jbrowse-plugin-graphgenomeviewer 4.0.13 → 4.0.14

package/dist/chunks/chunk-KULNKXPT.js

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+function o(t){return t.split("#")[0]}var i=new Set(["_gbwt_ref"]);function u(t){return i.has(t)}function p(t){let e=t.split("#");return e.length>=3?`${e[0]}#${e[1]}`:void 0}function d(t){let e=t.split("#");return e.length>=3?e.slice(2).join("#"):e.length===2?e[1]:t}function f(t,e){return e!==void 0&&(t===e||t.startsWith(e+"#"))}function s(t){return t.getConf("assemblyNameToPanSN")??{}}function c(t,e){return e===void 0?void 0:s(t)[e]??e}var a=new WeakMap;function g(t){let e=a.get(t);if(e===void 0){let r=s(t);e={};for(let n of new Set([...Object.keys(r),...t.getConf("assemblyNames")]))e[r[n]??n]=n;a.set(t,e)}return e}export{o as a,u as b,p as c,d,f as e,c as f,g};
+//# sourceMappingURL=chunk-KULNKXPT.js.map

package/dist/chunks/chunk-KULNKXPT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "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// 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\nexport function isGenericSample(sample: string) {\n  return GENERIC_SAMPLES.has(sample)\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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+  "names": ["panSNSample", "refName", "GENERIC_SAMPLES", "isGenericSample", "sample", "panSNHaplotype", "parts", "panSNContig", "panSNMatchesPrefix", "prefix", "assemblyNameToPanSN", "adapter", "resolvePanSNPrefix", "name", "asmByPrefixCache", "assemblyByPanSNPrefix", "out", "map", "asm"]
+}

package/dist/chunks/chunk-QSH263Y6.js

@@ -0,0 +1,2 @@
+import{b as u}from"./chunk-EFVAQ2KM.js";import{a as p,b as d,c as m,d as c}from"./chunk-KULNKXPT.js";var N=new Map([["hg38","GRCh38"],["hg19","GRCh37"],["hs1","CHM13"],["t2t-chm13","CHM13"],["chm13v2","CHM13"]]);function x(n){return N.get(n.toLowerCase())}function g(n){let t=n.includes("#")?p(n):void 0;return t===void 0||d(t)?void 0:t}function l(n){return m(n)??p(n)}function h(n){let t=new Set((n.anchorPaths??[]).map(e=>e.name));for(let e of n.nodes)e.stable&&t.add(e.stable.refName);let s=new Map;for(let e of t){let o=g(e);o!==void 0&&(s.get(o)??s.set(o,new Set).get(o)).add(l(e))}return s}function b(n,t){let s=new Set(n.map(f=>g(f.refName))),[e]=s;if(s.size!==1||e===void 0)return{contigs:n,prefixes:[],named:!1};let o=new Set(n.map(f=>l(f.refName))),i=[...t.get(e)??[]].every(f=>o.has(f)),r=new Set(n.map(f=>m(f.refName))),[a]=r;return{contigs:n,prefixes:[...i?[e]:[],...r.size===1&&a?[a]:[]],named:!0}}function B(n){let t=new Map;for(let e of n.nodes)if(u(e)){let{refName:o,start:i}=e.stable,r=i+e.length,a=t.get(o);a?(a.start=Math.min(a.start,i),a.end=Math.max(a.end,r)):t.set(o,{refName:o,contig:c(o),start:i,end:r})}let s=[...t.values()];return s.length?b(s,h(n)):void 0}function y(n,t){let s=r=>[r.name,...r.aliases??[]],e=r=>a=>s(a).some(f=>f.toLowerCase()===r.toLowerCase()),o=[...n?.prefixes??[]].reverse(),i=n?.prefixes.find(r=>!r.includes("#"))?.toLowerCase();for(let r of o){let a=t.find(e(r));if(a)return a}return i===void 0?void 0:t.find(r=>s(r).some(a=>x(a)?.toLowerCase()===i))}function M(n,t){let s=h(n);return n.anchorPaths?.find(e=>y(b([{refName:e.name,contig:c(e.name),start:e.start,end:e.start+e.length}],s),[t]))}function S(n){let t=new Set(n),s=new Map;for(let e of t){let o=c(e);s.set(o,s.has(o)?void 0:e)}return e=>t.has(e)?e:s.get(e)}function k(n,t){let s=S(t.contigs.map(e=>e.refName));return n.flatMap(e=>{let o=s(e.refName);return o===void 0?[]:[o===e.refName?e:{...e,refName:o}]})}export{x as a,B as b,y as c,M as d,k as e};
+//# sourceMappingURL=chunk-QSH263Y6.js.map

package/dist/chunks/chunk-QSH263Y6.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../packages/core/src/reference.ts"],
+  "sourcesContent": ["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// 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      ? []\n      : [refName === f.refName ? f : { ...f, refName }]\n  })\n}\n"],
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+  "names": ["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", "a", "naming", "prefix", "n", "prefixes", "assembly", "assemblyWalk", "walk", "refNameBinding", "exact", "byContig", "contig", "name", "featuresOnBackbone", "features", "bind", "f"]
+}

package/dist/chunks/chunk-UQEPPJEO.js

@@ -0,0 +1,2 @@
+function r(n){return n===void 0||n==="*"?void 0:n}function l(n){let e=n.split("	");return{refName:e[0],start:+e[1],end:+e[2],segmentCount:+e[3],pathCount:+e[4],inversion:e[5]==="1",shortestAlleleLength:+e[6],longestAlleleLength:+e[7],segments:e[11],shortestAllele:r(e[12]),longestAllele:r(e[13])}}function i(n,e){return n.refName===e.refName&&n.start===e.start&&n.end===e.end}function u(n){let{shortestAlleleLength:e,longestAlleleLength:t}=n;return e===t?`${t.toLocaleString()} bp`:`${e.toLocaleString()}-${t.toLocaleString()} bp`}var s=2147483647;function b(n){let{pathCount:e,segmentCount:t,inversion:o}=n;return[`${t} segments`,e===s?"more paths than gfatools counts":`up to ${e.toLocaleString()} paths`,...o?["inversion"]:[]].join(", ")}export{l as a,i as b,u as c,s as d,b as e};
+//# sourceMappingURL=chunk-UQEPPJEO.js.map

package/dist/chunks/{chunk-VAGPKHHS.js.map → chunk-UQEPPJEO.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../packages/core/src/bubbles/bubbleLine.ts"],
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+  "sourcesContent": ["// One row of `gfatools bubble` output. Column order is fixed by gfatools\n// main.c (main_bubble): stable sequence, span, then the bubble's shape, three\n// `-1` placeholders, the segments it spans, and the two extreme alleles.\n//\n//   1  stable sequence name        8  longest allele length\n//   2  start                       9  -1\n//   3  end                        10  -1\n//   4  segments in the bubble     11  -1\n//   5  paths through it           12  comma-separated segment ids\n//   6  1 if it involves an inversion  13  shortest allele sequence, or *\n//   7  shortest allele length     14  longest allele sequence, or *\nexport interface MinigraphBubble {\n  refName: string\n  start: number\n  end: number\n  segmentCount: number\n  pathCount: number\n  inversion: boolean\n  shortestAlleleLength: number\n  longestAlleleLength: number\n  segments: string\n  shortestAllele: string | undefined\n  longestAllele: string | undefined\n  // Set on a bubble derived from the graph itself (bubblesFromGraph.ts) whose\n  // reference route leaves the cut, so its lengths are a floor, not a fact.\n  partial?: boolean\n  // Every distinct route the walks take through a derived bubble, with the\n  // walks that take it. Only a graph with walks can state this.\n  routes?: BubbleRoute[]\n}\n\nexport interface BubbleRoute {\n  // the node ids between the bubble's two ends, in walk order\n  steps: string[]\n  bp: number\n  walks: string[]\n}\n\n// gfatools writes `*` for a zero-length allele (a pure insertion has no\n// shorter side), which is the GFA spec's \"no sequence here\" rather than a\n// sequence to show.\nfunction sequence(field: string | undefined) {\n  return field === undefined || field === '*' ? undefined : field\n}\n\nexport function parseBubbleLine(line: string): MinigraphBubble {\n  const cols = line.split('\\t')\n  return {\n    refName: cols[0]!,\n    start: +cols[1]!,\n    end: +cols[2]!,\n    segmentCount: +cols[3]!,\n    pathCount: +cols[4]!,\n    inversion: cols[5] === '1',\n    shortestAlleleLength: +cols[6]!,\n    longestAlleleLength: +cols[7]!,\n    segments: cols[11]!,\n    shortestAllele: sequence(cols[12]),\n    longestAllele: sequence(cols[13]),\n  }\n}\n\n// A bubble is its span on the reference, whichever array it was read into\nexport function sameBubble(a: MinigraphBubble, b: MinigraphBubble) {\n  return a.refName === b.refName && a.start === b.start && a.end === b.end\n}\n\n// How far apart the two extreme alleles are, which is the concrete thing a\n// bubble says: this stretch is between min and max bases long depending on the\n// haplotype.\nexport function bubbleLabel(bubble: MinigraphBubble) {\n  const { shortestAlleleLength: min, longestAlleleLength: max } = bubble\n  return min === max\n    ? `${max.toLocaleString()} bp`\n    : `${min.toLocaleString()}-${max.toLocaleString()} bp`\n}\n\n// gfatools counts paths into an int32 and clamps at its maximum rather than\n// overflowing, so this exact value is a \"more than I can count\" sentinel and not\n// a measurement. 406 of HPRC release 2's 130,510 bubbles hit it.\nexport const SATURATED_PATH_COUNT = 2147483647\n\n// The rest of the shape, for the description line. `pathCount` is the number of\n// ways through the bubble, which is combinatorial rather than a count of\n// observed haplotypes: one HLA class II bubble reports over 510 million across\n// its 91 segments. Hence \"up to\", and hence the label above leading with\n// lengths.\nexport function bubbleDescription(bubble: MinigraphBubble) {\n  const { pathCount, segmentCount, inversion } = bubble\n  return [\n    `${segmentCount} segments`,\n    pathCount === SATURATED_PATH_COUNT\n      ? 'more paths than gfatools counts'\n      : `up to ${pathCount.toLocaleString()} paths`,\n    ...(inversion ? ['inversion'] : []),\n  ].join(', ')\n}\n"],
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 }

package/dist/chunks/chunk-YWJ3RWYB.js

@@ -0,0 +1,4 @@
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