jbrowse-plugin-graphgenomeviewer 4.8.0 → 5.0.0

package/dist/chunks/LinearGraphDisplay-7YE624D5.js

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+//# sourceMappingURL=LinearGraphDisplay-7YE624D5.js.map

package/dist/chunks/LinearGraphDisplay-7YE624D5.js.map

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+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/display-kit/DisplayChrome", "global-externals:@jbrowse/core/ui/BaseTooltip", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx", "../../src/HaplotypeOverview/HaplotypeOverviewCanvas.tsx"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/display-kit/DisplayChrome\"];", "module.exports = JBrowseExports[\"@jbrowse/core/ui/BaseTooltip\"];", "import { DisplayStatusChrome } from '@jbrowse/display-kit/DisplayChrome'\nimport { observer } from 'mobx-react'\n\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\nimport HaplotypeOverviewCanvas from '../../HaplotypeOverview/HaplotypeOverviewCanvas'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <DisplayStatusChrome\n      model={model}\n      phase={model.displayPhase}\n      drawn={\n        model.showsOverview\n          ? model.overview !== undefined &&\n            model.overviewPainted === model.overview\n          : model.painted && model.geometryPainted\n      }\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      {model.showsOverview ? (\n        <HaplotypeOverviewCanvas model={model} />\n      ) : (\n        <GraphCanvas model={model} ownChrome={false} />\n      )}\n    </DisplayStatusChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n", "import { useEffect, useMemo, useRef, useState } from 'react'\n\nimport BaseTooltip from '@jbrowse/core/ui/BaseTooltip'\nimport { observer } from 'mobx-react'\n\nimport {\n  NOT_SHOWN,\n  binAt,\n  cellLabel,\n  describeBin,\n  drawOverview,\n  overviewLayout,\n  rowAt,\n  rowImages,\n} from './draw'\nimport { hostFrame } from '../GraphGenomeView/host'\n\nimport type { OverviewLayout } from './draw'\nimport type { HaplotypeOverviewData } from '../GetHaplotypeOverview'\nimport type { SubgraphRegion } from '../GetSubgraph'\nimport type { LinearHost } from '../GraphGenomeView/host'\n\nexport interface OverviewCanvasModel {\n  overview: HaplotypeOverviewData | undefined\n  overviewRegion: SubgraphRegion | undefined\n  overviewCounts: number[][] | undefined\n  overviewAllRows: boolean\n  height: number\n  host: LinearHost | undefined\n  setOverviewPainted: (data: HaplotypeOverviewData) => void\n}\n\ninterface Pointer {\n  bin: number\n  row: number | undefined\n  clientX: number\n  clientY: number\n}\n\nconst OverviewTooltip = observer(function OverviewTooltip({\n  data,\n  region,\n  pointer,\n}: {\n  data: HaplotypeOverviewData\n  region: SubgraphRegion\n  pointer: Pointer\n}) {\n  const bin = describeBin(data, pointer.bin)\n  const cell =\n    pointer.row === undefined\n      ? undefined\n      : data.cells[pointer.bin * data.rows.length + pointer.row]\n  return (\n    <BaseTooltip clientPoint={{ x: pointer.clientX, y: pointer.clientY }}>\n      <div>\n        {region.refName}:{bin.span}\n      </div>\n      {pointer.row !== undefined && cell !== undefined ? (\n        <div>\n          <strong>{data.rows[pointer.row]}</strong>: {cellLabel(cell)}\n        </div>\n      ) : (\n        <>\n          <div>{bin.classes}</div>\n          <div>{bin.excursions}</div>\n        </>\n      )}\n      <div style={{ opacity: 0.7 }}>{NOT_SHOWN}</div>\n    </BaseTooltip>\n  )\n})\n\n// The haplotype index's overview on the linear view's axis: a density row of\n// the haplotypes that differ from the reference, then a row per haplotype.\n// A click zooms to the bin under the pointer.\nconst HaplotypeOverviewCanvas = observer(function HaplotypeOverviewCanvas({\n  model,\n}: {\n  model: OverviewCanvasModel\n}) {\n  const ref = useRef<HTMLCanvasElement>(null)\n  const [pointer, setPointer] = useState<Pointer>()\n  const {\n    overview,\n    overviewRegion,\n    overviewCounts,\n    overviewAllRows,\n    height,\n    host,\n  } = model\n  const width = host?.width ?? 0\n  const frame =\n    host && overviewRegion ? hostFrame(host, overviewRegion) : undefined\n  const scale = frame?.scale\n  const translateX = frame?.translateX\n  const layout = useMemo<OverviewLayout | undefined>(\n    () =>\n      overview ? overviewLayout(overview, overviewAllRows, height) : undefined,\n    [overview, overviewAllRows, height],\n  )\n\n  const dpr = typeof window === 'undefined' ? 1 : window.devicePixelRatio || 1\n  const images = useMemo(\n    () => (overview && layout ? rowImages(overview, layout, dpr) : []),\n    [overview, layout, dpr],\n  )\n\n  useEffect(() => {\n    const canvas = ref.current\n    const ctx = canvas?.getContext('2d')\n    if (\n      !canvas ||\n      !ctx ||\n      !overview ||\n      !layout ||\n      scale === undefined ||\n      translateX === undefined\n    ) {\n      return\n    }\n    const deviceWidth = Math.round(width * dpr)\n    const deviceHeight = Math.round(height * dpr)\n    if (canvas.width !== deviceWidth || canvas.height !== deviceHeight) {\n      canvas.width = deviceWidth\n      canvas.height = deviceHeight\n    }\n    ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n    drawOverview(ctx, overview, overviewCounts, layout, images, {\n      xOf: bp => bp * scale + translateX,\n      width,\n      height,\n      dpr,\n    })\n    model.setOverviewPainted(overview)\n  }, [\n    model,\n    overview,\n    overviewCounts,\n    layout,\n    images,\n    scale,\n    translateX,\n    width,\n    height,\n    dpr,\n  ])\n\n  const locate = (event: React.MouseEvent<HTMLCanvasElement>) => {\n    if (!overview || !layout || !scale || translateX === undefined) {\n      return undefined\n    }\n    const rect = event.currentTarget.getBoundingClientRect()\n    const x = event.clientX - rect.left\n    const y = event.clientY - rect.top\n    const bin = binAt(overview, (x - translateX) / scale)\n    return bin === undefined\n      ? undefined\n      : {\n          bin,\n          row: rowAt(layout, y),\n          clientX: event.clientX,\n          clientY: event.clientY,\n        }\n  }\n\n  return (\n    <>\n      <canvas\n        ref={ref}\n        data-testid=\"haplotype-overview\"\n        style={{ width, height, display: 'block', cursor: 'pointer' }}\n        onMouseMove={event => {\n          setPointer(locate(event))\n        }}\n        onMouseLeave={() => {\n          setPointer(undefined)\n        }}\n        onClick={event => {\n          const at = locate(event)\n          const bin = at && overview?.bins[at.bin]\n          if (bin && overviewRegion && host?.navTo) {\n            host.navTo({\n              refName: overviewRegion.refName,\n              assemblyName: overviewRegion.assemblyName,\n              start: bin.start,\n              end: bin.end,\n            })\n          }\n        }}\n      />\n      {pointer && overview && overviewRegion ? (\n        <OverviewTooltip\n          data={overview}\n          region={overviewRegion}\n          pointer={pointer}\n        />\n      ) : null}\n    </>\n  )\n})\n\nexport default HaplotypeOverviewCanvas\n"],
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+}

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Yn="_gbwt_ref";function le(i){let e=`${i.sample}#${i.haplotype}#${i.contig}`;return i.end===void 0?e:`${e}[${i.fragment}-${i.end}]`}var es=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,ts=/^([^#]+?)(?:\[\d+-\d+\])?$/;function ns(i){let e=es.exec(i);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=ts.exec(i);if(t)return{contig:t[1]};throw new Error(`"${i}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function $e(i){return typeof i=="string"?ns(i):i}function He(i,e){return{sample:i.sample??Yn,contig:i.contig,haplotype:i.haplotype??0,fragment:e}}var ss=4096;function kt(i){let e=[];for(let t of i){let n=e[e.length-1];n&&t-n[1]<=ss?n[1]=t:e.push([t,t])}return e}var os=32768,gn={mostChosenPaths:32},It=class{byNode=new Map;get(e){return this.byNode.get(e.node)?.get(e.offset)}set(e,t){let n=this.byNode.get(e.node);n||(n=new Map,this.byNode.set(e.node,n)),n.set(e.offset,t)}},re=class extends Error{};function Ye(i,e,t,n){return i==="forward"?e+t:e-n}function mn(i,e,t,n){return i==="forward"?e-n:e+t}function yn(i){return Me(ne(i.handles[i.handles.length-1]),ne(i.handles[0]))}function Fe(i){return`${i.pathHandle}:${i.hapStart}:${i.hapEnd}`}async function xn(i){let{db:e,records:t,signal:n}=i,s=performance.now(),r=()=>{let S=performance.now(),M=S-s;return s=S,M},o={spacing:await e.haplotypeAnchorSpacing(),anchors:void 0,anchorsRead:0,chosenPaths:0,scans:[],scanRows:0,strays:void 0,pieces:0,sources:{reference:0,section:0,stray:0,chain:0,twin:0},walks:{},twins:{tried:0,found:0},graphFetches:0,fallback:void 0,ms:{scan:0,walks:0,check:0,twins:0}},a=(S,M)=>{let P=`${S}: ${M}`;o.walks[P]=(o.walks[P]??0)+1},h=await e.haplotypeSampleInterval()??4096,c=new Map,d=async S=>{let M=t.get(S)??c.get(S);if(M)return M;let P=await e.getRecord(S);if(o.graphFetches+=1,!P)throw new Error(`Node record ${S} is missing from the database`);return c.set(S,P),P},f=S=>t.get(S).sequenceLen,l=await e.pathsByHandle(),g=S=>{let M=l.get(S);return M!==void 0&&i.keep(M.name)},p=[],u=new It,m=new Map,E=new Set,I=new Set,w=async S=>{let M=(await d(S.node)).gbwt().lf(S.offset);return M===void 0||M.node===0?void 0:M},b=async(S,M)=>{let P=(await d(ne(S.node))).gbwt().predecessorAt(S.offset);if(P===void 0||M!==void 0&&!M.has(P))return;let H=(await d(P)).gbwt().offsetTo(S);if(H===void 0)throw new Error(`No offset in ${P} leads to ${S.node}:${S.offset}`);return{node:P,offset:H}},y=(S,M,P,H)=>{let T=P.map(V=>V.pos.node),j=P.map(V=>V.pos.offset),J=0;for(let V of T)J+=f(V);let L=M==="forward"?P[0].left:P[P.length-1].left,C=p.length;p.push({pathHandle:S,orientation:M,handles:T,offsets:j,len:J,hapStart:L,hapEnd:L+J,canonical:Me(T[0],T[T.length-1]),source:H});for(let V of P)u.set(V.pos,C);let W=m.get(S);return W?W.push(C):m.set(S,[C]),C},k=async(S,M,P,H)=>{let T=[],j=S;for(;;){n?.throwIfAborted();let L=await b(j.pos,t);if(!L)break;j={pos:L,left:mn(P,j.left,f(j.pos.node),f(L.node))},T.push(j)}T.reverse();let J=[S];for(j=S;;){n?.throwIfAborted();let L=await w(j.pos);if(!L||!t.has(L.node))break;j={pos:L,left:Ye(P,j.left,f(j.pos.node),f(L.node))},J.push(j)}return y(M,P,[...T,...J],H)},v=async(S,M,P,H)=>p[u.get(S.pos)??await k(S,M,P,H)],O=S=>{let M=S.handles[S.handles.length-1];return{pos:{node:M,offset:S.offsets[S.offsets.length-1]},left:S.orientation==="forward"?S.hapEnd-f(M):S.hapStart}},B=S=>{let M=S.handles[0];return{pos:{node:M,offset:S.offsets[0]},left:S.orientation==="forward"?S.hapStart:S.hapEnd-f(M)}},D=await k({pos:i.referencePos,left:i.referenceLeft},i.referenceHandle,"forward","reference"),q=p[D],$=()=>{if(o.fallback!==void 0)return{reference:q,pieces:[],stats:o};let S=new Map;p.forEach((P,H)=>{H!==D&&S.set(Fe(P),[...S.get(Fe(P))??[],P])});let M=[];for(let P of S.values()){let H=new Set;for(let T of P)T.canonical&&!H.has(T.orientation)&&(H.add(T.orientation),M.push(T),o.sources[T.source]+=1)}return o.sources.reference=1,o.pieces=M.length+1,{reference:q,pieces:M,stats:o}},N=async(S,M)=>{let P=M?E:I,H=M?I:E,T=S;for(;;){if(P.has(T))return;P.add(T);let j=p[T],J=M?O(j):B(j),L=0,C;for(;C===void 0;){n?.throwIfAborted();let W=M?await w(J.pos):await b(J.pos);if(!W){C="endmarker";break}let V=(await d(J.pos.node)).sequenceLen,ge=(await d(W.node)).sequenceLen,se=M?Ye(j.orientation,J.left,V,ge):mn(j.orientation,J.left,V,ge);if(t.has(W.node)){let Y=u.get(W);Y===void 0?(T=await k({pos:W,left:se},j.pathHandle,j.orientation,"chain"),H.add(T),C="landed"):(H.add(Y),C="merge")}else L>os?C="bound":(L+=ge,J={pos:W,left:se})}if(a("chain",C),C!=="landed")return}},Q=async S=>{if(i.context>S.context)throw new re(`the context of ${i.context} bp exceeds the ${S.context} bp the haplotype index's stray rows cover`);let M=o.spacing;if(M===void 0)throw new re("the haplotype index has no anchors");let{bin:P,bound:H}=S,{fills:T,inserted:j}=i.snarls;if(i.snarls.mode==="overlapping"&&T.length>0)throw new re("the haplotype index's stray rows cover contained snarls only");for(let x of T){if(x.inserted>0&&x.low===x.high)throw new re(`the haplotype index's stray rows leave out the snarl bounded by node ${x.low} at both ends`);if(x.inserted>0&&(S.snarlNodes===void 0||x.nodes>S.snarlNodes))throw new re(S.snarlNodes===void 0?"the haplotype index's stray rows leave snarls out":`a snarl of ${x.nodes} nodes exceeds the ${S.snarlNodes} the haplotype index's stray rows cover`)}let J=Math.floor(i.window.start/P),L=Math.floor((i.window.end-1)/P),C=J*P,W=(L+1)*P,V=new Map,ge=async(x,A)=>{let U=await e.haplotypeAnchorsBetween(i.referenceHandle,x*M,A*M);for(let _ of U)V.set(_.anchorOffset/M,_)},se=Math.max(0,Math.floor((C-H)/M)-1),Y=Math.ceil((W+H)/M)+1,[{listed:Ge,strays:ae}]=await Promise.all([e.haplotypeBinData(i.referenceHandle,J,L),ge(se,Y)]);for(let x of t.keys()){let A=R(x);if(!z(x)&&!Ge(A)&&!j.has(A))throw new re(`the haplotype index lists node ${A} of the subgraph in no bin that the window touches`)}o.scans=kt([...t.keys()].sort((x,A)=>x-A));let ce=Promise.all(o.scans.map(([x,A])=>e.haplotypeSamplesInRange(x,A)));for(ce.catch(()=>{});se>0&&(V.get(se)?.pathOffset??Number.POSITIVE_INFINITY)>=C-H;)se-=1,await ge(se,se);for(;V.has(Y)&&V.get(Y).pathOffset<=W+H;)Y+=1,await ge(Y,Y);let pe=[...V.keys()].sort((x,A)=>x-A),Se=V.get(pe[0]??-1);if(!Se)throw new re("the haplotype index has no anchors on this path");let de=x=>V.get(x).pathOffset,Le=new Map;for(let x of pe){let A=R(V.get(x).node);Le.set(A,[...Le.get(A)??[],x])}let bt=[...Le.keys()],Ut=bt.map(x=>V.get(Le.get(x)[0]).visits);if(!Ut[bt.indexOf(R(Se.node))].some(x=>x.pathHandle===i.referenceHandle&&x.orientation==="forward"&&x.pathOffset===Se.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path ${i.referenceHandle} at offset ${Se.pathOffset} (node ${R(Se.node)}); it does not match this graph`);let jt=pe.filter(x=>de(x)<=i.window.start),Vn=pe.filter(x=>de(x)>=i.window.end);o.anchors=[de(jt[jt.length-1]??pe[0]),de(Vn[0]??pe[pe.length-1])],o.anchorsRead=pe.length;let St=new Map,Vt=new Set;if(bt.forEach((x,A)=>{let U=Le.get(x),_=U.length===1?U[0]:void 0;for(let F of Ut[A])Vt.add(F.pathHandle),F.orientation==="forward"&&g(F.pathHandle)&&St.set(F.pathHandle,[...St.get(F.pathHandle)??[],{k:_,row:F}])}),o.chosenPaths=[...Vt].filter(g).length,o.chosenPaths>gn.mostChosenPaths)throw new re(`${o.chosenPaths} chosen paths pass the anchors, more than ${gn.mostChosenPaths}`);let Qe=[],ve=Number.POSITIVE_INFINITY,Ee=0;for(let[x,A]of St){A.sort((U,_)=>U.row.pathOffset-_.row.pathOffset);for(let U=0;U+1<A.length;U++){let _=A[U],F=A[U+1];if(_.k===void 0||F.k===void 0||Math.abs(_.k-F.k)!==1)continue;let[X,ee]=de(_.k)<=de(F.k)?[_,F]:[F,_],te=de(X.k),oe=de(ee.k);te<W&&oe>=C?(Qe.push({pathHandle:x,from:_.row,to:F.row}),ve=Math.min(ve,te-H),Ee=Math.max(Ee,oe+H)):te>=W&&te-W<=H?(Qe.push({pathHandle:x,from:X.row,to:void 0}),ve=Math.min(ve,te-H),Ee=Math.max(Ee,te+H)):oe<C&&C-oe<=H&&(Qe.push({pathHandle:x,from:ee.row,to:void 0}),ve=Math.min(ve,oe-H),Ee=Math.max(Ee,oe+H))}}let Gn=new Set(T.map(x=>`${x.low}:${x.high}`)),Qn=ae.filter(x=>g(x.pathHandle)&&(x.snarl===void 0||Gn.has(`${x.snarl[0]}:${x.snarl[1]}`))).sort((x,A)=>x.pathHandle-A.pathHandle||x.pathStart-A.pathStart);o.strays={bins:L-J+1,rows:ae.length,walked:0,outsideBp:0},Ee>0&&await i.prefetchReferenceRange(i.referenceHandle,Math.max(0,ve),Ee+1),o.ms.scan=r();let Gt=8*M+2*(i.window.end-i.window.start),Qt=o.strays,Be=0,Wt=x=>{if(Qt.outsideBp+=x,Be+=x,Be>Gt)throw new re(`a walk of a chosen path near the window went past its cap of ${Gt} bp`)},Et=new Map,Kt=(x,A,U)=>(Et.get(x)??[]).some(([_,F])=>_<=A&&U<F),Xt=(x,A,U)=>{Et.set(x,[...Et.get(x)??[],[A,U]])},Zt=async(x,A,U,_,F)=>{let X=A,ee=U,te=ee;for(;X&&ee<=_;){n?.throwIfAborted();let oe;if(t.has(X.node)){let Te=await v({pos:X,left:ee},x,"forward",F),Yt=O(Te);X=Yt.pos,ee=Yt.left,oe=f(X.node),te=Math.max(te,Te.hapEnd)}else oe=(await d(X.node)).sequenceLen,Wt(oe),te=Math.max(te,ee+oe);X=await w(X),ee+=oe}return te},Wn=async(x,A,U,_)=>{let F={pos:A,left:U},X=U;for(;F.left>_;){n?.throwIfAborted();let ee=await b(F.pos);if(!ee)break;let te=(await d(ee.node)).sequenceLen,oe=F.left-te;if(t.has(ee.node)){let Te=await v({pos:ee,left:oe},x,"forward","section");F=B(Te),X=Math.min(X,Te.hapStart)}else Wt(te),F={pos:ee,left:oe},X=Math.min(X,oe)}return X};for(let{pathHandle:x,from:A,to:U}of Qe){let _=A.pathOffset,F=(U??A).pathOffset+H;if(Kt(x,_-H,F))continue;let X={node:A.node,offset:A.offset};Be=0;let ee=await Zt(x,X,_,F,"section");Be=0;let te=await Wn(x,X,_,_-H);Xt(x,Math.min(te,_-H),Math.max(ee,F+1)),a(U?"section":"visit",U?"past the far anchor":"bound")}for(let x of Qn){if(Kt(x.pathHandle,x.pathStart,x.pathEnd))continue;Be=0;let A=await Zt(x.pathHandle,{node:x.node,offset:x.offset},x.pathStart,x.pathEnd,"stray");Xt(x.pathHandle,x.pathStart,Math.max(A,x.pathEnd+1)),Qt.walked+=1}o.ms.walks=r();let Jt=[];for(let x of await ce)for(let A of x)if(o.scanRows+=1,t.has(A.node)&&g(A.pathHandle)){if(!(m.get(A.pathHandle)??[]).some(U=>{let _=p[U];return _.hapStart<=A.pathOffset&&A.pathOffset<_.hapEnd}))throw new re(`chosen path ${A.pathHandle} has a sample at ${A.pathOffset} on the window's nodes that no walk reached`);A.orientation==="reverse"&&Jt.push(A)}for(let x of Jt)await v({pos:{node:x.node,offset:x.offset},left:x.pathOffset},x.pathHandle,"reverse","twin");o.ms.check=r()},Z=async()=>{let S=new Map,M=L=>{let C=Fe(L),W=S.get(C);W?W.add(L.orientation):S.set(C,new Set([L.orientation]))},P=0,H=()=>{for(;P<p.length;P++)M(p[P])};H();let 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n.solve(0,i.length,0,e.length),[n.pairs,n.total]}var rs=100,Pt=4e6,is=5e3,he=15,as=64,hs=8,Pn=1,Rt=-4,ie=-6,xe=-1,Ce=-(2**30),st=0,Mt=1,Rn=2;function Ae(i,e,t){let n=i.at(-1);t>0&&(n?.[0]===e?n[1]+=t:i.push([e,t]))}function nt(i,e,t){return i>=t&&i>=e?st:t>=e?Rn:Mt}function Nn(i,e,t){let n=i.length,s=e.length,r=s+1,o=new Uint8Array((n+1)*r),a=new Int32Array(r).fill(Ce),h=new Int32Array(r).fill(Ce),c=new Int32Array(r).fill(Ce);a[0]=0;for(let p=1;p<=s;p++)c[p]=ie+(p-1)*xe,o[p]=(p===1?st:Rn)<<4;for(let p=1;p<=n;p++){let u=new Int32Array(r).fill(Ce),m=new Int32Array(r).fill(Ce),E=new Int32Array(r).fill(Ce);m[0]=ie+(p-1)*xe,o[p*r]=(p===1?st:Mt)<<2;let I=i.charCodeAt(p-1);for(let w=1;w<=s;w++){let b=nt(a[w-1],h[w-1],c[w-1]);u[w]=Math.max(a[w-1],h[w-1],c[w-1])+(I===e.charCodeAt(w-1)?Pn:Rt);let y=nt(a[w]+ie,h[w]+xe,c[w]+ie);m[w]=Math.max(a[w]+ie,h[w]+xe,c[w]+ie);let k=nt(u[w-1]+ie,m[w-1]+ie,E[w-1]+xe);E[w]=Math.max(u[w-1]+ie,m[w-1]+ie,E[w-1]+xe),o[p*r+w]=b|y<<2|k<<4}a=u,h=m,c=E}let 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d)s.query[f]=Math.min(255,s.query[f]+1),s.target[l]=Math.min(255,s.target[l]+1);return d}),o={query:new Map,target:new Map};r.forEach((c,d)=>{for(let[f,l]of c)for(let[g,p]of[["query",f],["target",l]])if(s[g][p]>1){let u=o[g].get(p);u?u.at(-1)!==d&&u.push(d):o[g].set(p,[d])}});let a=new Map,h=(c,d,f)=>{let l=`${f}:${c}:${d}`,g=a.get(l);if(g===void 0){let[p,u]=kn(i[c],f),[m,E]=kn(i[d],f),I=Math.max(p,m),w=Math.min(u,E),[b,y]=[i[c],i[d]];g=[In(y,f,I,w)-In(b,f,I,w),y.sharedBases-b.sharedBases,c-d].find(v=>v!==0)>0,a.set(l,g)}return g};return i.flatMap((c,d)=>{let f=r[d],l=new Uint8Array(f.length);if(f.forEach(([u,m],E)=>{for(let[I,w]of[["query",u],["target",m]])!l[E]&&o[I].get(w)?.some(b=>b!==d&&h(d,b,I))&&(l[E]=1)}),!l.includes(1))return[c];let g=ws(c,l),p=g?.edits.reduce((u,[m,E])=>u+(m==="="?E:0),0)??0;return g&&p>=n?[g]:[]})}function vn(i,e){return i.map(t=>{let n=e(R(t));return z(t)?Je(n):n}).join("")}function Mn(i,e){let t=[0];for(let n of i)t.push(t.at(-1)+e(R(n)).length);return t}function An(i){let e=new Map,t=new Map;i.forEach((o,a)=>{let h=R(o);e.has(h)?t.set(h,a):e.set(h,a)});let n=new Int32Array(i.length+1);for(let[o,a]of t)n[e.get(o)]+=1,n[a+1]-=1;let s=new Uint8Array(i.length),r=0;for(let o=0;o<i.length;o++)r+=n[o],s[o]=r>0?1:0;return s}function ms(i,e,t,n){let s=An(i),r=An(e),o=new Map;e.forEach((f,l)=>{r[l]||o.set(R(f),[l])});let a=2*e.length,h=(f,l,g)=>f*a+2*l+(g?1:0),c=new Set;i.forEach((f,l)=>{for(let g of s[l]?[]:o.get(R(f))??[])c.add(h(l,g,z(f)!==z(e[g])))});let d=[];return i.forEach((f,l)=>{for(let g of s[l]?[]:o.get(R(f))??[]){let p=z(f)!==z(e[g]),u=p?-1:1,m=g-u;if(!(l>0&&m>=0&&m<e.length&&c.has(h(l-1,m,p)))){let I=l,w=g;for(;I<i.length&&w>=0&&w<e.length&&c.has(h(I,w,p));)I+=1,w+=u;let b=w-u;d.push({qs:t[l],qe:t[I],ts:n[Math.min(g,b)],te:n[Math.max(g,b)+1],flipped:p})}}}),d}function Hn(i){let{query:e,target:t,sequenceOf:n}=i,s=vn(e,n),r=vn(t,n),o=ms(e,t,Mn(e,n),Mn(t,n)),a=i.minMatch??rs,h=i.bases??!0,c=[];for(let d of Nt(o,i.maxGap??1/0,a,cs)){let f=[],l=d[0],g=d.at(-1),{flipped:p}=l.run;ot(d,s,r,f,h?(m,E,I,w,b)=>{for(let y of us(m,E,I,a)){let k=b+E.length;c.push({...y,queryStart:w+y.queryStart,queryEnd:w+y.queryEnd,targetStart:p?k-y.targetEnd:b+y.targetStart,targetEnd:p?k-y.targetStart:b+y.targetEnd,strand:p?"+":"-",edits:p?y.edits.reverse():y.edits,shared:[]})}}:qt),c.push({queryStart:l.run.qs+l.trim,queryEnd:g.run.qe,targetStart:p?g.run.ts:l.run.ts+l.trim,targetEnd:p?l.run.te-l.trim:g.run.te,strand:p?"-":"+",edits:p?f.reverse():f,sharedBases:d.reduce((m,{run:E,trim:I})=>m+E.qe-E.qs-I,0),shared:d.map(({run:m,trim:E})=>[m.qs+E,m.qe])})}return gs(c,s.length,r.length,a).map(({shared:d,...f})=>f).sort((d,f)=>d.queryStart-f.queryStart)}function Cn(i){return i.map(([e,t])=>`${t}${e}`).join("")}var we=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 ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Ct(i,e){return i[0]<e[0]||i[0]===e[0]&&(i[1]<e[1]||i[1]===e[1]&&i[2]<e[2])}var Ue=class{heap=[];push(e,t,n){let s=this.heap;s.push([e,t,n]);let r=s.length-1;for(;r>0;){let o=r-1>>1;if(Ct(s[r],s[o]))[s[r],s[o]]=[s[o],s[r]],r=o;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let s=0;for(;;){let r=2*s+1,o=r+1,a=s;if(r<e.length&&Ct(e[r],e[a])&&(a=r),o<e.length&&Ct(e[o],e[a])&&(a=o),a===s)break;[e[s],e[a]]=[e[a],e[s]],s=a}}return t}get size(){return this.heap.length}};function ys(i){let e=new Int32Array(i.length),t=new Int32Array(i.length);return i.forEach(([n,s],r)=>{e[r]=n,t[r]=s}),{pathAt:e,refAt:t,count:i.length}}function xs(i,e){let t=0,n=i.length;for(;t<n;){let s=t+n>>1;i[s]>e?n=s:t=s+1}return i[t]}function Pe(i){return`${i.node}:${i.offset}`}function ze(i){return i.map(e=>ne(e)).reverse()}function bs(i,e){let t=e.identity.hapStart-i.identity.hapEnd,n=i.strand==="+"?e.refStart-i.refEnd:i.refStart-e.refEnd;return i.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Ss(i,e,t){let[n,s]=i.strand==="+"?[i,e]:[e,i],r=n.edits.map(([c,d])=>[c,d]);Ln(r,t.insertion,t.deletion);for(let[c,d]of s.edits)K(r,c,d);let o=i.identity.walkForward,[a,h]=o?[i,e]:[e,i];return{strand:i.strand,refStart:n.refStart,refEnd:s.refEnd,edits:r,weight:void 0,path:[...a.path,...h.path],start:a.start,pieces:[...a.pieces,...h.pieces],soloAligned:[...a.soloAligned,...h.soloAligned],identity:{pathHandle:i.identity.pathHandle,name:i.identity.name,hapStart:i.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:o}}}function Es(i,e,t){if(i.some(o=>o.weight!==void 0))return i;let n=new Map;i.forEach((o,a)=>{if(o.identity){let h=n.get(o.identity.pathHandle);h?h.push(a):n.set(o.identity.pathHandle,[a])}});let s=new Map,r=new Set;for(let o of n.values()){o.sort((d,f)=>i[d].identity.hapStart-i[f].identity.hapStart);let a=o[0],h=i[a],c=[];for(let d of o.slice(1)){let f=i[d],l=c.length===0?bs(h,f):void 0;if(l){h=Ss(h,f,l),r.add(d);continue}if(!e(f)){c.push(d);continue}let g=e(h)?t([h,...c.map(p=>i[p]),f]):void 0;if(g){h=g;for(let p of[...c,d])r.add(p)}else s.set(a,h),a=d,h=f;c=[]}s.set(a,h)}return i.flatMap((o,a)=>r.has(a)?[]:[s.get(a)??o])}function rt(i,e){return{node:i.path[e],offset:i.offsets[e]}}var Is=32768;function ks(i){let e=[...i].sort((n,s)=>n-s),t=[];for(let n of e){let s=t[t.length-1];s&&n-s[1]<=Is?s[1]=n:t.push([n,n])}return t}var ht=class i{records=new Map;paths=[];twinStarts=new Set;twinDeferred=!1;unsettled;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 i(e,t)}get nodeCount(){return this.records.size/2}get pathCount(){return this.settleDeferred(),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(ue(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 we(this.limit);let t=await this.db.getRecord(ue(e,"forward")),n=await this.db.getRecord(ue(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.twinDeferred=!1,this.unsettled=void 0,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 ${le(e)}`);if(!t.isIndexed)throw new Error(`The fragment of ${le(t.name)} at ${t.name.fragment} has not been indexed for random access`);let n=e.fragment-t.name.fragment,s=await this.db.indexedPosition(t.handle,n);if(!s)throw new Error(`The fragment of ${le(t.name)} at ${t.name.fragment} has not been indexed for random access`);return this.findPathPosition(t,n,s.pathOffset,s.pos)}async findPathPosition(e,t,n,s){let r=n,o=s;for(;;){await this.ensureNode(R(o.node));let a=this.record(o.node);if(r+a.sequenceLen>t)return{position:{seqOffset:t,handle:o.node,nodeOffset:t-r,gbwtOffset:o.offset},name:e.name,handle:e.handle};r+=a.sequenceLen;let h=a.gbwt().lf(o.offset);if(!h)throw new Error(`The fragment of ${le(e.name)} at ${e.name.fragment} does not contain offset ${t}`);o=h}}async aroundPosition(e,t,n){let s=R(e);await this.ensureNode(s);let r=this.record(e),o=Ne(e),a=new Ue;return a.push(t,s,We(o)),a.push(r.sequenceLen-t-1,s,Ke(o)),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[s,r]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(s&&r){let o=s.pos.node,a=r.pos.node;if(!await this.db.prefetchRecords([[Math.min(o,a),Math.max(o,a)+1]])){let c=await this.db.indexedPositionsBetween(e,t,n);await this.db.prefetchRecords(ks(c.map(d=>d.pos.node)).map(([d,f])=>[d,f+2]),!0)}}return s}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(s){throw s instanceof we&&s.windowBp===void 0?new we(s.limit,{windowBp:t,walkedBp:this.walkedBp}):s}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let s={node:e.handle,offset:e.gbwtOffset},r=e.nodeOffset,o=t,a=new Ue;for(;;){let h=R(s.node),c=Ne(s.node);this.walkedBp=t-o,await this.ensureNode(h);let d=this.record(s.node);if(r>=d.sequenceLen)throw new Error(`Offset ${r} in node ${h} of length ${d.sequenceLen}`);a.push(r,h,We(c));let f=d.sequenceLen-r;if(o<=f){a.push(o===f?0:f-o-1,h,Ke(c));break}a.push(0,h,Ke(c));let l=d.gbwt().lf(s.offset);if(!l)throw new Error(`No successor for GBWT position (${s.node}, ${s.offset})`);s=l,r=0,o-=f}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new Ue;for(let s of e)await this.ensureNode(s),n.push(0,s,"left"),n.push(0,s,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths(),this.snarlMode="none",this.snarlFills=[],this.snarlNodes.clear(),this.stats.snarls={fills:0,inserted:0};let n=new Set,s=new Set;for(let o of this.records.keys())s.add(R(o));let r=0;for(;e.size>0;){let[o,a,h]=e.pop(),c=`${a}:${h}`;if(n.has(c))continue;n.add(c),s.delete(a),this.hasNode(a)||(await this.addNode(a),r+=1);let d=en(h);if(!n.has(`${a}:${d}`)){let g=this.record(ue(a,tn(h))),p=o+g.sequenceLen-1;p<=t&&e.push(p,a,d)}let f=this.record(ue(a,nn(h))),l=o+1;if(l<=t)for(let g of f.successors()){let p=R(g),u=We(Ne(g));n.has(`${p}:${u}`)||e.push(l,p,u)}}for(let o of s)this.records.delete(ue(o,"forward")),this.records.delete(ue(o,"reverse"));return{inserted:r,removed:s.size}}async betweenNodes(e,t){return(await this.fillBetween(e,t)).inserted.length}async fillBetween(e,t){this.clearPaths();let n=[e,ne(t)],s=new Set([R(e),R(t)]),r=[];for(;n.length>0;){let o=n.pop(),a=R(o);this.hasNode(a)||(await this.addNode(a),r.push(a));for(let h of this.record(o).successors()){let c=R(h);s.has(c)||(n.push(h,ne(h)),s.add(c))}}return{inserted:r,nodes:s.size-2}}async extractSnarls(e){let t=0;this.snarlMode=e;for(let[n,s]of await this.overlappingSnarls(e)){let{inserted:r,nodes:o}=await this.fillBetween(n,s),a=R(n),h=R(s);this.snarlFills.push({low:Math.min(a,h),high:Math.max(a,h),nodes:o,inserted:r.length});for(let c of r)this.snarlNodes.add(c);t+=r.length}return this.stats.snarls={fills:this.snarlFills.length,inserted:this.snarlNodes.size},t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let s of this.sortedHandles()){let r=this.record(s),o=r.next;o!==void 0&&(n=!0,this.hasHandle(o)?qe(s,o)&&t.push([s,o]):e==="overlapping"&&this.isSnarlEntryInSubgraph(r)&&t.push([s,o]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let s=await this.findCoveringSnarl();s&&t.push(s)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(s=>this.hasHandle(s));return n===void 0?!1:t.length>1||this.record(ne(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let s=this.records.get(n);if(s)return s;let r=t.get(n);if(!r){if(r=await this.db.getRecord(n),e?.(),!r)throw new Error(`Node record ${n} is missing from the database`);t.set(n,r)}return r}}async findCoveringSnarl(){let e=this.recordReader(),t=async h=>{let c=h.successors(),d=c[0];return d===void 0?!1:c.length>1||(await e(ne(d))).successors().length>1},n=async h=>{let c=await e(ne(h));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[ne(h),c.next]}:{kind:"chain"}:(await e(h)).next!==void 0?{kind:"chain"}:{kind:"regular"}},s=new Set,r=this.sortedHandles().flatMap(h=>this.record(h).successors()),o,a=!1;for(;!a&&r.length>0;){let h=r.shift(),c=R(h);if(!this.hasHandle(h)&&!s.has(c)){s.add(c);let d=await n(h);if(d.kind==="snarl-exit")o=d.snarl,a=!0;else if(d.kind==="chain")a=!0;else for(let f of["forward","reverse"])r.push(...(await e(ue(c,f))).successors())}}return o}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let s=this.sortedHandles(),r=s.length,o=new Map;s.forEach((y,k)=>o.set(y,k));let a=new Int32Array(r+1),h=new Int32Array(r),c=[];for(let y=0;y<r;y++){let k=this.record(s[y]),v=k.gbwt().decompressArrays();h[y]=k.sequenceLen,c.push(v),a[y+1]=a[y]+v.nodes.length}let d=a[r],f=new Int32Array(d),l=new Int32Array(d),g=new Uint8Array(d);for(let y=0;y<r;y++){let k=c[y];f.set(k.nodes,a[y]),l.set(k.offsets,a[y])}c.length=0;for(let y=0;y<d;y++){let k=o.get(f[y]);k===void 0?f[y]=-1:(f[y]=k,g[a[k]+l[y]]=1)}let p=n===void 0?void 0:o.get(n.handle),u=n?.gbwtOffset,m,E=(y,k,v)=>{let O=[],B=0,D=0,q=-1,$=y,N=k;for(;;){$===p&&N===u&&(q=B),v&&(v.push(s[$]),O.push(N)),B+=1,D+=h[$];let Q=a[$]+N,Z=f[Q];if(Z<0)break;N=l[Q],$=Z}return{offsets:O,len:D,refAt:q,last:$}},I=(y,k,v,O)=>{O>=0&&(this.refId=this.paths.length,m=O),this.paths.push({path:y,offsets:k,len:v,weight:void 0,identity:void 0})},w=new Int32Array(r);for(let y=0;y<r;y++){let k=s[y];if(!z(k)){let v=a[y],O=a[y+1]-v;for(let B=0;B<O;B++)if(g[v+B]===0){let D=[],{offsets:q,len:$,refAt:N,last:Q}=E(y,B,D),Z=s[Q];if(N>=0||Me(k,Z)){if(I(D,q,$,N),!z(Z)){let S=o.get(ne(Z));w[S]=w[S]+1}}else this.twinStarts.add(Pe({node:k,offset:B}))}}}for(let y=0;y<r;y++){let k=s[y];if(z(k)){let v=a[y],O=a[y+1]-v,B=0;for(let q=0;q<O;q++)g[v+q]===0&&(B+=1);let D=(p===void 0||m!==void 0)&&B===w[y];for(let q=0;q<O;q++)if(g[v+q]===0){let $=D?void 0:E(y,q,void 0);if($&&($.refAt>=0||Me(k,s[$.last]))){let N=[],{offsets:Q,len:Z,refAt:S}=E(y,q,N);I(N,Q,Z,S)}else this.twinStarts.add(Pe({node:k,offset:q}))}}}let b=this.refId===void 0?void 0:this.paths[this.refId];if(this.paths.sort((y,k)=>y.path[0]-k.path[0]||y.offsets[0]-k.offsets[0]),b&&(this.refId=this.paths.indexOf(b)),n){if(m===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let y=this.paths[this.refId],k=n.nodeOffset;for(let O of y.path.slice(0,m))k+=this.record(O).sequenceLen;let v=n.seqOffset-k;this.refInterval=[v,v+y.len],y.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:v,hapEnd:v+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],n=t?.path,s=n&&!_e(n)?ze(n):void 0,r=c=>s!==void 0&&Ot(c,s)===0||_e(ze(c)),o=e&&this.db.hasHaplotypeIndex;this.twinDeferred=!1,this.paths.sort((c,d)=>Ot(c.path,d.path)||c.len-d.len||(c===t?-1:d===t?1:0));let a=[],h;for(let c of this.paths){let d=a[a.length-1],f=o&&c!==t&&r(c.path);this.twinDeferred||=f,d&&Ot(d.path,c.path)===0&&!f?d.weight=(d.weight??1)+(c.weight??1):(c===t&&(h=a.length),a.push({...c,weight:c.weight??1}))}this.paths=a,this.refId=h}mergeDistinct(){this.twinDeferred?this.settleDeferred():this.distinctPaths(!1)}settleDeferred(){this.twinDeferred&&(this.unsettled={paths:[...this.paths],refId:this.refId},this.distinctPaths(!1))}dropTwins(){let e=this.refId===void 0?void 0:this.paths[this.refId],t=this.refInterval,n=o=>`${o.pathHandle}:${o.hapStart}-${o.hapEnd}`,s=new Set;e?.identity&&t&&s.add(n({...e.identity,hapStart:t[0],hapEnd:t[1]}));for(let o of this.paths)o!==e&&o.identity?.orientation==="forward"&&s.add(n(o.identity));let r=this.paths.filter(o=>o===e||o.identity?.orientation!=="reverse"||!s.has(n(o.identity)));r.length<this.paths.length&&(this.paths=r,this.refId=e===void 0?void 0:r.indexOf(e)),this.twinDeferred&&this.distinctPaths(!1)}keepHaplotypes(e){if(this.paths.some(o=>o.weight!==void 0))throw new Error("keepHaplotypes needs one walk per haplotype: extract with haplotypes 'all', then call mergeDistinct()");let t=this.paths.filter((o,a)=>a!==this.refId&&o.identity===void 0).length;if(t>0)throw new Error(`${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 n=this.refId===void 0?void 0:this.paths[this.refId],s=this.paths.filter((o,a)=>a===this.refId||o.identity!==void 0&&e(o.identity.name)),r=new Set;for(let o of s)for(let a of o.path)r.add(R(a));for(let o of[...this.records.keys()])r.has(R(o))||this.records.delete(o);this.paths=s,this.refId=n===void 0?void 0:s.indexOf(n)}async extractChosenPaths(e,t,n,s){this.clearPaths();let r=e.position.seqOffset,o=await xn({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:r-e.position.nodeOffset,window:{start:r,end:r+t},context:s,snarls:{mode:this.snarlMode,fills:this.snarlFills,inserted:this.snarlNodes},keep:n,signal:this.signal,prefetchReferenceRange:(d,f,l)=>this.prefetchReferenceRange(d,f,l)});if(this.stats.keep=o.stats,o.stats.fallback!==void 0)return!1;let a=await this.db.pathsByHandle(),h=d=>({path:d.handles,offsets:d.offsets,len:d.len,weight:void 0,identity:{pathHandle:d.pathHandle,name:d===o.reference?e.name:a.get(d.pathHandle).name,orientation:d.orientation,hapStart:d.hapStart,hapEnd:d.hapEnd}}),c=[o.reference,...o.pieces].sort(bn);return this.paths=c.map(h),this.refId=c.indexOf(o.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[o.reference.hapStart,o.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");this.unsettled&&({paths:this.paths,refId:this.refId}=this.unsettled,this.unsettled=void 0,this.twinDeferred=!0);let e=await this.db.haplotypeSampleGap()??4096,t=kt(this.sortedHandles());if(t.length===0)return;let n=new Map,s=await Promise.all(t.map(([u,m])=>this.db.haplotypeSamplesInRange(u,m)));for(let u of s.flat())n.set(Pe(u),u);let r=u=>{let m=0,E=t.length-1;for(;m<E;){let w=m+E+1>>1;t[w][0]<=u?m=w:E=w-1}let I=t[m];return I[0]<=u&&u<=I[1]},o=new Map;this.paths.forEach((u,m)=>{u.path.length>0&&m!==this.refId&&o.set(Pe(rt(u,0)),m)});let a=this.stats.identification;a.interval=e,a.scans=t,a.windowSamples=n.size,this.paths.forEach((u,m)=>{m!==this.refId&&a.fragmentLengths.push(u.len)});let h=this.recordReader(()=>{this.stats.identificationFetches+=1,a.graphFetches+=1}),c=u=>(a.graphLookups+=1,h(u)),d=async(u,m)=>{if(r(u.node))return n.get(Pe(u));this.stats.identificationFetches+=1,a.companionSeeks+=1,m.seeks+=1;let E=await this.db.haplotypeSampleAt(u.node,u.offset);return E||(a.companionMisses+=1),E},f=new Map,l=async u=>{let m=f.get(u);if(!m){let E=await this.db.getPath(u);if(!E)throw new Error(`Path ${u} is missing from the database`);m=E.name,f.set(u,m)}return m},g=(u,m,E)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+m+E},p=(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 E=[],I=new Set,w={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};a.chains.push(w);let b,y=0,k=u,v;for(;b===void 0;){if(this.signal?.throwIfAborted(),k!==void 0){if(I.has(k)){w.end="cycle";break}I.add(k);let $=this.paths[k];E.push({index:k,startBp:y}),w.fragments+=1;let N=y;for(let Z=0;Z<$.path.length;Z++){let S=rt($,Z),M=n.get(Pe(S)),P=this.record(S.node).sequenceLen;if(M){b=g(M,N,P);break}N+=P}if(y+=$.len,b){w.end="in-fragment sample";break}let Q=rt($,$.path.length-1);v=this.record(Q.node).gbwt().lf(Q.offset),k=void 0}if(v===void 0||v.node===0){w.end="endmarker";break}let O=Pe(v),B=o.get(O);if(B!==void 0){let $=this.paths[B].identity;if($){b=p($,y),w.end="identified sibling";break}k=B;continue}this.records.has(v.node)&&(w.reentries+=1),this.twinStarts.has(O)&&(w.twinLandings+=1);let D=await d(v,w),q=await c(v.node);if(D){b=g(D,y,q.sequenceLen),w.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,w.steps+=1,y-E[E.length-1].startBp>4*e+4*q.sequenceLen){w.end="bound";break}y+=q.sequenceLen,v=q.gbwt().lf(v.offset)}if(b){w.pathHandle=b.pathHandle;let O=await l(b.pathHandle);for(let{index:B,startBp:D}of E){let q=this.paths[B];q.identity=b.orientation==="forward"?{pathHandle:b.pathHandle,name:O,orientation:"forward",hapStart:b.base+D,hapEnd:b.base+D+q.len}:{pathHandle:b.pathHandle,name:O,orientation:"reverse",hapStart:b.base-D-q.len,hapEnd:b.base-D}}}}this.dropTwins()}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,s)=>{let r=t.get(n);r?r.push(s):t.set(n,[s])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,s)=>{t.push(t[s]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),s=new Int32Array(e.length),r=new Int32Array(e.length),o=0,a=-1;for(let h=0;h<e.length;h++){let c=n.get(e[h]);if(c){let d=xs(c,a);if(d===void 0)return;s[o]=h,r[o]=d,o+=1,a=d}}return{pathAt:s,refAt:r,count:o}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,s=0,r=0,o=0,a=0;for(;s<e.length&&r<t.length;){let h=this.record(e[s]).sequence,c=this.record(t[r]).sequence;for(;o<h.length&&a<c.length;){if(h[o]!==c[a])return n;o+=1,a+=1,n+=1}o===h.length&&(s+=1,o=0),a===c.length&&(r+=1,a=0)}return n}suffixMatches(e,t){let n=0,s=0,r=0,o=0,a=0;for(;s<e.length&&r<t.length;){let h=this.record(e[e.length-s-1]).sequence,c=this.record(t[t.length-r-1]).sequence;for(;o<h.length&&a<c.length;){if(h[h.length-o-1]!==c[c.length-a-1])return n;o+=1,a+=1,n+=1}o===h.length&&(s+=1,o=0),a===c.length&&(r+=1,a=0)}return n}align(e,t,n){let s=this.pathLen(e),r=this.pathLen(t),o=this.prefixMatches(e,t),a=this.suffixMatches(e,t);o+a>s&&(a=s-o),o+a>r&&(a=r-o),K(n,"M",o),Ln(n,s-o-a,r-o-a),K(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),s=0;for(let r of e)n.has(r)&&(s+=this.record(r).sequenceLen);return s}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let s=n??ys(Sn(e,t,f=>this.record(f).sequenceLen)[0]),r=[],o=this.refPrefix(t),a=(f,l,g,p)=>{f===l?K(r,"D",o[p]-o[g]):g===p?K(r,"I",this.pathLen(e.slice(f,l))):this.align(e.slice(f,l),t.slice(g,p),r)},h=0,c=0,d=0;for(let f=0;f<s.count;f++){let l=s.pathAt[f],g=s.refAt[f];(c!==l||d!==g)&&a(c,l,d,g);let p=this.record(e[l]).sequenceLen;K(r,"M",p),h+=p,c=l+1,d=g+1}return a(c,e.length,d,t.length),{edits:r,matched:h,matches:s}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,s;if(_e(n)&&(t.identity===void 0||!_e(ze(t.path))))s={...this.editsAgainst(t.path,n),flipped:!1};else{let r=ze(t.path),o=this.sharedWeight(t.path,n);if(this.sharedWeight(r,n)===0)s={...this.editsAgainst(t.path,n),flipped:!1};else if(o===0)s={...this.editsAgainst(r,n),flipped:!0};else{let h=this.editsAgainst(t.path,n),c=this.editsAgainst(r,n);s=c.matched>h.matched?{...c,flipped:!0}:{...h,flipped:!1}}}return s}alignToRef(e){return this.settleDeferred(),this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){this.settleDeferred();let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],s=(d,f,l,g)=>{let p=Ms(d),u=this.paths[l[0]],m=this.paths[l[l.length-1]],E=u.identity,I=E?.orientation==="forward",[w,b]=I?[u,m]:[m,u];return{strand:f,refStart:e.start+p.leading,refEnd:e.start+n-p.trailing,edits:p.edits,weight:u.weight,path:l.flatMap(y=>this.paths[y].path),start:rt(u,0),pieces:l,soloAligned:g,identity:E===void 0?void 0:{pathHandle:E.pathHandle,name:E.name,hapStart:E.name.fragment+w.identity.hapStart,hapEnd:E.name.fragment+b.identity.hapEnd,walkForward:I}}},r=d=>d.soloAligned.reduce((f,l)=>f+l,0),o=d=>d.pieces.reduce((f,l)=>f+this.paths[l].len,0),a=d=>2*r(d)>=o(d),h=d=>{let f=d[0],l=d[d.length-1],g=f.identity.walkForward;if(d.some((N,Q)=>N.strand!==f.strand||N.identity.walkForward!==g||Q>0&&N.identity.hapStart<d[Q-1].identity.hapEnd))return;let p=g?d:[...d].reverse(),u=p.flatMap(N=>N.pieces),m=p.flatMap(N=>N.soloAligned),E=f.strand==="+"!==g,I=u.map(N=>this.paths[N]),w=I.slice(1).map((N,Q)=>{let Z=I[Q].identity;return g?N.identity.hapStart-Z.hapEnd:Z.hapStart-N.identity.hapEnd}),b=E?[...I].reverse():I,y=E?[...w].reverse():w,k=b.flatMap(N=>E?ze(N.path):N.path),{edits:v}=this.editsAgainst(k,t),O=On(v,b.map(N=>N.len)),B=new Map((E?[...u].reverse():u).map((N,Q)=>[N,O[Q]])),D=N=>2*N.pieces.reduce((Q,Z)=>Q+B.get(Z),0)>=r(N);if(!D(f)||!D(l))return;let q=[],$=0;return b.slice(0,-1).forEach((N,Q)=>{$+=N.len,q.push([$,y[Q]])}),s(As(v,q),f.strand,u,m)},c=[];return this.paths.forEach((d,f)=>{if(f===this.refId)return;let{edits:l,flipped:g}=this.alignment(f),p=d.identity,u=p?p.orientation==="forward"!==g:!g;c.push(s(l,u?"+":"-",[f],On(l,[d.len])))}),Es(c,a,h).map(d=>{let{edits:f,identity:l,pieces:g,soloAligned:p,...u}=d,m={...u,cigar:Ps(f)};return l?{...m,resolved:!0,name:l.name,label:le({...l.name,fragment:l.hapStart,end:l.hapEnd}),pathHandle:l.pathHandle,hapStart:l.hapStart,hapEnd:l.hapEnd}:{...m,resolved:!1}})}pairAlignments(e){let{target:t,query:n,...s}=e,r=this.paths.flatMap(d=>{let{identity:f}=d;return f?[{name:f.name,start:f.name.fragment+f.hapStart,steps:at(d,f)}]:[]}),o=d=>f=>f.sample===d.sample&&f.haplotype===d.haplotype,a=o(t),h=n?o(n):d=>!a(d),c=d=>this.record(ue(d,"forward")).sequence;return r.filter(d=>a(d.name)).flatMap(d=>r.filter(f=>h(f.name)).flatMap(f=>Hn({...s,query:f.steps,target:d.steps,sequenceOf:c}).map(l=>({query:f.name,queryStart:f.start+l.queryStart,queryEnd:f.start+l.queryEnd,strand:l.strand,target:d.name,targetStart:d.start+l.targetStart,targetEnd:d.start+l.targetEnd,cigar:Cn(l.edits),matches:l.edits.reduce((g,[p,u])=>g+(p==="="?u:0),0),columns:l.edits.reduce((g,[,p])=>g+p,0),sharedBases:l.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let s=ue(e,n);for(let r of this.record(s).successors())this.hasHandle(r)&&qe(s,r)&&t.push([n==="reverse"?1:0,R(r),z(r)?1:0])}return t.sort((n,s)=>n[0]-s[0]||n[1]-s[1]||n[2]-s[2]),t.filter((n,s)=>s===0||n[0]!==t[s-1][0]||n[1]!==t[s-1][1]||n[2]!==t[s-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!z(n)){let s=R(n),r=`S	${s}	${this.record(n).sequence}
+`;for(let[o,a,h]of this.canonicalEdges(s))r+=`L	${s}	${o?"-":"+"}	${a}	${h?"-":"+"}
+`;t.push(e.encode(r))}return wn(t)}async toGFA(e={}){this.settleDeferred();let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...un(pn(await this.stableName(),await this.db.graphName()))],s=this.sortedHandles();for(let c of s)z(c)||n.push(`S	${R(c)}	${this.record(c).sequence}`);let r=c=>z(c)?"-":"+";for(let c of s)for(let d of this.record(c).successors())this.hasHandle(d)&&qe(c,d)&&n.push(`L	${R(c)}	${r(c)}	${R(d)}	${r(d)}	0M`);let o=(c,d,f,l,g)=>{let p=at(c,d).map(E=>`${z(E)?"<":">"}${R(E)}`).join(""),u=c.weight===void 0?"":`	WT:i:${c.weight}`,m=g===void 0?"":`	CG:Z:${g}`;return`W	${f.sample}	${f.haplotype}	${f.contig}	${f.fragment}	${l}	${p}${u}${m}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(o(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let h=1;return this.paths.forEach((c,d)=>{if(d!==this.refId){let f=e.names!=="anonymous"?c.identity:void 0,l=t?this.alignToRef(d):void 0;n.push(f?o(c,f,{...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd,l):o(c,void 0,{sample:"unknown",contig:a,haplotype:h,fragment:0},c.len,l)),h+=1}}),`${n.join(`
+`)}
+`}outputPaths(e){this.settleDeferred();let t=e.cigar??!1,n=[],s=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let o={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};n.push({info:this.paths[this.refId],identity:void 0,name:le({...o,end:this.refPath.fragment+this.refInterval[1]}),cigar:void 0})}let r=1;return this.paths.forEach((o,a)=>{if(a===this.refId)return;let h=e.names!=="anonymous"?o.identity:void 0;n.push({info:o,identity:h,name:h?le({...h.name,fragment:h.name.fragment+h.hapStart,end:h.name.fragment+h.hapEnd}):le({sample:"unknown",contig:s,haplotype:r,fragment:0,end:o.len}),cigar:t?this.alignToRef(a):void 0}),r+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&qe(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(r=>!z(r)).map(r=>({id:String(R(r)),sequence:this.record(r).sequence})),n=[];for(let[r,o]of this.outputEdges())n.push({from:String(R(r)),from_is_reverse:z(r),to:String(R(o)),to_is_reverse:z(o)});let s=this.outputPaths(e).map(r=>vs(r.info,r.identity,r.name,r.cigar));return{nodes:t,edges:n,paths:s}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(o=>!z(o)),n=new Int32Array(t.length),s=[];t.forEach((o,a)=>{n[a]=R(o),s.push(this.record(o).sequence)});let r=[];for(let[o,a]of this.outputEdges())r.push(o,a);return{nodeIds:n,nodeSequences:s,edges:Int32Array.from(r),paths:this.outputPaths(e).map(o=>({name:o.name,weight:o.info.weight,cigar:o.cigar,steps:Int32Array.from(at(o.info,o.identity))}))}}};function at(i,e){return e?.orientation==="reverse"?i.path.map(t=>ne(t)).reverse():i.path}function vs(i,e,t,n){return{name:t,...i.weight===void 0?{}:{weight:i.weight},...n===void 0?{}:{cigar:n},path:at(i,e).map(s=>({id:String(R(s)),is_reverse:z(s)}))}}function Ot(i,e){let t=Math.min(i.length,e.length);for(let n=0;n<t;n++){let s=i[n],r=e[n];if(s!==r)return s<r?-1:1}return i.length-e.length}function K(i,e,t){if(t===0)return;let n=i[i.length-1];n?.[0]===e?n[1]+=t:i.push([e,t])}function it(i){return i===0?0:6+(i-1)}function Ln(i,e,t){if(e===0)K(i,"D",t);else if(t===0)K(i,"I",e);else{let n=Math.min(e,t),s=4*n+it(e-n)+it(t-n),r=it(e)+it(t);s<=r?(K(i,"M",n),K(i,"I",e-n),K(i,"D",t-n)):(K(i,"I",e),K(i,"D",t))}}function Ms(i){let e=0;for(;e<i.length&&i[e][0]!=="M";)e+=1;if(e===i.length){let a=i.filter(([c])=>c==="I"),h=i.filter(([c])=>c==="D").reduce((c,[,d])=>c+d,0);return{edits:a.map(([c,d])=>[c,d]),leading:0,trailing:h}}let t=i.length;for(;i[t-1][0]!=="M";)t-=1;let n=a=>({inserted:a.reduce((h,[c,d])=>h+(c==="I"?d:0),0),deleted:a.reduce((h,[c,d])=>h+(c==="D"?d:0),0)}),s=n(i.slice(0,e)),r=n(i.slice(t)),o=[];K(o,"I",s.inserted);for(let[a,h]of i.slice(e,t))K(o,a,h);return K(o,"I",r.inserted),{edits:o,leading:s.deleted,trailing:r.deleted}}function On(i,e){let t=e.map(()=>0),n=e.length-1,s=0,r=e[0],o=0;for(let[a,h]of i){if(a==="D")continue;let c=h;for(;c>0;){for(;s<n&&o>=r;)s+=1,r+=e[s];let d=s<n?Math.min(c,r-o):c;a==="M"&&(t[s]+=d),o+=d,c-=d}}return t}function As(i,e){let t=[],n=0,s=0;for(let[r,o]of i){if(r==="D"){K(t,r,o);continue}let a=n;for(;s<e.length&&e[s][0]<n+o;){let[h,c]=e[s];K(t,r,h-a),K(t,"I",c),a=h,s+=1}K(t,r,n+o-a),n+=o}for(;s<e.length;s++)K(t,"I",e[s][1]);return t}function Ps(i){return i.map(([e,t])=>`${t}${e}`).join("")}function Ie(i,e,t=0){if(!Number.isSafeInteger(e)||e<t)throw new Error(`${i} must be a whole number${t>0?` of at least ${t}`:""}, not ${e}`);return e}function ct(i){return Ie("context",i.context??100)}function dt(i,e){return e.limit!==void 0&&Ie("limit",e.limit),ht.create(i,e)}async function Bn(i,e){let t=ct(e),n=dt(i,e),s=await n.pathPosition(He($e(e.path),Ie("offset",e.offset)));return await n.aroundPosition(s.position.handle,s.position.nodeOffset,t),await n.extractSnarls(e.snarls??"none"),n.extractPaths(s,e.haplotypes??"all"),n}async function Rs(i,e){let t=Ie("start",e.start),n=Ie("end",e.end),s=ct(e),r=dt(i,e);try{let o=await r.pathPosition(He($e(e.path),t));return await r.prefetchReferenceWalk(o,n-t),await r.aroundInterval(o.position,n-t,s),await r.extractSnarls(e.snarls??"none"),{subgraph:r,reference:o}}catch(o){throw o instanceof we&&o.windowBp===void 0?new we(o.limit,{windowBp:n-t,walkedBp:r.referenceWalkedBp??0}):o}}async function Lt(i,e){let{keep:t}=e,n=e.haplotypes??"all",s=n==="all"||n==="distinct";if(t!==void 0&&s&&!i.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:r,reference:o}=await Rs(i,e);return t===void 0||!s?(r.extractPaths(o,n),r):(await r.extractChosenPaths(o,e.end-e.start,t,ct(e))||(r.extractPaths(o,"all"),await r.identifyPaths()),r.keepHaplotypes(t),n==="distinct"&&r.mergeDistinct(),r)}async function Tn(i,e){let t=e.haplotypes??"all",n=e.snarls??"none";if(t==="reference-only")throw new Error("Cannot output a reference path in a node-based 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buffer");if(t=t*256+n,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function Ns(i,e,t){switch(t){case 1:return i.getInt8(e);case 2:return i.getInt16(e);case 3:return i.getInt8(e)<<16|i.getUint16(e+1);case 4:return i.getInt32(e);case 6:return i.getInt16(e)*4294967296+i.getUint32(e+2);default:{let n=i.getBigInt64(e);if(n>BigInt(Number.MAX_SAFE_INTEGER)||n<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${n} exceeds the safe integer range`);return Number(n)}}}var qs=new TextDecoder;function ft(i){let[e,t]=ye(i,0),n=[],s=t;for(;s<e;){let[a,h]=ye(i,s);n.push(a),s=h}let r=new DataView(i.buffer,i.byteOffset,i.byteLength),o=e;return n.map(a=>{if(a===0)return null;if(a>=1&&a<=6){let h=a<=4?a:a===5?6:8,c=Ns(r,o,h);return o+=h,c}if(a===7){let h=r.getFloat64(o);return o+=8,h}if(a===8)return 0;if(a===9)return 1;if(a>=12){let h=a-12>>1,c=i.subarray(o,o+h);return o+=h,a%2===0?c:qs.decode(c)}throw new Error(`SQLite serial type ${a} is reserved`)})}var pt=2,ut=5,Dn=10,lt=13;function Fn(i,e){return i[e]*256+i[e+1]}function ke(i,e){return i[e]*16777216+i[e+1]*65536+i[e+2]*256+i[e+3]}function $s(i,e){let t=i[e];if(t!==pt&&t!==ut&&t!==Dn&&t!==lt)throw new Error(`SQLite page has unknown b-tree type ${t}`);let n=t===pt||t===ut;return{type:t,cellCount:Fn(i,e+3),rightChild:n?ke(i,e+8):0,cellPointers:e+(n?12:8)}}function be(i,e,t){return Fn(i,e.cellPointers+2*t)}var Hs=4096,wt=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let n=this.usable,s=t?Math.floor((n-12)*64/255)-23:n-35;if(e<=s)return e;let r=Math.floor((n-12)*32/255)-23,o=r+(e-r)%(n-4);return o<=s?o:r}async payload(e,t,n,s){let r=this.localPayloadSize(n,s);if(r===n)return e.subarray(t,t+n);let o=new Uint8Array(n);o.set(e.subarray(t,t+r),0);let a=r,h=ke(e,t+r);for(;h!==0&&a<n;){let c=await this.pager.page(h),d=c.subarray(4,4+Math.min(this.usable-4,n-a));o.set(d,a),a+=d.length,h=ke(c,0)}if(a!==n)throw new Error("SQLite overflow chain ended before the payload was complete");return o}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:$s(t,e===1?100:0)}}tableDepth(e,t){let n=this.tableDepths.get(e);return n||(n=(async()=>{let s=e;for(let r=0;;r++){let{page:o,header:a}=await this.pageAt(s);if(a.type===lt)return r;if(a.type!==ut)throw new Error("SQLite table b-tree contains an index page");let h=this.childIndexFor(o,a,t);s=h===a.cellCount?a.rightChild:ke(o,be(o,a,h))}})(),this.tableDepths.set(e,n),n.catch(()=>this.tableDepths.delete(e))),n}childIndexFor(e,t,n){let s=0,r=t.cellCount;for(;s<r;){let o=s+r>>1,[a]=ye(e,be(e,t,o)+4);a<n?s=o+1:r=o}return s}async prefetchRowidRanges(e,t,n=!1){if(t.length===0)return!0;let s=await this.tableDepth(e,t[0][0]),r=t.map(()=>[e]);for(let o=0;o<s;o++){r=await Promise.all(r.map((h,c)=>this.childrenInRange(h,...t[c])));let a=r.flat();if(n)this.pager.prefetchLeading(a);else if(!this.pager.prefetch(a))return!1}return!0}async childrenInRange(e,t,n){let s=await Promise.all(e.map(o=>this.pageAt(o))),r=[];return s.forEach(({page:o,header:a},h)=>{let c=h===0?this.childIndexFor(o,a,t):0,d=h===s.length-1?this.childIndexFor(o,a,n):a.cellCount;for(let f=c;f<=d;f++)r.push(f===a.cellCount?a.rightChild:ke(o,be(o,a,f)))}),r}async tableRowid(e,t){let n=e;for(;;){let{page:s,header:r}=await this.pageAt(n);if(r.type===lt){let h=0,c=r.cellCount;for(;h<c;){let d=h+c>>1,f=be(s,r,d),[l,g]=ye(s,f),[p,u]=ye(s,g);if(p===t)return ft(await this.payload(s,u,l,!1));p<t?h=d+1:c=d}return}if(r.type!==ut)throw new Error("SQLite table b-tree contains an index page");let o=0,a=r.cellCount;for(;o<a;){let h=o+a>>1,c=be(s,r,h),[d]=ye(s,c+4);d<t?o=h+1:a=h}n=o===r.cellCount?r.rightChild:ke(s,be(s,r,o))}}async*tableScan(e){yield*this.scanPage(e,await this.tableDepth(e,0))}async*scanPage(e,t){let{page:n,header:s}=await this.pageAt(e);if(s.type===lt)for(let r=0;r<s.cellCount;r++){let o=be(n,s,r),[a,h]=ye(n,o),[c,d]=ye(n,h);yield{rowid:c,values:ft(await this.payload(n,d,a,!1))}}else{let r=[];for(let o=0;o<s.cellCount;o++)r.push(ke(n,be(n,s,o)));r.push(s.rightChild),t===1&&this.pager.prefetchLeading(r);for(let o of r)yield*this.scanPage(o,t-1)}}decodedCells(e,t){let n=this.decodedIndexPages.get(e);if(n)this.decodedIndexPages.delete(e);else if(n=new Array(t.cellCount),this.decodedIndexPages.size>=Hs){let s=this.decodedIndexPages.keys().next().value;s!==void 0&&this.decodedIndexPages.delete(s)}return this.decodedIndexPages.set(e,n),n}async indexCell(e,t,n,s){let r=this.decodedCells(e,n),o=r[s];if(!o){let a=be(t,n,s),h=n.type===pt,[c,d]=ye(t,h?a+4:a);o={values:ft(await this.payload(t,d,c,!0)),leftChild:h?ke(t,a):0},r[s]=o}return o}async lowerBound(e,t,n,s,r,o){let a=r,h=n.cellCount;for(;a<h;){let c=a+h>>1,d=await this.indexCell(e,t,n,c),f=Bt(d.values,s);f<0||o&&f===0?a=c+1:h=c}return a}async*indexScanFrom(e,t,n){let{page:s,header:r}=await this.pageAt(e),o=await this.lowerBound(e,s,r,t,0,!1),a=r.type===pt;if(a&&n){let h=await this.lowerBound(e,s,r,n,o,!0),c=[];for(let d=o;d<=h;d++)c.push(d===r.cellCount?r.rightChild:(await this.indexCell(e,s,r,d)).leftChild);this.pager.prefetchLeading(c)}for(let h=o;h<r.cellCount;h++){let c=await this.indexCell(e,s,r,h);if(a&&(yield*this.indexScanFrom(c.leftChild,t,n)),n&&Bt(c.values,n)>0)return;yield c.values}a&&(yield*this.indexScanFrom(r.rightChild,t,n))}async indexSeekLE(e,t){let n,s=e;for(;;){let{page:r,header:o}=await this.pageAt(s),a=0,h=o.cellCount,c=0;for(;a<h;){let d=a+h>>1,f=await this.indexCell(s,r,o,d);Bt(f.values,t)<=0?(n=f.values,a=d+1):(c=f.leftChild,h=d)}if(o.type===Dn)return n;s=a===o.cellCount?o.rightChild:c}}};function Bt(i,e){for(let t=0;t<e.length;t++){let n=i[t],s=e[t];if(typeof n!="number"||s===void 0)throw new Error("SQLite index key is not numeric");if(n!==s)return n<s?-1:1}return 0}function zn({blockSize:i,maxBlocks:e}){if(i!==void 0&&!(Number.isSafeInteger(i)&&i>0))throw new Error(`blockSize must be a positive integer, not ${i}`);if(e!==void 0&&!(Number.isSafeInteger(e)&&e>0))throw new Error(`maxBlocks must be a positive integer, not ${e}`)}var gt=class{blocks=new Map;blockSize;maxBlocks;plan;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,n,s={}){this.source=e,this.pageSize=t,this.fileSize=n;let r=s.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(r/t)*t),this.maxBlocks=s.maxBlocks??256}async read(e,t){let n=await this.readRetrying(e,t);if(this.bytesFetched+=n.length,n.length<e)throw new Error(`the file ends at byte ${t+n.length}, short of the ${this.fileSize} bytes its SQLite header gives`);return n}async readRetrying(e,t){let n=0;for(;;)try{return await this.source.read(e,t)}catch(s){if(n+=1,n>=3)throw s;await new Promise(r=>setTimeout(r,200*n))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){this.follow(e);let t=this.touch(e);if(t)return t;let n=e*this.blockSize,s=Math.min(this.blockSize,this.fileSize-n),r=this.read(s,n);return this.fetches+=1,this.store(e,r),this.evict(),r}touch(e){let t=this.blocks.get(e);return t&&(this.blocks.delete(e),this.blocks.set(e,t)),t}blockOf(e){return Math.floor((e-1)*this.pageSize/this.blockSize)}get prefetchBudget(){return Math.max(1,Math.floor(this.maxBlocks/2))}get chunk(){return Math.max(1,Math.floor(this.prefetchBudget/2))}prefetch(e){let t=new Set(e.map(n=>this.blockOf(n)));return t.size>this.prefetchBudget?!1:(this.fetchBlocks(t),!0)}prefetchLeading(e){let t=[],n=new Map;for(let s of e){let r=this.blockOf(s);n.has(r)||(n.set(r,t.length),t.push(r))}this.plan={blocks:t,position:n,next:0},this.advance(this.prefetchBudget)}advance(e){let t=this.plan;if(!t)return;let n=t.blocks.slice(t.next,t.next+e);t.next+=n.length,t.next>=t.blocks.length&&(this.plan=void 0),this.fetchBlocks(new Set(n))}follow(e){let t=this.plan,n=t?.position.get(e);t&&n!==void 0&&n>=t.next-Math.ceil(this.chunk/2)&&this.advance(this.chunk)}fetchBlocks(e){let t=[...e].filter(s=>!this.touch(s)).sort((s,r)=>s-r),n=0;for(;n<t.length;){let s=n+1;for(;s<t.length&&t[s]===t[s-1]+1;)s+=1;this.fetchRun(t[n],s-n),n=s}}fetchRun(e,t){let n=e*this.blockSize,s=Math.min(t*this.blockSize,this.fileSize-n),r=this.read(s,n);this.fetches+=1;for(let o=0;o<t;o++){let a=o*this.blockSize;this.store(e+o,r.then(h=>h.subarray(a,a+this.blockSize)))}this.evict()}store(e,t){this.blocks.set(e,t),t.catch(()=>{this.blocks.get(e)===t&&this.blocks.delete(e)})}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 n=await this.block(Math.floor(t/this.blockSize)),s=t%this.blockSize;return n.subarray(s,s+this.pageSize)}};var je=class i{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){zn(t);let n=await e.read(Math.max(512,t.blockSize??65536),0),s=n.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3"||s.length<100)throw new Error("Not a SQLite database");let o=new DataView(s.buffer,s.byteOffset,s.byteLength),a=o.getUint16(16),h=a===1?65536:a,c=s[20]??0,d=o.getUint32(56);if(d!==1)throw new Error(`SQLite text encoding ${d} is not UTF-8`);let f=o.getUint32(28);if(f===0||o.getUint32(24)!==o.getUint32(92))throw new Error("SQLite header has no valid database size; the file was written by SQLite older than 3.7.0");let l=f*h,g=new gt(e,h,l,t);g.seed(0,n),g.fetches+=1,g.bytesFetched+=n.length;let p=new wt(g,c),u=new Map;for await(let{values:m}of p.tableScan(1)){let[E,I,w,b,y]=m;typeof E=="string"&&typeof I=="string"&&typeof w=="string"&&typeof b=="number"&&u.set(I,{type:E,name:I,tableName:w,rootPage:b,sql:typeof y=="string"?y:""})}return new i(g,p,u)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}withoutRowid(e){let t=this.objects.get(e);return t?.type==="table"&&/without\s+rowid/i.test(t.sql)}indexOn(e){let t=[...this.objects.values()].find(n=>n.type==="index"&&n.tableName===e);if(t)return t.rootPage;if(this.withoutRowid(e))return this.rootPage(e);throw new Error(`SQLite table ${e} has no index`)}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n=!1){return this.btree.prefetchRowidRanges(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,n){return this.btree.indexScanFrom(this.indexOn(e),t,n)}has(e){return this.objects.has(e)}};var zt="GBZ-base version 4",mt=class extends Error{name="UnknownPathError";path;constructor(e){super(`the graph has no path named ${le(e)}`),this.path=e}},yt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},xt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: it has no version tag":`unsupported database schema "${e}"; this reader understands "${zt}"`),this.found=e}},Cs=0,Os=1,Ls=2,Bs=3;function Ts(i){if(i.length===1)return i[0];let e=new Uint8Array(i.reduce((n,s)=>n+s.length,0)),t=0;for(let n of i)e.set(n,t),t+=n.length;return e}var Tt=3,Oe=class{at=0;bytes;constructor(e){this.bytes=e}get done(){return this.at>=this.bytes.length}next(){let e=0,t=1;for(;;){let n=this.bytes[this.at++];if(n===void 0)throw new Error("a haplotype index blob ends inside a number");if(e+=(n&127)*t,t*=128,(n&128)===0)return e}}};function _s(i,e){let t=new Oe(i),n=0;for(;!t.done;){let s=n+t.next();n=s+t.next(),e.push([s,n])}}function Ds(i){i.sort((n,s)=>n[0]-s[0]);let e=[],t=[];for(let[n,s]of i){let r=t.length-1;r>=0&&n<=t[r]+1?t[r]=Math.max(t[r],s):(e.push(n),t.push(s))}return n=>{let s=0,r=e.length;for(;s<r;){let o=s+r>>1;e[o]<=n?s=o+1:r=o}return s>0&&n<=t[s-1]}}function Fs(i,e,t){let n=new Oe(e);for(;!n.done;){let s=n.next(),r=n.next(),o=n.next(),a=n.next(),h=n.next();t.push({bin:i,pathHandle:s,pathStart:r,pathEnd:o,snarl:h>0?[a,h]:void 0,node:n.next(),offset:n.next()})}}function zs(i,e,t){let n=R(i);for(let s of e){let r=new Oe(s);for(;!r.done;){let o=r.next(),a=o%2;t.push({node:2*n+a,offset:r.next(),pathHandle:(o-a)/2,orientation:"forward",pathOffset:r.next()})}}}var Dt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,s,r){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=s,this.next=r,this.sequenceLen=rn(s)}get id(){return R(this.handle)}get orientation(){return Ne(this.handle)}get sequence(){return this.decoded??=an(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 ${this.handle} is empty`);return new Ze(this.edges,this.bwt)}};function G(i,e){if(typeof i!="number")throw new Error(`${e} is not a number in the database`);return i}function Ve(i,e){if(typeof i!="string")throw new Error(`${e} is not text in the database`);return i}function Re(i,e){if(!(i instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return i}function Un(i,e){return{handle:i,fwStart:{node:G(e[1],"Paths.fw_node"),offset:G(e[2],"Paths.fw_offset")},revStart:{node:G(e[3],"Paths.rev_node"),offset:G(e[4],"Paths.rev_offset")},name:{sample:Ve(e[5],"Paths.sample"),contig:Ve(e[6],"Paths.contig"),haplotype:G(e[7],"Paths.haplotype"),fragment:G(e[8],"Paths.fragment")},isIndexed:G(e[9],"Paths.is_indexed")!==0}}function _t(i,e){return i.catch(e),i}async function jn(i){let e=new Map;for await(let{values:t}of i.scan("Tags"))e.set(Ve(t[0],"Tags.key"),Ve(t[1],"Tags.value"));return e}var Ft=class i{pathCache;pathMapCache;indexTags=new Map;overviewRowsCache;sqlite;index;tagMap;constructor(e,t,n){this.sqlite=e,this.index=t,this.tagMap=n}static async open(e){let{source:t,haplotypeIndex:n}=e,s={blockSize:e.blockSize,maxBlocks:e.maxBlocks},r=await je.open(t,s),o=r.objects.has("Tags")?await jn(r):new Map,a=o.get("version");if(a!==zt)throw new xt(a);for(let d of["Nodes","Paths","ReferenceIndex"])r.rootPage(d);let h=n?await je.open(n,s):void 0,c=new i(r,h,o);if(h){for(let u of["Tags","HaplotypeSamples","HaplotypeLengths"])if(!h.objects.has(u))throw new Error(`haplotypeIndex is not a gbz-base haplotype index: it has no ${u} table`);c.indexTags=await jn(h);let d=c.indexTags.get("haplotype_index_paths"),f=await c.tag("paths");if(d!==f)throw new Error(`haplotype index was built for ${d??"an unknown number of"} paths but the graph has ${f}`);let l=c.indexTags.get("haplotype_index_nodes"),g=await c.tag("nodes");if(l!==void 0&&l!==g)throw new Error(`haplotype index was built for a graph with ${l} nodes but this one has ${g}`);if(c.indexTags.get("haplotype_index_orientations")==="forward")throw new yt;let p=c.indexTags.get("haplotype_index_format");if(Number(p)!==Tt)throw new Error(p===void 0?`the haplotype index predates format ${Tt}; rebuild it with gbz-haplotype-index 0.3`:`the haplotype index has format ${p}; this version of @gmod/gbz-base reads format ${Tt}`)}return c}async tags(){return this.tagMap}async tag(e){return this.tagMap.get(e)}prefetchRecords(e,t=!1){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new Dt(e,on(Re(t[1],"Nodes.edges")),Re(t[2],"Nodes.bwt"),Re(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=_t(this.scanPaths(),()=>{this.pathCache=void 0}),this.pathCache}async scanPaths(){let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(Un(t,n));return e}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?Un(e,t):void 0}pathsByHandle(){return this.pathMapCache??=_t(this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),()=>{this.pathMapCache=void 0}),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,s)=>s.name.fragment-n.name.fragment)[0]}async pathsNamed(e){let t=He($e(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,s)=>n.name.fragment-s.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 o=await this.getPath(e);throw new Error(`${o?`The fragment of ${le(o.name)} at ${o.name.fragment}`:`Path ${e}`} has not been indexed for random access`)}let s=n.pathOffset,r=n.pos;for(;;){let o=await this.getRecord(r.node);if(!o)throw new Error(`Node ${r.node} does not exist in the graph`);s+=o.sequenceLen;let a=o.gbwt().lf(r.offset);if(!a||a.node===0)return s;r=a}}return t}async getPathFragments(e){let{start:t,end:n}=e;if(Number.isNaN(t)||Number.isNaN(n))throw new Error(`The window ${t}..${n} is not a number range`);let s=await this.pathsNamed(e.path);if(s.length===0)throw new mt(He($e(e.path),0));if(n<=t)return[];let r=s.filter(h=>h.name.fragment<=t).slice(-1),o=s.filter(h=>h.name.fragment>t&&h.name.fragment<n);return(await Promise.all([...r,...o].map(async h=>({path:h,start:h.name.fragment,end:h.name.fragment+await this.pathLength(h.handle)})))).filter(h=>t<h.end)}async subgraphForFragment(e,t){let{sample:n,contig:s,haplotype:r}=e.path.name,o=Math.max(t.start,e.start),a=t.haplotypes??"all";try{let h=await Lt(this,{...t,path:{sample:n,contig:s,haplotype:r},start:o,end:Math.min(t.end,e.end)});return t.keep===void 0&&this.hasHaplotypeIndex&&(a==="all"||a==="distinct")&&await h.identifyPaths(),h}catch(h){throw h instanceof we&&h.walkedBp!==void 0?new we(h.limit,{windowBp:t.end-t.start,walkedBp:o-t.start+h.walkedBp}):h}}async getSubgraphs(e){let t=await this.getPathFragments(e);return(await Promise.allSettled(t.map(s=>this.subgraphForFragment(s,e)))).map(s=>{if(s.status==="rejected")throw s.reason;return s.value})}async getAlignments(e){return(await this.getSubgraphs(e)).flatMap(t=>t.alignments())}subgraphInInterval(e){return Lt(this,e)}subgraphAtOffset(e){return Bn(this,e)}subgraphAroundNodes(e){return Tn(this,e)}subgraphBetween(e){return _n(this,e)}fetchStats(){let e=({pager:t})=>({fetches:t.fetches,bytesFetched:t.bytesFetched});return{graph:e(this.sqlite),haplotypeIndex:this.index?e(this.index):void 0}}async graphName(){let e=new Map;for(let[n,s]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),s);let t={name:void 0,subgraph:new Map,translation:new Map};try{t=ln(e)}catch{}return t}async hasChainLinks(){let e=await this.tag("chain_links");return e!==void 0&&Number(e)>0}get hasHaplotypeIndex(){return this.index!==void 0}get companion(){if(!this.index)throw new Error("no haplotype index was opened with this database");return this.index}async haplotypeSampleInterval(){let e=this.indexTags.get("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeSampleGap(){let e=await this.haplotypeSampleInterval(),t=this.indexTags.get("haplotype_index_reference_interval");return e===void 0?void 0:Math.max(e,t===void 0?0:Number(t))}async haplotypeAnchorSpacing(){let e=this.index?.has("HaplotypeAnchors")?this.indexTags.get("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeStrayOptions(){let e=n=>this.indexTags.get(`haplotype_index_stray_${n}`);if(!this.index?.has("HaplotypeBins")||e("format")!=="2")return;let t=e("snarls")==="modeled"&&e("chain_links")===(await this.tag("chain_links")??"0");return{context:Number(e("context")),bin:Number(e("bin")),bound:Number(e("bound")),snarlNodes:t?Number(e("snarl_nodes")):void 0}}async blobRows(e,t,n){let s=[],r=[];for await(let o of this.companion.indexScanFrom(e,t,n))r.push(G(o[o.length-1],`${e} rowid`));r.length>1&&await this.companion.prefetchRows(e,[[Math.min(...r),Math.max(...r)+1]],!0);for(let o of r){let a=await this.companion.byRowid(e,o);a&&s.push(a)}return s}async haplotypeBinData(e,t,n){let s=[],r=[];for(let o of await this.blobRows("HaplotypeBins",[e,t],[e,n])){let a=G(o[1],"HaplotypeBins.bin");_s(Re(o[3],"HaplotypeBins.nodes"),s),Fs(a,Re(o[4],"HaplotypeBins.strays"),r)}return{listed:Ds(s),strays:r}}async haplotypeAnchorsBetween(e,t,n){let s=[],r=[],o=()=>{let a=s[s.length-1];a&&zs(a.node,r,a.visits),r=[]};for(let a of await this.blobRows("HaplotypeAnchors",[e,t],[e,n])){let h=G(a[1],"HaplotypeAnchors.anchor_offset");s[s.length-1]?.anchorOffset!==h&&(o(),s.push({anchorOffset:h,node:G(a[3],"HaplotypeAnchors.node_handle"),pathOffset:G(a[4],"HaplotypeAnchors.path_offset"),visits:[]})),r.push(Re(a[5],"HaplotypeAnchors.visits"))}return o(),s}async haplotypeAnchor(e,t){let[n]=await this.haplotypeAnchorsBetween(e,t,t);return n&&{node:n.node,pathOffset:n.pathOffset}}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:G(e[0],"HaplotypeSamples.node_handle"),offset:G(e[1],"HaplotypeSamples.node_offset"),pathHandle:G(e[2],"HaplotypeSamples.path_handle"),orientation:G(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:G(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let n=[];for await(let s of this.companion.indexScanFrom("HaplotypeSamples",[e,0],[t,Number.MAX_SAFE_INTEGER]))n.push(this.sampleFromRow(s));return n}async haplotypeSampleAt(e,t){let n=await this.companion.indexSeekLE("HaplotypeSamples",[e,t]);return n?.[0]===e&&n[1]===t?this.sampleFromRow(n):void 0}overviewRows(){return this.overviewRowsCache??=_t((async()=>{let e=[];for await(let{rowid:t,values:n}of this.companion.scan("HaplotypeOverviewRows"))e[t]={sample:Ve(n[1],"HaplotypeOverviewRows.sample"),haplotype:G(n[2],"HaplotypeOverviewRows.haplotype")};return e})(),()=>{this.overviewRowsCache=void 0}),this.overviewRowsCache}async overviewChunks(e,t,n,s,r){let o=new Map;for(let a of await this.blobRows(e,[t,n,s],[t,n,r])){let h=G(a[2],`${e}.chunk`),c=o.get(h)??[];c.push(Re(a[4],`${e} blob`)),o.set(h,c)}return new Map([...o].map(([a,h])=>[a,Ts(h)]))}async haplotypeOverview(e){let t=p=>this.indexTags.get(`haplotype_index_overview_${p}`);if(!this.index?.has("HaplotypeOverviewClasses")||t("format")!=="1")return;let n=Number(t("bin")),s=Number(t("chunk")),r=Number(t("levels")),o=Math.max(0,Math.min(Math.floor(e.level??0)||0,r-1));if(e.level===void 0&&e.bpPerPixel!==void 0)for(;o+1<r&&n*4**(o+1)<=e.bpPerPixel;)o+=1;let a=n*4**o,[h,c]=await Promise.all([this.getPathFragments(e),this.overviewRows()]),d=Math.ceil(c.length/2),f=[],l=[];for(let p of h){let u=p.end-p.start,m=Math.max(e.start,p.start)-p.start,E=Math.min(e.end,p.end)-p.start,I=Math.floor(m/a),w=Math.floor((E-1)/a),b=Math.floor(I/s),y=Math.floor(w/s),[k,v]=await Promise.all([this.overviewChunks("HaplotypeOverviewBins",p.path.handle,o,b,y),this.overviewChunks("HaplotypeOverviewClasses",p.path.handle,o,b,y)]);for(let O=b;O<=y;O++){let B=new Oe(k.get(O)??new Uint8Array),D=v.get(O)??new Uint8Array;for(let q=O*s;!B.done;q++){let $=Array.from({length:7},()=>B.next());if(q<I||q>w)continue;f.push({start:p.start+q*a,end:p.start+Math.min((q+1)*a,u),classes:[$[0],$[1],$[2],$[3]],excursions:$[4],variants:$[5],longestExcursion:$[6]});let N=(q-O*s)*d;l.push(D.subarray(N,N+d))}}}if(f.length===0)return;let g=new Uint8Array(f.length*c.length);return l.forEach((p,u)=>{for(let m=0;m<c.length;m++)g[u*c.length+m]=(p[m>>1]??0)>>4*(m%2)&15}),{level:o,bin:a,haplotypes:c,bins:f,cells:g}}async haplotypeLength(e){let t=await this.companion.byRowid("HaplotypeLengths",e);return t?G(t[1],"HaplotypeLengths.length"):void 0}async indexedRow(e){let t=await this.sqlite.byRowid("ReferenceIndex",e);if(!t)throw new Error("ReferenceIndex row referenced by its index is missing");return{pathOffset:G(t[1],"ReferenceIndex.path_offset"),pos:{node:G(t[2],"ReferenceIndex.node_handle"),offset:G(t[3],"ReferenceIndex.node_offset")}}}async indexedRowid(e,t){let n=await this.sqlite.indexSeekLE("ReferenceIndex",[e,t]);return n?.[0]===e?G(n[2],"ReferenceIndex rowid"):void 0}async indexedPosition(e,t){let n=await this.indexedRowid(e,t);return n===void 0?void 0:this.indexedRow(n)}async indexedPositionsBetween(e,t,n){let[s,r]=await Promise.all([this.indexedRowid(e,t),this.indexedRowid(e,n)]),o=[];if(s!==void 0&&r!==void 0){await this.sqlite.prefetchRows("ReferenceIndex",[[s,r+1]]);for(let a=s;a<=r;a++)o.push(await this.indexedRow(a))}return o}};export{Cs as a,Os as b,Ls as c,Bs as d,Ft as e};
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