npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 8.3.5 → 8.3.6 - Mend

jbrowse-plugin-graphgenomeviewer 8.3.5 → 8.3.6

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package/dist/chunks/{GbzBaseSyntenyAdapter-RRLBONL5.js → GbzBaseSyntenyAdapter-BG6FNGHY.js} RENAMED Viewed

@@ -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-HMIJBEUE.js";import{a as te}from"./chunk-SYKOZDP6.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-EVKN4Y3R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as V,a as K,c as L}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-RRLBONL5.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-HLWIFWDZ.js";import{a as te}from"./chunk-SYKOZDP6.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-EVKN4Y3R.js";import"./chunk-M2D7NUOY.js";import{h as z,i as E}from"./chunk-HQ7FQACT.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as V,a as K,c as L}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{g as F,h as N,i as C}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import{e as G,h as X,i as Y,j as J}from"./chunk-6VNDP3UB.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{e as _,o as B}from"./chunk-J5RMHLFJ.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-BG6FNGHY.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-7COETKFB.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as ee}from"./chunk-KVZIGTH3.js";import{a as K,b as V,d as Z,e as J,f as B,g as Q,h as Y}from"./chunk-HLWIFWDZ.js";import"./chunk-SYKOZDP6.js";import{a as G}from"./chunk-KOB7YIMR.js";import{p as L,q as H,r as q}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-3HS6N7WB.js";import"./chunk-HICKAMKK.js";import{E as X,F as z,i as U}from"./chunk-DAF7EWRF.js";import"./chunk-YBLNN5FU.js";import"./chunk-ROZPEXN4.js";import{a as O,c as D,d as A,g as x,h as F,i as E}from"./chunk-L372SDUG.js";import"./chunk-OTBDKJEA.js";import"./chunk-3VGXCEMQ.js";import"./chunk-OGQ6OQDN.js";import"./chunk-3WG3GF2A.js";import{o as v}from"./chunk-J5RMHLFJ.js";var me=50;function le(r){let o=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=me&&(t==="I"&&s==="D"\|\|t==="D"&&s==="I")?(o.push(["X",a]),e++):o.push([t,a])}return o}function R(r){return Array.from(r.ids,(o,e)=>2*o+r.rev[e])}function P(r,o){let e=r.get(o);return e===void 0?0:e.end-e.start}function te(r){let o=new Map,e=s=>{let n=P(r,s),i=o.get(n);return i===void 0&&(i="N".repeat(n),o.set(n,i)),i},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=R(s),t.set(s,n)),n};return(s,n)=>H({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var _=100;function I(r,o,e){let t=r.at(-1);e>0&&(t?.[0]===o?t[1]+=e:r.push([o,e]))}function ae(r){let o=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+o(s)}),a};return(t,a)=>{let s=R(a),n=R(t),[i,c]=L(n,s,o),[h,d]=L(n.map(y=>y^1).reverse(),s,o),m=d>c,p=m?h:i,b=Math.max(c,d);if(b<_)return[];let f=e(s),g=e(n),u=y=>m?n.length-1-p[y][0]:p[y][0],k=[];p.forEach(([,y],N)=>{if(N>0){let[M,l]=[u(N-1),u(N)].sort((w,C)=>w-C);I(k,"I",g[l]-g[M+1]),I(k,"D",f[y]-f[p[N-1][1]+1])}I(k,"=",o(s[y]))});let[S,W]=[u(0),u(p.length-1)].sort((y,N)=>y-N);return[{queryStart:g[S],queryEnd:g[W+1],targetStart:f[p[0][1]],targetEnd:f[p.at(-1)[1]+1],strand:m?"-":"+",edits:k,sharedBases:b}]}}function ce(r){let o=new Map,e=new Set;r.ids.forEach((t,a)=>{o.has(t)?e.add(t):o.set(t,r.rev[a])});for(let t of e)o.delete(t);return o}function ne(r){let o=new Map,e=t=>{let a=o.get(t);return a===void 0&&(a=ce(t),o.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,i=0;for(let[c,h]of e(t)){let d=s.get(c);d===h?n+=P(r,c):d!==void 0&&(i+=P(r,c))}return{same:n,opposite:i}}}function se(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let{same:n,opposite:i}=t(a,s);return n>=_&&i>=_?e(a,s):o(a,s)}}var pe=1e4;function re(r){let o=ae(r),e=te(r),t=ne(r);return(a,s)=>{let n=o(a,s),i=n[0]?.strand,{same:c,opposite:h}=t(a,s);return i===void 0\|\|Math.min(c,h)<pe?n:[...n,...e(a,s).filter(d=>d.strand!==i)]}}function j({chain:r,target:o,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=le(r.edits);return Y({target:{name:o.name,assemblyName:t,refName:a,start:o.hapStart+r.targetStart,end:o.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:A(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:q(n),matches:n.reduce((i,[c,h])=>i+(c==="="?h:0),0),columns:n.reduce((i,[,c])=>i+c,0)})}function ie(r,o,e,t,a){let s=a==="leave",n=i=>i.kind==="elsewhere"&&(s?i.chunk.start>=r.refStart:i.chunk.start<r.refStart);for(let i of e){let{name:c,fragStart:h,hapStart:d,ids:m,rev:p,before:b,after:f}=i;if(c===r.name&&h===r.fragStart){let g=d;for(let u=0;u<m.length;u++){let k=t.get(m[u]),S=k===void 0?0:k.end-k.start;if(k?.rank===0&&k.refName===o&&(s?k.end===r.refStart:k.start===r.refEnd)){let W=n(f)!==n(b)?n(f):u>0!=u<m.length-1?u>0:s!==(p[u]===1);return{skip:r,at:W?g+S:g,strand:W===s?"+":"-"}}g+=S}}}}function oe({crossing:r,refName:o,assemblyName:e,mateAssemblyName:t}){let{skip:a,at:s,strand:n}=r,i=`${a.name}:${a.fragStart}:${a.piece}:skip`;return new K({uniqueId:i,assemblyName:e,refName:o,start:a.refStart,end:a.refEnd,type:"deletion",strand:n==="-"?-1:1,syntenyId:i,spansWindow:!0,mate:{refName:A(a.name),start:s,end:s,assemblyName:t}})}var T=({name:r})=>D(r)??r,$=class extends V{constructor(){super(...arguments);this.walks=new ee(X(this,["walksLocation"],["walksIndex"]),this);this.refNames=new z(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=F(this,a),n=E(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(i=>i!==s&&O(i)!==s).map(i=>({name:B(n,i),label:i,group:O(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0\|\|t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolveForCut(e,{signal:t.signal});return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let i=U(a,e);return v(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:i,expand:i,links:!1}).catch(c=>{throw Q(c,t.end-t.start)}))}async skipCrossings(e,t,a){let s=[],n=t;for(let i of["leave","rejoin"]){let c=await this.sideCrossings(e,n,i,a);for(let d of c)s.push(d);let h=new Set(c.map(d=>d.skip));n=n.filter(d=>!h.has(d))}return s}async sideCrossings(e,t,a,s){let{signal:n}=s,{chunk:i}=await this.walks.reader.header({signal:n}),c=m=>a==="leave"?m.refStart-1:m.refEnd,h=new Map;for(let m of t){let p=c(m),b=Math.floor(p/i),f=h.get(b);f?(f.group.push(m),f.start=Math.min(f.start,p),f.end=Math.max(f.end,p+1)):h.set(b,{group:[m],start:p,end:p+1})}return(await Promise.all([...h.values()].map(async({group:m,start:p,end:b})=>{let f=new Set(m.map(u=>u.name)),g=u=>f.has(u);try{let{graph:u,fragments:k}=await this.walks.reader.cut(e,{start:p,end:b},{...this.walks.budgets(),signal:n,keep:g,expand:g,context:0,contained:!0,links:!1});return m.map(S=>ie(S,e,k,u.nodes,a))}catch(u){if(n?.aborted)throw u;return[]}}))).flat().filter(m=>m!==void 0)}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(l=>F(this,l)):void 0,n=F(this,a.targetAssemblyName),i=n===void 0?s:s===void 0\|\|s.some(l=>x(n,l)\|\|x(l,n))?[n]:[];if(i?.length===0)return[];let{start:c,end:h}=t,d=`Reading walks ${t.refName}:${c.toLocaleString()}-${h.toLocaleString()}`,{graph:m,fragments:p,skips:b}=await this.laneWalks(e,t,i,a,d),f=({name:l})=>i===void 0?0:i.findIndex(w=>x(l,w)),g=new Set(p.map(T)),u=await v(d,a.statusCallback,()=>this.skipCrossings(e,b.filter(l=>f(l)>=0&&!g.has(T(l))&&l.refStart<=c&&l.refEnd>=h),a)),k=re(m.nodes),S=E(this),W=l=>B(S,T(l)),y=p.filter(l=>l.name===e),N=p.filter(l=>l.name!==e&&f(l)>=0).map(l=>({rank:f(l),features:y.flatMap(w=>k(l,w).map(C=>j({chain:C,target:w,query:l,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:W(l)})))})),M=u.map(l=>({rank:f(l.skip),features:[oe({crossing:l,refName:t.refName,assemblyName:t.assemblyName,mateAssemblyName:W(l.skip)})]}));return[...N,...M].sort((l,w)=>l.rank-w.rank).flatMap(l=>l.features)}async pairFeatures(e,t,a,s){let n=a.map(m=>({pair:m,featurePrefix:F(this,m.queryAssemblyName),matePrefix:F(this,m.targetAssemblyName)})),{graph:i,fragments:c}=await this.laneWalks(e,t,n.flatMap(m=>[m.featurePrefix,m.matePrefix]),s,J(a)),h=se(i.nodes),d=m=>c.filter(p=>x(p.name,m));return n.flatMap(({pair:m,featurePrefix:p,matePrefix:b})=>d(p).flatMap(f=>d(b).flatMap(g=>h(g,f).map(u=>j({chain:u,target:f,query:g,assemblyName:m.queryAssemblyName,refName:A(f.name),mateAssemblyName:m.targetAssemblyName})))))}getFeatures(e,t={}){return G(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=Z(t),i=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let c of i)a.next(c)}a.complete()},t.signal)}};export{$ as default};
2	+ //# sourceMappingURL=WalkTabixSyntenyAdapter-7COETKFB.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-7COETKFB.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
+  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments, pairCigar } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type {\n  WalkFragment,\n  WalkNode,\n  WalkSkip,\n  WalkStop,\n} from '@jbrowse/graph-walks'\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\n// A walk's steps as the handles gbz-base reads, 2 * id + reversed\nfunction handlesOf(fragment: WalkFragment) {\n  return Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n}\n\nfunction nodeLength(nodes: Map<number, WalkNode>, id: number) {\n  const node = nodes.get(id)\n  return node === undefined ? 0 : node.end - node.start\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 length = nodeLength(nodes, id)\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 cachedHandles = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = handlesOf(fragment)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: cachedHandles(query),\n      target: cachedHandles(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) => nodeLength(nodes, handle >> 1)\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\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// Each node a walk visits once, with the direction it passes it\nfunction singleVisits(fragment: WalkFragment) {\n  const rev = new Map<number, number>()\n  const twice = new Set<number>()\n  fragment.ids.forEach((id, i) => {\n    if (rev.has(id)) {\n      twice.add(id)\n    } else {\n      rev.set(id, fragment.rev[i]!)\n    }\n  })\n  for (const id of twice) {\n    rev.delete(id)\n  }\n  return rev\n}\n\n// The bases on singly visited nodes two walks pass the same way and the\n// opposite way\nfunction directionShares(nodes: Map<number, WalkNode>) {\n  const visits = new Map<WalkFragment, Map<number, number>>()\n  const visitsOf = (fragment: WalkFragment) => {\n    let found = visits.get(fragment)\n    if (found === undefined) {\n      found = singleVisits(fragment)\n      visits.set(fragment, found)\n    }\n    return found\n  }\n  return (query: WalkFragment, target: WalkFragment) => {\n    const theirs = visitsOf(target)\n    let same = 0\n    let opposite = 0\n    for (const [id, rev] of visitsOf(query)) {\n      const other = theirs.get(id)\n      if (other === rev) {\n        same += nodeLength(nodes, id)\n      } else if (other !== undefined) {\n        opposite += nodeLength(nodes, id)\n      }\n    }\n    return { same, opposite }\n  }\n}\n\n/**\n * Aligns one lane's walk fragment to another's. The weighted subsequence\n * (`referenceAligner`) is the fast route and matches through copy-number\n * arrays, but it reads one direction per pair, so an inversion between the\n * lanes comes out as an insertion beside a deletion. A pair sharing 100 bp\n * (MIN_MATCH_BP) or more of singly visited nodes in each direction goes to\n * pair chaining (`walkAligner`) instead, which answers the inverted stretch as\n * a reverse-strand record of its own. Chaining leaves out every node a walk\n * passes twice, so counting singly visited nodes misses no inversion it could\n * draw.\n */\nexport function lanePairAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const { same, opposite } = shares(query, target)\n    return same >= MIN_MATCH_BP && opposite >= MIN_MATCH_BP\n      ? chained(query, target)\n      : subsequence(query, target)\n  }\n}\n\n// The multi-way display's SPLIT_AT_GAP_BP, under which a turned stretch names\n// no inversion there\nconst TURNED_MIN_BP = 10_000\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as `referenceAligner`\n * does, then adds the stretches it reads the other way. A walk sharing\n * TURNED_MIN_BP or more of singly visited nodes in each direction is chained\n * too, and the chained records on the strand the subsequence did not take are\n * its turned stretches. The subsequence record stays, so a copy-number array,\n * which chaining leaves out, still matches one pass alike in every lane.\n */\nexport function anchorAligner(nodes: Map<number, WalkNode>) {\n  const subsequence = referenceAligner(nodes)\n  const chained = walkAligner(nodes)\n  const shares = directionShares(nodes)\n  return (query: WalkFragment, target: WalkFragment) => {\n    const records = subsequence(query, target)\n    const taken = records[0]?.strand\n    const { same, opposite } = shares(query, target)\n    return taken === undefined || Math.min(same, opposite) < TURNED_MIN_BP\n      ? records\n      : [\n          ...records,\n          ...chained(query, target).filter(chain => chain.strand !== taken),\n        ]\n  }\n}\n\n/**\n * One record of a walk aligned to another, with its short balanced bubbles as\n * mismatches\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 edits = bubblesAsMismatches(chain.edits)\n  return matchFeature({\n    target: {\n      name: target.name,\n      assemblyName,\n      refName,\n      start: target.hapStart + chain.targetStart,\n      end: target.hapStart + chain.targetEnd,\n    },\n    query: {\n      name: query.name,\n      assemblyName: mateAssemblyName,\n      refName: panSNContig(query.name),\n      start: query.hapStart + chain.queryStart,\n      end: query.hapStart + chain.queryEnd,\n    },\n    strand: chain.strand,\n    cigar: pairCigar(edits),\n    matches: edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0),\n    columns: edits.reduce((sum, [, n]) => sum + n, 0),\n  })\n}\n\n/** The point on a haplotype's contig where it crosses a skipped stretch */\nexport interface SkipCrossing {\n  skip: WalkSkip\n  at: number\n  strand: '+' | '-'\n}\n\n/**\n * The reference node either side of a skipped stretch: the one a haplotype\n * leaves, ending at `refStart`, or the one it rejoins, starting at `refEnd`\n */\nexport type SkipSide = 'leave' | 'rejoin'\n\n/**\n * Where a haplotype that skips the window crosses its deletion, from a cut\n * over the reference node on one `side` of it. The jump lies on whichever end\n * of the walk's fragment goes on to a chunk across the stretch; with neither\n * or both, on the end the fragment's other steps leave free, and failing that\n * on the end the node's own direction points to. A walk that passes the node\n * inverted between two forward steps still crosses after it.\n */\nexport function skipCrossing(\n  skip: WalkSkip,\n  refName: string,\n  fragments: WalkFragment[],\n  nodes: Map<number, WalkNode>,\n  side: SkipSide,\n): SkipCrossing | undefined {\n  const leaving = side === 'leave'\n  const across = (stop: WalkStop) =>\n    stop.kind === 'elsewhere' &&\n    (leaving\n      ? stop.chunk.start >= skip.refStart\n      : stop.chunk.start < skip.refStart)\n  for (const fragment of fragments) {\n    const { name, fragStart, hapStart, ids, rev, before, after } = fragment\n    if (name === skip.name && fragStart === skip.fragStart) {\n      let at = hapStart\n      for (let i = 0; i < ids.length; i++) {\n        const node = nodes.get(ids[i]!)\n        const length = node === undefined ? 0 : node.end - node.start\n        if (\n          node?.rank === 0 &&\n          node.refName === refName &&\n          (leaving ? node.end === skip.refStart : node.start === skip.refEnd)\n        ) {\n          const jumpsAfter =\n            across(after) !== across(before)\n              ? across(after)\n              : i > 0 !== i < ids.length - 1\n                ? i > 0\n                : leaving !== (rev[i] === 1)\n          return {\n            skip,\n            at: jumpsAfter ? at + length : at,\n            strand: jumpsAfter === leaving ? '+' : '-',\n          }\n        }\n        at += length\n      }\n    }\n  }\n  return undefined\n}\n\n/**\n * A haplotype whose deletion spans the whole window, as the record a\n * multi-way display lifts out as a deletion: `spansWindow`, the skipped\n * stretch whole so its length heads the lane, and the crossing as its mate.\n * The record carries no CIGAR and no identity, so no ramp or identity filter\n * reads it as an alignment.\n */\nexport function skipFeature({\n  crossing,\n  refName,\n  assemblyName,\n  mateAssemblyName,\n}: {\n  crossing: SkipCrossing\n  refName: string\n  assemblyName: string\n  mateAssemblyName: string\n}) {\n  const { skip, at, strand } = crossing\n  const id = `${skip.name}:${skip.fragStart}:${skip.piece}:skip`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start: skip.refStart,\n    end: skip.refEnd,\n    type: 'deletion',\n    strand: strand === '-' ? -1 : 1,\n    syntenyId: id,\n    spansWindow: true,\n    mate: {\n      refName: panSNContig(skip.name),\n      start: at,\n      end: at,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import {\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'\nimport { walksKept } from '@jbrowse/graph-walks'\n\nimport {\n  anchorAligner,\n  chainFeature,\n  lanePairAligner,\n  skipCrossing,\n  skipFeature,\n} from './walkLanes.ts'\nimport { WalkIndex } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SkipCrossing, SkipSide } from './walkLanes.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkSkip } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = ({ name }: { name: string }) => panSNHaplotype(name) ?? name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly walks: WalkIndex = new WalkIndex(\n    openTabixSlot(this, ['walksLocation'], ['walksIndex']),\n    this,\n  )\n  private readonly refNames: PanSNRefNames = new PanSNRefNames(\n    this.walks.file,\n    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    return this.walks.haplotypeNames(opts)\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 } = await this.walks.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      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(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  /**\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 refName = await this.refNames.resolveForCut(region, {\n      signal: opts.signal,\n    })\n    return this.walks.subgraph(refName, region, opts)\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  // Named lanes come back in full where format 5 abridged them: an abridged\n  // walk is two reference steps, which drew 15 of the HPRC MHC launch's 32\n  // lanes empty.\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    const keep = walksKept(prefixes, refName)\n    return updateStatus(status, opts.statusCallback, () =>\n      this.walks.reader\n        .cut(refName, region, {\n          ...this.walks.budgets(),\n          signal: opts.signal,\n          keep,\n          expand: keep,\n          links: false,\n        })\n        .catch((error: unknown) => {\n          throw laneZoomNotice(error, region.end - region.start)\n        }),\n    )\n  }\n\n  /**\n   * Where each skipping haplotype crosses its deletion, read from contained\n   * cuts over the reference node it leaves, one cut per chunk those nodes\n   * fall in, and for any that cut misses, over the node it rejoins. A cut\n   * that fails drops only its own haplotypes' crossings.\n   */\n  private async skipCrossings(\n    refName: string,\n    skips: WalkSkip[],\n    opts: LaneFeatureOptions,\n  ) {\n    const found: SkipCrossing[] = []\n    let missed = skips\n    for (const side of ['leave', 'rejoin'] as const) {\n      const crossings = await this.sideCrossings(refName, missed, side, opts)\n      for (const crossing of crossings) {\n        found.push(crossing)\n      }\n      const placed = new Set(crossings.map(crossing => crossing.skip))\n      missed = missed.filter(skip => !placed.has(skip))\n    }\n    return found\n  }\n\n  private async sideCrossings(\n    refName: string,\n    skips: WalkSkip[],\n    side: SkipSide,\n    opts: LaneFeatureOptions,\n  ) {\n    const { signal } = opts\n    const { chunk } = await this.walks.reader.header({ signal })\n    const boundary = (skip: WalkSkip) =>\n      side === 'leave' ? skip.refStart - 1 : skip.refEnd\n    const byChunk = new Map<\n      number,\n      { group: WalkSkip[]; start: number; end: number }\n    >()\n    for (const skip of skips) {\n      const at = boundary(skip)\n      const cs = Math.floor(at / chunk)\n      const held = byChunk.get(cs)\n      if (held) {\n        held.group.push(skip)\n        held.start = Math.min(held.start, at)\n        held.end = Math.max(held.end, at + 1)\n      } else {\n        byChunk.set(cs, { group: [skip], start: at, end: at + 1 })\n      }\n    }\n    const found = await Promise.all(\n      [...byChunk.values()].map(async ({ group, start, end }) => {\n        const names = new Set(group.map(skip => skip.name))\n        const keep = (name: string) => names.has(name)\n        try {\n          const { graph, fragments } = await this.walks.reader.cut(\n            refName,\n            { start, end },\n            {\n              ...this.walks.budgets(),\n              signal,\n              keep,\n              expand: keep,\n              context: 0,\n              contained: true,\n              links: false,\n            },\n          )\n          return group.map(skip =>\n            skipCrossing(skip, refName, fragments, graph.nodes, side),\n          )\n        } catch (error) {\n          if (signal?.aborted) {\n            throw error\n          }\n          return []\n        }\n      }),\n    )\n    return found.flat().filter(crossing => crossing !== undefined)\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. A haplotype whose\n   * deletion spans the window, with no walk there on any contig, is one\n   * `spansWindow` record of the skipped stretch.\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 status = `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`\n    const { graph, fragments, skips } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      status,\n    )\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 = ({ name }: { name: string }) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix => panSNMatchesPrefix(name, prefix))\n    // NA19036#1 skips the IGL locus on one contig and walks it on another\n    const walking = new Set(fragments.map(haplotypeOf))\n    const crossings = await updateStatus(status, opts.statusCallback, () =>\n      this.skipCrossings(\n        refName,\n        skips.filter(\n          skip =>\n            rank(skip) >= 0 &&\n            !walking.has(haplotypeOf(skip)) &&\n            skip.refStart <= start &&\n            skip.refEnd >= end,\n        ),\n        opts,\n      ),\n    )\n    const align = anchorAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const laneOf = (walk: { name: string }) =>\n      laneAssemblyName(asmByPrefix, haplotypeOf(walk))\n    const references = fragments.filter(f => f.name === refName)\n    const walked = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .map(query => ({\n        rank: rank(query),\n        features: 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(query),\n            }),\n          ),\n        ),\n      }))\n    const skipped = crossings.map(crossing => ({\n      rank: rank(crossing.skip),\n      features: [\n        skipFeature({\n          crossing,\n          refName: region.refName,\n          assemblyName: region.assemblyName,\n          mateAssemblyName: laneOf(crossing.skip),\n        }),\n      ],\n    }))\n    return [...walked, ...skipped]\n      .sort((a, b) => a.rank - b.rank)\n      .flatMap(lane => lane.features)\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 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      lanePairsStatus(pairs),\n    )\n    const align = lanePairAligner(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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+}

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