jbrowse-plugin-graphgenomeviewer 3.0.3 → 3.0.4

package/dist/chunks/GbzBaseSyntenyAdapter-6UTRY4CV.js

@@ -0,0 +1,8 @@
+import"./chunk-LGKM2PZH.js";import{a as so}from"./chunk-D7XFR2IV.js";import{a as bn,b as oo}from"./chunk-TN6FK5UD.js";import{a as ro}from"./chunk-KWAXLUPQ.js";import{a as Ae}from"./chunk-J4OLMLS5.js";import{a as Sn,d as Ee,e as ue,f as Lt}from"./chunk-F4C3BEPV.js";import{a as no,b as Y}from"./chunk-FY3BTKY4.js";var Qr=no((Mc,Wr)=>{Wr.exports=JBrowseExports["@jbrowse/core/util/installClearHoverOnSurfaceMove"]});function V(r,e){return 2*r+(e==="reverse"?1:0)}function A(r){return Math.floor(r/2)}function me(r){return r%2===0?"forward":"reverse"}function L(r){return r%2===1}function G(r){return r%2===0?r+1:r-1}function vn(r){return r==="left"?"right":"left"}function He(r){return r==="forward"?"left":"right"}function qe(r){return r==="forward"?"right":"left"}function In(r){return r==="left"?"forward":"reverse"}function An(r){return r==="right"?"forward":"reverse"}function ge(r,e){let t=A(r),n=A(e);return L(r)?n>t||n===t&&!L(e):n>=t}function En(r){return $e(r[0],r[r.length-1])}function $e(r,e){return r===void 0||e===void 0?!0:L(r)===L(e)?!L(r):ge(r,e)}var Ce=class{offset=0;bytes;constructor(e){this.bytes=e}get done(){return this.offset>=this.bytes.length}byte(){let e=this.bytes[this.offset];if(e!==void 0)return this.offset+=1,e}int(){let e=1,t=0;for(;this.offset<this.bytes.length;){let n=this.bytes[this.offset];if(this.offset+=1,t+=(n&127)*e,e*=128,(n&128)===0)return t}}},Cn=255,ao=256,Be=class{source;sigma;threshold;constructor(e,t){this.source=new Ce(e),this.sigma=t===0?Number.MAX_SAFE_INTEGER:t,this.threshold=this.sigma<Cn?Math.floor(ao/this.sigma):0}next(){if(this.sigma>=Cn){let o=this.source.int(),s=this.source.int();return o===void 0||s===void 0?void 0:{value:o,len:s+1}}let e=this.source.byte();if(e===void 0)return;let t=e%this.sigma,n=Math.floor(e/this.sigma)+1;if(n===this.threshold){let o=this.source.int();if(o===void 0)return;n+=o}return{value:t,len:n}}*[Symbol.iterator](){for(let e=this.next();e!==void 0;e=this.next())yield e}};function Rn(r){let e=new Ce(r),t=e.int();if(t===void 0||t===0)return[];let n=[],o=0;for(let s=0;s<t;s++){let i=e.int(),a=e.int();if(i===void 0||a===void 0)throw new Error("GBWT edge list ends early");o+=i,n.push({node:o,offset:a})}return n}var Ge=class{edges;bwt;constructor(e,t){this.edges=e,this.bwt=t}runs(){return new Be(this.bwt,this.edges.length)}edge(e){let t=this.edges[e];if(t===void 0)throw new Error(`GBWT run refers to edge rank ${e} of ${this.edges.length}`);return t}lf(e){let t=this.edges.map(o=>o.offset),n=0;for(let o of this.runs()){let s=this.edge(o.value),i=t[o.value];if(n+o.len>e)return s.node===0?void 0:{node:s.node,offset:i+(e-n)};t[o.value]=i+o.len,n+=o.len}}edgeTo(e){let t=0,n=this.edges.length;for(;t<n;){let o=t+n>>1,s=this.edges[o];if(s.node===e)return o;s.node<e?t=o+1:n=o}}offsetTo(e){if(e.node===0)return;let t=this.edgeTo(e.node);if(t===void 0)return;let n=this.edges[t].offset;if(n>e.offset)return;let o=0;for(let s of this.runs())if(o+=s.len,s.value===t&&(n+=s.len,n>e.offset))return o-(n-e.offset)}predecessorAt(e){let t=this.edges.map(o=>({node:o.node===0?0:G(o.node),count:0}));for(let o of this.runs()){let s=t[o.value];s&&(s.count+=o.len)}for(let o=1;o<t.length;o++){let s=t[o-1],i=t[o];A(s.node)===A(i.node)&&(t[o-1]=i,t[o]=s)}let n=0;for(let o of t)if(n+=o.count,n>e)return o.node===0?void 0:o.node}decompressArrays(){let e=this.edges.map(i=>i.offset),t=0;for(let i of this.runs())t+=i.len;let n=new Int32Array(t),o=new Int32Array(t),s=0;for(let i of this.runs()){let a=this.edge(i.value),c=e[i.value];for(let f=0;f<i.len;f++)n[s]=a.node,o[s]=c,c+=1,s+=1;e[i.value]=c}return{nodes:n,offsets:o}}decompress(){let e=this.edges.map(n=>n.offset),t=[];for(let n of this.runs()){let o=this.edge(n.value);for(let s=0;s<n.len;s++)t.push({node:o.node,offset:e[n.value]}),e[n.value]=e[n.value]+1}return t}};var fo=["","A","C","G","T","N"];function _n(r){let e=r[r.length-1];if(e===void 0)return 0;let t=e,n=0;for(let o=0;o<3&&t%6!==0;o++)t=Math.floor(t/6),n+=1;return 3*(r.length-1)+n}function Pn(r){let e="";for(let t of r){let n=t;for(let o=0;o<3;o++){let s=fo[n%6];if(s==="")return e;n=Math.floor(n/6),e+=s}}return e}var co={A:"T",C:"G",G:"C",T:"A",N:"N"};function De(r){let e="";for(let t=r.length-1;t>=0;t--)e+=co[r[t]]??"N";return e}function kn(r,e){let t=new Map;if(r!==void 0)for(let n of r.split(";")){let o=n.split(","),[s,i]=o;if(o.length!==2||!s||!i)throw new Error(`Invalid ${e} relationship: ${n}`);let a=t.get(s);a||(a=new Set,t.set(s,a)),a.add(i)}return t}function Ln(r){return{name:r.get("pggname"),subgraph:kn(r.get("subgraph"),"subgraph"),translation:kn(r.get("translation"),"translation")}}function Mn(r,e){for(let[t,n]of e){let o=r.get(t);o||(o=new Set,r.set(t,o));for(let s of n)o.add(s)}}function Tn(r,e){let t={name:r,subgraph:new Map,translation:new Map};return e.name!==void 0&&(t.subgraph.set(r,new Set([e.name])),Mn(t.subgraph,e.subgraph),Mn(t.translation,e.translation)),t}function On(r){return[...r.entries()].sort(([e],[t])=>e<t?-1:e>t?1:0).flatMap(([e,t])=>[...t].sort().map(n=>[e,n]))}function Nn(r){let e=[];r.name!==void 0&&e.push(`H	NM:Z:${r.name}`);for(let[t,n]of On(r.subgraph))e.push(`H	SG:Z:${t},${n}`);for(let[t,n]of On(r.translation))e.push(`H	TL:Z:${t},${n}`);return e}async function Fn(r){let e=r.reduce((s,i)=>s+i.length,0),t=new Uint8Array(e),n=0;for(let s of r)t.set(s,n),n+=s.length;let o=await globalThis.crypto.subtle.digest("SHA-256",t);return[...new Uint8Array(o)].map(s=>s.toString(16).padStart(2,"0")).join("")}var lo="_gbwt_ref";function q(r,e){return`${r.sample}#${r.haplotype}#${r.contig}[${r.fragment}-${e}]`}var po=/^([^#]+)#(\d+)#([^#]+?)(?:\[\d+-\d+\])?$/,ho=/^([^#]+?)(?:\[\d+-\d+\])?$/;function uo(r){let e=po.exec(r);if(e)return{sample:e[1],haplotype:Number(e[2]),contig:e[3]};let t=ho.exec(r);if(t)return{contig:t[1]};throw new Error(`"${r}" is not a path name; expected "sample#haplotype#contig" or a bare contig`)}function Hn(r){return typeof r=="string"?uo(r):r}function Re(r,e){return{sample:r.sample??lo,contig:r.contig,haplotype:r.haplotype??0,fragment:e}}function ze(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]<e?t=o+1:n=o}return t}var je=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 n=e;n>0;n-=n&-n){let o=this.tree[n];o!==-1&&(t===-1||this.ending[o]>this.ending[t])&&(t=o)}return t}raise(e,t){this.ending[e]=t;for(let n=e+1;n<this.tree.length;n+=n&-n){let o=this.tree[n];(o===-1||t>this.ending[o])&&(this.tree[n]=e)}}},Tt=class{pairs=[];total=0;a;b;weight;occurrences=new Map;constructor(e,t,n){this.a=e,this.b=t,this.weight=n,t.forEach((o,s)=>{let i=this.occurrences.get(o);i?i.push(s):this.occurrences.set(o,[s])})}solve(e,t,n,o){let s=0;for(;e+s<t&&n+s<o&&this.a[e+s]===this.b[n+s];)this.match(e+s,n+s),s+=1;let i=0;for(;t-i>e+s&&o-i>n+s&&this.a[t-i-1]===this.b[o-i-1];)i+=1;this.solveMiddle(e+s,t-i,n+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,n,o){if(e===t||n===o)return;let s=this.matchCount(e,t,n,o);if(s===0)return;if(s<=t-e+(o-n)){this.chain(e,t,n,o,s);return}let i=e+t>>1,a=this.split(e,i,t,n,o);this.solve(e,i,n,a),this.solve(i,t,a,o)}matchCount(e,t,n,o){let s=0;for(let i=e;i<t;i++){let a=this.occurrences.get(this.a[i]);a&&(s+=ze(a,o)-ze(a,n))}return s}sweep(e,t,n,o,s,i,a){for(let c=e;c!==t;c+=n){let f=this.occurrences.get(this.a[c]);if(!f)continue;let l=this.weight(this.a[c]),p=ze(f,o),d=ze(f,s);for(let h=0;h<d-p;h++){let u=n===1?f[d-1-h]-o:s-1-f[p+h],m=i.bestBefore(u),y=(m===-1?0:i.ending[m])+l;if(y>i.ending[u]&&(i.raise(u,y),a)){let x=a.count++;a.row[x]=c,a.column[x]=u,a.previous[x]=m===-1?-1:a.endingMatch[m],a.endingMatch[u]=x}}}}chain(e,t,n,o,s){let i=new je(o-n),a={row:new Int32Array(s),column:new Int32Array(s),previous:new Int32Array(s),endingMatch:new Int32Array(o-n),count:0};this.sweep(e,t,1,n,o,i,a);let c=i.bestBefore(o-n);if(c===-1)return;this.total+=i.ending[c];let f=[];for(let l=a.endingMatch[c];l!==-1;l=a.previous[l])f.push([a.row[l],n+a.column[l]]);for(let l=f.length-1;l>=0;l--)this.pairs.push(f[l])}frontier(e,t,n,o,s){let i=new je(s-o);this.sweep(e,t,n,o,s,i);let a=new Float64Array(s-o+1);for(let c=0;c<s-o;c++)a[c+1]=Math.max(a[c],i.ending[c]);return a}split(e,t,n,o,s){let i=s-o,a=this.frontier(e,t,1,o,s),c=this.frontier(n-1,t-1,-1,o,s),f=0,l=-1;for(let p=0;p<=i;p++){let d=a[p]+c[i-p];d>l&&(l=d,f=p)}return o+f}};function qn(r,e,t){let n=new Tt(r,e,t);return n.solve(0,r.length,0,e.length),[n.pairs,n.total]}var mo=100,Ht=4e6,go=5e3,D=15,yo=64,wo=8,Un=1,qt=-4,B=-6,ee=-1,ye=-(2**30),We=0,Nt=1,Wn=2;function te(r,e,t){let n=r.at(-1);t>0&&(n?.[0]===e?n[1]+=t:r.push([e,t]))}function Ue(r,e,t){return r>=t&&r>=e?We:t>=e?Wn:Nt}function Qn(r,e,t){let n=r.length,o=e.length,s=o+1,i=new Uint8Array((n+1)*s),a=new Int32Array(s).fill(ye),c=new Int32Array(s).fill(ye),f=new Int32Array(s).fill(ye);a[0]=0;for(let u=1;u<=o;u++)f[u]=B+(u-1)*ee,i[u]=(u===1?We:Wn)<<4;for(let u=1;u<=n;u++){let m=new Int32Array(s).fill(ye),y=new Int32Array(s).fill(ye),x=new Int32Array(s).fill(ye);y[0]=B+(u-1)*ee,i[u*s]=(u===1?We:Nt)<<2;let S=r.charCodeAt(u-1);for(let g=1;g<=o;g++){let b=Ue(a[g-1],c[g-1],f[g-1]);m[g]=Math.max(a[g-1],c[g-1],f[g-1])+(S===e.charCodeAt(g-1)?Un:qt);let w=Ue(a[g]+B,c[g]+ee,f[g]+B);y[g]=Math.max(a[g]+B,c[g]+ee,f[g]+B);let v=Ue(m[g-1]+B,y[g-1]+B,x[g-1]+ee);x[g]=Math.max(m[g-1]+B,y[g-1]+B,x[g-1]+ee),i[u*s+g]=b|w<<2|v<<4}a=m,c=y,f=x}let l=[],p=n,d=o,h=Ue(a[o],c[o],f[o]);for(;p>0||d>0;){let u=i[p*s+d]>>2*h&3;h===We?(l.push(r[p-1]===e[d-1]?"=":"X"),p-=1,d-=1):h===Nt?(l.push("I"),p-=1):(l.push("D"),d-=1),h=u}for(let u of l.reverse())te(t,u,1)}function xo(r,e){let t=Math.abs(r-e);return(t===0?0:Math.min(-B-(t-1)*ee,-B+10*Math.log2(t)))+(Math.min(r,e)>0?-qt:0)}function Yn(r,e){let t=Math.abs(r-e);return t===0?0:.01*D*t+.5*Math.log2(t)}function $n(r,e,t){return{qs:r.qs+e,qe:r.qs+t,ts:r.flipped?r.te-t:r.ts+e,te:r.flipped?r.te-e:r.ts+t,flipped:r.flipped}}function bo(r,e,t){let n=r.qe-r.qs,o=[];for(let[a,c]of e){let f=Math.max(0,a-r.qs),l=Math.min(n,c-r.qs);f<l&&o.push([f,l])}for(let[a,c]of t){let f=Math.max(0,r.flipped?r.te-c:a-r.ts),l=Math.min(n,r.flipped?r.te-a:c-r.ts);f<l&&o.push([f,l])}if(o.length===0)return[r];o.sort((a,c)=>a[0]-c[0]);let s=[],i=0;for(let[a,c]of o)a-i>=D&&s.push($n(r,i,a)),i=Math.max(i,c);return n-i>=D&&s.push($n(r,i,n)),s}function $t(r,e,t,n,o=1/0){let s=[],i={query:[],target:[]},a={forward:{query:[],target:[]},flipped:{query:[],target:[]}},c=[...r].sort((f,l)=>f.qs-l.qs||f.ts-l.ts);for(;c.length>0&&s.length<o;){let f=c.map(g=>g.qe-g.qs),l=new Int32Array(c.length).fill(-1),p=new Int32Array(c.length);for(let g=0;g<c.length;g++){let b=c[g],w=b.qe-b.qs;for(let v=g-1;v>=Math.max(0,g-go);v--){if(f[v]+w<=f[g])continue;let I=c[v];if(I.flipped===b.flipped&&I.qs<b.qs&&(b.flipped?b.te<I.te:I.ts<b.ts)){let C=Math.max(0,I.qe-b.qs,b.flipped?b.te-I.ts:I.te-b.ts),_=b.qs+C-I.qe,E=b.flipped?I.ts-(b.te-C):b.ts+C-I.te;if(C<w&&_<=e&&E<=e){let k=f[v]+w-C-n(_,E);k>f[g]&&(f[g]=k,l[g]=v,p[g]=C)}}}}let d=0;for(let g=1;g<c.length;g++)f[g]>f[d]&&(d=g);let h=[];for(let g=d;g>=0;g=l[g])h.push({run:c[g],trim:p[g]});if(h.reverse(),h.reduce((g,{run:b,trim:w})=>g+b.qe-b.qs-w,0)<t)break;s.push(h);let m=h[0],y=h.at(-1),{flipped:x}=m.run,S=x?a.flipped:a.forward;S.query.push([m.run.qs+m.trim,y.run.qe]),S.target.push(x?[y.run.ts,m.run.te-m.trim]:[m.run.ts+m.trim,y.run.te]);for(let{run:g,trim:b}of h)i.query.push([g.qs+b,g.qe]),i.target.push(g.flipped?[g.ts,g.te-b]:[g.ts+b,g.te]);c=c.flatMap(g=>{let b=g.flipped?a.flipped:a.forward;return bo(g,[...i.query,...b.query],[...i.target,...b.target])}).sort((g,b)=>g.qs-b.qs||g.ts-b.ts)}return s}function Ft(r,e){let t=new Map;for(let s=0;s+D<=e.length;s++){let i=e.slice(s,s+D),a=t.get(i);a?a.push(s):t.set(i,[s])}let n=[],o=new Map;for(let s=0;s+D<=r.length;s++){let i=t.get(r.slice(s,s+D));if(i&&i.length<=yo)for(let a of i){let c=a-s,f=o.get(c);if(f&&s<=f.qe)f.qe=s+D,f.te=a+D;else{let l={qs:s,qe:s+D,ts:a,te:a+D,flipped:!1};o.set(c,l),n.push(l)}}}return n}function So(r,e){return[...Ft(r,e),...Ft(r,De(e)).map(t=>({...t,ts:e.length-t.te,te:e.length-t.ts,flipped:!0}))]}function Qe(r,e,t,n,o){let s;for(let{run:i,trim:a}of r){let c=i.qs+a;if(s){let f=i.flipped?i.te-a:s.te,l=i.flipped?s.ts:i.ts+a,p=t.slice(f,l);o(e.slice(s.qe,c),i.flipped?De(p):p,n,s.qe,f)}te(n,"=",i.qe-c),s=i}}function Vn(r,e,t){r.length*e.length<=Ht?Qn(r,e,t):(te(t,"I",r.length),te(t,"D",e.length))}function Bt(r,e,t,n=0){let[o]=r.length*e.length>Ht&&n<wo?$t(Ft(r,e),1/0,D,Yn,1):[];if(!o){Vn(r,e,t);return}let s=(c,f,l)=>{Bt(c,f,l,n+1)},i=o[0].run,a=o.at(-1).run;s(r.slice(0,i.qs),e.slice(0,i.ts),t),Qe(o,r,e,t,s),s(r.slice(a.qe),e.slice(a.te),t)}function vo(r,e,t){Bt(r,e,t)}function Io(r,e,t){let n=[];Qe(r,e,t,n,vo);let o=r[0],s=r.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?n.reverse():n,sharedBases:0}}function Ao(r,e,t,n){let o=[];if(r.length*e.length<=Ht)Qn(r,e,t);else{let s=$t(So(r,e),1/0,Math.max(n,D),Yn),i=s.find(a=>!a[0].run.flipped);if(o=s.filter(a=>a[0].run.flipped).map(a=>Io(a,r,e)),i){let a=(l,p,d,h,u)=>{o.some(y=>h<y.queryEnd&&y.queryStart<h+l.length||u<y.targetEnd&&y.targetStart<u+p.length)?Vn(l,p,d):Bt(l,p,d)},c=i[0].run,f=i.at(-1).run;a(r.slice(0,c.qs),e.slice(0,c.ts),t,0,0),Qe(i,r,e,t,a),a(r.slice(f.qe),e.slice(f.te),t,f.qe,f.te)}else te(t,"I",r.length),te(t,"D",e.length)}return o}function Gt(r,e){let t=r.strand==="-",n=0,o=0;for(let[s,i]of r.edits)e(s,i,t?r.queryEnd-1-n:r.queryStart+n,r.targetStart+o),s!=="D"&&(n+=i),s!=="I"&&(o+=i)}function Bn(r,e,t,n){let o=e==="query"&&r.strand==="-"?-1:1,s=0;return Gt(r,(i,a,c,f)=>{let l=e==="query"?c:f,p=d=>{let h=l+o*d;return h>=t&&h<n};if(i==="="||i==="X")for(let d=0;d<a;d++)p(d)&&(s+=i==="="?Un:qt);else if(i==="I"==(e==="query"))for(let d=0;d<a;d++)p(d)&&(s+=d===0?B:ee);else p(0)&&(s+=B+(a-1)*ee)}),s}function Gn(r,e){return e==="query"?[r.queryStart,r.queryEnd]:[r.targetStart,r.targetEnd]}function Eo(r,e){let t=r.strand==="-",n=[],o=0,s=0,i=0,a=0,c=new Uint8Array(r.queryEnd-r.queryStart);for(let[h,u]of r.shared)c.fill(1,h-r.queryStart,u-r.queryStart);let f=h=>c[h-r.queryStart]===1,l=()=>{te(n,"I",o),te(n,"D",s),o=0,s=0};Gt(r,(h,u,m)=>{if(h==="I")o+=u;else if(h==="D")s+=u;else{for(let y=0;y<u;y++)e[i+y]?(o+=1,s+=1,f(t?m-y:m+y)&&(a+=1)):((o>0||s>0)&&l(),te(n,h,1));i+=u}}),l();let p={I:0,D:0};for(;n[0]?.[0]==="I"||n[0]?.[0]==="D";){let[h,u]=n.shift();p[h]+=u}let d={I:0,D:0};for(;n.at(-1)?.[0]==="I"||n.at(-1)?.[0]==="D";){let[h,u]=n.pop();d[h]+=u}return n.length===0?void 0:{...r,queryStart:r.queryStart+(t?d.I:p.I),queryEnd:r.queryEnd-(t?p.I:d.I),targetStart:r.targetStart+p.D,targetEnd:r.targetEnd-d.D,edits:n,sharedBases:r.sharedBases-a}}function Co(r,e,t,n){let o={query:new Uint8Array(e),target:new Uint8Array(t)},s=r.map(f=>{let l=[];Gt(f,(p,d,h,u)=>{if(p==="="||p==="X")for(let m=0;m<d;m++)l.push([f.strand==="-"?h-m:h+m,u+m])});for(let[p,d]of l)o.query[p]=Math.min(255,o.query[p]+1),o.target[d]=Math.min(255,o.target[d]+1);return l}),i={query:new Map,target:new Map};s.forEach((f,l)=>{for(let[p,d]of f)for(let[h,u]of[["query",p],["target",d]])if(o[h][u]>1){let m=i[h].get(u);m?m.at(-1)!==l&&m.push(l):i[h].set(u,[l])}});let a=new Map,c=(f,l,p)=>{let d=`${p}:${f}:${l}`,h=a.get(d);if(h===void 0){let[u,m]=Gn(r[f],p),[y,x]=Gn(r[l],p),S=Math.max(u,y),g=Math.min(m,x);h=Bn(r[f],p,S,g)<Bn(r[l],p,S,g),a.set(d,h)}return h};return r.flatMap((f,l)=>{let p=s[l],d=new Uint8Array(p.length);if(p.forEach(([m,y],x)=>{for(let[S,g]of[["query",m],["target",y]])!d[x]&&i[S].get(g)?.some(b=>b!==l&&c(l,b,S))&&(d[x]=1)}),!d.includes(1))return[f];let h=Eo(f,d),u=h?.edits.reduce((m,[y,x])=>m+(y==="="?x:0),0)??0;return h&&u>=n?[h]:[]})}function Dn(r,e){return r.map(t=>{let n=e(A(t));return L(t)?De(n):n}).join("")}function zn(r,e){let t=[0];for(let n of r)t.push(t.at(-1)+e(A(n)).length);return t}function jn(r){let e=new Map,t=new Map;r.forEach((i,a)=>{let c=A(i);e.has(c)?t.set(c,a):e.set(c,a)});let n=new Int32Array(r.length+1);for(let[i,a]of t)n[e.get(i)]+=1,n[a+1]-=1;let o=new Uint8Array(r.length),s=0;for(let i=0;i<r.length;i++)s+=n[i],o[i]=s>0?1:0;return o}function Ro(r,e,t,n){let o=jn(r),s=jn(e),i=new Map;e.forEach((p,d)=>{s[d]||i.set(A(p),[d])});let a=2*e.length,c=(p,d,h)=>p*a+2*d+(h?1:0),f=new Set;r.forEach((p,d)=>{for(let h of o[d]?[]:i.get(A(p))??[])f.add(c(d,h,L(p)!==L(e[h])))});let l=[];return r.forEach((p,d)=>{for(let h of o[d]?[]:i.get(A(p))??[]){let u=L(p)!==L(e[h]),m=u?-1:1;if(!f.has(c(d-1,h-m,u))){let y=d,x=h;for(;y<r.length&&x>=0&&x<e.length&&f.has(c(y,x,u));)y+=1,x+=m;let S=x-m;l.push({qs:t[d],qe:t[y],ts:n[Math.min(h,S)],te:n[Math.max(h,S)+1],flipped:u})}}}),l}function Kn(r,e,t,n={}){let o=Dn(r,t),s=Dn(e,t),i=Ro(r,e,zn(r,t),zn(e,t)),a=n.minMatch??mo,c=[];for(let f of $t(i,n.maxGap??1/0,a,xo)){let l=[],p=f[0],d=f.at(-1),{flipped:h}=p.run;Qe(f,o,s,l,(u,m,y,x,S)=>{for(let g of Ao(u,m,y,a)){let b=S+m.length;c.push({...g,queryStart:x+g.queryStart,queryEnd:x+g.queryEnd,targetStart:h?b-g.targetEnd:S+g.targetStart,targetEnd:h?b-g.targetStart:S+g.targetEnd,strand:h?"+":"-",edits:h?g.edits.reverse():g.edits,shared:[]})}}),c.push({queryStart:p.run.qs+p.trim,queryEnd:d.run.qe,targetStart:h?d.run.ts:p.run.ts+p.trim,targetEnd:h?p.run.te-p.trim:d.run.te,strand:h?"-":"+",edits:h?l.reverse():l,sharedBases:f.reduce((u,{run:m,trim:y})=>u+m.qe-m.qs-y,0),shared:f.map(({run:u,trim:m})=>[u.qs+m,u.qe])})}return Co(c,o.length,s.length,a).map(({shared:f,...l})=>l).sort((f,l)=>f.queryStart-l.queryStart)}function Xn(r){return r.map(([e,t])=>`${t}${e}`).join("")}var X=class extends Error{name="SubgraphLimitError";limit;windowBp;walkedBp;constructor(e,t){super(t===void 0?`Subgraph size limit of ${e} nodes exceeded`:`Subgraph size limit of ${e} nodes exceeded ${t.walkedBp} bp into a ${t.windowBp} bp window`),this.limit=e,this.windowBp=t?.windowBp,this.walkedBp=t?.walkedBp}};function Dt(r,e){return r[0]<e[0]||r[0]===e[0]&&(r[1]<e[1]||r[1]===e[1]&&r[2]<e[2])}var _e=class{heap=[];push(e,t,n){let o=this.heap;o.push([e,t,n]);let s=o.length-1;for(;s>0;){let i=s-1>>1;if(Dt(o[s],o[i]))[o[s],o[i]]=[o[i],o[s]],s=i;else break}}pop(){let e=this.heap,t=e[0],n=e.pop();if(e.length>0&&n!==void 0){e[0]=n;let o=0;for(;;){let s=2*o+1,i=s+1,a=o;if(s<e.length&&Dt(e[s],e[a])&&(a=s),i<e.length&&Dt(e[i],e[a])&&(a=i),a===o)break;[e[o],e[a]]=[e[a],e[o]],o=a}}return t}get size(){return this.heap.length}};function _o(r){let e=new Int32Array(r.length),t=new Int32Array(r.length);return r.forEach(([n,o],s)=>{e[s]=n,t[s]=o}),{pathAt:e,refAt:t,count:r.length}}function Po(r,e){let t=0,n=r.length;for(;t<n;){let o=t+n>>1;r[o]>e?n=o:t=o+1}return r[t]}function fe(r){return`${r.node}:${r.offset}`}function ko(r,e){let t=e.identity.hapStart-r.identity.hapEnd,n=r.strand==="+"?e.refStart-r.refEnd:r.refStart-e.refEnd;return r.strand===e.strand&&t>=0&&n>=0?{insertion:t,deletion:n}:void 0}function Mo(r,e,t){let[n,o]=r.strand==="+"?[r,e]:[e,r],s=n.edits.map(([f,l])=>[f,l]);Jn(s,t.insertion,t.deletion);for(let[f,l]of o.edits)z(s,f,l);let i=r.identity.walkForward,[a,c]=i?[r,e]:[e,r];return{strand:r.strand,refStart:n.refStart,refEnd:o.refEnd,edits:s,weight:void 0,path:[...a.path,...c.path],start:a.start,identity:{pathHandle:r.identity.pathHandle,name:r.identity.name,hapStart:r.identity.hapStart,hapEnd:e.identity.hapEnd,walkForward:i}}}function Oo(r){if(r.some(o=>o.weight!==void 0))return r;let e=new Map;r.forEach((o,s)=>{if(o.identity){let i=e.get(o.identity.pathHandle);i?i.push(s):e.set(o.identity.pathHandle,[s])}});let t=new Map,n=new Set;for(let o of e.values()){o.sort((a,c)=>r[a].identity.hapStart-r[c].identity.hapStart);let s=o[0],i=r[s];for(let a of o.slice(1)){let c=r[a],f=ko(i,c);f?(i=Mo(i,c,f),n.add(a)):(t.set(s,i),s=a,i=c)}t.set(s,i)}return r.flatMap((o,s)=>n.has(s)?[]:[t.get(s)??o])}function Ye(r,e){return{node:r.path[e],offset:r.offsets[e]}}var Lo=4096;function Zn(r){let e=[];for(let t of r){let n=e[e.length-1];n&&t-n[1]<=Lo?n[1]=t:e.push([t,t])}return e}var To=32768,No=65536;function Fo(r){let e=[...r].sort((n,o)=>n-o),t=[];for(let n of e){let o=t[t.length-1];o&&n-o[1]<=To?o[1]=n:t.push([n,n])}return t}var Pe=class{records=new Map;paths=[];twinStarts=new Set;refId;refPath;refHandle;refInterval;refIndexCache;refPrefixCache;walkedBp;stats={orderedAlignments:0,lcsAlignments:0,identificationSteps:0,identificationFetches:0,identification:{interval:0,scans:[],windowSamples:0,fragmentLengths:[],companionSeeks:0,companionMisses:0,graphLookups:0,graphFetches:0,chains:[]},anchorWalk:void 0};db;limit;signal;constructor(e,t={}){this.db=e,this.limit=t.limit,this.signal=t.signal}get nodeCount(){return this.records.size/2}get pathCount(){return this.paths.length}get referenceInterval(){return this.refInterval&&this.refPath?{name:this.refPath,start:this.refPath.fragment+this.refInterval[0],end:this.refPath.fragment+this.refInterval[1]}:void 0}hasNode(e){return this.records.has(V(e,"forward"))}hasHandle(e){return this.records.has(e)}record(e){let t=this.records.get(e);if(!t)throw new Error(`Subgraph has no record for handle ${e}`);return t}sortedHandles(){return[...this.records.keys()].sort((e,t)=>e-t)}async addNode(e){if(this.signal?.throwIfAborted(),this.limit!==void 0&&this.nodeCount>=this.limit)throw new X(this.limit);let t=await this.db.getRecord(V(e,"forward")),n=await this.db.getRecord(V(e,"reverse"));if(!t||!n)throw new Error(`Node ${e} does not exist in the graph`);this.records.set(t.handle,t),this.records.set(n.handle,n)}async ensureNode(e){this.hasNode(e)||await this.addNode(e)}clearPaths(){this.paths=[],this.twinStarts.clear(),this.refId=void 0,this.refPath=void 0,this.refHandle=void 0,this.refInterval=void 0,this.refIndexCache=void 0,this.refPrefixCache=void 0}async pathPosition(e){let t=await this.db.findPath(e);if(!t)throw new Error(`Cannot find a path covering ${q(e,e.fragment)}`);if(!t.isIndexed)throw new Error(`Path ${q(t.name,t.name.fragment)} has not been indexed for random access`);let n=e.fragment-t.name.fragment,o=await this.db.indexedPosition(t.handle,n);if(!o)throw new Error(`Path ${q(t.name,t.name.fragment)} has not been indexed for random access`);return this.findPathPosition(t,n,o.pathOffset,o.pos)}async findPathPosition(e,t,n,o){let s=n,i=o;for(;;){await this.ensureNode(A(i.node));let a=this.record(i.node);if(s+a.sequenceLen>t)return{position:{seqOffset:t,handle:i.node,nodeOffset:t-s,gbwtOffset:i.offset},name:e.name,handle:e.handle};s+=a.sequenceLen;let c=a.gbwt().lf(i.offset);if(!c)throw new Error(`Path ${q(e.name,e.name.fragment)} does not contain offset ${t}`);i=c}}async aroundPosition(e,t,n){let o=A(e);await this.ensureNode(o);let s=this.record(e),i=me(e),a=new _e;return a.push(t,o,He(i)),a.push(s.sequenceLen-t-1,o,qe(i)),this.insertContext(a,n)}prefetchReferenceWalk(e,t){return this.prefetchReferenceRange(e.handle,e.position.seqOffset,e.position.seqOffset+t)}async prefetchReferenceRange(e,t,n){let[o,s]=await Promise.all([this.db.indexedPosition(e,t),this.db.indexedPosition(e,n)]);if(o&&s){let i=o.pos.node,a=s.pos.node;if(!await this.db.prefetchRecords(Math.min(i,a),Math.max(i,a)+1)){let f=await this.db.indexedPositionsBetween(e,t,n),l=Fo(f.map(p=>p.pos.node));await Promise.all(l.map(([p,d])=>this.db.prefetchRecords(p,d+2)))}}return o}async aroundInterval(e,t,n){if(t===0)throw new Error("Interval length must be greater than 0");this.walkedBp=0;try{return await this.walkInterval(e,t,n)}catch(o){throw o instanceof X&&o.windowBp===void 0?new X(o.limit,{windowBp:t,walkedBp:this.walkedBp}):o}}get referenceWalkedBp(){return this.walkedBp}async walkInterval(e,t,n){let o={node:e.handle,offset:e.gbwtOffset},s=e.nodeOffset,i=t,a=new _e;for(;;){let c=A(o.node),f=me(o.node);this.walkedBp=t-i,await this.ensureNode(c);let l=this.record(o.node);if(s>=l.sequenceLen)throw new Error(`Offset ${s} in node ${c} of length ${l.sequenceLen}`);a.push(s,c,He(f));let p=l.sequenceLen-s;if(i<=p){a.push(i===p?0:p-i-1,c,qe(f));break}a.push(0,c,qe(f));let d=l.gbwt().lf(o.offset);if(!d)throw new Error(`No successor for GBWT position (${o.node}, ${o.offset})`);o=d,s=0,i-=p}return this.walkedBp=t,this.insertContext(a,n)}async aroundNodes(e,t){let n=new _e;for(let o of e)await this.ensureNode(o),n.push(0,o,"left"),n.push(0,o,"right");return this.insertContext(n,t)}async insertContext(e,t){this.clearPaths();let n=new Set,o=new Set;for(let i of this.records.keys())o.add(A(i));let s=0;for(;e.size>0;){let[i,a,c]=e.pop(),f=`${a}:${c}`;if(n.has(f))continue;n.add(f),o.delete(a),this.hasNode(a)||(await this.addNode(a),s+=1);let l=vn(c);if(!n.has(`${a}:${l}`)){let h=this.record(V(a,In(c))),u=i+h.sequenceLen-1;u<=t&&e.push(u,a,l)}let p=this.record(V(a,An(c))),d=i+1;if(d<=t)for(let h of p.successors()){let u=A(h),m=He(me(h));n.has(`${u}:${m}`)||e.push(d,u,m)}}for(let i of o)this.records.delete(V(i,"forward")),this.records.delete(V(i,"reverse"));return{inserted:s,removed:o.size}}async betweenNodes(e,t){this.clearPaths();let n=[e,G(t)],o=new Set([A(e),A(t)]),s=0;for(;n.length>0;){let i=n.pop(),a=A(i);this.hasNode(a)||(await this.addNode(a),s+=1);for(let c of this.record(i).successors()){let f=A(c);o.has(f)||(n.push(c,G(c)),o.add(f))}}return s}async extractSnarls(e){let t=0;for(let[n,o]of await this.overlappingSnarls(e))t+=await this.betweenNodes(n,o);return t}async overlappingSnarls(e){let t=[];if(e!=="none"){let n=!1;for(let o of this.sortedHandles()){let s=this.record(o),i=s.next;i!==void 0&&(n=!0,this.hasHandle(i)?ge(o,i)&&t.push([o,i]):e==="overlapping"&&this.isSnarlEntryInSubgraph(s)&&t.push([o,i]))}if(!n&&e==="overlapping"&&await this.db.hasChainLinks()){let o=await this.findCoveringSnarl();o&&t.push(o)}}return t}isSnarlEntryInSubgraph(e){let t=e.successors(),n=t.find(o=>this.hasHandle(o));return n===void 0?!1:t.length>1||this.record(G(n)).successors().length>1}recordReader(e){let t=new Map;return async n=>{let o=this.records.get(n);if(o)return o;let s=t.get(n);if(!s){if(s=await this.db.getRecord(n),e?.(),!s)throw new Error(`Node record ${n} is missing from the database`);t.set(n,s)}return s}}async findCoveringSnarl(){let e=this.recordReader(),t=async c=>{let f=c.successors(),l=f[0];return l===void 0?!1:f.length>1||(await e(G(l))).successors().length>1},n=async c=>{let f=await e(G(c));return f.next!==void 0?await t(f)?{kind:"snarl-exit",snarl:[G(c),f.next]}:{kind:"chain"}:(await e(c)).next!==void 0?{kind:"chain"}:{kind:"regular"}},o=new Set,s=this.sortedHandles().flatMap(c=>this.record(c).successors()),i,a=!1;for(;!a&&s.length>0;){let c=s.shift(),f=A(c);if(!this.hasHandle(c)&&!o.has(f)){o.add(f);let l=await n(c);if(l.kind==="snarl-exit")i=l.snarl,a=!0;else if(l.kind==="chain")a=!0;else for(let p of["forward","reverse"])s.push(...(await e(V(f,p))).successors())}}return i}extractPaths(e,t){if(this.clearPaths(),t==="none")return;let n=e?.position;this.refPath=e?.name,this.refHandle=e?.handle;let o=this.sortedHandles(),s=o.length,i=new Map;o.forEach((w,v)=>i.set(w,v));let a=new Int32Array(s+1),c=new Int32Array(s),f=[];for(let w=0;w<s;w++){let v=this.record(o[w]),I=v.gbwt().decompressArrays();c[w]=v.sequenceLen,f.push(I),a[w+1]=a[w]+I.nodes.length}let l=a[s],p=new Int32Array(l),d=new Int32Array(l),h=new Uint8Array(l);for(let w=0;w<s;w++){let v=f[w];p.set(v.nodes,a[w]),d.set(v.offsets,a[w])}f.length=0;for(let w=0;w<l;w++){let v=i.get(p[w]);v===void 0?p[w]=-1:(p[w]=v,h[a[v]+d[w]]=1)}let u=n===void 0?void 0:i.get(n.handle),m=n?.gbwtOffset,y,x=(w,v,I)=>{let R=[],C=0,_=0,E=-1,k=w,O=v;for(;;){k===u&&O===m&&(E=C),I&&(I.push(o[k]),R.push(O)),C+=1,_+=c[k];let N=a[k]+O,F=p[N];if(F<0)break;O=d[N],k=F}return{offsets:R,len:_,refAt:E,last:k}},S=(w,v,I,R)=>{R>=0&&(this.refId=this.paths.length,y=R),this.paths.push({path:w,offsets:v,len:I,weight:void 0,identity:void 0})},g=new Int32Array(s),b=u!==void 0&&L(o[u]);for(let w=0;w<s;w++){let v=o[w];if(!L(v)){let I=a[w],R=a[w+1]-I;for(let C=0;C<R;C++)if(h[I+C]===0){let _=[],{offsets:E,len:k,refAt:O,last:N}=x(w,C,_),F=o[N];if(O>=0||$e(v,F)){if(S(_,E,k,O),!L(F)){let H=i.get(G(F));g[H]=g[H]+1}}else this.twinStarts.add(fe({node:v,offset:C}))}}}for(let w=0;w<s;w++){let v=o[w];if(L(v)){let I=a[w],R=a[w+1]-I,C=0;for(let E=0;E<R;E++)h[I+E]===0&&(C+=1);let _=!b&&C===g[w];for(let E=0;E<R;E++)if(h[I+E]===0){let k=_?void 0:x(w,E,void 0);if(k&&(k.refAt>=0||$e(v,o[k.last]))){let O=[],{offsets:N,len:F,refAt:H}=x(w,E,O);S(O,N,F,H)}else this.twinStarts.add(fe({node:v,offset:E}))}}}if(n){if(y===void 0||this.refId===void 0)throw this.clearPaths(),new Error("Could not find the reference path");let w=this.paths[this.refId],v=n.nodeOffset;for(let R of w.path.slice(0,y))v+=this.record(R).sequenceLen;let I=n.seqOffset-v;this.refInterval=[I,I+w.len],w.identity={pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:I,hapEnd:I+w.len}}if(t==="distinct")this.distinctPaths();else if(t==="reference-only"){if(this.refId===void 0)throw new Error("Reference path is required for reference-only output");this.paths=[this.paths[this.refId]],this.refId=0}}distinctPaths(){let e=this.refId===void 0?void 0:this.paths[this.refId].path;this.paths.sort((o,s)=>zt(o.path,s.path)||o.len-s.len);let t=[],n;for(let o of this.paths){let s=t[t.length-1];s&&zt(s.path,o.path)===0?s.weight=(s.weight??0)+1:(e&&zt(o.path,e)===0&&(n=t.length),t.push({...o,weight:1}))}this.paths=t,this.refId=n}keepHaplotypes(e){let t=this.refId===void 0?void 0:this.paths[this.refId],n=this.paths.filter((s,i)=>i===this.refId||s.identity!==void 0&&e(s.identity.name)),o=new Set;for(let s of n)for(let i of s.path)o.add(A(i));for(let s of[...this.records.keys()])o.has(A(s))||this.records.delete(s);this.paths=n,this.refId=t===void 0?void 0:n.indexOf(t)}async walkHaplotypesFromAnchor(e,t,n,o,s){let i=e.position.seqOffset,a=i+t,c=Math.floor(i/n)*n,f=Math.min(n,No),l=4*(n+t)+f,p={spacing:n,anchorOffset:c,anchorNodeOffset:-1,anchorHandle:-1,referenceSteps:0,rows:0,walks:[],graphFetches:0,scans:[],scanRows:0,fallback:void 0,ms:{reference:0,rows:0,walks:0,scan:0,sampled:0}};this.stats.anchorWalk=p;let d=performance.now(),h=()=>{let M=performance.now(),U=M-d;return d=M,U};this.clearPaths(),this.records.clear();let u=this.recordReader(()=>{p.graphFetches+=1}),m=await this.db.haplotypeAnchor(e.handle,c);if(m===void 0)throw new Error(`The haplotype index names no anchor for ${q(e.name,e.name.fragment)} at offset ${c}; it was not built with anchors at ${n} bp for this graph`);p.anchorNodeOffset=m.pathOffset;let y=await this.prefetchReferenceRange(e.handle,m.pathOffset,a+f);if(!y)throw new Error(`Path ${q(e.name,e.name.fragment)} has not been indexed for random access`);let x=await this.walkReference(u,y,m,i,a,a+f),{anchor:S,refOffsetOf:g,refHandles:b,windowSteps:w}=x;p.anchorHandle=S.pos.node,p.referenceSteps=x.steps,this.walkedBp=t;let v=[],I=[],R=0;for(let M of w)await this.ensureNode(A(M.pos.node)),v.push(M.pos.node),I.push(M.pos.offset),R+=this.record(M.pos.node).sequenceLen;let C=w[0];if(C===void 0)throw new Error("The reference walk has no node in the window");this.refPath=e.name,this.refHandle=e.handle,this.refInterval=[C.refOffset,C.refOffset+R],this.refId=0,this.paths.push({path:v,offsets:I,len:R,weight:void 0,identity:{pathHandle:e.handle,name:e.name,orientation:"forward",hapStart:C.refOffset,hapEnd:C.refOffset+R}}),p.ms.reference=h();let _=await this.db.haplotypeSamplesAtNode(S.pos.node);p.rows=_.length,p.ms.rows=h();let E=_.find(M=>M.offset===S.pos.offset&&M.pathHandle===e.handle&&M.pathOffset===S.offset);if(E===void 0)throw new Error(`The haplotype index has no anchor row for ${q(e.name,e.name.fragment)} at offset ${S.offset} (node ${A(S.pos.node)}); it was not built with anchors at ${n} bp for this graph`);let k=await this.db.pathsByHandle(),O=M=>{let U=k.get(M);if(!U)throw new Error(`Path ${M} is missing from the database`);return U.name},N=new Set([e.handle]),F=new Map;for(let M of _)if(M!==E&&o(O(M.pathHandle))){let U=F.get(M.pathHandle);U?U.push(M):F.set(M.pathHandle,[M])}let H;for(let[M,U]of F)if(H===void 0){let he=ae=>Math.abs(ae.offset-E.offset);U.sort((ae,to)=>he(ae)-he(to));let de;for(let ae of U)N.has(M)||(de=await this.walkAndKeep(u,ae,"anchor",O(M),g,a,l,s,N,p));N.has(M)||(H=de)}p.ms.walks=h();let Ie=H===void 0?await this.samplesOfUnwalkedContigs(v,g,b,o,N,O,p):new Map;if(p.ms.scan=h(),Ie.size>0){await this.mapReferenceBefore(u,e.handle,Math.max(0,m.pathOffset-2*n),m.pathOffset,g,b);for(let[M,U]of Ie)if(H===void 0){let he=O(M),de;for(let ae of U)de??=await this.entryBefore(u,ae,g,b,this.refInterval[0],l);H=de===void 0?`no sample of ${q(he,he.fragment)} on the window's nodes runs with the reference`:await this.walkAndKeep(u,de,"sample",he,g,a,l,s,N,p)}p.ms.sampled=h()}return p.fallback=H,H}async walkAndKeep(e,t,n,o,s,i,a,c,f,l){let p=await this.walkFromRow(e,t,o,s,this.refInterval[0],i,a,c);l.walks.push({pathHandle:t.pathHandle,from:n,steps:p.steps,pieces:p.infos.length,end:p.end});let d;return p.end==="bound"||p.infos.length===0?d=`${q(o,t.pathOffset)} walked ${p.steps} steps from its ${n} without writing a walk through the window (${p.end})`:(f.add(t.pathHandle),this.paths.push(...p.infos)),d}async mapReferenceBefore(e,t,n,o,s,i){let a=await this.prefetchReferenceRange(t,n,o),c=a?.pos,f=a?.pathOffset??o;for(;c!==void 0&&c.node!==0&&f<o;){this.signal?.throwIfAborted();let l=await e(c.node),p=A(c.node);s.has(p)||(s.set(p,f),i.add(c.node)),f+=l.sequenceLen,c=l.gbwt().lf(c.offset)}}async runsWithReference(e,t,n,o,s){let i={node:t.node,offset:t.offset},a=0,c;for(;c===void 0;)if(this.signal?.throwIfAborted(),i===void 0||i.node===0||a>s)c=!1;else if(n.has(A(i.node)))c=o.has(i.node);else{let f=await e(i.node);a+=f.sequenceLen,i=f.gbwt().lf(i.offset)}return c}async entryBefore(e,t,n,o,s,i){let a=(await e(t.node)).sequenceLen,c=async(h,u)=>{let m=(await e(h.node)).sequenceLen;return{node:h.node,offset:h.offset,pathHandle:t.pathHandle,orientation:t.orientation,pathOffset:t.orientation==="forward"?t.pathOffset-u:t.pathOffset+a+u-m}},f={node:t.node,offset:t.offset},l=0,p,d=!await this.runsWithReference(e,t,n,o,i);for(;!d;){this.signal?.throwIfAborted();let h=n.get(A(f.node));if(h!==void 0&&h<s)p=await c(f,l),d=!0;else if(l>i)p={...t},d=!0;else{let m=(await e(G(f.node))).gbwt().predecessorAt(f.offset);if(m===void 0)p=await c(f,l),d=!0;else{let y=await e(m),x=y.gbwt().offsetTo(f);if(x===void 0)throw new Error(`No offset in ${m} leads to ${f.node}:${f.offset}`);f={node:m,offset:x},l+=y.sequenceLen}}}return p}async walkReference(e,t,n,o,s,i){let a=new Map,c=new Set,f=[],l,p=t.pos,d=t.pathOffset,h=0;for(;p!==void 0&&p.node!==0&&d<i;){this.signal?.throwIfAborted();let u=await e(p.node),m=d+u.sequenceLen;if(l===void 0&&d===n.pathOffset){if(p.node!==n.node)throw new Error(`The reference walk reaches node ${A(p.node)} at offset ${d} where the haplotype index names node ${A(n.node)} as the anchor`);l={pos:p,offset:d}}if(l!==void 0){h+=1;let y=A(p.node);a.has(y)||(a.set(y,d),c.add(p.node)),d<s&&m>o&&f.push({pos:p,refOffset:d})}d=m,p=u.gbwt().lf(p.offset)}if(l===void 0)throw new Error(`The reference walk from offset ${t.pathOffset} never starts a node at the anchor offset ${n.pathOffset}`);return{anchor:l,refOffsetOf:a,refHandles:c,windowSteps:f,steps:h}}async walkFromRow(e,t,n,o,s,i,a,c){let f=(await e(t.node)).sequenceLen,l=t.orientation==="forward"?t.pathOffset:t.pathOffset+f,p=[],d=[],h=[],u=0,m=0,y=0,x,S,g={node:t.node,offset:t.offset};for(;S===void 0;)if(this.signal?.throwIfAborted(),g===void 0||g.node===0)S=x===void 0?"before the window":"ended in the window";else if(m>a)S="bound";else{let w=o.get(A(g.node)),v=x!==void 0;if(w!==void 0&&w>=i)S=v?"through the window":"past the window";else{!v&&w!==void 0&&w>=s&&(x=m);let I=await e(g.node);if(x!==void 0){let R={pos:g,at:m,len:I.sequenceLen};w===void 0?(h.push(R),u+=R.len):(u>c&&w<s?(p.push(d),d=[]):d.push(...h),h=[],u=0,d.push(R))}y+=1,m+=I.sequenceLen,g=I.gbwt().lf(g.offset)}}p.push(d);let b=[];for(let w of p){let v=w[0],I=w[w.length-1];if(v!==void 0&&I!==void 0){let R=[],C=[],_=0;for(let O of w)await this.ensureNode(A(O.pos.node)),R.push(O.pos.node),C.push(O.pos.offset),_+=O.len;let E=v.at,k=I.at+I.len;b.push({path:R,offsets:C,len:_,weight:void 0,identity:t.orientation==="forward"?{pathHandle:t.pathHandle,name:n,orientation:"forward",hapStart:l+E,hapEnd:l+k}:{pathHandle:t.pathHandle,name:n,orientation:"reverse",hapStart:l-k,hapEnd:l-E}})}}return{steps:y,end:S,infos:b}}async samplesOfUnwalkedContigs(e,t,n,o,s,i,a){let c=Zn([...e].sort((l,p)=>l-p));a.scans=c;let f=new Map;for(let[l,p]of c){let d=await this.db.haplotypeSamplesInRange(l,p);a.scanRows+=d.length;for(let h of d){let u=t.has(A(h.node));if(!s.has(h.pathHandle)&&(!u||n.has(h.node))&&o(i(h.pathHandle))){let m=f.get(h.pathHandle)??[];u?m.unshift(h):m.push(h),f.set(h.pathHandle,m)}}}return f}async identifyPaths(){if(!this.db.hasHaplotypeIndex)throw new Error("The database has no HaplotypeSamples table; run gbz-haplotype-index on it");let e=await this.db.haplotypeSampleInterval()??4096,t=Zn(this.sortedHandles());if(t.length===0)return;let n=new Map;for(let[u,m]of t)for(let y of await this.db.haplotypeSamplesInRange(u,m))n.set(fe(y),y);let o=u=>{let m=0,y=t.length-1;for(;m<y;){let S=m+y+1>>1;t[S][0]<=u?m=S:y=S-1}let x=t[m];return x[0]<=u&&u<=x[1]},s=new Map;this.paths.forEach((u,m)=>{u.path.length>0&&m!==this.refId&&s.set(fe(Ye(u,0)),m)});let i=this.stats.identification;i.interval=e,i.scans=t,i.windowSamples=n.size,this.paths.forEach((u,m)=>{m!==this.refId&&i.fragmentLengths.push(u.len)});let a=this.recordReader(()=>{this.stats.identificationFetches+=1,i.graphFetches+=1}),c=u=>(i.graphLookups+=1,a(u)),f=async(u,m)=>{if(o(u.node))return n.get(fe(u));this.stats.identificationFetches+=1,i.companionSeeks+=1,m.seeks+=1;let y=await this.db.haplotypeSampleAt(u.node,u.offset);return y||(i.companionMisses+=1),y},l=new Map,p=async u=>{let m=l.get(u);if(!m){let y=await this.db.getPath(u);if(!y)throw new Error(`Path ${u} is missing from the database`);m=y.name,l.set(u,m)}return m},d=(u,m,y)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.pathOffset-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.pathOffset+m+y},h=(u,m)=>u.orientation==="forward"?{pathHandle:u.pathHandle,orientation:"forward",base:u.hapStart-m}:{pathHandle:u.pathHandle,orientation:"reverse",base:u.hapEnd+m};for(let u=0;u<this.paths.length;u++){let m=this.paths[u];if(u===this.refId||m.identity)continue;let y=[],x=new Set,S={fragments:0,steps:0,seeks:0,reentries:0,twinLandings:0,end:"endmarker",pathHandle:void 0};i.chains.push(S);let g,b=0,w=u,v;for(;g===void 0;){if(this.signal?.throwIfAborted(),w!==void 0){if(x.has(w)){S.end="cycle";break}x.add(w);let E=this.paths[w];y.push({index:w,startBp:b}),S.fragments+=1;let k=b;for(let N=0;N<E.path.length;N++){let F=Ye(E,N),H=n.get(fe(F)),Ie=this.record(F.node).sequenceLen;if(H){g=d(H,k,Ie);break}k+=Ie}if(b+=E.len,g){S.end="in-fragment sample";break}let O=Ye(E,E.path.length-1);v=this.record(O.node).gbwt().lf(O.offset),w=void 0}if(v===void 0||v.node===0){S.end="endmarker";break}let I=fe(v),R=s.get(I);if(R!==void 0){let E=this.paths[R].identity;if(E){g=h(E,b),S.end="identified sibling";break}w=R;continue}this.records.has(v.node)&&(S.reentries+=1),this.twinStarts.has(I)&&(S.twinLandings+=1);let C=await f(v,S),_=await c(v.node);if(C){g=d(C,b,_.sequenceLen),S.end="out-of-window sample";break}if(this.stats.identificationSteps+=1,S.steps+=1,b-y[y.length-1].startBp>4*e+4*_.sequenceLen){S.end="bound";break}b+=_.sequenceLen,v=_.gbwt().lf(v.offset)}if(g){S.pathHandle=g.pathHandle;let I=await p(g.pathHandle);for(let{index:R,startBp:C}of y){let _=this.paths[R];_.identity=g.orientation==="forward"?{pathHandle:g.pathHandle,name:I,orientation:"forward",hapStart:g.base+C,hapEnd:g.base+C+_.len}:{pathHandle:g.pathHandle,name:I,orientation:"reverse",hapStart:g.base-C-_.len,hapEnd:g.base-C}}}}}refIndex(e){if(this.refIndexCache===void 0){let t=new Map;e.forEach((n,o)=>{let s=t.get(n);s?s.push(o):t.set(n,[o])}),this.refIndexCache=t}return this.refIndexCache}refPrefix(e){if(this.refPrefixCache===void 0){let t=[0];e.forEach((n,o)=>{t.push(t[o]+this.record(n).sequenceLen)}),this.refPrefixCache=t}return this.refPrefixCache}orderedMatches(e,t){let n=this.refIndex(t),o=new Int32Array(e.length),s=new Int32Array(e.length),i=0,a=-1;for(let c=0;c<e.length;c++){let f=n.get(e[c]);if(f){let l=Po(f,a);if(l===void 0)return;o[i]=c,s[i]=l,i+=1,a=l}}return{pathAt:o,refAt:s,count:i}}pathLen(e){let t=0;for(let n of e)t+=this.record(n).sequenceLen;return t}prefixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let c=this.record(e[o]).sequence,f=this.record(t[s]).sequence;for(;i<c.length&&a<f.length;){if(c[i]!==f[a])return n;i+=1,a+=1,n+=1}i===c.length&&(o+=1,i=0),a===f.length&&(s+=1,a=0)}return n}suffixMatches(e,t){let n=0,o=0,s=0,i=0,a=0;for(;o<e.length&&s<t.length;){let c=this.record(e[e.length-o-1]).sequence,f=this.record(t[t.length-s-1]).sequence;for(;i<c.length&&a<f.length;){if(c[c.length-i-1]!==f[f.length-a-1])return n;i+=1,a+=1,n+=1}i===c.length&&(o+=1,i=0),a===f.length&&(s+=1,a=0)}return n}align(e,t,n){let o=this.pathLen(e),s=this.pathLen(t),i=this.prefixMatches(e,t),a=this.suffixMatches(e,t);i+a>o&&(a=o-i),i+a>s&&(a=s-i),z(n,"M",i),Jn(n,o-i-a,s-i-a),z(n,"M",a)}sharedWeight(e,t){let n=this.refIndex(t),o=0;for(let s of e)n.has(s)&&(o+=this.record(s).sequenceLen);return o}editsAgainst(e,t){let n=this.orderedMatches(e,t);n?this.stats.orderedAlignments+=1:this.stats.lcsAlignments+=1;let o=n??_o(qn(e,t,p=>this.record(p).sequenceLen)[0]),s=[],i=this.refPrefix(t),a=(p,d,h,u)=>{p===d?z(s,"D",i[u]-i[h]):h===u?z(s,"I",this.pathLen(e.slice(p,d))):this.align(e.slice(p,d),t.slice(h,u),s)},c=0,f=0,l=0;for(let p=0;p<o.count;p++){let d=o.pathAt[p],h=o.refAt[p];(f!==d||l!==h)&&a(f,d,l,h);let u=this.record(e[d]).sequenceLen;z(s,"M",u),c+=u,f=d+1,l=h+1}return a(f,e.length,l,t.length),{edits:s,matched:c}}alignment(e){let t=this.paths[e];if(this.refId===void 0||e===this.refId||!t)return;let n=this.paths[this.refId].path,o;if(En(n))o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else{let s=t.path.map(c=>G(c)).reverse(),i=this.sharedWeight(t.path,n);if(this.sharedWeight(s,n)===0)o={edits:this.editsAgainst(t.path,n).edits,flipped:!1};else if(i===0)o={edits:this.editsAgainst(s,n).edits,flipped:!0};else{let c=this.editsAgainst(t.path,n),f=this.editsAgainst(s,n);o=f.matched>c.matched?{edits:f.edits,flipped:!0}:{edits:c.edits,flipped:!1}}}return o}alignToRef(e){return this.alignment(e)?.edits.map(([t,n])=>`${n}${t}`).join("")}alignments(){let e=this.referenceInterval;if(this.refId===void 0||!e)throw new Error("Alignments need a reference path");let t=this.paths[this.refId].path,n=this.refPrefix(t)[t.length],o=[];return this.paths.forEach((s,i)=>{if(i===this.refId)return;let{edits:a,flipped:c}=this.alignment(i),f=0,l=0;for(;f<a.length&&a[f][0]==="D";)l+=a[f][1],f+=1;let p=a.length,d=0;for(;p>f&&a[p-1][0]==="D";)d+=a[p-1][1],p-=1;let h=s.identity,u=h?h.orientation==="forward"!==c:!c;o.push({strand:u?"+":"-",refStart:e.start+l,refEnd:e.start+n-d,edits:a.slice(f,p),weight:s.weight,path:s.path,start:Ye(s,0),identity:h===void 0?void 0:{pathHandle:h.pathHandle,name:h.name,hapStart:h.name.fragment+h.hapStart,hapEnd:h.name.fragment+h.hapEnd,walkForward:h.orientation==="forward"}})}),Oo(o).map(s=>{let{edits:i,identity:a,...c}=s,f={...c,cigar:qo(i)};return a?{...f,resolved:!0,name:a.name,label:q({...a.name,fragment:a.hapStart},a.hapEnd),pathHandle:a.pathHandle,hapStart:a.hapStart,hapEnd:a.hapEnd}:{...f,resolved:!1}})}pairAlignments(e){let{target:t,query:n,maxGap:o}=e,s=this.paths.flatMap(l=>{let{identity:p}=l;return p?[{name:p.name,start:p.name.fragment+p.hapStart,steps:Ke(l,p)}]:[]}),i=l=>p=>p.sample===l.sample&&p.haplotype===l.haplotype,a=i(t),c=n?i(n):l=>!a(l),f=l=>this.record(V(l,"forward")).sequence;return s.filter(l=>a(l.name)).flatMap(l=>s.filter(p=>c(p.name)).flatMap(p=>Kn(p.steps,l.steps,f,o===void 0?{}:{maxGap:o}).map(d=>({query:p.name,queryStart:p.start+d.queryStart,queryEnd:p.start+d.queryEnd,strand:d.strand,target:l.name,targetStart:l.start+d.targetStart,targetEnd:l.start+d.targetEnd,cigar:Xn(d.edits),matches:d.edits.reduce((h,[u,m])=>h+(u==="="?m:0),0),columns:d.edits.reduce((h,[,u])=>h+u,0),sharedBases:d.sharedBases}))))}canonicalEdges(e){let t=[];for(let n of["forward","reverse"]){let o=V(e,n);for(let s of this.record(o).successors())this.hasHandle(s)&&ge(o,s)&&t.push([n==="reverse"?1:0,A(s),L(s)?1:0])}return t.sort((n,o)=>n[0]-o[0]||n[1]-o[1]||n[2]-o[2]),t.filter((n,o)=>o===0||n[0]!==t[o-1][0]||n[1]!==t[o-1][1]||n[2]!==t[o-1][2])}async stableName(){let e=new TextEncoder,t=[];for(let n of this.sortedHandles())if(!L(n)){let o=A(n),s=`S	${o}	${this.record(n).sequence}
+`;for(let[i,a,c]of this.canonicalEdges(o))s+=`L	${o}	${i?"-":"+"}	${a}	${c?"-":"+"}
+`;t.push(e.encode(s))}return Fn(t)}async toGFA(e={}){let t=e.cigar??!1,n=[this.refPath?`H	VN:Z:1.1	RS:Z:${this.refPath.sample}`:"H	VN:Z:1.1",...Nn(Tn(await this.stableName(),await this.db.graphName()))],o=this.sortedHandles();for(let f of o)L(f)||n.push(`S	${A(f)}	${this.record(f).sequence}`);let s=f=>L(f)?"-":"+";for(let f of o)for(let l of this.record(f).successors())this.hasHandle(l)&&ge(f,l)&&n.push(`L	${A(f)}	${s(f)}	${A(l)}	${s(l)}	0M`);let i=(f,l,p,d,h)=>{let u=Ke(f,l).map(x=>`${L(x)?"<":">"}${A(x)}`).join(""),m=f.weight===void 0?"":`	WT:i:${f.weight}`,y=h===void 0?"":`	CG:Z:${h}`;return`W	${p.sample}	${p.haplotype}	${p.contig}	${p.fragment}	${d}	${u}${m}${y}`},a=this.refPath?.contig??"unknown";this.refId!==void 0&&this.refPath&&this.refInterval&&n.push(i(this.paths[this.refId],void 0,{...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]},this.refPath.fragment+this.refInterval[1],void 0));let c=1;return this.paths.forEach((f,l)=>{if(l!==this.refId){let p=e.names==="resolved"?f.identity:void 0,d=t?this.alignToRef(l):void 0;n.push(p?i(f,p,{...p.name,fragment:p.name.fragment+p.hapStart},p.name.fragment+p.hapEnd,d):i(f,void 0,{sample:"unknown",contig:a,haplotype:c,fragment:0},f.len,d)),c+=1}}),`${n.join(`
+`)}
+`}outputPaths(e){let t=e.cigar??!1,n=[],o=this.refPath?.contig??"unknown";if(this.refId!==void 0&&this.refPath&&this.refInterval){let i={...this.refPath,fragment:this.refPath.fragment+this.refInterval[0]};n.push({info:this.paths[this.refId],identity:void 0,name:q(i,this.refPath.fragment+this.refInterval[1]),cigar:void 0})}let s=1;return this.paths.forEach((i,a)=>{if(a===this.refId)return;let c=e.names==="resolved"?i.identity:void 0;n.push({info:i,identity:c,name:c?q({...c.name,fragment:c.name.fragment+c.hapStart},c.name.fragment+c.hapEnd):q({sample:"unknown",contig:o,haplotype:s,fragment:0},i.len),cigar:t?this.alignToRef(a):void 0}),s+=1}),n}*outputEdges(){for(let e of this.sortedHandles())for(let t of this.record(e).successors())this.hasHandle(t)&&ge(e,t)&&(yield[e,t])}toSubgraphJson(e={}){let t=this.sortedHandles().filter(s=>!L(s)).map(s=>({id:String(A(s)),sequence:this.record(s).sequence})),n=[];for(let[s,i]of this.outputEdges())n.push({from:String(A(s)),from_is_reverse:L(s),to:String(A(i)),to_is_reverse:L(i)});let o=this.outputPaths(e).map(s=>Ho(s.info,s.identity,s.name,s.cigar));return{nodes:t,edges:n,paths:o}}toCompactSubgraph(e={}){let t=this.sortedHandles().filter(i=>!L(i)),n=new Int32Array(t.length),o=[];t.forEach((i,a)=>{n[a]=A(i),o.push(this.record(i).sequence)});let s=[];for(let[i,a]of this.outputEdges())s.push(i,a);return{nodeIds:n,nodeSequences:o,edges:Int32Array.from(s),paths:this.outputPaths(e).map(i=>({name:i.name,weight:i.info.weight,cigar:i.cigar,steps:Int32Array.from(Ke(i.info,i.identity))}))}}};function Ke(r,e){return e?.orientation==="reverse"?r.path.map(t=>G(t)).reverse():r.path}function Ho(r,e,t,n){return{name:t,...r.weight===void 0?{}:{weight:r.weight},...n===void 0?{}:{cigar:n},path:Ke(r,e).map(o=>({id:String(A(o)),is_reverse:L(o)}))}}function zt(r,e){let t=Math.min(r.length,e.length);for(let n=0;n<t;n++){let o=r[n],s=e[n];if(o!==s)return o<s?-1:1}return r.length-e.length}function z(r,e,t){if(t===0)return;let n=r[r.length-1];n?.[0]===e?n[1]+=t:r.push([e,t])}function Ve(r){return r===0?0:6+(r-1)}function Jn(r,e,t){if(e===0)z(r,"D",t);else if(t===0)z(r,"I",e);else{let n=Math.min(e,t),o=4*n+Ve(e-n)+Ve(t-n),s=Ve(e)+Ve(t);o<=s?(z(r,"M",n),z(r,"I",e-n),z(r,"D",t-n)):(z(r,"I",e),z(r,"D",t))}}function qo(r){return r.map(([e,t])=>`${t}${e}`).join("")}async function Xe(r,e,t,n,o={}){let s=new Pe(r,o);try{let i=await s.pathPosition(Re(e,t));await s.prefetchReferenceWalk(i,n-t),await s.aroundInterval(i.position,n-t,o.context??100),await s.extractSnarls(o.snarls??"none"),s.extractPaths(i,o.haplotypes??"all")}catch(i){throw i instanceof X&&i.windowBp===void 0?new X(i.limit,{windowBp:n-t,walkedBp:s.referenceWalkedBp??0}):i}return s}async function er(r,e,t,n,o){if(!r.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let s=await r.haplotypeAnchorSpacing(),i,a;if(s!==void 0&&(o.haplotypes??"all")==="all"){let c=new Pe(r,o);try{let f=await c.pathPosition(Re(e,t));a=await c.walkHaplotypesFromAnchor(f,n-t,s,o.keep,o.context??100)}catch(f){throw f instanceof X&&f.windowBp===void 0?new X(f.limit,{windowBp:n-t,walkedBp:c.referenceWalkedBp??0}):f}if(a===void 0)i=c;else{a=`${a}; identified from the per-path samples instead`;let f=await Xe(r,e,t,n,o);await f.identifyPaths(),f.keepHaplotypes(o.keep),f.stats.anchorWalk=c.stats.anchorWalk,f.stats.anchorWalk&&(f.stats.anchorWalk.fallback=a),i=f}}else i=await Xe(r,e,t,n,o),await i.identifyPaths(),i.keepHaplotypes(o.keep);return i}function Z(r,e){let t=0;for(let o=0;o<8;o++){let s=r[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 n=r[e+8];if(n===void 0)throw new Error("SQLite varint runs past the end of the buffer");if(t=t*256+n,!Number.isSafeInteger(t))throw new Error("SQLite varint exceeds the safe integer range");return[t,e+9]}function $o(r,e,t){switch(t){case 1:return r.getInt8(e);case 2:return r.getInt16(e);case 3:return r.getInt8(e)<<16|r.getUint16(e+1);case 4:return r.getInt32(e);case 6:return r.getInt16(e)*4294967296+r.getUint32(e+2);default:{let n=r.getBigInt64(e);if(n>BigInt(Number.MAX_SAFE_INTEGER)||n<BigInt(Number.MIN_SAFE_INTEGER))throw new Error(`SQLite integer ${n} exceeds the safe integer range`);return Number(n)}}}var Bo=new TextDecoder;function Ze(r){let[e,t]=Z(r,0),n=[],o=t;for(;o<e;){let[a,c]=Z(r,o);n.push(a),o=c}let s=new DataView(r.buffer,r.byteOffset,r.byteLength),i=e;return n.map(a=>{if(a===0)return null;if(a>=1&&a<=6){let c=a<=4?a:a===5?6:8,f=$o(s,i,c);return i+=c,f}if(a===7){let c=s.getFloat64(i);return i+=8,c}if(a===8)return 0;if(a===9)return 1;if(a>=12){let c=a-12>>1,f=r.subarray(i,i+c);return i+=c,a%2===0?f:Bo.decode(f)}throw new Error(`SQLite serial type ${a} is reserved`)})}var ke=2,et=5,nr=10,Je=13;function rr(r,e){return r[e]*256+r[e+1]}function oe(r,e){return r[e]*16777216+r[e+1]*65536+r[e+2]*256+r[e+3]}function Go(r,e){let t=r[e];if(t!==ke&&t!==et&&t!==nr&&t!==Je)throw new Error(`SQLite page has unknown b-tree type ${t}`);let n=t===ke||t===et;return{type:t,cellCount:rr(r,e+3),rightChild:n?oe(r,e+8):0,cellPointers:e+(n?12:8)}}function ne(r,e,t){return rr(r,e.cellPointers+2*t)}var Do=4096,zo=4096,tt=class{usable;pager;decodedIndexPages=new Map;tableDepths=new Map;constructor(e,t){this.pager=e,this.usable=e.pageSize-t}localPayloadSize(e,t){let n=this.usable,o=t?Math.floor((n-12)*64/255)-23:n-35;if(e<=o)return e;let s=Math.floor((n-12)*32/255)-23,i=s+(e-s)%(n-4);return i<=o?i:s}async payload(e,t,n,o){let s=this.localPayloadSize(n,o);if(s===n)return e.subarray(t,t+n);let i=new Uint8Array(n);i.set(e.subarray(t,t+s),0);let a=s,c=oe(e,t+s);for(;c!==0&&a<n;){let f=await this.pager.page(c),l=f.subarray(4,4+Math.min(this.usable-4,n-a));i.set(l,a),a+=l.length,c=oe(f,0)}if(a!==n)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:Go(t,e===1?100:0)}}tableDepth(e,t){let n=this.tableDepths.get(e);return n||(n=(async()=>{let o=e;for(let s=0;;s++){let{page:i,header:a}=await this.pageAt(o);if(a.type===Je)return s;if(a.type!==et)throw new Error("SQLite table b-tree contains an index page");let c=this.childIndexFor(i,a,t);o=c===a.cellCount?a.rightChild:oe(i,ne(i,a,c))}})(),this.tableDepths.set(e,n),n.catch(()=>this.tableDepths.delete(e))),n}childIndexFor(e,t,n){let o=0,s=t.cellCount;for(;o<s;){let i=o+s>>1,[a]=Z(e,ne(e,t,i)+4);a<n?o=i+1:s=i}return o}async prefetchRowidRange(e,t,n){let o=await this.tableDepth(e,t),s=[e];for(let i=0;i<o;i++){let a=await Promise.all(s.map(f=>this.pageAt(f))),c=[];if(a.forEach(({page:f,header:l},p)=>{let d=p===0?this.childIndexFor(f,l,t):0,h=p===a.length-1?this.childIndexFor(f,l,n):l.cellCount;for(let u=d;u<=h;u++)c.push(u===l.cellCount?l.rightChild:oe(f,ne(f,l,u)))}),c.length>zo)return!1;this.pager.prefetch(c),s=c}return!0}async tableRowid(e,t){let n=e;for(;;){let{page:o,header:s}=await this.pageAt(n);if(s.type===Je){let c=0,f=s.cellCount;for(;c<f;){let l=c+f>>1,p=ne(o,s,l),[d,h]=Z(o,p),[u,m]=Z(o,h);if(u===t)return Ze(await this.payload(o,m,d,!1));u<t?c=l+1:f=l}return}if(s.type!==et)throw new Error("SQLite table b-tree contains an index page");let i=0,a=s.cellCount;for(;i<a;){let c=i+a>>1,f=ne(o,s,c),[l]=Z(o,f+4);l<t?i=c+1:a=c}n=i===s.cellCount?s.rightChild:oe(o,ne(o,s,i))}}async*tableScan(e){let{page:t,header:n}=await this.pageAt(e);if(n.type===Je)for(let o=0;o<n.cellCount;o++){let s=ne(t,n,o),[i,a]=Z(t,s),[c,f]=Z(t,a);yield{rowid:c,values:Ze(await this.payload(t,f,i,!1))}}else{let o=[];for(let s=0;s<n.cellCount;s++)o.push(oe(t,ne(t,n,s)));o.push(n.rightChild),this.pager.prefetch(o);for(let s of o)yield*this.tableScan(s)}}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>=Do){let o=this.decodedIndexPages.keys().next().value;o!==void 0&&this.decodedIndexPages.delete(o)}return this.decodedIndexPages.set(e,n),n}async indexCell(e,t,n,o){let s=this.decodedCells(e,n),i=s[o];if(!i){let a=ne(t,n,o),c=n.type===ke,[f,l]=Z(t,c?a+4:a);i={values:Ze(await this.payload(t,l,f,!0)),leftChild:c?oe(t,a):0},s[o]=i}return i}async*indexScanFrom(e,t){let{page:n,header:o}=await this.pageAt(e),s=0,i=o.cellCount;for(;s<i;){let a=s+i>>1,c=await this.indexCell(e,n,o,a);tr(c.values,t)<0?s=a+1:i=a}for(let a=s;a<o.cellCount;a++){let c=await this.indexCell(e,n,o,a);o.type===ke&&(yield*this.indexScanFrom(c.leftChild,t)),yield c.values}o.type===ke&&(yield*this.indexScanFrom(o.rightChild,t))}async indexSeekLE(e,t){let n,o=e;for(;;){let{page:s,header:i}=await this.pageAt(o),a=0,c=i.cellCount,f=0;for(;a<c;){let l=a+c>>1,p=await this.indexCell(o,s,i,l);tr(p.values,t)<=0?(n=p.values,a=l+1):(f=p.leftChild,c=l)}if(i.type===nr)return n;o=a===i.cellCount?i.rightChild:f}}};function tr(r,e){for(let t=0;t<e.length;t++){let n=r[t],o=e[t];if(typeof n!="number"||o===void 0)throw new Error("SQLite index key is not numeric");if(n!==o)return n<o?-1:1}return 0}var nt=class{blocks=new Map;blockSize;maxBlocks;bytesFetched=0;fetches=0;source;pageSize;fileSize;constructor(e,t,n,o={}){this.source=e,this.pageSize=t,this.fileSize=n;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 n=0;for(;;)try{let o=await this.source.read(e,t);return this.bytesFetched+=o.length,o}catch(o){if(n+=1,n>=3)throw o;await new Promise(s=>setTimeout(s,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){let t=this.blocks.get(e);if(t)return this.blocks.delete(e),this.blocks.set(e,t),t;let n=e*this.blockSize,o=Math.min(this.blockSize,this.fileSize-n),s=this.read(o,n);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),n=0;for(;n<t.length;){let o=n+1;for(;o<t.length&&t[o]===t[o-1]+1;)o+=1;this.fetchRun(t[n],o-n),n=o}}fetchRun(e,t){let n=e*this.blockSize,o=Math.min(t*this.blockSize,this.fileSize-n),s=this.read(o,n);this.fetches+=1;let i=[];for(let a=0;a<t;a++){let c=a*this.blockSize;i.push(e+a),this.blocks.set(e+a,s.then(f=>f.subarray(c,c+this.blockSize)))}this.forgetOnFailure(s,i),this.evict()}forgetOnFailure(e,t){e.catch(()=>{for(let n of t)this.blocks.delete(n)})}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)),o=t%this.blockSize;return n.subarray(o,o+this.pageSize)}};var Me=class r{pager;btree;objects;constructor(e,t,n){this.pager=e,this.btree=t,this.objects=n}static async open(e,t={}){let{size:n}=await e.stat(),o=await e.read(Math.min(t.blockSize??65536,n),0),s=o.subarray(0,100);if(new TextDecoder().decode(s.subarray(0,15))!=="SQLite format 3")throw new Error("Not a SQLite database");let a=new DataView(s.buffer,s.byteOffset,s.byteLength),c=a.getUint16(16),f=c===1?65536:c,l=s[20]??0,p=a.getUint32(56);if(p!==1)throw new Error(`SQLite text encoding ${p} is not UTF-8`);let d=new nt(e,f,n,t);d.seed(0,o),d.fetches+=1,d.bytesFetched+=o.length;let h=new tt(d,l),u=new Map;for await(let{values:m}of h.tableScan(1)){let[y,x,S,g,b]=m;typeof y=="string"&&typeof x=="string"&&typeof S=="string"&&typeof g=="number"&&u.set(x,{type:y,name:x,tableName:S,rootPage:g,sql:typeof b=="string"?b:""})}return new r(d,h,u)}rootPage(e){let t=this.objects.get(e);if(!t)throw new Error(`SQLite database has no object named ${e}`);return t.rootPage}indexOn(e){let t=[...this.objects.values()].find(n=>n.type==="index"&&n.tableName===e);if(!t)throw new Error(`SQLite table ${e} has no index`);return t.rootPage}byRowid(e,t){return this.btree.tableRowid(this.rootPage(e),t)}prefetchRows(e,t,n){return this.btree.prefetchRowidRange(this.rootPage(e),t,n)}scan(e){return this.btree.tableScan(this.rootPage(e))}indexSeekLE(e,t){return this.btree.indexSeekLE(this.indexOn(e),t)}indexScanFrom(e,t){return this.btree.indexScanFrom(this.indexOn(e),t)}has(e){return this.objects.has(e)}};var Ut="GBZ-base version 4",rt=class extends Error{name="ForwardOnlyIndexError";constructor(){super("the haplotype index was written with --forward-only, which cannot name the walks stored against their reference (about half of them); rebuild it with gbz-haplotype-index without --forward-only")}},ot=class extends Error{name="SchemaVersionError";found;constructor(e){super(e===void 0?"not a gbz-base database: its Tags table has no version":`unsupported database schema "${e}"; this reader understands "${Ut}"`),this.found=e}},st=class{sequenceLen;handle;edges;bwt;encodedSequence;next;decoded;constructor(e,t,n,o,s){this.handle=e,this.edges=t,this.bwt=n,this.encodedSequence=o,this.next=s,this.sequenceLen=_n(o)}get id(){return A(this.handle)}get orientation(){return me(this.handle)}get sequence(){return this.decoded??=Pn(this.encodedSequence),this.decoded}successors(){return this.edges.filter(e=>e.node!==0).map(e=>e.node)}gbwt(){if(this.edges.length===0)throw new Error(`GBWT record for handle ${this.handle} is empty`);return new Ge(this.edges,this.bwt)}};function T(r,e){if(typeof r!="number")throw new Error(`${e} is not a number in the database`);return r}function it(r,e){if(typeof r!="string")throw new Error(`${e} is not text in the database`);return r}function jt(r,e){if(!(r instanceof Uint8Array))throw new Error(`${e} is not a blob in the database`);return r}function or(r,e){return{handle:r,fwStart:{node:T(e[1],"Paths.fw_node"),offset:T(e[2],"Paths.fw_offset")},revStart:{node:T(e[3],"Paths.rev_node"),offset:T(e[4],"Paths.rev_offset")},name:{sample:it(e[5],"Paths.sample"),contig:it(e[6],"Paths.contig"),haplotype:T(e[7],"Paths.haplotype"),fragment:T(e[8],"Paths.fragment")},isIndexed:T(e[9],"Paths.is_indexed")!==0}}async function sr(r){let e=new Map;for await(let{values:t}of r.scan("Tags"))e.set(it(t[0],"Tags.key"),it(t[1],"Tags.value"));return e}var Oe=class r{tagCache;pathCache;pathMapCache;indexTags;sqlite;index;constructor(e,t){this.sqlite=e,this.index=t}static async open(e,t={}){let{haplotypeIndex:n,...o}=t,s=await Me.open(e,o);for(let f of["Tags","Nodes","Paths","ReferenceIndex"])s.rootPage(f);let i=n?await Me.open(n,o):s,a=new r(s,i),c=await a.tag("version");if(c!==Ut)throw new ot(c);if(n){for(let h of["Tags","HaplotypeSamples","HaplotypeLengths"])i.rootPage(h);a.indexTags=await sr(i);let f=a.indexTags.get("haplotype_index_paths"),l=await a.tag("paths");if(f!==l)throw new Error(`haplotype index was built for ${f??"an unknown number of"} paths but the graph has ${l}`);let p=a.indexTags.get("haplotype_index_nodes"),d=await a.tag("nodes");if(p!==void 0&&p!==d)throw new Error(`haplotype index was built for a graph with ${p} nodes but this one has ${d}`)}if(a.hasHaplotypeIndex&&await a.haplotypeIndexTag("haplotype_index_orientations")==="forward")throw new rt;return a}tags(){return this.tagCache??=sr(this.sqlite),this.tagCache}async tag(e){return(await this.tags()).get(e)}prefetchRecords(e,t){return this.sqlite.prefetchRows("Nodes",e,t)}async getRecord(e){let t=await this.sqlite.byRowid("Nodes",e);if(!t)return;let n=t[4];return new st(e,Rn(jt(t[1],"Nodes.edges")),jt(t[2],"Nodes.bwt"),jt(t[3],"Nodes.sequence"),typeof n=="number"?n:void 0)}paths(){return this.pathCache??=(async()=>{let e=[];for await(let{rowid:t,values:n}of this.sqlite.scan("Paths"))e.push(or(t,n));return e})(),this.pathCache}async getPath(e){let t=await this.sqlite.byRowid("Paths",e);return t?or(e,t):void 0}pathsByHandle(){return this.pathMapCache??=this.paths().then(e=>new Map(e.map(t=>[t.handle,t]))),this.pathMapCache}async findPath(e){return(await this.paths()).filter(n=>n.name.sample===e.sample&&n.name.contig===e.contig&&n.name.haplotype===e.haplotype&&n.name.fragment<=e.fragment).sort((n,o)=>o.name.fragment-n.name.fragment)[0]}async pathsForSample(e){return(await this.paths()).filter(t=>t.name.sample===e)}async pathsNamed(e){let t=Re(Hn(e),0);return(await this.paths()).filter(n=>n.name.sample===t.sample&&n.name.contig===t.contig&&n.name.haplotype===t.haplotype).sort((n,o)=>n.name.fragment-o.name.fragment)}async hasPath(e){return(await this.pathsNamed(e)).length>0}pathLengths=new Map;pathLength(e){let t=this.pathLengths.get(e);return t||(t=this.walkPathLength(e),this.pathLengths.set(e,t),t.catch(()=>this.pathLengths.delete(e))),t}async walkPathLength(e){let t=this.hasHaplotypeIndex?await this.haplotypeLength(e):void 0;if(t===void 0){let n=await this.indexedPosition(e,Number.MAX_SAFE_INTEGER);if(!n){let i=await this.getPath(e);throw new Error(`Path ${i?q(i.name,i.name.fragment):e} has not been indexed for random access`)}let o=n.pathOffset,s=n.pos;for(;;){let i=await this.getRecord(s.node);if(!i)throw new Error(`Node ${s.node} does not exist in the graph`);o+=i.sequenceLen;let a=i.gbwt().lf(s.offset);if(!a||a.node===0)return o;s=a}}return t}async pathFragmentsForRange(e,t,n){if(n<=t)return[];let o=await this.pathsNamed(e),s=o.filter(c=>c.name.fragment<=t).slice(-1),i=o.filter(c=>c.name.fragment>t&&c.name.fragment<n);return(await Promise.all([...s,...i].map(async c=>({path:c,start:c.name.fragment,end:c.name.fragment+await this.pathLength(c.handle)})))).filter(c=>t<c.end)}async subgraphForFragment(e,t,n,o){let{keep:s,...i}=o;if(s!==void 0&&!this.hasHaplotypeIndex)throw new Error("keep needs the haplotype index: this database cannot name its walks");let{sample:a,contig:c,haplotype:f}=e.path.name,l={sample:a,contig:c,haplotype:f},p=Math.max(t,e.start),d=Math.min(n,e.end),h=o.haplotypes??"all",u=h==="all"||h==="distinct",m;return s!==void 0&&h==="all"?m=await er(this,l,p,d,{...i,keep:s}):(m=await Xe(this,l,p,d,i),this.hasHaplotypeIndex&&u&&(await m.identifyPaths(),s!==void 0&&m.keepHaplotypes(s))),m}async getSubgraphForRange(e,t,n,o={}){let[s]=await this.pathFragmentsForRange(e,t,n);return s?this.subgraphForFragment(s,t,n,o):void 0}async getAlignmentsForRange(e,t,n,o={}){let s=[];for(let i of await this.pathFragmentsForRange(e,t,n)){let a=await this.subgraphForFragment(i,t,n,o);s.push(...a.alignments())}return s}async graphName(){let e=new Map;for(let[n,o]of await this.tags())n.startsWith("gbz_")&&e.set(n.slice(4),o);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.has("HaplotypeSamples")&&this.index.has("HaplotypeLengths")}async haplotypeIndexTag(e){return this.indexTags?this.indexTags.get(e):await this.tag(e)}async haplotypeSampleInterval(){let e=await this.haplotypeIndexTag("haplotype_index_interval");return e===void 0?void 0:Number(e)}async haplotypeAnchorSpacing(){let e=this.hasHaplotypeIndex&&this.index.has("HaplotypeAnchors")?await this.haplotypeIndexTag("haplotype_index_anchor_spacing"):void 0;return e===void 0?void 0:Number(e)}async haplotypeAnchor(e,t){let n=await this.index.indexSeekLE("HaplotypeAnchors",[e,t]),o=n?.[0]===e&&n[1]===t?await this.index.byRowid("HaplotypeAnchors",T(n[2],"HaplotypeAnchors rowid")):void 0;return o?{node:T(o[2],"HaplotypeAnchors.node_handle"),pathOffset:T(o[3],"HaplotypeAnchors.path_offset")}:void 0}haplotypeSamplesAtNode(e){return this.haplotypeSamplesInRange(e,e)}sampleFromRow(e){return{node:T(e[0],"HaplotypeSamples.node_handle"),offset:T(e[1],"HaplotypeSamples.node_offset"),pathHandle:T(e[2],"HaplotypeSamples.path_handle"),orientation:T(e[3],"HaplotypeSamples.orientation")===0?"forward":"reverse",pathOffset:T(e[4],"HaplotypeSamples.path_offset")}}async haplotypeSamplesInRange(e,t){let n=[];for await(let o of this.index.indexScanFrom("HaplotypeSamples",[e,0])){if(T(o[0],"HaplotypeSamples.node_handle")>t)break;let i=await this.index.byRowid("HaplotypeSamples",T(o[2],"HaplotypeSamples rowid"));i&&n.push(this.sampleFromRow(i))}return n}async haplotypeSampleAt(e,t){let n=await this.index.indexSeekLE("HaplotypeSamples",[e,t]);if(n?.[0]!==e||n[1]!==t)return;let o=await this.index.byRowid("HaplotypeSamples",T(n[2],"HaplotypeSamples rowid"));return o?this.sampleFromRow(o):void 0}async haplotypeLength(e){let t=await this.index.byRowid("HaplotypeLengths",e);return t?T(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:T(t[1],"ReferenceIndex.path_offset"),pos:{node:T(t[2],"ReferenceIndex.node_handle"),offset:T(t[3],"ReferenceIndex.node_offset")}}}async indexedRowid(e,t){let n=await this.sqlite.indexSeekLE("ReferenceIndex",[e,t]);return n?.[0]===e?T(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[o,s]=await Promise.all([this.indexedRowid(e,t),this.indexedRowid(e,n)]),i=[];if(o!==void 0&&s!==void 0){await this.sqlite.prefetchRows("ReferenceIndex",o,s+1);for(let a=o;a<=s;a++)i.push(await this.indexedRow(a))}return i}};var Jr=Y(bn(),1),hn=Y(Ae(),1),dn=Y(ro(),1),eo=Y(oo(),1);var Kr=Y(bn(),1),Xr=Y(Ae(),1);var Wt=function(r,e){return Wt=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,n){t.__proto__=n}||function(t,n){for(var o in n)Object.prototype.hasOwnProperty.call(n,o)&&(t[o]=n[o])},Wt(r,e)};function Le(r,e){if(typeof e!="function"&&e!==null)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");Wt(r,e);function t(){this.constructor=r}r.prototype=e===null?Object.create(e):(t.prototype=e.prototype,new t)}function ir(r,e,t,n){function o(s){return s instanceof t?s:new t(function(i){i(s)})}return new(t||(t=Promise))(function(s,i){function a(l){try{f(n.next(l))}catch(p){i(p)}}function c(l){try{f(n.throw(l))}catch(p){i(p)}}function f(l){l.done?s(l.value):o(l.value).then(a,c)}f((n=n.apply(r,e||[])).next())})}function at(r,e){var t={label:0,sent:function(){if(s[0]&1)throw s[1];return s[1]},trys:[],ops:[]},n,o,s,i=Object.create((typeof Iterator=="function"?Iterator:Object).prototype);return i.next=a(0),i.throw=a(1),i.return=a(2),typeof Symbol=="function"&&(i[Symbol.iterator]=function(){return this}),i;function a(f){return function(l){return c([f,l])}}function c(f){if(n)throw new TypeError("Generator is already executing.");for(;i&&(i=0,f[0]&&(t=0)),t;)try{if(n=1,o&&(s=f[0]&2?o.return:f[0]?o.throw||((s=o.return)&&s.call(o),0):o.next)&&!(s=s.call(o,f[1])).done)return s;switch(o=0,s&&(f=[f[0]&2,s.value]),f[0]){case 0:case 1:s=f;break;case 4:return t.label++,{value:f[1],done:!1};case 5:t.label++,o=f[1],f=[0];continue;case 7:f=t.ops.pop(),t.trys.pop();continue;default:if(s=t.trys,!(s=s.length>0&&s[s.length-1])&&(f[0]===6||f[0]===2)){t=0;continue}if(f[0]===3&&(!s||f[1]>s[0]&&f[1]<s[3])){t.label=f[1];break}if(f[0]===6&&t.label<s[1]){t.label=s[1],s=f;break}if(s&&t.label<s[2]){t.label=s[2],t.ops.push(f);break}s[2]&&t.ops.pop(),t.trys.pop();continue}f=e.call(r,t)}catch(l){f=[6,l],o=0}finally{n=s=0}if(f[0]&5)throw f[1];return{value:f[0]?f[1]:void 0,done:!0}}}function ce(r){var e=typeof Symbol=="function"&&Symbol.iterator,t=e&&r[e],n=0;if(t)return t.call(r);if(r&&typeof r.length=="number")return{next:function(){return r&&n>=r.length&&(r=void 0),{value:r&&r[n++],done:!r}}};throw new TypeError(e?"Object is not iterable.":"Symbol.iterator is not defined.")}function we(r,e){var t=typeof Symbol=="function"&&r[Symbol.iterator];if(!t)return r;var n=t.call(r),o,s=[],i;try{for(;(e===void 0||e-- >0)&&!(o=n.next()).done;)s.push(o.value)}catch(a){i={error:a}}finally{try{o&&!o.done&&(t=n.return)&&t.call(n)}finally{if(i)throw i.error}}return s}function xe(r,e,t){if(t||arguments.length===2)for(var n=0,o=e.length,s;n<o;n++)(s||!(n in e))&&(s||(s=Array.prototype.slice.call(e,0,n)),s[n]=e[n]);return r.concat(s||Array.prototype.slice.call(e))}function le(r){return this instanceof le?(this.v=r,this):new le(r)}function ar(r,e,t){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var n=t.apply(r,e||[]),o,s=[];return o=Object.create((typeof AsyncIterator=="function"?AsyncIterator:Object).prototype),a("next"),a("throw"),a("return",i),o[Symbol.asyncIterator]=function(){return this},o;function i(h){return function(u){return Promise.resolve(u).then(h,p)}}function a(h,u){n[h]&&(o[h]=function(m){return new Promise(function(y,x){s.push([h,m,y,x])>1||c(h,m)})},u&&(o[h]=u(o[h])))}function c(h,u){try{f(n[h](u))}catch(m){d(s[0][3],m)}}function f(h){h.value instanceof le?Promise.resolve(h.value.v).then(l,p):d(s[0][2],h)}function l(h){c("next",h)}function p(h){c("throw",h)}function d(h,u){h(u),s.shift(),s.length&&c(s[0][0],s[0][1])}}function fr(r){if(!Symbol.asyncIterator)throw new TypeError("Symbol.asyncIterator is not defined.");var e=r[Symbol.asyncIterator],t;return e?e.call(r):(r=typeof ce=="function"?ce(r):r[Symbol.iterator](),t={},n("next"),n("throw"),n("return"),t[Symbol.asyncIterator]=function(){return this},t);function n(s){t[s]=r[s]&&function(i){return new Promise(function(a,c){i=r[s](i),o(a,c,i.done,i.value)})}}function o(s,i,a,c){Promise.resolve(c).then(function(f){s({value:f,done:a})},i)}}function P(r){return typeof r=="function"}function cr(r){var e=function(n){Error.call(n),n.stack=new Error().stack},t=r(e);return t.prototype=Object.create(Error.prototype),t.prototype.constructor=t,t}var ft=cr(function(r){return function(t){r(this),this.message=t?t.length+` errors occurred during unsubscription:
+`+t.map(function(n,o){return o+1+") "+n.toString()}).join(`
+  `):"",this.name="UnsubscriptionError",this.errors=t}});function Qt(r,e){if(r){var t=r.indexOf(e);0<=t&&r.splice(t,1)}}var ct=(function(){function r(e){this.initialTeardown=e,this.closed=!1,this._parentage=null,this._finalizers=null}return r.prototype.unsubscribe=function(){var e,t,n,o,s;if(!this.closed){this.closed=!0;var i=this._parentage;if(i)if(this._parentage=null,Array.isArray(i))try{for(var a=ce(i),c=a.next();!c.done;c=a.next()){var f=c.value;f.remove(this)}}catch(m){e={error:m}}finally{try{c&&!c.done&&(t=a.return)&&t.call(a)}finally{if(e)throw e.error}}else i.remove(this);var l=this.initialTeardown;if(P(l))try{l()}catch(m){s=m instanceof ft?m.errors:[m]}var p=this._finalizers;if(p){this._finalizers=null;try{for(var d=ce(p),h=d.next();!h.done;h=d.next()){var u=h.value;try{lr(u)}catch(m){s=s??[],m instanceof ft?s=xe(xe([],we(s)),we(m.errors)):s.push(m)}}}catch(m){n={error:m}}finally{try{h&&!h.done&&(o=d.return)&&o.call(d)}finally{if(n)throw n.error}}}if(s)throw new ft(s)}},r.prototype.add=function(e){var t;if(e&&e!==this)if(this.closed)lr(e);else{if(e instanceof r){if(e.closed||e._hasParent(this))return;e._addParent(this)}(this._finalizers=(t=this._finalizers)!==null&&t!==void 0?t:[]).push(e)}},r.prototype._hasParent=function(e){var t=this._parentage;return t===e||Array.isArray(t)&&t.includes(e)},r.prototype._addParent=function(e){var t=this._parentage;this._parentage=Array.isArray(t)?(t.push(e),t):t?[t,e]:e},r.prototype._removeParent=function(e){var t=this._parentage;t===e?this._parentage=null:Array.isArray(t)&&Qt(t,e)},r.prototype.remove=function(e){var t=this._finalizers;t&&Qt(t,e),e instanceof r&&e._removeParent(this)},r.EMPTY=(function(){var e=new r;return e.closed=!0,e})(),r})();var Ii=ct.EMPTY;function lt(r){return r instanceof ct||r&&"closed"in r&&P(r.remove)&&P(r.add)&&P(r.unsubscribe)}function lr(r){P(r)?r():r.unsubscribe()}var K={onUnhandledError:null,onStoppedNotification:null,Promise:void 0,useDeprecatedSynchronousErrorHandling:!1,useDeprecatedNextContext:!1};var be={setTimeout:function(r,e){for(var t=[],n=2;n<arguments.length;n++)t[n-2]=arguments[n];var o=be.delegate;return o?.setTimeout?o.setTimeout.apply(o,xe([r,e],we(t))):setTimeout.apply(void 0,xe([r,e],we(t)))},clearTimeout:function(r){var e=be.delegate;return(e?.clearTimeout||clearTimeout)(r)},delegate:void 0};function pt(r){be.setTimeout(function(){var e=K.onUnhandledError;if(e)e(r);else throw r})}function Yt(){}var pr=(function(){return Vt("C",void 0,void 0)})();function hr(r){return Vt("E",void 0,r)}function dr(r){return Vt("N",r,void 0)}function Vt(r,e,t){return{kind:r,value:e,error:t}}var pe=null;function ur(r){if(K.useDeprecatedSynchronousErrorHandling){var e=!pe;if(e&&(pe={errorThrown:!1,error:null}),r(),e){var t=pe,n=t.errorThrown,o=t.error;if(pe=null,n)throw o}}else r()}function mr(r){K.useDeprecatedSynchronousErrorHandling&&pe&&(pe.errorThrown=!0,pe.error=r)}var Te=(function(r){Le(e,r);function e(t){var n=r.call(this)||this;return n.isStopped=!1,t?(n.destination=t,lt(t)&&t.add(n)):n.destination=Qo,n}return e.create=function(t,n,o){return new dt(t,n,o)},e.prototype.next=function(t){this.isStopped?Xt(dr(t),this):this._next(t)},e.prototype.error=function(t){this.isStopped?Xt(hr(t),this):(this.isStopped=!0,this._error(t))},e.prototype.complete=function(){this.isStopped?Xt(pr,this):(this.isStopped=!0,this._complete())},e.prototype.unsubscribe=function(){this.closed||(this.isStopped=!0,r.prototype.unsubscribe.call(this),this.destination=null)},e.prototype._next=function(t){this.destination.next(t)},e.prototype._error=function(t){try{this.destination.error(t)}finally{this.unsubscribe()}},e.prototype._complete=function(){try{this.destination.complete()}finally{this.unsubscribe()}},e})(ct);var jo=Function.prototype.bind;function Kt(r,e){return jo.call(r,e)}var Uo=(function(){function r(e){this.partialObserver=e}return r.prototype.next=function(e){var t=this.partialObserver;if(t.next)try{t.next(e)}catch(n){ht(n)}},r.prototype.error=function(e){var t=this.partialObserver;if(t.error)try{t.error(e)}catch(n){ht(n)}else ht(e)},r.prototype.complete=function(){var e=this.partialObserver;if(e.complete)try{e.complete()}catch(t){ht(t)}},r})(),dt=(function(r){Le(e,r);function e(t,n,o){var s=r.call(this)||this,i;if(P(t)||!t)i={next:t??void 0,error:n??void 0,complete:o??void 0};else{var a;s&&K.useDeprecatedNextContext?(a=Object.create(t),a.unsubscribe=function(){return s.unsubscribe()},i={next:t.next&&Kt(t.next,a),error:t.error&&Kt(t.error,a),complete:t.complete&&Kt(t.complete,a)}):i=t}return s.destination=new Uo(i),s}return e})(Te);function ht(r){K.useDeprecatedSynchronousErrorHandling?mr(r):pt(r)}function Wo(r){throw r}function Xt(r,e){var t=K.onStoppedNotification;t&&be.setTimeout(function(){return t(r,e)})}var Qo={closed:!0,next:Yt,error:Wo,complete:Yt};var Se=(function(){return typeof Symbol=="function"&&Symbol.observable||"@@observable"})();function gr(r){return r}function yr(r){return r.length===0?gr:r.length===1?r[0]:function(t){return r.reduce(function(n,o){return o(n)},t)}}var j=(function(){function r(e){e&&(this._subscribe=e)}return r.prototype.lift=function(e){var t=new r;return t.source=this,t.operator=e,t},r.prototype.subscribe=function(e,t,n){var o=this,s=Vo(e)?e:new dt(e,t,n);return ur(function(){var i=o,a=i.operator,c=i.source;s.add(a?a.call(s,c):c?o._subscribe(s):o._trySubscribe(s))}),s},r.prototype._trySubscribe=function(e){try{return this._subscribe(e)}catch(t){e.error(t)}},r.prototype.forEach=function(e,t){var n=this;return t=wr(t),new t(function(o,s){var i=new dt({next:function(a){try{e(a)}catch(c){s(c),i.unsubscribe()}},error:s,complete:o});n.subscribe(i)})},r.prototype._subscribe=function(e){var t;return(t=this.source)===null||t===void 0?void 0:t.subscribe(e)},r.prototype[Se]=function(){return this},r.prototype.pipe=function(){for(var e=[],t=0;t<arguments.length;t++)e[t]=arguments[t];return yr(e)(this)},r.prototype.toPromise=function(e){var t=this;return e=wr(e),new e(function(n,o){var s;t.subscribe(function(i){return s=i},function(i){return o(i)},function(){return n(s)})})},r.create=function(e){return new r(e)},r})();function wr(r){var e;return(e=r??K.Promise)!==null&&e!==void 0?e:Promise}function Yo(r){return r&&P(r.next)&&P(r.error)&&P(r.complete)}function Vo(r){return r&&r instanceof Te||Yo(r)&&lt(r)}function Ko(r){return P(r?.lift)}function W(r){return function(e){if(Ko(e))return e.lift(function(t){try{return r(t,this)}catch(n){this.error(n)}});throw new TypeError("Unable to lift unknown Observable type")}}function re(r,e,t,n,o){return new Xo(r,e,t,n,o)}var Xo=(function(r){Le(e,r);function e(t,n,o,s,i,a){var c=r.call(this,t)||this;return c.onFinalize=i,c.shouldUnsubscribe=a,c._next=n?function(f){try{n(f)}catch(l){t.error(l)}}:r.prototype._next,c._error=s?function(f){try{s(f)}catch(l){t.error(l)}finally{this.unsubscribe()}}:r.prototype._error,c._complete=o?function(){try{o()}catch(f){t.error(f)}finally{this.unsubscribe()}}:r.prototype._complete,c}return e.prototype.unsubscribe=function(){var t;if(!this.shouldUnsubscribe||this.shouldUnsubscribe()){var n=this.closed;r.prototype.unsubscribe.call(this),!n&&((t=this.onFinalize)===null||t===void 0||t.call(this))}},e})(Te);var ut=(function(r){return r&&typeof r.length=="number"&&typeof r!="function"});function mt(r){return P(r?.then)}function gt(r){return P(r[Se])}function yt(r){return Symbol.asyncIterator&&P(r?.[Symbol.asyncIterator])}function wt(r){return new TypeError("You provided "+(r!==null&&typeof r=="object"?"an invalid object":"'"+r+"'")+" where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.")}function Zo(){return typeof Symbol!="function"||!Symbol.iterator?"@@iterator":Symbol.iterator}var xt=Zo();function bt(r){return P(r?.[xt])}function St(r){return ar(this,arguments,function(){var t,n,o,s;return at(this,function(i){switch(i.label){case 0:t=r.getReader(),i.label=1;case 1:i.trys.push([1,,9,10]),i.label=2;case 2:return[4,le(t.read())];case 3:return n=i.sent(),o=n.value,s=n.done,s?[4,le(void 0)]:[3,5];case 4:return[2,i.sent()];case 5:return[4,le(o)];case 6:return[4,i.sent()];case 7:return i.sent(),[3,2];case 8:return[3,10];case 9:return t.releaseLock(),[7];case 10:return[2]}})})}function vt(r){return P(r?.getReader)}function J(r){if(r instanceof j)return r;if(r!=null){if(gt(r))return Jo(r);if(ut(r))return es(r);if(mt(r))return ts(r);if(yt(r))return xr(r);if(bt(r))return ns(r);if(vt(r))return rs(r)}throw wt(r)}function Jo(r){return new j(function(e){var t=r[Se]();if(P(t.subscribe))return t.subscribe(e);throw new TypeError("Provided object does not correctly implement Symbol.observable")})}function es(r){return new j(function(e){for(var t=0;t<r.length&&!e.closed;t++)e.next(r[t]);e.complete()})}function ts(r){return new j(function(e){r.then(function(t){e.closed||(e.next(t),e.complete())},function(t){return e.error(t)}).then(null,pt)})}function ns(r){return new j(function(e){var t,n;try{for(var o=ce(r),s=o.next();!s.done;s=o.next()){var i=s.value;if(e.next(i),e.closed)return}}catch(a){t={error:a}}finally{try{s&&!s.done&&(n=o.return)&&n.call(o)}finally{if(t)throw t.error}}e.complete()})}function xr(r){return new j(function(e){os(r,e).catch(function(t){return e.error(t)})})}function rs(r){return xr(St(r))}function os(r,e){var t,n,o,s;return ir(this,void 0,void 0,function(){var i,a;return at(this,function(c){switch(c.label){case 0:c.trys.push([0,5,6,11]),t=fr(r),c.label=1;case 1:return[4,t.next()];case 2:if(n=c.sent(),!!n.done)return[3,4];if(i=n.value,e.next(i),e.closed)return[2];c.label=3;case 3:return[3,1];case 4:return[3,11];case 5:return a=c.sent(),o={error:a},[3,11];case 6:return c.trys.push([6,,9,10]),n&&!n.done&&(s=t.return)?[4,s.call(t)]:[3,8];case 7:c.sent(),c.label=8;case 8:return[3,10];case 9:if(o)throw o.error;return[7];case 10:return[7];case 11:return e.complete(),[2]}})})}function Q(r,e,t,n,o){n===void 0&&(n=0),o===void 0&&(o=!1);var s=e.schedule(function(){t(),o?r.add(this.schedule(null,n)):this.unsubscribe()},n);if(r.add(s),!o)return s}function It(r,e){return e===void 0&&(e=0),W(function(t,n){t.subscribe(re(n,function(o){return Q(n,r,function(){return n.next(o)},e)},function(){return Q(n,r,function(){return n.complete()},e)},function(o){return Q(n,r,function(){return n.error(o)},e)}))})}function At(r,e){return e===void 0&&(e=0),W(function(t,n){n.add(r.schedule(function(){return t.subscribe(n)},e))})}function br(r,e){return J(r).pipe(At(e),It(e))}function Sr(r,e){return J(r).pipe(At(e),It(e))}function vr(r,e){return new j(function(t){var n=0;return e.schedule(function(){n===r.length?t.complete():(t.next(r[n++]),t.closed||this.schedule())})})}function Ir(r,e){return new j(function(t){var n;return Q(t,e,function(){n=r[xt](),Q(t,e,function(){var o,s,i;try{o=n.next(),s=o.value,i=o.done}catch(a){t.error(a);return}i?t.complete():t.next(s)},0,!0)}),function(){return P(n?.return)&&n.return()}})}function Et(r,e){if(!r)throw new Error("Iterable cannot be null");return new j(function(t){Q(t,e,function(){var n=r[Symbol.asyncIterator]();Q(t,e,function(){n.next().then(function(o){o.done?t.complete():t.next(o.value)})},0,!0)})})}function Ar(r,e){return Et(St(r),e)}function Er(r,e){if(r!=null){if(gt(r))return br(r,e);if(ut(r))return vr(r,e);if(mt(r))return Sr(r,e);if(yt(r))return Et(r,e);if(bt(r))return Ir(r,e);if(vt(r))return Ar(r,e)}throw wt(r)}function Zt(r,e){return e?Er(r,e):J(r)}function Ne(r,e){return W(function(t,n){var o=0;t.subscribe(re(n,function(s){n.next(r.call(e,s,o++))}))})}function Cr(r,e,t,n,o,s,i,a){var c=[],f=0,l=0,p=!1,d=function(){p&&!c.length&&!f&&e.complete()},h=function(m){return f<n?u(m):c.push(m)},u=function(m){s&&e.next(m),f++;var y=!1;J(t(m,l++)).subscribe(re(e,function(x){o?.(x),s?h(x):e.next(x)},function(){y=!0},void 0,function(){if(y)try{f--;for(var x=function(){var S=c.shift();i?Q(e,i,function(){return u(S)}):u(S)};c.length&&f<n;)x();d()}catch(S){e.error(S)}}))};return r.subscribe(re(e,h,function(){p=!0,d()})),function(){a?.()}}function ve(r,e,t){return t===void 0&&(t=1/0),P(e)?ve(function(n,o){return Ne(function(s,i){return e(n,s,o,i)})(J(r(n,o)))},t):(typeof e=="number"&&(t=e),W(function(n,o){return Cr(n,o,r,t)}))}function Rr(r,e,t,n,o){return function(s,i){var a=t,c=e,f=0;s.subscribe(re(i,function(l){var p=f++;c=a?r(c,l,p):(a=!0,l),n&&i.next(c)},o&&(function(){a&&i.next(c),i.complete()})))}}function _r(r,e){return W(Rr(r,e,arguments.length>=2,!1,!0))}var ss=function(r,e){return r.push(e),r};function Ct(){return W(function(r,e){_r(ss,[])(r).subscribe(e)})}function Pr(r){let e=[],t=0,n;for(let o=0,s=r.length;o<s;o++){let i=r.charCodeAt(o);if(i>=48&&i<=57)t=t*10+i-48;else if(i===58)n=t,t=0;else{let a=r[o];a==="M"||a==="="||a==="X"?e.push({own:n===void 0?t:n,mate:t,op:"M"}):a==="I"?e.push({own:0,mate:t,op:a}):(a==="D"||a==="N")&&e.push({own:t,mate:0,op:a}),n=void 0,t=0}}return e}function tn(r){let e="";for(let{own:t,mate:n,op:o}of Pr(r))e+=o==="M"?t===0?`${n}I`:n===0?`${t}D`:`${t}M`:`${o==="I"?n:t}${o}`;return e}var Jt=2**28-1;function en(r,e,t){for(let n=e;n>0;n-=Jt)r.push((Math.min(n,Jt)<<4|t)>>>0)}function is(r,e,t){if(e===t)en(r,e,0);else{let n=Math.ceil(Math.max(e,t)/Jt);for(let o=0;o<n;o++){let s=Math.floor(e*(o+1)/n)-Math.floor(e*o/n),i=Math.floor(t*(o+1)/n)-Math.floor(t*o/n);r.push((s<<4|9)>>>0,(i<<4|9)>>>0)}}}function nn(r){let e=[];for(let{own:t,mate:n,op:o}of Pr(r))o==="M"?is(e,t,n):o==="I"?en(e,n,1):en(e,t,o==="N"?3:2);return Uint32Array.from(e)}function as(r){return r>=48&&r<=57}function fs(r){return r!==void 0&&/[A-Za-z]/.test(r)}function kr(r,e){let t=e;for(;t<r.length&&fs(r[t]);)t++;return t}function Mr(r,e){let t=e,n=0;for(;t<r.length&&as(r.charCodeAt(t));)n=n*10+(r.charCodeAt(t)-48),t++;return{value:n,next:t}}function Fr(r,e){let t=0;for(;t<r.length;){let n=r[t];if(n===":"){let{value:o,next:s}=Mr(r,t+1);e(":",o,o,t+1,s),t=s}else if(n==="="){let o=kr(r,t+1),s=o-t-1;e("=",s,s,t+1,o),t=o}else if(n==="*")e("*",1,1,t+1,Math.min(t+3,r.length)),t+=3;else if(n==="+"||n==="-"){let o=kr(r,t+1),s=o-t-1;e(n,n==="-"?s:0,n==="+"?s:0,t+1,o),t=o}else if(n==="~"){let{value:o,next:s}=Mr(r,t+3),i=Math.min(s+2,r.length);e("~",o,0,t+1,i),t=i}else t++}}function rn(r,e,t,n){let o=t??Number.NEGATIVE_INFINITY,s=n??Number.POSITIVE_INFINITY,i=0;Fr(r,(a,c,f,l,p)=>{if(a==="*")i>=o&&i<s&&e(88,i,1,r[l+1]??"",-1,0,0);else if(a==="+"){if(i>=o&&i<=s){let d=r.slice(l,p);e(73,i,f,d,-1,0,f)}}else(a==="-"||a==="~")&&i<s&&i+c>o&&e(a==="-"?68:78,i,c,"",-1,0,0);i+=c})}function Hr(r,e,t,n){let o=0,s=0,i=[],a=t&&e;for(let c=0,f=r.length;c<f;c++){let l=r[c],p=l>>>4,d=l&15;if(d===0||d===7){if(a)for(let h=0;h<p;h++)(e.charCodeAt(s+h)|32)!==(t.charCodeAt(o+h)|32)&&i.push({start:o+h,type:"mismatch",base:e[s+h],altbase:t[o+h],length:1});s+=p,o+=p}else if(d===1)i.push({start:o,type:"insertion",insertlen:p,insertedBases:e?.slice(s,s+p),length:0}),s+=p;else if(d===2)i.push({start:o,type:"deletion",length:p}),o+=p;else if(d===3)i.push({start:o,type:"skip",length:p}),o+=p;else if(d===8){for(let h=0;h<p;h++)i.push({start:o+h,type:"mismatch",base:e?.[s+h]||"X",qual:n?.[s+h],length:1});s+=p,o+=p}else d===5?i.push({start:o,type:"hardclip",cliplen:p,length:1}):d===4&&(i.push({start:o,type:"softclip",cliplen:p,length:1}),s+=p)}return i}function qr(r,e,t,n,o){if(!e)return[];let s=[],i=e.length,a=n.length,c=o!==void 0,f=t.length,l=!1;for(let S=0;S<f;S++)if(t[S].type==="skip"){l=!0;break}let p=0,d=0,h=0,u=0,m=0,y=0,x=r.length;for(;y<x;){let S=r.charCodeAt(y);if(S>=48&&S<=57){let g=0;for(;y<x;){let b=r.charCodeAt(y);if(b>=48&&b<=57)g=g*10+(b-48),y++;else break}p+=g}else if(S===94)for(y++;y<x&&r.charCodeAt(y)>=65;)y++,p++;else if(S>=65){let g=r[y];if(y++,l&&f>0)for(let R=m;R<f;R++){let C=t[R];C.type==="skip"&&p>=C.start&&(p+=C.length,m=R+1)}let b=h,w=u;for(let R=d;R<i&&w<=p;R++,d=R){let C=e[R],_=C>>>4,E=C&15;E===4||E===1?b+=_:E===2||E===6||E===3?w+=_:E!==5&&(b+=_,w+=_)}h=b,u=w;let v=b-(w-p),I=v<a?n[v]:"X";s.push({start:p,base:I,qual:c?o[v]:void 0,altbase:g,length:1,type:"mismatch"}),p++}else y++}return s}var $r={77:0,73:1,68:2,78:3,83:4,72:5,80:6,61:7,88:8};function Br(r=""){let e=0,t=[];for(let n=0,o=r.length;n<o;n++){let s=r.charCodeAt(n);if(s>=48&&s<=57)e=e*10+(s-48);else{let i=$r[s];t.push(e<<4|i),e=0}}return t}function an(r=""){let e=0;for(let s=0,i=r.length;s<i;s++){let a=r.charCodeAt(s);(a<48||a>57)&&e++}let t=new Uint32Array(e),n=0,o=0;for(let s=0,i=r.length;s<i;s++){let a=r.charCodeAt(s);a>=48&&a<=57?n=n*10+(a-48):(t[o++]=n<<4|$r[a],n=0)}return t}function Mt(r,e,t,n,o){let s=Br(r),i=r?Hr(s,t,n,o):[];return e&&t?i.concat(qr(e,s,i,t,o)):i}var ps=397,hs=387,ds=385;function Gr(r){return(1<<r&ps)!==0}function Dr(r){return(1<<r&hs)!==0}function zr(r){return(1<<r&ds)!==0}function fn(r,e,t,n,o,s,i){let a=o===-1?-1:1,c=e,f=o===-1?n:t,l=[],p=1/0,d=-1/0,h=1/0,u=-1/0,m=(y,x)=>{h=Math.min(h,y,x),u=Math.max(u,y,x)};for(let y=0;y<r.length;y++){let x=r[y],S=x>>>4,g=x&15,b=g===9,w=b||Gr(g)?S:0,v=b?r[++y]>>>4:Dr(g)?S:0,I=c+w,R=f+v*a,C=c,_=I;if(_>=s&&C<=i)if(w>0){let E=Math.max(C,s),k=Math.min(_,i);if(k>E)if(p=Math.min(p,E),d=Math.max(d,k),b){let O=v/S,N=k-E,F=Math.round(N*O),H=Math.round(f+(E-c)*O*a);l.push(N<<4|9,F<<4|9),m(H,H+F*a)}else l.push(k-E<<4|g),zr(g)?m(f+(E-c)*a,f+(k-c)*a):m(f,f)}else v>0&&(b?l.push(x,r[y]):l.push(x),p=Math.min(p,c),d=Math.max(d,c),m(f,R));if(c=I,f=R,c>i)break}if(l.length!==0)return{start:p,end:d,mateStart:h,mateEnd:u,cigar:Uint32Array.from(l)}}function us(r){return r===1||r===2||r===3}function cn(r,e,t,n,o,s){let i=o===-1?-1:1,a=[],c=e,f=o===-1?n:t,l,p=!1,d=()=>{l!==void 0&&p&&l.qHi>l.qLo&&a.push({start:l.qLo,end:l.qHi,mateStart:l.tLo,mateEnd:l.tHi,cigar:Uint32Array.from(l.ops)}),l=void 0,p=!1};for(let h=0;h<r.length;h++){let u=r[h],m=u>>>4,y=u&15,x=y===9,S=x?r[++h]:void 0,g=x||Gr(y)?m:0,b=S!==void 0?S>>>4:Dr(y)?m:0,w=f+b*i;us(y)&&m>=s?d():(g>0||b>0)&&(l===void 0&&(l={qLo:c,qHi:c,tLo:f,tHi:f,ops:[]}),l.qHi=c+g,l.tLo=Math.min(l.tLo,f,w),l.tHi=Math.max(l.tHi,f,w),l.ops.push(u),S!==void 0&&l.ops.push(S),p=p||x||zr(y)),c+=g,f=w}return d(),a}function jr(r){let e=r.get("CIGAR");return typeof e=="string"?e:void 0}function Ur(r){let e=r.get("coarseCigar");return typeof e=="string"?e:void 0}function ln(r){let e=jr(r),t=e===void 0?Ur(r):void 0;return e!==void 0?an(e):t!==void 0?nn(t):void 0}var ms=Y(Ae(),1),gs=Y(Qr(),1);var ys=Y(Ae(),1);var ws=Y(so(),1);var Yr=Y(Ae(),1),se=class extends Yr.SimpleFeature{get(e){return e==="mismatches"?Mt(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"?tn(t):void 0}get clipLengthAtStartOfRead(){return this.mate?.start??0}forEachMismatch(e,t){let n=this.get("start"),o=t?.start===void 0?void 0:t.start-n,s=t?.end===void 0?void 0:t.end-n,i=this.get("cs");if(i)rn(i,e,o,s);else{let a=o??Number.NEGATIVE_INFINITY,c=s??Number.POSITIVE_INFINITY;for(let f of Mt(this.walkableCigar))(f.type==="deletion"||f.type==="skip"?f.start<c&&f.start+f.length>a:f.start>=a&&f.start<=c)&&(f.type==="mismatch"?e(88,f.start,f.length,f.base,f.qual??-1,0,0):f.type==="insertion"?e(73,f.start,f.length,f.insertedBases??"",-1,0,f.insertlen):f.type==="deletion"?e(68,f.start,f.length,"",-1,0,0):f.type==="skip"&&e(78,f.start,f.length,"",-1,0,0))}}};var xs=["CIGAR","cs","coarseCigar","cg","cr"];function bs(r){return typeof r=="object"&&r!==null&&"refName"in r&&"start"in r&&"end"in r&&typeof r.refName=="string"&&typeof r.start=="number"&&typeof r.end=="number"}function Ss(r){let e=r.get("mate");return bs(e)?e:void 0}function vs(r,e,t,n){let o=Math.max(r.start,n.start),s=Math.min(r.end,n.end),i=(e.end-e.start)/Math.max(r.end-r.start,1),a=l=>t===-1?e.end-(l-r.start)*i:e.start+(l-r.start)*i,c=Math.round(a(o)),f=Math.round(a(s));return s>o?{start:o,end:s,mateStart:Math.min(c,f),mateEnd:Math.max(c,f)}:void 0}function Is(r,e,t,n){let o={start:r.get("start"),end:r.get("end")},s=r.get("strand")===-1?-1:1,i=o.start>=t.start&&o.end<=t.end,a=i&&n===void 0?void 0:ln(r);if(a===void 0){let c=i?{...o,mateStart:e.start,mateEnd:e.end}:vs(o,e,s,t);return c===void 0?[]:[c]}else return(n===void 0?[{...o,mateStart:e.start,mateEnd:e.end,cigar:a}]:cn(a,o.start,e.start,e.end,s,n)).flatMap(f=>{let l=fn(f.cigar,f.start,f.mateStart,f.mateEnd,s,t.start,t.end);return l===void 0?[]:[l]})}function As(r,e,t,n,o){let s=`:${n.start}-${n.end}${o}`,i=r.toJSON(),a={...i,uniqueId:`${r.id()}${s}`,start:t.start,end:t.end,mate:{...e,start:t.mateStart,end:t.mateEnd}};i.syntenyId!==void 0&&(a.syntenyId=`${String(i.syntenyId)}${s}`);for(let c of xs)delete a[c];return new se(a)}function Vr(r,e,t){let n=Ss(r);if(n===void 0)return[r];{let o=Is(r,n,e,t);return o.map((s,i)=>As(r,n,s,e,o.length>1?`/${i}`:""))}}var Ot=class extends Kr.BaseFeatureDataAdapter{constructor(){super(...arguments);this.recordsAreAlignments=!0}static{this.capabilities=["getFeatures","getRefNames"]}async hasDataForRefName(){return!0}getFeaturesInMultipleRegions(t,n={}){let{clipToRegion:o,splitAtGapBp:s,...i}=n,a=o&&this.recordsAreAlignments,c=(0,Xr.createStatusFanOut)(i.statusCallback);return Zt(t).pipe(ve((f,l)=>this.getFeatures(f,{...i,statusCallback:c()}).pipe(ve(p=>a?Vr(p,p.get("assemblyName")===f.assemblyName?f:{start:p.get("start"),end:p.get("end")},s):[p]),Ct(),Ne(p=>({index:l,features:p})))),Ct(),ve(f=>f.sort((l,p)=>l.index-p.index).flatMap(l=>l.features)))}};var un=class extends Error{constructor(){super("this .gbz.db has no HaplotypeSamples/HaplotypeLengths tables, so its walks cannot be named; run gbz-haplotype-index (from @gmod/gbz-base) over it first");this.name="NoHaplotypeIndexError"}},mn=class extends Error{constructor(t,n){super(n.length===0?`the graph names no reference sample (gbwt_reference_samples) and the anchor "${t}" maps to none; set referenceSample`:`the anchor "${t}" is none of the graph's reference samples (${n.join(", ")}); set referenceSample or map it through assemblyNameToPanSN`);this.name="NoReferenceSampleError"}};function ie(r){return`${r.sample}#${r.haplotype}`}var gn=class extends Error{constructor(t){super(`a pair query names both lanes: queryAssemblyName ${t} came without a targetAssemblyName`);this.name="PairTargetError"}};function Es(r,e){let t=ie(r);return e===void 0||e.some(n=>Ee(t,n))}var yn=class extends Error{constructor(t,n){super(`the graph is cut on its reference, ${n}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${n} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}},wn=class extends Error{constructor(t,n,o){super(`this ${n.toLocaleString()} bp window reads more than nodeLimit (${t.toLocaleString()}) graph nodes; zoom in to about ${o.toLocaleString()} bp or raise nodeLimit`);this.name="NodeLimitError"}};function pn(r,e,t){if(r instanceof Error&&(r.name==="SubgraphLimitError"||/^Subgraph size limit of \d+ nodes exceeded/.test(r.message))){let o=r.walkedBp,s=typeof o=="number"&&o>0?Math.floor(o*.8):Math.floor(t/2);return new wn(e,t,Math.max(s,1))}else return}function Zr(r,e){let t=ie(e);return r[t]??r[e.sample]??t}function Cs({configured:r,anchorPrefix:e,referenceSamples:t}){let n=Sn(e);if(r!=="")return r;if(t.includes(n))return n;if(t.length===1)return t[0];throw new mn(e,t)}function Rs(r,e){return`${ie(r)}#${r.contig}@${e.start.node}.${e.start.offset}`}function _s({alignment:r,assemblyName:e,refName:t,lane:n}){let{refStart:o,refEnd:s,strand:i,cigar:a}=r;if(!(!r.resolved||s<=o)){let{name:c,hapStart:f,hapEnd:l}=r,p=Rs(c,r),d={uniqueId:p,assemblyName:e,refName:t,start:o,end:s,type:"match",strand:i==="-"?-1:1,CIGAR:a,syntenyId:p,mate:{refName:c.contig,start:f,end:l,assemblyName:n}};return new se(d)}}function Ps({pair:r,lane:e,mateLane:t}){let n=`${ie(r.target)}#${r.target.contig}:${r.targetStart}-${r.targetEnd}|${ie(r.query)}#${r.query.contig}:${r.queryStart}-${r.queryEnd}`;return new se({uniqueId:n,assemblyName:e,refName:r.target.contig,start:r.targetStart,end:r.targetEnd,type:"match",strand:r.strand==="-"?-1:1,CIGAR:r.cigar,syntenyId:n,identity:r.matches/Math.max(r.columns,1),numMatches:r.matches,blockLen:r.columns,mate:{refName:r.query.contig,start:r.queryStart,end:r.queryEnd,assemblyName:t}})}var xn=class extends Ot{constructor(){super(...arguments);this.graph=(0,Jr.cachedSetup)({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("haplotypeIndexLocation"),n=!("uri"in t)||t.uri!=="",o=await Oe.open((0,dn.openLocation)(this.getConf("gbzDbLocation"),this.pluginManager),n?{haplotypeIndex:(0,dn.openLocation)(t,this.pluginManager)}:{}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let i=(await o.tag("gbwt_reference_samples")??"").split(/\s+/).filter(c=>c!==""),a=Cs({configured:this.getConf("referenceSample"),anchorPrefix:ue(this,s),referenceSamples:i});return{db:o,anchor:s,referenceSample:a,referenceSamples:i}}})}async referenceQuery(t,n){let{db:o,referenceSample:s}=await this.graph(n),i=(await o.paths()).find(a=>a.isIndexed&&a.name.sample===s&&a.name.contig===t);return i?{sample:i.name.sample,contig:t,haplotype:i.name.haplotype}:void 0}async getHaplotypes(t={}){let{db:n,referenceSamples:o}=await this.graph(t),s=new Map;for(let i of await n.paths()){let a=ie(i.name),c=s.get(a);c?c.contigs.includes(i.name.contig)||c.contigs.push(i.name.contig):s.set(a,{prefix:a,sample:i.name.sample,haplotype:i.name.haplotype,contigs:[i.name.contig],isReference:o.includes(i.name.sample)})}return[...s.values()]}async getHeader(t={}){let{anchor:n,referenceSample:o,referenceSamples:s}=await this.graph(t),i=Lt(this),a=[];for(let c of await this.getHaplotypes(t))c.sample!==o&&a.push({name:Zr(i,c),label:c.prefix,group:c.sample});return{hasCoarseTier:!1,anchorAssemblyName:n,referenceSample:o,referenceSamples:s,lanes:a}}async getRefNames(t={}){let{db:n,anchor:o,referenceSample:s}=await this.graph(t),{assemblyName:i}=t,a=i===o?void 0:ue(this,i),c=(await n.paths()).filter(f=>i===o?f.isIndexed&&f.name.sample===s:Ee(ie(f.name),a)).map(f=>f.name.contig);return[...new Set(c)]}keepPredicate(t,n){let o=t===void 0||t.length===0?void 0:t.map(s=>ue(this,s));return o===void 0&&n===void 0?void 0:s=>Es(s,o)&&(n===void 0||Ee(ie(s),n))}async getSubgraph(t,n={}){let{db:o,anchor:s}=await this.graph(),{assemblyName:i,refName:a,start:c,end:f}=t;if(i!==s)throw new yn(i,s);let l=await this.referenceQuery(a,{}),p=this.getConf("nodeLimit"),d=this.keepPredicate(n.haplotypes),h=l?await o.getSubgraphForRange(l,c,f,{context:this.getConf("context"),snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:p,signal:n.signal,...d===void 0?{}:{keep:d}}).catch(u=>{throw pn(u,p,f-c)??u}):void 0;return h?h.toGFA({names:"resolved"}):""}async laneHaplotypes(t,n){let o=ue(this,t);return(await this.getHaplotypes(n)).filter(s=>Ee(s.prefix,o))}async referencePieces(t,n,o,s){let{db:i,referenceSample:a}=await this.graph(s),c=(await i.paths()).filter(l=>l.isIndexed&&l.name.sample===a&&l.name.contig===t&&l.name.fragment>n&&l.name.fragment<o).map(l=>l.name.fragment),f=[n,...[...new Set(c)].sort((l,p)=>l-p),o];return f.slice(1).map((l,p)=>({start:f[p],end:l}))}async anchorFeatures(t,n){let{db:o}=await this.graph(n),{assemblyName:s,refName:i,start:a,end:c}=t,f=ue(this,n.targetAssemblyName),l=Lt(this),p=this.keepPredicate(n.haplotypes,f),d=await this.referenceQuery(i,n),h=this.getConf("nodeLimit");return(d?await(0,hn.updateStatus)(`Reading graph ${i}:${a.toLocaleString()}-${c.toLocaleString()}`,n.statusCallback,()=>o.getAlignmentsForRange(d,a,c,{context:this.getConf("context"),haplotypes:"all",limit:h,signal:n.signal,...p===void 0?{}:{keep:p}}).catch(m=>{throw pn(m,h,c-a)??m})):[]).flatMap(m=>{let y=m.resolved?_s({alignment:m,assemblyName:s,refName:i,lane:Zr(l,m.name)}):void 0;return y===void 0?[]:[y]})}async pairFeatures(t,n,o){let{targetAssemblyName:s}=o;if(s===void 0)throw new gn(n);let{db:i}=await this.graph(o),{refName:a,start:c,end:f}=t,l=await this.laneHaplotypes(n,o),p=await this.laneHaplotypes(s,o),d=[...l,...p],h=await this.referenceQuery(a,o),u=this.getConf("nodeLimit"),m=await i.haplotypeAnchorSpacing()!==void 0,y=(g,b)=>i.getSubgraphForRange(g,b.start,b.end,{context:this.getConf("context"),haplotypes:"all",limit:u,signal:o.signal,keep:w=>d.some(v=>v.sample===w.sample&&v.haplotype===w.haplotype)}).catch(w=>{throw pn(w,u,f-c)??w}),x=h&&m&&l.length>0&&p.length>0?(await(0,hn.updateStatus)(`Aligning ${n} to ${s}`,o.statusCallback,async()=>Promise.all((await this.referencePieces(a,c,f,o)).map(g=>y(h,g))))).filter(g=>g!==void 0):[];return x.every(g=>{let b=g.stats.anchorWalk;return b!==void 0&&b.fallback===void 0})?x.flatMap(g=>l.flatMap(b=>p.flatMap(w=>g.pairAlignments({target:b,query:w}).map(v=>Ps({pair:v,lane:n,mateLane:s}))))):[]}getFeatures(t,n={}){return(0,eo.ObservableCreate)(async o=>{let{db:s,anchor:i}=await this.graph(n);if(!s.hasHaplotypeIndex)throw new un;if(t.assemblyName===i){let a=n.queryAssemblyName===void 0?await this.anchorFeatures(t,n):await this.pairFeatures(t,n.queryAssemblyName,n);for(let c of a)o.next(c)}o.complete()},n.signal)}};export{yn as HaplotypeWindowError,un as NoHaplotypeIndexError,mn as NoReferenceSampleError,wn as NodeLimitError,gn as PairTargetError,xn as default,_s as fragmentFeature,ie as haplotypePrefix,Zr as laneAssemblyName,pn as nodeLimitError,Ps as pairFeature,Cs as resolveReferenceSample};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-6UTRY4CV.js.map