jbrowse-plugin-graphgenomeviewer 6.18.1 → 6.19.0

package/dist/chunks/{GbzBaseSyntenyAdapter-VFDJ76X6.js → GbzBaseSyntenyAdapter-UZGHQM5I.js}

@@ -1,6 +1,6 @@
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as="_gbwt_ref";function fe(o){let e=`${o.sample}#${o.haplotype}#${o.contig}`;return o.end===void 0?e:`${e}[${o.fragment}-${o.end}]`}var os=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,is=/^([^#]+?)(?:\[\d+-\d+\])?$/;function hs(o){let e=os.exec(o);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=is.exec(o);if(t)return{contig:t[1]};throw new Error(`"${o}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function $e(o){return typeof o=="string"?hs(o):o}function Me(o,e){return{sample:o.sample??as,contig:o.contig,haplotype:o.haplotype??0,fragment:e}}var cs=4096;function Ht(o){let e=[];for(let t of o){let n=e[e.length-1];n&&t-n[1]<=cs?n[1]=t:e.push([t,t])}return e}var ds=32768,Hn={mostChosenPaths:32},Lt=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)}},ae=class extends Error{};function tt(o,e,t,n){return 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k=p.get(w);return k!==void 0&&o.keep(k.name)},m=[],l=new Lt,b=new Map,I=new Set,A=new Set,x=async w=>{let k=(await d(w.node)).gbwt().lf(w.offset);return k===void 0||k.node===0?void 0:k},E=async(w,k)=>{let N=(await d(te(w.node))).gbwt().predecessorAt(w.offset);if(N===void 0||k!==void 0&&!k.has(N))return;let $=(await d(N)).gbwt().offsetTo(w);if($===void 0)throw new Error(`No offset in ${N} leads to ${w.node}:${w.offset}`);return{node:N,offset:$}},g=(w,k,N,$)=>{let F=N.map(j=>j.pos.node),U=N.map(j=>j.pos.offset),K=0;for(let j of F)K+=f(j);let O=k==="forward"?N[0].left:N[N.length-1].left,L=m.length;m.push({pathHandle:w,orientation:k,handles:F,offsets:U,len:K,hapStart:O,hapEnd:O+K,canonical:Ae(F[0],F[F.length-1]),source:$});for(let j of N)l.set(j.pos,L);let V=b.get(w);return V?V.push(L):b.set(w,[L]),L},S=async(w,k,N,$)=>{let F=[],U=w;for(;;){n?.throwIfAborted();let O=await E(U.pos,t);if(!O)break;U={pos:O,left:On(N,U.left,f(U.pos.node),f(O.node))},F.push(U)}F.reverse();let K=[w];for(U=w;;){n?.throwIfAborted();let O=await x(U.pos);if(!O||!t.has(O.node))break;U={pos:O,left:tt(N,U.left,f(U.pos.node),f(O.node))},K.push(U)}return g(k,N,[...F,...K],$)},P=async(w,k,N,$)=>m[l.get(w.pos)??await S(w,k,N,$)],_=w=>{let k=w.handles[w.handles.length-1];return{pos:{node:k,offset:w.offsets[w.offsets.length-1]},left:w.orientation==="forward"?w.hapEnd-f(k):w.hapStart}},B=w=>{let k=w.handles[0];return{pos:{node:k,offset:w.offsets[0]},left:w.orientation==="forward"?w.hapStart:w.hapEnd-f(k)}},D=await S({pos:o.referencePos,left:o.referenceLeft},o.referenceHandle,"forward","reference"),C=m[D],H=()=>{if(a.fallback!==void 0)return{reference:C,pieces:[],stats:a};let w=new Map;m.forEach((N,$)=>{$!==D&&w.set(ze(N),[...w.get(ze(N))??[],N])});let k=[];for(let N of w.values()){let $=new Set;for(let F of N)F.canonical&&!$.has(F.orientation)&&($.add(F.orientation),k.push(F),a.sources[F.source]+=1)}return a.sources.reference=1,a.pieces=k.length+1,{reference:C,pieces:k,stats:a}},v=async(w,k)=>{let N=k?I:A,$=k?A:I,F=w;for(;;){if(N.has(F))return;N.add(F);let U=m[F],K=k?_(U):B(U),O=0,L;for(;L===void 0;){n?.throwIfAborted();let V=k?await x(K.pos):await E(K.pos);if(!V){L="endmarker";break}let j=(await d(K.pos.node)).sequenceLen,ge=(await d(V.node)).sequenceLen,ne=k?tt(U.orientation,K.left,j,ge):On(U.orientation,K.left,j,ge);if(t.has(V.node)){let Y=l.get(V);Y===void 0?(F=await S({pos:V,left:ne},U.pathHandle,U.orientation,"chain"),$.add(F),L="landed"):($.add(Y),L="merge")}else O>ds?L="bound":(O+=ge,K={pos:V,left:ne})}if(i("chain",L),L!=="landed")return}},G=async w=>{if(o.context>w.context)throw new ae(`the context of ${o.context} bp exceeds the ${w.context} bp the haplotype index's stray rows cover`);let k=a.spacing;if(k===void 0)throw new ae("the haplotype index has no anchors");let{bin:N,bound:$}=w,{fills:F,inserted:U}=o.snarls;if(o.snarls.mode==="overlapping"&&F.length>0)throw new ae("the haplotype index's stray rows cover contained snarls only");for(let u of F){if(u.inserted>0&&u.low===u.high)throw new ae(`the haplotype index's stray rows leave out the snarl bounded by node ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new ae(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let K=Math.floor(o.window.start/N),O=Math.floor((o.window.end-1)/N),L=K*N,V=(O+1)*N,j=new Map,ge=async(u,R)=>{let q=await e.haplotypeAnchorsBetween(o.referenceHandle,u*k,R*k);for(let T of q)j.set(T.anchorOffset/k,T)},ne=Math.max(0,Math.floor((L-$)/k)-1),Y=Math.ceil((V+$)/k)+1,[{listed:Ve,strays:ie}]=await Promise.all([e.haplotypeBinData(o.referenceHandle,K,O),ge(ne,Y)]);for(let u of t.keys()){let R=M(u);if(!re(u)&&!Ve(R)&&!U.has(R))throw new ae(`the haplotype index lists node ${R} of the subgraph in no bin that the window touches`)}a.scans=Ht([...t.keys()].sort((u,R)=>u-R));let he=Promise.all(a.scans.map(([u,R])=>e.haplotypeSamplesInRange(u,R)));for(he.catch(()=>{});ne>0&&(j.get(ne)?.pathOffset??Number.POSITIVE_INFINITY)>=L-$;)ne-=1,await ge(ne,ne);for(;j.has(Y)&&j.get(Y).pathOffset<=V+$;)Y+=1,await ge(Y,Y);let le=[...j.keys()].sort((u,R)=>u-R),be=j.get(le[0]??-1);if(!be)throw new ae("the haplotype index has no anchors on this path");let ce=u=>j.get(u).pathOffset,He=new Map;for(let u of le){let R=M(j.get(u).node);He.set(R,[...He.get(R)??[],u])}let bt=[...He.keys()],Vt=bt.map(u=>j.get(He.get(u)[0]).visits);if(!Vt[bt.indexOf(M(be.node))].some(u=>u.pathHandle===o.referenceHandle&&u.orientation==="forward"&&u.pathOffset===be.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${o.referenceHandle} at offset ${be.pathOffset} (node ${M(be.node)}); it does not match this graph`);let Wt=le.filter(u=>ce(u)<=o.window.start),Kn=le.filter(u=>ce(u)>=o.window.end);a.anchors=[ce(Wt[Wt.length-1]??le[0]),ce(Kn[0]??le[le.length-1])],a.anchorsRead=le.length;let xt=new Map,Zt=new Set;if(bt.forEach((u,R)=>{let q=He.get(u),T=q.length===1?q[0]:void 0;for(let z of Vt[R])Zt.add(z.pathHandle),z.orientation==="forward"&&y(z.pathHandle)&&xt.set(z.pathHandle,[...xt.get(z.pathHandle)??[],{k:T,row:z}])}),a.chosenPaths=[...Zt].filter(y).length,a.chosenPaths>Hn.mostChosenPaths)throw new ae(`${a.chosenPaths} chosen paths pass the anchors, more than ${Hn.mostChosenPaths}`);let We=[],Ee=Number.POSITIVE_INFINITY,xe=0;for(let[u,R]of xt){R.sort((q,T)=>q.row.pathOffset-T.row.pathOffset);for(let q=0;q+1<R.length;q++){let T=R[q],z=R[q+1];if(T.k===void 0||z.k===void 0||Math.abs(T.k-z.k)!==1)continue;let[Z,J]=ce(T.k)<=ce(z.k)?[T,z]:[z,T],ee=ce(Z.k),se=ce(J.k);ee<V&&se>=L?(We.push({pathHandle:u,from:T.row,to:z.row}),Ee=Math.min(Ee,ee-$),xe=Math.max(xe,se+$)):ee>=V&&ee-V<=$?(We.push({pathHandle:u,from:Z.row,to:void 0}),Ee=Math.min(Ee,ee-$),xe=Math.max(xe,ee+$)):se<L&&L-se<=$&&(We.push({pathHandle:u,from:J.row,to:void 0}),Ee=Math.min(Ee,se-$),xe=Math.max(xe,se+$))}}let Yn=new Set(F.map(u=>`${u.low}:${u.high}`)),Jn=ie.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Yn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,R)=>u.pathHandle-R.pathHandle||u.pathStart-R.pathStart);a.strays={bins:O-K+1,rows:ie.length,walked:0,outsideBp:0},xe>0&&await o.prefetchReferenceRange(o.referenceHandle,Math.max(0,Ee),xe+1),a.ms.scan=r();let Xt=8*k+2*(o.window.end-o.window.start),Kt=a.strays,Oe=0,Yt=u=>{if(Kt.outsideBp+=u,Oe+=u,Oe>Xt)throw new ae(`a walk of a chosen path near the window went past its cap of ${Xt} bp`)},St=new Map,Jt=(u,R,q)=>(St.get(u)??[]).some(([T,z])=>T<=R&&q<z),en=(u,R,q)=>{St.set(u,[...St.get(u)??[],[R,q]])},tn=async(u,R,q,T,z)=>{let Z=R,J=q,ee=J;for(;Z&&J<=T;){n?.throwIfAborted();let se;if(t.has(Z.node)){let Ce=await P({pos:Z,left:J},u,"forward",z),sn=_(Ce);Z=sn.pos,J=sn.left,se=f(Z.node),ee=Math.max(ee,Ce.hapEnd)}else se=(await d(Z.node)).sequenceLen,Yt(se),ee=Math.max(ee,J+se);Z=await x(Z),J+=se}return ee},es=async(u,R,q,T)=>{let z={pos:R,left:q},Z=q;for(;z.left>T;){n?.throwIfAborted();let J=await E(z.pos);if(!J)break;let ee=(await d(J.node)).sequenceLen,se=z.left-ee;if(t.has(J.node)){let Ce=await P({pos:J,left:se},u,"forward","section");z=B(Ce),Z=Math.min(Z,Ce.hapStart)}else Yt(ee),z={pos:J,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:u,from:R,to:q}of We){let T=R.pathOffset,z=(q??R).pathOffset+$;if(Jt(u,T-$,z))continue;let Z={node:R.node,offset:R.offset};Oe=0;let J=await tn(u,Z,T,z,"section");Oe=0;let ee=await es(u,Z,T,T-$);en(u,Math.min(ee,T-$),Math.max(J,z+1)),i(q?"section":"visit",q?"past the far anchor":"bound")}for(let u of Jn){if(Jt(u.pathHandle,u.pathStart,u.pathEnd))continue;Oe=0;let R=await tn(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");en(u.pathHandle,u.pathStart,Math.max(R,u.pathEnd+1)),Kt.walked+=1}a.ms.walks=r();let nn=[];for(let u of await he)for(let R of u)if(a.scanRows+=1,t.has(R.node)&&y(R.pathHandle)){if(!(b.get(R.pathHandle)??[]).some(q=>{let T=m[q];return T.hapStart<=R.pathOffset&&R.pathOffset<T.hapEnd}))throw new ae(`chosen path ${R.pathHandle} has a sample at ${R.pathOffset} on the window's nodes that no walk reached`);R.orientation==="reverse"&&nn.push(R)}for(let u of nn)await P({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");a.ms.check=r()},X=async()=>{let w=new Map,k=O=>{let L=ze(O),V=w.get(L);V?V.add(O.orientation):w.set(L,new Set([O.orientation]))},N=0,$=()=>{for(;N<m.length;N++)k(m[N])};$();let F=O=>(w.get(ze(O))?.size??0)>1,U=2*h,K=(O,L)=>L===D?y(o.referenceHandle)&&Cn(O):!O.canonical||Cn(O);for(let O=0;O<m.length;O++){let L=m[O];if(F(L)||!K(L,O))continue;a.twins.tried+=1;let V=L.orientation==="forward"?"reverse":"forward",j=_(L),ge=0,ne;for(;!ne&&ge<=U;){n?.throwIfAborted();let ie=await x(j.pos);if(!ie)break;let he=(await d(ie.node)).sequenceLen,le=tt(L.orientation,j.left,(await d(j.pos.node)).sequenceLen,he),be=te(ie.node);ne=(await e.haplotypeSamplesInRange(be,be)).find(ce=>ce.pathHandle===L.pathHandle&&ce.orientation===V&&ce.pathOffset===le),ge+=he,j={pos:ie,left:le}}let Y=ne&&{pos:{node:ne.node,offset:ne.offset},left:ne.pathOffset},Ve=0;for(;Y&&!F(L)&&Ve<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ie=await P(Y,L.pathHandle,V,"twin"),he=m.indexOf(ie);await v(he,!0),await v(he,!1),$(),Y=_(ie)}if(!F(L)){let ie=(await d(Y.pos.node)).sequenceLen;Ve+=ie;let he=await x(Y.pos);Y=he?{pos:he,left:tt(V,Y.left,ie,(await d(he.node)).sequenceLen)}:void 0}}if($(),!F(L))throw new ae(`piece ${ze(L)} was found in one orientation where extractPaths keeps the other`);a.twins.found+=1}a.ms.twins=r()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new ae("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await G(w),await X()}catch(w){if(!(w instanceof ae))throw w;a.fallback=w.message}return H()}function Fn(o,e){return o.handles[0]-e.handles[0]||o.offsets[0]-e.offsets[0]}var oe=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Ot(o,e){return o[0]<e[0]||o[0]===e[0]&&(o[1]<e[1]||o[1]===e[1]&&o[2]<e[2])}var De=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let r=s.length-1;for(;r>0;){let a=r-1>>1;if(Ot(s[r],s[a]))[s[r],s[a]]=[s[a],s[r]],r=a;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let r=2*s+1,a=r+1,i=s;if(r<e.length&&Ot(e[r],e[i])&&(i=r),a<e.length&&Ot(e[a],e[i])&&(i=a),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function fs(o){let e=new Int32Array(o.length),t=new Int32Array(o.length);return o.forEach(([n,s],r)=>{e[r]=n,t[r]=s}),{pathAt:e,refAt:t,count:o.length}}function ls(o,e){let t=0,n=o.length;for(;t<n;){let s=t+n>>1;o[s]>e?n=s:t=s+1}return o[t]}function ke(o){return`${o.node}:${o.offset}`}function qe(o){return o.map(e=>te(e)).reverse()}function ps(o,e){let t=e.identity.hapStart-o.identity.hapEnd,n=o.strand==="+"?e.refStart-o.refEnd:o.refStart-e.refEnd;return o.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function us(o,e,t){let[n,s]=o.strand==="+"?[o,e]:[e,o],r=n.edits.map(([c,d])=>[c,d]);Tn(r,t.insertion,t.deletion);for(let[c,d]of s.edits)W(r,c,d);let a=o.identity.walkForward,[i,h]=a?[o,e]:[e,o];return{strand:o.strand,refStart:n.refStart,refEnd:s.refEnd,edits:r,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:o.identity.pathHandle,name:o.identity.name,hapStart:o.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:a}}}function gs(o,e,t){if(o.some(a=>a.weight!==void 0))return o;let n=new Map;o.forEach((a,i)=>{if(a.identity){let h=n.get(a.identity.pathHandle);h?h.push(i):n.set(a.identity.pathHandle,[i])}});let s=new Map,r=new Set;for(let a of n.values()){a.sort((d,f)=>o[d].identity.hapStart-o[f].identity.hapStart);let i=a[0],h=o[i],c=[];for(let d of a.slice(1)){let f=o[d],p=c.length===0?ps(h,f):void 0;if(p){h=us(h,f,p),r.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(m=>o[m]),f]):void 0;if(y){h=y;for(let m of[...c,d])r.add(m)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return o.flatMap((a,i)=>r.has(i)?[]:[s.get(i)??a])}function nt(o,e){return{node:o.path[e],offset:o.offsets[e]}}var ws=32768;function ms(o){let e=[...o].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=ws?s[1]=n:t.push([n,n])}return t}var Ge=class o{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 o(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(ue(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 oe(this.limit);let t=await this.db.getRecord(ue(e,"forward")),n=await this.db.getRecord(ue(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 ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let r=n,a=s;for(;;){await this.ensureNode(M(a.node));let i=this.record(a.node);if(r+i.sequenceLen>t)return{position:{seqOffset:t,handle:a.node,nodeOffset:t-r,gbwtOffset:a.offset},name:e.name,handle:e.handle};r+=i.sequenceLen;let h=i.gbwt().lf(a.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);a=h}}async aroundPosition(e,t,n){let s=M(e);await this.ensureNode(s);let r=this.record(e),a=Re(e),i=new De;return i.push(t,s,Ke(a)),i.push(r.sequenceLen-t-1,s,Ye(a)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,r]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&r){let a=s.pos.node,i=r.pos.node;if(!await this.db.prefetchRecords([[Math.min(a,i),Math.max(a,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(ms(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}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(s){throw s instanceof oe&&s.windowBp===void 0?new oe(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},r=e.nodeOffset,a=t,i=new De;for(;;){let h=M(s.node),c=Re(s.node);this.walkedBp=t-a,await this.ensureNode(h);let d=this.record(s.node);if(r>=d.sequenceLen)throw new Error(`Offset ${r} in node ${h} of length ${d.sequenceLen}`);i.push(r,h,Ke(c));let f=d.sequenceLen-r;if(a<=f){i.push(a===f?0:f-a-1,h,Ye(c));break}i.push(0,h,Ye(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,r=0,a-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new De;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let a of this.records.keys())s.add(M(a));let r=0;for(;e.size>0;){let[a,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),r+=1);let d=dn(h);if(!n.has(`${i}:${d}`)){let y=this.record(ue(i,fn(h))),m=a+y.sequenceLen-1;m<=t&&e.push(m,i,d)}let f=this.record(ue(i,ln(h))),p=a+1;if(p<=t)for(let y of f.successors()){let m=M(y),l=Ke(Re(y));n.has(`${m}:${l}`)||e.push(p,m,l)}}for(let a of s)this.records.delete(ue(a,"forward")),this.records.delete(ue(a,"reverse"));return{inserted:r,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,te(t)],s=new Set([M(e),M(t)]),r=[];for(;n.length>0;){let a=n.pop(),i=M(a);this.hasNode(i)||(await this.addNode(i),r.push(i));for(let h of this.record(a).successors()){let c=M(h);s.has(c)||(n.push(h,te(h)),s.add(c))}}return{inserted:r,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:r,nodes:a}=await this.fillBetween(n,s),i=M(n),h=M(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:a,inserted:r.length});for(let c of r)this.snarlNodes.add(c);t+=r.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 s of this.sortedHandles()){let r=this.record(s),a=r.next;a!==void 0&&(n=!0,this.hasHandle(a)?Be(s,a)&&t.push([s,a]):e==="overlapping"&&this.isSnarlEntryInSubgraph(r)&&t.push([s,a]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(te(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let r=t.get(n);if(!r){if(r=await this.db.getRecord(n),e?.(),!r)throw new Error(`Node record ${n} is missing from the database`);t.set(n,r)}return r}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(te(d))).successors().length>1},n=async h=>{let c=await e(te(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[te(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,r=this.sortedHandles().flatMap(h=>this.record(h).successors()),a,i=!1;for(;!i&&r.length>0;){let h=r.shift(),c=M(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")a=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])r.push(...(await e(ue(c,f))).successors())}}return a}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),r=s.length,a=new Map;s.forEach((g,S)=>a.set(g,S));let i=new Int32Array(r+1),h=new Int32Array(r),c=[];for(let g=0;g<r;g++){let S=this.record(s[g]),P=S.gbwt().decompressArrays();h[g]=S.sequenceLen,c.push(P),i[g+1]=i[g]+P.nodes.length}let d=i[r],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let g=0;g<r;g++){let S=c[g];f.set(S.nodes,i[g]),p.set(S.offsets,i[g])}c.length=0;for(let g=0;g<d;g++){let S=a.get(f[g]);S===void 0?f[g]=-1:(f[g]=S,y[i[S]+p[g]]=1)}let m=n===void 0?void 0:a.get(n.handle),l=n?.gbwtOffset,b,I=(g,S,P)=>{let _=[],B=0,D=0,C=-1,H=g,v=S;for(;;){H===m&&v===l&&(C=B),P&&(P.push(s[H]),_.push(v)),B+=1,D+=h[H];let G=i[H]+v,X=f[G];if(X<0)break;v=p[G],H=X}return{offsets:_,len:D,refAt:C,last:H}},A=(g,S,P,_)=>{_>=0&&(this.refId=this.paths.length,b=_),this.paths.push({path:g,offsets:S,len:P,weight:void 0,identity:void 0})},x=new Int32Array(r);for(let g=0;g<r;g++){let S=s[g];if(!re(S)){let P=i[g],_=i[g+1]-P;for(let B=0;B<_;B++)if(y[P+B]===0){let D=[],{offsets:C,len:H,refAt:v,last:G}=I(g,B,D),X=s[G];if(v>=0||Ae(S,X)){if(A(D,C,H,v),!re(X)){let w=a.get(te(X));x[w]=x[w]+1}}else this.twinStarts.add(ke({node:S,offset:B}))}}}for(let g=0;g<r;g++){let S=s[g];if(re(S)){let P=i[g],_=i[g+1]-P,B=0;for(let C=0;C<_;C++)y[P+C]===0&&(B+=1);let D=(m===void 0||b!==void 0)&&B===x[g];for(let C=0;C<_;C++)if(y[P+C]===0){let H=D?void 0:I(g,C,void 0);if(H&&(H.refAt>=0||Ae(S,s[H.last]))){let v=[],{offsets:G,len:X,refAt:w}=I(g,C,v);A(v,G,X,w)}else this.twinStarts.add(ke({node:S,offset:C}))}}}let E=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((g,S)=>g.path[0]-S.path[0]||g.offsets[0]-S.offsets[0]),E&&(this.refId=this.paths.indexOf(E)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let g=this.paths[this.refId],S=n.nodeOffset;for(let _ of g.path.slice(0,b))S+=this.record(_).sequenceLen;let P=n.seqOffset-S;this.refInterval=[P,P+g.len],g.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:P,hapEnd:P+g.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,s=n&&!Fe(n)?qe(n):void 0,r=c=>s!==void 0&&Ct(c,s)===0||Fe(qe(c)),a=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>Ct(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=a&&c!==t&&r(c.path);this.twinDeferred||=f,d&&Ct(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}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=a=>`${a.pathHandle}:${a.hapStart}-${a.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let a of this.paths)a!==e&&a.identity?.orientation==="forward"&&s.add(n(a.identity));let r=this.paths.filter(a=>a===e||a.identity?.orientation!=="reverse"||!s.has(n(a.identity)));r.length<this.paths.length&&(this.paths=r,this.refId=e===void 0?void 0:r.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(a=>a.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((a,i)=>i!==this.refId&&a.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],s=this.paths.filter((a,i)=>i===this.refId||a.identity!==void 0&&e(a.identity.name)),r=new Set;for(let a of s)for(let i of a.path)r.add(M(i));for(let a of[...this.records.keys()])r.has(M(a))||this.records.delete(a);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let r=e.position.seqOffset,a=await Bn({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:r-e.position.nodeOffset,window:{start:r,end:r+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=a.stats,a.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===a.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[a.reference,...a.pieces].sort(Fn);return this.paths=c.map(h),this.refId=c.indexOf(a.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[a.reference.hapStart,a.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=Ht(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let r=l=>{let b=0,I=t.length-1;for(;b<I;){let x=b+I+1>>1;t[x][0]<=l?b=x:I=x-1}let A=t[b];return A[0]<=l&&l<=A[1]},a=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&a.set(ke(nt(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(r(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let I=await this.db.haplotypeSampleAt(l.node,l.offset);return I||(i.companionMisses+=1),I},f=new Map,p=async l=>{let b=f.get(l);if(!b){let I=await this.db.getPath(l);if(!I)throw new Error(`Path ${l} is missing from the database`);b=I.name,f.set(l,b)}return b},y=(l,b,I)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+I},m=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let I=[],A=new Set,x={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(x);let E,g=0,S=l,P;for(;E===void 0;){if(this.signal?.throwIfAborted(),S!==void 0){if(A.has(S)){x.end="cycle";break}A.add(S);let H=this.paths[S];I.push({index:S,startBp:g}),x.fragments+=1;let v=g;for(let X=0;X<H.path.length;X++){let w=nt(H,X),k=n.get(ke(w)),N=this.record(w.node).sequenceLen;if(k){E=y(k,v,N);break}v+=N}if(g+=H.len,E){x.end="in-fragment sample";break}let G=nt(H,H.path.length-1);P=this.record(G.node).gbwt().lf(G.offset),S=void 0}if(P===void 0||P.node===0){x.end="endmarker";break}let _=ke(P),B=a.get(_);if(B!==void 0){let H=this.paths[B].identity;if(H){E=m(H,g),x.end="identified sibling";break}S=B;continue}this.records.has(P.node)&&(x.reentries+=1),this.twinStarts.has(_)&&(x.twinLandings+=1);let D=await d(P,x),C=await c(P.node);if(D){E=y(D,g,C.sequenceLen),x.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,x.steps+=1,g-I[I.length-1].startBp>4*e+4*C.sequenceLen){x.end="bound";break}g+=C.sequenceLen,P=C.gbwt().lf(P.offset)}if(E){x.pathHandle=E.pathHandle;let _=await p(E.pathHandle);for(let{index:B,startBp:D}of I){let C=this.paths[B];C.identity=E.orientation==="forward"?{pathHandle:E.pathHandle,name:_,orientation:"forward",hapStart:E.base+D,hapEnd:E.base+D+C.len}:{pathHandle:E.pathHandle,name:_,orientation:"reverse",hapStart:E.base-D-C.len,hapEnd:E.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let r=t.get(n);r?r.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),r=new Int32Array(e.length),a=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=ls(c,i);if(d===void 0)return;s[a]=h,r[a]=d,a+=1,i=d}}return{pathAt:s,refAt:r,count:a}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,r=0,a=0,i=0;for(;s<e.length&&r<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[r]).sequence;for(;a<h.length&&i<c.length;){if(h[a]!==c[i])return n;a+=1,i+=1,n+=1}a===h.length&&(s+=1,a=0),i===c.length&&(r+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,r=0,a=0,i=0;for(;s<e.length&&r<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-r-1]).sequence;for(;a<h.length&&i<c.length;){if(h[h.length-a-1]!==c[c.length-i-1])return n;a+=1,i+=1,n+=1}a===h.length&&(s+=1,a=0),i===c.length&&(r+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),r=this.pathLen(t),a=this.prefixMatches(e,t),i=this.suffixMatches(e,t);a+i>s&&(i=s-a),a+i>r&&(i=r-a),W(n,"M",a),Tn(n,s-a-i,r-a-i),W(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let r of e)n.has(r)&&(s+=this.record(r).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??fs(gn(e,t,f=>this.record(f).sequenceLen)[0]),r=[],a=this.refPrefix(t),i=(f,p,y,m)=>{f===p?W(r,"D",a[m]-a[y]):y===m?W(r,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,m),r)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let m=this.record(e[p]).sequenceLen;W(r,"M",m),h+=m,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:r,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Fe(n)&&(t.identity===void 0||!Fe(qe(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let r=qe(t.path),a=this.sharedWeight(t.path,n);if(this.sharedWeight(r,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(a===0)s={...this.editsAgainst(r,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(r,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}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],s=(d,f,p,y)=>{let m=bs(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],I=l.identity,A=I?.orientation==="forward",[x,E]=A?[l,b]:[b,l];return{strand:f,refStart:e.start+m.leading,refEnd:e.start+n-m.trailing,edits:m.edits,weight:l.weight,path:p.flatMap(g=>this.paths[g].path),start:nt(l,0),pieces:p,soloAligned:y,identity:I===void 0?void 0:{pathHandle:I.pathHandle,name:I.name,hapStart:I.name.fragment+x.identity.hapStart,hapEnd:I.name.fragment+E.identity.hapEnd,walkForward:A}}},r=d=>d.soloAligned.reduce((f,p)=>f+p,0),a=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*r(d)>=a(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((v,G)=>v.strand!==f.strand||v.identity.walkForward!==y||G>0&&v.identity.hapStart<d[G-1].identity.hapEnd))return;let m=y?d:[...d].reverse(),l=m.flatMap(v=>v.pieces),b=m.flatMap(v=>v.soloAligned),I=f.strand==="+"!==y,A=l.map(v=>this.paths[v]),x=A.slice(1).map((v,G)=>{let X=A[G].identity;return y?v.identity.hapStart-X.hapEnd:X.hapStart-v.identity.hapEnd}),E=I?[...A].reverse():A,g=I?[...x].reverse():x,S=E.flatMap(v=>I?qe(v.path):v.path),{edits:P}=this.editsAgainst(S,t),_=_n(P,E.map(v=>v.len)),B=new Map((I?[...l].reverse():l).map((v,G)=>[v,_[G]])),D=v=>2*v.pieces.reduce((G,X)=>G+B.get(X),0)>=r(v);if(!D(f)||!D(p))return;let C=[],H=0;return E.slice(0,-1).forEach((v,G)=>{H+=v.len,C.push([H,g[G]])}),s(xs(P,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),m=d.identity,l=m?m.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],_n(p,[d.len])))}),gs(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:m,...l}=d,b={...l,cigar:Ss(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,r=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:rt(d,f)}]:[]}),a=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=a(t),h=n?a(n):d=>!i(d),c=d=>this.record(ue(d,"forward")).sequence;return r.filter(d=>i(d.name)).flatMap(d=>r.filter(f=>h(f.name)).flatMap(f=>wn({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:mn(p.edits),matches:p.edits.reduce((y,[m,l])=>y+(m==="="?l:0),0),columns:p.edits.reduce((y,[,m])=>y+m,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ue(e,n);for(let r of this.record(s).successors())this.hasHandle(r)&&Be(s,r)&&t.push([n==="reverse"?1:0,M(r),re(r)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!re(n)){let s=M(n),r=`S	${s}	${this.record(n).sequence}
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Nn(o){return{name:o.get("pggname"),subgraph:vn(o.get("subgraph"),"subgraph"),translation:vn(o.get("translation"),"translation")}}function Rn(o,e){for(let[t,n]of e){let s=o.get(t);s||(s=new Set,o.set(t,s));for(let r of n)s.add(r)}}function $n(o,e){let t={name:o,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(o,new Set([e.name])),Rn(t.subgraph,e.subgraph),Rn(t.translation,e.translation)),t}function An(o){return[...o.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function Mn(o){let e=[];o.name!==void 0&&e.push(`H	NM:Z:${o.name}`);for(let[t,n]of An(o.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of An(o.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function Ln(o){let e=o.reduce((a,i)=>a+i.length,0),t=new Uint8Array(e),n=0;for(let a of o)t.set(a,n),n+=a.length;let s=globalThis.crypto?.subtle;return[...s?new Uint8Array(await s.digest("SHA-256",t)):Pn(t)].map(a=>a.toString(16).padStart(2,"0")).join("")}var as="_gbwt_ref";function fe(o){let e=`${o.sample}#${o.haplotype}#${o.contig}`;return o.end===void 0?e:`${e}[${o.fragment}-${o.end}]`}var os=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,is=/^([^#]+?)(?:\[\d+-\d+\])?$/;function hs(o){let e=os.exec(o);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=is.exec(o);if(t)return{contig:t[1]};throw new Error(`"${o}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function $e(o){return typeof o=="string"?hs(o):o}function Me(o,e){return{sample:o.sample??as,contig:o.contig,haplotype:o.haplotype??0,fragment:e}}var cs=4096;function Ht(o){let e=[];for(let t of o){let n=e[e.length-1];n&&t-n[1]<=cs?n[1]=t:e.push([t,t])}return e}var ds=32768,Hn={mostChosenPaths:32},Lt=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},ae=class extends Error{};function tt(o,e,t,n){return o==="forward"?e+t:e-n}function On(o,e,t,n){return o==="forward"?e-n:e+t}function Cn(o){return Ae(te(o.handles[o.handles.length-1]),te(o.handles[0]))}function ze(o){return`${o.pathHandle}:${o.hapStart}:${o.hapEnd}`}async function Bn(o){let{db:e,records:t,signal:n}=o,s=performance.now(),r=()=>{let w=performance.now(),k=w-s;return s=w,k},a={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}},i=(w,k)=>{let N=`${w}: ${k}`;a.walks[N]=(a.walks[N]??0)+1},h=await e.haplotypeSampleInterval()??4096,c=new Map,d=async w=>{let k=t.get(w)??c.get(w);if(k)return k;let N=await e.getRecord(w);if(a.graphFetches+=1,!N)throw new Error(`Node record ${w} is missing from the database`);return c.set(w,N),N},f=w=>t.get(w).sequenceLen,p=await e.pathsByHandle(),y=w=>{let k=p.get(w);return k!==void 0&&o.keep(k.name)},m=[],l=new Lt,b=new Map,I=new Set,A=new Set,x=async w=>{let k=(await d(w.node)).gbwt().lf(w.offset);return k===void 0||k.node===0?void 0:k},E=async(w,k)=>{let N=(await d(te(w.node))).gbwt().predecessorAt(w.offset);if(N===void 0||k!==void 0&&!k.has(N))return;let $=(await d(N)).gbwt().offsetTo(w);if($===void 0)throw new Error(`No offset in ${N} leads to ${w.node}:${w.offset}`);return{node:N,offset:$}},g=(w,k,N,$)=>{let F=N.map(j=>j.pos.node),U=N.map(j=>j.pos.offset),K=0;for(let j of F)K+=f(j);let O=k==="forward"?N[0].left:N[N.length-1].left,L=m.length;m.push({pathHandle:w,orientation:k,handles:F,offsets:U,len:K,hapStart:O,hapEnd:O+K,canonical:Ae(F[0],F[F.length-1]),source:$});for(let j of N)l.set(j.pos,L);let V=b.get(w);return V?V.push(L):b.set(w,[L]),L},S=async(w,k,N,$)=>{let F=[],U=w;for(;;){n?.throwIfAborted();let O=await E(U.pos,t);if(!O)break;U={pos:O,left:On(N,U.left,f(U.pos.node),f(O.node))},F.push(U)}F.reverse();let K=[w];for(U=w;;){n?.throwIfAborted();let O=await x(U.pos);if(!O||!t.has(O.node))break;U={pos:O,left:tt(N,U.left,f(U.pos.node),f(O.node))},K.push(U)}return g(k,N,[...F,...K],$)},P=async(w,k,N,$)=>m[l.get(w.pos)??await S(w,k,N,$)],_=w=>{let k=w.handles[w.handles.length-1];return{pos:{node:k,offset:w.offsets[w.offsets.length-1]},left:w.orientation==="forward"?w.hapEnd-f(k):w.hapStart}},B=w=>{let k=w.handles[0];return{pos:{node:k,offset:w.offsets[0]},left:w.orientation==="forward"?w.hapStart:w.hapEnd-f(k)}},D=await S({pos:o.referencePos,left:o.referenceLeft},o.referenceHandle,"forward","reference"),C=m[D],H=()=>{if(a.fallback!==void 0)return{reference:C,pieces:[],stats:a};let w=new Map;m.forEach((N,$)=>{$!==D&&w.set(ze(N),[...w.get(ze(N))??[],N])});let k=[];for(let N of w.values()){let $=new Set;for(let F of N)F.canonical&&!$.has(F.orientation)&&($.add(F.orientation),k.push(F),a.sources[F.source]+=1)}return a.sources.reference=1,a.pieces=k.length+1,{reference:C,pieces:k,stats:a}},v=async(w,k)=>{let N=k?I:A,$=k?A:I,F=w;for(;;){if(N.has(F))return;N.add(F);let U=m[F],K=k?_(U):B(U),O=0,L;for(;L===void 0;){n?.throwIfAborted();let V=k?await x(K.pos):await E(K.pos);if(!V){L="endmarker";break}let j=(await d(K.pos.node)).sequenceLen,ge=(await d(V.node)).sequenceLen,ne=k?tt(U.orientation,K.left,j,ge):On(U.orientation,K.left,j,ge);if(t.has(V.node)){let Y=l.get(V);Y===void 0?(F=await S({pos:V,left:ne},U.pathHandle,U.orientation,"chain"),$.add(F),L="landed"):($.add(Y),L="merge")}else O>ds?L="bound":(O+=ge,K={pos:V,left:ne})}if(i("chain",L),L!=="landed")return}},G=async w=>{if(o.context>w.context)throw new ae(`the context of ${o.context} bp exceeds the ${w.context} bp the haplotype index's stray rows cover`);let k=a.spacing;if(k===void 0)throw new ae("the haplotype index has no anchors");let{bin:N,bound:$}=w,{fills:F,inserted:U}=o.snarls;if(o.snarls.mode==="overlapping"&&F.length>0)throw new ae("the haplotype index's stray rows cover contained snarls only");for(let u of F){if(u.inserted>0&&u.low===u.high)throw new ae(`the haplotype index's stray rows leave out the snarl bounded by node ${u.low} at both ends`);if(u.inserted>0&&(w.snarlNodes===void 0||u.nodes>w.snarlNodes))throw new ae(w.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${u.nodes} nodes exceeds the ${w.snarlNodes} the haplotype index's stray rows cover`)}let K=Math.floor(o.window.start/N),O=Math.floor((o.window.end-1)/N),L=K*N,V=(O+1)*N,j=new Map,ge=async(u,R)=>{let q=await e.haplotypeAnchorsBetween(o.referenceHandle,u*k,R*k);for(let T of q)j.set(T.anchorOffset/k,T)},ne=Math.max(0,Math.floor((L-$)/k)-1),Y=Math.ceil((V+$)/k)+1,[{listed:Ve,strays:ie}]=await Promise.all([e.haplotypeBinData(o.referenceHandle,K,O),ge(ne,Y)]);for(let u of t.keys()){let R=M(u);if(!re(u)&&!Ve(R)&&!U.has(R))throw new ae(`the haplotype index lists node ${R} of the subgraph in no bin that the window touches`)}a.scans=Ht([...t.keys()].sort((u,R)=>u-R));let he=Promise.all(a.scans.map(([u,R])=>e.haplotypeSamplesInRange(u,R)));for(he.catch(()=>{});ne>0&&(j.get(ne)?.pathOffset??Number.POSITIVE_INFINITY)>=L-$;)ne-=1,await ge(ne,ne);for(;j.has(Y)&&j.get(Y).pathOffset<=V+$;)Y+=1,await ge(Y,Y);let le=[...j.keys()].sort((u,R)=>u-R),be=j.get(le[0]??-1);if(!be)throw new ae("the haplotype index has no anchors on this path");let ce=u=>j.get(u).pathOffset,He=new Map;for(let u of le){let R=M(j.get(u).node);He.set(R,[...He.get(R)??[],u])}let bt=[...He.keys()],Vt=bt.map(u=>j.get(He.get(u)[0]).visits);if(!Vt[bt.indexOf(M(be.node))].some(u=>u.pathHandle===o.referenceHandle&&u.orientation==="forward"&&u.pathOffset===be.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${o.referenceHandle} at offset ${be.pathOffset} (node ${M(be.node)}); it does not match this graph`);let Wt=le.filter(u=>ce(u)<=o.window.start),Kn=le.filter(u=>ce(u)>=o.window.end);a.anchors=[ce(Wt[Wt.length-1]??le[0]),ce(Kn[0]??le[le.length-1])],a.anchorsRead=le.length;let xt=new Map,Zt=new Set;if(bt.forEach((u,R)=>{let q=He.get(u),T=q.length===1?q[0]:void 0;for(let z of Vt[R])Zt.add(z.pathHandle),z.orientation==="forward"&&y(z.pathHandle)&&xt.set(z.pathHandle,[...xt.get(z.pathHandle)??[],{k:T,row:z}])}),a.chosenPaths=[...Zt].filter(y).length,a.chosenPaths>Hn.mostChosenPaths)throw new ae(`${a.chosenPaths} chosen paths pass the anchors, more than ${Hn.mostChosenPaths}`);let We=[],Ee=Number.POSITIVE_INFINITY,xe=0;for(let[u,R]of xt){R.sort((q,T)=>q.row.pathOffset-T.row.pathOffset);for(let q=0;q+1<R.length;q++){let T=R[q],z=R[q+1];if(T.k===void 0||z.k===void 0||Math.abs(T.k-z.k)!==1)continue;let[Z,J]=ce(T.k)<=ce(z.k)?[T,z]:[z,T],ee=ce(Z.k),se=ce(J.k);ee<V&&se>=L?(We.push({pathHandle:u,from:T.row,to:z.row}),Ee=Math.min(Ee,ee-$),xe=Math.max(xe,se+$)):ee>=V&&ee-V<=$?(We.push({pathHandle:u,from:Z.row,to:void 0}),Ee=Math.min(Ee,ee-$),xe=Math.max(xe,ee+$)):se<L&&L-se<=$&&(We.push({pathHandle:u,from:J.row,to:void 0}),Ee=Math.min(Ee,se-$),xe=Math.max(xe,se+$))}}let Yn=new Set(F.map(u=>`${u.low}:${u.high}`)),Jn=ie.filter(u=>y(u.pathHandle)&&(u.snarl===void 0||Yn.has(`${u.snarl[0]}:${u.snarl[1]}`))).sort((u,R)=>u.pathHandle-R.pathHandle||u.pathStart-R.pathStart);a.strays={bins:O-K+1,rows:ie.length,walked:0,outsideBp:0},xe>0&&await o.prefetchReferenceRange(o.referenceHandle,Math.max(0,Ee),xe+1),a.ms.scan=r();let Xt=8*k+2*(o.window.end-o.window.start),Kt=a.strays,Oe=0,Yt=u=>{if(Kt.outsideBp+=u,Oe+=u,Oe>Xt)throw new ae(`a walk of a chosen path near the window went past its cap of ${Xt} bp`)},St=new Map,Jt=(u,R,q)=>(St.get(u)??[]).some(([T,z])=>T<=R&&q<z),en=(u,R,q)=>{St.set(u,[...St.get(u)??[],[R,q]])},tn=async(u,R,q,T,z)=>{let Z=R,J=q,ee=J;for(;Z&&J<=T;){n?.throwIfAborted();let se;if(t.has(Z.node)){let Ce=await P({pos:Z,left:J},u,"forward",z),sn=_(Ce);Z=sn.pos,J=sn.left,se=f(Z.node),ee=Math.max(ee,Ce.hapEnd)}else se=(await d(Z.node)).sequenceLen,Yt(se),ee=Math.max(ee,J+se);Z=await x(Z),J+=se}return ee},es=async(u,R,q,T)=>{let z={pos:R,left:q},Z=q;for(;z.left>T;){n?.throwIfAborted();let J=await E(z.pos);if(!J)break;let ee=(await d(J.node)).sequenceLen,se=z.left-ee;if(t.has(J.node)){let Ce=await P({pos:J,left:se},u,"forward","section");z=B(Ce),Z=Math.min(Z,Ce.hapStart)}else Yt(ee),z={pos:J,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:u,from:R,to:q}of We){let T=R.pathOffset,z=(q??R).pathOffset+$;if(Jt(u,T-$,z))continue;let Z={node:R.node,offset:R.offset};Oe=0;let J=await tn(u,Z,T,z,"section");Oe=0;let ee=await es(u,Z,T,T-$);en(u,Math.min(ee,T-$),Math.max(J,z+1)),i(q?"section":"visit",q?"past the far anchor":"bound")}for(let u of Jn){if(Jt(u.pathHandle,u.pathStart,u.pathEnd))continue;Oe=0;let R=await tn(u.pathHandle,{node:u.node,offset:u.offset},u.pathStart,u.pathEnd,"stray");en(u.pathHandle,u.pathStart,Math.max(R,u.pathEnd+1)),Kt.walked+=1}a.ms.walks=r();let nn=[];for(let u of await he)for(let R of u)if(a.scanRows+=1,t.has(R.node)&&y(R.pathHandle)){if(!(b.get(R.pathHandle)??[]).some(q=>{let T=m[q];return T.hapStart<=R.pathOffset&&R.pathOffset<T.hapEnd}))throw new ae(`chosen path ${R.pathHandle} has a sample at ${R.pathOffset} on the window's nodes that no walk reached`);R.orientation==="reverse"&&nn.push(R)}for(let u of nn)await P({pos:{node:u.node,offset:u.offset},left:u.pathOffset},u.pathHandle,"reverse","twin");a.ms.check=r()},X=async()=>{let w=new Map,k=O=>{let L=ze(O),V=w.get(L);V?V.add(O.orientation):w.set(L,new Set([O.orientation]))},N=0,$=()=>{for(;N<m.length;N++)k(m[N])};$();let F=O=>(w.get(ze(O))?.size??0)>1,U=2*h,K=(O,L)=>L===D?y(o.referenceHandle)&&Cn(O):!O.canonical||Cn(O);for(let O=0;O<m.length;O++){let L=m[O];if(F(L)||!K(L,O))continue;a.twins.tried+=1;let V=L.orientation==="forward"?"reverse":"forward",j=_(L),ge=0,ne;for(;!ne&&ge<=U;){n?.throwIfAborted();let ie=await x(j.pos);if(!ie)break;let he=(await d(ie.node)).sequenceLen,le=tt(L.orientation,j.left,(await d(j.pos.node)).sequenceLen,he),be=te(ie.node);ne=(await e.haplotypeSamplesInRange(be,be)).find(ce=>ce.pathHandle===L.pathHandle&&ce.orientation===V&&ce.pathOffset===le),ge+=he,j={pos:ie,left:le}}let Y=ne&&{pos:{node:ne.node,offset:ne.offset},left:ne.pathOffset},Ve=0;for(;Y&&!F(L)&&Ve<=U+L.len;){if(n?.throwIfAborted(),t.has(Y.pos.node)){let ie=await P(Y,L.pathHandle,V,"twin"),he=m.indexOf(ie);await v(he,!0),await v(he,!1),$(),Y=_(ie)}if(!F(L)){let ie=(await d(Y.pos.node)).sequenceLen;Ve+=ie;let he=await x(Y.pos);Y=he?{pos:he,left:tt(V,Y.left,ie,(await d(he.node)).sequenceLen)}:void 0}}if($(),!F(L))throw new ae(`piece ${ze(L)} was found in one orientation where extractPaths keeps the other`);a.twins.found+=1}a.ms.twins=r()};try{let w=await e.haplotypeStrayOptions();if(w===void 0)throw new ae("the haplotype index has no stray rows; gbz-haplotype-index 0.2.0 writes them");await G(w),await X()}catch(w){if(!(w instanceof ae))throw w;a.fallback=w.message}return H()}function Fn(o,e){return o.handles[0]-e.handles[0]||o.offsets[0]-e.offsets[0]}var oe=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Ot(o,e){return o[0]<e[0]||o[0]===e[0]&&(o[1]<e[1]||o[1]===e[1]&&o[2]<e[2])}var De=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let r=s.length-1;for(;r>0;){let a=r-1>>1;if(Ot(s[r],s[a]))[s[r],s[a]]=[s[a],s[r]],r=a;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let r=2*s+1,a=r+1,i=s;if(r<e.length&&Ot(e[r],e[i])&&(i=r),a<e.length&&Ot(e[a],e[i])&&(i=a),i===s)break;[e[s],e[i]]=[e[i],e[s]],s=i}}return t}get size(){return this.heap.length}};function fs(o){let e=new Int32Array(o.length),t=new Int32Array(o.length);return o.forEach(([n,s],r)=>{e[r]=n,t[r]=s}),{pathAt:e,refAt:t,count:o.length}}function ls(o,e){let t=0,n=o.length;for(;t<n;){let s=t+n>>1;o[s]>e?n=s:t=s+1}return o[t]}function ke(o){return`${o.node}:${o.offset}`}function qe(o){return o.map(e=>te(e)).reverse()}function ps(o,e){let t=e.identity.hapStart-o.identity.hapEnd,n=o.strand==="+"?e.refStart-o.refEnd:o.refStart-e.refEnd;return o.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function us(o,e,t){let[n,s]=o.strand==="+"?[o,e]:[e,o],r=n.edits.map(([c,d])=>[c,d]);Tn(r,t.insertion,t.deletion);for(let[c,d]of s.edits)W(r,c,d);let a=o.identity.walkForward,[i,h]=a?[o,e]:[e,o];return{strand:o.strand,refStart:n.refStart,refEnd:s.refEnd,edits:r,weight:void 0,path:[...i.path,...h.path],start:i.start,pieces:[...i.pieces,...h.pieces],soloAligned:[...i.soloAligned,...h.soloAligned],identity:{pathHandle:o.identity.pathHandle,name:o.identity.name,hapStart:o.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:a}}}function gs(o,e,t){if(o.some(a=>a.weight!==void 0))return o;let n=new Map;o.forEach((a,i)=>{if(a.identity){let h=n.get(a.identity.pathHandle);h?h.push(i):n.set(a.identity.pathHandle,[i])}});let s=new Map,r=new Set;for(let a of n.values()){a.sort((d,f)=>o[d].identity.hapStart-o[f].identity.hapStart);let i=a[0],h=o[i],c=[];for(let d of a.slice(1)){let f=o[d],p=c.length===0?ps(h,f):void 0;if(p){h=us(h,f,p),r.add(d);continue}if(!e(f)){c.push(d);continue}let y=e(h)?t([h,...c.map(m=>o[m]),f]):void 0;if(y){h=y;for(let m of[...c,d])r.add(m)}else s.set(i,h),i=d,h=f;c=[]}s.set(i,h)}return o.flatMap((a,i)=>r.has(i)?[]:[s.get(i)??a])}function nt(o,e){return{node:o.path[e],offset:o.offsets[e]}}var ws=32768;function ms(o){let e=[...o].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=ws?s[1]=n:t.push([n,n])}return t}var Ge=class o{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 o(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(ue(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 oe(this.limit);let t=await this.db.getRecord(ue(e,"forward")),n=await this.db.getRecord(ue(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 ${fe(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${fe(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let r=n,a=s;for(;;){await this.ensureNode(M(a.node));let i=this.record(a.node);if(r+i.sequenceLen>t)return{position:{seqOffset:t,handle:a.node,nodeOffset:t-r,gbwtOffset:a.offset},name:e.name,handle:e.handle};r+=i.sequenceLen;let h=i.gbwt().lf(a.offset);if(!h)throw new Error(`The fragment of ${fe(e.name)} at ${e.name.fragment} does not contain offset ${t}`);a=h}}async aroundPosition(e,t,n){let s=M(e);await this.ensureNode(s);let r=this.record(e),a=Re(e),i=new De;return i.push(t,s,Ke(a)),i.push(r.sequenceLen-t-1,s,Ye(a)),this.insertContext(i,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[s,r]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&r){let a=s.pos.node,i=r.pos.node;if(!await this.db.prefetchRecords([[Math.min(a,i),Math.max(a,i)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(ms(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}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(s){throw s instanceof oe&&s.windowBp===void 0?new oe(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},r=e.nodeOffset,a=t,i=new De;for(;;){let h=M(s.node),c=Re(s.node);this.walkedBp=t-a,await this.ensureNode(h);let d=this.record(s.node);if(r>=d.sequenceLen)throw new Error(`Offset ${r} in node ${h} of length ${d.sequenceLen}`);i.push(r,h,Ke(c));let f=d.sequenceLen-r;if(a<=f){i.push(a===f?0:f-a-1,h,Ye(c));break}i.push(0,h,Ye(c));let p=d.gbwt().lf(s.offset);if(!p)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=p,r=0,a-=f}return this.walkedBp=t,this.insertContext(i,n)}async aroundNodes(e,t){let n=new De;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let a of this.records.keys())s.add(M(a));let r=0;for(;e.size>0;){let[a,i,h]=e.pop(),c=`${i}:${h}`;if(n.has(c))continue;n.add(c),s.delete(i),this.hasNode(i)||(await this.addNode(i),r+=1);let d=dn(h);if(!n.has(`${i}:${d}`)){let y=this.record(ue(i,fn(h))),m=a+y.sequenceLen-1;m<=t&&e.push(m,i,d)}let f=this.record(ue(i,ln(h))),p=a+1;if(p<=t)for(let y of f.successors()){let m=M(y),l=Ke(Re(y));n.has(`${m}:${l}`)||e.push(p,m,l)}}for(let a of s)this.records.delete(ue(a,"forward")),this.records.delete(ue(a,"reverse"));return{inserted:r,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,te(t)],s=new Set([M(e),M(t)]),r=[];for(;n.length>0;){let a=n.pop(),i=M(a);this.hasNode(i)||(await this.addNode(i),r.push(i));for(let h of this.record(a).successors()){let c=M(h);s.has(c)||(n.push(h,te(h)),s.add(c))}}return{inserted:r,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:r,nodes:a}=await this.fillBetween(n,s),i=M(n),h=M(s);this.snarlFills.push({low:Math.min(i,h),high:Math.max(i,h),nodes:a,inserted:r.length});for(let c of r)this.snarlNodes.add(c);t+=r.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 s of this.sortedHandles()){let r=this.record(s),a=r.next;a!==void 0&&(n=!0,this.hasHandle(a)?Be(s,a)&&t.push([s,a]):e==="overlapping"&&this.isSnarlEntryInSubgraph(r)&&t.push([s,a]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(te(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let r=t.get(n);if(!r){if(r=await this.db.getRecord(n),e?.(),!r)throw new Error(`Node record ${n} is missing from the database`);t.set(n,r)}return r}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(te(d))).successors().length>1},n=async h=>{let c=await e(te(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[te(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,r=this.sortedHandles().flatMap(h=>this.record(h).successors()),a,i=!1;for(;!i&&r.length>0;){let h=r.shift(),c=M(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")a=d.snarl,i=!0;else if(d.kind==="chain")i=!0;else for(let f of["forward","reverse"])r.push(...(await e(ue(c,f))).successors())}}return a}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),r=s.length,a=new Map;s.forEach((g,S)=>a.set(g,S));let i=new Int32Array(r+1),h=new Int32Array(r),c=[];for(let g=0;g<r;g++){let S=this.record(s[g]),P=S.gbwt().decompressArrays();h[g]=S.sequenceLen,c.push(P),i[g+1]=i[g]+P.nodes.length}let d=i[r],f=new Int32Array(d),p=new Int32Array(d),y=new Uint8Array(d);for(let g=0;g<r;g++){let S=c[g];f.set(S.nodes,i[g]),p.set(S.offsets,i[g])}c.length=0;for(let g=0;g<d;g++){let S=a.get(f[g]);S===void 0?f[g]=-1:(f[g]=S,y[i[S]+p[g]]=1)}let m=n===void 0?void 0:a.get(n.handle),l=n?.gbwtOffset,b,I=(g,S,P)=>{let _=[],B=0,D=0,C=-1,H=g,v=S;for(;;){H===m&&v===l&&(C=B),P&&(P.push(s[H]),_.push(v)),B+=1,D+=h[H];let G=i[H]+v,X=f[G];if(X<0)break;v=p[G],H=X}return{offsets:_,len:D,refAt:C,last:H}},A=(g,S,P,_)=>{_>=0&&(this.refId=this.paths.length,b=_),this.paths.push({path:g,offsets:S,len:P,weight:void 0,identity:void 0})},x=new Int32Array(r);for(let g=0;g<r;g++){let S=s[g];if(!re(S)){let P=i[g],_=i[g+1]-P;for(let B=0;B<_;B++)if(y[P+B]===0){let D=[],{offsets:C,len:H,refAt:v,last:G}=I(g,B,D),X=s[G];if(v>=0||Ae(S,X)){if(A(D,C,H,v),!re(X)){let w=a.get(te(X));x[w]=x[w]+1}}else this.twinStarts.add(ke({node:S,offset:B}))}}}for(let g=0;g<r;g++){let S=s[g];if(re(S)){let P=i[g],_=i[g+1]-P,B=0;for(let C=0;C<_;C++)y[P+C]===0&&(B+=1);let D=(m===void 0||b!==void 0)&&B===x[g];for(let C=0;C<_;C++)if(y[P+C]===0){let H=D?void 0:I(g,C,void 0);if(H&&(H.refAt>=0||Ae(S,s[H.last]))){let v=[],{offsets:G,len:X,refAt:w}=I(g,C,v);A(v,G,X,w)}else this.twinStarts.add(ke({node:S,offset:C}))}}}let E=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((g,S)=>g.path[0]-S.path[0]||g.offsets[0]-S.offsets[0]),E&&(this.refId=this.paths.indexOf(E)),n){if(b===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let g=this.paths[this.refId],S=n.nodeOffset;for(let _ of g.path.slice(0,b))S+=this.record(_).sequenceLen;let P=n.seqOffset-S;this.refInterval=[P,P+g.len],g.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:P,hapEnd:P+g.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,s=n&&!Fe(n)?qe(n):void 0,r=c=>s!==void 0&&Ct(c,s)===0||Fe(qe(c)),a=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>Ct(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let i=[],h;for(let c of this.paths){let d=i[i.length-1],f=a&&c!==t&&r(c.path);this.twinDeferred||=f,d&&Ct(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=i.length),i.push({...c,weight:c.weight??1}))}this.paths=i,this.refId=h}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=a=>`${a.pathHandle}:${a.hapStart}-${a.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let a of this.paths)a!==e&&a.identity?.orientation==="forward"&&s.add(n(a.identity));let r=this.paths.filter(a=>a===e||a.identity?.orientation!=="reverse"||!s.has(n(a.identity)));r.length<this.paths.length&&(this.paths=r,this.refId=e===void 0?void 0:r.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(a=>a.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((a,i)=>i!==this.refId&&a.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],s=this.paths.filter((a,i)=>i===this.refId||a.identity!==void 0&&e(a.identity.name)),r=new Set;for(let a of s)for(let i of a.path)r.add(M(i));for(let a of[...this.records.keys()])r.has(M(a))||this.records.delete(a);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let r=e.position.seqOffset,a=await Bn({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:r-e.position.nodeOffset,window:{start:r,end:r+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,p)=>this.prefetchReferenceRange(d,f,p)});if(this.stats.keep=a.stats,a.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===a.reference?e.name:i.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[a.reference,...a.pieces].sort(Fn);return this.paths=c.map(h),this.refId=c.indexOf(a.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[a.reference.hapStart,a.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=Ht(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([l,b])=>this.db.haplotypeSamplesInRange(l,b)));for(let l of s.flat())n.set(ke(l),l);let r=l=>{let b=0,I=t.length-1;for(;b<I;){let x=b+I+1>>1;t[x][0]<=l?b=x:I=x-1}let A=t[b];return A[0]<=l&&l<=A[1]},a=new Map;this.paths.forEach((l,b)=>{l.path.length>0&&b!==this.refId&&a.set(ke(nt(l,0)),b)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((l,b)=>{b!==this.refId&&i.fragmentLengths.push(l.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=l=>(i.graphLookups+=1,h(l)),d=async(l,b)=>{if(r(l.node))return n.get(ke(l));this.stats.identificationFetches+=1,i.companionSeeks+=1,b.seeks+=1;let I=await this.db.haplotypeSampleAt(l.node,l.offset);return I||(i.companionMisses+=1),I},f=new Map,p=async l=>{let b=f.get(l);if(!b){let I=await this.db.getPath(l);if(!I)throw new Error(`Path ${l} is missing from the database`);b=I.name,f.set(l,b)}return b},y=(l,b,I)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.pathOffset-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.pathOffset+b+I},m=(l,b)=>l.orientation==="forward"?{pathHandle:l.pathHandle,orientation:"forward",base:l.hapStart-b}:{pathHandle:l.pathHandle,orientation:"reverse",base:l.hapEnd+b};for(let l=0;l<this.paths.length;l++){let b=this.paths[l];if(l===this.refId||b.identity)continue;let I=[],A=new Set,x={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(x);let E,g=0,S=l,P;for(;E===void 0;){if(this.signal?.throwIfAborted(),S!==void 0){if(A.has(S)){x.end="cycle";break}A.add(S);let H=this.paths[S];I.push({index:S,startBp:g}),x.fragments+=1;let v=g;for(let X=0;X<H.path.length;X++){let w=nt(H,X),k=n.get(ke(w)),N=this.record(w.node).sequenceLen;if(k){E=y(k,v,N);break}v+=N}if(g+=H.len,E){x.end="in-fragment sample";break}let G=nt(H,H.path.length-1);P=this.record(G.node).gbwt().lf(G.offset),S=void 0}if(P===void 0||P.node===0){x.end="endmarker";break}let _=ke(P),B=a.get(_);if(B!==void 0){let H=this.paths[B].identity;if(H){E=m(H,g),x.end="identified sibling";break}S=B;continue}this.records.has(P.node)&&(x.reentries+=1),this.twinStarts.has(_)&&(x.twinLandings+=1);let D=await d(P,x),C=await c(P.node);if(D){E=y(D,g,C.sequenceLen),x.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,x.steps+=1,g-I[I.length-1].startBp>4*e+4*C.sequenceLen){x.end="bound";break}g+=C.sequenceLen,P=C.gbwt().lf(P.offset)}if(E){x.pathHandle=E.pathHandle;let _=await p(E.pathHandle);for(let{index:B,startBp:D}of I){let C=this.paths[B];C.identity=E.orientation==="forward"?{pathHandle:E.pathHandle,name:_,orientation:"forward",hapStart:E.base+D,hapEnd:E.base+D+C.len}:{pathHandle:E.pathHandle,name:_,orientation:"reverse",hapStart:E.base-D-C.len,hapEnd:E.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let r=t.get(n);r?r.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),r=new Int32Array(e.length),a=0,i=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=ls(c,i);if(d===void 0)return;s[a]=h,r[a]=d,a+=1,i=d}}return{pathAt:s,refAt:r,count:a}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,r=0,a=0,i=0;for(;s<e.length&&r<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[r]).sequence;for(;a<h.length&&i<c.length;){if(h[a]!==c[i])return n;a+=1,i+=1,n+=1}a===h.length&&(s+=1,a=0),i===c.length&&(r+=1,i=0)}return n}suffixMatches(e,t){let n=0,s=0,r=0,a=0,i=0;for(;s<e.length&&r<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-r-1]).sequence;for(;a<h.length&&i<c.length;){if(h[h.length-a-1]!==c[c.length-i-1])return n;a+=1,i+=1,n+=1}a===h.length&&(s+=1,a=0),i===c.length&&(r+=1,i=0)}return n}align(e,t,n){let s=this.pathLen(e),r=this.pathLen(t),a=this.prefixMatches(e,t),i=this.suffixMatches(e,t);a+i>s&&(i=s-a),a+i>r&&(i=r-a),W(n,"M",a),Tn(n,s-a-i,r-a-i),W(n,"M",i)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let r of e)n.has(r)&&(s+=this.record(r).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??fs(gn(e,t,f=>this.record(f).sequenceLen)[0]),r=[],a=this.refPrefix(t),i=(f,p,y,m)=>{f===p?W(r,"D",a[m]-a[y]):y===m?W(r,"I",this.pathLen(e.slice(f,p))):this.align(e.slice(f,p),t.slice(y,m),r)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let p=s.pathAt[f],y=s.refAt[f];(c!==p||d!==y)&&i(c,p,d,y);let m=this.record(e[p]).sequenceLen;W(r,"M",m),h+=m,c=p+1,d=y+1}return i(c,e.length,d,t.length),{edits:r,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(Fe(n)&&(t.identity===void 0||!Fe(qe(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let r=qe(t.path),a=this.sharedWeight(t.path,n);if(this.sharedWeight(r,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(a===0)s={...this.editsAgainst(r,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(r,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}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],s=(d,f,p,y)=>{let m=bs(d),l=this.paths[p[0]],b=this.paths[p[p.length-1]],I=l.identity,A=I?.orientation==="forward",[x,E]=A?[l,b]:[b,l];return{strand:f,refStart:e.start+m.leading,refEnd:e.start+n-m.trailing,edits:m.edits,weight:l.weight,path:p.flatMap(g=>this.paths[g].path),start:nt(l,0),pieces:p,soloAligned:y,identity:I===void 0?void 0:{pathHandle:I.pathHandle,name:I.name,hapStart:I.name.fragment+x.identity.hapStart,hapEnd:I.name.fragment+E.identity.hapEnd,walkForward:A}}},r=d=>d.soloAligned.reduce((f,p)=>f+p,0),a=d=>d.pieces.reduce((f,p)=>f+this.paths[p].len,0),i=d=>2*r(d)>=a(d),h=d=>{let f=d[0],p=d[d.length-1],y=f.identity.walkForward;if(d.some((v,G)=>v.strand!==f.strand||v.identity.walkForward!==y||G>0&&v.identity.hapStart<d[G-1].identity.hapEnd))return;let m=y?d:[...d].reverse(),l=m.flatMap(v=>v.pieces),b=m.flatMap(v=>v.soloAligned),I=f.strand==="+"!==y,A=l.map(v=>this.paths[v]),x=A.slice(1).map((v,G)=>{let X=A[G].identity;return y?v.identity.hapStart-X.hapEnd:X.hapStart-v.identity.hapEnd}),E=I?[...A].reverse():A,g=I?[...x].reverse():x,S=E.flatMap(v=>I?qe(v.path):v.path),{edits:P}=this.editsAgainst(S,t),_=_n(P,E.map(v=>v.len)),B=new Map((I?[...l].reverse():l).map((v,G)=>[v,_[G]])),D=v=>2*v.pieces.reduce((G,X)=>G+B.get(X),0)>=r(v);if(!D(f)||!D(p))return;let C=[],H=0;return E.slice(0,-1).forEach((v,G)=>{H+=v.len,C.push([H,g[G]])}),s(xs(P,C),f.strand,l,b)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:p,flipped:y}=this.alignment(f),m=d.identity,l=m?m.orientation==="forward"!==y:!y;c.push(s(p,l?"+":"-",[f],_n(p,[d.len])))}),gs(c,i,h).map(d=>{let{edits:f,identity:p,pieces:y,soloAligned:m,...l}=d,b={...l,cigar:Ss(f)};return p?{...b,resolved:!0,name:p.name,label:fe({...p.name,fragment:p.hapStart,end:p.hapEnd}),pathHandle:p.pathHandle,hapStart:p.hapStart,hapEnd:p.hapEnd}:{...b,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,r=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:rt(d,f)}]:[]}),a=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,i=a(t),h=n?a(n):d=>!i(d),c=d=>this.record(ue(d,"forward")).sequence;return r.filter(d=>i(d.name)).flatMap(d=>r.filter(f=>h(f.name)).flatMap(f=>wn({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(p=>({query:f.name,queryStart:f.start+p.queryStart,queryEnd:f.start+p.queryEnd,strand:p.strand,target:d.name,targetStart:d.start+p.targetStart,targetEnd:d.start+p.targetEnd,cigar:mn(p.edits),matches:p.edits.reduce((y,[m,l])=>y+(m==="="?l:0),0),columns:p.edits.reduce((y,[,m])=>y+m,0),sharedBases:p.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ue(e,n);for(let r of this.record(s).successors())this.hasHandle(r)&&Be(s,r)&&t.push([n==="reverse"?1:0,M(r),re(r)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!re(n)){let s=M(n),r=`S	${s}	${this.record(n).sequence}
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n?[{name:n.name,start:n.name.fragment+n.hapStart,end:n.name.fragment+n.hapEnd}]:[]})}toSubgraphJson(e={}){let t=this.sortedHandles().filter(r=>!re(r)).map(r=>({id:String(M(r)),sequence:this.record(r).sequence})),n=[];for(let[r,a]of this.outputEdges())n.push({from:String(M(r)),from_is_reverse:re(r),to:String(M(a)),to_is_reverse:re(a)});let s=this.outputPaths(e).map(r=>ys(r.info,r.identity,r.name,r.cigar));return{nodes:t,edges:n,paths:s}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(a=>!re(a)),n=new Int32Array(t.length),s=[];t.forEach((a,i)=>{n[i]=M(a),s.push(this.record(a).sequence)});let r=[];for(let[a,i]of this.outputEdges())r.push(a,i);return{nodeIds:n,nodeSequences:s,edges:Int32Array.from(r),paths:this.outputPaths(e).map(a=>({name:a.name,weight:a.info.weight,cigar:a.cigar,steps:Int32Array.from(rt(a.info,a.identity))}))}}};function rt(o,e){return e?.orientation==="reverse"?o.path.map(t=>te(t)).reverse():o.path}function ys(o,e,t,n){return{name:t,...o.weight===void 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ot(o,e){return e.limit!==void 0&&Se("limit",e.limit),Ge.create(o,e)}async function zn(o,e){let t=at(e),n=ot(o,e),s=await n.pathPosition(Me($e(e.path),Se("offset",e.offset)));return await n.aroundPosition(s.position.handle,s.position.nodeOffset,t),await n.extractSnarls(e.snarls??"none"),n.extractPaths(s,e.haplotypes??"all"),n}async function Is(o,e){let t=Se("start",e.start),n=Se("end",e.end),s=at(e),r=ot(o,e);try{let a=await r.pathPosition(Me($e(e.path),t));return await r.prefetchReferenceWalk(a,n-t),await r.aroundInterval(a.position,n-t,s),await r.extractSnarls(e.snarls??"none"),{subgraph:r,reference:a}}catch(a){throw a instanceof oe&&a.windowBp===void 0?new oe(a.limit,{windowBp:n-t,walkedBp:r.referenceWalkedBp??0}):a}}async function Bt(o,e){let{keep:t}=e,n=e.haplotypes??"all",s=n==="all"||n==="distinct";if(t!==void 0&&s&&!o.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:r,reference:a}=await Is(o,e);return t===void 0||!s?(r.extractPaths(a,n),r):(await r.extractChosenPaths(a,e.end-e.start,t,at(e))||(r.extractPaths(a,"all"),await r.identifyPaths()),r.keepHaplotypes(t),n==="distinct"&&r.mergeDistinct(),r)}async function qn(o,e){let t=e.haplotypes??"all",n=e.snarls??"none";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");if(n==="overlapping"&&new Set(e.nodeIds).size>1)throw new Error("Overlapping snarls cannot be extracted for a node-based query with multiple nodes");let s=at(e);for(let a of e.nodeIds)Se("node id",a,1);let r=ot(o,e);return await r.aroundNodes(e.nodeIds,s),await r.extractSnarls(n),r.extractPaths(void 0,t),r}async function Dn(o,e){let t=e.haplotypes??"all";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");let n=ot(o,e);return await n.betweenNodes(Se("startHandle",e.startHandle,2),Se("endHandle",e.endHandle,2)),n.extractPaths(void 0,t),n}function me(o,e){let t=0;for(let s=0;s<8;s++){let r=o[e+s];if(r===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(r&127),(r&128)===0){if(s===7&&!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+s+1]}}let n=o[e+8];if(n===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+n,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function Es(o,e,t){switch(t){case 1:return o.getInt8(e);case 2:return o.getInt16(e);case 3:return o.getInt8(e)<<16|o.getUint16(e+1);case 4:return o.getInt32(e);case 6:return o.getInt16(e)*4294967296+o.getUint32(e+2);default:{let n=o.getBigInt64(e);if(n>BigInt(Number.MAX_SAFE_INTEGER)||n<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${n} exceeds the safe integer range`);return Number(n)}}}var ks=new TextDecoder;function it(o){let[e,t]=me(o,0),n=[],s=t;for(;s<e;){let[i,h]=me(o,s);n.push(i),s=h}let r=new DataView(o.buffer,o.byteOffset,o.byteLength),a=e;return n.map(i=>{if(i===0)return null;if(i>=1&&i<=6){let h=i<=4?i:i===5?6:8,c=Es(r,a,h);return a+=h,c}if(i===7){let h=r.getFloat64(a);return a+=8,h}if(i===8)return 0;if(i===9)return 1;if(i>=12){let h=i-12>>1,c=o.subarray(a,a+h);return a+=h,i%2===0?c:ks.decode(c)}throw new Error(`SQLite serial type ${i} is reserved`)})}var ct=2,dt=5,Gn=10,ht=13;function Un(o,e){return o[e]*256+o[e+1]}function Ie(o,e){return o[e]*16777216+o[e+1]*65536+o[e+2]*256+o[e+3]}function Ps(o,e){let t=o[e];if(t!==ct&&t!==dt&&t!==Gn&&t!==ht)throw new Error(`SQLite page has unknown b-tree type ${t}`);let n=t===ct||t===dt;return{type:t,cellCount:Un(o,e+3),rightChild:n?Ie(o,e+8):0,cellPointers:e+(n?12:8)}}function ye(o,e,t){return Un(o,e.cellPointers+2*t)}var vs=4096,ft=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let n=this.usable,s=t?Math.floor((n-12)*64/255)-23:n-35;if(e<=s)return e;let r=Math.floor((n-12)*32/255)-23,a=r+(e-r)%(n-4);return a<=s?a:r}async payload(e,t,n,s){let r=this.localPayloadSize(n,s);if(r===n)return e.subarray(t,t+n);let a=new Uint8Array(n);a.set(e.subarray(t,t+r),0);let i=r,h=Ie(e,t+r);for(;h!==0&&i<n;){let c=await this.pager.page(h),d=c.subarray(4,4+Math.min(this.usable-4,n-i));a.set(d,i),i+=d.length,h=Ie(c,0)}if(i!==n)throw new Error("SQLite overflow chain ended before the payload was complete");return a}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:Ps(t,e===1?100:0)}}tableDepth(e,t){let n=this.tableDepths.get(e);return n||(n=(async()=>{let s=e;for(let r=0;;r++){let{page:a,header:i}=await this.pageAt(s);if(i.type===ht)return r;if(i.type!==dt)throw new Error("SQLite table b-tree contains an index page");let h=this.childIndexFor(a,i,t);s=h===i.cellCount?i.rightChild:Ie(a,ye(a,i,h))}})(),this.tableDepths.set(e,n),n.catch(()=>this.tableDepths.delete(e))),n}childIndexFor(e,t,n){let s=0,r=t.cellCount;for(;s<r;){let a=s+r>>1,[i]=me(e,ye(e,t,a)+4);i<n?s=a+1:r=a}return s}async prefetchRowidRanges(e,t,n=!1){if(t.length===0)return!0;let s=await this.tableDepth(e,t[0][0]),r=t.map(()=>[e]);for(let a=0;a<s;a++){r=await Promise.all(r.map((h,c)=>this.childrenInRange(h,...t[c])));let i=r.flat();if(n)this.pager.prefetchLeading(i);else if(!this.pager.prefetch(i))return!1}return!0}async childrenInRange(e,t,n){let s=await Promise.all(e.map(a=>this.pageAt(a))),r=[];return s.forEach(({page:a,header:i},h)=>{let c=h===0?this.childIndexFor(a,i,t):0,d=h===s.length-1?this.childIndexFor(a,i,n):i.cellCount;for(let f=c;f<=d;f++)r.push(f===i.cellCount?i.rightChild:Ie(a,ye(a,i,f)))}),r}async tableRowid(e,t){let n=e;for(;;){let{page:s,header:r}=await this.pageAt(n);if(r.type===ht){let h=0,c=r.cellCount;for(;h<c;){let d=h+c>>1,f=ye(s,r,d),[p,y]=me(s,f),[m,l]=me(s,y);if(m===t)return it(await this.payload(s,l,p,!1));m<t?h=d+1:c=d}return}if(r.type!==dt)throw new Error("SQLite table b-tree contains an index page");let a=0,i=r.cellCount;for(;a<i;){let h=a+i>>1,c=ye(s,r,h),[d]=me(s,c+4);d<t?a=h+1:i=h}n=a===r.cellCount?r.rightChild:Ie(s,ye(s,r,a))}}async*tableScan(e){yield*this.scanPage(e,await this.tableDepth(e,0))}async*scanPage(e,t){let{page:n,header:s}=await this.pageAt(e);if(s.type===ht)for(let r=0;r<s.cellCount;r++){let a=ye(n,s,r),[i,h]=me(n,a),[c,d]=me(n,h);yield{rowid:c,values:it(await this.payload(n,d,i,!1))}}else{let r=[];for(let a=0;a<s.cellCount;a++)r.push(Ie(n,ye(n,s,a)));r.push(s.rightChild),t===1&&this.pager.prefetchLeading(r);for(let a of r)yield*this.scanPage(a,t-1)}}decodedCells(e,t){let n=this.decodedIndexPages.get(e);if(n)this.decodedIndexPages.delete(e);else if(n=new Array(t.cellCount),this.decodedIndexPages.size>=vs){let s=this.decodedIndexPages.keys().next().value;s!==void 0&&this.decodedIndexPages.delete(s)}return this.decodedIndexPages.set(e,n),n}async indexCell(e,t,n,s){let r=this.decodedCells(e,n),a=r[s];if(!a){let i=ye(t,n,s),h=n.type===ct,[c,d]=me(t,h?i+4:i);a={values:it(await this.payload(t,d,c,!0)),leftChild:h?Ie(t,i):0},r[s]=a}return a}async lowerBound(e,t,n,s,r,a){let i=r,h=n.cellCount;for(;i<h;){let c=i+h>>1,d=await this.indexCell(e,t,n,c),f=Ft(d.values,s);f<0||a&&f===0?i=c+1:h=c}return i}async*indexScanFrom(e,t,n){let{page:s,header:r}=await this.pageAt(e),a=await this.lowerBound(e,s,r,t,0,!1),i=r.type===ct;if(i&&n){let h=await this.lowerBound(e,s,r,n,a,!0),c=[];for(let d=a;d<=h;d++)c.push(d===r.cellCount?r.rightChild:(await this.indexCell(e,s,r,d)).leftChild);this.pager.prefetchLeading(c)}for(let h=a;h<r.cellCount;h++){let c=await this.indexCell(e,s,r,h);if(i&&(yield*this.indexScanFrom(c.leftChild,t,n)),n&&Ft(c.values,n)>0)return;yield c.values}i&&(yield*this.indexScanFrom(r.rightChild,t,n))}async indexSeekLE(e,t){let n,s=e;for(;;){let{page:r,header:a}=await this.pageAt(s),i=0,h=a.cellCount,c=0;for(;i<h;){let d=i+h>>1,f=await this.indexCell(s,r,a,d);Ft(f.values,t)<=0?(n=f.values,i=d+1):(c=f.leftChild,h=d)}if(a.type===Gn)return n;s=i===a.cellCount?a.rightChild:c}}};function Ft(o,e){for(let t=0;t<e.length;t++){let n=o[t],s=e[t];if(typeof n!="number"||s===void 0)throw new Error("SQLite index key is not numeric");if(n!==s)return n<s?-1:1}return 0}function jn({blockSize:o,maxBlocks:e}){if(o!==void 0&&!(Number.isSafeInteger(o)&&o>0))throw new Error(`blockSize must be a positive integer, not ${o}`);if(e!==void 0&&!(Number.isSafeInteger(e)&&e>0))throw new Error(`maxBlocks must be a positive integer, not ${e}`)}var lt=class{blocks=new Map;blockSize;maxBlocks;plan;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,n,s={}){this.source=e,this.pageSize=t,this.fileSize=n;let r=s.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(r/t)*t),this.maxBlocks=s.maxBlocks??256}async read(e,t){let n=await 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(s){if(n+=1,n>=3)throw s;await new Promise(r=>setTimeout(r,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,s=Math.min(this.blockSize,this.fileSize-n),r=this.read(s,n);return this.fetches+=1,this.store(e,r),this.evict(),r}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 s of e){let r=this.blockOf(s);n.has(r)||(n.set(r,t.length),t.push(r))}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(s=>!this.touch(s)).sort((s,r)=>s-r),n=0;for(;n<t.length;){let s=n+1;for(;s<t.length&&t[s]===t[s-1]+1;)s+=1;this.fetchRun(t[n],s-n),n=s}}fetchRun(e,t){let n=e*this.blockSize,s=Math.min(t*this.blockSize,this.fileSize-n),r=this.read(s,n);this.fetches+=1;for(let a=0;a<t;a++){let i=a*this.blockSize;this.store(e+a,r.then(h=>h.subarray(i,i+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)),s=t%this.blockSize;return n.subarray(s,s+this.pageSize)}};var Ue=class o{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){jn(t);let n=await e.read(Math.max(512,t.blockSize??65536),0),s=n.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3"||s.length<100)throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),i=a.getUint16(16),h=i===1?65536:i,c=s[20]??0,d=a.getUint32(56);if(d!==1)throw new Error(`SQLite text encoding ${d} is not UTF-8`);let f=a.getUint32(28);if(f===0||a.getUint32(24)!==a.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let p=f*h,y=new lt(e,h,p,t);y.seed(0,n),y.fetches+=1,y.bytesFetched+=n.length;let m=new ft(y,c),l=new Map;for await(let{values:b}of m.tableScan(1)){let[I,A,x,E,g]=b;typeof I=="string"&&typeof A=="string"&&typeof x=="string"&&typeof E=="number"&&l.set(A,{type:I,name:A,tableName:x,rootPage:E,sql:typeof g=="string"?g:""})}return new o(y,m,l)}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 qt="GBZ-base version 4",pt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${fe(e)}`),this.path=e}},ut=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},gt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${qt}"`),this.found=e}};function Rs(o){if(o.length===1)return o[0];let e=new Uint8Array(o.reduce((n,s)=>n+s.length,0)),t=0;for(let n of o)e.set(n,t),t+=n.length;return e}var _t=3,Le=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 As(o,e){let t=new Le(o),n=0;for(;!t.done;){let s=n+t.next();n=s+t.next(),e.push([s,n])}}function Ns(o){o.sort((n,s)=>n[0]-s[0]);let e=[],t=[];for(let[n,s]of o){let r=t.length-1;r>=0&&n<=t[r]+1?t[r]=Math.max(t[r],s):(e.push(n),t.push(s))}return n=>{let s=0,r=e.length;for(;s<r;){let a=s+r>>1;e[a]<=n?s=a+1:r=a}return s>0&&n<=t[s-1]}}function $s(o,e,t){let n=new Le(e);for(;!n.done;){let s=n.next(),r=n.next(),a=n.next(),i=n.next(),h=n.next();t.push({bin:o,pathHandle:s,pathStart:r,pathEnd:a,snarl:h>0?[i,h]:void 0,node:n.next(),offset:n.next()})}}function Ms(o,e,t){let n=M(o);for(let s of e){let r=new Le(s);for(;!r.done;){let a=r.next(),i=a%2;t.push({node:2*n+i,offset:r.next(),pathHandle:(a-i)/2,orientation:"forward",pathOffset:r.next()})}}}var zt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,s,r){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=s,this.next=r,this.sequenceLen=pn(s)}get id(){return M(this.handle)}get orientation(){return Re(this.handle)}get sequence(){return this.decoded??=un(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 ${this.handle} is empty`);return new et(this.edges,this.bwt)}};function Q(o,e){if(typeof o!="number")throw new Error(`${e} is not a number in the database`);return o}function je(o,e){if(typeof o!="string")throw new Error(`${e} is not text in the database`);return o}function Pe(o,e){if(!(o instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return o}function Qn(o,e){return{handle:o,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:je(e[5],"Paths.sample"),contig:je(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 Tt(o,e){return o.catch(e),o}async function Vn(o){let e=new Map;for await(let{values:t}of o.scan("Tags"))e.set(je(t[0],"Tags.key"),je(t[1],"Tags.value"));return e}var Qe=class o{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,s={blockSize:e.blockSize,maxBlocks:e.maxBlocks},r=await Ue.open(t,s),a=r.objects.has("Tags")?await Vn(r):new Map,i=a.get("version");if(i!==qt)throw new gt(i);for(let d of["Nodes","Paths","ReferenceIndex"])r.rootPage(d);let h=n?await Ue.open(n,s):void 0,c=new o(r,h,a);if(h){for(let l of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!h.objects.has(l))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${l} table`);c.indexTags=await Vn(h);let d=c.indexTags.get("haplotype_index_paths"),f=await c.tag("paths");if(d!==f)throw new Error(`haplotype index was built for ${d??"an unknown number of"} paths but the graph has ${f}`);let p=c.indexTags.get("haplotype_index_nodes"),y=await c.tag("nodes");if(p!==void 0&&p!==y)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${y}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new ut;let m=c.indexTags.get("haplotype_index_format");if(Number(m)!==_t)throw new Error(m===void 0?`the haplotype index predates format ${_t}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${m}; this version of @gmod/gbz-base reads format ${_t}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new zt(e,kn(Pe(t[1],"Nodes.edges")),Pe(t[2],"Nodes.bwt"),Pe(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=Tt(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(Qn(t,n));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?Qn(e,t):void 0}pathsByHandle(){return this.pathMapCache??=Tt(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,s)=>s.name.fragment-n.name.fragment)[0]}async pathsNamed(e){let t=Me($e(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,s)=>n.name.fragment-s.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 a=await this.getPath(e);throw new Error(`${a?`The fragment of ${fe(a.name)} at ${a.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let s=n.pathOffset,r=n.pos;for(;;){let a=await this.getRecord(r.node);if(!a)throw new Error(`Node ${r.node} does not exist in the graph`);s+=a.sequenceLen;let i=a.gbwt().lf(r.offset);if(!i||i.node===0)return s;r=i}}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 s=await this.pathsNamed(e.path);if(s.length===0)throw new pt(Me($e(e.path),0));if(n<=t)return[];let r=s.filter(h=>h.name.fragment<=t).slice(-1),a=s.filter(h=>h.name.fragment>t&&h.name.fragment<n);return(await Promise.all([...r,...a].map(async h=>({path:h,start:h.name.fragment,end:h.name.fragment+await this.pathLength(h.handle)})))).filter(h=>t<h.end)}async subgraphForFragment(e,t){let{sample:n,contig:s,haplotype:r}=e.path.name,a=Math.max(t.start,e.start),i=t.haplotypes??"all";try{let h=await Bt(this,{...t,path:{sample:n,contig:s,haplotype:r},start:a,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(i==="all"||i==="distinct")&&await h.identifyPaths(),h}catch(h){throw h instanceof oe&&h.walkedBp!==void 0?new oe(h.limit,{windowBp:t.end-t.start,walkedBp:a-t.start+h.walkedBp}):h}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(s=>this.subgraphForFragment(s,e)))).map(s=>{if(s.status==="rejected")throw s.reason;return s.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Bt(this,e)}subgraphAtOffset(e){return zn(this,e)}subgraphAroundNodes(e){return qn(this,e)}subgraphBetween(e){return Dn(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,s]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),s);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=Nn(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 s=[],r=[];for await(let a of this.companion.indexScanFrom(e,t,n))r.push(Q(a[a.length-1],`${e} rowid`));r.length>1&&await this.companion.prefetchRows(e,[[Math.min(...r),Math.max(...r)+1]],!0);for(let a of r){let i=await this.companion.byRowid(e,a);i&&s.push(i)}return s}async haplotypeBinData(e,t,n){let s=[],r=[];for(let a of await this.blobRows("HaplotypeBins",[e,t],[e,n])){let i=Q(a[1],"HaplotypeBins.bin");As(Pe(a[3],"HaplotypeBins.nodes"),s),$s(i,Pe(a[4],"HaplotypeBins.strays"),r)}return{listed:Ns(s),strays:r}}async haplotypeAnchorsBetween(e,t,n){let s=[],r=[],a=()=>{let i=s[s.length-1];i&&Ms(i.node,r,i.visits),r=[]};for(let i of await this.blobRows("HaplotypeAnchors",[e,t],[e,n])){let h=Q(i[1],"HaplotypeAnchors.anchor_offset");s[s.length-1]?.anchorOffset!==h&&(a(),s.push({anchorOffset:h,node:Q(i[3],"HaplotypeAnchors.node_handle"),pathOffset:Q(i[4],"HaplotypeAnchors.path_offset"),visits:[]})),r.push(Pe(i[5],"HaplotypeAnchors.visits"))}return a(),s}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 s of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))n.push(this.sampleFromRow(s));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??=Tt((async()=>{let e=[];for await(let{rowid:t,values:n}of this.companion.scan("HaplotypeOverviewRows"))e[t]={sample:je(n[1],"HaplotypeOverviewRows.sample"),haplotype:Q(n[2],"HaplotypeOverviewRows.haplotype")};return e})(),()=>{this.overviewRowsCache=void 0}),this.overviewRowsCache}async overviewChunks(e,t,n,s,r){let a=new Map;for(let i of await this.blobRows(e,[t,n,s],[t,n,r])){let h=Q(i[2],`${e}.chunk`),c=a.get(h)??[];c.push(Pe(i[4],`${e} blob`)),a.set(h,c)}return new Map([...a].map(([i,h])=>[i,Rs(h)]))}async haplotypeOverview(e){let{signal:t}=e;t?.throwIfAborted();let n=l=>this.indexTags.get(`haplotype_index_overview_${l}`);if(!this.index?.has("HaplotypeOverviewClasses")||n("format")!=="1")return;let s=Number(n("bin")),r=Number(n("chunk")),a=Number(n("levels")),i=Math.max(0,Math.min(Math.floor(e.level??0)||0,a-1));if(e.level===void 0&&e.bpPerPixel!==void 0)for(;i+1<a&&s*4**(i+1)<=e.bpPerPixel;)i+=1;let h=s*4**i,[c,d]=await Promise.all([this.getPathFragments(e),this.overviewRows()]);t?.throwIfAborted();let f=Math.ceil(d.length/2),p=[],y=[];for(let l of c){let b=l.end-l.start,I=Math.max(e.start,l.start)-l.start,A=Math.min(e.end,l.end)-l.start,x=Math.floor(I/h),E=Math.floor((A-1)/h),g=Math.floor(x/r),S=Math.floor(E/r),[P,_]=await Promise.all([this.overviewChunks("HaplotypeOverviewBins",l.path.handle,i,g,S),this.overviewChunks("HaplotypeOverviewClasses",l.path.handle,i,g,S)]);t?.throwIfAborted();for(let B=g;B<=S;B++){let D=new Le(P.get(B)??new Uint8Array),C=_.get(B)??new Uint8Array;for(let H=B*r;!D.done;H++){let v=Array.from({length:7},()=>D.next());if(H<x||H>E)continue;p.push({start:l.start+H*h,end:l.start+Math.min((H+1)*h,b),classes:[v[0],v[1],v[2],v[3]],excursions:v[4],variants:v[5],longestExcursion:v[6]});let G=(H-B*r)*f;y.push(C.subarray(G,G+f))}}}if(p.length===0)return;let m=new Uint8Array(p.length*d.length);return y.forEach((l,b)=>{for(let I=0;I<d.length;I++)m[b*d.length+I]=(l[I>>1]??0)>>4*(I%2)&15}),{level:i,bin:h,haplotypes:d,bins:p,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 n?.[0]===e?Q(n[2],"ReferenceIndex rowid"):void 0}async indexedPosition(e,t){let n=await this.indexedRowid(e,t);return n===void 0?void 0:this.indexedRow(n)}async indexedPositionsBetween(e,t,n){let[s,r]=await Promise.all([this.indexedRowid(e,t),this.indexedRowid(e,n)]),a=[];if(s!==void 0&&r!==void 0){await this.sqlite.prefetchRows("ReferenceIndex",[[s,r+1]]);for(let i=s;i<=r;i++)a.push(await this.indexedRow(i))}return a}};function wt(o){let e=/\.gbz\.db$/i;return e.test(o)?o.replace(e,".haplotype-index.db"):void 0}function Ls(o){return hn(o)&&wt(on(o))?cn(o,e=>wt(e)):void 0}function Hs(o){return o instanceof Error&&(/\bHTTP 40[34]\b/.test(o.message)||o.code==="ENOENT")}async function Wn(o,e){let t=Ls(o);if(!t)return{};try{return await Ne(t,e).stat(),{location:t}}catch(n){return Hs(n)?{}:{unreadable:String(n)}}}var Os=5e3,Cs=50*2**20,Dt=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function Bs(o,e){if(o.length<=e)return o;let t=o.length/e;return Array.from({length:e},(n,s)=>o[Math.floor(s*t)])}var Zn=(o,e)=>o.path.some(t=>e.has(t.name)),mt=class{constructor(e,t){this.file=e;this.tabix=t;this.whole=_e({setup:async({signal:e})=>{let{size:t}=await this.file.stat();if(t>Cs)throw new Dt(t);let n=await this.file.readFile({signal:e}),s=new TextDecoder().decode(n[0]===31&&n[1]===139?await bn(n):n);return $t(s)}})}async readIndexed(e,t,n){let s=1/0,r=-1/0;for(let i of t){let h=Number(i);Number.isInteger(h)&&(s=Math.min(s,h),r=Math.max(r,h))}let a=[];return s<=r&&await e.getLines("{node}",s,r+1,{signal:n,lineCallback:i=>{let h=Nt(i);h&&Zn(h,t)&&a.push(h)}}),a}async readsOver(e,{signal:t}={}){let n=this.tabix?await this.readIndexed(this.tabix,e,t):(await this.whole({signal:t})).filter(s=>Zn(s,e));return{records:Bs(n,Os),total:n.length}}};var yt=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},jt=class extends Error{constructor(t,n){super(`the graph is cut on its reference, ${n}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${n} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Xn(o,e){let t=pe(e);return o[t]??o[e.sample]??t}function Fs(o,e){return`${pe(o)}#${o.contig}@${e.start.node}.${e.start.offset}`}function _s({alignment:o,assemblyName:e,refName:t,lane:n}){let{refStart:s,refEnd:r,strand:a,cigar:i}=o;if(!(!o.resolved||r<=s)){let{name:h,hapStart:c,hapEnd:d}=o,f=Fs(h,o),p={uniqueId:f,assemblyName:e,refName:t,start:s,end:r,type:"match",strand:a==="-"?-1:1,CIGAR:i,syntenyId:f,mate:{refName:h.contig,start:c,end:d,assemblyName:n}};return new Mt(p)}}function Ts({pair:o,lane:e,mateLane:t}){let n=`${pe(o.target)}#${o.target.contig}:${o.targetStart}-${o.targetEnd}|${pe(o.query)}#${o.query.contig}:${o.queryStart}-${o.queryEnd}`;return new Mt({uniqueId:n,assemblyName:e,refName:o.target.contig,start:o.targetStart,end:o.targetEnd,type:"match",strand:o.strand==="-"?-1:1,CIGAR:o.cigar,syntenyId:n,identity:o.matches/Math.max(o.columns,1),numMatches:o.matches,blockLen:o.columns,mate:{refName:o.query.contig,start:o.queryStart,end:o.queryEnd,assemblyName:t}})}var zs=12e4;function qs(o,e){let t=new Map;for(let s of o)for(let{name:r,start:a,end:i}of s.walkSpans()){let h=pe(r);if(e.has(h)){let c=`${h}#${r.contig}`;t.set(c,[...t.get(c)??[],[a,i]])}}let n=0;for(let s of t.values()){s.sort((r,a)=>r[0]-a[0]);for(let r=1;r<s.length;r++){let a=s[r][0]-s[r-1][1];a>0&&a<=zs&&(n=Math.max(n,a))}}return n}function Gt(o,e){return o instanceof an&&(o.message=`Zoom in to about ${rn(o.fitsBp)} to see ${e}`),o}var Ut=o=>!("uri"in o)||o.uri!=="",Qt=class extends Sn{constructor(){super(...arguments);this.graph=_e({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),n=this.getConf("haplotypeIndexLocation"),s=Ut(n)?{location:n}:await Wn(t,this.pluginManager),r=s.location,a=await Qe.open({source:Ne(t,this.pluginManager),haplotypeIndex:r?Ne(r,this.pluginManager):void 0}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let h=await Pt(a),c=Xe({configured:this.getConf("referenceSample"),anchorPrefix:ve(this,i),referenceSamples:h});return{db:a,anchor:i,referenceSample:c,referenceSamples:h,unreadableIndex:s.unreadable}}});this.gaf=_e({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),n=this.getConf(["readsIndex","location"]);return Ut(t)?new mt(Ne(t,this.pluginManager),Ut(n)?xn(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,n){let{db:s,referenceSample:r}=await this.graph(n);return vt(s,r,t)}async getHaplotypes(t={}){let{db:n,referenceSamples:s}=await this.graph(t),r=new Map;for(let a of await n.paths()){let i=pe(a.name),h=r.get(i);h?h.contigs.includes(a.name.contig)||h.contigs.push(a.name.contig):r.set(i,{prefix:i,sample:a.name.sample,haplotype:a.name.haplotype,contigs:[a.name.contig],isReference:s.includes(a.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:n,referenceSample:s,referenceSamples:r}=await this.graph(t),a=Et(this),i=[];for(let h of await this.getHaplotypes(t))h.sample!==s&&i.push({name:Xn(a,h),label:h.prefix,group:h.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:s,referenceSamples:r,lanes:i}}async getRefNames(t={}){let{db:n,anchor:s,referenceSample:r}=await this.graph(t),{assemblyName:a}=t,i=a===s?void 0:ve(this,a),h=(await n.paths()).filter(c=>a===s?c.isIndexed&&c.name.sample===r:Ze(pe(c.name),i)).map(c=>c.name.contig);return[...new Set(h)]}keepPredicate(t,n){let s=t===void 0||t.length===0?void 0:t.map(r=>ve(this,r));return s===void 0&&n===void 0?void 0:r=>kt(r,s)&&(n===void 0||Ze(pe(r),n))}async getSubgraph(t,n={}){let{signal:s}=n,{db:r,anchor:a,referenceSample:i,unreadableIndex:h}=await this.graph({signal:s}),{assemblyName:c,refName:d,start:f,end:p}=t;if(c!==a)throw new jt(c,a);let y=await this.referenceQuery(d,{signal:s});if(!y)throw new Error(`${i} has no indexed path ${d} in this graph`);let m=this.keepPredicate(n.haplotypes);if(m!==void 0&&!r.hasHaplotypeIndex)throw new yt(h);return At(r,y,f,p,{context:this.getConf("context"),snarls:n.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:n.signal,keep:m}).catch(l=>{throw Gt(l,"the graph")})}async getReads(t,n={}){let s=await this.gaf(n);return s?s.readsOver(new Set(t),n):{records:[],total:0}}async laneHaplotypes(t,n){let s=ve(this,t);return(await this.getHaplotypes(n)).filter(r=>Ze(r.prefix,s))}async anchorFeatures(t,n){let{db:s}=await this.graph(n),{assemblyName:r,refName:a,start:i,end:h}=t,c=ve(this,n.targetAssemblyName),d=Et(this),f=this.keepPredicate(n.haplotypes,c),p=await this.referenceQuery(a,n),y=this.getConf("nodeLimit");return(p?await It(`Reading graph ${a}:${i.toLocaleString()}-${h.toLocaleString()}`,n.statusCallback,()=>s.getAlignments({path:p,start:i,end:h,context:this.getConf("context"),haplotypes:"all",limit:y,signal:n.signal,keep:f}).catch(l=>{throw Gt(Rt(l,y,h-i)??l,"lanes")})):[]).flatMap(l=>{let b=l.resolved?_s({alignment:l,assemblyName:r,refName:a,lane:Xn(d,l.name)}):void 0;return b===void 0?[]:[b]})}async pairFeatures(t,n,s){let{db:r}=await this.graph(s),{refName:a,start:i,end:h}=t,d=(await Promise.all(n.map(async x=>({pair:x,featureSide:await this.laneHaplotypes(x.queryAssemblyName,s),mateSide:await this.laneHaplotypes(x.targetAssemblyName,s)})))).filter(({featureSide:x,mateSide:E})=>x.length>0&&E.length>0),f=new Set(d.flatMap(({featureSide:x,mateSide:E})=>[...x,...E].map(pe))),p=await this.referenceQuery(a,s),y=this.getConf("nodeLimit"),m=this.getConf("context"),[l]=n,b=(x,E)=>r.getSubgraphs({path:x,start:i,end:h,context:E,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:s.signal,keep:g=>f.has(pe(g))}),I=async x=>{let E=await b(x,m).catch(P=>{throw Gt(Rt(P,y,h-i)??P,"lanes")}),g=qs(E,f),S=Math.ceil(g/2)+2e3;return g>0&&S>m?b(x,S).catch(P=>{if(P instanceof oe)return E;throw P}):E};return(p&&l&&d.length>0?await It(n.length===1?`Reading ${l.queryAssemblyName} against ${l.targetAssemblyName}`:`Reading ${n.length} lane pairs`,s.statusCallback,()=>I(p)):[]).flatMap(x=>d.flatMap(({pair:E,featureSide:g,mateSide:S})=>g.flatMap(P=>S.flatMap(_=>x.pairAlignments({target:P,query:_,bases:!1}).map(B=>Ts({pair:B,lane:E.queryAssemblyName,mateLane:E.targetAssemblyName}))))))}getFeatures(t,n={}){return yn(async s=>{let{db:r,anchor:a,unreadableIndex:i}=await this.graph(n);if(!r.hasHaplotypeIndex)throw new yt(i);if(t.assemblyName===a){let h=In(n),c=h.length>0?await this.pairFeatures(t,h,n):await this.anchorFeatures(t,n);for(let d of c)s.next(d)}s.complete()},n.signal)}};export{jt as HaplotypeWindowError,yt as NoHaplotypeIndexError,ts as NoReferenceSampleError,ns as PairTargetError,Qt as default,_s as fragmentFeature,Xn as laneAssemblyName,Ts as pairFeature,Xe as resolveReferenceSample,qs as widestWalkGap};
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