jbrowse-plugin-graphgenomeviewer 7.1.8 → 7.1.9

package/dist/chunks/AddTrackWorkflow-LK25EC3H.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-LK25EC3H.js.map

package/dist/chunks/AddTrackWorkflow-LK25EC3H.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/core/util/tss-react\"]\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/tss-react\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport {\n  addTrackFromWidget,\n  getEnv,\n  getSession,\n  makeTrackId,\n} from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot, isAlive } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  GRAPH_INDEX_FIELDS,\n  buildTrackConfig,\n  parseHaplotypes,\n} from './buildTrackConfig'\nimport { readGraphManifest } from './graphManifest'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'RgfaTabixWalks',\n  'GbzBaseSyntenyAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [readsLoc, setReadsLoc] = useState<FileLocation>()\n  const gbz = choice === 'GbzBaseSyntenyAdapter'\n  const walks = choice === 'RgfaTabixWalks'\n  const [sample, setSample] = useState('')\n  const [haplotypes, setHaplotypes] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n  const [submitting, setSubmitting] = useState(false)\n\n  async function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    setError(undefined)\n    setSubmitting(true)\n    const manifest =\n      choice === 'RgfaTabixAdapter'\n        ? await readGraphManifest(loc, getEnv(model).pluginManager)\n        : undefined\n    setSubmitting(false)\n    if (!isAlive(model) || !model.assembly) {\n      return\n    }\n    try {\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          readsLoc: gbz ? readsLoc : undefined,\n          manifest,\n          assembly: model.assembly,\n          sample,\n          haplotypes: walks ? parseHaplotypes(haplotypes) : undefined,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n            setIndexLoc(undefined)\n            setError(undefined)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name={GRAPH_INDEX_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      {gbz ? 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'Reading graph.json\u2026' : 'Submit'}\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n"],
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+}

package/dist/chunks/{GbzBaseSyntenyAdapter-3HGD7PKF.js → GbzBaseSyntenyAdapter-J55EZLSA.js}

@@ -1,2 +1,2 @@
-import{a as ae,b as re,c as de,d as oe,e as se,f as q,g as ie}from"./chunk-IP3ORVTU.js";import{a as te}from"./chunk-KOB7YIMR.js";import{a as W,b as Z,c as U,d as u,e as M,f as $,g as k,h as E,i as z,k as X}from"./chunk-IT7HZNZO.js";import"./chunk-TFPHVH5H.js";import{b as O,c as H}from"./chunk-TVFR5KBQ.js";import"./chunk-Y7UUDKJL.js";import"./chunk-T4HOC6O3.js";import{a as ne}from"./chunk-HVBY3TGB.js";import{a as V,c as L,m as ee}from"./chunk-SQUFY3QO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as F,f as P,g as C}from"./chunk-KM3QNC77.js";import"./chunk-E7J6SB5P.js";import{b as G,e as Y,f as J,g as K}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as j,o as I}from"./chunk-TENPGIPX.js";function A(n){let s=/\.gbz\.db$/i;return s.test(n)?n.replace(s,".haplotype-index.db"):void 0}function he(n){return J(n)&&A(Y(n))?K(n,s=>A(s)):void 0}function ue(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,s){let t=he(n);if(!t)return{};try{return await N(t,s).stat(),{location:t}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(n,s){if(n.length<=s)return n;let t=n.length/s;return Array.from({length:s},(e,a)=>n[Math.floor(a*t)])}var pe=(n,s)=>n.path.some(t=>s.has(t.name)),v=class{constructor(s,t){this.file=s;this.tabix=t;this.whole=L({setup:async({signal:s})=>{let{size:t}=await this.file.stat();if(t>ye)throw new T(t);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await V(e):e);return H(a)}})}async readIndexed(s,t,e){let a=1/0,r=-1/0;for(let i of t){let c=Number(i);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:i=>{let c=O(i);c&&pe(c,t)&&o.push(c)}}),o}async readsOver(s,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,t):(await this.whole({signal:t})).filter(a=>pe(a,s));return{records:be(e,ge),total:e.length}}};var B=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=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 ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function we(n,s){return`${u(n)}#${n.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:n,assemblyName:s,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:i}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,d=we(c,n),g={uniqueId:d,assemblyName:s,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:i,syntenyId:d,mate:{refName:c.contig,start:p,end:l,assemblyName:e}};return new ae(g)}}function Se({pair:n,lane:s,mateLane:t}){return ie({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:s,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:t,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Pe=12e4;function Ne(n,s){let t=new Map;for(let a of n)for(let{name:r,start:o,end:i}of a.walkSpans()){let c=u(r);if(s.has(c)){let p=`${c}#${r.contig}`,l=t.get(p);l?l.push([o,i]):t.set(p,[[o,i]])}}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<=Pe&&(e=Math.max(e,o))}}return e}function _(n,s){return n instanceof U&&(n.message=`Zoom in to about ${j(n.fitsBp)} to see ${s}`),n}var le=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),D=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await ce(t,this.pluginManager),r=a.location,o=await Z.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await $(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,i),referenceSamples:c});return{db:o,anchor:i,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?ee(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let i=u(o.name),c=r.get(i);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(i,{prefix:i,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a}=await this.graph(t),r=C(this),o=[];for(let i of await this.getHaplotypes(t))i.sample!==a&&o.push({name:q(r,i.prefix),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,lanes:o}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,i=o===a?void 0:P(this,o),c=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),i)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>M(r,a)&&(e===void 0||F(u(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:i,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:d,end:g}=le(t);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${i} has no indexed path ${l} in this graph`);let w=this.keepPredicate(e.haplotypes);if(w!==void 0&&!r.hasHaplotypeIndex)throw new B(c);let f=await X(r,y,d,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:w}).catch(x=>{throw _(x,"the graph")});return typeof f=="string"?f:ne(f,{start:d,end:g},e.walkRows)}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=P(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:i,end:c}=t,p=P(this,e.targetAssemblyName),l=C(this),d=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await I(`Reading graph ${o}:${i.toLocaleString()}-${c.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:i,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:d}).catch(f=>{throw _(z(f,y,c-i)??f,"lanes")})):[]).flatMap(f=>{let x=f.resolved?xe({alignment:f,assemblyName:r,refName:o,lane:q(l,u(f.name))}):void 0;return x===void 0?[]:[x]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:i,end:c}=t,l=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),d=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),w=this.getConf("context"),f=(m,h)=>r.getSubgraphs({path:m,start:i,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>d.has(u(S))}),x=async m=>{let h=await f(m,w).catch(b=>{throw _(z(b,y,c-i)??b,"lanes")}),S=Ne(h,d),R=Math.ceil(S/2)+2e3;return S>0&&R>w?f(m,R).catch(b=>{if(b instanceof W)return h;throw b}):h};return(g&&l.length>0?await I(se(e),a.statusCallback,()=>x(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(b=>R.flatMap(me=>m.pairAlignments({target:b,query:me,bases:!1}).map(fe=>Se({pair:fe,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=le(t);return te(async r=>{let{db:o,anchor:i,unreadableIndex:c}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new B(c);if(a.assemblyName===i){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let d of l)r.next(d)}r.complete()},e.signal)}};export{B as NoHaplotypeIndexError,de as PairTargetError,D as default,Ne as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-3HGD7PKF.js.map
+import{a as ae,b as re,c as de,d as oe,e as se,f as q,g as ie}from"./chunk-KVIIZV7R.js";import{a as te}from"./chunk-KOB7YIMR.js";import{a as W,b as Z,c as U,d as u,e as M,f as $,g as k,h as E,i as z,k as X}from"./chunk-IT7HZNZO.js";import"./chunk-TFPHVH5H.js";import{b as O,c as H}from"./chunk-TVFR5KBQ.js";import"./chunk-Y7UUDKJL.js";import"./chunk-T4HOC6O3.js";import{a as ne}from"./chunk-HVBY3TGB.js";import{a as V,c as L,m as ee}from"./chunk-JOPQA7GP.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as F,f as P,g as C}from"./chunk-KM3QNC77.js";import"./chunk-E7J6SB5P.js";import{d as G,g as Y,h as J,i as K}from"./chunk-IKJZPPOA.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as j,o as I}from"./chunk-TENPGIPX.js";function A(n){let s=/\.gbz\.db$/i;return s.test(n)?n.replace(s,".haplotype-index.db"):void 0}function he(n){return J(n)&&A(Y(n))?K(n,s=>A(s)):void 0}function ue(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,s){let t=he(n);if(!t)return{};try{return await N(t,s).stat(),{location:t}}catch(e){return ue(e)?{}:{unreadable:String(e)}}}var ge=5e3,ye=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function be(n,s){if(n.length<=s)return n;let t=n.length/s;return Array.from({length:s},(e,a)=>n[Math.floor(a*t)])}var pe=(n,s)=>n.path.some(t=>s.has(t.name)),v=class{constructor(s,t){this.file=s;this.tabix=t;this.whole=L({setup:async({signal:s})=>{let{size:t}=await this.file.stat();if(t>ye)throw new T(t);let e=await this.file.readFile({signal:s}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await V(e):e);return H(a)}})}async readIndexed(s,t,e){let a=1/0,r=-1/0;for(let i of t){let c=Number(i);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await s.getLines("{node}",a,r+1,{signal:e,lineCallback:i=>{let c=O(i);c&&pe(c,t)&&o.push(c)}}),o}async readsOver(s,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,s,t):(await this.whole({signal:t})).filter(a=>pe(a,s));return{records:be(e,ge),total:e.length}}};var B=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},Q=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 ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function we(n,s){return`${u(n)}#${n.contig}@${s.start.node}.${s.start.offset}`}function xe({alignment:n,assemblyName:s,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:i}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,d=we(c,n),g={uniqueId:d,assemblyName:s,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:i,syntenyId:d,mate:{refName:c.contig,start:p,end:l,assemblyName:e}};return new ae(g)}}function Se({pair:n,lane:s,mateLane:t}){return ie({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:s,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:t,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Pe=12e4;function Ne(n,s){let t=new Map;for(let a of n)for(let{name:r,start:o,end:i}of a.walkSpans()){let c=u(r);if(s.has(c)){let p=`${c}#${r.contig}`,l=t.get(p);l?l.push([o,i]):t.set(p,[[o,i]])}}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<=Pe&&(e=Math.max(e,o))}}return e}function _(n,s){return n instanceof U&&(n.message=`Zoom in to about ${j(n.fitsBp)} to see ${s}`),n}var le=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),D=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await ce(t,this.pluginManager),r=a.location,o=await Z.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await $(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,i),referenceSamples:c});return{db:o,anchor:i,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?ee(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let i=u(o.name),c=r.get(i);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(i,{prefix:i,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a}=await this.graph(t),r=C(this),o=[];for(let i of await this.getHaplotypes(t))i.sample!==a&&o.push({name:q(r,i.prefix),label:i.prefix,group:i.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,lanes:o}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,i=o===a?void 0:P(this,o),c=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),i)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>M(r,a)&&(e===void 0||F(u(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:i,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:d,end:g}=le(t);if(p!==o)throw new Q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${i} has no indexed path ${l} in this graph`);let w=this.keepPredicate(e.haplotypes);if(w!==void 0&&!r.hasHaplotypeIndex)throw new B(c);let f=await X(r,y,d,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:w}).catch(x=>{throw _(x,"the graph")});return typeof f=="string"?f:ne(f,{start:d,end:g},e.walkRows)}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=P(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:i,end:c}=t,p=P(this,e.targetAssemblyName),l=C(this),d=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await I(`Reading graph ${o}:${i.toLocaleString()}-${c.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:i,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:d}).catch(f=>{throw _(z(f,y,c-i)??f,"lanes")})):[]).flatMap(f=>{let x=f.resolved?xe({alignment:f,assemblyName:r,refName:o,lane:q(l,u(f.name))}):void 0;return x===void 0?[]:[x]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:i,end:c}=t,l=(await Promise.all(e.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),d=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),w=this.getConf("context"),f=(m,h)=>r.getSubgraphs({path:m,start:i,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>d.has(u(S))}),x=async m=>{let h=await f(m,w).catch(b=>{throw _(z(b,y,c-i)??b,"lanes")}),S=Ne(h,d),R=Math.ceil(S/2)+2e3;return S>0&&R>w?f(m,R).catch(b=>{if(b instanceof W)return h;throw b}):h};return(g&&l.length>0?await I(se(e),a.statusCallback,()=>x(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(b=>R.flatMap(me=>m.pairAlignments({target:b,query:me,bases:!1}).map(fe=>Se({pair:fe,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=le(t);return te(async r=>{let{db:o,anchor:i,unreadableIndex:c}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new B(c);if(a.assemblyName===i){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let d of l)r.next(d)}r.complete()},e.signal)}};export{B as NoHaplotypeIndexError,de as PairTargetError,D as default,Ne as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-J55EZLSA.js.map

package/dist/chunks/GraphGenomeView-Q2IW7AND.js

@@ -0,0 +1,10 @@
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+//# sourceMappingURL=GraphGenomeView-Q2IW7AND.js.map

package/dist/chunks/GraphGenomeView-Q2IW7AND.js.map

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+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/GraphLoadStatus.tsx", "../../src/GraphGenomeView/components/ImportForm.tsx", "../../src/GraphGenomeView/components/GraphGenomeView.tsx"],
+  "sourcesContent": ["import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs or waits on\n// its assembly, and after a load of a source it can retry was canceled or\n// failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (!model.error && !model.loadCanceled) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses\n            variant=\"h6\"\n            message={model.statusMessage || undefined}\n          />\n          {model.canCancelLoad ? (\n            <Button\n              size=\"small\"\n              data-testid=\"graph-genome-cancel\"\n              onClick={() => {\n                model.cancelLoad()\n              }}\n            >\n              Cancel\n            </Button>\n          ) : null}\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphGenomeViewModel } from '../viewModel'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphGenomeViewModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    const uri = url.trim()\n    if (uri) {\n      void model.openGfaLocation({ uri, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    // or picking the same file again fires no change\n    event.target.value = ''\n    if (file) {\n      void model.loadGFAFile(file, file.name)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2,.gz\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleUrlLoad()\n            }}\n            disabled={!url.trim()}\n          >\n            Open\n          </Button>\n        </div>\n      </div>\n\n      <div className={classes.footer}>\n        <Button\n          size=\"small\"\n          onClick={() => {\n            void model.loadGFA(EXAMPLE_GFA, 'Example graph')\n          }}\n        >\n          Load 4-node example\n        </Button>\n      </div>\n\n      {model.error ? <ErrorBanner error={model.error} /> : null}\n    </Paper>\n  )\n})\n\nexport default ImportForm\n", "import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphGenomeViewModel } from '../viewModel'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphGenomeViewModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it, including while its assembly loads\n  if (model.canRetryLoad) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n"],
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+  "names": ["useStyles", "makeStyles", "GraphLoadStatus", "observer", "model", "classes", "jsxs", "Paper", "jsx", "LoadingEllipses", "Button", "LinearProgress", "ErrorBanner", "Typography", "GraphLoadStatus_default", "EXAMPLE_GFA", "useStyles", "makeStyles", "ImportForm", "observer", "model", "classes", "url", "setUrl", "useState", "handleUrlLoad", "uri", "handleFileUpload", "event", "file", "jsxs", "Paper", "jsx", "Typography", "Button", "TextField", "e", "ErrorBanner", "ImportForm_default", "GraphGenomeView", "observer", "model", "jsx", "GraphCanvas_default", "GraphLoadStatus_default", "jsxs", "Fragment", "ImportForm_default", "GraphGenomeView_default"]
+}

package/dist/chunks/GraphTrackSettingsDialog-5UX65OSM.js

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+import{a as G,b as L}from"./chunk-3CIJSKCN.js";import{b as v,c as x,n as d}from"./chunk-RROZDQ35.js";import"./chunk-IPMAQCYX.js";import"./chunk-HYKQBZA4.js";import"./chunk-Y7UUDKJL.js";import"./chunk-MVVXRZXV.js";import"./chunk-KM3QNC77.js";import"./chunk-IKJZPPOA.js";import{g,h}from"./chunk-YU7T5WOQ.js";import{F as m,H as u,n as C}from"./chunk-UGCNPRKC.js";import{b as r,c as i,d as c}from"./chunk-JMBDTNUR.js";var P=d()({section:{marginBottom:24}}),T=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],w=c(function({model:t}){let{classes:l}=P(),o=t.sourceAdapter;return o?.type==="RgfaTabixAdapter"&&!v(o)?i("div",{className:l.section,children:[r(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:T,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),t.recut()}}),r(u,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),k=w;var F=d()({section:{marginBottom:24}});function M(n){return n.split(/[\s,]+/).filter(t=>t!=="")}var I=c(function({model:t}){let[l,o]=h(t.cutHaplotypes?.join(", ")??""),a=()=>{let e=M(l);e.join(`
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+`)!==(t.cutHaplotypes??[]).join(`
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+//# sourceMappingURL=GraphTrackSettingsDialog-5UX65OSM.js.map

package/dist/chunks/GraphTrackSettingsDialog-5UX65OSM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
+  "sourcesContent": ["import { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from '../../GraphGenomeView/components/LabelledSelect'\nimport { walkIndexed } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\n// Only an rGFA cut from segment rows reads hops: a GBZ cut widens by its\n// adapter's bp `context`, and a walk-indexed cut follows its walks.\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: '0', label: 'None' },\n  { value: '1', label: '1 hop' },\n  { value: '2', label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const adapter = model.sourceAdapter\n  return adapter?.type === 'RgfaTabixAdapter' && !walkIndexed(adapter) ? (\n    <div className={classes.section}>\n      <LabelledSelect\n        label=\"Graph context\"\n        sx={{ minWidth: 200 }}\n        value={String(model.subgraphContext)}\n        options={SUBGRAPH_CONTEXTS}\n        testId=\"graph-context-select\"\n        onChange={hops => {\n          model.setSubgraphContext(Number(hops))\n          model.recut()\n        }}\n      />\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        How far the cut follows links out of the region. At none, a detour that\n        leaves the window draws as two stubs. No effect on gfa-to-tabix&apos;s\n        default anchored index.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphContextSelect\n", "import { useRef, useState } from 'react'\n\nimport { Autocomplete, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { cutsByHaplotype } from '../../graphTrackConfig'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nfunction parseHaplotypeList(text: string) {\n  return text.split(/[\\s,]+/).filter(name => name !== '')\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft)\n    const unchanged =\n      parsed.join('\\n') === (model.cutHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      model.recut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// The haplotypes a walk-indexed graph's header names, searched as typed. A\n// typed prefix the list lacks (HG002 for both haplotypes) is kept too, on\n// Enter or when the field loses focus. The set applies when the list closes\n// or, with the list closed, as it changes. Not MUI's `autoSelect`: in a\n// multiple select its blur toggles the highlighted option, so a pick made by\n// keyboard was dropped again on Tab.\nconst HaplotypePickField = observer(function HaplotypePickField({\n  model,\n  names,\n}: {\n  model: LinearGraphCutModel\n  names: string[]\n}) {\n  const [draft, setDraft] = useState(model.cutHaplotypes ?? [])\n  const draftRef = useRef(draft)\n  const typed = useRef('')\n  const [open, setOpen] = useState(false)\n  const apply = (haplotypes: string[]) => {\n    if (haplotypes.join('\\n') !== (model.cutHaplotypes ?? []).join('\\n')) {\n      model.setSubgraphHaplotypes(haplotypes)\n      model.recut()\n    }\n  }\n  return (\n    <Autocomplete\n      multiple\n      freeSolo\n      disableCloseOnSelect\n      options={names}\n      value={draft}\n      open={open}\n      onOpen={() => {\n        setOpen(true)\n      }}\n      onInputChange={(_, text) => {\n        typed.current = text\n      }}\n      onClose={(_, reason) => {\n        setOpen(false)\n        const text = typed.current.trim()\n        if (reason === 'blur' && text && !draftRef.current.includes(text)) {\n          draftRef.current = [...draftRef.current, text]\n          setDraft(draftRef.current)\n        }\n        apply(draftRef.current)\n      }}\n      onChange={(_, value) => {\n        draftRef.current = value\n        setDraft(value)\n        if (!open) {\n          apply(value)\n        }\n      }}\n      renderInput={params => (\n        <TextField\n          {...params}\n          label=\"Haplotypes\"\n          placeholder={draft.length === 0 ? 'every haplotype' : undefined}\n          slotProps={{\n            ...params.slotProps,\n            htmlInput: {\n              ...params.slotProps.htmlInput,\n              'data-testid': 'graph-haplotypes-field',\n            },\n          }}\n        />\n      )}\n    />\n  )\n})\n\n// Only a GBZ cut and a walk-indexed rGFA cut read the set. The inner field is\n// keyed on it so an outside change (a restored session, a launch) resets the\n// draft rather than fighting it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  const names = model.haplotypeNames\n  const key = model.cutHaplotypes?.join(',') ?? ''\n  const adapter = model.sourceAdapter\n  return adapter && cutsByHaplotype(adapter) ? (\n    <div className={classes.section}>\n      {names ? (\n        <HaplotypePickField key={key} model={model} names={names} />\n      ) : (\n        <HaplotypeListField key={key} model={model} />\n      )}\n      <Typography variant=\"caption\" component=\"div\" color=\"text.secondary\">\n        {names\n          ? `Which of the graph's ${names.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`\n          : 'Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas.'}{' '}\n        Empty is every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
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+}

package/dist/chunks/{LinearGraphDisplay-GLJ3L2IZ.js → LinearGraphDisplay-JXPE3DGS.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=LinearGraphDisplay-JXPE3DGS.js.map

package/dist/chunks/MinigraphBubbleAdapter-BK35LCJR.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=MinigraphBubbleAdapter-BK35LCJR.js.map

package/dist/chunks/{MinigraphBubbleAdapter-FNP6DISL.js.map → MinigraphBubbleAdapter-BK35LCJR.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts"],
-  "sourcesContent": ["import {\n  bubbleDescription,\n  bubbleLabel,\n  parseBubbleLine,\n} from '@jbrowse/bandage-core/bubbles/bubbleLine'\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 { getLines } from '../tabixRange.ts'\n\nimport type { MinigraphBubbleAdapterConfig } from './configSchema.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nexport default class MinigraphBubbleAdapter extends BaseFeatureDataAdapter<MinigraphBubbleAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly bubbles = openTabixSlot(this, ['bubblesLocation'], ['index'])\n  // `gfatools bubble` names each row after the graph's stable sequence, so a\n  // Minigraph-Cactus graph produces PanSN rows (`GRCh38#0#chr6`) where a plain\n  // minigraph graph produces bare ones (`chr6`). Same resolution the segment\n  // adapter does, through the same `assemblyNameToPanSN` slot.\n  private readonly refNames = new PanSNRefNames(this.bubbles, this)\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.refNames.assemblyRefNames(opts)\n  }\n\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    return this.refNames.regionBytes(regions, opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading bubbles', statusCallback, () =>\n          getLines(this.bubbles, tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: (line, fileOffset) => {\n              const bubble = parseBubbleLine(line)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: `bubble-${fileOffset}`,\n                  refName: query.refName,\n                  start: bubble.start,\n                  end: bubble.end,\n                  // How variable this spot is, in two words, since that is the\n                  // whole point of the track.\n                  name: bubbleLabel(bubble),\n                  description: bubbleDescription(bubble),\n                  type: 'bubble',\n                  score: bubble.segmentCount,\n                  segmentCount: bubble.segmentCount,\n                  pathCount: bubble.pathCount,\n                  inversion: bubble.inversion,\n                  shortestAlleleLength: bubble.shortestAlleleLength,\n                  longestAlleleLength: bubble.longestAlleleLength,\n                  segments: bubble.segments,\n                  shortestAllele: bubble.shortestAllele,\n                  longestAllele: bubble.longestAllele,\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n}\n"],
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+  "sourcesContent": ["import {\n  bubbleDescription,\n  bubbleLabel,\n  parseBubbleLine,\n} from '@jbrowse/bandage-core/bubbles/bubbleLine'\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 { getLines } from '../tabixRange.ts'\n\nimport type { MinigraphBubbleAdapterConfig } from './configSchema.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nexport default class MinigraphBubbleAdapter extends BaseFeatureDataAdapter<MinigraphBubbleAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly bubbles = openTabixSlot(this, ['bubblesLocation'], ['index'])\n  // `gfatools bubble` names each row after the graph's stable sequence, so a\n  // Minigraph-Cactus graph produces PanSN rows (`GRCh38#0#chr6`) where a plain\n  // minigraph graph produces bare ones (`chr6`). Same resolution the segment\n  // adapter does, through the same `assemblyNameToPanSN` slot.\n  private readonly refNames = new PanSNRefNames(this.bubbles, this)\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.refNames.assemblyRefNames(opts)\n  }\n\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    return this.refNames.regionBytes(regions, opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.refNames.resolveMapped(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading bubbles', statusCallback, () =>\n          getLines(this.bubbles, tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: (line, fileOffset) => {\n              const bubble = parseBubbleLine(line)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: `bubble-${fileOffset}`,\n                  refName: query.refName,\n                  start: bubble.start,\n                  end: bubble.end,\n                  // How variable this spot is, in two words, since that is the\n                  // whole point of the track.\n                  name: bubbleLabel(bubble),\n                  description: bubbleDescription(bubble),\n                  type: 'bubble',\n                  score: bubble.segmentCount,\n                  segmentCount: bubble.segmentCount,\n                  pathCount: bubble.pathCount,\n                  inversion: bubble.inversion,\n                  shortestAlleleLength: bubble.shortestAlleleLength,\n                  longestAlleleLength: bubble.longestAlleleLength,\n                  segments: bubble.segments,\n                  shortestAllele: bubble.shortestAllele,\n                  longestAllele: bubble.longestAllele,\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n}\n"],
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   "names": ["MinigraphBubbleAdapter", "BaseFeatureDataAdapter", "openTabixSlot", "PanSNRefNames", "opts", "regions", "query", "signal", "statusCallback", "ObservableCreate", "observer", "tabixRefName", "updateStatus", "getLines", "line", "fileOffset", "bubble", "parseBubbleLine", "SimpleFeature", "bubbleLabel", "bubbleDescription"]
 }

package/dist/chunks/RgfaTabixAdapter-ODT4JA6Y.js

@@ -0,0 +1,3 @@
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+`)}function Z(s){return s.filter(n=>n.rank>0)}async function x(s,n,t){let a=[];return await d(s,n.refName,n.start,n.end,{signal:t,lineCallback:e=>{a.push($(e))}}),a}async function G(s,n,{hops:t=0,signal:a}={}){let e=new Map,r=new Map,i={anchored:!1};if(await d(s.segments,n.refName,n.start,n.end,{signal:a,lineCallback:f=>{let m=u(f);i.anchored||=m.anchored,e.set(m.segment.id,m.segment)}}),i.anchored){let f=O(e,await x(s.links,n,a),n);return R(f.segments,f.links)}let o=async f=>(await x(s.links,f,a)).flatMap(m=>S(e,r,m)),g=Z(await o(n));for(let f=0;f<t;f++){let m=await Promise.all(g.map(o));g=Z(m.flat())}if(t>0){let f=A([...e.values()],new Set(g.map(c=>c.id)),n),m=await Promise.all(f.map(c=>x(s.links,c,a)));for(let c of T(m.flat(),e,f))S(e,r,c)}return R(e,r)}var b=class extends L{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(t){let a=p(this,[...t,"segmentsLocation"],[...t,"segmentsIndex"]),e=p(this,[...t,"linksLocation"],[...t,"linksIndex"]),r=this.getConf("walksLocation"),i=t.length===0&&N(r)?new I(p(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:e,walks:i,refNames:new F(i?.file??a,this)}}async getHaplotypeNames(t={}){return this.fine.walks?.haplotypeNames(t)}index(t="fine"){return t==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(t={}){return this.fine.refNames.assemblyRefNames(t)}async getRegionByteSize(t,a={}){let{walks:e,refNames:r}=this.fine;return r.regionBytes(t,a,e&&(i=>e.reader.queryStart(i,a)))}async hasDataForRefName(){return!0}getFeatures(t,a={}){return w(async e=>{let r=await this.fine.refNames.resolveMapped(t,a);if(r!==void 0){let{walks:i}=this.fine,o=g=>{e.next(g)};await(i?this.walkFeatures(i,r,t,a,o):this.segmentFeatures(r,t,a,o))}e.complete()},a.signal)}async walkFeatures(t,a,e,r,i){let o=await h("Downloading walks",r.statusCallback,()=>t.referenceNodes(a,e,r));for(let g of o){let f=String(g.id);i(new k({uniqueId:f,refName:e.refName,start:g.start,end:g.end,name:f,type:"segment",rank:0,stableName:g.refName}))}}async segmentFeatures(t,a,e,r){await h("Downloading segments",e.statusCallback,()=>d(this.fine.segments,t,a.start,a.end,{signal:e.signal,lineCallback:i=>{let{segment:o,anchored:g}=u(i);if(g&&o.refName!==t)return;let f=v(o);r(new k({uniqueId:o.id,refName:a.refName,start:o.start,end:o.end,name:o.id,type:"segment",rank:o.rank,stableName:o.refName,...f&&{samples:f,sampleCount:f.length}}))}}))}async getSubgraph(t,a={}){let{hops:e,signal:r,tier:i}=a,o=this.index(i),g=await o.refNames.resolve(t,{signal:r});if(g===void 0)throw new Error(y(t));return o.walks?o.walks.subgraph(g,t,a):G(o,{refName:g,start:t.start,end:t.end},{hops:e,signal:r})}};export{b as default};
+//# sourceMappingURL=RgfaTabixAdapter-ODT4JA6Y.js.map

package/dist/chunks/{RgfaTabixAdapter-6NY7XZ6E.js.map → RgfaTabixAdapter-ODT4JA6Y.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/RgfaTabixAdapter/rgfaBed.ts", "../../src/RgfaTabixAdapter/rgfaCut.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// gfa-to-tabix writes both endpoints of a link into every row and files the\n// link under each endpoint's stable sequence, so a read covering both returns\n// it twice; linkKey dedupes it. Returns the endpoints the cut lacked.\nexport function addLink(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n  link: RgfaLink,\n) {\n  links.set(linkKey(link), link)\n  const added: RgfaSegment[] = []\n  for (const segment of [link.sourceSegment, link.targetSegment]) {\n    if (!segments.has(segment.id)) {\n      segments.set(segment.id, segment)\n      added.push(segment)\n    }\n  }\n  return added\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      addLink(segments, links, link)\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\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      segment => unread.has(segment.id),\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      () => true,\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  isUnread: (segment: RgfaSegment) => boolean,\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 || isUnread(segment)\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: isUnread(segment),\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 {\n  addLink,\n  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  parseLinkLine,\n  parseSegmentRow,\n} from './rgfaBed.ts'\nimport { getLines } from '../tabixRange.ts'\n\nimport type { RgfaLink, RgfaSegment, StableSpan } from './rgfaBed.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\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\nexport interface RgfaFiles {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n}\n\nasync function linksOver(\n  file: TabixIndexedFile,\n  span: StableSpan,\n  signal?: AbortSignal,\n) {\n  const found: RgfaLink[] = []\n  await getLines(file, span.refName, span.start, span.end, {\n    signal,\n    lineCallback: line => {\n      found.push(parseLinkLine(line))\n    },\n  })\n  return found\n}\n\n/**\n * The graph around a window of one stable sequence, as GFA text. The window's\n * own segments come from the segment file; the link file 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 window.\n *\n * `hops` is extra rounds of link-following past the window's own segments and\n * their immediate neighbours, each costing one tabix query per off-reference\n * segment newly reached. After the last round, one more read per stretch of\n * stable sequence the cut holds closes it (closingSpans), so an allele reached\n * from both ends draws whole. The view asks for one hop; a hopless cut stays\n * as cheap as it was. `signal` goes to every one of those queries, so a cut\n * the view has replaced stops.\n */\nexport async function rgfaCut(\n  files: RgfaFiles,\n  window: StableSpan,\n  { hops = 0, signal }: { hops?: number; signal?: AbortSignal } = {},\n) {\n  const segments = new Map<string, RgfaSegment>()\n  const links = new Map<string, RgfaLink>()\n  const layout = { anchored: false }\n  await getLines(files.segments, window.refName, window.start, window.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 window and there is nothing to hop to or close.\n  if (layout.anchored) {\n    const cut = anchoredCut(\n      segments,\n      await linksOver(files.links, window, signal),\n      window,\n    )\n    return formatSubgraph(cut.segments, cut.links)\n  }\n  const addLinksOver = async (span: StableSpan) =>\n    (await linksOver(files.links, span, signal)).flatMap(link =>\n      addLink(segments, links, link),\n    )\n  let frontier = offReference(await addLinksOver(window))\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, and the output is sorted\n    // at the end regardless of the order they arrive in.\n    const reached = await Promise.all(frontier.map(addLinksOver))\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      window,\n    )\n    const found = await Promise.all(\n      spans.map(span => linksOver(files.links, span, signal)),\n    )\n    for (const link of closingLinks(found.flat(), segments, spans)) {\n      addLink(segments, links, link)\n    }\n  }\n  return formatSubgraph(segments, links)\n}\n", "import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { locationIsSet } from '../locationName.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\nimport { parseSegmentRow, segmentSamples } from './rgfaBed.ts'\nimport { rgfaCut } from './rgfaCut.ts'\nimport { WalkIndex } from './walkReader.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { WalkCut } from './walkRowRuns.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkIndex\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine = this.openIndex([])\n  private coarse: GraphIndex | undefined\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. A walk-indexed graph's walk file names the same sequences,\n  // and it has no segment file.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const walks =\n      under.length === 0 && locationIsSet(walksLocation)\n        ? new WalkIndex(\n            openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n            this,\n          )\n        : undefined\n    return {\n      segments,\n      links,\n      walks,\n      refNames: new PanSNRefNames(walks?.file ?? 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    return this.fine.walks?.haplotypeNames(opts)\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  // getFeatures reads a walk file from the chunk before the window\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    const { walks, refNames } = this.fine\n    return refNames.regionBytes(\n      regions,\n      opts,\n      walks && (start => walks.reader.queryStart(start, opts)),\n    )\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        const { walks } = this.fine\n        const emit = (feature: Feature) => {\n          observer.next(feature)\n        }\n        await (walks\n          ? this.walkFeatures(walks, tabixRefName, query, opts, emit)\n          : this.segmentFeatures(tabixRefName, query, opts, emit))\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n\n  // A walk-indexed graph's reference nodes are its ref rows' steps\n  private async walkFeatures(\n    walks: WalkIndex,\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    const nodes = await updateStatus(\n      'Downloading walks',\n      opts.statusCallback,\n      () => walks.referenceNodes(tabixRefName, query, opts),\n    )\n    for (const node of nodes) {\n      const id = String(node.id)\n      emit(\n        new SimpleFeature({\n          uniqueId: id,\n          refName: query.refName,\n          start: node.start,\n          end: node.end,\n          name: id,\n          type: 'segment',\n          rank: 0,\n          stableName: node.refName,\n        }),\n      )\n    }\n  }\n\n  private async segmentFeatures(\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    await updateStatus('Downloading segments', opts.statusCallback, () =>\n      getLines(this.fine.segments, tabixRefName, query.start, query.end, {\n        signal: opts.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 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          emit(\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\n  // The graph around a region for GraphGenomeView: GFA text (rgfaCut), or a\n  // walk-indexed graph's tables (WalkIndex.subgraph). `tier: 'coarse'` reads\n  // the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops, signal, tier } = opts\n    const index = this.index(tier)\n    const tabixRefName = await index.refNames.resolve(region, { signal })\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 index.walks.subgraph(tabixRefName, region, opts)\n    }\n    return rgfaCut(\n      index,\n      { refName: tabixRefName, start: region.start, end: region.end },\n      { hops, signal },\n    )\n  }\n}\n"],
-  "mappings": 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-  "names": ["parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "s", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "addLink", "segments", "links", "added", "anchoredCut", "under", "found", "window", "side", "closingSpans", "held", "unread", "outside", "mergedSpans", "isUnread", "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", "k", "offReference", "segments", "segment", "linksOver", "file", "span", "signal", "found", "getLines", "line", "parseLinkLine", "rgfaCut", "files", "window", "hops", "links", "layout", "row", "parseSegmentRow", "cut", "anchoredCut", "formatSubgraph", "addLinksOver", "link", "addLink", "frontier", "hop", "reached", "spans", "closingSpans", "closingLinks", "RgfaTabixAdapter", "BaseFeatureDataAdapter", "under", "segments", "openTabixSlot", "links", "walksLocation", "walks", "locationIsSet", "WalkIndex", "PanSNRefNames", "opts", "tier", "regions", "refNames", "start", "query", "ObservableCreate", "observer", "tabixRefName", "emit", "feature", "nodes", "updateStatus", "node", "id", "SimpleFeature", "getLines", "line", "segment", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "signal", "index", "rgfaCut"]
+  "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// gfa-to-tabix writes both endpoints of a link into every row and files the\n// link under each endpoint's stable sequence, so a read covering both returns\n// it twice; linkKey dedupes it. Returns the endpoints the cut lacked.\nexport function addLink(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n  link: RgfaLink,\n) {\n  links.set(linkKey(link), link)\n  const added: RgfaSegment[] = []\n  for (const segment of [link.sourceSegment, link.targetSegment]) {\n    if (!segments.has(segment.id)) {\n      segments.set(segment.id, segment)\n      added.push(segment)\n    }\n  }\n  return added\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      addLink(segments, links, link)\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\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      segment => unread.has(segment.id),\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      () => true,\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  isUnread: (segment: RgfaSegment) => boolean,\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 || isUnread(segment)\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: isUnread(segment),\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 {\n  addLink,\n  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  parseLinkLine,\n  parseSegmentRow,\n} from './rgfaBed.ts'\nimport { getLines } from '../tabixRange.ts'\n\nimport type { RgfaLink, RgfaSegment, StableSpan } from './rgfaBed.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\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\nexport interface RgfaFiles {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n}\n\nasync function linksOver(\n  file: TabixIndexedFile,\n  span: StableSpan,\n  signal?: AbortSignal,\n) {\n  const found: RgfaLink[] = []\n  await getLines(file, span.refName, span.start, span.end, {\n    signal,\n    lineCallback: line => {\n      found.push(parseLinkLine(line))\n    },\n  })\n  return found\n}\n\n/**\n * The graph around a window of one stable sequence, as GFA text. The window's\n * own segments come from the segment file; the link file 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 window.\n *\n * `hops` is extra rounds of link-following past the window's own segments and\n * their immediate neighbours, each costing one tabix query per off-reference\n * segment newly reached. After the last round, one more read per stretch of\n * stable sequence the cut holds closes it (closingSpans), so an allele reached\n * from both ends draws whole. The view asks for one hop; a hopless cut stays\n * as cheap as it was. `signal` goes to every one of those queries, so a cut\n * the view has replaced stops.\n */\nexport async function rgfaCut(\n  files: RgfaFiles,\n  window: StableSpan,\n  { hops = 0, signal }: { hops?: number; signal?: AbortSignal } = {},\n) {\n  const segments = new Map<string, RgfaSegment>()\n  const links = new Map<string, RgfaLink>()\n  const layout = { anchored: false }\n  await getLines(files.segments, window.refName, window.start, window.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 window and there is nothing to hop to or close.\n  if (layout.anchored) {\n    const cut = anchoredCut(\n      segments,\n      await linksOver(files.links, window, signal),\n      window,\n    )\n    return formatSubgraph(cut.segments, cut.links)\n  }\n  const addLinksOver = async (span: StableSpan) =>\n    (await linksOver(files.links, span, signal)).flatMap(link =>\n      addLink(segments, links, link),\n    )\n  let frontier = offReference(await addLinksOver(window))\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, and the output is sorted\n    // at the end regardless of the order they arrive in.\n    const reached = await Promise.all(frontier.map(addLinksOver))\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      window,\n    )\n    const found = await Promise.all(\n      spans.map(span => linksOver(files.links, span, signal)),\n    )\n    for (const link of closingLinks(found.flat(), segments, spans)) {\n      addLink(segments, links, link)\n    }\n  }\n  return formatSubgraph(segments, links)\n}\n", "import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { locationIsSet } from '../locationName.ts'\nimport {\n  PanSNRefNames,\n  openTabixSlot,\n  unmappedRegionMessage,\n} from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\nimport { parseSegmentRow, segmentSamples } from './rgfaBed.ts'\nimport { rgfaCut } from './rgfaCut.ts'\nimport { WalkIndex } from './walkReader.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { WalkCut } from './walkRowRuns.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkIndex\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine = this.openIndex([])\n  private coarse: GraphIndex | undefined\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. A walk-indexed graph's walk file names the same sequences,\n  // and it has no segment file.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const walks =\n      under.length === 0 && locationIsSet(walksLocation)\n        ? new WalkIndex(\n            openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n            this,\n          )\n        : undefined\n    return {\n      segments,\n      links,\n      walks,\n      refNames: new PanSNRefNames(walks?.file ?? 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    return this.fine.walks?.haplotypeNames(opts)\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  // getFeatures reads a walk file from the chunk before the window\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    const { walks, refNames } = this.fine\n    return refNames.regionBytes(\n      regions,\n      opts,\n      walks && (start => walks.reader.queryStart(start, opts)),\n    )\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolveMapped(query, opts)\n      if (tabixRefName !== undefined) {\n        const { walks } = this.fine\n        const emit = (feature: Feature) => {\n          observer.next(feature)\n        }\n        await (walks\n          ? this.walkFeatures(walks, tabixRefName, query, opts, emit)\n          : this.segmentFeatures(tabixRefName, query, opts, emit))\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n\n  // A walk-indexed graph's reference nodes are its ref rows' steps\n  private async walkFeatures(\n    walks: WalkIndex,\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    const nodes = await updateStatus(\n      'Downloading walks',\n      opts.statusCallback,\n      () => walks.referenceNodes(tabixRefName, query, opts),\n    )\n    for (const node of nodes) {\n      const id = String(node.id)\n      emit(\n        new SimpleFeature({\n          uniqueId: id,\n          refName: query.refName,\n          start: node.start,\n          end: node.end,\n          name: id,\n          type: 'segment',\n          rank: 0,\n          stableName: node.refName,\n        }),\n      )\n    }\n  }\n\n  private async segmentFeatures(\n    tabixRefName: string,\n    query: Region,\n    opts: BaseOptions,\n    emit: (feature: Feature) => void,\n  ) {\n    await updateStatus('Downloading segments', opts.statusCallback, () =>\n      getLines(this.fine.segments, tabixRefName, query.start, query.end, {\n        signal: opts.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 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          emit(\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\n  // The graph around a region for GraphGenomeView: GFA text (rgfaCut), or a\n  // walk-indexed graph's tables (WalkIndex.subgraph). `tier: 'coarse'` reads\n  // the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops, signal, tier } = opts\n    const index = this.index(tier)\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n    if (tabixRefName === undefined) {\n      throw new Error(unmappedRegionMessage(region))\n    }\n    if (index.walks) {\n      return index.walks.subgraph(tabixRefName, region, opts)\n    }\n    return rgfaCut(\n      index,\n      { refName: tabixRefName, start: region.start, end: region.end },\n      { hops, signal },\n    )\n  }\n}\n"],
+  "mappings": 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+  "names": ["parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "s", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "addLink", "segments", "links", "added", "anchoredCut", "under", "found", "window", "side", "closingSpans", "held", "unread", "outside", "mergedSpans", "isUnread", "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", "k", "offReference", "segments", "segment", "linksOver", "file", "span", "signal", "found", "getLines", "line", "parseLinkLine", "rgfaCut", "files", "window", "hops", "links", "layout", "row", "parseSegmentRow", "cut", "anchoredCut", "formatSubgraph", "addLinksOver", "link", "addLink", "frontier", "hop", "reached", "spans", "closingSpans", "closingLinks", "RgfaTabixAdapter", "BaseFeatureDataAdapter", "under", "segments", "openTabixSlot", "links", "walksLocation", "walks", "locationIsSet", "WalkIndex", "PanSNRefNames", "opts", "tier", "regions", "refNames", "start", "query", "ObservableCreate", "observer", "tabixRefName", "emit", "feature", "nodes", "updateStatus", "node", "id", "SimpleFeature", "getLines", "line", "segment", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "signal", "index", "unmappedRegionMessage", "rgfaCut"]
 }

package/dist/chunks/{WalkTabixSyntenyAdapter-KRNEQL44.js → WalkTabixSyntenyAdapter-A5OPAELK.js}

@@ -1,2 +1,2 @@
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