jbrowse-plugin-graphgenomeviewer 3.0.3 → 3.0.4

package/dist/chunks/GbzBaseSyntenyAdapter-EFIOI2SN.js

@@ -1,8 +0,0 @@
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n.edits)D(s,c,l);let i=o.identity.walkForward,[a,f]=i?[o,e]:[e,o];return{strand:o.strand,refStart:r.refStart,refEnd:n.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,identity:{pathHandle:o.identity.pathHandle,name:o.identity.name,hapStart:o.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Dn(o){if(o.some(n=>n.weight!==void 0))return o;let e=new Map;o.forEach((n,s)=>{if(n.identity){let i=e.get(n.identity.pathHandle);i?i.push(s):e.set(n.identity.pathHandle,[s])}});let t=new Map,r=new Set;for(let n of e.values()){n.sort((a,f)=>o[a].identity.hapStart-o[f].identity.hapStart);let s=n[0],i=o[s];for(let a of n.slice(1)){let f=o[a],c=Bn(i,f);c?(i=Gn(i,f,c),r.add(a)):(t.set(s,i),s=a,i=f)}t.set(s,i)}return o.flatMap((n,s)=>r.has(s)?[]:[t.get(s)??n])}function Be(o,e){return{node:o.path[e],offset:o.offsets[e]}}var zn=4096;function yr(o){let e=[];for(let t of o){let r=e[e.length-1];r&&t-r[1]<=zn?r[1]=t:e.push([t,t])}return e}var jn=32768,qn=65536;function 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this.db.indexedPosition(t.handle,r);if(!n)throw new Error(`Path ${$(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,r,n.pathOffset,n.pos)}async findPathPosition(e,t,r,n){let s=r,i=n;for(;;){await this.ensureNode(A(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${$(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let n=A(e);await this.ensureNode(n);let s=this.record(e),i=ce(e),a=new ve;return a.push(t,n,Le(i)),a.push(s.sequenceLen-t-1,n,Te(i)),this.insertContext(a,r)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,r){let[n,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(n&&s){let i=n.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let c=await this.db.indexedPositionsBetween(e,t,r),l=Wn(c.map(p=>p.pos.node));await Promise.all(l.map(([p,u])=>this.db.prefetchRecords(p,u+2)))}}return n}async aroundInterval(e,t,r){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,r)}catch(n){throw n instanceof V&&n.windowBp===void 0?new V(n.limit,{windowBp:t,walkedBp:this.walkedBp}):n}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let n={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ve;for(;;){let f=A(n.node),c=ce(n.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(n.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,Le(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,Te(c));break}a.push(0,f,Te(c));let u=l.gbwt().lf(n.offset);if(!u)throw new Error(`No successor for GBWT position (${n.node}, ${n.offset})`);n=u,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new ve;for(let n of e)await this.ensureNode(n),r.push(0,n,"left"),r.push(0,n,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,n=new Set;for(let i of this.records.keys())n.add(A(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),n.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=rr(f);if(!r.has(`${a}:${l}`)){let h=this.record(Y(a,nr(f))),d=i+h.sequenceLen-1;d<=t&&e.push(d,a,l)}let p=this.record(Y(a,or(f))),u=i+1;if(u<=t)for(let h of p.successors()){let d=A(h),m=Le(ce(h));r.has(`${d}:${m}`)||e.push(u,d,m)}}for(let i of n)this.records.delete(Y(i,"forward")),this.records.delete(Y(i,"reverse"));return{inserted:s,removed:n.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,G(t)],n=new Set([A(e),A(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=A(f);n.has(c)||(r.push(f,G(f)),n.add(c))}}return s}async extractSnarls(e){let t=0;for(let[r,n]of await this.overlappingSnarls(e))t+=await this.betweenNodes(r,n);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let n of this.sortedHandles()){let s=this.record(n),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?le(n,i)&&t.push([n,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([n,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let n=await this.findCoveringSnarl();n&&t.push(n)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(n=>this.hasHandle(n));return r===void 0?!1:t.length>1||this.record(G(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let n=this.records.get(r);if(n)return n;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(G(l))).successors().length>1},r=async f=>{let c=await e(G(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[G(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},n=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=A(f);if(!this.hasHandle(f)&&!n.has(c)){n.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(Y(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let n=this.sortedHandles(),s=n.length,i=new Map;n.forEach((g,b)=>i.set(g,b));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let g=0;g<s;g++){let b=this.record(n[g]),E=b.gbwt().decompressArrays();f[g]=b.sequenceLen,c.push(E),a[g+1]=a[g]+E.nodes.length}let l=a[s],p=new Int32Array(l),u=new Int32Array(l),h=new Uint8Array(l);for(let g=0;g<s;g++){let b=c[g];p.set(b.nodes,a[g]),u.set(b.offsets,a[g])}c.length=0;for(let g=0;g<l;g++){let b=i.get(p[g]);b===void 0?p[g]=-1:(p[g]=b,h[a[b]+u[g]]=1)}let d=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,x,w=(g,b,E)=>{let I=[],C=0,_=0,v=-1,O=g,L=b;for(;;){O===d&&L===m&&(v=C),E&&(E.push(n[O]),I.push(L)),C+=1,_+=f[O];let N=a[O]+L,F=p[N];if(F<0)break;L=u[N],O=F}return{offsets:I,len:_,refAt:v,last:O}},y=(g,b,E,I)=>{I>=0&&(this.refId=this.paths.length,x=I),this.paths.push({path:g,offsets:b,len:E,weight:void 0,identity:void 0})},S=new Int32Array(s),R=d!==void 0&&M(n[d]);for(let g=0;g<s;g++){let b=n[g];if(!M(b)){let E=a[g],I=a[g+1]-E;for(let C=0;C<I;C++)if(h[E+C]===0){let _=[],{offsets:v,len:O,refAt:L,last:N}=w(g,C,_),F=n[N];if(L>=0||Me(b,F)){if(y(_,v,O,L),!M(F)){let H=i.get(G(F));S[H]=S[H]+1}}else this.twinStarts.add(re({node:b,offset:C}))}}}for(let g=0;g<s;g++){let b=n[g];if(M(b)){let E=a[g],I=a[g+1]-E,C=0;for(let v=0;v<I;v++)h[E+v]===0&&(C+=1);let _=!R&&C===S[g];for(let v=0;v<I;v++)if(h[E+v]===0){let O=_?void 0:w(g,v,void 0);if(O&&(O.refAt>=0||Me(b,n[O.last]))){let L=[],{offsets:N,len:F,refAt:H}=w(g,v,L);y(L,N,F,H)}else this.twinStarts.add(re({node:b,offset:v}))}}}if(r){if(x===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let g=this.paths[this.refId],b=r.nodeOffset;for(let I of g.path.slice(0,x))b+=this.record(I).sequenceLen;let E=r.seqOffset-b;this.refInterval=[E,E+g.len],g.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:E,hapEnd:E+g.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((n,s)=>Ct(n.path,s.path)||n.len-s.len);let t=[],r;for(let n of this.paths){let s=t[t.length-1];s&&Ct(s.path,n.path)===0?s.weight=(s.weight??0)+1:(e&&Ct(n.path,e)===0&&(r=t.length),t.push({...n,weight:1}))}this.paths=t,this.refId=r}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),n=new Set;for(let s of r)for(let i of s.path)n.add(A(i));for(let s of[...this.records.keys()])n.has(A(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async walkHaplotypesFromAnchor(e,t,r,n,s){let i=e.position.seqOffset,a=i+t,f=Math.floor(i/r)*r,c=Math.min(r,qn),l=4*(r+t)+c,p={spacing:r,anchorOffset:f,anchorNodeOffset:-1,anchorHandle:-1,referenceSteps:0,rows:0,walks:[],graphFetches:0,scans:[],scanRows:0,fallback:void 0,ms:{reference:0,rows:0,walks:0,scan:0,sampled:0}};this.stats.anchorWalk=p;let u=performance.now(),h=()=>{let k=performance.now(),j=k-u;return u=k,j};this.clearPaths(),this.records.clear();let d=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,f);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${$(e.name,e.name.fragment)} at offset ${f}; it was not built with anchors at ${r} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let x=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+c);if(!x)throw new Error(`Path ${$(e.name,e.name.fragment)} has not been indexed for random access`);let w=await this.walkReference(d,x,m,i,a,a+c),{anchor:y,refOffsetOf:S,refHandles:R,windowSteps:g}=w;p.anchorHandle=y.pos.node,p.referenceSteps=w.steps,this.walkedBp=t;let b=[],E=[],I=0;for(let k of g)await this.ensureNode(A(k.pos.node)),b.push(k.pos.node),E.push(k.pos.offset),I+=this.record(k.pos.node).sequenceLen;let C=g[0];if(C===void 0)throw new Error("The reference walk has no node in the window");this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[C.refOffset,C.refOffset+I],this.refId=0,this.paths.push({path:b,offsets:E,len:I,weight:void 0,identity:{pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:C.refOffset,hapEnd:C.refOffset+I}}),p.ms.reference=h();let _=await this.db.haplotypeSamplesAtNode(y.pos.node);p.rows=_.length,p.ms.rows=h();let v=_.find(k=>k.offset===y.pos.offset&&k.pathHandle===e.handle&&k.pathOffset===y.offset);if(v===void 0)throw new Error(`The haplotype index has no anchor row for ${$(e.name,e.name.fragment)} at offset ${y.offset} (node ${A(y.pos.node)}); it was not built with anchors at ${r} bp for this graph`);let O=await this.db.pathsByHandle(),L=k=>{let j=O.get(k);if(!j)throw new Error(`Path ${k} is missing from the database`);return j.name},N=new Set([e.handle]),F=new Map;for(let k of _)if(k!==v&&n(L(k.pathHandle))){let j=F.get(k.pathHandle);j?j.push(k):F.set(k.pathHandle,[k])}let H;for(let[k,j]of F)if(H===void 0){let ae=te=>Math.abs(te.offset-v.offset);j.sort((te,En)=>ae(te)-ae(En));let fe;for(let te of j)N.has(k)||(fe=await this.walkAndKeep(d,te,"anchor",L(k),S,a,l,s,N,p));N.has(k)||(H=fe)}p.ms.walks=h();let xe=H===void 0?await this.samplesOfUnwalkedContigs(b,S,R,n,N,L,p):new Map;if(p.ms.scan=h(),xe.size>0){await this.mapReferenceBefore(d,e.handle,Math.max(0,m.pathOffset-2*r),m.pathOffset,S,R);for(let[k,j]of xe)if(H===void 0){let ae=L(k),fe;for(let te of j)fe??=await this.entryBefore(d,te,S,R,this.refInterval[0],l);H=fe===void 0?`no sample of ${$(ae,ae.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(d,fe,"sample",ae,S,a,l,s,N,p)}p.ms.sampled=h()}return p.fallback=H,H}async walkAndKeep(e,t,r,n,s,i,a,f,c,l){let p=await this.walkFromRow(e,t,n,s,this.refInterval[0],i,a,f);l.walks.push({pathHandle:t.pathHandle,from:r,steps:p.steps,pieces:p.infos.length,end:p.end});let u;return p.end==="bound"?u=`${$(n,t.pathOffset)} walked ${p.steps} steps from its ${r} without reaching the window's end (${p.end})`:(c.add(t.pathHandle),this.paths.push(...p.infos)),u}async mapReferenceBefore(e,t,r,n,s,i){let a=await this.prefetchReferenceRange(t,r,n),f=a?.pos,c=a?.pathOffset??n;for(;f!==void 0&&f.node!==0&&c<n;){this.signal?.throwIfAborted();let l=await e(f.node),p=A(f.node);s.has(p)||(s.set(p,c),i.add(f.node)),c+=l.sequenceLen,f=l.gbwt().lf(f.offset)}}async runsWithReference(e,t,r,n,s){let i={node:t.node,offset:t.offset},a=0,f;for(;f===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)f=!1;else if(r.has(A(i.node)))f=n.has(i.node);else{let c=await e(i.node);a+=c.sequenceLen,i=c.gbwt().lf(i.offset)}return f}async entryBefore(e,t,r,n,s,i){let a=(await e(t.node)).sequenceLen,f=async(h,d)=>{let m=(await e(h.node)).sequenceLen;return{node:h.node,offset:h.offset,pathHandle:t.pathHandle,orientation:t.orientation,pathOffset:t.orientation==="forward"?t.pathOffset-d:t.pathOffset+a+d-m}},c={node:t.node,offset:t.offset},l=0,p,u=!await this.runsWithReference(e,t,r,n,i);for(;!u;){this.signal?.throwIfAborted();let h=r.get(A(c.node));if(h!==void 0&&h<s)p=await f(c,l),u=!0;else if(l>i)p={...t},u=!0;else{let m=(await e(G(c.node))).gbwt().predecessorAt(c.offset);if(m===void 0)p=await f(c,l),u=!0;else{let x=await e(m),w=x.gbwt().offsetTo(c);if(w===void 0)throw new Error(`No offset in ${m} leads to ${c.node}:${c.offset}`);c={node:m,offset:w},l+=x.sequenceLen}}}return p}async walkReference(e,t,r,n,s,i){let a=new Map,f=new Set,c=[],l,p=t.pos,u=t.pathOffset,h=0;for(;p!==void 0&&p.node!==0&&u<i;){this.signal?.throwIfAborted();let d=await e(p.node),m=u+d.sequenceLen;if(l===void 0&&u===r.pathOffset){if(p.node!==r.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${u} where the haplotype index names node ${A(r.node)} as the anchor`);l={pos:p,offset:u}}if(l!==void 0){h+=1;let x=A(p.node);a.has(x)||(a.set(x,u),f.add(p.node)),u<s&&m>n&&c.push({pos:p,refOffset:u})}u=m,p=d.gbwt().lf(p.offset)}if(l===void 0)throw new Error(`The reference walk from offset ${t.pathOffset} never starts a node at the anchor offset ${r.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:f,windowSteps:c,steps:h}}async walkFromRow(e,t,r,n,s,i,a,f){let c=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+c,p=[],u=[],h=[],d=0,m=0,x=0,w,y,S={node:t.node,offset:t.offset};for(;y===void 0;)if(this.signal?.throwIfAborted(),S===void 0||S.node===0)y=w===void 0?"before the window":"ended in the window";else if(m>a)y="bound";else{let g=n.get(A(S.node)),b=w!==void 0;if(g!==void 0&&g>=i)y=b?"through the window":"past the window";else{!b&&g!==void 0&&g>=s&&(w=m);let E=await e(S.node);if(w!==void 0){let I={pos:S,at:m,len:E.sequenceLen};g===void 0?(h.push(I),d+=I.len):(d>f&&g<s?(p.push(u),u=[]):u.push(...h),h=[],d=0,u.push(I))}x+=1,m+=E.sequenceLen,S=E.gbwt().lf(S.offset)}}p.push(u);let R=[];for(let g of p){let b=g[0],E=g[g.length-1];if(b!==void 0&&E!==void 0){let I=[],C=[],_=0;for(let L of g)await this.ensureNode(A(L.pos.node)),I.push(L.pos.node),C.push(L.pos.offset),_+=L.len;let v=b.at,O=E.at+E.len;R.push({path:I,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:r,orientation:"forward",hapStart:l+v,hapEnd:l+O}:{pathHandle:t.pathHandle,name:r,orientation:"reverse",hapStart:l-O,hapEnd:l-v}})}}return{steps:x,end:y,infos:R}}async samplesOfUnwalkedContigs(e,t,r,n,s,i,a){let f=yr([...e].sort((l,p)=>l-p));a.scans=f;let c=new Map;for(let[l,p]of f){let u=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=u.length;for(let h of u){let d=t.has(A(h.node));if(!s.has(h.pathHandle)&&(!d||r.has(h.node))&&n(i(h.pathHandle))){let m=c.get(h.pathHandle)??[];d?m.unshift(h):m.push(h),c.set(h.pathHandle,m)}}}return c}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=yr(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[d,m]of t)for(let x of await this.db.haplotypeSamplesInRange(d,m))r.set(re(x),x);let n=d=>{let m=0,x=t.length-1;for(;m<x;){let y=m+x+1>>1;t[y][0]<=d?m=y:x=y-1}let w=t[m];return w[0]<=d&&d<=w[1]},s=new Map;this.paths.forEach((d,m)=>{d.path.length>0&&m!==this.refId&&s.set(re(Be(d,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((d,m)=>{m!==this.refId&&i.fragmentLengths.push(d.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=d=>(i.graphLookups+=1,a(d)),c=async(d,m)=>{if(n(d.node))return r.get(re(d));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let x=await this.db.haplotypeSampleAt(d.node,d.offset);return x||(i.companionMisses+=1),x},l=new Map,p=async d=>{let m=l.get(d);if(!m){let x=await this.db.getPath(d);if(!x)throw new Error(`Path ${d} is missing from the database`);m=x.name,l.set(d,m)}return m},u=(d,m,x)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.pathOffset-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.pathOffset+m+x},h=(d,m)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.hapStart-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.hapEnd+m};for(let d=0;d<this.paths.length;d++){let m=this.paths[d];if(d===this.refId||m.identity)continue;let x=[],w=new Set,y={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(y);let S,R=0,g=d,b;for(;S===void 0;){if(this.signal?.throwIfAborted(),g!==void 0){if(w.has(g)){y.end="cycle";break}w.add(g);let v=this.paths[g];x.push({index:g,startBp:R}),y.fragments+=1;let O=R;for(let N=0;N<v.path.length;N++){let F=Be(v,N),H=r.get(re(F)),xe=this.record(F.node).sequenceLen;if(H){S=u(H,O,xe);break}O+=xe}if(R+=v.len,S){y.end="in-fragment sample";break}let L=Be(v,v.path.length-1);b=this.record(L.node).gbwt().lf(L.offset),g=void 0}if(b===void 0||b.node===0){y.end="endmarker";break}let E=re(b),I=s.get(E);if(I!==void 0){let v=this.paths[I].identity;if(v){S=h(v,R),y.end="identified sibling";break}g=I;continue}this.records.has(b.node)&&(y.reentries+=1),this.twinStarts.has(E)&&(y.twinLandings+=1);let C=await c(b,y),_=await f(b.node);if(C){S=u(C,R,_.sequenceLen),y.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,y.steps+=1,R-x[x.length-1].startBp>4*e+4*_.sequenceLen){y.end="bound";break}R+=_.sequenceLen,b=_.gbwt().lf(b.offset)}if(S){y.pathHandle=S.pathHandle;let E=await p(S.pathHandle);for(let{index:I,startBp:C}of x){let _=this.paths[I];_.identity=S.orientation==="forward"?{pathHandle:S.pathHandle,name:E,orientation:"forward",hapStart:S.base+C,hapEnd:S.base+C+_.len}:{pathHandle:S.pathHandle,name:E,orientation:"reverse",hapStart:S.base-C-_.len,hapEnd:S.base-C}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,n)=>{let s=t.get(r);s?s.push(n):t.set(r,[n])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,n)=>{t.push(t[n]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),n=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=$n(c,a);if(l===void 0)return;n[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:n,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,n=0,s=0,i=0,a=0;for(;n<e.length&&s<t.length;){let f=this.record(e[n]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(n+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,n=0,s=0,i=0,a=0;for(;n<e.length&&s<t.length;){let f=this.record(e[e.length-n-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(n+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let n=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>n&&(a=n-i),i+a>s&&(a=s-i),D(r,"M",i),br(r,n-i-a,s-i-a),D(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),n=0;for(let s of e)r.has(s)&&(n+=this.record(s).sequenceLen);return n}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let n=r??Hn(wr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,u,h,d)=>{p===u?D(s,"D",i[d]-i[h]):h===d?D(s,"I",this.pathLen(e.slice(p,u))):this.align(e.slice(p,u),t.slice(h,d),s)},f=0,c=0,l=0;for(let p=0;p<n.count;p++){let u=n.pathAt[p],h=n.refAt[p];(c!==u||l!==h)&&a(c,u,l,h);let d=this.record(e[u]).sequenceLen;D(s,"M",d),f+=d,c=u+1,l=h+1}return a(c,e.length,l,t.length),{edits:s,matched:f}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,n;if(sr(r))n={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else{let s=t.path.map(f=>G(f)).reverse(),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)n={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else if(i===0)n={edits:this.editsAgainst(s,r).edits,flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);n=c.matched>f.matched?{edits:c.edits,flipped:!0}:{edits:f.edits,flipped:!1}}}return n}alignToRef(e){return this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],n=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:f}=this.alignment(i),c=0,l=0;for(;c<a.length&&a[c][0]==="D";)l+=a[c][1],c+=1;let p=a.length,u=0;for(;p>c&&a[p-1][0]==="D";)u+=a[p-1][1],p-=1;let h=s.identity,d=h?h.orientation==="forward"!==f:!f;n.push({strand:d?"+":"-",refStart:e.start+l,refEnd:e.start+r-u,edits:a.slice(c,p),weight:s.weight,path:s.path,start:Be(s,0),identity:h===void 0?void 0:{pathHandle:h.pathHandle,name:h.name,hapStart:h.name.fragment+h.hapStart,hapEnd:h.name.fragment+h.hapEnd,walkForward:h.orientation==="forward"}})}),Dn(n).map(s=>{let{edits:i,identity:a,...f}=s,c={...f,cigar:Qn(i)};return a?{...c,resolved:!0,name:a.name,label:$({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...c,resolved:!1}})}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let n=Y(e,r);for(let s of this.record(n).successors())this.hasHandle(s)&&le(n,s)&&t.push([r==="reverse"?1:0,A(s),M(s)?1:0])}return t.sort((r,n)=>r[0]-n[0]||r[1]-n[1]||r[2]-n[2]),t.filter((r,n)=>n===0||r[0]!==t[n-1][0]||r[1]!==t[n-1][1]||r[2]!==t[n-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!M(r)){let n=A(r),s=`S	${n}	${this.record(r).sequence}
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-`;t.push(e.encode(s))}return gr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...mr(ur(await this.stableName(),await this.db.graphName()))],n=this.sortedHandles();for(let c of n)M(c)||r.push(`S	${A(c)}	${this.record(c).sequence}`);let s=c=>M(c)?"-":"+";for(let c of n)for(let l of this.record(c).successors())this.hasHandle(l)&&le(c,l)&&r.push(`L	${A(c)}	${s(c)}	${A(l)}	${s(l)}	0M`);let i=(c,l,p,u,h)=>{let d=Rt(c,l).map(w=>`${M(w)?"<":">"}${A(w)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,x=h===void 0?"":`	CG:Z:${h}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${u}	${d}${m}${x}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,u=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,u):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,u)),f+=1}}),`${r.join(`
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this.outputEdges())r.push({from:String(A(s)),from_is_reverse:M(s),to:String(A(i)),to_is_reverse:M(i)});let n=this.outputPaths(e).map(s=>Un(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:n}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!M(i)),r=new Int32Array(t.length),n=[];t.forEach((i,a)=>{r[a]=A(i),n.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:n,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Rt(i.info,i.identity))}))}}};function Rt(o,e){return e?.orientation==="reverse"?o.path.map(t=>G(t)).reverse():o.path}function Un(o,e,t,r){return{name:t,...o.weight===void 0?{}:{weight:o.weight},...r===void 0?{}:{cigar:r},path:Rt(o,e).map(n=>({id:String(A(n)),is_reverse:M(n)}))}}function Ct(o,e){let t=Math.min(o.length,e.length);for(let r=0;r<t;r++){let n=o[r],s=e[r];if(n!==s)return n<s?-1:1}return 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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 this.haplotypeLength(e):void 0;if(t===void 0){let r=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!r){let i=await this.getPath(e);throw new Error(`Path ${i?$(i.name,i.name.fragment):e} has not been indexed for random access`)}let n=r.pathOffset,s=r.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);n+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return n;s=a}}return t}async pathFragmentsForRange(e,t,r){if(r<=t)return[];let n=await this.pathsNamed(e),s=n.filter(f=>f.name.fragment<=t).slice(-1),i=n.filter(f=>f.name.fragment>t&&f.name.fragment<r);return(await Promise.all([...s,...i].map(async f=>({path:f,start:f.name.fragment,end:f.name.fragment+await this.pathLength(f.handle)})))).filter(f=>t<f.end)}async 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St(this.walkableCigar))(c.type==="deletion"||c.type==="skip"?c.start<f&&c.start+c.length>a:c.start>=a&&c.start<=f)&&(c.type==="mismatch"?e(88,c.start,c.length,c.base,c.qual??-1,0,0):c.type==="insertion"?e(73,c.start,c.length,c.insertedBases??"",-1,0,c.insertlen):c.type==="deletion"?e(68,c.start,c.length,"",-1,0,0):c.type==="skip"&&e(78,c.start,c.length,"",-1,0,0))}}};var Po=["CIGAR","cs","coarseCigar","cg","cr"];function ko(o){return typeof o=="object"&&o!==null&&"refName"in o&&"start"in o&&"end"in o&&typeof o.refName=="string"&&typeof o.start=="number"&&typeof o.end=="number"}function Oo(o){let e=o.get("mate");return ko(e)?e:void 0}function Lo(o,e,t,r){let n=Math.max(o.start,r.start),s=Math.min(o.end,r.end),i=(e.end-e.start)/Math.max(o.end-o.start,1),a=l=>t===-1?e.end-(l-o.start)*i:e.start+(l-o.start)*i,f=Math.round(a(n)),c=Math.round(a(s));return s>n?{start:n,end:s,mateStart:Math.min(f,c),mateEnd:Math.max(f,c)}:void 0}function To(o,e,t,r){let n={start:o.get("start"),end:o.get("end")},s=o.get("strand")===-1?-1:1,i=n.start>=t.start&&n.end<=t.end,a=i&&r===void 0?void 0:Qt(o);if(a===void 0){let f=i?{...n,mateStart:e.start,mateEnd:e.end}:Lo(n,e,s,t);return f===void 0?[]:[f]}else return(r===void 0?[{...n,mateStart:e.start,mateEnd:e.end,cigar:a}]:Ut(a,n.start,e.start,e.end,s,r)).flatMap(c=>{let l=Wt(c.cigar,c.start,c.mateStart,c.mateEnd,s,t.start,t.end);return l===void 0?[]:[l]})}function Mo(o,e,t,r,n){let s=`:${r.start}-${r.end}${n}`,i=o.toJSON(),a={...i,uniqueId:`${o.id()}${s}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};i.syntenyId!==void 0&&(a.syntenyId=`${String(i.syntenyId)}${s}`);for(let f of Po)delete a[f];return new ie(a)}function xn(o,e,t){let r=Oo(o);if(r===void 0)return[o];{let n=To(o,r,e,t);return n.map((s,i)=>Mo(o,r,s,e,n.length>1?`/${i}`:""))}}var vt=class extends wn.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:n,splitAtGapBp:s,...i}=r,a=n&&this.recordsAreAlignments,f=(0,yn.createStatusFanOut)(i.statusCallback);return Ft(t).pipe(me((c,l)=>this.getFeatures(c,{...i,statusCallback:f()}).pipe(me(p=>a?xn(p,c,s):[p]),gt(),Pe(p=>({index:l,features:p})))),gt(),me(c=>c.sort((l,p)=>l.index-p.index).flatMap(l=>l.features)))}};var Vt=class extends Error{constructor(){super("this .gbz.db has no HaplotypeSamples/HaplotypeLengths tables, so its walks cannot be named; run gbz-haplotype-index (from @gmod/gbz-base) over it first");this.name="NoHaplotypeIndexError"}},Kt=class extends Error{constructor(t,r){super(r.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${t}" maps to none; set referenceSample`:`the anchor "${t}" is none of the graph's reference samples (${r.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`);this.name="NoReferenceSampleError"}};function ge(o){return`${o.sample}#${o.haplotype}`}function No(o,e){let t=ge(o);return e===void 0||e.some(r=>Oe(t,r))}var Xt=class extends Error{constructor(t,r){super(`the graph is cut on its reference, ${r}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}},Zt=class extends Error{constructor(t,r,n){super(`this ${r.toLocaleString()} bp window reads more than nodeLimit (${t.toLocaleString()}) graph nodes; zoom in to about ${n.toLocaleString()} bp or raise nodeLimit`);this.name="NodeLimitError"}};function bn(o,e,t){if(o instanceof Error&&(o.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(o.message))){let n=o.walkedBp,s=typeof n=="number"&&n>0?Math.floor(n*.8):Math.floor(t/2);return new Zt(e,t,Math.max(s,1))}else return}function Sn(o,e){let t=ge(e);return o[t]??o[e.sample]??t}function Fo({configured:o,anchorPrefix:e,referenceSamples:t}){let r=tr(e);if(o!=="")return o;if(t.includes(r))return r;if(t.length===1)return t[0];throw new Kt(e,t)}function Ho(o,e){return`${ge(o)}#${o.contig}@${e.start.node}.${e.start.offset}`}function $o({alignment:o,assemblyName:e,refName:t,lane:r}){let{refStart:n,refEnd:s,strand:i,cigar:a}=o;if(!(!o.resolved||s<=n)){let{name:f,hapStart:c,hapEnd:l}=o,p=Ho(f,o),u={uniqueId:p,assemblyName:e,refName:t,start:n,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new ie(u)}}var Jt=class extends vt{constructor(){super(...arguments);this.graph=(0,vn.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),r=!("uri"in t)||t.uri!=="",n=await Ce.open((0,Yt.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),r?{haplotypeIndex:(0,Yt.openLocation)(t,this.pluginManager)}:{}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=(await n.tag("gbwt_reference_samples")??"").split(/\s+/).filter(f=>f!==""),a=Fo({configured:this.getConf("referenceSample"),anchorPrefix:ye(this,s),referenceSamples:i});return{db:n,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,r){let{db:n,referenceSample:s}=await this.graph(r),i=(await n.paths()).find(a=>a.isIndexed&&a.name.sample===s&&a.name.contig===t);return i?{sample:i.name.sample,contig:t,haplotype:i.name.haplotype}:void 0}async getHaplotypes(t={}){let{db:r,referenceSamples:n}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=ge(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:n.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:n,referenceSamples:s}=await this.graph(t),i=It(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==n&&a.push({name:Sn(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:n,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:n,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===n?void 0:ye(this,i),f=(await r.paths()).filter(c=>i===n?c.isIndexed&&c.name.sample===s:Oe(ge(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let n=t===void 0||t.length===0?void 0:t.map(s=>ye(this,s));return n===void 0&&r===void 0?void 0:s=>No(s,n)&&(r===void 0||Oe(ge(s),r))}async getSubgraph(t,r={}){let{db:n,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new Xt(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),u=this.keepPredicate(r.haplotypes),h=l?await n.getSubgraphForRange(l,f,c,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:r.signal,...u===void 0?{}:{keep:u}}).catch(d=>{throw bn(d,p,c-f)??d}):void 0;return h?h.toGFA({names:"resolved"}):""}getFeatures(t,r={}){return(0,An.ObservableCreate)(async n=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new Vt;let{assemblyName:a,refName:f,start:c,end:l}=t;if(a===i){let p=ye(this,r.targetAssemblyName),u=It(this),h=this.keepPredicate(r.haplotypes,p),d=await this.referenceQuery(f,r),m=this.getConf("nodeLimit"),x=d?await(0,In.updateStatus)(`Reading graph ${f}:${c.toLocaleString()}-${l.toLocaleString()}`,r.statusCallback,()=>s.getAlignmentsForRange(d,c,l,{context:this.getConf("context"),haplotypes:"all",limit:m,signal:r.signal,...h===void 0?{}:{keep:h}}).catch(w=>{throw bn(w,m,l-c)??w})):[];for(let w of x)if(w.resolved){let y=$o({alignment:w,assemblyName:a,refName:f,lane:Sn(u,w.name)});y!==void 0&&n.next(y)}}n.complete()},r.signal)}};export{Xt as HaplotypeWindowError,Vt as NoHaplotypeIndexError,Kt as NoReferenceSampleError,Zt as NodeLimitError,Jt as default,$o as fragmentFeature,ge as haplotypePrefix,Sn as laneAssemblyName,bn as nodeLimitError,Fo as resolveReferenceSample};
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