jbrowse-plugin-graphgenomeviewer 8.3.4 → 8.3.5

package/README.md

@@ -4,8 +4,8 @@
   - a [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) walk file
     (`<prefix>.<sample>.walks.bed.gz` beside its `.tbi`), opened with File →
     **Open track**
-  - a gfa-to-tabix segments index (`<prefix>.segs.bed.gz` beside
-    `<prefix>.links.bed.gz` and a `.tbi` for each), opened the same way
+  - a gfa-to-tabix graph index (`<prefix>.graph.bed.gz` beside its `.tbi`, or
+    format 1's `.segs.bed.gz` and `.links.bed.gz` pair), opened the same way
   - a [gbz-base](https://github.com/jltsiren/gbz-base) database (`.gbz.db`),
     opened the same way
   - a GFA file (`.gfa` or `.gfa.gz`), opened whole with Add → **Graph genome

package/dist/chunks/{GbzBaseSyntenyAdapter-GX3NGJHG.js → GbzBaseSyntenyAdapter-RRLBONL5.js}

@@ -1,2 +1,2 @@
-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-WANYNRGU.js";import{a as te}from"./chunk-SYKOZDP6.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 $,i as W,k as U}from"./chunk-EVKN4Y3R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as V,a as K,c as L}from"./chunk-EENENDGZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/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-GX3NGJHG.js.map
+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-HMIJBEUE.js";import{a as te}from"./chunk-SYKOZDP6.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 $,i as W,k as U}from"./chunk-EVKN4Y3R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as V,a as K,c as L}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/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-RRLBONL5.js.map

package/dist/chunks/{MinigraphBubbleAdapter-XYAUUM35.js → MinigraphBubbleAdapter-P66QLENP.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-QB5JERW4.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-EENENDGZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.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-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-XYAUUM35.js.map
+import{a as f,d as c,f as d}from"./chunk-QB5JERW4.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${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-P66QLENP.js.map

package/dist/chunks/{RgfaTabixAdapter-SBIUUIRI.js → RgfaTabixAdapter-CQJROUIP.js}

@@ -1,2 +1,2 @@
-import{a as F}from"./chunk-OXU7F4BR.js";import"./chunk-SYKOZDP6.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-EENENDGZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
-//# sourceMappingURL=RgfaTabixAdapter-SBIUUIRI.js.map
+import{a as F}from"./chunk-KVZIGTH3.js";import"./chunk-SYKOZDP6.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
+//# sourceMappingURL=RgfaTabixAdapter-CQJROUIP.js.map

package/dist/chunks/{WalkFormsAdapter-ANELMZU4.js → WalkFormsAdapter-YSYANJD5.js}

@@ -1,2 +1,2 @@
-import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-OHQ3WIPI.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-EENENDGZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-ANELMZU4.js.map
+import{a as x,b,c as N,d as R,f as c,g as C,h as P,i as T}from"./chunk-RCJQCBBI.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-YSYANJD5.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-4I32E62Y.js

@@ -0,0 +1,2 @@
+import{a as ee}from"./chunk-KVZIGTH3.js";import{b as Z,d as J,e as Q,f as B,g as Y,h as L}from"./chunk-HMIJBEUE.js";import"./chunk-SYKOZDP6.js";import{a as V}from"./chunk-KOB7YIMR.js";import{p as E,q as U,r as X}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as G,F as K,i as z}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as O,c as $,d as F,g as M,h as A,i as v}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as P}from"./chunk-J5RMHLFJ.js";var le=50;function ce(a){let i=[];for(let e=0;e<a.length;e++){let[t,n]=a[e],[r,s]=a[e+1]??[];n===s&&n<=le&&(t==="I"&&r==="D"||t==="D"&&r==="I")?(i.push(["X",n]),e++):i.push([t,n])}return i}function I(a){return Array.from(a.ids,(i,e)=>2*i+a.rev[e])}function C(a,i){let e=a.get(i);return e===void 0?0:e.end-e.start}function te(a){let i=new Map,e=r=>{let s=C(a,r),o=i.get(s);return o===void 0&&(o="N".repeat(s),i.set(s,o)),o},t=new Map,n=r=>{let s=t.get(r);return s===void 0&&(s=I(r),t.set(r,s)),s};return(r,s)=>U({query:n(r),target:n(s),sequenceOf:e,bases:!1})}var _=100;function R(a,i,e){let t=a.at(-1);e>0&&(t?.[0]===i?t[1]+=e:a.push([i,e]))}function ae(a){let i=t=>C(a,t>>1),e=t=>{let n=new Float64Array(t.length+1);return t.forEach((r,s)=>{n[s+1]=n[s]+i(r)}),n};return(t,n)=>{let r=I(n),s=I(t),[o,p]=E(s,r,i),[h,u]=E(s.map(k=>k^1).reverse(),r,i),y=u>p,l=y?h:o,S=Math.max(p,u);if(S<_)return[];let f=e(r),W=e(s),N=k=>y?s.length-1-l[k][0]:l[k][0],c=[];l.forEach(([,k],w)=>{if(w>0){let[m,b]=[N(w-1),N(w)].sort((x,me)=>x-me);R(c,"I",W[b]-W[m+1]),R(c,"D",f[k]-f[l[w-1][1]+1])}R(c,"=",i(r[k]))});let[g,d]=[N(0),N(l.length-1)].sort((k,w)=>k-w);return[{queryStart:W[g],queryEnd:W[d+1],targetStart:f[l[0][1]],targetEnd:f[l.at(-1)[1]+1],strand:y?"-":"+",edits:c,sharedBases:S}]}}function pe(a){let i=new Map,e=new Set;a.ids.forEach((t,n)=>{i.has(t)?e.add(t):i.set(t,a.rev[n])});for(let t of e)i.delete(t);return i}function ne(a){let i=new Map,e=t=>{let n=i.get(t);return n===void 0&&(n=pe(t),i.set(t,n)),n};return(t,n)=>{let r=e(n),s=0,o=0;for(let[p,h]of e(t)){let u=r.get(p);u===h?s+=C(a,p):u!==void 0&&(o+=C(a,p))}return{same:s,opposite:o}}}function se(a){let i=ae(a),e=te(a),t=ne(a);return(n,r)=>{let{same:s,opposite:o}=t(n,r);return s>=_&&o>=_?e(n,r):i(n,r)}}var ue=1e4;function re(a){let i=ae(a),e=te(a),t=ne(a);return(n,r)=>{let s=i(n,r),o=s[0]?.strand,{same:p,opposite:h}=t(n,r);return o===void 0||Math.min(p,h)<ue?s:[...s,...e(n,r).filter(u=>u.strand!==o)]}}function T({chain:a,target:i,query:e,assemblyName:t,refName:n,mateAssemblyName:r}){let s=ce(a.edits);return L({target:{name:i.name,assemblyName:t,refName:n,start:i.hapStart+a.targetStart,end:i.hapStart+a.targetEnd},query:{name:e.name,assemblyName:r,refName:F(e.name),start:e.hapStart+a.queryStart,end:e.hapStart+a.queryEnd},strand:a.strand,cigar:X(s),matches:s.reduce((o,[p,h])=>o+(p==="="?h:0),0),columns:s.reduce((o,[,p])=>o+p,0)})}function ie(a,i,e,t){for(let{name:n,fragStart:r,hapStart:s,ids:o,rev:p}of e)if(n===a.name&&r===a.fragStart){let h=s;for(let u=0;u<o.length;u++){let y=t.get(o[u]),l=y===void 0?0:y.end-y.start;if(y?.rank===0&&y.refName===i&&y.end===a.refStart)return p[u]?{skip:a,at:h,strand:"-"}:{skip:a,at:h+l,strand:"+"};h+=l}}}function oe(a,i){return{name:a.name,assemblyName:i,refName:F(a.name),start:a.hapStart,end:a.hapEnd}}function j({skip:a,at:i},e){return{name:a.name,assemblyName:e,refName:F(a.name),start:i,end:i}}function D({target:a,query:i,strand:e}){return L({target:a,query:i,strand:e,matches:0,columns:Math.max(a.end-a.start,i.end-i.start)})}var H=({name:a})=>$(a)??a,q=class extends Z{constructor(){super(...arguments);this.walks=new ee(G(this,["walksLocation"],["walksIndex"]),this);this.refNames=new K(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:n}=this,r=A(this,n),s=v(this);return{hasCoarseTier:!1,anchorAssemblyName:n,lanes:t.filter(o=>o!==r&&O(o)!==r).map(o=>({name:B(s,o),label:o,group:O(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let n=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(n,e,t)}async laneWalks(e,t,n,r,s){let o=z(n,e);return P(s,r.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:r.signal,keep:o,expand:o,links:!1}).catch(p=>{throw Y(p,t.end-t.start)}))}async skipCrossings(e,{skips:t,fragments:n},r){let{signal:s}=r,o=new Set(n.map(H)),p=t.filter(l=>!o.has(H(l))),{chunk:h}=await this.walks.reader.header({signal:s}),u=new Map;for(let l of p){let S=Math.floor((l.refStart-1)/h),f=u.get(S);f?(f.group.push(l),f.start=Math.min(f.start,l.refStart-1),f.end=Math.max(f.end,l.refStart)):u.set(S,{group:[l],start:l.refStart-1,end:l.refStart})}return(await Promise.all([...u.values()].map(async({group:l,start:S,end:f})=>{let W=new Set(l.map(d=>d.name)),N=d=>W.has(d),{graph:c,fragments:g}=await this.walks.reader.cut(e,{start:S,end:f},{signal:s,keep:N,expand:N,context:0,links:!1});return l.map(d=>ie(d,e,g,c.nodes))}))).flat().filter(l=>l!==void 0)}async anchorFeatures(e,t,n){let r=n.haplotypes?.length?n.haplotypes.map(m=>A(this,m)):void 0,s=A(this,n.targetAssemblyName),o=s===void 0?r:r===void 0||r.some(m=>M(s,m)||M(m,s))?[s]:[];if(o?.length===0)return[];let{start:p,end:h}=t,u=`Reading walks ${t.refName}:${p.toLocaleString()}-${h.toLocaleString()}`,{graph:y,fragments:l,skips:S}=await this.laneWalks(e,t,o,n,u),f=({name:m})=>o===void 0?0:o.findIndex(b=>M(m,b)),W=await P(u,n.statusCallback,()=>this.skipCrossings(e,{skips:S.filter(m=>f(m)>=0),fragments:l},n)),N=re(y.nodes),c=v(this),g=m=>B(c,H(m)),d=l.filter(m=>m.name===e),k=l.filter(m=>m.name!==e&&f(m)>=0).map(m=>({rank:f(m),features:d.flatMap(b=>N(m,b).map(x=>T({chain:x,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:g(m)})))})),w=W.map(m=>{let{skip:b}=m;return{rank:f(b),features:[D({target:{name:e,assemblyName:t.assemblyName,refName:t.refName,start:b.refStart,end:b.refEnd},query:j(m,g(b)),strand:m.strand})]}});return[...k,...w].sort((m,b)=>m.rank-b.rank).flatMap(m=>m.features)}async pairFeatures(e,t,n,r){let s=n.map(c=>({pair:c,featurePrefix:A(this,c.queryAssemblyName),matePrefix:A(this,c.targetAssemblyName)})),o=Q(n),{graph:p,fragments:h,skips:u}=await this.laneWalks(e,t,s.flatMap(c=>[c.featurePrefix,c.matePrefix]),r,o),y=await P(o,r.statusCallback,()=>this.skipCrossings(e,{skips:u,fragments:h},r)),l=se(p.nodes),S=c=>h.filter(g=>M(g.name,c)),f=(c,g)=>S(c).map(d=>oe(d,g)),W=(c,g)=>y.filter(({skip:d})=>M(d.name,c)).map(d=>j(d,g)),N=(c,g)=>c.flatMap(d=>g.map(k=>D({target:d,query:k,strand:"+"})));return s.flatMap(({pair:c,featurePrefix:g,matePrefix:d})=>{let{queryAssemblyName:k,targetAssemblyName:w}=c;return[...S(g).flatMap(m=>S(d).flatMap(b=>l(b,m).map(x=>T({chain:x,target:m,query:b,assemblyName:k,refName:F(m.name),mateAssemblyName:w})))),...N(f(g,k),W(d,w)),...N(W(g,k),f(d,w))]})}getFeatures(e,t={}){return V(async n=>{let r=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(r!==void 0){let s=J(t),o=s.length>0?await this.pairFeatures(r,e,s,t):await this.anchorFeatures(r,e,t);for(let p of o)n.next(p)}n.complete()},t.signal)}};export{q as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-4I32E62Y.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-4I32E62Y.js.map

@@ -0,0 +1,7 @@
+{
+  "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 { MatchSide } from '../synteny/matchFeature.ts'\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode, WalkSkip } 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// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\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  return (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, opposite }\n  }\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 shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\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\n/** The point on a haplotype's contig where it crosses a skipped stretch */\nexport interface SkipCrossing {\n  skip: WalkSkip\n  at: number\n  strand: '+' | '-'\n}\n\n/**\n * Where a haplotype that skips the window crosses its deletion, from a cut\n * over the reference node it leaves at `skip.refStart`: past that node, or\n * where it enters the node when it passes it backwards, arriving across the\n * deletion\n */\nexport function skipCrossing(\n  skip: WalkSkip,\n  refName: string,\n  fragments: WalkFragment[],\n  nodes: Map<number, WalkNode>,\n): SkipCrossing | undefined {\n  for (const { name, fragStart, hapStart, ids, rev } of fragments) {\n    if (name === skip.name && fragStart === skip.fragStart) {\n      let at = hapStart\n      for (let i = 0; i < ids.length; i++) {\n        const node = nodes.get(ids[i]!)\n        const length = node === undefined ? 0 : node.end - node.start\n        if (\n          node?.rank === 0 &&\n          node.refName === refName &&\n          node.end === skip.refStart\n        ) {\n          return rev[i]\n            ? { skip, at, strand: '-' }\n            : { skip, at: at + length, strand: '+' }\n        }\n        at += length\n      }\n    }\n  }\n  return undefined\n}\n\n/** One side of a record: a walk fragment's extent on its contig */\nexport function walkSide(fragment: WalkFragment, assemblyName: string) {\n  return {\n    name: fragment.name,\n    assemblyName,\n    refName: panSNContig(fragment.name),\n    start: fragment.hapStart,\n    end: fragment.hapEnd,\n  }\n}\n\n/** One side of a record: the point where a haplotype crosses its deletion */\nexport function crossingSide({ skip, at }: SkipCrossing, assemblyName: string) {\n  return {\n    name: skip.name,\n    assemblyName,\n    refName: panSNContig(skip.name),\n    start: at,\n    end: at,\n  }\n}\n\n/**\n * A record with one side a haplotype's deletion crossing. With no CIGAR, a\n * display clipping it to a window maps the window onto that point, so the\n * haplotype gets a lane that the window's ribbon narrows to.\n */\nexport function crossingFeature({\n  target,\n  query,\n  strand,\n}: {\n  target: MatchSide\n  query: MatchSide\n  strand: string\n}) {\n  return matchFeature({\n    target,\n    query,\n    strand,\n    matches: 0,\n    columns: Math.max(target.end - target.start, query.end - query.start),\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 {\n  anchorAligner,\n  chainFeature,\n  crossingFeature,\n  crossingSide,\n  lanePairAligner,\n  skipCrossing,\n  walkSide,\n} 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 { MatchSide } from '../synteny/matchFeature.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 { WalkSkip } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = ({ name }: { name: string }) => panSNHaplotype(name) ?? 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.resolveForCut(region, {\n      signal: opts.signal,\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  // Named lanes come back in full where format 5 abridged them: an abridged\n  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32\n  // lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * Where each haplotype that skips the window crosses its deletion, read\n   * from cuts over the reference nodes they leave at, one cut per chunk those\n   * nodes fall in. A haplotype with a walk in the window draws that instead:\n   * NA19036#1 skips the IGL locus on one contig and walks it on another.\n   */\n  private async skipCrossings(\n    refName: string,\n    { skips, fragments }: { skips: WalkSkip[]; fragments: { name: string }[] },\n    opts: LaneFeatureOptions,\n  ) {\n    const { signal } = opts\n    const walked = new Set(fragments.map(haplotypeOf))\n    const crossing = skips.filter(skip => !walked.has(haplotypeOf(skip)))\n    const { chunk } = await this.walks.reader.header({ signal })\n    const byChunk = new Map<\n      number,\n      { group: WalkSkip[]; start: number; end: number }\n    >()\n    for (const skip of crossing) {\n      const cs = Math.floor((skip.refStart - 1) / chunk)\n      const held = byChunk.get(cs)\n      if (held) {\n        held.group.push(skip)\n        held.start = Math.min(held.start, skip.refStart - 1)\n        held.end = Math.max(held.end, skip.refStart)\n      } else {\n        byChunk.set(cs, {\n          group: [skip],\n          start: skip.refStart - 1,\n          end: skip.refStart,\n        })\n      }\n    }\n    const found = await Promise.all(\n      [...byChunk.values()].map(async ({ group, start, end }) => {\n        const names = new Set(group.map(skip => skip.name))\n        const keep = (name: string) => names.has(name)\n        const { graph, fragments } = await this.walks.reader.cut(\n          refName,\n          { start, end },\n          { signal, keep, expand: keep, context: 0, links: false },\n        )\n        return group.map(skip =>\n          skipCrossing(skip, refName, fragments, graph.nodes),\n        )\n      }),\n    )\n    return found.flat().filter(crossing => crossing !== undefined)\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. A haplotype whose\n   * deletion spans the window is one record of the skipped stretch, its mate\n   * the point where the haplotype crosses the deletion.\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 status = `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`\n    const { graph, fragments, skips } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      status,\n    )\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 = ({ name }: { name: string }) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix => panSNMatchesPrefix(name, prefix))\n    const crossings = await updateStatus(status, opts.statusCallback, () =>\n      this.skipCrossings(\n        refName,\n        { skips: skips.filter(skip => rank(skip) >= 0), fragments },\n        opts,\n      ),\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const laneOf = (walk: { name: string }) =>\n      laneAssemblyName(asmByPrefix, haplotypeOf(walk))\n    const references = fragments.filter(f => f.name === refName)\n    const walked = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .map(query => ({\n        rank: rank(query),\n        features: references.flatMap(reference =>\n          align(query, reference).map(chain =>\n            chainFeature({\n              chain,\n              target: reference,\n              query,\n              assemblyName: region.assemblyName,\n              refName: region.refName,\n              mateAssemblyName: laneOf(query),\n            }),\n          ),\n        ),\n      }))\n    const skipped = crossings.map(crossing => {\n      const { skip } = crossing\n      return {\n        rank: rank(skip),\n        features: [\n          crossingFeature({\n            target: {\n              name: refName,\n              assemblyName: region.assemblyName,\n              refName: region.refName,\n              start: skip.refStart,\n              end: skip.refEnd,\n            },\n            query: crossingSide(crossing, laneOf(skip)),\n            strand: crossing.strand,\n          }),\n        ],\n      }\n    })\n    return [...walked, ...skipped]\n      .sort((a, b) => a.rank - b.rank)\n      .flatMap(lane => lane.features)\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. A lane that skips the window pairs as the\n   * point where it crosses its deletion.\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 status = lanePairsStatus(pairs)\n    const { graph, fragments, skips } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      status,\n    )\n    const crossings = await updateStatus(status, opts.statusCallback, () =>\n      this.skipCrossings(refName, { skips, fragments }, opts),\n    )\n    const align = lanePairAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    const walkSides = (prefix: string, assemblyName: string) =>\n      walksOf(prefix).map(walk => walkSide(walk, assemblyName))\n    const crossingSides = (prefix: string, assemblyName: string) =>\n      crossings\n        .filter(({ skip }) => panSNMatchesPrefix(skip.name, prefix))\n        .map(crossing => crossingSide(crossing, assemblyName))\n    const crossed = (own: MatchSide[], mates: MatchSide[]) =>\n      own.flatMap(target =>\n        mates.map(query => crossingFeature({ target, query, strand: '+' })),\n      )\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) => {\n      const { queryAssemblyName, targetAssemblyName } = pair\n      return [\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: queryAssemblyName,\n                refName: panSNContig(target.name),\n                mateAssemblyName: targetAssemblyName,\n              }),\n            ),\n          ),\n        ),\n        ...crossed(\n          walkSides(featurePrefix, queryAssemblyName),\n          crossingSides(matePrefix, targetAssemblyName),\n        ),\n        ...crossed(\n          crossingSides(featurePrefix, queryAssemblyName),\n          walkSides(matePrefix, targetAssemblyName),\n        ),\n      ]\n    })\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": "mpBAYA,IAAMA,GAAyB,GAOxB,SAASC,GAAoBC,EAAmB,CACrD,IAAMC,EAAkB,CAAC,EACzB,QAASC,EAAI,EAAGA,EAAIF,EAAM,OAAQE,IAAK,CACrC,GAAM,CAACC,EAAIC,CAAG,EAAIJ,EAAME,CAAC,EACnB,CAACG,EAAQC,CAAO,EAAIN,EAAME,EAAI,CAAC,GAAK,CAAC,EAEzCE,IAAQE,GACRF,GAAON,KACLK,IAAO,KAAOE,IAAW,KAASF,IAAO,KAAOE,IAAW,MAE7DJ,EAAI,KAAK,CAAC,IAAKG,CAAG,CAAC,EACnBF,KAEAD,EAAI,KAAK,CAACE,EAAIC,CAAG,CAAC,CAEtB,CACA,OAAOH,CACT,CAGA,SAASM,EAAUC,EAAwB,CACzC,OAAO,MAAM,KAAKA,EAAS,IAAK,CAACC,EAAIP,IAAM,EAAIO,EAAKD,EAAS,IAAIN,CAAC,CAAE,CACtE,CAEA,SAASQ,EAAWC,EAA8BF,EAAY,CAC5D,IAAMG,EAAOD,EAAM,IAAIF,CAAE,EACzB,OAAOG,IAAS,OAAY,EAAIA,EAAK,IAAMA,EAAK,KAClD,CAOO,SAASC,GAAYF,EAA8B,CACxD,IAAMG,EAAU,IAAI,IACdC,EAAcN,GAAe,CACjC,IAAMO,EAASN,EAAWC,EAAOF,CAAE,EAC/BQ,EAAWH,EAAQ,IAAIE,CAAM,EACjC,OAAIC,IAAa,SACfA,EAAW,IAAI,OAAOD,CAAM,EAC5BF,EAAQ,IAAIE,EAAQC,CAAQ,GAEvBA,CACT,EACMC,EAAU,IAAI,IACdC,EAAiBX,GAA2B,CAChD,IAAIY,EAAQF,EAAQ,IAAIV,CAAQ,EAChC,OAAIY,IAAU,SACZA,EAAQb,EAAUC,CAAQ,EAC1BU,EAAQ,IAAIV,EAAUY,CAAK,GAEtBA,CACT,EACA,MAAO,CAACC,EAAqBC,IAC3BC,EAAe,CACb,MAAOJ,EAAcE,CAAK,EAC1B,OAAQF,EAAcG,CAAM,EAC5B,WAAAP,EACA,MAAO,EACT,CAAC,CACL,CAIA,IAAMS,EAAe,IAErB,SAASC,EAAWzB,EAAmBG,EAAiBC,EAAa,CACnE,IAAMsB,EAAO1B,EAAM,GAAG,EAAE,EACpBI,EAAM,IACJsB,IAAO,CAAC,IAAMvB,EAChBuB,EAAK,CAAC,GAAKtB,EAEXJ,EAAM,KAAK,CAACG,EAAIC,CAAG,CAAC,EAG1B,CAUO,SAASuB,GAAiBhB,EAA8B,CAC7D,IAAMiB,EAAYC,GAAmBnB,EAAWC,EAAOkB,GAAU,CAAC,EAC5DC,EAAWZ,GAAsB,CACrC,IAAMjB,EAAM,IAAI,aAAaiB,EAAQ,OAAS,CAAC,EAC/C,OAAAA,EAAQ,QAAQ,CAACW,EAAQ3B,IAAM,CAC7BD,EAAIC,EAAI,CAAC,EAAID,EAAIC,CAAC,EAAK0B,EAASC,CAAM,CACxC,CAAC,EACM5B,CACT,EAEA,MAAO,CAACoB,EAAqBC,IAAsC,CACjE,IAAMS,EAAMxB,EAAUe,CAAM,EACtBU,EAAMzB,EAAUc,CAAK,EACrB,CAACY,EAAMC,CAAU,EAAIC,EAAYH,EAAKD,EAAKH,CAAQ,EACnD,CAACQ,EAAQC,CAAY,EAAIF,EAC7BH,EAAI,IAAIH,GAAUA,EAAS,CAAC,EAAE,QAAQ,EACtCE,EACAH,CACF,EACMU,EAAUD,EAAeH,EACzBK,EAAQD,EAAUF,EAASH,EAC3BO,EAAc,KAAK,IAAIN,EAAYG,CAAY,EACrD,GAAIG,EAAchB,EAChB,MAAO,CAAC,EAEV,IAAMiB,EAAQX,EAAQC,CAAG,EACnBW,EAAQZ,EAAQE,CAAG,EAEnBW,EAAU,GACdL,EAAUN,EAAI,OAAS,EAAIO,EAAM,CAAC,EAAG,CAAC,EAAIA,EAAM,CAAC,EAAG,CAAC,EACjDvC,EAAoB,CAAC,EAC3BuC,EAAM,QAAQ,CAAC,CAAC,CAAEK,CAAC,EAAGC,IAAM,CAC1B,GAAIA,EAAI,EAAG,CACT,GAAM,CAACC,EAAIC,CAAE,EAAI,CAACJ,EAAOE,EAAI,CAAC,EAAGF,EAAOE,CAAC,CAAC,EAAE,KAAK,CAAC,EAAGG,KAAM,EAAIA,EAAC,EAChEvB,EAAWzB,EAAO,IAAK0C,EAAMK,CAAG,EAAKL,EAAMI,EAAM,CAAC,CAAE,EACpDrB,EAAWzB,EAAO,IAAKyC,EAAMG,CAAC,EAAKH,EAAMF,EAAMM,EAAI,CAAC,EAAG,CAAC,EAAI,CAAC,CAAE,CACjE,CACApB,EAAWzB,EAAO,IAAK4B,EAASG,EAAIa,CAAC,CAAE,CAAC,CAC1C,CAAC,EACD,GAAM,CAACE,EAAIC,CAAE,EAAI,CAACJ,EAAO,CAAC,EAAGA,EAAOJ,EAAM,OAAS,CAAC,CAAC,EAAE,KAAK,CAACU,EAAGD,IAAMC,EAAID,CAAC,EAC3E,MAAO,CACL,CACE,WAAYN,EAAMI,CAAG,EACrB,SAAUJ,EAAMK,EAAM,CAAC,EACvB,YAAaN,EAAMF,EAAM,CAAC,EAAG,CAAC,CAAC,EAC/B,UAAWE,EAAMF,EAAM,GAAG,EAAE,EAAG,CAAC,EAAI,CAAC,EACrC,OAAQD,EAAU,IAAM,IACxB,MAAAtC,EACA,YAAAwC,CACF,CACF,CACF,CACF,CAGA,SAASU,GAAa1C,EAAwB,CAC5C,IAAM2C,EAAM,IAAI,IACVC,EAAQ,IAAI,IAClB5C,EAAS,IAAI,QAAQ,CAACC,EAAIP,IAAM,CAC1BiD,EAAI,IAAI1C,CAAE,EACZ2C,EAAM,IAAI3C,CAAE,EAEZ0C,EAAI,IAAI1C,EAAID,EAAS,IAAIN,CAAC,CAAE,CAEhC,CAAC,EACD,QAAWO,KAAM2C,EACfD,EAAI,OAAO1C,CAAE,EAEf,OAAO0C,CACT,CAIA,SAASE,GAAgB1C,EAA8B,CACrD,IAAM2C,EAAS,IAAI,IACbC,EAAY/C,GAA2B,CAC3C,IAAIgD,EAAQF,EAAO,IAAI9C,CAAQ,EAC/B,OAAIgD,IAAU,SACZA,EAAQN,GAAa1C,CAAQ,EAC7B8C,EAAO,IAAI9C,EAAUgD,CAAK,GAErBA,CACT,EACA,MAAO,CAACnC,EAAqBC,IAAyB,CACpD,IAAMmC,EAASF,EAASjC,CAAM,EAC1BW,EAAO,EACPyB,EAAW,EACf,OAAW,CAACjD,EAAI0C,CAAG,IAAKI,EAASlC,CAAK,EAAG,CACvC,IAAMsC,EAAQF,EAAO,IAAIhD,CAAE,EACvBkD,IAAUR,EACZlB,GAAQvB,EAAWC,EAAOF,CAAE,EACnBkD,IAAU,SACnBD,GAAYhD,EAAWC,EAAOF,CAAE,EAEpC,CACA,MAAO,CAAE,KAAAwB,EAAM,SAAAyB,CAAS,CAC1B,CACF,CAaO,SAASE,GAAgBjD,EAA8B,CAC5D,IAAMkD,EAAclC,GAAiBhB,CAAK,EACpCmD,EAAUjD,GAAYF,CAAK,EAC3BoD,EAASV,GAAgB1C,CAAK,EACpC,MAAO,CAACU,EAAqBC,IAAyB,CACpD,GAAM,CAAE,KAAAW,EAAM,SAAAyB,CAAS,EAAIK,EAAO1C,EAAOC,CAAM,EAC/C,OAAOW,GAAQT,GAAgBkC,GAAYlC,EACvCsC,EAAQzC,EAAOC,CAAM,EACrBuC,EAAYxC,EAAOC,CAAM,CAC/B,CACF,CAIA,IAAM0C,GAAgB,IAUf,SAASC,GAActD,EAA8B,CAC1D,IAAMkD,EAAclC,GAAiBhB,CAAK,EACpCmD,EAAUjD,GAAYF,CAAK,EAC3BoD,EAASV,GAAgB1C,CAAK,EACpC,MAAO,CAACU,EAAqBC,IAAyB,CACpD,IAAM4C,EAAUL,EAAYxC,EAAOC,CAAM,EACnC6C,EAAQD,EAAQ,CAAC,GAAG,OACpB,CAAE,KAAAjC,EAAM,SAAAyB,CAAS,EAAIK,EAAO1C,EAAOC,CAAM,EAC/C,OAAO6C,IAAU,QAAa,KAAK,IAAIlC,EAAMyB,CAAQ,EAAIM,GACrDE,EACA,CACE,GAAGA,EACH,GAAGJ,EAAQzC,EAAOC,CAAM,EAAE,OAAO8C,GAASA,EAAM,SAAWD,CAAK,CAClE,CACN,CACF,CAMO,SAASE,EAAa,CAC3B,MAAAD,EACA,OAAA9C,EACA,MAAAD,EACA,aAAAiD,EACA,QAAAC,EACA,iBAAAC,CACF,EAOG,CACD,IAAMxE,EAAQD,GAAoBqE,EAAM,KAAK,EAC7C,OAAOK,EAAa,CAClB,OAAQ,CACN,KAAMnD,EAAO,KACb,aAAAgD,EACA,QAAAC,EACA,MAAOjD,EAAO,SAAW8C,EAAM,YAC/B,IAAK9C,EAAO,SAAW8C,EAAM,SAC/B,EACA,MAAO,CACL,KAAM/C,EAAM,KACZ,aAAcmD,EACd,QAASE,EAAYrD,EAAM,IAAI,EAC/B,MAAOA,EAAM,SAAW+C,EAAM,WAC9B,IAAK/C,EAAM,SAAW+C,EAAM,QAC9B,EACA,OAAQA,EAAM,OACd,MAAOO,EAAU3E,CAAK,EACtB,QAASA,EAAM,OAAO,CAAC4E,EAAK,CAACzE,EAAI0E,CAAC,IAAMD,GAAOzE,IAAO,IAAM0E,EAAI,GAAI,CAAC,EACrE,QAAS7E,EAAM,OAAO,CAAC4E,EAAK,CAAC,CAAEC,CAAC,IAAMD,EAAMC,EAAG,CAAC,CAClD,CAAC,CACH,CAeO,SAASC,GACdC,EACAR,EACAS,EACArE,EAC0B,CAC1B,OAAW,CAAE,KAAAsE,EAAM,UAAAC,EAAW,SAAAC,EAAU,IAAAC,EAAK,IAAAjC,CAAI,IAAK6B,EACpD,GAAIC,IAASF,EAAK,MAAQG,IAAcH,EAAK,UAAW,CACtD,IAAIM,EAAKF,EACT,QAASjF,EAAI,EAAGA,EAAIkF,EAAI,OAAQlF,IAAK,CACnC,IAAMU,EAAOD,EAAM,IAAIyE,EAAIlF,CAAC,CAAE,EACxBc,EAASJ,IAAS,OAAY,EAAIA,EAAK,IAAMA,EAAK,MACxD,GACEA,GAAM,OAAS,GACfA,EAAK,UAAY2D,GACjB3D,EAAK,MAAQmE,EAAK,SAElB,OAAO5B,EAAIjD,CAAC,EACR,CAAE,KAAA6E,EAAM,GAAAM,EAAI,OAAQ,GAAI,EACxB,CAAE,KAAAN,EAAM,GAAIM,EAAKrE,EAAQ,OAAQ,GAAI,EAE3CqE,GAAMrE,CACR,CACF,CAGJ,CAGO,SAASsE,GAAS9E,EAAwB8D,EAAsB,CACrE,MAAO,CACL,KAAM9D,EAAS,KACf,aAAA8D,EACA,QAASI,EAAYlE,EAAS,IAAI,EAClC,MAAOA,EAAS,SAChB,IAAKA,EAAS,MAChB,CACF,CAGO,SAAS+E,EAAa,CAAE,KAAAR,EAAM,GAAAM,CAAG,EAAiBf,EAAsB,CAC7E,MAAO,CACL,KAAMS,EAAK,KACX,aAAAT,EACA,QAASI,EAAYK,EAAK,IAAI,EAC9B,MAAOM,EACP,IAAKA,CACP,CACF,CAOO,SAASG,EAAgB,CAC9B,OAAAlE,EACA,MAAAD,EACA,OAAAoE,CACF,EAIG,CACD,OAAOhB,EAAa,CAClB,OAAAnD,EACA,MAAAD,EACA,OAAAoE,EACA,QAAS,EACT,QAAS,KAAK,IAAInE,EAAO,IAAMA,EAAO,MAAOD,EAAM,IAAMA,EAAM,KAAK,CACtE,CAAC,CACH,CCtVA,IAAMqE,EAAc,CAAC,CAAE,KAAAC,CAAK,IAAwBC,EAAeD,CAAI,GAAKA,EAEvDE,EAArB,cAAqDC,CAAsD,CAA3G,kCACE,KAAiB,MAAmB,IAAIC,GACtCC,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,IACF,EACA,KAAiB,SAA0B,IAAIC,EAC7C,KAAK,MAAM,KACX,IACF,EAEA,IAAY,QAAS,CACnB,IAAMC,EAAS,KAAK,QAAQ,eAAe,EAAE,CAAC,EAC9C,GAAIA,IAAW,OACb,MAAM,IAAI,MACR,gHACF,EAEF,OAAOA,CACT,CAMA,MAAM,kBAAkBC,EAAoB,CAAC,EAAG,CAC9C,OAAO,KAAK,MAAM,eAAeA,CAAI,CACvC,CAOA,MAAM,UAAUA,EAAoB,CAAC,EAAG,CACtC,GAAM,CAAE,WAAAC,CAAW,EAAI,MAAM,KAAK,MAAM,OAAO,OAAOD,CAAI,EACpD,CAAE,OAAAD,CAAO,EAAI,KACbG,EAAeC,EAAmB,KAAMJ,CAAM,EAC9CK,EAAcC,EAAsB,IAAI,EAC9C,MAAO,CACL,cAAe,GACf,mBAAoBN,EACpB,MAAOE,EACJ,OACCK,GACEA,IAAWJ,GAAgBK,EAAYD,CAAM,IAAMJ,CACvD,EACC,IAAII,IAAW,CACd,KAAME,EAAiBJ,EAAaE,CAAM,EAC1C,MAAOA,EACP,MAAOC,EAAYD,CAAM,CAC3B,EAAE,CACN,CACF,CAIA,MAAM,YAAYN,EAAoB,CAAC,EAAG,CACxC,GAAM,CAAE,aAAAS,CAAa,EAAIT,EACzB,OAAOS,IAAiB,QAAaA,IAAiB,KAAK,OACvD,KAAK,SAAS,iBAAiB,CAAE,GAAGT,EAAM,aAAc,KAAK,MAAO,CAAC,EACrE,CAAC,CACP,CAOA,MAAM,YAAYU,EAAgBV,EAA+B,CAAC,EAAG,CACnE,IAAMW,EAAU,MAAM,KAAK,SAAS,cAAcD,EAAQ,CACxD,OAAQV,EAAK,MACf,CAAC,EACD,OAAO,KAAK,MAAM,SAASW,EAASD,EAAQV,CAAI,CAClD,CAOA,MAAc,UACZW,EACAD,EACAE,EACAZ,EACAa,EACA,CACA,IAAMC,EAAOC,EAAUH,EAAUD,CAAO,EACxC,OAAOK,EAAaH,EAAQb,EAAK,eAAgB,IAC/C,KAAK,MAAM,OACR,IAAIW,EAASD,EAAQ,CACpB,GAAG,KAAK,MAAM,QAAQ,EACtB,OAAQV,EAAK,OACb,KAAAc,EACA,OAAQA,EACR,MAAO,EACT,CAAC,EACA,MAAOG,GAAmB,CACzB,MAAMC,EAAeD,EAAOP,EAAO,IAAMA,EAAO,KAAK,CACvD,CAAC,CACL,CACF,CAQA,MAAc,cACZC,EACA,CAAE,MAAAQ,EAAO,UAAAC,CAAU,EACnBpB,EACA,CACA,GAAM,CAAE,OAAAqB,CAAO,EAAIrB,EACbsB,EAAS,IAAI,IAAIF,EAAU,IAAI7B,CAAW,CAAC,EAC3CgC,EAAWJ,EAAM,OAAOK,GAAQ,CAACF,EAAO,IAAI/B,EAAYiC,CAAI,CAAC,CAAC,EAC9D,CAAE,MAAAC,CAAM,EAAI,MAAM,KAAK,MAAM,OAAO,OAAO,CAAE,OAAAJ,CAAO,CAAC,EACrDK,EAAU,IAAI,IAIpB,QAAWF,KAAQD,EAAU,CAC3B,IAAMI,EAAK,KAAK,OAAOH,EAAK,SAAW,GAAKC,CAAK,EAC3CG,EAAOF,EAAQ,IAAIC,CAAE,EACvBC,GACFA,EAAK,MAAM,KAAKJ,CAAI,EACpBI,EAAK,MAAQ,KAAK,IAAIA,EAAK,MAAOJ,EAAK,SAAW,CAAC,EACnDI,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKJ,EAAK,QAAQ,GAE3CE,EAAQ,IAAIC,EAAI,CACd,MAAO,CAACH,CAAI,EACZ,MAAOA,EAAK,SAAW,EACvB,IAAKA,EAAK,QACZ,CAAC,CAEL,CAeA,OAdc,MAAM,QAAQ,IAC1B,CAAC,GAAGE,EAAQ,OAAO,CAAC,EAAE,IAAI,MAAO,CAAE,MAAAG,EAAO,MAAAC,EAAO,IAAAC,CAAI,IAAM,CACzD,IAAMC,EAAQ,IAAI,IAAIH,EAAM,IAAIL,GAAQA,EAAK,IAAI,CAAC,EAC5CV,EAAQtB,GAAiBwC,EAAM,IAAIxC,CAAI,EACvC,CAAE,MAAAyC,EAAO,UAAAb,CAAU,EAAI,MAAM,KAAK,MAAM,OAAO,IACnDT,EACA,CAAE,MAAAmB,EAAO,IAAAC,CAAI,EACb,CAAE,OAAAV,EAAQ,KAAAP,EAAM,OAAQA,EAAM,QAAS,EAAG,MAAO,EAAM,CACzD,EACA,OAAOe,EAAM,IAAIL,GACfU,GAAaV,EAAMb,EAASS,EAAWa,EAAM,KAAK,CACpD,CACF,CAAC,CACH,GACa,KAAK,EAAE,OAAOV,GAAYA,IAAa,MAAS,CAC/D,CAQA,MAAc,eACZZ,EACAD,EACAV,EACA,CACA,IAAMmC,EAASnC,EAAK,YAAY,OAC5BA,EAAK,WAAW,IAAIoC,GAAQjC,EAAmB,KAAMiC,CAAI,CAAC,EAC1D,OACEC,EAASlC,EAAmB,KAAMH,EAAK,kBAAkB,EACzDY,EACJyB,IAAW,OACPF,EACAA,IAAW,QACTA,EAAO,KACL7B,GACEgC,EAAmBD,EAAQ/B,CAAM,GACjCgC,EAAmBhC,EAAQ+B,CAAM,CACrC,EACA,CAACA,CAAM,EACP,CAAC,EACT,GAAIzB,GAAU,SAAW,EACvB,MAAO,CAAC,EAEV,GAAM,CAAE,MAAAkB,EAAO,IAAAC,CAAI,EAAIrB,EACjBG,EAAS,iBAAiBH,EAAO,OAAO,IAAIoB,EAAM,eAAe,CAAC,IAAIC,EAAI,eAAe,CAAC,GAC1F,CAAE,MAAAE,EAAO,UAAAb,EAAW,MAAAD,CAAM,EAAI,MAAM,KAAK,UAC7CR,EACAD,EACAE,EACAZ,EACAa,CACF,EAGM0B,EAAO,CAAC,CAAE,KAAA/C,CAAK,IACnBoB,IAAa,OACT,EACAA,EAAS,UAAUN,GAAUgC,EAAmB9C,EAAMc,CAAM,CAAC,EAC7DkC,EAAY,MAAMxB,EAAaH,EAAQb,EAAK,eAAgB,IAChE,KAAK,cACHW,EACA,CAAE,MAAOQ,EAAM,OAAOK,GAAQe,EAAKf,CAAI,GAAK,CAAC,EAAG,UAAAJ,CAAU,EAC1DpB,CACF,CACF,EACMyC,EAAQC,GAAcT,EAAM,KAAK,EACjC7B,EAAcC,EAAsB,IAAI,EACxCsC,EAAUC,GACdpC,EAAiBJ,EAAab,EAAYqD,CAAI,CAAC,EAC3CC,EAAazB,EAAU,OAAO0B,GAAKA,EAAE,OAASnC,CAAO,EACrDW,EAASF,EACZ,OAAO2B,GAAYA,EAAS,OAASpC,GAAW4B,EAAKQ,CAAQ,GAAK,CAAC,EACnE,IAAIC,IAAU,CACb,KAAMT,EAAKS,CAAK,EAChB,SAAUH,EAAW,QAAQI,GAC3BR,EAAMO,EAAOC,CAAS,EAAE,IAAIC,GAC1BC,EAAa,CACX,MAAAD,EACA,OAAQD,EACR,MAAAD,EACA,aAActC,EAAO,aACrB,QAASA,EAAO,QAChB,iBAAkBiC,EAAOK,CAAK,CAChC,CAAC,CACH,CACF,CACF,EAAE,EACEI,EAAUZ,EAAU,IAAIjB,GAAY,CACxC,GAAM,CAAE,KAAAC,CAAK,EAAID,EACjB,MAAO,CACL,KAAMgB,EAAKf,CAAI,EACf,SAAU,CACR6B,EAAgB,CACd,OAAQ,CACN,KAAM1C,EACN,aAAcD,EAAO,aACrB,QAASA,EAAO,QAChB,MAAOc,EAAK,SACZ,IAAKA,EAAK,MACZ,EACA,MAAO8B,EAAa/B,EAAUoB,EAAOnB,CAAI,CAAC,EAC1C,OAAQD,EAAS,MACnB,CAAC,CACH,CACF,CACF,CAAC,EACD,MAAO,CAAC,GAAGD,EAAQ,GAAG8B,CAAO,EAC1B,KAAK,CAACG,EAAG,IAAMA,EAAE,KAAO,EAAE,IAAI,EAC9B,QAAQnB,GAAQA,EAAK,QAAQ,CAClC,CASA,MAAc,aACZzB,EACAD,EACA8C,EACAxD,EACA,CACA,IAAMyD,EAAQD,EAAM,IAAIE,IAAS,CAC/B,KAAAA,EACA,cAAevD,EAAmB,KAAMuD,EAAK,iBAAiB,EAC9D,WAAYvD,EAAmB,KAAMuD,EAAK,kBAAkB,CAC9D,EAAE,EACI7C,EAAS8C,EAAgBH,CAAK,EAC9B,CAAE,MAAAvB,EAAO,UAAAb,EAAW,MAAAD,CAAM,EAAI,MAAM,KAAK,UAC7CR,EACAD,EACA+C,EAAM,QAAQG,GAAQ,CAACA,EAAK,cAAeA,EAAK,UAAU,CAAC,EAC3D5D,EACAa,CACF,EACM2B,EAAY,MAAMxB,EAAaH,EAAQb,EAAK,eAAgB,IAChE,KAAK,cAAcW,EAAS,CAAE,MAAAQ,EAAO,UAAAC,CAAU,EAAGpB,CAAI,CACxD,EACMyC,EAAQoB,GAAgB5B,EAAM,KAAK,EACnC6B,EAAWxD,GACfc,EAAU,OAAO0B,GAAKR,EAAmBQ,EAAE,KAAMxC,CAAM,CAAC,EACpDyD,EAAY,CAACzD,EAAgBG,IACjCqD,EAAQxD,CAAM,EAAE,IAAIsC,GAAQoB,GAASpB,EAAMnC,CAAY,CAAC,EACpDwD,EAAgB,CAAC3D,EAAgBG,IACrC+B,EACG,OAAO,CAAC,CAAE,KAAAhB,CAAK,IAAMc,EAAmBd,EAAK,KAAMlB,CAAM,CAAC,EAC1D,IAAIiB,GAAY+B,EAAa/B,EAAUd,CAAY,CAAC,EACnDyD,EAAU,CAACC,EAAkBC,IACjCD,EAAI,QAAQ9B,GACV+B,EAAM,IAAIpB,GAASK,EAAgB,CAAE,OAAAhB,EAAQ,MAAAW,EAAO,OAAQ,GAAI,CAAC,CAAC,CACpE,EACF,OAAOS,EAAM,QAAQ,CAAC,CAAE,KAAAC,EAAM,cAAAW,EAAe,WAAAC,CAAW,IAAM,CAC5D,GAAM,CAAE,kBAAAC,EAAmB,mBAAAC,CAAmB,EAAId,EAClD,MAAO,CACL,GAAGI,EAAQO,CAAa,EAAE,QAAQhC,GAChCyB,EAAQQ,CAAU,EAAE,QAAQtB,GAC1BP,EAAMO,EAAOX,CAAM,EAAE,IAAIa,GACvBC,EAAa,CACX,MAAAD,EACA,OAAAb,EACA,MAAAW,EACA,aAAcuB,EACd,QAASE,EAAYpC,EAAO,IAAI,EAChC,iBAAkBmC,CACpB,CAAC,CACH,CACF,CACF,EACA,GAAGN,EACDH,EAAUM,EAAeE,CAAiB,EAC1CN,EAAcK,EAAYE,CAAkB,CAC9C,EACA,GAAGN,EACDD,EAAcI,EAAeE,CAAiB,EAC9CR,EAAUO,EAAYE,CAAkB,CAC1C,CACF,CACF,CAAC,CACH,CAIA,YAAY9D,EAAgBV,EAA2B,CAAC,EAAG,CACzD,OAAO0E,EAA0B,MAAMC,GAAY,CACjD,IAAMhE,EACJD,EAAO,eAAiB,KAAK,OACzB,MAAM,KAAK,SAAS,QAAQA,EAAQV,CAAI,EACxC,OACN,GAAIW,IAAY,OAAW,CACzB,IAAM6C,EAAQoB,EAAe5E,CAAI,EAC3B6E,EACJrB,EAAM,OAAS,EACX,MAAM,KAAK,aAAa7C,EAASD,EAAQ8C,EAAOxD,CAAI,EACpD,MAAM,KAAK,eAAeW,EAASD,EAAQV,CAAI,EACrD,QAAW8E,KAAWD,EACpBF,EAAS,KAAKG,CAAO,CAEzB,CACAH,EAAS,SAAS,CACpB,EAAG3E,EAAK,MAAM,CAChB,CACF",
+  "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", "r", "k", "lo", "hi", "y", "x", "singleVisits", "rev", "twice", "directionShares", "visits", "visitsOf", "found", "theirs", "opposite", "other", "lanePairAligner", "subsequence", "chained", "shares", "TURNED_MIN_BP", "anchorAligner", "records", "taken", "chain", "chainFeature", "assemblyName", "refName", "mateAssemblyName", "matchFeature", "panSNContig", "pairCigar", "sum", "n", "skipCrossing", "skip", "fragments", "name", "fragStart", "hapStart", "ids", "at", "walkSide", "crossingSide", "crossingFeature", "strand", "haplotypeOf", "name", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "WalkIndex", "openTabixSlot", "PanSNRefNames", "anchor", "opts", "haplotypes", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "region", "refName", "prefixes", "status", "keep", "walksKept", "updateStatus", "error", "laneZoomNotice", "skips", "fragments", "signal", "walked", "crossing", "skip", "chunk", "byChunk", "cs", "held", "group", "start", "end", "names", "graph", "skipCrossing", "wanted", "lane", "target", "panSNMatchesPrefix", "rank", "crossings", "align", "anchorAligner", "laneOf", "walk", "references", "f", "fragment", "query", "reference", "chain", "chainFeature", "skipped", "crossingFeature", "crossingSide", "a", "pairs", "sides", "pair", "lanePairsStatus", "side", "lanePairAligner", "walksOf", "walkSides", "walkSide", "crossingSides", "crossed", "own", "mates", "featurePrefix", "matePrefix", "queryAssemblyName", "targetAssemblyName", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
+}