jbrowse-plugin-graphgenomeviewer 5.0.1 → 5.2.0

package/dist/chunks/{chunk-LGFKHSVJ.js.map → chunk-FNHKEAKB.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../packages/core/src/gbzJoin.ts", "../../packages/core/src/reference.ts", "../../packages/core/src/gbzWindow.ts"],
-  "sourcesContent": ["// One GFA from gbz-base cuts of consecutive reference fragments. A haplotype\n// bridging the gap between two fragments comes back from both cuts, each piece\n// the run inside its own cut's nodes, so the two can overlap without matching.\n\ninterface Walk {\n  fields: string[]\n  name: string\n  start: number\n  end: number\n}\n\nconst UNKNOWN_SAMPLE = 'unknown'\n\nfunction parseWalk(line: string): Walk {\n  const fields = line.split('\\t')\n  return {\n    fields,\n    name: fields.slice(1, 4).join('\\t'),\n    start: +fields[4]!,\n    end: +fields[5]!,\n  }\n}\n\nconst stepsOf = (walk: Walk) => walk.fields[6]!.match(/[<>][^<>]+/g) ?? []\n\nfunction segmentLengths(lines: string[]) {\n  const lengths = new Map<string, number>()\n  for (const line of lines) {\n    if (line.startsWith('S\\t')) {\n      const [, id, sequence, ...tags] = line.split('\\t')\n      const ln = tags.find(tag => tag.startsWith('LN:i:'))\n      lengths.set(\n        id!,\n        sequence === '*' && ln ? +ln.slice('LN:i:'.length) : sequence!.length,\n      )\n    }\n  }\n  return lengths\n}\n\n// `a` carried on by the steps of `b` past `a.end`, where `b` starts inside or\n// at the end of `a`; undefined when no step of `b` starts exactly at `a.end`,\n// which two pieces of one walk always share\nfunction extend(a: Walk, b: Walk, lengths: Map<string, number>) {\n  if (b.end <= a.end) {\n    return a\n  }\n  const steps = stepsOf(b)\n  let pos = b.start\n  for (const [i, step] of steps.entries()) {\n    if (pos === a.end) {\n      const fields = [...a.fields]\n      fields[5] = String(b.end)\n      fields[6] = a.fields[6]! + steps.slice(i).join('')\n      return { ...a, fields, end: b.end }\n    }\n    const length = lengths.get(step.slice(1))\n    if (pos > a.end || length === undefined) {\n      return undefined\n    }\n    pos += length\n  }\n  return undefined\n}\n\n// Whether one of a haplotype's own paths starts at `at` on its contig\nexport type StartsPath = (\n  sample: string,\n  haplotype: number,\n  contig: string,\n  at: number,\n) => boolean\n\n// Pieces of one walk, by start, with each pair that overlaps or meets joined\n// into one. Pieces that meet where one of the haplotype's own paths starts are\n// two paths, whether or not the graph links them; a walk a cut split never\n// has a path starting at the seam.\nfunction joinPieces(\n  pieces: Walk[],\n  lengths: Map<string, number>,\n  startsPath: StartsPath,\n) {\n  const joined: Walk[] = []\n  for (const piece of pieces.sort((a, b) => a.start - b.start)) {\n    const last = joined.at(-1)\n    const [, sample, haplotype, contig] = piece.fields\n    const joins =\n      last !== undefined &&\n      (piece.start < last.end ||\n        (piece.start === last.end &&\n          !startsPath(sample!, +haplotype!, contig!, piece.start)))\n    const extended = joins ? extend(last, piece, lengths) : undefined\n    if (extended) {\n      joined[joined.length - 1] = extended\n    } else {\n      joined.push(piece)\n    }\n  }\n  return joined\n}\n\nconst flip = (sign: string) => (sign === '+' ? '-' : '+')\n\n// The link each step of a walk takes, in both of the ways an L line can write\n// it. Where two pieces met in no cut's nodes, no cut wrote the link between\n// them.\nfunction* stepLinks(walk: Walk) {\n  const steps = stepsOf(walk).map(step => ({\n    id: step.slice(1),\n    sign: step.startsWith('>') ? '+' : '-',\n  }))\n  for (let i = 1; i < steps.length; i++) {\n    const a = steps[i - 1]!\n    const b = steps[i]!\n    yield {\n      forward: `L\\t${a.id}\\t${a.sign}\\t${b.id}\\t${b.sign}\\t0M`,\n      reverse: `L\\t${b.id}\\t${flip(b.sign)}\\t${a.id}\\t${flip(a.sign)}\\t0M`,\n    }\n  }\n}\n\n// Each segment and link once, every cut's reference walk (its first W line)\n// ahead of the haplotype walks, the pieces of each walk joined, the\n// reference's among them since a cut's context can reach the other fragment,\n// and each cut's `unknown#N` walks numbered on from the cut before's, since\n// gbz-base numbers them per cut. Unnamed walks start every cut at 0, so their\n// pieces cannot be joined.\nexport function joinCuts(gfas: string[], startsPath: StartsPath) {\n  if (gfas.length <= 1) {\n    return gfas[0] ?? ''\n  }\n  const cuts = gfas.map(gfa => gfa.split('\\n').filter(line => line !== ''))\n  const ofType = (cut: string[], type: string) =>\n    cut.filter(line => line.startsWith(`${type}\\t`))\n  const lengths = segmentLengths(cuts.flat())\n  let unknownOffset = 0\n  const walksByCut = cuts.map(cut => {\n    const walks = ofType(cut, 'W').map(parseWalk)\n    const offset = unknownOffset\n    for (const walk of walks.filter(w => w.fields[1] === UNKNOWN_SAMPLE)) {\n      const haplotype = +walk.fields[2]! + offset\n      walk.fields[2] = String(haplotype)\n      walk.name = walk.fields.slice(1, 4).join('\\t')\n      unknownOffset = Math.max(unknownOffset, haplotype)\n    }\n    return walks\n  })\n  const byName = new Map<string, Walk[]>()\n  for (const walk of [\n    ...walksByCut.flatMap(walks => walks.slice(0, 1)),\n    ...walksByCut.flatMap(walks => walks.slice(1)),\n  ]) {\n    const pieces = byName.get(walk.name)\n    if (pieces) {\n      pieces.push(walk)\n    } else {\n      byName.set(walk.name, [walk])\n    }\n  }\n  const walks = [...byName.values()].flatMap(pieces =>\n    joinPieces(pieces, lengths, startsPath),\n  )\n  const links = new Set(cuts.flatMap(cut => ofType(cut, 'L')))\n  for (const walk of walks) {\n    for (const link of stepLinks(walk)) {\n      if (!links.has(link.forward) && !links.has(link.reverse)) {\n        links.add(link.forward)\n      }\n    }\n  }\n  const lines = new Set([\n    ...ofType(cuts[0]!, 'H'),\n    ...cuts.flatMap(cut => ofType(cut, 'S')),\n    ...links,\n    ...walks.map(walk => walk.fields.join('\\t')),\n  ])\n  return `${[...lines].join('\\n')}\\n`\n}\n", "import { isBackbone } from './anchoredNodes'\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from './pansn'\n\nimport type { Graph, PathOrigin } from './types'\n\n// A graph's backbone names the sample it lies on (`GRCh38#0#chr6`), not an\n// assembly, and a bare contig (`chr6`) is in every human assembly at once. A\n// backbone binds to an assembly where its PanSN prefix is that assembly's name,\n// one of its aliases, or its well-known sample. One that names no sample binds\n// only where the host knows the assembly otherwise, as a track's config does.\n\nexport interface BackboneContig {\n  // as the graph names it, `GRCh38#0#chr6`\n  refName: string\n  // as an assembly names it, `chr6`\n  contig: string\n  start: number\n  end: number\n}\n\nexport interface Backbone {\n  contigs: BackboneContig[]\n  // The PanSN prefixes that name the backbone, sample then haplotype:\n  // `GRCh38`, `GRCh38#0`. The sample drops out where the graph walks another\n  // haplotype of it, as a diploid's `HG002` names `HG002#1` and `HG002#2`.\n  prefixes: string[]\n  // Whether the contigs name one real sample: false where every contig is bare\n  // (`chr6`) or generic (`_gbwt_ref#0#chr6`), or where the samples differ\n  named: boolean\n}\n\nexport interface AssemblyNames {\n  name: string\n  aliases?: string[]\n}\n\n// The sample a reference assembly's graphs name it by, keyed by the assembly's\n// name in lower case: HPRC writes `CHM13` where UCSC's assembly is `hs1`.\nexport const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string> = new Map([\n  ['hg38', 'GRCh38'],\n  ['hg19', 'GRCh37'],\n  ['hs1', 'CHM13'],\n  ['t2t-chm13', 'CHM13'],\n  ['chm13v2', 'CHM13'],\n])\n\nexport function wellKnownSample(assemblyName: string) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase())\n}\n\nfunction sampleOf(refName: string) {\n  const sample = refName.includes('#') ? panSNSample(refName) : undefined\n  return sample === undefined || isGenericSample(sample) ? undefined : sample\n}\n\n// `HG002#1`, or the sample of a two-part name, which states no haplotype\nfunction haplotypeOf(refName: string) {\n  return panSNHaplotype(refName) ?? panSNSample(refName)\n}\n\n// Each sample's haplotypes among the graph's walks and node refNames\nfunction graphHaplotypes(graph: Graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map(p => p.name))\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName)\n    }\n  }\n  const bySample = new Map<string, Set<string>>()\n  for (const refName of refNames) {\n    const sample = sampleOf(refName)\n    if (sample !== undefined) {\n      const haplotypes =\n        bySample.get(sample) ?? bySample.set(sample, new Set()).get(sample)!\n      haplotypes.add(haplotypeOf(refName))\n    }\n  }\n  return bySample\n}\n\nfunction backboneFrom(\n  contigs: BackboneContig[],\n  haplotypes: Map<string, Set<string>>,\n): Backbone {\n  const samples = new Set(contigs.map(c => sampleOf(c.refName)))\n  const [sample] = samples\n  if (samples.size !== 1 || sample === undefined) {\n    return { contigs, prefixes: [], named: false }\n  }\n  const own = new Set(contigs.map(c => haplotypeOf(c.refName)))\n  const unique = [...(haplotypes.get(sample) ?? [])].every(h => own.has(h))\n  const shared = new Set(contigs.map(c => panSNHaplotype(c.refName)))\n  const [haplotype] = shared\n  return {\n    contigs,\n    prefixes: [\n      ...(unique ? [sample] : []),\n      ...(shared.size === 1 && haplotype ? [haplotype] : []),\n    ],\n    named: true,\n  }\n}\n\n// The rank-0 nodes' refNames and the span each covers\nexport function graphBackbone(graph: Graph): Backbone | undefined {\n  const spans = new Map<string, BackboneContig>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable\n      const end = start + node.length\n      const span = spans.get(refName)\n      if (span) {\n        span.start = Math.min(span.start, start)\n        span.end = Math.max(span.end, end)\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end,\n        })\n      }\n    }\n  }\n  const contigs = [...spans.values()]\n  return contigs.length\n    ? backboneFrom(contigs, graphHaplotypes(graph))\n    : undefined\n}\n\n// The assembly the backbone's haplotype names by its name or an alias, else\n// the one its sample names, else the one whose well-known sample it is. A\n// backbone with no prefix binds to none.\nexport function backboneAssembly<T extends AssemblyNames>(\n  backbone: Backbone | undefined,\n  assemblies: T[],\n): T | undefined {\n  const names = (a: T) => [a.name, ...(a.aliases ?? [])]\n  const naming = (prefix: string) => (a: T) =>\n    names(a).some(n => n.toLowerCase() === prefix.toLowerCase())\n  const prefixes = [...(backbone?.prefixes ?? [])].reverse()\n  const sample = backbone?.prefixes.find(p => !p.includes('#'))?.toLowerCase()\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix))\n    if (assembly) {\n      return assembly\n    }\n  }\n  return sample === undefined\n    ? undefined\n    : assemblies.find(a =>\n        names(a).some(n => wellKnownSample(n)?.toLowerCase() === sample),\n      )\n}\n\n// The first of the graph's walks that a backbone along it would bind to\n// `assembly`, for putting x on the assembly a cut was made for\nexport function assemblyWalk(\n  graph: Graph,\n  assembly: AssemblyNames,\n): PathOrigin | undefined {\n  const haplotypes = graphHaplotypes(graph)\n  return graph.anchorPaths?.find(walk =>\n    backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length,\n          },\n        ],\n        haplotypes,\n      ),\n      [assembly],\n    ),\n  )\n}\n\n// The names a file from outside the graph may give a contig: its own, and the\n// same with or without UCSC's `chr`, the mitochondrion as M or MT either way\nexport function contigNames(contig: string) {\n  const bare = contig.replace(/^chr/i, '')\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? ['M', 'MT'] : [bare]\n  return [...new Set([contig, ...forms.flatMap(f => [f, `chr${f}`])])]\n}\n\n// Which of `refNames` a feature's refName names: the one it equals, else the\n// only one whose contig it names, by any of contigNames or the name `aliases`\n// gives that contig (`{ chr6: 'NC_000006.12' }`). A name two refNames share\n// names neither.\nexport function refNameBinding(\n  refNames: Iterable<string>,\n  aliases: Record<string, string> = {},\n) {\n  const exact = new Set(refNames)\n  const byName = new Map<string, string | undefined>()\n  for (const refName of exact) {\n    const contig = panSNContig(refName)\n    const alias = aliases[contig]\n    for (const name of new Set([\n      ...contigNames(contig),\n      ...(alias ? [alias] : []),\n    ])) {\n      byName.set(name, byName.has(name) ? undefined : refName)\n    }\n  }\n  return (name: string) => (exact.has(name) ? name : byName.get(name))\n}\n\n// An assembly's features on a backbone that binds to it, each renamed to the\n// backbone's refName for it, so the assembly's `chr6` becomes the graph's\n// `GRCh38#0#chr6`. genePins and tubeMapGenes take only the renamed.\nexport function featuresOnBackbone<T extends { refName: string }>(\n  features: readonly T[],\n  backbone: Backbone,\n  aliases?: Record<string, string>,\n): T[] {\n  const bind = refNameBinding(\n    backbone.contigs.map(c => c.refName),\n    aliases,\n  )\n  return features.flatMap(f => {\n    const refName = bind(f.refName)\n    return refName === undefined\n      ? []\n      : [refName === f.refName ? f : { ...f, refName }]\n  })\n}\n", "import { joinCuts } from './gbzJoin.ts'\nimport { panSNMatchesPrefix, panSNSample } from './pansn.ts'\nimport { wellKnownSample } from './reference.ts'\n\nimport type { GBZBase, PathName, PathQuery, SnarlOutput } from '@gmod/gbz-base'\n\n// A window of a gbz-base graph cut to GFA, with no host in it: the adapter\n// and a standalone page open the database their own way and share this.\n\nexport class NoReferenceSampleError extends Error {\n  override name = 'NoReferenceSampleError'\n\n  constructor(anchor: string, referenceSamples: string[]) {\n    super(\n      referenceSamples.length === 0\n        ? `the graph names no reference sample (gbwt_reference_samples) and the anchor \"${anchor}\" maps to none; set referenceSample`\n        : `the anchor \"${anchor}\" is none of the graph's reference samples (${referenceSamples.join(', ')}); set referenceSample or map it through assemblyNameToPanSN`,\n    )\n  }\n}\n\nexport class NodeLimitError extends Error {\n  override name = 'NodeLimitError'\n\n  constructor(limit: number, windowBp: number, fitsBp: number) {\n    super(\n      `this ${windowBp.toLocaleString()} bp window reads more than nodeLimit (${limit.toLocaleString()}) graph nodes; zoom in to about ${fitsBp.toLocaleString()} bp or raise nodeLimit`,\n    )\n  }\n}\n\nexport function haplotypePrefix(name: Pick<PathName, 'sample' | 'haplotype'>) {\n  return `${name.sample}#${name.haplotype}`\n}\n\n// Whether a walk is one of the haplotypes asked for, by PanSN prefix at sample\n// (`HG002`) or haplotype (`HG002#1`) depth; undefined wants every one.\nexport function haplotypeWanted(name: PathName, wanted: string[] | undefined) {\n  const prefix = haplotypePrefix(name)\n  return (\n    wanted === undefined ||\n    wanted.some(candidate => panSNMatchesPrefix(prefix, candidate))\n  )\n}\n\nexport async function referenceSamplesOf(db: GBZBase) {\n  return ((await db.tag('gbwt_reference_samples')) ?? '')\n    .split(/\\s+/)\n    .filter(sample => sample !== '')\n}\n\nfunction aliasedSample(anchorSample: string, referenceSamples: string[]) {\n  const lower = anchorSample.toLowerCase()\n  const alias = wellKnownSample(anchorSample)?.toLowerCase()\n  return (\n    referenceSamples.find(s => s === anchorSample) ??\n    referenceSamples.find(s => s.toLowerCase() === lower) ??\n    referenceSamples.find(s => s.toLowerCase() === alias)\n  )\n}\n\nexport function resolveReferenceSample({\n  configured,\n  anchorPrefix,\n  referenceSamples,\n}: {\n  configured: string\n  anchorPrefix: string\n  referenceSamples: string[]\n}) {\n  if (configured !== '') {\n    return configured\n  }\n  const sample =\n    aliasedSample(panSNSample(anchorPrefix), referenceSamples) ??\n    (referenceSamples.length === 1 ? referenceSamples[0] : undefined)\n  if (sample === undefined) {\n    throw new NoReferenceSampleError(anchorPrefix, referenceSamples)\n  }\n  return sample\n}\n\n// The indexed reference path a window on `refName` resolves against, or\n// undefined when the reference sample has no indexed path by that contig.\nexport async function referencePathQuery(\n  db: GBZBase,\n  referenceSample: string,\n  refName: string,\n): Promise<PathQuery | undefined> {\n  const path = (await db.paths()).find(\n    p =>\n      p.isIndexed &&\n      p.name.sample === referenceSample &&\n      p.name.contig === refName,\n  )\n  return path\n    ? {\n        sample: path.name.sample,\n        contig: refName,\n        haplotype: path.name.haplotype,\n      }\n    : undefined\n}\n\n// gbz-base reports the node limit with how far along the reference the walk\n// had got when it tripped, counted from the window's start; a window that fits\n// is that far, with a margin, or half the window when the limit tripped past\n// the reference.\nexport function nodeLimitError(\n  error: unknown,\n  limit: number,\n  windowBp: number,\n) {\n  const isLimit =\n    error instanceof Error &&\n    (error.name === 'SubgraphLimitError' ||\n      /^Subgraph size limit of \\d+ nodes exceeded/.test(error.message))\n  if (!isLimit) {\n    return undefined\n  } else {\n    const walked = (error as { walkedBp?: unknown }).walkedBp\n    const fits =\n      typeof walked === 'number' && walked > 0\n        ? Math.floor(walked * 0.8)\n        : Math.floor(windowBp / 2)\n    return new NodeLimitError(limit, windowBp, Math.max(fits, 1))\n  }\n}\n\nexport interface GbzWindowOptions {\n  context: number\n  snarls: SnarlOutput\n  limit: number\n  keep?: ((name: PathName) => boolean) | undefined\n  signal?: AbortSignal | undefined\n}\n\n// A cut's context and snarls unless told otherwise, and the nodes past which a\n// window fails rather than read a whole chromosome: what a gbz-base track's\n// slots default to, so a page or a script cuts the window the viewer would.\n// gbz-base counts every node it walks, which runs well past the nodes a cut\n// keeps.\nexport const GBZ_CUT_DEFAULTS = {\n  context: 1000,\n  snarls: 'contained',\n  limit: 100_000,\n} as const satisfies Pick<GbzWindowOptions, 'context' | 'snarls' | 'limit'>\n\n// The reference walk, the snarls in the window, and one W line per haplotype\n// walk (the reference walk first), PanSN-named when the database carries the\n// haplotype index. Empty when the query names no indexed path.\nexport async function cutWindowGFA(\n  db: GBZBase,\n  query: PathQuery | undefined,\n  start: number,\n  end: number,\n  opts: GbzWindowOptions,\n) {\n  if (!query) {\n    return ''\n  }\n  const subgraphs = await db\n    .getSubgraphs({ ...opts, path: query, start, end, haplotypes: 'all' })\n    .catch((error: unknown) => {\n      throw nodeLimitError(error, opts.limit, end - start) ?? error\n    })\n  const paths = await db.paths()\n  return joinCuts(\n    await Promise.all(subgraphs.map(subgraph => subgraph.toGFA())),\n    (sample, haplotype, contig, at) =>\n      paths.some(\n        ({ name }) =>\n          name.sample === sample &&\n          name.haplotype === haplotype &&\n          name.contig === contig &&\n          name.fragment === at,\n      ),\n  )\n}\n"],
-  "mappings": 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-  "names": ["UNKNOWN_SAMPLE", "parseWalk", "line", "fields", "stepsOf", "walk", "segmentLengths", "lines", "lengths", "id", "sequence", "tags", "ln", "tag", "extend", "a", "b", "steps", "pos", "step", "length", "joinPieces", "pieces", "startsPath", "joined", "piece", "last", "sample", "haplotype", "contig", "extended", "flip", "sign", "stepLinks", "i", "joinCuts", "gfas", "cuts", "gfa", "ofType", "cut", "type", "unknownOffset", "walksByCut", "walks", "offset", "w", "byName", "links", "link", "WELL_KNOWN_SAMPLES", "wellKnownSample", "assemblyName", "sampleOf", "refName", "sample", "panSNSample", "isGenericSample", "haplotypeOf", "panSNHaplotype", "graphHaplotypes", "graph", "refNames", "p", "node", "bySample", "backboneFrom", "contigs", "haplotypes", "samples", "c", "own", "unique", "h", "shared", "haplotype", "graphBackbone", "spans", "isBackbone", "start", "end", "span", "panSNContig", "backboneAssembly", "backbone", "assemblies", "names", "naming", "prefix", "a", "n", "prefixes", "assembly", "assemblyWalk", "walk", "contigNames", "contig", "bare", "forms", "f", "refNameBinding", "aliases", "exact", "byName", "alias", "name", "featuresOnBackbone", "features", "bind", "NoReferenceSampleError", "anchor", "referenceSamples", "NodeLimitError", "limit", "windowBp", "fitsBp", "haplotypePrefix", "name", "haplotypeWanted", "wanted", "prefix", "candidate", "panSNMatchesPrefix", "referenceSamplesOf", "db", "sample", "aliasedSample", "anchorSample", "lower", "alias", "wellKnownSample", "resolveReferenceSample", "configured", "anchorPrefix", "panSNSample", "referencePathQuery", "referenceSample", "refName", "path", "p", "nodeLimitError", "error", "walked", "fits", "GBZ_CUT_DEFAULTS", "cutWindowGFA", "query", "start", "end", "opts", "subgraphs", "paths", "joinCuts", "subgraph", "haplotype", "contig", "at"]
+  "sourcesContent": ["// One GFA from gbz-base cuts of consecutive reference fragments. A haplotype\n// bridging the gap between two fragments comes back from both cuts, each piece\n// the run inside its own cut's nodes, so the two can overlap without matching.\n\ninterface Walk {\n  fields: string[]\n  name: string\n  start: number\n  end: number\n}\n\nconst UNKNOWN_SAMPLE = 'unknown'\n\nfunction parseWalk(line: string): Walk {\n  const fields = line.split('\\t')\n  return {\n    fields,\n    name: fields.slice(1, 4).join('\\t'),\n    start: +fields[4]!,\n    end: +fields[5]!,\n  }\n}\n\nconst stepsOf = (walk: Walk) => walk.fields[6]!.match(/[<>][^<>]+/g) ?? []\n\nfunction segmentLengths(lines: string[]) {\n  const lengths = new Map<string, number>()\n  for (const line of lines) {\n    if (line.startsWith('S\\t')) {\n      const [, id, sequence, ...tags] = line.split('\\t')\n      const ln = tags.find(tag => tag.startsWith('LN:i:'))\n      lengths.set(\n        id!,\n        sequence === '*' && ln ? +ln.slice('LN:i:'.length) : sequence!.length,\n      )\n    }\n  }\n  return lengths\n}\n\n// `a` carried on by the steps of `b` past `a.end`, where `b` starts inside or\n// at the end of `a`; undefined when no step of `b` starts exactly at `a.end`,\n// which two pieces of one walk always share\nfunction extend(a: Walk, b: Walk, lengths: Map<string, number>) {\n  if (b.end <= a.end) {\n    return a\n  }\n  const steps = stepsOf(b)\n  let pos = b.start\n  for (const [i, step] of steps.entries()) {\n    if (pos === a.end) {\n      const fields = [...a.fields]\n      fields[5] = String(b.end)\n      fields[6] = a.fields[6]! + steps.slice(i).join('')\n      return { ...a, fields, end: b.end }\n    }\n    const length = lengths.get(step.slice(1))\n    if (pos > a.end || length === undefined) {\n      return undefined\n    }\n    pos += length\n  }\n  return undefined\n}\n\n// Whether one of a haplotype's own paths starts at `at` on its contig\nexport type StartsPath = (\n  sample: string,\n  haplotype: number,\n  contig: string,\n  at: number,\n) => boolean\n\n// Pieces of one walk, by start, with each pair that overlaps or meets joined\n// into one. Pieces that meet where one of the haplotype's own paths starts are\n// two paths, whether or not the graph links them; a walk a cut split never\n// has a path starting at the seam.\nfunction joinPieces(\n  pieces: Walk[],\n  lengths: Map<string, number>,\n  startsPath: StartsPath,\n) {\n  const joined: Walk[] = []\n  for (const piece of pieces.sort((a, b) => a.start - b.start)) {\n    const last = joined.at(-1)\n    const [, sample, haplotype, contig] = piece.fields\n    const joins =\n      last !== undefined &&\n      (piece.start < last.end ||\n        (piece.start === last.end &&\n          !startsPath(sample!, +haplotype!, contig!, piece.start)))\n    const extended = joins ? extend(last, piece, lengths) : undefined\n    if (extended) {\n      joined[joined.length - 1] = extended\n    } else {\n      joined.push(piece)\n    }\n  }\n  return joined\n}\n\nconst flip = (sign: string) => (sign === '+' ? '-' : '+')\n\n// The link each step of a walk takes, in both of the ways an L line can write\n// it. Where two pieces met in no cut's nodes, no cut wrote the link between\n// them.\nfunction* stepLinks(walk: Walk) {\n  const steps = stepsOf(walk).map(step => ({\n    id: step.slice(1),\n    sign: step.startsWith('>') ? '+' : '-',\n  }))\n  for (let i = 1; i < steps.length; i++) {\n    const a = steps[i - 1]!\n    const b = steps[i]!\n    yield {\n      forward: `L\\t${a.id}\\t${a.sign}\\t${b.id}\\t${b.sign}\\t0M`,\n      reverse: `L\\t${b.id}\\t${flip(b.sign)}\\t${a.id}\\t${flip(a.sign)}\\t0M`,\n    }\n  }\n}\n\n// Each segment and link once, every cut's reference walk (its first W line)\n// ahead of the haplotype walks, the pieces of each walk joined, the\n// reference's among them since a cut's context can reach the other fragment,\n// and each cut's `unknown#N` walks numbered on from the cut before's, since\n// gbz-base numbers them per cut. Unnamed walks start every cut at 0, so their\n// pieces cannot be joined.\nexport function joinCuts(gfas: string[], startsPath: StartsPath) {\n  if (gfas.length <= 1) {\n    return gfas[0] ?? ''\n  }\n  const cuts = gfas.map(gfa => gfa.split('\\n').filter(line => line !== ''))\n  const ofType = (cut: string[], type: string) =>\n    cut.filter(line => line.startsWith(`${type}\\t`))\n  const lengths = segmentLengths(cuts.flat())\n  let unknownOffset = 0\n  const walksByCut = cuts.map(cut => {\n    const walks = ofType(cut, 'W').map(parseWalk)\n    const offset = unknownOffset\n    for (const walk of walks.filter(w => w.fields[1] === UNKNOWN_SAMPLE)) {\n      const haplotype = +walk.fields[2]! + offset\n      walk.fields[2] = String(haplotype)\n      walk.name = walk.fields.slice(1, 4).join('\\t')\n      unknownOffset = Math.max(unknownOffset, haplotype)\n    }\n    return walks\n  })\n  const byName = new Map<string, Walk[]>()\n  for (const walk of [\n    ...walksByCut.flatMap(walks => walks.slice(0, 1)),\n    ...walksByCut.flatMap(walks => walks.slice(1)),\n  ]) {\n    const pieces = byName.get(walk.name)\n    if (pieces) {\n      pieces.push(walk)\n    } else {\n      byName.set(walk.name, [walk])\n    }\n  }\n  const walks = [...byName.values()].flatMap(pieces =>\n    joinPieces(pieces, lengths, startsPath),\n  )\n  const links = new Set(cuts.flatMap(cut => ofType(cut, 'L')))\n  for (const walk of walks) {\n    for (const link of stepLinks(walk)) {\n      if (!links.has(link.forward) && !links.has(link.reverse)) {\n        links.add(link.forward)\n      }\n    }\n  }\n  const lines = new Set([\n    ...ofType(cuts[0]!, 'H'),\n    ...cuts.flatMap(cut => ofType(cut, 'S')),\n    ...links,\n    ...walks.map(walk => walk.fields.join('\\t')),\n  ])\n  return `${[...lines].join('\\n')}\\n`\n}\n", "import { isBackbone } from './anchoredNodes'\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample,\n} from './pansn'\n\nimport type { Graph, PathOrigin } from './types'\n\n// A graph's backbone names the sample it lies on (`GRCh38#0#chr6`), not an\n// assembly, and a bare contig (`chr6`) is in every human assembly at once. A\n// backbone binds to an assembly where its PanSN prefix is that assembly's name,\n// one of its aliases, or its well-known sample. One that names no sample binds\n// only where the host knows the assembly otherwise, as a track's config does.\n\nexport interface BackboneContig {\n  // as the graph names it, `GRCh38#0#chr6`\n  refName: string\n  // as an assembly names it, `chr6`\n  contig: string\n  start: number\n  end: number\n}\n\nexport interface Backbone {\n  contigs: BackboneContig[]\n  // The PanSN prefixes that name the backbone, sample then haplotype:\n  // `GRCh38`, `GRCh38#0`. The sample drops out where the graph walks another\n  // haplotype of it, as a diploid's `HG002` names `HG002#1` and `HG002#2`.\n  prefixes: string[]\n  // Whether the contigs name one real sample: false where every contig is bare\n  // (`chr6`) or generic (`_gbwt_ref#0#chr6`), or where the samples differ\n  named: boolean\n}\n\nexport interface AssemblyNames {\n  name: string\n  aliases?: string[]\n}\n\n// The sample a reference assembly's graphs name it by, keyed by the assembly's\n// name in lower case: HPRC writes `CHM13` where UCSC's assembly is `hs1`.\nexport const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string> = new Map([\n  ['hg38', 'GRCh38'],\n  ['hg19', 'GRCh37'],\n  ['hs1', 'CHM13'],\n  ['t2t-chm13', 'CHM13'],\n  ['chm13v2', 'CHM13'],\n])\n\nexport function wellKnownSample(assemblyName: string) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase())\n}\n\nfunction sampleOf(refName: string) {\n  const sample = refName.includes('#') ? panSNSample(refName) : undefined\n  return sample === undefined || isGenericSample(sample) ? undefined : sample\n}\n\n// `HG002#1`, or the sample of a two-part name, which states no haplotype\nfunction haplotypeOf(refName: string) {\n  return panSNHaplotype(refName) ?? panSNSample(refName)\n}\n\n// Each sample's haplotypes among the graph's walks and node refNames\nfunction graphHaplotypes(graph: Graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map(p => p.name))\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName)\n    }\n  }\n  const bySample = new Map<string, Set<string>>()\n  for (const refName of refNames) {\n    const sample = sampleOf(refName)\n    if (sample !== undefined) {\n      const haplotypes =\n        bySample.get(sample) ?? bySample.set(sample, new Set()).get(sample)!\n      haplotypes.add(haplotypeOf(refName))\n    }\n  }\n  return bySample\n}\n\nfunction backboneFrom(\n  contigs: BackboneContig[],\n  haplotypes: Map<string, Set<string>>,\n): Backbone {\n  const samples = new Set(contigs.map(c => sampleOf(c.refName)))\n  const [sample] = samples\n  if (samples.size !== 1 || sample === undefined) {\n    return { contigs, prefixes: [], named: false }\n  }\n  const own = new Set(contigs.map(c => haplotypeOf(c.refName)))\n  const unique = [...(haplotypes.get(sample) ?? [])].every(h => own.has(h))\n  const shared = new Set(contigs.map(c => panSNHaplotype(c.refName)))\n  const [haplotype] = shared\n  return {\n    contigs,\n    prefixes: [\n      ...(unique ? [sample] : []),\n      ...(shared.size === 1 && haplotype ? [haplotype] : []),\n    ],\n    named: true,\n  }\n}\n\n// The rank-0 nodes' refNames and the span each covers\nexport function graphBackbone(graph: Graph): Backbone | undefined {\n  const spans = new Map<string, BackboneContig>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable\n      const end = start + node.length\n      const span = spans.get(refName)\n      if (span) {\n        span.start = Math.min(span.start, start)\n        span.end = Math.max(span.end, end)\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end,\n        })\n      }\n    }\n  }\n  const contigs = [...spans.values()]\n  return contigs.length\n    ? backboneFrom(contigs, graphHaplotypes(graph))\n    : undefined\n}\n\n// `GRCh38 chr6`: the window's contig, else the backbone's one contig, after the\n// sample a named backbone lies on. Undefined where there is no one contig, so\n// a range never follows a bare sample.\nexport function referenceLabel(graph: Graph, region?: { refName: string }) {\n  const backbone = graphBackbone(graph)\n  const contig = region\n    ? panSNContig(region.refName)\n    : backbone?.contigs.length === 1\n      ? backbone.contigs[0]!.contig\n      : undefined\n  const sample = backbone?.named\n    ? panSNSample(backbone.contigs[0]!.refName)\n    : undefined\n  return contig && (sample ? `${sample} ${contig}` : contig)\n}\n\n// The assembly the backbone's haplotype names by its name or an alias, else\n// the one its sample names, else the one whose well-known sample it is. A\n// backbone with no prefix binds to none.\nexport function backboneAssembly<T extends AssemblyNames>(\n  backbone: Backbone | undefined,\n  assemblies: T[],\n): T | undefined {\n  const names = (a: T) => [a.name, ...(a.aliases ?? [])]\n  const naming = (prefix: string) => (a: T) =>\n    names(a).some(n => n.toLowerCase() === prefix.toLowerCase())\n  const prefixes = [...(backbone?.prefixes ?? [])].reverse()\n  const sample = backbone?.prefixes.find(p => !p.includes('#'))?.toLowerCase()\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix))\n    if (assembly) {\n      return assembly\n    }\n  }\n  return sample === undefined\n    ? undefined\n    : assemblies.find(a =>\n        names(a).some(n => wellKnownSample(n)?.toLowerCase() === sample),\n      )\n}\n\n// The first of the graph's walks that a backbone along it would bind to\n// `assembly`, for putting x on the assembly a cut was made for\nexport function assemblyWalk(\n  graph: Graph,\n  assembly: AssemblyNames,\n): PathOrigin | undefined {\n  const haplotypes = graphHaplotypes(graph)\n  return graph.anchorPaths?.find(walk =>\n    backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length,\n          },\n        ],\n        haplotypes,\n      ),\n      [assembly],\n    ),\n  )\n}\n\n// The names a file from outside the graph may give a contig: its own, and the\n// same with or without UCSC's `chr`, the mitochondrion as M or MT either way\nexport function contigNames(contig: string) {\n  const bare = contig.replace(/^chr/i, '')\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? ['M', 'MT'] : [bare]\n  return [...new Set([contig, ...forms.flatMap(f => [f, `chr${f}`])])]\n}\n\n// Which of `refNames` a feature's refName names: the one it equals, else the\n// only one whose contig it names, by any of contigNames or the name `aliases`\n// gives that contig (`{ chr6: 'NC_000006.12' }`). A name two refNames share\n// names neither.\nexport function refNameBinding(\n  refNames: Iterable<string>,\n  aliases: Record<string, string> = {},\n) {\n  const exact = new Set(refNames)\n  const byName = new Map<string, string | undefined>()\n  for (const refName of exact) {\n    const contig = panSNContig(refName)\n    const alias = aliases[contig]\n    for (const name of new Set([\n      ...contigNames(contig),\n      ...(alias ? [alias] : []),\n    ])) {\n      byName.set(name, byName.has(name) ? undefined : refName)\n    }\n  }\n  return (name: string) => (exact.has(name) ? name : byName.get(name))\n}\n\n// An assembly's features on a backbone that binds to it, each renamed to the\n// backbone's refName for it, so the assembly's `chr6` becomes the graph's\n// `GRCh38#0#chr6`. genePins and tubeMapGenes take only the renamed.\nexport function featuresOnBackbone<T extends { refName: string }>(\n  features: readonly T[],\n  backbone: Backbone,\n  aliases?: Record<string, string>,\n): T[] {\n  const bind = refNameBinding(\n    backbone.contigs.map(c => c.refName),\n    aliases,\n  )\n  return features.flatMap(f => {\n    const refName = bind(f.refName)\n    return refName === undefined\n      ? []\n      : [refName === f.refName ? f : { ...f, refName }]\n  })\n}\n", "import { joinCuts } from './gbzJoin.ts'\nimport { panSNMatchesPrefix, panSNSample } from './pansn.ts'\nimport { wellKnownSample } from './reference.ts'\n\nimport type { GBZBase, PathName, PathQuery, SnarlOutput } from '@gmod/gbz-base'\n\n// A window of a gbz-base graph cut to GFA, with no host in it: the adapter\n// and a standalone page open the database their own way and share this.\n\nexport class NoReferenceSampleError extends Error {\n  override name = 'NoReferenceSampleError'\n\n  constructor(anchor: string, referenceSamples: string[]) {\n    super(\n      referenceSamples.length === 0\n        ? `the graph names no reference sample (gbwt_reference_samples) and the anchor \"${anchor}\" maps to none; set referenceSample`\n        : `the anchor \"${anchor}\" is none of the graph's reference samples (${referenceSamples.join(', ')}); set referenceSample or map it through assemblyNameToPanSN`,\n    )\n  }\n}\n\nexport class NodeLimitError extends Error {\n  override name = 'NodeLimitError'\n  readonly regionTooLarge = true\n\n  constructor(\n    limit: number,\n    windowBp: number,\n    readonly fitsBp: number,\n  ) {\n    super(\n      `this ${windowBp.toLocaleString()} bp window reads more than nodeLimit (${limit.toLocaleString()}) graph nodes; zoom in to about ${fitsBp.toLocaleString()} bp or raise nodeLimit`,\n    )\n  }\n}\n\nexport function haplotypePrefix(name: Pick<PathName, 'sample' | 'haplotype'>) {\n  return `${name.sample}#${name.haplotype}`\n}\n\n// Whether a walk is one of the haplotypes asked for, by PanSN prefix at sample\n// (`HG002`) or haplotype (`HG002#1`) depth; undefined wants every one.\nexport function haplotypeWanted(name: PathName, wanted: string[] | undefined) {\n  const prefix = haplotypePrefix(name)\n  return (\n    wanted === undefined ||\n    wanted.some(candidate => panSNMatchesPrefix(prefix, candidate))\n  )\n}\n\nexport async function referenceSamplesOf(db: GBZBase) {\n  return ((await db.tag('gbwt_reference_samples')) ?? '')\n    .split(/\\s+/)\n    .filter(sample => sample !== '')\n}\n\nfunction aliasedSample(anchorSample: string, referenceSamples: string[]) {\n  const lower = anchorSample.toLowerCase()\n  const alias = wellKnownSample(anchorSample)?.toLowerCase()\n  return (\n    referenceSamples.find(s => s === anchorSample) ??\n    referenceSamples.find(s => s.toLowerCase() === lower) ??\n    referenceSamples.find(s => s.toLowerCase() === alias)\n  )\n}\n\nexport function resolveReferenceSample({\n  configured,\n  anchorPrefix,\n  referenceSamples,\n}: {\n  configured: string\n  anchorPrefix: string\n  referenceSamples: string[]\n}) {\n  if (configured !== '') {\n    return configured\n  }\n  const sample =\n    aliasedSample(panSNSample(anchorPrefix), referenceSamples) ??\n    (referenceSamples.length === 1 ? referenceSamples[0] : undefined)\n  if (sample === undefined) {\n    throw new NoReferenceSampleError(anchorPrefix, referenceSamples)\n  }\n  return sample\n}\n\n// The indexed reference path a window on `refName` resolves against, or\n// undefined when the reference sample has no indexed path by that contig.\nexport async function referencePathQuery(\n  db: GBZBase,\n  referenceSample: string,\n  refName: string,\n): Promise<PathQuery | undefined> {\n  const path = (await db.paths()).find(\n    p =>\n      p.isIndexed &&\n      p.name.sample === referenceSample &&\n      p.name.contig === refName,\n  )\n  return path\n    ? {\n        sample: path.name.sample,\n        contig: refName,\n        haplotype: path.name.haplotype,\n      }\n    : undefined\n}\n\n// gbz-base reports the node limit with how far along the reference the walk\n// had got when it tripped, counted from the window's start; a window that fits\n// is that far, with a margin, or half the window when the limit tripped past\n// the reference.\nexport function nodeLimitError(\n  error: unknown,\n  limit: number,\n  windowBp: number,\n) {\n  const isLimit =\n    error instanceof Error &&\n    (error.name === 'SubgraphLimitError' ||\n      /^Subgraph size limit of \\d+ nodes exceeded/.test(error.message))\n  if (!isLimit) {\n    return undefined\n  } else {\n    const walked = (error as { walkedBp?: unknown }).walkedBp\n    const fits =\n      typeof walked === 'number' && walked > 0\n        ? Math.floor(walked * 0.8)\n        : Math.floor(windowBp / 2)\n    return new NodeLimitError(limit, windowBp, Math.max(fits, 1))\n  }\n}\n\nexport interface GbzWindowOptions {\n  context: number\n  snarls: SnarlOutput\n  limit: number\n  keep?: ((name: PathName) => boolean) | undefined\n  signal?: AbortSignal | undefined\n}\n\n// A cut's context and snarls unless told otherwise, and the nodes past which a\n// window fails rather than read a whole chromosome: what a gbz-base track's\n// slots default to, so a page or a script cuts the window the viewer would.\n// gbz-base counts every node it walks, which runs well past the nodes a cut\n// keeps.\nexport const GBZ_CUT_DEFAULTS = {\n  context: 1000,\n  snarls: 'contained',\n  limit: 100_000,\n} as const satisfies Pick<GbzWindowOptions, 'context' | 'snarls' | 'limit'>\n\n// The reference walk, the snarls in the window, and one W line per haplotype\n// walk (the reference walk first), PanSN-named when the database carries the\n// haplotype index. Empty when the query names no indexed path.\nexport async function cutWindowGFA(\n  db: GBZBase,\n  query: PathQuery | undefined,\n  start: number,\n  end: number,\n  opts: GbzWindowOptions,\n) {\n  if (!query) {\n    return ''\n  }\n  const subgraphs = await db\n    .getSubgraphs({ ...opts, path: query, start, end, haplotypes: 'all' })\n    .catch((error: unknown) => {\n      throw nodeLimitError(error, opts.limit, end - start) ?? error\n    })\n  const paths = await db.paths()\n  return joinCuts(\n    await Promise.all(subgraphs.map(subgraph => subgraph.toGFA())),\n    (sample, haplotype, contig, at) =>\n      paths.some(\n        ({ name }) =>\n          name.sample === sample &&\n          name.haplotype === haplotype &&\n          name.contig === contig &&\n          name.fragment === at,\n      ),\n  )\n}\n"],
+  "mappings": 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 }

package/dist/chunks/chunk-K5Z47YVI.js

@@ -0,0 +1,2 @@
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