npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 4.0.30 → 4.1.1 - Mend

jbrowse-plugin-graphgenomeviewer 4.0.30 → 4.1.1

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Files changed (35) hide show

package/dist/chunks/GbzBaseSyntenyAdapter-3BCUI2JI.js ADDED Viewed

@@ -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 N=(await l(P)).gbwt().offsetTo(v);if(N===void 0)throw new Error(`No offset in ${P} leads to ${v.node}:${v.offset}`);return{node:P,offset:N}},y=(v,C,P,N)=>{let B=P.map(te=>te.pos.node),W=P.map(te=>te.pos.offset),K=0;for(let te of B)K+=d(te);let H=C==="forward"?P[0].left:P[P.length-1].left,L=p.length;p.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:N});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,N)=>{let B=[],W=v;for(;;){r?.throwIfAborted();let H=await I(W.pos,t);if(!H)break;W={pos:H,left:Xr(P,W.left,d(W.pos.node),d(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:Et(P,W.left,d(W.pos.node),d(H.node))},K.push(W)}return y(C,P,[...B,...K],N)},A=async(v,C,P,N)=>p[m.get(v.pos)??await 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g(K.pos):await I(K.pos);if(!Y){L="endmarker";break}let te=(await l(K.pos.node)).sequenceLen,ie=(await l(Y.node)).sequenceLen,le=C?Et(W.orientation,K.left,te,ie):Xr(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"),N.add(B),L="landed"):(N.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:N}=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 b of B){if(b.inserted>0&&b.low===b.high)throw new fe(`the haplotype index's stray rows leave out the snarl bounded by node ${b.low} at both ends`);if(b.inserted>0&&(v.snarlNodes===void 0||b.nodes>v.snarlNodes))throw new fe(v.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${b.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 b of t.keys()){let k=R(b);if(!U(b)&&!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 b=>{let k=await e.haplotypeAnchor(n.referenceHandle,b*C);return k&&ie.set(b,k),k},ee=Math.max(0,Math.floor((L-N)/C)-1),_e=Math.ceil((Y+N)/C)+1;for(await Promise.all(Array.from({length:_e-ee+1},(b,k)=>le(ee+k)));ee>0&&(ie.get(ee)?.pathOffset??Number.POSITIVE_INFINITY)>=L-N;)ee-=1,await le(ee);for(;ie.has(_e)&&ie.get(_e).pathOffset<=Y+N;)_e+=1,await le(_e);let J=[...ie.keys()].sort((b,k)=>b-k),ae=ie.get(J[0]??-1);if(!ae)throw new fe("the haplotype index has no anchors on this path");let xe=b=>ie.get(b).pathOffset,Te=new Map;for(let b of J){let k=R(ie.get(b).node);Te.set(k,[...Te.get(k)??[],b])}let Ne=[...Te.keys()],mr=await Promise.all(Ne.map(b=>_(2*b)));if(!mr[Ne.indexOf(R(ae.node))].some(b=>b.pathHandle===n.referenceHandle&&b.orientation==="forward"&&b.pathOffset===ae.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${n.referenceHandle} at offset ${ae.pathOffset} (node ${R(ae.node)}); it does not match this graph`);let gr=J.filter(b=>xe(b)<=n.window.start),vs=J.filter(b=>xe(b)>=n.window.end);i.anchors=[xe(gr[gr.length-1]??J[0]),xe(vs[0]??J[J.length-1])],i.anchorsRead=J.length;let bn=new Map,wr=new Set;if(Ne.forEach((b,k)=>{let $=Te.get(b),Q=$.length===1?$[0]:void 0;for(let G of mr[k])wr.add(G.pathHandle),G.orientation==="forward"&&u(G.pathHandle)&&bn.set(G.pathHandle,[...bn.get(G.pathHandle)??[],{k:Q,row:G}])}),i.chosenPaths=[...wr].filter(u).length,i.chosenPaths>Vr.mostChosenPaths)throw new fe(`${i.chosenPaths} chosen paths pass the anchors, more than ${Vr.mostChosenPaths}`);let ut=[],Le=Number.POSITIVE_INFINITY,Pe=0;for(let[b,k]of bn){k.sort(($,Q)=>$.row.pathOffset-Q.row.pathOffset);for(let $=0;$+1<k.length;$++){let Q=k[$],G=k[$+1];if(Q.k===void 0||G.k===void 0||Math.abs(Q.k-G.k)!==1)continue;let[Z,ne]=xe(Q.k)<=xe(G.k)?[Q,G]:[G,Q],re=xe(Z.k),se=xe(ne.k);re<Y&&se>=L?(ut.push({pathHandle:b,from:Q.row,to:G.row}),Le=Math.min(Le,re-N),Pe=Math.max(Pe,se+N)):re>=Y&&re-Y<=N?(ut.push({pathHandle:b,from:Z.row,to:void 0}),Le=Math.min(Le,re-N),Pe=Math.max(Pe,re+N)):se<L&&L-se<=N&&(ut.push({pathHandle:b,from:ne.row,to:void 0}),Le=Math.min(Le,se-N),Pe=Math.max(Pe,se+N))}}let Es=new Set(B.map(b=>`${b.low}:${b.high}`)),yr=await 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0){let[p,m]=ro(n[c],d),[w,x]=ro(n[l],d),S=Math.max(p,w),g=Math.min(m,x),[I,y]=[n[c],n[l]];u=[no(y,d,S,g)-no(I,d,S,g),y.sharedBases-I.sharedBases,c-l].find(A=>A!==0)>0,a.set(h,u)}return u};return n.flatMap((c,l)=>{let d=s[l],h=new Uint8Array(d.length);if(d.forEach(([m,w],x)=>{for(let[S,g]of[["query",m],["target",w]])!h[x]&&i[S].get(g)?.some(I=>I!==l&&f(l,I,S))&&(h[x]=1)}),!h.includes(1))return[c];let u=Ks(c,h),p=u?.edits.reduce((m,[w,x])=>m+(w==="="?x:0),0)??0;return u&&p>=r?[u]:[]})}function oo(n,e){return n.map(t=>{let r=e(R(t));return U(t)?vt(r):r}).join("")}function so(n,e){let t=[0];for(let r of n)t.push(t.at(-1)+e(R(r)).length);return t}function io(n){let e=new Map,t=new Map;n.forEach((i,a)=>{let f=R(i);e.has(f)?t.set(f,a):e.set(f,a)});let r=new Int32Array(n.length+1);for(let[i,a]of t)r[e.get(i)]+=1,r[a+1]-=1;let o=new Uint8Array(n.length),s=0;for(let i=0;i<n.length;i++)s+=r[i],o[i]=s>0?1:0;return o}function Js(n,e,t,r){let o=io(n),s=io(e),i=new 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E=I+x.length;c.push({...y,queryStart:g+y.queryStart,queryEnd:g+y.queryEnd,targetStart:p?E-y.targetEnd:I+y.targetStart,targetEnd:p?E-y.targetStart:I+y.targetEnd,strand:p?"+":"-",edits:p?y.edits.reverse():y.edits,shared:[]})}}:Fn),c.push({queryStart:h.run.qs+h.trim,queryEnd:u.run.qe,targetStart:p?u.run.ts:h.run.ts+h.trim,targetEnd:p?h.run.te-h.trim:u.run.te,strand:p?"-":"+",edits:p?d.reverse():d,sharedBases:l.reduce((w,{run:x,trim:S})=>w+x.qe-x.qs-S,0),shared:l.map(({run:w,trim:x})=>[w.qs+x,w.qe])})}return Zs(c,o.length,s.length,a).map(({shared:l,...d})=>d).sort((l,d)=>l.queryStart-d.queryStart)}function uo(n){return n.map(([e,t])=>`${t}${e}`).join("")}var Se=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function qn(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var it=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(qn(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],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&&qn(e[s],e[a])&&(a=s),i<e.length&&qn(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function 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 st(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]);go(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,d)=>n[l].identity.hapStart-n[d].identity.hapStart);let a=i[0],f=n[a],c=[];for(let l of i.slice(1)){let d=n[l],h=c.length===0?ni(f,d):void 0;if(h){f=ri(f,d,h),s.add(l);continue}if(!e(d)){c.push(l);continue}let u=e(f)?t([f,...c.map(p=>n[p]),d]):void 0;if(u){f=u;for(let p of[...c,l])s.add(p)}else o.set(a,f),a=l,f=d;c=[]}o.set(a,f)}return n.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function Pt(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 qe=class n{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}static create(e,t={}){return new n(e,t)}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 Se(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 offset ${e.fragment} of ${ge(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${ge(t.name)} at ${t.name.fragment} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`The fragment of ${ge(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(R(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`The fragment of ${ge(e.name)} at ${e.name.fragment} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=R(e);await this.ensureNode(o);let s=this.record(e),i=je(e),a=new it;return a.push(t,o,yt(i)),a.push(s.sequenceLen-t-1,o,xt(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(d=>d.pos.node));await Promise.all(l.map(([d,h])=>this.db.prefetchRecords(d,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 Se&&o.windowBp===void 0?new Se(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 it;for(;;){let f=R(o.node),c=je(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,yt(c));let d=l.sequenceLen-s;if(i<=d){a.push(i===d?0:d-i-1,f,xt(c));break}a.push(0,f,xt(c));let h=l.gbwt().lf(o.offset);if(!h)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=h,s=0,i-=d}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new it;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let r=new Set,o=new Set;for(let i of this.records.keys())o.add(R(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=Lr(f);if(!r.has(`${a}:${l}`)){let u=this.record(be(a,Fr(f))),p=i+u.sequenceLen-1;p<=t&&e.push(p,a,l)}let d=this.record(be(a,Hr(f))),h=i+1;if(h<=t)for(let u of d.successors()){let p=R(u),m=yt(je(u));r.has(`${p}:${m}`)||e.push(h,p,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([R(e),R(t)]),s=[];for(;r.length>0;){let i=r.pop(),a=R(i);this.hasNode(a)||(await this.addNode(a),s.push(a));for(let f of this.record(i).successors()){let c=R(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=R(r),f=R(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)?Ue(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=R(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 d of["forward","reverse"])s.push(...(await e(be(c,d))).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((y,E)=>i.set(y,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let y=0;y<s;y++){let E=this.record(o[y]),A=E.gbwt().decompressArrays();f[y]=E.sequenceLen,c.push(A),a[y+1]=a[y]+A.nodes.length}let l=a[s],d=new Int32Array(l),h=new Int32Array(l),u=new Uint8Array(l);for(let y=0;y<s;y++){let E=c[y];d.set(E.nodes,a[y]),h.set(E.offsets,a[y])}c.length=0;for(let y=0;y<l;y++){let E=i.get(d[y]);E===void 0?d[y]=-1:(d[y]=E,u[a[E]+h[y]]=1)}let p=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,w,x=(y,E,A)=>{let T=[],O=0,F=0,M=-1,z=y,_=E;for(;;){z===p&&_===m&&(M=O),A&&(A.push(o[z]),T.push(_)),O+=1,F+=f[z];let j=a[z]+_,V=d[j];if(V<0)break;_=h[j],z=V}return{offsets:T,len:F,refAt:M,last:z}},S=(y,E,A,T)=>{T>=0&&(this.refId=this.paths.length,w=T),this.paths.push({path:y,offsets:E,len:A,weight:void 0,identity:void 0})},g=new Int32Array(s);for(let y=0;y<s;y++){let E=o[y];if(!U(E)){let A=a[y],T=a[y+1]-A;for(let O=0;O<T;O++)if(u[A+O]===0){let F=[],{offsets:M,len:z,refAt:_,last:j}=x(y,O,F),V=o[j];if(_>=0||Fe(E,V)){if(S(F,M,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 y=0;y<s;y++){let E=o[y];if(U(E)){let A=a[y],T=a[y+1]-A,O=0;for(let M=0;M<T;M++)u[A+M]===0&&(O+=1);let F=(p===void 0||w!==void 0)&&O===g[y];for(let M=0;M<T;M++)if(u[A+M]===0){let z=F?void 0:x(y,M,void 0);if(z&&(z.refAt>=0||Fe(E,o[z.last]))){let _=[],{offsets:j,len:V,refAt:ue}=x(y,M,_);S(_,j,V,ue)}else this.twinStarts.add($e({node:E,offset:M}))}}}let I=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((y,E)=>y.path[0]-E.path[0]||y.offsets[0]-E.offsets[0]),I&&(this.refId=this.paths.indexOf(I)),r){if(w===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let y=this.paths[this.refId],E=r.nodeOffset;for(let T of y.path.slice(0,w))E+=this.record(T).sequenceLen;let A=r.seqOffset-E;this.refInterval=[A,A+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:A,hapEnd:A+y.len}}if(t==="distinct")this.distinctPaths(!0);else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=t?.path,o=r&&!bt(r)?st(r):void 0,s=c=>o!==void 0&&kt(c,o)===0||kt(c,st(c))===0,i=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,l)=>kt(c.path,l.path)||c.len-l.len||(c===t?-1:l===t?1:0));let a=[],f;for(let c of this.paths){let l=a[a.length-1],d=i&&c!==t&&s(c.path);this.twinDeferred||=d,l&&kt(l.path,c.path)===0&&!d?l.weight=(l.weight??1)+(c.weight??1):(c===t&&(f=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=f}mergeDistinct(){this.distinctPaths(!1)}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,r=i=>`${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 ${this.paths.length} walks have no name, so the haplotypes to keep cannot be told from the rest; call identifyPaths() first, and check that the haplotype index was built for this graph`);let r=this.refId===void 0?void 0:this.paths[this.refId],o=this.paths.filter((i,a)=>a===this.refId||i.identity!==void 0&&e(i.identity.name)),s=new Set;for(let i of o)for(let a of i.path)s.add(R(a));for(let i of[...this.records.keys()])s.has(R(i))||this.records.delete(i);this.paths=o,this.refId=r===void 0?void 0:o.indexOf(r)}async extractChosenPaths(e,t,r,o){this.clearPaths();let s=e.position.seqOffset,i=await Zr({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:s-e.position.nodeOffset,window:{start:s,end:s+t},context:o,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:r,signal:this.signal,prefetchReferenceRange:(l,d,h)=>this.prefetchReferenceRange(l,d,h)});if(this.stats.keep=i.stats,i.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),f=l=>({path:l.handles,offsets:l.offsets,len:l.len,weight:void 0,identity:{pathHandle:l.pathHandle,name:l===i.reference?e.name:a.get(l.pathHandle).name,orientation:l.orientation,hapStart:l.hapStart,hapEnd:l.hapEnd}}),c=[i.reference,...i.pieces].sort(Jr);return this.paths=c.map(f),this.refId=c.indexOf(i.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[i.reference.hapStart,i.reference.hapEnd],this.dropTwins(),!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleGap()??4096,t=_n(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[p,m]of t)for(let w of await this.db.haplotypeSamplesInRange(p,m))r.set($e(w),w);let o=p=>{let m=0,w=t.length-1;for(;m<w;){let S=m+w+1>>1;t[S][0]<=p?m=S:w=S-1}let x=t[m];return x[0]<=p&&p<=x[1]},s=new Map;this.paths.forEach((p,m)=>{p.path.length>0&&m!==this.refId&&s.set($e(Pt(p,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((p,m)=>{m!==this.refId&&i.fragmentLengths.push(p.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=p=>(i.graphLookups+=1,a(p)),c=async(p,m)=>{if(o(p.node))return r.get($e(p));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let w=await this.db.haplotypeSampleAt(p.node,p.offset);return w||(i.companionMisses+=1),w},l=new Map,d=async p=>{let m=l.get(p);if(!m){let w=await this.db.getPath(p);if(!w)throw new Error(`Path ${p} is missing from the database`);m=w.name,l.set(p,m)}return m},h=(p,m,w)=>p.orientation==="forward"?{pathHandle:p.pathHandle,orientation:"forward",base:p.pathOffset-m}:{pathHandle:p.pathHandle,orientation:"reverse",base:p.pathOffset+m+w},u=(p,m)=>p.orientation==="forward"?{pathHandle:p.pathHandle,orientation:"forward",base:p.hapStart-m}:{pathHandle:p.pathHandle,orientation:"reverse",base:p.hapEnd+m};for(let p=0;p<this.paths.length;p++){let m=this.paths[p];if(p===this.refId||m.identity)continue;let w=[],x=new Set,S={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(S);let g,I=0,y=p,E;for(;g===void 0;){if(this.signal?.throwIfAborted(),y!==void 0){if(x.has(y)){S.end="cycle";break}x.add(y);let M=this.paths[y];w.push({index:y,startBp:I}),S.fragments+=1;let z=I;for(let j=0;j<M.path.length;j++){let V=Pt(M,j),ue=r.get($e(V)),v=this.record(V.node).sequenceLen;if(ue){g=h(ue,z,v);break}z+=v}if(I+=M.len,g){S.end="in-fragment sample";break}let _=Pt(M,M.path.length-1);E=this.record(_.node).gbwt().lf(_.offset),y=void 0}if(E===void 0||E.node===0){S.end="endmarker";break}let A=$e(E),T=s.get(A);if(T!==void 0){let M=this.paths[T].identity;if(M){g=u(M,I),S.end="identified sibling";break}y=T;continue}this.records.has(E.node)&&(S.reentries+=1),this.twinStarts.has(A)&&(S.twinLandings+=1);let O=await c(E,S),F=await f(E.node);if(O){g=h(O,I,F.sequenceLen),S.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,S.steps+=1,I-w[w.length-1].startBp>4*e+4*F.sequenceLen){S.end="bound";break}I+=F.sequenceLen,E=F.gbwt().lf(E.offset)}if(g){S.pathHandle=g.pathHandle;let A=await d(g.pathHandle);for(let{index:T,startBp:O}of w){let F=this.paths[T];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),go(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(eo(e,t,d=>this.record(d).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(d,h,u,p)=>{d===h?X(s,"D",i[p]-i[u]):u===p?X(s,"I",this.pathLen(e.slice(d,h))):this.align(e.slice(d,h),t.slice(u,p),s)},f=0,c=0,l=0;for(let d=0;d<o.count;d++){let h=o.pathAt[d],u=o.refAt[d];(c!==h||l!==u)&&a(c,h,l,u);let p=this.record(e[h]).sequenceLen;X(s,"M",p),f+=p,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(bt(r)&&(t.identity===void 0||!bt(st(t.path))))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=st(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,d,h,u)=>{let p=fi(l),m=this.paths[h[0]],w=this.paths[h[h.length-1]],x=m.identity,S=x?.orientation==="forward",[g,I]=S?[m,w]:[w,m];return{strand:d,refStart:e.start+p.leading,refEnd:e.start+r-p.trailing,edits:p.edits,weight:m.weight,path:h.flatMap(y=>this.paths[y].path),start:Pt(m,0),pieces:h,soloAligned:u,identity:x===void 0?void 0:{pathHandle:x.pathHandle,name:x.name,hapStart:x.name.fragment+g.identity.hapStart,hapEnd:x.name.fragment+I.identity.hapEnd,walkForward:S}}},s=l=>l.soloAligned.reduce((d,h)=>d+h,0),i=l=>l.pieces.reduce((d,h)=>d+this.paths[h].len,0),a=l=>2*s(l)>=i(l),f=l=>{let d=l[0],h=l[l.length-1],u=d.identity.walkForward;if(l.some((_,j)=>_.strand!==d.strand||_.identity.walkForward!==u||j>0&&_.identity.hapStart<l[j-1].identity.hapEnd))return;let p=u?l:[...l].reverse(),m=p.flatMap(_=>_.pieces),w=p.flatMap(_=>_.soloAligned),x=d.strand==="+"!==u,S=m.map(_=>this.paths[_]),g=S.slice(1).map((_,j)=>{let V=S[j].identity;return u?_.identity.hapStart-V.hapEnd:V.hapStart-_.identity.hapEnd}),I=x?[...S].reverse():S,y=x?[...g].reverse():g,E=I.flatMap(_=>x?st(_.path):_.path),{edits:A}=this.editsAgainst(E,t),T=mo(A,I.map(_=>_.len)),O=new Map((x?[...m].reverse():m).map((_,j)=>[_,T[j]])),F=_=>2*_.pieces.reduce((j,V)=>j+O.get(V),0)>=s(_);if(!F(d)||!F(h))return;let M=[],z=0;return I.slice(0,-1).forEach((_,j)=>{z+=_.len,M.push([z,y[j]])}),o(ci(A,M),d.strand,m,w)},c=[];return this.paths.forEach((l,d)=>{if(d===this.refId)return;let{edits:h,flipped:u}=this.alignment(d),p=l.identity,m=p?p.orientation==="forward"!==u:!u;c.push(o(h,m?"+":"-",[d],mo(h,[l.len])))}),oi(c,a,f).map(l=>{let{edits:d,identity:h,pieces:u,soloAligned:p,...m}=l,w={...m,cigar:li(d)};return h?{...w,resolved:!0,name:h.name,label:ge({...h.name,fragment:h.hapStart,end: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:d}=l;return d?[{name:d.name,start:d.name.fragment+d.hapStart,steps:Tt(l,d)}]:[]}),i=l=>d=>d.sample===l.sample&&d.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(d=>f(d.name)).flatMap(d=>po({...o,query:d.steps,target:l.steps,sequenceOf:c}).map(h=>({query:d.name,queryStart:d.start+h.queryStart,queryEnd:d.start+h.queryEnd,strand:h.strand,target:l.name,targetStart:l.start+h.targetStart,targetEnd:l.start+h.targetEnd,cigar:uo(h.edits),matches:h.edits.reduce((u,[p,m])=>u+(p==="="?m:0),0),columns:h.edits.reduce((u,[,p])=>u+p,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)&&Ue(o,s)&&t.push([r==="reverse"?1:0,R(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=R(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",...Qr(Wr(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)U(c)||r.push(`S	${R(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)&&Ue(c,l)&&r.push(`L	${R(c)}	${s(c)}	${R(l)}	${s(l)}	0M`);let i=(c,l,d,h,u)=>{let p=Tt(c,l).map(x=>`${U(x)?"<":">"}${R(x)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,w=u===void 0?"":`	CG:Z:${u}`;return`W	${d.sample}	${d.haplotype}	${d.contig}	${d.fragment}	${h}	${p}${m}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let d=e.names!=="anonymous"?c.identity:void 0,h=t?this.alignToRef(l):void 0;r.push(d?i(c,d,{...d.name,fragment:d.name.fragment+d.hapStart},d.name.fragment+d.hapEnd,h):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,h)),f+=1}}),`${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,end:this.refPath.fragment+this.refInterval[1]}),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names!=="anonymous"?i.identity:void 0;r.push({info:i,identity:f,name:f?ge({...f.name,fragment:f.name.fragment+f.hapStart,end:f.name.fragment+f.hapEnd}):ge({sample:"unknown",contig:o,haplotype:s,fragment:0,end: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)&&Ue(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!U(s)).map(s=>({id:String(R(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(R(s)),from_is_reverse:U(s),to:String(R(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]=R(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(Tt(i.info,i.identity))}))}}};function Tt(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:Tt(n,e).map(o=>({id:String(R(o)),is_reverse:U(o)}))}}function kt(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 Ot(n){return n===0?0:6+(n-1)}function go(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+Ot(e-r)+Ot(t-r),s=Ot(e)+Ot(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 mo(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 wo(n,e){let t=qe.create(n,e),r=await t.pathPosition(Qe(We(e.path),e.offset));return await t.aroundPosition(r.position.handle,r.position.nodeOffset,e.context??100),await t.extractSnarls(e.snarls??"none"),t.extractPaths(r,e.haplotypes??"all"),t}async function di(n,e){let{start:t,end:r}=e,o=qe.create(n,e);try{let s=await o.pathPosition(Qe(We(e.path),t));return await o.prefetchReferenceWalk(s,r-t),await o.aroundInterval(s.position,r-t,e.context??100),await o.extractSnarls(e.snarls??"none"),{subgraph:o,reference:s}}catch(s){throw s instanceof Se&&s.windowBp===void 0?new Se(s.limit,{windowBp:r-t,walkedBp:o.referenceWalkedBp??0}):s}}async function Bn(n,e){let{keep:t}=e,r=e.haplotypes??"all",o=r==="all"||r==="distinct";if(t!==void 0&&o&&!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:s,reference:i}=await di(n,e);return t===void 0||!o?(s.extractPaths(i,r),s):(await s.extractChosenPaths(i,e.end-e.start,t,e.context??100)||(s.extractPaths(i,"all"),await s.identifyPaths()),s.keepHaplotypes(t),r==="distinct"&&s.mergeDistinct(),s)}async function yo(n,e){let t=e.haplotypes??"all",r=e.snarls??"none";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");if(r==="overlapping"&&e.nodeIds.length>1)throw new Error("Overlapping snarls cannot be extracted for a node-based query with multiple nodes");let o=qe.create(n,e);return await o.aroundNodes(e.nodeIds,e.context??100),await o.extractSnarls(r),o.extractPaths(void 0,t),o}async function xo(n,e){let t=e.haplotypes??"all";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based query");let r=qe.create(n,e);return await r.betweenNodes(e.startHandle,e.endHandle),r.extractPaths(void 0,t),r}function ve(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 hi(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 pi=new TextDecoder;function Nt(n){let[e,t]=ve(n,0),r=[],o=t;for(;o<e;){let[a,f]=ve(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=hi(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:pi.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var at=2,Ft=5,So=10,Lt=13;function Io(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 ui(n,e){let t=n[e];if(t!==at&&t!==Ft&&t!==So&&t!==Lt)throw new Error(`SQLite page has unknown b-tree type ${t}`);let r=t===at||t===Ft;return{type:t,cellCount:Io(n,e+3),rightChild:r?ke(n,e+8):0,cellPointers:e+(r?12:8)}}function Me(n,e,t){return Io(n,e.cellPointers+2*t)}var mi=4096,gi=4096,Ht=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:ui(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===Lt)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:ke(i,Me(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]=ve(e,Me(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},d)=>{let h=d===0?this.childIndexFor(c,l,t):0,u=d===a.length-1?this.childIndexFor(c,l,r):l.cellCount;for(let p=h;p<=u;p++)f.push(p===l.cellCount?l.rightChild:ke(c,Me(c,l,p)))}),f.length>gi)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===Lt){let f=0,c=s.cellCount;for(;f<c;){let l=f+c>>1,d=Me(o,s,l),[h,u]=ve(o,d),[p,m]=ve(o,u);if(p===t)return Nt(await this.payload(o,m,h,!1));p<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=Me(o,s,f),[l]=ve(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:ke(o,Me(o,s,i))}}async*tableScan(e){let{page:t,header:r}=await this.pageAt(e);if(r.type===Lt)for(let o=0;o<r.cellCount;o++){let s=Me(t,r,o),[i,a]=ve(t,s),[f,c]=ve(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,Me(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>=mi){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=Me(t,r,o),f=r.type===at,[c,l]=ve(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);bo(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===at&&(yield*this.indexScanFrom(f.leftChild,t)),yield f.values}o.type===at&&(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,d=await this.indexCell(o,s,i,l);bo(d.values,t)<=0?(r=d.values,a=l+1):(c=d.leftChild,f=l)}if(i.type===So)return r;o=a===i.cellCount?i.rightChild:c}}};function bo(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 $t=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=await this.readRetrying(e,t);if(this.bytesFetched+=r.length,r.length<e)throw new Error(`the file ends at byte ${t+r.length}, short of the ${this.fileSize} bytes its SQLite header gives`);return r}async readRetrying(e,t){let r=0;for(;;)try{return await this.source.read(e,t)}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 ft=class n{pager;btree;objects;constructor(e,t,r){this.pager=e,this.btree=t,this.objects=r}static async open(e,t={}){let r=await e.read(t.blockSize??65536,0),o=r.subarray(0,100);if(new TextDecoder().decode(o.subarray(0,15))!=="SQLite format 3"||o.length<100)throw new Error("Not a SQLite database");let i=new DataView(o.buffer,o.byteOffset,o.byteLength),a=i.getUint16(16),f=a===1?65536:a,c=o[20]??0,l=i.getUint32(56);if(l!==1)throw new Error(`SQLite text encoding ${l} is not UTF-8`);let d=i.getUint32(28);if(d===0||i.getUint32(24)!==i.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let h=d*f,u=new $t(e,f,h,t);u.seed(0,r),u.fetches+=1,u.bytesFetched+=r.length;let p=new Ht(u,c),m=new Map;for await(let{values:w}of p.tableScan(1)){let[x,S,g,I,y]=w;typeof x=="string"&&typeof S=="string"&&typeof g=="string"&&typeof I=="number"&&m.set(S,{type:x,name:S,tableName:g,rootPage:I,sql:typeof y=="string"?y:""})}return new n(u,p,m)}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 Dn="GBZ-base version 4",Bt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${ge(e)}`),this.path=e}},Gt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Dt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Dn}"`),this.found=e}},Gn=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 R(this.handle)}get orientation(){return je(this.handle)}get sequence(){return this.decoded??=Gr(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new It(this.edges,this.bwt)}};function q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function zt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function qt(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function vo(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:zt(e[5],"Paths.sample"),contig:zt(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 Eo(n){let e=new Map;for await(let{values:t}of n.scan("Tags"))e.set(zt(t[0],"Tags.key"),zt(t[1],"Tags.value"));return e}var ct=class n{tagCache;pathCache;pathMapCache;indexTags=new Map;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e){let{source:t,haplotypeIndex:r}=e,o={blockSize:e.blockSize,maxBlocks:e.maxBlocks},s=await ft.open(t,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=r?await ft.open(r,o):void 0,a=new n(s,i),f=await a.tag("version");if(f!==Dn)throw new Dt(f);if(i){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(u);a.indexTags=await Eo(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 d=a.indexTags.get("haplotype_index_nodes"),h=await a.tag("nodes");if(d!==void 0&&d!==h)throw new Error(`haplotype index was built for a graph with ${d} nodes but this one has ${h}`);if(a.indexTags.get("haplotype_index_orientations")==="forward")throw new Gt}return a}tags(){return this.tagCache??=Eo(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let r=t[4];return new Gn(e,qr(qt(t[1],"Nodes.edges")),qt(t[2],"Nodes.bwt"),qt(t[3],"Nodes.sequence"),typeof r=="number"?r:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:r}of this.sqlite.scan("Paths"))e.push(vo(t,r));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?vo(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(r=>r.name.sample===e.sample&&r.name.contig===e.contig&&r.name.haplotype===e.haplotype&&r.name.fragment<=e.fragment).sort((r,o)=>o.name.fragment-r.name.fragment)[0]}async pathsNamed(e){let t=Qe(We(e),0);return(await this.paths()).filter(r=>r.name.sample===t.sample&&r.name.contig===t.contig&&r.name.haplotype===t.haplotype).sort((r,o)=>r.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let r=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!r){let i=await this.getPath(e);throw new Error(`${i?`The fragment of ${ge(i.name)} at ${i.name.fragment}`:`Path ${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 getPathFragments(e){let{start:t,end:r}=e,o=await this.pathsNamed(e.path);if(o.length===0)throw new Bt(Qe(We(e.path),0));if(r<=t)return[];let 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){let{sample:r,contig:o,haplotype:s}=e.path.name,i=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let f=await Bn(this,{...t,path:{sample:r,contig:o,haplotype:s},start:i,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await f.identifyPaths(),f}catch(f){throw f instanceof Se&&f.walkedBp!==void 0?new Se(f.limit,{windowBp:t.end-t.start,walkedBp:i-t.start+f.walkedBp}):f}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(o=>this.subgraphForFragment(o,e)))).map(o=>{if(o.status==="rejected")throw o.reason;return o.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Bn(this,e)}subgraphAtOffset(e){return wo(this,e)}subgraphAroundNodes(e){return yo(this,e)}subgraphBetween(e){return 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xs.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:o,splitAtGapBp:s,keepAlignment:i,...a}=r,f=o&&this.recordsAreAlignments,c=(0,bs.createStatusFanOut)(a.statusCallback);return Kn(t).pipe(Je((l,d)=>this.getFeatures(l,{...a,statusCallback:c()}).pipe(Je(h=>f?ys(h,h.get("assemblyName")===l.assemblyName?l:{start:h.get("start"),end:h.get("end")},s,i):[h]),dn(),ht(h=>({index:d,features:h})))),dn(),Je(l=>l.sort((d,h)=>d.index-h.index).flatMap(d=>d.features)))}};var xn=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},hr=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},pr=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 ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Ss(n,e){let t=Ae(e);return n[t]??n[e.sample]??t}function ra(n,e){return`${Ae(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function oa({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,d=ra(f,n),h={uniqueId:d,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:d,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new Oe(h)}}function sa({pair:n,lane:e,mateLane:t}){let r=`${Ae(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${Ae(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 cr=n=>!("uri"in n)||n.uri!=="",ur=class extends wn{constructor(){super(...arguments);this.graph=(0,lr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=cr(r)?{location:r}:await Co(t,this.pluginManager),s=o.location,i=await ct.open({source:(0,yn.openLocation)(t,this.pluginManager),haplotypeIndex:s?(0,yn.openLocation)(s,this.pluginManager):void 0}),a=this.getConf("assemblyNames")[0];if(a===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let f=await En(i),c=gt({configured:this.getConf("referenceSample"),anchorPrefix:ze(this,a),referenceSamples:f});return{db:i,anchor:a,referenceSample:c,referenceSamples:f,unreadableIndex:o.unreadable}}});this.gaf=(0,lr.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]);return cr(t)?new jt((0,yn.openLocation)(t,this.pluginManager),cr(r)?Nr(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return An(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=Ae(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=In(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Ss(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:ze(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:mt(Ae(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=>ze(this,s));return o===void 0&&r===void 0?void 0:s=>vn(s,o)&&(r===void 0||mt(Ae(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 pr(a,s);let d=await this.referenceQuery(f,{}),h=this.keepPredicate(r.haplotypes);if(h!==void 0&&!o.hasHaplotypeIndex)throw new xn(i);return Cn(o,d,c,l,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,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=ze(this,t);return(await this.getHaplotypes(r)).filter(s=>mt(s.prefix,o))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=ze(this,r.targetAssemblyName),l=In(this),d=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.getAlignments({path:h,start:a,end:f,context:this.getConf("context"),haplotypes:"all",limit:u,signal:r.signal,keep:d}).catch(m=>{throw wt(m,u,f-a)??m})):[]).flatMap(m=>{let w=m.resolved?oa({alignment:m,assemblyName:s,refName:i,lane:Ss(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 hr(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),d=await this.laneHaplotypes(s,o),h=[...l,...d],u=await this.referenceQuery(a,o),p=this.getConf("nodeLimit"),m=x=>i.getSubgraphs({path:x,start:f,end:c,context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:o.signal,keep:S=>h.some(g=>g.sample===S.sample&&g.haplotype===S.haplotype)}).catch(S=>{throw wt(S,p,c-f)??S});return(u&&l.length>0&&d.length>0?await(0,dr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,()=>m(u)):[]).flatMap(x=>l.flatMap(S=>d.flatMap(g=>x.pairAlignments({target:S,query:g,bases:!1}).map(I=>sa({pair:I,lane:r,mateLane:s})))))}getFeatures(t,r={}){return(0,Is.ObservableCreate)(async o=>{let{db:s,anchor:i,unreadableIndex:a}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new xn(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{pr as HaplotypeWindowError,xn as NoHaplotypeIndexError,Rs as NoReferenceSampleError,_s as NodeLimitError,hr as PairTargetError,ur as default,oa as fragmentFeature,Ae as haplotypePrefix,Ss as laneAssemblyName,wt as nodeLimitError,sa as pairFeature,gt as resolveReferenceSample};
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