jbrowse-plugin-graphgenomeviewer 4.0.20 → 4.0.22

package/README.md

@@ -24,14 +24,17 @@ session spec does the same with `loadedTrackId` and `loadedRegion`.
 
 ![KIV-2 walk rows: eight haplotypes, each bar tiled by the kringle unit](img/walk_rows_kiv2.png)
 
+![The KIV-2 cut side by side: GRCh38, HG00097 and HG00133 each followed through the same graph, start to end](img/force_kiv2_facet.png)
+
 ## Features
 
 - Seven layouts: force-directed (Bandage FMMM), ordered, anchored, sample rows,
   walk rows, and sequenceTubeMap's tube map on its own axis or the reference's
 - Genes from the session's annotation track, drawn on the graph
 - Bubbles from `gfatools bubble` or the graph itself, opened level by level
-- gbz-base haplotypes as walks: carriage as node thickness, several walks lifted
-  out at once, each lane coloured by progress, reference position or strand
+- gbz-base haplotypes as walks: carriage as node thickness, walks lifted out as
+  metro-map lanes or side by side, one panel per walk, each shading from its
+  start to its end
 - GAF reads in the tube map, with their mismatches, from a gbz-base track
 
 ## Usage

package/dist/chunks/AddTrackWorkflow-NKKGI6SM.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-NKKGI6SM.js.map

package/dist/chunks/{AddTrackWorkflow-WYRVQYH2.js.map → AddTrackWorkflow-NKKGI6SM.js.map}

@@ -2,6 +2,6 @@
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 }

package/dist/chunks/{GbzBaseSyntenyAdapter-KKSNCZXY.js → GbzBaseSyntenyAdapter-HNETLUW4.js}

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$s=["","A","C","G","T","N"];function Hr(n){let e=n[n.length-1];if(e===void 0)return 0;let t=e,r=0;for(let o=0;o<3&&t%6!==0;o++)t=Math.floor(t/6),r+=1;return 3*(n.length-1)+r}function Gr(n){let e="";for(let t of n){let r=t;for(let o=0;o<3;o++){let s=$s[r%6];if(s==="")return e;r=Math.floor(r/6),e+=s}}return e}var Hs={A:"T",C:"G",G:"C",T:"A",N:"N"};function At(n){let e="";for(let t=n.length-1;t>=0;t--)e+=Hs[n[t]]??"N";return e}function Br(n,e){let t=new Map;if(n!==void 0)for(let r of n.split(";")){let o=r.split(","),[s,i]=o;if(o.length!==2||!s||!i)throw new Error(`Invalid ${e} relationship: ${r}`);let a=t.get(s);a||(a=new Set,t.set(s,a)),a.add(i)}return t}function jr(n){return{name:n.get("pggname"),subgraph:Br(n.get("subgraph"),"subgraph"),translation:Br(n.get("translation"),"translation")}}function Dr(n,e){for(let[t,r]of e){let o=n.get(t);o||(o=new Set,n.set(t,o));for(let s of r)o.add(s)}}function Ur(n,e){let t={name:n,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(n,new Set([e.name])),Dr(t.subgraph,e.subgraph),Dr(t.translation,e.translation)),t}function zr(n){return[...n.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(r=>[e,r]))}function Wr(n){let e=[];n.name!==void 0&&e.push(`H	NM:Z:${n.name}`);for(let[t,r]of zr(n.subgraph))e.push(`H	SG:Z:${t},${r}`);for(let[t,r]of zr(n.translation))e.push(`H	TL:Z:${t},${r}`);return e}async function Qr(n){let e=n.reduce((s,i)=>s+i.length,0),t=new Uint8Array(e),r=0;for(let s of n)t.set(s,r),r+=s.length;let o=await globalThis.crypto.subtle.digest("SHA-256",t);return[...new Uint8Array(o)].map(s=>s.toString(16).padStart(2,"0")).join("")}var Gs="_gbwt_ref";function ge(n,e){return`${n.sample}#${n.haplotype}#${n.contig}[${n.fragment}-${e}]`}var Bs=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,Ds=/^([^#]+?)(?:\[\d+-\d+\])?$/;function zs(n){let e=Bs.exec(n);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=Ds.exec(n);if(t)return{contig:t[1]};throw new Error(`"${n}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Yr(n){return typeof n=="string"?zs(n):n}function Et(n,e){return{sample:n.sample??Gs,contig:n.contig,haplotype:n.haplotype??0,fragment:e}}var js=4096;function kn(n){let e=[];for(let t of n){let r=e[e.length-1];r&&t-r[1]<=js?r[1]=t:e.push([t,t])}return e}var Ee=32768,Vr={mostChosenPaths:32},_n=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let r=this.byNode.get(e.node);r||(r=new Map,this.byNode.set(e.node,r)),r.set(e.offset,t)}},ne=class extends Error{};function nt(n,e,t,r){return n==="forward"?e+t:e-r}function Mn(n,e,t,r){return n==="forward"?e-r:e+t}function Kr(n){return Ne(K(n.handles[n.handles.length-1]),K(n.handles[0]))}function Fe(n){return`${n.pathHandle}:${n.hapStart}:${n.hapEnd}`}async function Xr(n){let{db:e,records:t,signal:r}=n,o=performance.now(),s=()=>{let v=performance.now(),C=v-o;return o=v,C},i={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,seeds:0,pieces:0,sources:{reference:0,sample:0,interval:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,intervals:0,seeds:0,chains:0,twins:0}},a=(v,C)=>{let P=`${v}: ${C}`;i.walks[P]=(i.walks[P]??0)+1},f=await e.haplotypeSampleInterval()??4096,c=new Map,l=async v=>{let C=t.get(v)??c.get(v);if(C)return C;let P=await e.getRecord(v);if(i.graphFetches+=1,!P)throw new Error(`Node record ${v} is missing from the database`);return c.set(v,P),P},p=v=>t.get(v).sequenceLen,u=await e.pathsByHandle(),d=v=>{let C=u.get(v);return C!==void 0&&n.keep(C.name)},h=[],m=new _n,y=new Map,S=new Set,I=new Set,g=async v=>{let C=(await l(v.node)).gbwt().lf(v.offset);return C===void 0||C.node===0?void 0:C},b=async(v,C)=>{let P=(await l(K(v.node))).gbwt().predecessorAt(v.offset);if(P===void 0||C!==void 0&&!C.has(P))return;let G=(await l(P)).gbwt().offsetTo(v);if(G===void 0)throw new Error(`No offset in ${P} leads to ${v.node}:${v.offset}`);return{node:P,offset:G}},x=(v,C,P,G)=>{let j=P.map(ae=>ae.pos.node),X=P.map(ae=>ae.pos.offset),ee=0;for(let ae of j)ee+=p(ae);let te=C==="forward"?P[0].left:P[P.length-1].left,ve=h.length;h.push({pathHandle:v,orientation:C,handles:j,offsets:X,len:ee,hapStart:te,hapEnd:te+ee,canonical:Ne(j[0],j[j.length-1]),source:G});for(let ae of P)m.set(ae.pos,ve);let Oe=y.get(v);return Oe?Oe.push(ve):y.set(v,[ve]),ve},A=async(v,C,P,G)=>{let j=[],X=v;for(;;){r?.throwIfAborted();let te=await b(X.pos,t);if(!te)break;X={pos:te,left:Mn(P,X.left,p(X.pos.node),p(te.node))},j.push(X)}j.reverse();let ee=[v];for(X=v;;){r?.throwIfAborted();let te=await g(X.pos);if(!te||!t.has(te.node))break;X={pos:te,left:nt(P,X.left,p(X.pos.node),p(te.node))},ee.push(X)}return x(C,P,[...j,...ee],G)},M=async(v,C,P,G)=>h[m.get(v.pos)??await A(v,C,P,G)],L=v=>{let C=v.handles[v.handles.length-1];return{pos:{node:C,offset:v.offsets[v.offsets.length-1]},left:v.orientation==="forward"?v.hapEnd-p(C):v.hapStart}},k=v=>{let C=v.handles[0];return{pos:{node:C,offset:v.offsets[0]},left:v.orientation==="forward"?v.hapStart:v.hapEnd-p(C)}},T=await A({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),R=h[T],B=()=>{if(i.fallback!==void 0)return{reference:R,pieces:[],stats:i};let v=new Map;h.forEach((P,G)=>{G!==T&&v.set(Fe(P),[...v.get(Fe(P))??[],P])});let C=[];for(let P of v.values()){let G=new Set;for(let j of P)j.canonical&&!G.has(j.orientation)&&(G.add(j.orientation),C.push(j),i.sources[j.source]+=1)}return i.sources.reference=1,i.pieces=C.length,{reference:R,pieces:C,stats:i}};try{let v=i.spacing;if(v===void 0)throw new ne("the haplotype index has no anchors");let C=Math.floor(n.window.start/v),P=Math.ceil(n.window.end/v),G=w=>w>=0?e.haplotypeAnchor(n.referenceHandle,w*v):Promise.resolve(void 0),[j,X]=await 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Z=ht.get(O).filter(W=>W.pathHandle===E);if(Z.length>0)return{anchor:O,rows:Z}}},De=new Map,dt=(w,E)=>{let O=De.get(w);O[0]=Math.min(O[0],E),O[1]=Math.max(O[1],E)},ut=[],Sn=new Set,Rs=async w=>{let E=yr(Oe,w),O=yr(ae,w);if(!E&&!O)return;let Z=E?.rows??[],W=O?.rows??[],Y=[...Z,...W].map(z=>z.pathOffset);De.set(w,[Math.min(...Y),Math.max(...Y)]);let N=E?.anchor??ee,Q=O?.anchor??ve,$=Q.pathOffset-N.pathOffset,H=d(w),V=!1;for(let z of Z){let U=z.orientation==="forward"?1:-1,fe=W.filter(Ae=>Ae.orientation===z.orientation&&(Ae.pathOffset-z.pathOffset)*U>0).sort((Ae,xt)=>(Ae.pathOffset-xt.pathOffset)*U)[0];if(!fe)continue;let ye=z.node===N.node,Le=fe.node===Q.node,Ie=fe.pathOffset,Te=0;ye&&!Le?Ie+=U*((await l(fe.node)).sequenceLen+$):!ye&&Le&&(Te=$),dt(w,Ie),dt(w,z.pathOffset-U*Te),V=!0,H&&(ut.push({row:z,stopAt:Ie,back:Te,kind:ye===Le?"interval":"inversion"}),Sn.add(w))}if(!V){let z=De.get(w);dt(w,z[0]-$),dt(w,z[1]+$);for(let U of[...Z,...W])if(H&&(U.node===N.node||U.node===K(Q.node))){let fe=U.orientation==="forward"?1:-1;ut.push({row:U,stopAt:U.pathOffset+fe*$,back:0,kind:"one-sided"}),Sn.add(w)}}return V?"paired":"one-sided"},xr=new Set([...ht.values()].flat().map(w=>w.pathHandle)),mt=[...xr].filter(d);if(i.chosenPaths=mt.length,mt.length>Vr.mostChosenPaths)throw new ne(`${mt.length} chosen paths pass the anchors, more than ${Vr.mostChosenPaths}`);for(let w of xr)await Rs(w);let vn=[],In=[];i.scans=kn([...t.keys()].sort((w,E)=>w-E));for(let[w,E]of i.scans)for(let O of await e.haplotypeSamplesInRange(w,E))i.scanRows+=1,t.has(O.node)&&(In.push(O),d(O.pathHandle)&&vn.push(O));if(mt.length===0&&vn.length===0&&[...u.values()].some(w=>n.keep(w.name)))throw new ne("no chosen path passes the anchors or has a sample on the window's nodes");let Ps=new Set(In.map(w=>w.pathHandle).filter(w=>!De.has(w))),Ms=ae[ae.length-1].pathOffset-Oe[Oe.length-1].pathOffset;for(let w of Ps){let E=await e.haplotypeLength(w)??Number.POSITIVE_INFINITY;if(E>Ms+2*Ee)throw new ne(`path ${w} of ${E} 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W=w.orientation,Y=(J,ue)=>W==="forward"?ue-J:J-ue,N=w.pathOffset,Q=w.pathOffset,$,H={node:w.node,offset:w.offset},V=w.pathOffset,z=!1,U=0,fe=0,ye="past the far anchor";for(;H&&(r?.throwIfAborted(),!z&&Y(V,E)<=0&&(z=!0),!(z&&U>Ee));){let J;if(t.has(H.node)){$??=V;let ce=await M({pos:H,left:V},w.pathHandle,W,"interval"),Rn=L(ce);H=Rn.pos,V=Rn.left,J=p(Rn.pos.node),N=Math.min(N,ce.hapStart),Q=Math.max(Q,ce.hapEnd),U=0}else{if(J=(await l(H.node)).sequenceLen,U+=J,fe+=J,fe>br){ye="cap";break}N=Math.min(N,V),Q=Math.max(Q,V+J)}let ue=await g(H);ue&&(V=nt(W,V,J,(await l(ue.node)).sequenceLen)),H=ue}if(!H&&ye!=="cap"&&(ye="endmarker"),a(Z,ye),ye==="cap")throw new ne(`the walk of path ${w.pathHandle} between the anchors reached its cap of ${br} bp`);if(Z==="one-sided"&&ye!=="endmarker")throw new ne(`chosen path ${w.pathHandle} runs on past the stretch from its visit to one anchor without a visit to the other`);let Le=$===void 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Set,ks=h.map((w,E)=>({piece:w,id:E})).filter(({piece:w,id:E})=>E!==T&&!_s(w)).sort((w,E)=>Number(E.piece.canonical)-Number(w.piece.canonical));for(let{piece:w,id:E}of ks)Sr.has(Fe(w))||(Sr.add(Fe(w)),await gt(E,!0),await gt(E,!1));i.ms.chains=s();let En=new Map,Os=w=>{let E=Fe(w),O=En.get(E);O?O.add(w.orientation):En.set(E,new Set([w.orientation]))},wt=0,Cn=()=>{for(;wt<h.length;wt++)wt!==T&&Os(h[wt])};Cn();let yt=w=>(En.get(Fe(w))?.size??0)>1,vr=2*f;for(let w=0;w<h.length;w++){let E=h[w];if(w===T||yt(E)||E.canonical&&!Kr(E))continue;i.twins.tried+=1;let O=E.orientation==="forward"?"reverse":"forward",Z=L(E),W=0,Y;for(;!Y&&W<=vr;){r?.throwIfAborted();let $=await g(Z.pos);if(!$)break;let H=(await l($.node)).sequenceLen,V=nt(E.orientation,Z.left,(await l(Z.pos.node)).sequenceLen,H),z=K($.node);Y=(await e.haplotypeSamplesInRange(z,z)).find(U=>U.pathHandle===E.pathHandle&&U.orientation===O&&U.pathOffset===V),W+=H,Z={pos:$,left:V}}let 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qn(i,r.maxGap??1/0,a,Vs)){let p=[],u=l[0],d=l.at(-1),{flipped:h}=u.run;_t(l,o,s,p,f?(y,S,I,g,b)=>{for(let x of ei(y,S,I,a)){let A=b+S.length;c.push({...x,queryStart:g+x.queryStart,queryEnd:g+x.queryEnd,targetStart:h?A-x.targetEnd:b+x.targetStart,targetEnd:h?A-x.targetStart:b+x.targetEnd,strand:h?"+":"-",edits:h?x.edits.reverse():x.edits,shared:[]})}}:$n),c.push({queryStart:u.run.qs+u.trim,queryEnd:d.run.qe,targetStart:h?d.run.ts:u.run.ts+u.trim,targetEnd:h?u.run.te-u.trim:d.run.te,strand:h?"-":"+",edits:h?p.reverse():p,sharedBases:l.reduce((y,{run:S,trim:I})=>y+S.qe-S.qs-I,0),shared:l.map(({run:y,trim:S})=>[y.qs+S,y.qe])})}return ni(c,o.length,s.length,a).map(({shared:l,...p})=>p).sort((l,p)=>l.queryStart-p.queryStart)}function ho(n){return n.map(([e,t])=>`${t}${e}`).join("")}var Me=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 Bn(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var rt=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Bn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Bn(e[s],e[a])&&(a=s),i<e.length&&Bn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function oi(n){let e=new Int32Array(n.length),t=new Int32Array(n.length);return n.forEach(([r,o],s)=>{e[s]=r,t[s]=o}),{pathAt:e,refAt:t,count:n.length}}function si(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]>e?r=o:t=o+1}return n[t]}function $e(n){return`${n.node}:${n.offset}`}function ii(n,e){let t=e.identity.hapStart-n.identity.hapEnd,r=n.strand==="+"?e.refStart-n.refEnd:n.refStart-e.refEnd;return n.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function ai(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);uo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)se(s,c,l);let i=n.identity.walkForward,[a,f]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function fi(n){if(n.some(o=>o.weight!==void 0))return n;let e=new Map;n.forEach((o,s)=>{if(o.identity){let i=e.get(o.identity.pathHandle);i?i.push(s):e.set(o.identity.pathHandle,[s])}});let t=new Map,r=new Set;for(let o of e.values()){o.sort((a,f)=>n[a].identity.hapStart-n[f].identity.hapStart);let s=o[0],i=n[s];for(let a of o.slice(1)){let f=n[a],c=ii(i,f);c?(i=ai(i,f,c),r.add(a)):(t.set(s,i),s=a,i=f)}t.set(s,i)}return n.flatMap((o,s)=>r.has(s)?[]:[t.get(s)??o])}function kt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var ci=32768;function li(n){let e=[...n].sort((r,o)=>r-o),t=[];for(let r of e){let o=t[t.length-1];o&&r-o[1]<=ci?o[1]=r:t.push([r,r])}return t}var Tt=class{records=new Map;paths=[];twinStarts=new Set;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;stats={orderedAlignments:0,lcsAlignments: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}get nodeCount(){return this.records.size/2}get pathCount(){return 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(me(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 Me(this.limit);let t=await this.db.getRecord(me(e,"forward")),r=await this.db.getRecord(me(e,"reverse"));if(!t||!r)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(r.handle,r)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),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 ${ge(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${ge(t.name,t.name.fragment)} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`Path ${ge(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(_(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${ge(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=_(e);await this.ensureNode(o);let s=this.record(e),i=Ue(e),a=new rt;return a.push(t,o,bt(i)),a.push(s.sequenceLen-t-1,o,St(i)),this.insertContext(a,r)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,r){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let c=await this.db.indexedPositionsBetween(e,t,r),l=li(c.map(p=>p.pos.node));await Promise.all(l.map(([p,u])=>this.db.prefetchRecords(p,u+2)))}}return o}async aroundInterval(e,t,r){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,r)}catch(o){throw o instanceof Me&&o.windowBp===void 0?new Me(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new rt;for(;;){let f=_(o.node),c=Ue(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,bt(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,St(c));break}a.push(0,f,St(c));let u=l.gbwt().lf(o.offset);if(!u)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=u,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new rt;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,o=new Set;for(let i of this.records.keys())o.add(_(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Lr(f);if(!r.has(`${a}:${l}`)){let d=this.record(me(a,Tr(f))),h=i+d.sequenceLen-1;h<=t&&e.push(h,a,l)}let p=this.record(me(a,Nr(f))),u=i+1;if(u<=t)for(let d of p.successors()){let h=_(d),m=bt(Ue(d));r.has(`${h}:${m}`)||e.push(u,h,m)}}for(let i of o)this.records.delete(me(i,"forward")),this.records.delete(me(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,K(t)],o=new Set([_(e),_(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=_(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=_(f);o.has(c)||(r.push(f,K(f)),o.add(c))}}return s}async extractSnarls(e){let t=0;for(let[r,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(r,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?We(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(o=>this.hasHandle(o));return r===void 0?!1:t.length>1||this.record(K(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let o=this.records.get(r);if(o)return o;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(K(l))).successors().length>1},r=async f=>{let c=await e(K(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[K(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=_(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(me(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((x,A)=>i.set(x,A));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let x=0;x<s;x++){let A=this.record(o[x]),M=A.gbwt().decompressArrays();f[x]=A.sequenceLen,c.push(M),a[x+1]=a[x]+M.nodes.length}let l=a[s],p=new Int32Array(l),u=new Int32Array(l),d=new Uint8Array(l);for(let x=0;x<s;x++){let A=c[x];p.set(A.nodes,a[x]),u.set(A.offsets,a[x])}c.length=0;for(let x=0;x<l;x++){let A=i.get(p[x]);A===void 0?p[x]=-1:(p[x]=A,d[a[A]+u[x]]=1)}let h=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,y,S=(x,A,M)=>{let L=[],k=0,T=0,R=-1,B=x,v=A;for(;;){B===h&&v===m&&(R=k),M&&(M.push(o[B]),L.push(v)),k+=1,T+=f[B];let C=a[B]+v,P=p[C];if(P<0)break;v=u[C],B=P}return{offsets:L,len:T,refAt:R,last:B}},I=(x,A,M,L)=>{L>=0&&(this.refId=this.paths.length,y=L),this.paths.push({path:x,offsets:A,len:M,weight:void 0,identity:void 0})},g=new Int32Array(s),b=h!==void 0&&q(o[h]);for(let x=0;x<s;x++){let A=o[x];if(!q(A)){let M=a[x],L=a[x+1]-M;for(let k=0;k<L;k++)if(d[M+k]===0){let T=[],{offsets:R,len:B,refAt:v,last:C}=S(x,k,T),P=o[C];if(v>=0||Ne(A,P)){if(I(T,R,B,v),!q(P)){let G=i.get(K(P));g[G]=g[G]+1}}else this.twinStarts.add($e({node:A,offset:k}))}}}for(let x=0;x<s;x++){let A=o[x];if(q(A)){let M=a[x],L=a[x+1]-M,k=0;for(let R=0;R<L;R++)d[M+R]===0&&(k+=1);let T=!b&&k===g[x];for(let R=0;R<L;R++)if(d[M+R]===0){let B=T?void 0:S(x,R,void 0);if(B&&(B.refAt>=0||Ne(A,o[B.last]))){let v=[],{offsets:C,len:P,refAt:G}=S(x,R,v);I(v,C,P,G)}else this.twinStarts.add($e({node:A,offset:R}))}}}if(r){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let x=this.paths[this.refId],A=r.nodeOffset;for(let L of x.path.slice(0,y))A+=this.record(L).sequenceLen;let M=r.seqOffset-A;this.refInterval=[M,M+x.len],x.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:M,hapEnd:M+x.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((o,s)=>Dn(o.path,s.path)||o.len-s.len);let t=[],r;for(let o of this.paths){let s=t[t.length-1];s&&Dn(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&Dn(o.path,e)===0&&(r=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=r}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of r)for(let i of s.path)o.add(_(i));for(let s of[...this.records.keys()])o.has(_(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async extractChosenPaths(e,t,r){this.clearPaths();let o=e.position.seqOffset,s=await Xr({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},keep:r,signal:this.signal,prefetchReferenceRange:(c,l,p)=>this.prefetchReferenceRange(c,l,p)});if(this.stats.keep=s.stats,s.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),a=c=>({path:c.handles,offsets:c.offsets,len:c.len,weight:void 0,identity:{pathHandle:c.pathHandle,name:c===s.reference?e.name:i.get(c.pathHandle).name,orientation:c.orientation,hapStart:c.hapStart,hapEnd:c.hapEnd}}),f=[s.reference,...s.pieces].sort(Zr);return this.paths=f.map(a),this.refId=f.indexOf(s.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[s.reference.hapStart,s.reference.hapEnd],!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=kn(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[h,m]of t)for(let y of await this.db.haplotypeSamplesInRange(h,m))r.set($e(y),y);let o=h=>{let m=0,y=t.length-1;for(;m<y;){let I=m+y+1>>1;t[I][0]<=h?m=I:y=I-1}let S=t[m];return S[0]<=h&&h<=S[1]},s=new Map;this.paths.forEach((h,m)=>{h.path.length>0&&m!==this.refId&&s.set($e(kt(h,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((h,m)=>{m!==this.refId&&i.fragmentLengths.push(h.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=h=>(i.graphLookups+=1,a(h)),c=async(h,m)=>{if(o(h.node))return r.get($e(h));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(h.node,h.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async h=>{let m=l.get(h);if(!m){let y=await this.db.getPath(h);if(!y)throw new Error(`Path ${h} is missing from the database`);m=y.name,l.set(h,m)}return m},u=(h,m,y)=>h.orientation==="forward"?{pathHandle:h.pathHandle,orientation:"forward",base:h.pathOffset-m}:{pathHandle:h.pathHandle,orientation:"reverse",base:h.pathOffset+m+y},d=(h,m)=>h.orientation==="forward"?{pathHandle:h.pathHandle,orientation:"forward",base:h.hapStart-m}:{pathHandle:h.pathHandle,orientation:"reverse",base:h.hapEnd+m};for(let h=0;h<this.paths.length;h++){let m=this.paths[h];if(h===this.refId||m.identity)continue;let y=[],S=new Set,I={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(I);let g,b=0,x=h,A;for(;g===void 0;){if(this.signal?.throwIfAborted(),x!==void 0){if(S.has(x)){I.end="cycle";break}S.add(x);let R=this.paths[x];y.push({index:x,startBp:b}),I.fragments+=1;let B=b;for(let C=0;C<R.path.length;C++){let P=kt(R,C),G=r.get($e(P)),j=this.record(P.node).sequenceLen;if(G){g=u(G,B,j);break}B+=j}if(b+=R.len,g){I.end="in-fragment sample";break}let v=kt(R,R.path.length-1);A=this.record(v.node).gbwt().lf(v.offset),x=void 0}if(A===void 0||A.node===0){I.end="endmarker";break}let M=$e(A),L=s.get(M);if(L!==void 0){let R=this.paths[L].identity;if(R){g=d(R,b),I.end="identified sibling";break}x=L;continue}this.records.has(A.node)&&(I.reentries+=1),this.twinStarts.has(M)&&(I.twinLandings+=1);let k=await c(A,I),T=await f(A.node);if(k){g=u(k,b,T.sequenceLen),I.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,I.steps+=1,b-y[y.length-1].startBp>4*e+4*T.sequenceLen){I.end="bound";break}b+=T.sequenceLen,A=T.gbwt().lf(A.offset)}if(g){I.pathHandle=g.pathHandle;let M=await p(g.pathHandle);for(let{index:L,startBp:k}of y){let T=this.paths[L];T.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:M,orientation:"forward",hapStart:g.base+k,hapEnd:g.base+k+T.len}:{pathHandle:g.pathHandle,name:M,orientation:"reverse",hapStart:g.base-k-T.len,hapEnd:g.base-k}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,o)=>{let s=t.get(r);s?s.push(o):t.set(r,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,o)=>{t.push(t[o]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=si(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),se(r,"M",i),uo(r,o-i-a,s-i-a),se(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),o=0;for(let s of e)r.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=r??oi(Jr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,u,d,h)=>{p===u?se(s,"D",i[h]-i[d]):d===h?se(s,"I",this.pathLen(e.slice(p,u))):this.align(e.slice(p,u),t.slice(d,h),s)},f=0,c=0,l=0;for(let p=0;p<o.count;p++){let u=o.pathAt[p],d=o.refAt[p];(c!==u||l!==d)&&a(c,u,l,d);let h=this.record(e[u]).sequenceLen;se(s,"M",h),f+=h,c=u+1,l=d+1}return a(c,e.length,l,t.length),{edits:s,matched:f}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(Fr(r))o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else{let s=t.path.map(f=>K(f)).reverse(),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,r).edits,flipped:!0};else{let 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0:{pathHandle:d.pathHandle,name:d.name,hapStart:d.name.fragment+d.hapStart,hapEnd:d.name.fragment+d.hapEnd,walkForward:d.orientation==="forward"}})}),fi(o).map(s=>{let{edits:i,identity:a,...f}=s,c={...f,cigar:hi(i)};return a?{...c,resolved:!0,name:a.name,label:ge({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...c,resolved:!1}})}pairAlignments(e){let{target:t,query:r,...o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Lt(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),f=r?i(r):l=>!a(l),c=l=>this.record(me(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>f(p.name)).flatMap(p=>po(p.steps,l.steps,c,o).map(u=>({query:p.name,queryStart:p.start+u.queryStart,queryEnd:p.start+u.queryEnd,strand:u.strand,target:l.name,targetStart:l.start+u.targetStart,targetEnd:l.start+u.targetEnd,cigar:ho(u.edits),matches:u.edits.reduce((d,[h,m])=>d+(h==="="?m:0),0),columns:u.edits.reduce((d,[,h])=>d+h,0),sharedBases:u.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=me(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&We(o,s)&&t.push([r==="reverse"?1:0,_(s),q(s)?1:0])}return t.sort((r,o)=>r[0]-o[0]||r[1]-o[1]||r[2]-o[2]),t.filter((r,o)=>o===0||r[0]!==t[o-1][0]||r[1]!==t[o-1][1]||r[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!q(r)){let o=_(r),s=`S	${o}	${this.record(r).sequence}
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C=v.handles[v.handles.length-1];return{pos:{node:C,offset:v.offsets[v.offsets.length-1]},left:v.orientation==="forward"?v.hapEnd-p(C):v.hapStart}},k=v=>{let C=v.handles[0];return{pos:{node:C,offset:v.offsets[0]},left:v.orientation==="forward"?v.hapStart:v.hapEnd-p(C)}},T=await A({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),R=h[T],B=()=>{if(i.fallback!==void 0)return{reference:R,pieces:[],stats:i};let v=new Map;h.forEach((P,G)=>{G!==T&&v.set(Fe(P),[...v.get(Fe(P))??[],P])});let C=[];for(let P of v.values()){let G=new Set;for(let j of P)j.canonical&&!G.has(j.orientation)&&(G.add(j.orientation),C.push(j),i.sources[j.source]+=1)}return i.sources.reference=1,i.pieces=C.length,{reference:R,pieces:C,stats:i}};try{let v=i.spacing;if(v===void 0)throw new ne("the haplotype index has no anchors");let C=Math.floor(n.window.start/v),P=Math.ceil(n.window.end/v),G=w=>w>=0?e.haplotypeAnchor(n.referenceHandle,w*v):Promise.resolve(void 0),[j,X]=await Promise.all([Promise.all([0,1,2].map(w=>G(C-w))),Promise.all([0,1,2,3].map(w=>G(P+w)))]),ee=j[0],te=X.slice(0,2).findIndex(w=>w!==void 0&&w.pathOffset>=n.window.end),ve=X[te];if(!ee)throw new ne("the haplotype index has no anchor before the window");if(!ve)throw new ne("the haplotype index has no anchor after the window");i.anchors=[ee.pathOffset,ve.pathOffset];let Oe=j.filter(w=>w!==void 0),ae=X.slice(te,te+3).filter(w=>w!==void 0),Es=w=>{let E=w-w%2;return e.haplotypeSamplesInRange(E,E+1)},ht=new Map,bn=[...Oe,...ae],Cs=await Promise.all(bn.map(w=>Es(w.node)));if(bn.forEach((w,E)=>ht.set(w,Cs[E])),i.anchorsRead=bn.length,!ht.get(ee).some(w=>w.pathHandle===n.referenceHandle&&w.orientation==="forward"&&w.pathOffset===ee.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${ee.pathOffset} (node ${_(ee.node)}); it does not match this graph`);let yr=(w,E)=>{for(let O of w){let Z=ht.get(O).filter(W=>W.pathHandle===E);if(Z.length>0)return{anchor:O,rows:Z}}},De=new Map,dt=(w,E)=>{let O=De.get(w);O[0]=Math.min(O[0],E),O[1]=Math.max(O[1],E)},ut=[],Sn=new Set,Rs=async w=>{let E=yr(Oe,w),O=yr(ae,w);if(!E&&!O)return;let Z=E?.rows??[],W=O?.rows??[],Y=[...Z,...W].map(z=>z.pathOffset);De.set(w,[Math.min(...Y),Math.max(...Y)]);let N=E?.anchor??ee,Q=O?.anchor??ve,$=Q.pathOffset-N.pathOffset,H=d(w),V=!1;for(let z of Z){let U=z.orientation==="forward"?1:-1,fe=W.filter(Ae=>Ae.orientation===z.orientation&&(Ae.pathOffset-z.pathOffset)*U>0).sort((Ae,xt)=>(Ae.pathOffset-xt.pathOffset)*U)[0];if(!fe)continue;let ye=z.node===N.node,Le=fe.node===Q.node,Ie=fe.pathOffset,Te=0;ye&&!Le?Ie+=U*((await l(fe.node)).sequenceLen+$):!ye&&Le&&(Te=$),dt(w,Ie),dt(w,z.pathOffset-U*Te),V=!0,H&&(ut.push({row:z,stopAt:Ie,back:Te,kind:ye===Le?"interval":"inversion"}),Sn.add(w))}if(!V){let z=De.get(w);dt(w,z[0]-$),dt(w,z[1]+$);for(let U of[...Z,...W])if(H&&(U.node===N.node||U.node===K(Q.node))){let fe=U.orientation==="forward"?1:-1;ut.push({row:U,stopAt:U.pathOffset+fe*$,back:0,kind:"one-sided"}),Sn.add(w)}}return V?"paired":"one-sided"},xr=new Set([...ht.values()].flat().map(w=>w.pathHandle)),mt=[...xr].filter(d);if(i.chosenPaths=mt.length,mt.length>Vr.mostChosenPaths)throw new ne(`${mt.length} chosen paths pass the anchors, more than ${Vr.mostChosenPaths}`);for(let w of xr)await Rs(w);let vn=[],In=[];i.scans=kn([...t.keys()].sort((w,E)=>w-E));for(let[w,E]of i.scans)for(let O of await e.haplotypeSamplesInRange(w,E))i.scanRows+=1,t.has(O.node)&&(In.push(O),d(O.pathHandle)&&vn.push(O));if(mt.length===0&&vn.length===0&&[...u.values()].some(w=>n.keep(w.name)))throw new ne("no chosen path passes the anchors or has a sample on the window's nodes");let Ps=new Set(In.map(w=>w.pathHandle).filter(w=>!De.has(w))),Ms=ae[ae.length-1].pathOffset-Oe[Oe.length-1].pathOffset;for(let w of Ps){let E=await e.haplotypeLength(w)??Number.POSITIVE_INFINITY;if(E>Ms+2*Ee)throw new ne(`path ${w} of ${E} bp has a sample on the window's nodes and no visit to the anchors`);if(d(w)){let O=(await e.getPath(w))?.fwStart;if(!O)throw new Error(`Path ${w} is missing from the database`);ut.push({row:{node:O.node,offset:O.offset,pathHandle:w,orientation:"forward",pathOffset:0},stopAt:E,back:0,kind:"whole"})}}for(let w of De.keys())if(d(w)&&!Sn.has(w))throw new ne(`chosen path ${w} has no walk from its visits to the anchors`);for(let w of In){let E=De.get(w.pathHandle);if(E&&(w.pathOffset<E[0]-Ee||w.pathOffset>E[1]+Ee))throw new ne(`path ${w.pathHandle} has a sample at ${w.pathOffset} on the window's nodes far from its anchor visits at ${E[0]}-${E[1]}`)}i.ms.scan=s();let An=new Map;await n.prefetchReferenceRange(n.referenceHandle,ee.pathOffset,ve.pathOffset+1);let br=8*v+2*(n.window.end-n.window.start);for(let{row:w,stopAt:E,back:O,kind:Z}of ut){let W=w.orientation,Y=(J,ue)=>W==="forward"?ue-J:J-ue,N=w.pathOffset,Q=w.pathOffset,$,H={node:w.node,offset:w.offset},V=w.pathOffset,z=!1,U=0,fe=0,ye="past the far anchor";for(;H&&(r?.throwIfAborted(),!z&&Y(V,E)<=0&&(z=!0),!(z&&U>Ee));){let J;if(t.has(H.node)){$??=V;let ce=await M({pos:H,left:V},w.pathHandle,W,"interval"),Rn=L(ce);H=Rn.pos,V=Rn.left,J=p(Rn.pos.node),N=Math.min(N,ce.hapStart),Q=Math.max(Q,ce.hapEnd),U=0}else{if(J=(await l(H.node)).sequenceLen,U+=J,fe+=J,fe>br){ye="cap";break}N=Math.min(N,V),Q=Math.max(Q,V+J)}let ue=await g(H);ue&&(V=nt(W,V,J,(await l(ue.node)).sequenceLen)),H=ue}if(!H&&ye!=="cap"&&(ye="endmarker"),a(Z,ye),ye==="cap")throw new ne(`the walk of path ${w.pathHandle} between the anchors reached its cap of ${br} bp`);if(Z==="one-sided"&&ye!=="endmarker")throw new ne(`chosen path ${w.pathHandle} runs on past the stretch from its visit to one anchor without a visit to the other`);let Le=$===void 0?0:Ee-Y(w.pathOffset,$),Ie={pos:{node:w.node,offset:w.offset},left:w.pathOffset},Te=0,Ae=O;for(;Le>0||Ae>0;){r?.throwIfAborted();let J=await b(Ie.pos);if(!J)break;let ue=Mn(W,Ie.left,(await l(Ie.pos.node)).sequenceLen,(await l(J.node)).sequenceLen);if(t.has(J.node)){let ce=await M({pos:J,left:ue},w.pathHandle,W,"interval");Ie=k(ce),N=Math.min(N,ce.hapStart),Q=Math.max(Q,ce.hapEnd),Le=Ee,Te=0,Ae-=ce.len}else{let ce=(await l(J.node)).sequenceLen;if(Te+=ce,Te>Le&&Ae<=0)break;Ae-=ce,Ie={pos:J,left:ue},N=Math.min(N,ue),Q=Math.max(Q,ue+ce)}}let xt=An.get(w.pathHandle);xt?xt.push([N,Q]):An.set(w.pathHandle,[[N,Q]])}let _s=w=>(An.get(w.pathHandle)??[]).some(([E,O])=>E<=w.hapStart&&w.hapEnd<=O);i.ms.intervals=s();for(let w of vn)m.get(w)===void 0&&!(y.get(w.pathHandle)??[]).some(E=>{let O=h[E];return O.canonical&&!Kr(O)&&O.hapStart<=w.pathOffset&&w.pathOffset<O.hapEnd})&&(i.seeds+=1,await A({pos:{node:w.node,offset:w.offset},left:w.pathOffset},w.pathHandle,w.orientation,"sample"));i.ms.seeds=s();let gt=async(w,E)=>{let O=E?S:I,Z=E?I:S,W=w;for(;;){if(O.has(W))return;O.add(W);let Y=h[W],N=E?L(Y):k(Y),Q=0,$;for(;$===void 0;){r?.throwIfAborted();let H=E?await g(N.pos):await b(N.pos);if(!H){$="endmarker";break}let V=(await l(N.pos.node)).sequenceLen,z=(await l(H.node)).sequenceLen,U=E?nt(Y.orientation,N.left,V,z):Mn(Y.orientation,N.left,V,z);if(t.has(H.node)){let fe=m.get(H);fe===void 0?(W=await A({pos:H,left:U},Y.pathHandle,Y.orientation,"chain"),Z.add(W),$="landed"):(Z.add(fe),$="merge")}else Q>Ee?$="bound":(Q+=z,N={pos:H,left:U})}if(a("chain",$),$!=="landed")return}};await Promise.all([n.prefetchReferenceRange(n.referenceHandle,Math.max(0,R.hapStart-Ee),R.hapStart),n.prefetchReferenceRange(n.referenceHandle,R.hapEnd,R.hapEnd+Ee)]);let Sr=new Set,ks=h.map((w,E)=>({piece:w,id:E})).filter(({piece:w,id:E})=>E!==T&&!_s(w)).sort((w,E)=>Number(E.piece.canonical)-Number(w.piece.canonical));for(let{piece:w,id:E}of ks)Sr.has(Fe(w))||(Sr.add(Fe(w)),await gt(E,!0),await gt(E,!1));i.ms.chains=s();let En=new Map,Os=w=>{let E=Fe(w),O=En.get(E);O?O.add(w.orientation):En.set(E,new Set([w.orientation]))},wt=0,Cn=()=>{for(;wt<h.length;wt++)wt!==T&&Os(h[wt])};Cn();let yt=w=>(En.get(Fe(w))?.size??0)>1,vr=2*f;for(let w=0;w<h.length;w++){let E=h[w];if(w===T||yt(E)||E.canonical&&!Kr(E))continue;i.twins.tried+=1;let O=E.orientation==="forward"?"reverse":"forward",Z=L(E),W=0,Y;for(;!Y&&W<=vr;){r?.throwIfAborted();let $=await g(Z.pos);if(!$)break;let H=(await l($.node)).sequenceLen,V=nt(E.orientation,Z.left,(await l(Z.pos.node)).sequenceLen,H),z=K($.node);Y=(await e.haplotypeSamplesInRange(z,z)).find(U=>U.pathHandle===E.pathHandle&&U.orientation===O&&U.pathOffset===V),W+=H,Z={pos:$,left:V}}let N=Y&&{pos:{node:Y.node,offset:Y.offset},left:Y.pathOffset},Q=0;for(;N&&!yt(E)&&Q<=vr+E.len;){if(r?.throwIfAborted(),t.has(N.pos.node)){let $=await M(N,E.pathHandle,O,"twin"),H=h.indexOf($);await gt(H,!0),await gt(H,!1),Cn(),N=L($)}if(!yt(E)){let $=(await l(N.pos.node)).sequenceLen;Q+=$;let H=await g(N.pos);N=H?{pos:H,left:nt(O,N.left,$,(await l(H.node)).sequenceLen)}:void 0}}if(Cn(),!yt(E))throw new ne(`piece ${Fe(E)} was found in one orientation where extractPaths keeps the other`);i.twins.found+=1}i.ms.twins=s()}catch(v){if(!(v instanceof ne))throw v;i.fallback=v.message}return B()}function Zr(n,e){let t=n.handles[0],r=e.handles[0];return Number(q(t))-Number(q(r))||t-r||n.offsets[0]-e.offsets[0]}function Ct(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]<e?t=o+1:r=o}return t}var Rt=class{ending;tree;constructor(e){this.ending=new Float64Array(e),this.tree=new Int32Array(e+1).fill(-1)}bestBefore(e){let t=-1;for(let r=e;r>0;r-=r&-r){let 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a=this.occurrences.get(this.a[i]);a&&(s+=Ct(a,o)-Ct(a,r))}return s}sweep(e,t,r,o,s,i,a){for(let f=e;f!==t;f+=r){let c=this.occurrences.get(this.a[f]);if(!c)continue;let l=this.weight(this.a[f]),p=Ct(c,o),u=Ct(c,s);for(let d=0;d<u-p;d++){let h=r===1?c[u-1-d]-o:s-1-c[p+d],m=i.bestBefore(h),y=(m===-1?0:i.ending[m])+l;if(y>i.ending[h]&&(i.raise(h,y),a)){let S=a.count++;a.row[S]=f,a.column[S]=h,a.previous[S]=m===-1?-1:a.endingMatch[m],a.endingMatch[h]=S}}}}chain(e,t,r,o,s){let i=new Rt(o-r),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-r),count:0};this.sweep(e,t,1,r,o,i,a);let f=i.bestBefore(o-r);if(f===-1)return;this.total+=i.ending[f];let c=[];for(let l=a.endingMatch[f];l!==-1;l=a.previous[l])c.push([a.row[l],r+a.column[l]]);for(let l=c.length-1;l>=0;l--)this.pairs.push(c[l])}frontier(e,t,r,o,s){let i=new Rt(s-o);this.sweep(e,t,r,o,s,i);let a=new Float64Array(s-o+1);for(let f=0;f<s-o;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,r,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),f=this.frontier(r-1,t-1,-1,o,s),c=0,l=-1;for(let p=0;p<=i;p++){let u=a[p]+f[i-p];u>l&&(l=u,c=p)}return o+c}};function Jr(n,e,t){let r=new On(n,e,t);return r.solve(0,n.length,0,e.length),[r.pairs,r.total]}var Us=100,Nn=4e6,Ws=5e3,oe=15,Qs=64,Ys=8,io=1,Fn=-4,re=-6,Ce=-1,Qe=-(2**30),Mt=0,Ln=1,ao=2;function qe(n,e,t){let r=n.at(-1);t>0&&(r?.[0]===e?r[1]+=t:n.push([e,t]))}function Pt(n,e,t){return n>=t&&n>=e?Mt:t>=e?ao:Ln}function fo(n,e,t){let r=n.length,o=e.length,s=o+1,i=new Uint8Array((r+1)*s),a=new Int32Array(s).fill(Qe),f=new Int32Array(s).fill(Qe),c=new Int32Array(s).fill(Qe);a[0]=0;for(let h=1;h<=o;h++)c[h]=re+(h-1)*Ce,i[h]=(h===1?Mt:ao)<<4;for(let h=1;h<=r;h++){let m=new Int32Array(s).fill(Qe),y=new Int32Array(s).fill(Qe),S=new Int32Array(s).fill(Qe);y[0]=re+(h-1)*Ce,i[h*s]=(h===1?Mt:Ln)<<2;let I=n.charCodeAt(h-1);for(let g=1;g<=o;g++){let b=Pt(a[g-1],f[g-1],c[g-1]);m[g]=Math.max(a[g-1],f[g-1],c[g-1])+(I===e.charCodeAt(g-1)?io:Fn);let x=Pt(a[g]+re,f[g]+Ce,c[g]+re);y[g]=Math.max(a[g]+re,f[g]+Ce,c[g]+re);let A=Pt(m[g-1]+re,y[g-1]+re,S[g-1]+Ce);S[g]=Math.max(m[g-1]+re,y[g-1]+re,S[g-1]+Ce),i[h*s+g]=b|x<<2|A<<4}a=m,f=y,c=S}let l=[],p=r,u=o,d=Pt(a[o],f[o],c[o]);for(;p>0||u>0;){let h=i[p*s+u]>>2*d&3;d===Mt?(l.push(n[p-1]===e[u-1]?"=":"X"),p-=1,u-=1):d===Ln?(l.push("I"),p-=1):(l.push("D"),u-=1),d=h}for(let h of l.reverse())qe(t,h,1)}function Vs(n,e){let t=Math.abs(n-e);return(t===0?0:Math.min(-re-(t-1)*Ce,-re+10*Math.log2(t)))+(Math.min(n,e)>0?-Fn:0)}function co(n,e){let t=Math.abs(n-e);return t===0?0:.01*oe*t+.5*Math.log2(t)}function eo(n,e,t){return{qs:n.qs+e,qe:n.qs+t,ts:n.flipped?n.te-t:n.ts+e,te:n.flipped?n.te-e:n.ts+t,flipped:n.flipped}}function Ks(n,e,t){let r=n.qe-n.qs,o=[];for(let[a,f]of e){let c=Math.max(0,a-n.qs),l=Math.min(r,f-n.qs);c<l&&o.push([c,l])}for(let[a,f]of t){let 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g=u;g>=0;g=l[g])d.push({run:f[g],trim:p[g]});if(d.reverse(),d.reduce((g,{run:b,trim:x})=>g+b.qe-b.qs-x,0)<t)break;s.push(d);let m=d[0],y=d.at(-1),{flipped:S}=m.run,I=S?a.flipped:a.forward;I.query.push([m.run.qs+m.trim,y.run.qe]),I.target.push(S?[y.run.ts,m.run.te-m.trim]:[m.run.ts+m.trim,y.run.te]);for(let{run:g,trim:b}of d)i.query.push([g.qs+b,g.qe]),i.target.push(g.flipped?[g.ts,g.te-b]:[g.ts+b,g.te]);f=f.flatMap(g=>{let b=g.flipped?a.flipped:a.forward;return Ks(g,[...i.query,...b.query],[...i.target,...b.target])}).sort((g,b)=>g.qs-b.qs||g.ts-b.ts)}return s}function Tn(n,e){let t=new Map;for(let s=0;s+oe<=e.length;s++){let i=e.slice(s,s+oe),a=t.get(i);a?a.push(s):t.set(i,[s])}let r=[],o=new Map;for(let s=0;s+oe<=n.length;s++){let i=t.get(n.slice(s,s+oe));if(i&&i.length<=Qs)for(let a of i){let f=a-s,c=o.get(f);if(c&&s<=c.qe)c.qe=s+oe,c.te=a+oe;else{let l={qs:s,qe:s+oe,ts:a,te:a+oe,flipped:!1};o.set(f,l),r.push(l)}}}return r}function 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o=[];if(n.length*e.length<=Nn)fo(n,e,t);else{let s=qn(Xs(n,e),1/0,Math.max(r,oe),co),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>Js(a,n,e)),i){let a=(l,p,u,d,h)=>{o.some(y=>d<y.queryEnd&&y.queryStart<d+l.length||h<y.targetEnd&&y.targetStart<h+p.length)?lo(l,p,u):Hn(l,p,u)},f=i[0].run,c=i.at(-1).run;a(n.slice(0,f.qs),e.slice(0,f.ts),t,0,0),_t(i,n,e,t,a),a(n.slice(c.qe),e.slice(c.te),t,c.qe,c.te)}else $n(n,e,t)}return o}function Gn(n,e){let t=n.strand==="-",r=0,o=0;for(let[s,i]of n.edits)e(s,i,t?n.queryEnd-1-r:n.queryStart+r,n.targetStart+o),s!=="D"&&(r+=i),s!=="I"&&(o+=i)}function to(n,e,t,r){let o=e==="query"&&n.strand==="-"?-1:1,s=0;return Gn(n,(i,a,f,c)=>{let l=e==="query"?f:c,p=u=>{let d=l+o*u;return d>=t&&d<r};if(i==="="||i==="X")for(let u=0;u<a;u++)p(u)&&(s+=i==="="?io:Fn);else if(i==="I"==(e==="query"))for(let u=0;u<a;u++)p(u)&&(s+=u===0?re:Ce);else p(0)&&(s+=re+(a-1)*Ce)}),s}function no(n,e){return e==="query"?[n.queryStart,n.queryEnd]:[n.targetStart,n.targetEnd]}function ti(n,e){let t=n.strand==="-",r=[],o=0,s=0,i=0,a=0,f=new Uint8Array(n.queryEnd-n.queryStart);for(let[d,h]of n.shared)f.fill(1,d-n.queryStart,h-n.queryStart);let c=d=>f[d-n.queryStart]===1,l=()=>{qe(r,"I",o),qe(r,"D",s),o=0,s=0};Gn(n,(d,h,m)=>{if(d==="I")o+=h;else if(d==="D")s+=h;else{for(let y=0;y<h;y++)e[i+y]?(o+=1,s+=1,c(t?m-y:m+y)&&(a+=1)):((o>0||s>0)&&l(),qe(r,d,1));i+=h}}),l();let p={I:0,D:0};for(;r[0]?.[0]==="I"||r[0]?.[0]==="D";){let[d,h]=r.shift();p[d]+=h}let u={I:0,D:0};for(;r.at(-1)?.[0]==="I"||r.at(-1)?.[0]==="D";){let[d,h]=r.pop();u[d]+=h}return r.length===0?void 0:{...n,queryStart:n.queryStart+(t?u.I:p.I),queryEnd:n.queryEnd-(t?p.I:u.I),targetStart:n.targetStart+p.D,targetEnd:n.targetEnd-u.D,edits:r,sharedBases:n.sharedBases-a}}function ni(n,e,t,r){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=n.map(c=>{let l=[];Gn(c,(p,u,d,h)=>{if(p==="="||p==="X")for(let 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oo(n,e){let t=[0];for(let r of n)t.push(t.at(-1)+e(_(r)).length);return t}function so(n){let e=new Map,t=new Map;n.forEach((i,a)=>{let f=_(i);e.has(f)?t.set(f,a):e.set(f,a)});let r=new Int32Array(n.length+1);for(let[i,a]of t)r[e.get(i)]+=1,r[a+1]-=1;let o=new Uint8Array(n.length),s=0;for(let i=0;i<n.length;i++)s+=r[i],o[i]=s>0?1:0;return o}function ri(n,e,t,r){let o=so(n),s=so(e),i=new Map;e.forEach((p,u)=>{s[u]||i.set(_(p),[u])});let a=2*e.length,f=(p,u,d)=>p*a+2*u+(d?1:0),c=new Set;n.forEach((p,u)=>{for(let d of o[u]?[]:i.get(_(p))??[])c.add(f(u,d,q(p)!==q(e[d])))});let l=[];return n.forEach((p,u)=>{for(let d of o[u]?[]:i.get(_(p))??[]){let h=q(p)!==q(e[d]),m=h?-1:1;if(!c.has(f(u-1,d-m,h))){let y=u,S=d;for(;y<n.length&&S>=0&&S<e.length&&c.has(f(y,S,h));)y+=1,S+=m;let I=S-m;l.push({qs:t[u],qe:t[y],ts:r[Math.min(d,I)],te:r[Math.max(d,I)+1],flipped:h})}}}),l}function po(n,e,t,r={}){let o=ro(n,t),s=ro(e,t),i=ri(n,e,oo(n,t),oo(e,t)),a=r.minMatch??Us,f=r.bases??!0,c=[];for(let l of qn(i,r.maxGap??1/0,a,Vs)){let p=[],u=l[0],d=l.at(-1),{flipped:h}=u.run;_t(l,o,s,p,f?(y,S,I,g,b)=>{for(let x of ei(y,S,I,a)){let A=b+S.length;c.push({...x,queryStart:g+x.queryStart,queryEnd:g+x.queryEnd,targetStart:h?A-x.targetEnd:b+x.targetStart,targetEnd:h?A-x.targetStart:b+x.targetEnd,strand:h?"+":"-",edits:h?x.edits.reverse():x.edits,shared:[]})}}:$n),c.push({queryStart:u.run.qs+u.trim,queryEnd:d.run.qe,targetStart:h?d.run.ts:u.run.ts+u.trim,targetEnd:h?u.run.te-u.trim:d.run.te,strand:h?"-":"+",edits:h?p.reverse():p,sharedBases:l.reduce((y,{run:S,trim:I})=>y+S.qe-S.qs-I,0),shared:l.map(({run:y,trim:S})=>[y.qs+S,y.qe])})}return ni(c,o.length,s.length,a).map(({shared:l,...p})=>p).sort((l,p)=>l.queryStart-p.queryStart)}function ho(n){return n.map(([e,t])=>`${t}${e}`).join("")}var Me=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} 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t=e.identity.hapStart-n.identity.hapEnd,r=n.strand==="+"?e.refStart-n.refEnd:n.refStart-e.refEnd;return n.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function ai(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);uo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)se(s,c,l);let i=n.identity.walkForward,[a,f]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function fi(n){if(n.some(o=>o.weight!==void 0))return n;let e=new Map;n.forEach((o,s)=>{if(o.identity){let i=e.get(o.identity.pathHandle);i?i.push(s):e.set(o.identity.pathHandle,[s])}});let t=new Map,r=new Set;for(let o of e.values()){o.sort((a,f)=>n[a].identity.hapStart-n[f].identity.hapStart);let s=o[0],i=n[s];for(let a of o.slice(1)){let f=n[a],c=ii(i,f);c?(i=ai(i,f,c),r.add(a)):(t.set(s,i),s=a,i=f)}t.set(s,i)}return n.flatMap((o,s)=>r.has(s)?[]:[t.get(s)??o])}function kt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var ci=32768;function li(n){let e=[...n].sort((r,o)=>r-o),t=[];for(let r of e){let o=t[t.length-1];o&&r-o[1]<=ci?o[1]=r:t.push([r,r])}return t}var Tt=class{records=new Map;paths=[];twinStarts=new Set;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;stats={orderedAlignments:0,lcsAlignments: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}get nodeCount(){return this.records.size/2}get pathCount(){return 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(me(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 Me(this.limit);let t=await this.db.getRecord(me(e,"forward")),r=await this.db.getRecord(me(e,"reverse"));if(!t||!r)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(r.handle,r)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),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 ${ge(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${ge(t.name,t.name.fragment)} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`Path ${ge(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(_(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${ge(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=_(e);await this.ensureNode(o);let s=this.record(e),i=Ue(e),a=new rt;return a.push(t,o,bt(i)),a.push(s.sequenceLen-t-1,o,St(i)),this.insertContext(a,r)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,r){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let c=await this.db.indexedPositionsBetween(e,t,r),l=li(c.map(p=>p.pos.node));await Promise.all(l.map(([p,u])=>this.db.prefetchRecords(p,u+2)))}}return o}async aroundInterval(e,t,r){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,r)}catch(o){throw o instanceof Me&&o.windowBp===void 0?new Me(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new rt;for(;;){let f=_(o.node),c=Ue(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,bt(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,St(c));break}a.push(0,f,St(c));let u=l.gbwt().lf(o.offset);if(!u)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=u,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new rt;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,o=new Set;for(let i of this.records.keys())o.add(_(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Lr(f);if(!r.has(`${a}:${l}`)){let d=this.record(me(a,Tr(f))),h=i+d.sequenceLen-1;h<=t&&e.push(h,a,l)}let p=this.record(me(a,Nr(f))),u=i+1;if(u<=t)for(let d of p.successors()){let h=_(d),m=bt(Ue(d));r.has(`${h}:${m}`)||e.push(u,h,m)}}for(let i of o)this.records.delete(me(i,"forward")),this.records.delete(me(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,K(t)],o=new Set([_(e),_(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=_(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=_(f);o.has(c)||(r.push(f,K(f)),o.add(c))}}return s}async extractSnarls(e){let t=0;for(let[r,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(r,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?We(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(o=>this.hasHandle(o));return r===void 0?!1:t.length>1||this.record(K(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let o=this.records.get(r);if(o)return o;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(K(l))).successors().length>1},r=async f=>{let c=await e(K(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[K(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=_(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(me(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((x,A)=>i.set(x,A));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let x=0;x<s;x++){let A=this.record(o[x]),M=A.gbwt().decompressArrays();f[x]=A.sequenceLen,c.push(M),a[x+1]=a[x]+M.nodes.length}let l=a[s],p=new Int32Array(l),u=new Int32Array(l),d=new Uint8Array(l);for(let x=0;x<s;x++){let A=c[x];p.set(A.nodes,a[x]),u.set(A.offsets,a[x])}c.length=0;for(let x=0;x<l;x++){let A=i.get(p[x]);A===void 0?p[x]=-1:(p[x]=A,d[a[A]+u[x]]=1)}let h=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,y,S=(x,A,M)=>{let L=[],k=0,T=0,R=-1,B=x,v=A;for(;;){B===h&&v===m&&(R=k),M&&(M.push(o[B]),L.push(v)),k+=1,T+=f[B];let C=a[B]+v,P=p[C];if(P<0)break;v=u[C],B=P}return{offsets:L,len:T,refAt:R,last:B}},I=(x,A,M,L)=>{L>=0&&(this.refId=this.paths.length,y=L),this.paths.push({path:x,offsets:A,len:M,weight:void 0,identity:void 0})},g=new Int32Array(s),b=h!==void 0&&q(o[h]);for(let x=0;x<s;x++){let A=o[x];if(!q(A)){let M=a[x],L=a[x+1]-M;for(let k=0;k<L;k++)if(d[M+k]===0){let T=[],{offsets:R,len:B,refAt:v,last:C}=S(x,k,T),P=o[C];if(v>=0||Ne(A,P)){if(I(T,R,B,v),!q(P)){let G=i.get(K(P));g[G]=g[G]+1}}else this.twinStarts.add($e({node:A,offset:k}))}}}for(let x=0;x<s;x++){let A=o[x];if(q(A)){let M=a[x],L=a[x+1]-M,k=0;for(let R=0;R<L;R++)d[M+R]===0&&(k+=1);let T=!b&&k===g[x];for(let R=0;R<L;R++)if(d[M+R]===0){let B=T?void 0:S(x,R,void 0);if(B&&(B.refAt>=0||Ne(A,o[B.last]))){let v=[],{offsets:C,len:P,refAt:G}=S(x,R,v);I(v,C,P,G)}else this.twinStarts.add($e({node:A,offset:R}))}}}if(r){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let x=this.paths[this.refId],A=r.nodeOffset;for(let L of x.path.slice(0,y))A+=this.record(L).sequenceLen;let M=r.seqOffset-A;this.refInterval=[M,M+x.len],x.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:M,hapEnd:M+x.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((o,s)=>Dn(o.path,s.path)||o.len-s.len);let t=[],r;for(let o of this.paths){let s=t[t.length-1];s&&Dn(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&Dn(o.path,e)===0&&(r=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=r}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of r)for(let i of s.path)o.add(_(i));for(let s of[...this.records.keys()])o.has(_(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async extractChosenPaths(e,t,r){this.clearPaths();let o=e.position.seqOffset,s=await Xr({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},keep:r,signal:this.signal,prefetchReferenceRange:(c,l,p)=>this.prefetchReferenceRange(c,l,p)});if(this.stats.keep=s.stats,s.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),a=c=>({path:c.handles,offsets:c.offsets,len:c.len,weight:void 0,identity:{pathHandle:c.pathHandle,name:c===s.reference?e.name:i.get(c.pathHandle).name,orientation:c.orientation,hapStart:c.hapStart,hapEnd:c.hapEnd}}),f=[s.reference,...s.pieces].sort(Zr);return this.paths=f.map(a),this.refId=f.indexOf(s.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[s.reference.hapStart,s.reference.hapEnd],!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=kn(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[h,m]of t)for(let y of await this.db.haplotypeSamplesInRange(h,m))r.set($e(y),y);let o=h=>{let m=0,y=t.length-1;for(;m<y;){let I=m+y+1>>1;t[I][0]<=h?m=I:y=I-1}let S=t[m];return S[0]<=h&&h<=S[1]},s=new Map;this.paths.forEach((h,m)=>{h.path.length>0&&m!==this.refId&&s.set($e(kt(h,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((h,m)=>{m!==this.refId&&i.fragmentLengths.push(h.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=h=>(i.graphLookups+=1,a(h)),c=async(h,m)=>{if(o(h.node))return r.get($e(h));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(h.node,h.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async h=>{let m=l.get(h);if(!m){let y=await this.db.getPath(h);if(!y)throw new Error(`Path ${h} is missing from the database`);m=y.name,l.set(h,m)}return m},u=(h,m,y)=>h.orientation==="forward"?{pathHandle:h.pathHandle,orientation:"forward",base:h.pathOffset-m}:{pathHandle:h.pathHandle,orientation:"reverse",base:h.pathOffset+m+y},d=(h,m)=>h.orientation==="forward"?{pathHandle:h.pathHandle,orientation:"forward",base:h.hapStart-m}:{pathHandle:h.pathHandle,orientation:"reverse",base:h.hapEnd+m};for(let h=0;h<this.paths.length;h++){let m=this.paths[h];if(h===this.refId||m.identity)continue;let y=[],S=new Set,I={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(I);let g,b=0,x=h,A;for(;g===void 0;){if(this.signal?.throwIfAborted(),x!==void 0){if(S.has(x)){I.end="cycle";break}S.add(x);let R=this.paths[x];y.push({index:x,startBp:b}),I.fragments+=1;let B=b;for(let C=0;C<R.path.length;C++){let P=kt(R,C),G=r.get($e(P)),j=this.record(P.node).sequenceLen;if(G){g=u(G,B,j);break}B+=j}if(b+=R.len,g){I.end="in-fragment sample";break}let v=kt(R,R.path.length-1);A=this.record(v.node).gbwt().lf(v.offset),x=void 0}if(A===void 0||A.node===0){I.end="endmarker";break}let M=$e(A),L=s.get(M);if(L!==void 0){let R=this.paths[L].identity;if(R){g=d(R,b),I.end="identified sibling";break}x=L;continue}this.records.has(A.node)&&(I.reentries+=1),this.twinStarts.has(M)&&(I.twinLandings+=1);let k=await c(A,I),T=await f(A.node);if(k){g=u(k,b,T.sequenceLen),I.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,I.steps+=1,b-y[y.length-1].startBp>4*e+4*T.sequenceLen){I.end="bound";break}b+=T.sequenceLen,A=T.gbwt().lf(A.offset)}if(g){I.pathHandle=g.pathHandle;let M=await p(g.pathHandle);for(let{index:L,startBp:k}of y){let T=this.paths[L];T.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:M,orientation:"forward",hapStart:g.base+k,hapEnd:g.base+k+T.len}:{pathHandle:g.pathHandle,name:M,orientation:"reverse",hapStart:g.base-k-T.len,hapEnd:g.base-k}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,o)=>{let s=t.get(r);s?s.push(o):t.set(r,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,o)=>{t.push(t[o]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=si(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),se(r,"M",i),uo(r,o-i-a,s-i-a),se(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),o=0;for(let s of e)r.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=r??oi(Jr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,u,d,h)=>{p===u?se(s,"D",i[h]-i[d]):d===h?se(s,"I",this.pathLen(e.slice(p,u))):this.align(e.slice(p,u),t.slice(d,h),s)},f=0,c=0,l=0;for(let p=0;p<o.count;p++){let u=o.pathAt[p],d=o.refAt[p];(c!==u||l!==d)&&a(c,u,l,d);let h=this.record(e[u]).sequenceLen;se(s,"M",h),f+=h,c=u+1,l=d+1}return a(c,e.length,l,t.length),{edits:s,matched:f}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(Fr(r))o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else{let s=t.path.map(f=>K(f)).reverse(),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,r).edits,flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);o=c.matched>f.matched?{edits:c.edits,flipped:!0}:{edits:f.edits,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],o=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:f}=this.alignment(i),c=0,l=0;for(;c<a.length&&a[c][0]==="D";)l+=a[c][1],c+=1;let p=a.length,u=0;for(;p>c&&a[p-1][0]==="D";)u+=a[p-1][1],p-=1;let d=s.identity,h=d?d.orientation==="forward"!==f:!f;o.push({strand:h?"+":"-",refStart:e.start+l,refEnd:e.start+r-u,edits:a.slice(c,p),weight:s.weight,path:s.path,start:kt(s,0),identity:d===void 0?void 0:{pathHandle:d.pathHandle,name:d.name,hapStart:d.name.fragment+d.hapStart,hapEnd:d.name.fragment+d.hapEnd,walkForward:d.orientation==="forward"}})}),fi(o).map(s=>{let{edits:i,identity:a,...f}=s,c={...f,cigar:hi(i)};return a?{...c,resolved:!0,name:a.name,label:ge({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...c,resolved:!1}})}pairAlignments(e){let{target:t,query:r,...o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Lt(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),f=r?i(r):l=>!a(l),c=l=>this.record(me(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>f(p.name)).flatMap(p=>po(p.steps,l.steps,c,o).map(u=>({query:p.name,queryStart:p.start+u.queryStart,queryEnd:p.start+u.queryEnd,strand:u.strand,target:l.name,targetStart:l.start+u.targetStart,targetEnd:l.start+u.targetEnd,cigar:ho(u.edits),matches:u.edits.reduce((d,[h,m])=>d+(h==="="?m:0),0),columns:u.edits.reduce((d,[,h])=>d+h,0),sharedBases:u.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=me(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&We(o,s)&&t.push([r==="reverse"?1:0,_(s),q(s)?1:0])}return t.sort((r,o)=>r[0]-o[0]||r[1]-o[1]||r[2]-o[2]),t.filter((r,o)=>o===0||r[0]!==t[o-1][0]||r[1]!==t[o-1][1]||r[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!q(r)){let o=_(r),s=`S	${o}	${this.record(r).sequence}
 `;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
 `;t.push(e.encode(s))}return Qr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Wr(Ur(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)q(c)||r.push(`S	${_(c)}	${this.record(c).sequence}`);let s=c=>q(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&We(c,l)&&r.push(`L	${_(c)}	${s(c)}	${_(l)}	${s(l)}	0M`);let i=(c,l,p,u,d)=>{let h=Lt(c,l).map(S=>`${q(S)?"<":">"}${_(S)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,y=d===void 0?"":`	CG:Z:${d}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${u}	${h}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,u=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,u):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,u)),f+=1}}),`${r.join(`
 `)}
 `}outputPaths(e){let t=e.cigar??!1,r=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};r.push({info:this.paths[this.refId],identity:void 0,name:ge(i,this.refPath.fragment+this.refInterval[1]),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names==="resolved"?i.identity:void 0;r.push({info:i,identity:f,name:f?ge({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):ge({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),r}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&We(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!q(s)).map(s=>({id:String(_(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(_(s)),from_is_reverse:q(s),to:String(_(i)),to_is_reverse:q(i)});let o=this.outputPaths(e).map(s=>pi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!q(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=_(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Lt(i.info,i.identity))}))}}};function Lt(n,e){return e?.orientation==="reverse"?n.path.map(t=>K(t)).reverse():n.path}function pi(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Lt(n,e).map(o=>({id:String(_(o)),is_reverse:q(o)}))}}function Dn(n,e){let t=Math.min(n.length,e.length);for(let r=0;r<t;r++){let o=n[r],s=e[r];if(o!==s)return o<s?-1:1}return n.length-e.length}function se(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function Ot(n){return n===0?0:6+(n-1)}function uo(n,e,t){if(e===0)se(n,"D",t);else if(t===0)se(n,"I",e);else{let r=Math.min(e,t),o=4*r+Ot(e-r)+Ot(t-r),s=Ot(e)+Ot(t);o<=s?(se(n,"M",r),se(n,"I",e-r),se(n,"D",t-r)):(se(n,"I",e),se(n,"D",t))}}function hi(n){return n.map(([e,t])=>`${t}${e}`).join("")}async function mo(n,e,t,r,o){let s=new Tt(n,o);try{let i=await s.pathPosition(Et(e,t));return await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,o.context??100),await s.extractSnarls(o.snarls??"none"),{subgraph:s,reference:i}}catch(i){throw i instanceof Me&&i.windowBp===void 0?new Me(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}}async function go(n,e,t,r,o={}){let{subgraph:s,reference:i}=await mo(n,e,t,r,o);return s.extractPaths(i,o.haplotypes??"all"),s}async function wo(n,e,t,r,o){if(!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:s,reference:i}=await mo(n,e,t,r,o),a=o.haplotypes??"all";return(a!=="all"||!await s.extractChosenPaths(i,r-t,o.keep))&&(s.extractPaths(i,a),await s.identifyPaths()),s.keepHaplotypes(o.keep),s}function xe(n,e){let t=0;for(let o=0;o<8;o++){let s=n[e+o];if(s===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(s&127),(s&128)===0)return[t,e+o+1]}let r=n[e+8];if(r===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+r,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function di(n,e,t){switch(t){case 1:return n.getInt8(e);case 2:return n.getInt16(e);case 3:return n.getInt8(e)<<16|n.getUint16(e+1);case 4:return n.getInt32(e);case 6:return n.getInt16(e)*4294967296+n.getUint32(e+2);default:{let r=n.getBigInt64(e);if(r>BigInt(Number.MAX_SAFE_INTEGER)||r<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${r} exceeds the safe integer range`);return Number(r)}}}var ui=new TextDecoder;function Nt(n){let[e,t]=xe(n,0),r=[],o=t;for(;o<e;){let[a,f]=xe(n,o);r.push(a),o=f}let s=new DataView(n.buffer,n.byteOffset,n.byteLength),i=e;return r.map(a=>{if(a===0)return null;if(a>=1&&a<=6){let f=a<=4?a:a===5?6:8,c=di(s,i,f);return i+=f,c}if(a===7){let f=s.getFloat64(i);return i+=8,f}if(a===8)return 0;if(a===9)return 1;if(a>=12){let f=a-12>>1,c=n.subarray(i,i+f);return i+=f,a%2===0?c:ui.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var ot=2,qt=5,xo=10,Ft=13;function bo(n,e){return n[e]*256+n[e+1]}function _e(n,e){return n[e]*16777216+n[e+1]*65536+n[e+2]*256+n[e+3]}function mi(n,e){let t=n[e];if(t!==ot&&t!==qt&&t!==xo&&t!==Ft)throw new Error(`SQLite page has unknown b-tree type ${t}`);let r=t===ot||t===qt;return{type:t,cellCount:bo(n,e+3),rightChild:r?_e(n,e+8):0,cellPointers:e+(r?12:8)}}function Re(n,e,t){return bo(n,e.cellPointers+2*t)}var gi=4096,wi=4096,$t=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let r=this.usable,o=t?Math.floor((r-12)*64/255)-23:r-35;if(e<=o)return e;let s=Math.floor((r-12)*32/255)-23,i=s+(e-s)%(r-4);return i<=o?i:s}async payload(e,t,r,o){let s=this.localPayloadSize(r,o);if(s===r)return e.subarray(t,t+r);let i=new Uint8Array(r);i.set(e.subarray(t,t+s),0);let a=s,f=_e(e,t+s);for(;f!==0&&a<r;){let c=await this.pager.page(f),l=c.subarray(4,4+Math.min(this.usable-4,r-a));i.set(l,a),a+=l.length,f=_e(c,0)}if(a!==r)throw new Error("SQLite overflow chain ended before the payload was complete");return i}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:mi(t,e===1?100:0)}}tableDepth(e,t){let r=this.tableDepths.get(e);return r||(r=(async()=>{let o=e;for(let s=0;;s++){let{page:i,header:a}=await this.pageAt(o);if(a.type===Ft)return s;if(a.type!==qt)throw new Error("SQLite table b-tree contains an 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contains an index page");let i=0,a=s.cellCount;for(;i<a;){let f=i+a>>1,c=Re(o,s,f),[l]=xe(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:_e(o,Re(o,s,i))}}async*tableScan(e){let{page:t,header:r}=await this.pageAt(e);if(r.type===Ft)for(let o=0;o<r.cellCount;o++){let s=Re(t,r,o),[i,a]=xe(t,s),[f,c]=xe(t,a);yield{rowid:f,values:Nt(await this.payload(t,c,i,!1))}}else{let o=[];for(let s=0;s<r.cellCount;s++)o.push(_e(t,Re(t,r,s)));o.push(r.rightChild),this.pager.prefetch(o);for(let s of o)yield*this.tableScan(s)}}decodedCells(e,t){let r=this.decodedIndexPages.get(e);if(r)this.decodedIndexPages.delete(e);else if(r=new Array(t.cellCount),this.decodedIndexPages.size>=gi){let o=this.decodedIndexPages.keys().next().value;o!==void 0&&this.decodedIndexPages.delete(o)}return this.decodedIndexPages.set(e,r),r}async indexCell(e,t,r,o){let s=this.decodedCells(e,r),i=s[o];if(!i){let a=Re(t,r,o),f=r.type===ot,[c,l]=xe(t,f?a+4:a);i={values:Nt(await this.payload(t,l,c,!0)),leftChild:f?_e(t,a):0},s[o]=i}return i}async*indexScanFrom(e,t){let{page:r,header:o}=await this.pageAt(e),s=0,i=o.cellCount;for(;s<i;){let a=s+i>>1,f=await this.indexCell(e,r,o,a);yo(f.values,t)<0?s=a+1:i=a}for(let a=s;a<o.cellCount;a++){let f=await this.indexCell(e,r,o,a);o.type===ot&&(yield*this.indexScanFrom(f.leftChild,t)),yield f.values}o.type===ot&&(yield*this.indexScanFrom(o.rightChild,t))}async indexSeekLE(e,t){let r,o=e;for(;;){let{page:s,header:i}=await this.pageAt(o),a=0,f=i.cellCount,c=0;for(;a<f;){let l=a+f>>1,p=await this.indexCell(o,s,i,l);yo(p.values,t)<=0?(r=p.values,a=l+1):(c=p.leftChild,f=l)}if(i.type===xo)return r;o=a===i.cellCount?i.rightChild:c}}};function yo(n,e){for(let t=0;t<e.length;t++){let r=n[t],o=e[t];if(typeof r!="number"||o===void 0)throw new Error("SQLite index key is not numeric");if(r!==o)return r<o?-1:1}return 0}var Ht=class{blocks=new Map;blockSize;maxBlocks;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,r,o={}){this.source=e,this.pageSize=t,this.fileSize=r;let s=o.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(s/t)*t),this.maxBlocks=o.maxBlocks??256}async read(e,t){let r=0;for(;;)try{let o=await this.source.read(e,t);return this.bytesFetched+=o.length,o}catch(o){if(r+=1,r>=3)throw o;await new Promise(s=>setTimeout(s,200*r))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){let t=this.blocks.get(e);if(t)return this.blocks.delete(e),this.blocks.set(e,t),t;let r=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-r),s=this.read(o,r);return this.fetches+=1,this.blocks.set(e,s),this.forgetOnFailure(s,[e]),this.evict(),s}prefetch(e){let t=[...new Set(e.map(o=>Math.floor((o-1)*this.pageSize/this.blockSize)))].filter(o=>!this.blocks.has(o)).sort((o,s)=>o-s),r=0;for(;r<t.length;){let o=r+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[r],o-r),r=o}}fetchRun(e,t){let r=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-r),s=this.read(o,r);this.fetches+=1;let i=[];for(let a=0;a<t;a++){let f=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(c=>c.subarray(f,f+this.blockSize)))}this.forgetOnFailure(s,i),this.evict()}forgetOnFailure(e,t){e.catch(()=>{for(let r of t)this.blocks.delete(r)})}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 r=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return r.subarray(o,o+this.pageSize)}};var st=class n{pager;btree;objects;constructor(e,t,r){this.pager=e,this.btree=t,this.objects=r}static async open(e,t={}){let{size:r}=await e.stat(),o=await e.read(Math.min(t.blockSize??65536,r),0),s=o.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3")throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),f=a.getUint16(16),c=f===1?65536:f,l=s[20]??0,p=a.getUint32(56);if(p!==1)throw new Error(`SQLite text encoding ${p} is not UTF-8`);let u=new Ht(e,c,r,t);u.seed(0,o),u.fetches+=1,u.bytesFetched+=o.length;let d=new $t(u,l),h=new Map;for await(let{values:m}of d.tableScan(1)){let[y,S,I,g,b]=m;typeof y=="string"&&typeof S=="string"&&typeof I=="string"&&typeof g=="number"&&h.set(S,{type:y,name:S,tableName:I,rootPage:g,sql:typeof b=="string"?b:""})}return new n(u,d,h)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}indexOn(e){let t=[...this.objects.values()].find(r=>r.type==="index"&&r.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var jn="GBZ-base version 4",Gt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Bt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${jn}"`),this.found=e}},Dt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,o,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=o,this.next=s,this.sequenceLen=Hr(o)}get id(){return _(this.handle)}get orientation(){return Ue(this.handle)}get sequence(){return this.decoded??=Gr(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new It(this.edges,this.bwt)}};function D(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function zt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function zn(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function So(n,e){return{handle:n,fwStart:{node:D(e[1],"Paths.fw_node"),offset:D(e[2],"Paths.fw_offset")},revStart:{node:D(e[3],"Paths.rev_node"),offset:D(e[4],"Paths.rev_offset")},name:{sample:zt(e[5],"Paths.sample"),contig:zt(e[6],"Paths.contig"),haplotype:D(e[7],"Paths.haplotype"),fragment:D(e[8],"Paths.fragment")},isIndexed:D(e[9],"Paths.is_indexed")!==0}}async function vo(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(zt(t[0],"Tags.key"),zt(t[1],"Tags.value"));return e}var it=class n{tagCache;pathCache;pathMapCache;indexTags=new Map;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e,t={}){let{haplotypeIndex:r,...o}=t,s=await st.open(e,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=r?await st.open(r,o):void 0,a=new n(s,i),f=await a.tag("version");if(f!==jn)throw new Bt(f);if(i){for(let d of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(d);a.indexTags=await vo(i);let c=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(c!==l)throw new Error(`haplotype index was built for ${c??"an unknown number of"} paths but the graph has ${l}`);let p=a.indexTags.get("haplotype_index_nodes"),u=await a.tag("nodes");if(p!==void 0&&p!==u)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${u}`);if(a.indexTags.get("haplotype_index_orientations")==="forward")throw new Gt}return a}tags(){return this.tagCache??=vo(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new Dt(e,$r(zn(t[1],"Nodes.edges")),zn(t[2],"Nodes.bwt"),zn(t[3],"Nodes.sequence"),typeof r=="number"?r:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:r}of this.sqlite.scan("Paths"))e.push(So(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?So(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(r=>r.name.sample===e.sample&&r.name.contig===e.contig&&r.name.haplotype===e.haplotype&&r.name.fragment<=e.fragment).sort((r,o)=>o.name.fragment-r.name.fragment)[0]}async pathsForSample(e){return(await this.paths()).filter(t=>t.name.sample===e)}async pathsNamed(e){let t=Et(Yr(e),0);return(await this.paths()).filter(r=>r.name.sample===t.sample&&r.name.contig===t.contig&&r.name.haplotype===t.haplotype).sort((r,o)=>r.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let r=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!r){let i=await this.getPath(e);throw new Error(`Path ${i?ge(i.name,i.name.fragment):e} has not been indexed for random access`)}let o=r.pathOffset,s=r.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async pathFragmentsForRange(e,t,r){if(r<=t)return[];let o=await this.pathsNamed(e),s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<r);return(await Promise.all([...s,...i].map(async f=>({path:f,start:f.name.fragment,end:f.name.fragment+await this.pathLength(f.handle)})))).filter(f=>t<f.end)}async subgraphForFragment(e,t,r,o){let{keep:s,...i}=o;if(s!==void 0&&!this.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{sample:a,contig:f,haplotype:c}=e.path.name,l={sample:a,contig:f,haplotype:c},p=Math.max(t,e.start),u=Math.min(r,e.end),d=o.haplotypes??"all",h=d==="all"||d==="distinct",m;return s!==void 0&&d==="all"?m=await wo(this,l,p,u,{...i,keep:s}):(m=await go(this,l,p,u,i),this.hasHaplotypeIndex&&h&&(await m.identifyPaths(),s!==void 0&&m.keepHaplotypes(s))),m}async getSubgraphForRange(e,t,r,o={}){let[s]=await this.pathFragmentsForRange(e,t,r);return s?this.subgraphForFragment(s,t,r,o):void 0}async getAlignmentsForRange(e,t,r,o={}){let s=[];for(let i of await this.pathFragmentsForRange(e,t,r)){let a=await this.subgraphForFragment(i,t,r,o);s.push(...a.alignments())}return s}async graphName(){let e=new Map;for(let[r,o]of await this.tags())r.startsWith("gbz_")&&e.set(r.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=jr(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return 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getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Pn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Is(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:je(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:ze(be(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>je(this,s));return o===void 0&&r===void 0?void 0:s=>Io(s,o)&&(r===void 0||ze(be(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new gr(i,s);let l=await this.referenceQuery(a,{}),p=this.keepPredicate(r.haplotypes);return 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at(x,h,c-f)??x}),S=d&&m&&l.length>0&&p.length>0?(await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,f,c,o)).map(g=>y(d,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let b=g.stats.keep;return b!==void 0&&b.fallback===void 0})?S.flatMap(g=>l.flatMap(b=>p.flatMap(x=>g.pairAlignments({target:b,query:x,bases:!1}).map(A=>ia({pair:A,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,As.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new ur;if(t.assemblyName===i){let a=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let f of a)o.next(f)}o.complete()},r.signal)}};export{gr as HaplotypeWindowError,ur as NoHaplotypeIndexError,jt as NoReferenceSampleError,Ut as NodeLimitError,mr as PairTargetError,wr as default,sa as fragmentFeature,be as haplotypePrefix,Is as laneAssemblyName,at as nodeLimitError,ia as 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Ao(s),f=Un({configured:this.getConf("referenceSample"),anchorPrefix:je(this,i),referenceSamples:a});return{db:s,anchor:i,referenceSample:f,referenceSamples:a}}});this.gaf=(0,hr.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]),o=this.pluginManager;if(!pr(t))return;let s=(0,Je.openLocation)(t,o);return new Wt(s,pr(r)?new Ar({filehandle:s,...(0,Je.openTabixIndexFilehandle)(r,this.getConf(["readsIndex","indexType"]),o)}):void 0)}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return Eo(o,s,t)}async getHaplotypes(t={}){let{db:r,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=be(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Pn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Is(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:je(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:ze(be(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>je(this,s));return o===void 0&&r===void 0?void 0:s=>Io(s,o)&&(r===void 0||ze(be(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new gr(i,s);let l=await this.referenceQuery(a,{}),p=this.keepPredicate(r.haplotypes);return Co(o,l,f,c,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,...p===void 0?{}:{keep:p}})}async getReads(t,r={}){let o=await this.gaf(r);return o?o.readsOver(new Set(t),r):{records:[],total:0}}async laneHaplotypes(t,r){let o=je(this,t);return(await this.getHaplotypes(r)).filter(s=>ze(s.prefix,o))}async referencePieces(t,r,o,s){let{db:i,referenceSample:a}=await this.graph(s),f=(await i.paths()).filter(l=>l.isIndexed&&l.name.sample===a&&l.name.contig===t&&l.name.fragment>r&&l.name.fragment<o).map(l=>l.name.fragment),c=[r,...[...new Set(f)].sort((l,p)=>l-p),o];return c.slice(1).map((l,p)=>({start:c[p],end:l}))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=je(this,r.targetAssemblyName),l=Pn(this),p=this.keepPredicate(r.haplotypes,c),u=await this.referenceQuery(i,r),d=this.getConf("nodeLimit");return(u?await(0,dr.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignmentsForRange(u,a,f,{context:this.getConf("context"),haplotypes:"all",limit:d,signal:r.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw at(m,d,f-a)??m})):[]).flatMap(m=>{let y=m.resolved?sa({alignment:m,assemblyName:s,refName:i,lane:Is(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,r,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new mr(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),p=await this.laneHaplotypes(s,o),u=[...l,...p],d=await this.referenceQuery(a,o),h=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,b)=>i.getSubgraphForRange(g,b.start,b.end,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:h,signal:o.signal,keep:x=>u.some(A=>A.sample===x.sample&&A.haplotype===x.haplotype)}).catch(x=>{throw at(x,h,c-f)??x}),S=d&&m&&l.length>0&&p.length>0?(await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,f,c,o)).map(g=>y(d,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let b=g.stats.keep;return b!==void 0&&b.fallback===void 0})?S.flatMap(g=>l.flatMap(b=>p.flatMap(x=>g.pairAlignments({target:b,query:x,bases:!1}).map(A=>ia({pair:A,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,As.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new ur;if(t.assemblyName===i){let a=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let f of a)o.next(f)}o.complete()},r.signal)}};export{gr as HaplotypeWindowError,ur as NoHaplotypeIndexError,jt as NoReferenceSampleError,Ut as NodeLimitError,mr as PairTargetError,wr as default,sa as fragmentFeature,be as haplotypePrefix,Is as laneAssemblyName,at as nodeLimitError,ia as pairFeature,Un as resolveReferenceSample};
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