jbrowse-plugin-graphgenomeviewer 4.0.19 → 4.0.21

package/README.md

@@ -30,7 +30,8 @@ session spec does the same with `loadedTrackId` and `loadedRegion`.
   walk rows, and sequenceTubeMap's tube map on its own axis or the reference's
 - Genes from the session's annotation track, drawn on the graph
 - Bubbles from `gfatools bubble` or the graph itself, opened level by level
-- gbz-base haplotypes as walks: carriage as node thickness, one walk lifted out
+- gbz-base haplotypes as walks: carriage as node thickness, several walks lifted
+  out at once, each lane coloured by progress, reference position or strand
 - GAF reads in the tube map, with their mismatches, from a gbz-base track
 
 ## Usage

package/dist/chunks/{GbzBaseSyntenyAdapter-KKSNCZXY.js → GbzBaseSyntenyAdapter-7ZKFAEJG.js}

@@ -4,5 +4,5 @@ import{a as Ir,b as Ar,c as Rr,d as Ts}from"./chunk-JAQ2RQAE.js";import{a as Cr}
 `)}
 `}outputPaths(e){let t=e.cigar??!1,r=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};r.push({info:this.paths[this.refId],identity:void 0,name:ge(i,this.refPath.fragment+this.refInterval[1]),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names==="resolved"?i.identity:void 0;r.push({info:i,identity:f,name:f?ge({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):ge({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),r}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&We(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!q(s)).map(s=>({id:String(_(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(_(s)),from_is_reverse:q(s),to:String(_(i)),to_is_reverse:q(i)});let o=this.outputPaths(e).map(s=>pi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!q(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=_(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Lt(i.info,i.identity))}))}}};function Lt(n,e){return e?.orientation==="reverse"?n.path.map(t=>K(t)).reverse():n.path}function pi(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Lt(n,e).map(o=>({id:String(_(o)),is_reverse:q(o)}))}}function Dn(n,e){let t=Math.min(n.length,e.length);for(let r=0;r<t;r++){let o=n[r],s=e[r];if(o!==s)return o<s?-1:1}return n.length-e.length}function se(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function Ot(n){return n===0?0:6+(n-1)}function uo(n,e,t){if(e===0)se(n,"D",t);else if(t===0)se(n,"I",e);else{let r=Math.min(e,t),o=4*r+Ot(e-r)+Ot(t-r),s=Ot(e)+Ot(t);o<=s?(se(n,"M",r),se(n,"I",e-r),se(n,"D",t-r)):(se(n,"I",e),se(n,"D",t))}}function hi(n){return n.map(([e,t])=>`${t}${e}`).join("")}async function mo(n,e,t,r,o){let s=new Tt(n,o);try{let i=await s.pathPosition(Et(e,t));return await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,o.context??100),await s.extractSnarls(o.snarls??"none"),{subgraph:s,reference:i}}catch(i){throw i instanceof Me&&i.windowBp===void 0?new Me(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}}async function go(n,e,t,r,o={}){let{subgraph:s,reference:i}=await mo(n,e,t,r,o);return s.extractPaths(i,o.haplotypes??"all"),s}async function wo(n,e,t,r,o){if(!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: 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this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var jn="GBZ-base version 4",Gt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Bt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${jn}"`),this.found=e}},Dt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,o,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=o,this.next=s,this.sequenceLen=Hr(o)}get id(){return _(this.handle)}get orientation(){return Ue(this.handle)}get sequence(){return this.decoded??=Gr(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new It(this.edges,this.bwt)}};function D(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function zt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function zn(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function So(n,e){return{handle:n,fwStart:{node:D(e[1],"Paths.fw_node"),offset:D(e[2],"Paths.fw_offset")},revStart:{node:D(e[3],"Paths.rev_node"),offset:D(e[4],"Paths.rev_offset")},name:{sample:zt(e[5],"Paths.sample"),contig:zt(e[6],"Paths.contig"),haplotype:D(e[7],"Paths.haplotype"),fragment:D(e[8],"Paths.fragment")},isIndexed:D(e[9],"Paths.is_indexed")!==0}}async function vo(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(zt(t[0],"Tags.key"),zt(t[1],"Tags.value"));return e}var it=class n{tagCache;pathCache;pathMapCache;indexTags=new Map;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e,t={}){let{haplotypeIndex:r,...o}=t,s=await st.open(e,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=r?await st.open(r,o):void 0,a=new n(s,i),f=await a.tag("version");if(f!==jn)throw new Bt(f);if(i){for(let d of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(d);a.indexTags=await vo(i);let c=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(c!==l)throw new Error(`haplotype index was built for ${c??"an unknown number of"} paths but the graph has ${l}`);let p=a.indexTags.get("haplotype_index_nodes"),u=await a.tag("nodes");if(p!==void 0&&p!==u)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${u}`);if(a.indexTags.get("haplotype_index_orientations")==="forward")throw new Gt}return a}tags(){return this.tagCache??=vo(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new Dt(e,$r(zn(t[1],"Nodes.edges")),zn(t[2],"Nodes.bwt"),zn(t[3],"Nodes.sequence"),typeof r=="number"?r:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:r}of this.sqlite.scan("Paths"))e.push(So(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?So(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(r=>r.name.sample===e.sample&&r.name.contig===e.contig&&r.name.haplotype===e.haplotype&&r.name.fragment<=e.fragment).sort((r,o)=>o.name.fragment-r.name.fragment)[0]}async pathsForSample(e){return(await this.paths()).filter(t=>t.name.sample===e)}async pathsNamed(e){let t=Et(Yr(e),0);return(await this.paths()).filter(r=>r.name.sample===t.sample&&r.name.contig===t.contig&&r.name.haplotype===t.haplotype).sort((r,o)=>r.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await 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getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Pn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Is(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:je(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:ze(be(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>je(this,s));return o===void 0&&r===void 0?void 0:s=>Io(s,o)&&(r===void 0||ze(be(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new gr(i,s);let l=await this.referenceQuery(a,{}),p=this.keepPredicate(r.haplotypes);return 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at(x,h,c-f)??x}),S=d&&m&&l.length>0&&p.length>0?(await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,f,c,o)).map(g=>y(d,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let b=g.stats.keep;return b!==void 0&&b.fallback===void 0})?S.flatMap(g=>l.flatMap(b=>p.flatMap(x=>g.pairAlignments({target:b,query:x,bases:!1}).map(A=>ia({pair:A,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,As.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new ur;if(t.assemblyName===i){let a=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let f of a)o.next(f)}o.complete()},r.signal)}};export{gr as HaplotypeWindowError,ur as NoHaplotypeIndexError,jt as NoReferenceSampleError,Ut as NodeLimitError,mr as PairTargetError,wr as default,sa as fragmentFeature,be as haplotypePrefix,Is as laneAssemblyName,at as nodeLimitError,ia as 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Open the graph from a ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Is(n,e){let t=be(e);return n[t]??n[e.sample]??t}function oa(n,e){return`${be(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function sa({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,p=oa(f,n),u={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new ke(u)}}function ia({pair:n,lane:e,mateLane:t}){let r=`${be(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${be(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new ke({uniqueId:r,assemblyName:e,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:r,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 pr=n=>!("uri"in n)||n.uri!=="",wr=class extends xn{constructor(){super(...arguments);this.graph=(0,hr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=pr(r)?r:await Mo(t,this.pluginManager),s=await it.open((0,Je.openLocation)(t,this.pluginManager),o?{haplotypeIndex:(0,Je.openLocation)(o,this.pluginManager)}:{}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let a=await Ao(s),f=Un({configured:this.getConf("referenceSample"),anchorPrefix:je(this,i),referenceSamples:a});return{db:s,anchor:i,referenceSample:f,referenceSamples:a}}});this.gaf=(0,hr.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]),o=this.pluginManager;if(!pr(t))return;let s=(0,Je.openLocation)(t,o);return new Wt(s,pr(r)?new Ar({filehandle:s,...(0,Je.openTabixIndexFilehandle)(r,this.getConf(["readsIndex","indexType"]),o)}):void 0)}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return Eo(o,s,t)}async getHaplotypes(t={}){let{db:r,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=be(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Pn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Is(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:je(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:ze(be(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>je(this,s));return o===void 0&&r===void 0?void 0:s=>Io(s,o)&&(r===void 0||ze(be(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new gr(i,s);let l=await this.referenceQuery(a,{}),p=this.keepPredicate(r.haplotypes);return Co(o,l,f,c,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,...p===void 0?{}:{keep:p}})}async getReads(t,r={}){let o=await this.gaf(r);return o?o.readsOver(new Set(t),r):{records:[],total:0}}async laneHaplotypes(t,r){let o=je(this,t);return(await this.getHaplotypes(r)).filter(s=>ze(s.prefix,o))}async referencePieces(t,r,o,s){let{db:i,referenceSample:a}=await this.graph(s),f=(await i.paths()).filter(l=>l.isIndexed&&l.name.sample===a&&l.name.contig===t&&l.name.fragment>r&&l.name.fragment<o).map(l=>l.name.fragment),c=[r,...[...new Set(f)].sort((l,p)=>l-p),o];return c.slice(1).map((l,p)=>({start:c[p],end:l}))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=je(this,r.targetAssemblyName),l=Pn(this),p=this.keepPredicate(r.haplotypes,c),u=await this.referenceQuery(i,r),d=this.getConf("nodeLimit");return(u?await(0,dr.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignmentsForRange(u,a,f,{context:this.getConf("context"),haplotypes:"all",limit:d,signal:r.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw at(m,d,f-a)??m})):[]).flatMap(m=>{let y=m.resolved?sa({alignment:m,assemblyName:s,refName:i,lane:Is(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,r,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new mr(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),p=await this.laneHaplotypes(s,o),u=[...l,...p],d=await this.referenceQuery(a,o),h=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,b)=>i.getSubgraphForRange(g,b.start,b.end,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:h,signal:o.signal,keep:x=>u.some(A=>A.sample===x.sample&&A.haplotype===x.haplotype)}).catch(x=>{throw at(x,h,c-f)??x}),S=d&&m&&l.length>0&&p.length>0?(await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,f,c,o)).map(g=>y(d,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let b=g.stats.keep;return b!==void 0&&b.fallback===void 0})?S.flatMap(g=>l.flatMap(b=>p.flatMap(x=>g.pairAlignments({target:b,query:x,bases:!1}).map(A=>ia({pair:A,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,As.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new ur;if(t.assemblyName===i){let a=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let f of a)o.next(f)}o.complete()},r.signal)}};export{gr as HaplotypeWindowError,ur as NoHaplotypeIndexError,jt as NoReferenceSampleError,Ut as NodeLimitError,mr as PairTargetError,wr as default,sa as fragmentFeature,be as haplotypePrefix,Is as laneAssemblyName,at as nodeLimitError,ia as pairFeature,Un as resolveReferenceSample};
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