jbrowse-plugin-graphgenomeviewer 4.8.0 → 5.0.0

package/dist/chunks/chunk-2H7GDQ3R.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/gbwt/node.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/gbwt/bytecode.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/gbwt/record.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/gbwt/sequence.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/sha256.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/graphName.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/pathName.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/chosenPaths.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/lcs.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/pairAlignment.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/subgraph.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/query.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/sqlite/record.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/sqlite/btree.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/sqlite/pager.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/sqlite/database.ts", "../../node_modules/.pnpm/@gmod+gbz-base@7.0.0/node_modules/@gmod/gbz-base/src/db.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", "export class ByteCodeReader {\n  offset = 0\n  private bytes: Uint8Array\n\n  constructor(bytes: Uint8Array) {\n    this.bytes = bytes\n  }\n\n  get done() {\n    return this.offset >= this.bytes.length\n  }\n\n  byte() {\n    const value = this.bytes[this.offset]\n    if (value === undefined) {\n      return undefined\n    }\n    this.offset += 1\n    return value\n  }\n\n  int() {\n    let shift = 1\n    let result = 0\n    while (this.offset < this.bytes.length) {\n      const value = this.bytes[this.offset]!\n      this.offset += 1\n      result += (value & 0x7f) * shift\n      shift *= 128\n      if ((value & 0x80) === 0) {\n        return result\n      }\n    }\n    return undefined\n  }\n}\n\nexport interface Run {\n  value: number\n  len: number\n}\n\nconst RLE_THRESHOLD = 255\nconst RLE_UNIVERSE = 256\n\nexport class RunReader {\n  private source: ByteCodeReader\n  private sigma: number\n  private threshold: number\n\n  constructor(bytes: Uint8Array, sigma: number) {\n    this.source = new ByteCodeReader(bytes)\n    this.sigma = sigma === 0 ? Number.MAX_SAFE_INTEGER : sigma\n    this.threshold =\n      this.sigma < RLE_THRESHOLD ? Math.floor(RLE_UNIVERSE / this.sigma) : 0\n  }\n\n  next(): Run | undefined {\n    if (this.sigma >= RLE_THRESHOLD) {\n      const value = this.source.int()\n      const len = this.source.int()\n      return value === undefined || len === undefined\n        ? undefined\n        : { value, len: len + 1 }\n    }\n    const byte = this.source.byte()\n    if (byte === undefined) {\n      return undefined\n    }\n    const value = byte % this.sigma\n    let len = Math.floor(byte / this.sigma) + 1\n    if (len === this.threshold) {\n      const extra = this.source.int()\n      if (extra === undefined) {\n        return undefined\n      }\n      len += extra\n    }\n    return { value, len }\n  }\n\n  *[Symbol.iterator]() {\n    for (let run = this.next(); run !== undefined; run = this.next()) {\n      yield run\n    }\n  }\n}\n", "import { ByteCodeReader, RunReader } from './bytecode.ts'\nimport { ENDMARKER, flipNode, nodeId } from './node.ts'\n\nexport interface Pos {\n  node: number\n  offset: number\n}\n\nexport function decompressEdges(bytes: Uint8Array): Pos[] {\n  const reader = new ByteCodeReader(bytes)\n  const sigma = reader.int()\n  if (sigma === undefined || sigma === 0) {\n    return []\n  }\n  const edges: Pos[] = []\n  let prev = 0\n  for (let i = 0; i < sigma; i++) {\n    const delta = reader.int()\n    const offset = reader.int()\n    if (delta === undefined || offset === undefined) {\n      throw new Error('GBWT edge list ends early')\n    }\n    prev += delta\n    edges.push({ node: prev, offset })\n  }\n  return edges\n}\n\nexport class GbwtRecord {\n  readonly edges: Pos[]\n  readonly bwt: Uint8Array\n\n  constructor(edges: Pos[], bwt: Uint8Array) {\n    this.edges = edges\n    this.bwt = bwt\n  }\n\n  runs() {\n    return new RunReader(this.bwt, this.edges.length)\n  }\n\n  private edge(rank: number) {\n    const edge = this.edges[rank]\n    if (edge === undefined) {\n      throw new Error(\n        `GBWT run refers to edge rank ${rank} of ${this.edges.length}`,\n      )\n    }\n    return edge\n  }\n\n  lf(i: number): Pos | undefined {\n    const offsets = this.edges.map(e => e.offset)\n    let offset = 0\n    for (const run of this.runs()) {\n      const edge = this.edge(run.value)\n      const soFar = offsets[run.value]!\n      if (offset + run.len > i) {\n        return edge.node === ENDMARKER\n          ? undefined\n          : { node: edge.node, offset: soFar + (i - offset) }\n      }\n      offsets[run.value] = soFar + run.len\n      offset += run.len\n    }\n    return undefined\n  }\n\n  private edgeTo(node: number) {\n    let low = 0\n    let high = this.edges.length\n    while (low < high) {\n      const mid = (low + high) >> 1\n      const edge = this.edges[mid]!\n      if (edge.node === node) {\n        return mid\n      }\n      if (edge.node < node) {\n        low = mid + 1\n      } else {\n        high = mid\n      }\n    }\n    return undefined\n  }\n\n  offsetTo(pos: Pos): number | undefined {\n    if (pos.node === ENDMARKER) {\n      return undefined\n    }\n    const rank = this.edgeTo(pos.node)\n    if (rank === undefined) {\n      return undefined\n    }\n    let succRank = this.edges[rank]!.offset\n    if (succRank > pos.offset) {\n      return undefined\n    }\n    let offset = 0\n    for (const run of this.runs()) {\n      offset += run.len\n      if (run.value !== rank) {\n        continue\n      }\n      succRank += run.len\n      if (succRank > pos.offset) {\n        return offset - (succRank - pos.offset)\n      }\n    }\n    return undefined\n  }\n\n  predecessorAt(i: number): number | undefined {\n    const counts = this.edges.map(e => ({\n      node: e.node === ENDMARKER ? ENDMARKER : flipNode(e.node),\n      count: 0,\n    }))\n    for (const run of this.runs()) {\n      const entry = counts[run.value]\n      if (entry) {\n        entry.count += run.len\n      }\n    }\n    for (let rank = 1; rank < counts.length; rank++) {\n      const prev = counts[rank - 1] as { node: number; count: number }\n      const curr = counts[rank] as { node: number; count: number }\n      if (nodeId(prev.node) === nodeId(curr.node)) {\n        counts[rank - 1] = curr\n        counts[rank] = prev\n      }\n    }\n    let offset = 0\n    for (const entry of counts) {\n      offset += entry.count\n      if (offset > i) {\n        return entry.node === ENDMARKER ? undefined : entry.node\n      }\n    }\n    return undefined\n  }\n\n  decompressArrays() {\n    const offsets = this.edges.map(e => e.offset)\n    let total = 0\n    for (const run of this.runs()) {\n      total += run.len\n    }\n    const nodes = new Int32Array(total)\n    const nextOffsets = new Int32Array(total)\n    let i = 0\n    for (const run of this.runs()) {\n      const edge = this.edge(run.value)\n      let offset = offsets[run.value]!\n      for (let k = 0; k < run.len; k++) {\n        nodes[i] = edge.node\n        nextOffsets[i] = offset\n        offset += 1\n        i += 1\n      }\n      offsets[run.value] = offset\n    }\n    return { nodes, offsets: nextOffsets }\n  }\n\n  decompress(): Pos[] {\n    const offsets = this.edges.map(e => e.offset)\n    const result: Pos[] = []\n    for (const run of this.runs()) {\n      const edge = this.edge(run.value)\n      for (let k = 0; k < run.len; k++) {\n        result.push({ node: edge.node, offset: offsets[run.value]! })\n        offsets[run.value] = offsets[run.value]! + 1\n      }\n    }\n    return result\n  }\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", "const K = Uint32Array.from([\n  0x428a2f98, 0x71374491, 0xb5c0fbcf, 0xe9b5dba5, 0x3956c25b, 0x59f111f1,\n  0x923f82a4, 0xab1c5ed5, 0xd807aa98, 0x12835b01, 0x243185be, 0x550c7dc3,\n  0x72be5d74, 0x80deb1fe, 0x9bdc06a7, 0xc19bf174, 0xe49b69c1, 0xefbe4786,\n  0x0fc19dc6, 0x240ca1cc, 0x2de92c6f, 0x4a7484aa, 0x5cb0a9dc, 0x76f988da,\n  0x983e5152, 0xa831c66d, 0xb00327c8, 0xbf597fc7, 0xc6e00bf3, 0xd5a79147,\n  0x06ca6351, 0x14292967, 0x27b70a85, 0x2e1b2138, 0x4d2c6dfc, 0x53380d13,\n  0x650a7354, 0x766a0abb, 0x81c2c92e, 0x92722c85, 0xa2bfe8a1, 0xa81a664b,\n  0xc24b8b70, 0xc76c51a3, 0xd192e819, 0xd6990624, 0xf40e3585, 0x106aa070,\n  0x19a4c116, 0x1e376c08, 0x2748774c, 0x34b0bcb5, 0x391c0cb3, 0x4ed8aa4a,\n  0x5b9cca4f, 0x682e6ff3, 0x748f82ee, 0x78a5636f, 0x84c87814, 0x8cc70208,\n  0x90befffa, 0xa4506ceb, 0xbef9a3f7, 0xc67178f2,\n])\n\nconst rotr = (x: number, n: number) => (x >>> n) | (x << (32 - n))\n\n// FIPS 180-4, for pages without crypto.subtle (insecure contexts)\nexport function sha256(bytes: Uint8Array) {\n  const blocks = Math.ceil((bytes.length + 9) / 64)\n  const padded = new Uint8Array(blocks * 64)\n  padded.set(bytes)\n  padded[bytes.length] = 0x80\n  const view = new DataView(padded.buffer)\n  const bits = bytes.length * 8\n  view.setUint32(padded.length - 8, Math.floor(bits / 2 ** 32))\n  view.setUint32(padded.length - 4, bits >>> 0)\n  const h = Uint32Array.from([\n    0x6a09e667, 0xbb67ae85, 0x3c6ef372, 0xa54ff53a, 0x510e527f, 0x9b05688c,\n    0x1f83d9ab, 0x5be0cd19,\n  ])\n  const w = new Uint32Array(64)\n  for (let block = 0; block < blocks; block++) {\n    for (let t = 0; t < 16; t++) {\n      w[t] = view.getUint32(block * 64 + t * 4)\n    }\n    for (let t = 16; t < 64; t++) {\n      const a = w[t - 15]!\n      const b = w[t - 2]!\n      const s0 = rotr(a, 7) ^ rotr(a, 18) ^ (a >>> 3)\n      const s1 = rotr(b, 17) ^ rotr(b, 19) ^ (b >>> 10)\n      w[t] = w[t - 16]! + s0 + w[t - 7]! + s1\n    }\n    let a = h[0]!\n    let b = h[1]!\n    let c = h[2]!\n    let d = h[3]!\n    let e = h[4]!\n    let f = h[5]!\n    let g = h[6]!\n    let hh = h[7]!\n    for (let t = 0; t < 64; t++) {\n      const s1 = rotr(e, 6) ^ rotr(e, 11) ^ rotr(e, 25)\n      const ch = (e & f) ^ (~e & g)\n      const t1 = (hh + s1 + ch + K[t]! + w[t]!) | 0\n      const s0 = rotr(a, 2) ^ rotr(a, 13) ^ rotr(a, 22)\n      const maj = (a & b) ^ (a & c) ^ (b & c)\n      hh = g\n      g = f\n      f = e\n      e = (d + t1) | 0\n      d = c\n      c = b\n      b = a\n      a = (t1 + s0 + maj) | 0\n    }\n    ;[a, b, c, d, e, f, g, hh].forEach((value, i) => {\n      h[i] = h[i]! + value\n    })\n  }\n  const out = new Uint8Array(32)\n  const outView = new DataView(out.buffer)\n  for (let i = 0; i < 8; i++) {\n    outView.setUint32(i * 4, h[i]!)\n  }\n  return out\n}\n", "import { sha256 } from './sha256.ts'\n\nexport interface GraphName {\n  name: string | undefined\n  subgraph: Map<string, Set<string>>\n  translation: Map<string, Set<string>>\n}\n\nfunction parseRelationships(field: string | undefined, what: string) {\n  const relationships = new Map<string, Set<string>>()\n  if (field !== undefined) {\n    for (const rel of field.split(';')) {\n      const parts = rel.split(',')\n      const [from, to] = parts\n      if (parts.length !== 2 || !from || !to) {\n        throw new Error(`Invalid ${what} relationship: ${rel}`)\n      }\n      let targets = relationships.get(from)\n      if (!targets) {\n        targets = new Set()\n        relationships.set(from, targets)\n      }\n      targets.add(to)\n    }\n  }\n  return relationships\n}\n\nexport function graphNameFromTags(tags: Map<string, string>): GraphName {\n  return {\n    name: tags.get('pggname'),\n    subgraph: parseRelationships(tags.get('subgraph'), 'subgraph'),\n    translation: parseRelationships(tags.get('translation'), 'translation'),\n  }\n}\n\nfunction merge(into: Map<string, Set<string>>, from: Map<string, Set<string>>) {\n  for (const [key, values] of from) {\n    let targets = into.get(key)\n    if (!targets) {\n      targets = new Set()\n      into.set(key, targets)\n    }\n    for (const value of values) {\n      targets.add(value)\n    }\n  }\n}\n\nexport function subgraphName(name: string, parent: GraphName): GraphName {\n  const result: GraphName = {\n    name,\n    subgraph: new Map(),\n    translation: new Map(),\n  }\n  if (parent.name !== undefined) {\n    result.subgraph.set(name, new Set([parent.name]))\n    merge(result.subgraph, parent.subgraph)\n    merge(result.translation, parent.translation)\n  }\n  return result\n}\n\nfunction sortedEntries(relationships: Map<string, Set<string>>) {\n  return [...relationships.entries()]\n    .sort(([a], [b]) => (a < b ? -1 : a > b ? 1 : 0))\n    .flatMap(([from, tos]) => [...tos].sort().map(to => [from, to] as const))\n}\n\nexport function gfaHeaderLines(graphName: GraphName) {\n  const lines: string[] = []\n  if (graphName.name !== undefined) {\n    lines.push(`H\\tNM:Z:${graphName.name}`)\n  }\n  for (const [subgraph, supergraph] of sortedEntries(graphName.subgraph)) {\n    lines.push(`H\\tSG:Z:${subgraph},${supergraph}`)\n  }\n  for (const [from, to] of sortedEntries(graphName.translation)) {\n    lines.push(`H\\tTL:Z:${from},${to}`)\n  }\n  return lines\n}\n\nexport async function sha256Hex(chunks: Uint8Array[]) {\n  const total = chunks.reduce((sum, chunk) => sum + chunk.length, 0)\n  const bytes = new Uint8Array(total)\n  let offset = 0\n  for (const chunk of chunks) {\n    bytes.set(chunk, offset)\n    offset += chunk.length\n  }\n  const subtle = (globalThis.crypto as Crypto | undefined)?.subtle\n  const digest = subtle\n    ? new Uint8Array(await subtle.digest('SHA-256', bytes))\n    : sha256(bytes)\n  return [...digest].map(byte => byte.toString(16).padStart(2, '0')).join('')\n}\n", "export interface PathName {\n  sample: string\n  contig: string\n  haplotype: number\n  fragment: number\n}\n\nexport interface PathQuery {\n  sample?: string | undefined\n  contig: string\n  haplotype?: number | undefined\n}\n\nexport type PathRef = string | PathQuery\n\nexport const GENERIC_SAMPLE = '_gbwt_ref'\n\nexport function formatPathName(name: PathName & { end?: number | undefined }) {\n  const base = `${name.sample}#${name.haplotype}#${name.contig}`\n  return name.end === undefined ? base : `${base}[${name.fragment}-${name.end}]`\n}\n\nconst PAN_SN = /^([^#]+)#(\\d+)#([^#]+?)(?:\\[\\d+-\\d+\\])?$/\nconst BARE_CONTIG = /^([^#]+?)(?:\\[\\d+-\\d+\\])?$/\n\nexport function parsePathName(name: string): PathQuery {\n  const panSn = PAN_SN.exec(name)\n  if (panSn) {\n    return {\n      sample: panSn[1]!,\n      haplotype: Number(panSn[2]),\n      contig: panSn[3]!,\n    }\n  }\n  const bare = BARE_CONTIG.exec(name)\n  if (bare) {\n    return { contig: bare[1]! }\n  }\n  throw new Error(\n    `\"${name}\" is not a path name; expected \"sample#haplotype#contig\" or a bare contig`,\n  )\n}\n\nexport function toPathQuery(ref: PathRef) {\n  return typeof ref === 'string' ? parsePathName(ref) : ref\n}\n\nexport function pathNameFor(query: PathQuery, fragment: number): PathName {\n  return {\n    sample: query.sample ?? GENERIC_SAMPLE,\n    contig: query.contig,\n    haplotype: query.haplotype ?? 0,\n    fragment,\n  }\n}\n", "import {\n  ENDMARKER,\n  flipNode,\n  isReverse,\n  nodeId,\n  pathEndsAreCanonical,\n} from './gbwt/node.ts'\n\nimport type {\n  GBZBase,\n  GbzRecord,\n  HaplotypeAnchorRow,\n  HaplotypeSample,\n  HaplotypeStrayOptions,\n} from './db.ts'\nimport type { Orientation } from './gbwt/node.ts'\nimport type { Pos } from './gbwt/record.ts'\nimport type { PathName } from './pathName.ts'\nimport type { SnarlFill, SnarlOutput } from './subgraph.ts'\n\nconst SCAN_GAP = 4096\n\n// Runs of sorted handles close enough to read the haplotype index samples on\n// them with one scan each.\nexport function handleRuns(sortedHandles: number[]) {\n  const runs: [number, number][] = []\n  for (const handle of sortedHandles) {\n    const last = runs[runs.length - 1]\n    if (last && handle - last[1] <= SCAN_GAP) {\n      last[1] = handle\n    } else {\n      runs.push([handle, handle])\n    }\n  }\n  return runs\n}\n\n// How far a chain from a twin piece goes outside the subgraph before it stops.\nexport const CHAIN_BOUND = 32768\n\n// Above this many chosen paths at the anchors, extracting and identifying\n// every walk took less time than walking the chosen ones, on HPRC chr22 windows\n// with 42 haplotypes. Tests raise it to run the walks on large sets.\nexport const keepTuning = { mostChosenPaths: 32 }\n\nexport type ChosenPieceSource =\n  'reference' | 'section' | 'stray' | 'chain' | 'twin'\n\nexport interface ChosenPiece {\n  pathHandle: number\n  orientation: Orientation\n  handles: number[]\n  offsets: number[]\n  len: number\n  hapStart: number\n  hapEnd: number\n  canonical: boolean\n  source: ChosenPieceSource\n}\n\nexport type KeepWalkEnd =\n  'merge' | 'landed' | 'bound' | 'endmarker' | 'past the far anchor'\n\nexport interface KeepStats {\n  spacing: number | undefined\n  // The anchors before and after the window.\n  anchors: [number, number] | undefined\n  // The anchors within the walks' bound of the bins the window touches, and\n  // one beyond on each side.\n  anchorsRead: number\n  chosenPaths: number\n  scans: [number, number][]\n  scanRows: number\n  // The bins the window touches, the stray rows read in them, those of chosen\n  // paths walked, and the bases all walks took outside the subgraph.\n  strays:\n    | { bins: number; rows: number; walked: number; outsideBp: number }\n    | undefined\n  pieces: number\n  sources: Record<ChosenPieceSource, number>\n  walks: Record<string, number>\n  twins: { tried: number; found: number }\n  graphFetches: number\n  // Why the query extracted and identified every walk instead, when it did.\n  fallback: string | undefined\n  ms: {\n    scan: number\n    walks: number\n    check: number\n    twins: number\n  }\n}\n\nexport interface ChosenPathsInput {\n  db: GBZBase\n  records: Map<number, GbzRecord>\n  referenceHandle: number\n  referencePos: Pos\n  referenceLeft: number\n  window: { start: number; end: number }\n  context: number\n  // The snarls the subgraph filled and the nodes those fills added.\n  snarls: { mode: SnarlOutput; fills: SnarlFill[]; inserted: Set<number> }\n  keep: (name: PathName) => boolean\n  signal: AbortSignal | undefined\n  prefetchReferenceRange: (\n    pathHandle: number,\n    fromOffset: number,\n    toOffset: number,\n  ) => Promise<unknown>\n}\n\ninterface Cursor {\n  pos: Pos\n  left: number\n}\n\nclass PositionIndex {\n  private byNode = new Map<number, Map<number, number>>()\n\n  get(pos: Pos) {\n    return this.byNode.get(pos.node)?.get(pos.offset)\n  }\n\n  set(pos: Pos, id: number) {\n    let offsets = this.byNode.get(pos.node)\n    if (!offsets) {\n      offsets = new Map()\n      this.byNode.set(pos.node, offsets)\n    }\n    offsets.set(pos.offset, id)\n  }\n}\n\nclass Fallback extends Error {}\n\nfunction forwardLeft(\n  orientation: Orientation,\n  left: number,\n  currentLen: number,\n  nextLen: number,\n) {\n  return orientation === 'forward' ? left + currentLen : left - nextLen\n}\n\nfunction backwardLeft(\n  orientation: Orientation,\n  left: number,\n  currentLen: number,\n  previousLen: number,\n) {\n  return orientation === 'forward' ? left - previousLen : left + currentLen\n}\n\nfunction twinIsCanonical(piece: ChosenPiece) {\n  return pathEndsAreCanonical(\n    flipNode(piece.handles[piece.handles.length - 1]!),\n    flipNode(piece.handles[0]!),\n  )\n}\n\nfunction pieceKey(piece: ChosenPiece) {\n  return `${piece.pathHandle}:${piece.hapStart}:${piece.hapEnd}`\n}\n\n// The pieces a chosen set of haplotypes leaves in a subgraph: every maximal\n// run of one path's positions whose nodes all lie in the subgraph, the pieces\n// extractPaths and identifyPaths find by walking and naming every haplotype.\n// When the haplotype index cannot show that the walks below pass every such\n// piece, the result carries a fallback reason and no pieces, and the caller\n// identifies every walk.\nexport async function findChosenPieces(input: ChosenPathsInput) {\n  const { db, records, signal } = input\n  let clock = performance.now()\n  const lap = () => {\n    const now = performance.now()\n    const elapsed = now - clock\n    clock = now\n    return elapsed\n  }\n  const stats: KeepStats = {\n    spacing: await db.haplotypeAnchorSpacing(),\n    anchors: undefined,\n    anchorsRead: 0,\n    chosenPaths: 0,\n    scans: [],\n    scanRows: 0,\n    strays: undefined,\n    pieces: 0,\n    sources: {\n      reference: 0,\n      section: 0,\n      stray: 0,\n      chain: 0,\n      twin: 0,\n    },\n    walks: {},\n    twins: { tried: 0, found: 0 },\n    graphFetches: 0,\n    fallback: undefined,\n    ms: { scan: 0, walks: 0, check: 0, twins: 0 },\n  }\n  const countWalk = (kind: string, end: KeepWalkEnd) => {\n    const key = `${kind}: ${end}`\n    stats.walks[key] = (stats.walks[key] ?? 0) + 1\n  }\n  const interval = (await db.haplotypeSampleInterval()) ?? 4096\n  const outside = new Map<number, GbzRecord>()\n  const record = async (handle: number) => {\n    const inside = records.get(handle) ?? outside.get(handle)\n    if (inside) {\n      return inside\n    }\n    const fetched = await db.getRecord(handle)\n    stats.graphFetches += 1\n    if (!fetched) {\n      throw new Error(`Node record ${handle} is missing from the database`)\n    }\n    outside.set(handle, fetched)\n    return fetched\n  }\n  const lengthIn = (handle: number) => records.get(handle)!.sequenceLen\n  const pathsByHandle = await db.pathsByHandle()\n  const chosen = (pathHandle: number) => {\n    const path = pathsByHandle.get(pathHandle)\n    return path !== undefined && input.keep(path.name)\n  }\n\n  const pieces: ChosenPiece[] = []\n  const pieceAt = new PositionIndex()\n  const piecesOfPath = new Map<number, number[]>()\n  const forwardDone = new Set<number>()\n  const backwardDone = new Set<number>()\n\n  const next = async (pos: Pos): Promise<Pos | undefined> => {\n    const successor = (await record(pos.node)).gbwt().lf(pos.offset)\n    return successor === undefined || successor.node === ENDMARKER\n      ? undefined\n      : successor\n  }\n  const previous = async (\n    pos: Pos,\n    within?: Map<number, GbzRecord>,\n  ): Promise<Pos | undefined> => {\n    const predecessor = (await record(flipNode(pos.node)))\n      .gbwt()\n      .predecessorAt(pos.offset)\n    if (\n      predecessor === undefined ||\n      (within !== undefined && !within.has(predecessor))\n    ) {\n      return undefined\n    }\n    const offset = (await record(predecessor)).gbwt().offsetTo(pos)\n    if (offset === undefined) {\n      throw new Error(\n        `No offset in ${predecessor} leads to ${pos.node}:${pos.offset}`,\n      )\n    }\n    return { node: predecessor, offset }\n  }\n\n  const addPiece = (\n    pathHandle: number,\n    orientation: Orientation,\n    cursors: Cursor[],\n    source: ChosenPieceSource,\n  ) => {\n    const handles = cursors.map(c => c.pos.node)\n    const offsets = cursors.map(c => c.pos.offset)\n    let len = 0\n    for (const handle of handles) {\n      len += lengthIn(handle)\n    }\n    const hapStart =\n      orientation === 'forward'\n        ? cursors[0]!.left\n        : cursors[cursors.length - 1]!.left\n    const id = pieces.length\n    pieces.push({\n      pathHandle,\n      orientation,\n      handles,\n      offsets,\n      len,\n      hapStart,\n      hapEnd: hapStart + len,\n      canonical: pathEndsAreCanonical(handles[0], handles[handles.length - 1]),\n      source,\n    })\n    for (const cursor of cursors) {\n      pieceAt.set(cursor.pos, id)\n    }\n    const ofPath = piecesOfPath.get(pathHandle)\n    if (ofPath) {\n      ofPath.push(id)\n    } else {\n      piecesOfPath.set(pathHandle, [id])\n    }\n    return id\n  }\n\n  // The piece through a position in the subgraph, in that position's\n  // orientation of its path.\n  const pieceThrough = async (\n    seed: Cursor,\n    pathHandle: number,\n    orientation: Orientation,\n    source: ChosenPieceSource,\n  ) => {\n    const before: Cursor[] = []\n    let cursor = seed\n    for (;;) {\n      signal?.throwIfAborted()\n      const pos = await previous(cursor.pos, records)\n      if (!pos) {\n        break\n      }\n      cursor = {\n        pos,\n        left: backwardLeft(\n          orientation,\n          cursor.left,\n          lengthIn(cursor.pos.node),\n          lengthIn(pos.node),\n        ),\n      }\n      before.push(cursor)\n    }\n    before.reverse()\n    const after: Cursor[] = [seed]\n    cursor = seed\n    for (;;) {\n      signal?.throwIfAborted()\n      const pos = await next(cursor.pos)\n      if (!pos || !records.has(pos.node)) {\n        break\n      }\n      cursor = {\n        pos,\n        left: forwardLeft(\n          orientation,\n          cursor.left,\n          lengthIn(cursor.pos.node),\n          lengthIn(pos.node),\n        ),\n      }\n      after.push(cursor)\n    }\n    return addPiece(pathHandle, orientation, [...before, ...after], source)\n  }\n  const pieceAtOrThrough = async (\n    cursor: Cursor,\n    pathHandle: number,\n    orientation: Orientation,\n    source: ChosenPieceSource,\n  ) =>\n    pieces[\n      pieceAt.get(cursor.pos) ??\n        (await pieceThrough(cursor, pathHandle, orientation, source))\n    ]!\n\n  const lastCursor = (piece: ChosenPiece): Cursor => {\n    const node = piece.handles[piece.handles.length - 1]!\n    return {\n      pos: { node, offset: piece.offsets[piece.offsets.length - 1]! },\n      left:\n        piece.orientation === 'forward'\n          ? piece.hapEnd - lengthIn(node)\n          : piece.hapStart,\n    }\n  }\n  const firstCursor = (piece: ChosenPiece): Cursor => {\n    const node = piece.handles[0]!\n    return {\n      pos: { node, offset: piece.offsets[0]! },\n      left:\n        piece.orientation === 'forward'\n          ? piece.hapStart\n          : piece.hapEnd - lengthIn(node),\n    }\n  }\n\n  const referenceId = await pieceThrough(\n    { pos: input.referencePos, left: input.referenceLeft },\n    input.referenceHandle,\n    'forward',\n    'reference',\n  )\n  const reference = pieces[referenceId]!\n  const result = () => {\n    if (stats.fallback !== undefined) {\n      return { reference, pieces: [], stats }\n    }\n    // What extractPaths keeps: the canonical twin of each piece, and both twins\n    // when both are canonical.\n    const byKey = new Map<string, ChosenPiece[]>()\n    pieces.forEach((piece, id) => {\n      if (id !== referenceId) {\n        byKey.set(pieceKey(piece), [\n          ...(byKey.get(pieceKey(piece)) ?? []),\n          piece,\n        ])\n      }\n    })\n    const emitted: ChosenPiece[] = []\n    for (const group of byKey.values()) {\n      const orientations = new Set<Orientation>()\n      for (const piece of group) {\n        if (piece.canonical && !orientations.has(piece.orientation)) {\n          orientations.add(piece.orientation)\n          emitted.push(piece)\n          stats.sources[piece.source] += 1\n        }\n      }\n    }\n    stats.sources.reference = 1\n    stats.pieces = emitted.length + 1\n    return { reference, pieces: emitted, stats }\n  }\n\n  // A chain from a piece, forward or backward, through every piece it lands\n  // in, until it meets a known position or runs CHAIN_BOUND bp outside the\n  // subgraph.\n  const chain = async (id: number, forward: boolean) => {\n    const done = forward ? forwardDone : backwardDone\n    const other = forward ? backwardDone : forwardDone\n    let current = id\n    for (;;) {\n      if (done.has(current)) {\n        return\n      }\n      done.add(current)\n      const piece = pieces[current]!\n      let cursor = forward ? lastCursor(piece) : firstCursor(piece)\n      let bp = 0\n      let end: KeepWalkEnd | undefined\n      while (end === undefined) {\n        signal?.throwIfAborted()\n        const pos = forward\n          ? await next(cursor.pos)\n          : await previous(cursor.pos)\n        if (!pos) {\n          end = 'endmarker'\n          break\n        }\n        const currentLen = (await record(cursor.pos.node)).sequenceLen\n        const len = (await record(pos.node)).sequenceLen\n        const left = forward\n          ? forwardLeft(piece.orientation, cursor.left, currentLen, len)\n          : backwardLeft(piece.orientation, cursor.left, currentLen, len)\n        if (records.has(pos.node)) {\n          const known = pieceAt.get(pos)\n          if (known === undefined) {\n            current = await pieceThrough(\n              { pos, left },\n              piece.pathHandle,\n              piece.orientation,\n              'chain',\n            )\n            other.add(current)\n            end = 'landed'\n          } else {\n            other.add(known)\n            end = 'merge'\n          }\n        } else if (bp > CHAIN_BOUND) {\n          end = 'bound'\n        } else {\n          bp += len\n          cursor = { pos, left }\n        }\n      }\n      countWalk('chain', end)\n      if (end !== 'landed') {\n        return\n      }\n    }\n  }\n\n  // With HaplotypeStrays and HaplotypeBinNodes. The haplotype index lists the\n  // nodes of each bin of the reference path, and for each bin the stretches of\n  // each path whose visits to those nodes the section walks below can miss.\n  // The subgraph is checked against the bins the window touches, so every\n  // visit of a chosen path to it lies on a section walk or in a stray row,\n  // except inside a filled snarl, where the piece through a boundary node runs\n  // on into the snarl, and a path that stays inside the snarl has a row.\n  const strayRoute = async (strays: HaplotypeStrayOptions) => {\n    if (input.context > strays.context) {\n      throw new Fallback(\n        `the context of ${input.context} bp exceeds the ${strays.context} bp the haplotype index's stray rows cover`,\n      )\n    }\n    const spacing = stats.spacing\n    if (spacing === undefined) {\n      throw new Fallback('the haplotype index has no anchors')\n    }\n    const { bin, bound } = strays\n    const { fills, inserted } = input.snarls\n    if (input.snarls.mode === 'overlapping' && fills.length > 0) {\n      throw new Fallback(\n        \"the haplotype index's stray rows cover contained snarls only\",\n      )\n    }\n    for (const fill of fills) {\n      if (fill.inserted > 0 && fill.low === fill.high) {\n        throw new Fallback(\n          `the haplotype index's stray rows leave out the snarl bounded by node ${fill.low} at both ends`,\n        )\n      }\n      if (\n        fill.inserted > 0 &&\n        (strays.snarlNodes === undefined || fill.nodes > strays.snarlNodes)\n      ) {\n        throw new Fallback(\n          strays.snarlNodes === undefined\n            ? \"the haplotype index's stray rows leave snarls out\"\n            : `a snarl of ${fill.nodes} nodes exceeds the ${strays.snarlNodes} the haplotype index's stray rows cover`,\n        )\n      }\n    }\n    const firstBin = Math.floor(input.window.start / bin)\n    const lastBin = Math.floor((input.window.end - 1) / bin)\n    const lo = firstBin * bin\n    const hi = (lastBin + 1) * bin\n\n    // Every anchor within `bound` of the bins, and one beyond on each side.\n    // The indexer counts a section whose anchor lies exactly `bound` outside\n    // the bins as reaching the visits around it, so the anchor past that one\n    // must be read too, or the section between them is never planned. An\n    // anchor's node can start far before its multiple, so the first read\n    // does not settle it. The bins' node lists and stray rows come in the\n    // same round trip.\n    const anchorOf = new Map<number, HaplotypeAnchorRow>()\n    const readAnchors = async (fromK: number, toK: number) => {\n      const rows = await db.haplotypeAnchorsBetween(\n        input.referenceHandle,\n        fromK * spacing,\n        toK * spacing,\n      )\n      for (const row of rows) {\n        anchorOf.set(row.anchorOffset / spacing, row)\n      }\n    }\n    let lowest = Math.max(0, Math.floor((lo - bound) / spacing) - 1)\n    let highest = Math.ceil((hi + bound) / spacing) + 1\n    const [{ listed, strays: found }] = await Promise.all([\n      db.haplotypeBinData(input.referenceHandle, firstBin, lastBin),\n      readAnchors(lowest, highest),\n    ])\n    for (const handle of records.keys()) {\n      const id = nodeId(handle)\n      if (!isReverse(handle) && !listed(id) && !inserted.has(id)) {\n        throw new Fallback(\n          `the haplotype index lists node ${id} of the subgraph in no bin that the window touches`,\n        )\n      }\n    }\n    // The samples on the subgraph's nodes, for the check after the walks,\n    // read while the walks run.\n    stats.scans = handleRuns([...records.keys()].sort((x, y) => x - y))\n    const scanning = Promise.all(\n      stats.scans.map(([first, last]) =>\n        db.haplotypeSamplesInRange(first, last),\n      ),\n    )\n    scanning.catch(() => undefined)\n    while (\n      lowest > 0 &&\n      (anchorOf.get(lowest)?.pathOffset ?? Number.POSITIVE_INFINITY) >=\n        lo - bound\n    ) {\n      lowest -= 1\n      await readAnchors(lowest, lowest)\n    }\n    while (\n      anchorOf.has(highest) &&\n      anchorOf.get(highest)!.pathOffset <= hi + bound\n    ) {\n      highest += 1\n      await readAnchors(highest, highest)\n    }\n    const multiples = [...anchorOf.keys()].sort((x, y) => x - y)\n    const own = anchorOf.get(multiples[0] ?? -1)\n    if (!own) {\n      throw new Fallback('the haplotype index has no anchors on this path')\n    }\n    const anchorOffset = (k: number) => anchorOf.get(k)!.pathOffset\n    // A node that is the anchor of two multiples ends no section.\n    const multiplesOf = new Map<number, number[]>()\n    for (const k of multiples) {\n      const id = nodeId(anchorOf.get(k)!.node)\n      multiplesOf.set(id, [...(multiplesOf.get(id) ?? []), k])\n    }\n    const anchorNodes = [...multiplesOf.keys()]\n    const anchorRows = anchorNodes.map(\n      id => anchorOf.get(multiplesOf.get(id)![0]!)!.visits,\n    )\n    if (\n      !anchorRows[anchorNodes.indexOf(nodeId(own.node))]!.some(\n        row =>\n          row.pathHandle === input.referenceHandle &&\n          row.orientation === 'forward' &&\n          row.pathOffset === own.pathOffset,\n      )\n    ) {\n      throw new Error(\n        `The haplotype index has no anchor row for the reference path ${input.referenceHandle} at offset ${own.pathOffset} (node ${nodeId(own.node)}); it does not match this graph`,\n      )\n    }\n    const before = multiples.filter(k => anchorOffset(k) <= input.window.start)\n    const after = multiples.filter(k => anchorOffset(k) >= input.window.end)\n    stats.anchors = [\n      anchorOffset(before[before.length - 1] ?? multiples[0]!),\n      anchorOffset(after[0] ?? multiples[multiples.length - 1]!),\n    ]\n    stats.anchorsRead = multiples.length\n    const visits = new Map<\n      number,\n      { k: number | undefined; row: HaplotypeSample }[]\n    >()\n    const atAnchors = new Set<number>()\n    anchorNodes.forEach((id, i) => {\n      const ks = multiplesOf.get(id)!\n      const k = ks.length === 1 ? ks[0] : undefined\n      for (const row of anchorRows[i]!) {\n        atAnchors.add(row.pathHandle)\n        if (row.orientation === 'forward' && chosen(row.pathHandle)) {\n          visits.set(row.pathHandle, [\n            ...(visits.get(row.pathHandle) ?? []),\n            { k, row },\n          ])\n        }\n      }\n    })\n    stats.chosenPaths = [...atAnchors].filter(chosen).length\n    if (stats.chosenPaths > keepTuning.mostChosenPaths) {\n      throw new Fallback(\n        `${stats.chosenPaths} chosen paths pass the anchors, more than ${keepTuning.mostChosenPaths}`,\n      )\n    }\n\n    // A section between visits to adjacent anchors whose span meets the bins\n    // is walked whole, `bound` past both visits. One whose span ends up to\n    // `bound` outside the bins is walked `bound` to each side of the visit at\n    // that end. These are the walks the stray rows count on.\n    interface Plan {\n      pathHandle: number\n      from: HaplotypeSample\n      to: HaplotypeSample | undefined\n    }\n    const plans: Plan[] = []\n    let prefetchLo = Number.POSITIVE_INFINITY\n    let prefetchHi = 0\n    for (const [pathHandle, list] of visits) {\n      list.sort((x, y) => x.row.pathOffset - y.row.pathOffset)\n      for (let i = 0; i + 1 < list.length; i++) {\n        const from = list[i]!\n        const to = list[i + 1]!\n        if (\n          from.k === undefined ||\n          to.k === undefined ||\n          Math.abs(from.k - to.k) !== 1\n        ) {\n          continue\n        }\n        const [low, high] =\n          anchorOffset(from.k) <= anchorOffset(to.k) ? [from, to] : [to, from]\n        const a = anchorOffset(low.k!)\n        const b = anchorOffset(high.k!)\n        if (a < hi && b >= lo) {\n          plans.push({ pathHandle, from: from.row, to: to.row })\n          prefetchLo = Math.min(prefetchLo, a - bound)\n          prefetchHi = Math.max(prefetchHi, b + bound)\n        } else if (a >= hi && a - hi <= bound) {\n          plans.push({ pathHandle, from: low.row, to: undefined })\n          prefetchLo = Math.min(prefetchLo, a - bound)\n          prefetchHi = Math.max(prefetchHi, a + bound)\n        } else if (b < lo && lo - b <= bound) {\n          plans.push({ pathHandle, from: high.row, to: undefined })\n          prefetchLo = Math.min(prefetchLo, b - bound)\n          prefetchHi = Math.max(prefetchHi, b + bound)\n        }\n      }\n    }\n    const filled = new Set(fills.map(fill => `${fill.low}:${fill.high}`))\n    const rows = found\n      .filter(\n        row =>\n          chosen(row.pathHandle) &&\n          (row.snarl === undefined ||\n            filled.has(`${row.snarl[0]}:${row.snarl[1]}`)),\n      )\n      .sort((x, y) => x.pathHandle - y.pathHandle || x.pathStart - y.pathStart)\n    stats.strays = {\n      bins: lastBin - firstBin + 1,\n      rows: found.length,\n      walked: 0,\n      outsideBp: 0,\n    }\n    if (prefetchHi > 0) {\n      await input.prefetchReferenceRange(\n        input.referenceHandle,\n        Math.max(0, prefetchLo),\n        prefetchHi + 1,\n      )\n    }\n    stats.ms.scan = lap()\n\n    // A cap on each walk's bases outside the subgraph.\n    const cap = 8 * spacing + 2 * (input.window.end - input.window.start)\n    const counted = stats.strays\n    let walkBp = 0\n    const outside = (len: number) => {\n      counted.outsideBp += len\n      walkBp += len\n      if (walkBp > cap) {\n        throw new Fallback(\n          `a walk of a chosen path near the window went past its cap of ${cap} bp`,\n        )\n      }\n    }\n    // The stretches of each path that walks passed: every node that starts in\n    // [x, y). A visit is named by its node's start, so one at `to` is covered\n    // when the stretch ends past it.\n    const walkedRanges = new Map<number, [number, number][]>()\n    const covered = (pathHandle: number, from: number, to: number) =>\n      (walkedRanges.get(pathHandle) ?? []).some(([x, y]) => x <= from && to < y)\n    const markWalked = (pathHandle: number, from: number, to: number) => {\n      walkedRanges.set(pathHandle, [\n        ...(walkedRanges.get(pathHandle) ?? []),\n        [from, to],\n      ])\n    }\n    // Forward along a path from a position through every node that starts at\n    // or before `until`, jumping over the pieces it lands in; returns the\n    // offset it reached.\n    const walkForward = async (\n      pathHandle: number,\n      start: Pos,\n      startLeft: number,\n      until: number,\n      source: ChosenPieceSource,\n    ) => {\n      let pos: Pos | undefined = start\n      let left = startLeft\n      let reached = left\n      while (pos && left <= until) {\n        signal?.throwIfAborted()\n        let len: number\n        if (records.has(pos.node)) {\n          const piece = await pieceAtOrThrough(\n            { pos, left },\n            pathHandle,\n            'forward',\n            source,\n          )\n          const last = lastCursor(piece)\n          pos = last.pos\n          left = last.left\n          len = lengthIn(pos.node)\n          reached = Math.max(reached, piece.hapEnd)\n        } else {\n          len = (await record(pos.node)).sequenceLen\n          outside(len)\n          reached = Math.max(reached, left + len)\n        }\n        pos = await next(pos)\n        left += len\n      }\n      return reached\n    }\n    // Backward from a position through every node that ends after `until`;\n    // returns the offset reached.\n    const walkBackward = async (\n      pathHandle: number,\n      start: Pos,\n      startLeft: number,\n      until: number,\n    ) => {\n      let cursor: Cursor = { pos: start, left: startLeft }\n      let reached = startLeft\n      while (cursor.left > until) {\n        signal?.throwIfAborted()\n        const earlier = await previous(cursor.pos)\n        if (!earlier) {\n          break\n        }\n        const len = (await record(earlier.node)).sequenceLen\n        const earlierLeft = cursor.left - len\n        if (records.has(earlier.node)) {\n          const piece = await pieceAtOrThrough(\n            { pos: earlier, left: earlierLeft },\n            pathHandle,\n            'forward',\n            'section',\n          )\n          cursor = firstCursor(piece)\n          reached = Math.min(reached, piece.hapStart)\n        } else {\n          outside(len)\n          cursor = { pos: earlier, left: earlierLeft }\n          reached = Math.min(reached, earlierLeft)\n        }\n      }\n      return reached\n    }\n\n    for (const { pathHandle, from, to } of plans) {\n      const start = from.pathOffset\n      const stop = (to ?? from).pathOffset + bound\n      if (covered(pathHandle, start - bound, stop)) {\n        continue\n      }\n      const pos = { node: from.node, offset: from.offset }\n      walkBp = 0\n      const reachedEnd = await walkForward(\n        pathHandle,\n        pos,\n        start,\n        stop,\n        'section',\n      )\n      walkBp = 0\n      const reachedStart = await walkBackward(\n        pathHandle,\n        pos,\n        start,\n        start - bound,\n      )\n      markWalked(\n        pathHandle,\n        Math.min(reachedStart, start - bound),\n        Math.max(reachedEnd, stop + 1),\n      )\n      countWalk(to ? 'section' : 'visit', to ? 'past the far anchor' : 'bound')\n    }\n    for (const row of rows) {\n      if (covered(row.pathHandle, row.pathStart, row.pathEnd)) {\n        continue\n      }\n      walkBp = 0\n      const reachedEnd = await walkForward(\n        row.pathHandle,\n        { node: row.node, offset: row.offset },\n        row.pathStart,\n        row.pathEnd,\n        'stray',\n      )\n      markWalked(\n        row.pathHandle,\n        row.pathStart,\n        Math.max(reachedEnd, row.pathEnd + 1),\n      )\n      counted.walked += 1\n    }\n    stats.ms.walks = lap()\n\n    // A sample of a chosen path on the subgraph's nodes outside every piece\n    // would contradict the haplotype index's rows. A sample of the reverse\n    // orientation gives a position of the piece's twin.\n    const reversed: HaplotypeSample[] = []\n    for (const samples of await scanning) {\n      for (const sample of samples) {\n        stats.scanRows += 1\n        if (records.has(sample.node) && chosen(sample.pathHandle)) {\n          if (\n            !(piecesOfPath.get(sample.pathHandle) ?? []).some(id => {\n              const piece = pieces[id]!\n              return (\n                piece.hapStart <= sample.pathOffset &&\n                sample.pathOffset < piece.hapEnd\n              )\n            })\n          ) {\n            throw new Fallback(\n              `chosen path ${sample.pathHandle} has a sample at ${sample.pathOffset} on the window's nodes that no walk reached`,\n            )\n          }\n          if (sample.orientation === 'reverse') {\n            reversed.push(sample)\n          }\n        }\n      }\n    }\n    for (const sample of reversed) {\n      await pieceAtOrThrough(\n        {\n          pos: { node: sample.node, offset: sample.offset },\n          left: sample.pathOffset,\n        },\n        sample.pathHandle,\n        'reverse',\n        'twin',\n      )\n    }\n    stats.ms.check = lap()\n  }\n\n  const canonicalTwins = async () => {\n    // Canonical twins: a piece found only in the orientation extractPaths\n    // drops, or in one of two orientations it keeps, is walked on in that\n    // orientation while the samples of the other orientation at each node are\n    // read by coordinate. A matching sample gives a position of the other\n    // orientation, which is walked forward into the subgraph.\n    const orientationsOf = new Map<string, Set<Orientation>>()\n    const note = (piece: ChosenPiece) => {\n      const key = pieceKey(piece)\n      const seen = orientationsOf.get(key)\n      if (seen) {\n        seen.add(piece.orientation)\n      } else {\n        orientationsOf.set(key, new Set([piece.orientation]))\n      }\n    }\n    let noted = 0\n    const noteNew = () => {\n      for (; noted < pieces.length; noted++) {\n        note(pieces[noted]!)\n      }\n    }\n    noteNew()\n    const hasTwin = (piece: ChosenPiece) =>\n      (orientationsOf.get(pieceKey(piece))?.size ?? 0) > 1\n    const twinBound = 2 * interval\n    // extractPaths keeps the reference walk in either orientation, and its\n    // twin like any other walk, which matters when the reference is chosen.\n    const needsTwin = (piece: ChosenPiece, id: number) =>\n      id === referenceId\n        ? chosen(input.referenceHandle) && twinIsCanonical(piece)\n        : !piece.canonical || twinIsCanonical(piece)\n    for (let id = 0; id < pieces.length; id++) {\n      const piece = pieces[id]!\n      if (hasTwin(piece) || !needsTwin(piece, id)) {\n        continue\n      }\n      stats.twins.tried += 1\n      const other: Orientation =\n        piece.orientation === 'forward' ? 'reverse' : 'forward'\n      let cursor = lastCursor(piece)\n      let walkedBp = 0\n      let hit: HaplotypeSample | undefined\n      while (!hit && walkedBp <= twinBound) {\n        signal?.throwIfAborted()\n        const pos = await next(cursor.pos)\n        if (!pos) {\n          break\n        }\n        const len = (await record(pos.node)).sequenceLen\n        const left = forwardLeft(\n          piece.orientation,\n          cursor.left,\n          (await record(cursor.pos.node)).sequenceLen,\n          len,\n        )\n        const flipped = flipNode(pos.node)\n        hit = (await db.haplotypeSamplesInRange(flipped, flipped)).find(\n          s =>\n            s.pathHandle === piece.pathHandle &&\n            s.orientation === other &&\n            s.pathOffset === left,\n        )\n        walkedBp += len\n        cursor = { pos, left }\n      }\n      let walk: Cursor | undefined = hit && {\n        pos: { node: hit.node, offset: hit.offset },\n        left: hit.pathOffset,\n      }\n      let toPiece = 0\n      while (walk && !hasTwin(piece) && toPiece <= twinBound + piece.len) {\n        signal?.throwIfAborted()\n        if (records.has(walk.pos.node)) {\n          const landed = await pieceAtOrThrough(\n            walk,\n            piece.pathHandle,\n            other,\n            'twin',\n          )\n          const landedId = pieces.indexOf(landed)\n          await chain(landedId, true)\n          await chain(landedId, false)\n          noteNew()\n          walk = lastCursor(landed)\n        }\n        if (!hasTwin(piece)) {\n          const len: number = (await record(walk.pos.node)).sequenceLen\n          toPiece += len\n          const pos = await next(walk.pos)\n          walk = pos\n            ? {\n                pos,\n                left: forwardLeft(\n                  other,\n                  walk.left,\n                  len,\n                  (await record(pos.node)).sequenceLen,\n                ),\n              }\n            : undefined\n        }\n      }\n      noteNew()\n      if (!hasTwin(piece)) {\n        throw new Fallback(\n          `piece ${pieceKey(piece)} was found in one orientation where extractPaths keeps the other`,\n        )\n      }\n      stats.twins.found += 1\n    }\n    stats.ms.twins = lap()\n  }\n\n  try {\n    const strays = await db.haplotypeStrayOptions()\n    if (strays === undefined) {\n      throw new Fallback(\n        'the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them',\n      )\n    }\n    await strayRoute(strays)\n    await canonicalTwins()\n  } catch (error) {\n    if (!(error instanceof Fallback)) {\n      throw error\n    }\n    stats.fallback = error.message\n  }\n  return result()\n}\n\n// extractPaths's order, which is upstream's: by the walk's start position,\n// handle then offset.\nexport function extractionOrder(a: ChosenPiece, b: ChosenPiece) {\n  return a.handles[0]! - b.handles[0]! || a.offsets[0]! - b.offsets[0]!\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", "import { extractionOrder, findChosenPieces, handleRuns } from './chosenPaths.ts'\nimport {\n  ENDMARKER,\n  edgeIsCanonical,\n  encodeNode,\n  entryOrientation,\n  entrySide,\n  exitOrientation,\n  exitSide,\n  flipNode,\n  flipSide,\n  isReverse,\n  nodeId,\n  nodeOrientation,\n  pathEndsAreCanonical,\n  pathIsCanonical,\n} from './gbwt/node.ts'\nimport { gfaHeaderLines, sha256Hex, subgraphName } from './graphName.ts'\nimport { weightedLcs } from './lcs.ts'\nimport { pairAlignments, pairCigar } from './pairAlignment.ts'\nimport { formatPathName } from './pathName.ts'\n\nimport type { ChosenPiece, KeepStats } from './chosenPaths.ts'\nimport type { GBZBase, GbzPath, GbzRecord, HaplotypeSample } from './db.ts'\nimport type { NodeSide, Orientation } from './gbwt/node.ts'\nimport type { Pos } from './gbwt/record.ts'\nimport type { PathName } from './pathName.ts'\n\nexport type HaplotypeOutput = 'all' | 'distinct' | 'reference-only' | 'none'\n\nexport type SnarlOutput = 'none' | 'contained' | 'overlapping'\n\ntype HandleType =\n  | { kind: 'snarl-exit'; snarl: [number, number] }\n  | { kind: 'chain' }\n  | { kind: 'regular' }\n\n// A snarl filled between two boundary nodes: their ids, lower first, the\n// nodes between them, and how many of those the fill added to the subgraph.\nexport interface SnarlFill {\n  low: number\n  high: number\n  nodes: number\n  inserted: number\n}\n\nexport interface PathPosition {\n  seqOffset: number\n  handle: number\n  nodeOffset: number\n  gbwtOffset: number\n}\n\nexport interface ReferencePath {\n  position: PathPosition\n  name: PathName\n  handle: number\n}\n\nexport interface PathIdentity {\n  pathHandle: number\n  name: PathName\n  orientation: Orientation\n  hapStart: number\n  hapEnd: number\n}\n\ninterface PathInfo {\n  path: number[]\n  offsets: number[]\n  len: number\n  weight: number | undefined\n  identity: PathIdentity | undefined\n}\n\ntype EditOp = 'M' | 'I' | 'D'\ntype Edit = [EditOp, number]\n\nexport interface SubgraphPath {\n  name: string\n  weight?: number\n  cigar?: string\n  path: { id: string; is_reverse: boolean }[]\n}\n\nexport interface SubgraphJson {\n  nodes: { id: string; sequence: string }[]\n  edges: {\n    from: string\n    from_is_reverse: boolean\n    to: string\n    to_is_reverse: boolean\n  }[]\n  paths: SubgraphPath[]\n}\n\n// A step, and either end of an edge, is a GBWT handle: 2 * nodeId for the\n// forward orientation and 2 * nodeId + 1 for the reverse, which is how the\n// GBWT itself numbers them. nodeId and isReverse read the two halves back.\nexport interface CompactPath {\n  name: string\n  weight: number | undefined\n  cigar: string | undefined\n  steps: Int32Array\n}\n\nexport interface CompactSubgraph {\n  // Ascending, one entry per node; nodeSequences runs parallel to it.\n  nodeIds: Int32Array\n  nodeSequences: string[]\n  // Handle pairs laid end to end: edges[2i] -> edges[2i + 1].\n  edges: Int32Array\n  paths: CompactPath[]\n}\n\nexport interface AlignmentSpan {\n  strand: '+' | '-'\n  refStart: number\n  refEnd: number\n  cigar: string\n  weight: number | undefined\n  path: number[]\n  start: Pos\n}\n\nexport type HaplotypeAlignment = AlignmentSpan &\n  (\n    | {\n        resolved: true\n        name: PathName\n        label: string\n        pathHandle: number\n        hapStart: number\n        hapEnd: number\n      }\n    | { resolved: false }\n  )\n\nexport interface HaplotypeRef {\n  sample: string\n  haplotype: number\n}\n\nexport interface PairAlignmentOptions {\n  target: HaplotypeRef\n  query?: HaplotypeRef | undefined\n  maxGap?: number | undefined\n  minMatch?: number | undefined\n  bases?: boolean | undefined\n}\n\nexport interface PairAlignment {\n  query: PathName\n  queryStart: number\n  queryEnd: number\n  strand: '+' | '-'\n  target: PathName\n  targetStart: number\n  targetEnd: number\n  cigar: string\n  matches: number\n  columns: number\n  sharedBases: number\n}\n\nexport interface SubgraphOutputOptions {\n  cigar?: boolean | undefined\n  names?: 'anonymous' | 'resolved' | undefined\n}\n\nexport interface SubgraphOptions {\n  limit?: number | undefined\n  signal?: AbortSignal | undefined\n}\n\nexport class SubgraphLimitError extends Error {\n  override name = 'SubgraphLimitError'\n  readonly limit: number\n  readonly windowBp: number | undefined\n  readonly walkedBp: number | undefined\n\n  constructor(limit: number, walk?: { windowBp: number; walkedBp: number }) {\n    super(\n      walk === undefined\n        ? `Subgraph size limit of ${limit} nodes exceeded`\n        : `Subgraph size limit of ${limit} nodes exceeded ${walk.walkedBp} bp into a ${walk.windowBp} bp window`,\n    )\n    this.limit = limit\n    this.windowBp = walk?.windowBp\n    this.walkedBp = walk?.walkedBp\n  }\n}\n\nfunction sideBefore(\n  a: [number, number, NodeSide],\n  b: [number, number, NodeSide],\n) {\n  return (\n    a[0] < b[0] ||\n    (a[0] === b[0] && (a[1] < b[1] || (a[1] === b[1] && a[2] < b[2])))\n  )\n}\n\nclass SideQueue {\n  private heap: [number, number, NodeSide][] = []\n\n  push(distance: number, node: number, side: NodeSide) {\n    const heap = this.heap\n    heap.push([distance, node, side])\n    let i = heap.length - 1\n    while (i > 0) {\n      const parent = (i - 1) >> 1\n      if (sideBefore(heap[i]!, heap[parent]!)) {\n        ;[heap[i], heap[parent]] = [heap[parent]!, heap[i]!]\n        i = parent\n      } else {\n        break\n      }\n    }\n  }\n\n  pop() {\n    const heap = this.heap\n    const top = heap[0]\n    const last = heap.pop()\n    if (heap.length > 0 && last !== undefined) {\n      heap[0] = last\n      let i = 0\n      for (;;) {\n        const left = 2 * i + 1\n        const right = left + 1\n        let smallest = i\n        if (left < heap.length && sideBefore(heap[left]!, heap[smallest]!)) {\n          smallest = left\n        }\n        if (right < heap.length && sideBefore(heap[right]!, heap[smallest]!)) {\n          smallest = right\n        }\n        if (smallest === i) {\n          break\n        }\n        ;[heap[i], heap[smallest]] = [heap[smallest]!, heap[i]!]\n        i = smallest\n      }\n    }\n    return top\n  }\n\n  get size() {\n    return this.heap.length\n  }\n}\n\n// Which step of a walk matches which step of the reference, as two parallel\n// arrays rather than a list of pairs: there is one entry per step of every\n// walk being aligned, and a window at HPRC scale has millions of them.\ninterface Matches {\n  pathAt: Int32Array\n  refAt: Int32Array\n  count: number\n}\n\nfunction asMatches(pairs: [number, number][]): Matches {\n  const pathAt = new Int32Array(pairs.length)\n  const refAt = new Int32Array(pairs.length)\n  pairs.forEach(([a, b], i) => {\n    pathAt[i] = a\n    refAt[i] = b\n  })\n  return { pathAt, refAt, count: pairs.length }\n}\n\n// The first entry above `bound` of an ascending list, or undefined. Called\n// once per step of every walk being aligned, which is where `Array.find` hurt:\n// it allocated a closure over the bound each time, and scanned from the front\n// of a reference node's occurrence list, which a repeat locus makes long.\nfunction firstAbove(ascending: number[], bound: number) {\n  let lo = 0\n  let hi = ascending.length\n  while (lo < hi) {\n    const mid = (lo + hi) >> 1\n    if (ascending[mid]! > bound) {\n      hi = mid\n    } else {\n      lo = mid + 1\n    }\n  }\n  return ascending[lo]\n}\n\nfunction posKey(pos: Pos) {\n  return `${pos.node}:${pos.offset}`\n}\n\ninterface FragmentAlignment {\n  strand: '+' | '-'\n  refStart: number\n  refEnd: number\n  edits: Edit[]\n  weight: number | undefined\n  path: number[]\n  start: Pos\n  // Indices into the subgraph's paths, in walk order, and the bases of each\n  // that the CIGAR aligns when the piece is aligned alone.\n  pieces: number[]\n  soloAligned: number[]\n  identity:\n    | {\n        pathHandle: number\n        name: PathName\n        hapStart: number\n        hapEnd: number\n        walkForward: boolean\n      }\n    | undefined\n}\n\nfunction flipPath(path: number[]) {\n  return path.map(handle => flipNode(handle)).reverse()\n}\n\nfunction joinable(a: FragmentAlignment, b: FragmentAlignment) {\n  const insertion = b.identity!.hapStart - a.identity!.hapEnd\n  const deletion =\n    a.strand === '+' ? b.refStart - a.refEnd : a.refStart - b.refEnd\n  return a.strand === b.strand && insertion >= 0 && deletion >= 0\n    ? { insertion, deletion }\n    : undefined\n}\n\nfunction joinPair(\n  a: FragmentAlignment,\n  b: FragmentAlignment,\n  gap: { insertion: number; deletion: number },\n): FragmentAlignment {\n  const [left, right] = a.strand === '+' ? [a, b] : [b, a]\n  const edits = left.edits.map(([op, len]): Edit => [op, len])\n  appendGap(edits, gap.insertion, gap.deletion)\n  for (const [op, len] of right.edits) {\n    appendEdit(edits, op, len)\n  }\n  const walkForward = a.identity!.walkForward\n  const [first, second] = walkForward ? [a, b] : [b, a]\n  return {\n    strand: a.strand,\n    refStart: left.refStart,\n    refEnd: right.refEnd,\n    edits,\n    weight: undefined,\n    path: [...first.path, ...second.path],\n    start: first.start,\n    pieces: [...first.pieces, ...second.pieces],\n    soloAligned: [...first.soloAligned, ...second.soloAligned],\n    identity: {\n      pathHandle: a.identity!.pathHandle,\n      name: a.identity!.name,\n      hapStart: a.identity!.hapStart,\n      hapEnd: b.identity!.hapEnd,\n      walkForward,\n    },\n  }\n}\n\n// Pieces of one path in haplotype order, joined where they are colinear on\n// the reference, and otherwise aligned again as one walk. A piece aligned over\n// less than half its length joins only between two that are.\nfunction joinSiblings(\n  fragments: FragmentAlignment[],\n  mostlyAligned: (fragment: FragmentAlignment) => boolean,\n  alignJointly: (parts: FragmentAlignment[]) => FragmentAlignment | undefined,\n) {\n  if (fragments.some(f => f.weight !== undefined)) {\n    return fragments\n  }\n  const byPath = new Map<number, number[]>()\n  fragments.forEach((fragment, index) => {\n    if (fragment.identity) {\n      const siblings = byPath.get(fragment.identity.pathHandle)\n      if (siblings) {\n        siblings.push(index)\n      } else {\n        byPath.set(fragment.identity.pathHandle, [index])\n      }\n    }\n  })\n  const joined = new Map<number, FragmentAlignment>()\n  const consumed = new Set<number>()\n  for (const siblings of byPath.values()) {\n    siblings.sort(\n      (x, y) =>\n        fragments[x]!.identity!.hapStart - fragments[y]!.identity!.hapStart,\n    )\n    let head = siblings[0]!\n    let current = fragments[head]!\n    let between: number[] = []\n    for (const index of siblings.slice(1)) {\n      const next = fragments[index]!\n      const gap = between.length === 0 ? joinable(current, next) : undefined\n      if (gap) {\n        current = joinPair(current, next, gap)\n        consumed.add(index)\n        continue\n      }\n      if (!mostlyAligned(next)) {\n        between.push(index)\n        continue\n      }\n      const joint = mostlyAligned(current)\n        ? alignJointly([current, ...between.map(i => fragments[i]!), next])\n        : undefined\n      if (joint) {\n        current = joint\n        for (const i of [...between, index]) {\n          consumed.add(i)\n        }\n      } else {\n        joined.set(head, current)\n        head = index\n        current = next\n      }\n      between = []\n    }\n    joined.set(head, current)\n  }\n  return fragments.flatMap((fragment, index) =>\n    consumed.has(index) ? [] : [joined.get(index) ?? fragment],\n  )\n}\n\nfunction pathPosition(info: PathInfo, k: number): Pos {\n  return { node: info.path[k]!, offset: info.offsets[k]! }\n}\n\ninterface Anchor {\n  pathHandle: number\n  orientation: Orientation\n  base: number\n}\n\nexport type ChainEnd =\n  | 'in-fragment sample'\n  | 'identified sibling'\n  | 'out-of-window sample'\n  | 'bound'\n  | 'endmarker'\n  | 'cycle'\n\nexport interface ChainRecord {\n  fragments: number\n  steps: number\n  seeks: number\n  reentries: number\n  twinLandings: number\n  end: ChainEnd\n  pathHandle: number | undefined\n}\n\nexport interface IdentificationStats {\n  interval: number\n  scans: [number, number][]\n  windowSamples: number\n  fragmentLengths: number[]\n  companionSeeks: number\n  companionMisses: number\n  graphLookups: number\n  graphFetches: number\n  chains: ChainRecord[]\n}\n\ninterface SubgraphStats {\n  orderedAlignments: number\n  lcsAlignments: number\n  identificationSteps: number\n  identificationFetches: number\n  identification: IdentificationStats\n  // the top-level snarls the query filled, and the nodes those fills added\n  snarls: { fills: number; inserted: number }\n  keep: KeepStats | undefined\n}\n\nconst PREFETCH_RUN_GAP = 32768\n\nfunction rowidRuns(handles: number[]) {\n  const sorted = [...handles].sort((a, b) => a - b)\n  const runs: [number, number][] = []\n  for (const handle of sorted) {\n    const last = runs[runs.length - 1]\n    if (last && handle - last[1] <= PREFETCH_RUN_GAP) {\n      last[1] = handle\n    } else {\n      runs.push([handle, handle])\n    }\n  }\n  return runs\n}\n\nexport class Subgraph {\n  private records = new Map<number, GbzRecord>()\n  private paths: PathInfo[] = []\n  private twinStarts = new Set<string>()\n  private twinDeferred = false\n  private unsettled:\n    { paths: PathInfo[]; refId: number | undefined } | undefined\n  private refId: number | undefined\n  private refPath: PathName | undefined\n  private refHandle: number | undefined\n  private refInterval: [number, number] | undefined\n  private refIndexCache: Map<number, number[]> | undefined\n  private refPrefixCache: number[] | undefined\n  private walkedBp: number | undefined\n  private snarlMode: SnarlOutput = 'none'\n  private snarlFills: SnarlFill[] = []\n  private snarlNodes = new Set<number>()\n  /** @internal */\n  readonly stats: SubgraphStats = {\n    orderedAlignments: 0,\n    lcsAlignments: 0,\n    snarls: { fills: 0, inserted: 0 },\n    identificationSteps: 0,\n    identificationFetches: 0,\n    identification: {\n      interval: 0,\n      scans: [],\n      windowSamples: 0,\n      fragmentLengths: [],\n      companionSeeks: 0,\n      companionMisses: 0,\n      graphLookups: 0,\n      graphFetches: 0,\n      chains: [],\n    },\n    keep: undefined,\n  }\n\n  private db: GBZBase\n  private readonly limit: number | undefined\n  private readonly signal: AbortSignal | undefined\n\n  private constructor(db: GBZBase, opts: SubgraphOptions) {\n    this.db = db\n    this.limit = opts.limit\n    this.signal = opts.signal\n  }\n\n  /** @internal */\n  static create(db: GBZBase, opts: SubgraphOptions = {}) {\n    return new Subgraph(db, opts)\n  }\n\n  get nodeCount() {\n    return this.records.size / 2\n  }\n\n  get pathCount() {\n    this.settleDeferred()\n    return this.paths.length\n  }\n\n  get referenceInterval() {\n    return this.refInterval && this.refPath\n      ? {\n          name: this.refPath,\n          start: this.refPath.fragment + this.refInterval[0],\n          end: this.refPath.fragment + this.refInterval[1],\n        }\n      : undefined\n  }\n\n  hasNode(id: number) {\n    return this.records.has(encodeNode(id, 'forward'))\n  }\n\n  hasHandle(handle: number) {\n    return this.records.has(handle)\n  }\n\n  private record(handle: number) {\n    const record = this.records.get(handle)\n    if (!record) {\n      throw new Error(`Subgraph has no record for handle ${handle}`)\n    }\n    return record\n  }\n\n  private sortedHandles() {\n    return [...this.records.keys()].sort((a, b) => a - b)\n  }\n\n  private async addNode(id: number) {\n    this.signal?.throwIfAborted()\n    if (this.limit !== undefined && this.nodeCount >= this.limit) {\n      throw new SubgraphLimitError(this.limit)\n    }\n    const forward = await this.db.getRecord(encodeNode(id, 'forward'))\n    const reverse = await this.db.getRecord(encodeNode(id, 'reverse'))\n    if (!forward || !reverse) {\n      throw new Error(`Node ${id} does not exist in the graph`)\n    }\n    this.records.set(forward.handle, forward)\n    this.records.set(reverse.handle, reverse)\n  }\n\n  private async ensureNode(id: number) {\n    if (!this.hasNode(id)) {\n      await this.addNode(id)\n    }\n  }\n\n  private clearPaths() {\n    this.paths = []\n    this.twinStarts.clear()\n    this.twinDeferred = false\n    this.unsettled = undefined\n    this.refId = undefined\n    this.refPath = undefined\n    this.refHandle = undefined\n    this.refInterval = undefined\n    this.refIndexCache = undefined\n    this.refPrefixCache = undefined\n  }\n\n  /** @internal */\n  async pathPosition(query: PathName): Promise<ReferencePath> {\n    const path = await this.db.findPath(query)\n    if (!path) {\n      throw new Error(\n        `Cannot find a path covering offset ${query.fragment} of ${formatPathName(query)}`,\n      )\n    }\n    if (!path.isIndexed) {\n      throw new Error(\n        `The fragment of ${formatPathName(path.name)} at ${path.name.fragment} has not been indexed for random access`,\n      )\n    }\n    const queryOffset = query.fragment - path.name.fragment\n    const indexed = await this.db.indexedPosition(path.handle, queryOffset)\n    if (!indexed) {\n      throw new Error(\n        `The fragment of ${formatPathName(path.name)} at ${path.name.fragment} has not been indexed for random access`,\n      )\n    }\n    return this.findPathPosition(\n      path,\n      queryOffset,\n      indexed.pathOffset,\n      indexed.pos,\n    )\n  }\n\n  private async findPathPosition(\n    path: GbzPath,\n    queryOffset: number,\n    startOffset: number,\n    start: Pos,\n  ): Promise<ReferencePath> {\n    let pathOffset = startOffset\n    let pos = start\n    for (;;) {\n      await this.ensureNode(nodeId(pos.node))\n      const record = this.record(pos.node)\n      if (pathOffset + record.sequenceLen > queryOffset) {\n        return {\n          position: {\n            seqOffset: queryOffset,\n            handle: pos.node,\n            nodeOffset: queryOffset - pathOffset,\n            gbwtOffset: pos.offset,\n          },\n          name: path.name,\n          handle: path.handle,\n        }\n      }\n      pathOffset += record.sequenceLen\n      const next = record.gbwt().lf(pos.offset)\n      if (!next) {\n        throw new Error(\n          `The fragment of ${formatPathName(path.name)} at ${path.name.fragment} does not contain offset ${queryOffset}`,\n        )\n      }\n      pos = next\n    }\n  }\n\n  /** @internal */\n  async aroundPosition(handle: number, nodeOffset: number, context: number) {\n    const id = nodeId(handle)\n    await this.ensureNode(id)\n    const record = this.record(handle)\n    const orientation = nodeOrientation(handle)\n    const active = new SideQueue()\n    active.push(nodeOffset, id, entrySide(orientation))\n    active.push(record.sequenceLen - nodeOffset - 1, id, exitSide(orientation))\n    return this.insertContext(active, context)\n  }\n\n  /** @internal */\n  prefetchReferenceWalk(reference: ReferencePath, len: number) {\n    return this.prefetchReferenceRange(\n      reference.handle,\n      reference.position.seqOffset,\n      reference.position.seqOffset + len,\n    )\n  }\n\n  // One request for the reference walk's node records where their rowids are\n  // close, and one prefetch over the runs of them where the walk crosses a gap\n  // in node ids (AMY1's reference walk spans two gaps of millions), so the walk\n  // after it never fetches leaf pages one at a time.\n  private async prefetchReferenceRange(\n    pathHandle: number,\n    fromOffset: number,\n    toOffset: number,\n  ) {\n    const [first, last] = await Promise.all([\n      this.db.indexedPosition(pathHandle, fromOffset),\n      this.db.indexedPosition(pathHandle, toOffset),\n    ])\n    if (first && last) {\n      const a = first.pos.node\n      const b = last.pos.node\n      const whole = await this.db.prefetchRecords([\n        [Math.min(a, b), Math.max(a, b) + 1],\n      ])\n      if (!whole) {\n        const positions = await this.db.indexedPositionsBetween(\n          pathHandle,\n          fromOffset,\n          toOffset,\n        )\n        await this.db.prefetchRecords(\n          rowidRuns(positions.map(p => p.pos.node)).map(([lo, hi]) => [\n            lo,\n            hi + 2,\n          ]),\n          true,\n        )\n      }\n    }\n    return first\n  }\n\n  /** @internal */\n  async aroundInterval(start: PathPosition, len: number, context: number) {\n    if (!(len > 0)) {\n      throw new Error('Interval length must be greater than 0')\n    }\n    this.walkedBp = 0\n    try {\n      return await this.walkInterval(start, len, context)\n    } catch (error) {\n      throw error instanceof SubgraphLimitError && error.windowBp === undefined\n        ? new SubgraphLimitError(error.limit, {\n            windowBp: len,\n            walkedBp: this.walkedBp,\n          })\n        : error\n    }\n  }\n\n  /** @internal */\n  get referenceWalkedBp() {\n    return this.walkedBp\n  }\n\n  private async walkInterval(\n    start: PathPosition,\n    len: number,\n    context: number,\n  ) {\n    let pos: Pos = { node: start.handle, offset: start.gbwtOffset }\n    let offset = start.nodeOffset\n    let remaining = len\n    const active = new SideQueue()\n    for (;;) {\n      const id = nodeId(pos.node)\n      const orientation = nodeOrientation(pos.node)\n      this.walkedBp = len - remaining\n      await this.ensureNode(id)\n      const record = this.record(pos.node)\n      if (offset >= record.sequenceLen) {\n        throw new Error(\n          `Offset ${offset} in node ${id} of length ${record.sequenceLen}`,\n        )\n      }\n      active.push(offset, id, entrySide(orientation))\n      const distanceToNext = record.sequenceLen - offset\n      if (remaining <= distanceToNext) {\n        active.push(\n          remaining === distanceToNext ? 0 : distanceToNext - remaining - 1,\n          id,\n          exitSide(orientation),\n        )\n        break\n      }\n      active.push(0, id, exitSide(orientation))\n      const next = record.gbwt().lf(pos.offset)\n      if (!next) {\n        throw new Error(\n          `No successor for GBWT position (${pos.node}, ${pos.offset})`,\n        )\n      }\n      pos = next\n      offset = 0\n      remaining -= distanceToNext\n    }\n    this.walkedBp = len\n    return this.insertContext(active, context)\n  }\n\n  /** @internal */\n  async aroundNodes(nodes: Iterable<number>, context: number) {\n    const active = new SideQueue()\n    for (const id of nodes) {\n      await this.ensureNode(id)\n      active.push(0, id, 'left')\n      active.push(0, id, 'right')\n    }\n    return this.insertContext(active, context)\n  }\n\n  private async insertContext(active: SideQueue, context: number) {\n    this.clearPaths()\n    this.snarlMode = 'none'\n    this.snarlFills = []\n    this.snarlNodes.clear()\n    this.stats.snarls = { fills: 0, inserted: 0 }\n    const visited = new Set<string>()\n    const toRemove = new Set<number>()\n    for (const handle of this.records.keys()) {\n      toRemove.add(nodeId(handle))\n    }\n    let inserted = 0\n    while (active.size > 0) {\n      const [distance, id, side] = active.pop()!\n      const key = `${id}:${side}`\n      if (visited.has(key)) {\n        continue\n      }\n      visited.add(key)\n      toRemove.delete(id)\n      if (!this.hasNode(id)) {\n        await this.addNode(id)\n        inserted += 1\n      }\n      const otherSide = flipSide(side)\n      if (!visited.has(`${id}:${otherSide}`)) {\n        const record = this.record(encodeNode(id, entryOrientation(side)))\n        const nextDistance = distance + record.sequenceLen - 1\n        if (nextDistance <= context) {\n          active.push(nextDistance, id, otherSide)\n        }\n      }\n      const record = this.record(encodeNode(id, exitOrientation(side)))\n      const nextDistance = distance + 1\n      if (nextDistance <= context) {\n        for (const successor of record.successors()) {\n          const successorId = nodeId(successor)\n          const successorSide = entrySide(nodeOrientation(successor))\n          if (!visited.has(`${successorId}:${successorSide}`)) {\n            active.push(nextDistance, successorId, successorSide)\n          }\n        }\n      }\n    }\n    for (const id of toRemove) {\n      this.records.delete(encodeNode(id, 'forward'))\n      this.records.delete(encodeNode(id, 'reverse'))\n    }\n    return { inserted, removed: toRemove.size }\n  }\n\n  /** @internal */\n  async betweenNodes(start: number, end: number) {\n    return (await this.fillBetween(start, end)).inserted.length\n  }\n\n  private async fillBetween(start: number, end: number) {\n    this.clearPaths()\n    const active = [start, flipNode(end)]\n    const visited = new Set([nodeId(start), nodeId(end)])\n    const inserted: number[] = []\n    while (active.length > 0) {\n      const curr = active.pop()!\n      const id = nodeId(curr)\n      if (!this.hasNode(id)) {\n        await this.addNode(id)\n        inserted.push(id)\n      }\n      for (const successor of this.record(curr).successors()) {\n        const successorId = nodeId(successor)\n        if (!visited.has(successorId)) {\n          active.push(successor, flipNode(successor))\n          visited.add(successorId)\n        }\n      }\n    }\n    return { inserted, nodes: visited.size - 2 }\n  }\n\n  /** @internal */\n  async extractSnarls(snarls: SnarlOutput) {\n    let total = 0\n    this.snarlMode = snarls\n    for (const [start, end] of await this.overlappingSnarls(snarls)) {\n      const { inserted, nodes } = await this.fillBetween(start, end)\n      const a = nodeId(start)\n      const b = nodeId(end)\n      this.snarlFills.push({\n        low: Math.min(a, b),\n        high: Math.max(a, b),\n        nodes,\n        inserted: inserted.length,\n      })\n      for (const id of inserted) {\n        this.snarlNodes.add(id)\n      }\n      total += inserted.length\n    }\n    this.stats.snarls = {\n      fills: this.snarlFills.length,\n      inserted: this.snarlNodes.size,\n    }\n    return total\n  }\n\n  private async overlappingSnarls(snarls: SnarlOutput) {\n    const result: [number, number][] = []\n    if (snarls !== 'none') {\n      let foundLink = false\n      for (const handle of this.sortedHandles()) {\n        const record = this.record(handle)\n        const next = record.next\n        if (next !== undefined) {\n          foundLink = true\n          if (this.hasHandle(next)) {\n            if (edgeIsCanonical(handle, next)) {\n              result.push([handle, next])\n            }\n          } else if (\n            snarls === 'overlapping' &&\n            this.isSnarlEntryInSubgraph(record)\n          ) {\n            result.push([handle, next])\n          }\n        }\n      }\n      if (\n        !foundLink &&\n        snarls === 'overlapping' &&\n        (await this.db.hasChainLinks())\n      ) {\n        const covering = await this.findCoveringSnarl()\n        if (covering) {\n          result.push(covering)\n        }\n      }\n    }\n    return result\n  }\n\n  private isSnarlEntryInSubgraph(record: GbzRecord) {\n    const successors = record.successors()\n    const first = successors.find(handle => this.hasHandle(handle))\n    return first === undefined\n      ? false\n      : successors.length > 1 ||\n          this.record(flipNode(first)).successors().length > 1\n  }\n\n  private recordReader(onFetch?: () => void) {\n    const outside = new Map<number, GbzRecord>()\n    return async (handle: number) => {\n      const inside = this.records.get(handle)\n      if (inside) {\n        return inside\n      }\n      let record = outside.get(handle)\n      if (!record) {\n        record = await this.db.getRecord(handle)\n        onFetch?.()\n        if (!record) {\n          throw new Error(`Node record ${handle} is missing from the database`)\n        }\n        outside.set(handle, record)\n      }\n      return record\n    }\n  }\n\n  private async findCoveringSnarl() {\n    const read = this.recordReader()\n    const isSnarlEntry = async (record: GbzRecord) => {\n      const successors = record.successors()\n      const first = successors[0]\n      return first === undefined\n        ? false\n        : successors.length > 1 ||\n            (await read(flipNode(first))).successors().length > 1\n    }\n    const classify = async (handle: number): Promise<HandleType> => {\n      const reverse = await read(flipNode(handle))\n      return reverse.next !== undefined\n        ? (await isSnarlEntry(reverse))\n          ? { kind: 'snarl-exit', snarl: [flipNode(handle), reverse.next] }\n          : { kind: 'chain' }\n        : (await read(handle)).next !== undefined\n          ? { kind: 'chain' }\n          : { kind: 'regular' }\n    }\n    const visited = new Set<number>()\n    const queue = this.sortedHandles().flatMap(handle =>\n      this.record(handle).successors(),\n    )\n    let result: [number, number] | undefined\n    let done = false\n    while (!done && queue.length > 0) {\n      const handle = queue.shift()!\n      const id = nodeId(handle)\n      if (!this.hasHandle(handle) && !visited.has(id)) {\n        visited.add(id)\n        const type = await classify(handle)\n        if (type.kind === 'snarl-exit') {\n          result = type.snarl\n          done = true\n        } else if (type.kind === 'chain') {\n          done = true\n        } else {\n          for (const orientation of ['forward', 'reverse'] as const) {\n            queue.push(\n              ...(await read(encodeNode(id, orientation))).successors(),\n            )\n          }\n        }\n      }\n    }\n    return result\n  }\n\n  /** @internal */\n  extractPaths(reference: ReferencePath | undefined, output: HaplotypeOutput) {\n    this.clearPaths()\n    if (output === 'none') {\n      return\n    }\n    const refPos = reference?.position\n    this.refPath = reference?.name\n    this.refHandle = reference?.handle\n    const handles = this.sortedHandles()\n    const count = handles.length\n    const indexOf = new Map<number, number>()\n    handles.forEach((handle, i) => indexOf.set(handle, i))\n    // One flat pair for the whole subgraph, indexed by rowStart[node] + offset,\n    // rather than an Int32Array per node. walk() reads a successor on every one\n    // of a window's steps \u2014 9.9M of them at MHC class II \u2014 and through an array\n    // of forty thousand small buffers each of those is a pointer chase into\n    // scattered memory. The per-node arrays die before the walking starts.\n    const rowStart = new Int32Array(count + 1)\n    const seqLen = new Int32Array(count)\n    const rows: { nodes: Int32Array; offsets: Int32Array }[] = []\n    for (let i = 0; i < count; i++) {\n      const record = this.record(handles[i]!)\n      const row = record.gbwt().decompressArrays()\n      seqLen[i] = record.sequenceLen\n      rows.push(row)\n      rowStart[i + 1] = rowStart[i]! + row.nodes.length\n    }\n    const positions = rowStart[count]!\n    const nextIndex = new Int32Array(positions)\n    const nextOffset = new Int32Array(positions)\n    const hasPredecessor = new Uint8Array(positions)\n    for (let i = 0; i < count; i++) {\n      const row = rows[i]!\n      nextIndex.set(row.nodes, rowStart[i])\n      nextOffset.set(row.offsets, rowStart[i])\n    }\n    rows.length = 0\n    for (let k = 0; k < positions; k++) {\n      const j = indexOf.get(nextIndex[k]!)\n      if (j === undefined) {\n        nextIndex[k] = -1\n      } else {\n        nextIndex[k] = j\n        hasPredecessor[rowStart[j]! + nextOffset[k]!] = 1\n      }\n    }\n    const refIndex =\n      refPos === undefined ? undefined : indexOf.get(refPos.handle)\n    const refGbwtOffset = refPos?.gbwtOffset\n    let refOffset: number | undefined\n    const walk = (i: number, offset: number, path: number[] | undefined) => {\n      const offsets: number[] = []\n      let steps = 0\n      let len = 0\n      let refAt = -1\n      let cur = i\n      let off = offset\n      for (;;) {\n        if (cur === refIndex && off === refGbwtOffset) {\n          refAt = steps\n        }\n        if (path) {\n          path.push(handles[cur]!)\n          offsets.push(off)\n        }\n        steps += 1\n        len += seqLen[cur]!\n        const at = rowStart[cur]! + off\n        const next = nextIndex[at]!\n        if (next < 0) {\n          break\n        }\n        off = nextOffset[at]!\n        cur = next\n      }\n      return { offsets, len, refAt, last: cur }\n    }\n    const keep = (\n      path: number[],\n      offsets: number[],\n      len: number,\n      refAt: number,\n    ) => {\n      if (refAt >= 0) {\n        this.refId = this.paths.length\n        refOffset = refAt\n      }\n      this.paths.push({\n        path,\n        offsets,\n        len,\n        weight: undefined,\n        identity: undefined,\n      })\n    }\n    const twinsExpected = new Int32Array(count)\n    for (let i = 0; i < count; i++) {\n      const first = handles[i]!\n      if (!isReverse(first)) {\n        const from = rowStart[i]!\n        const degree = rowStart[i + 1]! - from\n        for (let offset = 0; offset < degree; offset++) {\n          if (hasPredecessor[from + offset] === 0) {\n            const path: number[] = []\n            const { offsets, len, refAt, last } = walk(i, offset, path)\n            const lastHandle = handles[last]!\n            if (refAt >= 0 || pathEndsAreCanonical(first, lastHandle)) {\n              keep(path, offsets, len, refAt)\n              if (!isReverse(lastHandle)) {\n                const twinRecord = indexOf.get(flipNode(lastHandle))!\n                twinsExpected[twinRecord] = twinsExpected[twinRecord]! + 1\n              }\n            } else {\n              this.twinStarts.add(posKey({ node: first, offset }))\n            }\n          }\n        }\n      }\n    }\n    for (let i = 0; i < count; i++) {\n      const first = handles[i]!\n      if (isReverse(first)) {\n        const from = rowStart[i]!\n        const degree = rowStart[i + 1]! - from\n        let startCount = 0\n        for (let offset = 0; offset < degree; offset++) {\n          if (hasPredecessor[from + offset] === 0) {\n            startCount += 1\n          }\n        }\n        // Until the reference walk is found, it can be one of these starts,\n        // with its twin kept above as a walk like any other.\n        const allTwins =\n          (refIndex === undefined || refOffset !== undefined) &&\n          startCount === twinsExpected[i]\n        for (let offset = 0; offset < degree; offset++) {\n          if (hasPredecessor[from + offset] === 0) {\n            const bare = allTwins ? undefined : walk(i, offset, undefined)\n            if (\n              bare &&\n              (bare.refAt >= 0 ||\n                pathEndsAreCanonical(first, handles[bare.last]))\n            ) {\n              const path: number[] = []\n              const { offsets, len, refAt } = walk(i, offset, path)\n              keep(path, offsets, len, refAt)\n            } else {\n              this.twinStarts.add(posKey({ node: first, offset }))\n            }\n          }\n        }\n      }\n    }\n    // Upstream lists walks by start position, handle then offset; the two\n    // passes above find the forward-start walks first.\n    const refInfo =\n      this.refId === undefined ? undefined : this.paths[this.refId]\n    this.paths.sort(\n      (x, y) => x.path[0]! - y.path[0]! || x.offsets[0]! - y.offsets[0]!,\n    )\n    if (refInfo) {\n      this.refId = this.paths.indexOf(refInfo)\n    }\n    if (refPos) {\n      if (refOffset === undefined || this.refId === undefined) {\n        this.clearPaths()\n        throw new Error('Could not find the reference path')\n      }\n      const info = this.paths[this.refId]!\n      let before = refPos.nodeOffset\n      for (const handle of info.path.slice(0, refOffset)) {\n        before += this.record(handle).sequenceLen\n      }\n      const start = refPos.seqOffset - before\n      this.refInterval = [start, start + info.len]\n      info.identity = {\n        pathHandle: reference.handle,\n        name: reference.name,\n        orientation: 'forward',\n        hapStart: start,\n        hapEnd: start + info.len,\n      }\n    }\n    if (output === 'distinct') {\n      this.distinctPaths(true)\n    } else if (output === 'reference-only') {\n      if (this.refId === undefined) {\n        throw new Error('Reference path is required for reference-only output')\n      }\n      this.paths = [this.paths[this.refId]!]\n      this.refId = 0\n    }\n  }\n\n  // Identical walks become one record whose weight counts them, and the\n  // reference walk stands for its own group, since the outputs read its\n  // offsets and identity. Walks that identification will drop as twins\n  // (dropTwins) stay apart until then, so that the record they would have\n  // merged into keeps a name and a weight of its own: the twin of a reference\n  // walk that is not canonical, which a haplotype stored against the reference\n  // walks handle for handle, and a walk canonical in both orientations, as\n  // through a hairpin, which extractPaths keeps twice.\n  private distinctPaths(deferTwins: boolean) {\n    const refInfo =\n      this.refId === undefined ? undefined : this.paths[this.refId]\n    const refPath = refInfo?.path\n    const referenceTwin =\n      refPath && !pathIsCanonical(refPath) ? flipPath(refPath) : undefined\n    const deferred = (path: number[]) =>\n      (referenceTwin !== undefined &&\n        comparePaths(path, referenceTwin) === 0) ||\n      pathIsCanonical(flipPath(path))\n    const defer = deferTwins && this.db.hasHaplotypeIndex\n    this.twinDeferred = false\n    this.paths.sort(\n      (x, y) =>\n        comparePaths(x.path, y.path) ||\n        x.len - y.len ||\n        (x === refInfo ? -1 : y === refInfo ? 1 : 0),\n    )\n    const merged: PathInfo[] = []\n    let refId: number | undefined\n    for (const info of this.paths) {\n      const last = merged[merged.length - 1]\n      const apart = defer && info !== refInfo && deferred(info.path)\n      this.twinDeferred ||= apart\n      if (last && comparePaths(last.path, info.path) === 0 && !apart) {\n        last.weight = (last.weight ?? 1) + (info.weight ?? 1)\n      } else {\n        if (info === refInfo) {\n          refId = merged.length\n        }\n        merged.push({ ...info, weight: info.weight ?? 1 })\n      }\n    }\n    this.paths = merged\n    this.refId = refId\n  }\n\n  // Merges identical walks into one record with a weight, as extractPaths does\n  // for 'distinct'. After keepHaplotypes the weights count kept haplotypes.\n  mergeDistinct() {\n    if (this.twinDeferred) {\n      this.settleDeferred()\n    } else {\n      this.distinctPaths(false)\n    }\n  }\n\n  // Output read before identifyPaths sees the walks merged as they would be\n  // without a haplotype index; identifyPaths takes them apart again.\n  private settleDeferred() {\n    if (this.twinDeferred) {\n      this.unsettled = { paths: [...this.paths], refId: this.refId }\n      this.distinctPaths(false)\n    }\n  }\n\n  // extractPaths keeps the canonical orientation of each walk, and both\n  // orientations are canonical when a walk starts and ends at one node in\n  // opposite orientations, as through a hairpin; the twin of a reference walk\n  // that is not canonical is kept too. Named, a twin is the same stretch of\n  // the same path as another walk, read the other way, and the reverse one\n  // goes.\n  private dropTwins() {\n    const refInfo =\n      this.refId === undefined ? undefined : this.paths[this.refId]\n    const interval = this.refInterval\n    const span = (identity: PathIdentity) =>\n      `${identity.pathHandle}:${identity.hapStart}-${identity.hapEnd}`\n    const forward = new Set<string>()\n    if (refInfo?.identity && interval) {\n      forward.add(\n        span({\n          ...refInfo.identity,\n          hapStart: interval[0],\n          hapEnd: interval[1],\n        }),\n      )\n    }\n    for (const info of this.paths) {\n      if (info !== refInfo && info.identity?.orientation === 'forward') {\n        forward.add(span(info.identity))\n      }\n    }\n    const kept = this.paths.filter(\n      info =>\n        info === refInfo ||\n        info.identity?.orientation !== 'reverse' ||\n        !forward.has(span(info.identity)),\n    )\n    if (kept.length < this.paths.length) {\n      this.paths = kept\n      this.refId = refInfo === undefined ? undefined : kept.indexOf(refInfo)\n    }\n    if (this.twinDeferred) {\n      this.distinctPaths(false)\n    }\n  }\n\n  // Narrows an identified subgraph to the reference walk and the named walks\n  // `wanted` accepts, and drops every node only the discarded walks visited,\n  // so a cut for a chosen set draws that set's private sequence and nothing\n  // else's. It needs a name for every walk, since a walk without one could\n  // belong to a wanted haplotype, and one walk per haplotype, since a record\n  // of merged walks carries the name of one of them.\n  keepHaplotypes(wanted: (name: PathName) => boolean) {\n    if (this.paths.some(info => info.weight !== undefined)) {\n      throw new Error(\n        \"keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()\",\n      )\n    }\n    const unnamed = this.paths.filter(\n      (info, index) => index !== this.refId && info.identity === undefined,\n    ).length\n    if (unnamed > 0) {\n      throw new Error(\n        `${unnamed} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`,\n      )\n    }\n    const refInfo =\n      this.refId === undefined ? undefined : this.paths[this.refId]\n    const kept = this.paths.filter(\n      (info, index) =>\n        index === this.refId ||\n        (info.identity !== undefined && wanted(info.identity.name)),\n    )\n    const visited = new Set<number>()\n    for (const info of kept) {\n      for (const handle of info.path) {\n        visited.add(nodeId(handle))\n      }\n    }\n    for (const handle of [...this.records.keys()]) {\n      if (!visited.has(nodeId(handle))) {\n        this.records.delete(handle)\n      }\n    }\n    this.paths = kept\n    this.refId = refInfo === undefined ? undefined : kept.indexOf(refInfo)\n  }\n\n  // The walks extractPaths and identifyPaths would give this subgraph for the\n  // haplotypes `keep` accepts, found from the haplotype index without walking\n  // the others. Returns false, leaving no walks, when the haplotype index\n  // cannot show that the walks it found are all of them; the caller then\n  // extracts and identifies every walk, and stats.keep.fallback says why.\n  /** @internal */\n  async extractChosenPaths(\n    reference: ReferencePath,\n    len: number,\n    keep: (name: PathName) => boolean,\n    context: number,\n  ) {\n    this.clearPaths()\n    const start = reference.position.seqOffset\n    const found = await findChosenPieces({\n      db: this.db,\n      records: this.records,\n      referenceHandle: reference.handle,\n      referencePos: {\n        node: reference.position.handle,\n        offset: reference.position.gbwtOffset,\n      },\n      referenceLeft: start - reference.position.nodeOffset,\n      window: { start, end: start + len },\n      context,\n      snarls: {\n        mode: this.snarlMode,\n        fills: this.snarlFills,\n        inserted: this.snarlNodes,\n      },\n      keep,\n      signal: this.signal,\n      prefetchReferenceRange: (pathHandle, fromOffset, toOffset) =>\n        this.prefetchReferenceRange(pathHandle, fromOffset, toOffset),\n    })\n    this.stats.keep = found.stats\n    if (found.stats.fallback !== undefined) {\n      return false\n    }\n    const pathsByHandle = await this.db.pathsByHandle()\n    const infoOf = (piece: ChosenPiece): PathInfo => ({\n      path: piece.handles,\n      offsets: piece.offsets,\n      len: piece.len,\n      weight: undefined,\n      identity: {\n        pathHandle: piece.pathHandle,\n        name:\n          piece === found.reference\n            ? reference.name\n            : pathsByHandle.get(piece.pathHandle)!.name,\n        orientation: piece.orientation,\n        hapStart: piece.hapStart,\n        hapEnd: piece.hapEnd,\n      },\n    })\n    const ordered = [found.reference, ...found.pieces].sort(extractionOrder)\n    this.paths = ordered.map(infoOf)\n    this.refId = ordered.indexOf(found.reference)\n    this.refPath = reference.name\n    this.refHandle = reference.handle\n    this.refInterval = [found.reference.hapStart, found.reference.hapEnd]\n    this.dropTwins()\n    return true\n  }\n\n  async identifyPaths() {\n    if (!this.db.hasHaplotypeIndex) {\n      throw new Error(\n        'The database has no HaplotypeSamples table; run gbz-haplotype-index on it',\n      )\n    }\n    if (this.unsettled) {\n      ;({ paths: this.paths, refId: this.refId } = this.unsettled)\n      this.unsettled = undefined\n      this.twinDeferred = true\n    }\n    const interval = (await this.db.haplotypeSampleGap()) ?? 4096\n    const runs = handleRuns(this.sortedHandles())\n    if (runs.length === 0) {\n      return\n    }\n    const samples = new Map<string, HaplotypeSample>()\n    const fetched = await Promise.all(\n      runs.map(([first, last]) => this.db.haplotypeSamplesInRange(first, last)),\n    )\n    for (const sample of fetched.flat()) {\n      samples.set(posKey(sample), sample)\n    }\n    const scanned = (handle: number) => {\n      let lo = 0\n      let hi = runs.length - 1\n      while (lo < hi) {\n        const mid = (lo + hi + 1) >> 1\n        if (runs[mid]![0] <= handle) {\n          lo = mid\n        } else {\n          hi = mid - 1\n        }\n      }\n      const run = runs[lo]!\n      return run[0] <= handle && handle <= run[1]\n    }\n    const starts = new Map<string, number>()\n    this.paths.forEach((info, index) => {\n      if (info.path.length > 0 && index !== this.refId) {\n        starts.set(posKey(pathPosition(info, 0)), index)\n      }\n    })\n    const identification = this.stats.identification\n    identification.interval = interval\n    identification.scans = runs\n    identification.windowSamples = samples.size\n    this.paths.forEach((info, index) => {\n      if (index !== this.refId) {\n        identification.fragmentLengths.push(info.len)\n      }\n    })\n    const readRecord = this.recordReader(() => {\n      this.stats.identificationFetches += 1\n      identification.graphFetches += 1\n    })\n    const recordAt = (handle: number) => {\n      identification.graphLookups += 1\n      return readRecord(handle)\n    }\n    const sampleAt = async (pos: Pos, chain: ChainRecord) => {\n      if (scanned(pos.node)) {\n        return samples.get(posKey(pos))\n      }\n      this.stats.identificationFetches += 1\n      identification.companionSeeks += 1\n      chain.seeks += 1\n      const sample = await this.db.haplotypeSampleAt(pos.node, pos.offset)\n      if (!sample) {\n        identification.companionMisses += 1\n      }\n      return sample\n    }\n    const names = new Map<number, PathName>()\n    const nameOf = async (pathHandle: number) => {\n      let name = names.get(pathHandle)\n      if (!name) {\n        const path = await this.db.getPath(pathHandle)\n        if (!path) {\n          throw new Error(`Path ${pathHandle} is missing from the database`)\n        }\n        name = path.name\n        names.set(pathHandle, name)\n      }\n      return name\n    }\n    const anchorFromSample = (\n      sample: HaplotypeSample,\n      counter: number,\n      nodeLen: number,\n    ): Anchor =>\n      sample.orientation === 'forward'\n        ? {\n            pathHandle: sample.pathHandle,\n            orientation: 'forward',\n            base: sample.pathOffset - counter,\n          }\n        : {\n            pathHandle: sample.pathHandle,\n            orientation: 'reverse',\n            base: sample.pathOffset + counter + nodeLen,\n          }\n    const anchorFromIdentity = (\n      identity: PathIdentity,\n      counter: number,\n    ): Anchor =>\n      identity.orientation === 'forward'\n        ? {\n            pathHandle: identity.pathHandle,\n            orientation: 'forward',\n            base: identity.hapStart - counter,\n          }\n        : {\n            pathHandle: identity.pathHandle,\n            orientation: 'reverse',\n            base: identity.hapEnd + counter,\n          }\n\n    for (let start = 0; start < this.paths.length; start++) {\n      const startInfo = this.paths[start]!\n      if (start === this.refId || startInfo.identity) {\n        continue\n      }\n      const chain: { index: number; startBp: number }[] = []\n      const visited = new Set<number>()\n      const record: ChainRecord = {\n        fragments: 0,\n        steps: 0,\n        seeks: 0,\n        reentries: 0,\n        twinLandings: 0,\n        end: 'endmarker',\n        pathHandle: undefined,\n      }\n      identification.chains.push(record)\n      let anchor: Anchor | undefined\n      let counter = 0\n      let current: number | undefined = start\n      let pos: Pos | undefined\n      while (anchor === undefined) {\n        this.signal?.throwIfAborted()\n        if (current !== undefined) {\n          if (visited.has(current)) {\n            record.end = 'cycle'\n            break\n          }\n          visited.add(current)\n          const info = this.paths[current]!\n          chain.push({ index: current, startBp: counter })\n          record.fragments += 1\n          let bp = counter\n          for (let k = 0; k < info.path.length; k++) {\n            const position = pathPosition(info, k)\n            const sample = samples.get(posKey(position))\n            const nodeLen = this.record(position.node).sequenceLen\n            if (sample) {\n              anchor = anchorFromSample(sample, bp, nodeLen)\n              break\n            }\n            bp += nodeLen\n          }\n          counter += info.len\n          if (anchor) {\n            record.end = 'in-fragment sample'\n            break\n          }\n          const last = pathPosition(info, info.path.length - 1)\n          pos = this.record(last.node).gbwt().lf(last.offset)\n          current = undefined\n        }\n        if (pos === undefined || pos.node === ENDMARKER) {\n          record.end = 'endmarker'\n          break\n        }\n        const key = posKey(pos)\n        const known = starts.get(key)\n        if (known !== undefined) {\n          const identity = this.paths[known]!.identity\n          if (identity) {\n            anchor = anchorFromIdentity(identity, counter)\n            record.end = 'identified sibling'\n            break\n          }\n          current = known\n          continue\n        }\n        if (this.records.has(pos.node)) {\n          record.reentries += 1\n        }\n        if (this.twinStarts.has(key)) {\n          record.twinLandings += 1\n        }\n        const sample = await sampleAt(pos, record)\n        const node = await recordAt(pos.node)\n        if (sample) {\n          anchor = anchorFromSample(sample, counter, node.sequenceLen)\n          record.end = 'out-of-window sample'\n          break\n        }\n        this.stats.identificationSteps += 1\n        record.steps += 1\n        if (\n          counter - (chain[chain.length - 1] as { startBp: number }).startBp >\n          4 * interval + 4 * node.sequenceLen\n        ) {\n          record.end = 'bound'\n          break\n        }\n        counter += node.sequenceLen\n        pos = node.gbwt().lf(pos.offset)\n      }\n      if (anchor) {\n        record.pathHandle = anchor.pathHandle\n        const name = await nameOf(anchor.pathHandle)\n        for (const { index, startBp } of chain) {\n          const info = this.paths[index]!\n          info.identity =\n            anchor.orientation === 'forward'\n              ? {\n                  pathHandle: anchor.pathHandle,\n                  name,\n                  orientation: 'forward',\n                  hapStart: anchor.base + startBp,\n                  hapEnd: anchor.base + startBp + info.len,\n                }\n              : {\n                  pathHandle: anchor.pathHandle,\n                  name,\n                  orientation: 'reverse',\n                  hapStart: anchor.base - startBp - info.len,\n                  hapEnd: anchor.base - startBp,\n                }\n        }\n      }\n    }\n    this.dropTwins()\n  }\n\n  private refIndex(ref: number[]) {\n    if (this.refIndexCache === undefined) {\n      const index = new Map<number, number[]>()\n      ref.forEach((handle, i) => {\n        const occurrences = index.get(handle)\n        if (occurrences) {\n          occurrences.push(i)\n        } else {\n          index.set(handle, [i])\n        }\n      })\n      this.refIndexCache = index\n    }\n    return this.refIndexCache\n  }\n\n  private refPrefix(ref: number[]) {\n    if (this.refPrefixCache === undefined) {\n      const prefix = [0]\n      ref.forEach((handle, i) => {\n        prefix.push(prefix[i]! + this.record(handle).sequenceLen)\n      })\n      this.refPrefixCache = prefix\n    }\n    return this.refPrefixCache\n  }\n\n  private orderedMatches(path: number[], ref: number[]): Matches | undefined {\n    const index = this.refIndex(ref)\n    const pathAt = new Int32Array(path.length)\n    const refAt = new Int32Array(path.length)\n    let count = 0\n    let last = -1\n    for (let i = 0; i < path.length; i++) {\n      const occurrences = index.get(path[i]!)\n      if (occurrences) {\n        const j = firstAbove(occurrences, last)\n        if (j === undefined) {\n          return undefined\n        }\n        pathAt[count] = i\n        refAt[count] = j\n        count += 1\n        last = j\n      }\n    }\n    return { pathAt, refAt, count }\n  }\n\n  private pathLen(path: number[]) {\n    let total = 0\n    for (const handle of path) {\n      total += this.record(handle).sequenceLen\n    }\n    return total\n  }\n\n  private prefixMatches(path: number[], ref: number[]) {\n    let result = 0\n    let pi = 0\n    let ri = 0\n    let pb = 0\n    let rb = 0\n    while (pi < path.length && ri < ref.length) {\n      const a = this.record(path[pi]!).sequence\n      const b = this.record(ref[ri]!).sequence\n      while (pb < a.length && rb < b.length) {\n        if (a[pb] !== b[rb]) {\n          return result\n        }\n        pb += 1\n        rb += 1\n        result += 1\n      }\n      if (pb === a.length) {\n        pi += 1\n        pb = 0\n      }\n      if (rb === b.length) {\n        ri += 1\n        rb = 0\n      }\n    }\n    return result\n  }\n\n  private suffixMatches(path: number[], ref: number[]) {\n    let result = 0\n    let pi = 0\n    let ri = 0\n    let pb = 0\n    let rb = 0\n    while (pi < path.length && ri < ref.length) {\n      const a = this.record(path[path.length - pi - 1]!).sequence\n      const b = this.record(ref[ref.length - ri - 1]!).sequence\n      while (pb < a.length && rb < b.length) {\n        if (a[a.length - pb - 1] !== b[b.length - rb - 1]) {\n          return result\n        }\n        pb += 1\n        rb += 1\n        result += 1\n      }\n      if (pb === a.length) {\n        pi += 1\n        pb = 0\n      }\n      if (rb === b.length) {\n        ri += 1\n        rb = 0\n      }\n    }\n    return result\n  }\n\n  private align(path: number[], ref: number[], edits: Edit[]) {\n    const pathLen = this.pathLen(path)\n    const refLen = this.pathLen(ref)\n    const prefix = this.prefixMatches(path, ref)\n    let suffix = this.suffixMatches(path, ref)\n    if (prefix + suffix > pathLen) {\n      suffix = pathLen - prefix\n    }\n    if (prefix + suffix > refLen) {\n      suffix = refLen - prefix\n    }\n    appendEdit(edits, 'M', prefix)\n    appendGap(edits, pathLen - prefix - suffix, refLen - prefix - suffix)\n    appendEdit(edits, 'M', suffix)\n  }\n\n  private sharedWeight(path: number[], ref: number[]) {\n    const index = this.refIndex(ref)\n    let weight = 0\n    for (const handle of path) {\n      if (index.has(handle)) {\n        weight += this.record(handle).sequenceLen\n      }\n    }\n    return weight\n  }\n\n  private editsAgainst(path: number[], ref: number[]) {\n    const ordered = this.orderedMatches(path, ref)\n    if (ordered) {\n      this.stats.orderedAlignments += 1\n    } else {\n      this.stats.lcsAlignments += 1\n    }\n    const lcs =\n      ordered ??\n      asMatches(\n        weightedLcs(path, ref, handle => this.record(handle).sequenceLen)[0],\n      )\n    const edits: Edit[] = []\n    const refPrefix = this.refPrefix(ref)\n    const alignGap = (\n      pathFrom: number,\n      pathTo: number,\n      refFrom: number,\n      refTo: number,\n    ) => {\n      if (pathFrom === pathTo) {\n        appendEdit(edits, 'D', refPrefix[refTo]! - refPrefix[refFrom]!)\n      } else if (refFrom === refTo) {\n        appendEdit(edits, 'I', this.pathLen(path.slice(pathFrom, pathTo)))\n      } else {\n        this.align(\n          path.slice(pathFrom, pathTo),\n          ref.slice(refFrom, refTo),\n          edits,\n        )\n      }\n    }\n    let matched = 0\n    let pathOffset = 0\n    let refOffset = 0\n    for (let m = 0; m < lcs.count; m++) {\n      const nextPath = lcs.pathAt[m]!\n      const nextRef = lcs.refAt[m]!\n      // Adjacent matches are the overwhelming majority of a walk's steps, and\n      // for those alignGap has nothing to append; only the gaps are worth a\n      // call.\n      if (pathOffset !== nextPath || refOffset !== nextRef) {\n        alignGap(pathOffset, nextPath, refOffset, nextRef)\n      }\n      const nodeLen = this.record(path[nextPath]!).sequenceLen\n      appendEdit(edits, 'M', nodeLen)\n      matched += nodeLen\n      pathOffset = nextPath + 1\n      refOffset = nextRef + 1\n    }\n    alignGap(pathOffset, path.length, refOffset, ref.length)\n    return { edits, matched, matches: lcs }\n  }\n\n  private alignment(pathIndex: number) {\n    const info = this.paths[pathIndex]\n    if (this.refId === undefined || pathIndex === this.refId || !info) {\n      return undefined\n    }\n    const ref = this.paths[this.refId]!.path\n    let result: { edits: Edit[]; matched: number; flipped: boolean }\n    if (\n      pathIsCanonical(ref) &&\n      (info.identity === undefined || !pathIsCanonical(flipPath(info.path)))\n    ) {\n      // A canonical walk against a canonical reference has nothing to gain\n      // from being flipped, so neither bound is worth the pass over its steps\n      // that measuring one costs. A walk through a hairpin is canonical both\n      // ways and either way aligns about half of it; once named, dropTwins\n      // has left one of them, and it takes the better way. Unnamed, both are\n      // walks as upstream prints them, each aligned as it stands.\n      result = { ...this.editsAgainst(info.path, ref), flipped: false }\n    } else {\n      const flippedPath = flipPath(info.path)\n      const forwardBound = this.sharedWeight(info.path, ref)\n      const flippedBound = this.sharedWeight(flippedPath, ref)\n      if (flippedBound === 0) {\n        result = { ...this.editsAgainst(info.path, ref), flipped: false }\n      } else if (forwardBound === 0) {\n        result = { ...this.editsAgainst(flippedPath, ref), flipped: true }\n      } else {\n        const forward = this.editsAgainst(info.path, ref)\n        const flipped = this.editsAgainst(flippedPath, ref)\n        result =\n          flipped.matched > forward.matched\n            ? { ...flipped, flipped: true }\n            : { ...forward, flipped: false }\n      }\n    }\n    return result\n  }\n\n  /** @internal */\n  alignToRef(pathIndex: number) {\n    this.settleDeferred()\n    return this.alignment(pathIndex)\n      ?.edits.map(([op, len]) => `${len}${op}`)\n      .join('')\n  }\n\n  alignments(): HaplotypeAlignment[] {\n    this.settleDeferred()\n    const reference = this.referenceInterval\n    if (this.refId === undefined || !reference) {\n      throw new Error('Alignments need a reference path')\n    }\n    const ref = this.paths[this.refId]!.path\n    const refTotal = this.refPrefix(ref)[ref.length]!\n    const fragment = (\n      edits: Edit[],\n      strand: '+' | '-',\n      pieces: number[],\n      soloAligned: number[],\n    ): FragmentAlignment => {\n      const trimmed = trimEnds(edits)\n      const first = this.paths[pieces[0]!]!\n      const last = this.paths[pieces[pieces.length - 1]!]!\n      const identity = first.identity\n      const walkForward = identity?.orientation === 'forward'\n      const [low, high] = walkForward ? [first, last] : [last, first]\n      return {\n        strand,\n        refStart: reference.start + trimmed.leading,\n        refEnd: reference.start + refTotal - trimmed.trailing,\n        edits: trimmed.edits,\n        weight: first.weight,\n        path: pieces.flatMap(index => this.paths[index]!.path),\n        start: pathPosition(first, 0),\n        pieces,\n        soloAligned,\n        identity:\n          identity === undefined\n            ? undefined\n            : {\n                pathHandle: identity.pathHandle,\n                name: identity.name,\n                hapStart: identity.name.fragment + low.identity!.hapStart,\n                hapEnd: identity.name.fragment + high.identity!.hapEnd,\n                walkForward,\n              },\n      }\n    }\n    // A walk that leaves the subgraph and comes back is two pieces here, and a\n    // piece whose tail touches reference nodes past where the next piece\n    // aligns cannot be joined after the fact. Aligned as one walk, with the\n    // bases outside the subgraph as an insertion between the pieces, they read\n    // as the detour they are. Each end of the join must be aligned over at\n    // least half its length alone, which keeps out a pass hundreds of kb away\n    // that the context reached through a rare edge, and must keep at least half\n    // its aligned bases jointly, which keeps out the second pass of a collapsed\n    // paralog. Pieces between the ends, often most of the detour, join with\n    // them whatever their alignment.\n    const aligned = (f: FragmentAlignment) =>\n      f.soloAligned.reduce((sum, bases) => sum + bases, 0)\n    const length = (f: FragmentAlignment) =>\n      f.pieces.reduce((sum, index) => sum + this.paths[index]!.len, 0)\n    const mostlyAligned = (f: FragmentAlignment) => 2 * aligned(f) >= length(f)\n    const alignJointly = (parts: FragmentAlignment[]) => {\n      const first = parts[0]!\n      const last = parts[parts.length - 1]!\n      const walkForward = first.identity!.walkForward\n      if (\n        parts.some(\n          (part, k) =>\n            part.strand !== first.strand ||\n            part.identity!.walkForward !== walkForward ||\n            (k > 0 && part.identity!.hapStart < parts[k - 1]!.identity!.hapEnd),\n        )\n      ) {\n        return undefined\n      }\n      const inWalkOrder = walkForward ? parts : [...parts].reverse()\n      const pieces = inWalkOrder.flatMap(part => part.pieces)\n      const soloAligned = inWalkOrder.flatMap(part => part.soloAligned)\n      const flipped = (first.strand === '+') !== walkForward\n      const infos = pieces.map(index => this.paths[index]!)\n      const gaps = infos.slice(1).map((info, k) => {\n        const before = infos[k]!.identity!\n        return walkForward\n          ? info.identity!.hapStart - before.hapEnd\n          : before.hapStart - info.identity!.hapEnd\n      })\n      const alignedInfos = flipped ? [...infos].reverse() : infos\n      const alignedGaps = flipped ? [...gaps].reverse() : gaps\n      const steps = alignedInfos.flatMap(info =>\n        flipped ? flipPath(info.path) : info.path,\n      )\n      const { edits } = this.editsAgainst(steps, ref)\n      const keptInOrder = alignedIn(\n        edits,\n        alignedInfos.map(info => info.len),\n      )\n      const kept = new Map(\n        (flipped ? [...pieces].reverse() : pieces).map((index, k) => [\n          index,\n          keptInOrder[k]!,\n        ]),\n      )\n      const keeps = (part: FragmentAlignment) =>\n        2 * part.pieces.reduce((sum, index) => sum + kept.get(index)!, 0) >=\n        aligned(part)\n      if (!keeps(first) || !keeps(last)) {\n        return undefined\n      }\n      const insertions: [number, number][] = []\n      let walked = 0\n      alignedInfos.slice(0, -1).forEach((info, k) => {\n        walked += info.len\n        insertions.push([walked, alignedGaps[k]!])\n      })\n      return fragment(\n        spliceInsertions(edits, insertions),\n        first.strand,\n        pieces,\n        soloAligned,\n      )\n    }\n    const fragments: FragmentAlignment[] = []\n    this.paths.forEach((info, index) => {\n      if (index === this.refId) {\n        return\n      }\n      const { edits, flipped } = this.alignment(index)!\n      const identity = info.identity\n      const alongReference = identity\n        ? (identity.orientation === 'forward') !== flipped\n        : !flipped\n      fragments.push(\n        fragment(\n          edits,\n          alongReference ? '+' : '-',\n          [index],\n          alignedIn(edits, [info.len]),\n        ),\n      )\n    })\n    return joinSiblings(fragments, mostlyAligned, alignJointly).map(joined => {\n      const { edits, identity, pieces, soloAligned, ...rest } = joined\n      const span: AlignmentSpan = { ...rest, cigar: cigarOf(edits) }\n      return identity\n        ? {\n            ...span,\n            resolved: true,\n            name: identity.name,\n            label: formatPathName({\n              ...identity.name,\n              fragment: identity.hapStart,\n              end: identity.hapEnd,\n            }),\n            pathHandle: identity.pathHandle,\n            hapStart: identity.hapStart,\n            hapEnd: identity.hapEnd,\n          }\n        : { ...span, resolved: false }\n    })\n  }\n\n  // One haplotype's walks aligned to another's, on both haplotypes' own\n  // coordinates, with the bases between two shared nodes compared unless bases\n  // is false. The reference path is a named walk like any other, on either\n  // side. With no query, every other named walk in the window is one.\n  pairAlignments(opts: PairAlignmentOptions): PairAlignment[] {\n    const { target, query, ...pairOptions } = opts\n    const walks = this.paths.flatMap(info => {\n      const { identity } = info\n      return identity\n        ? [\n            {\n              name: identity.name,\n              start: identity.name.fragment + identity.hapStart,\n              steps: haplotypeOrderedPath(info, identity),\n            },\n          ]\n        : []\n    })\n    const names = (haplotype: HaplotypeRef) => (name: PathName) =>\n      name.sample === haplotype.sample && name.haplotype === haplotype.haplotype\n    const isTarget = names(target)\n    const isQuery = query ? names(query) : (name: PathName) => !isTarget(name)\n    const sequenceOf = (id: number) =>\n      this.record(encodeNode(id, 'forward')).sequence\n    return walks\n      .filter(walk => isTarget(walk.name))\n      .flatMap(targetWalk =>\n        walks\n          .filter(walk => isQuery(walk.name))\n          .flatMap(queryWalk =>\n            pairAlignments({\n              ...pairOptions,\n              query: queryWalk.steps,\n              target: targetWalk.steps,\n              sequenceOf,\n            }).map(chain => ({\n              query: queryWalk.name,\n              queryStart: queryWalk.start + chain.queryStart,\n              queryEnd: queryWalk.start + chain.queryEnd,\n              strand: chain.strand,\n              target: targetWalk.name,\n              targetStart: targetWalk.start + chain.targetStart,\n              targetEnd: targetWalk.start + chain.targetEnd,\n              cigar: pairCigar(chain.edits),\n              matches: chain.edits.reduce(\n                (sum, [op, len]) => sum + (op === '=' ? len : 0),\n                0,\n              ),\n              columns: chain.edits.reduce((sum, [, len]) => sum + len, 0),\n              sharedBases: chain.sharedBases,\n            })),\n          ),\n      )\n  }\n\n  private canonicalEdges(id: number) {\n    const edges: [number, number, number][] = []\n    for (const orientation of ['forward', 'reverse'] as const) {\n      const handle = encodeNode(id, orientation)\n      for (const successor of this.record(handle).successors()) {\n        if (this.hasHandle(successor) && edgeIsCanonical(handle, successor)) {\n          edges.push([\n            orientation === 'reverse' ? 1 : 0,\n            nodeId(successor),\n            isReverse(successor) ? 1 : 0,\n          ])\n        }\n      }\n    }\n    edges.sort((a, b) => a[0] - b[0] || a[1] - b[1] || a[2] - b[2])\n    return edges.filter(\n      (edge, i) =>\n        i === 0 ||\n        edge[0] !== edges[i - 1]![0] ||\n        edge[1] !== edges[i - 1]![1] ||\n        edge[2] !== edges[i - 1]![2],\n    )\n  }\n\n  async stableName() {\n    const encoder = new TextEncoder()\n    const chunks: Uint8Array[] = []\n    for (const handle of this.sortedHandles()) {\n      if (!isReverse(handle)) {\n        const id = nodeId(handle)\n        let text = `S\\t${id}\\t${this.record(handle).sequence}\\n`\n        for (const [fromReverse, toId, toReverse] of this.canonicalEdges(id)) {\n          text += `L\\t${id}\\t${fromReverse ? '-' : '+'}\\t${toId}\\t${toReverse ? '-' : '+'}\\n`\n        }\n        chunks.push(encoder.encode(text))\n      }\n    }\n    return sha256Hex(chunks)\n  }\n\n  async toGFA(opts: SubgraphOutputOptions = {}) {\n    this.settleDeferred()\n    const cigar = opts.cigar ?? false\n    const lines = [\n      this.refPath ? `H\\tVN:Z:1.1\\tRS:Z:${this.refPath.sample}` : 'H\\tVN:Z:1.1',\n      ...gfaHeaderLines(\n        subgraphName(await this.stableName(), await this.db.graphName()),\n      ),\n    ]\n    const handles = this.sortedHandles()\n    for (const handle of handles) {\n      if (!isReverse(handle)) {\n        lines.push(`S\\t${nodeId(handle)}\\t${this.record(handle).sequence}`)\n      }\n    }\n    const sign = (handle: number) => (isReverse(handle) ? '-' : '+')\n    for (const handle of handles) {\n      for (const successor of this.record(handle).successors()) {\n        if (this.hasHandle(successor) && edgeIsCanonical(handle, successor)) {\n          lines.push(\n            `L\\t${nodeId(handle)}\\t${sign(handle)}\\t${nodeId(successor)}\\t${sign(successor)}\\t0M`,\n          )\n        }\n      }\n    }\n    const walk = (\n      info: PathInfo,\n      identity: PathIdentity | undefined,\n      name: PathName,\n      end: number,\n      cigarString: string | undefined,\n    ) => {\n      const steps = haplotypeOrderedPath(info, identity)\n        .map(handle => `${isReverse(handle) ? '<' : '>'}${nodeId(handle)}`)\n        .join('')\n      const weight = info.weight === undefined ? '' : `\\tWT:i:${info.weight}`\n      const cg = cigarString === undefined ? '' : `\\tCG:Z:${cigarString}`\n      return `W\\t${name.sample}\\t${name.haplotype}\\t${name.contig}\\t${name.fragment}\\t${end}\\t${steps}${weight}${cg}`\n    }\n    const contig = this.refPath?.contig ?? 'unknown'\n    if (this.refId !== undefined && this.refPath && this.refInterval) {\n      lines.push(\n        walk(\n          this.paths[this.refId]!,\n          undefined,\n          {\n            ...this.refPath,\n            fragment: this.refPath.fragment + this.refInterval[0],\n          },\n          this.refPath.fragment + this.refInterval[1],\n          undefined,\n        ),\n      )\n    }\n    let haplotype = 1\n    this.paths.forEach((info, index) => {\n      if (index !== this.refId) {\n        const resolved = opts.names !== 'anonymous' ? info.identity : undefined\n        const cigarString = cigar ? this.alignToRef(index) : undefined\n        lines.push(\n          resolved\n            ? walk(\n                info,\n                resolved,\n                {\n                  ...resolved.name,\n                  fragment: resolved.name.fragment + resolved.hapStart,\n                },\n                resolved.name.fragment + resolved.hapEnd,\n                cigarString,\n              )\n            : walk(\n                info,\n                undefined,\n                { sample: 'unknown', contig, haplotype, fragment: 0 },\n                info.len,\n                cigarString,\n              ),\n        )\n        haplotype += 1\n      }\n    })\n    return `${lines.join('\\n')}\\n`\n  }\n\n  // The reference walk first under the interval it covers, then one entry per\n  // haplotype in extraction order. Both outputs read this so a name, a weight\n  // or a CIGAR cannot mean one thing in the upstream JSON and another in the\n  // compact form.\n  private outputPaths(opts: SubgraphOutputOptions) {\n    this.settleDeferred()\n    const cigar = opts.cigar ?? false\n    const entries: {\n      info: PathInfo\n      identity: PathIdentity | undefined\n      name: string\n      cigar: string | undefined\n    }[] = []\n    const contig = this.refPath?.contig ?? 'unknown'\n    if (this.refId !== undefined && this.refPath && this.refInterval) {\n      const start = {\n        ...this.refPath,\n        fragment: this.refPath.fragment + this.refInterval[0],\n      }\n      entries.push({\n        info: this.paths[this.refId]!,\n        identity: undefined,\n        name: formatPathName({\n          ...start,\n          end: this.refPath.fragment + this.refInterval[1],\n        }),\n        cigar: undefined,\n      })\n    }\n    let haplotype = 1\n    this.paths.forEach((info, index) => {\n      if (index === this.refId) {\n        return\n      }\n      const identity = opts.names !== 'anonymous' ? info.identity : undefined\n      entries.push({\n        info,\n        identity,\n        name: identity\n          ? formatPathName({\n              ...identity.name,\n              fragment: identity.name.fragment + identity.hapStart,\n              end: identity.name.fragment + identity.hapEnd,\n            })\n          : formatPathName({\n              sample: 'unknown',\n              contig,\n              haplotype,\n              fragment: 0,\n              end: info.len,\n            }),\n        cigar: cigar ? this.alignToRef(index) : undefined,\n      })\n      haplotype += 1\n    })\n    return entries\n  }\n\n  private *outputEdges() {\n    for (const handle of this.sortedHandles()) {\n      for (const successor of this.record(handle).successors()) {\n        if (this.hasHandle(successor) && edgeIsCanonical(handle, successor)) {\n          yield [handle, successor] as const\n        }\n      }\n    }\n  }\n\n  toSubgraphJson(opts: SubgraphOutputOptions = {}): SubgraphJson {\n    const nodes = this.sortedHandles()\n      .filter(handle => !isReverse(handle))\n      .map(handle => ({\n        id: String(nodeId(handle)),\n        sequence: this.record(handle).sequence,\n      }))\n    const edges: SubgraphJson['edges'] = []\n    for (const [from, to] of this.outputEdges()) {\n      edges.push({\n        from: String(nodeId(from)),\n        from_is_reverse: isReverse(from),\n        to: String(nodeId(to)),\n        to_is_reverse: isReverse(to),\n      })\n    }\n    const paths = this.outputPaths(opts).map(entry =>\n      jsonPath(entry.info, entry.identity, entry.name, entry.cigar),\n    )\n    return { nodes, edges, paths }\n  }\n\n  // The same subgraph as typed arrays of GBWT handles. toSubgraphJson spends\n  // an object and a stringified id on every step of every walk, which a\n  // 200 kb human window has about 350,000 of; this hands back the numbers the\n  // extraction already holds, so it survives a structured clone into a worker\n  // for about the cost of the memcpy rather than of rebuilding the objects.\n  // Measured on HPRC chr20 CHM13#0#chr20 30.0-30.2 Mb, 5,943 nodes and 178\n  // haplotypes: 295 ms to clone the upstream shape against 1.9 ms for this one.\n  //\n  // Packing the other two fields the way bam-js packs NUMERIC_SEQ and\n  // NUMERIC_CIGAR was measured on the same window and rejected, because what\n  // pays there is a long per-record field and both of these are short. Node\n  // sequences average 34 bp: base-6 bytes plus offsets are 2.86x smaller but\n  // cost more to build than to hand over the cached strings (1.07 ms against\n  // 0.95 ms all in), and a consumer drawing the graph wants the strings for\n  // every node anyway. CIGARs average 323 chars over 17,555 total ops: packing\n  // them into one Int32Array per path is 1.7 ms against 2.4 ms to join the\n  // strings, but then clones SLOWER (0.20 ms against 0.09 ms) because 178 small\n  // typed arrays cost more than 178 strings. Steps are the only field here long\n  // enough to be worth it. The CIGAR phase is 103 ms of edit computation and\n  // 2 ms of string building, so neither field is where that time goes.\n  toCompactSubgraph(opts: SubgraphOutputOptions = {}): CompactSubgraph {\n    const forward = this.sortedHandles().filter(handle => !isReverse(handle))\n    const nodeIds = new Int32Array(forward.length)\n    const nodeSequences: string[] = []\n    forward.forEach((handle, i) => {\n      nodeIds[i] = nodeId(handle)\n      nodeSequences.push(this.record(handle).sequence)\n    })\n    const edgeHandles: number[] = []\n    for (const [from, to] of this.outputEdges()) {\n      edgeHandles.push(from, to)\n    }\n    return {\n      nodeIds,\n      nodeSequences,\n      edges: Int32Array.from(edgeHandles),\n      paths: this.outputPaths(opts).map(entry => ({\n        name: entry.name,\n        weight: entry.info.weight,\n        cigar: entry.cigar,\n        steps: Int32Array.from(\n          haplotypeOrderedPath(entry.info, entry.identity),\n        ),\n      })),\n    }\n  }\n}\n\n// The buffers a CompactSubgraph owns outright, for the transfer list of a\n// postMessage that hands it to another thread. Transferring detaches them, so\n// the sending side must not read the subgraph afterwards.\nexport function compactSubgraphTransferables(subgraph: CompactSubgraph) {\n  return [\n    subgraph.nodeIds.buffer,\n    subgraph.edges.buffer,\n    ...subgraph.paths.map(path => path.steps.buffer),\n  ]\n}\n\n// A named walk lists its steps in the haplotype's own direction, as the W line\n// spec and the start..end coordinates beside it require. extractPaths keeps\n// whichever twin of a walk is canonical, which is a property of the handles\n// and not of the haplotype, so the kept walk runs against the haplotype for\n// about half of them; identification records which.\nfunction haplotypeOrderedPath(\n  info: PathInfo,\n  identity: PathIdentity | undefined,\n) {\n  return identity?.orientation === 'reverse'\n    ? info.path.map(handle => flipNode(handle)).reverse()\n    : info.path\n}\n\nfunction jsonPath(\n  info: PathInfo,\n  identity: PathIdentity | undefined,\n  name: string,\n  cigar: string | undefined,\n): SubgraphPath {\n  return {\n    name,\n    ...(info.weight === undefined ? {} : { weight: info.weight }),\n    ...(cigar === undefined ? {} : { cigar }),\n    path: haplotypeOrderedPath(info, identity).map(handle => ({\n      id: String(nodeId(handle)),\n      is_reverse: isReverse(handle),\n    })),\n  }\n}\n\nfunction comparePaths(a: number[], b: number[]) {\n  const n = Math.min(a.length, b.length)\n  for (let i = 0; i < n; i++) {\n    const x = a[i]!\n    const y = b[i]!\n    if (x !== y) {\n      return x < y ? -1 : 1\n    }\n  }\n  return a.length - b.length\n}\n\nfunction appendEdit(edits: Edit[], op: EditOp, len: number) {\n  if (len === 0) {\n    return\n  }\n  const last = edits[edits.length - 1]\n  if (last?.[0] === op) {\n    last[1] += len\n  } else {\n    edits.push([op, len])\n  }\n}\n\nfunction gapPenalty(len: number) {\n  return len === 0 ? 0 : 6 + (len - 1)\n}\n\nfunction appendGap(edits: Edit[], pathMiddle: number, refMiddle: number) {\n  if (pathMiddle === 0) {\n    appendEdit(edits, 'D', refMiddle)\n  } else if (refMiddle === 0) {\n    appendEdit(edits, 'I', pathMiddle)\n  } else {\n    const mismatch = Math.min(pathMiddle, refMiddle)\n    const mismatchIndel =\n      4 * mismatch +\n      gapPenalty(pathMiddle - mismatch) +\n      gapPenalty(refMiddle - mismatch)\n    const insertionDeletion = gapPenalty(pathMiddle) + gapPenalty(refMiddle)\n    if (mismatchIndel <= insertionDeletion) {\n      appendEdit(edits, 'M', mismatch)\n      appendEdit(edits, 'I', pathMiddle - mismatch)\n      appendEdit(edits, 'D', refMiddle - mismatch)\n    } else {\n      appendEdit(edits, 'I', pathMiddle)\n      appendEdit(edits, 'D', refMiddle)\n    }\n  }\n}\n\n// A record starts and ends at an aligned base: the deletions in a run of\n// insertions and deletions at either end move its reference start or end, and\n// the insertions stay. An alignment with no aligned base keeps its insertion at\n// the reference start.\nfunction trimEnds(edits: Edit[]) {\n  let first = 0\n  while (first < edits.length && edits[first]![0] !== 'M') {\n    first += 1\n  }\n  if (first === edits.length) {\n    const inserted = edits.filter(([op]) => op === 'I')\n    const trailing = edits\n      .filter(([op]) => op === 'D')\n      .reduce((sum, [, len]) => sum + len, 0)\n    return {\n      edits: inserted.map(([op, len]): Edit => [op, len]),\n      leading: 0,\n      trailing,\n    }\n  }\n  let last = edits.length\n  while (edits[last - 1]![0] !== 'M') {\n    last -= 1\n  }\n  const ends = (run: Edit[]) => ({\n    inserted: run.reduce((sum, [op, len]) => sum + (op === 'I' ? len : 0), 0),\n    deleted: run.reduce((sum, [op, len]) => sum + (op === 'D' ? len : 0), 0),\n  })\n  const head = ends(edits.slice(0, first))\n  const tail = ends(edits.slice(last))\n  const trimmed: Edit[] = []\n  appendEdit(trimmed, 'I', head.inserted)\n  for (const [op, len] of edits.slice(first, last)) {\n    appendEdit(trimmed, op, len)\n  }\n  appendEdit(trimmed, 'I', tail.inserted)\n  return { edits: trimmed, leading: head.deleted, trailing: tail.deleted }\n}\n\n// The bases the CIGAR aligns within each of consecutive stretches of the walk.\nfunction alignedIn(edits: Edit[], lengths: number[]) {\n  const aligned = lengths.map(() => 0)\n  const last = lengths.length - 1\n  let piece = 0\n  let pieceEnd = lengths[0]!\n  let walked = 0\n  for (const [op, len] of edits) {\n    if (op === 'D') {\n      continue\n    }\n    let rest = len\n    while (rest > 0) {\n      while (piece < last && walked >= pieceEnd) {\n        piece += 1\n        pieceEnd += lengths[piece]!\n      }\n      const step = piece < last ? Math.min(rest, pieceEnd - walked) : rest\n      if (op === 'M') {\n        aligned[piece]! += step\n      }\n      walked += step\n      rest -= step\n    }\n  }\n  return aligned\n}\n\n// Insertions at walk offsets, after any deletions that end at the same offset.\nfunction spliceInsertions(edits: Edit[], insertions: [number, number][]) {\n  const spliced: Edit[] = []\n  let walked = 0\n  let next = 0\n  for (const [op, len] of edits) {\n    if (op === 'D') {\n      appendEdit(spliced, op, len)\n      continue\n    }\n    let from = walked\n    while (next < insertions.length && insertions[next]![0] < walked + len) {\n      const [at, inserted] = insertions[next]!\n      appendEdit(spliced, op, at - from)\n      appendEdit(spliced, 'I', inserted)\n      from = at\n      next += 1\n    }\n    appendEdit(spliced, op, walked + len - from)\n    walked += len\n  }\n  for (; next < insertions.length; next++) {\n    appendEdit(spliced, 'I', insertions[next]![1])\n  }\n  return spliced\n}\n\nfunction cigarOf(edits: Edit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n", "import { pathNameFor, toPathQuery } from './pathName.ts'\nimport { Subgraph, SubgraphLimitError } from './subgraph.ts'\n\nimport type { GBZBase } from './db.ts'\nimport type { PathName, PathRef } from './pathName.ts'\nimport type { HaplotypeOutput, SnarlOutput } from './subgraph.ts'\n\nexport interface QueryOptions {\n  context?: number | undefined\n  haplotypes?: HaplotypeOutput | undefined\n  snarls?: SnarlOutput | undefined\n  limit?: number | undefined\n  signal?: AbortSignal | undefined\n}\n\nexport interface PathWindow {\n  path: PathRef\n  start: number\n  end: number\n}\n\nexport interface IntervalQuery extends PathWindow, QueryOptions {\n  keep?: ((name: PathName) => boolean) | undefined\n}\n\nexport interface OffsetQuery extends QueryOptions {\n  path: PathRef\n  offset: number\n}\n\nexport type NodeHaplotypeOutput = Exclude<HaplotypeOutput, 'reference-only'>\n\nexport interface NodesQuery extends Omit<QueryOptions, 'haplotypes'> {\n  nodeIds: number[]\n  haplotypes?: NodeHaplotypeOutput | undefined\n}\n\nexport interface BetweenQuery {\n  startHandle: number\n  endHandle: number\n  haplotypes?: NodeHaplotypeOutput | undefined\n  limit?: number | undefined\n  signal?: AbortSignal | undefined\n}\n\nfunction wholeNumber(name: string, value: number, min = 0) {\n  if (!Number.isSafeInteger(value) || value < min) {\n    throw new Error(\n      `${name} must be a whole number${min > 0 ? ` of at least ${min}` : ''}, not ${value}`,\n    )\n  }\n  return value\n}\n\nfunction contextOf(opts: QueryOptions) {\n  return wholeNumber('context', opts.context ?? 100)\n}\n\nfunction createSubgraph(db: GBZBase, opts: QueryOptions | BetweenQuery) {\n  if (opts.limit !== undefined) {\n    wholeNumber('limit', opts.limit)\n  }\n  return Subgraph.create(db, opts)\n}\n\nexport async function subgraphAtOffset(db: GBZBase, opts: OffsetQuery) {\n  const context = contextOf(opts)\n  const subgraph = createSubgraph(db, opts)\n  const reference = await subgraph.pathPosition(\n    pathNameFor(toPathQuery(opts.path), wholeNumber('offset', opts.offset)),\n  )\n  await subgraph.aroundPosition(\n    reference.position.handle,\n    reference.position.nodeOffset,\n    context,\n  )\n  await subgraph.extractSnarls(opts.snarls ?? 'none')\n  subgraph.extractPaths(reference, opts.haplotypes ?? 'all')\n  return subgraph\n}\n\n// The subgraph both routes read a window from: the reference walk through it,\n// `context` bp around that, and the snarls `snarls` selects.\nasync function aroundWindow(db: GBZBase, opts: IntervalQuery) {\n  const start = wholeNumber('start', opts.start)\n  const end = wholeNumber('end', opts.end)\n  const context = contextOf(opts)\n  const subgraph = createSubgraph(db, opts)\n  try {\n    const reference = await subgraph.pathPosition(\n      pathNameFor(toPathQuery(opts.path), start),\n    )\n    await subgraph.prefetchReferenceWalk(reference, end - start)\n    await subgraph.aroundInterval(reference.position, end - start, context)\n    await subgraph.extractSnarls(opts.snarls ?? 'none')\n    return { subgraph, reference }\n  } catch (error) {\n    throw error instanceof SubgraphLimitError && error.windowBp === undefined\n      ? new SubgraphLimitError(error.limit, {\n          windowBp: end - start,\n          walkedBp: subgraph.referenceWalkedBp ?? 0,\n        })\n      : error\n  }\n}\n\n// With `keep`, the window for a chosen set of haplotypes: the same subgraph and\n// the same walks as the sampled route narrowed by keepHaplotypes, found from\n// the haplotype index without walking the haplotypes `keep` rejects, or by\n// extracting and identifying every walk when the index cannot show those walks\n// complete. 'distinct' merges the kept walks afterwards, so its weights count\n// kept haplotypes.\nexport async function subgraphInInterval(db: GBZBase, opts: IntervalQuery) {\n  const { keep } = opts\n  const haplotypes = opts.haplotypes ?? 'all'\n  const named = haplotypes === 'all' || haplotypes === 'distinct'\n  if (keep !== undefined && named && !db.hasHaplotypeIndex) {\n    throw new Error(\n      'keep needs the haplotype index: this database cannot name its walks',\n    )\n  }\n  const { subgraph, reference } = await aroundWindow(db, opts)\n  if (keep === undefined || !named) {\n    subgraph.extractPaths(reference, haplotypes)\n    return subgraph\n  }\n  if (\n    !(await subgraph.extractChosenPaths(\n      reference,\n      opts.end - opts.start,\n      keep,\n      contextOf(opts),\n    ))\n  ) {\n    subgraph.extractPaths(reference, 'all')\n    await subgraph.identifyPaths()\n  }\n  subgraph.keepHaplotypes(keep)\n  if (haplotypes === 'distinct') {\n    subgraph.mergeDistinct()\n  }\n  return subgraph\n}\n\nexport async function subgraphAroundNodes(db: GBZBase, opts: NodesQuery) {\n  const haplotypes = (opts.haplotypes ?? 'all') as HaplotypeOutput\n  const snarls = opts.snarls ?? 'none'\n  if (haplotypes === 'reference-only') {\n    throw new Error('Cannot output a reference path in a node-based query')\n  }\n  if (snarls === 'overlapping' && new Set(opts.nodeIds).size > 1) {\n    throw new Error(\n      'Overlapping snarls cannot be extracted for a node-based query with multiple nodes',\n    )\n  }\n  const context = contextOf(opts)\n  for (const id of opts.nodeIds) {\n    wholeNumber('node id', id, 1)\n  }\n  const subgraph = createSubgraph(db, opts)\n  await subgraph.aroundNodes(opts.nodeIds, context)\n  await subgraph.extractSnarls(snarls)\n  subgraph.extractPaths(undefined, haplotypes)\n  return subgraph\n}\n\nexport async function subgraphBetween(db: GBZBase, opts: BetweenQuery) {\n  const haplotypes = (opts.haplotypes ?? 'all') as HaplotypeOutput\n  if (haplotypes === 'reference-only') {\n    throw new Error('Cannot output a reference path in a node-based query')\n  }\n  const subgraph = createSubgraph(db, opts)\n  await subgraph.betweenNodes(\n    wholeNumber('startHandle', opts.startHandle, 2),\n    wholeNumber('endHandle', opts.endHandle, 2),\n  )\n  subgraph.extractPaths(undefined, haplotypes)\n  return subgraph\n}\n", "export type SqlValue = null | number | string | Uint8Array\n\nexport function readVarint(\n  bytes: Uint8Array,\n  offset: number,\n): [value: number, next: number] {\n  let value = 0\n  for (let i = 0; i < 8; i++) {\n    const byte = bytes[offset + i]\n    if (byte === undefined) {\n      throw new Error('SQLite varint runs past the end of the buffer')\n    }\n    value = value * 128 + (byte & 0x7f)\n    if ((byte & 0x80) === 0) {\n      if (i === 7 && !Number.isSafeInteger(value)) {\n        throw new Error('SQLite varint exceeds the safe integer range')\n      }\n      return [value, offset + i + 1]\n    }\n  }\n  const last = bytes[offset + 8]\n  if (last === undefined) {\n    throw new Error('SQLite varint runs past the end of the buffer')\n  }\n  value = value * 256 + last\n  if (!Number.isSafeInteger(value)) {\n    throw new Error('SQLite varint exceeds the safe integer range')\n  }\n  return [value, offset + 9]\n}\n\nfunction readSignedInt(view: DataView, offset: number, width: number) {\n  switch (width) {\n    case 1:\n      return view.getInt8(offset)\n    case 2:\n      return view.getInt16(offset)\n    case 3:\n      return (view.getInt8(offset) << 16) | view.getUint16(offset + 1)\n    case 4:\n      return view.getInt32(offset)\n    case 6:\n      return view.getInt16(offset) * 4294967296 + view.getUint32(offset + 2)\n    default: {\n      const big = view.getBigInt64(offset)\n      if (\n        big > BigInt(Number.MAX_SAFE_INTEGER) ||\n        big < BigInt(Number.MIN_SAFE_INTEGER)\n      ) {\n        throw new Error(`SQLite integer ${big} exceeds the safe integer range`)\n      }\n      return Number(big)\n    }\n  }\n}\n\nconst decoder = new TextDecoder()\n\nexport function decodeRecord(payload: Uint8Array): SqlValue[] {\n  const [headerSize, firstType] = readVarint(payload, 0)\n  const types: number[] = []\n  let offset = firstType\n  while (offset < headerSize) {\n    const [type, next] = readVarint(payload, offset)\n    types.push(type)\n    offset = next\n  }\n  const view = new DataView(\n    payload.buffer,\n    payload.byteOffset,\n    payload.byteLength,\n  )\n  let body = headerSize\n  return types.map(type => {\n    if (type === 0) {\n      return null\n    }\n    if (type >= 1 && type <= 6) {\n      const width = type <= 4 ? type : type === 5 ? 6 : 8\n      const value = readSignedInt(view, body, width)\n      body += width\n      return value\n    }\n    if (type === 7) {\n      const value = view.getFloat64(body)\n      body += 8\n      return value\n    }\n    if (type === 8) {\n      return 0\n    }\n    if (type === 9) {\n      return 1\n    }\n    if (type >= 12) {\n      const length = (type - 12) >> 1\n      const slice = payload.subarray(body, body + length)\n      body += length\n      return type % 2 === 0 ? slice : decoder.decode(slice)\n    }\n    throw new Error(`SQLite serial type ${type} is reserved`)\n  })\n}\n", "import { decodeRecord, readVarint } from './record.ts'\n\nimport type { Pager } from './pager.ts'\nimport type { SqlValue } from './record.ts'\n\nconst INTERIOR_INDEX = 0x02\nconst INTERIOR_TABLE = 0x05\nconst LEAF_INDEX = 0x0a\nconst LEAF_TABLE = 0x0d\n\ninterface PageHeader {\n  type: number\n  cellCount: number\n  rightChild: number\n  cellPointers: number\n}\n\nfunction readUint16(page: Uint8Array, offset: number) {\n  return page[offset]! * 256 + page[offset + 1]!\n}\n\nfunction readUint32(page: Uint8Array, offset: number) {\n  return (\n    page[offset]! * 16777216 +\n    page[offset + 1]! * 65536 +\n    page[offset + 2]! * 256 +\n    page[offset + 3]!\n  )\n}\n\nfunction readHeader(page: Uint8Array, start: number): PageHeader {\n  const type = page[start]\n  if (\n    type !== INTERIOR_INDEX &&\n    type !== INTERIOR_TABLE &&\n    type !== LEAF_INDEX &&\n    type !== LEAF_TABLE\n  ) {\n    throw new Error(`SQLite page has unknown b-tree type ${type}`)\n  }\n  const interior = type === INTERIOR_INDEX || type === INTERIOR_TABLE\n  return {\n    type,\n    cellCount: readUint16(page, start + 3),\n    rightChild: interior ? readUint32(page, start + 8) : 0,\n    cellPointers: start + (interior ? 12 : 8),\n  }\n}\n\nfunction cellOffset(page: Uint8Array, header: PageHeader, index: number) {\n  return readUint16(page, header.cellPointers + 2 * index)\n}\n\ninterface IndexCell {\n  values: SqlValue[]\n  leftChild: number\n}\n\nconst MAX_DECODED_INDEX_PAGES = 4096\n\nexport class BTree {\n  private readonly usable: number\n  private pager: Pager\n  private decodedIndexPages = new Map<number, (IndexCell | undefined)[]>()\n  private tableDepths = new Map<number, Promise<number>>()\n\n  constructor(pager: Pager, reservedBytes: number) {\n    this.pager = pager\n    this.usable = pager.pageSize - reservedBytes\n  }\n\n  private localPayloadSize(total: number, isIndex: boolean) {\n    const usable = this.usable\n    const maxLocal = isIndex\n      ? Math.floor(((usable - 12) * 64) / 255) - 23\n      : usable - 35\n    if (total <= maxLocal) {\n      return total\n    }\n    const minLocal = Math.floor(((usable - 12) * 32) / 255) - 23\n    const spill = minLocal + ((total - minLocal) % (usable - 4))\n    return spill <= maxLocal ? spill : minLocal\n  }\n\n  private async payload(\n    page: Uint8Array,\n    offset: number,\n    total: number,\n    isIndex: boolean,\n  ) {\n    const local = this.localPayloadSize(total, isIndex)\n    if (local === total) {\n      return page.subarray(offset, offset + total)\n    }\n    const result = new Uint8Array(total)\n    result.set(page.subarray(offset, offset + local), 0)\n    let filled = local\n    let next = readUint32(page, offset + local)\n    while (next !== 0 && filled < total) {\n      const overflow = await this.pager.page(next)\n      const chunk = overflow.subarray(\n        4,\n        4 + Math.min(this.usable - 4, total - filled),\n      )\n      result.set(chunk, filled)\n      filled += chunk.length\n      next = readUint32(overflow, 0)\n    }\n    if (filled !== total) {\n      throw new Error(\n        'SQLite overflow chain ended before the payload was complete',\n      )\n    }\n    return result\n  }\n\n  private async pageAt(pageNumber: number) {\n    const page = await this.pager.page(pageNumber)\n    return { page, header: readHeader(page, pageNumber === 1 ? 100 : 0) }\n  }\n\n  private tableDepth(root: number, towards: number) {\n    let depth = this.tableDepths.get(root)\n    if (!depth) {\n      depth = (async () => {\n        let pageNumber = root\n        for (let level = 0; ; level++) {\n          const { page, header } = await this.pageAt(pageNumber)\n          if (header.type === LEAF_TABLE) {\n            return level\n          }\n          if (header.type !== INTERIOR_TABLE) {\n            throw new Error('SQLite table b-tree contains an index page')\n          }\n          const child = this.childIndexFor(page, header, towards)\n          pageNumber =\n            child === header.cellCount\n              ? header.rightChild\n              : readUint32(page, cellOffset(page, header, child))\n        }\n      })()\n      this.tableDepths.set(root, depth)\n      depth.catch(() => this.tableDepths.delete(root))\n    }\n    return depth\n  }\n\n  private childIndexFor(page: Uint8Array, header: PageHeader, rowid: number) {\n    let low = 0\n    let high = header.cellCount\n    while (low < high) {\n      const mid = (low + high) >> 1\n      const [key] = readVarint(page, cellOffset(page, header, mid) + 4)\n      if (key < rowid) {\n        low = mid + 1\n      } else {\n        high = mid\n      }\n    }\n    return low\n  }\n\n  // Fetches the pages that hold the rows of the ranges, level by level. Up to\n  // the pager's budget they come at once; past it a strict prefetch gives up\n  // and returns false, and a streaming one fetches the leading blocks now and\n  // the rest in chunks as reads approach them.\n  async prefetchRowidRanges(\n    root: number,\n    ranges: [number, number][],\n    stream = false,\n  ) {\n    if (ranges.length === 0) {\n      return true\n    }\n    const leafLevel = await this.tableDepth(root, ranges[0]![0])\n    let frontiers = ranges.map(() => [root])\n    for (let level = 0; level < leafLevel; level++) {\n      frontiers = await Promise.all(\n        frontiers.map((pages, r) => this.childrenInRange(pages, ...ranges[r]!)),\n      )\n      const pages = frontiers.flat()\n      if (stream) {\n        this.pager.prefetchLeading(pages)\n      } else if (!this.pager.prefetch(pages)) {\n        return false\n      }\n    }\n    return true\n  }\n\n  private async childrenInRange(pages: number[], lo: number, hi: number) {\n    const decoded = await Promise.all(pages.map(n => this.pageAt(n)))\n    const children: number[] = []\n    decoded.forEach(({ page, header }, i) => {\n      const from = i === 0 ? this.childIndexFor(page, header, lo) : 0\n      const to =\n        i === decoded.length - 1\n          ? this.childIndexFor(page, header, hi)\n          : header.cellCount\n      for (let c = from; c <= to; c++) {\n        children.push(\n          c === header.cellCount\n            ? header.rightChild\n            : readUint32(page, cellOffset(page, header, c)),\n        )\n      }\n    })\n    return children\n  }\n\n  async tableRowid(\n    root: number,\n    rowid: number,\n  ): Promise<SqlValue[] | undefined> {\n    let pageNumber = root\n    for (;;) {\n      const { page, header } = await this.pageAt(pageNumber)\n      if (header.type === LEAF_TABLE) {\n        let low = 0\n        let high = header.cellCount\n        while (low < high) {\n          const mid = (low + high) >> 1\n          const offset = cellOffset(page, header, mid)\n          const [size, afterSize] = readVarint(page, offset)\n          const [key, afterKey] = readVarint(page, afterSize)\n          if (key === rowid) {\n            return decodeRecord(await this.payload(page, afterKey, size, false))\n          }\n          if (key < rowid) {\n            low = mid + 1\n          } else {\n            high = mid\n          }\n        }\n        return undefined\n      }\n      if (header.type !== INTERIOR_TABLE) {\n        throw new Error('SQLite table b-tree contains an index page')\n      }\n      let low = 0\n      let high = header.cellCount\n      while (low < high) {\n        const mid = (low + high) >> 1\n        const offset = cellOffset(page, header, mid)\n        const [key] = readVarint(page, offset + 4)\n        if (key < rowid) {\n          low = mid + 1\n        } else {\n          high = mid\n        }\n      }\n      pageNumber =\n        low === header.cellCount\n          ? header.rightChild\n          : readUint32(page, cellOffset(page, header, low))\n    }\n  }\n\n  async *tableScan(\n    root: number,\n  ): AsyncGenerator<{ rowid: number; values: SqlValue[] }> {\n    yield* this.scanPage(root, await this.tableDepth(root, 0))\n  }\n\n  // Prefetches only leaves: interior pages prefetched a level up would be\n  // evicted by the leaf prefetches below them before they were read\n  private async *scanPage(\n    pageNumber: number,\n    depth: number,\n  ): AsyncGenerator<{ rowid: number; values: SqlValue[] }> {\n    const { page, header } = await this.pageAt(pageNumber)\n    if (header.type === LEAF_TABLE) {\n      for (let i = 0; i < header.cellCount; i++) {\n        const offset = cellOffset(page, header, i)\n        const [size, afterSize] = readVarint(page, offset)\n        const [rowid, afterKey] = readVarint(page, afterSize)\n        yield {\n          rowid,\n          values: decodeRecord(await this.payload(page, afterKey, size, false)),\n        }\n      }\n    } else {\n      const children: number[] = []\n      for (let i = 0; i < header.cellCount; i++) {\n        children.push(readUint32(page, cellOffset(page, header, i)))\n      }\n      children.push(header.rightChild)\n      if (depth === 1) {\n        this.pager.prefetchLeading(children)\n      }\n      for (const child of children) {\n        yield* this.scanPage(child, depth - 1)\n      }\n    }\n  }\n\n  private decodedCells(pageNumber: number, header: PageHeader) {\n    let cells = this.decodedIndexPages.get(pageNumber)\n    if (cells) {\n      this.decodedIndexPages.delete(pageNumber)\n    } else {\n      cells = new Array<IndexCell | undefined>(header.cellCount)\n      if (this.decodedIndexPages.size >= MAX_DECODED_INDEX_PAGES) {\n        const oldest = this.decodedIndexPages.keys().next().value\n        if (oldest !== undefined) {\n          this.decodedIndexPages.delete(oldest)\n        }\n      }\n    }\n    this.decodedIndexPages.set(pageNumber, cells)\n    return cells\n  }\n\n  private async indexCell(\n    pageNumber: number,\n    page: Uint8Array,\n    header: PageHeader,\n    index: number,\n  ): Promise<IndexCell> {\n    const cells = this.decodedCells(pageNumber, header)\n    let cell = cells[index]\n    if (!cell) {\n      const offset = cellOffset(page, header, index)\n      const interior = header.type === INTERIOR_INDEX\n      const [size, afterSize] = readVarint(page, interior ? offset + 4 : offset)\n      cell = {\n        values: decodeRecord(await this.payload(page, afterSize, size, true)),\n        leftChild: interior ? readUint32(page, offset) : 0,\n      }\n      cells[index] = cell\n    }\n    return cell\n  }\n\n  // The first cell at or past `key`, by binary search from `from`.\n  private async lowerBound(\n    pageNumber: number,\n    page: Uint8Array,\n    header: PageHeader,\n    key: number[],\n    from: number,\n    inclusive: boolean,\n  ) {\n    let low = from\n    let high = header.cellCount\n    while (low < high) {\n      const mid = (low + high) >> 1\n      const cell = await this.indexCell(pageNumber, page, header, mid)\n      const order = compareKey(cell.values, key)\n      if (order < 0 || (inclusive && order === 0)) {\n        low = mid + 1\n      } else {\n        high = mid\n      }\n    }\n    return low\n  }\n\n  // The entries from `low` on in key order, and with `high` only those up to\n  // it, their pages read ahead.\n  async *indexScanFrom(\n    root: number,\n    low: number[],\n    high?: number[],\n  ): AsyncGenerator<SqlValue[]> {\n    const { page, header } = await this.pageAt(root)\n    const first = await this.lowerBound(root, page, header, low, 0, false)\n    const interior = header.type === INTERIOR_INDEX\n    if (interior && high) {\n      const past = await this.lowerBound(root, page, header, high, first, true)\n      const children: number[] = []\n      for (let c = first; c <= past; c++) {\n        children.push(\n          c === header.cellCount\n            ? header.rightChild\n            : (await this.indexCell(root, page, header, c)).leftChild,\n        )\n      }\n      this.pager.prefetchLeading(children)\n    }\n    for (let i = first; i < header.cellCount; i++) {\n      const cell = await this.indexCell(root, page, header, i)\n      if (interior) {\n        yield* this.indexScanFrom(cell.leftChild, low, high)\n      }\n      if (high && compareKey(cell.values, high) > 0) {\n        return\n      }\n      yield cell.values\n    }\n    if (interior) {\n      yield* this.indexScanFrom(header.rightChild, low, high)\n    }\n  }\n\n  async indexSeekLE(\n    root: number,\n    key: number[],\n  ): Promise<SqlValue[] | undefined> {\n    let best: SqlValue[] | undefined\n    let pageNumber = root\n    for (;;) {\n      const { page, header } = await this.pageAt(pageNumber)\n      let low = 0\n      let high = header.cellCount\n      let child = 0\n      while (low < high) {\n        const mid = (low + high) >> 1\n        const cell = await this.indexCell(pageNumber, page, header, mid)\n        if (compareKey(cell.values, key) <= 0) {\n          best = cell.values\n          low = mid + 1\n        } else {\n          child = cell.leftChild\n          high = mid\n        }\n      }\n      if (header.type === LEAF_INDEX) {\n        return best\n      }\n      pageNumber = low === header.cellCount ? header.rightChild : child\n    }\n  }\n}\n\nfunction compareKey(values: SqlValue[], key: number[]) {\n  for (let i = 0; i < key.length; i++) {\n    const a = values[i]\n    const b = key[i]\n    if (typeof a !== 'number' || b === undefined) {\n      throw new Error('SQLite index key is not numeric')\n    }\n    if (a !== b) {\n      return a < b ? -1 : 1\n    }\n  }\n  return 0\n}\n", "import type { ByteSource } from '../filehandle.ts'\n\nexport interface PagerOptions {\n  blockSize?: number | undefined\n  maxBlocks?: number | undefined\n}\n\nexport function checkPagerOptions({ blockSize, maxBlocks }: PagerOptions) {\n  if (\n    blockSize !== undefined &&\n    !(Number.isSafeInteger(blockSize) && blockSize > 0)\n  ) {\n    throw new Error(`blockSize must be a positive integer, not ${blockSize}`)\n  }\n  if (\n    maxBlocks !== undefined &&\n    !(Number.isSafeInteger(maxBlocks) && maxBlocks > 0)\n  ) {\n    throw new Error(`maxBlocks must be a positive integer, not ${maxBlocks}`)\n  }\n}\n\n// Blocks a reader asked for ahead of time, fetched in chunks as its reads\n// approach the end of what has been fetched.\ninterface Plan {\n  blocks: number[]\n  position: Map<number, number>\n  next: number\n}\n\nexport class Pager {\n  private blocks = new Map<number, Promise<Uint8Array>>()\n  private readonly blockSize: number\n  private readonly maxBlocks: number\n  private plan: Plan | undefined\n  bytesFetched = 0\n  fetches = 0\n\n  private source: ByteSource\n  readonly pageSize: number\n  private fileSize: number\n\n  constructor(\n    source: ByteSource,\n    pageSize: number,\n    fileSize: number,\n    opts: PagerOptions = {},\n  ) {\n    this.source = source\n    this.pageSize = pageSize\n    this.fileSize = fileSize\n    const requested = opts.blockSize ?? 65536\n    this.blockSize = Math.max(\n      pageSize,\n      Math.ceil(requested / pageSize) * pageSize,\n    )\n    this.maxBlocks = opts.maxBlocks ?? 256\n  }\n\n  private async read(length: number, start: number) {\n    const bytes = await this.readRetrying(length, start)\n    this.bytesFetched += bytes.length\n    if (bytes.length < length) {\n      throw new Error(\n        `the file ends at byte ${start + bytes.length}, short of the ${this.fileSize} bytes its SQLite header gives`,\n      )\n    }\n    return bytes\n  }\n\n  private async readRetrying(length: number, start: number) {\n    let attempt = 0\n    for (;;) {\n      try {\n        return await this.source.read(length, start)\n      } catch (error) {\n        attempt += 1\n        if (attempt >= 3) {\n          throw error\n        }\n        await new Promise(resolve => setTimeout(resolve, 200 * attempt))\n      }\n    }\n  }\n\n  seed(index: number, bytes: Uint8Array) {\n    if (\n      bytes.length ===\n      Math.min(this.blockSize, this.fileSize - index * this.blockSize)\n    ) {\n      this.blocks.set(index, Promise.resolve(bytes))\n    }\n  }\n\n  private block(index: number) {\n    this.follow(index)\n    const cached = this.touch(index)\n    if (cached) {\n      return cached\n    }\n    const start = index * this.blockSize\n    const length = Math.min(this.blockSize, this.fileSize - start)\n    const pending = this.read(length, start)\n    this.fetches += 1\n    this.store(index, pending)\n    this.evict()\n    return pending\n  }\n\n  private touch(index: number) {\n    const cached = this.blocks.get(index)\n    if (cached) {\n      this.blocks.delete(index)\n      this.blocks.set(index, cached)\n    }\n    return cached\n  }\n\n  private blockOf(pageNumber: number) {\n    return Math.floor(((pageNumber - 1) * this.pageSize) / this.blockSize)\n  }\n\n  // half the cache, so a prefetch cannot evict its own blocks\n  private get prefetchBudget() {\n    return Math.max(1, Math.floor(this.maxBlocks / 2))\n  }\n\n  private get chunk() {\n    return Math.max(1, Math.floor(this.prefetchBudget / 2))\n  }\n\n  // Fetches the pages' blocks when they fit the budget together.\n  prefetch(pageNumbers: number[]) {\n    const indexes = new Set(pageNumbers.map(n => this.blockOf(n)))\n    if (indexes.size > this.prefetchBudget) {\n      return false\n    }\n    this.fetchBlocks(indexes)\n    return true\n  }\n\n  // Fetches the first pages' blocks now, up to the budget, and plans the rest\n  // in the pages' order, to be fetched chunk by chunk as reads approach them.\n  prefetchLeading(pageNumbers: number[]) {\n    const blocks: number[] = []\n    const position = new Map<number, number>()\n    for (const pageNumber of pageNumbers) {\n      const index = this.blockOf(pageNumber)\n      if (!position.has(index)) {\n        position.set(index, blocks.length)\n        blocks.push(index)\n      }\n    }\n    this.plan = { blocks, position, next: 0 }\n    this.advance(this.prefetchBudget)\n  }\n\n  private advance(count: number) {\n    const plan = this.plan\n    if (!plan) {\n      return\n    }\n    const slice = plan.blocks.slice(plan.next, plan.next + count)\n    plan.next += slice.length\n    if (plan.next >= plan.blocks.length) {\n      this.plan = undefined\n    }\n    this.fetchBlocks(new Set(slice))\n  }\n\n  // A read within half a chunk of the end of the fetched part of the plan\n  // brings in the next chunk.\n  private follow(index: number) {\n    const plan = this.plan\n    const at = plan?.position.get(index)\n    if (\n      plan &&\n      at !== undefined &&\n      at >= plan.next - Math.ceil(this.chunk / 2)\n    ) {\n      this.advance(this.chunk)\n    }\n  }\n\n  private fetchBlocks(indexes: Set<number>) {\n    const wanted = [...indexes]\n      .filter(index => !this.touch(index))\n      .sort((a, b) => a - b)\n    let runStart = 0\n    while (runStart < wanted.length) {\n      let runEnd = runStart + 1\n      while (\n        runEnd < wanted.length &&\n        wanted[runEnd] === wanted[runEnd - 1]! + 1\n      ) {\n        runEnd += 1\n      }\n      this.fetchRun(wanted[runStart]!, runEnd - runStart)\n      runStart = runEnd\n    }\n  }\n\n  private fetchRun(firstIndex: number, count: number) {\n    const start = firstIndex * this.blockSize\n    const length = Math.min(count * this.blockSize, this.fileSize - start)\n    const pending = this.read(length, start)\n    this.fetches += 1\n    for (let i = 0; i < count; i++) {\n      const within = i * this.blockSize\n      this.store(\n        firstIndex + i,\n        pending.then(bytes => bytes.subarray(within, within + this.blockSize)),\n      )\n    }\n    this.evict()\n  }\n\n  private store(index: number, block: Promise<Uint8Array>) {\n    this.blocks.set(index, block)\n    block.catch(() => {\n      if (this.blocks.get(index) === block) {\n        this.blocks.delete(index)\n      }\n    })\n  }\n\n  private evict() {\n    while (this.blocks.size > this.maxBlocks) {\n      const oldest = this.blocks.keys().next().value\n      if (oldest === undefined) {\n        break\n      }\n      this.blocks.delete(oldest)\n    }\n  }\n\n  async page(pageNumber: number) {\n    const offset = (pageNumber - 1) * this.pageSize\n    if (pageNumber < 1 || offset + this.pageSize > this.fileSize) {\n      throw new Error(`SQLite page ${pageNumber} is outside the file`)\n    }\n    const bytes = await this.block(Math.floor(offset / this.blockSize))\n    const within = offset % this.blockSize\n    return bytes.subarray(within, within + this.pageSize)\n  }\n}\n", "import { BTree } from './btree.ts'\nimport { Pager, checkPagerOptions } from './pager.ts'\n\nimport type { ByteSource } from '../filehandle.ts'\nimport type { PagerOptions } from './pager.ts'\nimport type { SqlValue } from './record.ts'\n\nexport interface SqliteObject {\n  type: string\n  name: string\n  tableName: string\n  rootPage: number\n  sql: string\n}\n\nexport class SqliteDatabase {\n  readonly pager: Pager\n  readonly btree: BTree\n  readonly objects: Map<string, SqliteObject>\n\n  private constructor(\n    pager: Pager,\n    btree: BTree,\n    objects: Map<string, SqliteObject>,\n  ) {\n    this.pager = pager\n    this.btree = btree\n    this.objects = objects\n  }\n\n  static async open(source: ByteSource, opts: PagerOptions = {}) {\n    checkPagerOptions(opts)\n    const firstBlock = await source.read(\n      Math.max(512, opts.blockSize ?? 65536),\n      0,\n    )\n    const header = firstBlock.subarray(0, 100)\n    const magic = new TextDecoder().decode(header.subarray(0, 15))\n    if (magic !== 'SQLite format 3' || header.length < 100) {\n      throw new Error('Not a SQLite database')\n    }\n    const view = new DataView(\n      header.buffer,\n      header.byteOffset,\n      header.byteLength,\n    )\n    const rawPageSize = view.getUint16(16)\n    const pageSize = rawPageSize === 1 ? 65536 : rawPageSize\n    const reserved = header[20] ?? 0\n    const encoding = view.getUint32(56)\n    if (encoding !== 1) {\n      throw new Error(`SQLite text encoding ${encoding} is not UTF-8`)\n    }\n    const pageCount = view.getUint32(28)\n    if (pageCount === 0 || view.getUint32(24) !== view.getUint32(92)) {\n      throw new Error(\n        'SQLite header has no valid database size; the file was written by SQLite older than 3.7.0',\n      )\n    }\n    const size = pageCount * pageSize\n    const pager = new Pager(source, pageSize, size, opts)\n    pager.seed(0, firstBlock)\n    pager.fetches += 1\n    pager.bytesFetched += firstBlock.length\n    const btree = new BTree(pager, reserved)\n    const objects = new Map<string, SqliteObject>()\n    for await (const { values } of btree.tableScan(1)) {\n      const [type, name, tableName, rootPage, sql] = values\n      if (\n        typeof type === 'string' &&\n        typeof name === 'string' &&\n        typeof tableName === 'string' &&\n        typeof rootPage === 'number'\n      ) {\n        objects.set(name, {\n          type,\n          name,\n          tableName,\n          rootPage,\n          sql: typeof sql === 'string' ? sql : '',\n        })\n      }\n    }\n    return new SqliteDatabase(pager, btree, objects)\n  }\n\n  rootPage(name: string) {\n    const object = this.objects.get(name)\n    if (!object) {\n      throw new Error(`SQLite database has no object named ${name}`)\n    }\n    return object.rootPage\n  }\n\n  // Whether a table keeps its whole rows in the b-tree of its primary key.\n  withoutRowid(tableName: string) {\n    const table = this.objects.get(tableName)\n    return table?.type === 'table' && /without\\s+rowid/i.test(table.sql)\n  }\n\n  // The b-tree keyed by a table's primary key: its automatic index, or the\n  // table itself when it is WITHOUT ROWID.\n  indexOn(tableName: string) {\n    const index = [...this.objects.values()].find(\n      o => o.type === 'index' && o.tableName === tableName,\n    )\n    if (index) {\n      return index.rootPage\n    }\n    if (this.withoutRowid(tableName)) {\n      return this.rootPage(tableName)\n    }\n    throw new Error(`SQLite table ${tableName} has no index`)\n  }\n\n  byRowid(table: string, rowid: number) {\n    return this.btree.tableRowid(this.rootPage(table), rowid)\n  }\n\n  prefetchRows(table: string, ranges: [number, number][], stream = false) {\n    return this.btree.prefetchRowidRanges(this.rootPage(table), ranges, stream)\n  }\n\n  scan(table: string) {\n    return this.btree.tableScan(this.rootPage(table))\n  }\n\n  indexSeekLE(table: string, key: number[]): Promise<SqlValue[] | undefined> {\n    return this.btree.indexSeekLE(this.indexOn(table), key)\n  }\n\n  // The entries of a table's primary key from `low` on, or up to `high`.\n  indexScanFrom(table: string, low: number[], high?: number[]) {\n    return this.btree.indexScanFrom(this.indexOn(table), low, high)\n  }\n\n  has(name: string) {\n    return this.objects.has(name)\n  }\n}\n", "import { ENDMARKER, nodeId, nodeOrientation } from './gbwt/node.ts'\nimport { GbwtRecord, decompressEdges } from './gbwt/record.ts'\nimport { decodeSequence, encodedSequenceLength } from './gbwt/sequence.ts'\nimport { graphNameFromTags } from './graphName.ts'\nimport { formatPathName, pathNameFor, toPathQuery } from './pathName.ts'\nimport {\n  subgraphAroundNodes,\n  subgraphAtOffset,\n  subgraphBetween,\n  subgraphInInterval,\n} from './query.ts'\nimport { SqliteDatabase } from './sqlite/database.ts'\nimport { SubgraphLimitError } from './subgraph.ts'\n\nimport type { ByteSource } from './filehandle.ts'\nimport type { Pos } from './gbwt/record.ts'\nimport type { GraphName } from './graphName.ts'\nimport type { PathName, PathRef } from './pathName.ts'\nimport type {\n  BetweenQuery,\n  IntervalQuery,\n  NodesQuery,\n  OffsetQuery,\n  PathWindow,\n} from './query.ts'\nimport type { PagerOptions } from './sqlite/pager.ts'\nimport type { SqlValue } from './sqlite/record.ts'\nimport type { HaplotypeAlignment, Subgraph } from './subgraph.ts'\n\nexport const SCHEMA_VERSION = 'GBZ-base version 4'\n\nexport interface PathFragment {\n  path: GbzPath\n  start: number\n  end: number\n}\n\nexport type WindowQuery = IntervalQuery\n\nexport interface AlignmentQuery extends Omit<\n  WindowQuery,\n  'haplotypes' | 'snarls'\n> {\n  haplotypes?: 'all' | 'distinct' | undefined\n}\n\nexport class UnknownPathError extends Error {\n  override name = 'UnknownPathError'\n\n  readonly path: PathName\n\n  constructor(path: PathName) {\n    super(`the graph has no path named ${formatPathName(path)}`)\n    this.path = path\n  }\n}\n\nexport class ForwardOnlyIndexError extends Error {\n  override name = 'ForwardOnlyIndexError'\n\n  constructor() {\n    super(\n      'the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only',\n    )\n  }\n}\n\nexport class SchemaVersionError extends Error {\n  override name = 'SchemaVersionError'\n\n  readonly found: string | undefined\n\n  constructor(found: string | undefined) {\n    super(\n      found === undefined\n        ? `not a gbz-base database: it has no version tag`\n        : `unsupported database schema \"${found}\"; this reader understands \"${SCHEMA_VERSION}\"`,\n    )\n    this.found = found\n  }\n}\n\nexport interface IndexedPosition {\n  pathOffset: number\n  pos: Pos\n}\n\nexport interface HaplotypeSample {\n  node: number\n  offset: number\n  pathHandle: number\n  orientation: 'forward' | 'reverse'\n  pathOffset: number\n}\n\nexport interface HaplotypeAnchor {\n  node: number\n  pathOffset: number\n}\n\n// An anchor of a reference path with the forward samples at its node: one\n// visit of every haplotype that passes it, each with its GBWT position and\n// its offset along its own path.\nexport interface HaplotypeAnchorRow extends HaplotypeAnchor {\n  anchorOffset: number\n  visits: HaplotypeSample[]\n}\n\n// One bin of a reference path in the haplotype index's overview: how many\n// haplotypes fall in each class there, and the excursions from the reference\n// that start in it.\nexport interface OverviewBin {\n  start: number\n  end: number\n  // haplotypes that are absent, reference-like, partial and variant\n  classes: [number, number, number, number]\n  excursions: number\n  variants: number\n  longestExcursion: number\n}\n\nexport const OVERVIEW_ABSENT = 0\nexport const OVERVIEW_REFERENCE = 1\nexport const OVERVIEW_PARTIAL = 2\nexport const OVERVIEW_VARIANT = 3\n\n// A binned summary of every haplotype along a stretch of a reference path,\n// at one zoom level. `cells` holds bins.length \u00D7 haplotypes.length entries,\n// bin by bin: the class in the low two bits, and for a variant cell a bucket\n// of the bin's variant marks in the next two (1, 2 to 3, 4 to 15, 16 or\n// more).\nexport interface HaplotypeOverview {\n  level: number\n  bin: number\n  haplotypes: { sample: string; haplotype: number }[]\n  bins: OverviewBin[]\n  cells: Uint8Array\n}\n\nexport interface OverviewQuery extends PathWindow {\n  // The zoom level, clamped to those the index holds, or the bp per pixel to\n  // choose the coarsest level whose bins are no larger than it. Level 0\n  // without either.\n  level?: number | undefined\n  bpPerPixel?: number | undefined\n}\n\nfunction concatBytes(parts: Uint8Array[]) {\n  if (parts.length === 1) {\n    return parts[0]!\n  }\n  const whole = new Uint8Array(parts.reduce((n, p) => n + p.length, 0))\n  let at = 0\n  for (const part of parts) {\n    whole.set(part, at)\n    at += part.length\n  }\n  return whole\n}\n\n// The format of the haplotype index this reader understands: the samples in\n// their key b-tree, each anchor's visits with the anchor and each bin's stray\n// rows with its node list, which gbz-haplotype-index 0.3 writes.\nconst INDEX_FORMAT = 3\n\nclass Varints {\n  private at = 0\n  private bytes: Uint8Array\n\n  constructor(bytes: Uint8Array) {\n    this.bytes = bytes\n  }\n\n  get done() {\n    return this.at >= this.bytes.length\n  }\n\n  next() {\n    let value = 0\n    let scale = 1\n    for (;;) {\n      const byte = this.bytes[this.at++]\n      if (byte === undefined) {\n        throw new Error('a haplotype index blob ends inside a number')\n      }\n      value += (byte & 0x7f) * scale\n      scale *= 128\n      if ((byte & 0x80) === 0) {\n        return value\n      }\n    }\n  }\n}\n\n// Appends the runs of node ids a HaplotypeBins node-list part encodes: per\n// run, the gap from the previous run's last id and the length less one.\nfunction decodeRuns(bytes: Uint8Array, runs: [number, number][]) {\n  const reader = new Varints(bytes)\n  let previous = 0\n  while (!reader.done) {\n    const start = previous + reader.next()\n    previous = start + reader.next()\n    runs.push([start, previous])\n  }\n}\n\n// A test of membership in the union of the runs.\nfunction runTester(runs: [number, number][]) {\n  runs.sort((x, y) => x[0] - y[0])\n  const starts: number[] = []\n  const ends: number[] = []\n  for (const [start, end] of runs) {\n    const last = ends.length - 1\n    if (last >= 0 && start <= ends[last]! + 1) {\n      ends[last] = Math.max(ends[last]!, end)\n    } else {\n      starts.push(start)\n      ends.push(end)\n    }\n  }\n  return (id: number) => {\n    let lo = 0\n    let hi = starts.length\n    while (lo < hi) {\n      const mid = (lo + hi) >> 1\n      if (starts[mid]! <= id) {\n        lo = mid + 1\n      } else {\n        hi = mid\n      }\n    }\n    return lo > 0 && id <= ends[lo - 1]!\n  }\n}\n\nfunction decodeStrays(bin: number, bytes: Uint8Array, rows: HaplotypeStray[]) {\n  const reader = new Varints(bytes)\n  while (!reader.done) {\n    const pathHandle = reader.next()\n    const pathStart = reader.next()\n    const pathEnd = reader.next()\n    const low = reader.next()\n    const high = reader.next()\n    rows.push({\n      bin,\n      pathHandle,\n      pathStart,\n      pathEnd,\n      snarl: high > 0 ? [low, high] : undefined,\n      node: reader.next(),\n      offset: reader.next(),\n    })\n  }\n}\n\n// The visits of a format 3 anchor row: per visit, the path handle doubled\n// plus the orientation bit of the node handle, the node offset and the path\n// offset.\nfunction decodeVisits(\n  anchorNode: number,\n  parts: Uint8Array[],\n  visits: HaplotypeSample[],\n) {\n  const id = nodeId(anchorNode)\n  for (const part of parts) {\n    const reader = new Varints(part)\n    while (!reader.done) {\n      const pathAndBit = reader.next()\n      const bit = pathAndBit % 2\n      visits.push({\n        node: 2 * id + bit,\n        offset: reader.next(),\n        pathHandle: (pathAndBit - bit) / 2,\n        orientation: 'forward',\n        pathOffset: reader.next(),\n      })\n    }\n  }\n}\n\n// A row of HaplotypeStrays: a stretch of one path, from pathStart to the visit\n// at pathEnd, holding visits to nodes of one bin that the walks from anchor\n// visits can miss. `node` and `offset` are the GBWT position of its first\n// visit in the path's forward orientation. A row with a snarl names a path\n// that lies between those two boundary nodes from end to end.\nexport interface HaplotypeStray {\n  bin: number\n  pathHandle: number\n  pathStart: number\n  pathEnd: number\n  snarl: [number, number] | undefined\n  node: number\n  offset: number\n}\n\nexport interface HaplotypeStrayOptions {\n  // The largest query context the rows cover.\n  context: number\n  bin: number\n  bound: number\n  // The most nodes between a filled snarl's boundaries for the rows to cover\n  // it, or undefined when the rows leave snarls out.\n  snarlNodes: number | undefined\n}\n\nexport interface GbzPath {\n  handle: number\n  /** @internal */\n  fwStart: Pos\n  /** @internal */\n  revStart: Pos\n  name: PathName\n  isIndexed: boolean\n}\n\nexport class GbzRecord {\n  readonly sequenceLen: number\n  readonly handle: number\n  readonly edges: Pos[]\n  readonly bwt: Uint8Array\n  readonly encodedSequence: Uint8Array\n  readonly next: number | undefined\n  private decoded: string | undefined\n\n  constructor(\n    handle: number,\n    edges: Pos[],\n    bwt: Uint8Array,\n    encodedSequence: Uint8Array,\n    next: number | undefined,\n  ) {\n    this.handle = handle\n    this.edges = edges\n    this.bwt = bwt\n    this.encodedSequence = encodedSequence\n    this.next = next\n    this.sequenceLen = encodedSequenceLength(encodedSequence)\n  }\n\n  get id() {\n    return nodeId(this.handle)\n  }\n\n  get orientation() {\n    return nodeOrientation(this.handle)\n  }\n\n  get sequence() {\n    this.decoded ??= decodeSequence(this.encodedSequence)\n    return this.decoded\n  }\n\n  successors() {\n    return this.edges.filter(e => e.node !== ENDMARKER).map(e => e.node)\n  }\n\n  gbwt() {\n    if (this.edges.length === 0) {\n      throw new Error(`GBWT record for handle ${this.handle} is empty`)\n    }\n    return new GbwtRecord(this.edges, this.bwt)\n  }\n}\n\nfunction num(value: SqlValue | undefined, what: string) {\n  if (typeof value !== 'number') {\n    throw new Error(`${what} is not a number in the database`)\n  }\n  return value\n}\n\nfunction str(value: SqlValue | undefined, what: string) {\n  if (typeof value !== 'string') {\n    throw new Error(`${what} is not text in the database`)\n  }\n  return value\n}\n\nfunction blob(value: SqlValue | undefined, what: string) {\n  if (!(value instanceof Uint8Array)) {\n    throw new Error(`${what} is not a blob in the database`)\n  }\n  return value\n}\n\nfunction rowToPath(rowid: number, values: SqlValue[]): GbzPath {\n  return {\n    handle: rowid,\n    fwStart: {\n      node: num(values[1], 'Paths.fw_node'),\n      offset: num(values[2], 'Paths.fw_offset'),\n    },\n    revStart: {\n      node: num(values[3], 'Paths.rev_node'),\n      offset: num(values[4], 'Paths.rev_offset'),\n    },\n    name: {\n      sample: str(values[5], 'Paths.sample'),\n      contig: str(values[6], 'Paths.contig'),\n      haplotype: num(values[7], 'Paths.haplotype'),\n      fragment: num(values[8], 'Paths.fragment'),\n    },\n    isIndexed: num(values[9], 'Paths.is_indexed') !== 0,\n  }\n}\n\nexport interface OpenOptions {\n  source: ByteSource\n  haplotypeIndex?: ByteSource | undefined\n  blockSize?: number | undefined\n  maxBlocks?: number | undefined\n}\n\nexport interface FetchStats {\n  fetches: number\n  bytesFetched: number\n}\n\nfunction forgetOnRejection<T>(pending: Promise<T>, forget: () => void) {\n  pending.catch(forget)\n  return pending\n}\n\nasync function readTags(sqlite: SqliteDatabase) {\n  const tags = new Map<string, string>()\n  for await (const { values } of sqlite.scan('Tags')) {\n    tags.set(str(values[0], 'Tags.key'), str(values[1], 'Tags.value'))\n  }\n  return tags\n}\n\nexport class GBZBase {\n  private pathCache: Promise<GbzPath[]> | undefined\n  private pathMapCache: Promise<Map<number, GbzPath>> | undefined\n  private indexTags = new Map<string, string>()\n  private overviewRowsCache:\n    Promise<{ sample: string; haplotype: number }[]> | undefined\n\n  /** @internal */\n  readonly sqlite: SqliteDatabase\n  /** @internal */\n  readonly index: SqliteDatabase | undefined\n  private readonly tagMap: Map<string, string>\n\n  private constructor(\n    sqlite: SqliteDatabase,\n    index: SqliteDatabase | undefined,\n    tags: Map<string, string>,\n  ) {\n    this.sqlite = sqlite\n    this.index = index\n    this.tagMap = tags\n  }\n\n  static async open(opts: OpenOptions) {\n    const { source, haplotypeIndex } = opts\n    const pagerOptions: PagerOptions = {\n      blockSize: opts.blockSize,\n      maxBlocks: opts.maxBlocks,\n    }\n    const sqlite = await SqliteDatabase.open(source, pagerOptions)\n    const tags = sqlite.objects.has('Tags')\n      ? await readTags(sqlite)\n      : new Map<string, string>()\n    const version = tags.get('version')\n    if (version !== SCHEMA_VERSION) {\n      throw new SchemaVersionError(version)\n    }\n    for (const table of ['Nodes', 'Paths', 'ReferenceIndex']) {\n      sqlite.rootPage(table)\n    }\n    const index = haplotypeIndex\n      ? await SqliteDatabase.open(haplotypeIndex, pagerOptions)\n      : undefined\n    const db = new GBZBase(sqlite, index, tags)\n    if (index) {\n      for (const table of ['Tags', 'HaplotypeSamples', 'HaplotypeLengths']) {\n        if (!index.objects.has(table)) {\n          throw new Error(\n            `haplotypeIndex is not a gbz-base haplotype index: it has no ${table} table`,\n          )\n        }\n      }\n      db.indexTags = await readTags(index)\n      const indexed = db.indexTags.get('haplotype_index_paths')\n      const paths = await db.tag('paths')\n      if (indexed !== paths) {\n        throw new Error(\n          `haplotype index was built for ${indexed ?? 'an unknown number of'} paths but the graph has ${paths}`,\n        )\n      }\n      const indexedNodes = db.indexTags.get('haplotype_index_nodes')\n      const nodes = await db.tag('nodes')\n      if (indexedNodes !== undefined && indexedNodes !== nodes) {\n        throw new Error(\n          `haplotype index was built for a graph with ${indexedNodes} nodes but this one has ${nodes}`,\n        )\n      }\n      if (db.indexTags.get('haplotype_index_orientations') === 'forward') {\n        throw new ForwardOnlyIndexError()\n      }\n      const format = db.indexTags.get('haplotype_index_format')\n      if (Number(format) !== INDEX_FORMAT) {\n        throw new Error(\n          format === undefined\n            ? `the haplotype index predates format ${INDEX_FORMAT}; rebuild it with gbz-haplotype-index 0.3`\n            : `the haplotype index has format ${format}; this version of @gmod/gbz-base reads format ${INDEX_FORMAT}`,\n        )\n      }\n    }\n    return db\n  }\n\n  async tags() {\n    return this.tagMap\n  }\n\n  async tag(key: string) {\n    return this.tagMap.get(key)\n  }\n\n  /** @internal */\n  prefetchRecords(ranges: [number, number][], stream = false) {\n    return this.sqlite.prefetchRows('Nodes', ranges, stream)\n  }\n\n  /** @internal */\n  async getRecord(handle: number) {\n    const row = await this.sqlite.byRowid('Nodes', handle)\n    if (!row) {\n      return undefined\n    }\n    const next = row[4]\n    return new GbzRecord(\n      handle,\n      decompressEdges(blob(row[1], 'Nodes.edges')),\n      blob(row[2], 'Nodes.bwt'),\n      blob(row[3], 'Nodes.sequence'),\n      typeof next === 'number' ? next : undefined,\n    )\n  }\n\n  paths() {\n    this.pathCache ??= forgetOnRejection(this.scanPaths(), () => {\n      this.pathCache = undefined\n    })\n    return this.pathCache\n  }\n\n  private async scanPaths() {\n    const paths: GbzPath[] = []\n    for await (const { rowid, values } of this.sqlite.scan('Paths')) {\n      paths.push(rowToPath(rowid, values))\n    }\n    return paths\n  }\n\n  /** @internal */\n  async getPath(handle: number) {\n    const row = await this.sqlite.byRowid('Paths', handle)\n    return row ? rowToPath(handle, row) : undefined\n  }\n\n  /** @internal */\n  pathsByHandle() {\n    this.pathMapCache ??= forgetOnRejection(\n      this.paths().then(\n        paths => new Map(paths.map(path => [path.handle, path])),\n      ),\n      () => {\n        this.pathMapCache = undefined\n      },\n    )\n    return this.pathMapCache\n  }\n\n  /** @internal */\n  async findPath(name: PathName) {\n    const candidates = (await this.paths()).filter(\n      p =>\n        p.name.sample === name.sample &&\n        p.name.contig === name.contig &&\n        p.name.haplotype === name.haplotype &&\n        p.name.fragment <= name.fragment,\n    )\n    return candidates.sort((a, b) => b.name.fragment - a.name.fragment)[0]\n  }\n\n  private async pathsNamed(ref: PathRef) {\n    const name = pathNameFor(toPathQuery(ref), 0)\n    return (await this.paths())\n      .filter(\n        p =>\n          p.name.sample === name.sample &&\n          p.name.contig === name.contig &&\n          p.name.haplotype === name.haplotype,\n      )\n      .sort((a, b) => a.name.fragment - b.name.fragment)\n  }\n\n  async hasPath(ref: PathRef) {\n    return (await this.pathsNamed(ref)).length > 0\n  }\n\n  private pathLengths = new Map<number, Promise<number>>()\n\n  /** @internal */\n  pathLength(handle: number) {\n    let length = this.pathLengths.get(handle)\n    if (!length) {\n      length = this.walkPathLength(handle)\n      this.pathLengths.set(handle, length)\n      length.catch(() => this.pathLengths.delete(handle))\n    }\n    return length\n  }\n\n  private async walkPathLength(handle: number) {\n    const indexed = this.hasHaplotypeIndex\n      ? await this.haplotypeLength(handle)\n      : undefined\n    if (indexed === undefined) {\n      const last = await this.indexedPosition(handle, Number.MAX_SAFE_INTEGER)\n      if (!last) {\n        const path = await this.getPath(handle)\n        throw new Error(\n          `${path ? `The fragment of ${formatPathName(path.name)} at ${path.name.fragment}` : `Path ${handle}`} has not been indexed for random access`,\n        )\n      }\n      let length = last.pathOffset\n      let pos = last.pos\n      for (;;) {\n        const record = await this.getRecord(pos.node)\n        if (!record) {\n          throw new Error(`Node ${pos.node} does not exist in the graph`)\n        }\n        length += record.sequenceLen\n        const next = record.gbwt().lf(pos.offset)\n        if (!next || next.node === ENDMARKER) {\n          return length\n        }\n        pos = next\n      }\n    }\n    return indexed\n  }\n\n  async getPathFragments(opts: PathWindow): Promise<PathFragment[]> {\n    const { start, end } = opts\n    if (Number.isNaN(start) || Number.isNaN(end)) {\n      throw new Error(`The window ${start}..${end} is not a number range`)\n    }\n    const ordered = await this.pathsNamed(opts.path)\n    if (ordered.length === 0) {\n      throw new UnknownPathError(pathNameFor(toPathQuery(opts.path), 0))\n    }\n    if (end <= start) {\n      return []\n    }\n    const covering = ordered.filter(p => p.name.fragment <= start).slice(-1)\n    const within = ordered.filter(\n      p => p.name.fragment > start && p.name.fragment < end,\n    )\n    const fragments = await Promise.all(\n      [...covering, ...within].map(async path => ({\n        path,\n        start: path.name.fragment,\n        end: path.name.fragment + (await this.pathLength(path.handle)),\n      })),\n    )\n    return fragments.filter(f => start < f.end)\n  }\n\n  private async subgraphForFragment(fragment: PathFragment, opts: WindowQuery) {\n    const { sample, contig, haplotype } = fragment.path.name\n    const start = Math.max(opts.start, fragment.start)\n    const haplotypes = opts.haplotypes ?? 'all'\n    try {\n      const subgraph = await subgraphInInterval(this, {\n        ...opts,\n        path: { sample, contig, haplotype },\n        start,\n        end: Math.min(opts.end, fragment.end),\n      })\n      if (\n        opts.keep === undefined &&\n        this.hasHaplotypeIndex &&\n        (haplotypes === 'all' || haplotypes === 'distinct')\n      ) {\n        await subgraph.identifyPaths()\n      }\n      return subgraph\n    } catch (error) {\n      throw error instanceof SubgraphLimitError && error.walkedBp !== undefined\n        ? new SubgraphLimitError(error.limit, {\n            windowBp: opts.end - opts.start,\n            walkedBp: start - opts.start + error.walkedBp,\n          })\n        : error\n    }\n  }\n\n  async getSubgraphs(opts: WindowQuery): Promise<Subgraph[]> {\n    const fragments = await this.getPathFragments(opts)\n    const settled = await Promise.allSettled(\n      fragments.map(fragment => this.subgraphForFragment(fragment, opts)),\n    )\n    return settled.map(result => {\n      if (result.status === 'rejected') {\n        throw result.reason\n      }\n      return result.value\n    })\n  }\n\n  async getAlignments(opts: AlignmentQuery): Promise<HaplotypeAlignment[]> {\n    return (await this.getSubgraphs(opts)).flatMap(subgraph =>\n      subgraph.alignments(),\n    )\n  }\n\n  subgraphInInterval(opts: IntervalQuery) {\n    return subgraphInInterval(this, opts)\n  }\n\n  subgraphAtOffset(opts: OffsetQuery) {\n    return subgraphAtOffset(this, opts)\n  }\n\n  subgraphAroundNodes(opts: NodesQuery) {\n    return subgraphAroundNodes(this, opts)\n  }\n\n  subgraphBetween(opts: BetweenQuery) {\n    return subgraphBetween(this, opts)\n  }\n\n  fetchStats(): { graph: FetchStats; haplotypeIndex: FetchStats | undefined } {\n    const stats = ({ pager }: SqliteDatabase) => ({\n      fetches: pager.fetches,\n      bytesFetched: pager.bytesFetched,\n    })\n    return {\n      graph: stats(this.sqlite),\n      haplotypeIndex: this.index ? stats(this.index) : undefined,\n    }\n  }\n\n  async graphName() {\n    const gbzTags = new Map<string, string>()\n    for (const [key, value] of await this.tags()) {\n      if (key.startsWith('gbz_')) {\n        gbzTags.set(key.slice('gbz_'.length), value)\n      }\n    }\n    let name: GraphName = {\n      name: undefined,\n      subgraph: new Map(),\n      translation: new Map(),\n    }\n    try {\n      name = graphNameFromTags(gbzTags)\n    } catch {\n      // upstream falls back to an empty name when the tags do not parse\n    }\n    return name\n  }\n\n  async hasChainLinks() {\n    const links = await this.tag('chain_links')\n    return links !== undefined && Number(links) > 0\n  }\n\n  get hasHaplotypeIndex() {\n    return this.index !== undefined\n  }\n\n  private get companion() {\n    if (!this.index) {\n      throw new Error('no haplotype index was opened with this database')\n    }\n    return this.index\n  }\n\n  /** @internal */\n  async haplotypeSampleInterval() {\n    const value = this.indexTags.get('haplotype_index_interval')\n    return value === undefined ? undefined : Number(value)\n  }\n\n  // The most bp between two samples of any path: the reference paths take\n  // --reference-interval, which can exceed --interval.\n  /** @internal */\n  async haplotypeSampleGap() {\n    const interval = await this.haplotypeSampleInterval()\n    const reference = this.indexTags.get('haplotype_index_reference_interval')\n    return interval === undefined\n      ? undefined\n      : Math.max(interval, reference === undefined ? 0 : Number(reference))\n  }\n\n  /** @internal */\n  async haplotypeAnchorSpacing() {\n    const value = this.index?.has('HaplotypeAnchors')\n      ? this.indexTags.get('haplotype_index_anchor_spacing')\n      : undefined\n    return value === undefined ? undefined : Number(value)\n  }\n\n  // How the bins' node lists and stray rows were built, or undefined without\n  // them.\n  /** @internal */\n  async haplotypeStrayOptions(): Promise<HaplotypeStrayOptions | undefined> {\n    const tag = (key: string) =>\n      this.indexTags.get(`haplotype_index_stray_${key}`)\n    if (!this.index?.has('HaplotypeBins') || tag('format') !== '2') {\n      return undefined\n    }\n    const snarls =\n      tag('snarls') === 'modeled' &&\n      tag('chain_links') === ((await this.tag('chain_links')) ?? '0')\n    return {\n      context: Number(tag('context')),\n      bin: Number(tag('bin')),\n      bound: Number(tag('bound')),\n      snarlNodes: snarls ? Number(tag('snarl_nodes')) : undefined,\n    }\n  }\n\n  // The rows of a table with blobs whose keys lie in low..high: a key scan of\n  // its index, then its rows, which the indexer wrote in key order, prefetched\n  // as one range.\n  private async blobRows(table: string, low: number[], high: number[]) {\n    const rows: SqlValue[][] = []\n    const rowids: number[] = []\n    for await (const key of this.companion.indexScanFrom(table, low, high)) {\n      rowids.push(num(key[key.length - 1], `${table} rowid`))\n    }\n    if (rowids.length > 1) {\n      await this.companion.prefetchRows(\n        table,\n        [[Math.min(...rowids), Math.max(...rowids) + 1]],\n        true,\n      )\n    }\n    for (const rowid of rowids) {\n      const row = await this.companion.byRowid(table, rowid)\n      if (row) {\n        rows.push(row)\n      }\n    }\n    return rows\n  }\n\n  // The node lists and stray rows of the bins firstBin..lastBin of one\n  // reference path: a test of whether a node id is listed, and the rows.\n  /** @internal */\n  async haplotypeBinData(\n    referenceHandle: number,\n    firstBin: number,\n    lastBin: number,\n  ): Promise<{ listed: (id: number) => boolean; strays: HaplotypeStray[] }> {\n    const runs: [number, number][] = []\n    const strays: HaplotypeStray[] = []\n    for (const row of await this.blobRows(\n      'HaplotypeBins',\n      [referenceHandle, firstBin],\n      [referenceHandle, lastBin],\n    )) {\n      const bin = num(row[1], 'HaplotypeBins.bin')\n      decodeRuns(blob(row[3], 'HaplotypeBins.nodes'), runs)\n      decodeStrays(bin, blob(row[4], 'HaplotypeBins.strays'), strays)\n    }\n    return { listed: runTester(runs), strays }\n  }\n\n  // The anchors of one reference path at offsets from lowOffset to\n  // highOffset, each with the forward samples at its node.\n  /** @internal */\n  async haplotypeAnchorsBetween(\n    pathHandle: number,\n    lowOffset: number,\n    highOffset: number,\n  ): Promise<HaplotypeAnchorRow[]> {\n    const rows: HaplotypeAnchorRow[] = []\n    let parts: Uint8Array[] = []\n    const flush = () => {\n      const last = rows[rows.length - 1]\n      if (last) {\n        decodeVisits(last.node, parts, last.visits)\n      }\n      parts = []\n    }\n    for (const row of await this.blobRows(\n      'HaplotypeAnchors',\n      [pathHandle, lowOffset],\n      [pathHandle, highOffset],\n    )) {\n      const anchorOffset = num(row[1], 'HaplotypeAnchors.anchor_offset')\n      if (rows[rows.length - 1]?.anchorOffset !== anchorOffset) {\n        flush()\n        rows.push({\n          anchorOffset,\n          node: num(row[3], 'HaplotypeAnchors.node_handle'),\n          pathOffset: num(row[4], 'HaplotypeAnchors.path_offset'),\n          visits: [],\n        })\n      }\n      parts.push(blob(row[5], 'HaplotypeAnchors.visits'))\n    }\n    flush()\n    return rows\n  }\n\n  /** @internal */\n  async haplotypeAnchor(\n    pathHandle: number,\n    anchorOffset: number,\n  ): Promise<HaplotypeAnchor | undefined> {\n    const [row] = await this.haplotypeAnchorsBetween(\n      pathHandle,\n      anchorOffset,\n      anchorOffset,\n    )\n    return row && { node: row.node, pathOffset: row.pathOffset }\n  }\n\n  /** @internal */\n  haplotypeSamplesAtNode(handle: number) {\n    return this.haplotypeSamplesInRange(handle, handle)\n  }\n\n  private sampleFromRow(values: SqlValue[]): HaplotypeSample {\n    return {\n      node: num(values[0], 'HaplotypeSamples.node_handle'),\n      offset: num(values[1], 'HaplotypeSamples.node_offset'),\n      pathHandle: num(values[2], 'HaplotypeSamples.path_handle'),\n      orientation:\n        num(values[3], 'HaplotypeSamples.orientation') === 0\n          ? 'forward'\n          : 'reverse',\n      pathOffset: num(values[4], 'HaplotypeSamples.path_offset'),\n    }\n  }\n\n  // The samples at the node handles minHandle..maxHandle, from the b-tree of\n  // their key.\n  /** @internal */\n  async haplotypeSamplesInRange(minHandle: number, maxHandle: number) {\n    const samples: HaplotypeSample[] = []\n    for await (const row of this.companion.indexScanFrom(\n      'HaplotypeSamples',\n      [minHandle, 0],\n      [maxHandle, Number.MAX_SAFE_INTEGER],\n    )) {\n      samples.push(this.sampleFromRow(row))\n    }\n    return samples\n  }\n\n  /** @internal */\n  async haplotypeSampleAt(node: number, offset: number) {\n    const row = await this.companion.indexSeekLE('HaplotypeSamples', [\n      node,\n      offset,\n    ])\n    return row?.[0] === node && row[1] === offset\n      ? this.sampleFromRow(row)\n      : undefined\n  }\n\n  private overviewRows() {\n    this.overviewRowsCache ??= forgetOnRejection(\n      (async () => {\n        const rows: { sample: string; haplotype: number }[] = []\n        for await (const { rowid, values } of this.companion.scan(\n          'HaplotypeOverviewRows',\n        )) {\n          rows[rowid] = {\n            sample: str(values[1], 'HaplotypeOverviewRows.sample'),\n            haplotype: num(values[2], 'HaplotypeOverviewRows.haplotype'),\n          }\n        }\n        return rows\n      })(),\n      () => {\n        this.overviewRowsCache = undefined\n      },\n    )\n    return this.overviewRowsCache\n  }\n\n  // The parts of one overview table for the chunks firstChunk..lastChunk of\n  // one reference path at one level, joined per chunk.\n  private async overviewChunks(\n    table: string,\n    pathHandle: number,\n    level: number,\n    firstChunk: number,\n    lastChunk: number,\n  ) {\n    const parts = new Map<number, Uint8Array[]>()\n    for (const row of await this.blobRows(\n      table,\n      [pathHandle, level, firstChunk],\n      [pathHandle, level, lastChunk],\n    )) {\n      const chunk = num(row[2], `${table}.chunk`)\n      const list = parts.get(chunk) ?? []\n      list.push(blob(row[4], `${table} blob`))\n      parts.set(chunk, list)\n    }\n    return new Map(\n      [...parts].map(([chunk, list]) => [chunk, concatBytes(list)]),\n    )\n  }\n\n  // The haplotype index's binned summary of every haplotype over a window of\n  // a reference path, or undefined when the index has no overview or none for\n  // this path, which is not a reference path of a sample with anchors.\n  async haplotypeOverview(\n    opts: OverviewQuery,\n  ): Promise<HaplotypeOverview | undefined> {\n    const tag = (key: string) =>\n      this.indexTags.get(`haplotype_index_overview_${key}`)\n    if (!this.index?.has('HaplotypeOverviewClasses') || tag('format') !== '1') {\n      return undefined\n    }\n    const baseBin = Number(tag('bin'))\n    const chunkBins = Number(tag('chunk'))\n    const levels = Number(tag('levels'))\n    let level = Math.max(\n      0,\n      Math.min(Math.floor(opts.level ?? 0) || 0, levels - 1),\n    )\n    if (opts.level === undefined && opts.bpPerPixel !== undefined) {\n      while (\n        level + 1 < levels &&\n        baseBin * 4 ** (level + 1) <= opts.bpPerPixel\n      ) {\n        level += 1\n      }\n    }\n    const bin = baseBin * 4 ** level\n    const [fragments, haplotypes] = await Promise.all([\n      this.getPathFragments(opts),\n      this.overviewRows(),\n    ])\n    const bytesPerBin = Math.ceil(haplotypes.length / 2)\n    const bins: OverviewBin[] = []\n    const cellRows: Uint8Array[] = []\n    for (const fragment of fragments) {\n      const length = fragment.end - fragment.start\n      const from = Math.max(opts.start, fragment.start) - fragment.start\n      const to = Math.min(opts.end, fragment.end) - fragment.start\n      const firstBin = Math.floor(from / bin)\n      const lastBin = Math.floor((to - 1) / bin)\n      const firstChunk = Math.floor(firstBin / chunkBins)\n      const lastChunk = Math.floor(lastBin / chunkBins)\n      const [summaries, cells] = await Promise.all([\n        this.overviewChunks(\n          'HaplotypeOverviewBins',\n          fragment.path.handle,\n          level,\n          firstChunk,\n          lastChunk,\n        ),\n        this.overviewChunks(\n          'HaplotypeOverviewClasses',\n          fragment.path.handle,\n          level,\n          firstChunk,\n          lastChunk,\n        ),\n      ])\n      for (let chunk = firstChunk; chunk <= lastChunk; chunk++) {\n        const reader = new Varints(summaries.get(chunk) ?? new Uint8Array())\n        const packed = cells.get(chunk) ?? new Uint8Array()\n        for (let b = chunk * chunkBins; !reader.done; b++) {\n          const values = Array.from({ length: 7 }, () => reader.next())\n          if (b < firstBin || b > lastBin) {\n            continue\n          }\n          bins.push({\n            start: fragment.start + b * bin,\n            end: fragment.start + Math.min((b + 1) * bin, length),\n            classes: [values[0]!, values[1]!, values[2]!, values[3]!],\n            excursions: values[4]!,\n            variants: values[5]!,\n            longestExcursion: values[6]!,\n          })\n          const at = (b - chunk * chunkBins) * bytesPerBin\n          cellRows.push(packed.subarray(at, at + bytesPerBin))\n        }\n      }\n    }\n    if (bins.length === 0) {\n      return undefined\n    }\n    const cells = new Uint8Array(bins.length * haplotypes.length)\n    cellRows.forEach((packed, b) => {\n      for (let row = 0; row < haplotypes.length; row++) {\n        cells[b * haplotypes.length + row] =\n          ((packed[row >> 1] ?? 0) >> (4 * (row % 2))) & 0xf\n      }\n    })\n    return { level, bin, haplotypes, bins, cells }\n  }\n\n  /** @internal */\n  async haplotypeLength(pathHandle: number) {\n    const row = await this.companion.byRowid('HaplotypeLengths', pathHandle)\n    return row ? num(row[1], 'HaplotypeLengths.length') : undefined\n  }\n\n  private async indexedRow(rowid: number): Promise<IndexedPosition> {\n    const row = await this.sqlite.byRowid('ReferenceIndex', rowid)\n    if (!row) {\n      throw new Error('ReferenceIndex row referenced by its index is missing')\n    }\n    return {\n      pathOffset: num(row[1], 'ReferenceIndex.path_offset'),\n      pos: {\n        node: num(row[2], 'ReferenceIndex.node_handle'),\n        offset: num(row[3], 'ReferenceIndex.node_offset'),\n      },\n    }\n  }\n\n  private async indexedRowid(pathHandle: number, pathOffset: number) {\n    const key = await this.sqlite.indexSeekLE('ReferenceIndex', [\n      pathHandle,\n      pathOffset,\n    ])\n    return key?.[0] === pathHandle\n      ? num(key[2], 'ReferenceIndex rowid')\n      : undefined\n  }\n\n  /** @internal */\n  async indexedPosition(\n    pathHandle: number,\n    pathOffset: number,\n  ): Promise<IndexedPosition | undefined> {\n    const rowid = await this.indexedRowid(pathHandle, pathOffset)\n    return rowid === undefined ? undefined : this.indexedRow(rowid)\n  }\n\n  /** @internal */\n  async indexedPositionsBetween(\n    pathHandle: number,\n    fromOffset: number,\n    toOffset: number,\n  ) {\n    const [first, last] = await Promise.all([\n      this.indexedRowid(pathHandle, fromOffset),\n      this.indexedRowid(pathHandle, toOffset),\n    ])\n    const positions: IndexedPosition[] = []\n    if (first !== undefined && last !== undefined) {\n      await this.sqlite.prefetchRows('ReferenceIndex', [[first, last + 1]])\n      for (let rowid = first; rowid <= last; rowid++) {\n        positions.push(await this.indexedRow(rowid))\n      }\n    }\n    return positions\n  }\n}\n"],
+  "mappings": 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+}