jbrowse-plugin-graphgenomeviewer 4.0.29 → 4.0.30

package/dist/chunks/GbzBaseSyntenyAdapter-VXDXFND3.js

@@ -0,0 +1,8 @@
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l(oe(v.node))).gbwt().predecessorAt(v.offset);if(P===void 0||C!==void 0&&!C.has(P))return;let T=(await l(P)).gbwt().offsetTo(v);if(T===void 0)throw new Error(`No offset in ${P} leads to ${v.node}:${v.offset}`);return{node:P,offset:T}},x=(v,C,P,T)=>{let B=P.map(te=>te.pos.node),W=P.map(te=>te.pos.offset),K=0;for(let te of B)K+=p(te);let H=C==="forward"?P[0].left:P[P.length-1].left,L=d.length;d.push({pathHandle:v,orientation:C,handles:B,offsets:W,len:K,hapStart:H,hapEnd:H+K,canonical:Fe(B[0],B[B.length-1]),source:T});for(let te of P)m.set(te.pos,L);let Y=w.get(v);return Y?Y.push(L):w.set(v,[L]),L},E=async(v,C,P,T)=>{let B=[],W=v;for(;;){r?.throwIfAborted();let H=await b(W.pos,t);if(!H)break;W={pos:H,left:Vr(P,W.left,p(W.pos.node),p(H.node))},B.push(W)}B.reverse();let K=[v];for(W=v;;){r?.throwIfAborted();let H=await g(W.pos);if(!H||!t.has(H.node))break;W={pos:H,left:It(P,W.left,p(W.pos.node),p(H.node))},K.push(W)}return x(C,P,[...B,...K],T)},A=async(v,C,P,T)=>d[m.get(v.pos)??await E(v,C,P,T)],N=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}},O=v=>{let C=v.handles[0];return{pos:{node:C,offset:v.offsets[0]},left:v.orientation==="forward"?v.hapStart:v.hapEnd-p(C)}},F=await E({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),R=d[F],z=()=>{if(i.fallback!==void 0)return{reference:R,pieces:[],stats:i};let v=new Map;d.forEach((P,T)=>{T!==F&&v.set(tt(P),[...v.get(tt(P))??[],P])});let C=[];for(let P of v.values()){let T=new Set;for(let B of P)B.canonical&&!T.has(B.orientation)&&(T.add(B.orientation),C.push(B),i.sources[B.source]+=1)}return i.sources.reference=1,i.pieces=C.length,{reference:R,pieces:C,stats:i}},_=v=>{let C=v-v%2;return e.haplotypeSamplesInRange(C,C+1)},j=async(v,C)=>{let P=C?y:I,T=C?I:y,B=v;for(;;){if(P.has(B))return;P.add(B);let W=d[B],K=C?N(W):O(W),H=0,L;for(;L===void 0;){r?.throwIfAborted();let Y=C?await g(K.pos):await b(K.pos);if(!Y){L="endmarker";break}let te=(await l(K.pos.node)).sequenceLen,ie=(await l(Y.node)).sequenceLen,le=C?It(W.orientation,K.left,te,ie):Vr(W.orientation,K.left,te,ie);if(t.has(Y.node)){let ee=m.get(Y);ee===void 0?(B=await E({pos:Y,left:le},W.pathHandle,W.orientation,"chain"),T.add(B),L="landed"):(T.add(ee),L="merge")}else H>Bs?L="bound":(H+=ie,K={pos:Y,left:le})}if(a("chain",L),L!=="landed")return}},V=async v=>{if(n.context>v.context)throw new fe(`the context of ${n.context} bp exceeds the ${v.context} bp the haplotype index's stray rows cover`);let C=i.spacing;if(C===void 0)throw new fe("the haplotype index has no anchors");let{bin:P,bound:T}=v,{fills:B,inserted:W}=n.snarls;if(n.snarls.mode==="overlapping"&&B.length>0)throw new fe("the haplotype index's stray rows cover contained snarls only");for(let S of B){if(S.inserted>0&&S.low===S.high)throw new fe(`the haplotype index's stray rows leave out the snarl bounded by node ${S.low} at both ends`);if(S.inserted>0&&(v.snarlNodes===void 0||S.nodes>v.snarlNodes))throw new fe(v.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${S.nodes} nodes exceeds the ${v.snarlNodes} the haplotype index's stray rows cover`)}let K=Math.floor(n.window.start/P),H=Math.floor((n.window.end-1)/P),L=K*P,Y=(H+1)*P,te=await e.haplotypeBinNodes(n.referenceHandle,K,H);for(let S of t.keys()){let k=M(S);if(!U(S)&&!te(k)&&!W.has(k))throw new fe(`the haplotype index lists node ${k} of the subgraph in no bin that the window touches`)}let ie=new Map,le=async S=>{let k=await e.haplotypeAnchor(n.referenceHandle,S*C);return k&&ie.set(S,k),k},ee=Math.max(0,Math.floor((L-T)/C)-1),Me=Math.ceil((Y+T)/C)+1;for(await Promise.all(Array.from({length:Me-ee+1},(S,k)=>le(ee+k)));ee>0&&(ie.get(ee)?.pathOffset??Number.POSITIVE_INFINITY)>=L-T;)ee-=1,await le(ee);for(;ie.has(Me)&&ie.get(Me).pathOffset<=Y+T;)Me+=1,await le(Me);let J=[...ie.keys()].sort((S,k)=>S-k),ae=ie.get(J[0]??-1);if(!ae)throw new fe("the haplotype index has no anchors on this path");let xe=S=>ie.get(S).pathOffset,Ne=new Map;for(let S of J){let k=M(ie.get(S).node);Ne.set(k,[...Ne.get(k)??[],S])}let Te=[...Ne.keys()],hr=await Promise.all(Te.map(S=>_(2*S)));if(!hr[Te.indexOf(M(ae.node))].some(S=>S.pathHandle===n.referenceHandle&&S.orientation==="forward"&&S.pathOffset===ae.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${ae.pathOffset} (node ${M(ae.node)}); it does not match this graph`);let dr=J.filter(S=>xe(S)<=n.window.start),Is=J.filter(S=>xe(S)>=n.window.end);i.anchors=[xe(dr[dr.length-1]??J[0]),xe(Is[0]??J[J.length-1])],i.anchorsRead=J.length;let xn=new Map,ur=new Set;if(Te.forEach((S,k)=>{let $=Ne.get(S),Q=$.length===1?$[0]:void 0;for(let G of hr[k])ur.add(G.pathHandle),G.orientation==="forward"&&u(G.pathHandle)&&xn.set(G.pathHandle,[...xn.get(G.pathHandle)??[],{k:Q,row:G}])}),i.chosenPaths=[...ur].filter(u).length,i.chosenPaths>Yr.mostChosenPaths)throw new fe(`${i.chosenPaths} chosen paths pass the anchors, more than ${Yr.mostChosenPaths}`);let pt=[],Le=Number.POSITIVE_INFINITY,_e=0;for(let[S,k]of xn){k.sort(($,Q)=>$.row.pathOffset-Q.row.pathOffset);for(let $=0;$+1<k.length;$++){let Q=k[$],G=k[$+1];if(Q.k===void 0||G.k===void 0||Math.abs(Q.k-G.k)!==1)continue;let[Z,ne]=xe(Q.k)<=xe(G.k)?[Q,G]:[G,Q],re=xe(Z.k),se=xe(ne.k);re<Y&&se>=L?(pt.push({pathHandle:S,from:Q.row,to:G.row}),Le=Math.min(Le,re-T),_e=Math.max(_e,se+T)):re>=Y&&re-Y<=T?(pt.push({pathHandle:S,from:Z.row,to:void 0}),Le=Math.min(Le,re-T),_e=Math.max(_e,re+T)):se<L&&L-se<=T&&(pt.push({pathHandle:S,from:ne.row,to:void 0}),Le=Math.min(Le,se-T),_e=Math.max(_e,se+T))}}let vs=new Set(B.map(S=>`${S.low}:${S.high}`)),mr=await e.haplotypeStraysInBins(n.referenceHandle,K,H),Es=mr.filter(S=>u(S.pathHandle)&&(S.snarl===void 0||vs.has(`${S.snarl[0]}:${S.snarl[1]}`))).sort((S,k)=>S.pathHandle-k.pathHandle||S.pathStart-k.pathStart);i.strays={bins:H-K+1,rows:mr.length,walked:0,outsideBp:0},_e>0&&await n.prefetchReferenceRange(n.referenceHandle,Math.max(0,Le),_e+1),i.ms.scan=s();let gr=8*C+2*(n.window.end-n.window.start),wr=i.strays,Ke=0,yr=S=>{if(wr.outsideBp+=S,Ke+=S,Ke>gr)throw new fe(`a walk of a chosen path near the window went past its cap of ${gr} bp`)},bn=new Map,xr=(S,k,$)=>(bn.get(S)??[]).some(([Q,G])=>Q<=k&&$<G),br=(S,k,$)=>{bn.set(S,[...bn.get(S)??[],[k,$]])},Sr=async(S,k,$,Q,G)=>{let Z=k,ne=$,re=ne;for(;Z&&ne<=Q;){r?.throwIfAborted();let se;if(t.has(Z.node)){let Ze=await A({pos:Z,left:ne},S,"forward",G),vr=N(Ze);Z=vr.pos,ne=vr.left,se=p(Z.node),re=Math.max(re,Ze.hapEnd)}else se=(await l(Z.node)).sequenceLen,yr(se),re=Math.max(re,ne+se);Z=await g(Z),ne+=se}return re},As=async(S,k,$,Q)=>{let G={pos:k,left:$},Z=$;for(;G.left>Q;){r?.throwIfAborted();let ne=await b(G.pos);if(!ne)break;let re=(await l(ne.node)).sequenceLen,se=G.left-re;if(t.has(ne.node)){let Ze=await A({pos:ne,left:se},S,"forward","section");G=O(Ze),Z=Math.min(Z,Ze.hapStart)}else yr(re),G={pos:ne,left:se},Z=Math.min(Z,se)}return Z};for(let{pathHandle:S,from:k,to:$}of pt){let Q=k.pathOffset,G=($??k).pathOffset+T;if(xr(S,Q-T,G))continue;let Z={node:k.node,offset:k.offset};Ke=0;let ne=await Sr(S,Z,Q,G,"section");Ke=0;let re=await As(S,Z,Q,Q-T);br(S,Math.min(re,Q-T),Math.max(ne,G+1)),a($?"section":"visit",$?"past the far anchor":"bound")}for(let S of Es){if(xr(S.pathHandle,S.pathStart,S.pathEnd))continue;Ke=0;let k=await Sr(S.pathHandle,{node:S.node,offset:S.offset},S.pathStart,S.pathEnd,"stray");br(S.pathHandle,S.pathStart,Math.max(k,S.pathEnd+1)),wr.walked+=1}i.ms.walks=s();let Ir=[];i.scans=Mn([...t.keys()].sort((S,k)=>S-k));for(let[S,k]of i.scans)for(let $ of await 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Map;e.forEach((p,h)=>{s[h]||i.set(M(p),[h])});let a=2*e.length,f=(p,h,u)=>p*a+2*h+(u?1:0),c=new Set;n.forEach((p,h)=>{for(let u of o[h]?[]:i.get(M(p))??[])c.add(f(h,u,U(p)!==U(e[u])))});let l=[];return n.forEach((p,h)=>{for(let u of o[h]?[]:i.get(M(p))??[]){let d=U(p)!==U(e[u]),m=d?-1:1;if(!c.has(f(h-1,u-m,d))){let w=h,y=u;for(;w<n.length&&y>=0&&y<e.length&&c.has(f(w,y,d));)w+=1,y+=m;let I=y-m;l.push({qs:t[h],qe:t[w],ts:r[Math.min(u,I)],te:r[Math.max(u,I)+1],flipped:d})}}}),l}function po(n,e,t,r={}){let o=ro(n,t),s=ro(e,t),i=Js(n,e,oo(n,t),oo(e,t)),a=r.minMatch??Gs,f=r.bases??!0,c=[];for(let l of Tn(i,r.maxGap??1/0,a,Us)){let p=[],h=l[0],u=l.at(-1),{flipped:d}=h.run;Rt(l,o,s,p,f?(w,y,I,g,b)=>{for(let x of Xs(w,y,I,a)){let E=b+y.length;c.push({...x,queryStart:g+x.queryStart,queryEnd:g+x.queryEnd,targetStart:d?E-x.targetEnd:b+x.targetStart,targetEnd:d?E-x.targetStart:b+x.targetEnd,strand:d?"+":"-",edits:d?x.edits.reverse():x.edits,shared:[]})}}:Ln),c.push({queryStart:h.run.qs+h.trim,queryEnd:u.run.qe,targetStart:d?u.run.ts:h.run.ts+h.trim,targetEnd:d?h.run.te-h.trim:u.run.te,strand:d?"-":"+",edits:d?p.reverse():p,sharedBases:l.reduce((w,{run:y,trim:I})=>w+y.qe-y.qs-I,0),shared:l.map(({run:w,trim:y})=>[w.qs+y,w.qe])})}return Zs(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 Pe=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 $n(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var rt=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if($n(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&&$n(e[s],e[a])&&(a=s),i<e.length&&$n(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 ei(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 ti(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 nt(n){return n.map(e=>oe(e)).reverse()}function ni(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 ri(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);mo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=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,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function oi(n,e,t){if(n.some(i=>i.weight!==void 0))return n;let r=new Map;n.forEach((i,a)=>{if(i.identity){let f=r.get(i.identity.pathHandle);f?f.push(a):r.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of r.values()){i.sort((l,p)=>n[l].identity.hapStart-n[p].identity.hapStart);let a=i[0],f=n[a],c=[];for(let l of i.slice(1)){let p=n[l],h=c.length===0?ni(f,p):void 0;if(h){f=ri(f,p,h),s.add(l);continue}if(!e(p)){c.push(l);continue}let u=e(f)?t([f,...c.map(d=>n[d]),p]):void 0;if(u){f=u;for(let d of[...c,l])s.add(d)}else o.set(a,f),a=l,f=p;c=[]}o.set(a,f)}return n.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Mt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var si=32768;function ii(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]<=si?o[1]=r:t.push([r,r])}return t}var Ot=class{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;snarlMode="none";snarlFills=[];snarlNodes=new Set;stats={orderedAlignments:0,lcsAlignments:0,snarls:{fills:0,inserted:0},identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t={}){this.db=e,this.limit=t.limit,this.signal=t.signal}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(be(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 Pe(this.limit);let t=await this.db.getRecord(be(e,"forward")),r=await this.db.getRecord(be(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.twinDeferred=!1,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(M(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=M(e);await this.ensureNode(o);let s=this.record(e),i=ze(e),a=new rt;return a.push(t,o,mt(i)),a.push(s.sequenceLen-t-1,o,gt(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=ii(c.map(p=>p.pos.node));await Promise.all(l.map(([p,h])=>this.db.prefetchRecords(p,h+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 Pe&&o.windowBp===void 0?new Pe(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=M(o.node),c=ze(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 ${l.sequenceLen}`);a.push(s,f,mt(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,gt(c));break}a.push(0,f,gt(c));let h=l.gbwt().lf(o.offset);if(!h)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=h,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new rt;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let r=new Set,o=new Set;for(let i of this.records.keys())o.add(M(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Nr(f);if(!r.has(`${a}:${l}`)){let u=this.record(be(a,Tr(f))),d=i+u.sequenceLen-1;d<=t&&e.push(d,a,l)}let p=this.record(be(a,Lr(f))),h=i+1;if(h<=t)for(let u of p.successors()){let d=M(u),m=mt(ze(u));r.has(`${d}:${m}`)||e.push(h,d,m)}}for(let i of o)this.records.delete(be(i,"forward")),this.records.delete(be(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let r=[e,oe(t)],o=new Set([M(e),M(t)]),s=[];for(;r.length>0;){let i=r.pop(),a=M(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=M(f);o.has(c)||(r.push(f,oe(f)),o.add(c))}}return{inserted:s,nodes:o.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[r,o]of await this.overlappingSnarls(e)){let{inserted:s,nodes:i}=await this.fillBetween(r,o),a=M(r),f=M(o);this.snarlFills.push({low:Math.min(a,f),high:Math.max(a,f),nodes:i,inserted:s.length});for(let c of s)this.snarlNodes.add(c);t+=s.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?je(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(oe(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(oe(l))).successors().length>1},r=async f=>{let c=await e(oe(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[oe(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=M(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(be(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,E)=>i.set(x,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let x=0;x<s;x++){let E=this.record(o[x]),A=E.gbwt().decompressArrays();f[x]=E.sequenceLen,c.push(A),a[x+1]=a[x]+A.nodes.length}let l=a[s],p=new Int32Array(l),h=new Int32Array(l),u=new Uint8Array(l);for(let x=0;x<s;x++){let E=c[x];p.set(E.nodes,a[x]),h.set(E.offsets,a[x])}c.length=0;for(let x=0;x<l;x++){let E=i.get(p[x]);E===void 0?p[x]=-1:(p[x]=E,u[a[E]+h[x]]=1)}let d=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,w,y=(x,E,A)=>{let N=[],O=0,F=0,R=-1,z=x,_=E;for(;;){z===d&&_===m&&(R=O),A&&(A.push(o[z]),N.push(_)),O+=1,F+=f[z];let j=a[z]+_,V=p[j];if(V<0)break;_=h[j],z=V}return{offsets:N,len:F,refAt:R,last:z}},I=(x,E,A,N)=>{N>=0&&(this.refId=this.paths.length,w=N),this.paths.push({path:x,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let x=0;x<s;x++){let E=o[x];if(!U(E)){let A=a[x],N=a[x+1]-A;for(let O=0;O<N;O++)if(u[A+O]===0){let F=[],{offsets:R,len:z,refAt:_,last:j}=y(x,O,F),V=o[j];if(_>=0||Fe(E,V)){if(I(F,R,z,_),!U(V)){let ue=i.get(oe(V));g[ue]=g[ue]+1}}else this.twinStarts.add($e({node:E,offset:O}))}}}for(let x=0;x<s;x++){let E=o[x];if(U(E)){let A=a[x],N=a[x+1]-A,O=0;for(let R=0;R<N;R++)u[A+R]===0&&(O+=1);let F=(d===void 0||w!==void 0)&&O===g[x];for(let R=0;R<N;R++)if(u[A+R]===0){let z=F?void 0:y(x,R,void 0);if(z&&(z.refAt>=0||Fe(E,o[z.last]))){let _=[],{offsets:j,len:V,refAt:ue}=y(x,R,_);I(_,j,V,ue)}else this.twinStarts.add($e({node:E,offset:R}))}}}let b=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((x,E)=>x.path[0]-E.path[0]||x.offsets[0]-E.offsets[0]),b&&(this.refId=this.paths.indexOf(b)),r){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let x=this.paths[this.refId],E=r.nodeOffset;for(let N of x.path.slice(0,w))E+=this.record(N).sequenceLen;let A=r.seqOffset-E;this.refInterval=[A,A+x.len],x.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+x.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=t?.path,o=r&&!wt(r)?nt(r):void 0,s=c=>o!==void 0&&_t(c,o)===0||_t(c,nt(c))===0,i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>_t(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],p=i&&c!==t&&s(c.path);this.twinDeferred||=p,l&&_t(l.path,c.path)===0&&!p?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.distinctPaths(!1)}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,r=i=>`${i.pathHandle}:${i.hapStart}-${i.hapEnd}`,o=new Set;e?.identity&&t&&o.add(r({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let i of this.paths)i!==e&&i.identity?.orientation==="forward"&&o.add(r(i.identity));let s=this.paths.filter(i=>i===e||i.identity?.orientation!=="reverse"||!o.has(r(i.identity)));s.length<this.paths.length&&(this.paths=s,this.refId=e===void 0?void 0:s.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(i=>i.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((i,a)=>a!==this.refId&&i.identity===void 0).length;if(t>0)throw new Error(`${t} of the window's ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let r=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(M(a));for(let i of[...this.records.keys()])s.has(M(i))||this.records.delete(i);this.paths=o,this.refId=r===void 0?void 0:o.indexOf(r)}async extractChosenPaths(e,t,r,o){this.clearPaths();let s=e.position.seqOffset,i=await Kr({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:r,signal:this.signal,prefetchReferenceRange:(l,p,h)=>this.prefetchReferenceRange(l,p,h)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(Zr);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleGap()??4096,t=Mn(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[d,m]of t)for(let w of await this.db.haplotypeSamplesInRange(d,m))r.set($e(w),w);let o=d=>{let m=0,w=t.length-1;for(;m<w;){let I=m+w+1>>1;t[I][0]<=d?m=I:w=I-1}let y=t[m];return y[0]<=d&&d<=y[1]},s=new Map;this.paths.forEach((d,m)=>{d.path.length>0&&m!==this.refId&&s.set($e(Mt(d,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((d,m)=>{m!==this.refId&&i.fragmentLengths.push(d.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=d=>(i.graphLookups+=1,a(d)),c=async(d,m)=>{if(o(d.node))return r.get($e(d));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let w=await this.db.haplotypeSampleAt(d.node,d.offset);return w||(i.companionMisses+=1),w},l=new Map,p=async d=>{let m=l.get(d);if(!m){let w=await this.db.getPath(d);if(!w)throw new Error(`Path ${d} is missing from the database`);m=w.name,l.set(d,m)}return m},h=(d,m,w)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.pathOffset-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.pathOffset+m+w},u=(d,m)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.hapStart-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.hapEnd+m};for(let d=0;d<this.paths.length;d++){let m=this.paths[d];if(d===this.refId||m.identity)continue;let w=[],y=new Set,I={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(I);let g,b=0,x=d,E;for(;g===void 0;){if(this.signal?.throwIfAborted(),x!==void 0){if(y.has(x)){I.end="cycle";break}y.add(x);let R=this.paths[x];w.push({index:x,startBp:b}),I.fragments+=1;let z=b;for(let j=0;j<R.path.length;j++){let V=Mt(R,j),ue=r.get($e(V)),v=this.record(V.node).sequenceLen;if(ue){g=h(ue,z,v);break}z+=v}if(b+=R.len,g){I.end="in-fragment sample";break}let _=Mt(R,R.path.length-1);E=this.record(_.node).gbwt().lf(_.offset),x=void 0}if(E===void 0||E.node===0){I.end="endmarker";break}let A=$e(E),N=s.get(A);if(N!==void 0){let R=this.paths[N].identity;if(R){g=u(R,b),I.end="identified sibling";break}x=N;continue}this.records.has(E.node)&&(I.reentries+=1),this.twinStarts.has(A)&&(I.twinLandings+=1);let O=await c(E,I),F=await f(E.node);if(O){g=h(O,b,F.sequenceLen),I.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,I.steps+=1,b-w[w.length-1].startBp>4*e+4*F.sequenceLen){I.end="bound";break}b+=F.sequenceLen,E=F.gbwt().lf(E.offset)}if(g){I.pathHandle=g.pathHandle;let A=await p(g.pathHandle);for(let{index:N,startBp:O}of w){let F=this.paths[N];F.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:A,orientation:"forward",hapStart:g.base+O,hapEnd:g.base+O+F.len}:{pathHandle:g.pathHandle,name:A,orientation:"reverse",hapStart:g.base-O-F.len,hapEnd:g.base-O}}}}this.dropTwins()}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=ti(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),X(r,"M",i),mo(r,o-i-a,s-i-a),X(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??ei(Jr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,h,u,d)=>{p===h?X(s,"D",i[d]-i[u]):u===d?X(s,"I",this.pathLen(e.slice(p,h))):this.align(e.slice(p,h),t.slice(u,d),s)},f=0,c=0,l=0;for(let p=0;p<o.count;p++){let h=o.pathAt[p],u=o.refAt[p];(c!==h||l!==u)&&a(c,h,l,u);let d=this.record(e[h]).sequenceLen;X(s,"M",d),f+=d,c=h+1,l=u+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(wt(r)&&(t.identity===void 0||!wt(nt(t.path))))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=nt(t.path),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={...this.editsAgainst(t.path,r),flipped:!1};else if(i===0)o={...this.editsAgainst(s,r),flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);o=c.matched>f.matched?{...c,flipped:!0}:{...f,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=(l,p,h,u)=>{let d=fi(l),m=this.paths[h[0]],w=this.paths[h[h.length-1]],y=m.identity,I=y?.orientation==="forward",[g,b]=I?[m,w]:[w,m];return{strand:p,refStart:e.start+d.leading,refEnd:e.start+r-d.trailing,edits:d.edits,weight:m.weight,path:h.flatMap(x=>this.paths[x].path),start:Mt(m,0),pieces:h,soloAligned:u,identity:y===void 0?void 0:{pathHandle:y.pathHandle,name:y.name,hapStart:y.name.fragment+g.identity.hapStart,hapEnd:y.name.fragment+b.identity.hapEnd,walkForward:I}}},s=l=>l.soloAligned.reduce((p,h)=>p+h,0),i=l=>l.pieces.reduce((p,h)=>p+this.paths[h].len,0),a=l=>2*s(l)>=i(l),f=l=>{let p=l[0],h=l[l.length-1],u=p.identity.walkForward;if(l.some((_,j)=>_.strand!==p.strand||_.identity.walkForward!==u||j>0&&_.identity.hapStart<l[j-1].identity.hapEnd))return;let d=u?l:[...l].reverse(),m=d.flatMap(_=>_.pieces),w=d.flatMap(_=>_.soloAligned),y=p.strand==="+"!==u,I=m.map(_=>this.paths[_]),g=I.slice(1).map((_,j)=>{let V=I[j].identity;return u?_.identity.hapStart-V.hapEnd:V.hapStart-_.identity.hapEnd}),b=y?[...I].reverse():I,x=y?[...g].reverse():g,E=b.flatMap(_=>y?nt(_.path):_.path),{edits:A}=this.editsAgainst(E,t),N=uo(A,b.map(_=>_.len)),O=new Map((y?[...m].reverse():m).map((_,j)=>[_,N[j]])),F=_=>2*_.pieces.reduce((j,V)=>j+O.get(V),0)>=s(_);if(!F(p)||!F(h))return;let R=[],z=0;return b.slice(0,-1).forEach((_,j)=>{z+=_.len,R.push([z,x[j]])}),o(ci(A,R),p.strand,m,w)},c=[];return this.paths.forEach((l,p)=>{if(p===this.refId)return;let{edits:h,flipped:u}=this.alignment(p),d=l.identity,m=d?d.orientation==="forward"!==u:!u;c.push(o(h,m?"+":"-",[p],uo(h,[l.len])))}),oi(c,a,f).map(l=>{let{edits:p,identity:h,pieces:u,soloAligned:d,...m}=l,w={...m,cigar:li(p)};return h?{...w,resolved:!0,name:h.name,label:ge({...h.name,fragment:h.hapStart},h.hapEnd),pathHandle:h.pathHandle,hapStart:h.hapStart,hapEnd:h.hapEnd}:{...w,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:kt(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(be(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(h=>({query:p.name,queryStart:p.start+h.queryStart,queryEnd:p.start+h.queryEnd,strand:h.strand,target:l.name,targetStart:l.start+h.targetStart,targetEnd:l.start+h.targetEnd,cigar:ho(h.edits),matches:h.edits.reduce((u,[d,m])=>u+(d==="="?m:0),0),columns:h.edits.reduce((u,[,d])=>u+d,0),sharedBases:h.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=be(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&je(o,s)&&t.push([r==="reverse"?1:0,M(s),U(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(!U(r)){let o=M(r),s=`S	${o}	${this.record(r).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return Wr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Ur(jr(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)U(c)||r.push(`S	${M(c)}	${this.record(c).sequence}`);let s=c=>U(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&je(c,l)&&r.push(`L	${M(c)}	${s(c)}	${M(l)}	${s(l)}	0M`);let i=(c,l,p,h,u)=>{let d=kt(c,l).map(y=>`${U(y)?"<":">"}${M(y)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,w=u===void 0?"":`	CG:Z:${u}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${h}	${d}${m}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,h=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,h):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,h)),f+=1}}),`${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)&&je(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!U(s)).map(s=>({id:String(M(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(M(s)),from_is_reverse:U(s),to:String(M(i)),to_is_reverse:U(i)});let o=this.outputPaths(e).map(s=>ai(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!U(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=M(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(kt(i.info,i.identity))}))}}};function kt(n,e){return e?.orientation==="reverse"?n.path.map(t=>oe(t)).reverse():n.path}function ai(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:kt(n,e).map(o=>({id:String(M(o)),is_reverse:U(o)}))}}function _t(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 X(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function Pt(n){return n===0?0:6+(n-1)}function mo(n,e,t){if(e===0)X(n,"D",t);else if(t===0)X(n,"I",e);else{let r=Math.min(e,t),o=4*r+Pt(e-r)+Pt(t-r),s=Pt(e)+Pt(t);o<=s?(X(n,"M",r),X(n,"I",e-r),X(n,"D",t-r)):(X(n,"I",e),X(n,"D",t))}}function fi(n){let e=0;for(;e<n.length&&n[e][0]!=="M";)e+=1;if(e===n.length){let a=n.filter(([c])=>c==="I"),f=n.filter(([c])=>c==="D").reduce((c,[,l])=>c+l,0);return{edits:a.map(([c,l])=>[c,l]),leading:0,trailing:f}}let t=n.length;for(;n[t-1][0]!=="M";)t-=1;let r=a=>({inserted:a.reduce((f,[c,l])=>f+(c==="I"?l:0),0),deleted:a.reduce((f,[c,l])=>f+(c==="D"?l:0),0)}),o=r(n.slice(0,e)),s=r(n.slice(t)),i=[];X(i,"I",o.inserted);for(let[a,f]of n.slice(e,t))X(i,a,f);return X(i,"I",s.inserted),{edits:i,leading:o.deleted,trailing:s.deleted}}function uo(n,e){let t=e.map(()=>0),r=e.length-1,o=0,s=e[0],i=0;for(let[a,f]of n){if(a==="D")continue;let c=f;for(;c>0;){for(;o<r&&i>=s;)o+=1,s+=e[o];let l=o<r?Math.min(c,s-i):c;a==="M"&&(t[o]+=l),i+=l,c-=l}}return t}function ci(n,e){let t=[],r=0,o=0;for(let[s,i]of n){if(s==="D"){X(t,s,i);continue}let a=r;for(;o<e.length&&e[o][0]<r+i;){let[f,c]=e[o];X(t,s,f-a),X(t,"I",c),a=f,o+=1}X(t,s,r+i-a),r+=i}for(;o<e.length;o++)X(t,"I",e[o][1]);return t}function li(n){return n.map(([e,t])=>`${t}${e}`).join("")}async function go(n,e,t,r,o){let s=new Ot(n,o);try{let i=await s.pathPosition(St(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 Pe&&i.windowBp===void 0?new Pe(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}}async function wo(n,e,t,r,o={}){let{subgraph:s,reference:i}=await go(n,e,t,r,o);return s.extractPaths(i,o.haplotypes??"all"),s}async function yo(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 go(n,e,t,r,o),a=o.haplotypes??"all";return a==="reference-only"||a==="none"?s.extractPaths(i,a):await s.extractChosenPaths(i,r-t,o.keep,o.context??100)||(s.extractPaths(i,"all"),await s.identifyPaths()),s.keepHaplotypes(o.keep),a==="distinct"&&s.mergeDistinct(),s}function Ie(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 pi(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 hi=new TextDecoder;function Nt(n){let[e,t]=Ie(n,0),r=[],o=t;for(;o<e;){let[a,f]=Ie(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=pi(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:hi.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var ot=2,Lt=5,bo=10,Tt=13;function So(n,e){return n[e]*256+n[e+1]}function ke(n,e){return n[e]*16777216+n[e+1]*65536+n[e+2]*256+n[e+3]}function di(n,e){let t=n[e];if(t!==ot&&t!==Lt&&t!==bo&&t!==Tt)throw new Error(`SQLite page has unknown b-tree type ${t}`);let r=t===ot||t===Lt;return{type:t,cellCount:So(n,e+3),rightChild:r?ke(n,e+8):0,cellPointers:e+(r?12:8)}}function Ce(n,e,t){return So(n,e.cellPointers+2*t)}var ui=4096,mi=4096,Ft=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let 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=ke(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=ke(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:di(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===Tt)return s;if(a.type!==Lt)throw new Error("SQLite table b-tree contains an index page");let f=this.childIndexFor(i,a,t);o=f===a.cellCount?a.rightChild:ke(i,Ce(i,a,f))}})(),this.tableDepths.set(e,r),r.catch(()=>this.tableDepths.delete(e))),r}childIndexFor(e,t,r){let o=0,s=t.cellCount;for(;o<s;){let i=o+s>>1,[a]=Ie(e,Ce(e,t,i)+4);a<r?o=i+1:s=i}return o}async prefetchRowidRange(e,t,r){let o=await this.tableDepth(e,t),s=[e];for(let i=0;i<o;i++){let a=await Promise.all(s.map(c=>this.pageAt(c))),f=[];if(a.forEach(({page:c,header:l},p)=>{let h=p===0?this.childIndexFor(c,l,t):0,u=p===a.length-1?this.childIndexFor(c,l,r):l.cellCount;for(let d=h;d<=u;d++)f.push(d===l.cellCount?l.rightChild:ke(c,Ce(c,l,d)))}),f.length>mi)return!1;this.pager.prefetch(f),s=f}return!0}async tableRowid(e,t){let r=e;for(;;){let{page:o,header:s}=await this.pageAt(r);if(s.type===Tt){let f=0,c=s.cellCount;for(;f<c;){let l=f+c>>1,p=Ce(o,s,l),[h,u]=Ie(o,p),[d,m]=Ie(o,u);if(d===t)return Nt(await this.payload(o,m,h,!1));d<t?f=l+1:c=l}return}if(s.type!==Lt)throw new Error("SQLite table b-tree contains an index page");let i=0,a=s.cellCount;for(;i<a;){let f=i+a>>1,c=Ce(o,s,f),[l]=Ie(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:ke(o,Ce(o,s,i))}}async*tableScan(e){let{page:t,header:r}=await this.pageAt(e);if(r.type===Tt)for(let o=0;o<r.cellCount;o++){let s=Ce(t,r,o),[i,a]=Ie(t,s),[f,c]=Ie(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(ke(t,Ce(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>=ui){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=Ce(t,r,o),f=r.type===ot,[c,l]=Ie(t,f?a+4:a);i={values:Nt(await this.payload(t,l,c,!0)),leftChild:f?ke(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);xo(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);xo(p.values,t)<=0?(r=p.values,a=l+1):(c=p.leftChild,f=l)}if(i.type===bo)return r;o=a===i.cellCount?i.rightChild:c}}};function xo(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 h=new Ht(e,c,r,t);h.seed(0,o),h.fetches+=1,h.bytesFetched+=o.length;let u=new Ft(h,l),d=new Map;for await(let{values:m}of u.tableScan(1)){let[w,y,I,g,b]=m;typeof w=="string"&&typeof y=="string"&&typeof I=="string"&&typeof g=="number"&&d.set(y,{type:w,name:y,tableName:I,rootPage:g,sql:typeof b=="string"?b:""})}return new n(h,u,d)}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(o=>o.type==="index"&&o.tableName===e);if(t)return t.rootPage;let r=this.objects.get(e);if(r?.type==="table"&&/without\s+rowid/i.test(r.sql))return r.rootPage;throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var qn="GBZ-base version 4",qt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Bt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${qn}"`),this.found=e}},Gt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,o,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=o,this.next=s,this.sequenceLen=$r(o)}get id(){return M(this.handle)}get orientation(){return ze(this.handle)}get sequence(){return this.decoded??=qr(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 ${this.handle} is empty`);return new xt(this.edges,this.bwt)}};function q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function Dt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function $t(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function Io(n,e){return{handle:n,fwStart:{node:q(e[1],"Paths.fw_node"),offset:q(e[2],"Paths.fw_offset")},revStart:{node:q(e[3],"Paths.rev_node"),offset:q(e[4],"Paths.rev_offset")},name:{sample:Dt(e[5],"Paths.sample"),contig:Dt(e[6],"Paths.contig"),haplotype:q(e[7],"Paths.haplotype"),fragment:q(e[8],"Paths.fragment")},isIndexed:q(e[9],"Paths.is_indexed")!==0}}async function vo(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(Dt(t[0],"Tags.key"),Dt(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!==qn)throw new Bt(f);if(i){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(u);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"),h=await a.tag("nodes");if(p!==void 0&&p!==h)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${h}`);if(a.indexTags.get("haplotype_index_orientations")==="forward")throw new qt}return a}tags(){return this.tagCache??=vo(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new Gt(e,Hr($t(t[1],"Nodes.edges")),$t(t[2],"Nodes.bwt"),$t(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(Io(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?Io(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=St(Qr(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),h=Math.min(r,e.end),u=o.haplotypes??"all",d=u==="all"||u==="distinct",m;return s!==void 0&&d?m=await yo(this,l,p,h,{...i,keep:s}):(m=await wo(this,l,p,h,i),this.hasHaplotypeIndex&&d&&await m.identifyPaths()),m}async getSubgraphForRange(e,t,r,o={}){let s=await this.pathFragmentsForRange(e,t,r),[i]=s;if(s.length>1){let a=i.path.name;throw new Error(`the window ${t}-${r} spans ${s.length} fragments of ${ge(a,0)}: query each fragment from pathFragmentsForRange, or use getAlignmentsForRange`)}return i?this.subgraphForFragment(i,t,r,o):void 0}async getAlignmentsForRange(e,t,r,o={}){let s=[];for(let i of await this.pathFragmentsForRange(e,t,r)){let a=await this.subgraphForFragment(i,t,r,o);s.push(...a.alignments())}return s}async graphName(){let e=new Map;for(let[r,o]of await this.tags())r.startsWith("gbz_")&&e.set(r.slice(4),o);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=zr(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=r=>this.indexTags.get(`haplotype_index_stray_${r}`);if(!this.index?.has("HaplotypeStrays")||!this.index.has("HaplotypeBinNodes")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async haplotypeStraysInBins(e,t,r){let o=[];for await(let s of this.companion.indexScanFrom("HaplotypeStrays",[e,t])){let i=q(s[1],"HaplotypeStrays.bin");if(s[0]!==e||i>r)break;let a=q(s[4],"HaplotypeStrays.snarl_low"),f=q(s[5],"HaplotypeStrays.snarl_high");o.push({bin:i,pathHandle:q(s[2],"HaplotypeStrays.path_handle"),pathStart:q(s[3],"HaplotypeStrays.path_start"),snarl:f>0?[a,f]:void 0,pathEnd:q(s[6],"HaplotypeStrays.path_end"),node:q(s[7],"HaplotypeStrays.node_handle"),offset:q(s[8],"HaplotypeStrays.node_offset")})}return o}async haplotypeBinNodes(e,t,r){let o=[];for await(let a of this.companion.indexScanFrom("HaplotypeBinNodes",[e,t])){if(a[0]!==e||q(a[1],"HaplotypeBinNodes.bin")>r)break;let f=$t(a[3],"HaplotypeBinNodes.nodes"),c=0,l=0,p=()=>{let h=0,u=1;for(;;){let 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try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},cr=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},lr=class extends Error{constructor(t,r){super(`the graph is cut on its reference, ${r}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function bs(n,e){let t=Ee(e);return n[t]??n[e.sample]??t}function na(n,e){return`${Ee(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function ra({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,p=na(f,n),h={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new Oe(h)}}function oa({pair:n,lane:e,mateLane:t}){let r=`${Ee(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${Ee(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new Oe({uniqueId:r,assemblyName:e,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:r,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var ir=n=>!("uri"in n)||n.uri!=="",pr=class extends gn{constructor(){super(...arguments);this.graph=(0,ar.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=ir(r)?{location:r}:await Ao(t,this.pluginManager),s=o.location,i=await it.open((0,wn.openLocation)(t,this.pluginManager),s?{haplotypeIndex:(0,wn.openLocation)(s,this.pluginManager)}:{}),a=this.getConf("assemblyNames")[0];if(a===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let f=await vn(i),c=dt({configured:this.getConf("referenceSample"),anchorPrefix:De(this,a),referenceSamples:f});return{db:i,anchor:a,referenceSample:c,referenceSamples:f,unreadableIndex:o.unreadable}}});this.gaf=(0,ar.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]);return ir(t)?new zt((0,wn.openLocation)(t,this.pluginManager),ir(r)?Or(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return En(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=Ee(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=Sn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:bs(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:De(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:ht(Ee(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=>De(this,s));return o===void 0&&r===void 0?void 0:s=>In(s,o)&&(r===void 0||ht(Ee(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s,unreadableIndex:i}=await this.graph(),{assemblyName:a,refName:f,start:c,end:l}=t;if(a!==s)throw new lr(a,s);let p=await this.referenceQuery(f,{}),h=this.keepPredicate(r.haplotypes);if(h!==void 0&&!o.hasHaplotypeIndex)throw new yn(i);return An(o,p,c,l,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,...h===void 0?{}:{keep:h}})}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=De(this,t);return(await this.getHaplotypes(r)).filter(s=>ht(s.prefix,o))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=De(this,r.targetAssemblyName),l=Sn(this),p=this.keepPredicate(r.haplotypes,c),h=await this.referenceQuery(i,r),u=this.getConf("nodeLimit");return(h?await(0,fr.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignmentsForRange(h,a,f,{context:this.getConf("context"),haplotypes:"all",limit:u,signal:r.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw ut(m,u,f-a)??m})):[]).flatMap(m=>{let w=m.resolved?ra({alignment:m,assemblyName:s,refName:i,lane:bs(l,m.name)}):void 0;return w===void 0?[]:[w]})}async pairFeatures(t,r,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new cr(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),h=[...l,...p],u=await this.referenceQuery(a,o),d=this.getConf("nodeLimit"),m=(y,I)=>i.getSubgraphForRange(y,I.start,I.end,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:d,signal:o.signal,keep:g=>h.some(b=>b.sample===g.sample&&b.haplotype===g.haplotype)}).catch(g=>{throw ut(g,d,c-f,I.start-f)??g});return(u&&l.length>0&&p.length>0?(await(0,fr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await Er(i,u,f,c)).map(y=>m(u,y))))).filter(y=>y!==void 0):[]).flatMap(y=>l.flatMap(I=>p.flatMap(g=>y.pairAlignments({target:I,query:g,bases:!1}).map(b=>oa({pair:b,lane:r,mateLane:s})))))}getFeatures(t,r={}){return(0,Ss.ObservableCreate)(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new yn(a);if(t.assemblyName===i){let f=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let c of f)o.next(c)}o.complete()},r.signal)}};export{lr as HaplotypeWindowError,yn as NoHaplotypeIndexError,Rs as NoReferenceSampleError,Ms as NodeLimitError,cr as PairTargetError,pr as default,ra as fragmentFeature,Ee as haplotypePrefix,bs as laneAssemblyName,ut as nodeLimitError,oa as pairFeature,dt as resolveReferenceSample};
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