jbrowse-plugin-graphgenomeviewer 3.0.5 → 4.0.0

package/README.md

@@ -1,8 +1,7 @@
 # jbrowse-plugin-graphgenomeviewer
 
-A JBrowse 2 plugin that adds a **GraphGenomeView** for pangenome graphs (GFA /
-rGFA), plus a right-click launcher to open the local subgraph around a region
-from a linear genome view.
+A JBrowse 2 plugin that draws a pangenome graph (GFA / rGFA) as a track of a
+linear genome view, and as a **GraphGenomeView** of its own for a whole file.
 
 ## Screenshots
 
@@ -75,6 +74,59 @@ no index, a GBZ cut, a pggb file or a popped bubble, from the graph itself off
 the ordered layout's layering. Every node layout marks them as halos; the
 variant map draws them as glyphs.
 
+### The graph as a track
+
+A graph track's display is `LinearGraphDisplay`. It cuts the view's window plus
+a window-width each side and re-cuts once the view leaves the cut, keeping its
+sample rows in the order they were drawn. On a layout whose x is reference bp,
+such as Anchored or Sample rows, the graph draws under the view's own
+coordinates and pans and zooms with it. The force-directed, ordered and walk-row
+layouts draw in their own coordinates inside the track, fitted to it, with their
+own zoom in the track menu, the way a variant matrix does. The track menu also
+picks the layout, the colour, a walk to lift out, and opens the settings.
+
+```json
+{
+  "type": "FeatureTrack",
+  "trackId": "hprc_graph",
+  "name": "HPRC release 2 graph",
+  "assemblyNames": ["hg38"],
+  "adapter": { "type": "RgfaTabixAdapter", "uri": "https://example.com/hprc" },
+  "displays": [
+    {
+      "type": "LinearGraphDisplay",
+      "displayId": "hprc_graph-LinearGraphDisplay"
+    },
+    {
+      "type": "LinearBasicDisplay",
+      "displayId": "hprc_graph-LinearBasicDisplay"
+    }
+  ]
+}
+```
+
+The first display is the one the track opens with; the second is the segments
+lane, one block per segment, reachable from the track menu.
+
+A fine cut spans at most 5 Mb. An rGFA track can carry a coarse tier, one node
+per bubble, built by `build_bubble_tier.sh` in jbrowse-components; past
+`aboveBpPerPx` in the linear view the track cuts that pair instead, with no bp
+cap:
+
+```json
+{
+  "type": "RgfaTabixAdapter",
+  "uri": "https://example.com/hprc-v2.0-mc-grch38",
+  "coarse": {
+    "uri": "https://example.com/hprc-v2.0-mc-grch38.tier10000",
+    "aboveBpPerPx": 1000
+  }
+}
+```
+
+**Add → Graph genome view** opens a whole GFA file in a view of its own, with
+the same layouts and its own pan and zoom.
+
 ### Demonstration loci
 
 Six HPRC release 2 windows, the ones the

package/dist/chunks/{AddTrackWorkflow-Y3OBHM33.js → AddTrackWorkflow-TPCKXM2H.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/GbzBaseSyntenyAdapter-BLSUE5LT.js

@@ -0,0 +1,8 @@
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e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function ko(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function fe(r){return`${r.node}:${r.offset}`}function Mo(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Oo(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([c,l])=>[c,l]);er(s,t.insertion,t.deletion);for(let[c,l]of o.edits)z(s,c,l);let i=r.identity.walkForward,[a,f]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Lo(r){if(r.some(o=>o.weight!==void 0))return r;let e=new Map;r.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,n=new Set;for(let o of e.values()){o.sort((a,f)=>r[a].identity.hapStart-r[f].identity.hapStart);let s=o[0],i=r[s];for(let a of o.slice(1)){let f=r[a],c=Mo(i,f);c?(i=Oo(i,f,c),n.add(a)):(t.set(s,i),s=a,i=f)}t.set(s,i)}return r.flatMap((o,s)=>n.has(s)?[]:[t.get(s)??o])}function Ye(r,e){return{node:r.path[e],offset:r.offsets[e]}}var To=4096;function Jn(r){let e=[];for(let t of r){let n=e[e.length-1];n&&t-n[1]<=To?n[1]=t:e.push([t,t])}return e}var No=32768,Fo=65536;function Ho(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=No?o[1]=n:t.push([n,n])}return t}var Pe=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")),n=await this.db.getRecord(V(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}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 n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`Path ${q(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,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 f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${q(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,n){let o=A(e);await this.ensureNode(o);let s=this.record(e),i=me(e),a=new _e;return a.push(t,o,He(i)),a.push(s.sequenceLen-t-1,o,qe(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);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,n),l=Ho(c.map(p=>p.pos.node));await Promise.all(l.map(([p,h])=>this.db.prefetchRecords(p,h+2)))}}return o}async aroundInterval(e,t,n){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}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,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new _e;for(;;){let f=A(o.node),c=me(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 ${l.sequenceLen}`);a.push(s,f,He(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,qe(c));break}a.push(0,f,qe(c));let h=l.gbwt().lf(o.offset);if(!h)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=h,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new _e;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths();let n=new Set,o=new Set;for(let i of this.records.keys())o.add(A(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(n.has(c))continue;n.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=In(f);if(!n.has(`${a}:${l}`)){let d=this.record(V(a,An(f))),u=i+d.sequenceLen-1;u<=t&&e.push(u,a,l)}let p=this.record(V(a,En(f))),h=i+1;if(h<=t)for(let d of p.successors()){let u=A(d),m=He(me(d));n.has(`${u}:${m}`)||e.push(h,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 n=[e,G(t)],o=new Set([A(e),A(t)]),s=0;for(;n.length>0;){let i=n.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=A(f);o.has(c)||(n.push(f,G(f)),o.add(c))}}return s}async extractSnarls(e){let t=0;for(let[n,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(n,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?ge(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(G(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(G(l))).successors().length>1},n=async f=>{let c=await e(G(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[G(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=A(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await n(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(V(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((w,v)=>i.set(w,v));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let w=0;w<s;w++){let v=this.record(o[w]),I=v.gbwt().decompressArrays();f[w]=v.sequenceLen,c.push(I),a[w+1]=a[w]+I.nodes.length}let l=a[s],p=new Int32Array(l),h=new Int32Array(l),d=new Uint8Array(l);for(let w=0;w<s;w++){let v=c[w];p.set(v.nodes,a[w]),h.set(v.offsets,a[w])}c.length=0;for(let w=0;w<l;w++){let v=i.get(p[w]);v===void 0?p[w]=-1:(p[w]=v,d[a[v]+h[w]]=1)}let u=n===void 0?void 0:i.get(n.handle),m=n?.gbwtOffset,y,x=(w,v,I)=>{let R=[],C=0,_=0,E=-1,k=w,O=v;for(;;){k===u&&O===m&&(E=C),I&&(I.push(o[k]),R.push(O)),C+=1,_+=f[k];let N=a[k]+O,F=p[N];if(F<0)break;O=h[N],k=F}return{offsets:R,len:_,refAt:E,last:k}},S=(w,v,I,R)=>{R>=0&&(this.refId=this.paths.length,y=R),this.paths.push({path:w,offsets:v,len:I,weight:void 0,identity:void 0})},g=new Int32Array(s),b=u!==void 0&&L(o[u]);for(let w=0;w<s;w++){let v=o[w];if(!L(v)){let I=a[w],R=a[w+1]-I;for(let C=0;C<R;C++)if(d[I+C]===0){let _=[],{offsets:E,len:k,refAt:O,last:N}=x(w,C,_),F=o[N];if(O>=0||$e(v,F)){if(S(_,E,k,O),!L(F)){let H=i.get(G(F));g[H]=g[H]+1}}else this.twinStarts.add(fe({node:v,offset:C}))}}}for(let w=0;w<s;w++){let v=o[w];if(L(v)){let I=a[w],R=a[w+1]-I,C=0;for(let E=0;E<R;E++)d[I+E]===0&&(C+=1);let _=!b&&C===g[w];for(let E=0;E<R;E++)if(d[I+E]===0){let k=_?void 0:x(w,E,void 0);if(k&&(k.refAt>=0||$e(v,o[k.last]))){let O=[],{offsets:N,len:F,refAt:H}=x(w,E,O);S(O,N,F,H)}else this.twinStarts.add(fe({node:v,offset:E}))}}}if(n){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let w=this.paths[this.refId],v=n.nodeOffset;for(let R of w.path.slice(0,y))v+=this.record(R).sequenceLen;let I=n.seqOffset-v;this.refInterval=[I,I+w.len],w.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:I,hapEnd:I+w.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)=>jt(o.path,s.path)||o.len-s.len);let t=[],n;for(let o of this.paths){let s=t[t.length-1];s&&jt(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&jt(o.path,e)===0&&(n=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=n}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of n)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=n,this.refId=t===void 0?void 0:n.indexOf(t)}async walkHaplotypesFromAnchor(e,t,n,o,s){let i=e.position.seqOffset,a=i+t,f=Math.floor(i/n)*n,c=Math.min(n,Fo),l=4*(n+t)+c,p={spacing:n,anchorOffset:f,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 h=performance.now(),d=()=>{let M=performance.now(),U=M-h;return h=M,U};this.clearPaths(),this.records.clear();let u=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,f);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${q(e.name,e.name.fragment)} at offset ${f}; it was not built with anchors at ${n} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let y=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+c);if(!y)throw new Error(`Path ${q(e.name,e.name.fragment)} has not been indexed for random access`);let x=await this.walkReference(u,y,m,i,a,a+c),{anchor:S,refOffsetOf:g,refHandles:b,windowSteps:w}=x;p.anchorHandle=S.pos.node,p.referenceSteps=x.steps,this.walkedBp=t;let v=[],I=[],R=0;for(let M of w)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=w[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=d();let _=await this.db.haplotypeSamplesAtNode(S.pos.node);p.rows=_.length,p.ms.rows=d();let E=_.find(M=>M.offset===S.pos.offset&&M.pathHandle===e.handle&&M.pathOffset===S.offset);if(E===void 0)throw new Error(`The haplotype index has no anchor row for ${q(e.name,e.name.fragment)} at offset ${S.offset} (node ${A(S.pos.node)}); it was not built with anchors at ${n} 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 he=ie=>Math.abs(ie.offset-E.offset);U.sort((ie,no)=>he(ie)-he(no));let de;for(let ie of U)N.has(M)||(de=await this.walkAndKeep(u,ie,"anchor",O(M),g,a,l,s,N,p));N.has(M)||(H=de)}p.ms.walks=d();let Ie=H===void 0?await this.samplesOfUnwalkedContigs(v,g,b,o,N,O,p):new Map;if(p.ms.scan=d(),Ie.size>0){await this.mapReferenceBefore(u,e.handle,Math.max(0,m.pathOffset-2*n),m.pathOffset,g,b);for(let[M,U]of Ie)if(H===void 0){let he=O(M),de;for(let ie of U)de??=await this.entryBefore(u,ie,g,b,this.refInterval[0],l);H=de===void 0?`no sample of ${q(he,he.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(u,de,"sample",he,g,a,l,s,N,p)}p.ms.sampled=d()}return p.fallback=H,H}async walkAndKeep(e,t,n,o,s,i,a,f,c,l){let p=await this.walkFromRow(e,t,o,s,this.refInterval[0],i,a,f);l.walks.push({pathHandle:t.pathHandle,from:n,steps:p.steps,pieces:p.infos.length,end:p.end});let h;return p.end==="bound"||p.infos.length===0?h=`${q(o,t.pathOffset)} walked ${p.steps} steps from its ${n} without writing a walk through the window (${p.end})`:(c.add(t.pathHandle),this.paths.push(...p.infos)),h}async mapReferenceBefore(e,t,n,o,s,i){let a=await this.prefetchReferenceRange(t,n,o),f=a?.pos,c=a?.pathOffset??o;for(;f!==void 0&&f.node!==0&&c<o;){this.signal?.throwIfAborted();let l=await e(f.node),p=A(f.node);s.has(p)||(s.set(p,c),i.add(f.node)),c+=l.sequenceLen,f=l.gbwt().lf(f.offset)}}async runsWithReference(e,t,n,o,s){let i={node:t.node,offset:t.offset},a=0,f;for(;f===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)f=!1;else if(n.has(A(i.node)))f=o.has(i.node);else{let c=await e(i.node);a+=c.sequenceLen,i=c.gbwt().lf(i.offset)}return f}async entryBefore(e,t,n,o,s,i){let a=(await e(t.node)).sequenceLen,f=async(d,u)=>{let m=(await e(d.node)).sequenceLen;return{node:d.node,offset:d.offset,pathHandle:t.pathHandle,orientation:t.orientation,pathOffset:t.orientation==="forward"?t.pathOffset-u:t.pathOffset+a+u-m}},c={node:t.node,offset:t.offset},l=0,p,h=!await this.runsWithReference(e,t,n,o,i);for(;!h;){this.signal?.throwIfAborted();let d=n.get(A(c.node));if(d!==void 0&&d<s)p=await f(c,l),h=!0;else if(l>i)p={...t},h=!0;else{let m=(await e(G(c.node))).gbwt().predecessorAt(c.offset);if(m===void 0)p=await f(c,l),h=!0;else{let y=await e(m),x=y.gbwt().offsetTo(c);if(x===void 0)throw new Error(`No offset in ${m} leads to ${c.node}:${c.offset}`);c={node:m,offset:x},l+=y.sequenceLen}}}return p}async walkReference(e,t,n,o,s,i){let a=new Map,f=new Set,c=[],l,p=t.pos,h=t.pathOffset,d=0;for(;p!==void 0&&p.node!==0&&h<i;){this.signal?.throwIfAborted();let u=await e(p.node),m=h+u.sequenceLen;if(l===void 0&&h===n.pathOffset){if(p.node!==n.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${h} where the haplotype index names node ${A(n.node)} as the anchor`);l={pos:p,offset:h}}if(l!==void 0){d+=1;let y=A(p.node);a.has(y)||(a.set(y,h),f.add(p.node)),h<s&&m>o&&c.push({pos:p,refOffset:h})}h=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 ${n.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:f,windowSteps:c,steps:d}}async walkFromRow(e,t,n,o,s,i,a,f){let c=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+c,p=[],h=[],d=[],u=0,m=0,y=0,x,S,g={node:t.node,offset:t.offset};for(;S===void 0;)if(this.signal?.throwIfAborted(),g===void 0||g.node===0)S=x===void 0?"before the window":"ended in the window";else if(m>a)S="bound";else{let w=o.get(A(g.node)),v=x!==void 0;if(w!==void 0&&w>=i)S=v?"through the window":"past the window";else{!v&&w!==void 0&&w>=s&&(x=m);let I=await e(g.node);if(x!==void 0){let R={pos:g,at:m,len:I.sequenceLen};w===void 0?(d.push(R),u+=R.len):(u>f&&w<s?(p.push(h),h=[]):h.push(...d),d=[],u=0,h.push(R))}y+=1,m+=I.sequenceLen,g=I.gbwt().lf(g.offset)}}p.push(h);let b=[];for(let w of p){let v=w[0],I=w[w.length-1];if(v!==void 0&&I!==void 0){let R=[],C=[],_=0;for(let O of w)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;b.push({path:R,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:n,orientation:"forward",hapStart:l+E,hapEnd:l+k}:{pathHandle:t.pathHandle,name:n,orientation:"reverse",hapStart:l-k,hapEnd:l-E}})}}return{steps:y,end:S,infos:b}}async samplesOfUnwalkedContigs(e,t,n,o,s,i,a){let f=Jn([...e].sort((l,p)=>l-p));a.scans=f;let c=new Map;for(let[l,p]of f){let h=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=h.length;for(let d of h){let u=t.has(A(d.node));if(!s.has(d.pathHandle)&&(!u||n.has(d.node))&&o(i(d.pathHandle))){let m=c.get(d.pathHandle)??[];u?m.unshift(d):m.push(d),c.set(d.pathHandle,m)}}}return c}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=Jn(this.sortedHandles());if(t.length===0)return;let n=new Map;for(let[u,m]of t)for(let y of await this.db.haplotypeSamplesInRange(u,m))n.set(fe(y),y);let o=u=>{let m=0,y=t.length-1;for(;m<y;){let S=m+y+1>>1;t[S][0]<=u?m=S:y=S-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(fe(Ye(u,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.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}),f=u=>(i.graphLookups+=1,a(u)),c=async(u,m)=>{if(o(u.node))return n.get(fe(u));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(u.node,u.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async u=>{let m=l.get(u);if(!m){let y=await this.db.getPath(u);if(!y)throw new Error(`Path ${u} is missing from the database`);m=y.name,l.set(u,m)}return m},h=(u,m,y)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+m+y},d=(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 y=[],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,b=0,w=u,v;for(;g===void 0;){if(this.signal?.throwIfAborted(),w!==void 0){if(x.has(w)){S.end="cycle";break}x.add(w);let E=this.paths[w];y.push({index:w,startBp:b}),S.fragments+=1;let k=b;for(let N=0;N<E.path.length;N++){let F=Ye(E,N),H=n.get(fe(F)),Ie=this.record(F.node).sequenceLen;if(H){g=h(H,k,Ie);break}k+=Ie}if(b+=E.len,g){S.end="in-fragment sample";break}let O=Ye(E,E.path.length-1);v=this.record(O.node).gbwt().lf(O.offset),w=void 0}if(v===void 0||v.node===0){S.end="endmarker";break}let I=fe(v),R=s.get(I);if(R!==void 0){let E=this.paths[R].identity;if(E){g=d(E,b),S.end="identified sibling";break}w=R;continue}this.records.has(v.node)&&(S.reentries+=1),this.twinStarts.has(I)&&(S.twinLandings+=1);let C=await c(v,S),_=await f(v.node);if(C){g=h(C,b,_.sequenceLen),S.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,S.steps+=1,b-y[y.length-1].startBp>4*e+4*_.sequenceLen){S.end="bound";break}b+=_.sequenceLen,v=_.gbwt().lf(v.offset)}if(g){S.pathHandle=g.pathHandle;let I=await p(g.pathHandle);for(let{index:R,startBp:C}of y){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((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=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=n.get(e[f]);if(c){let l=ko(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 n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=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 n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=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 n;i+=1,a+=1,n+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return n}align(e,t,n){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(n,"M",i),er(n,o-i-a,s-i-a),z(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??Po($n(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,h,d,u)=>{p===h?z(s,"D",i[u]-i[d]):d===u?z(s,"I",this.pathLen(e.slice(p,h))):this.align(e.slice(p,h),t.slice(d,u),s)},f=0,c=0,l=0;for(let p=0;p<o.count;p++){let h=o.pathAt[p],d=o.refAt[p];(c!==h||l!==d)&&a(c,h,l,d);let u=this.record(e[h]).sequenceLen;z(s,"M",u),f+=u,c=h+1,l=d+1}return a(c,e.length,l,t.length),{edits:s,matched:f}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(Cn(n))o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else{let s=t.path.map(f=>G(f)).reverse(),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,n).edits,flipped:!0};else{let f=this.editsAgainst(t.path,n),c=this.editsAgainst(s,n);o=c.matched>f.matched?{edits:c.edits,flipped:!0}:{edits:f.edits,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,n])=>`${n}${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,n=this.refPrefix(t)[t.length],o=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:f}=this.alignment(i),c=0,l=0;for(;c<a.length&&a[c][0]==="D";)l+=a[c][1],c+=1;let p=a.length,h=0;for(;p>c&&a[p-1][0]==="D";)h+=a[p-1][1],p-=1;let d=s.identity,u=d?d.orientation==="forward"!==f:!f;o.push({strand:u?"+":"-",refStart:e.start+l,refEnd:e.start+n-h,edits:a.slice(c,p),weight:s.weight,path:s.path,start:Ye(s,0),identity:d===void 0?void 0:{pathHandle:d.pathHandle,name:d.name,hapStart:d.name.fragment+d.hapStart,hapEnd:d.name.fragment+d.hapEnd,walkForward:d.orientation==="forward"}})}),Lo(o).map(s=>{let{edits:i,identity:a,...f}=s,c={...f,cigar:$o(i)};return a?{...c,resolved:!0,name:a.name,label:q({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...c,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...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),f=n?i(n):l=>!a(l),c=l=>this.record(V(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>f(p.name)).flatMap(p=>Xn(p.steps,l.steps,c,o).map(h=>({query:p.name,queryStart:p.start+h.queryStart,queryEnd:p.start+h.queryEnd,strand:h.strand,target:l.name,targetStart:l.start+h.targetStart,targetEnd:l.start+h.targetEnd,cigar:Zn(h.edits),matches:h.edits.reduce((d,[u,m])=>d+(u==="="?m:0),0),columns:h.edits.reduce((d,[,u])=>d+u,0),sharedBases:h.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=V(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&ge(o,s)&&t.push([n==="reverse"?1:0,A(s),L(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!L(n)){let o=A(n),s=`S	${o}	${this.record(n).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return Hn(t)}async toGFA(e={}){let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Fn(Nn(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)L(c)||n.push(`S	${A(c)}	${this.record(c).sequence}`);let s=c=>L(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&ge(c,l)&&n.push(`L	${A(c)}	${s(c)}	${A(l)}	${s(l)}	0M`);let i=(c,l,p,h,d)=>{let u=Ke(c,l).map(x=>`${L(x)?"<":">"}${A(x)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,y=d===void 0?"":`	CG:Z:${d}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${h}	${u}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,h=t?this.alignToRef(l):void 0;n.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,h):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,h)),f+=1}}),`${n.join(`
+`)}
+`}outputPaths(e){let t=e.cigar??!1,n=[],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]};n.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 f=e.names==="resolved"?i.identity:void 0;n.push({info:i,identity:f,name:f?q({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):q({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&ge(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!L(s)).map(s=>({id:String(A(s)),sequence:this.record(s).sequence})),n=[];for(let[s,i]of this.outputEdges())n.push({from:String(A(s)),from_is_reverse:L(s),to:String(A(i)),to_is_reverse:L(i)});let o=this.outputPaths(e).map(s=>qo(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:n,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!L(i)),n=new Int32Array(t.length),o=[];t.forEach((i,a)=>{n[a]=A(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:n,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(r,e){return e?.orientation==="reverse"?r.path.map(t=>G(t)).reverse():r.path}function qo(r,e,t,n){return{name:t,...r.weight===void 0?{}:{weight:r.weight},...n===void 0?{}:{cigar:n},path:Ke(r,e).map(o=>({id:String(A(o)),is_reverse:L(o)}))}}function jt(r,e){let t=Math.min(r.length,e.length);for(let n=0;n<t;n++){let o=r[n],s=e[n];if(o!==s)return o<s?-1:1}return r.length-e.length}function z(r,e,t){if(t===0)return;let n=r[r.length-1];n?.[0]===e?n[1]+=t:r.push([e,t])}function Ve(r){return r===0?0:6+(r-1)}function er(r,e,t){if(e===0)z(r,"D",t);else if(t===0)z(r,"I",e);else{let n=Math.min(e,t),o=4*n+Ve(e-n)+Ve(t-n),s=Ve(e)+Ve(t);o<=s?(z(r,"M",n),z(r,"I",e-n),z(r,"D",t-n)):(z(r,"I",e),z(r,"D",t))}}function $o(r){return r.map(([e,t])=>`${t}${e}`).join("")}async function Xe(r,e,t,n,o={}){let s=new Pe(r,o);try{let i=await s.pathPosition(Re(e,t));await s.prefetchReferenceWalk(i,n-t),await s.aroundInterval(i.position,n-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:n-t,walkedBp:s.referenceWalkedBp??0}):i}return s}async function tr(r,e,t,n,o){if(!r.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let s=await r.haplotypeAnchorSpacing(),i,a;if(s!==void 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outside the file`);let n=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return n.subarray(o,o+this.pageSize)}};var Me=class r{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){let{size:n}=await e.stat(),o=await e.read(Math.min(t.blockSize??65536,n),0),s=o.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3")throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),f=a.getUint16(16),c=f===1?65536:f,l=s[20]??0,p=a.getUint32(56);if(p!==1)throw new Error(`SQLite text encoding ${p} is not UTF-8`);let h=new nt(e,c,n,t);h.seed(0,o),h.fetches+=1,h.bytesFetched+=o.length;let d=new tt(h,l),u=new Map;for await(let{values:m}of d.tableScan(1)){let[y,x,S,g,b]=m;typeof y=="string"&&typeof x=="string"&&typeof S=="string"&&typeof g=="number"&&u.set(x,{type:y,name:x,tableName:S,rootPage:g,sql:typeof b=="string"?b:""})}return new r(h,d,u)}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(n=>n.type==="index"&&n.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n){return this.btree.prefetchRowidRange(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Wt="GBZ-base version 4",rt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},ot=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Wt}"`),this.found=e}},st=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=Pn(o)}get id(){return A(this.handle)}get orientation(){return me(this.handle)}get sequence(){return this.decoded??=kn(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 ${this.handle} is empty`);return new Ge(this.edges,this.bwt)}};function T(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function it(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function Ut(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function sr(r,e){return{handle:r,fwStart:{node:T(e[1],"Paths.fw_node"),offset:T(e[2],"Paths.fw_offset")},revStart:{node:T(e[3],"Paths.rev_node"),offset:T(e[4],"Paths.rev_offset")},name:{sample:it(e[5],"Paths.sample"),contig:it(e[6],"Paths.contig"),haplotype:T(e[7],"Paths.haplotype"),fragment:T(e[8],"Paths.fragment")},isIndexed:T(e[9],"Paths.is_indexed")!==0}}async function ir(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(it(t[0],"Tags.key"),it(t[1],"Tags.value"));return e}var Oe=class r{tagCache;pathCache;pathMapCache;indexTags;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e,t={}){let{haplotypeIndex:n,...o}=t,s=await Me.open(e,o);for(let c of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(c);let i=n?await Me.open(n,o):s,a=new r(s,i),f=await a.tag("version");if(f!==Wt)throw new ot(f);if(n){for(let d of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(d);a.indexTags=await ir(i);let c=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(c!==l)throw new Error(`haplotype index was built for ${c??"an unknown number of"} paths but the graph has ${l}`);let p=a.indexTags.get("haplotype_index_nodes"),h=await a.tag("nodes");if(p!==void 0&&p!==h)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${h}`)}if(a.hasHaplotypeIndex&&await a.haplotypeIndexTag("haplotype_index_orientations")==="forward")throw new rt;return a}tags(){return this.tagCache??=ir(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 n=t[4];return new st(e,_n(Ut(t[1],"Nodes.edges")),Ut(t[2],"Nodes.bwt"),Ut(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(sr(t,n));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?sr(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(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsForSample(e){return(await this.paths()).filter(t=>t.name.sample===e)}async pathsNamed(e){let t=Re(qn(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.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 n=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!n){let i=await this.getPath(e);throw new Error(`Path ${i?q(i.name,i.name.fragment):e} has not been indexed for random access`)}let o=n.pathOffset,s=n.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async pathFragmentsForRange(e,t,n){if(n<=t)return[];let o=await this.pathsNamed(e),s=o.filter(f=>f.name.fragment<=t).slice(-1),i=o.filter(f=>f.name.fragment>t&&f.name.fragment<n);return(await Promise.all([...s,...i].map(async f=>({path:f,start:f.name.fragment,end:f.name.fragment+await this.pathLength(f.handle)})))).filter(f=>t<f.end)}async 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Ps({alignment:r,assemblyName:e,refName:t,lane:n}){let{refStart:o,refEnd:s,strand:i,cigar:a}=r;if(!(!r.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=r,p=_s(f,r),h={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:n}};return new oe(h)}}function ks({pair:r,lane:e,mateLane:t}){let n=`${se(r.target)}#${r.target.contig}:${r.targetStart}-${r.targetEnd}|${se(r.query)}#${r.query.contig}:${r.queryStart}-${r.queryEnd}`;return new oe({uniqueId:n,assemblyName:e,refName:r.target.contig,start:r.targetStart,end:r.targetEnd,type:"match",strand:r.strand==="-"?-1:1,CIGAR:r.cigar,syntenyId:n,identity:r.matches/Math.max(r.columns,1),numMatches:r.matches,blockLen:r.columns,mate:{refName:r.query.contig,start:r.queryStart,end:r.queryEnd,assemblyName:t}})}var bn=class extends Ot{constructor(){super(...arguments);this.graph=(0,eo.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),n=!("uri"in t)||t.uri!=="",o=await Oe.open((0,un.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),n?{haplotypeIndex:(0,un.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(f=>f!==""),a=Rs({configured:this.getConf("referenceSample"),anchorPrefix:ue(this,s),referenceSamples:i});return{db:o,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,n){let{db:o,referenceSample:s}=await this.graph(n),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:n,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await n.paths()){let a=se(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:n,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Lt(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Jr(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:n,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:ue(this,i),f=(await n.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:Ee(se(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,n){let o=t===void 0||t.length===0?void 0:t.map(s=>ue(this,s));return o===void 0&&n===void 0?void 0:s=>Cs(s,o)&&(n===void 0||Ee(se(s),n))}async getSubgraph(t,n={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new wn(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),h=this.keepPredicate(n.haplotypes),d=l?await o.getSubgraphForRange(l,f,c,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:n.signal,...h===void 0?{}:{keep:h}}).catch(u=>{throw hn(u,p,c-f)??u}):void 0;return d?d.toGFA({names:"resolved"}):""}async laneHaplotypes(t,n){let o=ue(this,t);return(await this.getHaplotypes(n)).filter(s=>Ee(s.prefix,o))}async referencePieces(t,n,o,s){let{db:i,referenceSample:a}=await this.graph(s),f=(await i.paths()).filter(l=>l.isIndexed&&l.name.sample===a&&l.name.contig===t&&l.name.fragment>n&&l.name.fragment<o).map(l=>l.name.fragment),c=[n,...[...new Set(f)].sort((l,p)=>l-p),o];return c.slice(1).map((l,p)=>({start:c[p],end:l}))}async anchorFeatures(t,n){let{db:o}=await this.graph(n),{assemblyName:s,refName:i,start:a,end:f}=t,c=ue(this,n.targetAssemblyName),l=Lt(this),p=this.keepPredicate(n.haplotypes,c),h=await this.referenceQuery(i,n),d=this.getConf("nodeLimit");return(h?await(0,dn.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,n.statusCallback,()=>o.getAlignmentsForRange(h,a,f,{context:this.getConf("context"),haplotypes:"all",limit:d,signal:n.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw hn(m,d,f-a)??m})):[]).flatMap(m=>{let y=m.resolved?Ps({alignment:m,assemblyName:s,refName:i,lane:Jr(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,n,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new yn(n);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(n,o),p=await this.laneHaplotypes(s,o),h=[...l,...p],d=await this.referenceQuery(a,o),u=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,b)=>i.getSubgraphForRange(g,b.start,b.end,{context:this.getConf("context"),haplotypes:"all",limit:u,signal:o.signal,keep:w=>h.some(v=>v.sample===w.sample&&v.haplotype===w.haplotype)}).catch(w=>{throw hn(w,u,c-f)??w}),x=d&&m&&l.length>0&&p.length>0?(await(0,dn.updateStatus)(`Reading ${n} against ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,f,c,o)).map(g=>y(d,g))))).filter(g=>g!==void 0):[];return x.every(g=>{let b=g.stats.anchorWalk;return b!==void 0&&b.fallback===void 0})?x.flatMap(g=>l.flatMap(b=>p.flatMap(w=>g.pairAlignments({target:b,query:w,bases:!1}).map(v=>ks({pair:v,lane:n,mateLane:s}))))):[]}getFeatures(t,n={}){return(0,to.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(n);if(!s.hasHaplotypeIndex)throw new mn;if(t.assemblyName===i){let a=n.queryAssemblyName===void 0?await this.anchorFeatures(t,n):await this.pairFeatures(t,n.queryAssemblyName,n);for(let f of a)o.next(f)}o.complete()},n.signal)}};export{wn as HaplotypeWindowError,mn as NoHaplotypeIndexError,gn as NoReferenceSampleError,xn as NodeLimitError,yn as PairTargetError,bn as default,Ps as fragmentFeature,se as haplotypePrefix,Jr as laneAssemblyName,hn as nodeLimitError,ks as pairFeature,Rs as resolveReferenceSample};
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