jbrowse-plugin-graphgenomeviewer 6.10.0 → 6.11.0

package/README.md

@@ -97,7 +97,8 @@ Needs JBrowse 5.0.0-beta.11 or later.
 ```
 
 - The track menu picks layout, colour and highlighted haplotypes, and switches
-  to the segments lane or, for gbz-base, the haplotype lanes
+  to the segments lane or, for gbz-base and walk-indexed graphs, the haplotype
+  lanes
 - Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
   `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)
 - Past the cut (5 Mb, or a gbz-base adapter's `nodeLimit`) the track asks you to
@@ -107,9 +108,12 @@ Needs JBrowse 5.0.0-beta.11 or later.
   `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
   `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
+- A walk-indexed graph (`gfa-to-tabix --walks`) swaps in
+  `{ "type": "WalkTabixSyntenyAdapter", "walksUri": "….GRCh38", "assemblyNames": ["hg38"] }`
+  and draws the same haplotype lanes from the walk files, with no database
+- `"reads": "….gaf.gz"` on the gbz-base 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
 
 ## Docs
 

package/dist/chunks/AddTrackWorkflow-WS3KWZRK.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-WS3KWZRK.js.map

package/dist/chunks/{AddTrackWorkflow-OBRE3QJE.js.map → AddTrackWorkflow-WS3KWZRK.js.map}

@@ -2,6 +2,6 @@
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 }

package/dist/chunks/GbzBaseSyntenyAdapter-SPT62NR4.js

@@ -0,0 +1,2 @@
+import{b as J,c as K,d as q,e as ne,f as me,g as ae}from"./chunk-KROCIQJP.js";import{b as G,c as V,d as ee,e as te}from"./chunk-X4NNWAXW.js";import{a as O,b as H}from"./chunk-NU53CDGF.js";import{f as le,g as Z,h,i as B,j as z,k as R,l as M,m as k,o as E}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as F,f as S,g as C}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import{b as U,c as X,d as Y}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function de(n){return X(n)&&A(U(n))?Y(n,i=>A(i)):void 0}function fe(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function re(n,i){let t=de(n);if(!t)return{};try{return await P(t,i).stat(),{location:t}}catch(e){return fe(e)?{}:{unreadable:String(e)}}}var he=5e3,ue=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ge(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var oe=(n,i)=>n.path.some(t=>i.has(t.name)),I=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=G({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new T(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&oe(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>oe(a,i));return{records:ge(e,he),total:e.length}}};var v=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function se(n,i){let t=h(i);return n[t]??n[i.sample]??t}function ye(n,i){return`${h(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function be({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(!n.resolved||r<=a)){let{name:s,hapStart:p,hapEnd:m}=n,u=ye(s,n),g={uniqueId:u,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:u,mate:{refName:s.contig,start:p,end:m,assemblyName:e}};return new q(g)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${h(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${h(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var we=12e4;function Se(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=h(r);if(i.has(s)){let p=`${s}#${r.contig}`;t.set(p,[...t.get(p)??[],[o,c]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=we&&(e=Math.max(e,o))}}return e}function _(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var Q=n=>!("uri"in n)||n.uri!=="",j=class extends ne{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=Q(e)?{location:e}:await re(t,this.pluginManager),r=a.location,o=await K.open({source:P(t,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await z(o),p=R({configured:this.getConf("referenceSample"),anchorPrefix:S(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return Q(t)?new I(P(t,this.pluginManager),Q(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return M(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let c=h(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(t),o=C(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:se(o,s),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:S(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(h(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>S(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||F(h(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:m,start:u,end:g}=t;if(p!==o)throw new D(p,o);let y=await this.referenceQuery(m,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${m} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(s);return E(r,y,u,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(d=>{throw _(d,"the graph")})}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=S(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=S(this,e.targetAssemblyName),m=C(this),u=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:u}).catch(d=>{throw _(k(d,y,s-c)??d,"lanes")})):[]).flatMap(d=>{let N=d.resolved?be({alignment:d,assemblyName:r,refName:o,lane:se(m,d.name)}):void 0;return N===void 0?[]:[N]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,m=(await Promise.all(e.map(async l=>({pair:l,featureSide:await this.laneHaplotypes(l.queryAssemblyName,a),mateSide:await this.laneHaplotypes(l.targetAssemblyName,a)})))).filter(({featureSide:l,mateSide:f})=>l.length>0&&f.length>0),u=new Set(m.flatMap(({featureSide:l,mateSide:f})=>[...l,...f].map(h))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[d]=e,N=(l,f)=>r.getSubgraphs({path:l,start:c,end:s,context:f,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:w=>u.has(h(w))}),ie=async l=>{let f=await N(l,x).catch(b=>{throw _(k(b,y,s-c)??b,"lanes")}),w=Se(f,u),L=Math.ceil(w/2)+2e3;return w>0&&L>x?N(l,L).catch(b=>{if(b instanceof J)return f;throw b}):f};return(g&&d&&m.length>0?await $(e.length===1?`Reading ${d.queryAssemblyName} against ${d.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>ie(g)):[]).flatMap(l=>m.flatMap(({pair:f,featureSide:w,mateSide:L})=>w.flatMap(b=>L.flatMap(ce=>l.pairAlignments({target:b,query:ce,bases:!1}).map(pe=>xe({pair:pe,lane:f.queryAssemblyName,mateLane:f.targetAssemblyName}))))))}getFeatures(t,e={}){return V(async a=>{let{db:r,anchor:o,unreadableIndex:c}=await this.graph(e);if(!r.hasHaplotypeIndex)throw new v(c);if(t.assemblyName===o){let s=ae(e),p=s.length>0?await this.pairFeatures(t,s,e):await this.anchorFeatures(t,e);for(let m of p)a.next(m)}a.complete()},e.signal)}};export{D as HaplotypeWindowError,v as NoHaplotypeIndexError,le as NoReferenceSampleError,me as PairTargetError,j as default,be as fragmentFeature,se as laneAssemblyName,xe as pairFeature,R as resolveReferenceSample,Se as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-SPT62NR4.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-SPT62NR4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.1.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-73RSLGZT.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample\n} from \"./chunk-LTUWJKHD.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  return { refName: m[1], start: n(m[2]), end: n(m[3]) };\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowGFA,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport {\n  NoReferenceSampleError,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? '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'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\nexport interface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\nexport interface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\nexport type { LanePair } from '../synteny/lanePairs.ts'\nexport type GbzFeatureOptions = LaneFeatureOptions\n\nexport class HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix. The fallback stays at\n * haplotype depth, unlike the multi-genome PAF adapters', because a diploid\n * sample's two walks are two lanes here.\n */\nexport function laneAssemblyName(\n  asmByPrefix: Record<string, string>,\n  name: Pick<PathName, 'sample' | 'haplotype'>,\n) {\n  const prefix = haplotypePrefix(name)\n  return asmByPrefix[prefix] ?? asmByPrefix[name.sample] ?? prefix\n}\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: HaplotypeAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: HaplotypeAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (!alignment.resolved || refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${haplotypePrefix(pair.target)}#${pair.target.contig}:${pair.targetStart}-${pair.targetEnd}|${haplotypePrefix(pair.query)}#${pair.query.contig}:${pair.queryStart}-${pair.queryEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName: lane,\n    refName: pair.target.contig,\n    start: pair.targetStart,\n    end: pair.targetEnd,\n    type: 'match',\n    strand: pair.strand === '-' ? -1 : 1,\n    CIGAR: pair.cigar,\n    syntenyId: id,\n    identity: pair.matches / Math.max(pair.columns, 1),\n    numMatches: pair.matches,\n    blockLen: pair.columns,\n    mate: {\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n      assemblyName: mateLane,\n    },\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        byPath.set(key, [...(byPath.get(key) ?? []), [start, end]])\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\nconst isSet = (location: FileLocation) =>\n  !('uri' in location) || location.uri !== ''\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = isSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample, referenceSamples } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSample,\n      referenceSamples,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window: the reference walk, every top-level\n   * snarl contained in it, and one W line per haplotype walk, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first W line, which is\n   * the one the view anchors on by default. With `haplotypes` the W lines are\n   * that set's and the nodes those walks visit, the reference walk kept.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = region\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    return cutWindowGFA(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return isSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            isSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: GbzFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw zoomInNotice(\n                  nodeLimitError(error, nodeLimit, end - start) ?? error,\n                  'lanes',\n                )\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(asmByPrefix, alignment.name),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: GbzFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const [first] = pairs\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw zoomInNotice(\n          nodeLimitError(error, nodeLimit, end - start) ?? error,\n          'lanes',\n        )\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && first && answerable.length > 0\n        ? await updateStatus(\n            pairs.length === 1\n              ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n              : `Reading ${pairs.length} lane pairs`,\n            opts.statusCallback,\n            () => bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(region: Region, opts: GbzFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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+  "names": ["haplotypeIndexBeside", "db", "GBZ_DB", "siblingCompanion", "gbzDb", "readsSiblings", "haplotypeIndexBeside", "locationName", "renamed", "name", "isMissing", "error", "findCompanion", "pluginManager", "candidate", "openLocation", "MAX_READS", "MAX_UNINDEXED_BYTES", "UnindexedGafTooLargeError", "size", "sample", "records", "max", "stride", "_", "k", "touches", "record", "names", "step", "GafFile", "file", "tabix", "cachedSetup", "signal", "bytes", "text", "unzip", "parseGaf", "lo", "hi", "name", "id", "line", "parseGafLine", "r", "NoHaplotypeIndexError", "unreadable", "HaplotypeWindowError", "assemblyName", "anchor", "laneAssemblyName", "asmByPrefix", "name", "prefix", "haplotypePrefix", "fragmentId", "alignment", "fragmentFeature", "refName", "lane", "refStart", "refEnd", "strand", "cigar", "hapStart", "hapEnd", "id", "data", "SyntenyFeature", "pairFeature", "pair", "mateLane", "BRIDGE_MAX_BP", "widestWalkGap", "subgraphs", "kept", "byPath", "subgraph", "start", "end", "key", "widest", "spans", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "isSet", "location", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "assemblyByPanSNPrefix", "lanes", "haplotype", "contigs", "panSNMatchesPrefix", "haplotypes", "targetPrefix", "wantedPrefixes", "haplotypeWanted", "region", "signal", "unreadableIndex", "query", "keep", "cutWindowGFA", "nodeNames", "gaf", "nodeLimit", "updateStatus", "nodeLimitError", "feature", "pairs", "answerable", "featureSide", "mateSide", "baseContext", "first", "cut", "context", "bridged", "SubgraphLimitError", "target", "mate", "ObservableCreate", "observer", "requestedPairs", "features"]
+}

package/dist/chunks/{GraphTrackSettingsDialog-F3YNSD54.js → GraphTrackSettingsDialog-IRX4NTT5.js}

@@ -1,6 +1,6 @@
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-//# sourceMappingURL=GraphTrackSettingsDialog-F3YNSD54.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-IRX4NTT5.js.map

package/dist/chunks/RgfaTabixAdapter-5ZRSJMIP.js

@@ -0,0 +1,3 @@
+import{a as u,b as v,c as P}from"./chunk-TVXMEJLJ.js";import{a as B,c as F,e as N,f as I}from"./chunk-X4NNWAXW.js";import"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{c as A,f as M}from"./chunk-XKN5LH2Z.js";import{a as $,o as T}from"./chunk-TENPGIPX.js";function y(i){let e=i.split("	"),a=e.length>=8,s=a?5:0;return{anchored:a,segment:{refName:e[s],start:+e[s+1],end:+e[s+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function j(i){let e=i.tags.split(" ").find(s=>s.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(s=>s.trim()).filter(Boolean);return a.length>0?a:void 0}function O(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function x(i){let e=i.split("	"),a=O(e[3]),s=O(e[4]);return{source:a.id,sourceStrand:a.strand,target:s.id,targetStrand:s.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:s.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let s=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),r=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||s(n.sourceSegment)*s(n.targetSegment)===-1){r.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&r.set(S(n),n);return{segments:t,links:r}}function W(i,e,a){let s=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...G(i.filter(t=>t.rank>0),e,a.end-a.start),...G(i.filter(t=>t.rank===0&&s(t)),new Set(i.map(t=>t.id)),0)]}function G(i,e,a){let s=[...i].sort((r,n)=>R(r.refName,n.refName)||r.start-n.start),t=[];for(let r of s){let n=t.at(-1);n?.refName===r.refName&&r.start-n.end<=a?(n.needed||=r.start>n.end||e.has(r.id),n.end=Math.max(n.end,r.end)):t.push({refName:r.refName,start:r.start,end:r.end,needed:e.has(r.id)})}return t.filter(r=>r.needed).map(({refName:r,start:n,end:o})=>({refName:r,start:n,end:o}))}function H(i,e,a){let s=t=>e.has(t.id)||a.some(r=>r.refName===t.refName&&t.start>=r.start&&t.end<=r.end);return i.filter(t=>s(t.sourceSegment)&&s(t.targetSegment))}var E=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function K(i){let{id:e,refName:a,start:s,end:t,rank:r,tags:n}=i,o=n.split(" ").filter(f=>E.test(f)),c=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-s}	SN:Z:${a}	SO:i:${s}	SR:i:${r}${c}`}function z(i){let{source:e,sourceStrand:a,target:s,targetStrand:t}=i;return`L	${e}	${a}	${s}	${t}	0M`}function R(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,r)=>R(t.refName,r.refName)||t.start-r.start||R(t.id,r.id)),s=[...e.keys()].sort((t,r)=>R(t,r));return["H	VN:Z:1.0",...a.map(t=>K(t)),...s.map(t=>z(e.get(t)))].join(`
+`)}function _(i){return i.filter(e=>e.rank>0)}var J=1e3,C=class extends B{static{this.capabilities=["getFeatures","getRefNames"]}constructor(e,a,s){super(e,a,s),this.fine=this.openIndex([])}openIndex(e){let a=N(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=this.getConf("walksLocation"),t=e.length===0&&(!("uri"in s)||s.uri!==""),r=N(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:r,walks:t?new P({walks:N(this,["walksLocation"],["walksIndex"]),nodes:a,links:r},this.getConf("walkChunk")):void 0,refNames:new I(a,this)}}async getHaplotypeNames(e={}){let a=await this.fine.walks?.header(e);return a?.haplotypes.length?a.haplotypes:void 0}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,a={}){let{signal:s,statusCallback:t}=a;return F(async r=>{let n=await this.fine.refNames.resolve(e,a);if(n!==void 0){let o=this.fine.walks?await this.fine.walks.queryStart(e.start,a):e.start;await T("Downloading segments",t,()=>u(this.fine.segments,n,o,e.end,{signal:s,lineCallback:c=>{let{segment:f,anchored:h}=y(c);if(h&&f.refName!==n)return;let l=j(f);r.next(new $({uniqueId:f.id,refName:e.refName,start:f.start,end:f.end,name:f.id,type:"segment",rank:f.rank,stableName:f.refName,...l&&{samples:l,sampleCount:l.length}}))}}))}r.complete()},s)}async getSubgraph(e,a={}){let{hops:s=0,signal:t,tier:r}=a,n=this.index(r),o=new Map,c=new Map,f=await n.refNames.resolve(e,{signal:t}),h=async(p,m,g)=>{let d=[];return await u(n.links,p,m,g,{signal:t,lineCallback:D=>{let k=x(D);c.set(S(k),k);for(let b of[k.sourceSegment,k.targetSegment])o.has(b.id)||(o.set(b.id,b),d.push(b))}}),d};if(f===void 0)throw new Error(`${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`);if(n.walks)return this.walkSubgraph(n.walks,f,e,a);let l={anchored:!1};if(await u(n.segments,f,e.start,e.end,{signal:t,lineCallback:p=>{let m=y(p);l.anchored||=m.anchored,o.set(m.segment.id,m.segment)}}),l.anchored){let p=[];await u(n.links,f,e.start,e.end,{signal:t,lineCallback:g=>{p.push(x(g))}});let m=Z(o,p,{refName:f,start:e.start,end:e.end});return L(m.segments,m.links)}let w=_(await h(f,e.start,e.end));for(let p=0;p<s;p++){let m=await Promise.all(w.map(g=>h(g.refName,g.start,g.end)));w=_(m.flat())}if(s>0){let p=W([...o.values()],new Set(w.map(g=>g.id)),{refName:f,start:e.start,end:e.end}),m=[];await Promise.all(p.map(g=>u(n.links,g.refName,g.start,g.end,{signal:t,lineCallback:d=>{m.push(x(d))}})));for(let g of H(m,o,p)){c.set(S(g),g);for(let d of[g.sourceSegment,g.targetSegment])o.has(d.id)||o.set(d.id,d)}}return L(o,c)}async walkSubgraph(e,a,s,t){let{graph:r,kept:n,fragments:o}=await e.cut(a,s,{signal:t.signal,keep:v(t.haplotypes?.map(c=>M(this,c)),A(a)),stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:J});return r.tables(n,o)}};export{C as default};
+//# sourceMappingURL=RgfaTabixAdapter-5ZRSJMIP.js.map

package/dist/chunks/RgfaTabixAdapter-5ZRSJMIP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/rgfaBed.ts", "../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts"],
+  "sourcesContent": ["// 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  return parseSegmentRow(line).segment\n}\n\n// gfa-to-tabix's anchored layout files a segment under the reference interval\n// its bubble hangs from and states the segment's own coordinate after the rank:\n// `anchorName anchorStart anchorEnd segmentId rank stableName start end [tags]`.\n// One query over a region then returns every segment of every bubble under it,\n// and `anchored` tells a cut it has nothing left to follow.\nexport function parseSegmentRow(line: string) {\n  const cols = line.split('\\t')\n  const anchored = cols.length >= 8\n  const own = anchored ? 5 : 0\n  return {\n    anchored,\n    segment: {\n      refName: cols[own]!,\n      start: +cols[own + 1]!,\n      end: +cols[own + 2]!,\n      id: cols[3]!,\n      rank: +cols[4]!,\n      tags: cols[anchored ? 8 : 5] ?? '',\n    } satisfies RgfaSegment,\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// The cut an anchored index gives: `under` is what the segment file returned\n// for the window, every segment of every bubble under it, and `found` is what\n// the link file returned. gfa-to-tabix files a link widely enough that `found`\n// holds every link touching a segment in `under` and every link between the\n// segments those lead to, plus links of neither kind, which are dropped here.\n// A backbone link that jumps the whole window, as a deletion or inversion\n// spanning it does, touches nothing in `under` and is kept by its own rule.\nexport function anchoredCut(\n  under: Map<string, RgfaSegment>,\n  found: RgfaLink[],\n  window: StableSpan,\n) {\n  const side = (segment: RgfaSegment) =>\n    segment.rank !== 0 || segment.refName !== window.refName\n      ? 0\n      : segment.end <= window.start\n        ? -1\n        : segment.start >= window.end\n          ? 1\n          : 0\n  const segments = new Map(under)\n  const links = new Map<string, RgfaLink>()\n  for (const link of found) {\n    if (\n      under.has(link.source) ||\n      under.has(link.target) ||\n      side(link.sourceSegment) * side(link.targetSegment) === -1\n    ) {\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  for (const link of found) {\n    if (segments.has(link.source) && segments.has(link.target)) {\n      links.set(linkKey(link), link)\n    }\n  }\n  return { segments, links }\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", "import { panSNHaplotype, resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { 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  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentRow,\n  segmentSamples,\n} from './rgfaBed.ts'\nimport { getLines } from './tabixRange.ts'\nimport { WalkReader } from './walkReader.ts'\nimport { walkNameFilter } from './walkRows.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 { GraphTables } from '@jbrowse/bandage-core/gfa/graphTables'\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 { FileLocation, 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  walks?: WalkReader\n  refNames: PanSNRefNames\n}\n\n// How much graph a walk cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\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    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const hasWalks =\n      under.length === 0 &&\n      (!('uri' in walksLocation) || walksLocation.uri !== '')\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    return {\n      segments,\n      links,\n      walks: hasWalks\n        ? new WalkReader(\n            {\n              walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n              nodes: segments,\n              links,\n            },\n            this.getConf('walkChunk'),\n          )\n        : undefined,\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const header = await this.fine.walks?.header(opts)\n    return header?.haplotypes.length ? header.haplotypes : undefined\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        // a walk-indexed node row names only its chunk's first base, and a\n        // node crossing in from a chunk before is filed there\n        const start = this.fine.walks\n          ? await this.fine.walks.queryStart(query.start, opts)\n          : query.start\n        await updateStatus('Downloading segments', statusCallback, () =>\n          getLines(this.fine.segments, tabixRefName, start, query.end, {\n            signal,\n            lineCallback: line => {\n              const { segment, anchored } = parseSegmentRow(line)\n              // An anchored index also returns the alleles under the region,\n              // which lie on other stable sequences and have no place on this\n              // one.\n              if (anchored && segment.refName !== tabixRefName) {\n                return\n              }\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 for GraphGenomeView: GFA text, or a\n  // walk-indexed graph's tables (walkSubgraph). 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(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | GraphTables> {\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 getLines(index.links, 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    if (index.walks) {\n      return this.walkSubgraph(index.walks, tabixRefName, region, opts)\n    }\n    const layout = { anchored: false }\n    await getLines(index.segments, tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const row = parseSegmentRow(line)\n        layout.anchored ||= row.anchored\n        segments.set(row.segment.id, row.segment)\n      },\n    })\n    // An anchored index files every allele and every link under the reference\n    // interval its bubble hangs from, so one read of each file holds the whole\n    // graph under the region and there is nothing to hop to or close.\n    if (layout.anchored) {\n      const found: RgfaLink[] = []\n      await getLines(index.links, tabixRefName, region.start, region.end, {\n        signal,\n        lineCallback: line => {\n          found.push(parseLinkLine(line))\n        },\n      })\n      const cut = anchoredCut(segments, found, {\n        refName: tabixRefName,\n        start: region.start,\n        end: region.end,\n      })\n      return formatSubgraph(cut.segments, cut.links)\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          getLines(index.links, 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  // Only the walks `haplotypes` asks for, and the reference's, are decoded\n  private async walkSubgraph(\n    walks: WalkReader,\n    refName: string,\n    region: Region,\n    opts: SubgraphAdapterOptions,\n  ) {\n    const { graph, kept, fragments } = await walks.cut(refName, region, {\n      signal: opts.signal,\n      keep: walkNameFilter(\n        opts.haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        panSNHaplotype(refName),\n      ),\n      stepBudget: this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      context: WALK_CONTEXT,\n    })\n    return graph.tables(kept, fragments)\n  }\n}\n"],
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+  "names": ["parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "anchoredCut", "under", "found", "window", "side", "segments", "links", "closingSpans", "held", "unread", "outside", "mergedSpans", "maxGap", "sorted", "a", "b", "compare", "spans", "span", "refName", "start", "end", "closingLinks", "inside", "GFA_TAG", "formatSegment", "id", "rank", "tags", "valid", "extra", "formatLink", "sourceStrand", "targetStrand", "formatSubgraph", "sortedSegments", "sortedLinks", "s", "k", "offReference", "segments", "segment", "WALK_CONTEXT", "RgfaTabixAdapter", "BaseFeatureDataAdapter", "config", "getSubAdapter", "pluginManager", "under", "openTabixSlot", "walksLocation", "hasWalks", "links", "WalkReader", "PanSNRefNames", "opts", "header", "tier", "query", "signal", "statusCallback", "ObservableCreate", "observer", "tabixRefName", "start", "updateStatus", "getLines", "line", "anchored", "parseSegmentRow", "samples", "segmentSamples", "SimpleFeature", "region", "hops", "index", "addLinksOver", "refName", "end", "reached", "link", "parseLinkLine", "linkKey", "layout", "row", "found", "cut", "anchoredCut", "formatSubgraph", "frontier", "hop", "spans", "closingSpans", "span", "closingLinks", "walks", "graph", "kept", "fragments", "walkNameFilter", "lane", "resolvePanSNPrefix", "panSNHaplotype"]
+}

package/dist/chunks/WalkTabixSyntenyAdapter-2KJTYCX3.js

@@ -0,0 +1,2 @@
+import{b as x,c as T}from"./chunk-TVXMEJLJ.js";import{a as B,d as $,e as E,g as v}from"./chunk-KROCIQJP.js";import{c as L,e as A,f as M}from"./chunk-X4NNWAXW.js";import{g as R}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{a as k,c as w,d as S,e as N,f as g,g as P}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import{o as W}from"./chunk-TENPGIPX.js";var _=50;function q(o){let e=[];for(let t=0;t<o.length;t++){let[s,r]=o[t],[a,n]=o[t+1]??[];r===n&&r<=_&&(s==="I"&&a==="D"||s==="D"&&a==="I")?(e.push(["X",r]),t++):e.push([s,r])}return e}function D(o){return o.map(([e,t])=>`${t}${e}`).join("")}function F(o){let e=new Map,t=a=>{let n=o.get(a),i=n===void 0?0:n.end-n.start,p=e.get(i);return p===void 0&&(p="N".repeat(i),e.set(i,p)),p},s=new Map,r=a=>{let n=s.get(a);return n===void 0&&(n=Array.from(a.ids,(i,p)=>2*i+a.rev[p]),s.set(a,n)),n};return(a,n)=>B({query:r(a),target:r(n),sequenceOf:t,bases:!1})}function C({chain:o,target:e,query:t,assemblyName:s,refName:r,mateAssemblyName:a}){let n=e.hapStart+o.targetStart,i=e.hapStart+o.targetEnd,p=t.hapStart+o.queryStart,f=t.hapStart+o.queryEnd,c=q(o.edits),l=c.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=c.reduce((d,[,h])=>d+h,0),y=`${e.name}:${n}-${i}|${t.name}:${p}-${f}`;return new $({uniqueId:y,assemblyName:s,refName:r,start:n,end:i,type:"match",strand:o.strand==="-"?-1:1,CIGAR:D(c),syntenyId:y,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:S(t.name),start:p,end:f,assemblyName:a}})}var H=1e3;function I(o,e){return o[e]??o[k(e)]??e}var X=o=>w(o.name)??o.name,O=class extends E{constructor(e,t,s){super(e,t,s);let r=A(this,["nodesLocation"],["nodesIndex"]);this.reader=new T({walks:A(this,["walksLocation"],["walksIndex"]),nodes:r,links:A(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new M(r,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:s}=await this.reader.header(e),{anchor:r}=this,a=g(this,r),n=P(this);return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSamples:s,lanes:t.filter(i=>i!==a&&k(i)!==a).map(i=>({name:I(n,i),label:i,group:k(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:H}}async getSubgraph(e,t={}){let{signal:s,haplotypes:r}=t,a=await this.refNames.resolve(e,{signal:s});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:n,kept:i,fragments:p}=await this.reader.cut(a,e,{...this.budgets(),signal:s,keep:x(r?.map(f=>g(this,f)),w(a))});return n.tables(i,p)}async laneWalks(e,t,s,r,a){return W(a,r.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:r.signal,keep:x(s,w(e)),links:!1}).catch(n=>{throw n instanceof R&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,s){let r=s.haplotypes?.length?s.haplotypes.map(m=>g(this,m)):void 0,a=g(this,s.targetAssemblyName),n=a===void 0?r:r===void 0||r.some(m=>N(a,m)||N(m,a))?[a]:[];if(n?.length===0)return[];let{start:i,end:p}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,n,s,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=F(f.nodes),u=P(this),y=c.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(b=>N(m.name,b));return c.filter(m=>m.name!==e&&d(m)>=0).sort((m,b)=>d(m)-d(b)).flatMap(m=>y.flatMap(b=>l(m,b).map(j=>C({chain:j,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:I(u,X(m))}))))}async pairFeatures(e,t,s,r){let[a]=s,n=s.map(l=>({pair:l,featurePrefix:g(this,l.queryAssemblyName),matePrefix:g(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),r,s.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${s.length} lane pairs`),f=F(i.nodes),c=l=>p.filter(u=>N(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:y})=>c(u).flatMap(d=>c(y).flatMap(h=>f(h,d).map(m=>C({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:S(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return L(async s=>{let r=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(r!==void 0){let a=v(t),n=a.length>0?await this.pairFeatures(r,e,a,t):await this.anchorFeatures(r,e,t);for(let i of n)s.next(i)}s.complete()},t.signal)}};export{O as default,I as laneOf};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-2KJTYCX3.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-2KJTYCX3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
+  "sourcesContent": ["import { pairAlignments } from '@gmod/gbz-base'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\n\nimport type { WalkFragment, WalkNode } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { PairChain, PairEdit } from '@gmod/gbz-base'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\nfunction cigarOf(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const node = nodes.get(id)\n    const length = node === undefined ? 0 : node.end - node.start\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const handlesOf = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: handlesOf(query),\n      target: handlesOf(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n/**\n * One record of a walk aligned to another: on the target walk's contig, with\n * the query walk as its mate and the CIGAR read along the target, a `D` being\n * target bases the query lacks.\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const start = target.hapStart + chain.targetStart\n  const end = target.hapStart + chain.targetEnd\n  const mateStart = query.hapStart + chain.queryStart\n  const mateEnd = query.hapStart + chain.queryEnd\n  const edits = bubblesAsMismatches(chain.edits)\n  const matches = edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0)\n  const columns = edits.reduce((sum, [, n]) => sum + n, 0)\n  const id = `${target.name}:${start}-${end}|${query.name}:${mateStart}-${mateEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start,\n    end,\n    type: 'match',\n    strand: chain.strand === '-' ? -1 : 1,\n    CIGAR: cigarOf(edits),\n    syntenyId: id,\n    identity: matches / Math.max(columns, 1),\n    numMatches: matches,\n    blockLen: columns,\n    mate: {\n      refName: panSNContig(query.name),\n      start: mateStart,\n      end: mateEnd,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import { NodeLimitError } from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { chainFeature, walkAligner } from './walkLanes.ts'\nimport { WalkReader } from '../RgfaTabixAdapter/walkReader.ts'\nimport { walkNameFilter } from '../RgfaTabixAdapter/walkRows.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { WalkFragment } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.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\n// How much graph a cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix\n */\nexport function laneOf(asmByPrefix: Record<string, string>, prefix: string) {\n  return asmByPrefix[prefix] ?? asmByPrefix[panSNSample(prefix)] ?? prefix\n}\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly reader\n  private readonly refNames\n\n  public constructor(\n    config: WalkTabixSyntenyAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const nodes = openTabixSlot(this, ['nodesLocation'], ['nodesIndex'])\n    this.reader = new WalkReader(\n      {\n        walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n        nodes,\n        links: openTabixSlot(this, ['linksLocation'], ['linksIndex']),\n      },\n      this.getConf('walkChunk'),\n    )\n    this.refNames = new PanSNRefNames(nodes, this)\n  }\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes, references } = await this.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSamples: references,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneOf(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  private budgets() {\n    return {\n      stepBudget: this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      context: WALK_CONTEXT,\n    }\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal, haplotypes } = opts\n    const refName = await this.refNames.resolve(region, { signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    const { graph, kept, fragments } = await this.reader.cut(refName, region, {\n      ...this.budgets(),\n      signal,\n      keep: walkNameFilter(\n        haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        panSNHaplotype(refName),\n      ),\n    })\n    return graph.tables(kept, fragments)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.reader\n        .cut(refName, region, {\n          ...this.budgets(),\n          signal: opts.signal,\n          keep: walkNameFilter(prefixes, panSNHaplotype(refName)),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          if (error instanceof NodeLimitError) {\n            error.message = error.message.replace(\n              'to see the graph',\n              'to see lanes',\n            )\n          }\n          throw error\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = walkAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneOf(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const [first] = pairs\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      pairs.length === 1 && first\n        ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n        : `Reading ${pairs.length} lane pairs`,\n    )\n    const align = walkAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": 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+  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "cigarOf", "walkAligner", "nodes", "standIn", "sequenceOf", "id", "node", "length", "sequence", "handles", "handlesOf", "fragment", "steps", "query", "target", "pairAlignments", "chainFeature", "chain", "assemblyName", "refName", "mateAssemblyName", "start", "end", "mateStart", "mateEnd", "matches", "sum", "n", "columns", "SyntenyFeature", "panSNContig", "WALK_CONTEXT", "laneOf", "asmByPrefix", "prefix", "panSNSample", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "config", "getSubAdapter", "pluginManager", "nodes", "openTabixSlot", "WalkReader", "PanSNRefNames", "anchor", "opts", "haplotypes", "references", "anchorPrefix", "resolvePanSNPrefix", "assemblyByPanSNPrefix", "assemblyName", "region", "signal", "refName", "graph", "kept", "fragments", "walkNameFilter", "lane", "prefixes", "status", "updateStatus", "error", "NodeLimitError", "wanted", "target", "panSNMatchesPrefix", "start", "end", "align", "walkAligner", "f", "rank", "a", "query", "reference", "chain", "chainFeature", "pairs", "first", "sides", "pair", "side", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
+}

package/dist/chunks/chunk-7WIBGKBU.js

@@ -0,0 +1,2 @@
+var e=JBrowseExports["@jbrowse/core/util/tracks"],s=o=>e!=null&&o in Object(e)?e[o]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+o+"' from '@jbrowse/core/util/tracks' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:o});var t=s("getTrackName");var r=s("makeIndexType");var n=e&&e.__esModule?e.default:e;export{t as a,r as b};
+//# sourceMappingURL=chunk-7WIBGKBU.js.map

package/dist/chunks/chunk-7WIBGKBU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/core/util/tracks"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tracks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/tracks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const UNKNOWN = /* @__PURE__ */ read(\"UNKNOWN\")\nexport const UNSUPPORTED = /* @__PURE__ */ read(\"UNSUPPORTED\")\nexport const addAdapterGuesser = /* @__PURE__ */ read(\"addAdapterGuesser\")\nexport const addTrackTypeGuesser = /* @__PURE__ */ read(\"addTrackTypeGuesser\")\nexport const allSessionTracks = /* @__PURE__ */ read(\"allSessionTracks\")\nexport const annotationTrackIds = /* @__PURE__ */ read(\"annotationTrackIds\")\nexport const canonicalAssemblyNames = /* @__PURE__ */ read(\"canonicalAssemblyNames\")\nexport const clearFileFromCache = /* @__PURE__ */ read(\"clearFileFromCache\")\nexport const ensureFileHandleReady = /* @__PURE__ */ read(\"ensureFileHandleReady\")\nexport const expandLooseTrackConfig = /* @__PURE__ */ read(\"expandLooseTrackConfig\")\nexport const filterTracks = /* @__PURE__ */ read(\"filterTracks\")\nexport const findFileHandleIds = /* @__PURE__ */ read(\"findFileHandleIds\")\nexport const generateUnknownTrackConf = /* @__PURE__ */ read(\"generateUnknownTrackConf\")\nexport const generateUnsupportedTrackConf = /* @__PURE__ */ read(\"generateUnsupportedTrackConf\")\nexport const getBlob = /* @__PURE__ */ read(\"getBlob\")\nexport const getBlobMap = /* @__PURE__ */ read(\"getBlobMap\")\nexport const getConfAssemblyNames = /* @__PURE__ */ read(\"getConfAssemblyNames\")\nexport const getConfAssemblyNamesOrNone = /* @__PURE__ */ read(\"getConfAssemblyNamesOrNone\")\nexport const getConfRpcSessionId = /* @__PURE__ */ read(\"getConfRpcSessionId\")\nexport const getFileFromCache = /* @__PURE__ */ read(\"getFileFromCache\")\nexport const getFileName = /* @__PURE__ */ read(\"getFileName\")\nexport const getRpcSessionId = /* @__PURE__ */ read(\"getRpcSessionId\")\nexport const getTrackAssemblyNames = /* @__PURE__ */ read(\"getTrackAssemblyNames\")\nexport const getTrackName = /* @__PURE__ */ read(\"getTrackName\")\nexport const guessAdapter = /* @__PURE__ */ read(\"guessAdapter\")\nexport const guessTabixIndex = /* @__PURE__ */ read(\"guessTabixIndex\")\nexport const guessTrackConf = /* @__PURE__ */ read(\"guessTrackConf\")\nexport const guessTrackConfForLocation = /* @__PURE__ */ read(\"guessTrackConfForLocation\")\nexport const guessTrackType = /* @__PURE__ */ read(\"guessTrackType\")\nexport const hasFileHandlesInCache = /* @__PURE__ */ read(\"hasFileHandlesInCache\")\nexport const hideTrackGeneric = /* @__PURE__ */ read(\"hideTrackGeneric\")\nexport const isLooseTrackConfig = /* @__PURE__ */ read(\"isLooseTrackConfig\")\nexport const isSameAssemblyName = /* @__PURE__ */ read(\"isSameAssemblyName\")\nexport const launchToggleTrackGeneric = /* @__PURE__ */ read(\"launchToggleTrackGeneric\")\nexport const launchTrackGeneric = /* @__PURE__ */ read(\"launchTrackGeneric\")\nexport const makeIndex = /* @__PURE__ */ read(\"makeIndex\")\nexport const makeIndexType = /* @__PURE__ */ read(\"makeIndexType\")\nexport const normalizeTrackInit = /* @__PURE__ */ read(\"normalizeTrackInit\")\nexport const offeredTracks = /* @__PURE__ */ read(\"offeredTracks\")\nexport const openAssemblyInLinearView = /* @__PURE__ */ read(\"openAssemblyInLinearView\")\nexport const openMateLabel = /* @__PURE__ */ read(\"openMateLabel\")\nexport const pickDisplayForView = /* @__PURE__ */ read(\"pickDisplayForView\")\nexport const restoreFileHandles = /* @__PURE__ */ read(\"restoreFileHandles\")\nexport const restoreFileHandlesFromSnapshot = /* @__PURE__ */ read(\"restoreFileHandlesFromSnapshot\")\nexport const setBlobMap = /* @__PURE__ */ read(\"setBlobMap\")\nexport const setFileInCache = /* @__PURE__ */ read(\"setFileInCache\")\nexport const showTrackGeneric = /* @__PURE__ */ read(\"showTrackGeneric\")\nexport const storeBlobLocation = /* @__PURE__ */ read(\"storeBlobLocation\")\nexport const storeFileHandleLocation = /* @__PURE__ */ read(\"storeFileHandleLocation\")\nexport const stripFileExtension = /* @__PURE__ */ read(\"stripFileExtension\")\nexport const stripTrackIds = /* @__PURE__ */ read(\"stripTrackIds\")\nexport const toggleTrackGeneric = /* @__PURE__ */ read(\"toggleTrackGeneric\")\nexport const viewCanDisplayTrack = /* @__PURE__ */ read(\"viewCanDisplayTrack\")\nexport const viewDisplayNames = /* @__PURE__ */ read(\"viewDisplayNames\")\nexport const warmTrackDisplayGeneric = /* @__PURE__ */ read(\"warmTrackDisplayGeneric\")\nexport default host && host.__esModule ? host.default : host"],
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+  "names": ["host", "read", "name", "getTrackName", "read", "makeIndexType", "read", "tracks_default", "host"]
+}