jbrowse-plugin-graphgenomeviewer 8.3.6 → 8.3.7

package/dist/chunks/{GbzBaseSyntenyAdapter-BG6FNGHY.js → GbzBaseSyntenyAdapter-4FATZPZG.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-HLWIFWDZ.js";import{a as te}from"./chunk-SYKOZDP6.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-EVKN4Y3R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as V,a as K,c as L}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-BG6FNGHY.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-DFWLOMRU.js";import{a as te}from"./chunk-SQBD75UZ.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-SVF6WK42.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-47KLT4FL.js";import"./chunk-YBLNN5FU.js";import"./chunk-UOWS2HEQ.js";import"./chunk-PVRRW4PM.js";import{E as V,a as K,c as L}from"./chunk-XK4HHKSP.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-3M3UH5JQ.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-4FATZPZG.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-BG6FNGHY.js.map → GbzBaseSyntenyAdapter-4FATZPZG.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BGEAXWE7.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-BGEAXWE7.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-4NUW2F2Y.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-JJNU2432.js → GraphGenomeView-H2Z5NQW4.js}

@@ -1,4 +1,4 @@
-import{b as C}from"./chunk-3S33TTXF.js";import"./chunk-4B3GQTHX.js";import"./chunk-NBS4FGQ6.js";import"./chunk-C5YAQNOO.js";import{p as d}from"./chunk-NFPLX56S.js";import"./chunk-CNFMSSE2.js";import"./chunk-YS3R3J2I.js";import"./chunk-LD6RX4AZ.js";import"./chunk-DKQFTMWL.js";import"./chunk-QB5JERW4.js";import"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import{i as L}from"./chunk-NIEZKWQV.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-5Z4VIKXZ.js";import{a as h,b as e,c as r,d as i}from"./chunk-JMBDTNUR.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-XTEZPFP4.js";import"./chunk-75WJWJ45.js";import"./chunk-VZNECPSI.js";import"./chunk-6YK4U5LT.js";import{p as d}from"./chunk-HVDE2ZKA.js";import"./chunk-YDJ6SDQM.js";import"./chunk-AILGRHTE.js";import"./chunk-6NR64IXK.js";import"./chunk-CI6VQ2KV.js";import"./chunk-IICQFAGJ.js";import"./chunk-47KLT4FL.js";import"./chunk-YBLNN5FU.js";import"./chunk-UOWS2HEQ.js";import"./chunk-PVRRW4PM.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import{i as L}from"./chunk-NIEZKWQV.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-5Z4VIKXZ.js";import{a as h,b as e,c as r,d as i}from"./chunk-JMBDTNUR.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-JJNU2432.js.map
+//# sourceMappingURL=GraphGenomeView-H2Z5NQW4.js.map

package/dist/chunks/{GraphTrackSettingsDialog-7NGUPDUJ.js → GraphTrackSettingsDialog-LFFJHC7F.js}

@@ -1,4 +1,4 @@
-import{a as G,b as L}from"./chunk-4B3GQTHX.js";import{b as v,c as x,p as f}from"./chunk-NFPLX56S.js";import"./chunk-LD6RX4AZ.js";import"./chunk-DKQFTMWL.js";import"./chunk-HICKAMKK.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-NIEZKWQV.js";import{F as m,H as h,n as H}from"./chunk-5Z4VIKXZ.js";import{b as p,c as l,d as u}from"./chunk-JMBDTNUR.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=u(function({model:t}){let{classes:n}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?l("div",{className:n.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),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(o){return o.split(/[\s,]+/).filter(t=>t!=="")}var N=(o,t)=>o.join(`
+import{a as G,b as L}from"./chunk-75WJWJ45.js";import{b as v,c as x,p as f}from"./chunk-HVDE2ZKA.js";import"./chunk-6NR64IXK.js";import"./chunk-CI6VQ2KV.js";import"./chunk-PVRRW4PM.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import{h as g,i as d}from"./chunk-NIEZKWQV.js";import{F as m,H as h,n as H}from"./chunk-5Z4VIKXZ.js";import{b as p,c as l,d as u}from"./chunk-JMBDTNUR.js";var k=f()({section:{marginBottom:24}}),w=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],F=u(function({model:t}){let{classes:n}=k(),e=t.sourceAdapter;return e?.type==="RgfaTabixAdapter"&&!v(e)?l("div",{className:n.section,children:[p(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:w,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),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(o){return o.split(/[\s,]+/).filter(t=>t!=="")}var N=(o,t)=>o.join(`
 `)===t.join(`
 `);function P(o,t){let n=o.cutHaplotypes??[],[e,a]=d(n);return N(n,e)||(a(n),t()),r=>{N(r,n)||(a(r),o.setSubgraphHaplotypes(r),o.recut())}}var D=u(function({model:t}){let[n,e]=d(t.cutHaplotypes?.join(", ")??""),a=P(t,()=>{e(t.cutHaplotypes?.join(", ")??"")}),r=()=>{a(A(n))};return p(m,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:n,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:i=>{e(i.target.value)},onBlur:()=>{r()},onKeyDown:i=>{i.key==="Enter"&&r()}})}),B=u(function({model:t,names:n}){let[e,a]=d(t.cutHaplotypes??[]),r=g(e),i=g(""),[S,b]=d(!1),C=P(t,()=>{r.current=t.cutHaplotypes??[],a(r.current)});return p(H,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:n,value:e,open:S,onOpen:()=>{b(!0)},onInputChange:(c,s)=>{i.current=s},onClose:(c,s)=>{b(!1);let y=i.current.trim();s==="blur"&&y&&!r.current.includes(y)&&(r.current=[...r.current,y],a(r.current)),C(r.current)},onChange:(c,s)=>{r.current=s,a(s),S||C(s)},renderInput:c=>p(m,{...c,label:"Haplotypes",placeholder:e.length===0?"every haplotype":void 0,slotProps:{...c.slotProps,htmlInput:{...c.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),O=u(function({model:t}){let{classes:n}=I(),e=t.haplotypeNames,a=t.sourceAdapter;return a&&x(a)?l("div",{className:n.section,children:[e?p(B,{model:t,names:e}):p(D,{model:t}),l(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;function R({model:o,onClose:t}){return l(L,{model:o,onClose:t,children:[p(M,{model:o}),p(T,{model:o})]})}export{R as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-7NGUPDUJ.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-LFFJHC7F.js.map

package/dist/chunks/{HighlightColorDialog-KFXSZXTC.js → HighlightColorDialog-76RJSXSV.js}

@@ -1,2 +1,2 @@
-import{x as v,y as C}from"./chunk-YS3R3J2I.js";import"./chunk-DKQFTMWL.js";import"./chunk-HICKAMKK.js";import"./chunk-L372SDUG.js";import{F as g,H as t,d as u,o as y,q as c,r as d,z as s}from"./chunk-5Z4VIKXZ.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
-//# sourceMappingURL=HighlightColorDialog-KFXSZXTC.js.map
+import{x as v,y as C}from"./chunk-AILGRHTE.js";import"./chunk-CI6VQ2KV.js";import"./chunk-PVRRW4PM.js";import"./chunk-3M3UH5JQ.js";import{F as g,H as t,d as u,o as y,q as c,r as d,z as s}from"./chunk-5Z4VIKXZ.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
+//# sourceMappingURL=HighlightColorDialog-76RJSXSV.js.map

package/dist/chunks/{LinearGraphDisplay-K3AT3S7J.js → LinearGraphDisplay-VYPF26DJ.js}

@@ -1,2 +1,2 @@
-import{a,b as i}from"./chunk-3S33TTXF.js";import"./chunk-4B3GQTHX.js";import"./chunk-NBS4FGQ6.js";import"./chunk-C5YAQNOO.js";import"./chunk-NFPLX56S.js";import"./chunk-CNFMSSE2.js";import"./chunk-YS3R3J2I.js";import"./chunk-LD6RX4AZ.js";import"./chunk-DKQFTMWL.js";import"./chunk-QB5JERW4.js";import"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.js";import{b as o,d as t}from"./chunk-JMBDTNUR.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-K3AT3S7J.js.map
+import{a,b as i}from"./chunk-XTEZPFP4.js";import"./chunk-75WJWJ45.js";import"./chunk-VZNECPSI.js";import"./chunk-6YK4U5LT.js";import"./chunk-HVDE2ZKA.js";import"./chunk-YDJ6SDQM.js";import"./chunk-AILGRHTE.js";import"./chunk-6NR64IXK.js";import"./chunk-CI6VQ2KV.js";import"./chunk-IICQFAGJ.js";import"./chunk-47KLT4FL.js";import"./chunk-YBLNN5FU.js";import"./chunk-UOWS2HEQ.js";import"./chunk-PVRRW4PM.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import"./chunk-3VGXCEMQ.js";import"./chunk-6VNDP3UB.js";import"./chunk-3WG3GF2A.js";import"./chunk-J5RMHLFJ.js";import"./chunk-NIEZKWQV.js";import"./chunk-5Z4VIKXZ.js";import{b as o,d as t}from"./chunk-JMBDTNUR.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-VYPF26DJ.js.map

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

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-QB5JERW4.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-P66QLENP.js.map
+import{a as f,d as c,f as d}from"./chunk-IICQFAGJ.js";import{a as g}from"./chunk-KOB7YIMR.js";import{E as p,F as u,b,z as m}from"./chunk-XK4HHKSP.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as i,o as l}from"./chunk-J5RMHLFJ.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-WQUZTNDM.js.map

package/dist/chunks/{RgfaTabixAdapter-CQJROUIP.js → RgfaTabixAdapter-K763K62E.js}

@@ -1,2 +1,2 @@
-import{a as F}from"./chunk-KVZIGTH3.js";import"./chunk-SYKOZDP6.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as p,F as d,b as h,u,v as w,w as k,x,y as b,z as g}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
-//# sourceMappingURL=RgfaTabixAdapter-CQJROUIP.js.map
+import{a as F}from"./chunk-477HYXB2.js";import"./chunk-SQBD75UZ.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-UOWS2HEQ.js";import"./chunk-PVRRW4PM.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-XK4HHKSP.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import{e as f}from"./chunk-6VNDP3UB.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as l,o as m}from"./chunk-J5RMHLFJ.js";var c=class extends h{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let t=this.getConf("walksLocation"),n=e.length===0&&f(t)?new F(p(this,["walksLocation"],["walksIndex"]),this):void 0,r=e.length===0?this.getConf("graphLocation"):this.getConf(["coarse","graphLocation"]);if(f(r)){let s=p(this,[...e,"graphLocation"],[...e,"graphIndex"]);return{graph:s,walks:n,refNames:new d(n?.file??s,this)}}let a=p(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),i=p(this,[...e,"linksLocation"],[...e,"linksIndex"]);return{segments:a,links:i,walks:n,refNames:new d(n?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,t={}){let{walks:n,refNames:r}=this.fine;return r.regionBytes(e,t,n&&((a,{start:i,end:s})=>n.reader.queryStart(i,{...t,refName:a,end:s})))}async hasDataForRefName(){return!0}getFeatures(e,t={}){return N(async n=>{let r=await this.fine.refNames.resolveMapped(e,t);if(r!==void 0){let{walks:a}=this.fine,i=s=>{n.next(s)};await(a?this.walkFeatures(a,r,e,t,i):this.segmentFeatures(r,e,t,i))}n.complete()},t.signal)}async walkFeatures(e,t,n,r,a){let i=await m("Downloading walks",r.statusCallback,()=>e.referenceNodes(t,n,r));for(let s of i){let o=String(s.id);a(new l({uniqueId:o,refName:n.refName,start:s.start,end:s.end,name:o,type:"segment",rank:0,stableName:s.refName}))}}async segmentRows(e,t,n,r){let a=this.fine;if("graph"in a){let i=k(await a.graph.getHeaderLines({signal:n.signal}));return g(a.graph,e,t.start,t.end,{signal:n.signal,lineCallback:s=>{let o=x(s,i);o?.kind==="N"&&r(o.segment,i.anchored)}})}return g(a.segments,e,t.start,t.end,{signal:n.signal,lineCallback:i=>{let{segment:s,anchored:o}=u(i);r(s,o)}})}async segmentFeatures(e,t,n,r){await m("Downloading segments",n.statusCallback,()=>this.segmentRows(e,t,n,(a,i)=>{if(i&&a.refName!==e)return;let s=w(a);r(new l({uniqueId:a.id,refName:t.refName,start:a.start,end:a.end,name:a.id,type:"segment",rank:a.rank,stableName:a.refName,...s&&{samples:s,sampleCount:s.length}}))}))}async getSubgraph(e,t={}){let{hops:n,signal:r,tier:a}=t,i=this.index(a),s=await i.refNames.resolveForCut(e,{signal:r});return i.walks?i.walks.subgraph(s,e,t):b(i,{refName:s,start:e.start,end:e.end},{hops:n,signal:r})}};export{c as default};
+//# sourceMappingURL=RgfaTabixAdapter-K763K62E.js.map

package/dist/chunks/{WalkFormsAdapter-YSYANJD5.js → WalkFormsAdapter-WJTEKIOB.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-RCJQCBBI.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-L372SDUG.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
-//# sourceMappingURL=WalkFormsAdapter-YSYANJD5.js.map
+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-VEI7EAE6.js";import{a as k}from"./chunk-KOB7YIMR.js";import{E as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-XK4HHKSP.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import"./chunk-3M3UH5JQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{a as m,o as u}from"./chunk-J5RMHLFJ.js";var v=r=>`${(r/1e6).toFixed(1)} MB`,O=r=>`${(r/1e6).toFixed(1)} M`;function E(r,f){if(!(r instanceof g))return r;let t=N(f);if(r instanceof F)return new Error(`The pinned window ${t} is too large to read every walk in full for structural forms: its walks take ${O(r.steps)} steps, over the ${O(r.limit)} step budget, and about ${p(r.fitsBp)} of it fits. Pin a narrower window`);let e=`walkByteBudget, ${v(r.limit)}`;return new Error(`The pinned window ${t} is too large to cut for structural forms: ${r.zoomHelps?`about ${p(r.fitsBp)} of it fits in ${e}. Pin a narrower window or raise walkByteBudget`:`its cut fetches ${v(r.bytes??0)}, over ${e}. Raise walkByteBudget`}`)}var L=8,i=new Map;function A(r,f){let t=i.get(r),e=t??f();if(i.delete(r),i.set(r,e),!t){e.catch(()=>{i.get(r)===e&&i.delete(r)});for(let s of i.keys()){if(i.size<=L)break;i.delete(s)}}return e}var d=class extends l{constructor(){super(...arguments);this.reader=new y($(this,["walksLocation"],["walksIndex"]))}static{this.capabilities=["getFeatures","getRefNames"]}async referenceSample(t){let{references:e}=await this.reader.header(t);return e[0]??""}async getRefNames(t={}){let e=await this.reader.referenceSequences(t),s=await this.referenceSample(t),a=e.filter(o=>h(o,s)).map(o=>w(o));return a.length>0?[...new Set(a)]:e}pinned(){let t=x(this.getConf("pinned"));if(!t)throw new Error("WalkFormsAdapter needs `pinned`, the window its forms come from: { refName, start, end }");return t}forms(t){if(!this.formsRead){let e=this.pinned(),s=`${JSON.stringify(this.getConf("walksLocation"))}	${e.refName}:${e.start}-${e.end}`,a=this.getConf("walkByteBudget"),o=A(`${s}	${a}`,()=>u("Cutting walks",t.statusCallback,()=>S(this.reader,e,{byteBudget:a,partial:!1}).catch(n=>{throw E(n,e)}))).then(n=>B(n,{window:e,floorBp:b(this.getConf("floorBp")),exclude:this.getConf("exclude")}));o.catch(()=>{this.formsRead===o&&(this.formsRead=void 0)}),this.formsRead=o}return this.formsRead}maxForms(){return this.getConf("maxForms")}async getSourcesAndWarnings(t={}){let e=await this.forms(t),s=R(this.pinned());return{sources:c(e,this.maxForms()),warnings:C(e,this.maxForms()).map(a=>s+a)}}async getSources(t,e={}){return c(await this.forms(e),this.maxForms())}async onPinnedSequence(t,e){let s=await this.referenceSample(e),[a,o]=await Promise.all([this.reader.sequenceFor(s,t,e),this.reader.sequenceFor(s,this.pinned().refName,e)]);return a!==void 0&&a===o}getFeatures(t,e={}){return k(async s=>{let a=await this.forms(e),o=await this.onPinnedSequence(t.refName,e)?T(a,this.maxForms()).filter(n=>n.start<t.end&&n.end>t.start):[];for(let n of o)s.next(new m({uniqueId:`forms-${a.floorBp}-${n.id}`,refName:t.refName,start:n.start,end:n.end,name:n.name,description:n.description,type:n.type,svType:n.svType,consequence:n.consequence,REF:"N",ALT:[n.alt],INFO:{SVTYPE:[n.svType],SVLEN:[n.mark.delta]},mark:n.mark,genotypes:n.genotypes}));if(o.length===0){let n=Math.floor(t.start);s.next(new m({uniqueId:`forms-reference-${t.refName}-${n}`,refName:t.refName,start:n,end:n+1,REF:"N",ALT:["."],genotypes:P(a,this.maxForms())}))}s.complete()},e.signal)}};export{d as default};
+//# sourceMappingURL=WalkFormsAdapter-WJTEKIOB.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-7COETKFB.js → WalkTabixSyntenyAdapter-PHRULBP7.js}

@@ -1,2 +1,2 @@
-import{a as ee}from"./chunk-KVZIGTH3.js";import{a as K,b as V,d as Z,e as J,f as B,g as Q,h as Y}from"./chunk-HLWIFWDZ.js";import"./chunk-SYKOZDP6.js";import{a as G}from"./chunk-KOB7YIMR.js";import{p as L,q as H,r as q}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as X,F as z,i as U}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as O,c as D,d as A,g as x,h as F,i as E}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as v}from"./chunk-J5RMHLFJ.js";var me=50;function le(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=me&&(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),[h,d]=L(n.map(y=>y^1).reverse(),s,o),m=d>c,p=m?h:i,b=Math.max(c,d);if(b<_)return[];let f=e(s),g=e(n),u=y=>m?n.length-1-p[y][0]:p[y][0],k=[];p.forEach(([,y],N)=>{if(N>0){let[M,l]=[u(N-1),u(N)].sort((w,C)=>w-C);I(k,"I",g[l]-g[M+1]),I(k,"D",f[y]-f[p[N-1][1]+1])}I(k,"=",o(s[y]))});let[S,W]=[u(0),u(p.length-1)].sort((y,N)=>y-N);return[{queryStart:g[S],queryEnd:g[W+1],targetStart:f[p[0][1]],targetEnd:f[p.at(-1)[1]+1],strand:m?"-":"+",edits:k,sharedBases:b}]}}function ce(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=ce(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,h]of e(t)){let d=s.get(c);d===h?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 pe=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:h}=t(a,s);return i===void 0||Math.min(c,h)<pe?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function j({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=le(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:A(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:q(n),matches:n.reduce((i,[c,h])=>i+(c==="="?h: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:h,hapStart:d,ids:m,rev:p,before:b,after:f}=i;if(c===r.name&&h===r.fragStart){let g=d;for(let u=0;u<m.length;u++){let k=t.get(m[u]),S=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 W=n(f)!==n(b)?n(f):u>0!=u<m.length-1?u>0:s!==(p[u]===1);return{skip:r,at:W?g+S:g,strand:W===s?"+":"-"}}g+=S}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r,i=`${a.name}:${a.fragStart}:${a.piece}:skip`;return new K({uniqueId:i,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,type:"deletion",strand:n==="-"?-1:1,syntenyId:i,spansWindow:!0,mate:{refName:A(a.name),start:s,end:s,assemblyName:t}})}var T=({name:r})=>D(r)??r,$=class extends V{constructor(){super(...arguments);this.walks=new ee(X(this,["walksLocation"],["walksIndex"]),this);this.refNames=new z(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=F(this,a),n=E(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&O(i)!==s).map(i=>({name:B(n,i),label:i,group:O(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=U(a,e);return v(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 h=new Set(c.map(d=>d.skip));n=n.filter(d=>!h.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=m=>a==="leave"?m.refStart-1:m.refEnd,h=new Map;for(let m of t){let p=c(m),b=Math.floor(p/i),f=h.get(b);f?(f.group.push(m),f.start=Math.min(f.start,p),f.end=Math.max(f.end,p+1)):h.set(b,{group:[m],start:p,end:p+1})}return(await Promise.all([...h.values()].map(async({group:m,start:p,end:b})=>{let f=new Set(m.map(u=>u.name)),g=u=>f.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:p,end:b},{...this.walks.budgets(),signal:n,keep:g,expand:g,context:0,contained:!0,links:!1});return m.map(S=>ie(S,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(m=>m!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(l=>F(this,l)):void 0,n=F(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(l=>x(n,l)||x(l,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:h}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${h.toLocaleString()}`,{graph:m,fragments:p,skips:b}=await this.laneWalks(e,t,i,a,d),f=({name:l})=>i===void 0?0:i.findIndex(w=>x(l,w)),g=new Set(p.map(T)),u=await v(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(l=>f(l)>=0&&!g.has(T(l))&&l.refStart<=c&&l.refEnd>=h),a)),k=re(m.nodes),S=E(this),W=l=>B(S,T(l)),y=p.filter(l=>l.name===e),N=p.filter(l=>l.name!==e&&f(l)>=0).map(l=>({rank:f(l),features:y.flatMap(w=>k(l,w).map(C=>j({chain:C,target:w,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:W(l)})))})),M=u.map(l=>({rank:f(l.skip),features:[oe({crossing:l,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:W(l.skip)})]}));return[...N,...M].sort((l,w)=>l.rank-w.rank).flatMap(l=>l.features)}async pairFeatures(e,t,a,s){let n=a.map(m=>({pair:m,featurePrefix:F(this,m.queryAssemblyName),matePrefix:F(this,m.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(m=>[m.featurePrefix,m.matePrefix]),s,J(a)),h=se(i.nodes),d=m=>c.filter(p=>x(p.name,m));return n.flatMap(({pair:m,featurePrefix:p,matePrefix:b})=>d(p).flatMap(f=>d(b).flatMap(g=>h(g,f).map(u=>j({chain:u,target:f,query:g,assemblyName:m.queryAssemblyName,refName:A(f.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return G(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=Z(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{$ as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-7COETKFB.js.map
+import{a as ee}from"./chunk-477HYXB2.js";import{a as K,b as V,d as Z,e as J,f as B,g as Q,h as Y}from"./chunk-DFWLOMRU.js";import"./chunk-SQBD75UZ.js";import{a as G}from"./chunk-KOB7YIMR.js";import{p as L,q as H,r as q}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-UOWS2HEQ.js";import"./chunk-PVRRW4PM.js";import{E as X,F as z,i as U}from"./chunk-XK4HHKSP.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as O,c as D,d as A,g as x,h as F,i as E}from"./chunk-3M3UH5JQ.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as v}from"./chunk-J5RMHLFJ.js";var me=50;function le(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=me&&(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),[h,d]=L(n.map(y=>y^1).reverse(),s,o),m=d>c,p=m?h:i,b=Math.max(c,d);if(b<_)return[];let f=e(s),g=e(n),u=y=>m?n.length-1-p[y][0]:p[y][0],k=[];p.forEach(([,y],N)=>{if(N>0){let[M,l]=[u(N-1),u(N)].sort((w,C)=>w-C);I(k,"I",g[l]-g[M+1]),I(k,"D",f[y]-f[p[N-1][1]+1])}I(k,"=",o(s[y]))});let[S,W]=[u(0),u(p.length-1)].sort((y,N)=>y-N);return[{queryStart:g[S],queryEnd:g[W+1],targetStart:f[p[0][1]],targetEnd:f[p.at(-1)[1]+1],strand:m?"-":"+",edits:k,sharedBases:b}]}}function ce(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=ce(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,h]of e(t)){let d=s.get(c);d===h?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 pe=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:h}=t(a,s);return i===void 0||Math.min(c,h)<pe?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function j({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=le(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:A(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:q(n),matches:n.reduce((i,[c,h])=>i+(c==="="?h: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:h,hapStart:d,ids:m,rev:p,before:b,after:f}=i;if(c===r.name&&h===r.fragStart){let g=d;for(let u=0;u<m.length;u++){let k=t.get(m[u]),S=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 W=n(f)!==n(b)?n(f):u>0!=u<m.length-1?u>0:s!==(p[u]===1);return{skip:r,at:W?g+S:g,strand:W===s?"+":"-"}}g+=S}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r,i=`${a.name}:${a.fragStart}:${a.piece}:skip`;return new K({uniqueId:i,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,type:"deletion",strand:n==="-"?-1:1,syntenyId:i,spansWindow:!0,mate:{refName:A(a.name),start:s,end:s,assemblyName:t}})}var T=({name:r})=>D(r)??r,$=class extends V{constructor(){super(...arguments);this.walks=new ee(X(this,["walksLocation"],["walksIndex"]),this);this.refNames=new z(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=F(this,a),n=E(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&O(i)!==s).map(i=>({name:B(n,i),label:i,group:O(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=U(a,e);return v(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 h=new Set(c.map(d=>d.skip));n=n.filter(d=>!h.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=m=>a==="leave"?m.refStart-1:m.refEnd,h=new Map;for(let m of t){let p=c(m),b=Math.floor(p/i),f=h.get(b);f?(f.group.push(m),f.start=Math.min(f.start,p),f.end=Math.max(f.end,p+1)):h.set(b,{group:[m],start:p,end:p+1})}return(await Promise.all([...h.values()].map(async({group:m,start:p,end:b})=>{let f=new Set(m.map(u=>u.name)),g=u=>f.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:p,end:b},{...this.walks.budgets(),signal:n,keep:g,expand:g,context:0,contained:!0,links:!1});return m.map(S=>ie(S,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(m=>m!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(l=>F(this,l)):void 0,n=F(this,a.targetAssemblyName),i=n===void 0?s:s===void 0||s.some(l=>x(n,l)||x(l,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:h}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${h.toLocaleString()}`,{graph:m,fragments:p,skips:b}=await this.laneWalks(e,t,i,a,d),f=({name:l})=>i===void 0?0:i.findIndex(w=>x(l,w)),g=new Set(p.map(T)),u=await v(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(l=>f(l)>=0&&!g.has(T(l))&&l.refStart<=c&&l.refEnd>=h),a)),k=re(m.nodes),S=E(this),W=l=>B(S,T(l)),y=p.filter(l=>l.name===e),N=p.filter(l=>l.name!==e&&f(l)>=0).map(l=>({rank:f(l),features:y.flatMap(w=>k(l,w).map(C=>j({chain:C,target:w,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:W(l)})))})),M=u.map(l=>({rank:f(l.skip),features:[oe({crossing:l,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:W(l.skip)})]}));return[...N,...M].sort((l,w)=>l.rank-w.rank).flatMap(l=>l.features)}async pairFeatures(e,t,a,s){let n=a.map(m=>({pair:m,featurePrefix:F(this,m.queryAssemblyName),matePrefix:F(this,m.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(m=>[m.featurePrefix,m.matePrefix]),s,J(a)),h=se(i.nodes),d=m=>c.filter(p=>x(p.name,m));return n.flatMap(({pair:m,featurePrefix:p,matePrefix:b})=>d(p).flatMap(f=>d(b).flatMap(g=>h(g,f).map(u=>j({chain:u,target:f,query:g,assemblyName:m.queryAssemblyName,refName:A(f.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return G(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=Z(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{$ as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-PHRULBP7.js.map

package/dist/chunks/{chunk-L372SDUG.js → chunk-3M3UH5JQ.js}

@@ -1,2 +1,2 @@
 var e="#";function l(t){return t.split(e)[0]}var r=new Set(["_gbwt_ref"]);function p(t){return r.has(t)}function c(t){let n=t.split(e);return n.length>=3?`${n[0]}${e}${n[1]}`:void 0}function u(t){let n=t.split(e);return n.length>=3?n.slice(2).join(e):n.length===2?n[1]:t}function N(t){let[n="",o="",...s]=t.split(e);return s.length>0?{sample:n,haplotype:+o,contig:s.join(e)}:void 0}function S(t){let n=t.split(e),o=n.length>=2&&n[1]!==""?Number(n[1]):Number.NaN;return{sample:n[0],haplotype:Number.isFinite(o)?o:void 0}}function f(t,n){return n!==void 0&&(t===n||t.startsWith(n+e))}function a(t){return t.getConf("assemblyNameToPanSN")??{}}function h(t,n){return n===void 0?void 0:a(t)[n]??n}var i=new WeakMap;function m(t){let n=i.get(t);if(n===void 0){let o=a(t);n={};for(let s of new Set([...Object.keys(o),...t.getConf("assemblyNames")]))n[o[s]??s]=s;i.set(t,n)}return n}export{l as a,p as b,c,u as d,N as e,S as f,f as g,h,m as i};
-//# sourceMappingURL=chunk-L372SDUG.js.map
+//# sourceMappingURL=chunk-3M3UH5JQ.js.map

package/dist/chunks/{chunk-L372SDUG.js.map → chunk-3M3UH5JQ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2JL2JVZ2.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-2JL2JVZ2.js"],
   "sourcesContent": ["// src/pansn.ts\nvar SEP = \"#\";\nfunction panSNSample(refName) {\n  return refName.split(SEP)[0];\n}\nvar GENERIC_SAMPLES = /* @__PURE__ */ new Set([\"_gbwt_ref\"]);\nfunction isGenericSample(sample) {\n  return GENERIC_SAMPLES.has(sample);\n}\nfunction panSNHaplotype(refName) {\n  const parts = refName.split(SEP);\n  return parts.length >= 3 ? `${parts[0]}${SEP}${parts[1]}` : void 0;\n}\nfunction panSNContig(refName) {\n  const parts = refName.split(SEP);\n  return parts.length >= 3 ? parts.slice(2).join(SEP) : parts.length === 2 ? parts[1] : refName;\n}\nfunction panSNFields(name) {\n  const [sample = \"\", haplotype = \"\", ...contig] = name.split(SEP);\n  return contig.length > 0 ? { sample, haplotype: +haplotype, contig: contig.join(SEP) } : void 0;\n}\nfunction parsePanSN(refName) {\n  const parts = refName.split(SEP);\n  const haplotype = parts.length >= 2 && parts[1] !== \"\" ? Number(parts[1]) : Number.NaN;\n  return {\n    sample: parts[0],\n    haplotype: Number.isFinite(haplotype) ? haplotype : void 0\n  };\n}\nfunction panSNMatchesPrefix(refName, prefix) {\n  return prefix !== void 0 && (refName === prefix || refName.startsWith(prefix + SEP));\n}\nfunction assemblyNameToPanSN(adapter) {\n  return adapter.getConf(\"assemblyNameToPanSN\") ?? {};\n}\nfunction resolvePanSNPrefix(adapter, name) {\n  return name === void 0 ? void 0 : assemblyNameToPanSN(adapter)[name] ?? name;\n}\nvar asmByPrefixCache = /* @__PURE__ */ new WeakMap();\nfunction assemblyByPanSNPrefix(adapter) {\n  let out = asmByPrefixCache.get(adapter);\n  if (out === void 0) {\n    const map = assemblyNameToPanSN(adapter);\n    out = {};\n    for (const asm of /* @__PURE__ */ new Set([\n      ...Object.keys(map),\n      ...adapter.getConf(\"assemblyNames\")\n    ])) {\n      out[map[asm] ?? asm] = asm;\n    }\n    asmByPrefixCache.set(adapter, out);\n  }\n  return out;\n}\n\nexport {\n  panSNSample,\n  isGenericSample,\n  panSNHaplotype,\n  panSNContig,\n  panSNFields,\n  parsePanSN,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n  assemblyByPanSNPrefix\n};\n"],
   "mappings": "AACA,IAAIA,EAAM,IACV,SAASC,EAAYC,EAAS,CAC5B,OAAOA,EAAQ,MAAMF,CAAG,EAAE,CAAC,CAC7B,CACA,IAAIG,EAAkC,IAAI,IAAI,CAAC,WAAW,CAAC,EAC3D,SAASC,EAAgBC,EAAQ,CAC/B,OAAOF,EAAgB,IAAIE,CAAM,CACnC,CACA,SAASC,EAAeJ,EAAS,CAC/B,IAAMK,EAAQL,EAAQ,MAAMF,CAAG,EAC/B,OAAOO,EAAM,QAAU,EAAI,GAAGA,EAAM,CAAC,CAAC,GAAGP,CAAG,GAAGO,EAAM,CAAC,CAAC,GAAK,MAC9D,CACA,SAASC,EAAYN,EAAS,CAC5B,IAAMK,EAAQL,EAAQ,MAAMF,CAAG,EAC/B,OAAOO,EAAM,QAAU,EAAIA,EAAM,MAAM,CAAC,EAAE,KAAKP,CAAG,EAAIO,EAAM,SAAW,EAAIA,EAAM,CAAC,EAAIL,CACxF,CACA,SAASO,EAAYC,EAAM,CACzB,GAAM,CAACL,EAAS,GAAIM,EAAY,GAAI,GAAGC,CAAM,EAAIF,EAAK,MAAMV,CAAG,EAC/D,OAAOY,EAAO,OAAS,EAAI,CAAE,OAAAP,EAAQ,UAAW,CAACM,EAAW,OAAQC,EAAO,KAAKZ,CAAG,CAAE,EAAI,MAC3F,CACA,SAASa,EAAWX,EAAS,CAC3B,IAAMK,EAAQL,EAAQ,MAAMF,CAAG,EACzBW,EAAYJ,EAAM,QAAU,GAAKA,EAAM,CAAC,IAAM,GAAK,OAAOA,EAAM,CAAC,CAAC,EAAI,OAAO,IACnF,MAAO,CACL,OAAQA,EAAM,CAAC,EACf,UAAW,OAAO,SAASI,CAAS,EAAIA,EAAY,MACtD,CACF,CACA,SAASG,EAAmBZ,EAASa,EAAQ,CAC3C,OAAOA,IAAW,SAAWb,IAAYa,GAAUb,EAAQ,WAAWa,EAASf,CAAG,EACpF,CACA,SAASgB,EAAoBC,EAAS,CACpC,OAAOA,EAAQ,QAAQ,qBAAqB,GAAK,CAAC,CACpD,CACA,SAASC,EAAmBD,EAASP,EAAM,CACzC,OAAOA,IAAS,OAAS,OAASM,EAAoBC,CAAO,EAAEP,CAAI,GAAKA,CAC1E,CACA,IAAIS,EAAmC,IAAI,QAC3C,SAASC,EAAsBH,EAAS,CACtC,IAAII,EAAMF,EAAiB,IAAIF,CAAO,EACtC,GAAII,IAAQ,OAAQ,CAClB,IAAMC,EAAMN,EAAoBC,CAAO,EACvCI,EAAM,CAAC,EACP,QAAWE,KAAuB,IAAI,IAAI,CACxC,GAAG,OAAO,KAAKD,CAAG,EAClB,GAAGL,EAAQ,QAAQ,eAAe,CACpC,CAAC,EACCI,EAAIC,EAAIC,CAAG,GAAKA,CAAG,EAAIA,EAEzBJ,EAAiB,IAAIF,EAASI,CAAG,CACnC,CACA,OAAOA,CACT",
   "names": ["SEP", "panSNSample", "refName", "GENERIC_SAMPLES", "isGenericSample", "sample", "panSNHaplotype", "parts", "panSNContig", "panSNFields", "name", "haplotype", "contig", "parsePanSN", "panSNMatchesPrefix", "prefix", "assemblyNameToPanSN", "adapter", "resolvePanSNPrefix", "asmByPrefixCache", "assemblyByPanSNPrefix", "out", "map", "asm"]

package/dist/chunks/{chunk-KVZIGTH3.js → chunk-477HYXB2.js}

@@ -1,2 +1,2 @@
-import{a as B}from"./chunk-SYKOZDP6.js";import{h as b,i as o,k as f,z as m}from"./chunk-DAF7EWRF.js";import{h as u}from"./chunk-L372SDUG.js";var O={steps:"walkStepBudget",bytes:"walkByteBudget"},y=64,k=class{constructor(e,t){this.file=e;this.adapter=t;this.reader=new f(e)}async haplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}budgets(){return{stepBudget:this.adapter.getConf("walkStepBudget"),byteBudget:this.adapter.getConf("walkByteBudget"),budgetNames:O}}async subgraph(e,t,{signal:i,haplotypes:d,walkRows:s,expand:r,expandSamples:n}){let g=this.budgets(),p=o(d?.map(a=>u(this.adapter,a)),e),l=s&&p&&(d?.length??0)<=y?p:void 0,c=s&&n?.length&&n.length<=y?o(n.map(a=>u(this.adapter,a)),e):void 0,h=r?.length?a=>r.includes(a):void 0,{graph:w,kept:A,fragments:S,skips:x}=await this.reader.cut(e,t,{...g,stepBudget:s?1/0:g.stepBudget,signal:i,keep:p,...l||c||h?{expand:a=>!!l?.(a)||!!c?.(a)||!!h?.(a)}:{}});return B(w.tables(A,S,x),t,s)}async referenceNodes(e,t,i){let d=[];await m(this.file,e,await this.reader.queryStart(t.start,{...i,refName:e,end:t.end}),t.end,{signal:i.signal,lineCallback:r=>{let n=r.split("	");n[3]==="ref"&&d.push(n)}});let s=new Set;return b(d).filter(r=>r.refName!==e||r.end<=t.start||r.start>=t.end||s.has(r.id)?!1:(s.add(r.id),!0))}};export{k as a};
-//# sourceMappingURL=chunk-KVZIGTH3.js.map
+import{a as B}from"./chunk-SQBD75UZ.js";import{h as b,i as o,k as f,z as m}from"./chunk-XK4HHKSP.js";import{h as u}from"./chunk-3M3UH5JQ.js";var O={steps:"walkStepBudget",bytes:"walkByteBudget"},y=64,k=class{constructor(e,t){this.file=e;this.adapter=t;this.reader=new f(e)}async haplotypeNames(e={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}budgets(){return{stepBudget:this.adapter.getConf("walkStepBudget"),byteBudget:this.adapter.getConf("walkByteBudget"),budgetNames:O}}async subgraph(e,t,{signal:i,haplotypes:d,walkRows:s,expand:r,expandSamples:n}){let g=this.budgets(),p=o(d?.map(a=>u(this.adapter,a)),e),l=s&&p&&(d?.length??0)<=y?p:void 0,c=s&&n?.length&&n.length<=y?o(n.map(a=>u(this.adapter,a)),e):void 0,h=r?.length?a=>r.includes(a):void 0,{graph:w,kept:A,fragments:S,skips:x}=await this.reader.cut(e,t,{...g,stepBudget:s?1/0:g.stepBudget,signal:i,keep:p,...l||c||h?{expand:a=>!!l?.(a)||!!c?.(a)||!!h?.(a)}:{}});return B(w.tables(A,S,x),t,s)}async referenceNodes(e,t,i){let d=[];await m(this.file,e,await this.reader.queryStart(t.start,{...i,refName:e,end:t.end}),t.end,{signal:i.signal,lineCallback:r=>{let n=r.split("	");n[3]==="ref"&&d.push(n)}});let s=new Set;return b(d).filter(r=>r.refName!==e||r.end<=t.start||r.start>=t.end||s.has(r.id)?!1:(s.add(r.id),!0))}};export{k as a};
+//# sourceMappingURL=chunk-477HYXB2.js.map

package/dist/chunks/{chunk-HQ7FQACT.js → chunk-47KLT4FL.js}

@@ -1,4 +1,4 @@
-import{a as Z,b as $,f as L,h as M}from"./chunk-3HS6N7WB.js";import{b as O,g as G,p as T}from"./chunk-HICKAMKK.js";import{a as y,b as I,c as C,d as v}from"./chunk-L372SDUG.js";var q=new Map([["hg38","GRCh38"],["hg19","GRCh37"],["hs1","CHM13"],["t2t-chm13","CHM13"],["chm13v2","CHM13"]]);function F(t){return q.get(t.toLowerCase())}function z(t){let s=t.includes("#")?y(t):void 0;return s===void 0||I(s)?void 0:s}function P(t){return C(t)??y(t)}function _(t){let s=new Set((t.anchorPaths??[]).map(n=>n.name));for(let n of t.nodes)n.stable&&s.add(n.stable.refName);let e=new Map;for(let n of s){let r=z(n);r!==void 0&&O(e,r,P(n))}return e}function B(t,s){let e=new Set(t.map(f=>z(f.refName))),[n]=e;if(e.size!==1||n===void 0)return{contigs:t,prefixes:[],named:!1};let r=new Set(t.map(f=>P(f.refName))),i=[...s.get(n)??[]].every(f=>r.has(f)),a=new Set(t.map(f=>C(f.refName))),[o]=a;return{contigs:t,prefixes:[...i?[n]:[],...a.size===1&&o?[o]:[]],named:!0}}function U(t){let s=new Map;for(let n of t.nodes)if(G(n)){let{refName:r,start:i}=n.stable,a=i+n.length,o=s.get(r);o?(o.start=Math.min(o.start,i),o.end=Math.max(o.end,a)):s.set(r,{refName:r,contig:v(r),start:i,end:a})}let e=[...s.values()];return e.length?B(e,_(t)):void 0}function de(t,s){let e=U(t),n=s?v(s.refName):e?.contigs.length===1?e.contigs[0].contig:void 0,r=e?.named?y(e.contigs[0].refName):void 0;return n&&(r?`${r} ${n}`:n)}function H(t,s){let e=a=>[a.name,...a.aliases??[]],n=a=>o=>e(o).some(f=>f.toLowerCase()===a.toLowerCase()),r=[...t?.prefixes??[]].reverse(),i=t?.prefixes.find(a=>!a.includes("#"))?.toLowerCase();for(let a of r){let o=s.find(n(a));if(o)return o}return i===void 0?void 0:s.find(a=>e(a).some(o=>F(o)?.toLowerCase()===i))}function pe(t,s){let e=_(t);return t.anchorPaths?.find(n=>H(B([{refName:n.name,contig:v(n.name),start:n.start,end:n.start+n.length}],e),[s]))}function D(t){let s=t.replace(/^chr/i,""),e=s?/^(M|MT)$/i.test(s)?["M","MT"]:[s]:[];return[...new Set([t,...e.flatMap(n=>[n,`chr${n}`])])]}function K(t,s={}){let e=new Set(t),n=new Map;for(let r of e){let i=v(r),a=s[i];for(let o of new Set([...D(i),...a?[a]:[]]))n.set(o,n.has(o)?void 0:r)}return r=>e.has(r)?r:n.get(r)}function me(t,s,e){let n=K(s.contigs.map(r=>r.refName),e);return t.flatMap(r=>{let i=n(r.refName);return i===void 0?[]:[i===r.refName?r:{...r,refName:i}]})}var Q=62,R=60,j=9,k=48,J=57,V=/^(?:LN:i|SN:Z|SO:i|SR:i):/,X=/^[PEOUFG]\t/,W=t=>t.endsWith("\r")?t.slice(0,-1):t;function Y(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var ee=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(t){return this.byName.has(t)}add(t){let s=this.names.length;this.byName.set(t,s),this.names.push(t);let e=+t;return Number.isSafeInteger(e)&&String(e)===t&&this.byNumber.set(e,s),s}of(t){return this.byName.get(t)??this.add(t)}ofNumber(t){return this.byNumber.get(t)}};function te(t){let[,s,e="*",...n]=t.split("	");if(!s||/^\d+$/.test(e))return;let r=e==="*"?0:e.length,i,a,o;for(let u of n){if(!V.test(u))return;let c=u.slice(5),p=u.slice(0,2);p==="LN"?r=+c:p==="SN"?i=c:p==="SO"?a=+c:o=+c}return{name:s,length:r,stable:i!==void 0&&a!==void 0&&o!==void 0?{refName:i,start:a,rank:o}:void 0}}function se(t,s,e,n){let r=0,i=-1,a=0,o=!0,f=c=>{if(i>=0&&c>i){let p=o&&c-i<16&&(c-i===1||t.charCodeAt(i)!==k)?e.ofNumber(a):void 0;n.nodes.push(p??e.of(t.slice(i,c))),n.reversed.push(r)}},u=s;for(;u<t.length;u++){let c=t.charCodeAt(u);if(c===Q||c===R)f(u),r=c===R?1:0,i=u+1,a=0,o=!0;else{if(c===j)break;o&&c>=k&&c<=J?a=a*10+c-k:o=!1}}return f(u),u}function ne(t){let s=[],e=0;for(;s.length<6;){let f=t.indexOf("	",e);if(f===-1)return;s.push(t.slice(e,f)),e=f+1}let[,n,r,i,a,o]=s;return n&&r&&i&&a&&o&&e<t.length?{sample:n,haplotype:r,contig:i,start:a,end:o,body:e}:void 0}function Ne(t){let s=t.split(`
+import{a as Z,b as $,f as L,h as M}from"./chunk-UOWS2HEQ.js";import{b as O,g as G,p as T}from"./chunk-PVRRW4PM.js";import{a as y,b as I,c as C,d as v}from"./chunk-3M3UH5JQ.js";var q=new Map([["hg38","GRCh38"],["hg19","GRCh37"],["hs1","CHM13"],["t2t-chm13","CHM13"],["chm13v2","CHM13"]]);function F(t){return q.get(t.toLowerCase())}function z(t){let s=t.includes("#")?y(t):void 0;return s===void 0||I(s)?void 0:s}function P(t){return C(t)??y(t)}function _(t){let s=new Set((t.anchorPaths??[]).map(n=>n.name));for(let n of t.nodes)n.stable&&s.add(n.stable.refName);let e=new Map;for(let n of s){let r=z(n);r!==void 0&&O(e,r,P(n))}return e}function B(t,s){let e=new Set(t.map(f=>z(f.refName))),[n]=e;if(e.size!==1||n===void 0)return{contigs:t,prefixes:[],named:!1};let r=new Set(t.map(f=>P(f.refName))),i=[...s.get(n)??[]].every(f=>r.has(f)),a=new Set(t.map(f=>C(f.refName))),[o]=a;return{contigs:t,prefixes:[...i?[n]:[],...a.size===1&&o?[o]:[]],named:!0}}function U(t){let s=new Map;for(let n of t.nodes)if(G(n)){let{refName:r,start:i}=n.stable,a=i+n.length,o=s.get(r);o?(o.start=Math.min(o.start,i),o.end=Math.max(o.end,a)):s.set(r,{refName:r,contig:v(r),start:i,end:a})}let e=[...s.values()];return e.length?B(e,_(t)):void 0}function de(t,s){let e=U(t),n=s?v(s.refName):e?.contigs.length===1?e.contigs[0].contig:void 0,r=e?.named?y(e.contigs[0].refName):void 0;return n&&(r?`${r} ${n}`:n)}function H(t,s){let e=a=>[a.name,...a.aliases??[]],n=a=>o=>e(o).some(f=>f.toLowerCase()===a.toLowerCase()),r=[...t?.prefixes??[]].reverse(),i=t?.prefixes.find(a=>!a.includes("#"))?.toLowerCase();for(let a of r){let o=s.find(n(a));if(o)return o}return i===void 0?void 0:s.find(a=>e(a).some(o=>F(o)?.toLowerCase()===i))}function pe(t,s){let e=_(t);return t.anchorPaths?.find(n=>H(B([{refName:n.name,contig:v(n.name),start:n.start,end:n.start+n.length}],e),[s]))}function D(t){let s=t.replace(/^chr/i,""),e=s?/^(M|MT)$/i.test(s)?["M","MT"]:[s]:[];return[...new Set([t,...e.flatMap(n=>[n,`chr${n}`])])]}function K(t,s={}){let e=new Set(t),n=new Map;for(let r of e){let i=v(r),a=s[i];for(let o of new Set([...D(i),...a?[a]:[]]))n.set(o,n.has(o)?void 0:r)}return r=>e.has(r)?r:n.get(r)}function me(t,s,e){let n=K(s.contigs.map(r=>r.refName),e);return t.flatMap(r=>{let i=n(r.refName);return i===void 0?[]:[i===r.refName?r:{...r,refName:i}]})}var Q=62,R=60,j=9,k=48,J=57,V=/^(?:LN:i|SN:Z|SO:i|SR:i):/,X=/^[PEOUFG]\t/,W=t=>t.endsWith("\r")?t.slice(0,-1):t;function Y(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var ee=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(t){return this.byName.has(t)}add(t){let s=this.names.length;this.byName.set(t,s),this.names.push(t);let e=+t;return Number.isSafeInteger(e)&&String(e)===t&&this.byNumber.set(e,s),s}of(t){return this.byName.get(t)??this.add(t)}ofNumber(t){return this.byNumber.get(t)}};function te(t){let[,s,e="*",...n]=t.split("	");if(!s||/^\d+$/.test(e))return;let r=e==="*"?0:e.length,i,a,o;for(let u of n){if(!V.test(u))return;let c=u.slice(5),p=u.slice(0,2);p==="LN"?r=+c:p==="SN"?i=c:p==="SO"?a=+c:o=+c}return{name:s,length:r,stable:i!==void 0&&a!==void 0&&o!==void 0?{refName:i,start:a,rank:o}:void 0}}function se(t,s,e,n){let r=0,i=-1,a=0,o=!0,f=c=>{if(i>=0&&c>i){let p=o&&c-i<16&&(c-i===1||t.charCodeAt(i)!==k)?e.ofNumber(a):void 0;n.nodes.push(p??e.of(t.slice(i,c))),n.reversed.push(r)}},u=s;for(;u<t.length;u++){let c=t.charCodeAt(u);if(c===Q||c===R)f(u),r=c===R?1:0,i=u+1,a=0,o=!0;else{if(c===j)break;o&&c>=k&&c<=J?a=a*10+c-k:o=!1}}return f(u),u}function ne(t){let s=[],e=0;for(;s.length<6;){let f=t.indexOf("	",e);if(f===-1)return;s.push(t.slice(e,f)),e=f+1}let[,n,r,i,a,o]=s;return n&&r&&i&&a&&o&&e<t.length?{sample:n,haplotype:r,contig:i,start:a,end:o,body:e}:void 0}function Ne(t){let s=t.split(`
 `),e=new ee,n=[],r=[],i=[],a=[],o=[],f=new Map;for(let d of s){if(X.test(d))return;if(d.startsWith("S	")){let l=te(W(d));if(!l||e.has(l.name))return;e.add(l.name),n.push(l.length);let h=-1;l.stable&&(h=f.get(l.stable.refName)??o.length,h===o.length&&(o.push(l.stable.refName),f.set(l.stable.refName,h))),r.push(h),i.push(l.stable?.start??0),a.push(l.stable?.rank??0)}}let u=[],c=[],p=[],b=[],x=[],E=[],S=[0],g=Y(),w=new M,A=new M;for(let d of s)if(d.startsWith("L	")){let[,l,h,N,m]=W(d).split("	");l&&N&&m&&(u.push(e.of(l)),c.push(e.of(N)),p.push((h==="-"?1:0)|(m==="-"?2:0)))}else if(d.startsWith("W	")){let l=W(d),h=ne(l);if(h){b.push(`${h.sample}#${h.haplotype}#${h.contig}`),x.push(h.start==="*"?0:+h.start),E.push(h.end==="*"?-1:+h.end);let N=se(l,h.body,e,g),m=re(l,N);if(m===void 0||(m.before&&w.push(m.before),m.after&&A.push(m.after),g.nodes.length===S.at(-1)))return;S.push(g.nodes.length)}}if(![w.kinds.length,A.kinds.length].some(d=>d>0&&d<b.length))return{nodes:{names:e.names,lengths:Int32Array.from(n),refs:Int32Array.from(r),starts:Float64Array.from(i),ranks:Int32Array.from(a),refNames:o},links:{from:Int32Array.from(u),to:Int32Array.from(c),strands:Uint8Array.from(p)},walks:{names:b,starts:Float64Array.from(x),ends:Float64Array.from(E),offsets:Int32Array.from(S),steps:g.nodes.data.slice(0,g.nodes.length),reversed:g.reversed.data.slice(0,g.reversed.length),...oe(b.length,w,A)}}}function re(t,s){let e={};for(let n of s<t.length?t.slice(s+1).split("	"):[]){let r=n.slice(5);if(n.startsWith(`${Z}:Z:`)){if(e.before=L(r),!e.before)return}else if(n.startsWith(`${$}:Z:`)&&(e.after=L(r),!e.after))return}return e}function oe(t,s,e){return{...s.kinds.length===t&&t>0?{before:s.table()}:{},...e.kinds.length===t&&t>0?{after:e.table()}:{}}}var ae=/([><])([^><]+)/g;function ie(t){if(!t.startsWith(">")&&!t.startsWith("<"))return;let s=[];for(let[,e,n]of t.matchAll(ae))s.push({name:n,strand:e===">"?"+":"-"});return s}function fe(t){let s=t.trimEnd(),e=s.split("	");if(e.length<12||s.startsWith("#"))return;let n=ie(e[5]);if(!n)return;let r,i=!1;for(let a=12;a<e.length;a++){let o=e[a];o.startsWith("cs:Z:")?r=o.slice(5):o==="tp:A:S"&&(i=!0)}return{name:e[0],queryLength:+e[1],queryStart:+e[2],queryEnd:+e[3],strand:e[4]==="-"?"-":"+",path:n,pathLength:+e[6],pathStart:+e[7],pathEnd:+e[8],matches:+e[9],blockLength:+e[10],mappingQuality:+e[11],secondary:i,...r===void 0?{}:{cs:r}}}function we(t){let s=[];for(let e of t.split(`
 `)){let n=fe(e);n&&s.push(n)}return s}var ce=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function Ae(t){let s=[];for(let e of t.matchAll(ce))e[1]!==void 0?s.push({op:"match",length:+e[1]}):e[2]!==void 0?s.push({op:"match",length:e[2].length}):e[3]!==void 0?s.push({op:"substitution",seq:e[3].toUpperCase()}):e[4]!==void 0?s.push({op:"insertion",seq:e[4].toUpperCase()}):e[5]!==void 0?s.push({op:"deletion",length:e[5].length}):e[6]!==void 0&&s.push({op:"match",length:+e[6]});return s}export{F as a,U as b,de as c,H as d,pe as e,me as f,Ne as g,fe as h,we as i,Ae as j};
-//# sourceMappingURL=chunk-HQ7FQACT.js.map
+//# sourceMappingURL=chunk-47KLT4FL.js.map

package/dist/chunks/{chunk-HQ7FQACT.js.map → chunk-47KLT4FL.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5ORP7EFJ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JQVS4DRW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.3.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5ORP7EFJ.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-JQVS4DRW.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
   "sourcesContent": ["import {\n  addTo\n} from \"./chunk-BSOZW3FC.js\";\nimport {\n  isBackbone\n} from \"./chunk-RJWPJCIB.js\";\nimport {\n  isGenericSample,\n  panSNContig,\n  panSNHaplotype,\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/reference.ts\nvar WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([\n  [\"hg38\", \"GRCh38\"],\n  [\"hg19\", \"GRCh37\"],\n  [\"hs1\", \"CHM13\"],\n  [\"t2t-chm13\", \"CHM13\"],\n  [\"chm13v2\", \"CHM13\"]\n]);\nfunction wellKnownSample(assemblyName) {\n  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());\n}\nfunction sampleOf(refName) {\n  const sample = refName.includes(\"#\") ? panSNSample(refName) : void 0;\n  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;\n}\nfunction haplotypeOf(refName) {\n  return panSNHaplotype(refName) ?? panSNSample(refName);\n}\nfunction graphHaplotypes(graph) {\n  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));\n  for (const node of graph.nodes) {\n    if (node.stable) {\n      refNames.add(node.stable.refName);\n    }\n  }\n  const bySample = /* @__PURE__ */ new Map();\n  for (const refName of refNames) {\n    const sample = sampleOf(refName);\n    if (sample !== void 0) {\n      addTo(bySample, sample, haplotypeOf(refName));\n    }\n  }\n  return bySample;\n}\nfunction backboneFrom(contigs, haplotypes) {\n  const samples = new Set(contigs.map((c) => sampleOf(c.refName)));\n  const [sample] = samples;\n  if (samples.size !== 1 || sample === void 0) {\n    return { contigs, prefixes: [], named: false };\n  }\n  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));\n  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));\n  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));\n  const [haplotype] = shared;\n  return {\n    contigs,\n    prefixes: [\n      ...unique ? [sample] : [],\n      ...shared.size === 1 && haplotype ? [haplotype] : []\n    ],\n    named: true\n  };\n}\nfunction graphBackbone(graph) {\n  const spans = /* @__PURE__ */ new Map();\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      const { refName, start } = node.stable;\n      const end = start + node.length;\n      const span = spans.get(refName);\n      if (span) {\n        span.start = Math.min(span.start, start);\n        span.end = Math.max(span.end, end);\n      } else {\n        spans.set(refName, {\n          refName,\n          contig: panSNContig(refName),\n          start,\n          end\n        });\n      }\n    }\n  }\n  const contigs = [...spans.values()];\n  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;\n}\nfunction referenceLabel(graph, region) {\n  const backbone = graphBackbone(graph);\n  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;\n  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;\n  return contig && (sample ? `${sample} ${contig}` : contig);\n}\nfunction backboneAssembly(backbone, assemblies) {\n  const names = (a) => [a.name, ...a.aliases ?? []];\n  const naming = (prefix) => (a) => names(a).some((n) => n.toLowerCase() === prefix.toLowerCase());\n  const prefixes = [...backbone?.prefixes ?? []].reverse();\n  const sample = backbone?.prefixes.find((p) => !p.includes(\"#\"))?.toLowerCase();\n  for (const prefix of prefixes) {\n    const assembly = assemblies.find(naming(prefix));\n    if (assembly) {\n      return assembly;\n    }\n  }\n  return sample === void 0 ? void 0 : assemblies.find(\n    (a) => names(a).some((n) => wellKnownSample(n)?.toLowerCase() === sample)\n  );\n}\nfunction assemblyWalk(graph, assembly) {\n  const haplotypes = graphHaplotypes(graph);\n  return graph.anchorPaths?.find(\n    (walk) => backboneAssembly(\n      backboneFrom(\n        [\n          {\n            refName: walk.name,\n            contig: panSNContig(walk.name),\n            start: walk.start,\n            end: walk.start + walk.length\n          }\n        ],\n        haplotypes\n      ),\n      [assembly]\n    )\n  );\n}\nfunction contigNames(contig) {\n  const bare = contig.replace(/^chr/i, \"\");\n  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? [\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\n};\n", "import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-VA5U4F23.js\";\nimport {\n  Column\n} from \"./chunk-BEUTROKU.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(text) {\n  const line = text.trimEnd();\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line);\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
   "mappings": "gLAcA,IAAIA,EAAqC,IAAI,IAAI,CAC/C,CAAC,OAAQ,QAAQ,EACjB,CAAC,OAAQ,QAAQ,EACjB,CAAC,MAAO,OAAO,EACf,CAAC,YAAa,OAAO,EACrB,CAAC,UAAW,OAAO,CACrB,CAAC,EACD,SAASC,EAAgBC,EAAc,CACrC,OAAOF,EAAmB,IAAIE,EAAa,YAAY,CAAC,CAC1D,CACA,SAASC,EAASC,EAAS,CACzB,IAAMC,EAASD,EAAQ,SAAS,GAAG,EAAIE,EAAYF,CAAO,EAAI,OAC9D,OAAOC,IAAW,QAAUE,EAAgBF,CAAM,EAAI,OAASA,CACjE,CACA,SAASG,EAAYJ,EAAS,CAC5B,OAAOK,EAAeL,CAAO,GAAKE,EAAYF,CAAO,CACvD,CACA,SAASM,EAAgBC,EAAO,CAC9B,IAAMC,EAAW,IAAI,KAAKD,EAAM,aAAe,CAAC,GAAG,IAAKE,GAAMA,EAAE,IAAI,CAAC,EACrE,QAAWC,KAAQH,EAAM,MACnBG,EAAK,QACPF,EAAS,IAAIE,EAAK,OAAO,OAAO,EAGpC,IAAMC,EAA2B,IAAI,IACrC,QAAWX,KAAWQ,EAAU,CAC9B,IAAMP,EAASF,EAASC,CAAO,EAC3BC,IAAW,QACbW,EAAMD,EAAUV,EAAQG,EAAYJ,CAAO,CAAC,CAEhD,CACA,OAAOW,CACT,CACA,SAASE,EAAaC,EAASC,EAAY,CACzC,IAAMC,EAAU,IAAI,IAAIF,EAAQ,IAAKG,GAAMlB,EAASkB,EAAE,OAAO,CAAC,CAAC,EACzD,CAAChB,CAAM,EAAIe,EACjB,GAAIA,EAAQ,OAAS,GAAKf,IAAW,OACnC,MAAO,CAAE,QAAAa,EAAS,SAAU,CAAC,EAAG,MAAO,EAAM,EAE/C,IAAMI,EAAM,IAAI,IAAIJ,EAAQ,IAAKG,GAAMb,EAAYa,EAAE,OAAO,CAAC,CAAC,EACxDE,EAAS,CAAC,GAAGJ,EAAW,IAAId,CAAM,GAAK,CAAC,CAAC,EAAE,MAAOmB,GAAMF,EAAI,IAAIE,CAAC,CAAC,EAClEC,EAAS,IAAI,IAAIP,EAAQ,IAAKG,GAAMZ,EAAeY,EAAE,OAAO,CAAC,CAAC,EAC9D,CAACK,CAAS,EAAID,EACpB,MAAO,CACL,QAAAP,EACA,SAAU,CACR,GAAGK,EAAS,CAAClB,CAAM,EAAI,CAAC,EACxB,GAAGoB,EAAO,OAAS,GAAKC,EAAY,CAACA,CAAS,EAAI,CAAC,CACrD,EACA,MAAO,EACT,CACF,CACA,SAASC,EAAchB,EAAO,CAC5B,IAAMiB,EAAwB,IAAI,IAClC,QAAWd,KAAQH,EAAM,MACvB,GAAIkB,EAAWf,CAAI,EAAG,CACpB,GAAM,CAAE,QAAAV,EAAS,MAAA0B,CAAM,EAAIhB,EAAK,OAC1BiB,EAAMD,EAAQhB,EAAK,OACnBkB,EAAOJ,EAAM,IAAIxB,CAAO,EAC1B4B,GACFA,EAAK,MAAQ,KAAK,IAAIA,EAAK,MAAOF,CAAK,EACvCE,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKD,CAAG,GAEjCH,EAAM,IAAIxB,EAAS,CACjB,QAAAA,EACA,OAAQ6B,EAAY7B,CAAO,EAC3B,MAAA0B,EACA,IAAAC,CACF,CAAC,CAEL,CAEF,IAAMb,EAAU,CAAC,GAAGU,EAAM,OAAO,CAAC,EAClC,OAAOV,EAAQ,OAASD,EAAaC,EAASR,EAAgBC,CAAK,CAAC,EAAI,MAC1E,CACA,SAASuB,GAAevB,EAAOwB,EAAQ,CACrC,IAAMC,EAAWT,EAAchB,CAAK,EAC9B0B,EAASF,EAASF,EAAYE,EAAO,OAAO,EAAIC,GAAU,QAAQ,SAAW,EAAIA,EAAS,QAAQ,CAAC,EAAE,OAAS,OAC9G/B,EAAS+B,GAAU,MAAQ9B,EAAY8B,EAAS,QAAQ,CAAC,EAAE,OAAO,EAAI,OAC5E,OAAOC,IAAWhC,EAAS,GAAGA,CAAM,IAAIgC,CAAM,GAAKA,EACrD,CACA,SAASC,EAAiBF,EAAUG,EAAY,CAC9C,IAAMC,EAAS,GAAM,CAAC,EAAE,KAAM,GAAG,EAAE,SAAW,CAAC,CAAC,EAC1CC,EAAUC,GAAYC,GAAMH,EAAMG,CAAC,EAAE,KAAMC,GAAMA,EAAE,YAAY,IAAMF,EAAO,YAAY,CAAC,EACzFG,EAAW,CAAC,GAAGT,GAAU,UAAY,CAAC,CAAC,EAAE,QAAQ,EACjD/B,EAAS+B,GAAU,SAAS,KAAMvB,GAAM,CAACA,EAAE,SAAS,GAAG,CAAC,GAAG,YAAY,EAC7E,QAAW6B,KAAUG,EAAU,CAC7B,IAAMC,EAAWP,EAAW,KAAKE,EAAOC,CAAM,CAAC,EAC/C,GAAII,EACF,OAAOA,CAEX,CACA,OAAOzC,IAAW,OAAS,OAASkC,EAAW,KAC5C,GAAMC,EAAM,CAAC,EAAE,KAAMI,GAAM3C,EAAgB2C,CAAC,GAAG,YAAY,IAAMvC,CAAM,CAC1E,CACF,CACA,SAAS0C,GAAapC,EAAOmC,EAAU,CACrC,IAAM3B,EAAaT,EAAgBC,CAAK,EACxC,OAAOA,EAAM,aAAa,KACvBqC,GAASV,EACRrB,EACE,CACE,CACE,QAAS+B,EAAK,KACd,OAAQf,EAAYe,EAAK,IAAI,EAC7B,MAAOA,EAAK,MACZ,IAAKA,EAAK,MAAQA,EAAK,MACzB,CACF,EACA7B,CACF,EACA,CAAC2B,CAAQ,CACX,CACF,CACF,CACA,SAASG,EAAYZ,EAAQ,CAC3B,IAAMa,EAAOb,EAAO,QAAQ,QAAS,EAAE,EACjCc,EAASD,EAAY,YAAY,KAAKA,CAAI,EAAI,CAAC,IAAK,IAAI,EAAI,CAACA,CAAI,EAAjD,CAAC,EACvB,MAAO,CAAC,GAAmB,IAAI,IAAI,CAACb,EAAQ,GAAGc,EAAM,QAASC,GAAM,CAACA,EAAG,MAAMA,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CACvF,CACA,SAASC,EAAezC,EAAU0C,EAAU,CAAC,EAAG,CAC9C,IAAMC,EAAQ,IAAI,IAAI3C,CAAQ,EACxB4C,EAAyB,IAAI,IACnC,QAAWpD,KAAWmD,EAAO,CAC3B,IAAMlB,EAASJ,EAAY7B,CAAO,EAC5BqD,EAAQH,EAAQjB,CAAM,EAC5B,QAAWqB,KAAwB,IAAI,IAAI,CACzC,GAAGT,EAAYZ,CAAM,EACrB,GAAGoB,EAAQ,CAACA,CAAK,EAAI,CAAC,CACxB,CAAC,EACCD,EAAO,IAAIE,EAAMF,EAAO,IAAIE,CAAI,EAAI,OAAStD,CAAO,CAExD,CACA,OAAQsD,GAASH,EAAM,IAAIG,CAAI,EAAIA,EAAOF,EAAO,IAAIE,CAAI,CAC3D,CACA,SAASC,GAAmBC,EAAUxB,EAAUkB,EAAS,CACvD,IAAMO,EAAOR,EACXjB,EAAS,QAAQ,IAAKf,GAAMA,EAAE,OAAO,EACrCiC,CACF,EACA,OAAOM,EAAS,QAASR,GAAM,CAC7B,IAAMhD,EAAUyD,EAAKT,EAAE,OAAO,EAC9B,OAAOhD,IAAY,OAAS,CAAC,EAAI,CAACA,IAAYgD,EAAE,QAAUA,EAAI,CAAE,GAAGA,EAAG,QAAAhD,CAAQ,CAAC,CACjF,CAAC,CACH,CCnJA,IAAI0D,EAAK,GACLC,EAAK,GACLC,EAAM,EACNC,EAAO,GACPC,EAAO,GACPC,EAAY,4BACZC,EAAkB,cAClBC,EAAUC,GAASA,EAAK,SAAS,IAAI,EAAIA,EAAK,MAAM,EAAG,EAAE,EAAIA,EACjE,SAASC,GAAc,CACrB,MAAO,CACL,MAAO,IAAIC,EAAO,IAAI,WAAW,KAAO,CAAC,EACzC,SAAU,IAAIA,EAAO,IAAI,WAAW,KAAO,CAAC,CAC9C,CACF,CACA,IAAIC,GAAe,KAAM,CACvB,aAAc,CACZ,KAAK,MAAQ,CAAC,EACd,KAAK,OAAyB,IAAI,IAGlC,KAAK,SAA2B,IAAI,GACtC,CACA,IAAIC,EAAM,CACR,OAAO,KAAK,OAAO,IAAIA,CAAI,CAC7B,CACA,IAAIA,EAAM,CACR,IAAMC,EAAI,KAAK,MAAM,OACrB,KAAK,OAAO,IAAID,EAAMC,CAAC,EACvB,KAAK,MAAM,KAAKD,CAAI,EACpB,IAAME,EAAI,CAACF,EACX,OAAI,OAAO,cAAcE,CAAC,GAAK,OAAOA,CAAC,IAAMF,GAC3C,KAAK,SAAS,IAAIE,EAAGD,CAAC,EAEjBA,CACT,CACA,GAAGD,EAAM,CACP,OAAO,KAAK,OAAO,IAAIA,CAAI,GAAK,KAAK,IAAIA,CAAI,CAC/C,CACA,SAASE,EAAG,CACV,OAAO,KAAK,SAAS,IAAIA,CAAC,CAC5B,CACF,EACA,SAASC,GAAYP,EAAM,CACzB,GAAM,CAAC,CAAEI,EAAMI,EAAW,IAAK,GAAGC,CAAI,EAAIT,EAAK,MAAM,GAAG,EACxD,GAAI,CAACI,GAAQ,QAAQ,KAAKI,CAAQ,EAChC,OAEF,IAAIE,EAASF,IAAa,IAAM,EAAIA,EAAS,OACzCG,EACAC,EACAC,EACJ,QAAWC,KAAOL,EAAM,CACtB,GAAI,CAACZ,EAAU,KAAKiB,CAAG,EACrB,OAEF,IAAMC,EAAQD,EAAI,MAAM,CAAC,EACnBE,EAAMF,EAAI,MAAM,EAAG,CAAC,EACtBE,IAAQ,KACVN,EAAS,CAACK,EACDC,IAAQ,KACjBL,EAAUI,EACDC,IAAQ,KACjBJ,EAAQ,CAACG,EAETF,EAAO,CAACE,CAEZ,CAEA,MAAO,CAAE,KAAAX,EAAM,OAAAM,EAAQ,OADRC,IAAY,QAAUC,IAAU,QAAUC,IAAS,OAAS,CAAE,QAAAF,EAAS,MAAAC,EAAO,KAAAC,CAAK,EAAI,MACxE,CAChC,CACA,SAASI,GAAajB,EAAMkB,EAAMC,EAAUC,EAAO,CACjD,IAAIC,EAAW,EACXT,EAAQ,GACRG,EAAQ,EACRO,EAAU,GACRC,EAAUC,GAAQ,CACtB,GAAIZ,GAAS,GAAKY,EAAMZ,EAAO,CAC7B,IAAMa,EAAOH,GAAWE,EAAMZ,EAAQ,KAAOY,EAAMZ,IAAU,GAAKZ,EAAK,WAAWY,CAAK,IAAMjB,GAAQwB,EAAS,SAASJ,CAAK,EAAI,OAChIK,EAAM,MAAM,KAAKK,GAAQN,EAAS,GAAGnB,EAAK,MAAMY,EAAOY,CAAG,CAAC,CAAC,EAC5DJ,EAAM,SAAS,KAAKC,CAAQ,CAC9B,CACF,EACIhB,EAAIa,EACR,KAAOb,EAAIL,EAAK,OAAQK,IAAK,CAC3B,IAAMqB,EAAK1B,EAAK,WAAWK,CAAC,EAC5B,GAAIqB,IAAOlC,GAAMkC,IAAOjC,EACtB8B,EAAOlB,CAAC,EACRgB,EAAWK,IAAOjC,EAAK,EAAI,EAC3BmB,EAAQP,EAAI,EACZU,EAAQ,EACRO,EAAU,OACL,IAAII,IAAOhC,EAChB,MACS4B,GAAWI,GAAM/B,GAAQ+B,GAAM9B,EACxCmB,EAAQA,EAAQ,GAAKW,EAAK/B,EAE1B2B,EAAU,GAEd,CACA,OAAAC,EAAOlB,CAAC,EACDA,CACT,CACA,SAASsB,GAAW3B,EAAM,CACxB,IAAM4B,EAAS,CAAC,EACZC,EAAK,EACT,KAAOD,EAAO,OAAS,GAAG,CACxB,IAAME,EAAM9B,EAAK,QAAQ,IAAK6B,CAAE,EAChC,GAAIC,IAAQ,GACV,OAEFF,EAAO,KAAK5B,EAAK,MAAM6B,EAAIC,CAAG,CAAC,EAC/BD,EAAKC,EAAM,CACb,CACA,GAAM,CAAC,CAAEC,EAAQC,EAAWC,EAAQrB,EAAOY,CAAG,EAAII,EAClD,OAAOG,GAAUC,GAAaC,GAAUrB,GAASY,GAAOK,EAAK7B,EAAK,OAAS,CAAE,OAAA+B,EAAQ,UAAAC,EAAW,OAAAC,EAAQ,MAAArB,EAAO,IAAAY,EAAK,KAAMK,CAAG,EAAI,MACnI,CACA,SAASK,GAAUC,EAAM,CACvB,IAAMC,EAAQD,EAAK,MAAM;AAAA,CAAI,EACvBhB,EAAW,IAAIhB,GACfkC,EAAU,CAAC,EACXC,EAAO,CAAC,EACRC,EAAS,CAAC,EACVC,EAAQ,CAAC,EACTC,EAAW,CAAC,EACZC,EAA2B,IAAI,IACrC,QAAWC,KAAOP,EAAO,CACvB,GAAItC,EAAgB,KAAK6C,CAAG,EAC1B,OAEF,GAAIA,EAAI,WAAW,IAAI,EAAG,CACxB,IAAMC,EAAIrC,GAAYR,EAAO4C,CAAG,CAAC,EACjC,GAAI,CAACC,GAAKzB,EAAS,IAAIyB,EAAE,IAAI,EAC3B,OAEFzB,EAAS,IAAIyB,EAAE,IAAI,EACnBP,EAAQ,KAAKO,EAAE,MAAM,EACrB,IAAIC,EAAM,GACND,EAAE,SACJC,EAAMH,EAAS,IAAIE,EAAE,OAAO,OAAO,GAAKH,EAAS,OAC7CI,IAAQJ,EAAS,SACnBA,EAAS,KAAKG,EAAE,OAAO,OAAO,EAC9BF,EAAS,IAAIE,EAAE,OAAO,QAASC,CAAG,IAGtCP,EAAK,KAAKO,CAAG,EACbN,EAAO,KAAKK,EAAE,QAAQ,OAAS,CAAC,EAChCJ,EAAM,KAAKI,EAAE,QAAQ,MAAQ,CAAC,CAChC,CACF,CACA,IAAM1B,EAAO,CAAC,EACR4B,EAAK,CAAC,EACNC,EAAU,CAAC,EACXC,EAAQ,CAAC,EACTC,EAAa,CAAC,EACdC,EAAW,CAAC,EACZC,EAAU,CAAC,CAAC,EACZ/B,EAAQnB,EAAY,EACpBmD,EAAS,IAAIC,EACbC,EAAQ,IAAID,EAClB,QAAWV,KAAOP,EAChB,GAAIO,EAAI,WAAW,IAAI,EAAG,CACxB,GAAM,CAAC,CAAEY,EAAQC,EAASC,EAAQC,CAAO,EAAI3D,EAAO4C,CAAG,EAAE,MAAM,GAAG,EAC9DY,GAAUE,GAAUC,IACtBxC,EAAK,KAAKC,EAAS,GAAGoC,CAAM,CAAC,EAC7BT,EAAG,KAAK3B,EAAS,GAAGsC,CAAM,CAAC,EAC3BV,EAAQ,MAAMS,IAAY,IAAM,EAAI,IAAME,IAAY,IAAM,EAAI,EAAE,EAEtE,SAAWf,EAAI,WAAW,IAAI,EAAG,CAC/B,IAAM3C,EAAOD,EAAO4C,CAAG,EACjBgB,EAAIhC,GAAW3B,CAAI,EACzB,GAAI2D,EAAG,CACLX,EAAM,KAAK,GAAGW,EAAE,MAAM,IAAIA,EAAE,SAAS,IAAIA,EAAE,MAAM,EAAE,EACnDV,EAAW,KAAKU,EAAE,QAAU,IAAM,EAAI,CAACA,EAAE,KAAK,EAC9CT,EAAS,KAAKS,EAAE,MAAQ,IAAM,GAAK,CAACA,EAAE,GAAG,EACzC,IAAMnC,EAAMP,GAAajB,EAAM2D,EAAE,KAAMxC,EAAUC,CAAK,EAChDX,EAAOmD,GAAS5D,EAAMwB,CAAG,EAU/B,GATIf,IAAS,SAGTA,EAAK,QACP2C,EAAO,KAAK3C,EAAK,MAAM,EAErBA,EAAK,OACP6C,EAAM,KAAK7C,EAAK,KAAK,EAEnBW,EAAM,MAAM,SAAW+B,EAAQ,GAAG,EAAE,GACtC,OAEFA,EAAQ,KAAK/B,EAAM,MAAM,MAAM,CACjC,CACF,CAEF,GAAI,EAACgC,EAAO,MAAM,OAAQE,EAAM,MAAM,MAAM,EAAE,KAC3ChD,GAAMA,EAAI,GAAKA,EAAI0C,EAAM,MAC5B,EAGA,MAAO,CACL,MAAO,CACL,MAAO7B,EAAS,MAChB,QAAS,WAAW,KAAKkB,CAAO,EAChC,KAAM,WAAW,KAAKC,CAAI,EAC1B,OAAQ,aAAa,KAAKC,CAAM,EAChC,MAAO,WAAW,KAAKC,CAAK,EAC5B,SAAAC,CACF,EACA,MAAO,CACL,KAAM,WAAW,KAAKvB,CAAI,EAC1B,GAAI,WAAW,KAAK4B,CAAE,EACtB,QAAS,WAAW,KAAKC,CAAO,CAClC,EACA,MAAO,CACL,MAAAC,EACA,OAAQ,aAAa,KAAKC,CAAU,EACpC,KAAM,aAAa,KAAKC,CAAQ,EAChC,QAAS,WAAW,KAAKC,CAAO,EAChC,MAAO/B,EAAM,MAAM,KAAK,MAAM,EAAGA,EAAM,MAAM,MAAM,EACnD,SAAUA,EAAM,SAAS,KAAK,MAAM,EAAGA,EAAM,SAAS,MAAM,EAC5D,GAAGyC,GAAYb,EAAM,OAAQI,EAAQE,CAAK,CAC5C,CACF,CACF,CACA,SAASM,GAAS5D,EAAMkB,EAAM,CAC5B,IAAM4C,EAAM,CAAC,EACb,QAAWhD,KAAOI,EAAOlB,EAAK,OAASA,EAAK,MAAMkB,EAAO,CAAC,EAAE,MAAM,GAAG,EAAI,CAAC,EAAG,CAC3E,IAAMH,EAAQD,EAAI,MAAM,CAAC,EACzB,GAAIA,EAAI,WAAW,GAAGiD,CAAc,KAAK,GAEvC,GADAD,EAAI,OAASE,EAAajD,CAAK,EAC3B,CAAC+C,EAAI,OACP,eAEOhD,EAAI,WAAW,GAAGmD,CAAY,KAAK,IAC5CH,EAAI,MAAQE,EAAajD,CAAK,EAC1B,CAAC+C,EAAI,OACP,MAGN,CACA,OAAOA,CACT,CACA,SAASD,GAAYK,EAAOd,EAAQE,EAAO,CACzC,MAAO,CACL,GAAGF,EAAO,MAAM,SAAWc,GAASA,EAAQ,EAAI,CAAE,OAAQd,EAAO,MAAM,CAAE,EAAI,CAAC,EAC9E,GAAGE,EAAM,MAAM,SAAWY,GAASA,EAAQ,EAAI,CAAE,MAAOZ,EAAM,MAAM,CAAE,EAAI,CAAC,CAC7E,CACF,CC/PA,IAAIa,GAAO,kBACX,SAASC,GAAaC,EAAQ,CAC5B,GAAI,CAACA,EAAO,WAAW,GAAG,GAAK,CAACA,EAAO,WAAW,GAAG,EACnD,OAEF,IAAMC,EAAQ,CAAC,EACf,OAAW,CAAC,CAAEC,EAAOC,CAAI,IAAKH,EAAO,SAASF,EAAI,EAChDG,EAAM,KAAK,CAAE,KAAAE,EAAM,OAAQD,IAAU,IAAM,IAAM,GAAI,CAAC,EAExD,OAAOD,CACT,CACA,SAASG,GAAaC,EAAM,CAC1B,IAAMC,EAAOD,EAAK,QAAQ,EACpBE,EAAUD,EAAK,MAAM,GAAG,EAC9B,GAAIC,EAAQ,OAAS,IAAMD,EAAK,WAAW,GAAG,EAC5C,OAEF,IAAME,EAAOT,GAAaQ,EAAQ,CAAC,CAAC,EACpC,GAAI,CAACC,EACH,OAEF,IAAIC,EACAC,EAAY,GAChB,QAASC,EAAI,GAAIA,EAAIJ,EAAQ,OAAQI,IAAK,CACxC,IAAMC,EAAML,EAAQI,CAAC,EACjBC,EAAI,WAAW,OAAO,EACxBH,EAAKG,EAAI,MAAM,CAAC,EACPA,IAAQ,WACjBF,EAAY,GAEhB,CACA,MAAO,CACL,KAAMH,EAAQ,CAAC,EACf,YAAa,CAACA,EAAQ,CAAC,EACvB,WAAY,CAACA,EAAQ,CAAC,EACtB,SAAU,CAACA,EAAQ,CAAC,EACpB,OAAQA,EAAQ,CAAC,IAAM,IAAM,IAAM,IACnC,KAAAC,EACA,WAAY,CAACD,EAAQ,CAAC,EACtB,UAAW,CAACA,EAAQ,CAAC,EACrB,QAAS,CAACA,EAAQ,CAAC,EACnB,QAAS,CAACA,EAAQ,CAAC,EACnB,YAAa,CAACA,EAAQ,EAAE,EACxB,eAAgB,CAACA,EAAQ,EAAE,EAC3B,UAAAG,EACA,GAAGD,IAAO,OAAS,CAAC,EAAI,CAAE,GAAAA,CAAG,CAC/B,CACF,CACA,SAASI,GAASR,EAAM,CACtB,IAAMS,EAAU,CAAC,EACjB,QAAWR,KAAQD,EAAK,MAAM;AAAA,CAAI,EAAG,CACnC,IAAMU,EAASX,GAAaE,CAAI,EAC5BS,GACFD,EAAQ,KAAKC,CAAM,CAEvB,CACA,OAAOD,CACT,CACA,IAAIE,GAAQ,8FACZ,SAASC,GAAQR,EAAI,CACnB,IAAMS,EAAM,CAAC,EACb,QAAWC,KAAKV,EAAG,SAASO,EAAK,EAC3BG,EAAE,CAAC,IAAM,OACXD,EAAI,KAAK,CAAE,GAAI,QAAS,OAAQ,CAACC,EAAE,CAAC,CAAE,CAAC,EAC9BA,EAAE,CAAC,IAAM,OAClBD,EAAI,KAAK,CAAE,GAAI,QAAS,OAAQC,EAAE,CAAC,EAAE,MAAO,CAAC,EACpCA,EAAE,CAAC,IAAM,OAClBD,EAAI,KAAK,CAAE,GAAI,eAAgB,IAAKC,EAAE,CAAC,EAAE,YAAY,CAAE,CAAC,EAC/CA,EAAE,CAAC,IAAM,OAClBD,EAAI,KAAK,CAAE,GAAI,YAAa,IAAKC,EAAE,CAAC,EAAE,YAAY,CAAE,CAAC,EAC5CA,EAAE,CAAC,IAAM,OAClBD,EAAI,KAAK,CAAE,GAAI,WAAY,OAAQC,EAAE,CAAC,EAAE,MAAO,CAAC,EACvCA,EAAE,CAAC,IAAM,QAClBD,EAAI,KAAK,CAAE,GAAI,QAAS,OAAQ,CAACC,EAAE,CAAC,CAAE,CAAC,EAG3C,OAAOD,CACT",
   "names": ["WELL_KNOWN_SAMPLES", "wellKnownSample", "assemblyName", "sampleOf", "refName", "sample", "panSNSample", "isGenericSample", "haplotypeOf", "panSNHaplotype", "graphHaplotypes", "graph", "refNames", "p", "node", "bySample", "addTo", "backboneFrom", "contigs", "haplotypes", "samples", "c", "own", "unique", "h", "shared", "haplotype", "graphBackbone", "spans", "isBackbone", "start", "end", "span", "panSNContig", "referenceLabel", "region", "backbone", "contig", "backboneAssembly", "assemblies", "names", "naming", "prefix", "a", "n", "prefixes", "assembly", "assemblyWalk", "walk", "contigNames", "bare", "forms", "f", "refNameBinding", "aliases", "exact", "byName", "alias", "name", "featuresOnBackbone", "features", "bind", "GT", "LT", "TAB", "ZERO", "NINE", "TABLE_TAG", "UNTABLED_RECORD", "trimCR", "line", "stepColumns", "Column", "SegmentIndex", "name", "i", "n", "readSegment", "sequence", "tags", "length", "refName", "start", "rank", "tag", "value", "key", "readWalkBody", "from", "segments", "steps", "reversed", "decimal", "finish", "end", "node", "ch", "walkFields", "fields", "at", "tab", "sample", "haplotype", "contig", "gfaTables", "text", "lines", "lengths", "refs", "starts", "ranks", "refNames", "refIndex", "raw", "s", "ref", "to", "strands", "names", "walkStarts", "walkEnds", "offsets", "before", "StopColumns", "after", "source", "strand1", "target", "strand2", "w", "walkTags", "stopColumns", "out", "START_STOP_TAG", "parseStopTag", "END_STOP_TAG", "walks", "STEP", "parseGafPath", "column", "steps", "arrow", "name", "parseGafLine", "text", "line", "columns", "path", "cs", "secondary", "i", "tag", "parseGaf", "records", "record", "CS_OP", "parseCs", "ops", "m"]

package/dist/chunks/{chunk-LD6RX4AZ.js → chunk-6NR64IXK.js}

@@ -1,2 +1,2 @@
 var tt;function ut(){return tt??(tt=import("./bandage-layout-UZEOCKMS.js").then(o=>o.default()).catch(o=>{throw tt=void 0,o})),tt}async function dt(o){return(await ut()).computeLayout(o.graph,o.options)}var Bt="\0deletion:";var kt=25*Math.PI/180,Pt=.25,St=150,nn=[0,-.35,.35,-.7,.7,-1.05,1.05,-1.4,1.4],pt=[0,1];function _t(o){return o?0:1}function lt(o,t){let n=t.x-o.x,e=t.y-o.y,s=Math.hypot(n,e)||1;return{x:n/s,y:e/s}}function gt(o,t,n){return{x:o.x+(t.x-o.x)*n,y:o.y+(t.y-o.y)*n}}function Dt(o){let t=0,n=0;for(let e of o)t+=e.x,n+=e.y;return{x:t/o.length,y:n/o.length}}function Gt(o){let t=new Float64Array(o.length);for(let n=1;n<o.length;n++)t[n]=t[n-1]+Math.hypot(o[n].x-o[n-1].x,o[n].y-o[n-1].y);return t}function Ut(o){var t;return(t=Gt(o)[o.length-1])!==null&&t!==void 0?t:0}var at=new Map;function en(o){let t=at.get(o);if(t!==void 0)return t;let n=on(o);return at.size>1e4&&at.clear(),at.set(o,n),n}function on(o){let t=1e-6,n=2*Math.PI-1e-6;for(let e=0;e<60;e++){let s=(t+n)/2;s/(2*Math.sin(s/2))<o?t=s:n=s}return(t+n)/2}function sn(o,t){if(o<1e-9)return Math.PI*t;let n=(o*o/4+t*t)/(2*t),e=2*Math.asin(Math.min(1,o/(2*n)));return n*(t>n?2*Math.PI-e:e)}function mt(o,t,n,e){let s=t-2*n,i=o<1e-9?2*Math.PI:en(s/o),r=s/i,l=Math.cos(i/2),d=o/2,c=e+n-r*l;return{at:a=>{if(a<=n)return{u:0,v:e+a};if(a>=t-n)return{u:o,v:e+t-a};let h=(a-n)/r-i/2;return{u:d+r*Math.sin(h),v:c+r*Math.cos(h)}},apex:e+n+r*(1-l),length:t}}function It(o,t,n){if(!n)return o;let e=Math.cos(n),s=Math.sin(n);return{...o,at:i=>{let{u:r,v:l}=o.at(i),d=r-t/2;return{u:t/2+d*e-l*s,v:d*s+l*e}}}}function rn(o){for(let t=0;t<=32;t++)if(o.at(o.length*t/32).v<-1e-6)return!0;return!1}function Ot(o,t,n,e,s){return{at:i=>({u:o+n*i,v:t+e*i}),apex:t+Math.max(0,e)*s,length:s}}var ot=class{constructor(t,n,e=!1){var s;this.pts=t,this.normals=n,this.straight=e,this.arc=Gt(t),this.total=(s=this.arc[t.length-1])!==null&&s!==void 0?s:0}segment(t){let{arc:n}=this,e=1,s=n.length-1;for(;e<s;){let i=e+s>>1;n[i]<t?e=i+1:s=i}return e}fraction(t,n){let e=this.arc[t]-this.arc[t-1];return e>0?(n-this.arc[t-1])/e:0}pointAt(t){let{pts:n}=this,e=n.length-1;if(e===0)return{...n[0]};if(t<=0){let i=lt(n[0],n[1]);return{x:n[0].x+i.x*t,y:n[0].y+i.y*t}}if(t>=this.total){let i=lt(n[e-1],n[e]),r=t-this.total;return{x:n[e].x+i.x*r,y:n[e].y+i.y*r}}let s=this.segment(t);return gt(n[s-1],n[s],this.fraction(s,t))}normalAt(t){let{normals:n}=this;if(n.length===1||t<=0)return n[0];if(t>=this.total)return n[n.length-1];let e=this.segment(t),{x:s,y:i}=gt(n[e-1],n[e],this.fraction(e,t)),r=Math.hypot(s,i)||1;return{x:s/r,y:i/r}}};function an(o,t){let n=Dt(o);return o.map((e,s)=>{let i=lt(o[Math.max(0,s-1)],o[Math.min(o.length-1,s+1)]),r={x:-i.y,y:i.x},l=e.x-n.x,d=e.y-n.y,c=Math.hypot(l,d),a=r.x*l+r.y*d,h=t[s],f=c>1e-9&&Math.abs(a)>.3*c?Math.sign(a):Math.sign(r.x*h.x+r.y*h.y)||1;return{x:r.x*f,y:r.y*f}})}function xt(o,t,n,e,s){let i=Math.min(s,Math.max(e.length/24,.5)),r=[],l=[];for(let d=0;d<=e.length+1e-9;d+=i){let{u:c,v:a}=e.at(Math.min(d,e.length)),h=o.pointAt(t+c),f=o.normalAt(t+c),u=f.x*n,g=f.y*n;r.push({x:h.x+u*a,y:h.y+g*a}),l.push({x:u,y:g})}return{pts:r,refs:l}}var Ft=5,cn=10.5/2;function yt(o,t,n,e,s,i){let r=s,l=xt(o,t,n,e(r),i);if(o.straight)return l;for(let d=0;d<6;d++){let c=Ut(l.pts);if(!(c>0)||Math.abs(c/s-1)<.001)break;r*=s/c,l=xt(o,t,n,e(r),i)}return l}function ct(o,t){return Array.from({length:t},(n,e)=>o+e*15/2)}function Tt(o){if(o.length===0)return 1/0;let t=1/0,n=-1/0;for(let e of o)t=Math.min(t,e.point.x),n=Math.max(n,e.point.x);return n-t}function Rt(o,t){return o*73856093^t*19349663}var ht=class{constructor(t){this.c=t,this.grid=new Map;let{ids:n,first:e,count:s,per:i,seedX:r,seedY:l,backbone:d}=t,c=n.length;this.points=Array.from({length:c},()=>{}),this.params=Array.from({length:c},()=>{}),this.curves=Array.from({length:c},()=>{}),this.links=t.links.map((f,u)=>f.map(g=>g.filter(([M])=>M!==u))),this.route=n.map(f=>f.startsWith(Bt));let a=1/0,h=-1/0;for(let f=0;f<c;f++){let u=e[f];!d[u]||Number.isNaN(r[u])||(a=Math.min(a,r[u]),h=Math.max(h,r[u]+i[f]*(s[f]-1)))}this.backbone=new ot([{x:a,y:0},{x:h,y:0}],[{x:0,y:1},{x:0,y:1}],!0),this.backboneCentroid={x:(a+h)/2,y:0};for(let f=0;f<c;f++){let u=e[f];if(!d[u]||Number.isNaN(r[u]))continue;let g=[],M=[];for(let b=0;b<s[f];b++){let U=r[u]+b*i[f];g.push({x:U,y:l[u]}),M.push(U-a)}this.points[f]=g,this.params[f]=M,this.curves[f]=this.backbone,this.occupy(g,this.backbone)}}static hasBackbone(t){for(let n=0;n<t.ids.length;n++){let e=t.first[n];if(t.backbone[e]&&!Number.isNaN(t.seedX[e]))return!0}return!1}run(){let t=[];for(let e=0;e<this.points.length;e++)this.points[e]||t.push(e);let n=this.componentsOf(t).map(e=>({members:e,anchors:this.anchorsOf(e)})).filter(e=>e.anchors.length).map(e=>({members:e.members,span:Tt(e.anchors),drawn:e.members.reduce((s,i)=>s+this.drawn(i),0),feet:e.anchors.map(s=>`${s.point.x},${s.point.y}`).sort().join(" ")})).sort((e,s)=>e.span-s.span||(e.feet===s.feet?s.drawn-e.drawn:e.drawn-s.drawn));for(let e of n)this.placePiece(e.members,this.backboneCentroid)}write(t,n){let{first:e}=this.c;this.points.forEach((s,i)=>{s?.forEach((r,l)=>{t[e[i]+l]=r.x,n[e[i]+l]=r.y})})}drawn(t){return this.c.per[t]*(this.c.count[t]-1)}endIndex(t,n){return n?this.c.count[t]-1:0}occupy(t,n){for(let e of t){let s=Rt(Math.floor(e.x/10.5),Math.floor(e.y/10.5)),i=this.grid.get(s),r={x:e.x,y:e.y,curve:n};i?i.push(r):this.grid.set(s,[r])}}violations(t,n,e,s){var i;let r=0;for(let l of t){if(e.some(a=>Math.hypot(l.x-a.x,l.y-a.y)<15))continue;let d=Math.floor(l.x/10.5),c=Math.floor(l.y/10.5);for(let a=d-1;a<=d+1;a++)for(let h=c-1;h<=c+1;h++)for(let f of(i=this.grid.get(Rt(a,h)))!==null&&i!==void 0?i:[])if(f.curve!==n&&Math.hypot(l.x-f.x,l.y-f.y)<10.5&&(r++,r>=s))return r}return r}choose(t,n,e){let s,i=1/0;for(let r of t){let l=this.violations(r(cn).pts,n,e,i);if(l===0)return r(Ft);l<i&&(i=l,s=r)}return s(Ft)}anchorsOf(t){let n=new Set(t),e=[];for(let s of t)for(let i of pt)for(let[r,l]of this.links[s][i]){let d=this.points[r];if(n.has(r)||!d)continue;let c=this.endIndex(r,l);e.push({u:s,uSide:i,v:r,vSide:l,point:d[c],curve:this.curves[r],t:this.params[r][c]})}return e}componentsOf(t){let n=new Set(t),e=new Set,s=[];for(let i of t){if(e.has(i))continue;let r=[i];e.add(i);for(let l of r)for(let d of pt)for(let[c]of this.links[l][d])n.has(c)&&!e.has(c)&&(e.add(c),r.push(c));s.push(r)}return s}spinePath(t,n,e,s,i){let r=new Set(t),l=(u,g)=>u*2+g,d=(u,g)=>u===s&&_t(g)===i,c=new Map([[l(n,e),-1]]),a=[[n,e]],h=[n,e];for(let[u,g]of a){if(h=[u,g],s!==void 0&&d(u,g))break;for(let[M,b]of this.links[u][_t(g)])!r.has(M)||c.has(l(M,b))||(c.set(l(M,b),l(u,g)),a.push([M,b]))}if(s!==void 0&&!d(h[0],h[1]))return;let f=[];for(let u=l(h[0],h[1]);u!==-1;u=c.get(u))f.push({k:u>>1,enter:u&1});return f.reverse()}loosePath(t,n,e){let s=new Set(t),i=new Map([[n,-1]]),r=new Map([[n,0]]),l=[n];for(let c of l){if(c===e)break;for(let a of pt)for(let[h,f]of this.links[c][a])!s.has(h)||i.has(h)||(i.set(h,c),r.set(h,f),l.push(h))}let d=[];for(let c=e;c!==-1;c=i.get(c))d.push({k:c,enter:r.get(c)});return d.reverse()}spineLength(t){let{link:n}=this.c;return t.reduce((e,{k:s})=>e+this.drawn(s)+n,n)}layAlong(t,n,e,s){let{count:i,per:r,link:l}=this.c,d=e,c=[];for(let{k:a,enter:h}of t){let f=s??r[a],u=[],g=[];for(let M=0;M<i[a];M++)u.push(n.pointAt(d+M*f)),g.push(d+M*f);h===1&&(u.reverse(),g.reverse()),this.points[a]=u,this.params[a]=g,this.curves[a]=n,c.push(...u),d+=f*(i[a]-1)+l}return c}arcCandidates(t,n,e,s,i){let r=(i-s)/2-1e-6,l=i>2*s?nn:[0],d=[];for(let c of ct(0,8))for(let a of l)for(let h=0;h<=16;h++){let f=r*h/16,u=It(mt(s,i,f,c),s,a);h<16&&u.apex<12||rn(u)||d.push(g=>yt(t,n,e,M=>It(mt(s,M,Math.min(f,(M-s)/2-1e-6),c),s,a),i,g))}return d}placePiece(t,n){var e;let{count:s,link:i}=this.c,r=this.anchorsOf(t);if(r.length===0)return;let l=t.every(x=>this.route[x]),d=r.every(x=>x.curve===r[0].curve)?r[0].curve:void 0,c,a,h,f;if(d)r.sort((x,T)=>x.t-T.t),c=d,a=r[0].t,h=r[r.length-1].t,f=c===this.backbone&&l?-1:1;else{r.sort((q,Q)=>q.point.x-Q.point.x||q.point.y-Q.point.y);let x=r[0].point,T=r[r.length-1].point,W=Math.hypot(T.x-x.x,T.y-x.y),B=W>1e-9?lt(x,T):{x:1,y:0},D={x:-B.y,y:B.x},H=gt(x,T,.5);f=r.some(q=>q.curve===this.backbone)?(l?-1:1)*(Math.sign(D.y)||1):(H.x-n.x)*D.x+(H.y-n.y)*D.y>=0?1:-1,c=new ot([x,T],[D,D],!0),a=0,h=W}let u=r[0],g=r[r.length-1],M=h-a,b=r.length===1||u.u===g.u&&u.uSide===g.uSide&&M<1e-9,U=[u.point,g.point],v=x=>this.choose(x,d,U),N,y,L=i,w;if(b){N=this.spinePath(t,u.u,u.uSide);let x=this.spineLength(N),T=u.vSide?Math.max(0,s[u.v]-2):Math.min(1,s[u.v]-1),B=(u.t>=this.params[u.v][T]?1:-1)*Math.cos(kt),D=Math.sin(kt);y=v(ct(0,12).map(H=>q=>yt(c,a,f,Q=>Ot(0,H,B,D,Q),x,q)))}else{N=(e=this.spinePath(t,u.u,u.uSide,g.u,g.uSide))!==null&&e!==void 0?e:this.loosePath(t,u.u,g.u);let x=this.spineLength(N);if(l){let T=Math.max(12,Math.min(Pt*M,St));y=v(ct(T,12).map(B=>D=>xt(c,a,f,mt(M,sn(M,B),0,0),D)));let W=Ut(y.pts);w=Math.max(.001,(W-2*i)/(s[N[0].k]-1))}else if(x>M+1e-6)y=v(this.arcCandidates(c,a,f,M,x));else{let T=x-2*i,W=Math.max(12,Math.min(Pt*(M-T),St));y=v(ct(W,12).map(B=>D=>yt(c,a,f,H=>Ot(M/2-H/2,B,1,0,H),T,D))),L=0}}let E=new ot(y.pts,an(y.pts,y.refs)),O=this.layAlong(N,E,L,w);this.occupy(O,E);let _=Dt(O),R=t.filter(x=>!this.points[x]),F=this.componentsOf(R).map(x=>({members:x,span:Tt(this.anchorsOf(x))})).sort((x,T)=>x.span-T.span);for(let x of F)this.placePiece(x.members,_)}};function Mt(o){let t=new Float64Array(o.n).fill(NaN),n=new Float64Array(o.n).fill(NaN);if(ht.hasBackbone(o)){let e=new ht(o);e.run(),e.write(t,n)}return{X:t,Y:n}}var ln=[{walks:2,iterations:15},{walks:4,iterations:30},{walks:8,iterations:60},{walks:12,iterations:90},{walks:16,iterations:120}],hn=20,fn=3,wt=.3,un=2,dn=200,pn=.1,mn=.5,yn=o=>{var t;return((t=o.stable)===null||t===void 0?void 0:t.rank)===0};function Ht(o,t){let n=t.at(-1);return(o==="+"||o==="-")&&(n==="+"||n==="-")&&o!==n}function gn(o){let t=Math.imul(o,2654435761)>>>0||1;return()=>(t^=t<<13,t>>>=0,t^=t>>>17,t^=t<<5,t>>>=0,t/4294967296)}function z(o,t){return typeof o=="number"&&Number.isFinite(o)?o:t}function Nt(o,t){return Math.max(z(o.nodeLengthPerMegabase,1e3)*t/1e6,z(o.minimumNodeLength,1))}function Ct(o){let{nodes:t,edges:n}=o.graph,e=o.options,s=z(e.nodeSegmentLength,1),i=z(e.edgeLength,1),r=t.map(w=>w.id),l=new Int32Array(t.length),d=new Int32Array(t.length),c=new Float64Array(t.length),a=0;t.forEach((w,E)=>{let O=Nt(e,w.length),_=Math.max(1,Math.ceil(O/s));l[E]=a,d[E]=_+1,c[E]=O/_,a+=_+1});let h=new Int32Array(a),f=new Int32Array(a),u=new Float64Array(a).fill(NaN),g=new Float64Array(a).fill(NaN),M=new Uint8Array(a),b=Array.from({length:a},()=>[]);t.forEach((w,E)=>{let O=typeof w.x=="number"&&typeof w.y=="number",_=yn(w)?1:0;for(let R=0;R<d[E];R++){let F=l[E]+R;h[F]=E,f[F]=R,M[F]=_,O&&(u[F]=w.x+R*c[E],g[F]=w.y),R>0&&(b[F-1].push([F,c[E]]),b[F].push([F-1,c[E]]))}});let U=new Map(r.map((w,E)=>[w,E])),v=t.map(()=>[[],[]]);for(let w of n){let E=U.get(w.from),O=U.get(w.to);if(E===void 0||O===void 0||E===O&&d[E]<=2)continue;let _=Ht(w.fromStrand,w.from)?0:1,R=Ht(w.toStrand,w.to)?1:0,F=l[E]+(_?d[E]-1:0),x=l[O]+(R?d[O]-1:0);b[F].push([x,i]),b[x].push([F,i]),v[E][_].push([O,R]),v[O][R].push([E,_])}let N=new Int32Array(a+1);for(let w=0;w<a;w++)N[w+1]=N[w]+b[w].length;let y=new Int32Array(N[a]),L=new Float64Array(N[a]);for(let w=0;w<a;w++)b[w].forEach(([E,O],_)=>{y[N[w]+_]=E,L[N[w]+_]=O});return{ids:r,first:l,count:d,per:c,links:v,chainOf:h,indexOf:f,seedX:u,seedY:g,backbone:M,off:N,nb:y,wt:L,n:a,link:i}}function xn(o){let{n:t,off:n,nb:e}=o,s=new Int32Array(t).fill(-1),i=[];for(let r=0;r<t;r++){if(s[r]>=0)continue;let l=[r];s[r]=i.length;for(let d of l)for(let c=n[d];c<n[d+1];c++){let a=e[c];s[a]<0&&(s[a]=i.length,l.push(a))}i.push(l)}return{comp:s,members:i}}function At(o,t={}){var n,e,s;let i=Ct(o),{n:r,off:l,nb:d,wt:c,seedX:a,seedY:h,first:f,count:u,per:g,link:M}=i,b=o.options,U=ln[Math.max(0,Math.min(4,z((n=t.quality)!==null&&n!==void 0?n:b.quality,2)))],v=z((e=t.componentSeparation)!==null&&e!==void 0?e:b.componentSeparation,15),N=gn(z((s=t.seed)!==null&&s!==void 0?s:b.seed,1)),y=new Float64Array(r),L=new Float64Array(r),w={};if(r===0)return{nodePositions:w};let{comp:E,members:O}=xn(i),_=1/0,R=0;for(let p=0;p<d.length;p++)_=Math.min(_,c[p]),R+=c[p];R/=2;let F=!1;for(let p=0;p<r;p++)if(!Number.isNaN(a[p])){F=!0;break}let x=F?Mt(i):void 0,T=Math.sqrt(r)*20;for(let p=0;p<r;p++)x&&!Number.isNaN(x.X[p])?(y[p]=x.X[p],L[p]=x.Y[p]):F&&!Number.isNaN(a[p])?(y[p]=a[p]+N()-.5,L[p]=h[p]+N()-.5):(y[p]=N()*T,L[p]=N()*T);let W=O.map(p=>x!==void 0&&p.every(A=>!Number.isNaN(x.X[A]))),B=[],D=!0;for(let p=0;p<r;p++)W[E[p]]||(B.push(p),D&&(D=!Number.isNaN(a[p])));let H=Math.max(R/4,_*10),q=H*H,Q=pn*_*_,{walks:Jt,iterations:rt}=U,Qt=Math.log(q/Q)/Math.max(1,rt-1),bt=Math.log(_),Zt=Math.log(H),Lt=(p,A,m,k)=>{let S=k/(m*m);S>1&&(S=1);let P=y[p]-y[A],I=L[p]-L[A],V=Math.sqrt(P*P+I*I)||1e-9,G=S*(V-m)/(2*V),j=G*P,C=G*I;y[p]=y[p]-j,L[p]=L[p]-C,y[A]=y[A]+j,L[A]=L[A]+C},et=0,Yt=(p,A)=>{let m=i.chainOf[p],k=i.indexOf[p],S=N()<.5?-1:1,P=A;for(let I=0;I<dn;I++){let V=u[m],G=g[m],j=(S>0?V-1-k:k)*G;if(P<=j){let J=Math.round(P/G);return et=A-P+J*G,f[m]+k+S*J}P-=j;let C=i.links[m][S>0?1:0];if(C.length===0)return et=A-P,f[m]+(S>0?V-1:0);let[Y,$]=C[Math.floor(N()*C.length)];if(P-=M,m=Y,S=$===0?1:-1,k=$===0?0:u[Y]-1,P<=0)return et=A-P,f[m]+k}return-1},Et=(p,A)=>{for(let m=l[p];m<l[p+1];m++){let k=d[m];k>p&&Lt(p,k,c[m],A)}},Z=Int32Array.from(B),Xt=D?Math.floor(mn*rt):0;for(let p=B.length?Xt:rt;p<rt;p++){let A=q*Math.exp(-Qt*p);for(let m=Z.length-1;m>0;m--){let k=Math.floor(N()*(m+1)),S=Z[m];Z[m]=Z[k],Z[k]=S}for(let m of Z){Et(m,A);for(let k=0;k<Jt;k++){let S=Math.exp(bt+N()*(Zt-bt)),P=Yt(m,S);P>=0&&P!==m&&et>0&&Lt(m,P,et,A)}}}let K=fn*M,tn=(p,A)=>Math.floor(p/K)*73856093^Math.floor(A/K)*19349663;for(let p=0;p<(B.length?hn:0);p++){let A=new Map;for(let m of B){let k=tn(y[m],L[m]),S=A.get(k);S?S.push(m):A.set(k,[m])}for(let m of B){let k=Math.floor(y[m]/K),S=Math.floor(L[m]/K);for(let P=k-1;P<=k+1;P++)for(let I=S-1;I<=S+1;I++){let V=A.get(P*73856093^I*19349663);if(V)for(let G of V){if(G<=m)continue;let j=!1;for(let X=l[m];X<l[m+1];X++)if(d[X]===G){j=!0;break}if(j)continue;let C=y[m]-y[G],Y=L[m]-L[G],$=Math.sqrt(C*C+Y*Y);if($>=K)continue;let J,it;if($>1e-6){let X=wt*(K-$)/(2*$);J=X*C,it=X*Y}else J=wt*K*(N()-.5),it=wt*K*(N()-.5);y[m]=y[m]+J,L[m]=L[m]+it,y[G]=y[G]-J,L[G]=L[G]-it}}}for(let m of B)Et(m,1/0)}for(let p=0;p<u.length;p++){let A=f[p],m=u[p];if(!(m<3)){for(let k=0;k<un;k++){let S=y.slice(A,A+m),P=L.slice(A,A+m);for(let I=1;I+1<m;I++)y[A+I]=.5*S[I]+.25*(S[I-1]+S[I+1]),L[A+I]=.5*P[I]+.25*(P[I-1]+P[I+1])}Mn(y,L,A,m,g[p])}}Nn(E,O,y,L,F,v);for(let p=0;p<i.ids.length;p++){let A=[];for(let m=0;m<u[p];m++)A.push({x:y[f[p]+m],y:L[f[p]+m]});w[i.ids[p]]=A}return{nodePositions:w}}function Mn(o,t,n,e,s){wn(o,t,n,e,s*(e-1));let i=new Float64Array(e);for(let a=1;a<e;a++)i[a]=i[a-1]+Math.hypot(o[n+a]-o[n+a-1],t[n+a]-t[n+a-1]);if(!i[e-1])return;let r=i[e-1],l=o.slice(n,n+e),d=t.slice(n,n+e),c=1;for(let a=1;a+1<e;a++){let h=r*a/(e-1);for(;c<e-1&&i[c]<h;)c++;let f=i[c]-i[c-1],u=f>0?(h-i[c-1])/f:0;o[n+a]=l[c-1]+(l[c]-l[c-1])*u,t[n+a]=d[c-1]+(d[c]-d[c-1])*u}}function wn(o,t,n,e,s){let i=n+e-1,r=o[n],l=t[n],d=Math.hypot(o[i]-r,t[i]-l),c=d>1e-9?(o[i]-r)/d:1,a=d>1e-9?(t[i]-l)/d:0,h=new Float64Array(e),f=new Float64Array(e),u=!0;for(let v=0;v<e;v++){let N=o[n+v]-r,y=t[n+v]-l;h[v]=N*c+y*a,f[v]=y*c-N*a,u&&(u=Math.abs(f[v])<1e-6)}let g=v=>{let N=0;for(let y=1;y<e;y++)N+=Math.hypot(h[y]-h[y-1],v*(f[y]-f[y-1]));return N};if(u||g(1)>=s)return;let M=1,b=2;for(;g(b)<s&&b<1e6;)M=b,b*=2;for(let v=0;v<40;v++){let N=(M+b)/2;g(N)<s?M=N:b=N}let U=(M+b)/2;for(let v=1;v+1<e;v++)o[n+v]=r+h[v]*c-U*f[v]*a,t[n+v]=l+h[v]*a+U*f[v]*c}function Nn(o,t,n,e,s,i){if(!s)for(let h of t)An(n,e,h);if(t.length<2)return;let r=new Float64Array(t.length).fill(1/0),l=new Float64Array(t.length).fill(1/0),d=new Float64Array(t.length).fill(-1/0);for(let h=0;h<n.length;h++){let f=o[h];r[f]=Math.min(r[f],n[h]),l[f]=Math.min(l[f],e[h]),d[f]=Math.max(d[f],e[h])}let c=new Float64Array(t.length),a=0;for(let h=0;h<t.length;h++)c[h]=a-l[h],a+=d[h]-l[h]+i;for(let h=0;h<n.length;h++){let f=o[h];n[h]=n[h]-r[f],e[h]=e[h]+c[f]}}function An(o,t,n){if(n.length<3)return;let e=0,s=0;for(let h of n)e+=o[h],s+=t[h];e/=n.length,s/=n.length;let i=0,r=0,l=0;for(let h of n){let f=o[h]-e,u=t[h]-s;i+=f*f,r+=u*u,l+=f*u}let d=-.5*Math.atan2(2*l,i-r),c=Math.cos(d),a=Math.sin(d);for(let h of n){let f=o[h]-e,u=t[h]-s;o[h]=e+c*f-a*u,t[h]=s+a*f+c*u}}var Wt=[{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."}],vn=Wt.map(o=>o.value);var bn=async o=>{let t=performance.now();return{result:o.options.engine==="stress"?At(o):await dt(o),duration:performance.now()-t}};var st=40,Kt=500,ft=5;function Ln(o,t){return Math.max(o.nodeLengthPerMegabase*t/1e6,o.minimumNodeLength)}function Vt(o,t=ft){let e=o.nodes.reduce((i,r)=>i+r.length,0)/1e6,s=Math.max(o.nodes.length*st,Kt);return{nodeLengthPerMegabase:e>0?s/e:1e4,minimumNodeLength:Math.max(ft,t),edgeLength:5,nodeSegmentLength:20}}var nt={power:1,effect:1};function jt(o){return o.power===1&&o.effect===1}function zt(o,t){let n=o.nodes.length,e=o.nodes.reduce((r,l)=>r+l.length,0),s=n>0?e/n:0,i=n>0?Math.max(n*st,Kt)/n:st;return r=>{if(s<=0)return i;let l=(r/s)**t.power;return Math.max(i*((l-1)*t.effect+1),ft)}}var qt=1e3,$t={law:nt,minNodeLength:0};function Qn(o,t=$t){let{law:n,minNodeLength:e}=t,s=Vt(o,e);if(jt(n))return{nodes:o.nodes,opts:s};let i=zt(o,n);return{nodes:o.nodes.map(r=>({...r,length:Math.round(i(r.length)*qt)})),opts:{...s,nodeLengthPerMegabase:1e6/qt,minimumNodeLength:ft}}}function Zn(o,t=$t){if(jt(t.law)){let n=Vt(o,t.minNodeLength);return e=>Ln(n,e)}return zt(o,t.law)}var vt=[{value:"auto",label:"Proportional",description:"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.",law:nt,minNodeFactor:0},{value:"open",label:"Open bubbles",description:"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.",law:nt,minNodeFactor:2.5},{value:"wide",label:"Wide bubbles",description:"As open, spread further. Best on a window of a dozen bubbles.",law:nt,minNodeFactor:10},{value:"compress",label:"Compress lengths",description:"Pull the longest and shortest nodes towards the graph\u2019s mean, so a cut spanning kb and bp fits one pane.",law:{power:.5,effect:.5},minNodeFactor:0}],En=vt.map(o=>o.value);function kn(o){let t=vt.find(n=>n.value===o);return{law:t?.law??nt,minNodeLength:(t?.minNodeFactor??0)*st}}export{Bt as a,Wt as b,vn as c,bn as d,Ln as e,Qn as f,Zn as g,vt as h,En as i,kn as j};
-//# sourceMappingURL=chunk-LD6RX4AZ.js.map
+//# sourceMappingURL=chunk-6NR64IXK.js.map