jbrowse-plugin-graphgenomeviewer 3.0.4 → 3.1.0

package/dist/chunks/MinigraphBubbleAdapter-A7SBF2XY.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts"],
+  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport {\n  bubbleDescription,\n  bubbleLabel,\n  parseBubbleLine,\n} from './bubbleLine.ts'\n\nimport type { MinigraphBubbleAdapterConfig } from './configSchema.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nexport default class MinigraphBubbleAdapter extends BaseFeatureDataAdapter<MinigraphBubbleAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly bubbles\n  // `gfatools bubble` names each row after the graph's stable sequence, so a\n  // Minigraph-Cactus graph produces PanSN rows (`GRCh38#0#chr6`) where a plain\n  // minigraph graph produces bare ones (`chr6`). Same resolution the segment\n  // adapter does, through the same `assemblyNameToPanSN` slot.\n  private readonly refNames\n\n  public constructor(\n    config: MinigraphBubbleAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.bubbles = openTabixSlot(this, ['bubblesLocation'], ['index'])\n    this.refNames = new PanSNRefNames(this.bubbles, this)\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading bubbles', statusCallback, () =>\n          this.bubbles.getLines(tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: (line, fileOffset) => {\n              const bubble = parseBubbleLine(line)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: `bubble-${fileOffset}`,\n                  refName: query.refName,\n                  start: bubble.start,\n                  end: bubble.end,\n                  // How variable this spot is, in two words, since that is the\n                  // whole point of the track.\n                  name: bubbleLabel(bubble),\n                  description: bubbleDescription(bubble),\n                  type: 'bubble',\n                  score: bubble.segmentCount,\n                  segmentCount: bubble.segmentCount,\n                  pathCount: bubble.pathCount,\n                  inversion: bubble.inversion,\n                  shortestAlleleLength: bubble.shortestAlleleLength,\n                  longestAlleleLength: bubble.longestAlleleLength,\n                  segments: bubble.segments,\n                  shortestAllele: bubble.shortestAllele,\n                  longestAllele: bubble.longestAllele,\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n}\n"],
+  "mappings": "4RAAA,IAAAA,EAAuC,SACvCC,EAA4C,SAC5CC,EAAiC,SAgBjC,IAAqBC,EAArB,cAAoD,wBAAqD,CACvG,YAAc,aAAe,CAAC,cAAe,aAAa,EASnD,YACLC,EACAC,EACAC,EACA,CACA,MAAMF,EAAQC,EAAeC,CAAa,EAC1C,KAAK,QAAUC,EAAc,KAAM,CAAC,iBAAiB,EAAG,CAAC,OAAO,CAAC,EACjE,KAAK,SAAW,IAAIC,EAAc,KAAK,QAAS,IAAI,CACtD,CAEA,MAAM,YAAYC,EAAoB,CAAC,EAAG,CACxC,OAAO,KAAK,SAAS,iBAAiBA,CAAI,CAC5C,CAEA,MAAa,mBAAoB,CAC/B,MAAO,EACT,CAEA,YAAYC,EAAeD,EAAoB,CAAC,EAAG,CACjD,GAAM,CAAE,OAAAE,EAAQ,eAAAC,CAAe,EAAIH,EACnC,SAAO,oBAA0B,MAAMI,GAAY,CACjD,IAAMC,EAAe,MAAM,KAAK,SAAS,QAAQJ,EAAOD,CAAI,EACxDK,IAAiB,QACnB,QAAM,gBAAa,sBAAuBF,EAAgB,IACxD,KAAK,QAAQ,SAASE,EAAcJ,EAAM,MAAOA,EAAM,IAAK,CAC1D,OAAAC,EACA,aAAc,CAACI,EAAMC,IAAe,CAClC,IAAMC,EAASC,EAAgBH,CAAI,EACnCF,EAAS,KACP,IAAI,gBAAc,CAChB,SAAU,UAAUG,CAAU,GAC9B,QAASN,EAAM,QACf,MAAOO,EAAO,MACd,IAAKA,EAAO,IAGZ,KAAME,EAAYF,CAAM,EACxB,YAAaG,EAAkBH,CAAM,EACrC,KAAM,SACN,MAAOA,EAAO,aACd,aAAcA,EAAO,aACrB,UAAWA,EAAO,UAClB,UAAWA,EAAO,UAClB,qBAAsBA,EAAO,qBAC7B,oBAAqBA,EAAO,oBAC5B,SAAUA,EAAO,SACjB,eAAgBA,EAAO,eACvB,cAAeA,EAAO,aACxB,CAAC,CACH,CACF,CACF,CAAC,CACH,EAEFJ,EAAS,SAAS,CACpB,EAAGF,CAAM,CACX,CACF",
+  "names": ["import_BaseAdapter", "import_util", "import_rxjs", "MinigraphBubbleAdapter", "config", "getSubAdapter", "pluginManager", "openTabixSlot", "PanSNRefNames", "opts", "query", "signal", "statusCallback", "observer", "tabixRefName", "line", "fileOffset", "bubble", "parseBubbleLine", "bubbleLabel", "bubbleDescription"]
+}

package/dist/chunks/RgfaTabixAdapter-7ZGKJJYW.js

@@ -0,0 +1,3 @@
+import{a as h,b as y}from"./chunk-HOM2Y6XS.js";import{a as O,b as P}from"./chunk-TN6FK5UD.js";import"./chunk-KWAXLUPQ.js";import{a as B}from"./chunk-J4OLMLS5.js";import"./chunk-F4C3BEPV.js";import{b as S}from"./chunk-FY3BTKY4.js";var C=S(O(),1),l=S(B(),1),M=S(P(),1);function b(t){let e=t.split("	");return{refName:e[0],start:+e[1],end:+e[2],id:e[3],rank:+e[4],tags:e[5]??""}}function $(t){let e=t.tags.split(" ").find(a=>a.startsWith("SM:Z:"));if(e===void 0)return;let n=e.slice(5).split(",").map(a=>a.trim()).filter(Boolean);return n.length>0?n:void 0}function L(t){return{id:t.slice(0,-1),strand:t.slice(-1)}}function A(t){let e=t.split("	"),n=L(e[3]),a=L(e[4]);return{source:n.id,sourceStrand:n.strand,target:a.id,targetStrand:a.strand,sourceSegment:{id:n.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:a.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function I(t){return`${t.source}${t.sourceStrand}${t.target}${t.targetStrand}`}var j=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function G(t){let{id:e,refName:n,start:a,end:r,rank:s,tags:m}=t,o=m.split(" ").filter(g=>j.test(g)),i=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${r-a}	SN:Z:${n}	SO:i:${a}	SR:i:${s}${i}`}function Z(t){let{source:e,sourceStrand:n,target:a,targetStrand:r}=t;return`L	${e}	${n}	${a}	${r}	0M`}function w(t,e){return t<e?-1:t>e?1:0}function T(t,e){let n=[...t.values()].sort((r,s)=>r.refName===s.refName?r.start-s.start:w(r.refName,s.refName)),a=[...e.keys()].sort((r,s)=>w(r,s));return["H	VN:Z:1.0",...n.map(r=>G(r)),...a.map(r=>Z(e.get(r)))].join(`
+`)}function F(t){return t.filter(e=>e.rank>0)}var N=class extends C.BaseFeatureDataAdapter{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,n,a){super(e,n,a),this.fine=this.openIndex([])}openIndex(e){let n=h(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]);return{segments:n,links:h(this,[...e,"linksLocation"],[...e,"linksIndex"]),refNames:new y(n,this)}}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,n={}){let{signal:a,statusCallback:r}=n;return(0,M.ObservableCreate)(async s=>{let m=await this.fine.refNames.resolve(e,n);m!==void 0&&await(0,l.updateStatus)("Downloading segments",r,()=>this.fine.segments.getLines(m,e.start,e.end,{signal:a,lineCallback:o=>{let i=b(o),g=$(i);s.next(new l.SimpleFeature({uniqueId:i.id,refName:e.refName,start:i.start,end:i.end,name:i.id,type:"segment",rank:i.rank,stableName:i.refName,...g&&{samples:g,carriers:g.length}}))}})),s.complete()},a)}async getSubgraph(e,n={}){let{hops:a=0,signal:r,tier:s}=n,m=this.index(s),o=new Map,i=new Map,g=await m.refNames.resolve(e,{signal:r}),x=async(f,p,c)=>{let k=[];return await m.links.getLines(f,p,c,{signal:r,lineCallback:v=>{let d=A(v);i.set(I(d),d);for(let u of[d.sourceSegment,d.targetSegment])o.has(u.id)||(o.set(u.id,u),k.push(u))}}),k};if(g===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${e.assemblyName} mapped to its prefix in assemblyNameToPanSN`);await m.segments.getLines(g,e.start,e.end,{signal:r,lineCallback:f=>{let p=b(f);o.set(p.id,p)}});let R=F(await x(g,e.start,e.end));for(let f=0;f<a;f++){let p=await Promise.all(R.map(c=>x(c.refName,c.start,c.end)));R=F(p.flat())}return T(o,i)}};export{N as default};
+//# sourceMappingURL=RgfaTabixAdapter-7ZGKJJYW.js.map

package/dist/chunks/RgfaTabixAdapter-7ZGKJJYW.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts", "../../src/RgfaTabixAdapter/rgfaBed.ts"],
+  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport {\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentLine,\n  segmentSamples,\n} from './rgfaBed.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { RgfaLink, RgfaSegment } from './rgfaBed.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// What a hop follows: alleles, never the backbone. A rank-0 segment reached\n// through a link is flanking backbone, usually outside the window, so querying\n// its links walks the reference away from the region, brings back more backbone,\n// and closes nothing. Every segment that closes a bubble is an allele interior,\n// and an allele interior is rank > 0 in both index formats (rGFA's SR tag, and\n// pggb's rank 0-or-1 against the anchor path). Reached backbone still becomes a\n// node and its edge still draws; it is only not walked through.\n//\n// This is gfabase's rule, arrived at from the other end. `gfabase sub` expands\n// from a seed either to the whole connected component (`--connected`, which its\n// own README calls overkill) or with `--cutpoints 1`, which takes the biconnected\n// component by *stopping at cutpoints*, the segments every end-to-end walk of\n// the chromosome must traverse. In a reference-anchored pangenome the cutpoints\n// are the backbone, and rank is what the index already states about it, so\n// `rank > 0` is that stopping rule without a connectivity index to build. The\n// third tool is the same shape again: `gfatools view -R` maps the region onto its\n// precomputed bubble decomposition and returns whole overlapping bubbles\n// (gfa_query_by_reg), which is complete for the same reason. Bandage's own\n// `--distance` is a node-step radius, but Bandage holds the entire graph in\n// memory, so its scope is a drawing filter rather than a fetch strategy.\n//\n// Measured with this rule: the E. coli paa window converges at one hop (17\n// segments at 1 and at 2), so the cut closes and stays closed. HPRC's amylase\n// window keeps growing (63 at 0, 78 at 1, 92 at 2) because its alleles have\n// alleles, and wall-clock is flat across all three, since a hop's queries go out\n// together and the remote index dominates.\n//\n// The exact version, when a graph ships a bubble index beside its segments:\n// gfatools' bubble rows carry the member segment ids of every bubble, so the\n// bubbles overlapping the region state which segments a complete cut must\n// contain. That turns the hop count into a termination condition rather than a\n// setting, and MinigraphBubbleAdapter already parses those rows.\nfunction offReference(segments: RgfaSegment[]) {\n  return segments.filter(segment => segment.rank > 0)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine\n  private coarse: GraphIndex | undefined\n\n  public constructor(\n    config: RgfaTabixAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.fine = this.openIndex([])\n  }\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    return {\n      segments,\n      links: openTabixSlot(\n        this,\n        [...under, 'linksLocation'],\n        [...under, 'linksIndex'],\n      ),\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading segments', statusCallback, () =>\n          this.fine.segments.getLines(tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: line => {\n              const segment = parseSegmentLine(line)\n              // `samples` is who, `carriers` is how many, and the second is not\n              // just a convenience: a lane colored by carriage is a jexl\n              // expression in a config, where counting a list means relying on\n              // jexl resolving `.length` through a member access on an array.\n              // The count is the axis the color reads, so the index states it.\n              const samples = segmentSamples(segment)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: segment.id,\n                  refName: query.refName,\n                  start: segment.start,\n                  end: segment.end,\n                  name: segment.id,\n                  type: 'segment',\n                  rank: segment.rank,\n                  stableName: segment.refName,\n                  ...(samples && { samples, carriers: samples.length }),\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n\n  // Extract the graph around a region as GFA text, for GraphGenomeView. The\n  // region's own segments come from segs.bed.gz; links.bed.gz supplies the edges\n  // incident to them *and* the coordinates of the segments on the other end,\n  // which typically sit on a different stable sequence (a rank>0 bubble) and so\n  // are not reachable by any coordinate query on this region.\n  //\n  // `hops` is extra rounds of link-following past the region's own segments\n  // and their immediate neighbours, each costing one tabix query per\n  // off-reference segment newly reached. One round is what closes a bubble, so\n  // it is the default the view asks for; see the frontier below. `signal` goes\n  // to every one of those queries, so a cut the view has replaced stops.\n  // `tier: 'coarse'` reads the `coarse` pair instead, the same way.\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { hops = 0, signal, tier } = opts\n    const index = this.index(tier)\n    const segments = new Map<string, RgfaSegment>()\n    const links = new Map<string, RgfaLink>()\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n\n    const addLinksOver = async (\n      refName: string,\n      start: number,\n      end: number,\n    ) => {\n      const reached: RgfaSegment[] = []\n      await index.links.getLines(refName, start, end, {\n        signal,\n        lineCallback: line => {\n          const link = parseLinkLine(line)\n          links.set(linkKey(link), link)\n          for (const segment of [link.sourceSegment, link.targetSegment]) {\n            if (!segments.has(segment.id)) {\n              segments.set(segment.id, segment)\n              reached.push(segment)\n            }\n          }\n        },\n      })\n      return reached\n    }\n\n    if (tabixRefName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${region.assemblyName} mapped to its prefix in assemblyNameToPanSN`,\n      )\n    }\n    await index.segments.getLines(tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const segment = parseSegmentLine(line)\n        segments.set(segment.id, segment)\n      },\n    })\n    let frontier = offReference(\n      await addLinksOver(tabixRefName, region.start, region.end),\n    )\n    for (let hop = 0; hop < hops; hop++) {\n      // One hop's queries are independent of each other, so they go out\n      // together rather than one round-trip at a time. Their callbacks share\n      // the segment and link maps, which is safe because only one of them runs\n      // at a time, and the output is sorted at the end regardless of the order\n      // they arrive in.\n      const reached = await Promise.all(\n        frontier.map(segment =>\n          addLinksOver(segment.refName, segment.start, segment.end),\n        ),\n      )\n      frontier = offReference(reached.flat())\n    }\n\n    return formatSubgraph(segments, links)\n  }\n}\n", "// A segment as it appears in segs.bed.gz, and as it is repeated inside every\n// links.bed.gz row: `stableName start end segmentId rank [tags]`. The first\n// five are the SN/SO/SR tags rGFA already carries, projected to BED by\n// `gfatools gfa2bed -m`.\n//\n// `tags` is a space-separated list of GFA tags, written verbatim onto the\n// S-line formatSegment synthesizes, where the GFA parser reads them into\n// `GraphNode.tags` with no work here. It is the extension point for everything\n// the five columns cannot say: carriage on a path-derived graph (`SM:Z:`), the\n// collapse summary on a level-of-detail tier (`ct:Z:`, `cn:i:`, ...), a\n// precomputed layout position later. rGFA files have no sixth column at all,\n// so this is empty for them and nothing changes.\nexport interface RgfaSegment {\n  refName: string\n  start: number\n  end: number\n  id: string\n  rank: number\n  tags: string\n}\n\nexport interface RgfaLink {\n  source: string\n  sourceStrand: string\n  target: string\n  targetStrand: string\n  sourceSegment: RgfaSegment\n  targetSegment: RgfaSegment\n}\n\nexport function parseSegmentLine(line: string): RgfaSegment {\n  const cols = line.split('\\t')\n  return {\n    refName: cols[0]!,\n    start: +cols[1]!,\n    end: +cols[2]!,\n    id: cols[3]!,\n    rank: +cols[4]!,\n    tags: cols[5] ?? '',\n  }\n}\n\n// Carriage as an ordinary feature attribute, for the linear track rather than\n// the graph. The tag column reaches the graph view through the synthesized\n// S-line (formatSegment below, then gfaConverter reads SM into\n// `GraphNode.samples`), and that route ends at the graph: `getFeatures` builds\n// its own features and had no way to say who carries a segment, so a lane\n// colored by carriage was not expressible.\n//\n// `SM:Z:` is its own grammar check here. build_pggb_tabix.sh wrote a bare\n// comma-separated list in this column before the tag column existed, and those\n// files are still hosted; a bare list has no prefix to match, so it is dropped\n// rather than read as one sample named `K12,Sakai,CFT073`.\n//\n// Undefined rather than [] when the tag is absent, matching gfaConverter: an\n// rGFA has no sixth column at all, so a segment that says nothing about\n// carriage stays distinguishable from one carried by nobody.\nexport function segmentSamples(segment: RgfaSegment) {\n  const tag = segment.tags.split(' ').find(t => t.startsWith('SM:Z:'))\n  if (tag === undefined) {\n    return undefined\n  }\n  const samples = tag\n    .slice('SM:Z:'.length)\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\n// `s322+` \u2014 the L-line's segment id with its orientation appended, mirroring\n// the GFA record it came from.\nfunction parseEndpoint(field: string) {\n  return { id: field.slice(0, -1), strand: field.slice(-1) }\n}\n\nexport function parseLinkLine(line: string): RgfaLink {\n  const cols = line.split('\\t')\n  const source = parseEndpoint(cols[3]!)\n  const target = parseEndpoint(cols[4]!)\n  return {\n    source: source.id,\n    sourceStrand: source.strand,\n    target: target.id,\n    targetStrand: target.strand,\n    sourceSegment: {\n      id: source.id,\n      refName: cols[5]!,\n      start: +cols[6]!,\n      end: +cols[7]!,\n      rank: +cols[8]!,\n      tags: cols[13] ?? '',\n    },\n    targetSegment: {\n      id: target.id,\n      refName: cols[9]!,\n      start: +cols[10]!,\n      end: +cols[11]!,\n      rank: +cols[12]!,\n      tags: cols[14] ?? '',\n    },\n  }\n}\n\nexport function linkKey(link: RgfaLink) {\n  return `${link.source}${link.sourceStrand}${link.target}${link.targetStrand}`\n}\n\n// Both endpoints of a link are written into every row, so the same link is\n// indexed under each endpoint's stable sequence and arrives twice for a region\n// covering both. Callers dedupe on linkKey.\n\n// Segments carry no sequence here \u2014 the BED records only their span \u2014 so every\n// S-line is written with `*` and an LN tag, which is what the GFA spec asks for\n// and what packages/graph-core's parser reads back as the node length.\n// `NM:i:0`, `SM:Z:HG002.1,HG002.2` \u2014 the GFA tag grammar, checked rather than\n// trusted. Files built before the tag column existed put a bare comma-separated\n// sample list here, and passing that through would put a field that is not a\n// tag on an S-line, which is a malformed GFA rather than a missing annotation.\n// Dropping it degrades to the pre-tag behaviour instead.\nconst GFA_TAG = /^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/\n\nfunction formatSegment(segment: RgfaSegment) {\n  const { id, refName, start, end, rank, tags } = segment\n  const valid = tags.split(' ').filter(t => GFA_TAG.test(t))\n  const extra = valid.length === 0 ? 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+}

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n=[...t.entries()].sort(([a,i],[c,u])=>Wt(i,u)||Y(a,c)).map(([a])=>a),r=n.length;for(let a of n){let i=t.get(a);for(let c of e.get(a)??[])t.has(c)||(t.set(c,{at:i.at,side:1,hops:i.hops+1}),n.push(c))}let o=new Set(n.slice(r)),s=new Set;for(let a of o){if(s.has(a))continue;let{at:i}=t.get(a),c=[a];s.add(a);let u=!0;for(let p of c){let{hops:l}=t.get(p),d=!0,m=!1;for(let f of e.get(p)??[]){let h=t.get(f);h.at===i&&o.has(f)?(d&&=h.hops<=l,s.has(f)||(s.add(f),c.push(f))):h.at!==i&&(m||=h.at<i,u&&=h.at<i)}u&&=!d||m}if(u)for(let p of c){let l=t.get(p);t.set(p,{...l,side:-1,hops:-l.hops})}}}function kr(e){let t=new Set(e.nodes.map(s=>s.id)),n=new Map;for(let s of e.edges)!t.has(s.from)||!t.has(s.to)||((n.get(s.from)??n.set(s.from,[]).get(s.from)).push(s.to),(n.get(s.to)??n.set(s.to,[]).get(s.to)).push(s.from));let r=e.nodes.filter(S).sort((s,a)=>Y(s.stable.start,a.stable.start)||Y(s.name,a.name)),o=new Map;return Or(e,r).forEach((s,a)=>{o.set(s,{at:a,side:0,hops:0})}),Ir(n,o),o}function Tr(e){let t=new Map(e.nodes.map(l=>[l.id,l])),n=Cr(e),r=new Map(n.map((l,d)=>[l,d])),o=l=>S(t.get(l)),s=new Map(n.map(l=>[l,[]])),a=new Map(n.map(l=>[l,[]])),i=(l,d)=>{s.get(d).push(l),a.get(l).push(d)};for(let l of e.edges)l.from===l.to||!r.has(l.from)||!r.has(l.to)||(r.get(l.from)<r.get(l.to)?i(l.from,l.to):i(l.to,l.from));let c=n.filter(o);for(let l=1;l<c.length;l++)i(c[l-1],c[l]);let u=new Map;for(let l of n){let d=0;for(let m of s.get(l))d=Math.max(d,u.get(m)+1);u.set(l,d)}for(let l=n.length-1;l>=0;l--){let d=n[l],m=a.get(d);if(o(d)||m.length===0)continue;let f=1/0;for(let b of m)f=Math.min(f,u.get(b));let h=u.get(d),g=Math.max(h,f-1);u.set(d,Math.floor((h+g)/2))}let p=[];for(let l of n)(p[u.get(l)]??=[]).push(l);return{layers:p,layerOf:u,preds:s}}function zt(e){if(!e.nodes.some(S))return;let t=new Map(e.nodes.map(l=>[l.id,l])),n=l=>S(t.get(l)),{layers:r,layerOf:o,preds:s}=Tr(e),a=r.map(l=>{let d=0;for(let m of l)d=Math.max(d,Ht(t.get(m)));return d}),i=[],c=0;for(let l=0;l<r.length;l++)i[l]=c,c+=a[l]+vr;let u=new Map;for(let l of r){let d=[];for(let f of l){if(n(f)){u.set(f,0);continue}let h=s.get(f).filter(b=>u.has(b)),g=0;for(let b of h)g+=u.get(b)/h.length;d.push({id:f,ideal:g===0?Ke:g})}d.sort((f,h)=>f.ideal-h.ideal);let m=new Set([0]);for(let{id:f,ideal:h}of d){let g=Math.round(h/Ke);g===0&&(g=h>=0?1:-1);for(let b=1;m.has(g);b++)m.has(g+b)?m.has(g-b)||(g-=b):g+=b;m.add(g),u.set(f,g*Ke)}}let p={};for(let l of e.nodes){let d=o.get(l.id),m=Ht(l),f=i[d]+a[d]/2,h=u.get(l.id);p[l.id]=[{x:f-m/2,y:h},{x:f+m/2,y:h}]}return{nodePositions:p,referenceAxis:!1,pixelRows:!0}}function Br(e,t){let n=new Map;for(let o of e.nodes)if(Se(o)){let{sample:s}=Ie(o.stable.refName);n.set(s,(n.get(s)??0)+o.length)}let r=new Map(t.map((o,s)=>[o,s]));return[...n.keys()].sort((o,s)=>(r.get(o)??1/0)-(r.get(s)??1/0)||n.get(s)-n.get(o)||o.localeCompare(s))}function Ft(e,t,n=[]){let r=X(e),o=Br(e,n);if(r.length===0||o.length===0)return;let s=Le(r,t),a=new Map(o.map((d,m)=>[d,m+1])),i=U(r),c=o.length+1,u=ke({graph:e,span:s,rowY:d=>{let m=d.stable;return((m?a.get(Ie(m.refName).sample):void 0)??c)*20},positions:i}),l=[{label:Ie(r[0].stable.refName).sample,y:0},...o.map(d=>({label:d,y:a.get(d)*20}))];return{nodePositions:i,rowLabels:l,sampleRows:o,referenceAxis:!0,pixelRows:!0,alleleDeletions:u}}function Xt(e){let t=X(e);if(t.length!==0)return{nodePositions:U(t),referenceAxis:!0,pixelRows:!0}}var Pr="Force-directed layout",K=e=>e.nodes.some(S),Ut=e=>K(e)&&(e.paths?.length??0)>1,Yt=e=>K(e)&&e.nodes.some(Se),Ve=[{value:"auto",label:"Anchored",description:"x is reference bp, one row per stable rank. Needs rGFA tags or a reference path.",run:Dt,available:K,drawsLocally:K},{value:"samplerows",label:"Sample rows",description:"x is reference bp, one row per contributing assembly. Needs rGFA tags or a reference path.",run:Ft,available:Yt,drawsLocally:Yt},{value:"walkrows",label:"Walk rows",description:"x is each walk's own bp: one bar per haplotype, sequence the reference also carries in blue and sequence it does not in purple, so a repeat expansion reads as bar length. Needs W or P lines.",run:Bt,available:Ut,drawsLocally:Ut},{value:"ordered",label:"Ordered",description:"x is reference order, not bp: every node gets room, bubbles read as lenses. Needs rGFA tags or a reference path.",run:zt,available:K,drawsLocally:K},{value:"variants",label:"Variant map",description:"The reference as a line with one typed glyph per bubble, from the bubble index or from the graph itself: SNP, indel, deletion, inversion, repeat array. 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