npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 4.1.1 → 4.3.0 - Mend

jbrowse-plugin-graphgenomeviewer 4.1.1 → 4.3.0

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Files changed (39) hide show

package/README.md CHANGED Viewed

@@ -22,7 +22,7 @@ above it.
 - **Copy number off a bar.** Walk rows tile each haplotype by the 5,548 bp
   kringle: GRCh38's six units are the six LPA exon pairs above, and HG00133
-  carries 27.
+  has 27.
 ![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)
@@ -49,9 +49,9 @@ node in the view bands its bp in the linear view:
 - Genes from the session's annotation track, drawn on the graph
 - Hovering a callset or MAF row in the same view lifts that haplotype's walk
 - Bubbles from `gfatools bubble` or the graph itself, opened level by level
-- gbz-base haplotypes as walks: carriage as node thickness, walks lifted out as
-  metro-map lanes or side by side, a panel per walk or a row per sample, each
-  shading from its start to its end
+- gbz-base haplotypes as walks: the number of walks through a node as its
+  thickness, walks lifted out as metro-map lanes or side by side, a panel per
+  walk or a row per sample, each shading from its start to its end
 - GAF reads in the tube map, with their mismatches, from a gbz-base track
 - Figures as SVG, from the view's Export SVG or from a JSON spec with no browser
   ([docs/figures.md](docs/figures.md))

package/dist/chunks/{GraphGenomeView-QOBHGMLE.js → GraphGenomeView-ZB4N6Q3H.js} RENAMED Viewed

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 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
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-`)}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 L(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=x(o),g=$(i);s.next(new l.SimpleFeature({uniqueId:i.id,refName:e.refName,start:i.start,end:i.end,name:i.id,type:"segment",rank:i.rank,stableName:i.refName,...g&&{samples:g,carriers:g.length}}))}})),s.complete()},a)}async getSubgraph(e,n={}){let{hops:a=0,signal:r,tier:s}=n,m=this.index(s),o=new Map,i=new Map,g=await m.refNames.resolve(e,{signal:r}),R=async(f,p,d)=>{let y=[];return await m.links.getLines(f,p,d,{signal:r,lineCallback:v=>{let c=A(v);i.set(I(c),c);for(let u of[c.sourceSegment,c.targetSegment])o.has(u.id)||(o.set(u.id,u),y.push(u))}}),y};if(g===void 0)throw new Error(`${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=x(f);o.set(p.id,p)}});let k=F(await R(g,e.start,e.end));for(let f=0;f<a;f++){let p=await Promise.all(k.map(d=>R(d.refName,d.start,d.end)));k=F(p.flat())}return T(o,i)}};export{N as default};
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+import{a as O,b as P,d as h,e as L}from"./chunk-KDIBFGZM.js";import"./chunk-KWAXLUPQ.js";import{a as B}from"./chunk-J4OLMLS5.js";import"./chunk-KULNKXPT.js";import{b as S}from"./chunk-FY3BTKY4.js";var F=S(O(),1),l=S(B(),1),M=S(P(),1);function x(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 $(t){let e=t.tags.split(" ").find(a=>a.startsWith("SM:Z:"));if(e===void 0)return;let n=e.slice(5).split(",").map(a=>a.trim()).filter(Boolean);return n.length>0?n:void 0}function w(t){return{id:t.slice(0,-1),strand:t.slice(-1)}}function A(t){let e=t.split("	"),n=w(e[3]),a=w(e[4]);return{source:n.id,sourceStrand:n.strand,target:a.id,targetStrand:a.strand,sourceSegment:{id:n.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:a.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function I(t){return`${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}	${r}	0M`}function b(t,e){return t<e?-1:t>e?1:0}function T(t,e){let n=[...t.values()].sort((r,s)=>b(r.refName,s.refName)||r.start-s.start||b(r.id,s.id)),a=[...e.keys()].sort((r,s)=>b(r,s));return["H	VN:Z:1.0",...n.map(r=>G(r)),...a.map(r=>Z(e.get(r)))].join(`
+`)}function C(t){return t.filter(e=>e.rank>0)}var N=class extends F.BaseFeatureDataAdapter{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,n,a){super(e,n,a),this.fine=this.openIndex([])}openIndex(e){let n=h(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]);return{segments:n,links:h(this,[...e,"linksLocation"],[...e,"linksIndex"]),refNames:new L(n,this)}}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async hasDataForRefName(){return!0}getFeatures(e,n={}){let{signal:a,statusCallback:r}=n;return(0,M.ObservableCreate)(async s=>{let m=await this.fine.refNames.resolve(e,n);m!==void 0&&await(0,l.updateStatus)("Downloading segments",r,()=>this.fine.segments.getLines(m,e.start,e.end,{signal:a,lineCallback:o=>{let i=x(o),g=$(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,sampleCount: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}),R=async(f,p,d)=>{let y=[];return await m.links.getLines(f,p,d,{signal:r,lineCallback:v=>{let c=A(v);i.set(I(c),c);for(let u of[c.sourceSegment,c.targetSegment])o.has(u.id)||(o.set(u.id,u),y.push(u))}}),y};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=x(f);o.set(p.id,p)}});let k=C(await R(g,e.start,e.end));for(let f=0;f<a;f++){let p=await Promise.all(k.map(d=>R(d.refName,d.start,d.end)));k=C(p.flat())}return T(o,i)}};export{N as default};
+//# sourceMappingURL=RgfaTabixAdapter-QPKEJZXA.js.map

package/dist/chunks/{RgfaTabixAdapter-5MD2ZZ2F.js.map → RgfaTabixAdapter-QPKEJZXA.js.map} RENAMED Viewed

@@ -1,7 +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}${link.targetStrand}`\n}\n\n// Both endpoints of a link are written into every row, so the same link is\n// indexed under each endpoint's stable sequence and arrives twice for a region\n// covering both. Callers dedupe on linkKey.\n\n// Segments carry no sequence here \u2014 the BED records only their span \u2014 so every\n// S-line is written with `*` and an LN tag, which is what the GFA spec asks for\n// and what packages/graph-core's parser reads back as the node length.\n// `NM:i:0`, `SM:Z:HG002.1,HG002.2` \u2014 the GFA tag grammar, checked rather than\n// trusted. Files built before the tag column existed put a bare comma-separated\n// sample list here, and passing that through would put a field that is not a\n// tag on an S-line, which is a malformed GFA rather than a missing annotation.\n// Dropping it degrades to the pre-tag behaviour instead.\nconst GFA_TAG = /^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/\n\nfunction formatSegment(segment: RgfaSegment) {\n  const { id, refName, start, end, rank, tags } = segment\n  const valid = tags.split(' ').filter(t => GFA_TAG.test(t))\n  const extra = valid.length === 0 ? '' : `\\t${valid.join('\\t')}`\n  return `S\\t${id}\\t*\\tLN:i:${end - start}\\tSN:Z:${refName}\\tSO:i:${start}\\tSR:i:${rank}${extra}`\n}\n\nfunction formatLink(link: RgfaLink) {\n  const { source, sourceStrand, target, targetStrand } = link\n  return `L\\t${source}\\t${sourceStrand}\\t${target}\\t${targetStrand}\\t0M`\n}\n\n// Codepoint order, not localeCompare: the byte-identical-output guarantee below\n// has to hold across locales.\nfunction compare(a: string, b: string) {\n  return a < b ? -1 : a > b ? 1 : 0\n}\n\n// Deterministic ordering: the same region always produces byte-identical GFA,\n// so a layout computed from it is reproducible.\nexport function formatSubgraph(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n) {\n  const sortedSegments = [...segments.values()].sort(\n    (a, b) =>\n      compare(a.refName, b.refName) || a.start - b.start || compare(a.id, b.id),\n  )\n  const sortedLinks = [...links.keys()].sort((a, b) => compare(a, b))\n  return [\n    'H\\tVN:Z:1.0',\n    ...sortedSegments.map(s => formatSegment(s)),\n    ...sortedLinks.map(k => formatLink(links.get(k)!)),\n  ].join('\\n')\n}\n"],
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+  "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` lists the haplotypes whose paths visit the segment and\n              // `sampleCount` counts them. A lane's color reads the count, and\n              // a count in jexl would otherwise rely on `.length` resolving\n              // through a member access on an array.\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, sampleCount: 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] ?? 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