jbrowse-plugin-graphgenomeviewer 8.8.2 → 8.9.0

package/README.md

@@ -23,7 +23,7 @@ short.
 
 ## Quick start
 
-1. Add the plugin to your JBrowse 5.0.0-beta.18 or later config:
+1. Add the plugin to your JBrowse 5.0.0-beta.20 or later config:
 
    ```json
    {

package/dist/chunks/{GbzBaseSyntenyAdapter-NAXISJUH.js → GbzBaseSyntenyAdapter-7SUMECKQ.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-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
+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-BHRMUIK6.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 $,i as W,k as U}from"./chunk-EFXNCI7R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-DEWVJ57F.js";import"./chunk-YBLNN5FU.js";import"./chunk-A27SW7X7.js";import"./chunk-SKB4GSET.js";import{E as V,a as K,c as L}from"./chunk-3WUOWIYO.js";import"./chunk-YBLNN5FU.js";import"./chunk-T7NMFIRW.js";import{g as F,h as N,i as C}from"./chunk-KBOVZ3GI.js";import"./chunk-FQI75MV6.js";import"./chunk-TMM73K4C.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{e as _,o as B}from"./chunk-TC265JAP.js";function A(n){let i=/\.gbz\.db$/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-7SUMECKQ.js.map

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

@@ -1,4 +1,4 @@
-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
+import{b as C}from"./chunk-RU3HHR5K.js";import"./chunk-MURQDZ33.js";import"./chunk-TFJLUI7X.js";import"./chunk-MTMW4HY6.js";import{s as d}from"./chunk-RJZG46KB.js";import"./chunk-ZNDMFZLV.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-T7NMFIRW.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-PPOVN5LA.js.map
+//# sourceMappingURL=GraphGenomeView-XIZVEDCF.js.map

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

@@ -1,4 +1,4 @@
-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(`
+import{a as G,b as L}from"./chunk-MURQDZ33.js";import{e as v,f as x,s as f}from"./chunk-RJZG46KB.js";import"./chunk-ZWHXVFZF.js";import"./chunk-CHLLRNBQ.js";import"./chunk-SKB4GSET.js";import"./chunk-T7NMFIRW.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-BRTDTVOJ.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-GHTWJVWE.js.map

package/dist/chunks/{LinearGraphDisplay-2AZ7X7TK.js → LinearGraphDisplay-CA2GSNK3.js}

@@ -1,2 +1,2 @@
-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
+import{a,b as i}from"./chunk-RU3HHR5K.js";import"./chunk-MURQDZ33.js";import"./chunk-TFJLUI7X.js";import"./chunk-MTMW4HY6.js";import"./chunk-RJZG46KB.js";import"./chunk-ZNDMFZLV.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-T7NMFIRW.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-CA2GSNK3.js.map

package/dist/chunks/{MinigraphBubbleAdapter-NR3MMUUG.js → MinigraphBubbleAdapter-YOIBRCD3.js}

@@ -1,2 +1,2 @@
-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-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-NR3MMUUG.js.map
+import{a as f,d as c,f as d}from"./chunk-LKD5NRWR.js";import{a as g}from"./chunk-V55TK2NP.js";import{E as p,F as u,b,z as m}from"./chunk-3WUOWIYO.js";import"./chunk-YBLNN5FU.js";import"./chunk-T7NMFIRW.js";import"./chunk-KBOVZ3GI.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as i,o as l}from"./chunk-TC265JAP.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${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-YOIBRCD3.js.map

package/dist/chunks/{RgfaTabixAdapter-JDQLVQVP.js → RgfaTabixAdapter-AOOEVRF6.js}

@@ -1,2 +1,2 @@
-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
+import{a as F}from"./chunk-VQVV42DS.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-3WUOWIYO.js";import"./chunk-YBLNN5FU.js";import"./chunk-T7NMFIRW.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-AOOEVRF6.js.map

package/dist/chunks/{TrackWarningsDialog-23WL6FPV.js → TrackWarningsDialog-V5YSUFRO.js}

@@ -1,2 +1,2 @@
 import{H as i,h as o,m as a}from"./chunk-WE7DQVXF.js";import{c as r,d as e}from"./chunk-DUU6T2I5.js";var u=e(function({model:n,title:s,children:l,handleClose:m}){return r(o,{open:!0,title:s,onClose:()=>{m()},children:[l,n.trackWarnings.flatMap(({name:f,warnings:g},p)=>g.map((t,c)=>r(a,{severity:"warning",style:{marginBottom:8},children:[r(i,{variant:"subtitle2",children:[f,": ",t.message]}),t.effect]},`${p}_${c}`)))]})}),x=u;export{x as default};
-//# sourceMappingURL=TrackWarningsDialog-23WL6FPV.js.map
+//# sourceMappingURL=TrackWarningsDialog-V5YSUFRO.js.map

package/dist/chunks/{TrackWarningsDialog-23WL6FPV.js.map → TrackWarningsDialog-V5YSUFRO.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.19_@emotion+react@11.14.0_@types+react@19.3.0_react@19_eb34fd01d29d05a1c3ac8167d41484d7/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.20_@emotion+react@11.14.0_@types+react@19.3.0_react@19_56a3e322b5b3da42dc5bccc6b71729c9/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
   "sourcesContent": ["import { jsxs as _jsxs } from \"react/jsx-runtime\";\nimport { InfoDialog } from '@jbrowse/core/ui';\nimport { Alert, Typography } from '@mui/material';\nimport { observer } from 'mobx-react';\n/**\n * The render-warnings report both comparative views open, over the rows\n * `collectTrackWarnings` builds for them. Reads them off the view rather than\n * taking a copy, so a refetch that raises or clears a warning while the dialog\n * is open shows in it.\n *\n * Grouped by track, with the track name leading each row: a stacked view's\n * levels raise the same swapped-assemblies warning verbatim, and so does every\n * overlaid track that hits it, so an ungrouped list repeated one sentence N\n * times without ever naming the file to go fix.\n *\n * Keyed by position \u2014 the message is not an identity, and neither is the track\n * name once one track raises two warnings.\n */\nconst TrackWarningsDialog = observer(function TrackWarningsDialog({ model, title, children, handleClose, }) {\n    return (_jsxs(InfoDialog, { open: true, title: title, onClose: () => {\n            handleClose();\n        }, children: [children, model.trackWarnings.flatMap(({ name, warnings }, i) => warnings.map((w, j) => (_jsxs(Alert\n            // eslint-disable-next-line @eslint-react/no-array-index-key -- see above\n            , { severity: \"warning\", style: { marginBottom: 8 }, children: [_jsxs(Typography, { variant: \"subtitle2\", children: [name, \": \", w.message] }), w.effect] }, `${i}_${j}`))))] }));\n});\nexport default TrackWarningsDialog;\n"],
   "mappings": "qGAkBA,IAAMA,EAAsBC,EAAS,SAA6B,CAAE,MAAAC,EAAO,MAAAC,EAAO,SAAAC,EAAU,YAAAC,CAAa,EAAG,CACxG,OAAQC,EAAMC,EAAY,CAAE,KAAM,GAAM,MAAOJ,EAAO,QAAS,IAAM,CAC7DE,EAAY,CAChB,EAAG,SAAU,CAACD,EAAUF,EAAM,cAAc,QAAQ,CAAC,CAAE,KAAAM,EAAM,SAAAC,CAAS,EAAGC,IAAMD,EAAS,IAAI,CAACE,EAAGC,IAAON,EAAMO,EAEvG,CAAE,SAAU,UAAW,MAAO,CAAE,aAAc,CAAE,EAAG,SAAU,CAACP,EAAMQ,EAAY,CAAE,QAAS,YAAa,SAAU,CAACN,EAAM,KAAMG,EAAE,OAAO,CAAE,CAAC,EAAGA,EAAE,MAAM,CAAE,EAAG,GAAGD,CAAC,IAAIE,CAAC,EAAE,CAAE,CAAC,CAAC,CAAE,CAAC,CAC3L,CAAC,EACMG,EAAQf",
   "names": ["TrackWarningsDialog", "observer", "model", "title", "children", "handleClose", "jsxs", "InfoDialog", "name", "warnings", "i", "w", "j", "Alert", "Typography", "TrackWarningsDialog_default"]

package/dist/chunks/WalkFormsAdapter-5ALR4RU4.js

@@ -0,0 +1,2 @@
+import{a as b,b as x,c as C,d as R,f,g as v,h as N}from"./chunk-LZUH4IUR.js";import{a as $}from"./chunk-V55TK2NP.js";import{E as k,b as l,d as w,e as g,f as h,g as m,k as y,o as B,s as F,t as S}from"./chunk-3WUOWIYO.js";import"./chunk-YBLNN5FU.js";import"./chunk-T7NMFIRW.js";import"./chunk-KBOVZ3GI.js";import"./chunk-D6TY2QEG.js";import"./chunk-FLKXKTS2.js";import{a as d,o as u}from"./chunk-TC265JAP.js";var P=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function T(r,p){if(!(r instanceof w))return r;let t=C(p);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 ${m(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${P(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${m(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${P(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var E=8,i=new Map;function L(r,p){let t=i.get(r),e=t??p();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=E)break;i.delete(s)}}return e}var c=class extends l{constructor(){super(...arguments);this.reader=new y(k(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>g(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=b(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=L(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw T(n,e)}))).then(n=>B(n,{window:e,floorBp:x(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:f(e,this.maxForms()),warnings:v(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return f(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 $(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?N(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new d({uniqueId:`forms-${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}));s.complete()},e.signal)}};export{c as default};
+//# sourceMappingURL=WalkFormsAdapter-5ALR4RU4.js.map

package/dist/chunks/WalkFormsAdapter-5ALR4RU4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkFormsAdapter/WalkFormsAdapter.ts"],
+  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport {\n  ExpansionTooLargeError,\n  RegionTooLargeError,\n  WalkReader,\n  bpString,\n  formsCut,\n  panSNContig,\n  panSNMatchesPrefix,\n  structuralForms,\n} from '@jbrowse/graph-walks'\n\nimport { formSources, formVariants, formWarnings } from './formRows.ts'\nimport { floorOf, pinnedLocus, pinnedOf, warningPrefix } from './pinned.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\n\nimport type { WalkFormsAdapterConfig } from './configSchema.ts'\nimport type { Pinned } from './pinned.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { HaplotypeDepartures, StructuralForms } from '@jbrowse/graph-walks'\n\nconst megabytes = (bytes: number) => `${(bytes / 1_000_000).toFixed(1)} MB`\n\nconst millions = (n: number) => `${(n / 1_000_000).toFixed(1)} M`\n\n// A zoom-in notice would mislead, since the view's zoom does not move the\n// pinned window\nfunction pinnedTooLarge(error: unknown, pinned: Pinned) {\n  if (!(error instanceof RegionTooLargeError)) {\n    return error\n  }\n  const window = pinnedLocus(pinned)\n  if (error instanceof ExpansionTooLargeError) {\n    return new Error(\n      `The pinned window ${window} is too large to read every walk in full for structural forms: its walks take ${millions(error.steps)} steps, over the ${millions(error.limit)} step budget, and about ${bpString(error.fitsBp)} of it fits. Pin a narrower window`,\n    )\n  }\n  const budget = `walkByteBudget, ${megabytes(error.limit)}`\n  return new Error(\n    `The pinned window ${window} is too large to cut for structural forms: ${\n      error.zoomHelps\n        ? `about ${bpString(error.fitsBp)} of it fits in ${budget}. Pin a narrower window or raise walkByteBudget`\n        : `its cut fetches ${megabytes(error.bytes ?? 0)}, over ${budget}. Raise walkByteBudget`\n    }`,\n  )\n}\n\n// The departures of each pinned window, shared across adapter instances:\n// dataAdapterCache keys an adapter on its whole config, so a new floor or\n// exclude list makes a new adapter, which regroups these without a new cut.\n// A cut at the MHC takes 8 s.\nconst CUTS_KEPT = 8\nconst cuts = new Map<string, Promise<HaplotypeDepartures[]>>()\n\nfunction cachedCut(key: string, cut: () => Promise<HaplotypeDepartures[]>) {\n  const kept = cuts.get(key)\n  const read = kept ?? cut()\n  cuts.delete(key)\n  cuts.set(key, read)\n  if (!kept) {\n    read.catch(() => {\n      if (cuts.get(key) === read) {\n        cuts.delete(key)\n      }\n    })\n    for (const old of cuts.keys()) {\n      if (cuts.size <= CUTS_KEPT) {\n        break\n      }\n      cuts.delete(old)\n    }\n  }\n  return read\n}\n\nexport default class WalkFormsAdapter extends BaseFeatureDataAdapter<WalkFormsAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly reader = new WalkReader(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n  )\n\n  private formsRead: Promise<StructuralForms> | undefined\n\n  private async referenceSample(opts: BaseOptions) {\n    const { references } = await this.reader.header(opts)\n    return references[0] ?? ''\n  }\n\n  // The reference sample's contigs, as the assembly names them\n  async getRefNames(opts: BaseOptions = {}) {\n    const names = await this.reader.referenceSequences(opts)\n    const sample = await this.referenceSample(opts)\n    const contigs = names\n      .filter(n => panSNMatchesPrefix(n, sample))\n      .map(n => panSNContig(n))\n    return contigs.length > 0 ? [...new Set(contigs)] : names\n  }\n\n  private pinned() {\n    const pinned = pinnedOf(this.getConf('pinned'))\n    if (!pinned) {\n      throw new Error(\n        'WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }',\n      )\n    }\n    return pinned\n  }\n\n  // Read once per adapter, and so once per floor and exclude list. The cut\n  // takes no caller's signal, since every later caller shares it. A partial\n  // expansion would leave some walks as net changes over a whole chunk, so a\n  // window too large to read them all errors instead.\n  private forms(opts: BaseOptions) {\n    if (!this.formsRead) {\n      const pinned = this.pinned()\n      const key = `${JSON.stringify(this.getConf('walksLocation'))}\\t${pinned.refName}:${pinned.start}-${pinned.end}`\n      const byteBudget = this.getConf('walkByteBudget')\n      const read = cachedCut(`${key}\\t${byteBudget}`, () =>\n        updateStatus('Cutting walks', opts.statusCallback, () =>\n          formsCut(this.reader, pinned, { byteBudget, partial: false }).catch(\n            (error: unknown) => {\n              throw pinnedTooLarge(error, pinned)\n            },\n          ),\n        ),\n      ).then(departures =>\n        structuralForms(departures, {\n          window: pinned,\n          floorBp: floorOf(this.getConf('floorBp')),\n          exclude: this.getConf('exclude'),\n        }),\n      )\n      read.catch(() => {\n        if (this.formsRead === read) {\n          this.formsRead = undefined\n        }\n      })\n      this.formsRead = read\n    }\n    return this.formsRead\n  }\n\n  private maxForms() {\n    return this.getConf('maxForms')\n  }\n\n  /**\n   * One source per form up to maxForms, which core's multi-sample variant\n   * display draws as a row, and warnings naming the haplotypes left\n   * abridged, unplaced or in the \"other forms\" row\n   */\n  async getSourcesAndWarnings(opts: BaseOptions = {}) {\n    const result = await this.forms(opts)\n    const prefix = warningPrefix(this.pinned())\n    return {\n      sources: formSources(result, this.maxForms()),\n      warnings: formWarnings(result, this.maxForms()).map(w => prefix + w),\n    }\n  }\n\n  async getSources(_regions: Region[], opts: BaseOptions = {}) {\n    return formSources(await this.forms(opts), this.maxForms())\n  }\n\n  private async onPinnedSequence(refName: string, opts: BaseOptions) {\n    const sample = await this.referenceSample(opts)\n    const [query, pinned] = await Promise.all([\n      this.reader.sequenceFor(sample, refName, opts),\n      this.reader.sequenceFor(sample, this.pinned().refName, opts),\n    ])\n    return query !== undefined && query === pinned\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const result = await this.forms(opts)\n      const variants = (await this.onPinnedSequence(query.refName, opts))\n        ? formVariants(result, this.maxForms()).filter(\n            v => v.start < query.end && v.end > query.start,\n          )\n        : []\n      for (const v of variants) {\n        observer.next(\n          new SimpleFeature({\n            uniqueId: `forms-${result.floorBp}-${v.id}`,\n            refName: query.refName,\n            start: v.start,\n            end: v.end,\n            name: v.name,\n            description: v.description,\n            type: v.type,\n            svType: v.svType,\n            consequence: v.consequence,\n            REF: 'N',\n            ALT: [v.alt],\n            INFO: { SVTYPE: [v.svType], SVLEN: [v.mark.delta] },\n            mark: v.mark,\n            genotypes: v.genotypes,\n          }),\n        )\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": "uZAyBA,IAAMA,EAAaC,GAAkB,IAAIA,EAAQ,KAAW,QAAQ,CAAC,CAAC,MAEhEC,EAAYC,GAAc,IAAIA,EAAI,KAAW,QAAQ,CAAC,CAAC,KAI7D,SAASC,EAAeC,EAAgBC,EAAgB,CACtD,GAAI,EAAED,aAAiBE,GACrB,OAAOF,EAET,IAAMG,EAASC,EAAYH,CAAM,EACjC,GAAID,aAAiBK,EACnB,OAAO,IAAI,MACT,qBAAqBF,CAAM,iFAAiFN,EAASG,EAAM,KAAK,CAAC,oBAAoBH,EAASG,EAAM,KAAK,CAAC,2BAA2BM,EAASN,EAAM,MAAM,CAAC,oCAC7N,EAEF,IAAMO,EAAS,mBAAmBZ,EAAUK,EAAM,KAAK,CAAC,GACxD,OAAO,IAAI,MACT,qBAAqBG,CAAM,8CACzBH,EAAM,UACF,SAASM,EAASN,EAAM,MAAM,CAAC,kBAAkBO,CAAM,kDACvD,mBAAmBZ,EAAUK,EAAM,OAAS,CAAC,CAAC,UAAUO,CAAM,wBACpE,EACF,CACF,CAMA,IAAMC,EAAY,EACZC,EAAO,IAAI,IAEjB,SAASC,EAAUC,EAAaC,EAA2C,CACzE,IAAMC,EAAOJ,EAAK,IAAIE,CAAG,EACnBG,EAAOD,GAAQD,EAAI,EAGzB,GAFAH,EAAK,OAAOE,CAAG,EACfF,EAAK,IAAIE,EAAKG,CAAI,EACd,CAACD,EAAM,CACTC,EAAK,MAAM,IAAM,CACXL,EAAK,IAAIE,CAAG,IAAMG,GACpBL,EAAK,OAAOE,CAAG,CAEnB,CAAC,EACD,QAAWI,KAAON,EAAK,KAAK,EAAG,CAC7B,GAAIA,EAAK,MAAQD,EACf,MAEFC,EAAK,OAAOM,CAAG,CACjB,CACF,CACA,OAAOD,CACT,CAEA,IAAqBE,EAArB,cAA8CC,CAA+C,CAA7F,kCAGE,KAAiB,OAAS,IAAIC,EAC5BC,EAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,CACvD,EAJA,YAAc,aAAe,CAAC,cAAe,aAAa,EAQ1D,MAAc,gBAAgBC,EAAmB,CAC/C,GAAM,CAAE,WAAAC,CAAW,EAAI,MAAM,KAAK,OAAO,OAAOD,CAAI,EACpD,OAAOC,EAAW,CAAC,GAAK,EAC1B,CAGA,MAAM,YAAYD,EAAoB,CAAC,EAAG,CACxC,IAAME,EAAQ,MAAM,KAAK,OAAO,mBAAmBF,CAAI,EACjDG,EAAS,MAAM,KAAK,gBAAgBH,CAAI,EACxCI,EAAUF,EACb,OAAOxB,GAAK2B,EAAmB3B,EAAGyB,CAAM,CAAC,EACzC,IAAIzB,GAAK4B,EAAY5B,CAAC,CAAC,EAC1B,OAAO0B,EAAQ,OAAS,EAAI,CAAC,GAAG,IAAI,IAAIA,CAAO,CAAC,EAAIF,CACtD,CAEQ,QAAS,CACf,IAAMrB,EAAS0B,EAAS,KAAK,QAAQ,QAAQ,CAAC,EAC9C,GAAI,CAAC1B,EACH,MAAM,IAAI,MACR,0FACF,EAEF,OAAOA,CACT,CAMQ,MAAMmB,EAAmB,CAC/B,GAAI,CAAC,KAAK,UAAW,CACnB,IAAMnB,EAAS,KAAK,OAAO,EACrBU,EAAM,GAAG,KAAK,UAAU,KAAK,QAAQ,eAAe,CAAC,CAAC,IAAKV,EAAO,OAAO,IAAIA,EAAO,KAAK,IAAIA,EAAO,GAAG,GACvG2B,EAAa,KAAK,QAAQ,gBAAgB,EAC1Cd,EAAOJ,EAAU,GAAGC,CAAG,IAAKiB,CAAU,GAAI,IAC9CC,EAAa,gBAAiBT,EAAK,eAAgB,IACjDU,EAAS,KAAK,OAAQ7B,EAAQ,CAAE,WAAA2B,EAAY,QAAS,EAAM,CAAC,EAAE,MAC3D5B,GAAmB,CAClB,MAAMD,EAAeC,EAAOC,CAAM,CACpC,CACF,CACF,CACF,EAAE,KAAK8B,GACLC,EAAgBD,EAAY,CAC1B,OAAQ9B,EACR,QAASgC,EAAQ,KAAK,QAAQ,SAAS,CAAC,EACxC,QAAS,KAAK,QAAQ,SAAS,CACjC,CAAC,CACH,EACAnB,EAAK,MAAM,IAAM,CACX,KAAK,YAAcA,IACrB,KAAK,UAAY,OAErB,CAAC,EACD,KAAK,UAAYA,CACnB,CACA,OAAO,KAAK,SACd,CAEQ,UAAW,CACjB,OAAO,KAAK,QAAQ,UAAU,CAChC,CAOA,MAAM,sBAAsBM,EAAoB,CAAC,EAAG,CAClD,IAAMc,EAAS,MAAM,KAAK,MAAMd,CAAI,EAC9Be,EAASC,EAAc,KAAK,OAAO,CAAC,EAC1C,MAAO,CACL,QAASC,EAAYH,EAAQ,KAAK,SAAS,CAAC,EAC5C,SAAUI,EAAaJ,EAAQ,KAAK,SAAS,CAAC,EAAE,IAAIK,GAAKJ,EAASI,CAAC,CACrE,CACF,CAEA,MAAM,WAAWC,EAAoBpB,EAAoB,CAAC,EAAG,CAC3D,OAAOiB,EAAY,MAAM,KAAK,MAAMjB,CAAI,EAAG,KAAK,SAAS,CAAC,CAC5D,CAEA,MAAc,iBAAiBqB,EAAiBrB,EAAmB,CACjE,IAAMG,EAAS,MAAM,KAAK,gBAAgBH,CAAI,EACxC,CAACsB,EAAOzC,CAAM,EAAI,MAAM,QAAQ,IAAI,CACxC,KAAK,OAAO,YAAYsB,EAAQkB,EAASrB,CAAI,EAC7C,KAAK,OAAO,YAAYG,EAAQ,KAAK,OAAO,EAAE,QAASH,CAAI,CAC7D,CAAC,EACD,OAAOsB,IAAU,QAAaA,IAAUzC,CAC1C,CAEA,YAAYyC,EAAetB,EAAoB,CAAC,EAAG,CACjD,OAAOuB,EAA0B,MAAMC,GAAY,CACjD,IAAMV,EAAS,MAAM,KAAK,MAAMd,CAAI,EAC9ByB,EAAY,MAAM,KAAK,iBAAiBH,EAAM,QAAStB,CAAI,EAC7D0B,EAAaZ,EAAQ,KAAK,SAAS,CAAC,EAAE,OACpCa,GAAKA,EAAE,MAAQL,EAAM,KAAOK,EAAE,IAAML,EAAM,KAC5C,EACA,CAAC,EACL,QAAWK,KAAKF,EACdD,EAAS,KACP,IAAII,EAAc,CAChB,SAAU,SAASd,EAAO,OAAO,IAAIa,EAAE,EAAE,GACzC,QAASL,EAAM,QACf,MAAOK,EAAE,MACT,IAAKA,EAAE,IACP,KAAMA,EAAE,KACR,YAAaA,EAAE,YACf,KAAMA,EAAE,KACR,OAAQA,EAAE,OACV,YAAaA,EAAE,YACf,IAAK,IACL,IAAK,CAACA,EAAE,GAAG,EACX,KAAM,CAAE,OAAQ,CAACA,EAAE,MAAM,EAAG,MAAO,CAACA,EAAE,KAAK,KAAK,CAAE,EAClD,KAAMA,EAAE,KACR,UAAWA,EAAE,SACf,CAAC,CACH,EAEFH,EAAS,SAAS,CACpB,EAAGxB,EAAK,MAAM,CAChB,CACF",
+  "names": ["megabytes", "bytes", "millions", "n", "pinnedTooLarge", "error", "pinned", "RegionTooLargeError", "window", "pinnedLocus", "ExpansionTooLargeError", "bpString", "budget", "CUTS_KEPT", "cuts", "cachedCut", "key", "cut", "kept", "read", "old", "WalkFormsAdapter", "BaseFeatureDataAdapter", "WalkReader", "openTabixSlot", "opts", "references", "names", "sample", "contigs", "panSNMatchesPrefix", "panSNContig", "pinnedOf", "byteBudget", "updateStatus", "formsCut", "departures", "structuralForms", "floorOf", "result", "prefix", "warningPrefix", "formSources", "formWarnings", "w", "_regions", "refName", "query", "ObservableCreate", "observer", "variants", "formVariants", "v", "SimpleFeature"]
+}

package/dist/chunks/{WalkTabixSyntenyAdapter-PBWN53PE.js → WalkTabixSyntenyAdapter-2SGCZXRI.js}

@@ -1,2 +1,2 @@
-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
+import{a as ee}from"./chunk-VQVV42DS.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-BHRMUIK6.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-3WUOWIYO.js";import"./chunk-YBLNN5FU.js";import"./chunk-T7NMFIRW.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-FQI75MV6.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-2SGCZXRI.js.map