jbrowse-plugin-graphgenomeviewer 8.3.6 → 8.3.7

package/dist/chunks/{chunk-NFPLX56S.js.map → chunk-HVDE2ZKA.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
+  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "host:tss-react/mui"],
   "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. 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package/dist/chunks/{chunk-QB5JERW4.js → chunk-IICQFAGJ.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-QB5JERW4.js.map → chunk-IICQFAGJ.js.map}

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package/dist/chunks/{chunk-HICKAMKK.js → chunk-PVRRW4PM.js}

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a=s.firstBy(r,e),h=a>=0?a:s.firstByName(r);return{...t,stable:{refName:s.paths[s.path[h]],start:s.start[h],rank:a>=0?l:R,strand:s.strand(h)},samples:n(r)}}function O(t){let s=[...new Set(t.samples)].sort(),e=new Map(s.map((h,o)=>[h,o])),n=Int32Array.from(t.samples,h=>e.get(h)),r=new Uint8Array(s.length),a=new Int32Array(s.length);return h=>{let o=0;for(let f=t.offsets[h];f<t.offsets[h+1];f++){let c=n[t.path[f]];r[c]===0&&(r[c]=1,a[o++]=c)}let i;if(o===s.length)i=s,r.fill(0);else if(o*8<s.length){let f=a.subarray(0,o);f.forEach(c=>r[c]=0),i=Array.from(f.sort(),c=>s[c])}else{i=[];for(let f=0;f<s.length;f++)r[f]===1&&(r[f]=0,i.push(s[f]))}return i}}function k(t,s){let{anchorPaths:e,pathVisits:n}=t,r=e&&n?P(e,s):void 0;if(!r||!e||!n)return t;let a=O(n),h=n.pathIndex(r.name);return{...t,nodes:t.nodes.map(o=>N(o,n,h,a)),anchoredBy:"paths",referencePath:r.name}}function Y(t,s){if(t.anchoredBy!=="tags")return k(t,s);let e=B(t);return e?{...t,referencePath:e}:t}function B(t){let s=t.nodes.find(e=>e.stable?.rank===0)?.stable?.refName;return s!==void 0&&t.anchorPaths?.some(e=>e.name===s)?s:void 0}function Z(t,s){if(!t.anchorPaths)return;let e=new Map(t.nodes.map(a=>[a.id,a.length])),n=(a,h=a.length)=>{let o=0;for(let i=0;i<h;i++)o+=e.get(a[i])??0;return o},r=m(t.paths??[],a=>E(a.name).name);return t.anchorPaths.map(a=>{let h=r.get(a.name),o=h?.length===1?h[0]:void 0,i=o&&s.get(o.name);return o&&i?{...a,start:a.start+n(o.nodeIds,i.first),length:n(i.nodeIds)}:a})}function tt(t){let{pathVisits:s}=t,e=new Map;return n=>{let r=e.get(n.id);if(!r){r=[];let a=s?s.slot(n.name):-1,h=a>=0?s.pathIndex(n.stable.refName):-1;if(h>=0)for(let o=s.offsets[a];o<s.offsets[a+1];o++)s.path[o]===h&&r.push(s.start[o]);r.length<2&&(r=[n.stable.start]),e.set(n.id,r)}return r}}export{b as a,S as b,m as c,g as d,l as e,_ as f,w as g,G as h,U as i,C as j,K as k,T as l,y as m,$ as n,A as o,p,d as q,E as r,Q as s,P as t,k as u,Y as v,Z as w,tt as x};
+//# sourceMappingURL=chunk-PVRRW4PM.js.map

package/dist/chunks/{chunk-HICKAMKK.js.map → chunk-PVRRW4PM.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BEUTROKU.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BRH73RCH.js"],
   "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // the visit of `slot` on the path first in name order, at its lowest offset\n  // there: where gfa-to-tabix places a segment the reference doesn't visit, so\n  // both place it alike whatever order the file lists its paths in\n  firstByName(slot) {\n    let best = this.offsets[slot];\n    for (let i = best + 1; i < this.offsets[slot + 1]; i++) {\n      const a = this.paths[this.path[i]];\n      const b = this.paths[this.path[best]];\n      if (a < b || a === b && this.start[i] < this.start[best]) {\n        best = i;\n      }\n    }\n    return best;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n", "import {\n  PathVisitsBuilder\n} from \"./chunk-BEUTROKU.js\";\nimport {\n  groupBy\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  REFERENCE_RANK\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/pathAnchoring.ts\nvar RANGE_SUFFIX = /:(\\d+)-\\d+$/;\nvar VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\\d+)(?:\\[(\\d+)-\\d+\\])?$/;\nvar VG_SUBRANGE = /\\[(\\d+)-\\d+\\]$/;\nfunction pathOrigin(pathName) {\n  const fragment = VG_FRAGMENT.exec(pathName);\n  if (fragment) {\n    return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };\n  }\n  const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);\n  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };\n}\nfunction surveyPaths(paths, lengthOf) {\n  const anchorPaths = [];\n  const visits = new PathVisitsBuilder();\n  for (const path of paths) {\n    const sample = panSNSample(path.name);\n    const p = visits.pathOf(path.name, sample);\n    let pos = path.start;\n    for (const step of path.steps) {\n      visits.addAt(visits.declare(step.id), p, pos, step.strand === \"-\");\n      pos += lengthOf(step.id);\n    }\n    anchorPaths.push({\n      name: path.name,\n      sample,\n      start: path.start,\n      length: pos - path.start\n    });\n  }\n  return { anchorPaths, pathVisits: visits.build() };\n}\nfunction chooseReferencePath(anchorPaths, preferred) {\n  const named = anchorPaths.find(\n    (p) => p.sample === preferred || p.name === preferred\n  );\n  return named ?? anchorPaths[0];\n}\nvar OFF_REFERENCE_RANK = 1;\nfunction anchorNode(node, visits, reference, samplesOf) {\n  const slot = visits.slot(node.name);\n  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {\n    return node;\n  }\n  const own = visits.firstBy(slot, reference);\n  const anchor = own >= 0 ? own : visits.firstByName(slot);\n  return {\n    ...node,\n    stable: {\n      refName: visits.paths[visits.path[anchor]],\n      start: visits.start[anchor],\n      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,\n      strand: visits.strand(anchor)\n    },\n    samples: samplesOf(slot)\n  };\n}\nfunction sampleSorter(visits) {\n  const sorted = [...new Set(visits.samples)].sort();\n  const rank = new Map(sorted.map((sample, i) => [sample, i]));\n  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));\n  const seen = new Uint8Array(sorted.length);\n  const ranks = new Int32Array(sorted.length);\n  return (slot) => {\n    let n = 0;\n    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {\n      const r = pathRank[visits.path[i]];\n      if (seen[r] === 0) {\n        seen[r] = 1;\n        ranks[n++] = r;\n      }\n    }\n    let out;\n    if (n === sorted.length) {\n      out = sorted;\n      seen.fill(0);\n    } else if (n * 8 < sorted.length) {\n      const found = ranks.subarray(0, n);\n      found.forEach((r) => seen[r] = 0);\n      out = Array.from(found.sort(), (r) => sorted[r]);\n    } else {\n      out = [];\n      for (let r = 0; r < sorted.length; r++) {\n        if (seen[r] === 1) {\n          seen[r] = 0;\n          out.push(sorted[r]);\n        }\n      }\n    }\n    return out;\n  };\n}\nfunction anchorFromPaths(graph, preferred) {\n  const { anchorPaths, pathVisits } = graph;\n  const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;\n  if (!reference || !anchorPaths || !pathVisits) {\n    return graph;\n  }\n  const samplesOf = sampleSorter(pathVisits);\n  const referenceIndex = pathVisits.pathIndex(reference.name);\n  return {\n    ...graph,\n    nodes: graph.nodes.map(\n      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)\n    ),\n    anchoredBy: \"paths\",\n    referencePath: reference.name\n  };\n}\nfunction anchorGraph(graph, preferred) {\n  if (graph.anchoredBy !== \"tags\") {\n    return anchorFromPaths(graph, preferred);\n  }\n  const referencePath = taggedReferencePath(graph);\n  return referencePath ? { ...graph, referencePath } : graph;\n}\nfunction taggedReferencePath(graph) {\n  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;\n  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;\n}\nfunction trimOrigins(graph, kept) {\n  if (!graph.anchorPaths) {\n    return void 0;\n  }\n  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));\n  const bp = (ids, end = ids.length) => {\n    let sum = 0;\n    for (let i = 0; i < end; i++) {\n      sum += lengthOf.get(ids[i]) ?? 0;\n    }\n    return sum;\n  };\n  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);\n  return graph.anchorPaths.map((o) => {\n    const pieces = byOrigin.get(o.name);\n    const path = pieces?.length === 1 ? pieces[0] : void 0;\n    const stretch = path && kept.get(path.name);\n    return path && stretch ? {\n      ...o,\n      start: o.start + bp(path.nodeIds, stretch.first),\n      length: bp(stretch.nodeIds)\n    } : o;\n  });\n}\nfunction referenceVisitStarts(graph) {\n  const { pathVisits } = graph;\n  const cache = /* @__PURE__ */ new Map();\n  return (node) => {\n    let starts = cache.get(node.id);\n    if (!starts) {\n      starts = [];\n      const slot = pathVisits ? pathVisits.slot(node.name) : -1;\n      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;\n      if (p >= 0) {\n        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {\n          if (pathVisits.path[i] === p) {\n            starts.push(pathVisits.start[i]);\n          }\n        }\n      }\n      if (starts.length < 2) {\n        starts = [node.stable.start];\n      }\n      cache.set(node.id, starts);\n    }\n    return starts;\n  };\n}\n\nexport {\n  pathOrigin,\n  surveyPaths,\n  chooseReferencePath,\n  anchorFromPaths,\n  anchorGraph,\n  trimOrigins,\n  referenceVisitStarts\n};\n"],
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package/dist/chunks/chunk-SQBD75UZ.js

@@ -0,0 +1,2 @@
+import{l as o}from"./chunk-UOWS2HEQ.js";function u(a,r,e){return e?{...a,walkRowRuns:o(a,r)}:a}export{u as a};
+//# sourceMappingURL=chunk-SQBD75UZ.js.map

package/dist/chunks/{chunk-EVKN4Y3R.js → chunk-SVF6WK42.js}

@@ -1,4 +1,4 @@
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re(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(a.window.start/A),O=Math.floor((a.window.end-1)/A),L=J*A,G=(O+1)*A,W=new Map,ue=async(u,v)=>{let z=await e.haplotypeAnchorsBetween(a.referenceHandle,u*S,v*S);for(let T of z)W.set(T.anchorOffset/S,T)},se=Math.max(0,Math.floor((L-M)/S)-1),Y=Math.ceil((G+M)/S)+1,[{listed:De,strays:ae}]=await Promise.all([e.haplotypeBinData(a.referenceHandle,J,O),ue(se,Y)]);for(let u of t.keys()){let v=N(u);if(!Q(u)&&!De(v)&&!U.has(v))throw new re(`the haplotype index lists node ${v} of the subgraph in no bin that the window touches`)}r.scans=pt([...t.keys()].sort((u,v)=>u-v));let ie=Promise.all(r.scans.map(([u,v])=>e.haplotypeSamplesInRange(u,v)));for(ie.catch(()=>{});se>0&&(W.get(se)?.pathOffset??Number.POSITIVE_INFINITY)>=L-M;)se-=1,await ue(se,se);for(;W.has(Y)&&W.get(Y).pathOffset<=G+M;)Y+=1,await ue(Y,Y);let pe=[...W.keys()].sort((u,v)=>u-v),ye=W.get(pe[0]??-1);if(!ye)throw new re("the haplotype index has no anchors on this path");let he=u=>W.get(u).pathOffset,Ne=new Map;for(let u of pe){let v=N(W.get(u).node);Ne.set(v,[...Ne.get(v)??[],u])}let ct=[...Ne.keys()],Et=ct.map(u=>W.get(Ne.get(u)[0]).visits);if(!Et[ct.indexOf(N(ye.node))].some(u=>u.pathHandle===a.referenceHandle&&u.orientation==="forward"&&u.pathOffset===ye.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${a.referenceHandle} at offset ${ye.pathOffset} (node ${N(ye.node)}); it does not match this graph`);let kt=pe.filter(u=>he(u)<=a.window.start),$n=pe.filter(u=>he(u)>=a.window.end);r.anchors=[he(kt[kt.length-1]??pe[0]),he($n[0]??pe[pe.length-1])],r.anchorsRead=pe.length;let dt=new Map,vt=new Set;if(ct.forEach((u,v)=>{let z=Ne.get(u),T=z.length===1?z[0]:void 0;for(let q of Et[v])vt.add(q.pathHandle),q.orientation==="forward"&&y(q.pathHandle)&&dt.set(q.pathHandle,[...dt.get(q.pathHandle)??[],{k:T,row:q}])}),r.chosenPaths=[...vt].filter(y).length,r.chosenPaths>Gt.mostChosenPaths)throw new re(`${r.chosenPaths} chosen paths pass the anchors, more than ${Gt.mostChosenPaths}`);let je=[],Ie=Number.POSITIVE_INFINITY,be=0;for(let[u,v]of dt){v.sort((z,T)=>z.row.pathOffset-T.row.pathOffset);for(let z=0;z+1<v.length;z++){let T=v[z],q=v[z+1];if(T.k===void 0||q.k===void 0||Math.abs(T.k-q.k)!==1)continue;let[Z,te]=he(T.k)<=he(q.k)?[T,q]:[q,T],ne=he(Z.k),oe=he(te.k);ne<G&&oe>=L?(je.push({pathHandle:u,from:T.row,to:q.row}),Ie=Math.min(Ie,ne-M),be=Math.max(be,oe+M)):ne>=G&&ne-G<=M?(je.push({pathHandle:u,from:Z.row,to:void 0}),Ie=Math.min(Ie,ne-M),be=Math.max(be,ne+M)):oe<L&&L-oe<=M&&(je.push({pathHandle:u,from:te.row,to:void 0}),Ie=Math.min(Ie,oe-M),be=Math.max(be,oe+M))}}let Rn=new Set(B.map(u=>`${u.low}:${u.high}`)),Nn=ae.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Rn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,v)=>u.pathHandle-v.pathHandle||u.pathStart-v.pathStart);r.strays={bins:O-J+1,rows:ae.length,walked:0,outsideBp:0},be>0&&await a.prefetchReferenceRange(a.referenceHandle,Math.max(0,Ie),be+1),r.ms.scan=o();let Pt=8*S+2*(a.window.end-a.window.start),At=r.strays,Me=0,$t=u=>{if(At.outsideBp+=u,Me+=u,Me>Pt)throw new re(`a walk of a chosen path near the window went past its cap of ${Pt} bp`)},ft=new Map,Rt=(u,v,z)=>(ft.get(u)??[]).some(([T,q])=>T<=v&&z<q),Nt=(u,v,z)=>{ft.set(u,[...ft.get(u)??[],[v,z]])},Mt=async(u,v,z,T,q)=>{let Z=v,te=z,ne=te;for(;Z&&te<=T;){n?.throwIfAborted();let oe;if(t.has(Z.node)){let Le=await $({pos:Z,left:te},u,"forward",q),Ht=F(Le);Z=Ht.pos,te=Ht.left,oe=f(Z.node),ne=Math.max(ne,Le.hapEnd)}else oe=(await d(Z.node)).sequenceLen,$t(oe),ne=Math.max(ne,te+oe);Z=await E(Z),te+=oe}return ne},Mn=async(u,v,z,T)=>{let q={pos:v,left:z},Z=z;for(;q.left>T;){n?.throwIfAborted();let te=await R(q.pos);if(!te)break;let ne=(await d(te.node)).sequenceLen,oe=q.left-ne;if(t.has(te.node)){let Le=await $({pos:te,left:oe},u,"forward","section");q=_(Le),Z=Math.min(Z,Le.hapStart)}else $t(ne),q={pos:te,left:oe},Z=Math.min(Z,oe)}return Z};for(let{pathHandle:u,from:v,to:z}of je){let T=v.pathOffset,q=(z??v).pathOffset+M;if(Rt(u,T-M,q))continue;let Z={node:v.node,offset:v.offset};Me=0;let te=await Mt(u,Z,T,q,"section");Me=0;let ne=await Mn(u,Z,T,T-M);Nt(u,Math.min(ne,T-M),Math.max(te,q+1)),i(z?"section":"visit",z?"past the far anchor":"bound")}for(let u of Nn){if(Rt(u.pathHandle,u.pathStart,u.pathEnd))continue;Me=0;let v=await Mt(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");Nt(u.pathHandle,u.pathStart,Math.max(v,u.pathEnd+1)),At.walked+=1}r.ms.walks=o();let Lt=[];for(let u of await ie)for(let v of u)if(r.scanRows+=1,t.has(v.node)&&y(v.pathHandle)){if(!(b.get(v.pathHandle)??[]).some(z=>{let T=g[z];return T.hapStart<=v.pathOffset&&v.pathOffset<T.hapEnd}))throw new re(`chosen path ${v.pathHandle} has a sample at ${v.pathOffset} on the window's nodes that no walk reached`);v.orientation==="reverse"&&Lt.push(v)}for(let u of Lt)await $({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");r.ms.check=o()},X=async()=>{let w=new Map,S=O=>{let L=Ce(O),G=w.get(L);G?G.add(O.orientation):w.set(L,new Set([O.orientation]))},A=0,M=()=>{for(;A<g.length;A++)S(g[A])};M();let B=O=>(w.get(Ce(O))?.size??0)>1,U=2*h,J=(O,L)=>L===D?y(a.referenceHandle)&&Kt(O):!O.canonical||Kt(O);for(let O=0;O<g.length;O++){let L=g[O];if(B(L)||!J(L,O))continue;r.twins.tried+=1;let G=L.orientation==="forward"?"reverse":"forward",W=F(L),ue=0,se;for(;!se&&ue<=U;){n?.throwIfAborted();let ae=await E(W.pos);if(!ae)break;let ie=(await d(ae.node)).sequenceLen,pe=Ve(L.orientation,W.left,(await d(W.pos.node)).sequenceLen,ie),ye=ee(ae.node);se=(await e.haplotypeSamplesInRange(ye,ye)).find(he=>he.pathHandle===L.pathHandle&&he.orientation===G&&he.pathOffset===pe),ue+=ie,W={pos:ae,left:pe}}let Y=se&&{pos:{node:se.node,offset:se.offset},left:se.pathOffset},De=0;for(;Y&&!B(L)&&De<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ae=await $(Y,L.pathHandle,G,"twin"),ie=g.indexOf(ae);await k(ie,!0),await k(ie,!1),M(),Y=F(ae)}if(!B(L)){let ae=(await d(Y.pos.node)).sequenceLen;De+=ae;let ie=await E(Y.pos);Y=ie?{pos:ie,left:Ve(G,Y.left,ae,(await d(ie.node)).sequenceLen)}:void 0}}if(M(),!B(L))throw new re(`piece ${Ce(L)} was found in one orientation where extractPaths keeps the other`);r.twins.found+=1}r.ms.twins=o()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new re("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await j(w),await X()}catch(w){if(!(w instanceof re))throw w;r.fallback=w.message}return H()}function Xt(a,e){return a.handles[0]-e.handles[0]||a.offsets[0]-e.offsets[0]}var On=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),we=(a,e)=>a>>>e|a<<32-e;function Jt(a){let e=Math.ceil((a.length+9)/64),t=new Uint8Array(e*64);t.set(a),t[a.length]=128;let n=new DataView(t.buffer),s=a.length*8;n.setUint32(t.length-8,Math.floor(s/2**32)),n.setUint32(t.length-4,s>>>0);let o=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),r=new Uint32Array(64);for(let c=0;c<e;c++){for(let P=0;P<16;P++)r[P]=n.getUint32(c*64+P*4);for(let P=16;P<64;P++){let E=r[P-15],R=r[P-2],m=we(E,7)^we(E,18)^E>>>3,I=we(R,17)^we(R,19)^R>>>10;r[P]=r[P-16]+m+r[P-7]+I}let d=o[0],f=o[1],p=o[2],y=o[3],g=o[4],l=o[5],b=o[6],x=o[7];for(let P=0;P<64;P++){let E=we(g,6)^we(g,11)^we(g,25),R=g&l^~g&b,m=x+E+R+On[P]+r[P]|0,I=we(d,2)^we(d,13)^we(d,22),$=d&f^d&p^f&p;x=b,b=l,l=g,g=y+m|0,y=p,p=f,f=d,d=m+I+$|0}[d,f,p,y,g,l,b,x].forEach((P,E)=>{o[E]=o[E]+P})}let i=new Uint8Array(32),h=new DataView(i.buffer);for(let c=0;c<8;c++)h.setUint32(c*4,o[c]);return i}function Yt(a,e){let t=new Map;if(a!==void 0)for(let n of a.split(";")){let s=n.split(","),[o,r]=s;if(s.length!==2||!o||!r)throw new Error(`Invalid ${e} relationship: ${n}`);let i=t.get(o);i||(i=new Set,t.set(o,i)),i.add(r)}return t}function nn(a){return{name:a.get("pggname"),subgraph:Yt(a.get("subgraph"),"subgraph"),translation:Yt(a.get("translation"),"translation")}}function en(a,e){for(let[t,n]of e){let s=a.get(t);s||(s=new Set,a.set(t,s));for(let o of n)s.add(o)}}function sn(a,e){let t={name:a,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(a,new Set([e.name])),en(t.subgraph,e.subgraph),en(t.translation,e.translation)),t}function tn(a){return[...a.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function on(a){let e=[];a.name!==void 0&&e.push(`H	NM:Z:${a.name}`);for(let[t,n]of tn(a.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of tn(a.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function rn(a){let e=a.reduce((r,i)=>r+i.length,0),t=new Uint8Array(e),n=0;for(let r of a)t.set(r,n),n+=r.length;let s=globalThis.crypto?.subtle;return[...s?new Uint8Array(await s.digest("SHA-256",t)):Jt(t)].map(r=>r.toString(16).padStart(2,"0")).join("")}var Cn="_gbwt_ref";function fe(a){let e=`${a.sample}#${a.haplotype}#${a.contig}`;return a.end===void 0?e:`${e}[${a.fragment}-${a.end}]`}var Bn=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,_n=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Tn(a){let e=Bn.exec(a);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=_n.exec(a);if(t)return{contig:t[1]};throw new Error(`"${a}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Ae(a){return typeof a=="string"?Tn(a):a}function $e(a,e){return{sample:a.sample??Cn,contig:a.contig,haplotype:a.haplotype??0,fragment:e}}var le=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function ut(a,e){return a[0]<e[0]||a[0]===e[0]&&(a[1]<e[1]||a[1]===e[1]&&a[2]<e[2])}var _e=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let o=s.length-1;for(;o>0;){let r=o-1>>1;if(ut(s[o],s[r]))[s[o],s[r]]=[s[r],s[o]],o=r;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let o=2*s+1,r=o+1,i=s;if(o<e.length&&ut(e[o],e[i])&&(i=o),r<e.length&&ut(e[r],e[i])&&(i=r),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function Fn(a){let e=new Int32Array(a.length),t=new Int32Array(a.length);return a.forEach(([n,s],o)=>{e[o]=n,t[o]=s}),{pathAt:e,refAt:t,count:a.length}}function qn(a,e){let t=0,n=a.length;for(;t<n;){let s=t+n>>1;a[s]>e?n=s:t=s+1}return a[t]}function ke(a){return`${a.node}:${a.offset}`}function Be(a){return a.map(e=>ee(e)).reverse()}function zn(a,e){let t=e.identity.hapStart-a.identity.hapEnd,n=a.strand==="+"?e.refStart-a.refEnd:a.refStart-e.refEnd;return a.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Dn(a,e,t){let[n,s]=a.strand==="+"?[a,e]:[e,a],o=n.edits.map(([c,d])=>[c,d]);hn(o,t.insertion,t.deletion);for(let[c,d]of s.edits)K(o,c,d);let r=a.identity.walkForward,[i,h]=r?[a,e]:[e,a];return{strand:a.strand,refStart:n.refStart,refEnd:s.refEnd,edits:o,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:a.identity.pathHandle,name:a.identity.name,hapStart:a.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:r}}}function jn(a,e,t){if(a.some(r=>r.weight!==void 0))return a;let n=new Map;a.forEach((r,i)=>{if(r.identity){let h=n.get(r.identity.pathHandle);h?h.push(i):n.set(r.identity.pathHandle,[i])}});let s=new Map,o=new Set;for(let r of n.values()){r.sort((d,f)=>a[d].identity.hapStart-a[f].identity.hapStart);let i=r[0],h=a[i],c=[];for(let d of r.slice(1)){let f=a[d],p=c.length===0?zn(h,f):void 0;if(p){h=Dn(h,f,p),o.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(g=>a[g]),f]):void 0;if(y){h=y;for(let g of[...c,d])o.add(g)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return a.flatMap((r,i)=>o.has(i)?[]:[s.get(i)??r])}function Ge(a,e){return{node:a.path[e],offset:a.offsets[e]}}var Un=32768;function Wn(a){let e=[...a].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=Un?s[1]=n:t.push([n,n])}return t}var Te=class a{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new a(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ce(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new le(this.limit);let t=await this.db.getRecord(ce(e,"forward")),n=await this.db.getRecord(ce(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let o=n,r=s;for(;;){await this.ensureNode(N(r.node));let i=this.record(r.node);if(o+i.sequenceLen>t)return{position:{seqOffset:t,handle:r.node,nodeOffset:t-o,gbwtOffset:r.offset},name:e.name,handle:e.handle};o+=i.sequenceLen;let h=i.gbwt().lf(r.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);r=h}}async aroundPosition(e,t,n){let s=N(e);await this.ensureNode(s);let o=this.record(e),r=Ee(e),i=new _e;return i.push(t,s,Ue(r)),i.push(o.sequenceLen-t-1,s,We(r)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,o]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&o){let r=s.pos.node,i=o.pos.node;if(!await this.db.prefetchRecords([[Math.min(r,i),Math.max(r,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(Wn(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(s){throw s instanceof le&&s.windowBp===void 0?new le(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},o=e.nodeOffset,r=t,i=new _e;for(;;){let h=N(s.node),c=Ee(s.node);this.walkedBp=t-r,await this.ensureNode(h);let d=this.record(s.node);if(o>=d.sequenceLen)throw new Error(`Offset ${o} in node ${h} of length ${d.sequenceLen}`);i.push(o,h,Ue(c));let f=d.sequenceLen-o;if(r<=f){i.push(r===f?0:f-r-1,h,We(c));break}i.push(0,h,We(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,o=0,r-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new _e;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let r of this.records.keys())s.add(N(r));let o=0;for(;e.size>0;){let[r,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),o+=1);let d=Ft(h);if(!n.has(`${i}:${d}`)){let y=this.record(ce(i,qt(h))),g=r+y.sequenceLen-1;g<=t&&e.push(g,i,d)}let f=this.record(ce(i,zt(h))),p=r+1;if(p<=t)for(let y of f.successors()){let g=N(y),l=Ue(Ee(y));n.has(`${g}:${l}`)||e.push(p,g,l)}}for(let r of s)this.records.delete(ce(r,"forward")),this.records.delete(ce(r,"reverse"));return{inserted:o,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,ee(t)],s=new Set([N(e),N(t)]),o=[];for(;n.length>0;){let r=n.pop(),i=N(r);this.hasNode(i)||(await this.addNode(i),o.push(i));for(let h of this.record(r).successors()){let c=N(h);s.has(c)||(n.push(h,ee(h)),s.add(c))}}return{inserted:o,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:o,nodes:r}=await this.fillBetween(n,s),i=N(n),h=N(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:r,inserted:o.length});for(let c of o)this.snarlNodes.add(c);t+=o.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let s of this.sortedHandles()){let o=this.record(s),r=o.next;r!==void 0&&(n=!0,this.hasHandle(r)?He(s,r)&&t.push([s,r]):e==="overlapping"&&this.isSnarlEntryInSubgraph(o)&&t.push([s,r]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(ee(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let o=t.get(n);if(!o){if(o=await this.db.getRecord(n),e?.(),!o)throw new Error(`Node record ${n} is missing from the database`);t.set(n,o)}return o}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(ee(d))).successors().length>1},n=async h=>{let c=await e(ee(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[ee(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,o=this.sortedHandles().flatMap(h=>this.record(h).successors()),r,i=!1;for(;!i&&o.length>0;){let h=o.shift(),c=N(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")r=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])o.push(...(await e(ce(c,f))).successors())}}return r}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),o=s.length,r=new Map;s.forEach((m,I)=>r.set(m,I));let i=new Int32Array(o+1),h=new Int32Array(o),c=[];for(let m=0;m<o;m++){let I=this.record(s[m]),$=I.gbwt().decompressArrays();h[m]=I.sequenceLen,c.push($),i[m+1]=i[m]+$.nodes.length}let d=i[o],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let m=0;m<o;m++){let I=c[m];f.set(I.nodes,i[m]),p.set(I.offsets,i[m])}c.length=0;for(let m=0;m<d;m++){let I=r.get(f[m]);I===void 0?f[m]=-1:(f[m]=I,y[i[I]+p[m]]=1)}let g=n===void 0?void 0:r.get(n.handle),l=n?.gbwtOffset,b,x=(m,I,$)=>{let F=[],_=0,D=0,C=-1,H=m,k=I;for(;;){H===g&&k===l&&(C=_),$&&($.push(s[H]),F.push(k)),_+=1,D+=h[H];let j=i[H]+k,X=f[j];if(X<0)break;k=p[j],H=X}return{offsets:F,len:D,refAt:C,last:H}},P=(m,I,$,F)=>{F>=0&&(this.refId=this.paths.length,b=F),this.paths.push({path:m,offsets:I,len:$,weight:void 0,identity:void 0})},E=new Int32Array(o);for(let m=0;m<o;m++){let I=s[m];if(!Q(I)){let $=i[m],F=i[m+1]-$;for(let _=0;_<F;_++)if(y[$+_]===0){let D=[],{offsets:C,len:H,refAt:k,last:j}=x(m,_,D),X=s[j];if(k>=0||Pe(I,X)){if(P(D,C,H,k),!Q(X)){let w=r.get(ee(X));E[w]=E[w]+1}}else this.twinStarts.add(ke({node:I,offset:_}))}}}for(let m=0;m<o;m++){let I=s[m];if(Q(I)){let $=i[m],F=i[m+1]-$,_=0;for(let C=0;C<F;C++)y[$+C]===0&&(_+=1);let D=(g===void 0||b!==void 0)&&_===E[m];for(let C=0;C<F;C++)if(y[$+C]===0){let H=D?void 0:x(m,C,void 0);if(H&&(H.refAt>=0||Pe(I,s[H.last]))){let k=[],{offsets:j,len:X,refAt:w}=x(m,C,k);P(k,j,X,w)}else this.twinStarts.add(ke({node:I,offset:C}))}}}let R=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((m,I)=>m.path[0]-I.path[0]||m.offsets[0]-I.offsets[0]),R&&(this.refId=this.paths.indexOf(R)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let m=this.paths[this.refId],I=n.nodeOffset;for(let F of m.path.slice(0,b))I+=this.record(F).sequenceLen;let $=n.seqOffset-I;this.refInterval=[$,$+m.len],m.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:$,hapEnd:$+m.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,s=n&&!Oe(n)?Be(n):void 0,o=c=>s!==void 0&&wt(c,s)===0||Oe(Be(c)),r=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>wt(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=r&&c!==t&&o(c.path);this.twinDeferred||=f,d&&wt(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=r=>`${r.pathHandle}:${r.hapStart}-${r.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let r of this.paths)r!==e&&r.identity?.orientation==="forward"&&s.add(n(r.identity));let o=this.paths.filter(r=>r===e||r.identity?.orientation!=="reverse"||!s.has(n(r.identity)));o.length<this.paths.length&&(this.paths=o,this.refId=e===void 0?void 0:o.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(r=>r.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((r,i)=>i!==this.refId&&r.identity===void 0).length;if(t>0)throw new Error(`${t} 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`);let n=this.refId===void 0?void 0:this.paths[this.refId],s=this.paths.filter((r,i)=>i===this.refId||r.identity!==void 0&&e(r.identity.name)),o=new Set;for(let r of s)for(let i of r.path)o.add(N(i));for(let r of[...this.records.keys()])o.has(N(r))||this.records.delete(r);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let o=e.position.seqOffset,r=await Zt({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=r.stats,r.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===r.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[r.reference,...r.pieces].sort(Xt);return this.paths=c.map(h),this.refId=c.indexOf(r.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[r.reference.hapStart,r.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=pt(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let o=l=>{let b=0,x=t.length-1;for(;b<x;){let E=b+x+1>>1;t[E][0]<=l?b=E:x=E-1}let P=t[b];return P[0]<=l&&l<=P[1]},r=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&r.set(ke(Ge(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(o(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let x=await this.db.haplotypeSampleAt(l.node,l.offset);return x||(i.companionMisses+=1),x},f=new Map,p=async l=>{let b=f.get(l);if(!b){let x=await this.db.getPath(l);if(!x)throw new Error(`Path ${l} is missing from the database`);b=x.name,f.set(l,b)}return b},y=(l,b,x)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+x},g=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let x=[],P=new Set,E={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(E);let R,m=0,I=l,$;for(;R===void 0;){if(this.signal?.throwIfAborted(),I!==void 0){if(P.has(I)){E.end="cycle";break}P.add(I);let H=this.paths[I];x.push({index:I,startBp:m}),E.fragments+=1;let k=m;for(let X=0;X<H.path.length;X++){let w=Ge(H,X),S=n.get(ke(w)),A=this.record(w.node).sequenceLen;if(S){R=y(S,k,A);break}k+=A}if(m+=H.len,R){E.end="in-fragment sample";break}let j=Ge(H,H.path.length-1);$=this.record(j.node).gbwt().lf(j.offset),I=void 0}if($===void 0||$.node===0){E.end="endmarker";break}let F=ke($),_=r.get(F);if(_!==void 0){let H=this.paths[_].identity;if(H){R=g(H,m),E.end="identified sibling";break}I=_;continue}this.records.has($.node)&&(E.reentries+=1),this.twinStarts.has(F)&&(E.twinLandings+=1);let D=await d($,E),C=await c($.node);if(D){R=y(D,m,C.sequenceLen),E.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,E.steps+=1,m-x[x.length-1].startBp>4*e+4*C.sequenceLen){E.end="bound";break}m+=C.sequenceLen,$=C.gbwt().lf($.offset)}if(R){E.pathHandle=R.pathHandle;let F=await p(R.pathHandle);for(let{index:_,startBp:D}of x){let C=this.paths[_];C.identity=R.orientation==="forward"?{pathHandle:R.pathHandle,name:F,orientation:"forward",hapStart:R.base+D,hapEnd:R.base+D+C.len}:{pathHandle:R.pathHandle,name:F,orientation:"reverse",hapStart:R.base-D-C.len,hapEnd:R.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let o=t.get(n);o?o.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),o=new Int32Array(e.length),r=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=qn(c,i);if(d===void 0)return;s[r]=h,o[r]=d,r+=1,i=d}}return{pathAt:s,refAt:o,count:r}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[o]).sequence;for(;r<h.length&&i<c.length;){if(h[r]!==c[i])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-o-1]).sequence;for(;r<h.length&&i<c.length;){if(h[h.length-r-1]!==c[c.length-i-1])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),o=this.pathLen(t),r=this.prefixMatches(e,t),i=this.suffixMatches(e,t);r+i>s&&(i=s-r),r+i>o&&(i=o-r),K(n,"M",r),hn(n,s-r-i,o-r-i),K(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let o of e)n.has(o)&&(s+=this.record(o).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??Fn(Ut(e,t,f=>this.record(f).sequenceLen)[0]),o=[],r=this.refPrefix(t),i=(f,p,y,g)=>{f===p?K(o,"D",r[g]-r[y]):y===g?K(o,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,g),o)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let g=this.record(e[p]).sequenceLen;K(o,"M",g),h+=g,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:o,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Oe(n)&&(t.identity===void 0||!Oe(Be(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let o=Be(t.path),r=this.sharedWeight(t.path,n);if(this.sharedWeight(o,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(r===0)s={...this.editsAgainst(o,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(o,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],s=(d,f,p,y)=>{let g=Gn(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],x=l.identity,P=x?.orientation==="forward",[E,R]=P?[l,b]:[b,l];return{strand:f,refStart:e.start+g.leading,refEnd:e.start+n-g.trailing,edits:g.edits,weight:l.weight,path:p.flatMap(m=>this.paths[m].path),start:Ge(l,0),pieces:p,soloAligned:y,identity:x===void 0?void 0:{pathHandle:x.pathHandle,name:x.name,hapStart:x.name.fragment+E.identity.hapStart,hapEnd:x.name.fragment+R.identity.hapEnd,walkForward:P}}},o=d=>d.soloAligned.reduce((f,p)=>f+p,0),r=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*o(d)>=r(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((k,j)=>k.strand!==f.strand||k.identity.walkForward!==y||j>0&&k.identity.hapStart<d[j-1].identity.hapEnd))return;let g=y?d:[...d].reverse(),l=g.flatMap(k=>k.pieces),b=g.flatMap(k=>k.soloAligned),x=f.strand==="+"!==y,P=l.map(k=>this.paths[k]),E=P.slice(1).map((k,j)=>{let X=P[j].identity;return y?k.identity.hapStart-X.hapEnd:X.hapStart-k.identity.hapEnd}),R=x?[...P].reverse():P,m=x?[...E].reverse():E,I=R.flatMap(k=>x?Be(k.path):k.path),{edits:$}=this.editsAgainst(I,t),F=an($,R.map(k=>k.len)),_=new Map((x?[...l].reverse():l).map((k,j)=>[k,F[j]])),D=k=>2*k.pieces.reduce((j,X)=>j+_.get(X),0)>=o(k);if(!D(f)||!D(p))return;let C=[],H=0;return R.slice(0,-1).forEach((k,j)=>{H+=k.len,C.push([H,m[j]])}),s(Qn($,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),g=d.identity,l=g?g.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],an(p,[d.len])))}),jn(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:g,...l}=d,b={...l,cigar:Kn(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,o=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:Ke(d,f)}]:[]}),r=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=r(t),h=n?r(n):d=>!i(d),c=d=>this.record(ce(d,"forward")).sequence;return o.filter(d=>i(d.name)).flatMap(d=>o.filter(f=>h(f.name)).flatMap(f=>Wt({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:Vt(p.edits),matches:p.edits.reduce((y,[g,l])=>y+(g==="="?l:0),0),columns:p.edits.reduce((y,[,g])=>y+g,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ce(e,n);for(let o of this.record(s).successors())this.hasHandle(o)&&He(s,o)&&t.push([n==="reverse"?1:0,N(o),Q(o)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!Q(n)){let s=N(n),o=`S	${s}	${this.record(n).sequence}
+import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j as zt,k as He,l as Oe,m as Pe,n as Dt,o as jt,p as Ut,q as Wt,r as Vt}from"./chunk-M2D7NUOY.js";import{a as _t,g as Tt}from"./chunk-47KLT4FL.js";import{c as Ot}from"./chunk-PVRRW4PM.js";import{a as Ct,g as Bt}from"./chunk-3M3UH5JQ.js";var Ln=4096;function pt(a){let e=[];for(let t of a){let n=e[e.length-1];n&&t-n[1]<=Ln?n[1]=t:e.push([t,t])}return e}var Hn=32768,Gt={mostChosenPaths:32},lt=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},re=class extends Error{};function Ve(a,e,t,n){return a==="forward"?e+t:e-n}function Qt(a,e,t,n){return a==="forward"?e-n:e+t}function Kt(a){return Pe(ee(a.handles[a.handles.length-1]),ee(a.handles[0]))}function Ce(a){return`${a.pathHandle}:${a.hapStart}:${a.hapEnd}`}async function Zt(a){let{db:e,records:t,signal:n}=a,s=performance.now(),o=()=>{let w=performance.now(),S=w-s;return s=w,S},r={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},i=(w,S)=>{let A=`${w}: ${S}`;r.walks[A]=(r.walks[A]??0)+1},h=await e.haplotypeSampleInterval()??4096,c=new Map,d=async w=>{let S=t.get(w)??c.get(w);if(S)return S;let A=await e.getRecord(w);if(r.graphFetches+=1,!A)throw new Error(`Node record ${w} is missing from the database`);return c.set(w,A),A},f=w=>t.get(w).sequenceLen,p=await e.pathsByHandle(),y=w=>{let S=p.get(w);return S!==void 0&&a.keep(S.name)},g=[],l=new lt,b=new Map,x=new Set,P=new Set,E=async w=>{let S=(await d(w.node)).gbwt().lf(w.offset);return S===void 0||S.node===0?void 0:S},R=async(w,S)=>{let A=(await d(ee(w.node))).gbwt().predecessorAt(w.offset);if(A===void 0||S!==void 0&&!S.has(A))return;let M=(await d(A)).gbwt().offsetTo(w);if(M===void 0)throw new Error(`No offset in ${A} leads to ${w.node}:${w.offset}`);return{node:A,offset:M}},m=(w,S,A,M)=>{let B=A.map(W=>W.pos.node),U=A.map(W=>W.pos.offset),J=0;for(let W of B)J+=f(W);let O=S==="forward"?A[0].left:A[A.length-1].left,L=g.length;g.push({pathHandle:w,orientation:S,handles:B,offsets:U,len:J,hapStart:O,hapEnd:O+J,canonical:Pe(B[0],B[B.length-1]),source:M});for(let W of A)l.set(W.pos,L);let G=b.get(w);return G?G.push(L):b.set(w,[L]),L},I=async(w,S,A,M)=>{let B=[],U=w;for(;;){n?.throwIfAborted();let O=await R(U.pos,t);if(!O)break;U={pos:O,left:Qt(A,U.left,f(U.pos.node),f(O.node))},B.push(U)}B.reverse();let J=[w];for(U=w;;){n?.throwIfAborted();let O=await E(U.pos);if(!O||!t.has(O.node))break;U={pos:O,left:Ve(A,U.left,f(U.pos.node),f(O.node))},J.push(U)}return m(S,A,[...B,...J],M)},$=async(w,S,A,M)=>g[l.get(w.pos)??await I(w,S,A,M)],F=w=>{let S=w.handles[w.handles.length-1];return{pos:{node:S,offset:w.offsets[w.offsets.length-1]},left:w.orientation==="forward"?w.hapEnd-f(S):w.hapStart}},_=w=>{let S=w.handles[0];return{pos:{node:S,offset:w.offsets[0]},left:w.orientation==="forward"?w.hapStart:w.hapEnd-f(S)}},D=await I({pos:a.referencePos,left:a.referenceLeft},a.referenceHandle,"forward","reference"),C=g[D],H=()=>{if(r.fallback!==void 0)return{reference:C,pieces:[],stats:r};let w=new Map;g.forEach((A,M)=>{M!==D&&w.set(Ce(A),[...w.get(Ce(A))??[],A])});let S=[];for(let A of w.values()){let M=new Set;for(let B of A)B.canonical&&!M.has(B.orientation)&&(M.add(B.orientation),S.push(B),r.sources[B.source]+=1)}return r.sources.reference=1,r.pieces=S.length+1,{reference:C,pieces:S,stats:r}},k=async(w,S)=>{let A=S?x:P,M=S?P:x,B=w;for(;;){if(A.has(B))return;A.add(B);let U=g[B],J=S?F(U):_(U),O=0,L;for(;L===void 0;){n?.throwIfAborted();let G=S?await E(J.pos):await R(J.pos);if(!G){L="endmarker";break}let W=(await d(J.pos.node)).sequenceLen,ue=(await d(G.node)).sequenceLen,se=S?Ve(U.orientation,J.left,W,ue):Qt(U.orientation,J.left,W,ue);if(t.has(G.node)){let Y=l.get(G);Y===void 0?(B=await I({pos:G,left:se},U.pathHandle,U.orientation,"chain"),M.add(B),L="landed"):(M.add(Y),L="merge")}else O>Hn?L="bound":(O+=ue,J={pos:G,left:se})}if(i("chain",L),L!=="landed")return}},j=async w=>{if(a.context>w.context)throw new re(`the context of ${a.context} bp exceeds the ${w.context} bp the haplotype index's stray rows cover`);let S=r.spacing;if(S===void 0)throw new re("the haplotype index has no anchors");let{bin:A,bound:M}=w,{fills:B,inserted:U}=a.snarls;if(a.snarls.mode==="overlapping"&&B.length>0)throw new re("the haplotype index's stray rows cover contained snarls only");for(let u of B){if(u.inserted>0&&u.low===u.high)throw new re(`the haplotype index's stray rows leave out the snarl bounded by node ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new re(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(a.window.start/A),O=Math.floor((a.window.end-1)/A),L=J*A,G=(O+1)*A,W=new Map,ue=async(u,v)=>{let z=await e.haplotypeAnchorsBetween(a.referenceHandle,u*S,v*S);for(let T of z)W.set(T.anchorOffset/S,T)},se=Math.max(0,Math.floor((L-M)/S)-1),Y=Math.ceil((G+M)/S)+1,[{listed:De,strays:ae}]=await Promise.all([e.haplotypeBinData(a.referenceHandle,J,O),ue(se,Y)]);for(let u of t.keys()){let v=N(u);if(!Q(u)&&!De(v)&&!U.has(v))throw new re(`the haplotype index lists node ${v} of the subgraph in no bin that the window touches`)}r.scans=pt([...t.keys()].sort((u,v)=>u-v));let ie=Promise.all(r.scans.map(([u,v])=>e.haplotypeSamplesInRange(u,v)));for(ie.catch(()=>{});se>0&&(W.get(se)?.pathOffset??Number.POSITIVE_INFINITY)>=L-M;)se-=1,await ue(se,se);for(;W.has(Y)&&W.get(Y).pathOffset<=G+M;)Y+=1,await ue(Y,Y);let pe=[...W.keys()].sort((u,v)=>u-v),ye=W.get(pe[0]??-1);if(!ye)throw new re("the haplotype index has no anchors on this path");let he=u=>W.get(u).pathOffset,Ne=new Map;for(let u of pe){let v=N(W.get(u).node);Ne.set(v,[...Ne.get(v)??[],u])}let ct=[...Ne.keys()],Et=ct.map(u=>W.get(Ne.get(u)[0]).visits);if(!Et[ct.indexOf(N(ye.node))].some(u=>u.pathHandle===a.referenceHandle&&u.orientation==="forward"&&u.pathOffset===ye.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${a.referenceHandle} at offset ${ye.pathOffset} (node ${N(ye.node)}); it does not match this graph`);let kt=pe.filter(u=>he(u)<=a.window.start),$n=pe.filter(u=>he(u)>=a.window.end);r.anchors=[he(kt[kt.length-1]??pe[0]),he($n[0]??pe[pe.length-1])],r.anchorsRead=pe.length;let dt=new Map,vt=new Set;if(ct.forEach((u,v)=>{let z=Ne.get(u),T=z.length===1?z[0]:void 0;for(let q of Et[v])vt.add(q.pathHandle),q.orientation==="forward"&&y(q.pathHandle)&&dt.set(q.pathHandle,[...dt.get(q.pathHandle)??[],{k:T,row:q}])}),r.chosenPaths=[...vt].filter(y).length,r.chosenPaths>Gt.mostChosenPaths)throw new re(`${r.chosenPaths} chosen paths pass the anchors, more than ${Gt.mostChosenPaths}`);let je=[],Ie=Number.POSITIVE_INFINITY,be=0;for(let[u,v]of dt){v.sort((z,T)=>z.row.pathOffset-T.row.pathOffset);for(let z=0;z+1<v.length;z++){let T=v[z],q=v[z+1];if(T.k===void 0||q.k===void 0||Math.abs(T.k-q.k)!==1)continue;let[Z,te]=he(T.k)<=he(q.k)?[T,q]:[q,T],ne=he(Z.k),oe=he(te.k);ne<G&&oe>=L?(je.push({pathHandle:u,from:T.row,to:q.row}),Ie=Math.min(Ie,ne-M),be=Math.max(be,oe+M)):ne>=G&&ne-G<=M?(je.push({pathHandle:u,from:Z.row,to:void 0}),Ie=Math.min(Ie,ne-M),be=Math.max(be,ne+M)):oe<L&&L-oe<=M&&(je.push({pathHandle:u,from:te.row,to:void 0}),Ie=Math.min(Ie,oe-M),be=Math.max(be,oe+M))}}let Rn=new Set(B.map(u=>`${u.low}:${u.high}`)),Nn=ae.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Rn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,v)=>u.pathHandle-v.pathHandle||u.pathStart-v.pathStart);r.strays={bins:O-J+1,rows:ae.length,walked:0,outsideBp:0},be>0&&await a.prefetchReferenceRange(a.referenceHandle,Math.max(0,Ie),be+1),r.ms.scan=o();let Pt=8*S+2*(a.window.end-a.window.start),At=r.strays,Me=0,$t=u=>{if(At.outsideBp+=u,Me+=u,Me>Pt)throw new re(`a walk of a chosen path near the window went past its cap of ${Pt} bp`)},ft=new Map,Rt=(u,v,z)=>(ft.get(u)??[]).some(([T,q])=>T<=v&&z<q),Nt=(u,v,z)=>{ft.set(u,[...ft.get(u)??[],[v,z]])},Mt=async(u,v,z,T,q)=>{let Z=v,te=z,ne=te;for(;Z&&te<=T;){n?.throwIfAborted();let oe;if(t.has(Z.node)){let Le=await $({pos:Z,left:te},u,"forward",q),Ht=F(Le);Z=Ht.pos,te=Ht.left,oe=f(Z.node),ne=Math.max(ne,Le.hapEnd)}else oe=(await d(Z.node)).sequenceLen,$t(oe),ne=Math.max(ne,te+oe);Z=await E(Z),te+=oe}return ne},Mn=async(u,v,z,T)=>{let q={pos:v,left:z},Z=z;for(;q.left>T;){n?.throwIfAborted();let te=await R(q.pos);if(!te)break;let ne=(await d(te.node)).sequenceLen,oe=q.left-ne;if(t.has(te.node)){let Le=await $({pos:te,left:oe},u,"forward","section");q=_(Le),Z=Math.min(Z,Le.hapStart)}else $t(ne),q={pos:te,left:oe},Z=Math.min(Z,oe)}return Z};for(let{pathHandle:u,from:v,to:z}of je){let T=v.pathOffset,q=(z??v).pathOffset+M;if(Rt(u,T-M,q))continue;let Z={node:v.node,offset:v.offset};Me=0;let te=await Mt(u,Z,T,q,"section");Me=0;let ne=await Mn(u,Z,T,T-M);Nt(u,Math.min(ne,T-M),Math.max(te,q+1)),i(z?"section":"visit",z?"past the far anchor":"bound")}for(let u of Nn){if(Rt(u.pathHandle,u.pathStart,u.pathEnd))continue;Me=0;let v=await Mt(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");Nt(u.pathHandle,u.pathStart,Math.max(v,u.pathEnd+1)),At.walked+=1}r.ms.walks=o();let Lt=[];for(let u of await ie)for(let v of u)if(r.scanRows+=1,t.has(v.node)&&y(v.pathHandle)){if(!(b.get(v.pathHandle)??[]).some(z=>{let T=g[z];return T.hapStart<=v.pathOffset&&v.pathOffset<T.hapEnd}))throw new re(`chosen path ${v.pathHandle} has a sample at ${v.pathOffset} on the window's nodes that no walk reached`);v.orientation==="reverse"&&Lt.push(v)}for(let u of Lt)await $({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");r.ms.check=o()},X=async()=>{let w=new Map,S=O=>{let L=Ce(O),G=w.get(L);G?G.add(O.orientation):w.set(L,new Set([O.orientation]))},A=0,M=()=>{for(;A<g.length;A++)S(g[A])};M();let B=O=>(w.get(Ce(O))?.size??0)>1,U=2*h,J=(O,L)=>L===D?y(a.referenceHandle)&&Kt(O):!O.canonical||Kt(O);for(let O=0;O<g.length;O++){let L=g[O];if(B(L)||!J(L,O))continue;r.twins.tried+=1;let G=L.orientation==="forward"?"reverse":"forward",W=F(L),ue=0,se;for(;!se&&ue<=U;){n?.throwIfAborted();let ae=await E(W.pos);if(!ae)break;let ie=(await d(ae.node)).sequenceLen,pe=Ve(L.orientation,W.left,(await d(W.pos.node)).sequenceLen,ie),ye=ee(ae.node);se=(await e.haplotypeSamplesInRange(ye,ye)).find(he=>he.pathHandle===L.pathHandle&&he.orientation===G&&he.pathOffset===pe),ue+=ie,W={pos:ae,left:pe}}let Y=se&&{pos:{node:se.node,offset:se.offset},left:se.pathOffset},De=0;for(;Y&&!B(L)&&De<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ae=await $(Y,L.pathHandle,G,"twin"),ie=g.indexOf(ae);await k(ie,!0),await k(ie,!1),M(),Y=F(ae)}if(!B(L)){let ae=(await d(Y.pos.node)).sequenceLen;De+=ae;let ie=await E(Y.pos);Y=ie?{pos:ie,left:Ve(G,Y.left,ae,(await d(ie.node)).sequenceLen)}:void 0}}if(M(),!B(L))throw new re(`piece ${Ce(L)} was found in one orientation where extractPaths keeps the other`);r.twins.found+=1}r.ms.twins=o()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new re("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await j(w),await X()}catch(w){if(!(w instanceof re))throw w;r.fallback=w.message}return H()}function Xt(a,e){return a.handles[0]-e.handles[0]||a.offsets[0]-e.offsets[0]}var On=Uint32Array.from([1116352408,1899447441,3049323471,3921009573,961987163,1508970993,2453635748,2870763221,3624381080,310598401,607225278,1426881987,1925078388,2162078206,2614888103,3248222580,3835390401,4022224774,264347078,604807628,770255983,1249150122,1555081692,1996064986,2554220882,2821834349,2952996808,3210313671,3336571891,3584528711,113926993,338241895,666307205,773529912,1294757372,1396182291,1695183700,1986661051,2177026350,2456956037,2730485921,2820302411,3259730800,3345764771,3516065817,3600352804,4094571909,275423344,430227734,506948616,659060556,883997877,958139571,1322822218,1537002063,1747873779,1955562222,2024104815,2227730452,2361852424,2428436474,2756734187,3204031479,3329325298]),we=(a,e)=>a>>>e|a<<32-e;function Jt(a){let e=Math.ceil((a.length+9)/64),t=new Uint8Array(e*64);t.set(a),t[a.length]=128;let n=new DataView(t.buffer),s=a.length*8;n.setUint32(t.length-8,Math.floor(s/2**32)),n.setUint32(t.length-4,s>>>0);let o=Uint32Array.from([1779033703,3144134277,1013904242,2773480762,1359893119,2600822924,528734635,1541459225]),r=new Uint32Array(64);for(let c=0;c<e;c++){for(let P=0;P<16;P++)r[P]=n.getUint32(c*64+P*4);for(let P=16;P<64;P++){let E=r[P-15],R=r[P-2],m=we(E,7)^we(E,18)^E>>>3,I=we(R,17)^we(R,19)^R>>>10;r[P]=r[P-16]+m+r[P-7]+I}let d=o[0],f=o[1],p=o[2],y=o[3],g=o[4],l=o[5],b=o[6],x=o[7];for(let P=0;P<64;P++){let E=we(g,6)^we(g,11)^we(g,25),R=g&l^~g&b,m=x+E+R+On[P]+r[P]|0,I=we(d,2)^we(d,13)^we(d,22),$=d&f^d&p^f&p;x=b,b=l,l=g,g=y+m|0,y=p,p=f,f=d,d=m+I+$|0}[d,f,p,y,g,l,b,x].forEach((P,E)=>{o[E]=o[E]+P})}let i=new Uint8Array(32),h=new DataView(i.buffer);for(let c=0;c<8;c++)h.setUint32(c*4,o[c]);return i}function Yt(a,e){let t=new Map;if(a!==void 0)for(let n of a.split(";")){let s=n.split(","),[o,r]=s;if(s.length!==2||!o||!r)throw new Error(`Invalid ${e} relationship: ${n}`);let i=t.get(o);i||(i=new Set,t.set(o,i)),i.add(r)}return t}function nn(a){return{name:a.get("pggname"),subgraph:Yt(a.get("subgraph"),"subgraph"),translation:Yt(a.get("translation"),"translation")}}function en(a,e){for(let[t,n]of e){let s=a.get(t);s||(s=new Set,a.set(t,s));for(let o of n)s.add(o)}}function sn(a,e){let t={name:a,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(a,new Set([e.name])),en(t.subgraph,e.subgraph),en(t.translation,e.translation)),t}function tn(a){return[...a.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function on(a){let e=[];a.name!==void 0&&e.push(`H	NM:Z:${a.name}`);for(let[t,n]of tn(a.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of tn(a.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function rn(a){let e=a.reduce((r,i)=>r+i.length,0),t=new Uint8Array(e),n=0;for(let r of a)t.set(r,n),n+=r.length;let s=globalThis.crypto?.subtle;return[...s?new Uint8Array(await s.digest("SHA-256",t)):Jt(t)].map(r=>r.toString(16).padStart(2,"0")).join("")}var Cn="_gbwt_ref";function fe(a){let e=`${a.sample}#${a.haplotype}#${a.contig}`;return a.end===void 0?e:`${e}[${a.fragment}-${a.end}]`}var Bn=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,_n=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Tn(a){let e=Bn.exec(a);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=_n.exec(a);if(t)return{contig:t[1]};throw new Error(`"${a}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Ae(a){return typeof a=="string"?Tn(a):a}function $e(a,e){return{sample:a.sample??Cn,contig:a.contig,haplotype:a.haplotype??0,fragment:e}}var le=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function ut(a,e){return a[0]<e[0]||a[0]===e[0]&&(a[1]<e[1]||a[1]===e[1]&&a[2]<e[2])}var _e=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let o=s.length-1;for(;o>0;){let r=o-1>>1;if(ut(s[o],s[r]))[s[o],s[r]]=[s[r],s[o]],o=r;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let o=2*s+1,r=o+1,i=s;if(o<e.length&&ut(e[o],e[i])&&(i=o),r<e.length&&ut(e[r],e[i])&&(i=r),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function Fn(a){let e=new Int32Array(a.length),t=new Int32Array(a.length);return a.forEach(([n,s],o)=>{e[o]=n,t[o]=s}),{pathAt:e,refAt:t,count:a.length}}function qn(a,e){let t=0,n=a.length;for(;t<n;){let s=t+n>>1;a[s]>e?n=s:t=s+1}return a[t]}function ke(a){return`${a.node}:${a.offset}`}function Be(a){return a.map(e=>ee(e)).reverse()}function zn(a,e){let t=e.identity.hapStart-a.identity.hapEnd,n=a.strand==="+"?e.refStart-a.refEnd:a.refStart-e.refEnd;return a.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Dn(a,e,t){let[n,s]=a.strand==="+"?[a,e]:[e,a],o=n.edits.map(([c,d])=>[c,d]);hn(o,t.insertion,t.deletion);for(let[c,d]of s.edits)K(o,c,d);let r=a.identity.walkForward,[i,h]=r?[a,e]:[e,a];return{strand:a.strand,refStart:n.refStart,refEnd:s.refEnd,edits:o,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:a.identity.pathHandle,name:a.identity.name,hapStart:a.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:r}}}function jn(a,e,t){if(a.some(r=>r.weight!==void 0))return a;let n=new Map;a.forEach((r,i)=>{if(r.identity){let h=n.get(r.identity.pathHandle);h?h.push(i):n.set(r.identity.pathHandle,[i])}});let s=new Map,o=new Set;for(let r of n.values()){r.sort((d,f)=>a[d].identity.hapStart-a[f].identity.hapStart);let i=r[0],h=a[i],c=[];for(let d of r.slice(1)){let f=a[d],p=c.length===0?zn(h,f):void 0;if(p){h=Dn(h,f,p),o.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(g=>a[g]),f]):void 0;if(y){h=y;for(let g of[...c,d])o.add(g)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return a.flatMap((r,i)=>o.has(i)?[]:[s.get(i)??r])}function Ge(a,e){return{node:a.path[e],offset:a.offsets[e]}}var Un=32768;function Wn(a){let e=[...a].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=Un?s[1]=n:t.push([n,n])}return t}var Te=class a{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new a(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ce(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new le(this.limit);let t=await this.db.getRecord(ce(e,"forward")),n=await this.db.getRecord(ce(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let o=n,r=s;for(;;){await this.ensureNode(N(r.node));let i=this.record(r.node);if(o+i.sequenceLen>t)return{position:{seqOffset:t,handle:r.node,nodeOffset:t-o,gbwtOffset:r.offset},name:e.name,handle:e.handle};o+=i.sequenceLen;let h=i.gbwt().lf(r.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);r=h}}async aroundPosition(e,t,n){let s=N(e);await this.ensureNode(s);let o=this.record(e),r=Ee(e),i=new _e;return i.push(t,s,Ue(r)),i.push(o.sequenceLen-t-1,s,We(r)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,o]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&o){let r=s.pos.node,i=o.pos.node;if(!await this.db.prefetchRecords([[Math.min(r,i),Math.max(r,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(Wn(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(s){throw s instanceof le&&s.windowBp===void 0?new le(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},o=e.nodeOffset,r=t,i=new _e;for(;;){let h=N(s.node),c=Ee(s.node);this.walkedBp=t-r,await this.ensureNode(h);let d=this.record(s.node);if(o>=d.sequenceLen)throw new Error(`Offset ${o} in node ${h} of length ${d.sequenceLen}`);i.push(o,h,Ue(c));let f=d.sequenceLen-o;if(r<=f){i.push(r===f?0:f-r-1,h,We(c));break}i.push(0,h,We(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,o=0,r-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new _e;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let r of this.records.keys())s.add(N(r));let o=0;for(;e.size>0;){let[r,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),o+=1);let d=Ft(h);if(!n.has(`${i}:${d}`)){let y=this.record(ce(i,qt(h))),g=r+y.sequenceLen-1;g<=t&&e.push(g,i,d)}let f=this.record(ce(i,zt(h))),p=r+1;if(p<=t)for(let y of f.successors()){let g=N(y),l=Ue(Ee(y));n.has(`${g}:${l}`)||e.push(p,g,l)}}for(let r of s)this.records.delete(ce(r,"forward")),this.records.delete(ce(r,"reverse"));return{inserted:o,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,ee(t)],s=new Set([N(e),N(t)]),o=[];for(;n.length>0;){let r=n.pop(),i=N(r);this.hasNode(i)||(await this.addNode(i),o.push(i));for(let h of this.record(r).successors()){let c=N(h);s.has(c)||(n.push(h,ee(h)),s.add(c))}}return{inserted:o,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:o,nodes:r}=await this.fillBetween(n,s),i=N(n),h=N(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:r,inserted:o.length});for(let c of o)this.snarlNodes.add(c);t+=o.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let s of this.sortedHandles()){let o=this.record(s),r=o.next;r!==void 0&&(n=!0,this.hasHandle(r)?He(s,r)&&t.push([s,r]):e==="overlapping"&&this.isSnarlEntryInSubgraph(o)&&t.push([s,r]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(ee(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let o=t.get(n);if(!o){if(o=await this.db.getRecord(n),e?.(),!o)throw new Error(`Node record ${n} is missing from the database`);t.set(n,o)}return o}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(ee(d))).successors().length>1},n=async h=>{let c=await e(ee(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[ee(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,o=this.sortedHandles().flatMap(h=>this.record(h).successors()),r,i=!1;for(;!i&&o.length>0;){let h=o.shift(),c=N(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")r=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])o.push(...(await e(ce(c,f))).successors())}}return r}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),o=s.length,r=new Map;s.forEach((m,I)=>r.set(m,I));let i=new Int32Array(o+1),h=new Int32Array(o),c=[];for(let m=0;m<o;m++){let I=this.record(s[m]),$=I.gbwt().decompressArrays();h[m]=I.sequenceLen,c.push($),i[m+1]=i[m]+$.nodes.length}let d=i[o],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let m=0;m<o;m++){let I=c[m];f.set(I.nodes,i[m]),p.set(I.offsets,i[m])}c.length=0;for(let m=0;m<d;m++){let I=r.get(f[m]);I===void 0?f[m]=-1:(f[m]=I,y[i[I]+p[m]]=1)}let g=n===void 0?void 0:r.get(n.handle),l=n?.gbwtOffset,b,x=(m,I,$)=>{let F=[],_=0,D=0,C=-1,H=m,k=I;for(;;){H===g&&k===l&&(C=_),$&&($.push(s[H]),F.push(k)),_+=1,D+=h[H];let j=i[H]+k,X=f[j];if(X<0)break;k=p[j],H=X}return{offsets:F,len:D,refAt:C,last:H}},P=(m,I,$,F)=>{F>=0&&(this.refId=this.paths.length,b=F),this.paths.push({path:m,offsets:I,len:$,weight:void 0,identity:void 0})},E=new Int32Array(o);for(let m=0;m<o;m++){let I=s[m];if(!Q(I)){let $=i[m],F=i[m+1]-$;for(let _=0;_<F;_++)if(y[$+_]===0){let D=[],{offsets:C,len:H,refAt:k,last:j}=x(m,_,D),X=s[j];if(k>=0||Pe(I,X)){if(P(D,C,H,k),!Q(X)){let w=r.get(ee(X));E[w]=E[w]+1}}else this.twinStarts.add(ke({node:I,offset:_}))}}}for(let m=0;m<o;m++){let I=s[m];if(Q(I)){let $=i[m],F=i[m+1]-$,_=0;for(let C=0;C<F;C++)y[$+C]===0&&(_+=1);let D=(g===void 0||b!==void 0)&&_===E[m];for(let C=0;C<F;C++)if(y[$+C]===0){let H=D?void 0:x(m,C,void 0);if(H&&(H.refAt>=0||Pe(I,s[H.last]))){let k=[],{offsets:j,len:X,refAt:w}=x(m,C,k);P(k,j,X,w)}else this.twinStarts.add(ke({node:I,offset:C}))}}}let R=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((m,I)=>m.path[0]-I.path[0]||m.offsets[0]-I.offsets[0]),R&&(this.refId=this.paths.indexOf(R)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let m=this.paths[this.refId],I=n.nodeOffset;for(let F of m.path.slice(0,b))I+=this.record(F).sequenceLen;let $=n.seqOffset-I;this.refInterval=[$,$+m.len],m.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:$,hapEnd:$+m.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,s=n&&!Oe(n)?Be(n):void 0,o=c=>s!==void 0&&wt(c,s)===0||Oe(Be(c)),r=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>wt(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=r&&c!==t&&o(c.path);this.twinDeferred||=f,d&&wt(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=r=>`${r.pathHandle}:${r.hapStart}-${r.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let r of this.paths)r!==e&&r.identity?.orientation==="forward"&&s.add(n(r.identity));let o=this.paths.filter(r=>r===e||r.identity?.orientation!=="reverse"||!s.has(n(r.identity)));o.length<this.paths.length&&(this.paths=o,this.refId=e===void 0?void 0:o.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(r=>r.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((r,i)=>i!==this.refId&&r.identity===void 0).length;if(t>0)throw new Error(`${t} 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`);let n=this.refId===void 0?void 0:this.paths[this.refId],s=this.paths.filter((r,i)=>i===this.refId||r.identity!==void 0&&e(r.identity.name)),o=new Set;for(let r of s)for(let i of r.path)o.add(N(i));for(let r of[...this.records.keys()])o.has(N(r))||this.records.delete(r);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let o=e.position.seqOffset,r=await Zt({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=r.stats,r.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===r.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[r.reference,...r.pieces].sort(Xt);return this.paths=c.map(h),this.refId=c.indexOf(r.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[r.reference.hapStart,r.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=pt(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let o=l=>{let b=0,x=t.length-1;for(;b<x;){let E=b+x+1>>1;t[E][0]<=l?b=E:x=E-1}let P=t[b];return P[0]<=l&&l<=P[1]},r=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&r.set(ke(Ge(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(o(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let x=await this.db.haplotypeSampleAt(l.node,l.offset);return x||(i.companionMisses+=1),x},f=new Map,p=async l=>{let b=f.get(l);if(!b){let x=await this.db.getPath(l);if(!x)throw new Error(`Path ${l} is missing from the database`);b=x.name,f.set(l,b)}return b},y=(l,b,x)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+x},g=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let x=[],P=new Set,E={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(E);let R,m=0,I=l,$;for(;R===void 0;){if(this.signal?.throwIfAborted(),I!==void 0){if(P.has(I)){E.end="cycle";break}P.add(I);let H=this.paths[I];x.push({index:I,startBp:m}),E.fragments+=1;let k=m;for(let X=0;X<H.path.length;X++){let w=Ge(H,X),S=n.get(ke(w)),A=this.record(w.node).sequenceLen;if(S){R=y(S,k,A);break}k+=A}if(m+=H.len,R){E.end="in-fragment sample";break}let j=Ge(H,H.path.length-1);$=this.record(j.node).gbwt().lf(j.offset),I=void 0}if($===void 0||$.node===0){E.end="endmarker";break}let F=ke($),_=r.get(F);if(_!==void 0){let H=this.paths[_].identity;if(H){R=g(H,m),E.end="identified sibling";break}I=_;continue}this.records.has($.node)&&(E.reentries+=1),this.twinStarts.has(F)&&(E.twinLandings+=1);let D=await d($,E),C=await c($.node);if(D){R=y(D,m,C.sequenceLen),E.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,E.steps+=1,m-x[x.length-1].startBp>4*e+4*C.sequenceLen){E.end="bound";break}m+=C.sequenceLen,$=C.gbwt().lf($.offset)}if(R){E.pathHandle=R.pathHandle;let F=await p(R.pathHandle);for(let{index:_,startBp:D}of x){let C=this.paths[_];C.identity=R.orientation==="forward"?{pathHandle:R.pathHandle,name:F,orientation:"forward",hapStart:R.base+D,hapEnd:R.base+D+C.len}:{pathHandle:R.pathHandle,name:F,orientation:"reverse",hapStart:R.base-D-C.len,hapEnd:R.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let o=t.get(n);o?o.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),o=new Int32Array(e.length),r=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=qn(c,i);if(d===void 0)return;s[r]=h,o[r]=d,r+=1,i=d}}return{pathAt:s,refAt:o,count:r}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[o]).sequence;for(;r<h.length&&i<c.length;){if(h[r]!==c[i])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,o=0,r=0,i=0;for(;s<e.length&&o<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-o-1]).sequence;for(;r<h.length&&i<c.length;){if(h[h.length-r-1]!==c[c.length-i-1])return n;r+=1,i+=1,n+=1}r===h.length&&(s+=1,r=0),i===c.length&&(o+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),o=this.pathLen(t),r=this.prefixMatches(e,t),i=this.suffixMatches(e,t);r+i>s&&(i=s-r),r+i>o&&(i=o-r),K(n,"M",r),hn(n,s-r-i,o-r-i),K(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let o of e)n.has(o)&&(s+=this.record(o).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??Fn(Ut(e,t,f=>this.record(f).sequenceLen)[0]),o=[],r=this.refPrefix(t),i=(f,p,y,g)=>{f===p?K(o,"D",r[g]-r[y]):y===g?K(o,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,g),o)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let g=this.record(e[p]).sequenceLen;K(o,"M",g),h+=g,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:o,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Oe(n)&&(t.identity===void 0||!Oe(Be(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let o=Be(t.path),r=this.sharedWeight(t.path,n);if(this.sharedWeight(o,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(r===0)s={...this.editsAgainst(o,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(o,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],s=(d,f,p,y)=>{let g=Gn(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],x=l.identity,P=x?.orientation==="forward",[E,R]=P?[l,b]:[b,l];return{strand:f,refStart:e.start+g.leading,refEnd:e.start+n-g.trailing,edits:g.edits,weight:l.weight,path:p.flatMap(m=>this.paths[m].path),start:Ge(l,0),pieces:p,soloAligned:y,identity:x===void 0?void 0:{pathHandle:x.pathHandle,name:x.name,hapStart:x.name.fragment+E.identity.hapStart,hapEnd:x.name.fragment+R.identity.hapEnd,walkForward:P}}},o=d=>d.soloAligned.reduce((f,p)=>f+p,0),r=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*o(d)>=r(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((k,j)=>k.strand!==f.strand||k.identity.walkForward!==y||j>0&&k.identity.hapStart<d[j-1].identity.hapEnd))return;let g=y?d:[...d].reverse(),l=g.flatMap(k=>k.pieces),b=g.flatMap(k=>k.soloAligned),x=f.strand==="+"!==y,P=l.map(k=>this.paths[k]),E=P.slice(1).map((k,j)=>{let X=P[j].identity;return y?k.identity.hapStart-X.hapEnd:X.hapStart-k.identity.hapEnd}),R=x?[...P].reverse():P,m=x?[...E].reverse():E,I=R.flatMap(k=>x?Be(k.path):k.path),{edits:$}=this.editsAgainst(I,t),F=an($,R.map(k=>k.len)),_=new Map((x?[...l].reverse():l).map((k,j)=>[k,F[j]])),D=k=>2*k.pieces.reduce((j,X)=>j+_.get(X),0)>=o(k);if(!D(f)||!D(p))return;let C=[],H=0;return R.slice(0,-1).forEach((k,j)=>{H+=k.len,C.push([H,m[j]])}),s(Qn($,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),g=d.identity,l=g?g.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],an(p,[d.len])))}),jn(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:g,...l}=d,b={...l,cigar:Kn(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,o=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:Ke(d,f)}]:[]}),r=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=r(t),h=n?r(n):d=>!i(d),c=d=>this.record(ce(d,"forward")).sequence;return o.filter(d=>i(d.name)).flatMap(d=>o.filter(f=>h(f.name)).flatMap(f=>Wt({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:Vt(p.edits),matches:p.edits.reduce((y,[g,l])=>y+(g==="="?l:0),0),columns:p.edits.reduce((y,[,g])=>y+g,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ce(e,n);for(let o of this.record(s).successors())this.hasHandle(o)&&He(s,o)&&t.push([n==="reverse"?1:0,N(o),Q(o)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!Q(n)){let s=N(n),o=`S	${s}	${this.record(n).sequence}
 `;for(let[r,i,h]of this.canonicalEdges(s))o+=`L	${s}	${r?"-":"+"}	${i}	${h?"-":"+"}
 `;t.push(e.encode(o))}return rn(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...on(sn(await this.stableName(),await this.db.graphName()))],s=this.sortedHandles();for(let c of s)Q(c)||n.push(`S	${N(c)}	${this.record(c).sequence}`);let o=c=>Q(c)?"-":"+";for(let c of s)for(let d of this.record(c).successors())this.hasHandle(d)&&He(c,d)&&n.push(`L	${N(c)}	${o(c)}	${N(d)}	${o(d)}	0M`);let r=(c,d,f,p,y)=>{let g=Ke(c,d).map(x=>`${Q(x)?"<":">"}${N(x)}`).join(""),l=c.weight===void 0?"":`	WT:i:${c.weight}`,b=y===void 0?"":`	CG:Z:${y}`;return`W	${f.sample}	${f.haplotype}	${f.contig}	${f.fragment}	${p}	${g}${l}${b}`},i=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(r(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let h=1;return this.paths.forEach((c,d)=>{if(d!==this.refId){let f=e.names!=="anonymous"?c.identity:void 0,p=t?this.alignToRef(d):void 0;n.push(f?r(c,f,{...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd,p):r(c,void 0,{sample:"unknown",contig:i,haplotype:h,fragment:0},c.len,p)),h+=1}}),`${n.join(`
 `)}
@@ -6,4 +6,4 @@ import{a as ce,b as N,c as Ee,d as Q,e as ee,f as Ft,g as Ue,h as We,i as qt,j a
 `).filter(p=>p!=="")),n=(f,p)=>f.filter(y=>y.startsWith(`${p}	`)),s=cs(t.flat()),o=0,r=t.map(f=>{let p=n(f,"W").map(hs),y=o;for(let g of p.filter(l=>l.fields[1]===is)){let l=+g.fields[2]+y;g.fields[2]=String(l),g.name=g.fields.slice(1,4).join("	"),o=Math.max(o,l)}return p}),h=[...Ot([...r.flatMap(f=>f.slice(0,1)),...r.flatMap(f=>f.slice(1))],f=>f.name).values()].flatMap(f=>fs(f,s,e)),c=new Set(t.flatMap(f=>n(f,"L")));for(let f of h)for(let p of ls(f))!c.has(p.forward)&&!c.has(p.reverse)&&c.add(p.forward);return`${[...new Set([...n(t[0],"H"),...t.flatMap(f=>n(f,"S")),...c,...h.map(f=>f.fields.join("	"))])].join(`
 `)}
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