jbrowse-plugin-graphgenomeviewer 6.5.0 → 6.7.0

package/dist/chunks/{GbzBaseSyntenyAdapter-KVJKGGQ4.js → GbzBaseSyntenyAdapter-NULWNOBT.js}

@@ -1,8 +1,8 @@
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M=d.get(I);return M!==void 0&&r.keep(M.name)},m=[],u=new qn,w=new Map,b=new Set,S=new Set,g=async I=>{let M=(await l(I.node)).gbwt().lf(I.offset);return M===void 0||M.node===0?void 0:M},x=async(I,M)=>{let _=(await l(re(I.node))).gbwt().predecessorAt(I.offset);if(_===void 0||M!==void 0&&!M.has(_))return;let L=(await l(_)).gbwt().offsetTo(I);if(L===void 0)throw new Error(`No offset in ${_} leads to ${I.node}:${I.offset}`);return{node:_,offset:L}},y=(I,M,_,L)=>{let B=_.map(V=>V.pos.node),W=_.map(V=>V.pos.offset),J=0;for(let V of B)J+=h(V);let q=M==="forward"?_[0].left:_[_.length-1].left,$=m.length;m.push({pathHandle:I,orientation:M,handles:B,offsets:W,len:J,hapStart:q,hapEnd:q+J,canonical:Fe(B[0],B[B.length-1]),source:L});for(let V of _)u.set(V.pos,$);let K=w.get(I);return K?K.push($):w.set(I,[$]),$},E=async(I,M,_,L)=>{let B=[],W=I;for(;;){n?.throwIfAborted();let q=await x(W.pos,t);if(!q)break;W={pos:q,left:io(_,W.left,h(W.pos.node),h(q.node))},B.push(W)}B.reverse();let J=[I];for(W=I;;){n?.throwIfAborted();let q=await g(W.pos);if(!q||!t.has(q.node))break;W={pos:q,left:Pt(_,W.left,h(W.pos.node),h(q.node))},J.push(W)}return y(M,_,[...B,...J],L)},A=async(I,M,_,L)=>m[u.get(I.pos)??await E(I,M,_,L)],N=I=>{let M=I.handles[I.handles.length-1];return{pos:{node:M,offset:I.offsets[I.offsets.length-1]},left:I.orientation==="forward"?I.hapEnd-h(M):I.hapStart}},k=I=>{let M=I.handles[0];return{pos:{node:M,offset:I.offsets[0]},left:I.orientation==="forward"?I.hapStart:I.hapEnd-h(M)}},F=await E({pos:r.referencePos,left:r.referenceLeft},r.referenceHandle,"forward","reference"),R=m[F],T=()=>{if(i.fallback!==void 0)return{reference:R,pieces:[],stats:i};let I=new Map;m.forEach((_,L)=>{L!==F&&I.set(at(_),[...I.get(at(_))??[],_])});let M=[];for(let _ of I.values()){let L=new Set;for(let B of _)B.canonical&&!L.has(B.orientation)&&(L.add(B.orientation),M.push(B),i.sources[B.source]+=1)}return i.sources.reference=1,i.pieces=M.length+1,{reference:R,pieces:M,stats:i}},C=async(I,M)=>{let _=M?b:S,L=M?S:b,B=I;for(;;){if(_.has(B))return;_.add(B);let W=m[B],J=M?N(W):k(W),q=0,$;for(;$===void 0;){n?.throwIfAborted();let K=M?await g(J.pos):await x(J.pos);if(!K){$="endmarker";break}let V=(await l(J.pos.node)).sequenceLen,Ie=(await l(K.node)).sequenceLen,oe=M?Pt(W.orientation,J.left,V,Ie):io(W.orientation,J.left,V,Ie);if(t.has(K.node)){let ee=u.get(K);ee===void 0?(B=await E({pos:K,left:oe},W.pathHandle,W.orientation,"chain"),L.add(B),$="landed"):(L.add(ee),$="merge")}else q>Xs?$="bound":(q+=Ie,J={pos:K,left:oe})}if(a("chain",$),$!=="landed")return}},D=async I=>{if(r.context>I.context)throw new ie(`the context of ${r.context} bp exceeds the ${I.context} bp the haplotype index's stray rows cover`);let M=i.spacing;if(M===void 0)throw new ie("the haplotype index has no anchors");let{bin:_,bound:L}=I,{fills:B,inserted:W}=r.snarls;if(r.snarls.mode==="overlapping"&&B.length>0)throw new ie("the haplotype index's stray rows cover contained snarls only");for(let v of B){if(v.inserted>0&&v.low===v.high)throw new ie(`the haplotype index's stray rows leave out the snarl bounded by node ${v.low} at both ends`);if(v.inserted>0&&(I.snarlNodes===void 0||v.nodes>I.snarlNodes))throw new ie(I.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${v.nodes} nodes exceeds the ${I.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(r.window.start/_),q=Math.floor((r.window.end-1)/_),$=J*_,K=(q+1)*_,V=new Map,Ie=async(v,P)=>{let U=await e.haplotypeAnchorsBetween(r.referenceHandle,v*M,P*M);for(let G of U)V.set(G.anchorOffset/M,G)},oe=Math.max(0,Math.floor(($-L)/M)-1),ee=Math.ceil((K+L)/M)+1,[{listed:yt,strays:ce}]=await Promise.all([e.haplotypeBinData(r.referenceHandle,J,q),Ie(oe,ee)]);for(let v of t.keys()){let P=O(v);if(!j(v)&&!yt(P)&&!W.has(P))throw new ie(`the haplotype index lists node ${P} of the subgraph in no bin that the window 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t}function wo(r){let e=new Map,t=new Map;r.forEach((i,a)=>{let f=O(i);e.has(f)?t.set(f,a):e.set(f,a)});let n=new Int32Array(r.length+1);for(let[i,a]of t)n[e.get(i)]+=1,n[a+1]-=1;let o=new Uint8Array(r.length),s=0;for(let i=0;i<r.length;i++)s+=n[i],o[i]=s>0?1:0;return o}function li(r,e,t,n){let o=wo(r),s=wo(e),i=new Map;e.forEach((h,d)=>{s[d]||i.set(O(h),[d])});let a=2*e.length,f=(h,d,p)=>h*a+2*d+(p?1:0),c=new Set;r.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[])c.add(f(d,p,j(h)!==j(e[p])))});let l=[];return r.forEach((h,d)=>{for(let p of o[d]?[]:i.get(O(h))??[]){let m=j(h)!==j(e[p]),u=m?-1:1,w=p-u;if(!(d>0&&w>=0&&w<e.length&&c.has(f(d-1,w,m)))){let S=d,g=p;for(;S<r.length&&g>=0&&g<e.length&&c.has(f(S,g,m));)S+=1,g+=u;let x=g-u;l.push({qs:t[d],qe:t[S],ts:n[Math.min(p,x)],te:n[Math.max(p,x)+1],flipped:m})}}}),l}function Io(r){let{query:e,target:t,sequenceOf:n}=r,o=mo(e,n),s=mo(t,n),i=li(e,t,go(e,n),go(t,n)),a=r.minMatch??Zs,f=r.bases??!0,c=[];for(let l of Un(i,r.maxGap??1/0,a,ni)){let h=[],d=l[0],p=l.at(-1),{flipped:m}=d.run;Tt(l,o,s,h,f?(w,b,S,g,x)=>{for(let y of ai(w,b,S,a)){let E=x+b.length;c.push({...y,queryStart:g+y.queryStart,queryEnd:g+y.queryEnd,targetStart:m?E-y.targetEnd:x+y.targetStart,targetEnd:m?E-y.targetStart:x+y.targetEnd,strand:m?"+":"-",edits:m?y.edits.reverse():y.edits,shared:[]})}}:Wn),c.push({queryStart:d.run.qs+d.trim,queryEnd:p.run.qe,targetStart:m?p.run.ts:d.run.ts+d.trim,targetEnd:m?d.run.te-d.trim:p.run.te,strand:m?"-":"+",edits:m?h.reverse():h,sharedBases:l.reduce((w,{run:b,trim:S})=>w+b.qe-b.qs-S,0),shared:l.map(({run:w,trim:b})=>[w.qs+b,w.qe])})}return ci(c,o.length,s.length,a).map(({shared:l,...h})=>h).sort((l,h)=>l.queryStart-h.queryStart)}function Eo(r){return r.map(([e,t])=>`${t}${e}`).join("")}var fe=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Yn(r,e){return r[0]<e[0]||r[0]===e[0]&&(r[1]<e[1]||r[1]===e[1]&&r[2]<e[2])}var ct=class{heap=[];push(e,t,n){let o=this.heap;o.push([e,t,n]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Yn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Yn(e[s],e[a])&&(a=s),i<e.length&&Yn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function hi(r){let e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function di(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function qe(r){return`${r.node}:${r.offset}`}function ft(r){return r.map(e=>re(e)).reverse()}function pi(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function ui(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([c,l])=>[c,l]);Co(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=r.identity.walkForward,[a,f]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function mi(r,e,t){if(r.some(i=>i.weight!==void 0))return r;let n=new Map;r.forEach((i,a)=>{if(i.identity){let f=n.get(i.identity.pathHandle);f?f.push(a):n.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of n.values()){i.sort((l,h)=>r[l].identity.hapStart-r[h].identity.hapStart);let a=i[0],f=r[a],c=[];for(let l of i.slice(1)){let h=r[l],d=c.length===0?pi(f,h):void 0;if(d){f=ui(f,h,d),s.add(l);continue}if(!e(h)){c.push(l);continue}let p=e(f)?t([f,...c.map(m=>r[m]),h]):void 0;if(p){f=p;for(let m of[...c,l])s.add(m)}else o.set(a,f),a=l,f=h;c=[]}o.set(a,f)}return r.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Lt(r,e){return{node:r.path[e],offset:r.offsets[e]}}var gi=32768;function wi(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=gi?o[1]=n:t.push([n,n])}return t}var lt=class r{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new r(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(Se(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new fe(this.limit);let t=await this.db.getRecord(Se(e,"forward")),n=await this.db.getRecord(Se(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${we(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${we(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`The fragment of ${we(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,i=o;for(;;){await this.ensureNode(O(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(`The fragment of ${we(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,n){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new ct;return a.push(t,o,Et(i)),a.push(s.sequenceLen-t-1,o,At(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(o&&s){let i=o.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,n);await this.db.prefetchRecords(wi(c.map(l=>l.pos.node)).map(([l,h])=>[l,h+2]),!0)}}return o}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(o){throw o instanceof fe&&o.windowBp===void 0?new fe(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ct;for(;;){let f=O(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,Et(c));let h=l.sequenceLen-s;if(i<=h){a.push(i===h?0:h-i-1,f,At(c));break}a.push(0,f,At(c));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=h}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new ct;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(n.has(c))continue;n.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=jr(f);if(!n.has(`${a}:${l}`)){let p=this.record(Se(a,Ur(f))),m=i+p.sequenceLen-1;m<=t&&e.push(m,a,l)}let h=this.record(Se(a,Wr(f))),d=i+1;if(d<=t)for(let p of h.successors()){let m=O(p),u=Et(je(p));n.has(`${m}:${u}`)||e.push(d,m,u)}}for(let i of o)this.records.delete(Se(i,"forward")),this.records.delete(Se(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,re(t)],o=new Set([O(e),O(t)]),s=[];for(;n.length>0;){let i=n.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(n.push(f,re(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(n,o),a=O(n),f=O(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?Ue(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(re(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,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(re(l))).successors().length>1},n=async f=>{let c=await e(re(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[re(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await n(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let h of["forward","reverse"])s.push(...(await e(Se(c,h))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((y,E)=>i.set(y,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let y=0;y<s;y++){let E=this.record(o[y]),A=E.gbwt().decompressArrays();f[y]=E.sequenceLen,c.push(A),a[y+1]=a[y]+A.nodes.length}let l=a[s],h=new Int32Array(l),d=new Int32Array(l),p=new Uint8Array(l);for(let y=0;y<s;y++){let E=c[y];h.set(E.nodes,a[y]),d.set(E.offsets,a[y])}c.length=0;for(let y=0;y<l;y++){let E=i.get(h[y]);E===void 0?h[y]=-1:(h[y]=E,p[a[E]+d[y]]=1)}let m=n===void 0?void 0:i.get(n.handle),u=n?.gbwtOffset,w,b=(y,E,A)=>{let N=[],k=0,F=0,R=-1,T=y,C=E;for(;;){T===m&&C===u&&(R=k),A&&(A.push(o[T]),N.push(C)),k+=1,F+=f[T];let D=a[T]+C,Y=h[D];if(Y<0)break;C=d[D],T=Y}return{offsets:N,len:F,refAt:R,last:T}},S=(y,E,A,N)=>{N>=0&&(this.refId=this.paths.length,w=N),this.paths.push({path:y,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let y=0;y<s;y++){let E=o[y];if(!j(E)){let A=a[y],N=a[y+1]-A;for(let k=0;k<N;k++)if(p[A+k]===0){let F=[],{offsets:R,len:T,refAt:C,last:D}=b(y,k,F),Y=o[D];if(C>=0||Fe(E,Y)){if(S(F,R,T,C),!j(Y)){let I=i.get(re(Y));g[I]=g[I]+1}}else this.twinStarts.add(qe({node:E,offset:k}))}}}for(let y=0;y<s;y++){let E=o[y];if(j(E)){let A=a[y],N=a[y+1]-A,k=0;for(let R=0;R<N;R++)p[A+R]===0&&(k+=1);let F=(m===void 0||w!==void 0)&&k===g[y];for(let R=0;R<N;R++)if(p[A+R]===0){let T=F?void 0:b(y,R,void 0);if(T&&(T.refAt>=0||Fe(E,o[T.last]))){let C=[],{offsets:D,len:Y,refAt:I}=b(y,R,C);S(C,D,Y,I)}else this.twinStarts.add(qe({node:E,offset:R}))}}}let x=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((y,E)=>y.path[0]-E.path[0]||y.offsets[0]-E.offsets[0]),x&&(this.refId=this.paths.indexOf(x)),n){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let y=this.paths[this.refId],E=n.nodeOffset;for(let N of y.path.slice(0,w))E+=this.record(N).sequenceLen;let A=n.seqOffset-E;this.refInterval=[A,A+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+y.len}}if(t==="distinct")this.distinctPaths(!0);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(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,o=n&&!st(n)?ft(n):void 0,s=c=>o!==void 0&&Kn(c,o)===0||st(ft(c)),i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>Kn(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],h=i&&c!==t&&s(c.path);this.twinDeferred||=h,l&&Kn(l.path,c.path)===0&&!h?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(n(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(n(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let n=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(O(a));for(let i of[...this.records.keys()])s.has(O(i))||this.records.delete(i);this.paths=o,this.refId=n===void 0?void 0:o.indexOf(n)}async extractChosenPaths(e,t,n,o){this.clearPaths();let s=e.position.seqOffset,i=await fo({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(l,h,d)=>this.prefetchReferenceRange(l,h,d)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(co);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=Bn(this.sortedHandles());if(t.length===0)return;let n=new Map,o=await Promise.all(t.map(([u,w])=>this.db.haplotypeSamplesInRange(u,w)));for(let u of o.flat())n.set(qe(u),u);let s=u=>{let w=0,b=t.length-1;for(;w<b;){let g=w+b+1>>1;t[g][0]<=u?w=g:b=g-1}let S=t[w];return S[0]<=u&&u<=S[1]},i=new Map;this.paths.forEach((u,w)=>{u.path.length>0&&w!==this.refId&&i.set(qe(Lt(u,0)),w)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=n.size,this.paths.forEach((u,w)=>{w!==this.refId&&a.fragmentLengths.push(u.len)});let f=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=u=>(a.graphLookups+=1,f(u)),l=async(u,w)=>{if(s(u.node))return n.get(qe(u));this.stats.identificationFetches+=1,a.companionSeeks+=1,w.seeks+=1;let b=await this.db.haplotypeSampleAt(u.node,u.offset);return b||(a.companionMisses+=1),b},h=new Map,d=async u=>{let w=h.get(u);if(!w){let b=await this.db.getPath(u);if(!b)throw new Error(`Path ${u} is missing from the database`);w=b.name,h.set(u,w)}return w},p=(u,w,b)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+w+b},m=(u,w)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+w};for(let u=0;u<this.paths.length;u++){let w=this.paths[u];if(u===this.refId||w.identity)continue;let b=[],S=new Set,g={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(g);let x,y=0,E=u,A;for(;x===void 0;){if(this.signal?.throwIfAborted(),E!==void 0){if(S.has(E)){g.end="cycle";break}S.add(E);let T=this.paths[E];b.push({index:E,startBp:y}),g.fragments+=1;let C=y;for(let Y=0;Y<T.path.length;Y++){let I=Lt(T,Y),M=n.get(qe(I)),_=this.record(I.node).sequenceLen;if(M){x=p(M,C,_);break}C+=_}if(y+=T.len,x){g.end="in-fragment sample";break}let D=Lt(T,T.path.length-1);A=this.record(D.node).gbwt().lf(D.offset),E=void 0}if(A===void 0||A.node===0){g.end="endmarker";break}let N=qe(A),k=i.get(N);if(k!==void 0){let T=this.paths[k].identity;if(T){x=m(T,y),g.end="identified sibling";break}E=k;continue}this.records.has(A.node)&&(g.reentries+=1),this.twinStarts.has(N)&&(g.twinLandings+=1);let F=await l(A,g),R=await c(A.node);if(F){x=p(F,y,R.sequenceLen),g.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,g.steps+=1,y-b[b.length-1].startBp>4*e+4*R.sequenceLen){g.end="bound";break}y+=R.sequenceLen,A=R.gbwt().lf(A.offset)}if(x){g.pathHandle=x.pathHandle;let N=await d(x.pathHandle);for(let{index:k,startBp:F}of b){let R=this.paths[k];R.identity=x.orientation==="forward"?{pathHandle:x.pathHandle,name:N,orientation:"forward",hapStart:x.base+F,hapEnd:x.base+F+R.len}:{pathHandle:x.pathHandle,name:N,orientation:"reverse",hapStart:x.base-F-R.len,hapEnd:x.base-F}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=n.get(e[f]);if(c){let l=di(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-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 n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}align(e,t,n){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(n,"M",i),Co(n,o-i-a,s-i-a),X(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??hi(lo(e,t,h=>this.record(h).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(h,d,p,m)=>{h===d?X(s,"D",i[m]-i[p]):p===m?X(s,"I",this.pathLen(e.slice(h,d))):this.align(e.slice(h,d),t.slice(p,m),s)},f=0,c=0,l=0;for(let h=0;h<o.count;h++){let d=o.pathAt[h],p=o.refAt[h];(c!==d||l!==p)&&a(c,d,l,p);let m=this.record(e[d]).sequenceLen;X(s,"M",m),f+=m,c=d+1,l=p+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(st(n)&&(t.identity===void 0||!st(ft(t.path))))o={...this.editsAgainst(t.path,n),flipped:!1};else{let s=ft(t.path),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={...this.editsAgainst(t.path,n),flipped:!1};else if(i===0)o={...this.editsAgainst(s,n),flipped:!0};else{let f=this.editsAgainst(t.path,n),c=this.editsAgainst(s,n);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();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,n=this.refPrefix(t)[t.length],o=(l,h,d,p)=>{let m=yi(l),u=this.paths[d[0]],w=this.paths[d[d.length-1]],b=u.identity,S=b?.orientation==="forward",[g,x]=S?[u,w]:[w,u];return{strand:h,refStart:e.start+m.leading,refEnd:e.start+n-m.trailing,edits:m.edits,weight:u.weight,path:d.flatMap(y=>this.paths[y].path),start:Lt(u,0),pieces:d,soloAligned:p,identity:b===void 0?void 0:{pathHandle:b.pathHandle,name:b.name,hapStart:b.name.fragment+g.identity.hapStart,hapEnd:b.name.fragment+x.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((h,d)=>h+d,0),i=l=>l.pieces.reduce((h,d)=>h+this.paths[d].len,0),a=l=>2*s(l)>=i(l),f=l=>{let h=l[0],d=l[l.length-1],p=h.identity.walkForward;if(l.some((C,D)=>C.strand!==h.strand||C.identity.walkForward!==p||D>0&&C.identity.hapStart<l[D-1].identity.hapEnd))return;let m=p?l:[...l].reverse(),u=m.flatMap(C=>C.pieces),w=m.flatMap(C=>C.soloAligned),b=h.strand==="+"!==p,S=u.map(C=>this.paths[C]),g=S.slice(1).map((C,D)=>{let Y=S[D].identity;return p?C.identity.hapStart-Y.hapEnd:Y.hapStart-C.identity.hapEnd}),x=b?[...S].reverse():S,y=b?[...g].reverse():g,E=x.flatMap(C=>b?ft(C.path):C.path),{edits:A}=this.editsAgainst(E,t),N=Ao(A,x.map(C=>C.len)),k=new Map((b?[...u].reverse():u).map((C,D)=>[C,N[D]])),F=C=>2*C.pieces.reduce((D,Y)=>D+k.get(Y),0)>=s(C);if(!F(h)||!F(d))return;let R=[],T=0;return x.slice(0,-1).forEach((C,D)=>{T+=C.len,R.push([T,y[D]])}),o(bi(A,R),h.strand,u,w)},c=[];return this.paths.forEach((l,h)=>{if(h===this.refId)return;let{edits:d,flipped:p}=this.alignment(h),m=l.identity,u=m?m.orientation==="forward"!==p:!p;c.push(o(d,u?"+":"-",[h],Ao(d,[l.len])))}),mi(c,a,f).map(l=>{let{edits:h,identity:d,pieces:p,soloAligned:m,...u}=l,w={...u,cigar:Si(h)};return d?{...w,resolved:!0,name:d.name,label:we({...d.name,fragment:d.hapStart,end:d.hapEnd}),pathHandle:d.pathHandle,hapStart:d.hapStart,hapEnd:d.hapEnd}:{...w,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...o}=e,s=this.paths.flatMap(l=>{let{identity:h}=l;return h?[{name:h.name,start:h.name.fragment+h.hapStart,steps:$t(l,h)}]:[]}),i=l=>h=>h.sample===l.sample&&h.haplotype===l.haplotype,a=i(t),f=n?i(n):l=>!a(l),c=l=>this.record(Se(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(h=>f(h.name)).flatMap(h=>Io({...o,query:h.steps,target:l.steps,sequenceOf:c}).map(d=>({query:h.name,queryStart:h.start+d.queryStart,queryEnd:h.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Eo(d.edits),matches:d.edits.reduce((p,[m,u])=>p+(m==="="?u:0),0),columns:d.edits.reduce((p,[,m])=>p+m,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=Se(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&Ue(o,s)&&t.push([n==="reverse"?1:0,O(s),j(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!j(n)){let o=O(n),s=`S	${o}	${this.record(n).sequence}
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Ws="_gbwt_ref";function ge(r){let e=`${r.sample}#${r.haplotype}#${r.contig}`;return r.end===void 0?e:`${e}[${r.fragment}-${r.end}]`}var Vs=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,Qs=/^([^#]+?)(?:\[\d+-\d+\])?$/;function Ys(r){let e=Vs.exec(r);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=Qs.exec(r);if(t)return{contig:t[1]};throw new Error(`"${r}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function We(r){return typeof r=="string"?Ys(r):r}function Ve(r,e){return{sample:r.sample??Ws,contig:r.contig,haplotype:r.haplotype??0,fragment:e}}var Ks=4096;function qn(r){let e=[];for(let t of r){let n=e[e.length-1];n&&t-n[1]<=Ks?n[1]=t:e.push([t,t])}return e}var Xs=32768,io={mostChosenPaths:32},$n=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},ie=class extends Error{};function Rt(r,e,t,n){return r==="forward"?e+t:e-n}function ao(r,e,t,n){return r==="forward"?e-n:e+t}function fo(r){return Fe(re(r.handles[r.handles.length-1]),re(r.handles[0]))}function at(r){return`${r.pathHandle}:${r.hapStart}:${r.hapEnd}`}async function co(r){let{db:e,records:t,signal:n}=r,o=performance.now(),s=()=>{let I=performance.now(),M=I-o;return o=I,M},i={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},a=(I,M)=>{let _=`${I}: ${M}`;i.walks[_]=(i.walks[_]??0)+1},f=await e.haplotypeSampleInterval()??4096,c=new Map,l=async I=>{let M=t.get(I)??c.get(I);if(M)return M;let _=await e.getRecord(I);if(i.graphFetches+=1,!_)throw new Error(`Node record ${I} is missing from the database`);return c.set(I,_),_},h=I=>t.get(I).sequenceLen,d=await e.pathsByHandle(),p=I=>{let M=d.get(I);return M!==void 0&&r.keep(M.name)},m=[],u=new $n,w=new Map,b=new Set,S=new Set,g=async I=>{let M=(await l(I.node)).gbwt().lf(I.offset);return M===void 0||M.node===0?void 0:M},x=async(I,M)=>{let _=(await l(re(I.node))).gbwt().predecessorAt(I.offset);if(_===void 0||M!==void 0&&!M.has(_))return;let L=(await l(_)).gbwt().offsetTo(I);if(L===void 0)throw new Error(`No offset in ${_} leads to ${I.node}:${I.offset}`);return{node:_,offset:L}},y=(I,M,_,L)=>{let B=_.map(V=>V.pos.node),W=_.map(V=>V.pos.offset),J=0;for(let V of B)J+=h(V);let q=M==="forward"?_[0].left:_[_.length-1].left,$=m.length;m.push({pathHandle:I,orientation:M,handles:B,offsets:W,len:J,hapStart:q,hapEnd:q+J,canonical:Fe(B[0],B[B.length-1]),source:L});for(let V of _)u.set(V.pos,$);let K=w.get(I);return K?K.push($):w.set(I,[$]),$},E=async(I,M,_,L)=>{let B=[],W=I;for(;;){n?.throwIfAborted();let q=await x(W.pos,t);if(!q)break;W={pos:q,left:ao(_,W.left,h(W.pos.node),h(q.node))},B.push(W)}B.reverse();let J=[I];for(W=I;;){n?.throwIfAborted();let q=await g(W.pos);if(!q||!t.has(q.node))break;W={pos:q,left:Rt(_,W.left,h(W.pos.node),h(q.node))},J.push(W)}return y(M,_,[...B,...J],L)},A=async(I,M,_,L)=>m[u.get(I.pos)??await E(I,M,_,L)],N=I=>{let M=I.handles[I.handles.length-1];return{pos:{node:M,offset:I.offsets[I.offsets.length-1]},left:I.orientation==="forward"?I.hapEnd-h(M):I.hapStart}},k=I=>{let M=I.handles[0];return{pos:{node:M,offset:I.offsets[0]},left:I.orientation==="forward"?I.hapStart:I.hapEnd-h(M)}},F=await E({pos:r.referencePos,left:r.referenceLeft},r.referenceHandle,"forward","reference"),R=m[F],T=()=>{if(i.fallback!==void 0)return{reference:R,pieces:[],stats:i};let I=new Map;m.forEach((_,L)=>{L!==F&&I.set(at(_),[...I.get(at(_))??[],_])});let M=[];for(let _ of I.values()){let L=new Set;for(let B of _)B.canonical&&!L.has(B.orientation)&&(L.add(B.orientation),M.push(B),i.sources[B.source]+=1)}return i.sources.reference=1,i.pieces=M.length+1,{reference:R,pieces:M,stats:i}},C=async(I,M)=>{let _=M?b:S,L=M?S:b,B=I;for(;;){if(_.has(B))return;_.add(B);let W=m[B],J=M?N(W):k(W),q=0,$;for(;$===void 0;){n?.throwIfAborted();let K=M?await g(J.pos):await x(J.pos);if(!K){$="endmarker";break}let V=(await l(J.pos.node)).sequenceLen,Ie=(await l(K.node)).sequenceLen,oe=M?Rt(W.orientation,J.left,V,Ie):ao(W.orientation,J.left,V,Ie);if(t.has(K.node)){let ee=u.get(K);ee===void 0?(B=await E({pos:K,left:oe},W.pathHandle,W.orientation,"chain"),L.add(B),$="landed"):(L.add(ee),$="merge")}else q>Xs?$="bound":(q+=Ie,J={pos:K,left:oe})}if(a("chain",$),$!=="landed")return}},D=async I=>{if(r.context>I.context)throw new ie(`the context of ${r.context} bp exceeds the ${I.context} bp the haplotype index's stray rows cover`);let M=i.spacing;if(M===void 0)throw new ie("the haplotype index has no anchors");let{bin:_,bound:L}=I,{fills:B,inserted:W}=r.snarls;if(r.snarls.mode==="overlapping"&&B.length>0)throw new ie("the haplotype index's stray rows cover contained snarls only");for(let v of B){if(v.inserted>0&&v.low===v.high)throw new ie(`the haplotype index's stray rows leave out the snarl bounded by node ${v.low} at both ends`);if(v.inserted>0&&(I.snarlNodes===void 0||v.nodes>I.snarlNodes))throw new ie(I.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${v.nodes} nodes exceeds the ${I.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(r.window.start/_),q=Math.floor((r.window.end-1)/_),$=J*_,K=(q+1)*_,V=new Map,Ie=async(v,P)=>{let U=await e.haplotypeAnchorsBetween(r.referenceHandle,v*M,P*M);for(let G of U)V.set(G.anchorOffset/M,G)},oe=Math.max(0,Math.floor(($-L)/M)-1),ee=Math.ceil((K+L)/M)+1,[{listed:yt,strays:ce}]=await Promise.all([e.haplotypeBinData(r.referenceHandle,J,q),Ie(oe,ee)]);for(let v of t.keys()){let P=O(v);if(!j(v)&&!yt(P)&&!W.has(P))throw new ie(`the haplotype index lists node ${P} of the subgraph in no bin that the window touches`)}i.scans=qn([...t.keys()].sort((v,P)=>v-P));let pe=Promise.all(i.scans.map(([v,P])=>e.haplotypeSamplesInRange(v,P)));for(pe.catch(()=>{});oe>0&&(V.get(oe)?.pathOffset??Number.POSITIVE_INFINITY)>=$-L;)oe-=1,await Ie(oe,oe);for(;V.has(ee)&&V.get(ee).pathOffset<=K+L;)ee+=1,await Ie(ee,ee);let ye=[...V.keys()].sort((v,P)=>v-P),ke=V.get(ye[0]??-1);if(!ke)throw new ie("the haplotype index has no anchors on this path");let ue=v=>V.get(v).pathOffset,tt=new Map;for(let v of ye){let P=O(V.get(v).node);tt.set(P,[...tt.get(P)??[],v])}let An=[...tt.keys()],Mr=An.map(v=>V.get(tt.get(v)[0]).visits);if(!Mr[An.indexOf(O(ke.node))].some(v=>v.pathHandle===r.referenceHandle&&v.orientation==="forward"&&v.pathOffset===ke.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${r.referenceHandle} at offset ${ke.pathOffset} (node ${O(ke.node)}); it does not match this graph`);let Rr=ye.filter(v=>ue(v)<=r.window.start),Ts=ye.filter(v=>ue(v)>=r.window.end);i.anchors=[ue(Rr[Rr.length-1]??ye[0]),ue(Ts[0]??ye[ye.length-1])],i.anchorsRead=ye.length;let Cn=new Map,Pr=new Set;if(An.forEach((v,P)=>{let U=tt.get(v),G=U.length===1?U[0]:void 0;for(let z of Mr[P])Pr.add(z.pathHandle),z.orientation==="forward"&&p(z.pathHandle)&&Cn.set(z.pathHandle,[...Cn.get(z.pathHandle)??[],{k:G,row:z}])}),i.chosenPaths=[...Pr].filter(p).length,i.chosenPaths>io.mostChosenPaths)throw new ie(`${i.chosenPaths} chosen paths pass the anchors, more than ${io.mostChosenPaths}`);let bt=[],Le=Number.POSITIVE_INFINITY,_e=0;for(let[v,P]of Cn){P.sort((U,G)=>U.row.pathOffset-G.row.pathOffset);for(let U=0;U+1<P.length;U++){let G=P[U],z=P[U+1];if(G.k===void 0||z.k===void 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jn(i,r.maxGap??1/0,a,ni)){let h=[],d=l[0],p=l.at(-1),{flipped:m}=d.run;Nt(l,o,s,h,f?(w,b,S,g,x)=>{for(let y of ai(w,b,S,a)){let E=x+b.length;c.push({...y,queryStart:g+y.queryStart,queryEnd:g+y.queryEnd,targetStart:m?E-y.targetEnd:x+y.targetStart,targetEnd:m?E-y.targetStart:x+y.targetEnd,strand:m?"+":"-",edits:m?y.edits.reverse():y.edits,shared:[]})}}:Un),c.push({queryStart:d.run.qs+d.trim,queryEnd:p.run.qe,targetStart:m?p.run.ts:d.run.ts+d.trim,targetEnd:m?d.run.te-d.trim:p.run.te,strand:m?"-":"+",edits:m?h.reverse():h,sharedBases:l.reduce((w,{run:b,trim:S})=>w+b.qe-b.qs-S,0),shared:l.map(({run:w,trim:b})=>[w.qs+b,w.qe])})}return ci(c,o.length,s.length,a).map(({shared:l,...h})=>h).sort((l,h)=>l.queryStart-h.queryStart)}function Ao(r){return r.map(([e,t])=>`${t}${e}`).join("")}var fe=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Qn(r,e){return r[0]<e[0]||r[0]===e[0]&&(r[1]<e[1]||r[1]===e[1]&&r[2]<e[2])}var ct=class{heap=[];push(e,t,n){let o=this.heap;o.push([e,t,n]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Qn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Qn(e[s],e[a])&&(a=s),i<e.length&&Qn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function hi(r){let e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function di(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function qe(r){return`${r.node}:${r.offset}`}function ft(r){return r.map(e=>re(e)).reverse()}function pi(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function ui(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([c,l])=>[c,l]);Mo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=r.identity.walkForward,[a,f]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function mi(r,e,t){if(r.some(i=>i.weight!==void 0))return r;let n=new Map;r.forEach((i,a)=>{if(i.identity){let f=n.get(i.identity.pathHandle);f?f.push(a):n.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of n.values()){i.sort((l,h)=>r[l].identity.hapStart-r[h].identity.hapStart);let a=i[0],f=r[a],c=[];for(let l of i.slice(1)){let h=r[l],d=c.length===0?pi(f,h):void 0;if(d){f=ui(f,h,d),s.add(l);continue}if(!e(h)){c.push(l);continue}let p=e(f)?t([f,...c.map(m=>r[m]),h]):void 0;if(p){f=p;for(let m of[...c,l])s.add(m)}else o.set(a,f),a=l,f=h;c=[]}o.set(a,f)}return r.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Tt(r,e){return{node:r.path[e],offset:r.offsets[e]}}var gi=32768;function wi(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=gi?o[1]=n:t.push([n,n])}return t}var lt=class r{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t){this.db=e,this.limit=t.limit,this.signal=t.signal}static create(e,t={}){return new r(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(Se(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new fe(this.limit);let t=await this.db.getRecord(Se(e,"forward")),n=await this.db.getRecord(Se(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.twinDeferred=!1,this.unsettled=void 0,this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering offset ${e.fragment} of ${ge(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${ge(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`The fragment of ${ge(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,i=o;for(;;){await this.ensureNode(O(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(`The fragment of ${ge(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,n){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new ct;return a.push(t,o,It(i)),a.push(s.sequenceLen-t-1,o,Et(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(o&&s){let i=o.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,n);await this.db.prefetchRecords(wi(c.map(l=>l.pos.node)).map(([l,h])=>[l,h+2]),!0)}}return o}async aroundInterval(e,t,n){if(!(t>0))throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(o){throw o instanceof fe&&o.windowBp===void 0?new fe(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new ct;for(;;){let f=O(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,It(c));let h=l.sequenceLen-s;if(i<=h){a.push(i===h?0:h-i-1,f,Et(c));break}a.push(0,f,Et(c));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=h}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new ct;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(n.has(c))continue;n.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Ur(f);if(!n.has(`${a}:${l}`)){let p=this.record(Se(a,Wr(f))),m=i+p.sequenceLen-1;m<=t&&e.push(m,a,l)}let h=this.record(Se(a,Vr(f))),d=i+1;if(d<=t)for(let p of h.successors()){let m=O(p),u=It(je(p));n.has(`${m}:${u}`)||e.push(d,m,u)}}for(let i of o)this.records.delete(Se(i,"forward")),this.records.delete(Se(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,re(t)],o=new Set([O(e),O(t)]),s=[];for(;n.length>0;){let i=n.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(n.push(f,re(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(n,o),a=O(n),f=O(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?Ue(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(re(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,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(re(l))).successors().length>1},n=async f=>{let c=await e(re(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[re(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await n(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let h of["forward","reverse"])s.push(...(await e(Se(c,h))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((y,E)=>i.set(y,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let y=0;y<s;y++){let E=this.record(o[y]),A=E.gbwt().decompressArrays();f[y]=E.sequenceLen,c.push(A),a[y+1]=a[y]+A.nodes.length}let l=a[s],h=new Int32Array(l),d=new Int32Array(l),p=new Uint8Array(l);for(let y=0;y<s;y++){let E=c[y];h.set(E.nodes,a[y]),d.set(E.offsets,a[y])}c.length=0;for(let y=0;y<l;y++){let E=i.get(h[y]);E===void 0?h[y]=-1:(h[y]=E,p[a[E]+d[y]]=1)}let m=n===void 0?void 0:i.get(n.handle),u=n?.gbwtOffset,w,b=(y,E,A)=>{let N=[],k=0,F=0,R=-1,T=y,C=E;for(;;){T===m&&C===u&&(R=k),A&&(A.push(o[T]),N.push(C)),k+=1,F+=f[T];let D=a[T]+C,Y=h[D];if(Y<0)break;C=d[D],T=Y}return{offsets:N,len:F,refAt:R,last:T}},S=(y,E,A,N)=>{N>=0&&(this.refId=this.paths.length,w=N),this.paths.push({path:y,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let y=0;y<s;y++){let E=o[y];if(!j(E)){let A=a[y],N=a[y+1]-A;for(let k=0;k<N;k++)if(p[A+k]===0){let F=[],{offsets:R,len:T,refAt:C,last:D}=b(y,k,F),Y=o[D];if(C>=0||Fe(E,Y)){if(S(F,R,T,C),!j(Y)){let I=i.get(re(Y));g[I]=g[I]+1}}else this.twinStarts.add(qe({node:E,offset:k}))}}}for(let y=0;y<s;y++){let E=o[y];if(j(E)){let A=a[y],N=a[y+1]-A,k=0;for(let R=0;R<N;R++)p[A+R]===0&&(k+=1);let F=(m===void 0||w!==void 0)&&k===g[y];for(let R=0;R<N;R++)if(p[A+R]===0){let T=F?void 0:b(y,R,void 0);if(T&&(T.refAt>=0||Fe(E,o[T.last]))){let C=[],{offsets:D,len:Y,refAt:I}=b(y,R,C);S(C,D,Y,I)}else this.twinStarts.add(qe({node:E,offset:R}))}}}let x=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((y,E)=>y.path[0]-E.path[0]||y.offsets[0]-E.offsets[0]),x&&(this.refId=this.paths.indexOf(x)),n){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let y=this.paths[this.refId],E=n.nodeOffset;for(let N of y.path.slice(0,w))E+=this.record(N).sequenceLen;let A=n.seqOffset-E;this.refInterval=[A,A+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+y.len}}if(t==="distinct")this.distinctPaths(!0);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(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=t?.path,o=n&&!st(n)?ft(n):void 0,s=c=>o!==void 0&&Yn(c,o)===0||st(ft(c)),i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>Yn(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],h=i&&c!==t&&s(c.path);this.twinDeferred||=h,l&&Yn(l.path,c.path)===0&&!h?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(n(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(n(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let n=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(O(a));for(let i of[...this.records.keys()])s.has(O(i))||this.records.delete(i);this.paths=o,this.refId=n===void 0?void 0:o.indexOf(n)}async extractChosenPaths(e,t,n,o){this.clearPaths();let s=e.position.seqOffset,i=await co({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(l,h,d)=>this.prefetchReferenceRange(l,h,d)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(lo);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=qn(this.sortedHandles());if(t.length===0)return;let n=new Map,o=await Promise.all(t.map(([u,w])=>this.db.haplotypeSamplesInRange(u,w)));for(let u of o.flat())n.set(qe(u),u);let s=u=>{let w=0,b=t.length-1;for(;w<b;){let g=w+b+1>>1;t[g][0]<=u?w=g:b=g-1}let S=t[w];return S[0]<=u&&u<=S[1]},i=new Map;this.paths.forEach((u,w)=>{u.path.length>0&&w!==this.refId&&i.set(qe(Tt(u,0)),w)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=n.size,this.paths.forEach((u,w)=>{w!==this.refId&&a.fragmentLengths.push(u.len)});let f=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=u=>(a.graphLookups+=1,f(u)),l=async(u,w)=>{if(s(u.node))return n.get(qe(u));this.stats.identificationFetches+=1,a.companionSeeks+=1,w.seeks+=1;let b=await this.db.haplotypeSampleAt(u.node,u.offset);return b||(a.companionMisses+=1),b},h=new Map,d=async u=>{let w=h.get(u);if(!w){let b=await this.db.getPath(u);if(!b)throw new Error(`Path ${u} is missing from the database`);w=b.name,h.set(u,w)}return w},p=(u,w,b)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+w+b},m=(u,w)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-w}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+w};for(let u=0;u<this.paths.length;u++){let w=this.paths[u];if(u===this.refId||w.identity)continue;let b=[],S=new Set,g={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(g);let x,y=0,E=u,A;for(;x===void 0;){if(this.signal?.throwIfAborted(),E!==void 0){if(S.has(E)){g.end="cycle";break}S.add(E);let T=this.paths[E];b.push({index:E,startBp:y}),g.fragments+=1;let C=y;for(let Y=0;Y<T.path.length;Y++){let I=Tt(T,Y),M=n.get(qe(I)),_=this.record(I.node).sequenceLen;if(M){x=p(M,C,_);break}C+=_}if(y+=T.len,x){g.end="in-fragment sample";break}let D=Tt(T,T.path.length-1);A=this.record(D.node).gbwt().lf(D.offset),E=void 0}if(A===void 0||A.node===0){g.end="endmarker";break}let N=qe(A),k=i.get(N);if(k!==void 0){let T=this.paths[k].identity;if(T){x=m(T,y),g.end="identified sibling";break}E=k;continue}this.records.has(A.node)&&(g.reentries+=1),this.twinStarts.has(N)&&(g.twinLandings+=1);let F=await l(A,g),R=await c(A.node);if(F){x=p(F,y,R.sequenceLen),g.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,g.steps+=1,y-b[b.length-1].startBp>4*e+4*R.sequenceLen){g.end="bound";break}y+=R.sequenceLen,A=R.gbwt().lf(A.offset)}if(x){g.pathHandle=x.pathHandle;let N=await d(x.pathHandle);for(let{index:k,startBp:F}of b){let R=this.paths[k];R.identity=x.orientation==="forward"?{pathHandle:x.pathHandle,name:N,orientation:"forward",hapStart:x.base+F,hapEnd:x.base+F+R.len}:{pathHandle:x.pathHandle,name:N,orientation:"reverse",hapStart:x.base-F-R.len,hapEnd:x.base-F}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=n.get(e[f]);if(c){let l=di(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-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 n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}align(e,t,n){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(n,"M",i),Mo(n,o-i-a,s-i-a),X(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??hi(ho(e,t,h=>this.record(h).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(h,d,p,m)=>{h===d?X(s,"D",i[m]-i[p]):p===m?X(s,"I",this.pathLen(e.slice(h,d))):this.align(e.slice(h,d),t.slice(p,m),s)},f=0,c=0,l=0;for(let h=0;h<o.count;h++){let d=o.pathAt[h],p=o.refAt[h];(c!==d||l!==p)&&a(c,d,l,p);let m=this.record(e[d]).sequenceLen;X(s,"M",m),f+=m,c=d+1,l=p+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(st(n)&&(t.identity===void 0||!st(ft(t.path))))o={...this.editsAgainst(t.path,n),flipped:!1};else{let s=ft(t.path),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={...this.editsAgainst(t.path,n),flipped:!1};else if(i===0)o={...this.editsAgainst(s,n),flipped:!0};else{let f=this.editsAgainst(t.path,n),c=this.editsAgainst(s,n);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();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,n=this.refPrefix(t)[t.length],o=(l,h,d,p)=>{let m=yi(l),u=this.paths[d[0]],w=this.paths[d[d.length-1]],b=u.identity,S=b?.orientation==="forward",[g,x]=S?[u,w]:[w,u];return{strand:h,refStart:e.start+m.leading,refEnd:e.start+n-m.trailing,edits:m.edits,weight:u.weight,path:d.flatMap(y=>this.paths[y].path),start:Tt(u,0),pieces:d,soloAligned:p,identity:b===void 0?void 0:{pathHandle:b.pathHandle,name:b.name,hapStart:b.name.fragment+g.identity.hapStart,hapEnd:b.name.fragment+x.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((h,d)=>h+d,0),i=l=>l.pieces.reduce((h,d)=>h+this.paths[d].len,0),a=l=>2*s(l)>=i(l),f=l=>{let h=l[0],d=l[l.length-1],p=h.identity.walkForward;if(l.some((C,D)=>C.strand!==h.strand||C.identity.walkForward!==p||D>0&&C.identity.hapStart<l[D-1].identity.hapEnd))return;let m=p?l:[...l].reverse(),u=m.flatMap(C=>C.pieces),w=m.flatMap(C=>C.soloAligned),b=h.strand==="+"!==p,S=u.map(C=>this.paths[C]),g=S.slice(1).map((C,D)=>{let Y=S[D].identity;return p?C.identity.hapStart-Y.hapEnd:Y.hapStart-C.identity.hapEnd}),x=b?[...S].reverse():S,y=b?[...g].reverse():g,E=x.flatMap(C=>b?ft(C.path):C.path),{edits:A}=this.editsAgainst(E,t),N=Co(A,x.map(C=>C.len)),k=new Map((b?[...u].reverse():u).map((C,D)=>[C,N[D]])),F=C=>2*C.pieces.reduce((D,Y)=>D+k.get(Y),0)>=s(C);if(!F(h)||!F(d))return;let R=[],T=0;return x.slice(0,-1).forEach((C,D)=>{T+=C.len,R.push([T,y[D]])}),o(bi(A,R),h.strand,u,w)},c=[];return this.paths.forEach((l,h)=>{if(h===this.refId)return;let{edits:d,flipped:p}=this.alignment(h),m=l.identity,u=m?m.orientation==="forward"!==p:!p;c.push(o(d,u?"+":"-",[h],Co(d,[l.len])))}),mi(c,a,f).map(l=>{let{edits:h,identity:d,pieces:p,soloAligned:m,...u}=l,w={...u,cigar:Si(h)};return d?{...w,resolved:!0,name:d.name,label:ge({...d.name,fragment:d.hapStart,end:d.hapEnd}),pathHandle:d.pathHandle,hapStart:d.hapStart,hapEnd:d.hapEnd}:{...w,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...o}=e,s=this.paths.flatMap(l=>{let{identity:h}=l;return h?[{name:h.name,start:h.name.fragment+h.hapStart,steps:Ft(l,h)}]:[]}),i=l=>h=>h.sample===l.sample&&h.haplotype===l.haplotype,a=i(t),f=n?i(n):l=>!a(l),c=l=>this.record(Se(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(h=>f(h.name)).flatMap(h=>Eo({...o,query:h.steps,target:l.steps,sequenceOf:c}).map(d=>({query:h.name,queryStart:h.start+d.queryStart,queryEnd:h.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Ao(d.edits),matches:d.edits.reduce((p,[m,u])=>p+(m==="="?u:0),0),columns:d.edits.reduce((p,[,m])=>p+m,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=Se(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&Ue(o,s)&&t.push([n==="reverse"?1:0,O(s),j(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!j(n)){let o=O(n),s=`S	${o}	${this.record(n).sequence}
 `;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
-`;t.push(e.encode(s))}return oo(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...ro(no(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)j(c)||n.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>j(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&Ue(c,l)&&n.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,h,d,p)=>{let m=$t(c,l).map(b=>`${j(b)?"<":">"}${O(b)}`).join(""),u=c.weight===void 0?"":`	WT:i:${c.weight}`,w=p===void 0?"":`	CG:Z:${p}`;return`W	${h.sample}	${h.haplotype}	${h.contig}	${h.fragment}	${d}	${m}${u}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let h=e.names!=="anonymous"?c.identity:void 0,d=t?this.alignToRef(l):void 0;n.push(h?i(c,h,{...h.name,fragment:h.name.fragment+h.hapStart},h.name.fragment+h.hapEnd,d):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,d)),f+=1}}),`${n.join(`
+`;t.push(e.encode(s))}return so(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...oo(ro(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)j(c)||n.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>j(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&Ue(c,l)&&n.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,h,d,p)=>{let m=Ft(c,l).map(b=>`${j(b)?"<":">"}${O(b)}`).join(""),u=c.weight===void 0?"":`	WT:i:${c.weight}`,w=p===void 0?"":`	CG:Z:${p}`;return`W	${h.sample}	${h.haplotype}	${h.contig}	${h.fragment}	${d}	${m}${u}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let h=e.names!=="anonymous"?c.identity:void 0,d=t?this.alignToRef(l):void 0;n.push(h?i(c,h,{...h.name,fragment:h.name.fragment+h.hapStart},h.name.fragment+h.hapEnd,d):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,d)),f+=1}}),`${n.join(`
 `)}
-`}outputPaths(e){this.settleDeferred();let t=e.cigar??!1,n=[],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]};n.push({info:this.paths[this.refId],identity:void 0,name:we({...i,end: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!=="anonymous"?i.identity:void 0;n.push({info:i,identity:f,name:f?we({...f.name,fragment:f.name.fragment+f.hapStart,end:f.name.fragment+f.hapEnd}):we({sample:"unknown",contig:o,haplotype:s,fragment:0,end:i.len}),cigar:t?this.alignToRef(a):void 0}),s+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&Ue(e,t)&&(yield[e,t])}walkSpans(){return this.settleDeferred(),this.paths.flatMap((e,t)=>{let n=t===this.refId?void 0:e.identity;return n?[{name:n.name,start:n.name.fragment+n.hapStart,end:n.name.fragment+n.hapEnd}]:[]})}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!j(s)).map(s=>({id:String(O(s)),sequence:this.record(s).sequence})),n=[];for(let[s,i]of this.outputEdges())n.push({from:String(O(s)),from_is_reverse:j(s),to:String(O(i)),to_is_reverse:j(i)});let o=this.outputPaths(e).map(s=>xi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:n,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!j(i)),n=new Int32Array(t.length),o=[];t.forEach((i,a)=>{n[a]=O(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:n,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($t(i.info,i.identity))}))}}};function $t(r,e){return e?.orientation==="reverse"?r.path.map(t=>re(t)).reverse():r.path}function xi(r,e,t,n){return{name:t,...r.weight===void 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Set(e.map(n=>this.blockOf(n)));return t.size>this.prefetchBudget?!1:(this.fetchBlocks(t),!0)}prefetchLeading(e){let t=[],n=new Map;for(let o of e){let s=this.blockOf(o);n.has(s)||(n.set(s,t.length),t.push(s))}this.plan={blocks:t,position:n,next:0},this.advance(this.prefetchBudget)}advance(e){let t=this.plan;if(!t)return;let n=t.blocks.slice(t.next,t.next+e);t.next+=n.length,t.next>=t.blocks.length&&(this.plan=void 0),this.fetchBlocks(new Set(n))}follow(e){let t=this.plan,n=t?.position.get(e);t&&n!==void 0&&n>=t.next-Math.ceil(this.chunk/2)&&this.advance(this.chunk)}fetchBlocks(e){let t=[...e].filter(o=>!this.touch(o)).sort((o,s)=>o-s),n=0;for(;n<t.length;){let o=n+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[n],o-n),n=o}}fetchRun(e,t){let n=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-n),s=this.read(o,n);this.fetches+=1;for(let i=0;i<t;i++){let 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t=[...this.objects.values()].find(n=>n.type==="index"&&n.tableName===e);if(t)return t.rootPage;if(this.withoutRowid(e))return this.rootPage(e);throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n=!1){return this.btree.prefetchRowidRanges(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t,n){return this.btree.indexScanFrom(this.indexOn(e),t,n)}has(e){return this.objects.has(e)}};var nr="GBZ-base version 4",Wt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${we(e)}`),this.path=e}},Vt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Qt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${nr}"`),this.found=e}};function Mi(r){if(r.length===1)return r[0];let e=new Uint8Array(r.reduce((n,o)=>n+o.length,0)),t=0;for(let n of r)e.set(n,t),t+=n.length;return e}var Jn=3,Ye=class{at=0;bytes;constructor(e){this.bytes=e}get done(){return this.at>=this.bytes.length}next(){let e=0,t=1;for(;;){let n=this.bytes[this.at++];if(n===void 0)throw new Error("a haplotype index blob ends inside a number");if(e+=(n&127)*t,t*=128,(n&128)===0)return e}}};function Ri(r,e){let t=new Ye(r),n=0;for(;!t.done;){let o=n+t.next();n=o+t.next(),e.push([o,n])}}function Pi(r){r.sort((n,o)=>n[0]-o[0]);let e=[],t=[];for(let[n,o]of r){let s=t.length-1;s>=0&&n<=t[s]+1?t[s]=Math.max(t[s],o):(e.push(n),t.push(o))}return n=>{let o=0,s=e.length;for(;o<s;){let i=o+s>>1;e[i]<=n?o=i+1:s=i}return o>0&&n<=t[o-1]}}function ki(r,e,t){let n=new Ye(e);for(;!n.done;){let o=n.next(),s=n.next(),i=n.next(),a=n.next(),f=n.next();t.push({bin:r,pathHandle:o,pathStart:s,pathEnd:i,snarl:f>0?[a,f]:void 0,node:n.next(),offset:n.next()})}}function _i(r,e,t){let n=O(r);for(let o of e){let s=new Ye(o);for(;!s.done;){let i=s.next(),a=i%2;t.push({node:2*n+a,offset:s.next(),pathHandle:(i-a)/2,orientation:"forward",pathOffset:s.next()})}}}var tr=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=Yr(o)}get id(){return O(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Kr(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 ${this.handle} is empty`);return new Mt(this.edges,this.bwt)}};function Q(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function dt(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function Be(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function No(r,e){return{handle:r,fwStart:{node:Q(e[1],"Paths.fw_node"),offset:Q(e[2],"Paths.fw_offset")},revStart:{node:Q(e[3],"Paths.rev_node"),offset:Q(e[4],"Paths.rev_offset")},name:{sample:dt(e[5],"Paths.sample"),contig:dt(e[6],"Paths.contig"),haplotype:Q(e[7],"Paths.haplotype"),fragment:Q(e[8],"Paths.fragment")},isIndexed:Q(e[9],"Paths.is_indexed")!==0}}function er(r,e){return r.catch(e),r}async function To(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(dt(t[0],"Tags.key"),dt(t[1],"Tags.value"));return e}var pt=class r{pathCache;pathMapCache;indexTags=new Map;overviewRowsCache;sqlite;index;tagMap;constructor(e,t,n){this.sqlite=e,this.index=t,this.tagMap=n}static async open(e){let{source:t,haplotypeIndex:n}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await ht.open(t,o),i=s.objects.has("Tags")?await To(s):new Map,a=i.get("version");if(a!==nr)throw new Qt(a);for(let l of["Nodes","Paths","ReferenceIndex"])s.rootPage(l);let f=n?await ht.open(n,o):void 0,c=new r(s,f,i);if(f){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!f.objects.has(u))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${u} table`);c.indexTags=await To(f);let l=c.indexTags.get("haplotype_index_paths"),h=await c.tag("paths");if(l!==h)throw new Error(`haplotype index was built for ${l??"an unknown number of"} paths but the graph has ${h}`);let d=c.indexTags.get("haplotype_index_nodes"),p=await c.tag("nodes");if(d!==void 0&&d!==p)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${p}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new Vt;let m=c.indexTags.get("haplotype_index_format");if(Number(m)!==Jn)throw new Error(m===void 0?`the haplotype index predates format ${Jn}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${m}; this version of @gmod/gbz-base reads format ${Jn}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new tr(e,Qr(Be(t[1],"Nodes.edges")),Be(t[2],"Nodes.bwt"),Be(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=er(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(No(t,n));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?No(e,t):void 0}pathsByHandle(){return this.pathMapCache??=er(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsNamed(e){let t=Ve(We(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let n=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!n){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${we(i.name)} at ${i.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let o=n.pathOffset,s=n.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async getPathFragments(e){let{start:t,end:n}=e;if(Number.isNaN(t)||Number.isNaN(n))throw new Error(`The window ${t}..${n} is not a number range`);let o=await this.pathsNamed(e.path);if(o.length===0)throw new Wt(Ve(We(e.path),0));if(n<=t)return[];let s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<n);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 subgraphForFragment(e,t){let{sample:n,contig:o,haplotype:s}=e.path.name,i=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let f=await Xn(this,{...t,path:{sample:n,contig:o,haplotype:s},start:i,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await f.identifyPaths(),f}catch(f){throw f instanceof fe&&f.walkedBp!==void 0?new fe(f.limit,{windowBp:t.end-t.start,walkedBp:i-t.start+f.walkedBp}):f}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(o=>this.subgraphForFragment(o,e)))).map(o=>{if(o.status==="rejected")throw o.reason;return o.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Xn(this,e)}subgraphAtOffset(e){return Mo(this,e)}subgraphAroundNodes(e){return Ro(this,e)}subgraphBetween(e){return Po(this,e)}fetchStats(){let e=({pager:t})=>({fetches:t.fetches,bytesFetched:t.bytesFetched});return{graph:e(this.sqlite),haplotypeIndex:this.index?e(this.index):void 0}}async graphName(){let e=new Map;for(let[n,o]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=to(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=n=>this.indexTags.get(`haplotype_index_stray_${n}`);if(!this.index?.has("HaplotypeBins")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async blobRows(e,t,n){let o=[],s=[];for await(let i of this.companion.indexScanFrom(e,t,n))s.push(Q(i[i.length-1],`${e} rowid`));s.length>1&&await this.companion.prefetchRows(e,[[Math.min(...s),Math.max(...s)+1]],!0);for(let i of s){let a=await this.companion.byRowid(e,i);a&&o.push(a)}return o}async haplotypeBinData(e,t,n){let o=[],s=[];for(let i of await this.blobRows("HaplotypeBins",[e,t],[e,n])){let a=Q(i[1],"HaplotypeBins.bin");Ri(Be(i[3],"HaplotypeBins.nodes"),o),ki(a,Be(i[4],"HaplotypeBins.strays"),s)}return{listed:Pi(o),strays:s}}async haplotypeAnchorsBetween(e,t,n){let o=[],s=[],i=()=>{let a=o[o.length-1];a&&_i(a.node,s,a.visits),s=[]};for(let a of await this.blobRows("HaplotypeAnchors",[e,t],[e,n])){let f=Q(a[1],"HaplotypeAnchors.anchor_offset");o[o.length-1]?.anchorOffset!==f&&(i(),o.push({anchorOffset:f,node:Q(a[3],"HaplotypeAnchors.node_handle"),pathOffset:Q(a[4],"HaplotypeAnchors.path_offset"),visits:[]})),s.push(Be(a[5],"HaplotypeAnchors.visits"))}return i(),o}async haplotypeAnchor(e,t){let[n]=await this.haplotypeAnchorsBetween(e,t,t);return n&&{node:n.node,pathOffset:n.pathOffset}}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:Q(e[0],"HaplotypeSamples.node_handle"),offset:Q(e[1],"HaplotypeSamples.node_offset"),pathHandle:Q(e[2],"HaplotypeSamples.path_handle"),orientation:Q(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:Q(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let n=[];for await(let o of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))n.push(this.sampleFromRow(o));return n}async haplotypeSampleAt(e,t){let n=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);return n?.[0]===e&&n[1]===t?this.sampleFromRow(n):void 0}overviewRows(){return this.overviewRowsCache??=er((async()=>{let e=[];for await(let{rowid:t,values:n}of this.companion.scan("HaplotypeOverviewRows"))e[t]={sample:dt(n[1],"HaplotypeOverviewRows.sample"),haplotype:Q(n[2],"HaplotypeOverviewRows.haplotype")};return e})(),()=>{this.overviewRowsCache=void 0}),this.overviewRowsCache}async overviewChunks(e,t,n,o,s){let i=new Map;for(let a of await this.blobRows(e,[t,n,o],[t,n,s])){let f=Q(a[2],`${e}.chunk`),c=i.get(f)??[];c.push(Be(a[4],`${e} blob`)),i.set(f,c)}return new Map([...i].map(([a,f])=>[a,Mi(f)]))}async haplotypeOverview(e){let{signal:t}=e;t?.throwIfAborted();let n=u=>this.indexTags.get(`haplotype_index_overview_${u}`);if(!this.index?.has("HaplotypeOverviewClasses")||n("format")!=="1")return;let o=Number(n("bin")),s=Number(n("chunk")),i=Number(n("levels")),a=Math.max(0,Math.min(Math.floor(e.level??0)||0,i-1));if(e.level===void 0&&e.bpPerPixel!==void 0)for(;a+1<i&&o*4**(a+1)<=e.bpPerPixel;)a+=1;let f=o*4**a,[c,l]=await Promise.all([this.getPathFragments(e),this.overviewRows()]);t?.throwIfAborted();let h=Math.ceil(l.length/2),d=[],p=[];for(let u of c){let w=u.end-u.start,b=Math.max(e.start,u.start)-u.start,S=Math.min(e.end,u.end)-u.start,g=Math.floor(b/f),x=Math.floor((S-1)/f),y=Math.floor(g/s),E=Math.floor(x/s),[A,N]=await Promise.all([this.overviewChunks("HaplotypeOverviewBins",u.path.handle,a,y,E),this.overviewChunks("HaplotypeOverviewClasses",u.path.handle,a,y,E)]);t?.throwIfAborted();for(let k=y;k<=E;k++){let F=new Ye(A.get(k)??new Uint8Array),R=N.get(k)??new Uint8Array;for(let T=k*s;!F.done;T++){let C=Array.from({length:7},()=>F.next());if(T<g||T>x)continue;d.push({start:u.start+T*f,end:u.start+Math.min((T+1)*f,w),classes:[C[0],C[1],C[2],C[3]],excursions:C[4],variants:C[5],longestExcursion:C[6]});let D=(T-k*s)*h;p.push(R.subarray(D,D+h))}}}if(d.length===0)return;let m=new Uint8Array(d.length*l.length);return p.forEach((u,w)=>{for(let b=0;b<l.length;b++)m[w*l.length+b]=(u[b>>1]??0)>>4*(b%2)&15}),{level:a,bin:f,haplotypes:l,bins:d,cells:m}}async haplotypeLength(e){let t=await this.companion.byRowid("HaplotypeLengths",e);return t?Q(t[1],"HaplotypeLengths.length"):void 0}async indexedRow(e){let t=await this.sqlite.byRowid("ReferenceIndex",e);if(!t)throw new Error("ReferenceIndex row referenced by its index is missing");return{pathOffset:Q(t[1],"ReferenceIndex.path_offset"),pos:{node:Q(t[2],"ReferenceIndex.node_handle"),offset:Q(t[3],"ReferenceIndex.node_offset")}}}async indexedRowid(e,t){let n=await this.sqlite.indexSeekLE("ReferenceIndex",[e,t]);return 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this.readRetrying(e,t);if(this.bytesFetched+=n.length,n.length<e)throw new Error(`the file ends at byte ${t+n.length}, short of the ${this.fileSize} bytes its SQLite header gives`);return n}async readRetrying(e,t){let n=0;for(;;)try{return await this.source.read(e,t)}catch(o){if(n+=1,n>=3)throw o;await new Promise(s=>setTimeout(s,200*n))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){this.follow(e);let t=this.touch(e);if(t)return t;let n=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-n),s=this.read(o,n);return this.fetches+=1,this.store(e,s),this.evict(),s}touch(e){let t=this.blocks.get(e);return t&&(this.blocks.delete(e),this.blocks.set(e,t)),t}blockOf(e){return Math.floor((e-1)*this.pageSize/this.blockSize)}get prefetchBudget(){return Math.max(1,Math.floor(this.maxBlocks/2))}get chunk(){return Math.max(1,Math.floor(this.prefetchBudget/2))}prefetch(e){let t=new Set(e.map(n=>this.blockOf(n)));return t.size>this.prefetchBudget?!1:(this.fetchBlocks(t),!0)}prefetchLeading(e){let t=[],n=new Map;for(let o of e){let s=this.blockOf(o);n.has(s)||(n.set(s,t.length),t.push(s))}this.plan={blocks:t,position:n,next:0},this.advance(this.prefetchBudget)}advance(e){let t=this.plan;if(!t)return;let n=t.blocks.slice(t.next,t.next+e);t.next+=n.length,t.next>=t.blocks.length&&(this.plan=void 0),this.fetchBlocks(new Set(n))}follow(e){let t=this.plan,n=t?.position.get(e);t&&n!==void 0&&n>=t.next-Math.ceil(this.chunk/2)&&this.advance(this.chunk)}fetchBlocks(e){let t=[...e].filter(o=>!this.touch(o)).sort((o,s)=>o-s),n=0;for(;n<t.length;){let o=n+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[n],o-n),n=o}}fetchRun(e,t){let n=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-n),s=this.read(o,n);this.fetches+=1;for(let i=0;i<t;i++){let a=i*this.blockSize;this.store(e+i,s.then(f=>f.subarray(a,a+this.blockSize)))}this.evict()}store(e,t){this.blocks.set(e,t),t.catch(()=>{this.blocks.get(e)===t&&this.blocks.delete(e)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is outside the file`);let n=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return n.subarray(o,o+this.pageSize)}};var ht=class r{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){No(t);let n=await e.read(Math.max(512,t.blockSize??65536),0),o=n.subarray(0,100);if(new TextDecoder().decode(o.subarray(0,15))!=="SQLite format 3"||o.length<100)throw new Error("Not a SQLite database");let i=new DataView(o.buffer,o.byteOffset,o.byteLength),a=i.getUint16(16),f=a===1?65536:a,c=o[20]??0,l=i.getUint32(56);if(l!==1)throw new Error(`SQLite text encoding ${l} is not UTF-8`);let h=i.getUint32(28);if(h===0||i.getUint32(24)!==i.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let d=h*f,p=new jt(e,f,d,t);p.seed(0,n),p.fetches+=1,p.bytesFetched+=n.length;let m=new zt(p,c),u=new Map;for await(let{values:w}of m.tableScan(1)){let[b,S,g,x,y]=w;typeof b=="string"&&typeof S=="string"&&typeof g=="string"&&typeof x=="number"&&u.set(S,{type:b,name:S,tableName:g,rootPage:x,sql:typeof y=="string"?y:""})}return new r(p,m,u)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}withoutRowid(e){let t=this.objects.get(e);return t?.type==="table"&&/without\s+rowid/i.test(t.sql)}indexOn(e){let t=[...this.objects.values()].find(n=>n.type==="index"&&n.tableName===e);if(t)return t.rootPage;if(this.withoutRowid(e))return this.rootPage(e);throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n=!1){return this.btree.prefetchRowidRanges(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t,n){return this.btree.indexScanFrom(this.indexOn(e),t,n)}has(e){return this.objects.has(e)}};var tr="GBZ-base version 4",Ut=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${ge(e)}`),this.path=e}},Wt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Vt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${tr}"`),this.found=e}};function Mi(r){if(r.length===1)return r[0];let e=new Uint8Array(r.reduce((n,o)=>n+o.length,0)),t=0;for(let n of r)e.set(n,t),t+=n.length;return e}var Zn=3,Ye=class{at=0;bytes;constructor(e){this.bytes=e}get done(){return this.at>=this.bytes.length}next(){let e=0,t=1;for(;;){let n=this.bytes[this.at++];if(n===void 0)throw new Error("a haplotype index blob ends inside a number");if(e+=(n&127)*t,t*=128,(n&128)===0)return e}}};function Ri(r,e){let t=new Ye(r),n=0;for(;!t.done;){let o=n+t.next();n=o+t.next(),e.push([o,n])}}function Pi(r){r.sort((n,o)=>n[0]-o[0]);let e=[],t=[];for(let[n,o]of r){let s=t.length-1;s>=0&&n<=t[s]+1?t[s]=Math.max(t[s],o):(e.push(n),t.push(o))}return n=>{let o=0,s=e.length;for(;o<s;){let i=o+s>>1;e[i]<=n?o=i+1:s=i}return o>0&&n<=t[o-1]}}function ki(r,e,t){let n=new Ye(e);for(;!n.done;){let o=n.next(),s=n.next(),i=n.next(),a=n.next(),f=n.next();t.push({bin:r,pathHandle:o,pathStart:s,pathEnd:i,snarl:f>0?[a,f]:void 0,node:n.next(),offset:n.next()})}}function _i(r,e,t){let n=O(r);for(let o of e){let s=new Ye(o);for(;!s.done;){let i=s.next(),a=i%2;t.push({node:2*n+a,offset:s.next(),pathHandle:(i-a)/2,orientation:"forward",pathOffset:s.next()})}}}var er=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=Kr(o)}get id(){return O(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Xr(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 ${this.handle} is empty`);return new Ct(this.edges,this.bwt)}};function Q(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function dt(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function Be(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function To(r,e){return{handle:r,fwStart:{node:Q(e[1],"Paths.fw_node"),offset:Q(e[2],"Paths.fw_offset")},revStart:{node:Q(e[3],"Paths.rev_node"),offset:Q(e[4],"Paths.rev_offset")},name:{sample:dt(e[5],"Paths.sample"),contig:dt(e[6],"Paths.contig"),haplotype:Q(e[7],"Paths.haplotype"),fragment:Q(e[8],"Paths.fragment")},isIndexed:Q(e[9],"Paths.is_indexed")!==0}}function Jn(r,e){return r.catch(e),r}async function Lo(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(dt(t[0],"Tags.key"),dt(t[1],"Tags.value"));return e}var pt=class r{pathCache;pathMapCache;indexTags=new Map;overviewRowsCache;sqlite;index;tagMap;constructor(e,t,n){this.sqlite=e,this.index=t,this.tagMap=n}static async open(e){let{source:t,haplotypeIndex:n}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await ht.open(t,o),i=s.objects.has("Tags")?await Lo(s):new Map,a=i.get("version");if(a!==tr)throw new Vt(a);for(let l of["Nodes","Paths","ReferenceIndex"])s.rootPage(l);let f=n?await ht.open(n,o):void 0,c=new r(s,f,i);if(f){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!f.objects.has(u))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${u} table`);c.indexTags=await Lo(f);let l=c.indexTags.get("haplotype_index_paths"),h=await c.tag("paths");if(l!==h)throw new Error(`haplotype index was built for ${l??"an unknown number of"} paths but the graph has ${h}`);let d=c.indexTags.get("haplotype_index_nodes"),p=await c.tag("nodes");if(d!==void 0&&d!==p)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${p}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new Wt;let m=c.indexTags.get("haplotype_index_format");if(Number(m)!==Zn)throw new Error(m===void 0?`the haplotype index predates format ${Zn}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${m}; this version of @gmod/gbz-base reads format ${Zn}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new er(e,Yr(Be(t[1],"Nodes.edges")),Be(t[2],"Nodes.bwt"),Be(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=Jn(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(To(t,n));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?To(e,t):void 0}pathsByHandle(){return this.pathMapCache??=Jn(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsNamed(e){let t=Ve(We(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let n=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!n){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${ge(i.name)} at ${i.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let o=n.pathOffset,s=n.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async getPathFragments(e){let{start:t,end:n}=e;if(Number.isNaN(t)||Number.isNaN(n))throw new Error(`The window ${t}..${n} is not a number range`);let o=await this.pathsNamed(e.path);if(o.length===0)throw new Ut(Ve(We(e.path),0));if(n<=t)return[];let s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<n);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 subgraphForFragment(e,t){let{sample:n,contig:o,haplotype:s}=e.path.name,i=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let f=await Kn(this,{...t,path:{sample:n,contig:o,haplotype:s},start:i,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await f.identifyPaths(),f}catch(f){throw f instanceof fe&&f.walkedBp!==void 0?new fe(f.limit,{windowBp:t.end-t.start,walkedBp:i-t.start+f.walkedBp}):f}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(o=>this.subgraphForFragment(o,e)))).map(o=>{if(o.status==="rejected")throw o.reason;return o.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Kn(this,e)}subgraphAtOffset(e){return Ro(this,e)}subgraphAroundNodes(e){return Po(this,e)}subgraphBetween(e){return ko(this,e)}fetchStats(){let e=({pager:t})=>({fetches:t.fetches,bytesFetched:t.bytesFetched});return{graph:e(this.sqlite),haplotypeIndex:this.index?e(this.index):void 0}}async graphName(){let e=new Map;for(let[n,o]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=no(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=n=>this.indexTags.get(`haplotype_index_stray_${n}`);if(!this.index?.has("HaplotypeBins")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async blobRows(e,t,n){let o=[],s=[];for await(let i of this.companion.indexScanFrom(e,t,n))s.push(Q(i[i.length-1],`${e} rowid`));s.length>1&&await this.companion.prefetchRows(e,[[Math.min(...s),Math.max(...s)+1]],!0);for(let i of s){let a=await this.companion.byRowid(e,i);a&&o.push(a)}return o}async haplotypeBinData(e,t,n){let o=[],s=[];for(let i of await this.blobRows("HaplotypeBins",[e,t],[e,n])){let a=Q(i[1],"HaplotypeBins.bin");Ri(Be(i[3],"HaplotypeBins.nodes"),o),ki(a,Be(i[4],"HaplotypeBins.strays"),s)}return{listed:Pi(o),strays:s}}async haplotypeAnchorsBetween(e,t,n){let o=[],s=[],i=()=>{let a=o[o.length-1];a&&_i(a.node,s,a.visits),s=[]};for(let a of await this.blobRows("HaplotypeAnchors",[e,t],[e,n])){let f=Q(a[1],"HaplotypeAnchors.anchor_offset");o[o.length-1]?.anchorOffset!==f&&(i(),o.push({anchorOffset:f,node:Q(a[3],"HaplotypeAnchors.node_handle"),pathOffset:Q(a[4],"HaplotypeAnchors.path_offset"),visits:[]})),s.push(Be(a[5],"HaplotypeAnchors.visits"))}return i(),o}async haplotypeAnchor(e,t){let[n]=await this.haplotypeAnchorsBetween(e,t,t);return n&&{node:n.node,pathOffset:n.pathOffset}}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:Q(e[0],"HaplotypeSamples.node_handle"),offset:Q(e[1],"HaplotypeSamples.node_offset"),pathHandle:Q(e[2],"HaplotypeSamples.path_handle"),orientation:Q(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:Q(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let n=[];for await(let o of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))n.push(this.sampleFromRow(o));return n}async 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t=this.getConf("gbzDbLocation"),n=this.getConf("haplotypeIndexLocation"),o=vr(n)?{location:n}:await $o(t,this.pluginManager),s=o.location,i=await pt.open({source:(0,In.openLocation)(t,this.pluginManager),haplotypeIndex:s?(0,In.openLocation)(s,this.pluginManager):void 0}),a=this.getConf("assemblyNames")[0];if(a===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let f=await kn(i),c=vt({configured:this.getConf("referenceSample"),anchorPrefix:ze(this,a),referenceSamples:f});return{db:i,anchor:a,referenceSample:c,referenceSamples:f,unreadableIndex:o.unreadable}}});this.gaf=(0,Ir.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),n=this.getConf(["readsIndex","location"]);return vr(t)?new Yt((0,In.openLocation)(t,this.pluginManager),vr(n)?jr(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,n){let{db:o,referenceSample:s}=await this.graph(n);return _n(o,s,t)}async getHaplotypes(t={}){let{db:n,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await n.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:n,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Rn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Os(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:n,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:ze(this,i),f=(await n.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:St(be(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,n){let o=t===void 0||t.length===0?void 0:t.map(s=>ze(this,s));return o===void 0&&n===void 0?void 0:s=>Pn(s,o)&&(n===void 0||St(be(s),n))}async getSubgraph(t,n={}){let{signal:o}=n,{db:s,anchor:i,referenceSample:a,unreadableIndex:f}=await this.graph({signal:o}),{assemblyName:c,refName:l,start:h,end:d}=t;if(c!==i)throw new Ar(c,i);let p=await this.referenceQuery(l,{signal:o});if(!p)throw new Error(`${a} has no indexed path ${l} in this graph`);let m=this.keepPredicate(n.haplotypes);if(m!==void 0&&!s.hasHaplotypeIndex)throw new En(f);return Nn(s,p,h,d,{context:this.getConf("context"),snarls:n.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:n.signal,keep:m}).catch(u=>{throw Sr(u,"the graph")})}async getReads(t,n={}){let o=await this.gaf(n);return o?o.readsOver(new Set(t),n):{records:[],total:0}}async laneHaplotypes(t,n){let o=ze(this,t);return(await this.getHaplotypes(n)).filter(s=>St(s.prefix,o))}async anchorFeatures(t,n){let{db:o}=await this.graph(n),{assemblyName:s,refName:i,start:a,end:f}=t,c=ze(this,n.targetAssemblyName),l=Rn(this),h=this.keepPredicate(n.haplotypes,c),d=await this.referenceQuery(i,n),p=this.getConf("nodeLimit");return(d?await(0,xt.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,n.statusCallback,()=>o.getAlignments({path:d,start:a,end:f,context:this.getConf("context"),haplotypes:"all",limit:p,signal:n.signal,keep:h}).catch(u=>{throw Sr(On(u,p,f-a)??u,"lanes")})):[]).flatMap(u=>{let w=u.resolved?ba({alignment:u,assemblyName:s,refName:i,lane:Os(l,u.name)}):void 0;return w===void 0?[]:[w]})}async pairFeatures(t,n,o){let{db:s}=await this.graph(o),{refName:i,start:a,end:f}=t,l=(await Promise.all(n.map(async g=>({pair:g,featureSide:await this.laneHaplotypes(g.queryAssemblyName,o),mateSide:await this.laneHaplotypes(g.targetAssemblyName,o)})))).filter(({featureSide:g,mateSide:x})=>g.length>0&&x.length>0),h=new Set(l.flatMap(({featureSide:g,mateSide:x})=>[...g,...x].map(be))),d=await this.referenceQuery(i,o),p=this.getConf("nodeLimit"),m=this.getConf("context"),[u]=n,w=(g,x)=>s.getSubgraphs({path:g,start:a,end:f,context:x,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:o.signal,keep:y=>h.has(be(y))}),b=async g=>{let x=await w(g,m).catch(A=>{throw Sr(On(A,p,f-a)??A,"lanes")}),y=Ia(x,h),E=Math.ceil(y/2)+2e3;return y>0&&E>m?w(g,E).catch(A=>{if(A instanceof fe)return x;throw A}):x};return(d&&u&&l.length>0?await(0,xt.updateStatus)(n.length===1?`Reading ${u.queryAssemblyName} against ${u.targetAssemblyName}`:`Reading ${n.length} lane pairs`,o.statusCallback,()=>b(d)):[]).flatMap(g=>l.flatMap(({pair:x,featureSide:y,mateSide:E})=>y.flatMap(A=>E.flatMap(N=>g.pairAlignments({target:A,query:N,bases:!1}).map(k=>Sa({pair:k,lane:x.queryAssemblyName,mateLane:x.targetAssemblyName}))))))}getFeatures(t,n={}){return(0,Ns.ObservableCreate)(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(n);if(!s.hasHaplotypeIndex)throw new En(a);if(t.assemblyName===i){let f=n.lanePairs?.length?await this.pairFeatures(t,n.lanePairs,n):n.queryAssemblyName===void 0?await this.anchorFeatures(t,n):await this.pairFeatures(t,[xa(n.queryAssemblyName,n.targetAssemblyName)],n);for(let c of f)o.next(c)}o.complete()},n.signal)}};export{Ar as HaplotypeWindowError,En as NoHaplotypeIndexError,Bs as NoReferenceSampleError,Er as PairTargetError,Cr as default,ba as fragmentFeature,Os as laneAssemblyName,Sa as pairFeature,vt as resolveReferenceSample,Ia as widestWalkGap};
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