, b), Infinity, KMER, kmerJumpCost, 1)\n      : []\n  if (!chain) {\n    alignExact(a, b, edits)\n    return\n  }\n  const deeper = (qa: string, tb: string, into: PairEdit[]) => {\n    fillGap(qa, tb, into, depth + 1)\n  }\n  const first = chain[0]!.run\n  const last = chain.at(-1)!.run\n  deeper(a.slice(0, first.qs), b.slice(0, first.ts), edits)\n  chainEdits(chain, a, b, edits, deeper)\n  deeper(a.slice(last.qe), b.slice(last.te), edits)\n}\n\nfunction fill(a: string, b: string, edits: PairEdit[]) {\n  fillGap(a, b, edits)\n}\n\n// A chain as a record in the coordinates of the two strings it was made on\nfunction recordOf(chain: Link[], a: string, b: string): PairChain {\n  const edits: PairEdit[] = []\n  chainEdits(chain, a, b, edits, fill)\n  const first = chain[0]!\n  const last = chain.at(-1)!\n  const { flipped } = first.run\n  return {\n    queryStart: first.run.qs + first.trim,\n    queryEnd: last.run.qe,\n    targetStart: flipped ? last.run.ts : first.run.ts + first.trim,\n    targetEnd: flipped ? first.run.te - first.trim : last.run.te,\n    strand: flipped ? '-' : '+',\n    edits: flipped ? edits.reverse() : edits,\n    sharedBases: 0,\n  }\n}\n\n// The private bases between two shared nodes. A pair too large for the exact\n// alignment is seeded on shared k-mers in both orientations and chained the\n// way the walks are, which aligns two long copies of one sequence the graph\n// left apart. The best forward chain becomes edits. A flipped chain is an\n// inversion, which no CIGAR holds, so it comes back as a record of its own in\n// the coordinates of a and b. What no chain reaches is an insertion and a\n// deletion, which claims no homology.\nfunction alignPrivate(\n  a: string,\n  b: string,\n  edits: PairEdit[],\n  minMatch: number,\n): PairChain[] {\n  let inversions: PairChain[] = []\n  if (a.length * b.length <= MAX_ALIGNED_CELLS) {\n    affineAlignment(a, b, edits)\n  } else {\n    const chains = chainRuns(\n      kmerRuns(a, b),\n      Infinity,\n      Math.max(minMatch, KMER),\n      kmerJumpCost,\n    )\n    const forward = chains.find(chain => !chain[0]!.run.flipped)\n    inversions = chains\n      .filter(chain => chain[0]!.run.flipped)\n      .map(chain => recordOf(chain, a, b))\n    if (forward) {\n      // The forward record holds no inversion, so an inversion's bases stay\n      // unaligned in it. A gap that hides one is not seeded again: at a tandem\n      // array that finds only a neighbouring copy, matched forward over bases\n      // the inversion's own record already claims.\n      const forwardFill: GapFill = (qa, tb, into, queryFrom, targetFrom) => {\n        const hidesInversion = inversions.some(\n          inversion =>\n            (queryFrom < inversion.queryEnd &&\n              inversion.queryStart < queryFrom + qa.length) ||\n            (targetFrom < inversion.targetEnd &&\n              inversion.targetStart < targetFrom + tb.length),\n        )\n        if (hidesInversion) {\n          alignExact(qa, tb, into)\n        } else {\n          fillGap(qa, tb, into)\n        }\n      }\n      const first = forward[0]!.run\n      const last = forward.at(-1)!.run\n      forwardFill(a.slice(0, first.qs), b.slice(0, first.ts), edits, 0, 0)\n      chainEdits(forward, a, b, edits, forwardFill)\n      forwardFill(a.slice(last.qe), b.slice(last.te), edits, last.qe, last.te)\n    } else {\n      unaligned(a, b, edits)\n    }\n  }\n  return inversions\n}\n\ninterface Claimed extends PairChain {\n  // query stretches on nodes both walks visit\n  shared: Interval[]\n}\n\ntype Side = 'query' | 'target'\n\n// Each edit of a record with the query and target position it sits at. A `-`\n// record's edits read along the target, so its query runs down from queryEnd.\nfunction forEachEdit(\n  r: PairChain,\n  visit: (op: PairOp, len: number, query: number, target: number) => void,\n) {\n  const flipped = r.strand === '-'\n  let qi = 0\n  let ti = 0\n  for (const [op, len] of r.edits) {\n    visit(\n      op,\n      len,\n      flipped ? r.queryEnd - 1 - qi : r.queryStart + qi,\n      r.targetStart + ti,\n    )\n    if (op !== 'D') {\n      qi += len\n    }\n    if (op !== 'I') {\n      ti += len\n    }\n  }\n}\n\n// A record's score under vg's model over [lo, hi) on one side: a column counts\n// where its base on that side does, and a gap where it opens on that side.\nfunction scoreOver(r: PairChain, side: Side, lo: number, hi: number) {\n  const step = side === 'query' && r.strand === '-' ? -1 : 1\n  let score = 0\n  forEachEdit(r, (op, len, query, target) => {\n    const from = side === 'query' ? query : target\n    const inside = (k: number) => {\n      const at = from + step * k\n      return at >= lo && at < hi\n    }\n    if (op === '=' || op === 'X') {\n      for (let k = 0; k < len; k++) {\n        if (inside(k)) {\n          score += op === '=' ? MATCH : MISMATCH\n        }\n      }\n    } else if ((op === 'I') === (side === 'query')) {\n      for (let k = 0; k < len; k++) {\n        if (inside(k)) {\n          score += k === 0 ? GAP_OPEN : GAP_EXTEND\n        }\n      }\n    } else if (inside(0)) {\n      score += GAP_OPEN + (len - 1) * GAP_EXTEND\n    }\n  })\n  return score\n}\n\nfunction spanOf(r: PairChain, side: Side): Interval {\n  return side === 'query'\n    ? [r.queryStart, r.queryEnd]\n    : [r.targetStart, r.targetEnd]\n}\n\n// A record's edits with the aligned columns `lost` marks turned into an\n// insertion and a deletion, and its ends trimmed to the columns it keeps.\nfunction withoutColumns(r: Claimed, lost: Uint8Array): Claimed | undefined {\n  const flipped = r.strand === '-'\n  const edits: PairEdit[] = []\n  let pendingQuery = 0\n  let pendingTarget = 0\n  let column = 0\n  let sharedLost = 0\n  const sharedMask = new Uint8Array(r.queryEnd - r.queryStart)\n  for (const [s, e] of r.shared) {\n    sharedMask.fill(1, s - r.queryStart, e - r.queryStart)\n  }\n  const inShared = (at: number) => sharedMask[at - r.queryStart] === 1\n  const flush = () => {\n    appendEdit(edits, 'I', pendingQuery)\n    appendEdit(edits, 'D', pendingTarget)\n    pendingQuery = 0\n    pendingTarget = 0\n  }\n  forEachEdit(r, (op, len, query) => {\n    if (op === 'I') {\n      pendingQuery += len\n    } else if (op === 'D') {\n      pendingTarget += len\n    } else {\n      for (let k = 0; k < len; k++) {\n        if (lost[column + k]) {\n          pendingQuery += 1\n          pendingTarget += 1\n          if (inShared(flipped ? query - k : query + k)) {\n            sharedLost += 1\n          }\n        } else {\n          if (pendingQuery > 0 || pendingTarget > 0) {\n            flush()\n          }\n          appendEdit(edits, op, 1)\n        }\n      }\n      column += len\n    }\n  })\n  flush()\n  const lead = { I: 0, D: 0 }\n  while (edits[0]?.[0] === 'I' || edits[0]?.[0] === 'D') {\n    const [op, len] = edits.shift()!\n    lead[op as 'I' | 'D'] += len\n  }\n  const tail = { I: 0, D: 0 }\n  while (edits.at(-1)?.[0] === 'I' || edits.at(-1)?.[0] === 'D') {\n    const [op, len] = edits.pop()!\n    tail[op as 'I' | 'D'] += len\n  }\n  return edits.length === 0\n    ? undefined\n    : {\n        ...r,\n        queryStart: r.queryStart + (flipped ? tail.I : lead.I),\n        queryEnd: r.queryEnd - (flipped ? lead.I : tail.I),\n        targetStart: r.targetStart + lead.D,\n        targetEnd: r.targetEnd - tail.D,\n        edits,\n        sharedBases: r.sharedBases - sharedLost,\n      }\n}\n\n// A base aligns in one record at most. Where two records align the same bases\n// on either walk, the one scoring higher over the stretch their spans share\n// keeps them, and the other gives them up as an insertion and a deletion. In a\n// tandem array whose copies run both ways, one query copy aligns forward to one\n// target copy and inverted to another, and both are homology; the scoring\n// decides which one the pair's picture shows. A tie goes to the record with\n// more bases on shared nodes: alignPrivate finds an inversion a walk takes\n// through shared nodes again, base for base, in the gap of the forward record\n// spanning it.\nfunction claimOnce(\n  records: Claimed[],\n  queryLength: number,\n  targetLength: number,\n  minMatch: number,\n) {\n  const claims = {\n    query: new Uint8Array(queryLength),\n    target: new Uint8Array(targetLength),\n  }\n  const columnsOf = records.map(r => {\n    const columns: [number, number][] = []\n    forEachEdit(r, (op, len, query, target) => {\n      if (op === '=' || op === 'X') {\n        for (let k = 0; k < len; k++) {\n          columns.push([r.strand === '-' ? query - k : query + k, target + k])\n        }\n      }\n    })\n    for (const [query, target] of columns) {\n      claims.query[query] = Math.min(255, claims.query[query]! + 1)\n      claims.target[target] = Math.min(255, claims.target[target]! + 1)\n    }\n    return columns\n  })\n  const holders = {\n    query: new Map<number, number[]>(),\n    target: new Map<number, number[]>(),\n  }\n  columnsOf.forEach((columns, i) => {\n    for (const [query, target] of columns) {\n      for (const [side, at] of [\n        ['query', query],\n        ['target', target],\n      ] as const) {\n        if (claims[side][at]! > 1) {\n          const held = holders[side].get(at)\n          if (!held) {\n            holders[side].set(at, [i])\n          } else if (held.at(-1) !== i) {\n            held.push(i)\n          }\n        }\n      }\n    }\n  })\n  const beaten = new Map<string, boolean>()\n  const losesTo = (i: number, j: number, side: Side) => {\n    const key = `${side}:${i}:${j}`\n    let loses = beaten.get(key)\n    if (loses === undefined) {\n      const [si, ei] = spanOf(records[i]!, side)\n      const [sj, ej] = spanOf(records[j]!, side)\n      const lo = Math.max(si, sj)\n      const hi = Math.min(ei, ej)\n      const [mine, theirs] = [records[i]!, records[j]!]\n      const margins = [\n        scoreOver(theirs, side, lo, hi) - scoreOver(mine, side, lo, hi),\n        theirs.sharedBases - mine.sharedBases,\n        i - j,\n      ]\n      loses = margins.find(margin => margin !== 0)! > 0\n      beaten.set(key, loses)\n    }\n    return loses\n  }\n  return records.flatMap((r, i) => {\n    const columns = columnsOf[i]!\n    const lost = new Uint8Array(columns.length)\n    columns.forEach(([query, target], c) => {\n      for (const [side, at] of [\n        ['query', query],\n        ['target', target],\n      ] as const) {\n        if (\n          !lost[c] &&\n          holders[side].get(at)?.some(j => j !== i && losesTo(i, j, side))\n        ) {\n          lost[c] = 1\n        }\n      }\n    })\n    if (!lost.includes(1)) {\n      return [r]\n    }\n    const kept = withoutColumns(r, lost)\n    const matched =\n      kept?.edits.reduce((sum, [op, len]) => sum + (op === '=' ? len : 0), 0) ??\n      0\n    return kept && matched >= minMatch ? [kept] : []\n  })\n}\n\nfunction walkSequence(walk: number[], sequenceOf: (id: number) => string) {\n  return walk\n    .map(handle => {\n      const sequence = sequenceOf(nodeId(handle))\n      return isReverse(handle) ? reverseComplement(sequence) : sequence\n    })\n    .join('')\n}\n\nfunction walkOffsets(walk: number[], sequenceOf: (id: number) => string) {\n  const offsets = [0]\n  for (const handle of walk) {\n    offsets.push(offsets.at(-1)! + sequenceOf(nodeId(handle)).length)\n  }\n  return offsets\n}\n\n// The steps between a walk's first and last visit to any node it visits more\n// than once. Copies of a repeat folded onto one node say nothing about which\n// copy of one haplotype pairs with which copy of the other, and a graph can\n// pair them out of register, so there the bases decide.\nfunction repeatSteps(walk: number[]) {\n  const first = new Map<number, number>()\n  const last = new Map<number, number>()\n  walk.forEach((handle, i) => {\n    const id = nodeId(handle)\n    if (first.has(id)) {\n      last.set(id, i)\n    } else {\n      first.set(id, i)\n    }\n  })\n  const change = new Int32Array(walk.length + 1)\n  for (const [id, end] of last) {\n    change[first.get(id)!]! += 1\n    change[end + 1]! -= 1\n  }\n  const inside = new Uint8Array(walk.length)\n  let depth = 0\n  for (let i = 0; i < walk.length; i++) {\n    depth += change[i]!\n    inside[i] = depth > 0 ? 1 : 0\n  }\n  return inside\n}\n\n// Every stretch of steps the two walks take through the same nodes, in the\n// same order or the opposite one, outside both walks' repeats.\nfunction sharedRuns(\n  query: number[],\n  target: number[],\n  queryOffsets: number[],\n  targetOffsets: number[],\n) {\n  const queryRepeat = repeatSteps(query)\n  const targetRepeat = repeatSteps(target)\n  const visits = new Map<number, number[]>()\n  target.forEach((handle, rank) => {\n    if (!targetRepeat[rank]) {\n      visits.set(nodeId(handle), [rank])\n    }\n  })\n  const width = 2 * target.length\n  const key = (i: number, rank: number, flipped: boolean) =>\n    i * width + 2 * rank + (flipped ? 1 : 0)\n  const seeds = new Set<number>()\n  query.forEach((handle, i) => {\n    for (const rank of queryRepeat[i]\n      ? []\n      : (visits.get(nodeId(handle)) ?? [])) {\n      seeds.add(key(i, rank, isReverse(handle) !== isReverse(target[rank]!)))\n    }\n  })\n  const runs: Run[] = []\n  query.forEach((handle, i) => {\n    for (const rank of queryRepeat[i]\n      ? []\n      : (visits.get(nodeId(handle)) ?? [])) {\n      const flipped = isReverse(handle) !== isReverse(target[rank]!)\n      const step = flipped ? -1 : 1\n      const previous = rank - step\n      const continues =\n        i > 0 &&\n        previous >= 0 &&\n        previous < target.length &&\n        seeds.has(key(i - 1, previous, flipped))\n      if (!continues) {\n        let j = i\n        let r = rank\n        while (\n          j < query.length &&\n          r >= 0 &&\n          r < target.length &&\n          seeds.has(key(j, r, flipped))\n        ) {\n          j += 1\n          r += step\n        }\n        const lastRank = r - step\n        runs.push({\n          qs: queryOffsets[i]!,\n          qe: queryOffsets[j]!,\n          ts: targetOffsets[Math.min(rank, lastRank)]!,\n          te: targetOffsets[Math.max(rank, lastRank) + 1]!,\n          flipped,\n        })\n      }\n    }\n  })\n  return runs\n}\n\n// A query walk's alignments to a target walk. A stretch of nodes both walks\n// visit is a run of `=`, a record is the best collinear chain of those\n// stretches, and what lies between two of them is aligned base by base under\n// vg's scoring, an inversion there coming back as a record of its own. With\n// bases false it is an insertion and a deletion instead. A chain pays for the\n// gap it spans, so by default nothing bounds how far it reaches but the window;\n// maxGap caps that to bound the work. A record matching under minMatch bases is\n// dropped. Coordinates count from each walk's first base; a `-` record's edits\n// read along the target, the way minimap2 writes a reverse-strand row.\nexport function pairAlignments(opts: PairOptions): PairChain[] {\n  const { query, target, sequenceOf } = opts\n  const a = walkSequence(query, sequenceOf)\n  const b = walkSequence(target, sequenceOf)\n  const runs = sharedRuns(\n    query,\n    target,\n    walkOffsets(query, sequenceOf),\n    walkOffsets(target, sequenceOf),\n  )\n  const minMatch = opts.minMatch ?? DEFAULT_MIN_MATCH\n  const bases = opts.bases ?? true\n  const records: Claimed[] = []\n  for (const chain of chainRuns(\n    runs,\n    opts.maxGap ?? Infinity,\n    minMatch,\n    stepJumpCost,\n  )) {\n    const edits: PairEdit[] = []\n    const first = chain[0]!\n    const last = chain.at(-1)!\n    const { flipped } = first.run\n    const alignBetween: GapFill = (qa, tb, into, queryFrom, targetFrom) => {\n      for (const inversion of alignPrivate(qa, tb, into, minMatch)) {\n        const targetTo = targetFrom + tb.length\n        records.push({\n          ...inversion,\n          queryStart: queryFrom + inversion.queryStart,\n          queryEnd: queryFrom + inversion.queryEnd,\n          targetStart: flipped\n            ? targetTo - inversion.targetEnd\n            : targetFrom + inversion.targetStart,\n          targetEnd: flipped\n            ? targetTo - inversion.targetStart\n            : targetFrom + inversion.targetEnd,\n          strand: flipped ? '+' : '-',\n          edits: flipped ? inversion.edits.reverse() : inversion.edits,\n          shared: [],\n        })\n      }\n    }\n    chainEdits(chain, a, b, edits, bases ? alignBetween : unaligned)\n    records.push({\n      queryStart: first.run.qs + first.trim,\n      queryEnd: last.run.qe,\n      targetStart: flipped ? last.run.ts : first.run.ts + first.trim,\n      targetEnd: flipped ? first.run.te - first.trim : last.run.te,\n      strand: flipped ? '-' : '+',\n      edits: flipped ? edits.reverse() : edits,\n      sharedBases: chain.reduce(\n        (sum, { run, trim }) => sum + run.qe - run.qs - trim,\n        0,\n      ),\n      shared: chain.map(({ run, trim }) => [run.qs + trim, run.qe]),\n    })\n  }\n  return claimOnce(records, a.length, b.length, minMatch)\n    .map(({ shared: _, ...record }) => record)\n    .sort((x, y) => x.queryStart - y.queryStart)\n}\n\nexport function pairCigar(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n", "// The GBZ adapter's own refusal, marked regionTooLarge so core shows it as a\n// zoom-in notice, or gbz-base's when it reaches the display unwrapped\nexport function isNodeLimitError(error: unknown) {\n  return (\n    error instanceof Error &&\n    (error.name === 'NodeLimitError' ||\n      (error as { regionTooLarge?: unknown }).regionTooLarge === true ||\n      /reads more than nodeLimit|^Subgraph size limit of \\d+ nodes exceeded/.test(\n        error.message,\n      ))\n  )\n}\n"],
+  "mappings": 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 }