jbrowse-plugin-graphgenomeviewer 6.11.0 → 6.13.0

package/dist/chunks/{GbzBaseSyntenyAdapter-SPT62NR4.js → GbzBaseSyntenyAdapter-SFTZXPG5.js}

@@ -1,2 +1,2 @@
-import{b as J,c as K,d as q,e as ne,f as me,g as ae}from"./chunk-KROCIQJP.js";import{b as G,c as V,d as ee,e as te}from"./chunk-X4NNWAXW.js";import{a as O,b as H}from"./chunk-NU53CDGF.js";import{f as le,g as Z,h,i as B,j as z,k as R,l as M,m as k,o as E}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as F,f as S,g as C}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import{b as U,c as X,d as Y}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function de(n){return X(n)&&A(U(n))?Y(n,i=>A(i)):void 0}function fe(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function re(n,i){let t=de(n);if(!t)return{};try{return await P(t,i).stat(),{location:t}}catch(e){return fe(e)?{}:{unreadable:String(e)}}}var he=5e3,ue=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ge(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var oe=(n,i)=>n.path.some(t=>i.has(t.name)),I=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=G({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new T(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&oe(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>oe(a,i));return{records:ge(e,he),total:e.length}}};var v=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function se(n,i){let t=h(i);return n[t]??n[i.sample]??t}function ye(n,i){return`${h(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function be({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(!n.resolved||r<=a)){let{name:s,hapStart:p,hapEnd:m}=n,u=ye(s,n),g={uniqueId:u,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:u,mate:{refName:s.contig,start:p,end:m,assemblyName:e}};return new q(g)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${h(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${h(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var we=12e4;function Se(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=h(r);if(i.has(s)){let p=`${s}#${r.contig}`;t.set(p,[...t.get(p)??[],[o,c]])}}let e=0;for(let a of t.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<=we&&(e=Math.max(e,o))}}return e}function _(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var Q=n=>!("uri"in n)||n.uri!=="",j=class extends ne{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=Q(e)?{location:e}:await re(t,this.pluginManager),r=a.location,o=await K.open({source:P(t,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await z(o),p=R({configured:this.getConf("referenceSample"),anchorPrefix:S(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return Q(t)?new I(P(t,this.pluginManager),Q(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return M(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let c=h(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(t),o=C(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:se(o,s),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:S(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(h(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>S(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||F(h(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:m,start:u,end:g}=t;if(p!==o)throw new D(p,o);let y=await this.referenceQuery(m,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${m} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(s);return E(r,y,u,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(d=>{throw _(d,"the graph")})}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=S(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=S(this,e.targetAssemblyName),m=C(this),u=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:u}).catch(d=>{throw _(k(d,y,s-c)??d,"lanes")})):[]).flatMap(d=>{let N=d.resolved?be({alignment:d,assemblyName:r,refName:o,lane:se(m,d.name)}):void 0;return N===void 0?[]:[N]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,m=(await Promise.all(e.map(async l=>({pair:l,featureSide:await this.laneHaplotypes(l.queryAssemblyName,a),mateSide:await this.laneHaplotypes(l.targetAssemblyName,a)})))).filter(({featureSide:l,mateSide:f})=>l.length>0&&f.length>0),u=new Set(m.flatMap(({featureSide:l,mateSide:f})=>[...l,...f].map(h))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[d]=e,N=(l,f)=>r.getSubgraphs({path:l,start:c,end:s,context:f,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:w=>u.has(h(w))}),ie=async l=>{let f=await N(l,x).catch(b=>{throw _(k(b,y,s-c)??b,"lanes")}),w=Se(f,u),L=Math.ceil(w/2)+2e3;return w>0&&L>x?N(l,L).catch(b=>{if(b instanceof J)return f;throw b}):f};return(g&&d&&m.length>0?await $(e.length===1?`Reading ${d.queryAssemblyName} against ${d.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>ie(g)):[]).flatMap(l=>m.flatMap(({pair:f,featureSide:w,mateSide:L})=>w.flatMap(b=>L.flatMap(ce=>l.pairAlignments({target:b,query:ce,bases:!1}).map(pe=>xe({pair:pe,lane:f.queryAssemblyName,mateLane:f.targetAssemblyName}))))))}getFeatures(t,e={}){return V(async a=>{let{db:r,anchor:o,unreadableIndex:c}=await this.graph(e);if(!r.hasHaplotypeIndex)throw new v(c);if(t.assemblyName===o){let s=ae(e),p=s.length>0?await this.pairFeatures(t,s,e):await this.anchorFeatures(t,e);for(let m of p)a.next(m)}a.complete()},e.signal)}};export{D as HaplotypeWindowError,v as NoHaplotypeIndexError,le as NoReferenceSampleError,me as PairTargetError,j as default,be as fragmentFeature,se as laneAssemblyName,xe as pairFeature,R as resolveReferenceSample,Se as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-SPT62NR4.js.map
+import{c as J,d as K,e as q,f as ne,g as me,h as ae}from"./chunk-SYETHCAR.js";import{b as G,c as V,d as ee,e as te}from"./chunk-X4NNWAXW.js";import{a as O,b as H}from"./chunk-NU53CDGF.js";import{f as le,g as Z,h,i as B,j as z,k as R,l as M,m as k,o as E}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{e as F,f as S,g as C}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import{b as U,c as X,d as Y}from"./chunk-R3TRNF7N.js";import"./chunk-7WIBGKBU.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function de(n){return X(n)&&A(U(n))?Y(n,i=>A(i)):void 0}function fe(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function re(n,i){let t=de(n);if(!t)return{};try{return await P(t,i).stat(),{location:t}}catch(e){return fe(e)?{}:{unreadable:String(e)}}}var he=5e3,ue=50*2**20,T=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ge(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var oe=(n,i)=>n.path.some(t=>i.has(t.name)),I=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=G({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new T(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&oe(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>oe(a,i));return{records:ge(e,he),total:e.length}}};var v=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function se(n,i){let t=h(i);return n[t]??n[i.sample]??t}function ye(n,i){return`${h(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function be({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(!n.resolved||r<=a)){let{name:s,hapStart:p,hapEnd:m}=n,u=ye(s,n),g={uniqueId:u,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:u,mate:{refName:s.contig,start:p,end:m,assemblyName:e}};return new q(g)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${h(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${h(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var we=12e4;function Se(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=h(r);if(i.has(s)){let p=`${s}#${r.contig}`;t.set(p,[...t.get(p)??[],[o,c]])}}let e=0;for(let a of t.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<=we&&(e=Math.max(e,o))}}return e}function _(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var Q=n=>!("uri"in n)||n.uri!=="",j=class extends ne{constructor(){super(...arguments);this.graph=G({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=Q(e)?{location:e}:await re(t,this.pluginManager),r=a.location,o=await K.open({source:P(t,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await z(o),p=R({configured:this.getConf("referenceSample"),anchorPrefix:S(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=G({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return Q(t)?new I(P(t,this.pluginManager),Q(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return M(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let c=h(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(t),o=C(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:se(o,s),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:S(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(h(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>S(this,r));return a===void 0&&e===void 0?void 0:r=>B(r,a)&&(e===void 0||F(h(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:m,start:u,end:g}=t;if(p!==o)throw new D(p,o);let y=await this.referenceQuery(m,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${m} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new v(s);return E(r,y,u,g,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(d=>{throw _(d,"the graph")})}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=S(this,t);return(await this.getHaplotypes(e)).filter(r=>F(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=S(this,e.targetAssemblyName),m=C(this),u=this.keepPredicate(e.haplotypes,p),g=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(g?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:g,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:u}).catch(d=>{throw _(k(d,y,s-c)??d,"lanes")})):[]).flatMap(d=>{let N=d.resolved?be({alignment:d,assemblyName:r,refName:o,lane:se(m,d.name)}):void 0;return N===void 0?[]:[N]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,m=(await Promise.all(e.map(async l=>({pair:l,featureSide:await this.laneHaplotypes(l.queryAssemblyName,a),mateSide:await this.laneHaplotypes(l.targetAssemblyName,a)})))).filter(({featureSide:l,mateSide:f})=>l.length>0&&f.length>0),u=new Set(m.flatMap(({featureSide:l,mateSide:f})=>[...l,...f].map(h))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[d]=e,N=(l,f)=>r.getSubgraphs({path:l,start:c,end:s,context:f,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:w=>u.has(h(w))}),ie=async l=>{let f=await N(l,x).catch(b=>{throw _(k(b,y,s-c)??b,"lanes")}),w=Se(f,u),L=Math.ceil(w/2)+2e3;return w>0&&L>x?N(l,L).catch(b=>{if(b instanceof J)return f;throw b}):f};return(g&&d&&m.length>0?await $(e.length===1?`Reading ${d.queryAssemblyName} against ${d.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>ie(g)):[]).flatMap(l=>m.flatMap(({pair:f,featureSide:w,mateSide:L})=>w.flatMap(b=>L.flatMap(ce=>l.pairAlignments({target:b,query:ce,bases:!1}).map(pe=>xe({pair:pe,lane:f.queryAssemblyName,mateLane:f.targetAssemblyName}))))))}getFeatures(t,e={}){return V(async a=>{let{db:r,anchor:o,unreadableIndex:c}=await this.graph(e);if(!r.hasHaplotypeIndex)throw new v(c);if(t.assemblyName===o){let s=ae(e),p=s.length>0?await this.pairFeatures(t,s,e):await this.anchorFeatures(t,e);for(let m of p)a.next(m)}a.complete()},e.signal)}};export{D as HaplotypeWindowError,v as NoHaplotypeIndexError,le as NoReferenceSampleError,me as PairTargetError,j as default,be as fragmentFeature,se as laneAssemblyName,xe as pairFeature,R as resolveReferenceSample,Se as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-SFTZXPG5.js.map

package/dist/chunks/{GraphGenomeView-BSJYTSFN.js → GraphGenomeView-D3TBUFNW.js}

@@ -1,4 +1,4 @@
-import{a as C}from"./chunk-DOLO4I5J.js";import"./chunk-I574RVHG.js";import"./chunk-UQT5WHCD.js";import"./chunk-MDRNFKXW.js";import{p as d}from"./chunk-LEWWQ7ZK.js";import"./chunk-6AYSOQOK.js";import"./chunk-BXZLLHYP.js";import"./chunk-AB2XVNNS.js";import"./chunk-FSCO2SM4.js";import"./chunk-NU53CDGF.js";import"./chunk-PR5YUSXN.js";import"./chunk-YBLNN5FU.js";import"./chunk-XKN5LH2Z.js";import"./chunk-ELLLNUKS.js";import"./chunk-TENPGIPX.js";import{g as x}from"./chunk-6OPB7FOJ.js";import{E as L,G as p,d as s,h as v,n,w as G,z as l}from"./chunk-ECD5B2ZM.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=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}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
+import{a as C}from"./chunk-MIY4JCDL.js";import"./chunk-I574RVHG.js";import"./chunk-BXFEZVDW.js";import"./chunk-5DRS22TL.js";import{p as d}from"./chunk-LEWWQ7ZK.js";import"./chunk-KIXOGZKJ.js";import"./chunk-BXZLLHYP.js";import"./chunk-AB2XVNNS.js";import"./chunk-FSCO2SM4.js";import"./chunk-NU53CDGF.js";import"./chunk-PR5YUSXN.js";import"./chunk-YBLNN5FU.js";import"./chunk-XKN5LH2Z.js";import"./chunk-ELLLNUKS.js";import"./chunk-TENPGIPX.js";import{g as x}from"./chunk-6OPB7FOJ.js";import{E as L,G as p,d as s,h as v,n,w as G,z as l}from"./chunk-ECD5B2ZM.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=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}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`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`,S=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"}}),T=i(function({model:e}){let{classes:t}=S(),[m,M]=x("");function u(){let o=m.trim();o&&e.loadGFAFromLocation({uri:o,locationType:"UriLocation"})}function N(o){let c=o.target.files?.[0];o.target.value="",c&&c.text().then(f=>e.loadGFA(f,c.name)).catch(f=>{e.setError(f)})}return r(l,{className:t.paper,children:[a("div",{className:t.header,children:a(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",a("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:o=>{N(o)}})]}),a(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[a(L,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{M(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),a(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),a("div",{className:t.footer,children:a(n,{size:"small",onClick:()=>{e.loadGFA(F,"Example graph")},children:"Load 4-node example"})}),e.error?a(s,{error:e.error}):null]})}),P=T;var A=i(function({model:e}){return e.hasGraph?a(C,{model:e}):e.canRetryLoad&&(e.error||e.loadCanceled)?a(g,{model:e}):r(y,{children:[e.isLoading?a(g,{model:e}):null,a("div",{hidden:e.isLoading,children:a(P,{model:e})})]})}),J=A;export{J as default};
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+//# sourceMappingURL=GraphGenomeView-D3TBUFNW.js.map

package/dist/chunks/{LinearGraphDisplay-VW7DGOVT.js → LinearGraphDisplay-YKGK4KBD.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=LinearGraphDisplay-YKGK4KBD.js.map

package/dist/chunks/RgfaTabixAdapter-2PJS7QDO.js

@@ -0,0 +1,3 @@
+import{a as u,b as P,c as O}from"./chunk-WSZ6RCMI.js";import{a as v}from"./chunk-P6FDUP52.js";import{a as B,c as I,e as R,f as T}from"./chunk-X4NNWAXW.js";import"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{c as F,f as M}from"./chunk-XKN5LH2Z.js";import{a as $,o as A}from"./chunk-TENPGIPX.js";function y(i){let e=i.split("	"),a=e.length>=8,r=a?5:0;return{anchored:a,segment:{refName:e[r],start:+e[r+1],end:+e[r+2],id:e[3],rank:+e[4],tags:e[a?8:5]??""}}}function G(i){let e=i.tags.split(" ").find(r=>r.startsWith("SM:Z:"));if(e===void 0)return;let a=e.slice(5).split(",").map(r=>r.trim()).filter(Boolean);return a.length>0?a:void 0}function W(i){return{id:i.slice(0,-1),strand:i.slice(-1)}}function w(i){let e=i.split("	"),a=W(e[3]),r=W(e[4]);return{source:a.id,sourceStrand:a.strand,target:r.id,targetStrand:r.strand,sourceSegment:{id:a.id,refName:e[5],start:+e[6],end:+e[7],rank:+e[8],tags:e[13]??""},targetSegment:{id:r.id,refName:e[9],start:+e[10],end:+e[11],rank:+e[12],tags:e[14]??""}}}function S(i){return`${i.source}${i.sourceStrand}${i.target}${i.targetStrand}`}function Z(i,e,a){let r=n=>n.rank!==0||n.refName!==a.refName?0:n.end<=a.start?-1:n.start>=a.end?1:0,t=new Map(i),s=new Map;for(let n of e)if(i.has(n.source)||i.has(n.target)||r(n.sourceSegment)*r(n.targetSegment)===-1){s.set(S(n),n);for(let o of[n.sourceSegment,n.targetSegment])t.has(o.id)||t.set(o.id,o)}for(let n of e)t.has(n.source)&&t.has(n.target)&&s.set(S(n),n);return{segments:t,links:s}}function H(i,e,a){let r=t=>t.refName!==a.refName||t.end<=a.start||t.start>=a.end;return[...j(i.filter(t=>t.rank>0),e,a.end-a.start),...j(i.filter(t=>t.rank===0&&r(t)),new Set(i.map(t=>t.id)),0)]}function j(i,e,a){let r=[...i].sort((s,n)=>b(s.refName,n.refName)||s.start-n.start),t=[];for(let s of r){let n=t.at(-1);n?.refName===s.refName&&s.start-n.end<=a?(n.needed||=s.start>n.end||e.has(s.id),n.end=Math.max(n.end,s.end)):t.push({refName:s.refName,start:s.start,end:s.end,needed:e.has(s.id)})}return t.filter(s=>s.needed).map(({refName:s,start:n,end:o})=>({refName:s,start:n,end:o}))}function _(i,e,a){let r=t=>e.has(t.id)||a.some(s=>s.refName===t.refName&&t.start>=s.start&&t.end<=s.end);return i.filter(t=>r(t.sourceSegment)&&r(t.targetSegment))}var K=/^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/;function z(i){let{id:e,refName:a,start:r,end:t,rank:s,tags:n}=i,o=n.split(" ").filter(f=>K.test(f)),c=o.length===0?"":`	${o.join("	")}`;return`S	${e}	*	LN:i:${t-r}	SN:Z:${a}	SO:i:${r}	SR:i:${s}${c}`}function J(i){let{source:e,sourceStrand:a,target:r,targetStrand:t}=i;return`L	${e}	${a}	${r}	${t}	0M`}function b(i,e){return i<e?-1:i>e?1:0}function L(i,e){let a=[...i.values()].sort((t,s)=>b(t.refName,s.refName)||t.start-s.start||b(t.id,s.id)),r=[...e.keys()].sort((t,s)=>b(t,s));return["H	VN:Z:1.0",...a.map(t=>z(t)),...r.map(t=>J(e.get(t)))].join(`
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package/dist/chunks/RgfaTabixAdapter-2PJS7QDO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/RgfaTabixAdapter/rgfaBed.ts", "../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts"],
+  "sourcesContent": ["// A segment as it appears in segs.bed.gz, and as it is repeated inside every\n// links.bed.gz row: `stableName start end segmentId rank [tags]`. The first\n// five are the SN/SO/SR tags rGFA already carries, projected to BED by\n// `gfatools gfa2bed -m`.\n//\n// `tags` is a space-separated list of GFA tags, written verbatim onto the\n// S-line formatSegment synthesizes, where the GFA parser reads them into\n// `GraphNode.tags` with no work here. It is the extension point for everything\n// the five columns cannot say: carriage on a path-derived graph (`SM:Z:`), the\n// collapse summary on a level-of-detail tier (`ct:Z:`, `cn:i:`, ...), a\n// precomputed layout position later. rGFA files have no sixth column at all,\n// so this is empty for them and nothing changes.\nexport interface RgfaSegment {\n  refName: string\n  start: number\n  end: number\n  id: string\n  rank: number\n  tags: string\n}\n\nexport interface RgfaLink {\n  source: string\n  sourceStrand: string\n  target: string\n  targetStrand: string\n  sourceSegment: RgfaSegment\n  targetSegment: RgfaSegment\n}\n\nexport function parseSegmentLine(line: string): RgfaSegment {\n  return parseSegmentRow(line).segment\n}\n\n// gfa-to-tabix's anchored layout files a segment under the reference interval\n// its bubble hangs from and states the segment's own coordinate after the rank:\n// `anchorName anchorStart anchorEnd segmentId rank stableName start end [tags]`.\n// One query over a region then returns every segment of every bubble under it,\n// and `anchored` tells a cut it has nothing left to follow.\nexport function parseSegmentRow(line: string) {\n  const cols = line.split('\\t')\n  const anchored = cols.length >= 8\n  const own = anchored ? 5 : 0\n  return {\n    anchored,\n    segment: {\n      refName: cols[own]!,\n      start: +cols[own + 1]!,\n      end: +cols[own + 2]!,\n      id: cols[3]!,\n      rank: +cols[4]!,\n      tags: cols[anchored ? 8 : 5] ?? '',\n    } satisfies RgfaSegment,\n  }\n}\n\n// Carriage as an ordinary feature attribute, for the linear track rather than\n// the graph. The tag column reaches the graph view through the synthesized\n// S-line (formatSegment below, then gfaConverter reads SM into\n// `GraphNode.samples`), and that route ends at the graph: `getFeatures` builds\n// its own features and had no way to say who carries a segment, so a lane\n// colored by carriage was not expressible.\n//\n// `SM:Z:` is its own grammar check here. build_pggb_tabix.sh wrote a bare\n// comma-separated list in this column before the tag column existed, and those\n// files are still hosted; a bare list has no prefix to match, so it is dropped\n// rather than read as one sample named `K12,Sakai,CFT073`.\n//\n// Undefined rather than [] when the tag is absent, matching gfaConverter: an\n// rGFA has no sixth column at all, so a segment that says nothing about\n// carriage stays distinguishable from one carried by nobody.\nexport function segmentSamples(segment: RgfaSegment) {\n  const tag = segment.tags.split(' ').find(t => t.startsWith('SM:Z:'))\n  if (tag === undefined) {\n    return undefined\n  }\n  const samples = tag\n    .slice('SM:Z:'.length)\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\n// `s322+` \u2014 the L-line's segment id with its orientation appended, mirroring\n// the GFA record it came from.\nfunction parseEndpoint(field: string) {\n  return { id: field.slice(0, -1), strand: field.slice(-1) }\n}\n\nexport function parseLinkLine(line: string): RgfaLink {\n  const cols = line.split('\\t')\n  const source = parseEndpoint(cols[3]!)\n  const target = parseEndpoint(cols[4]!)\n  return {\n    source: source.id,\n    sourceStrand: source.strand,\n    target: target.id,\n    targetStrand: target.strand,\n    sourceSegment: {\n      id: source.id,\n      refName: cols[5]!,\n      start: +cols[6]!,\n      end: +cols[7]!,\n      rank: +cols[8]!,\n      tags: cols[13] ?? '',\n    },\n    targetSegment: {\n      id: target.id,\n      refName: cols[9]!,\n      start: +cols[10]!,\n      end: +cols[11]!,\n      rank: +cols[12]!,\n      tags: cols[14] ?? '',\n    },\n  }\n}\n\nexport function linkKey(link: RgfaLink) {\n  return `${link.source}${link.sourceStrand}${link.target}${link.targetStrand}`\n}\n\n// The cut an anchored index gives: `under` is what the segment file returned\n// for the window, every segment of every bubble under it, and `found` is what\n// the link file returned. gfa-to-tabix files a link widely enough that `found`\n// holds every link touching a segment in `under` and every link between the\n// segments those lead to, plus links of neither kind, which are dropped here.\n// A backbone link that jumps the whole window, as a deletion or inversion\n// spanning it does, touches nothing in `under` and is kept by its own rule.\nexport function anchoredCut(\n  under: Map<string, RgfaSegment>,\n  found: RgfaLink[],\n  window: StableSpan,\n) {\n  const side = (segment: RgfaSegment) =>\n    segment.rank !== 0 || segment.refName !== window.refName\n      ? 0\n      : segment.end <= window.start\n        ? -1\n        : segment.start >= window.end\n          ? 1\n          : 0\n  const segments = new Map(under)\n  const links = new Map<string, RgfaLink>()\n  for (const link of found) {\n    if (\n      under.has(link.source) ||\n      under.has(link.target) ||\n      side(link.sourceSegment) * side(link.targetSegment) === -1\n    ) {\n      links.set(linkKey(link), link)\n      for (const segment of [link.sourceSegment, link.targetSegment]) {\n        if (!segments.has(segment.id)) {\n          segments.set(segment.id, segment)\n        }\n      }\n    }\n  }\n  for (const link of found) {\n    if (segments.has(link.source) && segments.has(link.target)) {\n      links.set(linkKey(link), link)\n    }\n  }\n  return { segments, links }\n}\n\n// Both endpoints of a link are written into every row, so the same link is\n// indexed under each endpoint's stable sequence and arrives twice for a region\n// covering both. Callers dedupe on linkKey.\n\nexport interface StableSpan {\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a cut reads links once more to close itself. A hop reads the links of\n// the segments the round before it reached, so a link between two segments of\n// the last round is never read and an allele reached from both ends draws as\n// two stubs. rGFA lays an allele out as one stretch of the stable sequence that\n// introduced it, so pieces of one sequence within the window's length of each\n// other merge into a span, and reading it brings the pieces between too.\n// Backbone reached past the window is unread for the same reason; its spans\n// join only abutting pieces, since the reference past the window is not the\n// cut's to fill. A span whose segments were all read and abut is skipped.\nexport function closingSpans(\n  held: RgfaSegment[],\n  unread: Set<string>,\n  window: StableSpan,\n) {\n  const outside = (segment: RgfaSegment) =>\n    segment.refName !== window.refName ||\n    segment.end <= window.start ||\n    segment.start >= window.end\n  return [\n    ...mergedSpans(\n      held.filter(segment => segment.rank > 0),\n      unread,\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      new Set(held.map(segment => segment.id)),\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  unread: Set<string>,\n  maxGap: number,\n) {\n  const sorted = [...segments].sort(\n    (a, b) => compare(a.refName, b.refName) || a.start - b.start,\n  )\n  const spans: (StableSpan & { needed: boolean })[] = []\n  for (const segment of sorted) {\n    const span = spans.at(-1)\n    if (\n      span?.refName === segment.refName &&\n      segment.start - span.end <= maxGap\n    ) {\n      span.needed ||= segment.start > span.end || unread.has(segment.id)\n      span.end = Math.max(span.end, segment.end)\n    } else {\n      spans.push({\n        refName: segment.refName,\n        start: segment.start,\n        end: segment.end,\n        needed: unread.has(segment.id),\n      })\n    }\n  }\n  return spans\n    .filter(span => span.needed)\n    .map(({ refName, start, end }): StableSpan => ({ refName, start, end }))\n}\n\n// The links a closing read keeps: each end is a segment the cut holds or one\n// lying inside a span. Following anything else is what another hop is for.\nexport function closingLinks(\n  found: RgfaLink[],\n  held: Map<string, RgfaSegment>,\n  spans: StableSpan[],\n) {\n  const inside = (segment: RgfaSegment) =>\n    held.has(segment.id) ||\n    spans.some(\n      span =>\n        span.refName === segment.refName &&\n        segment.start >= span.start &&\n        segment.end <= span.end,\n    )\n  return found.filter(\n    link => inside(link.sourceSegment) && inside(link.targetSegment),\n  )\n}\n\n// Segments carry no sequence here \u2014 the BED records only their span \u2014 so every\n// S-line is written with `*` and an LN tag, which is what the GFA spec asks for\n// and what packages/graph-core's parser reads back as the node length.\n// `NM:i:0`, `SM:Z:HG002.1,HG002.2` \u2014 the GFA tag grammar, checked rather than\n// trusted. Files built before the tag column existed put a bare comma-separated\n// sample list here, and passing that through would put a field that is not a\n// tag on an S-line, which is a malformed GFA rather than a missing annotation.\n// Dropping it degrades to the pre-tag behaviour instead.\nconst GFA_TAG = /^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/\n\nfunction formatSegment(segment: RgfaSegment) {\n  const { id, refName, start, end, rank, tags } = segment\n  const valid = tags.split(' ').filter(t => GFA_TAG.test(t))\n  const extra = valid.length === 0 ? '' : `\\t${valid.join('\\t')}`\n  return `S\\t${id}\\t*\\tLN:i:${end - start}\\tSN:Z:${refName}\\tSO:i:${start}\\tSR:i:${rank}${extra}`\n}\n\nfunction formatLink(link: RgfaLink) {\n  const { source, sourceStrand, target, targetStrand } = link\n  return `L\\t${source}\\t${sourceStrand}\\t${target}\\t${targetStrand}\\t0M`\n}\n\n// Codepoint order, not localeCompare: the byte-identical-output guarantee below\n// has to hold across locales.\nfunction compare(a: string, b: string) {\n  return a < b ? -1 : a > b ? 1 : 0\n}\n\n// Deterministic ordering: the same region always produces byte-identical GFA,\n// so a layout computed from it is reproducible.\nexport function formatSubgraph(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n) {\n  const sortedSegments = [...segments.values()].sort(\n    (a, b) =>\n      compare(a.refName, b.refName) || a.start - b.start || compare(a.id, b.id),\n  )\n  const sortedLinks = [...links.keys()].sort((a, b) => compare(a, b))\n  return [\n    'H\\tVN:Z:1.0',\n    ...sortedSegments.map(s => formatSegment(s)),\n    ...sortedLinks.map(k => formatLink(links.get(k)!)),\n  ].join('\\n')\n}\n", "import { panSNHaplotype, resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport {\n  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentRow,\n  segmentSamples,\n} from './rgfaBed.ts'\nimport { getLines } from './tabixRange.ts'\nimport { WalkReader } from './walkReader.ts'\nimport { walkCutFor } from './walkRowRuns.ts'\nimport { walkNameFilter } from './walkRows.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { RgfaLink, RgfaSegment } from './rgfaBed.ts'\nimport type { WalkCut } from './walkRowRuns.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\n// What a hop follows: alleles, never the backbone. A rank-0 segment reached\n// through a link is flanking backbone, usually outside the window, so querying\n// its links walks the reference away from the region, brings back more backbone,\n// and closes nothing. Every segment that closes a bubble is an allele interior,\n// and an allele interior is rank > 0 in both index formats (rGFA's SR tag, and\n// pggb's rank 0-or-1 against the anchor path). Reached backbone still becomes a\n// node and its edge still draws; it is only not walked through.\n//\n// This is gfabase's rule, arrived at from the other end. `gfabase sub` expands\n// from a seed either to the whole connected component (`--connected`, which its\n// own README calls overkill) or with `--cutpoints 1`, which takes the biconnected\n// component by *stopping at cutpoints*, the segments every end-to-end walk of\n// the chromosome must traverse. In a reference-anchored pangenome the cutpoints\n// are the backbone, and rank is what the index already states about it, so\n// `rank > 0` is that stopping rule without a connectivity index to build. The\n// third tool is the same shape again: `gfatools view -R` maps the region onto its\n// precomputed bubble decomposition and returns whole overlapping bubbles\n// (gfa_query_by_reg), which is complete for the same reason. Bandage's own\n// `--distance` is a node-step radius, but Bandage holds the entire graph in\n// memory, so its scope is a drawing filter rather than a fetch strategy.\n//\n// Measured with this rule: the E. coli paa window converges at one hop (17\n// segments at 1 and at 2), so the cut closes and stays closed. HPRC's amylase\n// window keeps growing (63 at 0, 78 at 1, 92 at 2) because its alleles have\n// alleles, and wall-clock is flat across all three, since a hop's queries go out\n// together and the remote index dominates.\n//\n// The exact version, when a graph ships a bubble index beside its segments:\n// gfatools' bubble rows carry the member segment ids of every bubble, so the\n// bubbles overlapping the region state which segments a complete cut must\n// contain. That turns the hop count into a termination condition rather than a\n// setting, and MinigraphBubbleAdapter already parses those rows.\nfunction offReference(segments: RgfaSegment[]) {\n  return segments.filter(segment => segment.rank > 0)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkReader\n  refNames: PanSNRefNames\n}\n\n// How much graph a walk cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine\n  private coarse: GraphIndex | undefined\n\n  public constructor(\n    config: RgfaTabixAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.fine = this.openIndex([])\n  }\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const hasWalks =\n      under.length === 0 &&\n      (!('uri' in walksLocation) || walksLocation.uri !== '')\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    return {\n      segments,\n      links,\n      walks: hasWalks\n        ? new WalkReader(\n            {\n              walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n              nodes: segments,\n              links,\n            },\n            this.getConf('walkChunk'),\n          )\n        : undefined,\n      refNames: new PanSNRefNames(segments, this),\n    }\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const header = await this.fine.walks?.header(opts)\n    return header?.haplotypes.length ? header.haplotypes : undefined\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        // a walk-indexed node row names only its chunk's first base, and a\n        // node crossing in from a chunk before is filed there\n        const start = this.fine.walks\n          ? await this.fine.walks.queryStart(query.start, opts)\n          : query.start\n        await updateStatus('Downloading segments', statusCallback, () =>\n          getLines(this.fine.segments, tabixRefName, start, query.end, {\n            signal,\n            lineCallback: line => {\n              const { segment, anchored } = parseSegmentRow(line)\n              // An anchored index also returns the alleles under the region,\n              // which lie on other stable sequences and have no place on this\n              // one.\n              if (anchored && segment.refName !== tabixRefName) {\n                return\n              }\n              // `samples` lists the haplotypes whose paths visit the segment and\n              // `sampleCount` counts them. A lane's color reads the count, and\n              // a count in jexl would otherwise rely on `.length` resolving\n              // through a member access on an array.\n              const samples = segmentSamples(segment)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: segment.id,\n                  refName: query.refName,\n                  start: segment.start,\n                  end: segment.end,\n                  name: segment.id,\n                  type: 'segment',\n                  rank: segment.rank,\n                  stableName: segment.refName,\n                  ...(samples && { samples, sampleCount: samples.length }),\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n\n  // Extract the graph around a region for GraphGenomeView: GFA text, or a\n  // walk-indexed graph's tables (walkSubgraph). The\n  // region's own segments come from segs.bed.gz; links.bed.gz supplies the edges\n  // incident to them *and* the coordinates of the segments on the other end,\n  // which typically sit on a different stable sequence (a rank>0 bubble) and so\n  // are not reachable by any coordinate query on this region.\n  //\n  // `hops` is extra rounds of link-following past the region's own segments\n  // and their immediate neighbours, each costing one tabix query per\n  // off-reference segment newly reached. After the last round, one more read\n  // per stretch of stable sequence the cut holds closes it (closingSpans), so\n  // an allele reached from both ends draws whole. The view asks for one hop; a\n  // hopless cut stays as cheap as it was. `signal` goes to every one of those\n  // queries, so a cut the view has replaced stops.\n  // `tier: 'coarse'` reads the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops = 0, signal, tier } = opts\n    const index = this.index(tier)\n    const segments = new Map<string, RgfaSegment>()\n    const links = new Map<string, RgfaLink>()\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n\n    const addLinksOver = async (\n      refName: string,\n      start: number,\n      end: number,\n    ) => {\n      const reached: RgfaSegment[] = []\n      await getLines(index.links, refName, start, end, {\n        signal,\n        lineCallback: line => {\n          const link = parseLinkLine(line)\n          links.set(linkKey(link), link)\n          for (const segment of [link.sourceSegment, link.targetSegment]) {\n            if (!segments.has(segment.id)) {\n              segments.set(segment.id, segment)\n              reached.push(segment)\n            }\n          }\n        },\n      })\n      return reached\n    }\n\n    if (tabixRefName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${region.assemblyName} mapped to its prefix in assemblyNameToPanSN`,\n      )\n    }\n    if (index.walks) {\n      return this.walkSubgraph(index.walks, tabixRefName, region, opts)\n    }\n    const layout = { anchored: false }\n    await getLines(index.segments, tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const row = parseSegmentRow(line)\n        layout.anchored ||= row.anchored\n        segments.set(row.segment.id, row.segment)\n      },\n    })\n    // An anchored index files every allele and every link under the reference\n    // interval its bubble hangs from, so one read of each file holds the whole\n    // graph under the region and there is nothing to hop to or close.\n    if (layout.anchored) {\n      const found: RgfaLink[] = []\n      await getLines(index.links, tabixRefName, region.start, region.end, {\n        signal,\n        lineCallback: line => {\n          found.push(parseLinkLine(line))\n        },\n      })\n      const cut = anchoredCut(segments, found, {\n        refName: tabixRefName,\n        start: region.start,\n        end: region.end,\n      })\n      return formatSubgraph(cut.segments, cut.links)\n    }\n    let frontier = offReference(\n      await addLinksOver(tabixRefName, region.start, region.end),\n    )\n    for (let hop = 0; hop < hops; hop++) {\n      // One hop's queries are independent of each other, so they go out\n      // together rather than one round-trip at a time. Their callbacks share\n      // the segment and link maps, which is safe because only one of them runs\n      // at a time, and the output is sorted at the end regardless of the order\n      // they arrive in.\n      const reached = await Promise.all(\n        frontier.map(segment =>\n          addLinksOver(segment.refName, segment.start, segment.end),\n        ),\n      )\n      frontier = offReference(reached.flat())\n    }\n    if (hops > 0) {\n      const spans = closingSpans(\n        [...segments.values()],\n        new Set(frontier.map(segment => segment.id)),\n        { refName: tabixRefName, start: region.start, end: region.end },\n      )\n      const found: RgfaLink[] = []\n      await Promise.all(\n        spans.map(span =>\n          getLines(index.links, span.refName, span.start, span.end, {\n            signal,\n            lineCallback: line => {\n              found.push(parseLinkLine(line))\n            },\n          }),\n        ),\n      )\n      for (const link of closingLinks(found, segments, spans)) {\n        links.set(linkKey(link), link)\n        for (const segment of [link.sourceSegment, link.targetSegment]) {\n          if (!segments.has(segment.id)) {\n            segments.set(segment.id, segment)\n          }\n        }\n      }\n    }\n\n    return formatSubgraph(segments, links)\n  }\n\n  // Only the walks `haplotypes` asks for, and the reference's, are decoded\n  private async walkSubgraph(\n    walks: WalkReader,\n    refName: string,\n    region: Region,\n    opts: SubgraphAdapterOptions,\n  ) {\n    const { graph, kept, fragments } = await walks.cut(refName, region, {\n      signal: opts.signal,\n      keep: walkNameFilter(\n        opts.haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        panSNHaplotype(refName),\n      ),\n      stepBudget: opts.walkRows ? Infinity : this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      context: WALK_CONTEXT,\n    })\n    return walkCutFor(graph.tables(kept, fragments), region, opts.walkRows)\n  }\n}\n"],
+  "mappings": 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+  "names": ["parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "s", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "anchoredCut", "under", "found", "window", "side", "segments", "links", "closingSpans", "held", "unread", "outside", "mergedSpans", "maxGap", "sorted", "a", "b", "compare", "spans", "span", "refName", "start", "end", "closingLinks", "inside", "GFA_TAG", "formatSegment", "id", "rank", "tags", "valid", "extra", "formatLink", "sourceStrand", "targetStrand", "formatSubgraph", "sortedSegments", "sortedLinks", "k", "offReference", "segments", "segment", "WALK_CONTEXT", "RgfaTabixAdapter", "BaseFeatureDataAdapter", "config", "getSubAdapter", "pluginManager", "under", "openTabixSlot", "walksLocation", "hasWalks", "links", "WalkReader", "PanSNRefNames", "opts", "header", "tier", "query", "signal", "statusCallback", "ObservableCreate", "observer", "tabixRefName", "start", "updateStatus", "getLines", "line", "anchored", "parseSegmentRow", "samples", "segmentSamples", "SimpleFeature", "region", "hops", "index", "addLinksOver", "refName", "end", "reached", "link", "parseLinkLine", "linkKey", "layout", "row", "found", "cut", "anchoredCut", "formatSubgraph", "frontier", "hop", "spans", "closingSpans", "span", "closingLinks", "walks", "graph", "kept", "fragments", "walkNameFilter", "lane", "resolvePanSNPrefix", "panSNHaplotype", "walkCutFor"]
+}

package/dist/chunks/WalkTabixSyntenyAdapter-Q5Q5XS4C.js

@@ -0,0 +1,2 @@
+import{b as O,c as D}from"./chunk-WSZ6RCMI.js";import{a as j}from"./chunk-P6FDUP52.js";import{a as C,b as $,e as T,f as _,h as q}from"./chunk-SYETHCAR.js";import{c as v,e as x,f as I}from"./chunk-X4NNWAXW.js";import{g as L}from"./chunk-R4DSKZ5P.js";import"./chunk-PR5YUSXN.js";import"./chunk-OGQ6OQDN.js";import"./chunk-YBLNN5FU.js";import{a as S,c as P,d as F,e as A,f as N,g as W}from"./chunk-XKN5LH2Z.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import{o as R}from"./chunk-TENPGIPX.js";var Y=50;function Z(i){let e=[];for(let t=0;t<i.length;t++){let[r,s]=i[t],[a,n]=i[t+1]??[];s===n&&s<=Y&&(r==="I"&&a==="D"||r==="D"&&a==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function ee(i){return i.map(([e,t])=>`${t}${e}`).join("")}function H(i){let e=new Map,t=a=>{let n=i.get(a),o=n===void 0?0:n.end-n.start,p=e.get(o);return p===void 0&&(p="N".repeat(o),e.set(o,p)),p},r=new Map,s=a=>{let n=r.get(a);return n===void 0&&(n=Array.from(a.ids,(o,p)=>2*o+a.rev[p]),r.set(a,n)),n};return(a,n)=>$({query:s(a),target:s(n),sequenceOf:t,bases:!1})}var te=100;function E(i,e,t){let r=i.at(-1);t>0&&(r?.[0]===e?r[1]+=t:i.push([e,t]))}function X(i){let e=s=>{let a=i.get(s>>1);return a===void 0?0:a.end-a.start},t=s=>{let a=new Float64Array(s.length+1);return s.forEach((n,o)=>{a[o+1]=a[o]+e(n)}),a},r=s=>Array.from(s.ids,(a,n)=>2*a+s.rev[n]);return(s,a)=>{let n=r(a),o=r(s),[p,g]=C(o,n,e),[f,l]=C(o.map(b=>b^1).reverse(),n,e),u=l>g,c=u?f:p,d=Math.max(g,l);if(d<te)return[];let h=t(n),m=t(o),y=b=>u?o.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],k)=>{if(k>0){let[U,J]=[y(k-1),y(k)].sort((Q,V)=>Q-V);E(w,"I",m[J]-m[U+1]),E(w,"D",h[b]-h[c[k-1][1]+1])}E(w,"=",e(n[b]))});let[z,K]=[y(0),y(c.length-1)].sort((b,k)=>b-k);return[{queryStart:m[z],queryEnd:m[K+1],targetStart:h[c[0][1]],targetEnd:h[c.at(-1)[1]+1],strand:u?"-":"+",edits:w,sharedBases:d}]}}function M({chain:i,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:a}){let n=e.hapStart+i.targetStart,o=e.hapStart+i.targetEnd,p=t.hapStart+i.queryStart,g=t.hapStart+i.queryEnd,f=Z(i.edits),l=f.reduce((d,[h,m])=>d+(h==="="?m:0),0),u=f.reduce((d,[,h])=>d+h,0),c=`${e.name}:${n}-${o}|${t.name}:${p}-${g}`;return new T({uniqueId:c,assemblyName:r,refName:s,start:n,end:o,type:"match",strand:i.strand==="-"?-1:1,CIGAR:ee(f),syntenyId:c,identity:l/Math.max(u,1),numMatches:l,blockLen:u,mate:{refName:F(t.name),start:p,end:g,assemblyName:a}})}var ae=1e3;function G(i,e){return i[e]??i[S(e)]??e}var ne=i=>P(i.name)??i.name,B=class extends _{constructor(e,t,r){super(e,t,r);let s=x(this,["nodesLocation"],["nodesIndex"]);this.reader=new D({walks:x(this,["walksLocation"],["walksIndex"]),nodes:s,links:x(this,["linksLocation"],["linksIndex"])},this.getConf("walkChunk")),this.refNames=new I(s,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={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,a=N(this,s),n=W(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(o=>o!==a&&S(o)!==a).map(o=>({name:G(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}):[]}budgets(e){return{stepBudget:e?1/0:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),context:ae}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:a}=t,n=await this.refNames.resolve(e,{signal:r});if(n===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);let{graph:o,kept:p,fragments:g}=await this.reader.cut(n,e,{...this.budgets(a),signal:r,keep:O(s?.map(f=>N(this,f)),P(n))});return j(o.tables(p,g),e,a)}async laneWalks(e,t,r,s,a){return R(a,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:O(r,P(e)),links:!1}).catch(n=>{throw n instanceof L&&(n.message=n.message.replace("to see the graph","to see lanes")),n}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(m=>N(this,m)):void 0,a=N(this,r.targetAssemblyName),n=a===void 0?s:s===void 0||s.some(m=>A(a,m)||A(m,a))?[a]:[];if(n?.length===0)return[];let{start:o,end:p}=t,{graph:g,fragments:f}=await this.laneWalks(e,t,n,r,`Reading walks ${t.refName}:${o.toLocaleString()}-${p.toLocaleString()}`),l=X(g.nodes),u=W(this),c=f.filter(m=>m.name===e),d=m=>n===void 0?0:n.findIndex(y=>A(m.name,y));return f.filter(m=>m.name!==e&&d(m)>=0).sort((m,y)=>d(m)-d(y)).flatMap(m=>c.flatMap(y=>l(m,y).map(w=>M({chain:w,target:y,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:G(u,ne(m))}))))}async pairFeatures(e,t,r,s){let[a]=r,n=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:o,fragments:p}=await this.laneWalks(e,t,n.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&a?`Reading ${a.queryAssemblyName} against ${a.targetAssemblyName}`:`Reading ${r.length} lane pairs`),g=H(o.nodes),f=l=>p.filter(u=>A(u.name,l));return n.flatMap(({pair:l,featurePrefix:u,matePrefix:c})=>f(u).flatMap(d=>f(c).flatMap(h=>g(h,d).map(m=>M({chain:m,target:d,query:h,assemblyName:l.queryAssemblyName,refName:F(d.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return v(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let a=q(t),n=a.length>0?await this.pairFeatures(s,e,a,t):await this.anchorFeatures(s,e,t);for(let o of n)r.next(o)}r.complete()},t.signal)}};export{B as default,G as laneOf};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-Q5Q5XS4C.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-Q5Q5XS4C.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
+  "sourcesContent": ["import { pairAlignments, weightedLcs } from '@gmod/gbz-base'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\n\nimport type { WalkFragment, WalkNode } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { PairChain, PairEdit } from '@gmod/gbz-base'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\nfunction cigarOf(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const node = nodes.get(id)\n    const length = node === undefined ? 0 : node.end - node.start\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const handlesOf = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: handlesOf(query),\n      target: handlesOf(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => {\n    const node = nodes.get(handle >> 1)\n    return node === undefined ? 0 : node.end - node.start\n  }\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n  const handlesOf = (fragment: WalkFragment) =>\n    Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n/**\n * One record of a walk aligned to another: on the target walk's contig, with\n * the query walk as its mate and the CIGAR read along the target, a `D` being\n * target bases the query lacks.\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const start = target.hapStart + chain.targetStart\n  const end = target.hapStart + chain.targetEnd\n  const mateStart = query.hapStart + chain.queryStart\n  const mateEnd = query.hapStart + chain.queryEnd\n  const edits = bubblesAsMismatches(chain.edits)\n  const matches = edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0)\n  const columns = edits.reduce((sum, [, n]) => sum + n, 0)\n  const id = `${target.name}:${start}-${end}|${query.name}:${mateStart}-${mateEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start,\n    end,\n    type: 'match',\n    strand: chain.strand === '-' ? -1 : 1,\n    CIGAR: cigarOf(edits),\n    syntenyId: id,\n    identity: matches / Math.max(columns, 1),\n    numMatches: matches,\n    blockLen: columns,\n    mate: {\n      refName: panSNContig(query.name),\n      start: mateStart,\n      end: mateEnd,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import { NodeLimitError } from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { chainFeature, referenceAligner, walkAligner } from './walkLanes.ts'\nimport { WalkReader } from '../RgfaTabixAdapter/walkReader.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { walkNameFilter } from '../RgfaTabixAdapter/walkRows.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport { requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { WalkFragment } from '../RgfaTabixAdapter/walkRows.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\n// How much graph a cut keeps around the window, on the reference\nconst WALK_CONTEXT = 1000\n\n/**\n * The lane a haplotype draws on: the JBrowse assembly the config maps to it at\n * haplotype or sample depth, else its own PanSN prefix\n */\nexport function laneOf(asmByPrefix: Record<string, string>, prefix: string) {\n  return asmByPrefix[prefix] ?? asmByPrefix[panSNSample(prefix)] ?? prefix\n}\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly reader\n  private readonly refNames\n\n  public constructor(\n    config: WalkTabixSyntenyAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const nodes = openTabixSlot(this, ['nodesLocation'], ['nodesIndex'])\n    this.reader = new WalkReader(\n      {\n        walks: openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n        nodes,\n        links: openTabixSlot(this, ['linksLocation'], ['linksIndex']),\n      },\n      this.getConf('walkChunk'),\n    )\n    this.refNames = new PanSNRefNames(nodes, this)\n  }\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes, references } = await this.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSamples: references,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneOf(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  private budgets(walkRows?: boolean) {\n    return {\n      stepBudget: walkRows ? Infinity : this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      context: WALK_CONTEXT,\n    }\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal, haplotypes, walkRows } = opts\n    const refName = await this.refNames.resolve(region, { signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    const { graph, kept, fragments } = await this.reader.cut(refName, region, {\n      ...this.budgets(walkRows),\n      signal,\n      keep: walkNameFilter(\n        haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        panSNHaplotype(refName),\n      ),\n    })\n    return walkCutFor(graph.tables(kept, fragments), region, walkRows)\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.reader\n        .cut(refName, region, {\n          ...this.budgets(),\n          signal: opts.signal,\n          keep: walkNameFilter(prefixes, panSNHaplotype(refName)),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          if (error instanceof NodeLimitError) {\n            error.message = error.message.replace(\n              'to see the graph',\n              'to see lanes',\n            )\n          }\n          throw error\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = referenceAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneOf(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const [first] = pairs\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      pairs.length === 1 && first\n        ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n        : `Reading ${pairs.length} lane pairs`,\n    )\n    const align = walkAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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+}

package/dist/chunks/{chunk-MDRNFKXW.js → chunk-5DRS22TL.js}

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