jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.1

package/README.md

@@ -84,24 +84,33 @@ In reading order:
 - [sequenceTubeMap, MemPanG26 edition](https://github.com/cmdcolin/sequenceTubeMap):
   our fork of the tube map app
 
-### Programmatic usage
+Supporting utility libraries
 
-- [@jbrowse/bandage-core](https://github.com/GMOD/bandage-core) (npm): layout
-  and drawing engine, plus `bandage-figure` for SVGs with no browser
-- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout)
-  (npm): stress layout
+- [@jbrowse/bandage-core](https://github.com/GMOD/bandage-core) (npm): bandage
+  layout and drawing engine
 - [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) (npm): tube map
   layout
 - [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) (npm): `.gbz.db` reader
-- [ggbandage](https://github.com/GMOD/ggbandage) (R): Bandage layout as ggplot2
-  layers
-- [ggtubemap](https://github.com/GMOD/ggtubemap) (R): tube map as ggplot2 layers
+
+Supporting graph layout libraries
+
+- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout)
+- [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout)
+
+Supporting data preparation toolkits
+
 - [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix): indexes a GFA
 - [gbz-haplotype-index](https://github.com/GMOD/gbz-haplotype-index): names
   every walk in a gbz-base cut
 - [gfa-to-pairwise-paf](https://github.com/cmdcolin/gfa-to-pairwise-paf-rs):
   graph to PAF, for synteny views
 
+Standalone R packages
+
+- [ggbandage](https://github.com/GMOD/ggbandage) (R): Bandage layout as ggplot2
+  layers
+- [ggtubemap](https://github.com/GMOD/ggtubemap) (R): tube map as ggplot2 layers
+
 ## License
 
 GPL-3.0-or-later, based on work from Bandage and OGDF, both GPL.

package/dist/chunks/{GbzBaseSyntenyAdapter-TIXR4Y3J.js → GbzBaseSyntenyAdapter-A56NDFW7.js}

@@ -1,2 +1,2 @@
-import{a as q,b as re,c as de,d as oe,e as T}from"./chunk-SAMJE6GH.js";import{a as ne}from"./chunk-KOB7YIMR.js";import{a as Z,b as U,c as X,d as g,e as C,f as M,g as k,h as E,i as z,k as Y}from"./chunk-YJHYBDYF.js";import"./chunk-EWFJBQDV.js";import{a as O,b as H}from"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-IXQK7JAW.js";import{a as ae}from"./chunk-TXI43PEN.js";import{a as ee,c as L,f as te}from"./chunk-AMFIBQVR.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as A,f as P,g as B}from"./chunk-446RWIA3.js";import"./chunk-E7J6SB5P.js";import{b as G,e as J,f as K,g as V}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function F(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function fe(n){return K(n)&&F(J(n))?V(n,i=>F(i)):void 0}function he(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function se(n,i){let t=fe(n);if(!t)return{};try{return await N(t,i).stat(),{location:t}}catch(e){return he(e)?{}:{unreadable:String(e)}}}var ge=5e3,ue=50*2**20,_=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ye(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var ie=(n,i)=>n.path.some(t=>i.has(t.name)),v=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=L({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new _(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&ie(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>ie(a,i));return{records:ye(e,ge),total:e.length}}};var I=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${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 ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function be(n,i){return`${g(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function we({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(r<=a)){let{name:s,hapStart:p,hapEnd:l}=n,f=be(s,n),u={uniqueId:f,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:s.contig,start:p,end:l,assemblyName:e}};return new q(u)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${g(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${g(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var Se=12e4;function Pe(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=g(r);if(i.has(s)){let p=`${s}#${r.contig}`,l=t.get(p);l?l.push([o,c]):t.set(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<=Se&&(e=Math.max(e,o))}}return e}function Q(n,i){return n instanceof X&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var ce=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),j=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await se(t,this.pluginManager),r=a.location,o=await U.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(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 M(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(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=g(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=B(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:T(o,s.prefix),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:P(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:A(g(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=>P(this,r));return a===void 0&&e===void 0?void 0:r=>C(r,a)&&(e===void 0||A(g(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:l,start:f,end:u}=ce(t);if(p!==o)throw new D(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${l} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new I(s);let m=await Y(r,y,f,u,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw Q(b,"the graph")});return typeof m=="string"?m:ae(m,{start:f,end:u},e.walkRows)}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=P(this,t);return(await this.getHaplotypes(e)).filter(r=>A(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=P(this,e.targetAssemblyName),l=B(this),f=this.keepPredicate(e.haplotypes,p),u=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(u?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:u,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(m=>{throw Q(z(m,y,s-c)??m,"lanes")})):[]).flatMap(m=>{let b=m.resolved?we({alignment:m,assemblyName:r,refName:o,lane:T(l,g(m.name))}):void 0;return b===void 0?[]:[b]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,l=(await Promise.all(e.map(async d=>({pair:d,featureSide:await this.laneHaplotypes(d.queryAssemblyName,a),mateSide:await this.laneHaplotypes(d.targetAssemblyName,a)})))).filter(({featureSide:d,mateSide:h})=>d.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:d,mateSide:h})=>[...d,...h].map(g))),u=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[m]=e,b=(d,h)=>r.getSubgraphs({path:d,start:c,end:s,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(g(S))}),pe=async d=>{let h=await b(d,x).catch(w=>{throw Q(z(w,y,s-c)??w,"lanes")}),S=Pe(h,f),R=Math.ceil(S/2)+2e3;return S>0&&R>x?b(d,R).catch(w=>{if(w instanceof Z)return h;throw w}):h};return(u&&m&&l.length>0?await $(e.length===1?`Reading ${m.queryAssemblyName} against ${m.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(u)):[]).flatMap(d=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(w=>R.flatMap(le=>d.pairAlignments({target:w,query:le,bases:!1}).map(me=>xe({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=ce(t);return ne(async r=>{let{db:o,anchor:c,unreadableIndex:s}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new I(s);if(a.assemblyName===c){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of l)r.next(f)}r.complete()},e.signal)}};export{D as HaplotypeWindowError,I as NoHaplotypeIndexError,de as PairTargetError,j as default,we as fragmentFeature,xe as pairFeature,Pe as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-TIXR4Y3J.js.map
+import{a as q,b as re,c as de,d as oe,e as T}from"./chunk-WI7LRX6I.js";import{a as ne}from"./chunk-KOB7YIMR.js";import{a as Z,b as U,c as X,d as g,e as C,f as M,g as k,h as E,i as z,k as Y}from"./chunk-FAVU7473.js";import"./chunk-S3QFRJR3.js";import{a as O,b as H}from"./chunk-JT3RXYIL.js";import"./chunk-77GS3NVS.js";import"./chunk-T4HOC6O3.js";import{a as ae}from"./chunk-TXI43PEN.js";import{a as ee,c as L,f as te}from"./chunk-4IJKHORO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as A,f as P,g as B}from"./chunk-IIGYYZI5.js";import"./chunk-E7J6SB5P.js";import{b as G,e as J,f as K,g as V}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function F(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function fe(n){return K(n)&&F(J(n))?V(n,i=>F(i)):void 0}function he(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function se(n,i){let t=fe(n);if(!t)return{};try{return await N(t,i).stat(),{location:t}}catch(e){return he(e)?{}:{unreadable:String(e)}}}var ge=5e3,ue=50*2**20,_=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ye(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var ie=(n,i)=>n.path.some(t=>i.has(t.name)),v=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=L({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new _(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&ie(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>ie(a,i));return{records:ye(e,ge),total:e.length}}};var I=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${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 ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function be(n,i){return`${g(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function we({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(r<=a)){let{name:s,hapStart:p,hapEnd:l}=n,f=be(s,n),u={uniqueId:f,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:s.contig,start:p,end:l,assemblyName:e}};return new q(u)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${g(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${g(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var Se=12e4;function Pe(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=g(r);if(i.has(s)){let p=`${s}#${r.contig}`,l=t.get(p);l?l.push([o,c]):t.set(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<=Se&&(e=Math.max(e,o))}}return e}function Q(n,i){return n instanceof X&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var ce=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),j=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await se(t,this.pluginManager),r=a.location,o=await U.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(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 M(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(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=g(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=B(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:T(o,s.prefix),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:P(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:A(g(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=>P(this,r));return a===void 0&&e===void 0?void 0:r=>C(r,a)&&(e===void 0||A(g(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:l,start:f,end:u}=ce(t);if(p!==o)throw new D(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${l} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new I(s);let m=await Y(r,y,f,u,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw Q(b,"the graph")});return typeof m=="string"?m:ae(m,{start:f,end:u},e.walkRows)}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=P(this,t);return(await this.getHaplotypes(e)).filter(r=>A(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=P(this,e.targetAssemblyName),l=B(this),f=this.keepPredicate(e.haplotypes,p),u=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(u?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:u,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(m=>{throw Q(z(m,y,s-c)??m,"lanes")})):[]).flatMap(m=>{let b=m.resolved?we({alignment:m,assemblyName:r,refName:o,lane:T(l,g(m.name))}):void 0;return b===void 0?[]:[b]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,l=(await Promise.all(e.map(async d=>({pair:d,featureSide:await this.laneHaplotypes(d.queryAssemblyName,a),mateSide:await this.laneHaplotypes(d.targetAssemblyName,a)})))).filter(({featureSide:d,mateSide:h})=>d.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:d,mateSide:h})=>[...d,...h].map(g))),u=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[m]=e,b=(d,h)=>r.getSubgraphs({path:d,start:c,end:s,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(g(S))}),pe=async d=>{let h=await b(d,x).catch(w=>{throw Q(z(w,y,s-c)??w,"lanes")}),S=Pe(h,f),R=Math.ceil(S/2)+2e3;return S>0&&R>x?b(d,R).catch(w=>{if(w instanceof Z)return h;throw w}):h};return(u&&m&&l.length>0?await $(e.length===1?`Reading ${m.queryAssemblyName} against ${m.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(u)):[]).flatMap(d=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(w=>R.flatMap(le=>d.pairAlignments({target:w,query:le,bases:!1}).map(me=>xe({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=ce(t);return ne(async r=>{let{db:o,anchor:c,unreadableIndex:s}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new I(s);if(a.assemblyName===c){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of l)r.next(f)}r.complete()},e.signal)}};export{D as HaplotypeWindowError,I as NoHaplotypeIndexError,de as PairTargetError,j as default,we as fragmentFeature,xe as pairFeature,Pe as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-A56NDFW7.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-TIXR4Y3J.js.map → GbzBaseSyntenyAdapter-A56NDFW7.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VQWHMWLF.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.5/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VQWHMWLF.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
   "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample\n} from \"./chunk-Q7LYHGGQ.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { laneAssemblyName, requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\nexport interface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\nexport type { LanePair } from '../synteny/lanePairs.ts'\n\nexport class HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${haplotypePrefix(pair.target)}#${pair.target.contig}:${pair.targetStart}-${pair.targetEnd}|${haplotypePrefix(pair.query)}#${pair.query.contig}:${pair.queryStart}-${pair.queryEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName: lane,\n    refName: pair.target.contig,\n    start: pair.targetStart,\n    end: pair.targetEnd,\n    type: 'match',\n    strand: pair.strand === '-' ? -1 : 1,\n    CIGAR: pair.cigar,\n    syntenyId: id,\n    identity: pair.matches / Math.max(pair.columns, 1),\n    numMatches: pair.matches,\n    blockLen: pair.columns,\n    mate: {\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n      assemblyName: mateLane,\n    },\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample, referenceSamples } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSample,\n      referenceSamples,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw zoomInNotice(\n                  nodeLimitError(error, nodeLimit, end - start) ?? error,\n                  'lanes',\n                )\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const [first] = pairs\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw zoomInNotice(\n          nodeLimitError(error, nodeLimit, end - start) ?? error,\n          'lanes',\n        )\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && first && answerable.length > 0\n        ? await updateStatus(\n            pairs.length === 1\n              ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n              : `Reading ${pairs.length} lane pairs`,\n            opts.statusCallback,\n            () => bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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package/dist/chunks/{HighlightColorDialog-EYBKFSJU.js → HighlightColorDialog-YT55H62Y.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{LinearGraphDisplay-WIBVWRQE.js → LinearGraphDisplay-SPILNH4J.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=LinearGraphDisplay-WIBVWRQE.js.map
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+//# sourceMappingURL=LinearGraphDisplay-SPILNH4J.js.map

package/dist/chunks/{MinigraphBubbleAdapter-AGI2UYQR.js → MinigraphBubbleAdapter-2XGZPDI4.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=MinigraphBubbleAdapter-AGI2UYQR.js.map
+import{a as d}from"./chunk-WRH2EJKX.js";import{a as g,d as f,f as c}from"./chunk-ABNOMXT3.js";import{a as u}from"./chunk-KOB7YIMR.js";import{b,f as p,g as m}from"./chunk-4IJKHORO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-IIGYYZI5.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var r=class extends b{static{this.capabilities=["getFeatures","getRefNames"]}constructor(t,a,s){super(t,a,s),this.bubbles=p(this,["bubblesLocation"],["index"]),this.refNames=new m(this.bubbles,this)}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async hasDataForRefName(){return!0}getFeatures(t,a={}){let{signal:s,statusCallback:h}=a;return u(async o=>{let n=await this.refNames.resolve(t,a);n!==void 0&&await l("Downloading bubbles",h,()=>d(this.bubbles,n,t.start,t.end,{signal:s,lineCallback:(A,y)=>{let e=g(A);o.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:f(e),description:c(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),o.complete()},s)}};export{r as default};
+//# sourceMappingURL=MinigraphBubbleAdapter-2XGZPDI4.js.map

package/dist/chunks/{RgfaTabixAdapter-2OL5X3HF.js → RgfaTabixAdapter-ZTFVNM4G.js}

@@ -1,3 +1,3 @@
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package/dist/chunks/{WalkTabixSyntenyAdapter-UKFHCFOF.js → WalkTabixSyntenyAdapter-I6E6HAN4.js}

@@ -1,2 +1,2 @@
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the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return G(this.reader,a,e,{...this.budgets(),signal:r,prefixes:s?.map(i=>N(this,i)),walkRows:n})}async laneWalks(e,t,r,s,n){return C(n,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:q(r,F(e)),links:!1}).catch(a=>{throw _(a)&&a instanceof Error&&(a.message=a.message.replace("to see the graph","to see lanes")),a}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(o=>N(this,o)):void 0,n=N(this,r.targetAssemblyName),a=n===void 0?s:s===void 0||s.some(o=>k(n,o)||k(o,n))?[n]:[];if(a?.length===0)return[];let{start:i,end:p}=t,{graph:y,fragments:h}=await this.laneWalks(e,t,a,r,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=X(y.nodes),d=x(this),c=h.filter(o=>o.name===e),f=o=>a===void 0?0:a.findIndex(g=>k(o.name,g));return h.filter(o=>o.name!==e&&f(o)>=0).sort((o,g)=>f(o)-f(g)).flatMap(o=>c.flatMap(g=>l(o,g).map(w=>O({chain:w,target:g,query:o,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:B(d,ne(o))}))))}async pairFeatures(e,t,r,s){let[n]=r,a=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&n?`Reading ${n.queryAssemblyName} against ${n.targetAssemblyName}`:`Reading ${r.length} lane pairs`),y=U(i.nodes),h=l=>p.filter(d=>k(d.name,l));return a.flatMap(({pair:l,featurePrefix:d,matePrefix:c})=>h(d).flatMap(f=>h(c).flatMap(u=>y(u,f).map(o=>O({chain:o,target:f,query:u,assemblyName:l.queryAssemblyName,refName:A(f.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return R(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=j(t),a=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let i of a)r.next(i)}r.complete()},t.signal)}};export{M as default};
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+import{b as q,c as D,d as H,e as G}from"./chunk-2QQDYK5V.js";import{a as _}from"./chunk-LUTMKRXY.js";import{a as T,b as I,d as j,e as B}from"./chunk-WI7LRX6I.js";import{a as R}from"./chunk-KOB7YIMR.js";import{p as W,q as L}from"./chunk-T4HOC6O3.js";import"./chunk-TXI43PEN.js";import{f as $,g as v}from"./chunk-4IJKHORO.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as P,c as F,d as A,e as k,f as N,g as x}from"./chunk-IIGYYZI5.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as C}from"./chunk-TENPGIPX.js";var Z=50;function ee(m){let e=[];for(let t=0;t<m.length;t++){let[r,s]=m[t],[n,a]=m[t+1]??[];s===a&&s<=Z&&(r==="I"&&n==="D"||r==="D"&&n==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function te(m){return m.map(([e,t])=>`${t}${e}`).join("")}function U(m){let e=new Map,t=n=>{let a=m.get(n),i=a===void 0?0:a.end-a.start,p=e.get(i);return p===void 0&&(p="N".repeat(i),e.set(i,p)),p},r=new Map,s=n=>{let a=r.get(n);return a===void 0&&(a=Array.from(n.ids,(i,p)=>2*i+n.rev[p]),r.set(n,a)),a};return(n,a)=>L({query:s(n),target:s(a),sequenceOf:t,bases:!1})}var ae=100;function E(m,e,t){let r=m.at(-1);t>0&&(r?.[0]===e?r[1]+=t:m.push([e,t]))}function X(m){let e=s=>{let n=m.get(s>>1);return n===void 0?0:n.end-n.start},t=s=>{let n=new Float64Array(s.length+1);return s.forEach((a,i)=>{n[i+1]=n[i]+e(a)}),n},r=s=>Array.from(s.ids,(n,a)=>2*n+s.rev[a]);return(s,n)=>{let a=r(n),i=r(s),[p,y]=W(i,a,e),[h,l]=W(i.map(b=>b^1).reverse(),a,e),d=l>y,c=d?h:p,f=Math.max(y,l);if(f<ae)return[];let u=t(a),o=t(i),g=b=>d?i.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],S)=>{if(S>0){let[K,Q]=[g(S-1),g(S)].sort((V,Y)=>V-Y);E(w,"I",o[Q]-o[K+1]),E(w,"D",u[b]-u[c[S-1][1]+1])}E(w,"=",e(a[b]))});let[z,J]=[g(0),g(c.length-1)].sort((b,S)=>b-S);return[{queryStart:o[z],queryEnd:o[J+1],targetStart:u[c[0][1]],targetEnd:u[c.at(-1)[1]+1],strand:d?"-":"+",edits:w,sharedBases:f}]}}function O({chain:m,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:n}){let a=e.hapStart+m.targetStart,i=e.hapStart+m.targetEnd,p=t.hapStart+m.queryStart,y=t.hapStart+m.queryEnd,h=ee(m.edits),l=h.reduce((f,[u,o])=>f+(u==="="?o:0),0),d=h.reduce((f,[,u])=>f+u,0),c=`${e.name}:${a}-${i}|${t.name}:${p}-${y}`;return new T({uniqueId:c,assemblyName:r,refName:s,start:a,end:i,type:"match",strand:m.strand==="-"?-1:1,CIGAR:te(h),syntenyId:c,identity:l/Math.max(d,1),numMatches:l,blockLen:d,mate:{refName:A(t.name),start:p,end:y,assemblyName:n}})}var ne=m=>F(m.name)??m.name,M=class extends I{constructor(e,t,r){super(e,t,r);let s=$(this,["walksLocation"],["walksIndex"]);this.reader=new D(s),this.refNames=new v(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,n=N(this,s),a=x(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(i=>i!==n&&P(i)!==n).map(i=>({name:B(a,i),label:i,group:P(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),budgetNames:H}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:n}=t,a=await this.refNames.resolve(e,{signal:r});if(a===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`);return G(this.reader,a,e,{...this.budgets(),signal:r,prefixes:s?.map(i=>N(this,i)),walkRows:n})}async laneWalks(e,t,r,s,n){return C(n,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:q(r,F(e)),links:!1}).catch(a=>{throw _(a)&&a instanceof Error&&(a.message=a.message.replace("to see the graph","to see lanes")),a}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(o=>N(this,o)):void 0,n=N(this,r.targetAssemblyName),a=n===void 0?s:s===void 0||s.some(o=>k(n,o)||k(o,n))?[n]:[];if(a?.length===0)return[];let{start:i,end:p}=t,{graph:y,fragments:h}=await this.laneWalks(e,t,a,r,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=X(y.nodes),d=x(this),c=h.filter(o=>o.name===e),f=o=>a===void 0?0:a.findIndex(g=>k(o.name,g));return h.filter(o=>o.name!==e&&f(o)>=0).sort((o,g)=>f(o)-f(g)).flatMap(o=>c.flatMap(g=>l(o,g).map(w=>O({chain:w,target:g,query:o,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:B(d,ne(o))}))))}async pairFeatures(e,t,r,s){let[n]=r,a=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&n?`Reading ${n.queryAssemblyName} against ${n.targetAssemblyName}`:`Reading ${r.length} lane pairs`),y=U(i.nodes),h=l=>p.filter(d=>k(d.name,l));return a.flatMap(({pair:l,featurePrefix:d,matePrefix:c})=>h(d).flatMap(f=>h(c).flatMap(u=>y(u,f).map(o=>O({chain:o,target:f,query:u,assemblyName:l.queryAssemblyName,refName:A(f.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return R(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=j(t),a=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let i of a)r.next(i)}r.complete()},t.signal)}};export{M as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-I6E6HAN4.js.map

package/dist/chunks/{chunk-WX26KTZM.js → chunk-2QQDYK5V.js}

@@ -1,2 +1,2 @@
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_t={steps:"walkStepBudget",bytes:"walkByteBudget"};async function Jt(r,t,n,e){let{graph:o,kept:s,fragments:i}=await r.cut(t,n,{signal:e.signal,keep:ot(e.prefixes,ft(t)),stepBudget:e.walkRows?1/0:e.stepBudget,byteBudget:e.byteBudget,budgetNames:_t});return ht(o.tables(s,i),n,e.walkRows)}export{Et as a,ot as b,lt as c,_t as d,Jt as e};
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g=$(a[p]),x=c[p];f.set(g,x),w.nodes.has(g)||w.nodes.set(g,{refName:l[4],start:u,end:u+x,rank:0}),u+=x}w.ends.push({name:l[4],fragStart:+l[5],piece:+l[7],first:a[0],last:a.at(-1)}),(t===void 0||t(l[4]))&&w.rows.push({chunkStart:+l[1],name:l[4],fragStart:+l[5],hapOffset:d,piece:+l[7],n:a.length,steps:{ids:Int32Array.from(a,$),rev:Uint8Array.from(a,p=>p&1)},...ut(l,11,k)})}for(let l of r)if(l[3]==="nodes"){let k=D(l[4]),a=D(l[5]),c=0;for(let d=0;d<k.length;d++)c+=k[d],k[d]=c,f.set(c,a[d]);n&&dt(l,6,k,a,w.sequences)}else if(l[3]==="route"){let k=U(l[4],S,[]),a=U(l[5],S,[]),c=U(l[6],S,[]);y.push({entry:(e=k[0])!==null&&e!==void 0?e:-1,interior:a,exit:(o=c[0])!==null&&o!==void 0?o:-1})}let b=l=>{let k=y[l];if(!k)throw new L(`route ${l} is not in the chunk`);return k};for(let l of r){if(l[3]!=="walk")continue;let k=Nt(l[11]);w.chunk.walks.push({cols:l,choices:k});let a=l[4],c=+l[9],d=l[10],u=d.indexOf(":"),p=c,g=c+ +(u<0?d:d.slice(0,u));if(k.length>0){let x=b(k[0]),h=k[1]===1;tt(x,h)===-1&&(p=G(x,h,0));let m=k.length-3,N=b(k[m]),M=k[m+1]===1;pt(N,M)===-1&&(g=G(N,M,N.interior.length-1))}if(w.ends.push({name:a,fragStart:+l[5],piece:+l[7],first:p,last:g}),t===void 0||t(a)){let x=+l[8];for(let h=0;h<k.length;h+=3)for(let m of b(k[h]).interior){let N=$(m);if(!w.nodes.has(N)){let M=(s=f.get(N))!==null&&s!==void 0?s:0;w.nodes.set(N,{refName:a,start:0,end:M,rank:1})}}w.rows.push({chunkStart:+l[1],name:a,fragStart:+l[5],hapOffset:+l[6],piece:+l[7],n:x,steps:St(i,y,l,k,x),...ut(l,12,l[0])})}}return w}function kt(r,t,n,e){let o=new Map;for(let{path:s,routes:i,walks:f,lengths:y}of r){let w=s.handles;for(let a=1;a<w.length;a++)t.has($(w[a-1]))&&t.has($(w[a]))&&e(...Z(w[a-1],w[a]));let S=new Uint8Array(i.length);for(let a=0;a<i.length;a++){let{entry:c,interior:d,exit:u}=i[a],p=!1,g=c;for(let x of d){let h=t.has($(x));p||(p=h),h&&g!==-1&&t.has($(g))&&e(...Z(g,x)),g=x}g!==-1&&u!==-1&&t.has($(g))&&t.has($(u))&&e(...Z(g,u)),S[a]=p?1:0}let v=a=>{var c;return(c=y.get($(a)))!==null&&c!==void 0?c:0},b=new Float64Array(i.length).fill(-1),l=a=>(b[a]<0&&(b[a]=i[a].interior.reduce((c,d)=>c+v(d),0)),b[a]),k=new Uint8Array(i.length);for(let{cols:a,choices:c}of f){let d=0;for(let g=0;g<c.length;g+=3){let x=c[g];S[x]&&!k[x]&&d++}if(d===0)continue;let u=a[4],p=+a[6];gt(s,i,+a[9],a[10],c,{step(g){p+=v(g)},stretch(g,x,h){p+=h?s.bp(x+1)-s.bp(g+1):s.bp(g)-s.bp(x)},route(g,x){if(!S[g]||k[g])return p+=l(g),!0;k[g]=1;let h=i[g];for(let m=0;m<h.interior.length;m++){let N=G(h,x,m),M=$(N),A=v(N);if(t.has(M)){let E=o.get(M);(!E||u<E.refName||u===E.refName&&p<E.start)&&o.set(M,{refName:u,start:p,end:p+A,rank:1})}p+=A}return d--,d>0}})}}for(let[s,i]of o)n(s,i)}function Et(r){let t=[];for(let n of r){if(n[3]!=="ref")continue;let e=U(n[9],{id:0},[]),o=D(n[10]),s=+n[6];for(let i=0;i<e.length;i++){let f=o[i];t.push({id:$(e[i]),refName:n[4],start:s,end:s+f,rank:0}),s+=f}}return t}function mt(r){let t=new Map;for(let e of r){let o=`${e.name}	${e.fragStart}`,s=t.get(o);s||(s=new Map,t.set(o,s)),s.set(e.piece,e)}let n=[];for(let e of t.values())for(let[o,s]of e){let i=e.get(o+1);i&&n.push(Z(s.last,i.first))}return n}var q=class extends Error{constructor(t,n,e,o){super(t),this.regionTooLarge=!0,this.name="NodeLimitError",this.limit=n,this.windowBp=e,this.fitsBp=o}},Mt="#";function Q(r,t){return t!==void 0&&(r===t||r.startsWith(t+Mt))}var yt=r=>Number.parseFloat(r.toPrecision(3));function P(r){let t=yt(r/1e6);return t>=1?`${t.toLocaleString("en-US")}Mbp`:r>=1e3?`${yt(r/1e3).toLocaleString("en-US")}Kbp`:`${Math.floor(r)}bp`}function et(r,t){let n=new RegExp(`(?:^|\\t)${t}:i:(\\d+)`).exec(r);return n?+n[1]:void 0}function nt(r){var t,n,e;let o={references:[],haplotypes:[]};for(let s of r){let[i,f=""]=s.split("	");i==="#reference"?o.references.push(f):i==="#haplotype"?o.haplotypes.push(f):((t=o.format)!==null&&t!==void 0||(o.format=et(s,"format")),(n=o.chunk)!==null&&n!==void 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c?.rank===0?c:void 0},s=new Map,i=a=>{a&&s.set(`${a.refName}:${a.start}`,a)},f=(a,c,d)=>{let{ids:u}=a,p=c+d;for(;p>=0&&p<u.length&&o(u[p])===void 0;)p+=d;if(p<0||p>=u.length)return i(d<0?a.prev:a.next),p-d;let g=o(u[c]),x=o(u[p]);return x.refName!==n?p-d:p===c+d&&(x.start===g.end||x.end===g.start)?c:p},y=1/0,w=-1/0,S=[];for(let a of r){let{ids:c}=a,d=-1,u=-1;for(let p=0;p<c.length;p++)e(c[p])&&(d<0&&(d=p),u=p);if(d>=0){if(a.name!==n){d=f(a,d,-1),u=f(a,u,1);for(let p of[d,u]){let g=o(c[p]);g&&(y=Math.min(y,g.start),w=Math.max(w,g.end))}}S.push({run:a,first:d,last:u})}}let v=a=>{let c=o(a);return e(a)||c?.refName===n&&c.end>y&&c.start<w},b=new Set;for(let[a,c]of t)c.onWindow&&b.add(a);for(let a of S){let{ids:c}=a.run;if(a.run.name===n){for(;a.first>0&&v(c[a.first-1]);)a.first--;for(;a.last<c.length-1&&v(c[a.last+1]);)a.last++}for(let d=a.first;d<=a.last;d++)b.add(c[d])}let l=a=>{let c=t.get(a);return c===void 0?0:c.end-c.start},k=[];for(let{run:a,first:c,last:d}of S){let{ids:u,rev:p}=a,g=c,x=d;for(;g>0&&b.has(u[g-1]);)g--;for(;x<u.length-1&&b.has(u[x+1]);)x++;let h=a.hapOffset;for(let N=0;N<g;N++)h+=l(u[N]);let m=h;for(let N=g;N<=x;N++)m+=l(u[N]);k.push({name:a.name,hapStart:h,hapEnd:m,ids:u.subarray(g,x+1),rev:p.subarray(g,x+1)})}return{kept:b,fragments:k,open:[...s.values()]}}var T=class{constructor(t){this.nodes=new Map,this.sequences=new Map,this.links=[],this.chunks=[],this.window=t}placeNode(t,n){if(this.nodes.has(t))return;let{window:e}=this;this.nodes.set(t,{...n,onWindow:n.rank===0&&n.refName===e.refName&&n.end>e.start-e.context&&n.start<e.end+e.context})}addLinkEnds(t,n){this.links.push(t,n)}addChunk(t){this.chunks.push(t)}addSequences(t){if(this.window.sequences)for(let[n,e]of t)this.sequences.set(n,e)}tables(t,n){this.chunks.length>0&&kt(this.chunks,t,(h,m)=>{let N=this.nodes.get(h);N&&this.nodes.set(h,{...N,...m})},(h,m)=>{this.links.push(h,m)});let e=[];for(let h of t){let m=this.nodes.get(h);m&&e.push({...m,id:h})}e.sort((h,m)=>h.refName<m.refName?-1:h.refName>m.refName?1:h.start-m.start||h.id-m.id);let o=new Map,s=[],i=[],f=new Map,y=new Int32Array(e.length),w=new Int32Array(e.length),S=new Float64Array(e.length),v=new Int32Array(e.length);e.forEach(({id:h,refName:m,start:N,end:M,rank:A},E)=>{o.set(h,E),s.push(String(h));let O=f.get(m);O===void 0&&(O=i.length,f.set(m,O),i.push(m)),y[E]=M-N,w[E]=O,S[E]=N,v[E]=A});let b=h=>{let m=o.get(h);return m===void 0&&(m=s.length,o.set(h,m),s.push(String(h))),m},l=new Map;for(let h=0;h<this.links.length;h+=2){let m=this.links[h],N=this.links[h+1],M=Math.floor(m/2),A=Math.floor(N/2);t.has(M)&&t.has(A)&&l.set(`${M}	${m%2?"-":"+"}	${A}	${N%2?"-":"+"}`,h)}let k=[...l.keys()].sort(),a=new Int32Array(k.length),c=new Int32Array(k.length),d=new Uint8Array(k.length);k.forEach((h,m)=>{let N=l.get(h),M=this.links[N],A=this.links[N+1];a[m]=b(Math.floor(M/2)),c[m]=b(Math.floor(A/2)),d[m]=M%2|A%2<<1});let u=this.referenceFirst(n),p=new Int32Array(u.length+1);u.forEach(({ids:h},m)=>{p[m+1]=p[m]+h.length});let g=new Int32Array(p[u.length]),x=new Uint8Array(g.length);return u.forEach(({ids:h,rev:m},N)=>{let M=p[N];for(let A=0;A<h.length;A++)g[M+A]=b(h[A]);x.set(m,M)}),{nodes:{names:s,lengths:y,refs:w,starts:S,ranks:v,refNames:i},links:{from:a,to:c,strands:d},walks:{names:u.map(h=>h.name),starts:Float64Array.from(u,h=>h.hapStart),ends:Float64Array.from(u,h=>h.hapEnd),offsets:p,steps:g,reversed:x}}}referenceFirst(t){let{refName:n}=this.window;return[...t].sort((e,o)=>+(o.name===n)-+(e.name===n)||(e.name<o.name?-1:e.name>o.name?1:e.hapStart-o.hapStart))}},rt={steps:"the step budget",bytes:"a byte budget of"};function at(r,t,n,e,o,s,i=rt){var f;let y=0,w=new Map,S=new Set;for(let c of r)y+=c.n,w.set(c.chunkStart,((f=w.get(c.chunkStart))!==null&&f!==void 0?f:0)+c.n),S.add(c.name);let v=t*n;if(y<=v)return;let b=e.end-e.start,l=0,k=0;for(let c of[...w.keys()].sort((d,u)=>d-u)){if(l+=w.get(c),l>v)break;k=Math.max(k,c+o-e.start)}let a=!s&&S.size>2&&2*y/S.size<=v;return new q(k>0?`Zoom in to about ${P(k)}${a?", or choose fewer haplotypes,":""} to see the graph`:`Too many haplotype steps here to draw ${s?"these haplotypes":"every haplotype"} (${l.toLocaleString()} steps read, over ${n} \xD7 ${i.steps} of ${t.toLocaleString()}); choose fewer haplotypes`,v,b,Math.max(k,1))}function it(r,t,n,e){let o=r.reduce((f,y)=>f+y.ids.length,0);if(o<=t)return;let s=n.end-n.start,i=Math.max(1,Math.floor(s*t/o));return new q(`Zoom in to about ${P(i)}${e?"":", or choose fewer haplotypes,"} to see the graph`,t,s,i)}async function ct(r,t,n,e,o=rt){let s=await r(n.end);if(s<=t)return;let i=0,f;for(let w=Math.floor(n.start/e)*e;w<n.end;w+=e){let S=await r(w+1);if(f??(f=S),S>t)break;i=w+e-n.start}let y=n.end-n.start;return new q(i>0?`Zoom in to about ${P(i)} to see the graph`:`Too much graph here to fetch (${bt(f??s)} against ${o.bytes} ${bt(t)})`,t,y,Math.max(i,1))}var bt=r=>`${(r/1e6).toFixed(1)} MB`;var $t=8,Ot=3,Lt=4,Bt=1e3,J=class extends Error{constructor(){super(...arguments),this.name="WalkFormatError"}};function xt(r,t,n){if(!Number.isFinite(t)||!Number.isFinite(n))throw new Error(`${r}:${t}-${n} is not a finite range to query the graph's index for`)}function Ct(r,t){return t?(t.throwIfAborted(),new Promise((n,e)=>{let o=()=>{e(t.reason instanceof Error?t.reason:new Error(String(t.reason)))};t.addEventListener("abort",o,{once:!0}),r.then(n,e).finally(()=>{t.removeEventListener("abort",o)})})):r}var lt=class{constructor(t){this.walks=t}header(t={}){if(!this.headerRead){let n=this.walks.getHeaderLines().then(e=>{var o;let s=nt(e);if(s.format!==2)throw new J("This walk file is format 1, from gfa-to-tabix 0.12 or earlier; rebuild it with gfa-to-tabix 1.0 or later");let i=(o=s.chunk)!==null&&o!==void 0?o:65536;return{...s,chunk:i,lookback:st(s.maxNode,i)}});n.catch(()=>{this.headerRead===n&&(this.headerRead=void 0)}),this.headerRead=n}return Ct(this.headerRead,t.signal)}referenceSequences(t={}){return this.walks.getReferenceSequenceNames(t)}async queryStart(t,n={}){let{chunk:e,lookback:o}=await this.header(n);return K(t,e,o)}async cut(t,n,e={}){var o;let{signal:s,keep:i,context:f=Bt,stepBudget:y=1/0,byteBudget:w=1/0,links:S=!0}=e,{chunk:v,lookback:b}=await this.header({signal:s}),l=K(n.start,v,b),k=(o=this.walks.bytesForRegions)===null||o===void 0?void 0:o.bind(this.walks),a=Number.isFinite(w)&&k!==void 0,c=async E=>a?k(E.map(O=>({refName:t,...O})),{signal:s}):0,d=a?await ct(async E=>(xt(t,l,E),c([{start:l,end:E}])),w,n,v,e.budgetNames):void 0;if(d)throw d;let u=new AbortController,p=()=>{u.abort(s?.reason)};s?.throwIfAborted(),s?.addEventListener("abort",p,{once:!0});let g=[],x,h=new T({refName:t,start:n.start,end:n.end,context:f,sequences:e.sequences}),m=new Set,N=[],M=async(E,O)=>{xt(t,E,O);let _=new Map;await this.walks.getLines(t,E,O,{signal:u.signal,lineCallback:F=>{let R=F.split("	"),B=+R[1],W=_.get(B);W?W.push(R):_.set(B,[R])}});for(let[F,R]of _){if(m.has(F))continue;m.add(F);let B=wt(R,i,e.sequences);g.push(...B.rows);for(let[W,j]of B.nodes)h.placeNode(W,j);h.addSequences(B.sequences),h.addChunk(B.chunk),N.push(...B.ends)}if(S)for(let[F,R]of mt(N))h.addLinkEnds(F,R)};try{await M(l,n.end);let E=at(g,y,$t,n,v,i!==void 0,e.budgetNames);if(E)throw E;let O=l,_=Math.floor((n.end-1)/v)*v,F=Lt*v,[R,B]=[O-F,_+F];x=X(z(g),h.nodes,t);let W=await c([{start:l,end:n.end}]);for(let j=0;j<Ot;j++){let H=x.open.filter(C=>C.refName===t&&C.start>=R&&C.start<=B).map(C=>C.start),V=[{start:Math.min(O,...H),end:O},{start:_+v,end:Math.max(_,...H)+1}].filter(C=>C.end>C.start);if(V.length===0||(W+=await c(V),W>w))break;O=Math.min(O,...H),_=Math.max(_,...H),await Promise.all(V.map(({start:C,end:vt})=>M(C,vt))),x=X(z(g),h.nodes,t)}}catch(E){throw u.abort(),E}finally{s?.removeEventListener("abort",p)}let A=it(x.fragments,y,n,i!==void 0);if(A)throw A;return{graph:h,...x}}};var _t={steps:"walkStepBudget",bytes:"walkByteBudget"};async function Jt(r,t,n,e){let{graph:o,kept:s,fragments:i}=await r.cut(t,n,{signal:e.signal,keep:ot(e.prefixes,ft(t)),stepBudget:e.walkRows?1/0:e.stepBudget,byteBudget:e.byteBudget,budgetNames:_t});return ht(o.tables(s,i),n,e.walkRows)}export{Et as a,ot as b,lt as c,_t as d,Jt as e};
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