jbrowse-plugin-graphgenomeviewer 4.0.24 → 4.0.25

package/dist/chunks/GbzBaseSyntenyAdapter-LTKB3OX7.js

@@ -0,0 +1,8 @@
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l(X(x.node))).gbwt().predecessorAt(x.offset);if(R===void 0||C!==void 0&&!C.has(R))return;let D=(await l(R)).gbwt().offsetTo(x);if(D===void 0)throw new Error(`No offset in ${R} leads to ${x.node}:${x.offset}`);return{node:R,offset:D}},b=(x,C,R,D)=>{let V=R.map(he=>he.pos.node),Z=R.map(he=>he.pos.offset),J=0;for(let he of V)J+=p(he);let ee=C==="forward"?R[0].left:R[R.length-1].left,Ae=d.length;d.push({pathHandle:x,orientation:C,handles:V,offsets:Z,len:J,hapStart:ee,hapEnd:ee+J,canonical:Ne(V[0],V[V.length-1]),source:D});for(let he of R)m.set(he.pos,Ae);let Te=y.get(x);return Te?Te.push(Ae):y.set(x,[Ae]),Ae},E=async(x,C,R,D)=>{let V=[],Z=x;for(;;){r?.throwIfAborted();let ee=await v(Z.pos,t);if(!ee)break;Z={pos:ee,left:Mn(R,Z.left,p(Z.pos.node),p(ee.node))},V.push(Z)}V.reverse();let J=[x];for(Z=x;;){r?.throwIfAborted();let ee=await g(Z.pos);if(!ee||!t.has(ee.node))break;Z={pos:ee,left:ot(R,Z.left,p(Z.pos.node),p(ee.node))},J.push(Z)}return b(C,R,[...V,...J],D)},M=async(x,C,R,D)=>d[m.get(x.pos)??await E(x,C,R,D)],L=x=>{let C=x.handles[x.handles.length-1];return{pos:{node:C,offset:x.offsets[x.offsets.length-1]},left:x.orientation==="forward"?x.hapEnd-p(C):x.hapStart}},k=x=>{let C=x.handles[0];return{pos:{node:C,offset:x.offsets[0]},left:x.orientation==="forward"?x.hapStart:x.hapEnd-p(C)}},T=await E({pos:n.referencePos,left:n.referenceLeft},n.referenceHandle,"forward","reference"),P=d[T],G=()=>{if(i.fallback!==void 0)return{reference:P,pieces:[],stats:i};let x=new Map;d.forEach((R,D)=>{D!==T&&x.set(Fe(R),[...x.get(Fe(R))??[],R])});let C=[];for(let R of x.values()){let D=new Set;for(let V of R)V.canonical&&!D.has(V.orientation)&&(D.add(V.orientation),C.push(V),i.sources[V.source]+=1)}return i.sources.reference=1,i.pieces=C.length,{reference:P,pieces:C,stats:i}};try{let x=i.spacing;if(x===void 0)throw new oe("the haplotype index has no anchors");let C=Math.floor(n.window.start/x),R=Math.ceil(n.window.end/x),D=w=>w>=0?e.haplotypeAnchor(n.referenceHandle,w*x):Promise.resolve(void 0),[V,Z]=await Promise.all([Promise.all([0,1,2].map(w=>D(C-w))),Promise.all([0,1,2,3].map(w=>D(R+w)))]),J=V[0],ee=Z.slice(0,2).findIndex(w=>w!==void 0&&w.pathOffset>=n.window.end),Ae=Z[ee];if(!J)throw new oe("the haplotype index has no anchor before the window");if(!Ae)throw new oe("the haplotype index has no anchor after the window");i.anchors=[J.pathOffset,Ae.pathOffset];let Te=V.filter(w=>w!==void 0),he=Z.slice(ee,ee+3).filter(w=>w!==void 0),ks=w=>{let A=w-w%2;return e.haplotypeSamplesInRange(A,A+1)},ut=new Map,xn=[...Te,...he],_s=await Promise.all(xn.map(w=>ks(w.node)));if(xn.forEach((w,A)=>ut.set(w,_s[A])),i.anchorsRead=xn.length,!ut.get(J).some(w=>w.pathHandle===n.referenceHandle&&w.orientation==="forward"&&w.pathOffset===J.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${J.pathOffset} (node ${O(J.node)}); it does not match this graph`);let yr=(w,A)=>{for(let _ of w){let z=ut.get(_).filter(U=>U.pathHandle===A);if(z.length>0)return{anchor:_,rows:z}}},De=new Map,tt=[],bn=new Set,Os=async w=>{let A=yr(Te,w),_=yr(he,w);if(!A&&!_)return;let z=A?.rows??[],U=_?.rows??[],W=[],N=new Set,j=A?.anchor??J,F=_?.anchor??Ae,$=F.pathOffset-j.pathOffset,ce=u(w),te=!1;for(let q of z){let ie=q.orientation==="forward"?1:-1,Ee=U.filter(ke=>ke.orientation===q.orientation&&(ke.pathOffset-q.pathOffset)*ie>0).sort((ke,$s)=>(ke.pathOffset-$s.pathOffset)*ie)[0];if(!Ee)continue;let Me=q.node===j.node,ze=Ee.node===F.node,Y=Ee.pathOffset,ne=0;Me&&!ze?Y+=ie*((await l(Ee.node)).sequenceLen+$):!Me&&ze&&(ne=$);let re=q.pathOffset-ie*ne;W.push([Math.min(re,Y),Math.max(re,Y)]),N.add(q.pathOffset),N.add(Ee.pathOffset),te=!0,ce&&(tt.push({row:q,stopAt:Y,back:ne,kind:Me===ze?"interval":"inversion"}),bn.add(w))}let de=new Map;for(let q of[...z,...U])te?N.has(q.pathOffset)||(W.push([q.pathOffset,q.pathOffset]),de.set(q.pathOffset,q)):W.push([q.pathOffset-$,q.pathOffset+$]);let se=Ks(W,ae);if(se.length>1)throw new oe(`path ${w} visits the anchors from ${se.length} copies of the region, at ${se.map(([q,ie])=>`${q}-${ie}`).join(", ")}`);if(De.set(w,se[0]),ce)for(let q of de.values())tt.push({row:q,stopAt:q.pathOffset,back:0,kind:"interval"});if(!te){for(let q of[...z,...U])if(ce&&(q.node===j.node||q.node===X(F.node))){let ie=q.orientation==="forward"?1:-1;tt.push({row:q,stopAt:q.pathOffset+ie*$,back:0,kind:"one-sided"}),bn.add(w)}}return te?"paired":"one-sided"},xr=new Set([...ut.values()].flat().map(w=>w.pathHandle)),mt=[...xr].filter(u);if(i.chosenPaths=mt.length,mt.length>Zr.mostChosenPaths)throw new oe(`${mt.length} chosen paths pass the anchors, more than ${Zr.mostChosenPaths}`);for(let w of xr)await Os(w);let Sn=[],vn=[];i.scans=_n([...t.keys()].sort((w,A)=>w-A));for(let[w,A]of i.scans)for(let _ of await e.haplotypeSamplesInRange(w,A))i.scanRows+=1,t.has(_.node)&&(vn.push(_),u(_.pathHandle)&&Sn.push(_));if(mt.length===0&&Sn.length===0&&[...h.values()].some(w=>n.keep(w.name)))throw new oe("no chosen path passes the anchors or has a sample on the window's nodes");let In=new Set(vn.map(w=>w.pathHandle).filter(w=>!De.has(w))),Ls=he[he.length-1].pathOffset-Te[Te.length-1].pathOffset,br=w=>`${w.sample}#${w.haplotype}#${w.contig}`,An=new Map;for(let[w,[A,_]]of De){let z=h.get(w)?.name;if(z&&u(w)){let U=br(z),W=z.fragment+A-ae,N=z.fragment+_+ae,j=An.get(U);An.set(U,j?[Math.min(j[0],W),Math.max(j[1],N)]:[W,N])}}let Sr=[];for(let[w,A]of h){let _=An.get(br(A.name));if(_&&!De.has(w)&&!In.has(w)&&n.keep(A.name)){let z=await e.haplotypeLength(w)??0;A.name.fragment<_[1]&&A.name.fragment+z>_[0]&&Sr.push(w)}}for(let w of[...In,...Sr]){let A=await e.haplotypeLength(w)??Number.POSITIVE_INFINITY;if(A>Ls+2*ae)throw new oe(In.has(w)?`path ${w} of ${A} bp has a sample on the window's nodes and no visit to the anchors`:`chosen fragment ${w} of ${A} bp lies beside its contig's visits to the anchors without a visit of its own`);if(u(w)){let _=(await e.getPath(w))?.fwStart;if(!_)throw new Error(`Path ${w} is missing from the database`);tt.push({row:{node:_.node,offset:_.offset,pathHandle:w,orientation:"forward",pathOffset:0},stopAt:A,back:0,kind:"whole"})}}for(let w of De.keys())if(u(w)&&!bn.has(w))throw new oe(`chosen path ${w} has no walk from its visits to the anchors`);for(let w of vn){let A=De.get(w.pathHandle);if(A&&(w.pathOffset<A[0]-Xr||w.pathOffset>A[1]+Xr))throw new oe(`path ${w.pathHandle} has a sample at ${w.pathOffset} on the window's nodes far from its anchor visits at ${A[0]}-${A[1]}`)}i.ms.scan=s();let En=new Map;await n.prefetchReferenceRange(n.referenceHandle,Math.max(0,J.pathOffset-ae),Ae.pathOffset+ae+1);let vr=8*x+2*(n.window.end-n.window.start);for(let{row:w,stopAt:A,back:_,kind:z}of tt){let U=w.orientation,W=(Y,ne)=>U==="forward"?ne-Y:Y-ne,N=w.pathOffset,j=w.pathOffset,F={node:w.node,offset:w.offset},$=w.pathOffset,ce=!1,te=0,de=0,se="past the far anchor";for(;F&&(r?.throwIfAborted(),!ce&&W($,A)<=-ae&&(ce=!0),!(ce&&te>ae));){let Y;if(t.has(F.node)){let re=await M({pos:F,left:$},w.pathHandle,U,"interval"),ke=L(re);F=ke.pos,$=ke.left,Y=p(ke.pos.node),N=Math.min(N,re.hapStart),j=Math.max(j,re.hapEnd),te=0}else{if(Y=(await l(F.node)).sequenceLen,te+=Y,de+=Y,de>vr){se="cap";break}N=Math.min(N,$),j=Math.max(j,$+Y)}let ne=await g(F);ne&&($=ot(U,$,Y,(await l(ne.node)).sequenceLen)),F=ne}if(!F&&se!=="cap"&&(se="endmarker"),a(z,se),se==="cap")throw new oe(`the walk of path ${w.pathHandle} between the anchors reached its cap of ${vr} bp`);if(z==="one-sided"&&se!=="endmarker")throw new oe(`chosen path ${w.pathHandle} runs on past the stretch from its visit to one anchor without a visit to the other`);let q=ae,ie={pos:{node:w.node,offset:w.offset},left:w.pathOffset},Ee=0,Me=_;for(;q>0||Me>0;){r?.throwIfAborted();let Y=await v(ie.pos);if(!Y)break;let ne=Mn(U,ie.left,(await l(ie.pos.node)).sequenceLen,(await l(Y.node)).sequenceLen);if(t.has(Y.node)){let re=await M({pos:Y,left:ne},w.pathHandle,U,"interval");ie=k(re),N=Math.min(N,re.hapStart),j=Math.max(j,re.hapEnd),q=ae,Ee=0,Me-=re.len}else{let re=(await l(Y.node)).sequenceLen;if(Ee+=re,Ee>q&&Me<=0)break;Me-=re,ie={pos:Y,left:ne},N=Math.min(N,ne),j=Math.max(j,ne+re)}}let ze=En.get(w.pathHandle);ze?ze.push([N,j]):En.set(w.pathHandle,[[N,j]])}let Ts=w=>(En.get(w.pathHandle)??[]).some(([A,_])=>A<=w.hapStart&&w.hapEnd<=_);i.ms.intervals=s();for(let w of Sn)m.get(w)===void 0&&!(y.get(w.pathHandle)??[]).some(A=>{let _=d[A];return _.canonical&&!Jr(_)&&_.hapStart<=w.pathOffset&&w.pathOffset<_.hapEnd})&&(i.seeds+=1,await E({pos:{node:w.node,offset:w.offset},left:w.pathOffset},w.pathHandle,w.orientation,"sample"));i.ms.seeds=s();let gt=async(w,A)=>{let _=A?S:I,z=A?I:S,U=w;for(;;){if(_.has(U))return;_.add(U);let W=d[U],N=A?L(W):k(W),j=0,F;for(;F===void 0;){r?.throwIfAborted();let $=A?await g(N.pos):await v(N.pos);if(!$){F="endmarker";break}let ce=(await l(N.pos.node)).sequenceLen,te=(await l($.node)).sequenceLen,de=A?ot(W.orientation,N.left,ce,te):Mn(W.orientation,N.left,ce,te);if(t.has($.node)){let se=m.get($);se===void 0?(U=await E({pos:$,left:de},W.pathHandle,W.orientation,"chain"),z.add(U),F="landed"):(z.add(se),F="merge")}else j>ae?F="bound":(j+=te,N={pos:$,left:de})}if(a("chain",F),F!=="landed")return}};await Promise.all([n.prefetchReferenceRange(n.referenceHandle,Math.max(0,P.hapStart-ae),P.hapStart),n.prefetchReferenceRange(n.referenceHandle,P.hapEnd,P.hapEnd+ae)]);let Ir=new Set,Ns=d.map((w,A)=>({piece:w,id:A})).filter(({piece:w,id:A})=>A!==T&&!Ts(w)).sort((w,A)=>Number(A.piece.canonical)-Number(w.piece.canonical));for(let{piece:w,id:A}of Ns)Ir.has(Fe(w))||(Ir.add(Fe(w)),await gt(A,!0),await 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p=[],h=l[0],u=l.at(-1),{flipped:d}=h.run;Mt(l,o,s,p,f?(y,S,I,g,v)=>{for(let b of ii(y,S,I,a)){let E=v+S.length;c.push({...b,queryStart:g+b.queryStart,queryEnd:g+b.queryEnd,targetStart:d?E-b.targetEnd:v+b.targetStart,targetEnd:d?E-b.targetStart:v+b.targetEnd,strand:d?"+":"-",edits:d?b.edits.reverse():b.edits,shared:[]})}}:qn),c.push({queryStart:h.run.qs+h.trim,queryEnd:u.run.qe,targetStart:d?u.run.ts:h.run.ts+h.trim,targetEnd:d?h.run.te-h.trim:u.run.te,strand:d?"-":"+",edits:d?p.reverse():p,sharedBases:l.reduce((y,{run:S,trim:I})=>y+S.qe-S.qs-I,0),shared:l.map(({run:y,trim:S})=>[y.qs+S,y.qe])})}return fi(c,o.length,s.length,a).map(({shared:l,...p})=>p).sort((l,p)=>l.queryStart-p.queryStart)}function go(n){return n.map(([e,t])=>`${t}${e}`).join("")}var _e=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Bn(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var st=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Bn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Bn(e[s],e[a])&&(a=s),i<e.length&&Bn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function li(n){let e=new Int32Array(n.length),t=new Int32Array(n.length);return n.forEach(([r,o],s)=>{e[s]=r,t[s]=o}),{pathAt:e,refAt:t,count:n.length}}function pi(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]>e?r=o:t=o+1}return n[t]}function qe(n){return`${n.node}:${n.offset}`}function wo(n){return n.map(e=>X(e)).reverse()}function hi(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 di(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);xo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)K(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 ui(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?hi(f,p):void 0;if(h){f=di(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 kt(n,e){return{node:n.path[e],offset:n.offsets[e]}}var mi=32768;function gi(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]<=mi?o[1]=r:t.push([r,r])}return t}var Lt=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(ye(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 _e(this.limit);let t=await this.db.getRecord(ye(e,"forward")),r=await this.db.getRecord(ye(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 ${xe(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${xe(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 ${xe(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(O(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${xe(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=We(e),a=new st;return a.push(t,o,xt(i)),a.push(s.sequenceLen-t-1,o,bt(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=gi(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 _e&&o.windowBp===void 0?new _e(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 st;for(;;){let f=O(o.node),c=We(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 ${l.sequenceLen}`);a.push(s,f,xt(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,bt(c));break}a.push(0,f,bt(c));let h=l.gbwt().lf(o.offset);if(!h)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=h,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new st;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${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}:${l}`)){let u=this.record(ye(a,Fr(f))),d=i+u.sequenceLen-1;d<=t&&e.push(d,a,l)}let p=this.record(ye(a,$r(f))),h=i+1;if(h<=t)for(let u of p.successors()){let d=O(u),m=xt(We(u));r.has(`${d}:${m}`)||e.push(h,d,m)}}for(let i of o)this.records.delete(ye(i,"forward")),this.records.delete(ye(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,X(t)],o=new Set([O(e),O(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(r.push(f,X(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)?Qe(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(X(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(X(l))).successors().length>1},r=async f=>{let c=await e(X(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[X(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await 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(ye(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((b,E)=>i.set(b,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let b=0;b<s;b++){let E=this.record(o[b]),M=E.gbwt().decompressArrays();f[b]=E.sequenceLen,c.push(M),a[b+1]=a[b]+M.nodes.length}let l=a[s],p=new Int32Array(l),h=new Int32Array(l),u=new Uint8Array(l);for(let b=0;b<s;b++){let E=c[b];p.set(E.nodes,a[b]),h.set(E.offsets,a[b])}c.length=0;for(let b=0;b<l;b++){let E=i.get(p[b]);E===void 0?p[b]=-1:(p[b]=E,u[a[E]+h[b]]=1)}let d=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,y,S=(b,E,M)=>{let L=[],k=0,T=0,P=-1,G=b,x=E;for(;;){G===d&&x===m&&(P=k),M&&(M.push(o[G]),L.push(x)),k+=1,T+=f[G];let C=a[G]+x,R=p[C];if(R<0)break;x=h[C],G=R}return{offsets:L,len:T,refAt:P,last:G}},I=(b,E,M,L)=>{L>=0&&(this.refId=this.paths.length,y=L),this.paths.push({path:b,offsets:E,len:M,weight:void 0,identity:void 0})},g=new Int32Array(s),v=d!==void 0&&B(o[d]);for(let b=0;b<s;b++){let E=o[b];if(!B(E)){let M=a[b],L=a[b+1]-M;for(let k=0;k<L;k++)if(u[M+k]===0){let T=[],{offsets:P,len:G,refAt:x,last:C}=S(b,k,T),R=o[C];if(x>=0||Ne(E,R)){if(I(T,P,G,x),!B(R)){let D=i.get(X(R));g[D]=g[D]+1}}else this.twinStarts.add(qe({node:E,offset:k}))}}}for(let b=0;b<s;b++){let E=o[b];if(B(E)){let M=a[b],L=a[b+1]-M,k=0;for(let P=0;P<L;P++)u[M+P]===0&&(k+=1);let T=!v&&k===g[b];for(let P=0;P<L;P++)if(u[M+P]===0){let G=T?void 0:S(b,P,void 0);if(G&&(G.refAt>=0||Ne(E,o[G.last]))){let x=[],{offsets:C,len:R,refAt:D}=S(b,P,x);I(x,C,R,D)}else this.twinStarts.add(qe({node:E,offset:P}))}}}if(r){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let b=this.paths[this.refId],E=r.nodeOffset;for(let L of b.path.slice(0,y))E+=this.record(L).sequenceLen;let M=r.seqOffset-E;this.refInterval=[M,M+b.len],b.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:M,hapEnd:M+b.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(O(i));for(let s of[...this.records.keys()])o.has(O(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 eo({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(to);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=_n(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[d,m]of t)for(let y of await this.db.haplotypeSamplesInRange(d,m))r.set(qe(y),y);let o=d=>{let m=0,y=t.length-1;for(;m<y;){let I=m+y+1>>1;t[I][0]<=d?m=I:y=I-1}let S=t[m];return S[0]<=d&&d<=S[1]},s=new Map;this.paths.forEach((d,m)=>{d.path.length>0&&m!==this.refId&&s.set(qe(kt(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(qe(d));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(d.node,d.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async d=>{let m=l.get(d);if(!m){let y=await this.db.getPath(d);if(!y)throw new Error(`Path ${d} is missing from the database`);m=y.name,l.set(d,m)}return m},h=(d,m,y)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.pathOffset-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.pathOffset+m+y},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 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,v=0,b=d,E;for(;g===void 0;){if(this.signal?.throwIfAborted(),b!==void 0){if(S.has(b)){I.end="cycle";break}S.add(b);let P=this.paths[b];y.push({index:b,startBp:v}),I.fragments+=1;let G=v;for(let C=0;C<P.path.length;C++){let R=kt(P,C),D=r.get(qe(R)),V=this.record(R.node).sequenceLen;if(D){g=h(D,G,V);break}G+=V}if(v+=P.len,g){I.end="in-fragment sample";break}let x=kt(P,P.path.length-1);E=this.record(x.node).gbwt().lf(x.offset),b=void 0}if(E===void 0||E.node===0){I.end="endmarker";break}let M=qe(E),L=s.get(M);if(L!==void 0){let P=this.paths[L].identity;if(P){g=u(P,v),I.end="identified sibling";break}b=L;continue}this.records.has(E.node)&&(I.reentries+=1),this.twinStarts.has(M)&&(I.twinLandings+=1);let k=await c(E,I),T=await f(E.node);if(k){g=h(k,v,T.sequenceLen),I.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,I.steps+=1,v-y[y.length-1].startBp>4*e+4*T.sequenceLen){I.end="bound";break}v+=T.sequenceLen,E=T.gbwt().lf(E.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=pi(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),K(r,"M",i),xo(r,o-i-a,s-i-a),K(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??li(no(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,h,u,d)=>{p===h?K(s,"D",i[d]-i[u]):u===d?K(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;K(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(qr(r))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=wo(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=yi(l),m=this.paths[h[0]],y=this.paths[h[h.length-1]],S=m.identity,I=S?.orientation==="forward",[g,v]=I?[m,y]:[y,m];return{strand:p,refStart:e.start+d.leading,refEnd:e.start+r-d.trailing,edits:d.edits,weight:m.weight,path:h.flatMap(b=>this.paths[b].path),start:kt(m,0),pieces:h,soloAligned:u,identity:S===void 0?void 0:{pathHandle:S.pathHandle,name:S.name,hapStart:S.name.fragment+g.identity.hapStart,hapEnd:S.name.fragment+v.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((x,C)=>x.strand!==p.strand||x.identity.walkForward!==u||C>0&&x.identity.hapStart<l[C-1].identity.hapEnd))return;let d=u?l:[...l].reverse(),m=d.flatMap(x=>x.pieces),y=d.flatMap(x=>x.soloAligned),S=p.strand==="+"!==u,I=m.map(x=>this.paths[x]),g=I.slice(1).map((x,C)=>{let R=I[C].identity;return u?x.identity.hapStart-R.hapEnd:R.hapStart-x.identity.hapEnd}),v=S?[...I].reverse():I,b=S?[...g].reverse():g,E=v.flatMap(x=>S?wo(x.path):x.path),{edits:M}=this.editsAgainst(E,t),L=yo(M,v.map(x=>x.len)),k=new Map((S?[...m].reverse():m).map((x,C)=>[x,L[C]])),T=x=>2*x.pieces.reduce((C,R)=>C+k.get(R),0)>=s(x);if(!T(p)||!T(h))return;let P=[],G=0;return v.slice(0,-1).forEach((x,C)=>{G+=x.len,P.push([G,b[C]])}),o(xi(M,P),p.strand,m,y)},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],yo(h,[l.len])))}),ui(c,a,f).map(l=>{let{edits:p,identity:h,pieces:u,soloAligned:d,...m}=l,y={...m,cigar:bi(p)};return h?{...y,resolved:!0,name:h.name,label:xe({...h.name,fragment:h.hapStart},h.hapEnd),pathHandle:h.pathHandle,hapStart:h.hapStart,hapEnd:h.hapEnd}:{...y,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:Ot(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(ye(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>f(p.name)).flatMap(p=>mo(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:go(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=ye(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&Qe(o,s)&&t.push([r==="reverse"?1:0,O(s),B(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(!B(r)){let o=O(r),s=`S	${o}	${this.record(r).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return Yr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Vr(Qr(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)B(c)||r.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>B(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&Qe(c,l)&&r.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,p,h,u)=>{let d=Ot(c,l).map(S=>`${B(S)?"<":">"}${O(S)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,y=u===void 0?"":`	CG:Z:${u}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${h}	${d}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,h=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,h):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,h)),f+=1}}),`${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:xe(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?xe({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):xe({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)&&Qe(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!B(s)).map(s=>({id:String(O(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(O(s)),from_is_reverse:B(s),to:String(O(i)),to_is_reverse:B(i)});let o=this.outputPaths(e).map(s=>wi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!B(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=O(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(Ot(i.info,i.identity))}))}}};function Ot(n,e){return e?.orientation==="reverse"?n.path.map(t=>X(t)).reverse():n.path}function wi(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Ot(n,e).map(o=>({id:String(O(o)),is_reverse:B(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 K(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function _t(n){return n===0?0:6+(n-1)}function xo(n,e,t){if(e===0)K(n,"D",t);else if(t===0)K(n,"I",e);else{let r=Math.min(e,t),o=4*r+_t(e-r)+_t(t-r),s=_t(e)+_t(t);o<=s?(K(n,"M",r),K(n,"I",e-r),K(n,"D",t-r)):(K(n,"I",e),K(n,"D",t))}}function yi(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=[];K(i,"I",o.inserted);for(let[a,f]of n.slice(e,t))K(i,a,f);return K(i,"I",s.inserted),{edits:i,leading:o.deleted,trailing:s.deleted}}function yo(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 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database cannot name its walks");let{subgraph:s,reference:i}=await bo(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 Se(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 Si(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 ${r} exceeds the 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Ai=4096,Ei=4096,$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=Oe(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=Oe(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:Ii(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===Nt)return s;if(a.type!==Ft)throw new Error("SQLite table b-tree contains an index page");let f=this.childIndexFor(i,a,t);o=f===a.cellCount?a.rightChild:Oe(i,Re(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]=Se(e,Re(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:Oe(c,Re(c,l,d)))}),f.length>Ei)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===Nt){let f=0,c=s.cellCount;for(;f<c;){let l=f+c>>1,p=Re(o,s,l),[h,u]=Se(o,p),[d,m]=Se(o,u);if(d===t)return Tt(await this.payload(o,m,h,!1));d<t?f=l+1:c=l}return}if(s.type!==Ft)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=Re(o,s,f),[l]=Se(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:Oe(o,Re(o,s,i))}}async*tableScan(e){let{page:t,header:r}=await this.pageAt(e);if(r.type===Nt)for(let o=0;o<r.cellCount;o++){let s=Re(t,r,o),[i,a]=Se(t,s),[f,c]=Se(t,a);yield{rowid:f,values:Tt(await this.payload(t,c,i,!1))}}else{let o=[];for(let s=0;s<r.cellCount;s++)o.push(Oe(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>=Ai){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===it,[c,l]=Se(t,f?a+4:a);i={values:Tt(await this.payload(t,l,c,!0)),leftChild:f?Oe(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);Io(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===it&&(yield*this.indexScanFrom(f.leftChild,t)),yield f.values}o.type===it&&(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);Io(p.values,t)<=0?(r=p.values,a=l+1):(c=p.leftChild,f=l)}if(i.type===Ao)return r;o=a===i.cellCount?i.rightChild:c}}};function Io(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 qt=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 at=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 qt(e,c,r,t);h.seed(0,o),h.fetches+=1,h.bytesFetched+=o.length;let u=new $t(h,l),d=new Map;for await(let{values:m}of u.tableScan(1)){let[y,S,I,g,v]=m;typeof y=="string"&&typeof S=="string"&&typeof I=="string"&&typeof g=="number"&&d.set(S,{type:y,name:S,tableName:I,rootPage:g,sql:typeof v=="string"?v:""})}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(r=>r.type==="index"&&r.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var jn="GBZ-base version 4",Ht=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Gt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${jn}"`),this.found=e}},Bt=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=Br(o)}get id(){return O(this.handle)}get orientation(){return We(this.handle)}get sequence(){return this.decoded??=Dr(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 ${this.handle} is empty`);return new vt(this.edges,this.bwt)}};function Q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function Dt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function zn(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function Co(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 Ro(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 ft=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 at.open(e,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=r?await at.open(r,o):void 0,a=new n(s,i),f=await a.tag("version");if(f!==jn)throw new Gt(f);if(i){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(u);a.indexTags=await Ro(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 Ht}return a}tags(){return this.tagCache??=Ro(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 Bt(e,Gr(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(Co(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?Co(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=At(Kr(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?xe(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&&u==="all"?m=await vo(this,l,p,h,{...i,keep:s}):(m=await So(this,l,p,h,i),this.hasHaplotypeIndex&&d&&(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=Wr(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 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 haplotypeAnchor(e,t){let r=await this.companion.indexSeekLE("HaplotypeAnchors",[e,t]),o=r?.[0]===e&&r[1]===t?await this.companion.byRowid("HaplotypeAnchors",Q(r[2],"HaplotypeAnchors rowid")):void 0;return o?{node:Q(o[2],"HaplotypeAnchors.node_handle"),pathOffset:Q(o[3],"HaplotypeAnchors.path_offset")}:void 0}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:Q(e[0],"HaplotypeSamples.node_handle"),offset:Q(e[1],"HaplotypeSamples.node_offset"),pathHandle:Q(e[2],"HaplotypeSamples.path_handle"),orientation:Q(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:Q(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let r=[];for await(let o of this.companion.indexScanFrom("HaplotypeSamples",[e,0])){if(Q(o[0],"HaplotypeSamples.node_handle")>t)break;let i=await this.companion.byRowid("HaplotypeSamples",Q(o[2],"HaplotypeSamples rowid"));i&&r.push(this.sampleFromRow(i))}return r}async haplotypeSampleAt(e,t){let r=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);if(r?.[0]!==e||r[1]!==t)return;let o=await this.companion.byRowid("HaplotypeSamples",Q(r[2],"HaplotypeSamples rowid"));return o?this.sampleFromRow(o):void 0}async haplotypeLength(e){let t=await this.companion.byRowid("HaplotypeLengths",e);return 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without a targetAssemblyName`);this.name="PairTargetError"}},gr=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. 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Le({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 pr=n=>!("uri"in n)||n.uri!=="",wr=class extends yn{constructor(){super(...arguments);this.graph=(0,hr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=pr(r)?r:await To(t,this.pluginManager),s=await ft.open((0,et.openLocation)(t,this.pluginManager),o?{haplotypeIndex:(0,et.openLocation)(o,this.pluginManager)}:{}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let a=await Mo(s),f=Un({configured:this.getConf("referenceSample"),anchorPrefix:Ue(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,et.openLocation)(t,o);return new Ut(s,pr(r)?new Cr({filehandle:s,...(0,et.openTabixIndexFilehandle)(r,this.getConf(["readsIndex","indexType"]),o)}):void 0)}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return ko(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=ve(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:Ps(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:Ue(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:je(ve(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=>Ue(this,s));return o===void 0&&r===void 0?void 0:s=>Po(s,o)&&(r===void 0||je(ve(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 _o(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=Ue(this,t);return(await this.getHaplotypes(r)).filter(s=>je(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=Ue(this,r.targetAssemblyName),l=Pn(this),p=this.keepPredicate(r.haplotypes,c),h=await this.referenceQuery(i,r),u=this.getConf("nodeLimit");return(h?await(0,dr.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 ct(m,u,f-a)??m})):[]).flatMap(m=>{let y=m.resolved?da({alignment:m,assemblyName:s,refName:i,lane:Ps(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),h=[...l,...p],u=await this.referenceQuery(a,o),d=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,v)=>i.getSubgraphForRange(g,v.start,v.end,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:d,signal:o.signal,keep:b=>h.some(E=>E.sample===b.sample&&E.haplotype===b.haplotype)}).catch(b=>{throw ct(b,d,c-f)??b}),S=u&&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(u,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let v=g.stats.keep;return v!==void 0&&v.fallback===void 0})?S.flatMap(g=>l.flatMap(v=>p.flatMap(b=>g.pairAlignments({target:v,query:b,bases:!1}).map(E=>ua({pair:E,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,Ms.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,zt as NoReferenceSampleError,jt as NodeLimitError,mr as PairTargetError,wr as default,da as fragmentFeature,ve as haplotypePrefix,Ps as laneAssemblyName,ct as nodeLimitError,ua as pairFeature,Un as resolveReferenceSample};
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