jbrowse-plugin-graphgenomeviewer 4.0.13 → 4.0.15

package/dist/chunks/chunk-IFRDWMQ2.js

@@ -1,2 +0,0 @@
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package/dist/chunks/chunk-IFRDWMQ2.js.map

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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\n// vg names a reference path that states no sample `_gbwt_ref`, and gbz-base\n// writes its walk as `W _gbwt_ref 0 chr6`\nconst GENERIC_SAMPLES = new Set(['_gbwt_ref'])\n\nfunction sampleOf(refName: string) {\n  const sample = refName.includes('#') ? panSNSample(refName) : undefined\n  return sample === undefined || GENERIC_SAMPLES.has(sample)\n    ? undefined\n    : 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 ?? 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[])].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// Which of `refNames` a feature's refName names: the one it equals, else the\n// only one whose contig it is. A contig two refNames share names neither.\nexport function refNameBinding(refNames: Iterable<string>) {\n  const exact = new Set(refNames)\n  const byContig = new Map<string, string | undefined>()\n  for (const refName of exact) {\n    const contig = panSNContig(refName)\n    byContig.set(contig, byContig.has(contig) ? undefined : refName)\n  }\n  return (name: string) => (exact.has(name) ? name : byContig.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): T[] {\n  const bind = refNameBinding(backbone.contigs.map(c => c.refName))\n  return features.flatMap(f => {\n    const refName = bind(f.refName)\n    return refName === undefined\n      ? 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-}

package/dist/chunks/chunk-M4YEAXSR.js

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package/dist/chunks/chunk-MUK3KYB4.js

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-{
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-  "sources": ["../../packages/core/src/pansn.ts"],
-  "sourcesContent": ["import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// PanSN naming convention: `sample#haplotype#contig`. Shared by the all-vs-all\n// PAF adapters (in-memory and tabix-indexed), which anchor on the sample prefix\n// and strip it to recover each assembly's own refName.\nconst SEP = '#'\n\n// The PanSN sample name is the token before the first separator, e.g.\n// `grape#1#chr1` -> `grape`.\nexport function panSNSample(refName: string) {\n  return refName.split(SEP)[0]!\n}\n\n// The haplotype a three-part PanSN name belongs to, `sample#hap`, which is the\n// assembly that contributed it where one sample is two haplotypes (HPRC release\n// 2.1 names every node `NA20809#2#CM094351.1`); undefined for a name that\n// states no haplotype.\nexport function panSNHaplotype(refName: string) {\n  const parts = refName.split(SEP)\n  return parts.length >= 3 ? `${parts[0]}${SEP}${parts[1]}` : undefined\n}\n\n// Strip the PanSN prefix to recover the assembly's own refName: `sample#hap#chr1`\n// -> `chr1`, `sample#chr1` -> `chr1`. A contig that itself contains the\n// separator is assumed not to occur (PanSN uses `#` only as the delimiter).\nexport function panSNContig(refName: string) {\n  const parts = refName.split(SEP)\n  return parts.length >= 3\n    ? parts.slice(2).join(SEP)\n    : parts.length === 2\n      ? parts[1]!\n      : refName\n}\n\n// Whether a PanSN name belongs to a prefix at either depth: `grape#1#chr1`\n// matches `grape` and `grape#1`, not `grape#2` or `grapefruit`. An undefined\n// prefix is \"no assembly supplied\", which nothing belongs to.\nexport function panSNMatchesPrefix(\n  refName: string,\n  prefix: string | undefined,\n) {\n  return (\n    prefix !== undefined &&\n    (refName === prefix || refName.startsWith(prefix + SEP))\n  )\n}\n\n// How a config maps the session's assembly names onto the PanSN spelling a\n// graph uses, and back. Every adapter here declares an `assemblyNameToPanSN`\n// slot for it \u2014 the graph says `GRCh38#0` where the assembly is `hg38` \u2014 so\n// resolving a name is the same question in all of them, and it used to be\n// answered by two copies of these functions in two directories.\n//\n// `?? {}` so an adapter whose schema lacks the slot identity-maps rather than\n// throwing a TypeError deep inside a query.\nfunction assemblyNameToPanSN(adapter: BaseFeatureDataAdapter) {\n  return (adapter.getConf('assemblyNameToPanSN') ?? {}) as Record<\n    string,\n    string\n  >\n}\n\n// One assembly name as its PanSN sample prefix, identity when the config maps\n// it to nothing. Overloaded rather than widened: undefined passes through, so a\n// caller can express \"no anchor/target supplied\", and a caller that has a name\n// gets a `string` back instead of having to re-assert one.\nexport function resolvePanSNPrefix(\n  adapter: BaseFeatureDataAdapter,\n  name: string,\n): string\nexport function resolvePanSNPrefix(\n  adapter: BaseFeatureDataAdapter,\n  name: string | undefined,\n): string | undefined\nexport function resolvePanSNPrefix(\n  adapter: BaseFeatureDataAdapter,\n  name: string | undefined,\n) {\n  return name === undefined\n    ? undefined\n    : (assemblyNameToPanSN(adapter)[name] ?? name)\n}\n\nconst asmByPrefixCache = new WeakMap<\n  BaseFeatureDataAdapter,\n  Record<string, string>\n>()\n\n// The inverse: PanSN prefix -> the assembly name this session loads it as, for\n// naming the lane a haplotype draws on. A mapped assembly counts whether or not\n// `assemblyNames` also lists it.\nexport function assemblyByPanSNPrefix(adapter: BaseFeatureDataAdapter) {\n  let out = asmByPrefixCache.get(adapter)\n  if (out === undefined) {\n    const map = assemblyNameToPanSN(adapter)\n    out = {}\n    for (const asm of new Set([\n      ...Object.keys(map),\n      ...(adapter.getConf('assemblyNames') as string[]),\n    ])) {\n      out[map[asm] ?? asm] = asm\n    }\n    asmByPrefixCache.set(adapter, out)\n  }\n  return out\n}\n"],
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-}

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