jbrowse-plugin-graphgenomeviewer 4.0.26 → 4.0.28

package/README.md

@@ -47,6 +47,7 @@ node in the view bands its bp in the linear view:
 - Seven layouts: force-directed (Bandage FMMM), ordered, anchored, sample rows,
   walk rows, and sequenceTubeMap's tube map on its own axis or the reference's
 - Genes from the session's annotation track, drawn on the graph
+- Hovering a callset or MAF row in the same view lifts that haplotype's walk
 - Bubbles from `gfatools bubble` or the graph itself, opened level by level
 - gbz-base haplotypes as walks: carriage as node thickness, walks lifted out as
   metro-map lanes or side by side, a panel per walk or a row per sample, each

package/dist/chunks/{AddTrackWorkflow-WYRVQYH2.js → AddTrackWorkflow-F6FBBEJM.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=AddTrackWorkflow-WYRVQYH2.js.map
+import{b as F,c as T,i as y}from"./chunk-4T7DPQTR.js";import{a as N}from"./chunk-J4OLMLS5.js";import{a as W}from"./chunk-FCWXYIFC.js";import{a as C,b as B,c as H,d as _,e as O}from"./chunk-XEJ47DLD.js";import{a as w,b as t}from"./chunk-FY3BTKY4.js";var S=w((q,L)=>{L.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var s=t(O(),1),i=t(_(),1),l=t(N(),1),A=t(S(),1),R=t(W(),1),e=t(H(),1),x=t(B(),1);var o=t(C(),1),j=(0,A.makeStyles)()(n=>({paper:{margin:n.spacing(),padding:n.spacing()},field:{marginTop:n.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),D=["RgfaTabixAdapter","MinigraphBubbleAdapter"],J=(0,x.observer)(function({model:r}){let{classes:c}=j(),h=(0,l.getSession)(r),b=(0,R.getRoot)(r),[m,G]=(0,s.useState)("RgfaTabixAdapter"),[p,v]=(0,s.useState)(),[g,P]=(0,s.useState)(),[u,I]=(0,s.useState)(""),[d,M]=(0,s.useState)("Pangenome graph"),[f,k]=(0,s.useState)();function E(){if(!(!p||!r.assembly))try{k(void 0);let a=d.trim();(0,l.addTrackFromWidget)({model:r,session:h,conf:y({choice:m,loc:p,indexLoc:g,assembly:r.assembly,sample:u,trackId:(0,l.makeTrackId)({name:a}),name:a})})}catch(a){k(a)}}return(0,o.jsxs)(e.Paper,{className:c.paper,children:[f?(0,o.jsx)(i.ErrorMessage,{error:f}):null,(0,o.jsxs)(e.FormControl,{children:[(0,o.jsx)(e.FormLabel,{children:"File type"}),(0,o.jsx)(e.RadioGroup,{value:m,onChange:a=>{G(a.target.value)},children:D.map(a=>(0,o.jsx)(e.FormControlLabel,{value:a,control:(0,o.jsx)(e.Radio,{}),label:F[a]},a))})]}),(0,o.jsx)(i.FileSelector,{location:p,name:T[m],rootModel:b,setLocation:v}),(0,o.jsx)(i.FileSelector,{location:g,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:b,setLocation:P}),(0,o.jsx)(e.TextField,{className:c.field,value:u,onChange:a=>{I(a.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),(0,o.jsx)(e.TextField,{className:c.field,value:d,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:a=>{M(a.target.value)}}),(0,o.jsx)(i.AssemblySelector,{session:h,helperText:"Select assembly to add track to",selected:r.assembly,onChange:a=>{r.setAssembly(a)},fullWidth:!0}),(0,o.jsx)(e.Button,{variant:"contained",className:c.submit,disabled:!p||!d.trim()||!r.assembly,onClick:E,children:"Submit"})]})}),K=J;export{K as default};
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package/dist/chunks/GbzBaseSyntenyAdapter-FK6PVNBV.js

@@ -0,0 +1,8 @@
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haplotype index has no anchors");let C=Math.floor(n.window.start/x),R=Math.ceil(n.window.end/x),D=w=>w>=0?e.haplotypeAnchor(n.referenceHandle,w*x):Promise.resolve(void 0),[V,Z]=await Promise.all([Promise.all([0,1,2].map(w=>D(C-w))),Promise.all([0,1,2,3].map(w=>D(R+w)))]),J=V[0],ee=Z.slice(0,2).findIndex(w=>w!==void 0&&w.pathOffset>=n.window.end),Ie=Z[ee];if(!J)throw new oe("the haplotype index has no anchor before the window");if(!Ie)throw new oe("the haplotype index has no anchor after the window");i.anchors=[J.pathOffset,Ie.pathOffset];let Te=V.filter(w=>w!==void 0),de=Z.slice(ee,ee+3).filter(w=>w!==void 0),Ms=w=>{let A=w-w%2;return e.haplotypeSamplesInRange(A,A+1)},pt=new Map,yn=[...Te,...de],_s=await Promise.all(yn.map(w=>Ms(w.node)));if(yn.forEach((w,A)=>pt.set(w,_s[A])),i.anchorsRead=yn.length,!pt.get(J).some(w=>w.pathHandle===n.referenceHandle&&w.orientation==="forward"&&w.pathOffset===J.pathOffset))throw new Error(`The haplotype index has no anchor row for the reference path 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of[...z,...U])te?N.has(q.pathOffset)||(W.push([q.pathOffset,q.pathOffset]),ue.set(q.pathOffset,q)):W.push([q.pathOffset-$,q.pathOffset+$]);let se=Ks(W,ae);if(se.length>1)throw new oe(`path ${w} visits the anchors from ${se.length} copies of the region, at ${se.map(([q,ie])=>`${q}-${ie}`).join(", ")}`);if(De.set(w,se[0]),ce)for(let q of ue.values())Je.push({row:q,stopAt:q.pathOffset,back:0,kind:"interval"});if(!te){for(let q of[...z,...U])if(ce&&(q.node===j.node||q.node===K(F.node))){let ie=q.orientation==="forward"?1:-1;Je.push({row:q,stopAt:q.pathOffset+ie*$,back:0,kind:"one-sided"}),xn.add(w)}}return te?"paired":"one-sided"},Ir=new Set([...pt.values()].flat().map(w=>w.pathHandle)),ht=[...Ir].filter(u);if(i.chosenPaths=ht.length,ht.length>to.mostChosenPaths)throw new oe(`${ht.length} chosen paths pass the anchors, more than ${to.mostChosenPaths}`);for(let w of Ir)await ks(w);let bn=[],Sn=[];i.scans=Nn([...t.keys()].sort((w,A)=>w-A));for(let[w,A]of i.scans)for(let k of await e.haplotypeSamplesInRange(w,A))i.scanRows+=1,t.has(k.node)&&(Sn.push(k),u(k.pathHandle)&&bn.push(k));if(ht.length===0&&bn.length===0&&[...h.values()].some(w=>n.keep(w.name)))throw new oe("no chosen path passes the anchors or has a sample on the window's nodes");let vn=new Set(Sn.map(w=>w.pathHandle).filter(w=>!De.has(w))),Os=de[de.length-1].pathOffset-Te[Te.length-1].pathOffset,Ar=w=>`${w.sample}#${w.haplotype}#${w.contig}`,In=new Map;for(let[w,[A,k]]of De){let z=h.get(w)?.name;if(z&&u(w)){let U=Ar(z),W=z.fragment+A-ae,N=z.fragment+k+ae,j=In.get(U);In.set(U,j?[Math.min(j[0],W),Math.max(j[1],N)]:[W,N])}}let Er=[];for(let[w,A]of h){let k=In.get(Ar(A.name));if(k&&!De.has(w)&&!vn.has(w)&&n.keep(A.name)){let z=await e.haplotypeLength(w)??0;A.name.fragment<k[1]&&A.name.fragment+z>k[0]&&Er.push(w)}}for(let w of[...vn,...Er]){let A=await e.haplotypeLength(w)??Number.POSITIVE_INFINITY;if(A>Os+2*ae)throw new oe(vn.has(w)?`path ${w} of ${A} bp has a sample on the window's nodes and no visit to the anchors`:`chosen fragment ${w} of ${A} bp lies beside its contig's visits to the anchors without a visit of its own`);if(u(w)){let k=(await e.getPath(w))?.fwStart;if(!k)throw new Error(`Path ${w} is missing from the database`);Je.push({row:{node:k.node,offset:k.offset,pathHandle:w,orientation:"forward",pathOffset:0},stopAt:A,back:0,kind:"whole"})}}for(let w of De.keys())if(u(w)&&!xn.has(w))throw new oe(`chosen path ${w} has no walk from its visits to the anchors`);for(let w of Sn){let A=De.get(w.pathHandle);if(A&&(w.pathOffset<A[0]-eo||w.pathOffset>A[1]+eo))throw new oe(`path ${w.pathHandle} has a sample at ${w.pathOffset} on the window's nodes far from its anchor visits at ${A[0]}-${A[1]}`)}i.ms.scan=s();let An=new Map;await n.prefetchReferenceRange(n.referenceHandle,Math.max(0,J.pathOffset-ae),Ie.pathOffset+ae+1);let Cr=8*x+2*(n.window.end-n.window.start);for(let{row:w,stopAt:A,back:k,kind:z}of Je){let U=w.orientation,W=(Y,ne)=>U==="forward"?ne-Y:Y-ne,N=w.pathOffset,j=w.pathOffset,F={node:w.node,offset:w.offset},$=w.pathOffset,ce=!1,te=0,ue=0,se="past the far anchor";for(;F&&(r?.throwIfAborted(),!ce&&W($,A)<=-ae&&(ce=!0),!(ce&&te>ae));){let Y;if(t.has(F.node)){let re=await M({pos:F,left:$},w.pathHandle,U,"interval"),_e=L(re);F=_e.pos,$=_e.left,Y=p(_e.pos.node),N=Math.min(N,re.hapStart),j=Math.max(j,re.hapEnd),te=0}else{if(Y=(await l(F.node)).sequenceLen,te+=Y,ue+=Y,ue>Cr){se="cap";break}N=Math.min(N,$),j=Math.max(j,$+Y)}let ne=await g(F);ne&&($=nt(U,$,Y,(await l(ne.node)).sequenceLen)),F=ne}if(!F&&se!=="cap"&&(se="endmarker"),a(z,se),se==="cap")throw new oe(`the walk of path ${w.pathHandle} between the anchors reached its cap of ${Cr} bp`);if(z==="one-sided"&&se!=="endmarker")throw new oe(`chosen path ${w.pathHandle} runs on past the stretch from its visit to one anchor without a visit to the other`);let q=ae,ie={pos:{node:w.node,offset:w.offset},left:w.pathOffset},Ae=0,Me=k;for(;q>0||Me>0;){r?.throwIfAborted();let Y=await v(ie.pos);if(!Y)break;let ne=Ln(U,ie.left,(await l(ie.pos.node)).sequenceLen,(await l(Y.node)).sequenceLen);if(t.has(Y.node)){let re=await M({pos:Y,left:ne},w.pathHandle,U,"interval");ie=_(re),N=Math.min(N,re.hapStart),j=Math.max(j,re.hapEnd),q=ae,Ae=0,Me-=re.len}else{let re=(await l(Y.node)).sequenceLen;if(Ae+=re,Ae>q&&Me<=0)break;Me-=re,ie={pos:Y,left:ne},N=Math.min(N,ne),j=Math.max(j,ne+re)}}let ze=An.get(w.pathHandle);ze?ze.push([N,j]):An.set(w.pathHandle,[[N,j]])}let Ls=w=>(An.get(w.pathHandle)??[]).some(([A,k])=>A<=w.hapStart&&w.hapEnd<=k);i.ms.intervals=s();for(let w of bn)m.get(w)===void 0&&!(y.get(w.pathHandle)??[]).some(A=>{let k=d[A];return k.canonical&&!no(k)&&k.hapStart<=w.pathOffset&&w.pathOffset<k.hapEnd})&&(i.seeds+=1,await E({pos:{node:w.node,offset:w.offset},left:w.pathOffset},w.pathHandle,w.orientation,"sample"));i.ms.seeds=s();let dt=async(w,A)=>{let k=A?S:I,z=A?I:S,U=w;for(;;){if(k.has(U))return;k.add(U);let W=d[U],N=A?L(W):_(W),j=0,F;for(;F===void 0;){r?.throwIfAborted();let $=A?await g(N.pos):await v(N.pos);if(!$){F="endmarker";break}let ce=(await l(N.pos.node)).sequenceLen,te=(await l($.node)).sequenceLen,ue=A?nt(W.orientation,N.left,ce,te):Ln(W.orientation,N.left,ce,te);if(t.has($.node)){let se=m.get($);se===void 0?(U=await E({pos:$,left:ue},W.pathHandle,W.orientation,"chain"),z.add(U),F="landed"):(z.add(se),F="merge")}else j>ae?F="bound":(j+=te,N={pos:$,left:ue})}if(a("chain",F),F!=="landed")return}};await Promise.all([n.prefetchReferenceRange(n.referenceHandle,Math.max(0,P.hapStart-ae),P.hapStart),n.prefetchReferenceRange(n.referenceHandle,P.hapEnd,P.hapEnd+ae)]);let Rr=new Set,Ts=d.map((w,A)=>({piece:w,id:A})).filter(({piece:w,id:A})=>A!==T&&!Ls(w)).sort((w,A)=>Number(A.piece.canonical)-Number(w.piece.canonical));for(let{piece:w,id:A}of Ts)Rr.has(Fe(w))||(Rr.add(Fe(w)),await dt(A,!0),await dt(A,!1));i.ms.chains=s();let En=new Map,Ns=w=>{let A=Fe(w),k=En.get(A);k?k.add(w.orientation):En.set(A,new Set([w.orientation]))},ut=0,Cn=()=>{for(;ut<d.length;ut++)ut!==T&&Ns(d[ut])};Cn();let mt=w=>(En.get(Fe(w))?.size??0)>1,Pr=2*f;for(let w=0;w<d.length;w++){let A=d[w];if(w===T||mt(A)||A.canonical&&!no(A))continue;i.twins.tried+=1;let k=A.orientation==="forward"?"reverse":"forward",z=L(A),U=0,W;for(;!W&&U<=Pr;){r?.throwIfAborted();let F=await g(z.pos);if(!F)break;let $=(await l(F.node)).sequenceLen,ce=nt(A.orientation,z.left,(await l(z.pos.node)).sequenceLen,$),te=K(F.node);W=(await e.haplotypeSamplesInRange(te,te)).find(ue=>ue.pathHandle===A.pathHandle&&ue.orientation===k&&ue.pathOffset===ce),U+=$,z={pos:F,left:ce}}let N=W&&{pos:{node:W.node,offset:W.offset},left:W.pathOffset},j=0;for(;N&&!mt(A)&&j<=Pr+A.len;){if(r?.throwIfAborted(),t.has(N.pos.node)){let F=await M(N,A.pathHandle,k,"twin"),$=d.indexOf(F);await dt($,!0),await dt($,!1),Cn(),N=L(F)}if(!mt(A)){let F=(await l(N.pos.node)).sequenceLen;j+=F;let $=await g(N.pos);N=$?{pos:$,left:nt(k,N.left,F,(await l($.node)).sequenceLen)}:void 0}}if(Cn(),!mt(A))throw new oe(`piece ${Fe(A)} was found in one orientation where extractPaths keeps the other`);i.twins.found+=1}i.ms.twins=s()}catch(x){if(!(x instanceof oe))throw x;i.fallback=x.message}return G()}function oo(n,e){let t=n.handles[0],r=e.handles[0];return Number(B(t))-Number(B(r))||t-r||n.offsets[0]-e.offsets[0]}function Et(n,e){let t=0,r=n.length;for(;t<r;){let o=t+r>>1;n[o]<e?t=o+1:r=o}return t}var Ct=class{ending;tree;constructor(e){this.ending=new Float64Array(e),this.tree=new Int32Array(e+1).fill(-1)}bestBefore(e){let t=-1;for(let r=e;r>0;r-=r&-r){let o=this.tree[r];o!==-1&&(t===-1||this.ending[o]>this.ending[t])&&(t=o)}return t}raise(e,t){this.ending[e]=t;for(let r=e+1;r<this.tree.length;r+=r&-r){let o=this.tree[r];(o===-1||t>this.ending[o])&&(this.tree[r]=e)}}},Fn=class{pairs=[];total=0;a;b;weight;occurrences=new Map;constructor(e,t,r){this.a=e,this.b=t,this.weight=r,t.forEach((o,s)=>{let i=this.occurrences.get(o);i?i.push(s):this.occurrences.set(o,[s])})}solve(e,t,r,o){let s=0;for(;e+s<t&&r+s<o&&this.a[e+s]===this.b[r+s];)this.match(e+s,r+s),s+=1;let i=0;for(;t-i>e+s&&o-i>r+s&&this.a[t-i-1]===this.b[o-i-1];)i+=1;this.solveMiddle(e+s,t-i,r+s,o-i);for(let a=i;a>0;a--)this.match(t-a,o-a)}match(e,t){this.pairs.push([e,t]),this.total+=this.weight(this.a[e])}solveMiddle(e,t,r,o){if(e===t||r===o)return;let s=this.matchCount(e,t,r,o);if(s===0)return;if(s<=t-e+(o-r)){this.chain(e,t,r,o,s);return}let i=e+t>>1,a=this.split(e,i,t,r,o);this.solve(e,i,r,a),this.solve(i,t,a,o)}matchCount(e,t,r,o){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=Et(a,o)-Et(a,r))}return s}sweep(e,t,r,o,s,i,a){for(let f=e;f!==t;f+=r){let c=this.occurrences.get(this.a[f]);if(!c)continue;let l=this.weight(this.a[f]),p=Et(c,o),h=Et(c,s);for(let u=0;u<h-p;u++){let d=r===1?c[h-1-u]-o:s-1-c[p+u],m=i.bestBefore(d),y=(m===-1?0:i.ending[m])+l;if(y>i.ending[d]&&(i.raise(d,y),a)){let S=a.count++;a.row[S]=f,a.column[S]=d,a.previous[S]=m===-1?-1:a.endingMatch[m],a.endingMatch[d]=S}}}}chain(e,t,r,o,s){let i=new Ct(o-r),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-r),count:0};this.sweep(e,t,1,r,o,i,a);let f=i.bestBefore(o-r);if(f===-1)return;this.total+=i.ending[f];let c=[];for(let l=a.endingMatch[f];l!==-1;l=a.previous[l])c.push([a.row[l],r+a.column[l]]);for(let l=c.length-1;l>=0;l--)this.pairs.push(c[l])}frontier(e,t,r,o,s){let i=new Ct(s-o);this.sweep(e,t,r,o,s,i);let a=new Float64Array(s-o+1);for(let f=0;f<s-o;f++)a[f+1]=Math.max(a[f],i.ending[f]);return a}split(e,t,r,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),f=this.frontier(r-1,t-1,-1,o,s),c=0,l=-1;for(let p=0;p<=i;p++){let h=a[p]+f[i-p];h>l&&(l=h,c=p)}return o+c}};function so(n,e,t){let r=new Fn(n,e,t);return r.solve(0,n.length,0,e.length),[r.pairs,r.total]}var Zs=100,Hn=4e6,Js=5e3,pe=15,ei=64,ti=8,ho=1,Gn=-4,fe=-6,Ce=-1,Qe=-(2**30),Pt=0,$n=1,uo=2;function $e(n,e,t){let r=n.at(-1);t>0&&(r?.[0]===e?r[1]+=t:n.push([e,t]))}function Rt(n,e,t){return n>=t&&n>=e?Pt:t>=e?uo:$n}function mo(n,e,t){let r=n.length,o=e.length,s=o+1,i=new Uint8Array((r+1)*s),a=new Int32Array(s).fill(Qe),f=new Int32Array(s).fill(Qe),c=new Int32Array(s).fill(Qe);a[0]=0;for(let d=1;d<=o;d++)c[d]=fe+(d-1)*Ce,i[d]=(d===1?Pt:uo)<<4;for(let d=1;d<=r;d++){let m=new Int32Array(s).fill(Qe),y=new Int32Array(s).fill(Qe),S=new Int32Array(s).fill(Qe);y[0]=fe+(d-1)*Ce,i[d*s]=(d===1?Pt:$n)<<2;let I=n.charCodeAt(d-1);for(let g=1;g<=o;g++){let v=Rt(a[g-1],f[g-1],c[g-1]);m[g]=Math.max(a[g-1],f[g-1],c[g-1])+(I===e.charCodeAt(g-1)?ho:Gn);let b=Rt(a[g]+fe,f[g]+Ce,c[g]+fe);y[g]=Math.max(a[g]+fe,f[g]+Ce,c[g]+fe);let E=Rt(m[g-1]+fe,y[g-1]+fe,S[g-1]+Ce);S[g]=Math.max(m[g-1]+fe,y[g-1]+fe,S[g-1]+Ce),i[d*s+g]=v|b<<2|E<<4}a=m,f=y,c=S}let l=[],p=r,h=o,u=Rt(a[o],f[o],c[o]);for(;p>0||h>0;){let d=i[p*s+h]>>2*u&3;u===Pt?(l.push(n[p-1]===e[h-1]?"=":"X"),p-=1,h-=1):u===$n?(l.push("I"),p-=1):(l.push("D"),h-=1),u=d}for(let d of l.reverse())$e(t,d,1)}function ni(n,e){let t=Math.abs(n-e);return(t===0?0:Math.min(-fe-(t-1)*Ce,-fe+10*Math.log2(t)))+(Math.min(n,e)>0?-Gn:0)}function go(n,e){let t=Math.abs(n-e);return t===0?0:.01*pe*t+.5*Math.log2(t)}function io(n,e,t){return{qs:n.qs+e,qe:n.qs+t,ts:n.flipped?n.te-t:n.ts+e,te:n.flipped?n.te-e:n.ts+t,flipped:n.flipped}}function ri(n,e,t){let r=n.qe-n.qs,o=[];for(let[a,f]of e){let c=Math.max(0,a-n.qs),l=Math.min(r,f-n.qs);c<l&&o.push([c,l])}for(let[a,f]of t){let c=Math.max(0,n.flipped?n.te-f:a-n.ts),l=Math.min(r,n.flipped?n.te-a:f-n.ts);c<l&&o.push([c,l])}if(o.length===0)return[n];o.sort((a,f)=>a[0]-f[0]);let s=[],i=0;for(let[a,f]of o)a-i>=pe&&s.push(io(n,i,a)),i=Math.max(i,f);return r-i>=pe&&s.push(io(n,i,r)),s}function Bn(n,e,t,r,o=1/0){let 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m=u[0],y=u.at(-1),{flipped:S}=m.run,I=S?a.flipped:a.forward;I.query.push([m.run.qs+m.trim,y.run.qe]),I.target.push(S?[y.run.ts,m.run.te-m.trim]:[m.run.ts+m.trim,y.run.te]);for(let{run:g,trim:v}of u)i.query.push([g.qs+v,g.qe]),i.target.push(g.flipped?[g.ts,g.te-v]:[g.ts+v,g.te]);f=f.flatMap(g=>{let v=g.flipped?a.flipped:a.forward;return ri(g,[...i.query,...v.query],[...i.target,...v.target])}).sort((g,v)=>g.qs-v.qs||g.ts-v.ts)}return s}function qn(n,e){let t=new Map;for(let s=0;s+pe<=e.length;s++){let i=e.slice(s,s+pe),a=t.get(i);a?a.push(s):t.set(i,[s])}let r=[],o=new Map;for(let s=0;s+pe<=n.length;s++){let i=t.get(n.slice(s,s+pe));if(i&&i.length<=ei)for(let a of i){let f=a-s,c=o.get(f);if(c&&s<=c.qe)c.qe=s+pe,c.te=a+pe;else{let l={qs:s,qe:s+pe,ts:a,te:a+pe,flipped:!1};o.set(f,l),r.push(l)}}}return r}function oi(n,e){return[...qn(n,e),...qn(n,It(e)).map(t=>({...t,ts:e.length-t.te,te:e.length-t.ts,flipped:!0}))]}function Mt(n,e,t,r,o){let s;for(let{run:i,trim:a}of n){let f=i.qs+a;if(s){let c=i.flipped?i.te-a:s.te,l=i.flipped?s.ts:i.ts+a,p=t.slice(c,l);o(e.slice(s.qe,f),i.flipped?It(p):p,r,s.qe,c)}$e(r,"=",i.qe-f),s=i}}function Dn(n,e,t){$e(t,"I",n.length),$e(t,"D",e.length)}function wo(n,e,t){n.length*e.length<=Hn?mo(n,e,t):Dn(n,e,t)}function zn(n,e,t,r=0){let[o]=n.length*e.length>Hn&&r<ti?Bn(qn(n,e),1/0,pe,go,1):[];if(!o){wo(n,e,t);return}let s=(f,c,l)=>{zn(f,c,l,r+1)},i=o[0].run,a=o.at(-1).run;s(n.slice(0,i.qs),e.slice(0,i.ts),t),Mt(o,n,e,t,s),s(n.slice(a.qe),e.slice(a.te),t)}function si(n,e,t){zn(n,e,t)}function ii(n,e,t){let r=[];Mt(n,e,t,r,si);let o=n[0],s=n.at(-1),{flipped:i}=o.run;return{queryStart:o.run.qs+o.trim,queryEnd:s.run.qe,targetStart:i?s.run.ts:o.run.ts+o.trim,targetEnd:i?o.run.te-o.trim:s.run.te,strand:i?"-":"+",edits:i?r.reverse():r,sharedBases:0}}function ai(n,e,t,r){let o=[];if(n.length*e.length<=Hn)mo(n,e,t);else{let s=Bn(oi(n,e),1/0,Math.max(r,pe),go),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>ii(a,n,e)),i){let a=(l,p,h,u,d)=>{o.some(y=>u<y.queryEnd&&y.queryStart<u+l.length||d<y.targetEnd&&y.targetStart<d+p.length)?wo(l,p,h):zn(l,p,h)},f=i[0].run,c=i.at(-1).run;a(n.slice(0,f.qs),e.slice(0,f.ts),t,0,0),Mt(i,n,e,t,a),a(n.slice(c.qe),e.slice(c.te),t,c.qe,c.te)}else Dn(n,e,t)}return o}function jn(n,e){let t=n.strand==="-",r=0,o=0;for(let[s,i]of n.edits)e(s,i,t?n.queryEnd-1-r:n.queryStart+r,n.targetStart+o),s!=="D"&&(r+=i),s!=="I"&&(o+=i)}function ao(n,e,t,r){let o=e==="query"&&n.strand==="-"?-1:1,s=0;return jn(n,(i,a,f,c)=>{let l=e==="query"?f:c,p=h=>{let u=l+o*h;return u>=t&&u<r};if(i==="="||i==="X")for(let h=0;h<a;h++)p(h)&&(s+=i==="="?ho:Gn);else if(i==="I"==(e==="query"))for(let h=0;h<a;h++)p(h)&&(s+=h===0?fe:Ce);else p(0)&&(s+=fe+(a-1)*Ce)}),s}function fo(n,e){return e==="query"?[n.queryStart,n.queryEnd]:[n.targetStart,n.targetEnd]}function fi(n,e){let t=n.strand==="-",r=[],o=0,s=0,i=0,a=0,f=new Uint8Array(n.queryEnd-n.queryStart);for(let[u,d]of n.shared)f.fill(1,u-n.queryStart,d-n.queryStart);let c=u=>f[u-n.queryStart]===1,l=()=>{$e(r,"I",o),$e(r,"D",s),o=0,s=0};jn(n,(u,d,m)=>{if(u==="I")o+=d;else if(u==="D")s+=d;else{for(let y=0;y<d;y++)e[i+y]?(o+=1,s+=1,c(t?m-y:m+y)&&(a+=1)):((o>0||s>0)&&l(),$e(r,u,1));i+=d}}),l();let p={I:0,D:0};for(;r[0]?.[0]==="I"||r[0]?.[0]==="D";){let[u,d]=r.shift();p[u]+=d}let h={I:0,D:0};for(;r.at(-1)?.[0]==="I"||r.at(-1)?.[0]==="D";){let[u,d]=r.pop();h[u]+=d}return r.length===0?void 0:{...n,queryStart:n.queryStart+(t?h.I:p.I),queryEnd:n.queryEnd-(t?p.I:h.I),targetStart:n.targetStart+p.D,targetEnd:n.targetEnd-h.D,edits:r,sharedBases:n.sharedBases-a}}function ci(n,e,t,r){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=n.map(c=>{let l=[];jn(c,(p,h,u,d)=>{if(p==="="||p==="X")for(let m=0;m<h;m++)l.push([c.strand==="-"?u-m:u+m,d+m])});for(let[p,h]of l)o.query[p]=Math.min(255,o.query[p]+1),o.target[h]=Math.min(255,o.target[h]+1);return l}),i={query:new Map,target:new Map};s.forEach((c,l)=>{for(let[p,h]of c)for(let[u,d]of[["query",p],["target",h]])if(o[u][d]>1){let m=i[u].get(d);m?m.at(-1)!==l&&m.push(l):i[u].set(d,[l])}});let a=new Map,f=(c,l,p)=>{let h=`${p}:${c}:${l}`,u=a.get(h);if(u===void 0){let[d,m]=fo(n[c],p),[y,S]=fo(n[l],p),I=Math.max(d,y),g=Math.min(m,S),[v,b]=[n[c],n[l]];u=[ao(b,p,I,g)-ao(v,p,I,g),b.sharedBases-v.sharedBases,c-l].find(M=>M!==0)>0,a.set(h,u)}return u};return n.flatMap((c,l)=>{let p=s[l],h=new Uint8Array(p.length);if(p.forEach(([m,y],S)=>{for(let[I,g]of[["query",m],["target",y]])!h[S]&&i[I].get(g)?.some(v=>v!==l&&f(l,v,I))&&(h[S]=1)}),!h.includes(1))return[c];let u=fi(c,h),d=u?.edits.reduce((m,[y,S])=>m+(y==="="?S:0),0)??0;return u&&d>=r?[u]:[]})}function co(n,e){return n.map(t=>{let r=e(O(t));return B(t)?It(r):r}).join("")}function lo(n,e){let t=[0];for(let r of n)t.push(t.at(-1)+e(O(r)).length);return t}function po(n){let e=new Map,t=new Map;n.forEach((i,a)=>{let f=O(i);e.has(f)?t.set(f,a):e.set(f,a)});let r=new Int32Array(n.length+1);for(let[i,a]of t)r[e.get(i)]+=1,r[a+1]-=1;let o=new Uint8Array(n.length),s=0;for(let i=0;i<n.length;i++)s+=r[i],o[i]=s>0?1:0;return o}function li(n,e,t,r){let o=po(n),s=po(e),i=new Map;e.forEach((p,h)=>{s[h]||i.set(O(p),[h])});let a=2*e.length,f=(p,h,u)=>p*a+2*h+(u?1:0),c=new Set;n.forEach((p,h)=>{for(let u of o[h]?[]:i.get(O(p))??[])c.add(f(h,u,B(p)!==B(e[u])))});let l=[];return n.forEach((p,h)=>{for(let u of o[h]?[]:i.get(O(p))??[]){let d=B(p)!==B(e[u]),m=d?-1:1;if(!c.has(f(h-1,u-m,d))){let y=h,S=u;for(;y<n.length&&S>=0&&S<e.length&&c.has(f(y,S,d));)y+=1,S+=m;let I=S-m;l.push({qs:t[h],qe:t[y],ts:r[Math.min(u,I)],te:r[Math.max(u,I)+1],flipped:d})}}}),l}function yo(n,e,t,r={}){let o=co(n,t),s=co(e,t),i=li(n,e,lo(n,t),lo(e,t)),a=r.minMatch??Zs,f=r.bases??!0,c=[];for(let l of Bn(i,r.maxGap??1/0,a,ni)){let p=[],h=l[0],u=l.at(-1),{flipped:d}=h.run;Mt(l,o,s,p,f?(y,S,I,g,v)=>{for(let b of ai(y,S,I,a)){let E=v+S.length;c.push({...b,queryStart:g+b.queryStart,queryEnd:g+b.queryEnd,targetStart:d?E-b.targetEnd:v+b.targetStart,targetEnd:d?E-b.targetStart:v+b.targetEnd,strand:d?"+":"-",edits:d?b.edits.reverse():b.edits,shared:[]})}}:Dn),c.push({queryStart:h.run.qs+h.trim,queryEnd:u.run.qe,targetStart:d?u.run.ts:h.run.ts+h.trim,targetEnd:d?h.run.te-h.trim:u.run.te,strand:d?"-":"+",edits:d?p.reverse():p,sharedBases:l.reduce((y,{run:S,trim:I})=>y+S.qe-S.qs-I,0),shared:l.map(({run:y,trim:S})=>[y.qs+S,y.qe])})}return ci(c,o.length,s.length,a).map(({shared:l,...p})=>p).sort((l,p)=>l.queryStart-p.queryStart)}function xo(n){return n.map(([e,t])=>`${t}${e}`).join("")}var ke=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 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t=e.identity.hapStart-n.identity.hapEnd,r=n.strand==="+"?e.refStart-n.refEnd:n.refStart-e.refEnd;return n.strand===e.strand&&t>=0&&r>=0?{insertion:t,deletion:r}:void 0}function ui(n,e,t){let[r,o]=n.strand==="+"?[n,e]:[e,n],s=r.edits.map(([c,l])=>[c,l]);vo(s,t.insertion,t.deletion);for(let[c,l]of o.edits)X(s,c,l);let i=n.identity.walkForward,[a,f]=i?[n,e]:[e,n];return{strand:n.strand,refStart:r.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...f.path],start:a.start,pieces:[...a.pieces,...f.pieces],soloAligned:[...a.soloAligned,...f.soloAligned],identity:{pathHandle:n.identity.pathHandle,name:n.identity.name,hapStart:n.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function mi(n,e,t){if(n.some(i=>i.weight!==void 0))return n;let r=new Map;n.forEach((i,a)=>{if(i.identity){let f=r.get(i.identity.pathHandle);f?f.push(a):r.set(i.identity.pathHandle,[a])}});let o=new Map,s=new Set;for(let i of r.values()){i.sort((l,p)=>n[l].identity.hapStart-n[p].identity.hapStart);let a=i[0],f=n[a],c=[];for(let l of i.slice(1)){let p=n[l],h=c.length===0?di(f,p):void 0;if(h){f=ui(f,p,h),s.add(l);continue}if(!e(p)){c.push(l);continue}let u=e(f)?t([f,...c.map(d=>n[d]),p]):void 0;if(u){f=u;for(let d of[...c,l])s.add(d)}else o.set(a,f),a=l,f=p;c=[]}o.set(a,f)}return n.flatMap((i,a)=>s.has(a)?[]:[o.get(a)??i])}function _t(n,e){return{node:n.path[e],offset:n.offsets[e]}}var gi=32768;function wi(n){let e=[...n].sort((r,o)=>r-o),t=[];for(let r of e){let o=t[t.length-1];o&&r-o[1]<=gi?o[1]=r:t.push([r,r])}return t}var Lt=class{records=new Map;paths=[];twinStarts=new Set;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;stats={orderedAlignments:0,lcsAlignments:0,identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},keep:void 0};db;limit;signal;constructor(e,t={}){this.db=e,this.limit=t.limit,this.signal=t.signal}get nodeCount(){return this.records.size/2}get pathCount(){return this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(ye(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new ke(this.limit);let t=await this.db.getRecord(ye(e,"forward")),r=await this.db.getRecord(ye(e,"reverse"));if(!t||!r)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(r.handle,r)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering ${xe(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${xe(t.name,t.name.fragment)} has not been indexed for random access`);let r=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,r);if(!o)throw new Error(`Path ${xe(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,r,o.pathOffset,o.pos)}async findPathPosition(e,t,r,o){let s=r,i=o;for(;;){await this.ensureNode(O(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let f=a.gbwt().lf(i.offset);if(!f)throw new Error(`Path ${xe(e.name,e.name.fragment)} does not contain offset ${t}`);i=f}}async aroundPosition(e,t,r){let o=O(e);await this.ensureNode(o);let s=this.record(e),i=Ue(e),a=new rt;return a.push(t,o,xt(i)),a.push(s.sequenceLen-t-1,o,bt(i)),this.insertContext(a,r)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,r){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,r)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let c=await this.db.indexedPositionsBetween(e,t,r),l=wi(c.map(p=>p.pos.node));await Promise.all(l.map(([p,h])=>this.db.prefetchRecords(p,h+2)))}}return o}async aroundInterval(e,t,r){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,r)}catch(o){throw o instanceof ke&&o.windowBp===void 0?new ke(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,r){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new rt;for(;;){let f=O(o.node),c=Ue(o.node);this.walkedBp=t-i,await this.ensureNode(f);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${f} of length ${l.sequenceLen}`);a.push(s,f,xt(c));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,f,bt(c));break}a.push(0,f,bt(c));let h=l.gbwt().lf(o.offset);if(!h)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=h,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,r)}async aroundNodes(e,t){let r=new rt;for(let o of e)await this.ensureNode(o),r.push(0,o,"left"),r.push(0,o,"right");return this.insertContext(r,t)}async insertContext(e,t){this.clearPaths();let r=new Set,o=new Set;for(let i of this.records.keys())o.add(O(i));let s=0;for(;e.size>0;){let[i,a,f]=e.pop(),c=`${a}:${f}`;if(r.has(c))continue;r.add(c),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=qr(f);if(!r.has(`${a}:${l}`)){let u=this.record(ye(a,Hr(f))),d=i+u.sequenceLen-1;d<=t&&e.push(d,a,l)}let p=this.record(ye(a,Gr(f))),h=i+1;if(h<=t)for(let u of p.successors()){let d=O(u),m=xt(Ue(u));r.has(`${d}:${m}`)||e.push(h,d,m)}}for(let i of o)this.records.delete(ye(i,"forward")),this.records.delete(ye(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let r=[e,K(t)],o=new Set([O(e),O(t)]),s=0;for(;r.length>0;){let i=r.pop(),a=O(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let f of this.record(i).successors()){let c=O(f);o.has(c)||(r.push(f,K(f)),o.add(c))}}return s}async extractSnarls(e){let t=0;for(let[r,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(r,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let r=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(r=!0,this.hasHandle(i)?We(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!r&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),r=t.find(o=>this.hasHandle(o));return r===void 0?!1:t.length>1||this.record(K(r)).successors().length>1}recordReader(e){let t=new Map;return async r=>{let o=this.records.get(r);if(o)return o;let s=t.get(r);if(!s){if(s=await this.db.getRecord(r),e?.(),!s)throw new Error(`Node record ${r} is missing from the database`);t.set(r,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async f=>{let c=f.successors(),l=c[0];return l===void 0?!1:c.length>1||(await e(K(l))).successors().length>1},r=async f=>{let c=await e(K(f));return c.next!==void 0?await t(c)?{kind:"snarl-exit",snarl:[K(f),c.next]}:{kind:"chain"}:(await e(f)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(f=>this.record(f).successors()),i,a=!1;for(;!a&&s.length>0;){let f=s.shift(),c=O(f);if(!this.hasHandle(f)&&!o.has(c)){o.add(c);let l=await r(f);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(ye(c,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let r=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((b,E)=>i.set(b,E));let a=new Int32Array(s+1),f=new Int32Array(s),c=[];for(let b=0;b<s;b++){let E=this.record(o[b]),M=E.gbwt().decompressArrays();f[b]=E.sequenceLen,c.push(M),a[b+1]=a[b]+M.nodes.length}let l=a[s],p=new Int32Array(l),h=new Int32Array(l),u=new Uint8Array(l);for(let b=0;b<s;b++){let E=c[b];p.set(E.nodes,a[b]),h.set(E.offsets,a[b])}c.length=0;for(let b=0;b<l;b++){let E=i.get(p[b]);E===void 0?p[b]=-1:(p[b]=E,u[a[E]+h[b]]=1)}let d=r===void 0?void 0:i.get(r.handle),m=r?.gbwtOffset,y,S=(b,E,M)=>{let L=[],_=0,T=0,P=-1,G=b,x=E;for(;;){G===d&&x===m&&(P=_),M&&(M.push(o[G]),L.push(x)),_+=1,T+=f[G];let C=a[G]+x,R=p[C];if(R<0)break;x=h[C],G=R}return{offsets:L,len:T,refAt:P,last:G}},I=(b,E,M,L)=>{L>=0&&(this.refId=this.paths.length,y=L),this.paths.push({path:b,offsets:E,len:M,weight:void 0,identity:void 0})},g=new Int32Array(s),v=d!==void 0&&B(o[d]);for(let b=0;b<s;b++){let E=o[b];if(!B(E)){let M=a[b],L=a[b+1]-M;for(let _=0;_<L;_++)if(u[M+_]===0){let T=[],{offsets:P,len:G,refAt:x,last:C}=S(b,_,T),R=o[C];if(x>=0||Ne(E,R)){if(I(T,P,G,x),!B(R)){let D=i.get(K(R));g[D]=g[D]+1}}else this.twinStarts.add(qe({node:E,offset:_}))}}}for(let b=0;b<s;b++){let E=o[b];if(B(E)){let M=a[b],L=a[b+1]-M,_=0;for(let P=0;P<L;P++)u[M+P]===0&&(_+=1);let T=!v&&_===g[b];for(let P=0;P<L;P++)if(u[M+P]===0){let G=T?void 0:S(b,P,void 0);if(G&&(G.refAt>=0||Ne(E,o[G.last]))){let x=[],{offsets:C,len:R,refAt:D}=S(b,P,x);I(x,C,R,D)}else this.twinStarts.add(qe({node:E,offset:P}))}}}if(r){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let b=this.paths[this.refId],E=r.nodeOffset;for(let L of b.path.slice(0,y))E+=this.record(L).sequenceLen;let M=r.seqOffset-E;this.refInterval=[M,M+b.len],b.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:M,hapEnd:M+b.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((o,s)=>Wn(o.path,s.path)||o.len-s.len);let t=[],r;for(let o of this.paths){let s=t[t.length-1];s&&Wn(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&Wn(o.path,e)===0&&(r=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=r}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],r=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of r)for(let i of s.path)o.add(O(i));for(let s of[...this.records.keys()])o.has(O(s))||this.records.delete(s);this.paths=r,this.refId=t===void 0?void 0:r.indexOf(t)}async extractChosenPaths(e,t,r){this.clearPaths();let o=e.position.seqOffset,s=await ro({db:this.db,records:this.records,referenceHandle:e.handle,referencePos:{node:e.position.handle,offset:e.position.gbwtOffset},referenceLeft:o-e.position.nodeOffset,window:{start:o,end:o+t},keep:r,signal:this.signal,prefetchReferenceRange:(c,l,p)=>this.prefetchReferenceRange(c,l,p)});if(this.stats.keep=s.stats,s.stats.fallback!==void 0)return!1;let i=await this.db.pathsByHandle(),a=c=>({path:c.handles,offsets:c.offsets,len:c.len,weight:void 0,identity:{pathHandle:c.pathHandle,name:c===s.reference?e.name:i.get(c.pathHandle).name,orientation:c.orientation,hapStart:c.hapStart,hapEnd:c.hapEnd}}),f=[s.reference,...s.pieces].sort(oo);return this.paths=f.map(a),this.refId=f.indexOf(s.reference),this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[s.reference.hapStart,s.reference.hapEnd],!0}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=Nn(this.sortedHandles());if(t.length===0)return;let r=new Map;for(let[d,m]of t)for(let y of await this.db.haplotypeSamplesInRange(d,m))r.set(qe(y),y);let o=d=>{let m=0,y=t.length-1;for(;m<y;){let I=m+y+1>>1;t[I][0]<=d?m=I:y=I-1}let S=t[m];return S[0]<=d&&d<=S[1]},s=new Map;this.paths.forEach((d,m)=>{d.path.length>0&&m!==this.refId&&s.set(qe(_t(d,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=r.size,this.paths.forEach((d,m)=>{m!==this.refId&&i.fragmentLengths.push(d.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),f=d=>(i.graphLookups+=1,a(d)),c=async(d,m)=>{if(o(d.node))return r.get(qe(d));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(d.node,d.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async d=>{let m=l.get(d);if(!m){let y=await this.db.getPath(d);if(!y)throw new Error(`Path ${d} is missing from the database`);m=y.name,l.set(d,m)}return m},h=(d,m,y)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.pathOffset-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.pathOffset+m+y},u=(d,m)=>d.orientation==="forward"?{pathHandle:d.pathHandle,orientation:"forward",base:d.hapStart-m}:{pathHandle:d.pathHandle,orientation:"reverse",base:d.hapEnd+m};for(let d=0;d<this.paths.length;d++){let m=this.paths[d];if(d===this.refId||m.identity)continue;let y=[],S=new Set,I={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(I);let g,v=0,b=d,E;for(;g===void 0;){if(this.signal?.throwIfAborted(),b!==void 0){if(S.has(b)){I.end="cycle";break}S.add(b);let P=this.paths[b];y.push({index:b,startBp:v}),I.fragments+=1;let G=v;for(let C=0;C<P.path.length;C++){let R=_t(P,C),D=r.get(qe(R)),V=this.record(R.node).sequenceLen;if(D){g=h(D,G,V);break}G+=V}if(v+=P.len,g){I.end="in-fragment sample";break}let x=_t(P,P.path.length-1);E=this.record(x.node).gbwt().lf(x.offset),b=void 0}if(E===void 0||E.node===0){I.end="endmarker";break}let M=qe(E),L=s.get(M);if(L!==void 0){let P=this.paths[L].identity;if(P){g=u(P,v),I.end="identified sibling";break}b=L;continue}this.records.has(E.node)&&(I.reentries+=1),this.twinStarts.has(M)&&(I.twinLandings+=1);let _=await c(E,I),T=await f(E.node);if(_){g=h(_,v,T.sequenceLen),I.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,I.steps+=1,v-y[y.length-1].startBp>4*e+4*T.sequenceLen){I.end="bound";break}v+=T.sequenceLen,E=T.gbwt().lf(E.offset)}if(g){I.pathHandle=g.pathHandle;let M=await p(g.pathHandle);for(let{index:L,startBp:_}of y){let T=this.paths[L];T.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:M,orientation:"forward",hapStart:g.base+_,hapEnd:g.base+_+T.len}:{pathHandle:g.pathHandle,name:M,orientation:"reverse",hapStart:g.base-_-T.len,hapEnd:g.base-_}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((r,o)=>{let s=t.get(r);s?s.push(o):t.set(r,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((r,o)=>{t.push(t[o]+this.record(r).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let r=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let f=0;f<e.length;f++){let c=r.get(e[f]);if(c){let l=hi(c,a);if(l===void 0)return;o[i]=f,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let r of e)t+=this.record(r).sequenceLen;return t}prefixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[o]).sequence,c=this.record(t[s]).sequence;for(;i<f.length&&a<c.length;){if(f[i]!==c[a])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}suffixMatches(e,t){let r=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let f=this.record(e[e.length-o-1]).sequence,c=this.record(t[t.length-s-1]).sequence;for(;i<f.length&&a<c.length;){if(f[f.length-i-1]!==c[c.length-a-1])return r;i+=1,a+=1,r+=1}i===f.length&&(o+=1,i=0),a===c.length&&(s+=1,a=0)}return r}align(e,t,r){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),X(r,"M",i),vo(r,o-i-a,s-i-a),X(r,"M",a)}sharedWeight(e,t){let r=this.refIndex(t),o=0;for(let s of e)r.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let r=this.orderedMatches(e,t);r?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=r??pi(so(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,h,u,d)=>{p===h?X(s,"D",i[d]-i[u]):u===d?X(s,"I",this.pathLen(e.slice(p,h))):this.align(e.slice(p,h),t.slice(u,d),s)},f=0,c=0,l=0;for(let p=0;p<o.count;p++){let h=o.pathAt[p],u=o.refAt[p];(c!==h||l!==u)&&a(c,h,l,u);let d=this.record(e[h]).sequenceLen;X(s,"M",d),f+=d,c=h+1,l=u+1}return a(c,e.length,l,t.length),{edits:s,matched:f,matches:o}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let r=this.paths[this.refId].path,o;if(Br(r))o={...this.editsAgainst(t.path,r),flipped:!1};else{let s=bo(t.path),i=this.sharedWeight(t.path,r);if(this.sharedWeight(s,r)===0)o={...this.editsAgainst(t.path,r),flipped:!1};else if(i===0)o={...this.editsAgainst(s,r),flipped:!0};else{let f=this.editsAgainst(t.path,r),c=this.editsAgainst(s,r);o=c.matched>f.matched?{...c,flipped:!0}:{...f,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,r])=>`${r}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,r=this.refPrefix(t)[t.length],o=(l,p,h,u)=>{let d=xi(l),m=this.paths[h[0]],y=this.paths[h[h.length-1]],S=m.identity,I=S?.orientation==="forward",[g,v]=I?[m,y]:[y,m];return{strand:p,refStart:e.start+d.leading,refEnd:e.start+r-d.trailing,edits:d.edits,weight:m.weight,path:h.flatMap(b=>this.paths[b].path),start:_t(m,0),pieces:h,soloAligned:u,identity:S===void 0?void 0:{pathHandle:S.pathHandle,name:S.name,hapStart:S.name.fragment+g.identity.hapStart,hapEnd:S.name.fragment+v.identity.hapEnd,walkForward:I}}},s=l=>l.soloAligned.reduce((p,h)=>p+h,0),i=l=>l.pieces.reduce((p,h)=>p+this.paths[h].len,0),a=l=>2*s(l)>=i(l),f=l=>{let p=l[0],h=l[l.length-1],u=p.identity.walkForward;if(l.some((x,C)=>x.strand!==p.strand||x.identity.walkForward!==u||C>0&&x.identity.hapStart<l[C-1].identity.hapEnd))return;let d=u?l:[...l].reverse(),m=d.flatMap(x=>x.pieces),y=d.flatMap(x=>x.soloAligned),S=p.strand==="+"!==u,I=m.map(x=>this.paths[x]),g=I.slice(1).map((x,C)=>{let R=I[C].identity;return u?x.identity.hapStart-R.hapEnd:R.hapStart-x.identity.hapEnd}),v=S?[...I].reverse():I,b=S?[...g].reverse():g,E=v.flatMap(x=>S?bo(x.path):x.path),{edits:M}=this.editsAgainst(E,t),L=So(M,v.map(x=>x.len)),_=new Map((S?[...m].reverse():m).map((x,C)=>[x,L[C]])),T=x=>2*x.pieces.reduce((C,R)=>C+_.get(R),0)>=s(x);if(!T(p)||!T(h))return;let P=[],G=0;return v.slice(0,-1).forEach((x,C)=>{G+=x.len,P.push([G,b[C]])}),o(bi(M,P),p.strand,m,y)},c=[];return this.paths.forEach((l,p)=>{if(p===this.refId)return;let{edits:h,flipped:u}=this.alignment(p),d=l.identity,m=d?d.orientation==="forward"!==u:!u;c.push(o(h,m?"+":"-",[p],So(h,[l.len])))}),mi(c,a,f).map(l=>{let{edits:p,identity:h,pieces:u,soloAligned:d,...m}=l,y={...m,cigar:Si(p)};return h?{...y,resolved:!0,name:h.name,label:xe({...h.name,fragment:h.hapStart},h.hapEnd),pathHandle:h.pathHandle,hapStart:h.hapStart,hapEnd:h.hapEnd}:{...y,resolved:!1}})}pairAlignments(e){let{target:t,query:r,...o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Ot(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),f=r?i(r):l=>!a(l),c=l=>this.record(ye(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>f(p.name)).flatMap(p=>yo(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:xo(h.edits),matches:h.edits.reduce((u,[d,m])=>u+(d==="="?m:0),0),columns:h.edits.reduce((u,[,d])=>u+d,0),sharedBases:h.sharedBases}))))}canonicalEdges(e){let t=[];for(let r of["forward","reverse"]){let o=ye(e,r);for(let s of this.record(o).successors())this.hasHandle(s)&&We(o,s)&&t.push([r==="reverse"?1:0,O(s),B(s)?1:0])}return t.sort((r,o)=>r[0]-o[0]||r[1]-o[1]||r[2]-o[2]),t.filter((r,o)=>o===0||r[0]!==t[o-1][0]||r[1]!==t[o-1][1]||r[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let r of this.sortedHandles())if(!B(r)){let o=O(r),s=`S	${o}	${this.record(r).sequence}
+`;for(let[i,a,f]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${f?"-":"+"}
+`;t.push(e.encode(s))}return Zr(t)}async toGFA(e={}){let t=e.cigar??!1,r=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Kr(Xr(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let c of o)B(c)||r.push(`S	${O(c)}	${this.record(c).sequence}`);let s=c=>B(c)?"-":"+";for(let c of o)for(let l of this.record(c).successors())this.hasHandle(l)&&We(c,l)&&r.push(`L	${O(c)}	${s(c)}	${O(l)}	${s(l)}	0M`);let i=(c,l,p,h,u)=>{let d=Ot(c,l).map(S=>`${B(S)?"<":">"}${O(S)}`).join(""),m=c.weight===void 0?"":`	WT:i:${c.weight}`,y=u===void 0?"":`	CG:Z:${u}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${h}	${d}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&r.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let f=1;return this.paths.forEach((c,l)=>{if(l!==this.refId){let p=e.names==="resolved"?c.identity:void 0,h=t?this.alignToRef(l):void 0;r.push(p?i(c,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,h):i(c,void 0,{sample:"unknown",contig:a,haplotype:f,fragment:0},c.len,h)),f+=1}}),`${r.join(`
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+`}outputPaths(e){let t=e.cigar??!1,r=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};r.push({info:this.paths[this.refId],identity:void 0,name:xe(i,this.refPath.fragment+this.refInterval[1]),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let f=e.names==="resolved"?i.identity:void 0;r.push({info:i,identity:f,name:f?xe({...f.name,fragment:f.name.fragment+f.hapStart},f.name.fragment+f.hapEnd):xe({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),r}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&We(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!B(s)).map(s=>({id:String(O(s)),sequence:this.record(s).sequence})),r=[];for(let[s,i]of this.outputEdges())r.push({from:String(O(s)),from_is_reverse:B(s),to:String(O(i)),to_is_reverse:B(i)});let o=this.outputPaths(e).map(s=>yi(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:r,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!B(i)),r=new Int32Array(t.length),o=[];t.forEach((i,a)=>{r[a]=O(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:r,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Ot(i.info,i.identity))}))}}};function Ot(n,e){return e?.orientation==="reverse"?n.path.map(t=>K(t)).reverse():n.path}function yi(n,e,t,r){return{name:t,...n.weight===void 0?{}:{weight:n.weight},...r===void 0?{}:{cigar:r},path:Ot(n,e).map(o=>({id:String(O(o)),is_reverse:B(o)}))}}function Wn(n,e){let t=Math.min(n.length,e.length);for(let r=0;r<t;r++){let o=n[r],s=e[r];if(o!==s)return o<s?-1:1}return 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c=f;for(;c>0;){for(;o<r&&i>=s;)o+=1,s+=e[o];let l=o<r?Math.min(c,s-i):c;a==="M"&&(t[o]+=l),i+=l,c-=l}}return t}function bi(n,e){let t=[],r=0,o=0;for(let[s,i]of n){if(s==="D"){X(t,s,i);continue}let a=r;for(;o<e.length&&e[o][0]<r+i;){let[f,c]=e[o];X(t,s,f-a),X(t,"I",c),a=f,o+=1}X(t,s,r+i-a),r+=i}for(;o<e.length;o++)X(t,"I",e[o][1]);return t}function Si(n){return n.map(([e,t])=>`${t}${e}`).join("")}async function Io(n,e,t,r,o){let s=new Lt(n,o);try{let i=await s.pathPosition(At(e,t));return await s.prefetchReferenceWalk(i,r-t),await s.aroundInterval(i.position,r-t,o.context??100),await s.extractSnarls(o.snarls??"none"),{subgraph:s,reference:i}}catch(i){throw i instanceof ke&&i.windowBp===void 0?new ke(i.limit,{windowBp:r-t,walkedBp:s.referenceWalkedBp??0}):i}}async function Ao(n,e,t,r,o={}){let{subgraph:s,reference:i}=await Io(n,e,t,r,o);return s.extractPaths(i,o.haplotypes??"all"),s}async function Eo(n,e,t,r,o){if(!n.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{subgraph:s,reference:i}=await Io(n,e,t,r,o),a=o.haplotypes??"all";return(a!=="all"||!await s.extractChosenPaths(i,r-t,o.keep))&&(s.extractPaths(i,a),await s.identifyPaths()),s.keepHaplotypes(o.keep),s}function Se(n,e){let t=0;for(let o=0;o<8;o++){let s=n[e+o];if(s===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*128+(s&127),(s&128)===0)return[t,e+o+1]}let r=n[e+8];if(r===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+r,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function vi(n,e,t){switch(t){case 1:return n.getInt8(e);case 2:return n.getInt16(e);case 3:return n.getInt8(e)<<16|n.getUint16(e+1);case 4:return n.getInt32(e);case 6:return n.getInt16(e)*4294967296+n.getUint32(e+2);default:{let r=n.getBigInt64(e);if(r>BigInt(Number.MAX_SAFE_INTEGER)||r<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${r} exceeds the 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Ei=4096,Ci=4096,$t=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let r=this.usable,o=t?Math.floor((r-12)*64/255)-23:r-35;if(e<=o)return e;let s=Math.floor((r-12)*32/255)-23,i=s+(e-s)%(r-4);return i<=o?i:s}async payload(e,t,r,o){let s=this.localPayloadSize(r,o);if(s===r)return e.subarray(t,t+r);let i=new Uint8Array(r);i.set(e.subarray(t,t+s),0);let a=s,f=Oe(e,t+s);for(;f!==0&&a<r;){let c=await this.pager.page(f),l=c.subarray(4,4+Math.min(this.usable-4,r-a));i.set(l,a),a+=l.length,f=Oe(c,0)}if(a!==r)throw new Error("SQLite overflow chain ended before the payload was complete");return i}async pageAt(e){let t=await this.pager.page(e);return{page:t,header:Ai(t,e===1?100:0)}}tableDepth(e,t){let r=this.tableDepths.get(e);return r||(r=(async()=>{let o=e;for(let s=0;;s++){let{page:i,header:a}=await this.pageAt(o);if(a.type===Nt)return s;if(a.type!==Ft)throw new Error("SQLite table b-tree contains an 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contains an index page");let i=0,a=s.cellCount;for(;i<a;){let f=i+a>>1,c=Re(o,s,f),[l]=Se(o,c+4);l<t?i=f+1:a=f}r=i===s.cellCount?s.rightChild:Oe(o,Re(o,s,i))}}async*tableScan(e){let{page:t,header:r}=await this.pageAt(e);if(r.type===Nt)for(let o=0;o<r.cellCount;o++){let s=Re(t,r,o),[i,a]=Se(t,s),[f,c]=Se(t,a);yield{rowid:f,values:Tt(await this.payload(t,c,i,!1))}}else{let o=[];for(let s=0;s<r.cellCount;s++)o.push(Oe(t,Re(t,r,s)));o.push(r.rightChild),this.pager.prefetch(o);for(let s of o)yield*this.tableScan(s)}}decodedCells(e,t){let r=this.decodedIndexPages.get(e);if(r)this.decodedIndexPages.delete(e);else if(r=new Array(t.cellCount),this.decodedIndexPages.size>=Ei){let o=this.decodedIndexPages.keys().next().value;o!==void 0&&this.decodedIndexPages.delete(o)}return this.decodedIndexPages.set(e,r),r}async indexCell(e,t,r,o){let s=this.decodedCells(e,r),i=s[o];if(!i){let a=Re(t,r,o),f=r.type===ot,[c,l]=Se(t,f?a+4:a);i={values:Tt(await this.payload(t,l,c,!0)),leftChild:f?Oe(t,a):0},s[o]=i}return i}async*indexScanFrom(e,t){let{page:r,header:o}=await this.pageAt(e),s=0,i=o.cellCount;for(;s<i;){let a=s+i>>1,f=await this.indexCell(e,r,o,a);Co(f.values,t)<0?s=a+1:i=a}for(let a=s;a<o.cellCount;a++){let f=await this.indexCell(e,r,o,a);o.type===ot&&(yield*this.indexScanFrom(f.leftChild,t)),yield f.values}o.type===ot&&(yield*this.indexScanFrom(o.rightChild,t))}async indexSeekLE(e,t){let r,o=e;for(;;){let{page:s,header:i}=await this.pageAt(o),a=0,f=i.cellCount,c=0;for(;a<f;){let l=a+f>>1,p=await this.indexCell(o,s,i,l);Co(p.values,t)<=0?(r=p.values,a=l+1):(c=p.leftChild,f=l)}if(i.type===Ro)return r;o=a===i.cellCount?i.rightChild:c}}};function Co(n,e){for(let t=0;t<e.length;t++){let r=n[t],o=e[t];if(typeof r!="number"||o===void 0)throw new Error("SQLite index key is not numeric");if(r!==o)return r<o?-1:1}return 0}var qt=class{blocks=new Map;blockSize;maxBlocks;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,r,o={}){this.source=e,this.pageSize=t,this.fileSize=r;let s=o.blockSize??65536;this.blockSize=Math.max(t,Math.ceil(s/t)*t),this.maxBlocks=o.maxBlocks??256}async read(e,t){let r=0;for(;;)try{let o=await this.source.read(e,t);return this.bytesFetched+=o.length,o}catch(o){if(r+=1,r>=3)throw o;await new Promise(s=>setTimeout(s,200*r))}}seed(e,t){t.length===Math.min(this.blockSize,this.fileSize-e*this.blockSize)&&this.blocks.set(e,Promise.resolve(t))}block(e){let t=this.blocks.get(e);if(t)return this.blocks.delete(e),this.blocks.set(e,t),t;let r=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-r),s=this.read(o,r);return this.fetches+=1,this.blocks.set(e,s),this.forgetOnFailure(s,[e]),this.evict(),s}prefetch(e){let t=[...new Set(e.map(o=>Math.floor((o-1)*this.pageSize/this.blockSize)))].filter(o=>!this.blocks.has(o)).sort((o,s)=>o-s),r=0;for(;r<t.length;){let o=r+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[r],o-r),r=o}}fetchRun(e,t){let r=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-r),s=this.read(o,r);this.fetches+=1;let i=[];for(let a=0;a<t;a++){let f=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(c=>c.subarray(f,f+this.blockSize)))}this.forgetOnFailure(s,i),this.evict()}forgetOnFailure(e,t){e.catch(()=>{for(let r of t)this.blocks.delete(r)})}evict(){for(;this.blocks.size>this.maxBlocks;){let e=this.blocks.keys().next().value;if(e===void 0)break;this.blocks.delete(e)}}async page(e){let t=(e-1)*this.pageSize;if(e<1||t+this.pageSize>this.fileSize)throw new Error(`SQLite page ${e} is outside the file`);let r=await this.block(Math.floor(t/this.blockSize)),o=t%this.blockSize;return r.subarray(o,o+this.pageSize)}};var st=class n{pager;btree;objects;constructor(e,t,r){this.pager=e,this.btree=t,this.objects=r}static async open(e,t={}){let{size:r}=await e.stat(),o=await e.read(Math.min(t.blockSize??65536,r),0),s=o.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3")throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),f=a.getUint16(16),c=f===1?65536:f,l=s[20]??0,p=a.getUint32(56);if(p!==1)throw new Error(`SQLite text encoding ${p} is not UTF-8`);let h=new qt(e,c,r,t);h.seed(0,o),h.fetches+=1,h.bytesFetched+=o.length;let u=new $t(h,l),d=new Map;for await(let{values:m}of u.tableScan(1)){let[y,S,I,g,v]=m;typeof y=="string"&&typeof S=="string"&&typeof I=="string"&&typeof g=="number"&&d.set(S,{type:y,name:S,tableName:I,rootPage:g,sql:typeof v=="string"?v:""})}return new n(h,u,d)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}indexOn(e){let t=[...this.objects.values()].find(r=>r.type==="index"&&r.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,r){return this.btree.prefetchRowidRange(this.rootPage(e),t,r)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Vn="GBZ-base version 4",Ht=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},Gt=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Vn}"`),this.found=e}},Bt=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,r,o,s){this.handle=e,this.edges=t,this.bwt=r,this.encodedSequence=o,this.next=s,this.sequenceLen=jr(o)}get id(){return O(this.handle)}get orientation(){return Ue(this.handle)}get sequence(){return this.decoded??=Ur(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new vt(this.edges,this.bwt)}};function Q(n,e){if(typeof n!="number")throw new Error(`${e} is not a number in the database`);return n}function Dt(n,e){if(typeof n!="string")throw new Error(`${e} is not text in the database`);return n}function Qn(n,e){if(!(n instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return n}function 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e!==void 0?pr(e):t!==void 0?ar(t):void 0}var na=le(et(),1),ra=le(vs(),1);var oa=le(et(),1);var sa=le(Bs(),1);var Is=le(et(),1),Le=class extends Is.SimpleFeature{get(e){return e==="mismatches"?mn(this.walkableCigar):e==="clipLengthAtStartOfRead"?this.clipLengthAtStartOfRead:e==="name"?super.get("name")??this.mate?.refName:super.get(e)}get mate(){return super.get("mate")}get walkableCigar(){let e=super.get("CIGAR"),t=super.get("coarseCigar");return typeof e=="string"?e:typeof t=="string"?ir(t):void 0}get clipLengthAtStartOfRead(){return this.mate?.start??0}forEachMismatch(e,t){let r=this.get("start"),o=t?.start===void 0?void 0:t.start-r,s=t?.end===void 0?void 0:t.end-r,i=this.get("cs");if(i)fr(i,e,o,s);else{let a=o??Number.NEGATIVE_INFINITY,f=s??Number.POSITIVE_INFINITY;for(let c of mn(this.walkableCigar))(c.type==="deletion"||c.type==="skip"?c.start<f&&c.start+c.length>a:c.start>=a&&c.start<=f)&&(c.type==="mismatch"?e(88,c.start,c.length,c.base,c.qual??-1,0,0):c.type==="insertion"?e(73,c.start,c.length,c.insertedBases??"",-1,0,c.insertlen):c.type==="deletion"?e(68,c.start,c.length,"",-1,0,0):c.type==="skip"&&e(78,c.start,c.length,"",-1,0,0))}}};var ia=["CIGAR","cs","coarseCigar","cg","cr"];function aa(n){return typeof n=="object"&&n!==null&&"refName"in n&&"start"in n&&"end"in n&&typeof n.refName=="string"&&typeof n.start=="number"&&typeof n.end=="number"}function fa(n){let e=n.get("mate");return aa(e)?e:void 0}function ca(n,e,t,r){let o=Math.max(n.start,r.start),s=Math.min(n.end,r.end),i=(e.end-e.start)/Math.max(n.end-n.start,1),a=l=>t===-1?e.end-(l-n.start)*i:e.start+(l-n.start)*i,f=Math.round(a(o)),c=Math.round(a(s));return s>o?{start:o,end:s,mateStart:Math.min(f,c),mateEnd:Math.max(f,c)}:void 0}function la(n,e,t,r,o){let s={start:n.get("start"),end:n.get("end")},i=n.get("strand")===-1?-1:1,a=s.start>=t.start&&s.end<=t.end,f=a&&r===void 0&&!o?void 0:ur(n);if(f===void 0){let c=a?{...s,mateStart:e.start,mateEnd:e.end}:ca(s,e,i,t);return c===void 0?[]:[c]}else return(r===void 0?[{...s,mateStart:e.start,mateEnd:e.end,cigar:f}]:dr(f,s.start,e.start,e.end,i,r)).flatMap(l=>{let p=hr(l.cigar,l.start,l.mateStart,l.mateEnd,i,t.start,t.end);return p===void 0?[]:[p]})}function pa(n,e,t,r,o,s){let i=`:${r.start}-${r.end}${o}`,a=n.toJSON(),f={...a,uniqueId:`${n.id()}${i}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};a.syntenyId!==void 0&&(f.syntenyId=`${String(a.syntenyId)}${i}`);for(let c of ia)delete f[c];return s&&t.cigar&&(f.alignmentOps=t.cigar),new Le(f)}function As(n,e,t,r=!1){let o=fa(n);if(o===void 0)return[n];{let s=la(n,o,e,t,r);return s.map((i,a)=>pa(n,o,i,e,s.length>1?`/${a}`:"",r))}}var gn=class extends Es.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,r={}){let{clipToRegion:o,splitAtGapBp:s,keepAlignment:i,...a}=r,f=o&&this.recordsAreAlignments,c=(0,Cs.createStatusFanOut)(a.statusCallback);return rr(t).pipe(Ze((l,p)=>this.getFeatures(l,{...a,statusCallback:c()}).pipe(Ze(h=>f?As(h,h.get("assemblyName")===l.assemblyName?l:{start:h.get("start"),end:h.get("end")},s,i):[h]),ln(),ct(h=>({index:p,features:h})))),ln(),Ze(l=>l.sort((p,h)=>p.index-h.index).flatMap(p=>p.features)))}};var yr=class extends Error{constructor(){super("no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation");this.name="NoHaplotypeIndexError"}},xr=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}},br=class extends Error{constructor(t,r){super(`the graph is cut on its reference, ${r}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${r} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Rs(n,e){let t=Ee(e);return n[t]??n[e.sample]??t}function ha(n,e){return`${Ee(n)}#${n.contig}@${e.start.node}.${e.start.offset}`}function da({alignment:n,assemblyName:e,refName:t,lane:r}){let{refStart:o,refEnd:s,strand:i,cigar:a}=n;if(!(!n.resolved||s<=o)){let{name:f,hapStart:c,hapEnd:l}=n,p=ha(f,n),h={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:f.contig,start:c,end:l,assemblyName:r}};return new Le(h)}}function ua({pair:n,lane:e,mateLane:t}){let r=`${Ee(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${Ee(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new Le({uniqueId:r,assemblyName:e,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:r,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var mr=n=>!("uri"in n)||n.uri!=="",Sr=class extends gn{constructor(){super(...arguments);this.graph=(0,gr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),r=this.getConf("haplotypeIndexLocation"),o=mr(r)?r:await Oo(t,this.pluginManager),s=await it.open((0,wn.openLocation)(t,this.pluginManager),o?{haplotypeIndex:(0,wn.openLocation)(o,this.pluginManager)}:{}),i=this.getConf("assemblyNames")[0];if(i===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let a=await Mn(s),f=wt({configured:this.getConf("referenceSample"),anchorPrefix:je(this,i),referenceSamples:a});return{db:s,anchor:i,referenceSample:f,referenceSamples:a}}});this.gaf=(0,gr.cachedSetup)({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),r=this.getConf(["readsIndex","location"]);return mr(t)?new zt((0,wn.openLocation)(t,this.pluginManager),mr(r)?$r(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,r){let{db:o,referenceSample:s}=await this.graph(r);return _n(o,s,t)}async getHaplotypes(t={}){let{db:r,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await r.paths()){let a=Ee(i.name),f=s.get(a);f?f.contigs.includes(i.name.contig)||f.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:r,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Rn(this),a=[];for(let f of await this.getHaplotypes(t))f.sample!==o&&a.push({name:Rs(i,f),label:f.prefix,group:f.sample});return{hasCoarseTier:!1,anchorAssemblyName:r,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:r,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:je(this,i),f=(await r.paths()).filter(c=>i===o?c.isIndexed&&c.name.sample===s:gt(Ee(c.name),a)).map(c=>c.name.contig);return[...new Set(f)]}keepPredicate(t,r){let o=t===void 0||t.length===0?void 0:t.map(s=>je(this,s));return o===void 0&&r===void 0?void 0:s=>Pn(s,o)&&(r===void 0||gt(Ee(s),r))}async getSubgraph(t,r={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:f,end:c}=t;if(i!==s)throw new br(i,s);let l=await this.referenceQuery(a,{}),p=this.keepPredicate(r.haplotypes);return kn(o,l,f,c,{context:this.getConf("context"),snarls:r.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:r.signal,...p===void 0?{}:{keep:p}})}async getReads(t,r={}){let o=await this.gaf(r);return o?o.readsOver(new Set(t),r):{records:[],total:0}}async laneHaplotypes(t,r){let o=je(this,t);return(await this.getHaplotypes(r)).filter(s=>gt(s.prefix,o))}async anchorFeatures(t,r){let{db:o}=await this.graph(r),{assemblyName:s,refName:i,start:a,end:f}=t,c=je(this,r.targetAssemblyName),l=Rn(this),p=this.keepPredicate(r.haplotypes,c),h=await this.referenceQuery(i,r),u=this.getConf("nodeLimit");return(h?await(0,wr.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${f.toLocaleString()}`,r.statusCallback,()=>o.getAlignmentsForRange(h,a,f,{context:this.getConf("context"),haplotypes:"all",limit:u,signal:r.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw yt(m,u,f-a)??m})):[]).flatMap(m=>{let y=m.resolved?da({alignment:m,assemblyName:s,refName:i,lane:Rs(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,r,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new xr(r);let{db:i}=await this.graph(o),{refName:a,start:f,end:c}=t,l=await this.laneHaplotypes(r,o),p=await this.laneHaplotypes(s,o),h=[...l,...p],u=await this.referenceQuery(a,o),d=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,v)=>i.getSubgraphForRange(g,v.start,v.end,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:d,signal:o.signal,keep:b=>h.some(E=>E.sample===b.sample&&E.haplotype===b.haplotype)}).catch(b=>{throw yt(b,d,c-f)??b}),S=u&&m&&l.length>0&&p.length>0?(await(0,wr.updateStatus)(`Reading ${r} against ${s}`,o.statusCallback,async()=>Promise.all((await Mr(i,u,f,c)).map(g=>y(u,g))))).filter(g=>g!==void 0):[];return S.every(g=>{let v=g.stats.keep;return v!==void 0&&v.fallback===void 0})?S.flatMap(g=>l.flatMap(v=>p.flatMap(b=>g.pairAlignments({target:v,query:b,bases:!1}).map(E=>ua({pair:E,lane:r,mateLane:s}))))):[]}getFeatures(t,r={}){return(0,Ps.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(r);if(!s.hasHaplotypeIndex)throw new yr;if(t.assemblyName===i){let a=r.queryAssemblyName===void 0?await this.anchorFeatures(t,r):await this.pairFeatures(t,r.queryAssemblyName,r);for(let f of a)o.next(f)}o.complete()},r.signal)}};export{br as HaplotypeWindowError,yr as NoHaplotypeIndexError,qs as NoReferenceSampleError,Hs as NodeLimitError,xr as PairTargetError,Sr as default,da as fragmentFeature,Ee as haplotypePrefix,Rs as laneAssemblyName,yt as nodeLimitError,ua as pairFeature,wt as resolveReferenceSample};
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