jbrowse-plugin-graphgenomeviewer 3.0.3 → 3.0.5

package/README.md

@@ -145,7 +145,7 @@ Load the plugin from any JBrowse config, 5.0.0-beta.9 or later, with an
   "plugins": [
     {
       "name": "GraphGenomeView",
-      "esmUrl": "https://your-host/jbrowse-plugin-graphgenomeviewer.esm.js"
+      "esmUrl": "https://unpkg.com/jbrowse-plugin-graphgenomeviewer/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
     }
   ]
 }

package/dist/chunks/GbzBaseSyntenyAdapter-QT5CVRL2.js

@@ -0,0 +1,8 @@
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0:{...n,queryStart:n.queryStart+(t?d.I:p.I),queryEnd:n.queryEnd-(t?p.I:d.I),targetStart:n.targetStart+p.D,targetEnd:n.targetEnd-d.D,edits:r,sharedBases:n.sharedBases-a}}function Eo(n,e,t,r){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=n.map(f=>{let l=[];Gt(f,(p,d,h,u)=>{if(p==="="||p==="X")for(let m=0;m<d;m++)l.push([f.strand==="-"?h-m:h+m,u+m])});for(let[p,d]of l)o.query[p]=Math.min(255,o.query[p]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((f,l)=>{for(let[p,d]of f)for(let[h,u]of[["query",p],["target",d]])if(o[h][u]>1){let m=i[h].get(u);m?m.at(-1)!==l&&m.push(l):i[h].set(u,[l])}});let a=new Map,c=(f,l,p)=>{let d=`${p}:${f}:${l}`,h=a.get(d);if(h===void 0){let[u,m]=Hr(n[f],p),[w,x]=Hr(n[l],p),b=Math.max(u,w),g=Math.min(m,x);h=Fr(n[f],p,b,g)<Fr(n[l],p,b,g),a.set(d,h)}return h};return n.flatMap((f,l)=>{let p=s[l],d=new 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u=T(p)!==T(e[h]),m=u?-1:1;if(!f.has(c(d-1,h-m,u))){let w=d,x=h;for(;w<n.length&&x>=0&&x<e.length&&f.has(c(w,x,u));)w+=1,x+=m;let b=x-m;l.push({qs:t[d],qe:t[w],ts:r[Math.min(h,b)],te:r[Math.max(h,b)+1],flipped:u})}}}),l}function Wr(n,e,t,r={}){let o=qr(n,t),s=qr(e,t),i=Co(n,e,$r(n,t),$r(e,t)),a=r.minMatch??uo,c=[];for(let f of $t(i,r.maxGap??1/0,a,yo)){let l=[],p=f[0],d=f.at(-1),{flipped:h}=p.run;Qe(f,o,s,l,(u,m,w,x,b)=>{for(let g of Io(u,m,w,a)){let S=b+m.length;c.push({...g,queryStart:x+g.queryStart,queryEnd:x+g.queryEnd,targetStart:h?S-g.targetEnd:b+g.targetStart,targetEnd:h?S-g.targetStart:b+g.targetEnd,strand:h?"+":"-",edits:h?g.edits.reverse():g.edits,shared:[]})}}),c.push({queryStart:p.run.qs+p.trim,queryEnd:d.run.qe,targetStart:h?d.run.ts:p.run.ts+p.trim,targetEnd:h?p.run.te-p.trim:d.run.te,strand:h?"-":"+",edits:h?l.reverse():l,sharedBases:f.reduce((u,{run:m,trim:w})=>u+m.qe-m.qs-w,0),shared:f.map(({run:u,trim:m})=>[u.qs+m,u.qe])})}return Eo(c,o.length,s.length,a).map(({shared:f,...l})=>l).sort((f,l)=>f.queryStart-l.queryStart)}function Qr(n){return n.map(([e,t])=>`${t}${e}`).join("")}var X=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Dt(n,e){return n[0]<e[0]||n[0]===e[0]&&(n[1]<e[1]||n[1]===e[1]&&n[2]<e[2])}var Re=class{heap=[];push(e,t,r){let o=this.heap;o.push([e,t,r]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Dt(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],r=e.pop();if(e.length>0&&r!==void 0){e[0]=r;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Dt(e[s],e[a])&&(a=s),i<e.length&&Dt(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function Ro(n){let e=new Int32Array(n.length),t=new Int32Array(n.length);return n.forEach(([r,o],s)=>{e[s]=r,t[s]=o}),{pathAt:e,refAt:t,count:n.length}}function _o(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]>e?r=o:t=o+1}return n[t]}function ie(n){return`${n.node}:${n.offset}`}function Po(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 ko(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([f,l])=>[f,l]);Vr(s,t.insertion,t.deletion);for(let[f,l]of o.edits)z(s,f,l);let i=n.identity.walkForward,[a,c]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...c.path],start:a.start,identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Mo(n){if(n.some(o=>o.weight!==void 0))return n;let e=new Map;n.forEach((o,s)=>{if(o.identity){let i=e.get(o.identity.pathHandle);i?i.push(s):e.set(o.identity.pathHandle,[s])}});let t=new Map,r=new Set;for(let o of e.values()){o.sort((a,c)=>n[a].identity.hapStart-n[c].identity.hapStart);let s=o[0],i=n[s];for(let a of o.slice(1)){let c=n[a],f=Po(i,c);f?(i=ko(i,c,f),r.add(a)):(t.set(s,i),s=a,i=c)}t.set(s,i)}return n.flatMap((o,s)=>r.has(s)?[]:[t.get(s)??o])}function Ye(n,e){return{node:n.path[e],offset:n.offsets[e]}}var Oo=4096;function Yr(n){let e=[];for(let t of n){let r=e[e.length-1];r&&t-r[1]<=Oo?r[1]=t:e.push([t,t])}return e}var To=32768,Lo=65536;function No(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]<=To?o[1]=r:t.push([r,r])}return t}var _e=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:[]},anchorWalk: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(V(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 X(this.limit);let t=await this.db.getRecord(V(e,"forward")),r=await this.db.getRecord(V(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 ${q(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${q(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 ${q(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(A(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 c=a.gbwt().lf(i.offset);if(!c)throw new Error(`Path ${q(e.name,e.name.fragment)} does not contain offset ${t}`);i=c}}async aroundPosition(e,t,r){let o=A(e);await this.ensureNode(o);let s=this.record(e),i=de(e),a=new Re;return a.push(t,o,He(i)),a.push(s.sequenceLen-t-1,o,qe(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 f=await this.db.indexedPositionsBetween(e,t,r),l=No(f.map(p=>p.pos.node));await Promise.all(l.map(([p,d])=>this.db.prefetchRecords(p,d+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 X&&o.windowBp===void 0?new X(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 Re;for(;;){let c=A(o.node),f=de(o.node);this.walkedBp=t-i,await this.ensureNode(c);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${c} of length ${l.sequenceLen}`);a.push(s,c,He(f));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,c,qe(f));break}a.push(0,c,qe(f));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new Re;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,o=new Set;for(let i of this.records.keys())o.add(A(i));let s=0;for(;e.size>0;){let[i,a,c]=e.pop(),f=`${a}:${c}`;if(r.has(f))continue;r.add(f),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=yr(c);if(!r.has(`${a}:${l}`)){let h=this.record(V(a,xr(c))),u=i+h.sequenceLen-1;u<=t&&e.push(u,a,l)}let p=this.record(V(a,br(c))),d=i+1;if(d<=t)for(let h of p.successors()){let u=A(h),m=He(de(h));r.has(`${u}:${m}`)||e.push(d,u,m)}}for(let i of o)this.records.delete(V(i,"forward")),this.records.delete(V(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,G(t)],o=new Set([A(e),A(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let c of this.record(i).successors()){let f=A(c);o.has(f)||(r.push(c,G(c)),o.add(f))}}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)?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(G(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 ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async c=>{let f=c.successors(),l=f[0];return l===void 0?!1:f.length>1||(await e(G(l))).successors().length>1},r=async c=>{let f=await e(G(c));return f.next!==void 0?await t(f)?{kind:"snarl-exit",snarl:[G(c),f.next]}:{kind:"chain"}:(await e(c)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(c=>this.record(c).successors()),i,a=!1;for(;!a&&s.length>0;){let c=s.shift(),f=A(c);if(!this.hasHandle(c)&&!o.has(f)){o.add(f);let l=await r(c);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(V(f,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((y,v)=>i.set(y,v));let a=new Int32Array(s+1),c=new Int32Array(s),f=[];for(let y=0;y<s;y++){let v=this.record(o[y]),I=v.gbwt().decompressArrays();c[y]=v.sequenceLen,f.push(I),a[y+1]=a[y]+I.nodes.length}let l=a[s],p=new Int32Array(l),d=new Int32Array(l),h=new Uint8Array(l);for(let y=0;y<s;y++){let v=f[y];p.set(v.nodes,a[y]),d.set(v.offsets,a[y])}f.length=0;for(let y=0;y<l;y++){let v=i.get(p[y]);v===void 0?p[y]=-1:(p[y]=v,h[a[v]+d[y]]=1)}let u=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,w,x=(y,v,I)=>{let R=[],C=0,_=0,E=-1,k=y,O=v;for(;;){k===u&&O===m&&(E=C),I&&(I.push(o[k]),R.push(O)),C+=1,_+=c[k];let N=a[k]+O,F=p[N];if(F<0)break;O=d[N],k=F}return{offsets:R,len:_,refAt:E,last:k}},b=(y,v,I,R)=>{R>=0&&(this.refId=this.paths.length,w=R),this.paths.push({path:y,offsets:v,len:I,weight:void 0,identity:void 0})},g=new Int32Array(s),S=u!==void 0&&T(o[u]);for(let y=0;y<s;y++){let v=o[y];if(!T(v)){let I=a[y],R=a[y+1]-I;for(let C=0;C<R;C++)if(h[I+C]===0){let _=[],{offsets:E,len:k,refAt:O,last:N}=x(y,C,_),F=o[N];if(O>=0||$e(v,F)){if(b(_,E,k,O),!T(F)){let H=i.get(G(F));g[H]=g[H]+1}}else this.twinStarts.add(ie({node:v,offset:C}))}}}for(let y=0;y<s;y++){let v=o[y];if(T(v)){let I=a[y],R=a[y+1]-I,C=0;for(let E=0;E<R;E++)h[I+E]===0&&(C+=1);let _=!S&&C===g[y];for(let E=0;E<R;E++)if(h[I+E]===0){let k=_?void 0:x(y,E,void 0);if(k&&(k.refAt>=0||$e(v,o[k.last]))){let O=[],{offsets:N,len:F,refAt:H}=x(y,E,O);b(O,N,F,H)}else this.twinStarts.add(ie({node:v,offset:E}))}}}if(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],v=r.nodeOffset;for(let R of y.path.slice(0,w))v+=this.record(R).sequenceLen;let I=r.seqOffset-v;this.refInterval=[I,I+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:I,hapEnd:I+y.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)=>zt(o.path,s.path)||o.len-s.len);let t=[],r;for(let o of this.paths){let s=t[t.length-1];s&&zt(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&zt(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(A(i));for(let s of[...this.records.keys()])o.has(A(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async walkHaplotypesFromAnchor(e,t,r,o,s){let i=e.position.seqOffset,a=i+t,c=Math.floor(i/r)*r,f=Math.min(r,Lo),l=4*(r+t)+f,p={spacing:r,anchorOffset:c,anchorNodeOffset:-1,anchorHandle:-1,referenceSteps:0,rows:0,walks:[],graphFetches:0,scans:[],scanRows:0,fallback:void 0,ms:{reference:0,rows:0,walks:0,scan:0,sampled:0}};this.stats.anchorWalk=p;let d=performance.now(),h=()=>{let M=performance.now(),U=M-d;return d=M,U};this.clearPaths(),this.records.clear();let u=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,c);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${q(e.name,e.name.fragment)} at offset ${c}; it was not built with anchors at ${r} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let w=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+f);if(!w)throw new Error(`Path ${q(e.name,e.name.fragment)} has not been indexed for random access`);let x=await this.walkReference(u,w,m,i,a,a+f),{anchor:b,refOffsetOf:g,refHandles:S,windowSteps:y}=x;p.anchorHandle=b.pos.node,p.referenceSteps=x.steps,this.walkedBp=t;let v=[],I=[],R=0;for(let M of y)await this.ensureNode(A(M.pos.node)),v.push(M.pos.node),I.push(M.pos.offset),R+=this.record(M.pos.node).sequenceLen;let C=y[0];if(C===void 0)throw new Error("The reference walk has no node in the window");this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[C.refOffset,C.refOffset+R],this.refId=0,this.paths.push({path:v,offsets:I,len:R,weight:void 0,identity:{pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:C.refOffset,hapEnd:C.refOffset+R}}),p.ms.reference=h();let _=await this.db.haplotypeSamplesAtNode(b.pos.node);p.rows=_.length,p.ms.rows=h();let E=_.find(M=>M.offset===b.pos.offset&&M.pathHandle===e.handle&&M.pathOffset===b.offset);if(E===void 0)throw new Error(`The haplotype index has no anchor row for ${q(e.name,e.name.fragment)} at offset ${b.offset} (node ${A(b.pos.node)}); it was not built with anchors at ${r} bp for this graph`);let k=await this.db.pathsByHandle(),O=M=>{let U=k.get(M);if(!U)throw new Error(`Path ${M} is missing from the database`);return U.name},N=new Set([e.handle]),F=new Map;for(let M of _)if(M!==E&&o(O(M.pathHandle))){let U=F.get(M.pathHandle);U?U.push(M):F.set(M.pathHandle,[M])}let H;for(let[M,U]of F)if(H===void 0){let pe=se=>Math.abs(se.offset-E.offset);U.sort((se,eo)=>pe(se)-pe(eo));let he;for(let se of U)N.has(M)||(he=await this.walkAndKeep(u,se,"anchor",O(M),g,a,l,s,N,p));N.has(M)||(H=he)}p.ms.walks=h();let ve=H===void 0?await this.samplesOfUnwalkedContigs(v,g,S,o,N,O,p):new Map;if(p.ms.scan=h(),ve.size>0){await this.mapReferenceBefore(u,e.handle,Math.max(0,m.pathOffset-2*r),m.pathOffset,g,S);for(let[M,U]of ve)if(H===void 0){let pe=O(M),he;for(let se of U)he??=await this.entryBefore(u,se,g,S,this.refInterval[0],l);H=he===void 0?`no sample of ${q(pe,pe.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(u,he,"sample",pe,g,a,l,s,N,p)}p.ms.sampled=h()}return p.fallback=H,H}async walkAndKeep(e,t,r,o,s,i,a,c,f,l){let p=await this.walkFromRow(e,t,o,s,this.refInterval[0],i,a,c);l.walks.push({pathHandle:t.pathHandle,from:r,steps:p.steps,pieces:p.infos.length,end:p.end});let d;return p.end==="bound"||p.infos.length===0?d=`${q(o,t.pathOffset)} walked ${p.steps} steps from its ${r} without writing a walk through the window (${p.end})`:(f.add(t.pathHandle),this.paths.push(...p.infos)),d}async mapReferenceBefore(e,t,r,o,s,i){let a=await this.prefetchReferenceRange(t,r,o),c=a?.pos,f=a?.pathOffset??o;for(;c!==void 0&&c.node!==0&&f<o;){this.signal?.throwIfAborted();let l=await e(c.node),p=A(c.node);s.has(p)||(s.set(p,f),i.add(c.node)),f+=l.sequenceLen,c=l.gbwt().lf(c.offset)}}async runsWithReference(e,t,r,o,s){let i={node:t.node,offset:t.offset},a=0,c;for(;c===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)c=!1;else if(r.has(A(i.node)))c=o.has(i.node);else{let f=await e(i.node);a+=f.sequenceLen,i=f.gbwt().lf(i.offset)}return c}async entryBefore(e,t,r,o,s,i){let a=(await e(t.node)).sequenceLen,c=async(h,u)=>{let m=(await e(h.node)).sequenceLen;return{node:h.node,offset:h.offset,pathHandle:t.pathHandle,orientation:t.orientation,pathOffset:t.orientation==="forward"?t.pathOffset-u:t.pathOffset+a+u-m}},f={node:t.node,offset:t.offset},l=0,p,d=!await this.runsWithReference(e,t,r,o,i);for(;!d;){this.signal?.throwIfAborted();let h=r.get(A(f.node));if(h!==void 0&&h<s)p=await c(f,l),d=!0;else if(l>i)p={...t},d=!0;else{let m=(await e(G(f.node))).gbwt().predecessorAt(f.offset);if(m===void 0)p=await c(f,l),d=!0;else{let w=await e(m),x=w.gbwt().offsetTo(f);if(x===void 0)throw new Error(`No offset in ${m} leads to ${f.node}:${f.offset}`);f={node:m,offset:x},l+=w.sequenceLen}}}return p}async walkReference(e,t,r,o,s,i){let a=new Map,c=new Set,f=[],l,p=t.pos,d=t.pathOffset,h=0;for(;p!==void 0&&p.node!==0&&d<i;){this.signal?.throwIfAborted();let u=await e(p.node),m=d+u.sequenceLen;if(l===void 0&&d===r.pathOffset){if(p.node!==r.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${d} where the haplotype index names node ${A(r.node)} as the anchor`);l={pos:p,offset:d}}if(l!==void 0){h+=1;let w=A(p.node);a.has(w)||(a.set(w,d),c.add(p.node)),d<s&&m>o&&f.push({pos:p,refOffset:d})}d=m,p=u.gbwt().lf(p.offset)}if(l===void 0)throw new Error(`The reference walk from offset ${t.pathOffset} never starts a node at the anchor offset ${r.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:c,windowSteps:f,steps:h}}async walkFromRow(e,t,r,o,s,i,a,c){let f=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+f,p=[],d=[],h=[],u=0,m=0,w=0,x,b,g={node:t.node,offset:t.offset};for(;b===void 0;)if(this.signal?.throwIfAborted(),g===void 0||g.node===0)b=x===void 0?"before the window":"ended in the window";else if(m>a)b="bound";else{let y=o.get(A(g.node)),v=x!==void 0;if(y!==void 0&&y>=i)b=v?"through the window":"past the window";else{!v&&y!==void 0&&y>=s&&(x=m);let I=await e(g.node);if(x!==void 0){let R={pos:g,at:m,len:I.sequenceLen};y===void 0?(h.push(R),u+=R.len):(u>c&&y<s?(p.push(d),d=[]):d.push(...h),h=[],u=0,d.push(R))}w+=1,m+=I.sequenceLen,g=I.gbwt().lf(g.offset)}}p.push(d);let S=[];for(let y of p){let v=y[0],I=y[y.length-1];if(v!==void 0&&I!==void 0){let R=[],C=[],_=0;for(let O of y)await this.ensureNode(A(O.pos.node)),R.push(O.pos.node),C.push(O.pos.offset),_+=O.len;let E=v.at,k=I.at+I.len;S.push({path:R,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:r,orientation:"forward",hapStart:l+E,hapEnd:l+k}:{pathHandle:t.pathHandle,name:r,orientation:"reverse",hapStart:l-k,hapEnd:l-E}})}}return{steps:w,end:b,infos:S}}async samplesOfUnwalkedContigs(e,t,r,o,s,i,a){let c=Yr([...e].sort((l,p)=>l-p));a.scans=c;let f=new Map;for(let[l,p]of c){let d=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=d.length;for(let h of d){let u=t.has(A(h.node));if(!s.has(h.pathHandle)&&(!u||r.has(h.node))&&o(i(h.pathHandle))){let m=f.get(h.pathHandle)??[];u?m.unshift(h):m.push(h),f.set(h.pathHandle,m)}}}return f}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=Yr(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[u,m]of t)for(let w of await this.db.haplotypeSamplesInRange(u,m))r.set(ie(w),w);let o=u=>{let m=0,w=t.length-1;for(;m<w;){let b=m+w+1>>1;t[b][0]<=u?m=b:w=b-1}let x=t[m];return x[0]<=u&&u<=x[1]},s=new Map;this.paths.forEach((u,m)=>{u.path.length>0&&m!==this.refId&&s.set(ie(Ye(u,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((u,m)=>{m!==this.refId&&i.fragmentLengths.push(u.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=u=>(i.graphLookups+=1,a(u)),f=async(u,m)=>{if(o(u.node))return r.get(ie(u));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let w=await this.db.haplotypeSampleAt(u.node,u.offset);return w||(i.companionMisses+=1),w},l=new Map,p=async u=>{let m=l.get(u);if(!m){let w=await this.db.getPath(u);if(!w)throw new Error(`Path ${u} is missing from the database`);m=w.name,l.set(u,m)}return m},d=(u,m,w)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+m+w},h=(u,m)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+m};for(let u=0;u<this.paths.length;u++){let m=this.paths[u];if(u===this.refId||m.identity)continue;let w=[],x=new Set,b={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(b);let g,S=0,y=u,v;for(;g===void 0;){if(this.signal?.throwIfAborted(),y!==void 0){if(x.has(y)){b.end="cycle";break}x.add(y);let E=this.paths[y];w.push({index:y,startBp:S}),b.fragments+=1;let k=S;for(let N=0;N<E.path.length;N++){let F=Ye(E,N),H=r.get(ie(F)),ve=this.record(F.node).sequenceLen;if(H){g=d(H,k,ve);break}k+=ve}if(S+=E.len,g){b.end="in-fragment sample";break}let O=Ye(E,E.path.length-1);v=this.record(O.node).gbwt().lf(O.offset),y=void 0}if(v===void 0||v.node===0){b.end="endmarker";break}let I=ie(v),R=s.get(I);if(R!==void 0){let E=this.paths[R].identity;if(E){g=h(E,S),b.end="identified sibling";break}y=R;continue}this.records.has(v.node)&&(b.reentries+=1),this.twinStarts.has(I)&&(b.twinLandings+=1);let C=await f(v,b),_=await c(v.node);if(C){g=d(C,S,_.sequenceLen),b.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,b.steps+=1,S-w[w.length-1].startBp>4*e+4*_.sequenceLen){b.end="bound";break}S+=_.sequenceLen,v=_.gbwt().lf(v.offset)}if(g){b.pathHandle=g.pathHandle;let I=await p(g.pathHandle);for(let{index:R,startBp:C}of w){let _=this.paths[R];_.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:I,orientation:"forward",hapStart:g.base+C,hapEnd:g.base+C+_.len}:{pathHandle:g.pathHandle,name:I,orientation:"reverse",hapStart:g.base-C-_.len,hapEnd:g.base-C}}}}}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 c=0;c<e.length;c++){let f=r.get(e[c]);if(f){let l=_o(f,a);if(l===void 0)return;o[i]=c,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 c=this.record(e[o]).sequence,f=this.record(t[s]).sequence;for(;i<c.length&&a<f.length;){if(c[i]!==f[a])return r;i+=1,a+=1,r+=1}i===c.length&&(o+=1,i=0),a===f.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 c=this.record(e[e.length-o-1]).sequence,f=this.record(t[t.length-s-1]).sequence;for(;i<c.length&&a<f.length;){if(c[c.length-i-1]!==f[f.length-a-1])return r;i+=1,a+=1,r+=1}i===c.length&&(o+=1,i=0),a===f.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),z(r,"M",i),Vr(r,o-i-a,s-i-a),z(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??Ro(Lr(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,d,h,u)=>{p===d?z(s,"D",i[u]-i[h]):h===u?z(s,"I",this.pathLen(e.slice(p,d))):this.align(e.slice(p,d),t.slice(h,u),s)},c=0,f=0,l=0;for(let p=0;p<o.count;p++){let d=o.pathAt[p],h=o.refAt[p];(f!==d||l!==h)&&a(f,d,l,h);let u=this.record(e[d]).sequenceLen;z(s,"M",u),c+=u,f=d+1,l=h+1}return a(f,e.length,l,t.length),{edits:s,matched:c}}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(Sr(r))o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else{let s=t.path.map(c=>G(c)).reverse(),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={edits:this.editsAgainst(t.path,r).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,r).edits,flipped:!0};else{let c=this.editsAgainst(t.path,r),f=this.editsAgainst(s,r);o=f.matched>c.matched?{edits:f.edits,flipped:!0}:{edits:c.edits,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],o=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:c}=this.alignment(i),f=0,l=0;for(;f<a.length&&a[f][0]==="D";)l+=a[f][1],f+=1;let p=a.length,d=0;for(;p>f&&a[p-1][0]==="D";)d+=a[p-1][1],p-=1;let h=s.identity,u=h?h.orientation==="forward"!==c:!c;o.push({strand:u?"+":"-",refStart:e.start+l,refEnd:e.start+r-d,edits:a.slice(f,p),weight:s.weight,path:s.path,start:Ye(s,0),identity:h===void 0?void 0:{pathHandle:h.pathHandle,name:h.name,hapStart:h.name.fragment+h.hapStart,hapEnd:h.name.fragment+h.hapEnd,walkForward:h.orientation==="forward"}})}),Mo(o).map(s=>{let{edits:i,identity:a,...c}=s,f={...c,cigar:Ho(i)};return a?{...f,resolved:!0,name:a.name,label:q({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...f,resolved:!1}})}pairAlignments(e){let{target:t,query:r,maxGap:o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Ke(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),c=r?i(r):l=>!a(l),f=l=>this.record(V(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>c(p.name)).flatMap(p=>Wr(p.steps,l.steps,f,o===void 0?{}:{maxGap:o}).map(d=>({query:p.name,queryStart:p.start+d.queryStart,queryEnd:p.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Qr(d.edits),matches:d.edits.reduce((h,[u,m])=>h+(u==="="?m:0),0),columns:d.edits.reduce((h,[,u])=>h+u,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=V(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&ue(o,s)&&t.push([r==="reverse"?1:0,A(s),T(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(!T(r)){let o=A(r),s=`S	${o}	${this.record(r).sequence}
+`;for(let[i,a,c]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${c?"-":"+"}
+`;t.push(e.encode(s))}return Or(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Mr(kr(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let f of o)T(f)||r.push(`S	${A(f)}	${this.record(f).sequence}`);let s=f=>T(f)?"-":"+";for(let f of o)for(let l of this.record(f).successors())this.hasHandle(l)&&ue(f,l)&&r.push(`L	${A(f)}	${s(f)}	${A(l)}	${s(l)}	0M`);let i=(f,l,p,d,h)=>{let u=Ke(f,l).map(x=>`${T(x)?"<":">"}${A(x)}`).join(""),m=f.weight===void 0?"":`	WT:i:${f.weight}`,w=h===void 0?"":`	CG:Z:${h}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${d}	${u}${m}${w}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let c=1;return this.paths.forEach((f,l)=>{if(l!==this.refId){let p=e.names==="resolved"?f.identity:void 0,d=t?this.alignToRef(l):void 0;r.push(p?i(f,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,d):i(f,void 0,{sample:"unknown",contig:a,haplotype:c,fragment:0},f.len,d)),c+=1}}),`${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:q(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 c=e.names==="resolved"?i.identity:void 0;r.push({info:i,identity:c,name:c?q({...c.name,fragment:c.name.fragment+c.hapStart},c.name.fragment+c.hapEnd):q({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)&&ue(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!T(s)).map(s=>({id:String(A(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(A(s)),from_is_reverse:T(s),to:String(A(i)),to_is_reverse:T(i)});let o=this.outputPaths(e).map(s=>Fo(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!T(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=A(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Ke(i.info,i.identity))}))}}};function Ke(n,e){return e?.orientation==="reverse"?n.path.map(t=>G(t)).reverse():n.path}function Fo(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Ke(n,e).map(o=>({id:String(A(o)),is_reverse:T(o)}))}}function zt(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 z(n,e,t){if(t===0)return;let r=n[n.length-1];r?.[0]===e?r[1]+=t:n.push([e,t])}function Ve(n){return n===0?0:6+(n-1)}function Vr(n,e,t){if(e===0)z(n,"D",t);else if(t===0)z(n,"I",e);else{let r=Math.min(e,t),o=4*r+Ve(e-r)+Ve(t-r),s=Ve(e)+Ve(t);o<=s?(z(n,"M",r),z(n,"I",e-r),z(n,"D",t-r)):(z(n,"I",e),z(n,"D",t))}}function Ho(n){return n.map(([e,t])=>`${t}${e}`).join("")}async function Xe(n,e,t,r,o={}){let s=new _e(n,o);try{let i=await s.pathPosition(Ce(e,t));await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,o.context??100),await s.extractSnarls(o.snarls??"none"),s.extractPaths(i,o.haplotypes??"all")}catch(i){throw i instanceof X&&i.windowBp===void 0?new X(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}return s}async function Kr(n,e,t,r,o){if(!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let s=await n.haplotypeAnchorSpacing(),i,a;if(s!==void 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oe(n,e){return n[e]*16777216+n[e+1]*65536+n[e+2]*256+n[e+3]}function Bo(n,e){let t=n[e];if(t!==Pe&&t!==et&&t!==Zr&&t!==Je)throw new Error(`SQLite page has unknown b-tree type ${t}`);let r=t===Pe||t===et;return{type:t,cellCount:Jr(n,e+3),rightChild:r?oe(n,e+8):0,cellPointers:e+(r?12:8)}}function re(n,e,t){return Jr(n,e.cellPointers+2*t)}var Go=4096,Do=4096,tt=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,c=oe(e,t+s);for(;c!==0&&a<r;){let f=await this.pager.page(c),l=f.subarray(4,4+Math.min(this.usable-4,r-a));i.set(l,a),a+=l.length,c=oe(f,0)}if(a!==r)throw new Error("SQLite overflow chain ended before the 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u=d;u<=h;u++)c.push(u===l.cellCount?l.rightChild:oe(f,re(f,l,u)))}),c.length>Do)return!1;this.pager.prefetch(c),s=c}return!0}async tableRowid(e,t){let r=e;for(;;){let{page:o,header:s}=await this.pageAt(r);if(s.type===Je){let c=0,f=s.cellCount;for(;c<f;){let l=c+f>>1,p=re(o,s,l),[d,h]=Z(o,p),[u,m]=Z(o,h);if(u===t)return Ze(await this.payload(o,m,d,!1));u<t?c=l+1:f=l}return}if(s.type!==et)throw new Error("SQLite table b-tree contains an index page");let i=0,a=s.cellCount;for(;i<a;){let c=i+a>>1,f=re(o,s,c),[l]=Z(o,f+4);l<t?i=c+1:a=c}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===Je)for(let o=0;o<r.cellCount;o++){let s=re(t,r,o),[i,a]=Z(t,s),[c,f]=Z(t,a);yield{rowid:c,values:Ze(await this.payload(t,f,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 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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 c=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(f=>f.subarray(c,c+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 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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 ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Ut="GBZ-base version 4",nt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},ot=class extends 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o={start:n.get("start"),end:n.get("end")},s=n.get("strand")===-1?-1:1,i=o.start>=t.start&&o.end<=t.end,a=i&&r===void 0?void 0:cr(n);if(a===void 0){let c=i?{...o,mateStart:e.start,mateEnd:e.end}:Ss(o,e,s,t);return c===void 0?[]:[c]}else return(r===void 0?[{...o,mateStart:e.start,mateEnd:e.end,cigar:a}]:fr(a,o.start,e.start,e.end,s,r)).flatMap(f=>{let l=ar(f.cigar,f.start,f.mateStart,f.mateEnd,s,t.start,t.end);return l===void 0?[]:[l]})}function Is(n,e,t,r,o){let s=`:${r.start}-${r.end}${o}`,i=n.toJSON(),a={...i,uniqueId:`${n.id()}${s}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};i.syntenyId!==void 0&&(a.syntenyId=`${String(i.syntenyId)}${s}`);for(let c of ys)delete a[c];return new le(a)}function Wn(n,e,t){let r=bs(n);if(r===void 0)return[n];{let o=vs(n,r,e,t);return o.map((s,i)=>Is(n,r,s,e,o.length>1?`/${i}`:""))}}var Ot=class extends Qn.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:o,splitAtGapBp:s,...i}=r,a=o&&this.recordsAreAlignments,c=(0,Yn.createStatusFanOut)(i.statusCallback);return Zt(t).pipe(be((f,l)=>this.getFeatures(f,{...i,statusCallback:c()}).pipe(be(p=>a?Wn(p,p.get("assemblyName")===f.assemblyName?f:{start:p.get("start"),end:p.get("end")},s):[p]),Ct(),Le(p=>({index:l,features:p})))),Ct(),be(f=>f.sort((l,p)=>l.index-p.index).flatMap(l=>l.features)))}};var pr=class extends Error{constructor(){super("this .gbz.db has no HaplotypeSamples/HaplotypeLengths tables, so its walks cannot be named; run gbz-haplotype-index (from @gmod/gbz-base) over it first");this.name="NoHaplotypeIndexError"}},hr=class extends Error{constructor(t,r){super(r.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${t}" maps to none; set referenceSample`:`the anchor "${t}" is none of the graph's reference samples (${r.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`);this.name="NoReferenceSampleError"}};function Se(n){return`${n.sample}#${n.haplotype}`}function As(n,e){let t=Se(n);return e===void 0||e.some(r=>Fe(t,r))}var dr=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"}},ur=class extends Error{constructor(t,r,o){super(`this ${r.toLocaleString()} bp window reads more than nodeLimit (${t.toLocaleString()}) graph nodes; zoom in to about ${o.toLocaleString()} bp or raise nodeLimit`);this.name="NodeLimitError"}};function Vn(n,e,t){if(n instanceof Error&&(n.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(n.message))){let o=n.walkedBp,s=typeof o=="number"&&o>0?Math.floor(o*.8):Math.floor(t/2);return new ur(e,t,Math.max(s,1))}else return}function Kn(n,e){let t=Se(e);return n[t]??n[e.sample]??t}function Es({configured:n,anchorPrefix:e,referenceSamples:t}){let r=wr(e);if(n!=="")return n;if(t.includes(r))return r;if(t.length===1)return t[0];throw new hr(e,t)}function Cs(n,e){return`${Se(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function Rs({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:c,hapStart:f,hapEnd:l}=n,p=Cs(c,n),d={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:c.contig,start:f,end:l,assemblyName:r}};return new le(d)}}var mr=class extends Ot{constructor(){super(...arguments);this.graph=(0,Xn.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),r=!("uri"in t)||t.uri!=="",o=await Me.open((0,lr.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),r?{haplotypeIndex:(0,lr.openLocation)(t,this.pluginManager)}:{}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=(await o.tag("gbwt_reference_samples")??"").split(/\s+/).filter(c=>c!==""),a=Es({configured:this.getConf("referenceSample"),anchorPrefix:Ae(this,s),referenceSamples:i});return{db:o,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r),i=(await o.paths()).find(a=>a.isIndexed&&a.name.sample===s&&a.name.contig===t);return i?{sample:i.name.sample,contig:t,haplotype:i.name.haplotype}:void 0}async getHaplotypes(t={}){let{db:r,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=Se(i.name),c=s.get(a);c?c.contigs.includes(i.name.contig)||c.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=Tt(this),a=[];for(let c of await this.getHaplotypes(t))c.sample!==o&&a.push({name:Kn(i,c),label:c.prefix,group:c.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:Ae(this,i),c=(await r.paths()).filter(f=>i===o?f.isIndexed&&f.name.sample===s:Fe(Se(f.name),a)).map(f=>f.name.contig);return[...new Set(c)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>Ae(this,s));return o===void 0&&r===void 0?void 0:s=>As(s,o)&&(r===void 0||Fe(Se(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:c,end:f}=t;if(i!==s)throw new dr(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),d=this.keepPredicate(r.haplotypes),h=l?await o.getSubgraphForRange(l,c,f,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:r.signal,...d===void 0?{}:{keep:d}}).catch(u=>{throw Vn(u,p,f-c)??u}):void 0;return h?h.toGFA({names:"resolved"}):""}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:c}=t,f=Ae(this,r.targetAssemblyName),l=Tt(this),p=this.keepPredicate(r.haplotypes,f),d=await this.referenceQuery(i,r),h=this.getConf("nodeLimit");return(d?await(0,Zn.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${c.toLocaleString()}`,r.statusCallback,()=>o.getAlignmentsForRange(d,a,c,{context:this.getConf("context"),haplotypes:"all",limit:h,signal:r.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw Vn(m,h,c-a)??m})):[]).flatMap(m=>{let w=m.resolved?Rs({alignment:m,assemblyName:s,refName:i,lane:Kn(l,m.name)}):void 0;return w===void 0?[]:[w]})}getFeatures(t,r={}){return(0,Jn.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new pr;if(t.assemblyName===i){let a=await this.anchorFeatures(t,r);for(let c of a)o.next(c)}o.complete()},r.signal)}};export{dr as HaplotypeWindowError,pr as NoHaplotypeIndexError,hr as NoReferenceSampleError,ur as NodeLimitError,mr as default,Rs as fragmentFeature,Se as haplotypePrefix,Kn as laneAssemblyName,Vn as nodeLimitError,Es as resolveReferenceSample};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-QT5CVRL2.js.map