jbrowse-plugin-graphgenomeviewer 8.8.0 → 8.8.2

package/dist/chunks/{GbzBaseSyntenyAdapter-SDYLJG5H.js → GbzBaseSyntenyAdapter-NAXISJUH.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-7HJWQFKE.js";import{a as te}from"./chunk-KACKTX2U.js";import{a as ee}from"./chunk-V55TK2NP.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 $,i as W,k as U}from"./chunk-VQVQXMNM.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-VPZZ6XMM.js";import"./chunk-YBLNN5FU.js";import"./chunk-5TT5TG4Q.js";import"./chunk-WJHTNDTQ.js";import{E as V,a as K,c as L}from"./chunk-YNMEZ4EZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{g as F,h as N,i as C}from"./chunk-2FG67WIZ.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{e as _,o as B}from"./chunk-TC265JAP.js";function A(n){let i=/\.gbz\.db$/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-SDYLJG5H.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-LFQFVYNY.js";import{a as te}from"./chunk-APSXG7SV.js";import{a as ee}from"./chunk-V55TK2NP.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 $,i as W,k as U}from"./chunk-EFXNCI7R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-DEWVJ57F.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.js";import{E as V,a as K,c as L}from"./chunk-GLSUAMGV.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{g as F,h as N,i as C}from"./chunk-KBOVZ3GI.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{e as _,o as B}from"./chunk-TC265JAP.js";function A(n){let i=/\.gbz\.db$/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-NAXISJUH.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-SDYLJG5H.js.map → GbzBaseSyntenyAdapter-NAXISJUH.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-QPKSULKV.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-QPKSULKV.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
   "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  NoReferenceSampleError,\n  aliasedSample,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf\n} from \"./chunk-RQHIDUZR.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction gbzLocations({ db, index }) {\n  return db === \"hprc\" ? { db: HPRC_GBZ.db, index: index ?? HPRC_GBZ.index } : { db, index };\n}\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*(\\S+?):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a 0-based region like chr6:160,614,797-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  if (ref) {\n    return aliasedSample(panSNSample(ref), samples) ?? ref;\n  }\n  const first = samples[0];\n  if (first === void 0) {\n    throw new NoReferenceSampleError(\"\", samples);\n  }\n  return first;\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  gbzLocations,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkCut.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\ninterface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\n\nclass HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nfunction fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n// gbz-base writes the CIGAR along the target, which is the side a JBrowse\n// feature is, so it passes through unchanged\nfunction pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  return matchFeature({\n    target: {\n      name: `${haplotypePrefix(pair.target)}#${pair.target.contig}`,\n      assemblyName: lane,\n      refName: pair.target.contig,\n      start: pair.targetStart,\n      end: pair.targetEnd,\n    },\n    query: {\n      name: `${haplotypePrefix(pair.query)}#${pair.query.contig}`,\n      assemblyName: mateLane,\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n    },\n    strand: pair.strand,\n    cigar: pair.cigar,\n    matches: pair.matches,\n    columns: pair.columns,\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\nconst laneLimitNotice = (error: unknown, nodeLimit: number, windowBp: number) =>\n  laneZoomNotice(\n    zoomInNotice(nodeLimitError(error, nodeLimit, windowBp) ?? error, 'lanes'),\n    windowBp,\n  )\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw laneLimitNotice(error, nodeLimit, end - start)\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw laneLimitNotice(error, nodeLimit, end - start)\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && answerable.length > 0\n        ? await updateStatus(lanePairsStatus(pairs), opts.statusCallback, () =>\n            bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
   "mappings": "o0BAsBA,SAASA,EAAqBC,EAAI,CAChC,IAAMC,EAAS,cACf,OAAOA,EAAO,KAAKD,CAAE,EAAIA,EAAG,QAAQC,EAAQ,qBAAqB,EAAI,MACvE,CCjBO,SAASC,GAAiBC,EAAqB,CACpD,OAAOC,EAAcD,CAAK,GAAKE,EAAqBC,EAAaH,CAAK,CAAC,EACnEI,EAAQJ,EAAOK,GAAQH,EAAqBG,CAAI,CAAE,EAClD,MACN,CAIA,SAASC,GAAUC,EAAgB,CACjC,OACEA,aAAiB,QAChB,kBAAkB,KAAKA,EAAM,OAAO,GAClCA,EAA6B,OAAS,SAE7C,CAIA,eAAsBC,GACpBR,EACAS,EAC2D,CAC3D,IAAMC,EAAYX,GAAiBC,CAAK,EACxC,GAAI,CAACU,EACH,MAAO,CAAC,EAEV,GAAI,CACF,aAAMC,EAAaD,EAAWD,CAAa,EAAE,KAAK,EAC3C,CAAE,SAAUC,CAAU,CAC/B,OAASH,EAAO,CACd,OAAOD,GAAUC,CAAK,EAAI,CAAC,EAAI,CAAE,WAAY,OAAOA,CAAK,CAAE,CAC7D,CACF,CCrBO,IAAMK,GAAY,IAGnBC,GAAsB,GAAK,GAAK,GAEzBC,EAAN,cAAwC,KAAM,CAGnD,YAAYC,EAAc,CACxB,MACE,gBAAgBA,EAAO,GAAK,IAAI,QAAQ,CAAC,CAAC,+DAC5C,EALF,KAAS,KAAO,2BAMhB,CACF,EAGA,SAASC,GAAOC,EAAsBC,EAAa,CACjD,GAAID,EAAQ,QAAUC,EACpB,OAAOD,EAET,IAAME,EAASF,EAAQ,OAASC,EAChC,OAAO,MAAM,KAAK,CAAE,OAAQA,CAAI,EAAG,CAACE,EAAGC,IAAMJ,EAAQ,KAAK,MAAMI,EAAIF,CAAM,CAAC,CAAE,CAC/E,CAEA,IAAMG,GAAU,CAACC,EAAmBC,IAClCD,EAAO,KAAK,KAAKE,GAAQD,EAAM,IAAIC,EAAK,IAAI,CAAC,EAKlCC,EAAN,KAAc,CAiBnB,YACUC,EACAC,EACR,CAFQ,UAAAD,EACA,WAAAC,EAhBV,KAAQ,MAAQC,EAAY,CAC1B,MAAO,MAAO,CAAE,OAAAC,CAAO,IAAM,CAC3B,GAAM,CAAE,KAAAf,CAAK,EAAI,MAAM,KAAK,KAAK,KAAK,EACtC,GAAIA,EAAOF,GACT,MAAM,IAAIC,EAA0BC,CAAI,EAE1C,IAAMgB,EAAQ,MAAM,KAAK,KAAK,SAAS,CAAE,OAAAD,CAAO,CAAC,EAC3CE,EAAO,IAAI,YAAY,EAAE,OAC7BD,EAAM,CAAC,IAAM,IAAQA,EAAM,CAAC,IAAM,IAAO,MAAME,EAAMF,CAAK,EAAIA,CAChE,EACA,OAAOG,EAASF,CAAI,CACtB,CACF,CAAC,CAKE,CAEH,MAAc,YACZJ,EACAJ,EACAM,EACA,CACA,IAAIK,EAAK,IACLC,EAAK,KACT,QAAWC,KAAQb,EAAO,CACxB,IAAMc,EAAK,OAAOD,CAAI,EAClB,OAAO,UAAUC,CAAE,IACrBH,EAAK,KAAK,IAAIA,EAAIG,CAAE,EACpBF,EAAK,KAAK,IAAIA,EAAIE,CAAE,EAExB,CACA,IAAMrB,EAAuB,CAAC,EAC9B,OAAIkB,GAAMC,GAGR,MAAMR,EAAM,SAAS,SAAUO,EAAIC,EAAK,EAAG,CACzC,OAAAN,EACA,aAAcS,GAAQ,CACpB,IAAMhB,EAASiB,EAAaD,CAAI,EAC5BhB,GAAUD,GAAQC,EAAQC,CAAK,GACjCP,EAAQ,KAAKM,CAAM,CAEvB,CACF,CAAC,EAEIN,CACT,CAEA,MAAM,UACJO,EACA,CAAE,OAAAM,CAAO,EAA8B,CAAC,EACrB,CACnB,IAAMb,EAAU,KAAK,MACjB,MAAM,KAAK,YAAY,KAAK,MAAOO,EAAOM,CAAM,GAC/C,MAAM,KAAK,MAAM,CAAE,OAAAA,CAAO,CAAC,GAAG,OAAOW,GAAKnB,GAAQmB,EAAGjB,CAAK,CAAC,EAChE,MAAO,CAAE,QAASR,GAAOC,EAASL,EAAS,EAAG,MAAOK,EAAQ,MAAO,CACtE,CACF,EC3DO,IAAMyB,EAAN,cAAoC,KAAM,CAG/C,YAAYC,EAAqB,CAC/B,MACEA,IAAe,OACX,uKACA,uEAAuEA,CAAU,qGACvF,EAPF,KAAS,KAAO,uBAQhB,CACF,EAwBMC,EAAN,cAAmC,KAAM,CAGvC,YAAYC,EAAsBC,EAAgB,CAChD,MACE,sCAAsCA,CAAM,iBAAiBD,CAAY,kEAAkEC,CAAM,6CACnJ,EALF,KAAS,KAAO,sBAMhB,CACF,EAUA,SAASC,GAAWC,EAAgBC,EAA8B,CAChE,MAAO,GAAGC,EAAgBF,CAAI,CAAC,IAAIA,EAAK,MAAM,IAAIC,EAAU,MAAM,IAAI,IAAIA,EAAU,MAAM,MAAM,EAClG,CAEA,SAASE,GAAgB,CACvB,UAAAF,EACA,aAAAJ,EACA,QAAAO,EACA,KAAAC,CACF,EAKG,CACD,GAAM,CAAE,SAAAC,EAAU,OAAAC,EAAQ,OAAAC,EAAQ,MAAAC,CAAM,EAAIR,EAC5C,GAAI,EAAAM,GAAUD,GAEP,CACL,GAAM,CAAE,KAAAN,EAAM,SAAAU,EAAU,OAAAC,CAAO,EAAIV,EAC7BW,EAAKb,GAAWC,EAAMC,CAAS,EAC/BY,EAAgC,CACpC,SAAUD,EACV,aAAAf,EACA,QAAAO,EACA,MAAOE,EACP,IAAKC,EACL,KAAM,QACN,OAAQC,IAAW,IAAM,GAAK,EAC9B,MAAOC,EACP,UAAWG,EACX,KAAM,CACJ,QAASZ,EAAK,OACd,MAAOU,EACP,IAAKC,EACL,aAAcN,CAChB,CACF,EACA,OAAO,IAAIS,GAAeD,CAAI,CAChC,CACF,CAIA,SAASE,GAAY,CACnB,KAAAC,EACA,KAAAX,EACA,SAAAY,CACF,EAIG,CACD,OAAOC,GAAa,CAClB,OAAQ,CACN,KAAM,GAAGhB,EAAgBc,EAAK,MAAM,CAAC,IAAIA,EAAK,OAAO,MAAM,GAC3D,aAAcX,EACd,QAASW,EAAK,OAAO,OACrB,MAAOA,EAAK,YACZ,IAAKA,EAAK,SACZ,EACA,MAAO,CACL,KAAM,GAAGd,EAAgBc,EAAK,KAAK,CAAC,IAAIA,EAAK,MAAM,MAAM,GACzD,aAAcC,EACd,QAASD,EAAK,MAAM,OACpB,MAAOA,EAAK,WACZ,IAAKA,EAAK,QACZ,EACA,OAAQA,EAAK,OACb,MAAOA,EAAK,MACZ,QAASA,EAAK,QACd,QAASA,EAAK,OAChB,CAAC,CACH,CAGA,IAAMG,GAAgB,KAQf,SAASC,GAAcC,EAAuBC,EAAmB,CACtE,IAAMC,EAAS,IAAI,IACnB,QAAWC,KAAYH,EACrB,OAAW,CAAE,KAAArB,EAAM,MAAAyB,EAAO,IAAAC,CAAI,IAAKF,EAAS,UAAU,EAAG,CACvD,IAAMG,EAASzB,EAAgBF,CAAI,EACnC,GAAIsB,EAAK,IAAIK,CAAM,EAAG,CACpB,IAAMC,EAAM,GAAGD,CAAM,IAAI3B,EAAK,MAAM,GAC9B6B,EAAQN,EAAO,IAAIK,CAAG,EACxBC,EACFA,EAAM,KAAK,CAACJ,EAAOC,CAAG,CAAC,EAEvBH,EAAO,IAAIK,EAAK,CAAC,CAACH,EAAOC,CAAG,CAAC,CAAC,CAElC,CACF,CAEF,IAAII,EAAS,EACb,QAAWD,KAASN,EAAO,OAAO,EAAG,CACnCM,EAAM,KAAK,CAACE,EAAGC,IAAMD,EAAE,CAAC,EAAIC,EAAE,CAAC,CAAC,EAChC,QAASC,EAAI,EAAGA,EAAIJ,EAAM,OAAQI,IAAK,CACrC,IAAMC,EAAML,EAAMI,CAAC,EAAG,CAAC,EAAIJ,EAAMI,EAAI,CAAC,EAAG,CAAC,EACtCC,EAAM,GAAKA,GAAOf,KACpBW,EAAS,KAAK,IAAIA,EAAQI,CAAG,EAEjC,CACF,CACA,OAAOJ,CACT,CAIA,SAASK,GAAaC,EAAgBC,EAAc,CAClD,OAAID,aAAiBE,IACnBF,EAAM,QAAU,oBAAoBG,EAAgBH,EAAM,MAAM,CAAC,WAAWC,CAAI,IAE3ED,CACT,CAEA,IAAMI,GAAkB,CAACJ,EAAgBK,EAAmBC,IAC1DC,GACER,GAAaS,EAAeR,EAAOK,EAAWC,CAAQ,GAAKN,EAAO,OAAO,EACzEM,CACF,EAGIG,GAAWC,IAAoB,CACnC,GAAGA,EACH,MAAO,KAAK,MAAMA,EAAO,KAAK,EAC9B,IAAK,KAAK,KAAKA,EAAO,GAAG,CAC3B,GAEqBC,EAArB,cAAmDC,EAAoD,CAAvG,kCACE,KAAQ,MAAQC,EAAY,CAC1B,MAAO,6BACP,MAAO,SAAY,CACjB,IAAMC,EAAsB,KAAK,QAAQ,eAAe,EAClDC,EAA2B,KAAK,QAAQ,wBAAwB,EAChEC,EAAYC,EAAcF,CAAU,EACtC,CAAE,SAAUA,CAAW,EACvB,MAAMG,GAAcJ,EAAO,KAAK,aAAa,EAC3CK,EAAgBH,EAAU,SAC1BI,EAAK,MAAMC,EAAQ,KAAK,CAC5B,OAAQC,EAAaR,EAAO,KAAK,aAAa,EAC9C,eAAgBK,EACZG,EAAaH,EAAe,KAAK,aAAa,EAC9C,MACN,CAAC,EACKzD,EAAS,KAAK,QAAQ,eAAe,EAAE,CAAC,EAC9C,GAAIA,IAAW,OACb,MAAM,IAAI,MACR,8GACF,EAEF,IAAM6D,EAAmB,MAAMC,EAAmBJ,CAAE,EAC9CK,EAAkBC,EAAuB,CAC7C,WAAY,KAAK,QAAQ,iBAAiB,EAC1C,aAAcC,EAAmB,KAAMjE,CAAM,EAC7C,iBAAA6D,CACF,CAAC,EACD,MAAO,CACL,GAAAH,EACA,OAAA1D,EACA,gBAAA+D,EACA,iBAAAF,EACA,gBAAiBP,EAAU,UAC7B,CACF,CACF,CAAC,EA8JD,KAAQ,IAAMH,EAAY,CACxB,MAAO,gBACP,MAAO,SAAY,CACjB,IAAMe,EAAyB,KAAK,QAAQ,eAAe,EACrDC,EAAsB,KAAK,QAAQ,CAAC,aAAc,UAAU,CAAC,EACnE,OAAOZ,EAAcW,CAAQ,EACzB,IAAIE,EACFR,EAAaM,EAAU,KAAK,aAAa,EACzCX,EAAcY,CAAK,EACfE,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,MACN,EACA,MACN,CACF,CAAC,EAtKD,MAAc,eACZ/D,EACAgE,EACgC,CAChC,GAAM,CAAE,GAAAZ,EAAI,gBAAAK,CAAgB,EAAI,MAAM,KAAK,MAAMO,CAAI,EACrD,OAAOC,EAAmBb,EAAIK,EAAiBzD,CAAO,CACxD,CAOA,MAAM,cAAcgE,EAAoB,CAAC,EAA4B,CACnE,GAAM,CAAE,GAAAZ,EAAI,iBAAAG,CAAiB,EAAI,MAAM,KAAK,MAAMS,CAAI,EAChDE,EAAW,IAAI,IACrB,QAAWC,KAAQ,MAAMf,EAAG,MAAM,EAAG,CACnC,IAAM7B,EAASzB,EAAgBqE,EAAK,IAAI,EAClCC,EAAQF,EAAS,IAAI3C,CAAM,EAC7B6C,EACGA,EAAM,QAAQ,SAASD,EAAK,KAAK,MAAM,GAC1CC,EAAM,QAAQ,KAAKD,EAAK,KAAK,MAAM,EAGrCD,EAAS,IAAI3C,EAAQ,CACnB,OAAAA,EACA,OAAQ4C,EAAK,KAAK,OAClB,UAAWA,EAAK,KAAK,UACrB,QAAS,CAACA,EAAK,KAAK,MAAM,EAC1B,YAAaZ,EAAiB,SAASY,EAAK,KAAK,MAAM,CACzD,CAAC,CAEL,CACA,MAAO,CAAC,GAAGD,EAAS,OAAO,CAAC,CAC9B,CAOA,MAAM,UAAUF,EAAoB,CAAC,EAAG,CACtC,GAAM,CAAE,OAAAtE,EAAQ,gBAAA+D,CAAgB,EAAI,MAAM,KAAK,MAAMO,CAAI,EACnDK,EAAcC,EAAsB,IAAI,EACxCC,EAAyB,CAAC,EAChC,QAAWC,KAAa,MAAM,KAAK,cAAcR,CAAI,EAC/CQ,EAAU,SAAWf,GACvBc,EAAM,KAAK,CACT,KAAME,EAAiBJ,EAAaG,EAAU,MAAM,EACpD,MAAOA,EAAU,OACjB,MAAOA,EAAU,MACnB,CAAC,EAGL,MAAO,CACL,cAAe,GACf,mBAAoB9E,EACpB,MAAA6E,CACF,CACF,CAEA,MAAM,YAAYP,EAAoB,CAAC,EAAG,CACxC,GAAM,CAAE,GAAAZ,EAAI,OAAA1D,EAAQ,gBAAA+D,CAAgB,EAAI,MAAM,KAAK,MAAMO,CAAI,EACvD,CAAE,aAAAvE,CAAa,EAAIuE,EACnBzC,EACJ9B,IAAiBC,EACb,OACAiE,EAAmB,KAAMlE,CAAY,EACrCiF,GAAW,MAAMtB,EAAG,MAAM,GAC7B,OAAOe,GACN1E,IAAiBC,EACbyE,EAAK,WAAaA,EAAK,KAAK,SAAWV,EACvCkB,EAAmB7E,EAAgBqE,EAAK,IAAI,EAAG5C,CAAM,CAC3D,EACC,IAAI4C,GAAQA,EAAK,KAAK,MAAM,EAC/B,MAAO,CAAC,GAAG,IAAI,IAAIO,CAAO,CAAC,CAC7B,CAcQ,cACNE,EACAC,EACA,CACA,IAAMC,EACJF,IAAe,QAAaA,EAAW,SAAW,EAC9C,OACAA,EAAW,IAAI3E,GAAQ0D,EAAmB,KAAM1D,CAAI,CAAC,EAC3D,OAAO6E,IAAmB,QAAaD,IAAiB,OACpD,OACCjF,GACCmF,EAAgBnF,EAAMkF,CAAc,IACnCD,IAAiB,QAChBF,EAAmB7E,EAAgBF,CAAI,EAAGiF,CAAY,EAChE,CAeA,MAAM,YAAYnC,EAAgBsB,EAA+B,CAAC,EAAG,CACnE,GAAM,CAAE,OAAAgB,CAAO,EAAIhB,EACb,CAAE,GAAAZ,EAAI,OAAA1D,EAAQ,gBAAA+D,EAAiB,gBAAAwB,CAAgB,EAAI,MAAM,KAAK,MAAM,CACxE,OAAAD,CACF,CAAC,EACK,CAAE,aAAAvF,EAAc,QAAAO,EAAS,MAAAqB,EAAO,IAAAC,CAAI,EAAImB,GAAQC,CAAM,EAC5D,GAAIjD,IAAiBC,EACnB,MAAM,IAAIF,EAAqBC,EAAcC,CAAM,EAErD,IAAMwF,EAAQ,MAAM,KAAK,eAAelF,EAAS,CAAE,OAAAgF,CAAO,CAAC,EAC3D,GAAI,CAACE,EACH,MAAM,IAAI,MACR,GAAGzB,CAAe,wBAAwBzD,CAAO,gBACnD,EAEF,IAAMmF,EAAO,KAAK,cAAcnB,EAAK,UAAU,EAC/C,GAAImB,IAAS,QAAa,CAAC/B,EAAG,kBAC5B,MAAM,IAAI9D,EAAsB2F,CAAe,EAEjD,IAAMG,EAAM,MAAMC,EAAgBjC,EAAI8B,EAAO7D,EAAOC,EAAK,CACvD,QAAS,KAAK,QAAQ,SAAS,EAC/B,OAAQ0C,EAAK,QAAU,KAAK,QAAQ,gBAAgB,EACpD,MAAO,KAAK,QAAQ,WAAW,EAC/B,OAAQA,EAAK,OACb,KAAAmB,CACF,CAAC,EAAE,MAAOnD,GAAmB,CAC3B,MAAMD,GAAaC,EAAO,WAAW,CACvC,CAAC,EACD,OAAO,OAAOoD,GAAQ,SAClBA,EACAE,GAAWF,EAAK,CAAE,MAAA/D,EAAO,IAAAC,CAAI,EAAG0C,EAAK,QAAQ,CACnD,CAsBA,MAAM,SACJuB,EACAvB,EAAoB,CAAC,EACF,CACnB,IAAMwB,EAAM,MAAM,KAAK,IAAIxB,CAAI,EAC/B,OAAOwB,EACHA,EAAI,UAAU,IAAI,IAAID,CAAS,EAAGvB,CAAI,EACtC,CAAE,QAAS,CAAC,EAAG,MAAO,CAAE,CAC9B,CAEA,MAAc,eACZvE,EACAuE,EACyB,CACzB,IAAMzC,EAASoC,EAAmB,KAAMlE,CAAY,EACpD,OAAQ,MAAM,KAAK,cAAcuE,CAAI,GAAG,OAAOQ,GAC7CG,EAAmBH,EAAU,OAAQjD,CAAM,CAC7C,CACF,CAEA,MAAc,eAAemB,EAAgBsB,EAA0B,CACrE,GAAM,CAAE,GAAAZ,CAAG,EAAI,MAAM,KAAK,MAAMY,CAAI,EAC9B,CAAE,aAAAvE,EAAc,QAAAO,EAAS,MAAAqB,EAAO,IAAAC,CAAI,EAAIoB,EACxCmC,EAAelB,EAAmB,KAAMK,EAAK,kBAAkB,EAC/DK,EAAcC,EAAsB,IAAI,EACxCa,EAAO,KAAK,cAAcnB,EAAK,WAAYa,CAAY,EACvDK,EAAQ,MAAM,KAAK,eAAelF,EAASgE,CAAI,EAC/C3B,EAAoB,KAAK,QAAQ,WAAW,EAsBlD,OArBmB6C,EACf,MAAMO,EACJ,iBAAiBzF,CAAO,IAAIqB,EAAM,eAAe,CAAC,IAAIC,EAAI,eAAe,CAAC,GAC1E0C,EAAK,eACL,IACEZ,EACG,cAAc,CACb,KAAM8B,EACN,MAAA7D,EACA,IAAAC,EACA,QAAS,KAAK,QAAQ,SAAS,EAC/B,WAAY,MACZ,MAAOe,EACP,OAAQ2B,EAAK,OACb,KAAAmB,CACF,CAAC,EACA,MAAOnD,GAAmB,CACzB,MAAMI,GAAgBJ,EAAOK,EAAWf,EAAMD,CAAK,CACrD,CAAC,CACP,EACA,CAAC,GACa,QAAQxB,GAAa,CACrC,IAAM6F,EAAU7F,EAAU,SACtBE,GAAgB,CACd,UAAAF,EACA,aAAAJ,EACA,QAAAO,EACA,KAAMyE,EACJJ,EACAvE,EAAgBD,EAAU,IAAI,CAChC,CACF,CAAC,EACD,OACJ,OAAO6F,IAAY,OAAY,CAAC,EAAI,CAACA,CAAO,CAC9C,CAAC,CACH,CAWA,MAAc,aACZhD,EACAiD,EACA3B,EACA,CACA,GAAM,CAAE,GAAAZ,CAAG,EAAI,MAAM,KAAK,MAAMY,CAAI,EAC9B,CAAE,QAAAhE,EAAS,MAAAqB,EAAO,IAAAC,CAAI,EAAIoB,EAQ1BkD,GAPQ,MAAM,QAAQ,IAC1BD,EAAM,IAAI,MAAM/E,IAAS,CACvB,KAAAA,EACA,YAAa,MAAM,KAAK,eAAeA,EAAK,kBAAmBoD,CAAI,EACnE,SAAU,MAAM,KAAK,eAAepD,EAAK,mBAAoBoD,CAAI,CACnE,EAAE,CACJ,GACyB,OACvB,CAAC,CAAE,YAAA6B,EAAa,SAAAC,CAAS,IACvBD,EAAY,OAAS,GAAKC,EAAS,OAAS,CAChD,EACM5E,EAAO,IAAI,IACf0E,EAAW,QAAQ,CAAC,CAAE,YAAAC,EAAa,SAAAC,CAAS,IAC1C,CAAC,GAAGD,EAAa,GAAGC,CAAQ,EAAE,IAAIhG,CAAe,CACnD,CACF,EACMoF,EAAQ,MAAM,KAAK,eAAelF,EAASgE,CAAI,EAC/C3B,EAAoB,KAAK,QAAQ,WAAW,EAC5C0D,EAAsB,KAAK,QAAQ,SAAS,EAC5CX,EAAM,CAACjB,EAAiB6B,IAC5B5C,EAAG,aAAa,CACd,KAAAe,EACA,MAAA9C,EACA,IAAAC,EACA,QAAA0E,EACA,OAAQ,KAAK,QAAQ,gBAAgB,EACrC,WAAY,MACZ,MAAO3D,EACP,OAAQ2B,EAAK,OACb,KAAMpE,GAAQsB,EAAK,IAAIpB,EAAgBF,CAAI,CAAC,CAC9C,CAAC,EAEGqG,EAAU,MAAO9B,GAAoB,CACzC,IAAMlD,EAAY,MAAMmE,EAAIjB,EAAM4B,CAAW,EAAE,MAAO/D,GAAmB,CACvE,MAAMI,GAAgBJ,EAAOK,EAAWf,EAAMD,CAAK,CACrD,CAAC,EACKS,EAAMd,GAAcC,EAAWC,CAAI,EACnC8E,EAAU,KAAK,KAAKlE,EAAM,CAAC,EAAI,IACrC,OAAOA,EAAM,GAAKkE,EAAUD,EACxBX,EAAIjB,EAAM6B,CAAO,EAAE,MAAOhE,GAAmB,CAC3C,GAAIA,aAAiBkE,EACnB,OAAOjF,EAET,MAAMe,CACR,CAAC,EACDf,CACN,EAOA,OALEiE,GAASU,EAAW,OAAS,EACzB,MAAMH,EAAaU,GAAgBR,CAAK,EAAG3B,EAAK,eAAgB,IAC9DiC,EAAQf,CAAK,CACf,EACA,CAAC,GACU,QAAQ9D,GACvBwE,EAAW,QAAQ,CAAC,CAAE,KAAAhF,EAAM,YAAAiF,EAAa,SAAAC,CAAS,IAChDD,EAAY,QAAQO,GAClBN,EAAS,QAAQO,IACfjF,EACG,eAAe,CAAE,OAAAgF,EAAQ,MAAOC,GAAM,MAAO,EAAM,CAAC,EACpD,IAAIxG,IACHc,GAAY,CACV,KAAMd,GACN,KAAMe,EAAK,kBACX,SAAUA,EAAK,kBACjB,CAAC,CACH,CACJ,CACF,CACF,CACF,CACF,CAEA,YAAY0F,EAAetC,EAA2B,CAAC,EAAG,CACxD,IAAMtB,EAASD,GAAQ6D,CAAK,EAC5B,OAAOC,GAA0B,MAAMC,GAAY,CACjD,GAAM,CAAE,GAAApD,EAAI,OAAA1D,EAAQ,gBAAAuF,CAAgB,EAAI,MAAM,KAAK,MAAMjB,CAAI,EAC7D,GAAI,CAACZ,EAAG,kBACN,MAAM,IAAI9D,EAAsB2F,CAAe,EAIjD,GAAIvC,EAAO,eAAiBhD,EAAQ,CAClC,IAAMiG,EAAQc,GAAezC,CAAI,EAC3B0C,EACJf,EAAM,OAAS,EACX,MAAM,KAAK,aAAajD,EAAQiD,EAAO3B,CAAI,EAC3C,MAAM,KAAK,eAAetB,EAAQsB,CAAI,EAC5C,QAAW0B,KAAWgB,EACpBF,EAAS,KAAKd,CAAO,CAEzB,CACAc,EAAS,SAAS,CACpB,EAAGxC,EAAK,MAAM,CAChB,CACF",
   "names": ["haplotypeIndexBeside", "db", "GBZ_DB", "siblingCompanion", "gbzDb", "readsSiblings", "haplotypeIndexBeside", "locationName", "renamed", "name", "isMissing", "error", "findCompanion", "pluginManager", "candidate", "openLocation", "MAX_READS", "MAX_UNINDEXED_BYTES", "UnindexedGafTooLargeError", "size", "sample", "records", "max", "stride", "_", "k", "touches", "record", "names", "step", "GafFile", "file", "tabix", "cachedSetup", "signal", "bytes", "text", "unzip", "parseGaf", "lo", "hi", "name", "id", "line", "parseGafLine", "r", "NoHaplotypeIndexError", "unreadable", "HaplotypeWindowError", "assemblyName", "anchor", "fragmentId", "name", "alignment", "haplotypePrefix", "fragmentFeature", "refName", "lane", "refStart", "refEnd", "strand", "cigar", "hapStart", "hapEnd", "id", "data", "SyntenyFeature", "pairFeature", "pair", "mateLane", "matchFeature", "BRIDGE_MAX_BP", "widestWalkGap", "subgraphs", "kept", "byPath", "subgraph", "start", "end", "prefix", "key", "spans", "widest", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "laneLimitNotice", "nodeLimit", "windowBp", "laneZoomNotice", "nodeLimitError", "wholeBp", "region", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "locationIsSet", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "location", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "asmByPrefix", "assemblyByPanSNPrefix", "lanes", "haplotype", "laneAssemblyName", "contigs", "panSNMatchesPrefix", "haplotypes", "targetPrefix", "wantedPrefixes", "haplotypeWanted", "signal", "unreadableIndex", "query", "keep", "cut", "cutWindowTables", "walkCutFor", "nodeNames", "gaf", "updateStatus", "feature", "pairs", "answerable", "featureSide", "mateSide", "baseContext", "context", "bridged", "SubgraphLimitError", "lanePairsStatus", "target", "mate", "asked", "ObservableCreate", "observer", "requestedPairs", "features"]

package/dist/chunks/{GraphGenomeView-YRHBZFKL.js → GraphGenomeView-PPOVN5LA.js}

@@ -1,4 +1,4 @@
-import{b as C}from"./chunk-TUYN7C3O.js";import"./chunk-Y5Q3XQOP.js";import"./chunk-5WIUEMTH.js";import"./chunk-WWF7N6AP.js";import{s as d}from"./chunk-LPUQPLW7.js";import"./chunk-TFV57AXQ.js";import"./chunk-T3FHGWNW.js";import"./chunk-PXYYKSGK.js";import"./chunk-46O3IEW3.js";import"./chunk-G6NFDDMN.js";import"./chunk-VPZZ6XMM.js";import"./chunk-YBLNN5FU.js";import"./chunk-5TT5TG4Q.js";import"./chunk-WJHTNDTQ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import{i as L}from"./chunk-J2PN6CG3.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-WE7DQVXF.js";import{a as h,b as e,c as r,d as i}from"./chunk-DUU6T2I5.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
+import{b as C}from"./chunk-MWQGJP3J.js";import"./chunk-RS274NAD.js";import"./chunk-HKGTCZOL.js";import"./chunk-NSQ4VXKR.js";import{s as d}from"./chunk-5HDIVUAZ.js";import"./chunk-EH5OCKSE.js";import"./chunk-FM4T47WH.js";import"./chunk-ZWHXVFZF.js";import"./chunk-CHLLRNBQ.js";import"./chunk-LKD5NRWR.js";import"./chunk-DEWVJ57F.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import{i as L}from"./chunk-J2PN6CG3.js";import{A as l,F as G,H as p,e as s,j as v,o as n,x as y}from"./chunk-WE7DQVXF.js";import{a as h,b as e,c as r,d as i}from"./chunk-DUU6T2I5.js";var N=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),S=i(function({model:a}){let{classes:t}=N();return!a.error&&!a.loadCanceled?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[e(v,{variant:"h6",message:a.statusMessage||void 0}),a.canCancelLoad?e(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{a.cancelLoad()},children:"Cancel"}):null]}),e(y,{variant:"indeterminate"})]}):a.error?e(l,{className:t.paper,children:e(s,{error:a.error,onReset:()=>{a.retryLoad()}})}):e(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[e(p,{variant:"h6",children:"Loading canceled"}),e(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{a.retryLoad()},children:"Retry"})]})})}),f=S;var T=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,E=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),F=i(function({model:a}){let{classes:t}=E(),[m,w]=L("");function u(){let o=m.trim();o&&a.openGfaLocation({uri:o,locationType:"UriLocation"})}function M(o){let c=o.target.files?.[0];o.target.value="",c&&a.loadGFAFile(c,c.name)}return r(l,{className:t.paper,children:[e("div",{className:t.header,children:e(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",e("input",{type:"file",accept:".gfa,.gfa1,.gfa2,.gz",hidden:!0,onChange:o=>{M(o)}})]}),e(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[e(G,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{w(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),e(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),e("div",{className:t.footer,children:e(n,{size:"small",onClick:()=>{a.loadGFA(T,"Example graph")},children:"Load 4-node example"})}),a.error?e(s,{error:a.error}):null]})}),x=F;var B=i(function({model:a}){return a.hasGraph?e(C,{model:a}):a.canRetryLoad?e(f,{model:a}):r(h,{children:[a.isLoading?e(f,{model:a}):null,e("div",{hidden:a.isLoading,children:e(x,{model:a})})]})}),q=B;export{q as default};
-//# sourceMappingURL=GraphGenomeView-YRHBZFKL.js.map
+//# sourceMappingURL=GraphGenomeView-PPOVN5LA.js.map

package/dist/chunks/{GraphTrackSettingsDialog-HBLIHBB5.js → GraphTrackSettingsDialog-BRTDTVOJ.js}

@@ -1,4 +1,4 @@
-import{a as G,b as L}from"./chunk-Y5Q3XQOP.js";import{e as v,f as x,s as f}from"./chunk-LPUQPLW7.js";import"./chunk-PXYYKSGK.js";import"./chunk-46O3IEW3.js";import"./chunk-WJHTNDTQ.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-J2PN6CG3.js";import{F as y,H as h,n as H}from"./chunk-WE7DQVXF.js";import{b as p,c as i,d as s}from"./chunk-DUU6T2I5.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=s(function({model:t}){let{classes:o}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?i("div",{className:o.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:n=>{t.setSubgraphContext(Number(n)),t.recut()}}),p(h,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),M=F;var I=f()({section:{marginBottom:24}});function A(a){return a.split(/[\s,]+/).filter(t=>t!=="")}var N=(a,t)=>a.join(`
+import{a as G,b as L}from"./chunk-RS274NAD.js";import{e as v,f as x,s as f}from"./chunk-5HDIVUAZ.js";import"./chunk-ZWHXVFZF.js";import"./chunk-CHLLRNBQ.js";import"./chunk-SKB4GSET.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-J2PN6CG3.js";import{F as y,H as h,n as H}from"./chunk-WE7DQVXF.js";import{b as p,c as i,d as s}from"./chunk-DUU6T2I5.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=s(function({model:t}){let{classes:o}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?i("div",{className:o.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:n=>{t.setSubgraphContext(Number(n)),t.recut()}}),p(h,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),M=F;var I=f()({section:{marginBottom:24}});function A(a){return a.split(/[\s,]+/).filter(t=>t!=="")}var N=(a,t)=>a.join(`
 `)===t.join(`
 `);function P(a,t){let o=a.cutHaplotypes??[],[e,n]=d(o);return N(o,e)||(n(o),t()),r=>{N(r,o)||(n(r),a.setSubgraphHaplotypes(r),a.recut())}}var D=s(function({model:t}){let[o,e]=d(t.cutHaplotypes?.join(", ")??""),n=P(t,()=>{e(t.cutHaplotypes?.join(", ")??"")}),r=()=>{n(A(o))};return p(y,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:o,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:c=>{e(c.target.value)},onBlur:()=>{r()},onKeyDown:c=>{c.key==="Enter"&&r()}})}),B=s(function({model:t,names:o}){let[e,n]=d(t.cutHaplotypes??[]),r=g(e),c=g(""),[b,S]=d(!1),C=P(t,()=>{r.current=t.cutHaplotypes??[],n(r.current)});return p(H,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:o,value:e,open:b,onOpen:()=>{S(!0)},onInputChange:(u,l)=>{c.current=l},onClose:(u,l)=>{S(!1);let m=c.current.trim();l==="blur"&&m&&!r.current.includes(m)&&(r.current=[...r.current,m],n(r.current)),C(r.current)},onChange:(u,l)=>{r.current=l,n(l),b||C(l)},renderInput:u=>p(y,{...u,label:"Haplotypes",placeholder:e.length===0?"every haplotype":void 0,slotProps:{...u.slotProps,htmlInput:{...u.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),O=s(function({model:t}){let{classes:o}=I(),e=t.haplotypeNames,n=t.sourceAdapter;return n&&x(n)?i("div",{className:o.section,children:[e?p(B,{model:t,names:e}):p(D,{model:t}),i(h,{variant:"caption",component:"div",color:"text.secondary",children:[e?`Which of the graph's ${e.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),T=O;var ot=s(function({model:t,onClose:o}){return i(L,{model:t,onClose:o,children:[p(M,{model:t}),p(T,{model:t})]})});export{ot as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-HBLIHBB5.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-BRTDTVOJ.js.map

package/dist/chunks/{HighlightColorDialog-3H2H2LPS.js → HighlightColorDialog-CGW7J3SK.js}

@@ -1,2 +1,2 @@
-import{x as v,y as C}from"./chunk-T3FHGWNW.js";import"./chunk-46O3IEW3.js";import"./chunk-WJHTNDTQ.js";import"./chunk-2FG67WIZ.js";import{F as h,H as r,d as m,o as y,q as c,r as d,z as g}from"./chunk-WE7DQVXF.js";import{a as u,b as l,c as p,d as s}from"./chunk-DUU6T2I5.js";var f=s(function({model:o,onClose:t}){return p(m,{open:!0,onClose:t,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(r,{variant:"subtitle2",children:"Haplotype"}),l(r,{variant:"subtitle2",children:"Color by"}),l(r,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(S,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:i=>{o.setWalkColor(a,{field:i})},onScheme:i=>{o.setWalkColor(a,{scheme:i})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:t,children:"Done"})})]})}),S=s(function({label:o,field:t,scheme:a,onField:n,onScheme:i}){return p(u,{children:[l(r,{variant:"body2",children:o}),l(h,{select:!0,size:"small",value:t,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${o} by`}}},onChange:e=>{n(e.target.value)},children:v.map(e=>l(g,{value:e.value,children:e.label},e.value))}),l(h,{select:!0,size:"small",value:a,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${o}`}}},onChange:e=>{i(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||t==="reference").map(e=>l(g,{value:e.value,children:e.label},e.value))})]})}),T=f;export{T as default};
-//# sourceMappingURL=HighlightColorDialog-3H2H2LPS.js.map
+import{x as v,y as C}from"./chunk-FM4T47WH.js";import"./chunk-CHLLRNBQ.js";import"./chunk-SKB4GSET.js";import"./chunk-KBOVZ3GI.js";import{F as h,H as r,d as m,o as y,q as c,r as d,z as g}from"./chunk-WE7DQVXF.js";import{a as u,b as l,c as p,d as s}from"./chunk-DUU6T2I5.js";var f=s(function({model:o,onClose:t}){return p(m,{open:!0,onClose:t,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(r,{variant:"subtitle2",children:"Haplotype"}),l(r,{variant:"subtitle2",children:"Color by"}),l(r,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(S,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:i=>{o.setWalkColor(a,{field:i})},onScheme:i=>{o.setWalkColor(a,{scheme:i})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:t,children:"Done"})})]})}),S=s(function({label:o,field:t,scheme:a,onField:n,onScheme:i}){return p(u,{children:[l(r,{variant:"body2",children:o}),l(h,{select:!0,size:"small",value:t,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${o} by`}}},onChange:e=>{n(e.target.value)},children:v.map(e=>l(g,{value:e.value,children:e.label},e.value))}),l(h,{select:!0,size:"small",value:a,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${o}`}}},onChange:e=>{i(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||t==="reference").map(e=>l(g,{value:e.value,children:e.label},e.value))})]})}),T=f;export{T as default};
+//# sourceMappingURL=HighlightColorDialog-CGW7J3SK.js.map

package/dist/chunks/{LinearGraphDisplay-KD7PNZMQ.js → LinearGraphDisplay-2AZ7X7TK.js}

@@ -1,2 +1,2 @@
-import{a,b as i}from"./chunk-TUYN7C3O.js";import"./chunk-Y5Q3XQOP.js";import"./chunk-5WIUEMTH.js";import"./chunk-WWF7N6AP.js";import"./chunk-LPUQPLW7.js";import"./chunk-TFV57AXQ.js";import"./chunk-T3FHGWNW.js";import"./chunk-PXYYKSGK.js";import"./chunk-46O3IEW3.js";import"./chunk-G6NFDDMN.js";import"./chunk-VPZZ6XMM.js";import"./chunk-YBLNN5FU.js";import"./chunk-5TT5TG4Q.js";import"./chunk-WJHTNDTQ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as o,d as t}from"./chunk-DUU6T2I5.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
-//# sourceMappingURL=LinearGraphDisplay-KD7PNZMQ.js.map
+import{a,b as i}from"./chunk-MWQGJP3J.js";import"./chunk-RS274NAD.js";import"./chunk-HKGTCZOL.js";import"./chunk-NSQ4VXKR.js";import"./chunk-5HDIVUAZ.js";import"./chunk-EH5OCKSE.js";import"./chunk-FM4T47WH.js";import"./chunk-ZWHXVFZF.js";import"./chunk-CHLLRNBQ.js";import"./chunk-LKD5NRWR.js";import"./chunk-DEWVJ57F.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import"./chunk-TMM73K4C.js";import"./chunk-6VNDP3UB.js";import"./chunk-FLKXKTS2.js";import"./chunk-TC265JAP.js";import"./chunk-J2PN6CG3.js";import"./chunk-WE7DQVXF.js";import{b as o,d as t}from"./chunk-DUU6T2I5.js";var e=JBrowseExports["@jbrowse/display-kit/DisplayChrome"];var s=e&&e.__esModule?e.default:e;var p=t(function({model:r}){return o(s,{model:r,factory:a,testid:"linear-graph-display","data-layout":r.chosenLayoutMode,"data-cut-tier":r.cutTier,"data-recuts":r.recuts,"data-node-count":r.hasGraph?r.nodeCount:void 0,"data-loading":r.isLoading?"":void 0,style:{width:r.paneWidth,height:r.height,overflow:"hidden"},children:n=>o(i,{model:r,handle:n})})}),c=p;export{c as default};
+//# sourceMappingURL=LinearGraphDisplay-2AZ7X7TK.js.map

package/dist/chunks/{MinigraphBubbleAdapter-TTGZ45BF.js → MinigraphBubbleAdapter-NR3MMUUG.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-G6NFDDMN.js";import{a as g}from"./chunk-V55TK2NP.js";import{E as p,F as u,b,z as m}from"./chunk-YNMEZ4EZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as i,o as l}from"./chunk-TC265JAP.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-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-TTGZ45BF.js.map
+import{a as f,d as c,f as d}from"./chunk-LKD5NRWR.js";import{a as g}from"./chunk-V55TK2NP.js";import{E as p,F as u,b,z as m}from"./chunk-GLSUAMGV.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as i,o as l}from"./chunk-TC265JAP.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${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-NR3MMUUG.js.map

package/dist/chunks/{RgfaTabixAdapter-A274AVUU.js → RgfaTabixAdapter-JDQLVQVP.js}

@@ -1,2 +1,2 @@
-import{a as F}from"./chunk-HTH7NAV4.js";import"./chunk-KACKTX2U.js";import{a as N}from"./chunk-V55TK2NP.js";import"./chunk-YBLNN5FU.js";import"./chunk-5TT5TG4Q.js";import"./chunk-WJHTNDTQ.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-YNMEZ4EZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as l,o as m}from"./chunk-TC265JAP.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-A274AVUU.js.map
+import{a as F}from"./chunk-ZBFIEBO6.js";import"./chunk-APSXG7SV.js";import{a as N}from"./chunk-V55TK2NP.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.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-GLSUAMGV.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as l,o as m}from"./chunk-TC265JAP.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-JDQLVQVP.js.map

package/dist/chunks/{WalkFormsAdapter-7RD7ZAHG.js → WalkFormsAdapter-YMQC3NLG.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-5QJ2ANXK.js";import{a as k}from"./chunk-V55TK2NP.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-YNMEZ4EZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-2FG67WIZ.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as m,o as u}from"./chunk-TC265JAP.js";var v=r=>`${(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-7RD7ZAHG.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-EEWEXRY6.js";import{a as k}from"./chunk-V55TK2NP.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-GLSUAMGV.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import"./chunk-KBOVZ3GI.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as m,o as u}from"./chunk-TC265JAP.js";var v=r=>`${(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-YMQC3NLG.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-CLC2CJJT.js → WalkTabixSyntenyAdapter-PBWN53PE.js}

@@ -1,2 +1,2 @@
-import{a as ee}from"./chunk-HTH7NAV4.js";import{a as V,b as Z,d as q,e as J,f as B,g as Q,h as Y}from"./chunk-7HJWQFKE.js";import"./chunk-KACKTX2U.js";import{a as K}from"./chunk-V55TK2NP.js";import{p as L,q as H,r as U}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-5TT5TG4Q.js";import"./chunk-WJHTNDTQ.js";import{E as z,F as G,i as X}from"./chunk-YNMEZ4EZ.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{a as E,c as T,d as F,g as x,h as A,i as O}from"./chunk-2FG67WIZ.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{o as M}from"./chunk-TC265JAP.js";var ce=50;function fe(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=ce&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(o.push(["X",a]),e++):o.push([t,a])}return o}function R(r){return Array.from(r.ids,(o,e)=>2*o+r.rev[e])}function P(r,o){let e=r.get(o);return e===void 0?0:e.end-e.start}function te(r){let o=new Map,e=s=>{let n=P(r,s),i=o.get(n);return i===void 0&&(i="N".repeat(n),o.set(n,i)),i},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=R(s),t.set(s,n)),n};return(s,n)=>H({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var _=100;function I(r,o,e){let t=r.at(-1);e>0&&(t?.[0]===o?t[1]+=e:r.push([o,e]))}function ae(r){let o=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+o(s)}),a};return(t,a)=>{let s=R(a),n=R(t),[i,c]=L(n,s,o),[g,d]=L(n.map(y=>y^1).reverse(),s,o),l=d>c,f=l?g:i,b=Math.max(c,d);if(b<_)return[];let p=e(s),h=e(n),u=y=>l?n.length-1-f[y][0]:f[y][0],k=[];f.forEach(([,y],w)=>{if(w>0){let[v,m]=[u(w-1),u(w)].sort((W,C)=>W-C);I(k,"I",h[m]-h[v+1]),I(k,"D",p[y]-p[f[w-1][1]+1])}I(k,"=",o(s[y]))});let[N,S]=[u(0),u(f.length-1)].sort((y,w)=>y-w);return[{queryStart:h[N],queryEnd:h[S+1],targetStart:p[f[0][1]],targetEnd:p[f.at(-1)[1]+1],strand:l?"-":"+",edits:k,sharedBases:b}]}}function pe(r){let o=new Map,e=new Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=pe(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,g]of e(t)){let d=s.get(c);d===g?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var ue=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:g}=t(a,s);return i===void 0||Math.min(c,g)<ue?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function $({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=fe(r.edits);return Y({target:{name:o.name,assemblyName:t,refName:a,start:o.hapStart+r.targetStart,end:o.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:F(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:U(n),matches:n.reduce((i,[c,g])=>i+(c==="="?g:0),0),columns:n.reduce((i,[,c])=>i+c,0)})}function ie(r,o,e,t,a){let s=a==="leave",n=i=>i.kind==="elsewhere"&&(s?i.chunk.start>=r.refStart:i.chunk.start<r.refStart);for(let i of e){let{name:c,fragStart:g,hapStart:d,ids:l,rev:f,before:b,after:p}=i;if(c===r.name&&g===r.fragStart){let h=d;for(let u=0;u<l.length;u++){let k=t.get(l[u]),N=k===void 0?0:k.end-k.start;if(k?.rank===0&&k.refName===o&&(s?k.end===r.refStart:k.start===r.refEnd)){let S=n(p)!==n(b)?n(p):u>0!=u<l.length-1?u>0:s!==(f[u]===1);return{skip:r,at:S?h+N:h,strand:S===s?"+":"-"}}h+=N}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r;return le({id:`${a.name}:${a.fragStart}:${a.piece}:skip`,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,reverse:n==="-",mate:{refName:F(a.name),start:s,end:s,assemblyName:t}})}function me({fragment:r,crossing:o,refName:e,assemblyName:t,mateAssemblyName:a}){let{name:s,fragStart:n,hapStart:i,hapEnd:c}=r;return le({id:`${s}:${n}:${i}:crossing`,assemblyName:t,refName:e,start:o.refStart,end:o.refEnd,reverse:o.reverse,mate:{refName:F(s),start:i,end:c,assemblyName:a}})}function le({id:r,assemblyName:o,refName:e,start:t,end:a,reverse:s,mate:n}){return new V({uniqueId:r,assemblyName:o,refName:e,start:t,end:a,type:"skip",strand:s?-1:1,syntenyId:r,spansWindow:!0,mate:n})}var j=({name:r})=>T(r)??r,D=class extends Z{constructor(){super(...arguments);this.walks=new ee(z(this,["walksLocation"],["walksIndex"]),this);this.refNames=new G(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:a}=this,s=A(this,a),n=O(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&E(i)!==s).map(i=>({name:B(n,i),label:i,group:E(i)}))}}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 a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=X(a,e);return M(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let g=new Set(c.map(d=>d.skip));n=n.filter(d=>!g.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=l=>a==="leave"?l.refStart-1:l.refEnd,g=new Map;for(let l of t){let f=c(l),b=Math.floor(f/i),p=g.get(b);p?(p.group.push(l),p.start=Math.min(p.start,f),p.end=Math.max(p.end,f+1)):g.set(b,{group:[l],start:f,end:f+1})}return(await Promise.all([...g.values()].map(async({group:l,start:f,end:b})=>{let p=new Set(l.map(u=>u.name)),h=u=>p.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:f,end:b},{...this.walks.budgets(),signal:n,keep:h,expand:h,context:0,contained:!0,links:!1});return l.map(N=>ie(N,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(l=>l!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>A(this,m)):void 0,n=A(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(m=>x(n,m)||x(m,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:g}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${g.toLocaleString()}`,{graph:l,fragments:f,skips:b}=await this.laneWalks(e,t,i,a,d),p=({name:m})=>i===void 0?0:i.findIndex(W=>x(m,W)),h=new Set(f.map(j)),u=await M(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(m=>p(m)>=0&&!h.has(j(m))&&m.refStart<=c&&m.refEnd>=g),a)),k=re(l.nodes),N=O(this),S=m=>B(N,j(m)),y=f.filter(m=>m.name===e),w=f.filter(m=>m.name!==e&&p(m)>=0).map(m=>({rank:p(m),features:m.crossing?[me({fragment:m,crossing:m.crossing,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})]:y.flatMap(W=>k(m,W).map(C=>$({chain:C,target:W,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})))})),v=u.map(m=>({rank:p(m.skip),features:[oe({crossing:m,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:S(m.skip)})]}));return[...w,...v].sort((m,W)=>m.rank-W.rank).flatMap(m=>m.features)}async pairFeatures(e,t,a,s){let n=a.map(l=>({pair:l,featurePrefix:A(this,l.queryAssemblyName),matePrefix:A(this,l.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,J(a)),g=se(i.nodes),d=l=>c.filter(f=>x(f.name,l));return n.flatMap(({pair:l,featurePrefix:f,matePrefix:b})=>d(f).flatMap(p=>d(b).flatMap(h=>g(h,p).map(u=>$({chain:u,target:p,query:h,assemblyName:l.queryAssemblyName,refName:F(p.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return K(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=q(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{D as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-CLC2CJJT.js.map
+import{a as ee}from"./chunk-ZBFIEBO6.js";import{a as V,b as Z,d as q,e as J,f as B,g as Q,h as Y}from"./chunk-LFQFVYNY.js";import"./chunk-APSXG7SV.js";import{a as K}from"./chunk-V55TK2NP.js";import{p as L,q as H,r as U}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.js";import{E as z,F as G,i as X}from"./chunk-GLSUAMGV.js";import"./chunk-YBLNN5FU.js";import"./chunk-QUDJ7AM3.js";import{a as E,c as T,d as F,g as x,h as A,i as O}from"./chunk-KBOVZ3GI.js";import"./chunk-AGUEPVOR.js";import"./chunk-TMM73K4C.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{o as M}from"./chunk-TC265JAP.js";var ce=50;function fe(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=ce&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(o.push(["X",a]),e++):o.push([t,a])}return o}function R(r){return Array.from(r.ids,(o,e)=>2*o+r.rev[e])}function P(r,o){let e=r.get(o);return e===void 0?0:e.end-e.start}function te(r){let o=new Map,e=s=>{let n=P(r,s),i=o.get(n);return i===void 0&&(i="N".repeat(n),o.set(n,i)),i},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=R(s),t.set(s,n)),n};return(s,n)=>H({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var _=100;function I(r,o,e){let t=r.at(-1);e>0&&(t?.[0]===o?t[1]+=e:r.push([o,e]))}function ae(r){let o=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+o(s)}),a};return(t,a)=>{let s=R(a),n=R(t),[i,c]=L(n,s,o),[g,d]=L(n.map(y=>y^1).reverse(),s,o),l=d>c,f=l?g:i,b=Math.max(c,d);if(b<_)return[];let p=e(s),h=e(n),u=y=>l?n.length-1-f[y][0]:f[y][0],k=[];f.forEach(([,y],w)=>{if(w>0){let[v,m]=[u(w-1),u(w)].sort((W,C)=>W-C);I(k,"I",h[m]-h[v+1]),I(k,"D",p[y]-p[f[w-1][1]+1])}I(k,"=",o(s[y]))});let[N,S]=[u(0),u(f.length-1)].sort((y,w)=>y-w);return[{queryStart:h[N],queryEnd:h[S+1],targetStart:p[f[0][1]],targetEnd:p[f.at(-1)[1]+1],strand:l?"-":"+",edits:k,sharedBases:b}]}}function pe(r){let o=new Map,e=new Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=pe(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,g]of e(t)){let d=s.get(c);d===g?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var ue=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:g}=t(a,s);return i===void 0||Math.min(c,g)<ue?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function $({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=fe(r.edits);return Y({target:{name:o.name,assemblyName:t,refName:a,start:o.hapStart+r.targetStart,end:o.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:F(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:U(n),matches:n.reduce((i,[c,g])=>i+(c==="="?g:0),0),columns:n.reduce((i,[,c])=>i+c,0)})}function ie(r,o,e,t,a){let s=a==="leave",n=i=>i.kind==="elsewhere"&&(s?i.chunk.start>=r.refStart:i.chunk.start<r.refStart);for(let i of e){let{name:c,fragStart:g,hapStart:d,ids:l,rev:f,before:b,after:p}=i;if(c===r.name&&g===r.fragStart){let h=d;for(let u=0;u<l.length;u++){let k=t.get(l[u]),N=k===void 0?0:k.end-k.start;if(k?.rank===0&&k.refName===o&&(s?k.end===r.refStart:k.start===r.refEnd)){let S=n(p)!==n(b)?n(p):u>0!=u<l.length-1?u>0:s!==(f[u]===1);return{skip:r,at:S?h+N:h,strand:S===s?"+":"-"}}h+=N}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r;return le({id:`${a.name}:${a.fragStart}:${a.piece}:skip`,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,reverse:n==="-",mate:{refName:F(a.name),start:s,end:s,assemblyName:t}})}function me({fragment:r,crossing:o,refName:e,assemblyName:t,mateAssemblyName:a}){let{name:s,fragStart:n,hapStart:i,hapEnd:c}=r;return le({id:`${s}:${n}:${i}:crossing`,assemblyName:t,refName:e,start:o.refStart,end:o.refEnd,reverse:o.reverse,mate:{refName:F(s),start:i,end:c,assemblyName:a}})}function le({id:r,assemblyName:o,refName:e,start:t,end:a,reverse:s,mate:n}){return new V({uniqueId:r,assemblyName:o,refName:e,start:t,end:a,type:"skip",strand:s?-1:1,syntenyId:r,spansWindow:!0,mate:n})}var j=({name:r})=>T(r)??r,D=class extends Z{constructor(){super(...arguments);this.walks=new ee(z(this,["walksLocation"],["walksIndex"]),this);this.refNames=new G(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:a}=this,s=A(this,a),n=O(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&E(i)!==s).map(i=>({name:B(n,i),label:i,group:E(i)}))}}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 a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=X(a,e);return M(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let g=new Set(c.map(d=>d.skip));n=n.filter(d=>!g.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=l=>a==="leave"?l.refStart-1:l.refEnd,g=new Map;for(let l of t){let f=c(l),b=Math.floor(f/i),p=g.get(b);p?(p.group.push(l),p.start=Math.min(p.start,f),p.end=Math.max(p.end,f+1)):g.set(b,{group:[l],start:f,end:f+1})}return(await Promise.all([...g.values()].map(async({group:l,start:f,end:b})=>{let p=new Set(l.map(u=>u.name)),h=u=>p.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:f,end:b},{...this.walks.budgets(),signal:n,keep:h,expand:h,context:0,contained:!0,links:!1});return l.map(N=>ie(N,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(l=>l!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>A(this,m)):void 0,n=A(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(m=>x(n,m)||x(m,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:g}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${g.toLocaleString()}`,{graph:l,fragments:f,skips:b}=await this.laneWalks(e,t,i,a,d),p=({name:m})=>i===void 0?0:i.findIndex(W=>x(m,W)),h=new Set(f.map(j)),u=await M(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(m=>p(m)>=0&&!h.has(j(m))&&m.refStart<=c&&m.refEnd>=g),a)),k=re(l.nodes),N=O(this),S=m=>B(N,j(m)),y=f.filter(m=>m.name===e),w=f.filter(m=>m.name!==e&&p(m)>=0).map(m=>({rank:p(m),features:m.crossing?[me({fragment:m,crossing:m.crossing,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})]:y.flatMap(W=>k(m,W).map(C=>$({chain:C,target:W,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:S(m)})))})),v=u.map(m=>({rank:p(m.skip),features:[oe({crossing:m,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:S(m.skip)})]}));return[...w,...v].sort((m,W)=>m.rank-W.rank).flatMap(m=>m.features)}async pairFeatures(e,t,a,s){let n=a.map(l=>({pair:l,featurePrefix:A(this,l.queryAssemblyName),matePrefix:A(this,l.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,J(a)),g=se(i.nodes),d=l=>c.filter(f=>x(f.name,l));return n.flatMap(({pair:l,featurePrefix:f,matePrefix:b})=>d(f).flatMap(p=>d(b).flatMap(h=>g(h,p).map(u=>$({chain:u,target:p,query:h,assemblyName:l.queryAssemblyName,refName:F(p.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return K(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=q(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{D as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-PBWN53PE.js.map

package/dist/chunks/{chunk-LPUQPLW7.js → chunk-5HDIVUAZ.js}

@@ -1,2 +1,2 @@
-import{b as D}from"./chunk-PXYYKSGK.js";import{d as x}from"./chunk-QUDJ7AM3.js";import{a as w,d as P}from"./chunk-TMM73K4C.js";import{f as B}from"./chunk-6VNDP3UB.js";var g;function N(){return g??(g=import("./bandage-layout-UZEOCKMS.js").then(e=>e.default()).catch(e=>{throw g=void 0,e})),g}async function E(e){return(await N()).computeLayout(e.graph,e.options)}var G=[{value:"fmmm",label:"Bandage (FMMM)",description:"Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm."},{value:"stress",label:"Stress",description:"Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference."}],V=G.map(e=>e.value);var Y=async e=>{let n=performance.now();return{result:e.options.engine==="stress"?D(e):await E(e),duration:performance.now()-n}};function K(e){return Array.isArray(e)&&e.every(n=>typeof n=="string")}function we(e){let n=w(e).slice(1);return n.length>0?n:void 0}function $(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||B(e.walksLocation))}function Ne(e){return e.type==="GbzBaseSyntenyAdapter"||$(e)}function Ee(e){let{defaultHaplotypes:n}=e;return $(e)&&K(n)&&n.length>0?n:void 0}function Re(e){return w(e)[0]}function Le(e){return P(e).adapter}function Se(e,n){return e===void 0||e===n?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,n){return typeof e.get=="function"?e.get(n):e[n]}function b(e,n){return e.find(t=>t.trackId===n)}function h(e){return`${e.trackId} ${e.name??""}`}var J=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),S=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function ot(e,n){let t=n?b(e,n):void 0;return t||e.filter(o=>J.has(o.adapterType)).find(o=>S.test(h(o)))}var v=/^\w+=[^;]*(;\w+=[^;]*)*$/;function W(e){let n=i(e,"name");if(!(typeof n!="string"||!v.test(n)))return Object.fromEntries(n.split(";").map(t=>{let r=t.indexOf("=");return[t.slice(0,r),t.slice(r+1)]}))}function d(e,n){let t=i(e,n);return t!==void 0?t:i(e,"INFO")?.[n]??W(e)?.[n]}var U=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],z=["RUL","period","PERIOD","consensusSize","unit","unitLength"],X=["TRID","REPID","VARID","ID","name","id"];function k(e,n){for(let t of n){let r=d(e,t),o=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(o!==""&&o!==".")return o}}var H=/^[ACGTURYSWKMBDHVN]+$/i;function Q(e){let n=Number(k(e,z));if(Number.isFinite(n)&&n>0)return Math.round(n);let t=k(e,U);return t&&H.test(t)?t.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(t=>{let r=t===""||t===null||t===void 0?NaN:Number(t);return Number.isFinite(r)?r:void 0})}function L(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(t=>{let r=String(t??"").trim();return r===""||r==="."?void 0:r})}var R="<CNV:TR>";function q(e){let n=L(i(e,"ALT"));if(!n.includes(R))return;let t=m(d(e,"RN")),r=L(d(e,"RUS")),o=m(d(e,"RUL")),s=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return n.map((u,f)=>{let p=t[f]??(u===R?1:0),y=0,_=0;for(let C=0;C<p;C++,c++){let A=r[c],I=o[c]??(A&&H.test(A)?A.length:void 0),O=s[c],M=a[c]??(I&&O!==void 0?Math.round(I*O):void 0);M!==void 0&&(y+=M,_++)}return u===R&&p>0&&_===p?y:void 0})}function Z(e,n,t){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((o,s)=>{let a=o===""?NaN:Number(o),c=a>0?n[a-1]:t;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:s+1}:{}}]})}function ee(e,n,t){let r=i(e,"samples"),o={};for(let[s,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,y)=>p!==void 0&&p>0?[c[y]===void 0?{bp:p}:{bp:p,spanningReads:c[y]}]:[]),f=u.length>0||!n?u:Z(L(a.GT)[0],n,t);f.length>0&&(o[s]=f)}return Object.keys(o).length>0?o:void 0}function te(e,n){let t=d(e,"start"),r=d(e,"end"),o=m(d(e,"SVLEN"))[0];return n&&o!==void 0?{start:t+1,end:t+1+o}:{start:t,end:r}}function st(e){let n=[];for(let t of e){let r=q(t),{start:o,end:s}=te(t,r!==void 0),a=Q(t);if(!(s>o)||a===void 0)continue;let c=d(t,"refName"),u=k(t,U),f=k(t,X);n.push({key:`${c}:${o}-${s}`,name:(f&&!v.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(o+1).toLocaleString("en-US")}-${s.toLocaleString("en-US")}`),refName:c,start:o,end:s,unit:a,motif:u,calls:ee(t,r,s-o)})}return n.sort((t,r)=>t.start-r.start)}function T(e){let n=[];for(let t of[...e].sort((r,o)=>r.start-o.start)){let r=n.at(-1);r&&t.start<=r.end?r.end=Math.max(r.end,t.end):n.push({...t})}return n}function F(e){let n=[],t=new Map;for(let r of[...e].sort((o,s)=>o.start-s.start)){let o=`${r.refName}	${r.strand}	${r.name}`,s=t.get(o);if(s&&r.start<s.end)s.end=Math.max(s.end,r.end),s.exons=T([...s.exons,...r.exons]);else{let a={...r,exons:T(r.exons)};n.push(a),t.set(o,a)}}return n}var ne=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),re=/gene|refseq|gencode|ensembl|annotation/i,oe=new Set(["BedTabixAdapter","BedAdapter"]);function yt(e,n){let t=n?b(e,n):void 0;if(t)return t;let r=e.filter(o=>ne.has(o.adapterType)&&!S.test(h(o)));return r.find(o=>re.test(h(o)))??r.find(o=>!oe.has(o.adapterType))}var se=/\bTEs?\b|transpos/i;function Tt(e){return e&&se.test(h(e))?"TE":"gene"}function bt(e,n){let t=e.tracks?.find(r=>x(r.configuration,"trackId")===n)?.displays[0];return t?x(t.configuration,"filter")??[]:[]}var ie=new Set(["chromosome","region","contig","supercontig","scaffold"]),ae=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function j(e,n){let t=i(e,"type");typeof t=="string"&&ae.has(t)&&n.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let o of r??[])j(o,n)}function kt(e){let n=[];for(let t of e){let r=i(t,"gene_name")??i(t,"name")??i(t,"gene")??i(t,"gene_id"),o=i(t,"start"),s=i(t,"end");if(!r||!(s>o)||ie.has(i(t,"type")))continue;let a=[];j(t,a),n.push({name:r,refName:i(t,"refName"),start:o,end:s,strand:i(t,"strand")??0,exons:a.length?T(a):[{start:o,end:s}]})}return F(n)}var l=JBrowseExports["tss-react/mui"],ce=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var xt=ce("makeStyles"),wt=l&&l.__esModule?l.default:l;export{G as a,V as b,Y as c,we as d,$ as e,Ne as f,Ee as g,Re as h,Le as i,Se as j,J as k,ot as l,st as m,ne as n,yt as o,Tt as p,bt as q,kt as r,xt as s};
-//# sourceMappingURL=chunk-LPUQPLW7.js.map
+import{b as D}from"./chunk-ZWHXVFZF.js";import{d as x}from"./chunk-QUDJ7AM3.js";import{a as w,d as P}from"./chunk-TMM73K4C.js";import{f as B}from"./chunk-6VNDP3UB.js";var g;function N(){return g??(g=import("./bandage-layout-UZEOCKMS.js").then(e=>e.default()).catch(e=>{throw g=void 0,e})),g}async function E(e){return(await N()).computeLayout(e.graph,e.options)}var G=[{value:"fmmm",label:"Bandage (FMMM)",description:"Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm."},{value:"stress",label:"Stress",description:"Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference."}],V=G.map(e=>e.value);var Y=async e=>{let n=performance.now();return{result:e.options.engine==="stress"?D(e):await E(e),duration:performance.now()-n}};function K(e){return Array.isArray(e)&&e.every(n=>typeof n=="string")}function we(e){let n=w(e).slice(1);return n.length>0?n:void 0}function $(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||B(e.walksLocation))}function Ne(e){return e.type==="GbzBaseSyntenyAdapter"||$(e)}function Ee(e){let{defaultHaplotypes:n}=e;return $(e)&&K(n)&&n.length>0?n:void 0}function Re(e){return w(e)[0]}function Le(e){return P(e).adapter}function Se(e,n){return e===void 0||e===n?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,n){return typeof e.get=="function"?e.get(n):e[n]}function b(e,n){return e.find(t=>t.trackId===n)}function h(e){return`${e.trackId} ${e.name??""}`}var J=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),S=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function ot(e,n){let t=n?b(e,n):void 0;return t||e.filter(o=>J.has(o.adapterType)).find(o=>S.test(h(o)))}var v=/^\w+=[^;]*(;\w+=[^;]*)*$/;function W(e){let n=i(e,"name");if(!(typeof n!="string"||!v.test(n)))return Object.fromEntries(n.split(";").map(t=>{let r=t.indexOf("=");return[t.slice(0,r),t.slice(r+1)]}))}function d(e,n){let t=i(e,n);return t!==void 0?t:i(e,"INFO")?.[n]??W(e)?.[n]}var U=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],z=["RUL","period","PERIOD","consensusSize","unit","unitLength"],X=["TRID","REPID","VARID","ID","name","id"];function k(e,n){for(let t of n){let r=d(e,t),o=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(o!==""&&o!==".")return o}}var H=/^[ACGTURYSWKMBDHVN]+$/i;function Q(e){let n=Number(k(e,z));if(Number.isFinite(n)&&n>0)return Math.round(n);let t=k(e,U);return t&&H.test(t)?t.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(t=>{let r=t===""||t===null||t===void 0?NaN:Number(t);return Number.isFinite(r)?r:void 0})}function L(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(t=>{let r=String(t??"").trim();return r===""||r==="."?void 0:r})}var R="<CNV:TR>";function q(e){let n=L(i(e,"ALT"));if(!n.includes(R))return;let t=m(d(e,"RN")),r=L(d(e,"RUS")),o=m(d(e,"RUL")),s=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return n.map((u,f)=>{let p=t[f]??(u===R?1:0),y=0,_=0;for(let C=0;C<p;C++,c++){let A=r[c],I=o[c]??(A&&H.test(A)?A.length:void 0),O=s[c],M=a[c]??(I&&O!==void 0?Math.round(I*O):void 0);M!==void 0&&(y+=M,_++)}return u===R&&p>0&&_===p?y:void 0})}function Z(e,n,t){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((o,s)=>{let a=o===""?NaN:Number(o),c=a>0?n[a-1]:t;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:s+1}:{}}]})}function ee(e,n,t){let r=i(e,"samples"),o={};for(let[s,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,y)=>p!==void 0&&p>0?[c[y]===void 0?{bp:p}:{bp:p,spanningReads:c[y]}]:[]),f=u.length>0||!n?u:Z(L(a.GT)[0],n,t);f.length>0&&(o[s]=f)}return Object.keys(o).length>0?o:void 0}function te(e,n){let t=d(e,"start"),r=d(e,"end"),o=m(d(e,"SVLEN"))[0];return n&&o!==void 0?{start:t+1,end:t+1+o}:{start:t,end:r}}function st(e){let n=[];for(let t of e){let r=q(t),{start:o,end:s}=te(t,r!==void 0),a=Q(t);if(!(s>o)||a===void 0)continue;let c=d(t,"refName"),u=k(t,U),f=k(t,X);n.push({key:`${c}:${o}-${s}`,name:(f&&!v.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(o+1).toLocaleString("en-US")}-${s.toLocaleString("en-US")}`),refName:c,start:o,end:s,unit:a,motif:u,calls:ee(t,r,s-o)})}return n.sort((t,r)=>t.start-r.start)}function T(e){let n=[];for(let t of[...e].sort((r,o)=>r.start-o.start)){let r=n.at(-1);r&&t.start<=r.end?r.end=Math.max(r.end,t.end):n.push({...t})}return n}function F(e){let n=[],t=new Map;for(let r of[...e].sort((o,s)=>o.start-s.start)){let o=`${r.refName}	${r.strand}	${r.name}`,s=t.get(o);if(s&&r.start<s.end)s.end=Math.max(s.end,r.end),s.exons=T([...s.exons,...r.exons]);else{let a={...r,exons:T(r.exons)};n.push(a),t.set(o,a)}}return n}var ne=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),re=/gene|refseq|gencode|ensembl|annotation/i,oe=new Set(["BedTabixAdapter","BedAdapter"]);function yt(e,n){let t=n?b(e,n):void 0;if(t)return t;let r=e.filter(o=>ne.has(o.adapterType)&&!S.test(h(o)));return r.find(o=>re.test(h(o)))??r.find(o=>!oe.has(o.adapterType))}var se=/\bTEs?\b|transpos/i;function Tt(e){return e&&se.test(h(e))?"TE":"gene"}function bt(e,n){let t=e.tracks?.find(r=>x(r.configuration,"trackId")===n)?.displays[0];return t?x(t.configuration,"filter")??[]:[]}var ie=new Set(["chromosome","region","contig","supercontig","scaffold"]),ae=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function j(e,n){let t=i(e,"type");typeof t=="string"&&ae.has(t)&&n.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let o of r??[])j(o,n)}function kt(e){let n=[];for(let t of e){let r=i(t,"gene_name")??i(t,"name")??i(t,"gene")??i(t,"gene_id"),o=i(t,"start"),s=i(t,"end");if(!r||!(s>o)||ie.has(i(t,"type")))continue;let a=[];j(t,a),n.push({name:r,refName:i(t,"refName"),start:o,end:s,strand:i(t,"strand")??0,exons:a.length?T(a):[{start:o,end:s}]})}return F(n)}var l=JBrowseExports["tss-react/mui"],ce=e=>l!=null&&e in Object(l)?l[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var xt=ce("makeStyles"),wt=l&&l.__esModule?l.default:l;export{G as a,V as b,Y as c,we as d,$ as e,Ne as f,Ee as g,Re as h,Le as i,Se as j,J as k,ot as l,st as m,ne as n,yt as o,Tt as p,bt as q,kt as r,xt as s};
+//# sourceMappingURL=chunk-5HDIVUAZ.js.map

package/dist/chunks/{chunk-LPUQPLW7.js.map → chunk-5HDIVUAZ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/loadFmmm.js", "../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/fmmmLayout.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CO6RGQAD.js", "../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "jbrowse-host:tss-react/mui"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/loadFmmm.js", "../../node_modules/.pnpm/@jbrowse+graph-fmmm-layout@1.0.2/node_modules/@jbrowse/graph-fmmm-layout/esm/fmmmLayout.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-CO6RGQAD.js", "../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "jbrowse-host:tss-react/mui"],
   "sourcesContent": ["let cached;\nexport function loadFmmm() {\n    cached !== null && cached !== void 0 ? cached : (cached = import('./bandage-layout.js')\n        .then(mod => mod.default())\n        .catch((e) => {\n        cached = undefined;\n        throw e;\n    }));\n    return cached;\n}\n", "import { loadFmmm } from \"./loadFmmm.js\";\nexport async function fmmmLayout(request) {\n    const engine = await loadFmmm();\n    return engine.computeLayout(request.graph, request.options);\n}\n", "// src/layoutEngines.ts\nimport { fmmmLayout } from \"@jbrowse/graph-fmmm-layout\";\nimport { stressLayout } from \"@jbrowse/graph-stress-layout\";\nvar LAYOUT_ENGINES = [\n  {\n    value: \"fmmm\",\n    label: \"Bandage (FMMM)\",\n    description: \"Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.\"\n  },\n  {\n    value: \"stress\",\n    label: \"Stress\",\n    description: \"Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference.\"\n  }\n];\nvar LAYOUT_ENGINE_VALUES = LAYOUT_ENGINES.map((e) => e.value);\nfunction isLayoutEngineKind(value) {\n  return LAYOUT_ENGINE_VALUES.includes(value);\n}\nvar layoutEngine = async (request) => {\n  const start = performance.now();\n  const result = request.options.engine === \"stress\" ? stressLayout(request) : await fmmmLayout(request);\n  return { result, duration: performance.now() - start };\n};\n\nexport {\n  LAYOUT_ENGINES,\n  LAYOUT_ENGINE_VALUES,\n  isLayoutEngineKind,\n  layoutEngine\n};\n", "import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = ownField(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\n    const last = out.at(-1);\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end);\n    } else {\n      out.push({ ...iv });\n    }\n  }\n  return out;\n}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
   "mappings": "uKAAA,IAAIA,EACG,SAASC,GAAW,CACvB,OAAAD,IAAiDA,EAAS,OAAO,8BAAqB,EACjF,KAAKE,GAAOA,EAAI,QAAQ,CAAC,EACzB,MAAO,GAAM,CACd,MAAAF,EAAS,OACH,CACV,CAAC,GACMA,CACX,CCRA,eAAsBG,EAAWC,EAAS,CAEtC,OADe,MAAMC,EAAS,GAChB,cAAcD,EAAQ,MAAOA,EAAQ,OAAO,CAC9D,CCDA,IAAIE,EAAiB,CACnB,CACE,MAAO,OACP,MAAO,iBACP,YAAa,6FACf,EACA,CACE,MAAO,SACP,MAAO,SACP,YAAa,yNACf,CACF,EACIC,EAAuBD,EAAe,IAAK,GAAM,EAAE,KAAK,EAI5D,IAAIE,EAAe,MAAOC,GAAY,CACpC,IAAMC,EAAQ,YAAY,IAAI,EAE9B,MAAO,CAAE,OADMD,EAAQ,QAAQ,SAAW,SAAWE,EAAaF,CAAO,EAAI,MAAMG,EAAWH,CAAO,EACpF,SAAU,YAAY,IAAI,EAAIC,CAAM,CACvD,ECdA,SAASG,EAAcC,EAAmC,CACxD,OAAO,MAAM,QAAQA,CAAK,GAAKA,EAAM,MAAMC,GAAQ,OAAOA,GAAS,QAAQ,CAC7E,CAIO,SAASC,GAAWC,EAAuB,CAChD,IAAMC,EAAQC,EAA2BF,CAAK,EAAE,MAAM,CAAC,EACvD,OAAOC,EAAM,OAAS,EAAIA,EAAQ,MACpC,CAKO,SAASE,EAAYC,EAAwC,CAClE,OACEA,EAAc,OAAS,2BACtBA,EAAc,OAAS,qBACpB,OAAOA,EAAc,UAAa,UAClCA,EAAc,WAAa,IAC3BC,EAAkBD,EAAc,aAAa,EAErD,CAIO,SAASE,GAAgBF,EAAwC,CACtE,OACEA,EAAc,OAAS,yBAA2BD,EAAYC,CAAa,CAE/E,CAIO,SAASG,GAAiBH,EAAwC,CACvE,GAAM,CAAE,kBAAAI,CAAkB,EAAIJ,EAC9B,OAAOD,EAAYC,CAAa,GAC9BR,EAAcY,CAAiB,GAC/BA,EAAkB,OAAS,EACzBA,EACA,MACN,CAMO,SAASC,GAAuBT,EAAuB,CAC5D,OAAOE,EAA2BF,CAAK,EAAE,CAAC,CAC5C,CAGO,SAASU,GAAqBV,EAAuB,CAC1D,OAAOW,EAAmBX,CAAK,EAAE,OACnC,CAEO,SAASY,GACdC,EACAC,EACA,CACA,OAAOD,IAAsB,QAAaA,IAAsBC,EAC5D,OACA,sCAAsCD,CAAiB,4BAA4BA,CAAiB,EAC1G,CCpEO,SAASE,EAASC,EAAgBC,EAAuB,CAC9D,OAAO,OAAQD,EAAc,KAAQ,WAChCA,EAAc,IAAIC,CAAI,EACtBD,EAA8BC,CAAI,CACzC,CAQO,SAASC,EAAkCC,EAAaC,EAAe,CAC5E,OAAOD,EAAO,KAAK,GAAK,EAAE,UAAYC,CAAK,CAC7C,CAGO,SAASC,EAAWC,EAAgB,CACzC,MAAO,GAAGA,EAAE,OAAO,IAAIA,EAAE,MAAQ,EAAE,EACrC,CCgBO,IAAMC,EAAuB,IAAI,IAAI,CAC1C,aACA,kBACA,gBACA,aACA,iBACF,CAAC,EAEYC,EACX,gEAEK,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,OAAIC,GAGeF,EAAO,OAAOI,GAAKP,EAAqB,IAAIO,EAAE,WAAW,CAAC,EAC3D,KAAKA,GAAKN,EAAkB,KAAKO,EAAWD,CAAC,CAAC,CAAC,CACnE,CAKA,IAAME,EAAc,2BAEpB,SAASC,EAAWC,EAAgB,CAClC,IAAMC,EAAOC,EAASF,EAAG,MAAM,EAC/B,GAAI,SAAOC,GAAS,UAAY,CAACH,EAAY,KAAKG,CAAI,GAGtD,OAAO,OAAO,YACZA,EAAK,MAAM,GAAG,EAAE,IAAIE,GAAQ,CAC1B,IAAMC,EAAID,EAAK,QAAQ,GAAG,EAC1B,MAAO,CAACA,EAAK,MAAM,EAAGC,CAAC,EAAGD,EAAK,MAAMC,EAAI,CAAC,CAAC,CAC7C,CAAC,CACH,CACF,CAIA,SAASC,EAAML,EAAgBC,EAAuB,CACpD,IAAMK,EAAMJ,EAASF,EAAGC,CAAI,EAC5B,OAAIK,IAAQ,OACHA,EAEIJ,EAASF,EAAG,MAAM,IACjBC,CAAI,GAAKF,EAAWC,CAAC,IAAIC,CAAI,CAC7C,CAEA,IAAMM,EAAe,CACnB,MACA,SACA,KACA,SACA,QACA,WACA,WACF,EACMC,EAAgB,CACpB,MACA,SACA,SACA,gBACA,OACA,YACF,EACMC,EAAc,CAAC,OAAQ,QAAS,QAAS,KAAM,OAAQ,IAAI,EAKjE,SAASC,EAAMV,EAAgBW,EAAiB,CAC9C,QAAWV,KAAQU,EAAO,CACxB,IAAMC,EAAQP,EAAML,EAAGC,CAAI,EACrBY,EAAM,QAAQ,MAAM,QAAQD,CAAK,EAAIA,EAAM,CAAC,EAAIA,IAAU,EAAE,EAC/D,MAAM,GAAG,EAAE,CAAC,EACZ,KAAK,EACR,GAAIC,IAAQ,IAAMA,IAAQ,IACxB,OAAOA,CAEX,CAEF,CAEA,IAAMC,EAAQ,yBAGP,SAASC,EAAaf,EAAgB,CAC3C,IAAMgB,EAAS,OAAON,EAAMV,EAAGQ,CAAa,CAAC,EAC7C,GAAI,OAAO,SAASQ,CAAM,GAAKA,EAAS,EACtC,OAAO,KAAK,MAAMA,CAAM,EAE1B,IAAMC,EAAQP,EAAMV,EAAGO,CAAY,EACnC,OAAOU,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,MACrD,CAKA,SAASC,EAAQN,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMM,EACJN,IAAQ,IAAMA,IAAQ,MAAQA,IAAQ,OAAY,IAAM,OAAOA,CAAG,EACpE,OAAO,OAAO,SAASM,CAAC,EAAIA,EAAI,MAClC,CAAC,CACH,CAEA,SAASC,EAAQR,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMQ,EAAO,OAAOR,GAAO,EAAE,EAAE,KAAK,EACpC,OAAOQ,IAAS,IAAMA,IAAS,IAAM,OAAYA,CACnD,CAAC,CACH,CAEA,IAAMC,EAAgB,WAMtB,SAASC,EAAevB,EAAgB,CACtC,IAAMwB,EAAOJ,EAAQlB,EAASF,EAAG,KAAK,CAAC,EACvC,GAAI,CAACwB,EAAK,SAASF,CAAa,EAC9B,OAEF,IAAMG,EAAKP,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC3B0B,EAAMN,EAAQf,EAAML,EAAG,KAAK,CAAC,EAC7B2B,EAAMT,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B4B,EAAMV,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B6B,EAAKX,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC7B8B,EAAI,EACR,OAAON,EAAK,IAAI,CAACO,EAAK3B,IAAM,CAC1B,IAAMe,EAAIM,EAAGrB,CAAC,IAAM2B,IAAQT,EAAgB,EAAI,GAC5CU,EAAK,EACLC,EAAQ,EACZ,QAASC,EAAI,EAAGA,EAAIf,EAAGe,IAAKJ,IAAK,CAC/B,IAAMb,EAAQS,EAAII,CAAC,EACbK,EACJR,EAAIG,CAAC,IAAMb,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,QACnDmB,EAAQR,EAAIE,CAAC,EACbO,EACJR,EAAGC,CAAC,IACHK,GAAcC,IAAU,OACrB,KAAK,MAAMD,EAAaC,CAAK,EAC7B,QACFC,IAAU,SACZL,GAAMK,EACNJ,IAEJ,CACA,OAAOF,IAAQT,GAAiBH,EAAI,GAAKc,IAAUd,EAAIa,EAAK,MAC9D,CAAC,CACH,CAKA,SAASM,EACPC,EACAC,EACAC,EACA,CACA,IAAMC,EAASH,GAAI,SAAS,GAAG,EAC/B,OAAQA,GAAM,IAAI,MAAM,MAAM,EAAE,QAAQ,CAACI,EAAOb,IAAoB,CAClE,IAAM1B,EAAIuC,IAAU,GAAK,IAAM,OAAOA,CAAK,EACrCX,EAAK5B,EAAI,EAAIoC,EAASpC,EAAI,CAAC,EAAIqC,EACrC,MAAI,CAAC,OAAO,UAAUrC,CAAC,GAAK4B,IAAO,OAC1B,CAAC,EAEH,CAAC,CAAE,GAAAA,EAAI,GAAIU,EAAS,CAAE,UAAWZ,EAAI,CAAE,EAAI,CAAC,CAAG,CAAC,CACzD,CAAC,CACH,CAEA,SAASc,GACP5C,EACAwC,EACAC,EACA,CACA,IAAMI,EAAU3C,EAASF,EAAG,SAAS,EAE/B8C,EAAuC,CAAC,EAC9C,OAAW,CAACC,EAAQC,CAAM,IAAK,OAAO,QAAQH,GAAW,CAAC,CAAC,EAAG,CAC5D,IAAMI,EAAQ/B,EAAQ8B,EAAO,EAAE,EACzBE,EAAUhC,EAAQ8B,EAAO,EAAE,EAAE,QAAQ,CAAChB,EAAI5B,IAC9C4B,IAAO,QAAaA,EAAK,EACrB,CAACiB,EAAM7C,CAAC,IAAM,OAAY,CAAE,GAAA4B,CAAG,EAAI,CAAE,GAAAA,EAAI,cAAeiB,EAAM7C,CAAC,CAAE,CAAC,EAClE,CAAC,CACP,EACM+C,EACJD,EAAQ,OAAS,GAAK,CAACV,EACnBU,EACAZ,EAAUlB,EAAQ4B,EAAO,EAAE,EAAE,CAAC,EAAGR,EAAUC,CAAW,EACxDU,EAAM,OAAS,IACjBL,EAAOC,CAAM,EAAII,EAErB,CACA,OAAO,OAAO,KAAKL,CAAM,EAAE,OAAS,EAAIA,EAAS,MACnD,CAIA,SAASM,GAAOpD,EAAgBqD,EAAiB,CAC/C,IAAMC,EAAQjD,EAAML,EAAG,OAAO,EACxBuD,EAAMlD,EAAML,EAAG,KAAK,EACpBwD,EAAQtC,EAAQb,EAAML,EAAG,OAAO,CAAC,EAAE,CAAC,EAC1C,OAAOqD,GAAUG,IAAU,OACvB,CAAE,MAAOF,EAAQ,EAAG,IAAKA,EAAQ,EAAIE,CAAM,EAC3C,CAAE,MAAAF,EAAO,IAAAC,CAAI,CACnB,CAEO,SAASE,GAAiBC,EAAwC,CACvE,IAAMC,EAAwB,CAAC,EAC/B,QAAW3D,KAAK0D,EAAU,CACxB,IAAMlB,EAAWjB,EAAevB,CAAC,EAC3B,CAAE,MAAAsD,EAAO,IAAAC,CAAI,EAAIH,GAAOpD,EAAGwC,IAAa,MAAS,EACjDoB,EAAO7C,EAAaf,CAAC,EAC3B,GAAI,EAAEuD,EAAMD,IAAUM,IAAS,OAC7B,SAEF,IAAMC,EAAUxD,EAAML,EAAG,SAAS,EAC5BiB,EAAQP,EAAMV,EAAGO,CAAY,EAC7BuD,EAASpD,EAAMV,EAAGS,CAAW,EACnCkD,EAAO,KAAK,CACV,IAAK,GAAGE,CAAO,IAAIP,CAAK,IAAIC,CAAG,GAC/B,MACGO,GAAU,CAAChE,EAAY,KAAKgE,CAAM,EAAIA,EAAS,UAC/C7C,GAASA,EAAM,QAAU,GACtB,IAAIA,CAAK,KACT,GAAG4C,CAAO,KAAKP,EAAQ,GAAG,eAAe,OAAO,CAAC,IAAIC,EAAI,eAAe,OAAO,CAAC,IACtF,QAAAM,EACA,MAAAP,EACA,IAAAC,EACA,KAAAK,EACA,MAAA3C,EACA,MAAO2B,GAAQ5C,EAAGwC,EAAUe,EAAMD,CAAK,CACzC,CAAC,CACH,CACA,OAAOK,EAAO,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,CAChD,CC3RA,SAASC,EAAgBC,EAAW,CAClC,IAAMC,EAAM,CAAC,EACb,QAAWC,IAAM,CAAC,GAAGF,CAAS,EAAE,KAAK,CAACG,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CACjE,IAAMC,EAAOJ,EAAI,GAAG,EAAE,EAClBI,GAAQH,EAAG,OAASG,EAAK,IAC3BA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKH,EAAG,GAAG,EAEpCD,EAAI,KAAK,CAAE,GAAGC,CAAG,CAAC,CAEtB,CACA,OAAOD,CACT,CA2GA,SAASK,EAAuBC,EAAO,CACrC,IAAMC,EAAM,CAAC,EACPC,EAAuB,IAAI,IACjC,QAAWC,IAAK,CAAC,GAAGH,CAAK,EAAE,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CAC5D,IAAMC,EAAM,GAAGH,EAAE,OAAO,IAAIA,EAAE,MAAM,IAAIA,EAAE,IAAI,GACxCI,EAAOL,EAAK,IAAII,CAAG,EACzB,GAAIC,GAAQJ,EAAE,MAAQI,EAAK,IACzBA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKJ,EAAE,GAAG,EACnCI,EAAK,MAAQC,EAAgB,CAAC,GAAGD,EAAK,MAAO,GAAGJ,EAAE,KAAK,CAAC,MACnD,CACL,IAAMM,EAAO,CAAE,GAAGN,EAAG,MAAOK,EAAgBL,EAAE,KAAK,CAAE,EACrDF,EAAI,KAAKQ,CAAI,EACbP,EAAK,IAAII,EAAKG,CAAI,CACpB,CACF,CACA,OAAOR,CACT,CC1HO,IAAMS,GAAqB,IAAI,IAAI,CACxC,mBACA,cACA,kBACA,aACA,kBACA,aACA,gBACA,eACF,CAAC,EAEKC,GAAkB,0CAIlBC,GAAoB,IAAI,IAAI,CAAC,kBAAmB,YAAY,CAAC,EAO5D,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,GAAIC,EACF,OAAOA,EAET,IAAME,EAAaJ,EAAO,OACxBK,GACET,GAAmB,IAAIS,EAAE,WAAW,GACpC,CAACC,EAAkB,KAAKC,EAAWF,CAAC,CAAC,CACzC,EACA,OACED,EAAW,KAAKC,GAAKR,GAAgB,KAAKU,EAAWF,CAAC,CAAC,CAAC,GACxDD,EAAW,KAAKC,GAAK,CAACP,GAAkB,IAAIO,EAAE,WAAW,CAAC,CAE9D,CAEA,IAAMG,GAAgB,qBAIf,SAASC,GAAeC,EAAgC,CAC7D,OAAOA,GAASF,GAAc,KAAKD,EAAWG,CAAK,CAAC,EAAI,KAAO,MACjE,CAYO,SAASC,GAAYC,EAAcC,EAA6B,CACrE,IAAMC,EAAQF,EAAkB,QAAQ,KACtCP,GAAKU,EAAeV,EAAE,cAAe,SAAS,IAAMQ,CACtD,GAAG,SAAS,CAAC,EACb,OAAOC,EACDC,EAAeD,EAAK,cAAe,QAAQ,GAC3C,CAAC,EACH,CAAC,CACP,CAKA,IAAME,GAAuB,IAAI,IAAI,CACnC,aACA,SACA,SACA,cACA,UACF,CAAC,EAIKC,GAAa,IAAI,IAAI,CACzB,OACA,MACA,iBACA,kBACA,KACF,CAAC,EAED,SAASC,EAAQC,EAAgBC,EAAwC,CACvE,IAAMC,EAAOC,EAASH,EAAG,MAAM,EAC3B,OAAOE,GAAS,UAAYJ,GAAW,IAAII,CAAI,GACjDD,EAAK,KAAK,CACR,MAAOE,EAASH,EAAG,OAAO,EAC1B,IAAKG,EAASH,EAAG,KAAK,CACxB,CAAC,EAEH,IAAMI,EAAWD,EAASH,EAAG,aAAa,EAC1C,QAAWK,KAASD,GAAY,CAAC,EAC/BL,EAAQM,EAAOJ,CAAI,CAEvB,CAUO,SAASK,GAAeC,EAAsC,CACnE,IAAMC,EAAqB,CAAC,EAC5B,QAAWR,KAAKO,EAAU,CACxB,IAAME,EACHN,EAASH,EAAG,WAAW,GACvBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,SAAS,EAClBU,EAAQP,EAASH,EAAG,OAAO,EAC3BW,EAAMR,EAASH,EAAG,KAAK,EAC7B,GACE,CAACS,GACD,EAAEE,EAAMD,IACRb,GAAqB,IAAIM,EAASH,EAAG,MAAM,CAAW,EAEtD,SAEF,IAAMY,EAA0C,CAAC,EACjDb,EAAQC,EAAGY,CAAK,EAChBJ,EAAM,KAAK,CACT,KAAAC,EACA,QAASN,EAASH,EAAG,SAAS,EAC9B,MAAAU,EACA,IAAAC,EACA,OAASR,EAASH,EAAG,QAAQ,GAA4B,EACzD,MAAOY,EAAM,OAASC,EAAgBD,CAAK,EAAI,CAAC,CAAE,MAAAF,EAAO,IAAAC,CAAI,CAAC,CAChE,CAAC,CACH,CACA,OAAOG,EAAuBN,CAAK,CACrC,CC5JA,IAAMO,EAAO,eAAe,eAAe,EACrCC,GAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MAAM,kCAAoCA,EAAO,+HAA8I,CAC3M,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,GAA6BC,GAAK,YAAY,EACpDC,GAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
   "names": ["cached", "loadFmmm", "mod", "fmmmLayout", "request", "loadFmmm", "LAYOUT_ENGINES", "LAYOUT_ENGINE_VALUES", "layoutEngine", "request", "start", "stressLayout", "fmmmLayout", "isStringArray", "value", "item", "trackLanes", "track", "lanes", "getConfAssemblyNamesOrNone", "walkIndexed", "adapterConfig", "snapshotNamesFile", "cutsByHaplotype", "configHaplotypes", "defaultHaplotypes", "graphReferenceAssembly", "trackAdapterSnapshot", "toTrackConfigEntry", "offReferenceProblem", "referenceAssembly", "assemblyName", "ownField", "f", "name", "namedTrack", "tracks", "named", "trackLabel", "t", "REPEAT_ADAPTER_TYPES", "REPEAT_TRACK_HINT", "pickRepeatTrack", "tracks", "named", "chosen", "namedTrack", "t", "trackLabel", "PACKED_NAME", "packedName", "f", "name", "ownField", "pair", "i", "field", "top", "MOTIF_FIELDS", "PERIOD_FIELDS", "NAME_FIELDS", "first", "names", "value", "one", "IUPAC", "repeatUnitOf", "period", "motif", "numbers", "n", "strings", "text", "TANDEM_REPEAT", "tandemAlleleBp", "alts", "rn", "rus", "rul", "ruc", "rb", "k", "alt", "bp", "known", "j", "unitLength", "count", "runBp", "genotyped", "gt", "alleleBp", "referenceBp", "phased", "index", "callsOf", "samples", "called", "sample", "fields", "reads", "lengths", "calls", "spanOf", "tandem", "start", "end", "svlen", "repeatArraysFrom", "features", "arrays", "unit", "refName", "stated", "a", "b", "mergedIntervals", "intervals", "out", "iv", "a", "b", "last", "mergeOverlappingByName", "genes", "out", "open", "g", "a", "b", "key", "last", "mergedIntervals", "gene", "GENE_ADAPTER_TYPES", "GENE_TRACK_HINT", "BED_ADAPTER_TYPES", "pickGeneTrack", "tracks", "named", "chosen", "namedTrack", "candidates", "t", "REPEAT_TRACK_HINT", "trackLabel", "TE_TRACK_HINT", "annotationNoun", "track", "laneFilters", "view", "trackId", "lane", "readConfObject", "WHOLE_SEQUENCE_TYPES", "EXON_PARTS", "exonsOf", "f", "into", "type", "ownField", "children", "child", "geneModelsFrom", "features", "genes", "name", "start", "end", "exons", "mergedIntervals", "mergeOverlappingByName", "host", "read", "name", "makeStyles", "read", "mui_default", "host"]

package/dist/chunks/{chunk-5TT5TG4Q.js → chunk-A27SW7X7.js}

@@ -1,2 +1,2 @@
-import{c as se,o as re,r as ht}from"./chunk-WJHTNDTQ.js";import{a as Tt,c as ne,d as Gt,e as Pt}from"./chunk-2FG67WIZ.js";var Se="ws",Ae="we",oe=["elsewhere","break","end"],Te={missing:"not in the graph",elsewhere:"on nodes filed elsewhere",unknown:"gap, cause unknown",abridged:"abridged: steps not loaded",deleted:"no step on the reference"},Pe="outside the extracted subgraph";function ie(t,e,s){if(!e&&!s)return[{bp:t}];let n=Math.min(e?.trimmed??0,t),r=Math.min(s?.trimmed??0,t-n),a=t-n-r,p=e?.kind==="break"?Math.min(e.bp,a):0;a-=p;let l=s?.kind==="break"?Math.min(s.bp,a):0;a-=l;let d=[e,s].find(f=>f?.kind==="elsewhere");return[{bp:n},{bp:p,cause:"missing"},d?.kind==="elsewhere"?{bp:a,cause:"elsewhere",chunk:d.chunk}:{bp:a,cause:"unknown"},{bp:l,cause:"missing"},{bp:r}].filter(f=>f.bp>0)}function Lt(t,e){let s=t.bp[e],n=t.chunkRefs[e];return ce(t.kindNames[t.kinds[e]],Number.isNaN(s)?void 0:s,t.trimmed[e],n<0?void 0:{refName:t.chunkRefNames[n],start:t.chunkStarts[e]})}function ce(t,e,s,n){let r=s>0?{trimmed:s}:{};return t==="elsewhere"&&n?{kind:t,chunk:n,...e===void 0?{}:{bp:e},...r}:t==="break"&&e!==void 0?{kind:t,bp:e,...n?{chunk:n}:{},...r}:t==="end"?{kind:t,...r}:void 0}function ae(t){let[e,...s]=t.split(","),n,r=0,a;for(let p of s)if(p.startsWith("bp="))n=+p.slice(3);else if(p.startsWith("trimmed="))r=+p.slice(8);else if(p.startsWith("chunk=")){let l=p.lastIndexOf(":");a={refName:p.slice(6,l),start:+p.slice(l+1)}}return ce(e,n,r,a)}function Wt(t,e){return{...t?{before:t}:{},...e?{after:e}:{}}}function _e(t){let e=t[Se],s=t[Ae];return Wt(typeof e=="string"?ae(e):void 0,typeof s=="string"?ae(s):void 0)}var Ue=class{constructor(){this.kinds=[],this.bp=[],this.trimmed=[],this.chunkRefs=[],this.chunkStarts=[],this.chunkRefNames=[],this.refIndex=new Map}push(t){this.kinds.push(oe.indexOf(t.kind)),this.bp.push("bp"in t&&t.bp!==void 0?t.bp:NaN),this.trimmed.push(t.trimmed??0);let e="chunk"in t?t.chunk:void 0;if(e){let s=this.refIndex.get(e.refName);s===void 0&&(s=this.chunkRefNames.length,this.refIndex.set(e.refName,s),this.chunkRefNames.push(e.refName)),this.chunkRefs.push(s),this.chunkStarts.push(e.start)}else this.chunkRefs.push(-1),this.chunkStarts.push(NaN)}table(){return{kinds:Uint8Array.from(this.kinds),kindNames:[...oe],bp:Float64Array.from(this.bp),trimmed:Float64Array.from(this.trimmed),chunkRefs:Int32Array.from(this.chunkRefs),chunkStarts:Float64Array.from(this.chunkStarts),chunkRefNames:this.chunkRefNames}}};function Ie(t,e,s){return e===0?t:`${t}:${e}-${s}`}function Dt(t,e){let s=t.names[e],n=Pt(s),r=t.starts[e],a=t.abridgedSteps?.[e]??Number.NaN,p=Number.isNaN(a)?{}:{abridged:{steps:a,bp:t.abridgedBp?.[e]??0}};return n?{name:`${n.sample}#${n.haplotype}#${n.contig}`,start:r,...n,...Wt(t.before&&Lt(t.before,e),t.after&&Lt(t.after,e)),...p}:{name:Ie(s,r,t.ends[e]),start:r}}function Re(t,e,s,n){let r=new Int32Array(s+1);for(let d of t)r[d+1]++;for(let d=0;d<s;d++)r[d+1]+=r[d];let a=r.slice(0,s),p=new Int32Array(t.length);t.forEach((d,k)=>{p[a[d]++]=e[k]});let l=new Int32Array(n.length).fill(-1);return Array.from({length:s},(d,k)=>{let f=[];for(let T=r[k];T<r[k+1];T++){let b=p[T];l[b]!==k&&(l[b]=k,f.push(n[b]))}return f})}function Vt({nodes:t,links:e,walks:s},n){let r=new Uint8Array(t.names.length),a=(l,d)=>{r[l]===0&&(r[l]=d?2:1)};for(let l=0;l<e.from.length;l++)a(e.from[l],e.strands[l]&1),a(e.to[l],e.strands[l]&2);let p=s.offsets[s.names.length]??0;for(let l=0;l<p;l++){let d=s.steps[l];a(d,s.reversed[l]),n&&n[d]++}return t.names.map((l,d)=>`${l}${r[d]===2?"-":"+"}`)}function De({nodes:t,links:e,walks:s,skips:n},r="Imported GFA"){let a=t.names.length,p=t.lengths.length,l=[];for(let o=0;o<s.names.length;o++)s.offsets[o+1]>s.offsets[o]&&l.push(o);let d=new Int32Array(a),k=Vt({nodes:t,links:e,walks:s},d),f=[];for(let o=0;o<p;o++){let w=t.refs[o];f.push({id:k[o],name:t.names[o],length:t.lengths[o],depth:Math.max(d[o],1),stable:w<0?void 0:{refName:t.refNames[w],start:t.starts[o],rank:t.ranks[o]},samples:void 0})}let T=[],b=new Array(a),O=(o,w)=>{let g=b[o];if(g){for(let I=0;I<g.length;I+=2)if(g[I]===w)return g[I+1]}},B=(o,w,g)=>{let I=b[o];I?I.push(w,g):b[o]=[w,g]},dt=[],Y=0;for(let o=0;o<e.from.length;o++){let w=e.from[o],g=e.to[o];T.push({from:k[w],to:k[g],fromStrand:e.strands[o]&1?"-":"+",toStrand:e.strands[o]&2?"-":"+"});let I=O(w,g);I===void 0&&(I=Y++,B(w,g,I),B(g,w,I)),dt.push(I)}let U=new Int32Array(a+1);for(let o=0;o<a;o++)U[o+1]=U[o]+(b[o]?.length??0)/2;let pt=new Int32Array(U[a]),mt=new Int32Array(U[a]);b.forEach((o,w)=>{for(let g=0;g<o.length;g+=2)pt[U[w]+g/2]=o[g],mt[U[w]+g/2]=o[g+1]});let tt=(o,w)=>{for(let g=U[o];g<U[o+1];g++)if(pt[g]===w)return mt[g];return-1},ut=new Map,P=[],et=new Int32Array(s.offsets[s.names.length]??0),st=new Int32Array(et.length),Z=0,X=new Int32Array(Y).fill(-1),F=[],wt=[],_=s.offsets[s.names.length]??0,nt=new Int32Array(_),gt=new Float64Array(_),St=new Uint8Array(_),C=new Int32Array(a).fill(-1),$=[],E=[0],rt=[],At=new Map,L=[];for(let o of l){let w=Dt(s,o),{start:g,name:I}=w,z=w.sample===void 0?s.names[o]:I,K=ut.get(z);K===void 0&&(K=P.length,ut.set(z,K),P.push(z),rt.push(Tt(z)));let at=At.get(I);at===void 0&&(at=L.length,At.set(I,at),L.push(I));let _t=rt[K],Nt=s.offsets[o],It=new Array(s.offsets[o+1]-Nt),bt=g,i=-1;for(let h=Nt;h<s.offsets[o+1];h++){let N=s.steps[h];It[h-Nt]=k[N],C[N]===-1&&(C[N]=E.at(-1),E.push(C[N]+d[N]),$.push(N));let M=C[N]++;if(nt[M]=K,gt[M]=bt,St[M]=s.reversed[h],bt+=N<p?t.lengths[N]:0,i>=0){let x=tt(i,N);x>=0&&X[x]!==o&&(X[x]=o,et[Z]=x,st[Z++]=at)}i=N}F.push({...w,nodeIds:It}),wt.push({name:z,sample:_t,start:g,length:bt-g})}let H=Re(et.subarray(0,Z),st,Y,L);T.forEach((o,w)=>{let g=H[dt[w]];g.length>0&&(o.pathIds=g)});let ot=l.length>0;return{name:r,nodes:f,edges:T,paths:ot?F:void 0,anchorPaths:ot?wt:void 0,pathVisits:ot?new re({segments:$.map(o=>t.names[o]),offsets:Int32Array.from(E),path:nt.subarray(0,E.at(-1)),start:gt.subarray(0,E.at(-1)),reversed:St.subarray(0,E.at(-1)),paths:P,samples:rt}):void 0,anchoredBy:f.some(o=>o.stable)?"tags":void 0,...n?.names.length?{skips:n}:{}}}var Zt=1,de=2,kt=4,pe=[void 0,"missing","elsewhere","unknown","abridged","deleted"],me=3,fe=t=>pe.indexOf(t)<<me;function ue(t,e,s){return e!==void 0&&t.includes(e)?e:t.find(n=>s.has(n))??t[0]}function $e(t){return ue((t.paths??[]).map(e=>ht(e.name).name),t.referencePath,new Set(t.nodes.flatMap(e=>e.stable?.rank===0?[e.stable.refName]:[])))}var ge=t=>{let e=t&&Gt(t);return s=>s!==void 0&&(s===t||s===e)};function xe(t){let e=new Map,s=[],n=[],r=b=>{let O=e.get(b);return O===void 0&&(O=s.length,e.set(b,O),s.push(b),n.push(0)),O},a=$e(t),p=ge(a),l=new Map;for(let b of t.nodes){let O=r(b.id);n[O]=b.length,b.stable?.rank===0&&p(b.stable.refName)&&l.set(O,b.stable.start)}let d=t.paths??[],k=new Int32Array(d.length),f=new Int32Array(d.length),T=[];return d.forEach((b,O)=>{k[O]=T.length;for(let B of b.nodeIds)T.push(r(B));f[O]=T.length}),{heads:d,from:k,to:f,steps:Int32Array.from(T),lengths:Int32Array.from(n),names:s,reference:a,stableStart:b=>l.get(b)??Number.NaN}}function Me(t,e,s){let{nodes:n,walks:r}=t,a=[];for(let f=0;f<r.names.length;f++)r.offsets[f+1]>r.offsets[f]&&a.push(f);let p=a.map(f=>Dt(r,f)),l=new Set;for(let f=0;f<n.lengths.length;f++)n.refs[f]>=0&&n.ranks[f]===0&&l.add(n.refNames[n.refs[f]]);let d=ue(p.map(f=>ht(f.name).name),e,l),k=ge(d);return{heads:p,from:Int32Array.from(a,f=>r.offsets[f]),to:Int32Array.from(a,f=>r.offsets[f+1]),steps:r.steps,lengths:n.lengths,names:s?Vt(t):n.names,reference:d,stableStart:f=>f<n.lengths.length&&n.ranks[f]===0&&k(n.refNames[n.refs[f]])?n.starts[f]:Number.NaN}}function Ht(t){return t.sample??Tt(t.name)}function le(t){return t.haplotype!==void 0&&t.sample!==void 0?`${t.sample}#${t.haplotype}`:Ht(t)}var he=class{constructor(t){this.offsets=[0],this.values=Array.from({length:t},()=>[])}get length(){return this.values[0].length}push(t,e,s,n,r){let a=this.values;a[0].push(t),a[1].push(e),a[2].push(s),a[3].push(n),r!==void 0&&a[4].push(r)}endRow(){this.offsets.push(this.length)}reorder(t,e){let s=new Uint32Array(t.length+1);t.forEach((r,a)=>{s[a+1]=s[a]+this.offsets[r+1]-this.offsets[r]});let n=e.map((r,a)=>{let p=this.values[a],l=r(this.length),d=0;for(let k of t)for(let f=this.offsets[k];f<this.offsets[k+1];f++)l[d++]=p[f];return l});return{offsets:s,columns:n}}},yt=t=>new Float64Array(t);function qe(t,e,s={}){let{heads:n,from:r,to:a,steps:p,lengths:l,names:d,reference:k,stableStart:f}="walks"in t?Me(t,s.referencePath,s.visits):xe(t),T=l.length,b=i=>i<T?l[i]:0,O=i=>ht(n[i].name).name,B=i=>n[i].start,dt=(i,h)=>(B(i)??0)-(B(h)??0),Y=n.map((i,h)=>h),U=Y.filter(i=>O(i)===k).sort(dt),pt=U[0],mt=Y.filter(i=>O(i)!==k),{skips:tt}=t;if(pt===void 0||mt.length===0&&!tt?.names.length)return;let ut=se(mt,O),P=new Float64Array(d.length).fill(Number.NaN),et=new Float64Array(d.length),st=new Map,Z=-1/0,X=1/0,F=e&&e.end>e.start?e:void 0;for(let i of U){let h=B(i)??0;for(let N=r[i],M=a[i];N<M;N++){let x=p[N],A=b(x);if(Number.isNaN(P[x]))P[x]=h,et[x]=h+A,F&&(h+A<=F.start&&(Z=Math.max(Z,h+A)),h>=F.end&&(X=Math.min(X,h)));else{let W=st.get(x);W?W.push(h):st.set(x,[P[x],h])}h+=A}}let wt=F===void 0||Z>-1/0&&X<1/0,_=new he(5),nt=[],gt=new Map,St=i=>{if(!i)return-1;let h=`${i.refName}:${i.start}`,N=gt.get(h);return N===void 0&&(N=nt.length,gt.set(h,N),nt.push(i)),N},C=s.visits?new he(4):void 0,$=new Int32Array(0),E=new Float64Array(0),rt=i=>{let h=n[i[0]],N=[...i].sort(dt),M=N.length-1,x=0;for(let c of N)M+=a[c]-r[c]+(n[c].abridged?1:0),x+=n[c].abridged?.steps??0;M>$.length&&($=new Int32Array(M*2),E=new Float64Array(M*2));let A=0,W=!1,Rt,$t,q=new Map,Ut=0;for(let c of N){let m=B(c),y=m===void 0||Rt===void 0?0:m-Rt;(m===void 0||y<0)&&(W=!0),y<0&&n[$t].abridged&&(Ut-=y);let S=Math.min(Ut,Math.max(y,0));Ut-=S;let u=y-S;u>0&&(q.set(A,ie(u,$t===void 0?void 0:n[$t].after,n[c].before)),$[A]=-u,E[A++]=Rt);let v=m??0,R=n[c].abridged;for(let j=r[c],Q=a[c];j<Q;j++){let G=p[j],V=R?R.bp-(v-(m??0))-b(G):0;V>0&&j===Q-1&&j>r[c]&&(q.set(A,[{bp:V,cause:"abridged"}]),$[A]=-V,E[A++]=v,v+=V),$[A]=G,E[A++]=v,v+=b(G)}Rt=m===void 0?void 0:v,$t=c}let Xt=c=>c>=0&&c<A&&$[c]>=0&&!Number.isNaN(P[$[c]]),jt=c=>{let m=$[c];return E[c]+(m<0?-m:b(m))},Ne=(c,m)=>{let y=c>=0?c:m,S=-1;for(let G=1;S<0&&G<A;G++)S=[y-G,y+G].find(Xt)??-1;if(S<0)return;let u=S>y==P[$[S]]>P[$[y]],v=u===(y===c),R=v?A-1:0,j=Xt(R);return{stop:{contigEnds:j,shortBp:j?Math.max(0,F.start-et[$[R]],P[$[R]]-F.end):0},lo:v?y+1:0,hi:v?A:y,backward:!u,axisStart:u?v?jt(y):E[0]:v?jt(A-1):E[y]}},xt=0,Mt=A,it=!1,zt=!0,vt=-1,Kt=-1,Bt,qt,Jt=(c,m)=>{let S=q.get(c)?.[0];if(m<=0||S?.cause!=="abridged")return 0;let u=Math.min(m,S.bp);return q.set(c,S.bp>u?[{...S,bp:S.bp-u}]:[]),$[c]+=u,u},Qt=c=>q.get(c)?.[0]?.cause==="abridged",be=c=>{let m=$[c];return m<0||q.has(c)?Number.NaN:Number.isNaN(P[m])&&(Qt(c-1)||Qt(c+1))?f(m):P[m]},Ot=0,Yt=0;if(F&&wt){let c=-1,m=-1,y=-1/0,S=1/0;for(let u=0;u<A;u++){let v=be(u);if(!Number.isNaN(v)){let R=v+b($[u]);R<=F.start&&R>y&&(y=R,c=u),v>=F.end&&v<S&&(S=v,m=u)}}if(c<0||m<0){zt=!1;let u=c>=0||m>=0?Ne(c,m):void 0;u&&({lo:xt,hi:Mt,backward:it,axisStart:Bt,stop:qt}=u)}else{xt=Math.min(c,m)+1,Mt=Math.max(c,m),it=c>m,vt=c,Kt=m;let u=it?-1:1;Ot=Jt(c+u,Z-y),Yt=Jt(m-u,S-X)}}let Et=h.contig??Gt(ht(h.name).name),ve=W||A===0?void 0:Bt!==void 0?{contig:Et,start:Bt,reversed:it}:vt<0?{contig:Et,start:E[0],reversed:!1}:vt<Kt?{contig:Et,start:jt(vt)+Ot,reversed:!1}:{contig:Et,start:E[vt]-Ot,reversed:!0},ct=0,te=0,ee=0,ft=0,D=-1,lt=0,J=Number.NaN,Ft=Number.NaN,ke=c=>{let m=st.get(c);if(!m||Number.isNaN(Ft))return P[c];let y=b(c),S=m[0],u=1/0;for(let v of m){let R=Math.min(Math.abs(v-Ft),Math.abs(v+y-Ft));R<u&&(S=v,u=R)}return S},[,Ct,ye,we]=_.values;for(let c=xt;c<Mt;c++){let m=it?Mt-1-(c-xt):c,y=$[m],S=q.get(m);if(S){for(let V of it?[...S].reverse():S)_.push(ct,V.bp,Number.NaN,kt|fe(V.cause),St(V.chunk)),ct+=V.bp;D=_.length-1,lt=kt,J=Number.NaN,ee+=-y,ft=0;continue}let u=b(y),v=ke(y),R=!Number.isNaN(v);C?.push(y,ct,u,R?1:0);let j=D>=0&&!Number.isNaN(J),Q=R&&j&&ft>=0&&J+(Ct[D]??0)===v,G=R&&j&&ft<=0&&v+u===J;!R&&D>=0&&!(lt&(Zt|kt))?Ct[D]+=u:Q||G?(Ct[D]+=u,Q||(J=v,ye[D]=v,lt|=de,we[D]=lt),ft=Q?1:-1):(lt=R?Zt:0,J=R?v:Number.NaN,_.push(ct,u,J,lt,-1),D=_.length-1,ft=0),ct+=u,R?Ft=ft<0?v:v+u:te+=u}return _.endRow(),C?.endRow(),{name:h.name,label:le(h),sample:Ht(h),haplotype:h.haplotype,bp:ct,offReferenceBp:te,gapBp:ee,complete:zt,stop:qt,axis:ve,...x>0?{abridgedSteps:x}:{},...Ot+Yt>0?{estimated:!0}:{}}},At=(i,h,N,M)=>{let x=M?Math.max(h,M.start):h,A=Math.max((M?Math.min(N,M.end):N)-x,0);_.push(x-(M?M.start:h),A,Number.NaN,kt|fe("deleted"),-1),_.endRow(),C?.endRow();let W={name:i,...Pt(i)};return{name:i,label:le(W),sample:Ht(W),haplotype:W.haplotype,bp:0,offReferenceBp:0,gapBp:A,complete:!0,stop:void 0,axis:void 0,deletionBp:N-h}},L=rt(U),H=[...ut.values()].map((i,h)=>({meta:rt(i),row:h+1})),ot=new Set(ut.keys()),{axis:o}=L,w=o?{start:o.start,end:o.start+L.bp+L.gapBp}:F;tt?.names.forEach((i,h)=>{let N=ht(i).name;ot.has(N)||(ot.add(N),H.push({meta:At(N,tt.starts[h],tt.ends[h],w),row:H.length+1}))});let g=[L,...H.map(i=>i.meta)];if(new Set(g.map(i=>i.label)).size<g.length)for(let i of g)i.label=ne(i.name)??i.label;H.sort((i,h)=>Number(h.meta.complete)-Number(i.meta.complete)||h.meta.bp-i.meta.bp||i.meta.label.localeCompare(h.meta.label));let I=[0,...H.map(i=>i.row)],{offsets:z,columns:K}=_.reorder(I,[yt,yt,yt,i=>new Uint8Array(i),i=>new Int32Array(i)]),[at,_t,Nt,It,bt]=K;return{origin:F?F.start:B(pt)??0,rows:[L,...H.map(i=>i.meta)],offsets:z,start:at,bp:_t,referenceStart:Nt,flags:It,chunk:bt,chunks:nt,visits:C&&Oe(C,I,d)}}function Oe(t,e,s){let{offsets:n,columns:r}=t.reorder(e,[k=>new Int32Array(k),yt,yt,k=>new Uint8Array(k)]),[a,p,l,d]=r;return{offsets:n,node:a,start:p,bp:l,onReference:d,names:s}}function Ee(t,e){let s=t.flags[e],n={start:t.start[e],bp:t.bp[e],onReference:(s&Zt)!==0};if(s&kt){n.gap=!0;let r=pe[s>>me&7];r&&(n.cause=r);let a=t.chunks[t.chunk[e]];a&&(n.chunk=a)}else n.referenceStart=Number.isNaN(t.referenceStart[e])?void 0:t.referenceStart[e];return s&de&&(n.reversed=!0),n}function Fe(t,e){let s=[];for(let n=t.offsets[e];n<t.offsets[e+1];n++)s.push({node:t.names[t.node[n]],start:t.start[n],bp:t.bp[n],onReference:t.onReference[n]===1});return s}function Je(t,e){let s=t.rows.map((n,r)=>{let a=[];for(let p=t.offsets[r];p<t.offsets[r+1];p++)a.push(Ee(t,p));return{...n,runs:a,visits:t.visits&&Fe(t.visits,r)}});return{origin:t.origin,unit:e,reference:s[0],rows:s.slice(1)}}export{Se as a,Ae as b,Te as c,Pe as d,ie as e,ae as f,_e as g,Ue as h,Dt as i,De as j,$e as k,qe as l,Je as m};
-//# sourceMappingURL=chunk-5TT5TG4Q.js.map
+import{c as se,o as re,r as ht}from"./chunk-SKB4GSET.js";import{a as Tt,c as ne,d as Gt,e as Pt}from"./chunk-KBOVZ3GI.js";var Se="ws",Ae="we",oe=["elsewhere","break","end"],Te={missing:"not in the graph",elsewhere:"on nodes filed elsewhere",unknown:"gap, cause unknown",abridged:"abridged: steps not loaded",deleted:"no step on the reference"},Pe="outside the extracted subgraph";function ie(t,e,s){if(!e&&!s)return[{bp:t}];let n=Math.min(e?.trimmed??0,t),r=Math.min(s?.trimmed??0,t-n),a=t-n-r,p=e?.kind==="break"?Math.min(e.bp,a):0;a-=p;let l=s?.kind==="break"?Math.min(s.bp,a):0;a-=l;let d=[e,s].find(f=>f?.kind==="elsewhere");return[{bp:n},{bp:p,cause:"missing"},d?.kind==="elsewhere"?{bp:a,cause:"elsewhere",chunk:d.chunk}:{bp:a,cause:"unknown"},{bp:l,cause:"missing"},{bp:r}].filter(f=>f.bp>0)}function Lt(t,e){let s=t.bp[e],n=t.chunkRefs[e];return ce(t.kindNames[t.kinds[e]],Number.isNaN(s)?void 0:s,t.trimmed[e],n<0?void 0:{refName:t.chunkRefNames[n],start:t.chunkStarts[e]})}function ce(t,e,s,n){let r=s>0?{trimmed:s}:{};return t==="elsewhere"&&n?{kind:t,chunk:n,...e===void 0?{}:{bp:e},...r}:t==="break"&&e!==void 0?{kind:t,bp:e,...n?{chunk:n}:{},...r}:t==="end"?{kind:t,...r}:void 0}function ae(t){let[e,...s]=t.split(","),n,r=0,a;for(let p of s)if(p.startsWith("bp="))n=+p.slice(3);else if(p.startsWith("trimmed="))r=+p.slice(8);else if(p.startsWith("chunk=")){let l=p.lastIndexOf(":");a={refName:p.slice(6,l),start:+p.slice(l+1)}}return ce(e,n,r,a)}function Wt(t,e){return{...t?{before:t}:{},...e?{after:e}:{}}}function _e(t){let e=t[Se],s=t[Ae];return Wt(typeof e=="string"?ae(e):void 0,typeof s=="string"?ae(s):void 0)}var Ue=class{constructor(){this.kinds=[],this.bp=[],this.trimmed=[],this.chunkRefs=[],this.chunkStarts=[],this.chunkRefNames=[],this.refIndex=new Map}push(t){this.kinds.push(oe.indexOf(t.kind)),this.bp.push("bp"in t&&t.bp!==void 0?t.bp:NaN),this.trimmed.push(t.trimmed??0);let e="chunk"in t?t.chunk:void 0;if(e){let s=this.refIndex.get(e.refName);s===void 0&&(s=this.chunkRefNames.length,this.refIndex.set(e.refName,s),this.chunkRefNames.push(e.refName)),this.chunkRefs.push(s),this.chunkStarts.push(e.start)}else this.chunkRefs.push(-1),this.chunkStarts.push(NaN)}table(){return{kinds:Uint8Array.from(this.kinds),kindNames:[...oe],bp:Float64Array.from(this.bp),trimmed:Float64Array.from(this.trimmed),chunkRefs:Int32Array.from(this.chunkRefs),chunkStarts:Float64Array.from(this.chunkStarts),chunkRefNames:this.chunkRefNames}}};function Ie(t,e,s){return e===0?t:`${t}:${e}-${s}`}function Dt(t,e){let s=t.names[e],n=Pt(s),r=t.starts[e],a=t.abridgedSteps?.[e]??Number.NaN,p=Number.isNaN(a)?{}:{abridged:{steps:a,bp:t.abridgedBp?.[e]??0}};return n?{name:`${n.sample}#${n.haplotype}#${n.contig}`,start:r,...n,...Wt(t.before&&Lt(t.before,e),t.after&&Lt(t.after,e)),...p}:{name:Ie(s,r,t.ends[e]),start:r}}function Re(t,e,s,n){let r=new Int32Array(s+1);for(let d of t)r[d+1]++;for(let d=0;d<s;d++)r[d+1]+=r[d];let a=r.slice(0,s),p=new Int32Array(t.length);t.forEach((d,k)=>{p[a[d]++]=e[k]});let l=new Int32Array(n.length).fill(-1);return Array.from({length:s},(d,k)=>{let f=[];for(let T=r[k];T<r[k+1];T++){let b=p[T];l[b]!==k&&(l[b]=k,f.push(n[b]))}return f})}function Vt({nodes:t,links:e,walks:s},n){let r=new Uint8Array(t.names.length),a=(l,d)=>{r[l]===0&&(r[l]=d?2:1)};for(let l=0;l<e.from.length;l++)a(e.from[l],e.strands[l]&1),a(e.to[l],e.strands[l]&2);let p=s.offsets[s.names.length]??0;for(let l=0;l<p;l++){let d=s.steps[l];a(d,s.reversed[l]),n&&n[d]++}return t.names.map((l,d)=>`${l}${r[d]===2?"-":"+"}`)}function De({nodes:t,links:e,walks:s,skips:n},r="Imported GFA"){let a=t.names.length,p=t.lengths.length,l=[];for(let o=0;o<s.names.length;o++)s.offsets[o+1]>s.offsets[o]&&l.push(o);let d=new Int32Array(a),k=Vt({nodes:t,links:e,walks:s},d),f=[];for(let o=0;o<p;o++){let w=t.refs[o];f.push({id:k[o],name:t.names[o],length:t.lengths[o],depth:Math.max(d[o],1),stable:w<0?void 0:{refName:t.refNames[w],start:t.starts[o],rank:t.ranks[o]},samples:void 0})}let T=[],b=new Array(a),O=(o,w)=>{let g=b[o];if(g){for(let I=0;I<g.length;I+=2)if(g[I]===w)return g[I+1]}},B=(o,w,g)=>{let I=b[o];I?I.push(w,g):b[o]=[w,g]},dt=[],Y=0;for(let o=0;o<e.from.length;o++){let w=e.from[o],g=e.to[o];T.push({from:k[w],to:k[g],fromStrand:e.strands[o]&1?"-":"+",toStrand:e.strands[o]&2?"-":"+"});let I=O(w,g);I===void 0&&(I=Y++,B(w,g,I),B(g,w,I)),dt.push(I)}let U=new Int32Array(a+1);for(let o=0;o<a;o++)U[o+1]=U[o]+(b[o]?.length??0)/2;let pt=new Int32Array(U[a]),mt=new Int32Array(U[a]);b.forEach((o,w)=>{for(let g=0;g<o.length;g+=2)pt[U[w]+g/2]=o[g],mt[U[w]+g/2]=o[g+1]});let tt=(o,w)=>{for(let g=U[o];g<U[o+1];g++)if(pt[g]===w)return mt[g];return-1},ut=new Map,P=[],et=new Int32Array(s.offsets[s.names.length]??0),st=new Int32Array(et.length),Z=0,X=new Int32Array(Y).fill(-1),F=[],wt=[],_=s.offsets[s.names.length]??0,nt=new Int32Array(_),gt=new Float64Array(_),St=new Uint8Array(_),C=new Int32Array(a).fill(-1),$=[],E=[0],rt=[],At=new Map,L=[];for(let o of l){let w=Dt(s,o),{start:g,name:I}=w,z=w.sample===void 0?s.names[o]:I,K=ut.get(z);K===void 0&&(K=P.length,ut.set(z,K),P.push(z),rt.push(Tt(z)));let at=At.get(I);at===void 0&&(at=L.length,At.set(I,at),L.push(I));let _t=rt[K],Nt=s.offsets[o],It=new Array(s.offsets[o+1]-Nt),bt=g,i=-1;for(let h=Nt;h<s.offsets[o+1];h++){let N=s.steps[h];It[h-Nt]=k[N],C[N]===-1&&(C[N]=E.at(-1),E.push(C[N]+d[N]),$.push(N));let M=C[N]++;if(nt[M]=K,gt[M]=bt,St[M]=s.reversed[h],bt+=N<p?t.lengths[N]:0,i>=0){let x=tt(i,N);x>=0&&X[x]!==o&&(X[x]=o,et[Z]=x,st[Z++]=at)}i=N}F.push({...w,nodeIds:It}),wt.push({name:z,sample:_t,start:g,length:bt-g})}let H=Re(et.subarray(0,Z),st,Y,L);T.forEach((o,w)=>{let g=H[dt[w]];g.length>0&&(o.pathIds=g)});let ot=l.length>0;return{name:r,nodes:f,edges:T,paths:ot?F:void 0,anchorPaths:ot?wt:void 0,pathVisits:ot?new re({segments:$.map(o=>t.names[o]),offsets:Int32Array.from(E),path:nt.subarray(0,E.at(-1)),start:gt.subarray(0,E.at(-1)),reversed:St.subarray(0,E.at(-1)),paths:P,samples:rt}):void 0,anchoredBy:f.some(o=>o.stable)?"tags":void 0,...n?.names.length?{skips:n}:{}}}var Zt=1,de=2,kt=4,pe=[void 0,"missing","elsewhere","unknown","abridged","deleted"],me=3,fe=t=>pe.indexOf(t)<<me;function ue(t,e,s){return e!==void 0&&t.includes(e)?e:t.find(n=>s.has(n))??t[0]}function $e(t){return ue((t.paths??[]).map(e=>ht(e.name).name),t.referencePath,new Set(t.nodes.flatMap(e=>e.stable?.rank===0?[e.stable.refName]:[])))}var ge=t=>{let e=t&&Gt(t);return s=>s!==void 0&&(s===t||s===e)};function xe(t){let e=new Map,s=[],n=[],r=b=>{let O=e.get(b);return O===void 0&&(O=s.length,e.set(b,O),s.push(b),n.push(0)),O},a=$e(t),p=ge(a),l=new Map;for(let b of t.nodes){let O=r(b.id);n[O]=b.length,b.stable?.rank===0&&p(b.stable.refName)&&l.set(O,b.stable.start)}let d=t.paths??[],k=new Int32Array(d.length),f=new Int32Array(d.length),T=[];return d.forEach((b,O)=>{k[O]=T.length;for(let B of b.nodeIds)T.push(r(B));f[O]=T.length}),{heads:d,from:k,to:f,steps:Int32Array.from(T),lengths:Int32Array.from(n),names:s,reference:a,stableStart:b=>l.get(b)??Number.NaN}}function Me(t,e,s){let{nodes:n,walks:r}=t,a=[];for(let f=0;f<r.names.length;f++)r.offsets[f+1]>r.offsets[f]&&a.push(f);let p=a.map(f=>Dt(r,f)),l=new Set;for(let f=0;f<n.lengths.length;f++)n.refs[f]>=0&&n.ranks[f]===0&&l.add(n.refNames[n.refs[f]]);let d=ue(p.map(f=>ht(f.name).name),e,l),k=ge(d);return{heads:p,from:Int32Array.from(a,f=>r.offsets[f]),to:Int32Array.from(a,f=>r.offsets[f+1]),steps:r.steps,lengths:n.lengths,names:s?Vt(t):n.names,reference:d,stableStart:f=>f<n.lengths.length&&n.ranks[f]===0&&k(n.refNames[n.refs[f]])?n.starts[f]:Number.NaN}}function Ht(t){return t.sample??Tt(t.name)}function le(t){return t.haplotype!==void 0&&t.sample!==void 0?`${t.sample}#${t.haplotype}`:Ht(t)}var he=class{constructor(t){this.offsets=[0],this.values=Array.from({length:t},()=>[])}get length(){return this.values[0].length}push(t,e,s,n,r){let a=this.values;a[0].push(t),a[1].push(e),a[2].push(s),a[3].push(n),r!==void 0&&a[4].push(r)}endRow(){this.offsets.push(this.length)}reorder(t,e){let s=new Uint32Array(t.length+1);t.forEach((r,a)=>{s[a+1]=s[a]+this.offsets[r+1]-this.offsets[r]});let n=e.map((r,a)=>{let p=this.values[a],l=r(this.length),d=0;for(let k of t)for(let f=this.offsets[k];f<this.offsets[k+1];f++)l[d++]=p[f];return l});return{offsets:s,columns:n}}},yt=t=>new Float64Array(t);function qe(t,e,s={}){let{heads:n,from:r,to:a,steps:p,lengths:l,names:d,reference:k,stableStart:f}="walks"in t?Me(t,s.referencePath,s.visits):xe(t),T=l.length,b=i=>i<T?l[i]:0,O=i=>ht(n[i].name).name,B=i=>n[i].start,dt=(i,h)=>(B(i)??0)-(B(h)??0),Y=n.map((i,h)=>h),U=Y.filter(i=>O(i)===k).sort(dt),pt=U[0],mt=Y.filter(i=>O(i)!==k),{skips:tt}=t;if(pt===void 0||mt.length===0&&!tt?.names.length)return;let ut=se(mt,O),P=new Float64Array(d.length).fill(Number.NaN),et=new Float64Array(d.length),st=new Map,Z=-1/0,X=1/0,F=e&&e.end>e.start?e:void 0;for(let i of U){let h=B(i)??0;for(let N=r[i],M=a[i];N<M;N++){let x=p[N],A=b(x);if(Number.isNaN(P[x]))P[x]=h,et[x]=h+A,F&&(h+A<=F.start&&(Z=Math.max(Z,h+A)),h>=F.end&&(X=Math.min(X,h)));else{let W=st.get(x);W?W.push(h):st.set(x,[P[x],h])}h+=A}}let wt=F===void 0||Z>-1/0&&X<1/0,_=new he(5),nt=[],gt=new Map,St=i=>{if(!i)return-1;let h=`${i.refName}:${i.start}`,N=gt.get(h);return N===void 0&&(N=nt.length,gt.set(h,N),nt.push(i)),N},C=s.visits?new he(4):void 0,$=new Int32Array(0),E=new Float64Array(0),rt=i=>{let h=n[i[0]],N=[...i].sort(dt),M=N.length-1,x=0;for(let c of N)M+=a[c]-r[c]+(n[c].abridged?1:0),x+=n[c].abridged?.steps??0;M>$.length&&($=new Int32Array(M*2),E=new Float64Array(M*2));let A=0,W=!1,Rt,$t,q=new Map,Ut=0;for(let c of N){let m=B(c),y=m===void 0||Rt===void 0?0:m-Rt;(m===void 0||y<0)&&(W=!0),y<0&&n[$t].abridged&&(Ut-=y);let S=Math.min(Ut,Math.max(y,0));Ut-=S;let u=y-S;u>0&&(q.set(A,ie(u,$t===void 0?void 0:n[$t].after,n[c].before)),$[A]=-u,E[A++]=Rt);let v=m??0,R=n[c].abridged;for(let j=r[c],Q=a[c];j<Q;j++){let G=p[j],V=R?R.bp-(v-(m??0))-b(G):0;V>0&&j===Q-1&&j>r[c]&&(q.set(A,[{bp:V,cause:"abridged"}]),$[A]=-V,E[A++]=v,v+=V),$[A]=G,E[A++]=v,v+=b(G)}Rt=m===void 0?void 0:v,$t=c}let Xt=c=>c>=0&&c<A&&$[c]>=0&&!Number.isNaN(P[$[c]]),jt=c=>{let m=$[c];return E[c]+(m<0?-m:b(m))},Ne=(c,m)=>{let y=c>=0?c:m,S=-1;for(let G=1;S<0&&G<A;G++)S=[y-G,y+G].find(Xt)??-1;if(S<0)return;let u=S>y==P[$[S]]>P[$[y]],v=u===(y===c),R=v?A-1:0,j=Xt(R);return{stop:{contigEnds:j,shortBp:j?Math.max(0,F.start-et[$[R]],P[$[R]]-F.end):0},lo:v?y+1:0,hi:v?A:y,backward:!u,axisStart:u?v?jt(y):E[0]:v?jt(A-1):E[y]}},xt=0,Mt=A,it=!1,zt=!0,vt=-1,Kt=-1,Bt,qt,Jt=(c,m)=>{let S=q.get(c)?.[0];if(m<=0||S?.cause!=="abridged")return 0;let u=Math.min(m,S.bp);return q.set(c,S.bp>u?[{...S,bp:S.bp-u}]:[]),$[c]+=u,u},Qt=c=>q.get(c)?.[0]?.cause==="abridged",be=c=>{let m=$[c];return m<0||q.has(c)?Number.NaN:Number.isNaN(P[m])&&(Qt(c-1)||Qt(c+1))?f(m):P[m]},Ot=0,Yt=0;if(F&&wt){let c=-1,m=-1,y=-1/0,S=1/0;for(let u=0;u<A;u++){let v=be(u);if(!Number.isNaN(v)){let R=v+b($[u]);R<=F.start&&R>y&&(y=R,c=u),v>=F.end&&v<S&&(S=v,m=u)}}if(c<0||m<0){zt=!1;let u=c>=0||m>=0?Ne(c,m):void 0;u&&({lo:xt,hi:Mt,backward:it,axisStart:Bt,stop:qt}=u)}else{xt=Math.min(c,m)+1,Mt=Math.max(c,m),it=c>m,vt=c,Kt=m;let u=it?-1:1;Ot=Jt(c+u,Z-y),Yt=Jt(m-u,S-X)}}let Et=h.contig??Gt(ht(h.name).name),ve=W||A===0?void 0:Bt!==void 0?{contig:Et,start:Bt,reversed:it}:vt<0?{contig:Et,start:E[0],reversed:!1}:vt<Kt?{contig:Et,start:jt(vt)+Ot,reversed:!1}:{contig:Et,start:E[vt]-Ot,reversed:!0},ct=0,te=0,ee=0,ft=0,D=-1,lt=0,J=Number.NaN,Ft=Number.NaN,ke=c=>{let m=st.get(c);if(!m||Number.isNaN(Ft))return P[c];let y=b(c),S=m[0],u=1/0;for(let v of m){let R=Math.min(Math.abs(v-Ft),Math.abs(v+y-Ft));R<u&&(S=v,u=R)}return S},[,Ct,ye,we]=_.values;for(let c=xt;c<Mt;c++){let m=it?Mt-1-(c-xt):c,y=$[m],S=q.get(m);if(S){for(let V of it?[...S].reverse():S)_.push(ct,V.bp,Number.NaN,kt|fe(V.cause),St(V.chunk)),ct+=V.bp;D=_.length-1,lt=kt,J=Number.NaN,ee+=-y,ft=0;continue}let u=b(y),v=ke(y),R=!Number.isNaN(v);C?.push(y,ct,u,R?1:0);let j=D>=0&&!Number.isNaN(J),Q=R&&j&&ft>=0&&J+(Ct[D]??0)===v,G=R&&j&&ft<=0&&v+u===J;!R&&D>=0&&!(lt&(Zt|kt))?Ct[D]+=u:Q||G?(Ct[D]+=u,Q||(J=v,ye[D]=v,lt|=de,we[D]=lt),ft=Q?1:-1):(lt=R?Zt:0,J=R?v:Number.NaN,_.push(ct,u,J,lt,-1),D=_.length-1,ft=0),ct+=u,R?Ft=ft<0?v:v+u:te+=u}return _.endRow(),C?.endRow(),{name:h.name,label:le(h),sample:Ht(h),haplotype:h.haplotype,bp:ct,offReferenceBp:te,gapBp:ee,complete:zt,stop:qt,axis:ve,...x>0?{abridgedSteps:x}:{},...Ot+Yt>0?{estimated:!0}:{}}},At=(i,h,N,M)=>{let x=M?Math.max(h,M.start):h,A=Math.max((M?Math.min(N,M.end):N)-x,0);_.push(x-(M?M.start:h),A,Number.NaN,kt|fe("deleted"),-1),_.endRow(),C?.endRow();let W={name:i,...Pt(i)};return{name:i,label:le(W),sample:Ht(W),haplotype:W.haplotype,bp:0,offReferenceBp:0,gapBp:A,complete:!0,stop:void 0,axis:void 0,deletionBp:N-h}},L=rt(U),H=[...ut.values()].map((i,h)=>({meta:rt(i),row:h+1})),ot=new Set(ut.keys()),{axis:o}=L,w=o?{start:o.start,end:o.start+L.bp+L.gapBp}:F;tt?.names.forEach((i,h)=>{let N=ht(i).name;ot.has(N)||(ot.add(N),H.push({meta:At(N,tt.starts[h],tt.ends[h],w),row:H.length+1}))});let g=[L,...H.map(i=>i.meta)];if(new Set(g.map(i=>i.label)).size<g.length)for(let i of g)i.label=ne(i.name)??i.label;H.sort((i,h)=>Number(h.meta.complete)-Number(i.meta.complete)||h.meta.bp-i.meta.bp||i.meta.label.localeCompare(h.meta.label));let I=[0,...H.map(i=>i.row)],{offsets:z,columns:K}=_.reorder(I,[yt,yt,yt,i=>new Uint8Array(i),i=>new Int32Array(i)]),[at,_t,Nt,It,bt]=K;return{origin:F?F.start:B(pt)??0,rows:[L,...H.map(i=>i.meta)],offsets:z,start:at,bp:_t,referenceStart:Nt,flags:It,chunk:bt,chunks:nt,visits:C&&Oe(C,I,d)}}function Oe(t,e,s){let{offsets:n,columns:r}=t.reorder(e,[k=>new Int32Array(k),yt,yt,k=>new Uint8Array(k)]),[a,p,l,d]=r;return{offsets:n,node:a,start:p,bp:l,onReference:d,names:s}}function Ee(t,e){let s=t.flags[e],n={start:t.start[e],bp:t.bp[e],onReference:(s&Zt)!==0};if(s&kt){n.gap=!0;let r=pe[s>>me&7];r&&(n.cause=r);let a=t.chunks[t.chunk[e]];a&&(n.chunk=a)}else n.referenceStart=Number.isNaN(t.referenceStart[e])?void 0:t.referenceStart[e];return s&de&&(n.reversed=!0),n}function Fe(t,e){let s=[];for(let n=t.offsets[e];n<t.offsets[e+1];n++)s.push({node:t.names[t.node[n]],start:t.start[n],bp:t.bp[n],onReference:t.onReference[n]===1});return s}function Je(t,e){let s=t.rows.map((n,r)=>{let a=[];for(let p=t.offsets[r];p<t.offsets[r+1];p++)a.push(Ee(t,p));return{...n,runs:a,visits:t.visits&&Fe(t.visits,r)}});return{origin:t.origin,unit:e,reference:s[0],rows:s.slice(1)}}export{Se as a,Ae as b,Te as c,Pe as d,ie as e,ae as f,_e as g,Ue as h,Dt as i,De as j,$e as k,qe as l,Je as m};
+//# sourceMappingURL=chunk-A27SW7X7.js.map