jbrowse-plugin-graphgenomeviewer 7.5.0 → 7.6.0

package/dist/chunks/{GbzBaseSyntenyAdapter-4KVWVUN6.js → GbzBaseSyntenyAdapter-3PVPTKNW.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-HHMJNAA3.js";import{a as te}from"./chunk-UR2MJJUP.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 $,i as W,k as U}from"./chunk-HTTONSO4.js";import"./chunk-M2D7NUOY.js";import"./chunk-22ANI2KL.js";import{b as z,c as E}from"./chunk-POUV7OPY.js";import"./chunk-YBLNN5FU.js";import"./chunk-DEWZOJSC.js";import"./chunk-SPL3UO2D.js";import{C as V,a as K,c as L}from"./chunk-ZV5FNOHS.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{g as F,h as N,i as C}from"./chunk-FCMXEFJA.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import{d as G,g as X,h as Y,i as J}from"./chunk-IKJZPPOA.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as _,o as B}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-4KVWVUN6.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-4PHM6JNU.js";import{a as te}from"./chunk-3AC33AXB.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 $,i as W,k as U}from"./chunk-SI5VLKVN.js";import"./chunk-M2D7NUOY.js";import"./chunk-CNEUOM7X.js";import{b as z,c as E}from"./chunk-2CPD5NX2.js";import"./chunk-YBLNN5FU.js";import"./chunk-G4OPM6G7.js";import"./chunk-ZFJGNGIB.js";import{C as V,a as K,c as L}from"./chunk-XF6GU4GK.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{g as F,h as N,i as C}from"./chunk-TWPUVVYH.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import{d as G,g as X,h as Y,i as J}from"./chunk-IKJZPPOA.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as _,o as B}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-3PVPTKNW.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-4KVWVUN6.js.map → GbzBaseSyntenyAdapter-3PVPTKNW.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.11.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FNDNSDKW.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.14.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FNDNSDKW.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-ZKSC7QVE.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"],
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package/dist/chunks/{GraphGenomeView-KI4FQ5A7.js → GraphGenomeView-GQW4YC23.js}

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package/dist/chunks/{GraphTrackSettingsDialog-UQNMDXTE.js → GraphTrackSettingsDialog-ARWCWJW4.js}

@@ -1,4 +1,4 @@
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-//# sourceMappingURL=GraphTrackSettingsDialog-UQNMDXTE.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-ARWCWJW4.js.map

package/dist/chunks/{HighlightColorDialog-D4RCUCUF.js → HighlightColorDialog-PD3KMF2U.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=HighlightColorDialog-D4RCUCUF.js.map
+import{x as v,y as C}from"./chunk-SGP63UMC.js";import"./chunk-GRLNDNX4.js";import"./chunk-ZFJGNGIB.js";import"./chunk-TWPUVVYH.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-UGCNPRKC.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-PD3KMF2U.js.map

package/dist/chunks/{LinearGraphDisplay-RPZUZSM2.js → LinearGraphDisplay-QNS4EAL3.js}

@@ -1,2 +1,2 @@
-import{a as h}from"./chunk-42KD4AVY.js";import"./chunk-OZEKEYT3.js";import"./chunk-KOC23YNN.js";import"./chunk-DAPI7M4M.js";import"./chunk-Z3IKZAYC.js";import"./chunk-BCOXRUNQ.js";import"./chunk-VTMJQFN5.js";import"./chunk-XZGYJ3JC.js";import"./chunk-4NIWMRKH.js";import"./chunk-GYY6LF5L.js";import"./chunk-22ANI2KL.js";import"./chunk-POUV7OPY.js";import"./chunk-YBLNN5FU.js";import"./chunk-DEWZOJSC.js";import"./chunk-SPL3UO2D.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-FCMXEFJA.js";import"./chunk-IKJZPPOA.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as T}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as r,c as d,d as i}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var f=n&&n.__esModule?n.default:n;var l=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var v=l&&l.__esModule?l.default:l;var p=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=p&&p.__esModule?p.default:p;var c=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var L=c&&c.__esModule?c.default:c;var s=JBrowseExports["@jbrowse/display-ui"],u=e=>s!=null&&e in Object(s)?s[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var w=u("BottomRightCornerContext");var g=u("TrackOverlayPortal");var C=u("useChromeOverlayOverride");var U=s&&s.__esModule?s.default:s;var k={TooLarge:L,ErrorBar:v,Loading:O,BackgroundProgress:f},m="Zoom in to see features, or force load this track for the rest of the session (may be slow)",M="Force load this track for the rest of the session (may be slow)";function H(e){let{error:o}=e,t=o instanceof Error&&o.regionTooLarge===!0;return{error:{error:o,onRetry:t?void 0:()=>{e.reload()}},tooLarge:{message:[e.regionTooLargeReason,e.zoomCanReleaseGate?m:M].filter(Boolean).join(". "),onForceLoad:()=>{e.forceLoad()}},loading:{message:e.statusMessage,progress:e.statusProgress,canceled:e.fetchCanceled,onCancel:()=>{e.cancelFetchByUser()},onRetry:()=>{e.reload()}},background:{message:e.statusMessage,progress:e.statusProgress}}}var _=i(function({model:o,phase:t,drawn:x,testid:E,style:B,children:G,...S}){let{TooLarge:b,ErrorBar:P,Loading:A,BackgroundProgress:D}=C()??k,[R,I]=T(null),a=H(o),y={...S,"data-testid":E,"data-display-id":o.configuration.displayId,"data-display-drawn":x,"data-display-phase":t};return t==="tooLarge"?r("div",{style:{display:"contents"},...y,children:r(g,{children:r("div",{style:{pointerEvents:"auto"},children:r(b,{model:o,...a.tooLarge})})})}):d("div",{style:{position:"relative",height:o.height,...B},...y,children:[r(w,{value:R,children:G}),d(g,{children:[t==="error"&&o.error!==void 0?r(P,{model:o,visible:!0,...a.error}):null,r(A,{model:o,...a.loading,visible:t==="loading"||t==="canceled",immediate:!x}),r("div",{ref:I,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:t==="ready"&&o.statusMessage?r(D,{model:o,visible:!0,...a.background}):null})]})]})});var j=i(function({model:o}){return r(_,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:r(h,{model:o,ownChrome:!1})})}),so=j;export{so as default};
-//# sourceMappingURL=LinearGraphDisplay-RPZUZSM2.js.map
+import{a as h}from"./chunk-LGV6BTOY.js";import"./chunk-5LFPNQWH.js";import"./chunk-PTDOYJFH.js";import"./chunk-ZI7RFIA2.js";import"./chunk-JYYF3U2H.js";import"./chunk-KDXVLEHS.js";import"./chunk-SGP63UMC.js";import"./chunk-LJ7O3736.js";import"./chunk-GRLNDNX4.js";import"./chunk-DOC7QIE2.js";import"./chunk-CNEUOM7X.js";import"./chunk-2CPD5NX2.js";import"./chunk-YBLNN5FU.js";import"./chunk-G4OPM6G7.js";import"./chunk-ZFJGNGIB.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-TWPUVVYH.js";import"./chunk-IKJZPPOA.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as T}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as r,c as d,d as i}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var f=n&&n.__esModule?n.default:n;var l=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var v=l&&l.__esModule?l.default:l;var p=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=p&&p.__esModule?p.default:p;var c=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var L=c&&c.__esModule?c.default:c;var s=JBrowseExports["@jbrowse/display-ui"],u=e=>s!=null&&e in Object(s)?s[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var w=u("BottomRightCornerContext");var g=u("TrackOverlayPortal");var C=u("useChromeOverlayOverride");var U=s&&s.__esModule?s.default:s;var k={TooLarge:L,ErrorBar:v,Loading:O,BackgroundProgress:f},m="Zoom in to see features, or force load this track for the rest of the session (may be slow)",M="Force load this track for the rest of the session (may be slow)";function H(e){let{error:o}=e,t=o instanceof Error&&o.regionTooLarge===!0;return{error:{error:o,onRetry:t?void 0:()=>{e.reload()}},tooLarge:{message:[e.regionTooLargeReason,e.zoomCanReleaseGate?m:M].filter(Boolean).join(". "),onForceLoad:()=>{e.forceLoad()}},loading:{message:e.statusMessage,progress:e.statusProgress,canceled:e.fetchCanceled,onCancel:()=>{e.cancelFetchByUser()},onRetry:()=>{e.reload()}},background:{message:e.statusMessage,progress:e.statusProgress}}}var _=i(function({model:o,phase:t,drawn:x,testid:E,style:B,children:G,...S}){let{TooLarge:b,ErrorBar:P,Loading:A,BackgroundProgress:D}=C()??k,[R,I]=T(null),a=H(o),y={...S,"data-testid":E,"data-display-id":o.configuration.displayId,"data-display-drawn":x,"data-display-phase":t};return t==="tooLarge"?r("div",{style:{display:"contents"},...y,children:r(g,{children:r("div",{style:{pointerEvents:"auto"},children:r(b,{model:o,...a.tooLarge})})})}):d("div",{style:{position:"relative",height:o.height,...B},...y,children:[r(w,{value:R,children:G}),d(g,{children:[t==="error"&&o.error!==void 0?r(P,{model:o,visible:!0,...a.error}):null,r(A,{model:o,...a.loading,visible:t==="loading"||t==="canceled",immediate:!x}),r("div",{ref:I,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:t==="ready"&&o.statusMessage?r(D,{model:o,visible:!0,...a.background}):null})]})]})});var j=i(function({model:o}){return r(_,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:r(h,{model:o,ownChrome:!1})})}),so=j;export{so as default};
+//# sourceMappingURL=LinearGraphDisplay-QNS4EAL3.js.map

package/dist/chunks/{MinigraphBubbleAdapter-TJYI7KEN.js → MinigraphBubbleAdapter-L6JSQIOL.js}

@@ -1,2 +1,2 @@
-import{a as f,d as c,f as d}from"./chunk-GYY6LF5L.js";import{a as g}from"./chunk-KOB7YIMR.js";import{C as p,D as u,b,x as m}from"./chunk-ZV5FNOHS.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-FCMXEFJA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
-//# sourceMappingURL=MinigraphBubbleAdapter-TJYI7KEN.js.map
+import{a as f,d as c,f as d}from"./chunk-DOC7QIE2.js";import{a as g}from"./chunk-KOB7YIMR.js";import{C as p,D as u,b,x as m}from"./chunk-XF6GU4GK.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-TWPUVVYH.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-L6JSQIOL.js.map

package/dist/chunks/{RgfaTabixAdapter-5ZMJLFZP.js → RgfaTabixAdapter-5HCAJ7QI.js}

@@ -1,2 +1,2 @@
-import{a as N}from"./chunk-LTNFVL2F.js";import"./chunk-UR2MJJUP.js";import{a as x}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-DEWZOJSC.js";import"./chunk-SPL3UO2D.js";import{C as m,D as w,b as c,u as g,v as u,w as h,x as k}from"./chunk-ZV5FNOHS.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-FCMXEFJA.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as l}from"./chunk-TENPGIPX.js";var f=class extends c{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let a=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),i=e.length===0&&d(n)?new N(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:s,walks:i,refNames:new w(i?.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,a={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,a,s&&((i,{start:t,end:r})=>s.reader.queryStart(t,{...a,refName:i,end:r})))}async hasDataForRefName(){return!0}getFeatures(e,a={}){return x(async s=>{let n=await this.fine.refNames.resolveMapped(e,a);if(n!==void 0){let{walks:i}=this.fine,t=r=>{s.next(r)};await(i?this.walkFeatures(i,n,e,a,t):this.segmentFeatures(n,e,a,t))}s.complete()},a.signal)}async walkFeatures(e,a,s,n,i){let t=await l("Downloading walks",n.statusCallback,()=>e.referenceNodes(a,s,n));for(let r of t){let o=String(r.id);i(new p({uniqueId:o,refName:s.refName,start:r.start,end:r.end,name:o,type:"segment",rank:0,stableName:r.refName}))}}async segmentFeatures(e,a,s,n){await l("Downloading segments",s.statusCallback,()=>k(this.fine.segments,e,a.start,a.end,{signal:s.signal,lineCallback:i=>{let{segment:t,anchored:r}=g(i);if(r&&t.refName!==e)return;let o=u(t);n(new p({uniqueId:t.id,refName:a.refName,start:t.start,end:t.end,name:t.id,type:"segment",rank:t.rank,stableName:t.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,a={}){let{hops:s,signal:n,tier:i}=a,t=this.index(i),r=await t.refNames.resolveForCut(e,{signal:n});return t.walks?t.walks.subgraph(r,e,a):h(t,{refName:r,start:e.start,end:e.end},{hops:s,signal:n})}};export{f as default};
-//# sourceMappingURL=RgfaTabixAdapter-5ZMJLFZP.js.map
+import{a as N}from"./chunk-OQHN2GWX.js";import"./chunk-3AC33AXB.js";import{a as x}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-G4OPM6G7.js";import"./chunk-ZFJGNGIB.js";import{C as m,D as w,b as c,u as g,v as u,w as h,x as k}from"./chunk-XF6GU4GK.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-TWPUVVYH.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as l}from"./chunk-TENPGIPX.js";var f=class extends c{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let a=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),i=e.length===0&&d(n)?new N(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:s,walks:i,refNames:new w(i?.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,a={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,a,s&&((i,{start:t,end:r})=>s.reader.queryStart(t,{...a,refName:i,end:r})))}async hasDataForRefName(){return!0}getFeatures(e,a={}){return x(async s=>{let n=await this.fine.refNames.resolveMapped(e,a);if(n!==void 0){let{walks:i}=this.fine,t=r=>{s.next(r)};await(i?this.walkFeatures(i,n,e,a,t):this.segmentFeatures(n,e,a,t))}s.complete()},a.signal)}async walkFeatures(e,a,s,n,i){let t=await l("Downloading walks",n.statusCallback,()=>e.referenceNodes(a,s,n));for(let r of t){let o=String(r.id);i(new p({uniqueId:o,refName:s.refName,start:r.start,end:r.end,name:o,type:"segment",rank:0,stableName:r.refName}))}}async segmentFeatures(e,a,s,n){await l("Downloading segments",s.statusCallback,()=>k(this.fine.segments,e,a.start,a.end,{signal:s.signal,lineCallback:i=>{let{segment:t,anchored:r}=g(i);if(r&&t.refName!==e)return;let o=u(t);n(new p({uniqueId:t.id,refName:a.refName,start:t.start,end:t.end,name:t.id,type:"segment",rank:t.rank,stableName:t.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,a={}){let{hops:s,signal:n,tier:i}=a,t=this.index(i),r=await t.refNames.resolveForCut(e,{signal:n});return t.walks?t.walks.subgraph(r,e,a):h(t,{refName:r,start:e.start,end:e.end},{hops:s,signal:n})}};export{f as default};
+//# sourceMappingURL=RgfaTabixAdapter-5HCAJ7QI.js.map

package/dist/chunks/{WalkFormsAdapter-CAJOWOEX.js → WalkFormsAdapter-NX36GP35.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-K4JL57NR.js";import{a as k}from"./chunk-KOB7YIMR.js";import{C as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-ZV5FNOHS.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-FCMXEFJA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as m,o as u}from"./chunk-TENPGIPX.js";var v=r=>`${(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-CAJOWOEX.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-XSDGE4RF.js";import{a as k}from"./chunk-KOB7YIMR.js";import{C as $,b as l,d as g,e as w,f as h,g as p,k as y,o as B,s as F,t as S}from"./chunk-XF6GU4GK.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-TWPUVVYH.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as m,o as u}from"./chunk-TENPGIPX.js";var v=r=>`${(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-NX36GP35.js.map

package/dist/chunks/{WalkTabixSyntenyAdapter-VI3KA2GX.js → WalkTabixSyntenyAdapter-JFNFX3JP.js}

@@ -1,2 +1,2 @@
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G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends ${constructor(){super(...arguments);this.walks=new K(D(this,["walksLocation"],["walksIndex"]),this);this.refNames=new H(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=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),h=c.filter(m=>m.name===e),d=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&d(m)>=0).sort((m,b)=>d(m)-d(b)).flatMap(m=>h.flatMap(b=>p(m,b).map(P=>C({chain:P,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(h=>f(N).flatMap(d=>u(d,h).map(y=>C({chain:y,target:h,query:d,assemblyName:c.queryAssemblyName,refName:W(h.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return q(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 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this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&S(o)!==s).map(o=>({name:O(n,o),label:o,group:S(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=j(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks 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package/dist/chunks/{chunk-POUV7OPY.js.map → chunk-2CPD5NX2.js.map}

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package/dist/chunks/chunk-3AC33AXB.js

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