jbrowse-plugin-graphgenomeviewer 5.0.0 → 5.1.0

package/README.md

@@ -104,7 +104,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
   Needs an index from `gbz-haplotype-index` 0.3 or later
 - gbz-base swaps in `{ "type": "GbzBaseSyntenyAdapter", "uri": "….gbz.db" }`; an
   `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
-  `assemblyNameToPanSN` covers other names
+  `assemblyNameToPanSN` covers other names. A haplotype's lane draws on the
+  assembly aliased by its PanSN name (`HG002#1`) with no map entry
 - `"reads": "….gaf.gz"` on that adapter draws GAF reads in the tube map layouts,
   fetched through its tabix index; [docs/layouts.md](docs/layouts.md#reads) has
   the config and how to make one

package/dist/chunks/{GbzBaseSyntenyAdapter-CKKVHC2R.js → GbzBaseSyntenyAdapter-C2IGNBR4.js}

@@ -1,4 +1,4 @@
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i={start:e.get("start"),end:e.get("end")},a=e.get("strand")===-1?-1:1,s=i.start>=t.start&&i.end<=t.end,p=s&&o===void 0&&!n?void 0:ot(e);if(p===void 0){let f=s?{...i,mateStart:r.start,mateEnd:r.end}:fo(i,r,a,t);return f===void 0?[]:[f]}else return(o===void 0?[{...i,mateStart:r.start,mateEnd:r.end,cigar:p}]:rt(p,i.start,r.start,r.end,a,o)).flatMap(c=>{let l=tt(c.cigar,c.start,c.mateStart,c.mateEnd,a,t.start,t.end);return l===void 0?[]:[l]})}function co(e,r,t,o,n,i){let a=`:${o.start}-${o.end}${n}`,s=e.toJSON(),p={...s,uniqueId:`${e.id()}${a}`,start:t.start,end:t.end,mate:{...r,start:t.mateStart,end:t.mateEnd}};s.syntenyId!==void 0&&(p.syntenyId=`${String(s.syntenyId)}${a}`);for(let f of io)delete p[f];return i&&t.cigar&&(p.alignmentOps=t.cigar),new L(p)}function xr(e,r,t,o=!1){let n=so(e);if(n===void 0)return[e];{let i=po(e,n,r,t,o);return i.map((a,s)=>co(e,n,a,r,i.length>1?`/${s}`:"",o))}}var Re=class extends yr.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,o={}){let{clipToRegion:n,splitAtGapBp:i,keepAlignment:a,...s}=o,p=n&&this.recordsAreAlignments,f=(0,gr.createStatusFanOut)(s.statusCallback);return Ye(t).pipe(W((c,l)=>this.getFeatures(c,{...s,statusCallback:f()}).pipe(W(u=>p?xr(u,u.get("assemblyName")===c.assemblyName?c:{start:u.get("start"),end:u.get("end")},i,a):[u]),Ae(),X(u=>({index:l,features:u})))),Ae(),W(c=>c.sort((l,u)=>l.index-u.index).flatMap(l=>l.features)))}};var Me=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},ft=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},Fe=class extends Error{constructor(t,o){super(`the graph is cut on its reference, ${o}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${o} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function nt(e,r){let t=T(r);return e[t]??e[r.sample]??t}function lo(e,r){return`${T(e)}#${e.contig}@${r.start.node}.${r.start.offset}`}function uo({alignment:e,assemblyName:r,refName:t,lane:o}){let{refStart:n,refEnd:i,strand:a,cigar:s}=e;if(!(!e.resolved||i<=n)){let{name:p,hapStart:f,hapEnd:c}=e,l=lo(p,e),u={uniqueId:l,assemblyName:r,refName:t,start:n,end:i,type:"match",strand:a==="-"?-1:1,CIGAR:s,syntenyId:l,mate:{refName:p.contig,start:f,end:c,assemblyName:o}};return new L(u)}}function mo({pair:e,lane:r,mateLane:t}){let o=`${T(e.target)}#${e.target.contig}:${e.targetStart}-${e.targetEnd}|${T(e.query)}#${e.query.contig}:${e.queryStart}-${e.queryEnd}`;return new L({uniqueId:o,assemblyName:r,refName:e.target.contig,start:e.targetStart,end:e.targetEnd,type:"match",strand:e.strand==="-"?-1:1,CIGAR:e.cigar,syntenyId:o,identity:e.matches/Math.max(e.columns,1),numMatches:e.matches,blockLen:e.columns,mate:{refName:e.query.contig,start:e.queryStart,end:e.queryEnd,assemblyName:t}})}function ho(e,r,t){let o=re(e,r,t);return o&&(o.message+="; the track's Graph display draws every haplotype's overview at any size"),o}var it=e=>!("uri"in e)||e.uri!=="",pt=class extends Re{constructor(){super(...arguments);this.graph=(0,at.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),o=this.getConf("haplotypeIndexLocation"),n=it(o)?{location:o}:await Ct(t,this.pluginManager),i=n.location,a=await dt.open({source:(0,Te.openLocation)(t,this.pluginManager),haplotypeIndex:i?(0,Te.openLocation)(i,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let p=await Le(a),f=te({configured:this.getConf("referenceSample"),anchorPrefix:k(this,s),referenceSamples:p});return{db:a,anchor:s,referenceSample:f,referenceSamples:p,unreadableIndex:n.unreadable}}});this.gaf=(0,at.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),o=this.getConf(["readsIndex","location"]);return it(t)?new oe((0,Te.openLocation)(t,this.pluginManager),it(o)?wt(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,o){let{db:n,referenceSample:i}=await this.graph(o);return Ne(n,i,t)}async getHaplotypes(t={}){let{db:o,referenceSamples:n}=await this.graph(t),i=new Map;for(let a of await o.paths()){let s=T(a.name),p=i.get(s);p?p.contigs.includes(a.name.contig)||p.contigs.push(a.name.contig):i.set(s,{prefix:s,sample:a.name.sample,haplotype:a.name.haplotype,contigs:[a.name.contig],isReference:n.includes(a.name.sample)})}return[...i.values()]}async getHeader(t={}){let{anchor:o,referenceSample:n,referenceSamples:i}=await this.graph(t),a=ee(this),s=[];for(let p of await this.getHaplotypes(t))p.sample!==n&&s.push({name:nt(a,p),label:p.prefix,group:p.sample});return{hasCoarseTier:!1,anchorAssemblyName:o,referenceSample:n,referenceSamples:i,lanes:s}}async getRefNames(t={}){let{db:o,anchor:n,referenceSample:i}=await this.graph(t),{assemblyName:a}=t,s=a===n?void 0:k(this,a),p=(await o.paths()).filter(f=>a===n?f.isIndexed&&f.name.sample===i:V(T(f.name),s)).map(f=>f.name.contig);return[...new Set(p)]}keepPredicate(t,o){let n=t===void 0||t.length===0?void 0:t.map(i=>k(this,i));return n===void 0&&o===void 0?void 0:i=>Pe(i,n)&&(o===void 0||V(T(i),o))}async getSubgraph(t,o={}){let{db:n,anchor:i,unreadableIndex:a}=await this.graph(),{assemblyName:s,refName:p,start:f,end:c}=t;if(s!==i)throw new Fe(s,i);let l=await this.referenceQuery(p,{}),u=this.keepPredicate(o.haplotypes);if(u!==void 0&&!n.hasHaplotypeIndex)throw new Me(a);return Ge(n,l,f,c,{context:this.getConf("context"),snarls:o.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:o.signal,keep:u})}async getOverview(t,o){let{db:n,anchor:i,referenceSample:a}=await this.graph(),{assemblyName:s,refName:p,start:f,end:c}=t;if(s!==i)throw new Fe(s,i);let l=await this.referenceQuery(p,{}),u=l?await n.haplotypeOverview({path:l,start:f,end:c,bpPerPixel:o.bpPerPx}):void 0;if(!u)return;let m=ee(this),y=u.haplotypes.map(h=>T(h)),d=new Set;for(let h of o.haplotypes??[]){let g=k(this,h);y.forEach((x,S)=>{V(x,g)&&d.add(S)})}return{level:u.level,bin:u.bin,rows:u.haplotypes.map(h=>nt(m,h)),pinned:[...d],reference:u.haplotypes.flatMap((h,g)=>h.sample===a?[g]:[]),bins:u.bins,cells:u.cells}}async getReads(t,o={}){let n=await this.gaf(o);return n?n.readsOver(new Set(t),o):{records:[],total:0}}async laneHaplotypes(t,o){let n=k(this,t);return(await this.getHaplotypes(o)).filter(i=>V(i.prefix,n))}async anchorFeatures(t,o){let{db:n}=await this.graph(o),{assemblyName:i,refName:a,start:s,end:p}=t,f=k(this,o.targetAssemblyName),c=ee(this),l=this.keepPredicate(o.haplotypes,f),u=await this.referenceQuery(a,o),m=this.getConf("nodeLimit");return(u?await(0,st.updateStatus)(`Reading graph ${a}:${s.toLocaleString()}-${p.toLocaleString()}`,o.statusCallback,()=>n.getAlignments({path:u,start:s,end:p,context:this.getConf("context"),haplotypes:"all",limit:m,signal:o.signal,keep:l}).catch(d=>{throw ho(d,m,p-s)??d})):[]).flatMap(d=>{let h=d.resolved?uo({alignment:d,assemblyName:i,refName:a,lane:nt(c,d.name)}):void 0;return h===void 0?[]:[h]})}async pairFeatures(t,o,n){let{targetAssemblyName:i}=n;if(i===void 0)throw new ft(o);let{db:a}=await this.graph(n),{refName:s,start:p,end:f}=t,c=await this.laneHaplotypes(o,n),l=await this.laneHaplotypes(i,n),u=[...c,...l],m=await this.referenceQuery(s,n),y=this.getConf("nodeLimit"),d=g=>a.getSubgraphs({path:g,start:p,end:f,context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:n.signal,keep:x=>u.some(S=>S.sample===x.sample&&S.haplotype===x.haplotype)}).catch(x=>{throw re(x,y,f-p)??x});return(m&&c.length>0&&l.length>0?await(0,st.updateStatus)(`Reading ${o} against ${i}`,n.statusCallback,()=>d(m)):[]).flatMap(g=>c.flatMap(x=>l.flatMap(S=>g.pairAlignments({target:x,query:S,bases:!1}).map(v=>mo({pair:v,lane:o,mateLane:i})))))}getFeatures(t,o={}){return(0,br.ObservableCreate)(async n=>{let{db:i,anchor:a,unreadableIndex:s}=await this.graph(o);if(!i.hasHaplotypeIndex)throw new Me(s);if(t.assemblyName===a){let p=o.queryAssemblyName===void 0?await this.anchorFeatures(t,o):await this.pairFeatures(t,o.queryAssemblyName,o);for(let f of p)n.next(f)}n.complete()},o.signal)}};export{Fe as HaplotypeWindowError,Me as NoHaplotypeIndexError,vr as NoReferenceSampleError,wr as NodeLimitError,ft as PairTargetError,pt as default,uo as fragmentFeature,T as haplotypePrefix,nt as laneAssemblyName,re as nodeLimitError,mo as pairFeature,te as resolveReferenceSample};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-CKKVHC2R.js.map
+//# sourceMappingURL=GbzBaseSyntenyAdapter-C2IGNBR4.js.map

package/dist/chunks/{GraphGenomeView-YYP4IFSI.js → GraphGenomeView-TKK67NXR.js}

@@ -1,4 +1,4 @@
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+//# sourceMappingURL=GraphGenomeView-TKK67NXR.js.map

package/dist/chunks/{GraphTrackSettingsDialog-2WPJRAJC.js → GraphTrackSettingsDialog-RKZ5XIKY.js}

@@ -1,4 +1,4 @@
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package/dist/chunks/{LinearGraphDisplay-7YE624D5.js → LinearGraphDisplay-I2DJRM36.js}

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package/dist/chunks/RgfaTabixAdapter-LQGQXCVO.js

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package/dist/chunks/RgfaTabixAdapter-LQGQXCVO.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  closingLinks,\n  closingSpans,\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. After the last round, one more read\n  // per stretch of stable sequence the cut holds closes it (closingSpans), so\n  // an allele reached from both ends draws whole. The view asks for one hop; a\n  // hopless cut stays as cheap as it was. `signal` goes to every one of those\n  // 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    if (hops > 0) {\n      const spans = closingSpans(\n        [...segments.values()],\n        new Set(frontier.map(segment => segment.id)),\n        { refName: tabixRefName, start: region.start, end: region.end },\n      )\n      const found: RgfaLink[] = []\n      await Promise.all(\n        spans.map(span =>\n          index.links.getLines(span.refName, span.start, span.end, {\n            signal,\n            lineCallback: line => {\n              found.push(parseLinkLine(line))\n            },\n          }),\n        ),\n      )\n      for (const link of closingLinks(found, segments, spans)) {\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          }\n        }\n      }\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\nexport interface StableSpan {\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a cut reads links once more to close itself. A hop reads the links of\n// the segments the round before it reached, so a link between two segments of\n// the last round is never read and an allele reached from both ends draws as\n// two stubs. rGFA lays an allele out as one stretch of the stable sequence that\n// introduced it, so pieces of one sequence within the window's length of each\n// other merge into a span, and reading it brings the pieces between too.\n// Backbone reached past the window is unread for the same reason; its spans\n// join only abutting pieces, since the reference past the window is not the\n// cut's to fill. A span whose segments were all read and abut is skipped.\nexport function closingSpans(\n  held: RgfaSegment[],\n  unread: Set<string>,\n  window: StableSpan,\n) {\n  const outside = (segment: RgfaSegment) =>\n    segment.refName !== window.refName ||\n    segment.end <= window.start ||\n    segment.start >= window.end\n  return [\n    ...mergedSpans(\n      held.filter(segment => segment.rank > 0),\n      unread,\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      new Set(held.map(segment => segment.id)),\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  unread: Set<string>,\n  maxGap: number,\n) {\n  const sorted = [...segments].sort(\n    (a, b) => compare(a.refName, b.refName) || a.start - b.start,\n  )\n  const spans: (StableSpan & { needed: boolean })[] = []\n  for (const segment of sorted) {\n    const span = spans.at(-1)\n    if (\n      span?.refName === segment.refName &&\n      segment.start - span.end <= maxGap\n    ) {\n      span.needed ||= segment.start > span.end || unread.has(segment.id)\n      span.end = Math.max(span.end, segment.end)\n    } else {\n      spans.push({\n        refName: segment.refName,\n        start: segment.start,\n        end: segment.end,\n        needed: unread.has(segment.id),\n      })\n    }\n  }\n  return spans\n    .filter(span => span.needed)\n    .map(({ refName, start, end }): StableSpan => ({ refName, start, end }))\n}\n\n// The links a closing read keeps: each end is a segment the cut holds or one\n// lying inside a span. Following anything else is what another hop is for.\nexport function closingLinks(\n  found: RgfaLink[],\n  held: Map<string, RgfaSegment>,\n  spans: StableSpan[],\n) {\n  const inside = (segment: RgfaSegment) =>\n    held.has(segment.id) ||\n    spans.some(\n      span =>\n        span.refName === segment.refName &&\n        segment.start >= span.start &&\n        segment.end <= span.end,\n    )\n  return found.filter(\n    link => inside(link.sourceSegment) && inside(link.targetSegment),\n  )\n}\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"],
+  "mappings": 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