jbrowse-plugin-graphgenomeviewer 7.2.0 → 7.3.0

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts

@@ -1,4 +1,5 @@
 import { graphTablesGFA } from '@jbrowse/bandage-core/gfa/graphTables'
+import { walkRowsOf } from '@jbrowse/bandage-core/layout/walkRowRuns'
 import { walkRows } from '@jbrowse/bandage-core/layout/walkRows'
 import { loadGraph } from '@jbrowse/bandage-core/pipeline'
 import PluginManager from '@jbrowse/core/PluginManager'
@@ -10,11 +11,11 @@ import Adapter from './WalkTabixSyntenyAdapter.ts'
 import configSchema from './configSchema.ts'
 import WalkTabixSyntenyAdapterF from './index.ts'
 import {
+  anchorAligner,
   bubblesAsMismatches,
   referenceAligner,
   walkAligner,
 } from './walkLanes.ts'
-import { walkRowsOf } from '../RgfaTabixAdapter/walkRowRuns.ts'
 import { PairTargetError } from '../synteny/lanePairs.ts'
 
 import type { PairChain } from '@gmod/gbz-base/pairAlignment'
@@ -512,6 +513,81 @@ test('an inversion between two lanes is a reverse-strand record of its own when
   ])
 })
 
+// The same shape at a size the multi-way display names: 20 kb flanks around
+// a 15 kb stretch the haplotype runs backwards
+const largeInversionNodes = new Map(
+  [1, 2, 3, 4, 5].map(id => [
+    id,
+    {
+      refName: 'ref',
+      start: id * 100_000,
+      end: id * 100_000 + (id === 1 || id === 5 ? 20_000 : 5000),
+      rank: 0,
+      onWindow: true,
+    },
+  ]),
+)
+
+test('a walk turned against the reference for 10 kb or more gains a reverse-strand record of the turned stretch beside its own', () => {
+  expect(
+    drawn(anchorAligner(largeInversionNodes)(invertedLane, upperLane)),
+  ).toEqual([
+    {
+      query: '0-55000',
+      target: '0-55000',
+      strand: '+',
+      cigar: '20000=15000I15000D20000=',
+    },
+    {
+      query: '20000-35000',
+      target: '20000-35000',
+      strand: '-',
+      cigar: '15000=',
+    },
+  ])
+})
+
+// gfa-to-tabix --walks --refs GRCh38 --chunk 10000 over 20 kb flanks and three
+// 5 kb nodes:
+//   W GRCh38  0 chr1 >1>2>3>4>5
+//   W HG002   1 chr1 >1<4<3<2>5
+//   W HG00097 1 chr1 >1>2>3>4>5
+test('the anchor window answers a haplotype turned against the reference with a reverse-strand record of the turned stretch', async () => {
+  const records = await firstValueFrom(
+    makeAdapter({}, 'walks3_inversion')
+      .getFeatures({ ...window, end: 55_000 }, {})
+      .pipe(toArray()),
+  )
+  expect(
+    records
+      .filter(f => mateOf(f).assemblyName !== 'HG00097#1')
+      .map(f => ({
+        strand: f.get('strand'),
+        start: f.get('start'),
+        end: f.get('end'),
+      })),
+  ).toEqual([
+    { strand: 1, start: 0, end: 55_000 },
+    { strand: -1, start: 20_000, end: 35_000 },
+  ])
+})
+
+test('a walk turned for under 10 kb, or reversed whole, keeps its one record', () => {
+  expect(drawn(anchorAligner(inversionNodes)(invertedLane, upperLane))).toEqual(
+    drawn(referenceAligner(inversionNodes)(invertedLane, upperLane)),
+  )
+  const reversed = fragment('HG002#3#chr1', [
+    [5, 1],
+    [4, 1],
+    [3, 1],
+    [2, 1],
+    [1, 1],
+  ])
+  expect(
+    drawn(anchorAligner(largeInversionNodes)(reversed, upperLane)),
+  ).toEqual(drawn(referenceAligner(largeInversionNodes)(reversed, upperLane)))
+})
+
 test.each([
   ['the whole reference', window],
   ['a window inside it', { ...window, start: 1300, end: 2300 }],

package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts

@@ -10,7 +10,7 @@ import { updateStatus } from '@jbrowse/core/util'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { walksKept } from '@jbrowse/graph-walks'
 
-import { chainFeature, lanePairAligner, referenceAligner } from './walkLanes.ts'
+import { anchorAligner, chainFeature, lanePairAligner } from './walkLanes.ts'
 import { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'
 import { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'
 import { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'
@@ -168,7 +168,7 @@ export default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<Walk
       opts,
       `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,
     )
-    const align = referenceAligner(graph.nodes)
+    const align = anchorAligner(graph.nodes)
     const asmByPrefix = assemblyByPanSNPrefix(this)
     const references = fragments.filter(f => f.name === refName)
     // lanes come back in the order the fetch names them, which is the order

package/src/WalkTabixSyntenyAdapter/walkLanes.ts

@@ -173,20 +173,9 @@ function singleVisits(fragment: WalkFragment) {
   return rev
 }
 
-/**
- * Aligns one lane's walk fragment to another's. The weighted subsequence
- * (`referenceAligner`) is the fast route and matches through copy-number
- * arrays, but it reads one direction per pair, so an inversion between the
- * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp
- * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to
- * pair chaining (`walkAligner`) instead, which answers the inverted stretch as
- * a reverse-strand record of its own. Chaining leaves out every node a walk
- * passes twice, so counting singly visited nodes misses no inversion it could
- * draw.
- */
-export function lanePairAligner(nodes: Map<number, WalkNode>) {
-  const subsequence = referenceAligner(nodes)
-  const chained = walkAligner(nodes)
+// The bases on singly visited nodes two walks pass the same way and the
+// opposite way
+function directionShares(nodes: Map<number, WalkNode>) {
   const visits = new Map<WalkFragment, Map<number, number>>()
   const visitsOf = (fragment: WalkFragment) => {
     let found = visits.get(fragment)
@@ -196,7 +185,7 @@ export function lanePairAligner(nodes: Map<number, WalkNode>) {
     }
     return found
   }
-  const inverted = (query: WalkFragment, target: WalkFragment) => {
+  return (query: WalkFragment, target: WalkFragment) => {
     const theirs = visitsOf(target)
     let same = 0
     let opposite = 0
@@ -208,12 +197,60 @@ export function lanePairAligner(nodes: Map<number, WalkNode>) {
         opposite += nodeLength(nodes, id)
       }
     }
-    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP
+    return { same, opposite }
   }
-  return (query: WalkFragment, target: WalkFragment) =>
-    inverted(query, target)
+}
+
+/**
+ * Aligns one lane's walk fragment to another's. The weighted subsequence
+ * (`referenceAligner`) is the fast route and matches through copy-number
+ * arrays, but it reads one direction per pair, so an inversion between the
+ * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp
+ * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to
+ * pair chaining (`walkAligner`) instead, which answers the inverted stretch as
+ * a reverse-strand record of its own. Chaining leaves out every node a walk
+ * passes twice, so counting singly visited nodes misses no inversion it could
+ * draw.
+ */
+export function lanePairAligner(nodes: Map<number, WalkNode>) {
+  const subsequence = referenceAligner(nodes)
+  const chained = walkAligner(nodes)
+  const shares = directionShares(nodes)
+  return (query: WalkFragment, target: WalkFragment) => {
+    const { same, opposite } = shares(query, target)
+    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP
       ? chained(query, target)
       : subsequence(query, target)
+  }
+}
+
+// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names
+// no inversion there
+const TURNED_MIN_BP = 10_000
+
+/**
+ * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`
+ * does, then adds the stretches it reads the other way. A walk sharing
+ * TURNED_MIN_BP or more of singly visited nodes in each direction is chained
+ * too, and the chained records on the strand the subsequence did not take are
+ * its turned stretches. The subsequence record stays, so a copy-number array,
+ * which chaining leaves out, still matches one pass alike in every lane.
+ */
+export function anchorAligner(nodes: Map<number, WalkNode>) {
+  const subsequence = referenceAligner(nodes)
+  const chained = walkAligner(nodes)
+  const shares = directionShares(nodes)
+  return (query: WalkFragment, target: WalkFragment) => {
+    const records = subsequence(query, target)
+    const taken = records[0]?.strand
+    const { same, opposite } = shares(query, target)
+    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP
+      ? records
+      : [
+          ...records,
+          ...chained(query, target).filter(chain => chain.strand !== taken),
+        ]
+  }
 }
 
 /**

package/src/version.ts

@@ -1 +1 @@
-export const version = '7.2.0'
+export const version = '7.3.0'

package/dist/chunks/GbzBaseSyntenyAdapter-NB6WBBZH.js

@@ -1,2 +0,0 @@
-import{a as ne,b as ae,c as ue,d as re,e as oe,f as O,g as ie,h as se}from"./chunk-JLGPQO5L.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-LXCMWL7B.js";import"./chunk-O7Y7LYN6.js";import{b as z,c as E}from"./chunk-N4WBX2OS.js";import"./chunk-BWP3XYKD.js";import"./chunk-M2D7NUOY.js";import{a as te}from"./chunk-PFAHNHMM.js";import"./chunk-VDHDEEMF.js";import{a as K,c as L,m as V}from"./chunk-EDSIYH4H.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{g as F,h as N,i as C}from"./chunk-GUXZESDR.js";import"./chunk-T4R3ZVEM.js";import{d as G,g as X,h as Y,i as J}from"./chunk-IKJZPPOA.js";import"./chunk-7WIBGKBU.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as _,o as B}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), 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(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.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<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.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),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-NB6WBBZH.js.map

package/dist/chunks/MinigraphBubbleAdapter-HDLUZ6YF.js

@@ -1,2 +0,0 @@
-import{a as f,d as c,f as d}from"./chunk-6WA6WF6A.js";import{a as g}from"./chunk-KOB7YIMR.js";import{b,h as m,m as p,o as u}from"./chunk-EDSIYH4H.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-GUXZESDR.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-HDLUZ6YF.js.map

package/dist/chunks/RgfaTabixAdapter-XZRTWQMZ.js

@@ -1,3 +0,0 @@
-import{a as I}from"./chunk-ZNT7TQLN.js";import{a as w}from"./chunk-KOB7YIMR.js";import"./chunk-PFAHNHMM.js";import"./chunk-VDHDEEMF.js";import{b as L,h as d,m as p,n as y,o as F}from"./chunk-EDSIYH4H.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-GUXZESDR.js";import{d as N}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as k,o as h}from"./chunk-TENPGIPX.js";function u(s){let n=s.split("	"),t=n.length>=8,a=t?5:0;return{anchored:t,segment:{refName:n[a],start:+n[a+1],end:+n[a+2],id:n[3],rank:+n[4],tags:n[t?8:5]??""}}}function v(s){let n=s.tags.split(" ").find(a=>a.startsWith("SM:Z:"));if(n===void 0)return;let t=n.slice(5).split(",").map(a=>a.trim()).filter(Boolean);return t.length>0?t:void 0}function M(s){return{id:s.slice(0,-1),strand:s.slice(-1)}}function $(s){let n=s.split("	"),t=M(n[3]),a=M(n[4]);return{source:t.id,sourceStrand:t.strand,target:a.id,targetStrand:a.strand,sourceSegment:{id:t.id,refName:n[5],start:+n[6],end:+n[7],rank:+n[8],tags:n[13]??""},targetSegment:{id:a.id,refName:n[9],start:+n[10],end:+n[11],rank:+n[12],tags:n[14]??""}}}function B(s){return`${s.source}${s.sourceStrand}${s.target}${s.targetStrand}`}function S(s,n,t){n.set(B(t),t);let a=[];for(let e of[t.sourceSegment,t.targetSegment])s.has(e.id)||(s.set(e.id,e),a.push(e));return a}function O(s,n,t){let a=i=>i.rank!==0||i.refName!==t.refName?0:i.end<=t.start?-1:i.start>=t.end?1:0,e=new Map(s),r=new Map;for(let i of n)(s.has(i.source)||s.has(i.target)||a(i.sourceSegment)*a(i.targetSegment)===-1)&&S(e,r,i);for(let i of n)e.has(i.source)&&e.has(i.target)&&r.set(B(i),i);return{segments:e,links:r}}function A(s,n,t){let a=e=>e.refName!==t.refName||e.end<=t.start||e.start>=t.end;return[...C(s.filter(e=>e.rank>0),e=>n.has(e.id),t.end-t.start),...C(s.filter(e=>e.rank===0&&a(e)),()=>!0,0)]}function C(s,n,t){let a=[...s].sort((r,i)=>l(r.refName,i.refName)||r.start-i.start),e=[];for(let r of a){let i=e.at(-1);i?.refName===r.refName&&r.start-i.end<=t?(i.needed||=r.start>i.end||n(r),i.end=Math.max(i.end,r.end)):e.push({refName:r.refName,start:r.start,end:r.end,needed:n(r)})}return e.filter(r=>r.needed).map(({refName:r,start:i,end:o})=>({refName:r,start:i,end:o}))}function T(s,n,t){let a=e=>n.has(e.id)||t.some(r=>r.refName===e.refName&&e.start>=r.start&&e.end<=r.end);return s.filter(e=>a(e.sourceSegment)&&a(e.targetSegment))}var W=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function j(s){let{id:n,refName:t,start:a,end:e,rank:r,tags:i}=s,o=i.split(" ").filter(f=>W.test(f)),g=o.length===0?"":`	${o.join("	")}`;return`S	${n}	*	LN:i:${e-a}	SN:Z:${t}	SO:i:${a}	SR:i:${r}${g}`}function P(s){let{source:n,sourceStrand:t,target:a,targetStrand:e}=s;return`L	${n}	${t}	${a}	${e}	0M`}function l(s,n){return s<n?-1:s>n?1:0}function R(s,n){let t=[...s.values()].sort((e,r)=>l(e.refName,r.refName)||e.start-r.start||l(e.id,r.id)),a=[...n.keys()].sort((e,r)=>l(e,r));return["H	VN:Z:1.0",...t.map(e=>j(e)),...a.map(e=>P(n.get(e)))].join(`
-`)}function Z(s){return s.filter(n=>n.rank>0)}async function x(s,n,t){let a=[];return await d(s,n.refName,n.start,n.end,{signal:t,lineCallback:e=>{a.push($(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-XZRTWQMZ.js.map

package/dist/chunks/RgfaTabixAdapter-XZRTWQMZ.js.map

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-{
-  "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 {\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"],
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-}

package/dist/chunks/WalkTabixSyntenyAdapter-WBHOZLAN.js

@@ -1,2 +0,0 @@
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the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(n,e,t)}async laneWalks(e,t,n,r,a){return I(a,r.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:r.signal,keep:j(n,e),links:!1}).catch(s=>{throw K(s,t.end-t.start)}))}async anchorFeatures(e,t,n){let r=n.haplotypes?.length?n.haplotypes.map(l=>w(this,l)):void 0,a=w(this,n.targetAssemblyName),s=a===void 0?r:r===void 0||r.some(l=>F(a,l)||F(l,a))?[a]:[];if(s?.length===0)return[];let{start:c,end:u}=t,{graph:h,fragments:m}=await this.laneWalks(e,t,s,n,`Reading walks ${t.refName}:${c.toLocaleString()}-${u.toLocaleString()}`),p=C(h.nodes),g=x(this),d=m.filter(l=>l.name===e),f=l=>s===void 0?0:s.findIndex(y=>F(l.name,y));return m.filter(l=>l.name!==e&&f(l)>=0).sort((l,y)=>f(l)-f(y)).flatMap(l=>d.flatMap(y=>p(l,y).map(S=>L({chain:S,target:y,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(g,re(l))}))))}async pairFeatures(e,t,n,r){let a=n.map(m=>({pair:m,featurePrefix:w(this,m.queryAssemblyName),matePrefix:w(this,m.targetAssemblyName)})),{graph:s,fragments:c}=await this.laneWalks(e,t,a.flatMap(m=>[m.featurePrefix,m.matePrefix]),r,G(n)),u=Z(s.nodes),h=m=>c.filter(p=>F(p.name,m));return a.flatMap(({pair:m,featurePrefix:p,matePrefix:g})=>h(p).flatMap(d=>h(g).flatMap(f=>u(f,d).map(N=>L({chain:N,target:d,query:f,assemblyName:m.queryAssemblyName,refName:P(d.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return D(async n=>{let r=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(r!==void 0){let a=z(t),s=a.length>0?await this.pairFeatures(r,e,a,t):await this.anchorFeatures(r,e,t);for(let c of s)n.next(c)}n.complete()},t.signal)}};export{R as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-WBHOZLAN.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-WBHOZLAN.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
-  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const length = nodeLength(nodes, id)\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => nodeLength(nodes, handle >> 1)\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  const inverted = (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    inverted(query, target)\n      ? chained(query, target)\n      : subsequence(query, target)\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport { chainFeature, lanePairAligner, referenceAligner } from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.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'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    this,\n  )\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    return this.walks.haplotypeNames(opts)\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.walks.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const refName = await this.refNames.resolve(region, { signal: opts.signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    return this.walks.subgraph(refName, region, opts)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep: walksKept(prefixes, refName),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = referenceAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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-  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "handlesOf", "fragment", "id", "nodeLength", "nodes", "node", "walkAligner", "standIn", "sequenceOf", "length", "sequence", "handles", "cachedHandles", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "singleVisits", "rev", "twice", "lanePairAligner", "subsequence", "chained", "visits", "visitsOf", "found", "inverted", "theirs", "opposite", "other", "chainFeature", "chain", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openTabixSlot", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "updateStatus", "walksKept", "error", "laneZoomNotice", "wanted", "lane", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "align", "referenceAligner", "references", "f", "rank", "a", "b", "query", "reference", "chain", "chainFeature", "pairs", "sides", "pair", "side", "lanePairsStatus", "lanePairAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
-}

package/dist/chunks/chunk-BWP3XYKD.js

@@ -1,2 +0,0 @@
-function c(t,s,e){let i=t.get(s);i?i.push(e):t.set(s,[e])}function v(t,s,e){let i=t.get(s);i?i.add(e):t.set(s,new Set([e]))}function w(t,s){let e=new Map;for(let i of t)c(e,s(i),i);return e}function p(t,s){let e=0,i=t;for(;e<i;){let n=e+i>>1;s(n)?e=n+1:i=n}return e}var d=0;function I(t){return t.stable!==void 0}function g(t){return t.stable?.rank===d}function k(t){return t.stable!==void 0&&t.stable.rank>d}function M(t){return t.nodes.filter(g)}function O(t,s){return t.stable.start<s.end&&t.stable.start+t.length>s.start}function E(t){let s={};for(let e of t)s[e.id]=[{x:e.stable.start,y:0},{x:e.stable.start+e.length,y:0}];return s}function P(t,s){return p(t.length,e=>t[e].stable.start<s)}function m(t){let s=1/0,e=-1/0;for(let i of t)s=Math.min(s,i.stable.start),e=Math.max(e,i.stable.start+i.length);return e-s}function S(t,s){return s&&s.end>s.start?s.end-s.start:m(t)}var b=class{constructor(t){this.segments=t.segments,this.offsets=t.offsets,this.path=t.path,this.start=t.start,this.reversed=t.reversed,this.paths=t.paths,this.samples=t.samples,this.slots=new Map(this.segments.map((s,e)=>[s,e]))}static from(t){let s=new u;for(let[e,i]of t){s.declare(e);for(let n of i)s.add(e,n.path,n.sample,n.start,n.strand==="-")}return s.build()}get size(){return this.segments.length}slot(t){return this.slots.get(t)??-1}pathIndex(t){return this.paths.indexOf(t)}firstBy(t,s){for(let e=this.offsets[t];e<this.offsets[t+1];e++)if(this.path[e]===s)return e;return-1}replay(){let t=new Map;return(s,e)=>{if(s<0||e<0)return-1;let i=s*this.paths.length+e,n=this.offsets[s+1],h=t.get(i)??this.offsets[s];for(;h<n&&this.path[h]!==e;)h++;return t.set(i,h+1),h<n?h:-1}}filter(t,s=()=>!0){let e=this.paths.map(t),i=new u;return this.segments.forEach((n,h)=>{if(!s(n))return;let o=i.declare(n);for(let a=this.offsets[h];a<this.offsets[h+1];a++){let r=this.path[a];e[r]&&i.addAt(o,i.pathOf(this.paths[r],this.samples[r]),this.start[a],this.reversed[a]===1)}}),i.build()}strand(t){return this.reversed[t]?"-":"+"}visit(t){let s=this.path[t];return{path:this.paths[s],sample:this.samples[s],start:this.start[t],strand:this.strand(t)}}visitsAt(t){let s=[];for(let e=this.offsets[t];e<this.offsets[t+1];e++)s.push(this.visit(e));return s}get(t){let s=this.slot(t);return s<0?void 0:this.visitsAt(s)}has(t){return this.slots.has(t)}keys(){return this.segments[Symbol.iterator]()}*values(){for(let t=0;t<this.segments.length;t++)yield this.visitsAt(t)}*entries(){for(let t=0;t<this.segments.length;t++)yield[this.segments[t],this.visitsAt(t)]}[Symbol.iterator](){return this.entries()}},l=class{constructor(t){this.data=t,this.length=0}push(t){if(this.length===this.data.length){let s=new this.data.constructor(this.data.length*2);s.set(this.data),this.data=s}this.data[this.length++]=t}},u=class{constructor(){this.segments=[],this.slots=new Map,this.paths=[],this.samples=[],this.pathIndex=new Map,this.slot=new l(new Int32Array(1024)),this.path=new l(new Int32Array(1024)),this.start=new l(new Float64Array(1024)),this.reversed=new l(new Uint8Array(1024))}declare(t){let s=this.slots.get(t);return s===void 0&&(s=this.segments.length,this.slots.set(t,s),this.segments.push(t)),s}pathOf(t,s){let e=this.pathIndex.get(t);return e===void 0&&(e=this.paths.length,this.pathIndex.set(t,e),this.paths.push(t),this.samples.push(s)),e}add(t,s,e,i,n){this.addAt(this.declare(t),this.pathOf(s,e),i,n)}addAt(t,s,e,i){this.slot.push(t),this.path.push(s),this.start.push(e),this.reversed.push(i?1:0)}build(){let t=this.slot.length,s=this.segments.length,e=new Int32Array(s+1),i=this.slot.data;for(let r=0;r<t;r++)e[i[r]+1]++;for(let r=0;r<s;r++)e[r+1]+=e[r];let n=e.slice(0,s),h=new Int32Array(t),o=new Float64Array(t),a=new Uint8Array(t);for(let r=0;r<t;r++){let f=n[i[r]]++;h[f]=this.path.data[r],o[f]=this.start.data[r],a[f]=this.reversed.data[r]}return new b({segments:this.segments,offsets:e,path:h,start:o,reversed:a,paths:this.paths,samples:this.samples})}};export{c as a,v as b,w as c,p as d,d as e,I as f,g,k as h,M as i,O as j,E as k,P as l,m,S as n,b as o,l as p,u as q};
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package/dist/chunks/chunk-BWP3XYKD.js.map

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-{
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-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BSOZW3FC.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HOAIOEI7.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-RJWPJCIB.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-ZPZ7GNBT.js"],
-  "sourcesContent": ["// src/util/groups.ts\nfunction pushTo(map, key, value) {\n  const list = map.get(key);\n  if (list) {\n    list.push(value);\n  } else {\n    map.set(key, [value]);\n  }\n}\nfunction addTo(map, key, value) {\n  const set = map.get(key);\n  if (set) {\n    set.add(value);\n  } else {\n    map.set(key, /* @__PURE__ */ new Set([value]));\n  }\n}\nfunction groupBy(items, keyOf) {\n  const groups = /* @__PURE__ */ new Map();\n  for (const item of items) {\n    pushTo(groups, keyOf(item), item);\n  }\n  return groups;\n}\n\nexport {\n  pushTo,\n  addTo,\n  groupBy\n};\n", "// src/util/partitionPoint.ts\nfunction partitionPoint(n, pred) {\n  let lo = 0;\n  let hi = n;\n  while (lo < hi) {\n    const mid = lo + hi >> 1;\n    if (pred(mid)) {\n      lo = mid + 1;\n    } else {\n      hi = mid;\n    }\n  }\n  return lo;\n}\n\nexport {\n  partitionPoint\n};\n", "import {\n  partitionPoint\n} from \"./chunk-HOAIOEI7.js\";\n\n// src/anchoredNodes.ts\nvar REFERENCE_RANK = 0;\nfunction isAnchored(node) {\n  return node.stable !== void 0;\n}\nfunction isBackbone(node) {\n  return node.stable?.rank === REFERENCE_RANK;\n}\nfunction isOffReference(node) {\n  return node.stable !== void 0 && node.stable.rank > REFERENCE_RANK;\n}\nfunction backboneNodes(graph) {\n  return graph.nodes.filter(isBackbone);\n}\nfunction overlapsWindow(node, window) {\n  return node.stable.start < window.end && node.stable.start + node.length > window.start;\n}\nfunction backbonePositions(backbone) {\n  const positions = {};\n  for (const node of backbone) {\n    positions[node.id] = [\n      { x: node.stable.start, y: 0 },\n      { x: node.stable.start + node.length, y: 0 }\n    ];\n  }\n  return positions;\n}\nfunction firstNodeAtOrAfter(nodes, bp) {\n  return partitionPoint(nodes.length, (i) => nodes[i].stable.start < bp);\n}\nfunction backboneSpan(backbone) {\n  let min = Infinity;\n  let max = -Infinity;\n  for (const node of backbone) {\n    min = Math.min(min, node.stable.start);\n    max = Math.max(max, node.stable.start + node.length);\n  }\n  return max - min;\n}\nfunction referenceSpan(backbone, region) {\n  return region && region.end > region.start ? region.end - region.start : backboneSpan(backbone);\n}\n\nexport {\n  REFERENCE_RANK,\n  isAnchored,\n  isBackbone,\n  isOffReference,\n  backboneNodes,\n  overlapsWindow,\n  backbonePositions,\n  firstNodeAtOrAfter,\n  backboneSpan,\n  referenceSpan\n};\n", "// src/pathVisits.ts\nvar PathVisits = class {\n  constructor(columns) {\n    this.segments = columns.segments;\n    this.offsets = columns.offsets;\n    this.path = columns.path;\n    this.start = columns.start;\n    this.reversed = columns.reversed;\n    this.paths = columns.paths;\n    this.samples = columns.samples;\n    this.slots = new Map(this.segments.map((s, i) => [s, i]));\n  }\n  static from(entries) {\n    const builder = new PathVisitsBuilder();\n    for (const [segment, visits] of entries) {\n      builder.declare(segment);\n      for (const v of visits) {\n        builder.add(segment, v.path, v.sample, v.start, v.strand === \"-\");\n      }\n    }\n    return builder.build();\n  }\n  get size() {\n    return this.segments.length;\n  }\n  // the segment's index into `segments` and `offsets`, -1 when unvisited\n  slot(segment) {\n    return this.slots.get(segment) ?? -1;\n  }\n  pathIndex(path) {\n    return this.paths.indexOf(path);\n  }\n  // the first of `slot`'s visits by path `p`, -1 for none\n  firstBy(slot, p) {\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      if (this.path[i] === p) {\n        return i;\n      }\n    }\n    return -1;\n  }\n  // Paths' steps replayed in walk order against their visits: the k-th call\n  // for one path and segment answers that path's k-th visit there, -1 past\n  // its last. A walk in pieces lists its pieces in path order, so replaying\n  // the pieces in order reads each step's own visit.\n  replay() {\n    const cursor = /* @__PURE__ */ new Map();\n    return (slot, p) => {\n      if (slot < 0 || p < 0) {\n        return -1;\n      }\n      const key = slot * this.paths.length + p;\n      const end = this.offsets[slot + 1];\n      let at = cursor.get(key) ?? this.offsets[slot];\n      while (at < end && this.path[at] !== p) {\n        at++;\n      }\n      cursor.set(key, at + 1);\n      return at < end ? at : -1;\n    };\n  }\n  // the visits of paths `keepPath` accepts, at segments `keepSegment` does\n  filter(keepPath, keepSegment = () => true) {\n    const kept = this.paths.map(keepPath);\n    const builder = new PathVisitsBuilder();\n    this.segments.forEach((segment, s) => {\n      if (!keepSegment(segment)) {\n        return;\n      }\n      const slot = builder.declare(segment);\n      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {\n        const p = this.path[i];\n        if (kept[p]) {\n          builder.addAt(\n            slot,\n            builder.pathOf(this.paths[p], this.samples[p]),\n            this.start[i],\n            this.reversed[i] === 1\n          );\n        }\n      }\n    });\n    return builder.build();\n  }\n  strand(i) {\n    return this.reversed[i] ? \"-\" : \"+\";\n  }\n  visit(i) {\n    const p = this.path[i];\n    return {\n      path: this.paths[p],\n      sample: this.samples[p],\n      start: this.start[i],\n      strand: this.strand(i)\n    };\n  }\n  visitsAt(slot) {\n    const out = [];\n    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {\n      out.push(this.visit(i));\n    }\n    return out;\n  }\n  get(segment) {\n    const slot = this.slot(segment);\n    return slot < 0 ? void 0 : this.visitsAt(slot);\n  }\n  has(segment) {\n    return this.slots.has(segment);\n  }\n  keys() {\n    return this.segments[Symbol.iterator]();\n  }\n  *values() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield this.visitsAt(s);\n    }\n  }\n  *entries() {\n    for (let s = 0; s < this.segments.length; s++) {\n      yield [this.segments[s], this.visitsAt(s)];\n    }\n  }\n  [Symbol.iterator]() {\n    return this.entries();\n  }\n};\nvar Column = class {\n  constructor(data) {\n    this.data = data;\n    this.length = 0;\n  }\n  push(value) {\n    if (this.length === this.data.length) {\n      const grown = new this.data.constructor(\n        this.data.length * 2\n      );\n      grown.set(this.data);\n      this.data = grown;\n    }\n    this.data[this.length++] = value;\n  }\n};\nvar PathVisitsBuilder = class {\n  constructor() {\n    this.segments = [];\n    this.slots = /* @__PURE__ */ new Map();\n    this.paths = [];\n    this.samples = [];\n    this.pathIndex = /* @__PURE__ */ new Map();\n    this.slot = new Column(new Int32Array(1024));\n    this.path = new Column(new Int32Array(1024));\n    this.start = new Column(new Float64Array(1024));\n    this.reversed = new Column(new Uint8Array(1024));\n  }\n  // a segment's place in iteration order, though it has no visits yet\n  declare(segment) {\n    let s = this.slots.get(segment);\n    if (s === void 0) {\n      s = this.segments.length;\n      this.slots.set(segment, s);\n      this.segments.push(segment);\n    }\n    return s;\n  }\n  // a path's index, so a caller adding many of its visits names it once\n  pathOf(path, sample) {\n    let p = this.pathIndex.get(path);\n    if (p === void 0) {\n      p = this.paths.length;\n      this.pathIndex.set(path, p);\n      this.paths.push(path);\n      this.samples.push(sample);\n    }\n    return p;\n  }\n  add(segment, path, sample, start, reversed) {\n    this.addAt(\n      this.declare(segment),\n      this.pathOf(path, sample),\n      start,\n      reversed\n    );\n  }\n  addAt(slot, path, start, reversed) {\n    this.slot.push(slot);\n    this.path.push(path);\n    this.start.push(start);\n    this.reversed.push(reversed ? 1 : 0);\n  }\n  build() {\n    const n = this.slot.length;\n    const segments = this.segments.length;\n    const offsets = new Int32Array(segments + 1);\n    const slot = this.slot.data;\n    for (let i = 0; i < n; i++) {\n      offsets[slot[i] + 1]++;\n    }\n    for (let s = 0; s < segments; s++) {\n      offsets[s + 1] += offsets[s];\n    }\n    const fill = offsets.slice(0, segments);\n    const path = new Int32Array(n);\n    const start = new Float64Array(n);\n    const reversed = new Uint8Array(n);\n    for (let i = 0; i < n; i++) {\n      const at = fill[slot[i]]++;\n      path[at] = this.path.data[i];\n      start[at] = this.start.data[i];\n      reversed[at] = this.reversed.data[i];\n    }\n    return new PathVisits({\n      segments: this.segments,\n      offsets,\n      path,\n      start,\n      reversed,\n      paths: this.paths,\n      samples: this.samples\n    });\n  }\n};\n\nexport {\n  PathVisits,\n  Column,\n  PathVisitsBuilder\n};\n"],
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-}