chromosomix 0.16.0 → 0.17.0

package/dist/assets/reader.worker-Zet76cxB.js

@@ -0,0 +1,9 @@
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n===""?this.group:Hi(this.group==="/"?`/${n}`:`${this.group}/${n}`)}describe(t){return`${this.uri} :: ${this.resolve(t)}`}entity(t){this.assertOpen();const n=this.resolve(t);return n==="/"?this.file:this.file.get(n)}dataset(t){const n=this.entity(t);if(n===null)throw new st(`${this.describe(t)} does not exist`,{uri:this.uri,path:this.resolve(t)});if(!(n instanceof this.h5.Dataset))throw new st(`${this.describe(t)} is not a dataset`,{uri:this.uri,path:this.resolve(t)});return n}range(t,n,s){const o=t.metadata.shape;if(!o||o.length!==1)throw new st(`/${t.path.replace(/^\//,"")} is ${o?`${o.length}-D`:"scalar"}; this reader only slices 1-D columns`,{path:t.path,shape:o});const r=o[0],i=Math.min(Math.max(Math.trunc(n??0),0),r),a=Math.min(Math.max(Math.trunc(s??r),i),r);return[i,a]}decodeAttr(t,n,s,o){if(s.type===this.h5.Module.H5T_class_t.H5T_STRING.value&&!s.vlen){const r=this.readFixedStringAttr(t,n,s);if(r!==null)return r}return El(o)}readFixedStringAttr(t,n,s){const 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qt=4096,es={binsPerCell:1,contigsPerCell:1};function qi(e,t,n,s=es,o){const r=Math.max(0,Math.trunc(e));if(r===0)return{slot:new Int32Array(0),cellStart:new Int32Array(1),cellSegments:new Int32Array(0),cells:0,plan:es};const i=t.length>0?t.length:1,a=Math.max(1,Math.trunc(n)),c=h=>t.length>0?t[h]:0,l=h=>(h+1<i?c(h+1):r)-c(h),u=Math.max(s.binsPerCell,Wi(i,l,a,o));return Cl(r,i,c,l,u,o)}function vl(e,t,n,s){let o=0,r=0,i=-1;for(let a=0;a<e;a++){const c=t(a);if(c>=n){o+=Math.ceil(c/n),r=0,i=-1;continue}const l=s===void 0?0:s[a];r===0||r+c>n||l!==i?(o++,r=c,i=l):r+=c}return o}function Wi(e,t,n,s){let o=s;const r=c=>vl(e,t,c,o)<=n;let i=1;for(;!r(i);)if(i>=Number.MAX_SAFE_INTEGER/2){if(o===void 0)return i;o=void 0,i=1}else i*=2;let a=1;for(;a<i;){const c=a+i>>1;r(c)?i=c:a=c+1}return a}function Cl(e,t,n,s,o,r){const i=new Int32Array(e),a=[],c=[];let l=0,u=0,h=-1;for(let d=0;d<t;d++){const m=n(d),g=s(d),w=m+g;if(g>=o){u=0,h=-1;for(let 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Yo(e,t,n){const s=e.ids.length;if(s<=t)return{grouping:e,perCell:1};const o=Int32Array.from({length:s},(l,u)=>u),r=n===void 0?void 0:Int32Array.from(e.ids,n),i=qi(s,o,t,es,r),a=new Int32Array(e.slot.length);for(let l=0;l<a.length;l++){const u=e.slot[l];a[l]=u<0?-1:i.slot[u]}const c=new Int32Array(i.cells);for(let l=0;l<i.cells;l++)c[l]=e.ids[i.cellStart[l]];return{grouping:{slot:a,ids:c},perCell:i.plan.contigsPerCell}}function Ol(e,t,n,s,o,r,i=!0,a=Number.POSITIVE_INFINITY){const c=m=>o==="contig"?Qi(n,m[0],m[1]):Yi(n,s,m[0],m[1]),l=e[0]===t[0]&&e[1]===t[1],u=o==="contig"&&s.length>0?m=>s[m]??-1:void 0,h=Yo(c(e),a,u),f=l?h:Yo(c(t),a,u),d=Vs(e,t,h.grouping,f.grouping,r,i);return{place:d.place,finish:()=>({...d.finish(),level:o}),perCell:Math.max(h.perCell,f.perCell)}}function Vs(e,t,n,s,o,r=!0,i=!1){const c=e[0]===t[0]&&e[1]===t[1]&&r,l=n.ids.length,u=s.ids.length,h=i&&c&&l===u,f=new Float64Array(h?l*(l+1)/2:l*u),[d,m]=e,[g,w]=t,p=o!=="transpose",b=o!=="direct"&&!c,y=o==="symmetric",A=(x,E,S)=>{const v=n.slot[x],I=s.slot[E];if(!(v<0||I<0)){if(h){const N=v<I?v:I,B=v<I?I:v;f[N*l-N*(N-1)/2+(B-N)]+=S;return}f[c&&v>I?I*u+v:v*u+I]+=S}};return{place(x,E,S){Number.isNaN(S)||(p&&x>=d&&x<m&&E>=g&&E<w&&A(x-d,E-g,S),b&&!(y&&x===E)&&E>=d&&E<m&&x>=g&&x<w&&A(E-d,x-g,S))},finish(){if(h){const x=new Float32Array(l*l);let E=0;for(let S=0;S<l;S++)for(let v=S;v<l;v++,E++){const I=f[E];x[S*l+v]=I,x[v*l+S]=I}return{nrows:l,ncols:u,values:x,rowIds:n.ids,colIds:s.ids}}if(c)for(let x=0;x<l;x++)for(let E=x+1;E<u;E++)f[E*u+x]=f[x*u+E];return{nrows:l,ncols:u,values:f,rowIds:n.ids,colIds:s.ids}}}}function kl(e,t,n,s,o=!0){const r=l=>s==="contig"?Qi(t,l[0],l[1]):Yi(t,n,l[0],l[1]),i=e.rowExtent[0]===e.colExtent[0]&&e.rowExtent[1]===e.colExtent[1],a=r(e.rowExtent),c=i?a:r(e.colExtent);return Bl(e,a,c,s,i&&o)}function _l(e,t){let n=0,s=e.length-1;for(;n<s;){const o=n+s+1>>1;e[o]<=t?n=o:s=o-1}return n}class Tl{binsize;chromOffset;contigLengths;constructor(t,n,s){this.binsize=t,this.chromOffset=n,this.contigLengths=s}get nContigs(){return this.contigLengths.length}get nBins(){return this.chromOffset.length>0?this.chromOffset[this.chromOffset.length-1]:0}binsInContig(t){return Math.ceil(this.contigLengths[t]/this.binsize)}contigStartBin(t){return this.chromOffset[t]}contigBinExtent(t){return[this.chromOffset[t],this.chromOffset[t+1]]}binIndex(t,n){return this.chromOffset[t]+Math.floor(n/this.binsize)}contigOfBin(t){return _l(this.chromOffset,t)}binStart(t){const n=this.contigOfBin(t);return(t-this.chromOffset[n])*this.binsize}binEnd(t){const n=this.contigOfBin(t),s=(t-this.chromOffset[n])*this.binsize;return Math.min(s+this.binsize,this.contigLengths[n])}contigsOfBins(t,n){const s=new Int32Array(Math.max(0,n-t));if(s.length===0)return s;let o=this.contigOfBin(t),r=this.chromOffset[o+1];for(let i=t;i<n;i++){for(;i>=r&&o+1<this.nContigs;)o+=1,r=this.chromOffset[o+1];s[i-t]=o}return s}}function Fl(e,t,n){if(e===t||e.binsize===t.binsize)return[n[0],n[1]];if(n[1]<=n[0]){const g=Math.min(Math.max(n[0],0),t.nBins);return[g,g]}const s=g=>Math.min(Math.max(g,0),Math.max(0,e.nBins-1)),o=e.contigOfBin(s(n[0])),[r]=e.contigBinExtent(o),[i,a]=t.contigBinExtent(o),c=n[0]<=r?i:Math.min(Math.max(i,a-1),i+Math.floor((n[0]-r)*e.binsize/t.binsize)),l=e.contigOfBin(s(n[1]-1)),[u,h]=e.contigBinExtent(l),[f,d]=t.contigBinExtent(l),m=n[1]>=h?d:Math.min(d,f+Math.ceil((n[1]-u)*e.binsize/t.binsize));return[Math.min(c,Math.max(0,m-1)),Math.min(t.nBins,Math.max(c+1,m))]}class Vi{constructor(t,n,s){this.handle=t,this.nBins=n,this.countKind=s}offsets=null;get nnz(){return this.handle.datasetLength("pixels/bin1_id")}scoreColumns(){return Dc(this.handle)}binOffsets(){return this.offsets??=this.handle.readNumeric("indexes/bin1_offset"),this.offsets}async forEachWindow(t,n,s,o,r={}){return 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m.gap=="number"&&m.gap>0&&h.push({gap:Math.round(m.gap)});continue}if(typeof m.sequence!="string"||typeof m.start!="number"||typeof m.end!="number"||m.strand!==1&&m.strand!==-1)continue;const g=i(m.sequence,m.start,m.end);g!==null&&(r(m.sequence,g[0],g[1]),h.push({id:n.next(m.sequence),sequence:m.sequence,start:g[0],end:g[1],strand:m.strand}))}for(;h.length>0&&at(h[0]);)h.shift();for(;h.length>0&&at(h[h.length-1]);)h.pop();if(h.length===0)continue;const f=typeof u.name=="string"?u.name:"",d=f!==""&&!a.has(f)?f:Xt(f===""?"seq":f,a);a.add(d),c.push({name:d,parts:Pt(h),...u.circular===!0?{circular:!0}:{}})}const l=[];for(const u of Array.isArray(e.aside)?e.aside:[]){if(u===null||typeof u!="object"||typeof u.sequence!="string"||!Jl.includes(u.why))continue;const h=i(u.sequence,u.start,u.end);if(h===null)continue;r(u.sequence,h[0],h[1]);const f=typeof u.genome=="string"&&u.genome!==""?u.genome:void 0;l.push({piece:{id:n.next(u.sequence),sequence:u.sequence,start:h[0],end:h[1],strand:1},why:u.why,...f===void 0?{}:{genome:f}})}for(let u=0;u<t.names.length;u++){const h=t.names[u],f=(o.get(h)??[]).sort((m,g)=>m[0]-g[0]);let d=0;for(const[m,g]of f)m>d&&l.push({piece:{id:n.next(h),sequence:h,start:d,end:m,strand:1},why:"unplaced"}),d=Math.max(d,g);d<t.lengths[u]&&l.push({piece:{id:n.next(h),sequence:h,start:d,end:t.lengths[u],strand:1},why:"unplaced"})}return{sequences:c,aside:l}}function on(e){return e.replace(/_e\d+$/,"")}function fs(e,t){let n=0,s=null;for(const i of e.parts){if(at(i)||i.strand!==1||i.start!==n||s!==null&&i.sequence!==s)return!1;s=i.sequence,n=i.end}if(s===null)return!1;const o=t.names.indexOf(s);if(o>=0)return n===t.lengths[o];const r=t.elsewhere?.find(i=>i.name===s);return r!==void 0&&n===r.length}function ru(e,t){const n=new Set(us(t).keys()),s=new Set(e.sequences.map(o=>o.name));for(const o of e.sequences)n.has(o.name)&&!fs(o,t)&&(s.delete(o.name),o.name=Xt(on(o.name),s),s.add(o.name));for(const o of e.sequences){if(o.named===!0)continue;const r=Ji(o,t);r!==null&&o.name!==r&&!s.has(r)&&(s.delete(o.name),o.name=r,s.add(r))}return e}function Ji(e,t){if(!fs(e,t))return null;const n=e.parts[0];return at(n)?null:n.sequence}class pn{original;sequences;aside;offsets=new Map;byOriginal=new Map;constructor(t,n){this.original=t,this.sequences=n.sequences,this.aside=n.aside;for(const s of n.sequences){const o=[];let r=0;for(const i of s.parts){if(o.push(r),!at(i)){const a=this.byOriginal.get(i.sequence)??[];a.push({sequence:s.name,offset:r,piece:i}),this.byOriginal.set(i.sequence,a)}r+=hs(i)}o.push(r),this.offsets.set(s.name,o)}for(const s of this.byOriginal.values())s.sort((o,r)=>o.piece.start-r.piece.start)}static of(t){const n=new eu;let s=nu(t.original);const o=Zt(t.cursor,0,t.history.length);for(let r=0;r<o;r++)s=ru(su(s,t.history[r].step,t.original,n),t.original);return new pn(t.original,s)}get isIdentity(){return this.aside.length===0&&this.sequences.length===this.original.names.length&&this.sequences.every((t,n)=>t.name===this.original.names[n]&&fs(t,this.original))}sequence(t){return this.sequences.find(n=>n.name===t)??null}lengthOf(t){const n=this.offsets.get(t);return n===void 0?null:n[n.length-1]}contigs(){return this.sequences.map(t=>({name:t.name,length:this.lengthOf(t.name)??0}))}toOriginal(t,n){const s=this.sequence(t),o=this.offsets.get(t);if(s===null||o===void 0)return null;const r=iu(o,n);if(r<0)return null;const i=s.parts[r];if(at(i))return null;const a=n-o[r];return i.strand===1?{sequence:i.sequence,bp:i.start+a,strand:1}:{sequence:i.sequence,bp:i.end-1-a,strand:-1}}toEdited(t,n){const s=[];for(const o of this.landings(t)){const r=o.piece;n<r.start||n>=r.end||s.push(r.strand===1?{sequence:o.sequence,bp:o.offset+(n-r.start),strand:1}:{sequence:o.sequence,bp:o.offset+(r.end-1-n),strand:-1})}return s}landings(t){return this.byOriginal.get(t)??[]}piecesIn(t,n,s){const o=this.sequence(t),r=this.offsets.get(t);if(o===null||r===void 0)return[];const i=[];for(let a=0;a<o.parts.length;a++){const c=o.parts[a],l=r[a],u=r[a+1];if(at(c)||u<=n||l>=s)continue;const h=Math.max(n,l)-l,f=Math.min(s,u)-l,d=c.strand===1?{...c,start:c.start+h,end:c.start+f}:{...c,start:c.end-f,end:c.end-h};i.push({offset:l+h,piece:d})}return i}junctions(){const t=[];for(const n of this.sequences){const s=this.offsets.get(n.name)??[];for(let o=1;o<n.parts.length;o++)t.push({sequence:n.name,at:s[o]})}return t}}function iu(e,t){if(t<0||t>=e[e.length-1])return-1;let n=0,s=e.length-2;for(;n<=s;){const o=n+s>>1;if(t<e[o])s=o-1;else if(t>=e[o+1])n=o+1;else return o}return-1}function au(e){const t=JSON.stringify(e.history.slice(0,e.cursor).map(s=>s.step));let n=2166136261;for(let s=0;s<t.length;s++)n^=t.charCodeAt(s),n=Math.imul(n,16777619);return`${e.cursor}:${(n>>>0).toString(36)}`}function cu(e,t,n){const s=e.original;if(s.genome!==void 0){const o=new Map(t.map((r,i)=>[r,n[i]]));for(const[r,i]of us(s)){const a=o.get(r);if(a===void 0)return`the edit names ${r}, which this file does not have`;if(a!==i)return`${r} is ${i} bp in the edit and ${a} bp here`}return null}if(s.names.length!==t.length)return`the edit was made on ${s.names.length} sequences and this file has ${t.length}`;for(let o=0;o<t.length;o++){if(s.names[o]!==t[o])return`sequence ${o+1} is ${s.names[o]} in the edit and ${t[o]} here`;if(s.lengths[o]!==n[o])return`${t[o]} is ${s.lengths[o]} bp in the edit and ${n[o]} bp here`}return null}const lu=64;class bo{names;lengths;chromOffset;toOriginal;landingStart;landings;originalBins;constructor(t){this.names=t.names,this.lengths=t.lengths,this.chromOffset=t.chromOffset,this.toOriginal=t.toOriginal,this.originalBins=t.originalBins;const n=new Int32Array(t.originalBins+1);for(const r of t.toOriginal)r>=0&&n[r+1]++;for(let r=0;r<t.originalBins;r++)n[r+1]+=n[r];const s=n.slice(0,t.originalBins),o=new Int32Array(n[t.originalBins]);t.toOriginal.forEach((r,i)=>{r>=0&&(o[s[r]++]=i)}),this.landingStart=n,this.landings=o}get nBins(){return this.toOriginal.length}static of(t,n,s){const o=t.binsize,r=new Map(n.map((u,h)=>[u,h])),i=[],a=[],c=[],l=[0];for(const u of s.sequences){const h=s.lengthOf(u.name)??0,f=Math.ceil(h/o);let d=0;u.parts.forEach((m,g)=>{const w=at(m)?m.gap:m.end-m.start,p=Math.min(f,Math.round(d/o));d+=w;const b=g===u.parts.length-1?f:Math.min(f,Math.round(d/o)),y=Math.max(0,b-p),A=at(m)?void 0:r.get(m.sequence);if(at(m)||A===void 0){for(let R=0;R<y;R++)i.push(-1);return}const[x,E]=t.contigBinExtent(A),S=E-x,v=t.contigLengths[A],I=R=>R>=v?S:Math.max(0,Math.min(S,Math.round(R/o)));let N=I(m.start),B=I(m.end);B<=N&&(N=Math.max(0,Math.min(S-1,Math.floor((m.start+m.end)/2/o))),B=N+1);const z=B-N;for(let R=0;R<y;R++){const P=Math.min(z-1,Math.floor((R+.5)*z/y));i.push(x+(m.strand===1?N+P:B-1-P))}}),a.push(u.name),c.push(h),l.push(i.length)}return new bo({names:a,lengths:Float64Array.from(c),chromOffset:Float64Array.from(l),toOriginal:Int32Array.from(i),originalBins:t.nBins})}originalBands(t){const n=new Uint8Array(this.originalBins);for(const[s,o]of t)for(let r=Math.max(0,s);r<Math.min(this.nBins,o);r++){const i=this.toOriginal[r];i>=0&&(n[i]=1)}return this.bandsOf(n)}windowBands(t,n){const s=([r,i])=>{let a=-1;for(let c=Math.max(0,r);c<Math.min(this.nBins,i);c++)a=Math.max(a,this.toOriginal[c]);return a},o=new Uint8Array(this.originalBins);for(const[[r,i],a]of[[t,s(n)],[n,s(t)]])for(let c=Math.max(0,r);c<Math.min(this.nBins,i);c++){const l=this.toOriginal[c];l>=0&&l<=a&&(o[l]=1)}return this.bandsOf(o)}bandsOf(t){const n=[];let s=-1;for(let o=0;o<=this.originalBins;o++){const r=o<this.originalBins&&t[o]===1;r&&s<0&&(s=o),!r&&s>=0&&(n.push([s,o]),s=-1)}return n}originalRectangles(t,n,s){const o=new Uint8Array(this.originalBins);for(const[[l,u],h]of[[t,1],[n,2]])for(let f=Math.max(0,l);f<Math.min(this.nBins,u);f++){const d=this.toOriginal[f];d>=0&&(o[d]|=h)}const r=[];let i=-1,a=0;for(let l=0;l<=this.originalBins;l++){const u=l<this.originalBins?o[l]:0;u!==0?(i<0&&(i=l,a=0),a|=u):i>=0&&(r.push({extent:[i,l],bits:a}),i=-1)}const c=[];for(let l=0;l<r.length;l++)for(let u=l;u<r.length;u++){const h=r[l].bits,f=r[u].bits;if(h&1&&f&2||h&2&&f&1){if(c.length===s)return null;c.push([r[l].extent,r[u].extent])}}return c}translate(t,n,s,o){s.reset();const{landingStart:r,landings:i}=this,[[a,c],[l,u]]=o??[[0,this.originalBins],[0,this.originalBins]];for(let h=0;h<t.length;h++){const f=t.bin1[h],d=t.bin2[h];if(o!==void 0&&!(f>=a&&f<c&&d>=l&&d<u)&&!(f>=l&&f<u&&d>=a&&d<c))continue;const m=r[f],g=r[f+1];if(m===g)continue;const w=r[d],p=r[d+1];if(w===p)continue;const b=t.count[h];if(f===d&&n){for(let y=m;y<g;y++)for(let A=y;A<g;A++)s.push(i[y],i[A],b,n);continue}for(let y=m;y<g;y++)for(let A=w;A<p;A++)s.push(i[y],i[A],b,n)}return s.chunk()}gather(t,n=0,s=this.nBins){const o=new Float64Array(Math.max(0,s-n));for(let r=n;r<s;r++){const i=this.toOriginal[r];o[r-n]=i>=0&&i<t.length?t[i]:Number.NaN}return o}gatherText(t,n=0,s=this.nBins){const o=[];for(let r=n;r<s;r++){const i=this.toOriginal[r];o.push(i>=0&&i<t.length?t[i]:"")}return o}}class ta{bin1=new Int32Array(1024);bin2=new Int32Array(1024);count=new Float64Array(1024);length=0;reset(){this.length=0}push(t,n,s,o){this.length===this.bin1.length&&this.grow();const r=o&&t>n;this.bin1[this.length]=r?n:t,this.bin2[this.length]=r?t:n,this.count[this.length]=s,this.length++}chunk(){return{bin1:this.bin1,bin2:this.bin2,count:this.count,length:this.length}}grow(){const t=this.bin1.length*2,n=new Int32Array(t);n.set(this.bin1);const s=new Int32Array(t);s.set(this.bin2);const o=new Float64Array(t);o.set(this.count),this.bin1=n,this.bin2=s,this.count=o}}class uu{constructor(t,n,s){this.inner=t,this.lens=n,this.upper=s}buffer=new ta;get nnz(){return this.inner.nnz}get countKind(){return this.inner.countKind}scoreColumns(){return this.inner.scoreColumns()}binOffsets(){const t=this.inner.binOffsets(),n=new Float64Array(this.lens.nBins+1);for(let s=0;s<this.lens.nBins;s++){const o=this.lens.toOriginal[s];n[s+1]=n[s]+(o>=0?t[o+1]-t[o]:0)}return n}async forEachWindow(t,n,s,o,r){const i=this.inner.rectangular===!0?this.lens.originalRectangles(t,n,lu):null;if(i===null){const c=this.upper?this.lens.windowBands(t,n):this.lens.originalBands([t]);return c.length===0?!0:this.inner.forEachBands(c,l=>o(this.lens.translate(l,this.upper,this.buffer)),r)}const a=this.upper?"symmetric-upper":"square";for(const c of i){const[l,u]=c;if(!await this.inner.forEachWindow(l,u,Te(l,u,a),f=>o(this.lens.translate(f,this.upper,this.buffer,c)),r))return!1}return!0}forEachBands(t,n,s){const o=this.lens.originalBands(t);return o.length===0?Promise.resolve(!0):this.inner.forEachBands(o,r=>n(this.lens.translate(r,this.upper,this.buffer)),s)}scanAll(t){return this.inner.scanAll({...t,onChunk:n=>t.onChunk(this.lens.translate(n,this.upper,this.buffer))})}}function hu(e,t,n,s){const o=new Map,r=new Map,i=c=>c.startsWith("bins/"),a=c=>c==="chroms"||c==="contigs";return new Proxy(e,{get(c,l){switch(l){case"attrs":return()=>s;case"datasetLength":return u=>i(u)?t.nBins:u.startsWith("chroms/")||u.startsWith("contigs/")?n.length:c.datasetLength(u);case"readNumeric":return(u,h,f)=>{if(!i(u))return c.readNumeric(u,h,f);let d=o.get(u);return d===void 0&&(d=c.readNumeric(u),o.set(u,d)),t.gather(d,h??0,f??t.nBins)};case"readStrings":return(u,h,f)=>{if(!i(u))return c.readStrings(u,h,f);let d=r.get(u);return d===void 0&&(d=c.readStrings(u),r.set(u,d)),t.gatherText(d,h??0,f??t.nBins)};case"readTable":return(u,h,f,d)=>a(u)?n:c.readTable(u,h,f,d);default:{const u=Reflect.get(c,l,c);return typeof u=="function"?u.bind(c):u}}}})}function fu(e){return De(e.names.length,["name","length"],{name:e.names,length:e.lengths})}function du(e,t,n,s={}){const o=cu(e,t,Array.from(n));if(o!==null)return{refusal:`The edit was made on another assembly: ${o}.`};const r=pn.of(e);return r.isIdentity&&s.always!==!0?null:{assembly:r}}class yo{constructor(t,n,s){this.factor=t,this.fineOffset=n,this.chromOffset=s}static of(t,n){const s=Float64Array.from(t),o=new Float64Array(s.length);for(let r=0;r+1<s.length;r++)o[r+1]=o[r]+Math.ceil((s[r+1]-s[r])/n);return new yo(n,s,o)}get nBins(){return this.chromOffset[this.chromOffset.length-1]??0}get fineBins(){return this.fineOffset[this.fineOffset.length-1]??0}coarseBin(t){if(t>=this.fineBins)return this.nBins;const n=Ko(this.fineOffset,t);return this.chromOffset[n]+Math.floor((t-this.fineOffset[n])/this.factor)}fineBin(t){if(t>=this.nBins)return this.fineBins;const n=Ko(this.chromOffset,t);return this.fineOffset[n]+(t-this.chromOffset[n])*this.factor}toFine(t){return[this.fineBin(t[0]),this.fineBin(t[1])]}toCoarse(t){const n=this.coarseBin(t[0]);return t[1]<=t[0]?[n,n]:[n,this.coarseBin(t[1]-1)+1]}coarseIndex(){const t=new Int32Array(this.fineBins);for(let n=0;n+1<this.fineOffset.length;n++){const s=this.chromOffset[n],o=this.fineOffset[n];for(let r=o;r<this.fineOffset[n+1];r++)t[r]=s+Math.floor((r-o)/this.factor)}return t}}function Ko(e,t){let n=0,s=e.length-1;for(;n<s;){const o=n+s>>>1;e[o]<=t?n=o+1:s=o}return Math.max(0,n-1)}const mu="weight",gu=65536;class wu{constructor(t,n,s){this.inner=t,this.grid=n,this.storageMode=s}index=null;get nnz(){return null}get countKind(){return this.inner.countKind}get rectangular(){return this.inner.rectangular}scoreColumns(){return this.inner.scoreColumns()}binOffsets(){const t=this.inner.binOffsets(),n=new Float64Array(this.grid.nBins+1);for(let s=0;s<=this.grid.nBins;s++)n[s]=t[this.grid.fineBin(s)]??0;return n}async forEachWindow(t,n,s,o,r){const i=this.grid.toFine(t),a=this.grid.toFine(n),c=Te(i,a,this.storageMode),l=new ys(this.coarseIndex(),{rows:t,cols:n,mode:c.mode},o),u=await this.inner.forEachWindow(i,a,c,h=>l.add(h),r);return u&&l.finish(),u}forEachBands(t,n,s){const o=t.map(i=>this.grid.toFine(i)).filter(([i,a])=>a>i);if(o.length===0)return Promise.resolve(!0);const r=new ys(this.coarseIndex(),this.grid.nBins,n);return this.inner.forEachBands(o,i=>r.add(i),s).then(i=>(i&&r.finish(),i))}async scanAll(t){let n=!1;const s=new ys(this.coarseIndex(),this.grid.nBins,o=>{n||t.onChunk(o)===!1&&(n=!0)});await this.inner.scanAll({...t,onChunk:o=>(s.add(o),!n)}),n||s.finish()}coarseIndex(){return this.index??=this.grid.coarseIndex(),this.index}}class ys{constructor(t,n,s){this.coarseOf=t,this.reach=n,this.emit=s,typeof n=="number"?(this.colLo=0,this.colSpan=n,this.rowLo=0,this.sums=new Float64Array(n)):(this.colLo=n.cols[0],this.colSpan=n.cols[1]-n.cols[0],this.rowLo=n.rows[0],this.sums=new Float64Array(this.colSpan+(n.rows[1]-n.rows[0]))),this.stamp=new Int32Array(this.sums.length)}sums;stamp;touched=new Int32Array(256);nTouched=0;row=-1;generation=0;out=new ta;held=0;colLo;colSpan;rowLo;add(t){const{bin1:n,bin2:s,count:o,length:r}=t,i=this.coarseOf,a=typeof this.reach=="number"?null:this.reach;for(let c=0;c<r;c++){const l=i[n[c]],u=i[s[c]];if(l===void 0||u===void 0||a!==null&&!pu(a,l,u))continue;l!==this.row&&this.startRow(l);let h=u-this.colLo;if((h<0||h>=this.colSpan)&&(h=this.colSpan+(u-this.rowLo)),!(h<0||h>=this.sums.length))if(this.stamp[h]!==this.generation){if(this.stamp[h]=this.generation,this.sums[h]=o[c],this.nTouched===this.touched.length){const f=new Int32Array(this.touched.length*2);f.set(this.touched),this.touched=f}this.touched[this.nTouched++]=u}else this.sums[h]+=o[c]}this.held>0&&this.handOn()}finish(){this.closeRow(),this.row=-1,this.held>0&&this.handOn()}startRow(t){this.closeRow(),this.row=t,this.generation++}closeRow(){if(this.nTouched===0)return;const t=this.touched.subarray(0,this.nTouched).sort();for(const n of t){let s=n-this.colLo;(s<0||s>=this.colSpan)&&(s=this.colSpan+(n-this.rowLo)),this.out.push(this.row,n,this.sums[s],!1),this.held++}this.nTouched=0,this.held>=gu&&this.handOn()}handOn(){this.emit(this.out.chunk()),this.out.reset(),this.held=0}}function pu(e,t,n){const{rows:s,cols:o,mode:r}=e;return r!=="transpose"&&t>=s[0]&&t<s[1]&&n>=o[0]&&n<o[1]?!0:r!=="direct"&&n>=s[0]&&n<s[1]&&t>=o[0]&&t<o[1]}function bu(e,t,n){const s=new Map,o=new Map,r=c=>c.startsWith("bins/"),i=c=>{let l=s.get(c);return l===void 0&&(l=yu(c.slice(5),e.readNumeric(c),t),s.set(c,l)),l},a=c=>{let l=o.get(c);if(l===void 0){const u=e.readStrings(c);l=[];for(let h=0;h<t.nBins;h++)l.push(u[t.fineBin(h)]??"");o.set(c,l)}return l};return new Proxy(e,{get(c,l){switch(l){case"attrs":return()=>n;case"datasetLength":return u=>r(u)?t.nBins:c.datasetLength(u);case"readNumeric":return(u,h,f)=>r(u)?i(u).slice(h??0,f??t.nBins):c.readNumeric(u,h,f);case"readStrings":return(u,h,f)=>r(u)?a(u).slice(h??0,f??t.nBins):c.readStrings(u,h,f);default:{const u=Reflect.get(c,l,c);return typeof u=="function"?u.bind(c):u}}}})}function yu(e,t,n){const s=new Float64Array(n.nBins);for(let o=0;o<n.nBins;o++){const r=n.fineBin(o),i=n.fineBin(o+1);if(e==="chrom"||e==="start")s[o]=t[r];else if(e==="end")s[o]=t[i-1];else if(e===mu){let a=0,c=0;for(let l=r;l<i;l++){const u=t[l];Number.isFinite(u)&&u>0&&(a++,c+=1/u)}s[o]=a===0?Number.NaN:a/c}else{let a=0,c=0;for(let l=r;l<i;l++){const u=t[l];Number.isFinite(u)&&(a++,c+=u)}s[o]=a===0?Number.NaN:c/a}}return s}const 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Resampling reads raw counts — whole numbers, one per contact.`,{value:E}),!1;if(E===0)continue;const S=p[x],v=b[x];if(v<S)return l=Jt("This map stores pixels below its diagonal, so each contact would be drawn twice. Resampling reads upper-triangular files — cooler’s default."),!1;const I=s.of(S),N=v<t[I+1]?I:s.of(v);c++,i!==null?i[I*o+N]+=E:a.set(I*o+N,(a.get(I*o+N)??0)+E)}return!0},onProgress:n.onProgress}),l!==null)throw l;if(u)throw new DOMException("The census was cancelled.","AbortError");const h=[];if(i!==null)for(let w=0;w<i.length;w++)i[w]>0&&h.push(w);else{for(const w of a.keys())h.push(w);h.sort((w,p)=>w-p)}const f=new Int32Array(h.length),d=new Int32Array(h.length),m=new Float64Array(h.length);let g=0;for(let w=0;w<h.length;w++){const p=h[w];f[w]=Math.floor(p/o),d[w]=p-f[w]*o,m[w]=i!==null?i[p]:a.get(p),g+=m[w]}return{total:g,nnz:c,sequences:o,nBins:r,a:f,b:d,sum:m}}function Zu(e){if(!Number.isFinite(e)||!Number.isInteger(e)||e<=0)throw Jt(`${e} is not a number of contacts: it must be a positive whole number.`,{contacts:e});if(e>Number.MAX_SAFE_INTEGER)throw Jt(`${e} contacts is past what can be counted exactly here (2⁵³).`,{contacts:e});return e}function Ju(e,t,n,s){const o=Zu(t.contacts),r=e.total;if(!(r>0))throw Jt("This map holds no contacts, so there is nothing to draw from it.",{total:r});const i=t.seed??qu,a=t.alpha??Ao,c=Wu(r,o),l=new Map,u={mode:c,contacts:o,total:r,seed:i,alpha:a,shares:l,weightScale:Math.sqrt(r/o)};if(c==="none")return u;const h=new na(ea(i,ju,c==="sub"?ra:ia)),f=e.sum.length;if(c==="sub"){let g=o,w=r;for(let p=0;p<f&&g>0;p++){const b=e.sum[p],y=oa(h,b,w-b,g);y>0&&l.set(e.a[p]*e.sequences+e.b[p],y),g-=y,w-=b}return u}if(!(a>0))throw Jt(`Boost-HiC’s alpha must be above zero; ${a} was given.`,{alpha:a});for(let g=0;g<f;g++){const w=e.a[g];if(e.b[g]!==w)continue;const p=n[w+1]-n[w];if(p>As){const b=s?.[w]??`sequence ${w+1}`;throw Jt(`${b} is ${p.toLocaleString("en-US")} bins at this resolution, and Boost-HiC — which oversamples it — walks every path between them: at most ${As.toLocaleString("en-US")}. Open a coarser resolution to oversample this map.`,{sequence:b,bins:p,limit:As})}}let d=o-r,m=r;for(let g=0;g<f&&d>0;g++){const w=e.sum[g],p=g===f-1?d:sa(h,d,Math.min(1,w/m));p>0&&l.set(e.a[g]*e.sequences+e.b[g],p),d-=p,m-=w}return u}class or{bin1;bin2;count;length=0;constructor(t=1024){this.bin1=new Int32Array(t),this.bin2=new Int32Array(t),this.count=new Float64Array(t)}push(t,n,s){this.length===this.bin1.length&&this.grow(this.length*2),this.bin1[this.length]=t,this.bin2[this.length]=n,this.count[this.length]=s,this.length++}grow(t){const n=new Int32Array(t),s=new Int32Array(t),o=new Float64Array(t);n.set(this.bin1.subarray(0,this.length)),s.set(this.bin2.subarray(0,this.length)),o.set(this.count.subarray(0,this.length)),this.bin1=n,this.bin2=s,this.count=o}}function th(e,t,n,s,o){let r=t,i=n;const{bin1:a,bin2:c,count:l}=e;for(let u=0;u<l.length&&r>0;u++){const h=l[u];if(h===0)continue;let f;if(r===i)f=h,i-=h;else if(h<=Vu){f=0;for(let d=0;d<h;d++)s.nextDouble()*i<r-f&&f++,i--}else f=oa(s,h,i-h,r),i-=h;r-=f,f>0&&o.push(a[u],c[u],f)}}function aa(e,t,n){const s=e.length,o=new Float64Array(s);if(t<=0||s===0)return o;const r=new Float64Array(s+1);let i=-1;for(let c=s-1;c>=0;c--){const l=e[c]>0?e[c]:0;r[c]=r[c+1]+l,l>0&&i<0&&(i=c)}if(i<0)return o;let a=t;for(let c=0;c<s&&a>0;c++){const l=e[c];if(!(l>0))continue;const u=c===i?a:sa(n,a,Math.min(1,l/r[c]));o[c]=u,a-=u}return o}function eh(e,t,n,s){const o=aa(e.count,t,n),{bin1:r,bin2:i,count:a}=e;for(let c=0;c<a.length;c++){const l=a[c]+o[c];l>0&&s.push(r[c],i[c],l)}}function nh(e,t,n){const s=new Float64Array(n*n),{bin1:o,bin2:r,count:i}=e;for(let a=0;a<i.length;a++){const c=o[a]-t,l=r[a]-t;s[c*n+l]+=i[a],c!==l&&(s[l*n+c]+=i[a])}return s}function sh(e,t,n,s,o,r,i){const a=nh(e,t,n),c=vu(new Float64Array(a),n,o),l=n*(n+1)/2,u=new Float64Array(l);let h=0;for(let d=0;d<n;d++)for(let m=d;m<n;m++)u[h++]=a[d*n+m];if(c!==null){const{kept:d,counts:m}=c,g=d.length;let w=0,p=0;for(let y=0;y<g;y++)for(let A=y;A<g;A++)w+=a[d[y]*n+d[A]],p+=m[y*g+A];const b=p>0?w/p:0;for(let y=0;y<g;y++){const A=d[y],x=A*n-A*(A-1)/2-A;for(let E=y;E<g;E++)u[x+d[E]]=m[y*g+E]*b}}const f=aa(u,s,r);h=0;for(let d=0;d<n;d++)for(let m=d;m<n;m++,h++){const g=a[d*n+m]+f[h];g>0&&i.push(t+d,t+m,g)}}class oh{constructor(t,n,s,o){this.inner=t,this.geometry=n,this.spec=s,this.index=new Wn(n.starts),this.census=o}countKind="i";index;census;planned=null;plan=null;bands=new Map;bytes=0;get nnz(){return this.inner.nnz}get weightScale(){return this.plan?.weightScale??1}ready(){return this.planned??=this.census.then(t=>{if(t.nBins!==this.geometry.starts[this.index.count])throw Jt("This census was taken over another map.",{bins:t.nBins,nBins:this.geometry.starts[this.index.count]});const n=Ju(t,this.spec,this.geometry.starts,this.geometry.names);return this.plan=n,n}),this.planned}scoreColumns(){return["count"]}binOffsets(){return this.inner.binOffsets()}async forEachWindow(t,n,s,o,r={}){return(await this.ready()).mode==="none"?this.inner.forEachWindow(t,n,s,o,r):this.walk([[s.span[0],s.span[1]]],o,r)}async forEachBands(t,n,s={}){return(await this.ready()).mode==="none"?this.inner.forEachBands(t,n,s):this.walk(t,n,s)}async scanAll(t){if((await this.ready()).mode==="none")return this.inner.scanAll(t);const n=this.geometry.starts[this.index.count];let s=!1;await this.walk([[0,n]],o=>{s||t.onChunk(o)===!1&&(s=!0)},{cancelled:()=>s,onProgress:(o,r)=>t.onProgress?.(o,r)})}async walk(t,n,s){if(s.value!==void 0&&s.value!=="count")throw Jt(`A resampled map is drawn from its contacts, and “${s.value}” is not a count of them. Read the counts, or balance them, while the map is resampled.`,{value:s.value});const o=await this.ready(),r=rh(t),i=[];for(const[l,u]of r)for(const h of this.index.touching(l,u))i[i.length-1]!==h&&i.push(h);const a=[...new Set(i)].sort((l,u)=>l-u);let c=0;for(let l=0;l<a.length;){if(s.cancelled?.()===!0)return!1;const u=[];let h=0;for(;l<a.length;){const d=a[l],m=this.geometry.starts[d+1]-this.geometry.starts[d];if(u.length>0&&h+m>Yu)break;u.push(d),h+=m,l++}const f=u.filter(d=>!this.bands.has(d));if(f.length>0&&await this.draw(f,o,s)===null)return!1;for(const d of u){const m=this.bands.get(d);this.touch(d);for(const[g,w]of r){const p=Math.max(g,m.from)-m.from,b=Math.min(w,m.from+m.rows.length-1)-m.from;if(b<=p)continue;const y=m.rows[p],A=m.rows[b];A>y&&n({bin1:m.bin1.subarray(y,A),bin2:m.bin2.subarray(y,A),count:m.count.subarray(y,A),length:A-y})}c++,s.onProgress?.(c,a.length)}this.evict(new Set(u)),await St()}return!0}async draw(t,n,s){const o=this.geometry.starts,r=new Map;for(const u of t)r.set(u,new or);const i=new Wn(o);let a=-1,c;if(!await this.inner.forEachBands(t.map(u=>[o[u],o[u+1]]),u=>{const{bin1:h,bin2:f,count:d,length:m}=u;for(let g=0;g<m;g++){if(d[g]===0)continue;const w=i.of(h[g]);w!==a&&(a=w,c=r.get(w)),c?.push(h[g],f[g],d[g])}},...s.cancelled===void 0?[]:[{cancelled:s.cancelled}]))return null;for(const u of t){if(this.store(this.drawBand(u,r.get(u),n)),r.delete(u),s.cancelled?.()===!0)return null;await St()}return!0}drawBand(t,n,s){const o=this.geometry.starts,r=o[t],i=o[t+1],a=this.index.count,c=n.length,l=ih(n),u=new Wn(o),h=new Int32Array(c),f=new Map,d=[];let m=-1,g=-1;for(let S=0;S<c;S++){const v=u.of(n.bin2[l[S]]);if(v!==m){let I=f.get(v);I===void 0&&(I=d.length,f.set(v,I),d.push(v)),m=v,g=I}h[S]=g}const w=new Int32Array(d.length+1);for(let S=0;S<c;S++)w[h[S]+1]++;for(let S=0;S<d.length;S++)w[S+1]+=w[S];const p=w.slice(0,d.length),b=new Int32Array(c),y=new Int32Array(c),A=new Float64Array(c);for(let S=0;S<c;S++){const v=l[S],I=p[h[S]]++;b[I]=n.bin1[v],y[I]=n.bin2[v],A[I]=n.count[v]}const x=new or(Math.max(1024,s.mode==="sub"?Math.ceil(c/2):c)),E=d.map((S,v)=>({b:S,local:v})).sort((S,v)=>S.b-v.b);for(const{b:S,local:v}of E){const I=w[v],N=w[v+1],B={bin1:b.subarray(I,N),bin2:y.subarray(I,N),count:A.subarray(I,N)};if(s.mode==="none"){for(let P=0;P<B.count.length;P++)x.push(B.bin1[P],B.bin2[P],B.count[P]);continue}const z=s.shares.get(t*a+S)??0,R=new na(ea(s.seed,s.mode==="sub"?ra:ia,t,S));if(s.mode==="sub"){let P=0;for(let L=0;L<B.count.length;L++)P+=B.count[L];th(B,z,P,R,x)}else S===t?sh(B,r,i-r,z,s.alpha,R,x):eh(B,z,R,x)}return ah(t,r,i,x)}store(t){this.bands.set(t.sequence,t),this.bytes+=t.bytes}touch(t){const n=this.bands.get(t);n!==void 0&&(this.bands.delete(t),this.bands.set(t,n))}evict(t){for(const[n,s]of this.bands){if(this.bytes<=Qu)return;t.has(n)||(this.bands.delete(n),this.bytes-=s.bytes)}}}function rh(e){const t=e.filter(([s,o])=>o>s).map(([s,o])=>[s,o]);t.sort((s,o)=>s[0]-o[0]);const n=[];for(const s of t){const o=n[n.length-1];o!==void 0&&s[0]<=o[1]?o[1]=Math.max(o[1],s[1]):n.push(s)}return n}function ih(e){const t=e.length,n=new Int32Array(t);let s=!0;for(let i=0;i<t;i++)n[i]=i,i>0&&(e.bin1[i]<e.bin1[i-1]||e.bin1[i]===e.bin1[i-1]&&e.bin2[i]<e.bin2[i-1])&&(s=!1);if(s)return n;const{bin1:o,bin2:r}=e;return n.sort((i,a)=>o[i]-o[a]||r[i]-r[a])}function ah(e,t,n,s){const o=n-t,r=new Int32Array(o+1);for(let u=0;u<s.length;u++)r[s.bin1[u]-t+1]++;for(let u=0;u<o;u++)r[u+1]+=r[u];const i=r.slice(0,o),a=new Int32Array(s.length),c=new Int32Array(s.length),l=new Float64Array(s.length);for(let u=0;u<s.length;u++){const h=i[s.bin1[u]-t]++;a[h]=s.bin1[u],c[h]=s.bin2[u],l[h]=s.count[u]}return{sequence:e,from:t,bin1:a,bin2:c,count:l,rows:r,bytes:s.length*16+r.length*4}}class rn{constructor(t,n,s,o,r){this.nBins=o,this.countKind=r,this.cells=s.map(i=>({name:i,store:new Vi(t.at(ts(n,i)),o,r)}))}countKind;cells;offsets=null;onCells=null;get names(){return this.cells.map(t=>t.name)}get nnz(){let t=0;for(const n of this.cells)t+=n.store.nnz;return t}scoreColumns(){const[t,...n]=this.cells;if(t===void 0)return[ee];let s=t.store.scoreColumns();for(const o of n){const r=new Set(o.store.scoreColumns());s=s.filter(i=>r.has(i))}return s.length>0?s:[ee]}binOffsets(){if(this.offsets!==null)return this.offsets;const t=new Float64Array(this.nBins+1);for(const n of this.cells){const s=n.store.binOffsets(),o=Math.min(t.length,s.length);for(let r=0;r<o;r++)t[r]+=s[r]}return this.offsets=t,t}async forEachWindow(t,n,s,o,r={}){let i=0;for(const a of this.cells){if(!await a.store.forEachWindow(t,n,s,o,r))return!1;await St(),this.onCells?.(++i,this.cells.length)}return!0}async forEachBands(t,n,s={}){let o=0;for(const r of this.cells){if(!await r.store.forEachBands(t,n,s))return!1;await St(),this.onCells?.(++o,this.cells.length)}return!0}async scanAll(t){const n=this.nnz;let s=0,o=!1;for(const r of this.cells){if(o)return;const i=s;await r.store.scanAll({...t.chunkSize===void 0?{}:{chunkSize:t.chunkSize},...t.storedRows===void 0?{}:{storedRows:t.storedRows},onChunk:a=>{const c=t.onChunk(a);return c===!1&&(o=!0),c},onProgress:a=>{s=i+a,t.onProgress?.(s,n)}}),s=i+r.store.nnz,t.onProgress?.(Math.min(s,n),n)}}async scanPerCell(t){const n=this.nnz;let s=0;for(let o=0;o<this.cells.length;o++){const r=this.cells[o];t.onCell?.(o,r.name);const i=s;let a=!1;if(await r.store.scanAll({...t.chunkSize===void 0?{}:{chunkSize:t.chunkSize},onChunk:c=>{const l=t.onChunk(o,c);return l===!1&&(a=!0),l},onProgress:c=>{s=i+c,t.onProgress?.(s,n)}}),a)return;s=i+r.store.nnz,t.onProgress?.(Math.min(s,n),n),await St()}}}function rr(e,t){if(t===null||t.length===0)return[...e];const n=new Set(e),s=t.filter(r=>!n.has(r));if(s.length>0)throw new C("cell-not-found",`This file has no ${s.length===1?"cell":"cells"} ${Dt(s.slice(0,8))}. It carries ${e.length} ${e.length===1?"cell":"cells"}, starting ${Dt(e.slice(0,3))}.`,{missing:s,available:e.length});const o=new Set(t);return e.filter(r=>o.has(r))}function xt(e,t){const n=ua(e),s=ha(n,t);if(s===null)return n;throw new C("format",`The ${t.field} of this ${t.format} reads ${Zs(e)}, ${s.reason}. `+Fe,{format:t.format,field:t.field,value:typeof e=="bigint"?e.toString():e,ceiling:t.ceiling,...t.available===void 0?{}:{available:t.available},...s.most===void 0?{}:{most:s.most}})}function ch(e,t){return ha(ua(e),t)===null}function ds(e,t,n){const s={format:n.format,field:n.field,offset:e,length:t,size:n.size};if(!Xs(e)||!Xs(t))throw new C("format",`The ${n.field} of this ${n.format} points at ${Zs(t)} bytes from byte ${Zs(e)}, which is not a place in a file. ${Fe}`,s);if(n.ceiling!==void 0&&t>n.ceiling)throw new C("format",`The ${n.field} of this ${n.format} is ${At.int(t)} bytes long, more than the ${At.int(n.ceiling)} any real one holds. ${Fe}`,{...s,ceiling:n.ceiling});if(e+t>n.size)throw new C("format",`The ${n.field} of this ${n.format} points at bytes ${At.int(e)} to ${At.int(e+t)}, past the end of a file of ${At.int(n.size)}. ${Fe}`,s)}const ir=65536,Mo=2**29;async function xo(e,t){if(typeof DecompressionStream>"u")throw new C("unsupported",`Reading a ${t.format} needs DecompressionStream, which this runtime does not have. Every browser since 2023 has it; a very old one does not.`,{format:t.format});const n=new DecompressionStream(t.encoding),s=n.writable.getWriter(),o=n.readable.getReader(),r=[];let i=0,a=!1;const c=(async()=>{for(;;){const{done:g,value:w}=await o.read();if(g)return;if(i+=w.byteLength,i>t.maxBytes){a=!0,await o.cancel();return}r.push(w)}})(),l=(async()=>{for(let g=0;g<e.byteLength;g+=ir){if(a)return;const w=e.subarray(g,Math.min(g+ir,e.byteLength));await s.write(w)}a||await s.close()})(),[u,h]=await Promise.allSettled([c,l]);if(a)throw la(t,t.maxBytes,e.byteLength);const f=u.status==="rejected"?u.reason:h.status==="rejected"?h.reason:null;if(f!==null){const g=f instanceof Error?f.message:String(f);throw new C("format",`The ${t.field} of this ${t.format} does not inflate (${g.replace(/\.$/,"")}). ${Fe}`,{format:t.format,field:t.field})}if(r.length===1)return r[0];const d=new Uint8Array(i);let m=0;for(const g of r)d.set(g,m),m+=g.length;return d}function ca(e,t){return Math.min(t.ceiling,Math.max(t.floor,Math.ceil(e*t.ratio)))}function la(e,t,n){return new C("format",`The ${e.field} of this ${e.format} inflates to more than ${At.bytes(t)}, past what any real one holds. ${Fe}`,{format:e.format,field:e.field,maxBytes:t,compressed:n})}const Fe="The file is truncated, corrupt, or not the format its first bytes claim.";function ua(e){return typeof e=="number"?e:e>=BigInt(Number.MIN_SAFE_INTEGER)&&e<=BigInt(Number.MAX_SAFE_INTEGER)?Number(e):Number.NaN}function Xs(e){return Number.isSafeInteger(e)&&e>=0}function ha(e,t){if(!Xs(e))return{reason:"which is not a count"};if(e>t.ceiling)return{reason:`more than the ${At.int(t.ceiling)} any real one declares`};if(t.available!==void 0){const n=Math.floor(Math.max(0,t.available)/Math.max(1,t.bytesPerItem??1));if(e>n){const s=Math.max(0,t.available);return{reason:`and the ${At.int(s)} byte${s===1?"":"s"} after it could hold at most ${At.int(n)}`,most:n}}}return null}function Zs(e){return typeof e=="bigint"?e.toString():Number.isSafeInteger(e)?At.int(e):String(e)}const ar=[7,8,9],ht=".hic",fa=2**31-1,lh=2**40;class jt extends RangeError{needed;constructor(t){super(`a read needs ${t} bytes of a shorter buffer`),this.name="Truncated",this.needed=t}}class Ue{constructor(t){this.bytes=t,this.view=new DataView(t.buffer,t.byteOffset,t.byteLength)}view;at=0;get position(){return this.at}set position(t){this.at=t}get remaining(){return this.bytes.byteLength-this.at}need(t){if(this.at+t>this.bytes.byteLength)throw new jt(this.at+t)}int8(){this.need(1);const t=this.view.getInt8(this.at);return this.at+=1,t}int16(){this.need(2);const t=this.view.getInt16(this.at,!0);return this.at+=2,t}int32(){this.need(4);const t=this.view.getInt32(this.at,!0);return this.at+=4,t}int64(){this.need(8);const t=this.view.getBigInt64(this.at,!0);return this.at+=8,t>BigInt(Number.MAX_SAFE_INTEGER)||t<BigInt(Number.MIN_SAFE_INTEGER)?Number.NaN:Number(t)}float32(){this.need(4);const t=this.view.getFloat32(this.at,!0);return this.at+=4,t}float64(){this.need(8);const t=this.view.getFloat64(this.at,!0);return this.at+=8,t}string(){const t=this.at,n=this.bytes.indexOf(0,t);if(n<0)throw new jt(Math.max(t,this.bytes.byteLength)+1);const s=new TextDecoder().decode(this.bytes.subarray(t,n));return this.at=n+1,s}skip(t){if(!(t>=0))throw new RangeError(`a cursor cannot skip ${t} bytes`);this.at+=t}}const uh=512*1024;function da(e){return e.length>=4&&e[0]===72&&e[1]===73&&e[2]===67&&e[3]===0}function hh(e){let t=Math.min(uh,e.size);for(;;){const n=e.readBytes(0,t);try{return fh(n,e.size)}catch(s){if(!(s instanceof jt))throw s;if(t>=e.size)throw new C("format",`This .hic ends inside its header, ${e.size.toLocaleString("en-US")} bytes in. The file is truncated, or is not the format its first four bytes claim.`,{size:e.size});t=Math.min(e.size,Math.max(t*4,s.needed))}}}function fh(e,t=e.byteLength){if(!da(e))throw new C("format","This file does not begin with the `.hic` magic bytes.",{});const n=new Ue(e);n.position=4;const s=n.int32();if(!ar.includes(s))throw new C("unsupported",`This is a version ${s} .hic file, and this reader accepts versions ${ar.join(", ")}. Versions below 7 predate the block index this reader navigates by, and a version above the list is a format this build has not seen. Convert it with \`hic2cool\` or re-run Juicer Tools \`pre\`.`,{version:s});const o=n.int64(),r=n.string();let i=null,a=null;s>=9&&(i=n.int64(),a=n.int64());const c=()=>t-n.position,l={},u=xt(n.int32(),{format:ht,field:"header attribute count",ceiling:1e6,available:c(),bytesPerItem:2});for(let g=0;g<u;g++){const w=n.string();l[w]=n.string()}const h=xt(n.int32(),{format:ht,field:"chromosome count",ceiling:1e7,available:c(),bytesPerItem:1+(s>=9?8:4)});xs(h>0,"chromosome count");const f=[];for(let g=0;g<h;g++){const w=n.string(),p=xt(s>=9?n.int64():n.int32(),{format:ht,field:`length of chromosome ${w}`,ceiling:lh});f.push({name:w,length:p})}const d=xt(n.int32(),{format:ht,field:"resolution count",ceiling:1e4,available:c(),bytesPerItem:4});xs(d>0,"resolution count");const m=[];for(let g=0;g<d;g++){const w=n.int32();xs(w>0,"bin size"),m.push(w)}return{version:s,footerPosition:o,genomeId:r,attributes:l,chroms:f,bpResolutions:m,normVectorIndexPosition:i,normVectorIndexLength:a,headerBytes:n.position}}function xs(e,t){if(!e)throw new C("format",`The ${t} in this .hic header is not a plausible number. The file is either truncated or is not the format its first four bytes claim.`,{what:t})}function Js(e,t,n,s){return`${e}/${t}/${n}/${s}`}function dh(e,t){const{version:n,footerPosition:s}=t,o=n>=9?8:4;ds(s,o+4,{format:ht,field:"footer position",size:e.size});const r=e.size-s,i=new Ue(e.readBytes(s,o)),a=xt(n>=9?i.int64():i.int32(),{format:ht,field:"footer length",ceiling:Number.MAX_SAFE_INTEGER,available:r-o}),c={fileSize:e.size,footerPosition:s};let l=Math.min(r,Math.max(a+o+(1<<20),65536));for(;;){const u=e.readBytes(s,l);try{return gh(u,n,o,c)}catch(h){if(!(h instanceof jt))throw h;if(l>=r)throw new C("format",`This .hic ends inside its footer, which begins ${s.toLocaleString("en-US")} bytes in. The file is truncated, or its header does not point at its footer.`,{footerPosition:s,size:e.size});l=Math.min(r,Math.max(l*4,h.needed))}}}const mh=13;function gh(e,t,n,s){const o=new Ue(e);o.position=n;const r=s?.fileSize??e.byteLength,i=s?.footerPosition??0,a=()=>r-(i+o.position),c=new Map,l=xt(o.int32(),{format:ht,field:"master index size",ceiling:1e8,available:a(),bytesPerItem:mh});let u=0;for(let d=0;d<l;d++){const m=o.string(),g=o.int64(),w=o.int32();if(s!==void 0&&(ds(g,w,{format:ht,field:`matrix record for ${m}`,size:s.fileSize}),u+=w,u>s.fileSize))throw new C("format",`The master index of this .hic gives its matrix records ${u.toLocaleString("en-US")} bytes between them by entry ${d+1}, more than the whole file's ${s.fileSize.toLocaleString("en-US")}. The file is corrupt, or not the format its first bytes claim.`,{entries:d+1,bytes:u,size:s.fileSize});c.set(m,{key:m,position:g,size:w})}cr(o,t,!1,a),cr(o,t,!0,a);const h=new Map,f=[];if(a()>=4){const d=o.int32(),m=18+(t>=9?8:4),g={ceiling:1e8,available:a(),bytesPerItem:m};if(ch(d,g)){let w=0;for(let p=0;p<d;p++){const b=o.string(),y=o.int32(),A=o.string(),x=o.int32(),E=o.int64(),S=t>=9?o.int64():o.int32();h.set(Js(b,y,A,x),{type:b,chromIdx:y,unit:A,binSize:x,position:E,nBytes:S}),f.includes(b)||f.push(b),w+=S}s!==void 0&&!(w<=s.fileSize)&&(h.clear(),f.length=0)}}return{masterIndex:c,normVectors:h,normTypes:f}}function cr(e,t,n,s){if(s()<4)return;const o=t>=9?4:8,r=xt(e.int32(),{format:ht,field:`${n?"normalised ":""}expected-value vector count`,ceiling:1e6,available:s(),bytesPerItem:(n?1:0)+1+4+(t>=9?8:4)+4});for(let i=0;i<r;i++){n&&e.string(),e.string(),e.int32();const a=xt(t>=9?e.int64():e.int32(),{format:ht,field:"expected-value vector length",ceiling:fa,available:s(),bytesPerItem:o});e.skip(a*o);const c=xt(e.int32(),{format:ht,field:"expected-value scale factor count",ceiling:1e7,available:s(),bytesPerItem:4+o});e.skip(c*(4+o))}if(e.remaining<0)throw new jt(e.position)}function wh(e,t,n){const s=`${n.type} normalisation vector of chromosome ${n.chromIdx}`,o=t>=9?8:4,r=t>=9?4:8;ds(n.position,n.nBytes,{format:ht,field:s,size:e.size});const i=e.readBytes(n.position,o);if(i.byteLength<o)throw new C("format",`The ${s} begins in the last ${i.byteLength} bytes of this .hic, too few for its length. The file is truncated, or its normalisation index does not point at its vectors.`,{type:n.type,chromIdx:n.chromIdx,position:n.position});const a=new Ue(i),c=xt(t>=9?a.int64():a.int32(),{format:ht,field:`length of the ${s}`,ceiling:fa,available:n.nBytes-o,bytesPerItem:r}),l=e.readBytes(n.position+o,c*r),u=new DataView(l.buffer,l.byteOffset,l.byteLength),h=new Float64Array(c);for(let f=0;f<c;f++){const d=r===4?u.getFloat32(f*4,!0):u.getFloat64(f*8,!0);h[f]=d>0&&Number.isFinite(d)?1/d:Number.NaN}return h}const lr={ratio:64,floor:16<<20,ceiling:1<<30},to=2**26,ph=37,ur=16,jn=2**31-1,Ss=4096;function ms(e,t,n,s){const o=new Ue(e),r=()=>s===void 0?void 0:s-o.position;o.int32(),o.int32();const i=xt(o.int32(),{format:ht,field:"resolution count of a matrix record",ceiling:1e4,available:r(),bytesPerItem:ph});for(let a=0;a<i;a++){const c=o.string();o.int32();const l=o.float32();o.float32(),o.float32(),o.float32();const u=o.int32(),h=o.int32(),f=o.int32(),d=xt(o.int32(),{format:ht,field:"block count of a matrix record",ceiling:jn,available:r(),bytesPerItem:ur});if(c!==t||u!==n){o.skip(d*ur);continue}if(!(h>=1)||!(f>=1))throw new C("format",`This .hic's ${u} bp matrix declares blocks of ${h} bins in ${f} columns, which no block grid has. The file is truncated, corrupt, or not the format its first bytes claim.`,{binSize:u,blockBinCount:h,blockColumnCount:f});const m=new Map;for(let g=0;g<d;g++){const w=o.int32(),p=o.int64(),b=o.int32();m.set(w,{number:w,position:p,size:b})}return{unit:c,binSize:u,blockBinCount:h,blockColumnCount:f,blocks:m,sumCounts:l}}return null}function bh(e,t,n,s,o){if(o>0&&o<t.size){try{return{zoom:ms(e(t.position,o),n,s,t.size),beyondHead:!1}}catch(r){if(!(r instanceof jt))throw r}return{zoom:Pe(e(t.position,t.size),t,n,s),beyondHead:!0}}return{zoom:Pe(e(t.position,t.size),t,n,s),beyondHead:!1}}async function yh(e,t,n,s,o){if(o>0&&o<t.size){try{return{zoom:ms(await e(t.position,o),n,s,t.size),beyondHead:!1}}catch(r){if(!(r instanceof jt))throw r}return{zoom:Pe(await e(t.position,t.size),t,n,s),beyondHead:!0}}return{zoom:Pe(await e(t.position,t.size),t,n,s),beyondHead:!1}}function Pe(e,t,n,s){try{return ms(e,n,s,t.size)}catch(o){throw o instanceof jt?new C("format",`The matrix record for ${t.key} in this .hic ends inside its block index, ${e.byteLength.toLocaleString("en-US")} bytes in. The file is truncated, or its master index does not point at its records.`,{key:t.key,position:t.position,size:t.size}):o}}function Cn(e,t,n){const s=[...e].sort((r,i)=>r.position-i.position),o=[];for(const r of s){const i=o[o.length-1],a=r.position+r.size;if(i!==void 0&&r.position-(i.position+i.length)<=t&&a-i.position<=n){i.length=Math.max(i.length,a-i.position),i.refs.push(r);continue}o.push({position:r.position,length:r.size,refs:[r]})}return o}function hr(e,t,n,s,o){const r=n&&t>=9?xh(e,s,o):Mh(e,n,s,o);let i=0;for(const c of r)i+=Math.max(0,c.r2-c.r1+1)*Math.max(0,c.c2-c.c1+1);if(i>Math.max(Ah,e.blocks.size))return Sh(e,r);const a=new Set;for(const{r1:c,r2:l,c1:u,c2:h}of r)for(let f=c;f<=l;f++)for(let d=u;d<=h;d++)a.add(f*e.blockColumnCount+d);return[...a]}const Ah=1<<20;function Mh(e,t,n,s){const{blockBinCount:o}=e,r=Math.floor(n[0]/o),i=Math.floor(Math.max(n[0],n[1]-1)/o),a=Math.floor(s[0]/o),c=Math.floor(Math.max(s[0],s[1]-1)/o),l=[{r1:a,r2:c,c1:r,c2:i}];return t&&l.push({r1:r,r2:i,c1:a,c2:c}),l}function xh(e,t,n){const{blockBinCount:s}=e,[o,r]=[t[0],Math.max(t[0],t[1]-1)],[i,a]=[n[0],Math.max(n[0],n[1]-1)],c=Math.floor((o+i)/2/s),l=Math.floor((r+a)/2/s)+1,u=Math.floor(Math.log2(1+Math.abs(o-a)/Math.SQRT2/s)),h=Math.floor(Math.log2(1+Math.abs(r-i)/Math.SQRT2/s)),d=o>a&&r<i||r>i&&o<a?0:Math.min(u,h),m=Math.max(u,h)+1;return[{r1:Math.max(0,d),r2:m,c1:Math.max(0,c),c2:l}]}function Sh(e,t){const n=e.blockColumnCount,s=[];for(const o of e.blocks.keys()){const r=Math.floor(o/n),i=o-r*n;t.some(a=>r>=a.r1&&r<=a.r2&&i>=a.c1&&i<=a.c2)&&s.push(o)}return s.sort((o,r)=>o-r)}function Ih(e,t){try{return Eh(e,t)}catch(n){throw n instanceof jt?new C("format",`A block of this .hic ends before its records do, ${e.byteLength.toLocaleString("en-US")} bytes in. The file is truncated, corrupt, or not the format its first bytes claim.`,{bytes:e.byteLength}):n}}function Eh(e,t){const n=new Ue(e),s=n.int32();if(s===0)return{x:new Int32Array(0),y:new Int32Array(0),value:new Float32Array(0),length:0};const o=n.int32(),r=n.int32(),i=n.int8()===0,a=t>8?n.int8()===0:!0,c=t>8?n.int8()===0:!0,l=n.int8();if(l!==1&&l!==2)throw new C("format",`A block of this .hic is in encoding ${l}, and the format has two: 1, a list of rows, and 2, a dense rectangle. The file is corrupt, or was written by a tool this reader has not seen.`,{type:l});const u=i?2:4,h=l===1?(a?2:4)+u:u,f=xt(s,{format:ht,field:"record count of a block",ceiling:to,available:n.remaining,bytesPerItem:h});let d=new Int32Array(f),m=new Int32Array(f),g=new Float32Array(f),w=0;const p=()=>i?n.int16():n.float32();if(l===1){const A=xt(c?n.int16():n.int32(),{format:ht,field:"row count of a block",ceiling:jn,available:n.remaining,bytesPerItem:(c?2:4)+(a?2:4)});for(let x=0;x<A;x++){const E=r+(c?n.int16():n.int32()),S=xt(a?n.int16():n.int32(),{format:ht,field:"column count of a block row",ceiling:jn,available:n.remaining,bytesPerItem:h});for(let v=0;v<S;v++){const I=o+(a?n.int16():n.int32()),N=p();(i?N===-32768:!Number.isFinite(N))||(w===d.length&&([d,m,g]=fr(d,m,g,n.remaining,h)),d[w]=I,m[w]=E,g[w]=N,w+=1)}}return{x:d,y:m,value:g,length:w}}const b=xt(n.int32(),{format:ht,field:"cell count of a dense block",ceiling:jn,available:n.remaining-2,bytesPerItem:u}),y=n.int16();if(b>0&&!(y>=1))throw new C("format",`A dense block of this .hic is ${y} bins wide, which no rectangle is. The file is truncated, corrupt, or not the format its first bytes claim.`,{width:y});for(let A=0;A<b;A++){const x=p();if(i?x===-32768:!Number.isFinite(x))continue;const E=Math.floor(A/y);w===d.length&&([d,m,g]=fr(d,m,g,n.remaining,h)),d[w]=o+(A-E*y),m[w]=r+E,g[w]=x,w+=1}return{x:d,y:m,value:g,length:w}}function fr(e,t,n,s,o){const r=e.length,i=Math.floor(Math.max(0,s)/o)+1,a=r+Math.min(Math.max(r,1024),i);if(a>to)throw new C("format",`A block of this .hic holds more than ${to.toLocaleString("en-US")} records, more than any real one. The file is corrupt, or not the format its first bytes claim.`,{records:a});const c=new Int32Array(a),l=new Int32Array(a),u=new Float32Array(a);return c.set(e),l.set(t),u.set(n),[c,l,u]}const eo=48<<20,dr=4,vh=6,Ch=64<<20,mr=28,$n=65536,Nn=16<<20,$h=4096,Nh=eo/2,Bh=1024,gr=["SCALE","KR","INTER_KR","GW_KR","VC_SQRT","VC"],ue="BP";class wr{free;waiting=[];constructor(t){this.free=Math.max(1,t)}async run(t){this.free>0?this.free-=1:await new Promise(n=>this.waiting.push(n));try{return await t()}finally{const n=this.waiting.shift();n===void 0?this.free+=1:n()}}}class So{header;footer;chroms;binSize;resolutions;chromOffset;nBins;normType;source;fileIndex;zooms=new Map;zoomsInFlight=new Map;beyondHead=!1;blockCache=new Map;blockCacheBytes=0;normCache=new Map;normFallbacks=new Map;exactSlots;backgroundSlots;constructor(t,n,s,o){this.source=t,this.header=n,this.footer=s;const r=[],i=[];n.chroms.forEach((c,l)=>{c.name.toLowerCase()!=="all"&&(r.push(c),i.push(l))}),this.chroms=r,this.fileIndex=Int32Array.from(i),this.resolutions=[...n.bpResolutions].sort((c,l)=>c-l),this.binSize=o,this.chromOffset=new Float64Array(r.length+1);for(let c=0;c<r.length;c++)this.chromOffset[c+1]=this.chromOffset[c]+Math.ceil(r[c].length/o);this.nBins=this.chromOffset[r.length];const a=this.walkAhead();this.exactSlots=new wr(a===dr?vh:a),this.backgroundSlots=new wr(a),this.normType=gr.find(c=>r.some((l,u)=>s.normVectors.has(Js(c,this.fileIndex[u],ue,o))))??null}static open(t,n={}){const s=hh(t),o=dh(t,s),r=[...s.bpResolutions].sort((a,c)=>a-c);if(r.length===0)throw new C("unsupported","This .hic carries no base-pair resolutions. Fragment-resolution matrices are variable-bin and are excluded from this viewer.",{});const i=n.binSize??gl(r);if(!r.includes(i))throw new C("unsupported",`This .hic has no ${i} bp resolution. It offers ${r.join(", ")}.`,{binSize:i,available:r});return new So(t,s,o,i)}stats(){return this.source.stats()}fileIndexOf(t){return this.fileIndex[t]}chromExtent(t){return[this.chromOffset[t],this.chromOffset[t+1]]}chromAt(t){let n=0,s=this.chroms.length-1;for(;n<s;){const o=n+s+1>>1;this.chromOffset[o]<=t?n=o:s=o-1}return n}chromsSpanning(t){const n=[];if(t[1]<=t[0])return n;const s=this.chromAt(t[0]),o=this.chromAt(Math.min(t[1]-1,this.nBins-1));for(let r=s;r<=o;r++)n.push(r);return n}totalCount(){let t=0;for(const n of this.footer.masterIndex.keys()){const s=this.zoomAt(n);s!==null&&(t+=s.sumCounts)}return t}weights(t,n){const s=new Float64Array(Math.max(0,n-t)).fill(Number.NaN);if(this.normType===null||n<=t)return s;for(const o of this.chromsSpanning([t,n])){const r=this.normVector(o);if(r===null)continue;const i=this.chromOffset[o],a=Math.max(t,i),c=Math.min(n,this.chromOffset[o+1]);for(let l=a;l<c;l++){const u=l-i;s[l-t]=u<r.length?r[u]:Number.NaN}}return s}normVector(t){if(this.normCache.has(t))return this.normCache.get(t)??null;let n=null;if(this.normType!==null){const s=this.normType,o=[s,...gr.filter(r=>r!==s)];for(const r of o){const i=this.footer.normVectors.get(Js(r,this.fileIndex[t],ue,this.binSize));if(i===void 0)continue;const a=wh(this.source,this.header.version,i);if(a.some(c=>Number.isFinite(c))){n=a,r!==s&&this.normFallbacks.set(t,r);break}}}return this.normCache.set(t,n),n}normTypeFor(t){return this.normType===null||(this.normCache.has(t)||this.normVector(t),(this.normCache.get(t)??null)===null)?null:this.normFallbacks.get(t)??this.normType}zoomAt(t){if(this.zooms.has(t))return this.zooms.get(t)??null;const n=this.footer.masterIndex.get(t);let s=null;if(n!==void 0){const o=bh((r,i)=>this.source.readBytes(r,i),n,ue,this.binSize,this.beyondHead?0:Ss);s=this.fitted(t,o.zoom),o.beyondHead&&(this.beyondHead=!0)}return this.zooms.set(t,s),s}fitted(t,n){if(n===null)return null;let s=0;for(const o of n.blocks.values())s+=Math.max(0,o.size);if(!(s<=this.source.size))throw new C("format",`The ${this.binSize} bp blocks of this .hic's ${t} matrix claim ${s.toLocaleString("en-US")} bytes between them, more than the whole file's ${this.source.size.toLocaleString("en-US")}. The file is corrupt, or not the format its first bytes claim.`,{key:t,binSize:this.binSize,bytes:s,size:this.source.size});return n}zoomAtSparse(t){if(this.zooms.has(t))return Promise.resolve(this.zooms.get(t)??null);const n=this.zoomsInFlight.get(t);if(n!==void 0)return n;const s=this.footer.masterIndex.get(t);if(s===void 0||this.source.readExact===void 0)return Promise.resolve(this.zoomAt(t));const o=yh((r,i)=>this.exactRead(r,i),s,ue,this.binSize,this.beyondHead?0:Ss).then(r=>{r.beyondHead&&(this.beyondHead=!0);const i=this.fitted(t,r.zoom);return this.zooms.set(t,i),i}).finally(()=>this.zoomsInFlight.delete(t));return this.zoomsInFlight.set(t,o),o}zoomFor(t,n){return this.zoomAt(this.pairKey(t,n))}pairKey(t,n){return`${this.fileIndex[t]}_${this.fileIndex[n]}`}walkAhead(){let t=0;for(let s=0;s<this.chroms.length;s++)t=Math.max(t,this.chromOffset[s+1]-this.chromOffset[s]);const n=Math.max(1,t*t*mr);return Math.max(1,Math.min(dr,Math.floor(Ch/n)))}walkPlans(t){const n=[];let s=[],o=0;for(const r of t){const i=this.binsOf(r[0])*this.binsOf(r[1])*mr;s.length>0&&(o+i>Nh||s.length>=Bh)&&(n.push(s),s=[],o=0),s.push(r),o+=i}return s.length>0&&n.push(s),n}async prefetchWalk(t,n={}){if(this.source.readExact===void 0)return!0;const s=[],o=new Set;for(const h of t){const f=this.pairKey(Math.min(h.a,h.b),Math.max(h.a,h.b));if(o.has(f)||this.zooms.has(f))continue;o.add(f);const d=this.footer.masterIndex.get(f);d===void 0?this.zooms.set(f,null):s.push(d)}const r=[];for(const h of s){const f=this.beyondHead?h.size:Math.min(h.size,Ss);r.push({position:h.position,size:f,entry:h,head:!0});const d=h.position+h.size,m=Math.min($h,this.source.size-d);m>0&&r.push({position:d,size:m,entry:h,head:!1})}const i=new Map,a=[];if(!await this.fetchRuns(Cn(r,$n,Nn),n,(h,f)=>{for(const d of h.refs){const m=d.position-h.position,g=f.subarray(m,m+d.size);if(!d.head){i.set(d.entry.key,{position:d.position,bytes:g.slice()});continue}const{entry:w}=d;try{const p=d.size===w.size?Pe(g,w,ue,this.binSize):ms(g,ue,this.binSize,w.size);this.zooms.set(w.key,this.fitted(w.key,p))}catch(p){if(!(p instanceof jt))throw p;this.beyondHead=!0,a.push({position:w.position,size:w.size,entry:w})}}})||a.length>0&&!await this.fetchRuns(Cn(a,$n,Nn),n,(f,d)=>{for(const m of f.refs){const g=m.position-f.position,w=Pe(d.subarray(g,g+m.size),m.entry,ue,this.binSize);this.zooms.set(m.entry.key,this.fitted(m.entry.key,w))}}))return!1;const l=[],u=new Set;for(const h of t){const f=this.windowOf(h.a,h.b,h.rows,h.cols);if(f===null)continue;const d=this.pairKey(f.low,f.high),m=this.zooms.get(d);if(m==null)continue;const g=i.get(d);for(const w of hr(m,this.header.version,f.intra,f.lowSpan,f.highSpan)){const p=m.blocks.get(w);if(p===void 0||p.size<=0)continue;const b=this.blockKey(p);if(u.has(b)||this.blockCache.has(b))continue;u.add(b),this.checkBlock(p);const y=g===void 0?-1:p.position-g.position;g!==void 0&&y>=0&&y+p.size<=g.bytes.byteLength?await this.decode(p,g.bytes.subarray(y,y+p.size)):l.push(p)}}return this.fetchRuns(Cn(l,$n,Nn),n,async(h,f)=>{for(const d of h.refs){const m=d.position-h.position;await this.decode(d,f.subarray(m,m+d.size))}})}async fetchRuns(t,n,s){let o=!1;return await Promise.all(t.map(async r=>{await n.pause?.();const i=()=>this.exactSlots.run(async()=>o||n.cancelled?.()===!0?(o=!0,null):this.readExactNow(r.position,r.length)),a=n.pause===void 0?await i():await this.backgroundSlots.run(i);a!==null&&await s(r,a)})),!o}exactRead(t,n){return this.exactSlots.run(()=>this.readExactNow(t,n))}readExactNow(t,n){const s=this.source,o=s.readExact;return o===void 0?Promise.resolve(s.readBytes(t,n)):o.call(s,t,n)}binsOf(t){return this.chromOffset[t+1]-this.chromOffset[t]}hasAnyMatrix(){for(let t=0;t<this.chroms.length;t++)if(this.zoomFor(t,t)!==null)return!0;return!1}indexedPairs(){const t=new Map;this.fileIndex.forEach((o,r)=>t.set(o,r));const n=new Set,s=[];for(const o of this.footer.masterIndex.keys()){const[r,i]=o.split("_").map(h=>Number.parseInt(h,10)),a=t.get(r),c=t.get(i);if(a===void 0||c===void 0)continue;const l=a<=c?[a,c]:[c,a],u=`${l[0]}_${l[1]}`;n.has(u)||(n.add(u),s.push(l))}return s.sort((o,r)=>o[0]-r[0]||o[1]-r[1]),s}async pairRecords(t,n,s,o,r=!1){const[i,a]=t<=n?[t,n]:[n,t],c=r?await this.zoomAtSparse(this.pairKey(i,a)):this.zoomFor(i,a);if(c===null)return null;const l=this.windowOf(t,n,s,o);if(l===null)return null;const{intra:u,lowSpan:h,highSpan:f}=l,d=hr(c,this.header.version,u,h,f),m=this.chromOffset[i],g=this.chromOffset[a];let w=0;const p=await this.blocks(c,d,r);for(const E of p)w+=E.length;if(w===0)return null;const b=new Int32Array(w),y=new Int32Array(w),A=new Float64Array(w);let x=0;for(const E of p)for(let S=0;S<E.length;S++){const v=m+E.x[S],I=g+E.y[S];v<=I?(b[x]=v,y[x]=I):(b[x]=I,y[x]=v),A[x]=E.value[S],x+=1}return{bin1:b,bin2:y,count:A,length:x}}windowOf(t,n,s,o){const[r,i]=t<=n?[t,n]:[n,t],a=r===i,[c,l]=a?[this.clipSpan(r,s),this.clipSpan(r,o)]:[this.localSpan(r,s,o),this.localSpan(i,s,o)];return c===null||l===null?null:{low:r,high:i,intra:a,lowSpan:c,highSpan:l}}clipSpan(t,n){const s=this.chromOffset[t],o=Math.max(n[0],s),r=Math.min(n[1],this.chromOffset[t+1]);return r>o?[o-s,r-s]:null}localSpan(t,n,s){const o=this.chromOffset[t],r=this.chromOffset[t+1];let i=Number.POSITIVE_INFINITY,a=Number.NEGATIVE_INFINITY;for(const c of[n,s]){const l=Math.max(c[0],o),u=Math.min(c[1],r);u<=l||(i=Math.min(i,l-o),a=Math.max(a,u-o))}return Number.isFinite(i)?[i,a]:null}async blocks(t,n,s){const o=new Map,r=[];for(const a of n){const c=t.blocks.get(a);if(c===void 0||c.size<=0)continue;const l=this.held(c);if(l!==void 0){o.set(a,l);continue}this.checkBlock(c),r.push(c)}if(s&&this.source.readExact!==void 0)for(const a of Cn(r,$n,Nn)){const c=await this.exactRead(a.position,a.length);for(const l of a.refs){const u=l.position-a.position;o.set(l.number,await this.decode(l,c.subarray(u,u+l.size)))}}else for(const a of r)o.set(a.number,await this.decode(a,this.source.readBytes(a.position,a.size)));const i=[];for(const a of n){const c=o.get(a);c!==void 0&&i.push(c)}return i}checkBlock(t){ds(t.position,t.size,{format:ht,field:`block ${t.number} of the ${this.binSize} bp matrix`,size:this.source.size,ceiling:lr.ceiling})}held(t){const n=this.blockKey(t),s=this.blockCache.get(n);if(s!==void 0)return this.blockCache.delete(n),this.blockCache.set(n,s),s}async decode(t,n){const s=await xo(n,{format:ht,field:`block ${t.number} of the ${this.binSize} bp matrix`,encoding:"deflate",maxBytes:ca(n.byteLength,lr)}),o=Ih(s,this.header.version);return this.remember(this.blockKey(t),o),o}blockKey(t){return`${this.binSize}/${t.position}`}remember(t,n){const s=n.x.byteLength+n.y.byteLength+n.value.byteLength;if(!(s>eo)){this.blockCache.set(t,n),this.blockCacheBytes+=s;for(const o of this.blockCache.keys()){if(this.blockCacheBytes<=eo)break;const r=this.blockCache.get(o);r!==void 0&&(this.blockCacheBytes-=r.x.byteLength+r.y.byteLength+r.value.byteLength),this.blockCache.delete(o)}}}close(){this.zooms.clear(),this.blockCache.clear(),this.normCache.clear(),this.blockCacheBytes=0}}function pr(e){throw new C("unsupported",`A .hic has no ${e}: it is indexed per chromosome pair and per block, not as one sorted pixel table. Read pixels through PixelStore (metacooler/store.ts), which is the seam that exists for exactly this difference.`,{path:e})}function Oh(e,t){const n=()=>De(t.chroms.length,["name","length"],{name:t.chroms.map(o=>o.name),length:Float64Array.from(t.chroms,o=>o.length)}),s={format:"HIC","format-url":"https://github.com/aidenlab/juicer/wiki/Data-structure","format-version":t.header.version,"bin-size":t.binSize,"bin-type":"fixed",ordering:"genome-then-length","storage-mode":"symmetric-upper",assembly:t.header.genomeId,nbins:t.nBins,ncontigs:t.chroms.length,nnz:null,sum:null,ngenomes:null,...t.header.attributes,...t.normType===null?{}:{"hic-normalisation":t.normType}};return{uri:e,group:"/",rootEntries:t.resolutions.map(o=>String(o)),rootEntryGroup:"resolutions",attrs:()=>({...s}),attrsAt:o=>o===""||o==="/"?{...s}:{},has(o){return o==="bins/weight"?t.normType!==null:["chroms","chroms/name","chroms/length","indexes","pixels","bins"].includes(o)},keys(o){return o===""||o==="/"?["chroms","bins","pixels","indexes"]:o==="chroms"?["name","length"]:o==="pixels"?["bin1_id","bin2_id","count"]:o==="bins"?t.normType===null?[]:["weight"]:[]},isSoftLink:()=>!1,datasetLength(o){return o==="chroms/name"||o==="chroms/length"?t.chroms.length:o==="bins/weight"?t.nBins:(o.startsWith("pixels/"),0)},dtype(o){return o==="pixels/count"?"<f":o==="chroms/length"?"<i":o==="chroms/name"?"S":"<d"},readNumeric(o,r=0,i){if(o==="indexes/chrom_offset")return t.chromOffset.slice();if(o==="chroms/length"){const a=i??t.chroms.length;return Float64Array.from(t.chroms.slice(r,a),c=>c.length)}if(o==="bins/weight"){if(t.normType===null)throw new C("unsupported","This .hic carries no normalisation vectors, so there are no weights to balance with. Re-run Juicer Tools `addNorm`, or view the raw counts.",{});return t.weights(r,i??t.nBins)}throw(o==="indexes/bin1_offset"||o.startsWith("pixels/"))&&pr(o),new C("unsupported",`A .hic has no ${o}.`,{path:o})},readInt32(o){throw o.startsWith("pixels/")&&pr(o),new C("unsupported",`A .hic has no ${o}.`,{path:o})},readStrings(o,r=0,i){if(o==="chroms/name")return t.chroms.slice(r,i??t.chroms.length).map(a=>a.name);throw new C("unsupported",`A .hic has no ${o}.`,{path:o})},readTable(o){if(o==="chroms"||o==="contigs")return n();throw new C("unsupported",`A .hic has no /${o} table.`,{path:o})},at(o){throw new C("unsupported",`A .hic has no /${o} group to open.`,{path:o})},close:()=>t.close()}}function kh(e,t){return e*1e6+t}class _h{constructor(t){this.file=t}nnz=null;countKind="f";rectangular=!0;scoreColumns(){return["count"]}binOffsets(){throw new C("unsupported","A .hic has no per-bin pixel index, so the stored-pixel density column cannot be computed for one. It is a metagenome diagnostic and a .hic has no genomes, so nothing that draws asks for it.",{})}async forEachWindow(t,n,s,o,r={}){this.refuseOtherColumns(r.value);const i=this.pairsFor(t,n),a=i.length>1;return this.walk(i,(c,l)=>this.file.pairRecords(c,l,t,n,a),o,r,()=>[t,n])}async forEachBands(t,n,s={}){this.refuseOtherColumns(s.value);const o=new Set;for(const l of t)for(const u of this.file.chromsSpanning(l))o.add(u);const r=[0,this.file.nBins],i=this.file.indexedPairs().filter(([l])=>o.has(l)),a=i.length>1,c=l=>{const u=this.clipTo(l,t);return u===null?null:[u,r]};return this.walk(i,(l,u)=>{const h=c(l);return h===null?Promise.resolve(null):this.file.pairRecords(l,u,h[0],h[1],a)},n,s,c)}async scanAll(t){const n=[0,this.file.nBins],s=this.file.indexedPairs(),o=s.length>1;await this.inOrder(s,(r,i)=>this.file.pairRecords(r,i,n,n,o),(r,i)=>{const a=r!==null&&t.onChunk(r)===!1;return t.onProgress?.(i,s.length),!a},void 0,t.pause,()=>[n,n])}pairsFor(t,n){const s=this.file.chromsSpanning(t),o=this.file.chromsSpanning(n),r=new Set,i=[];for(const a of s)for(const c of o){const l=a<=c?[a,c]:[c,a],u=kh(l[0],l[1]);r.has(u)||(r.add(u),i.push(l))}return i}clipTo(t,n){const[s,o]=this.file.chromExtent(t);let r=Number.POSITIVE_INFINITY,i=Number.NEGATIVE_INFINITY;for(const a of n){const c=Math.max(a[0],s),l=Math.min(a[1],o);l<=c||(r=Math.min(r,c),i=Math.max(i,l))}return Number.isFinite(r)?[r,i]:null}walk(t,n,s,o,r){return this.inOrder(t,n,(i,a)=>(i!==null&&i.length>0&&s(i),o.onProgress?.(a,t.length),!0),()=>o.cancelled?.()===!0,void 0,r)}async inOrder(t,n,s,o,r,i){const a=t.length>1?this.file.walkAhead():1,c=this.planned(t,o,r,i),l=[];let u=0,h=0;for(;h<t.length;){if(await(r?.()??St()),o?.()===!0)return!1;for(;l.length<a&&u<t.length;){const[d,m]=t[u],g=c(u).then(w=>w?n(d,m):null);u+=1,g.catch(()=>{}),l.push(g)}const f=await l.shift();if(h+=1,!s(f,h))return!1}return!0}planned(t,n,s,o){if(t.length<2||o===void 0)return()=>Promise.resolve(!0);const r=this.file.walkPlans(t),i=[];r.forEach((c,l)=>c.forEach(()=>i.push(l)));const a=new Map;return c=>{const l=i[c];let u=a.get(l);if(u===void 0){const h=r[l].flatMap(([f,d])=>{const m=o(f,d);return m===null?[]:[{a:f,b:d,rows:m[0],cols:m[1]}]});u=this.file.prefetchWalk(h,{pause:s,cancelled:n}),a.set(l,u)}return u}}refuseOtherColumns(t){if(!(t===void 0||t==="count"))throw new C("unsupported",`A .hic stores one value per record, so there is no '${t}' column to draw. Extra per-pixel columns are a cooler feature.`,{value:t})}}const Io=4<<20,Eo=12,Th=65536;function ma(e){return e.length>=2&&e[0]===31&&e[1]===139}function ga(e,t=0){return e.length<t+Eo||e[t]!==31||e[t+1]!==139||e[t+2]!==8||(e[t+3]&4)===0?!1:vo(e,t)!==null}function vo(e,t=0){if(e.length<t+Eo)return null;const n=new DataView(e.buffer,e.byteOffset,e.byteLength),s=n.getUint16(t+10,!0);let o=t+12;const r=Math.min(o+s,e.length);for(;o+4<=r;){const i=e[o],a=e[o+1],c=n.getUint16(o+2,!0);if(i===66&&a===67&&c===2)return n.getUint16(o+4,!0)+1;o+=4+c}return null}async function wa(e){return e.length===0?e:xo(e,{format:"BGZF file",field:"member",encoding:"deflate-raw",maxBytes:Th})}function Fh(e,t,n){return new DataView(e.buffer,e.byteOffset,e.byteLength).getUint32(t+n-4,!0)}function zh(e,t,n){const o=new DataView(e.buffer,e.byteOffset,e.byteLength).getUint16(t+10,!0);return e.subarray(t+12+o,t+n-8)}function Co(e,t={}){const n=e.readBytes(0,Math.min(e.size,64));return ga(n)?Ph(e,t):ma(n)?br(e,t,Rh).pipeThrough(new DecompressionStream("gzip")):br(e,t,Io)}const Rh=65536;function br(e,t,n){const s=t.from??0,o=Math.min(t.to??e.size,e.size),r=Math.max(0,o-s);let i=s,a=0;return new ReadableStream({pull(c){if(t.cancelled?.()===!0||i>=o){c.close();return}const l=e.readBytes(i,Math.min(Io,o-i));if(l.length===0){c.close();return}i+=l.length,a+=l.length;for(let u=0;u<l.length;u+=n)c.enqueue(l.subarray(u,Math.min(u+n,l.length)));t.onProgress?.(a,r)}})}function Ph(e,t){const n=t.from??0,s=Math.min(t.to??e.size,e.size),o=Math.max(0,s-n);let r=n,i=0,a=new Uint8Array(0),c=!1;const l=u=>{t.onFraming?.({partialMember:a.length>0,endedOnEofMarker:c}),u.close()};return new ReadableStream({async pull(u){for(;;){if(t.cancelled?.()===!0){u.close();return}const h=a.length>=Eo?vo(a):null;if(h!==null&&a.length>=h){const d=zh(a,0,h),m=Fh(a,0,h);if(a=a.subarray(h),c=m===0,m>0){u.enqueue(await wa(d));return}continue}if(r>=s){l(u);return}const f=e.readBytes(r,Math.min(Io,s-r));if(f.length===0){l(u);return}if(r+=f.length,i+=f.length,t.onProgress?.(i,o),a.length===0)a=f.slice();else{const d=new Uint8Array(a.length+f.length);d.set(a),d.set(f,a.length),a=d}}}})}async function $o(e,t,n){const s=e.getReader();let o=[],r=0;const i=a=>{if(r===0)return a;const c=new Uint8Array(r+a.length);let l=0;for(const u of o)c.set(u,l),l+=u.length;return c.set(a,l),o=[],r=0,c};try{for(;;){if(n?.()===!0)return!1;const{done:a,value:c}=await s.read();if(a)break;let l=0;for(let u=c.indexOf(10);u>=0;u=c.indexOf(10,l)){const h=i(c.subarray(l,u)),f=h.length>0&&h[h.length-1]===13?h.length-1:h.length;t(h.subarray(0,f)),l=u+1}if(l<c.length&&(o.push(c.slice(l)),r+=c.length-l,r>Is))throw new C("format",`A line of this .pairs file runs past ${Is>>20} MiB without ending, and no pairs line is that long. The file is corrupt, or is not a .pairs file.`,{maxLineBytes:Is})}return r>0&&t(i(new Uint8Array(0))),!0}finally{s.releaseLock()}}const Is=64<<20,Lh=["readID","chr1","pos1","chr2","pos2","strand1","strand2"],Bn={chrom1:["chr1","chrom1","chromosome1"],pos1:["pos1","position1"],chrom2:["chr2","chrom2","chromosome2"],pos2:["pos2","position2"]},yr={strand1:["strand1","strand_1"],strand2:["strand2","strand_2"]},Dh=["pair_type","pairtype"],Uh=64<<20,Gh=64,Hh=65536;function pa(e){return/^##\s*pairs\s+format/i.test(e)}async function qh(e){let t=null;try{await $o(Co(e,{to:Wh(e)}),n=>{t??=new TextDecoder().decode(n)},()=>t!==null)}catch{}return t!==null&&pa(t)}function Wh(e){const t=e.readBytes(0,Math.min(e.size,Gh));if(ga(t)){const n=vo(t);if(n!==null)return Math.min(e.size,n)}return Math.min(e.size,Hh)}async function ba(e){const t=[],n=new Set,s=[];let o=null,r=null,i=null,a=null,c=null,l=0,u=!1;const h=new TextDecoder,f=Co(e,{to:Math.min(e.size,Uh)});if(await $o(f,d=>{if(u)return;if(l+=d.length+1,d.length===0||d[0]!==35){u=!0;return}const m=h.decode(d);if(s.push(m),o===null&&pa(m)){o=m.replace(/^##\s*/,"").trim();return}const g=m.indexOf(":");if(g<0)return;const w=m.slice(1,g).trim().toLowerCase(),p=m.slice(g+1).trim();if(w==="chromsize"||w==="chromosome"){const b=p.split(/\s+/);b.length>=2&&Ar(t,n,b[0],Number(b[1]))}else if(w==="samheader"){const b=/^@SQ\s.*\bSN:(\S+).*\bLN:(\d+)/.exec(p);b!==null&&Ar(t,n,b[1],Number(b[2]))}else w==="genome_assembly"?r=p:w==="sorted"?i=p:w==="shape"?a=p:w==="columns"&&(c=p.split(/\s+/).filter(b=>b!==""))},()=>u).catch(()=>!1),o===null)throw new C("format","This file does not begin with a `## pairs format` line, so it is not a 4DN pairs file. If it is a headerless contact list, add a header with `pairtools header generate`, or bin it with `cooler cload pairs` and open the cooler.",{bytesRead:l});if(t.length===0)throw new C("format","This .pairs file declares no `#chromsize:` lines, so there is no bin table to build. Chromosome sizes cannot be inferred from the records — a grid guessed from the largest coordinate seen would differ between two subsamples of the same library. Add them with `pairtools header generate --chroms-path <chrom.sizes>`.",{contigs:0});return{version:o,assembly:r,sorted:i,shape:a,contigs:t,columns:jh(c??Lh,c!==null),text:s.join(`
+`)}}function Ar(e,t,n,s){t.has(n)||!Number.isFinite(s)||s<=0||(t.add(n),e.push({name:n,length:s}))}function jh(e,t){const n=e.map(i=>i.toLowerCase()),s=i=>{for(const a of i){const c=n.indexOf(a);if(c>=0)return c}return-1},o={chrom1:s(Bn.chrom1),pos1:s(Bn.pos1),chrom2:s(Bn.chrom2),pos2:s(Bn.pos2),strand1:s(yr.strand1),strand2:s(yr.strand2),pairType:s(Dh)},r=["chrom1","pos1","chrom2","pos2"].filter(i=>o[i]<0);if(r.length>0)throw new C("unsupported",`This .pairs file's ${t?"`#columns:` line":"assumed column layout"} has no ${r.join(", ")} column. It declares ${e.join(", ")}. The importer needs two chromosome columns and two position columns.`,{missing:r,columns:[...e]});return o}function No(e,t){const n=new Float64Array(e.length+1);let s=0;for(let o=0;o<e.length;o++)n[o]=s,s+=Math.ceil(e[o].length/t);return n[e.length]=s,n}function ya(e,t){let n=0;for(const s of e)n+=Math.ceil(s.length/t);return n}function Mr(e){throw new C("unsupported",`A map binned from a .pairs file serves ${e} through PixelStore (metacooler/store.ts), not through the handle. Reaching for the column by name bypasses the chunking and the cancellation every other read has.`,{path:e})}function Qh(e){const{header:t,pixels:n}=e,s=()=>De(n.contigs.length,["name","length"],{name:n.contigs.map(r=>r.name),length:Float64Array.from(n.contigs,r=>r.length)}),o={format:"PAIRS","format-url":"https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md","format-version":Yh(t.version),"bin-size":n.binSize,"bin-type":"fixed","contig-ordering":"genome-then-length","storage-mode":"symmetric-upper","genome-assembly":t.assembly,nbins:n.nBins,nchroms:n.contigs.length,nnz:n.nnz,sum:n.sum,ngenomes:null,"pairs-source":e.uri,"pairs-header":t.text,"pairs-sorted":t.sorted,"pairs-shape":t.shape,"pairs-indexed":e.indexed,"pairs-records":n.sum,...e.declaredRecords==null?{}:{"pairs-declared-records":e.declaredRecords},...n.skippedUnknownContig===0?{}:{"pairs-skipped-unknown-contig":n.skippedUnknownContig},...n.skippedBadPosition===0?{}:{"pairs-skipped-bad-position":n.skippedBadPosition},...n.clampedPosition===0?{}:{"pairs-clamped-positions":n.clampedPosition},...n.wasUnsorted?{"pairs-required-merge":!0}:{},...n.truncated?{"pairs-truncated":!0}:{},...n.contigsWithoutCisContacts.length===0?{}:{"pairs-sequences-without-cis-contacts":n.contigsWithoutCisContacts.join(", ")}};return{uri:e.uri,group:"/",rootEntries:e.rungs.map(r=>String(r)),rootEntryGroup:"resolutions",attrs:()=>({...o}),attrsAt:r=>r===""||r==="/"?{...o}:{},has(r){return["chroms","chroms/name","chroms/length","contigs","indexes","indexes/chrom_offset","pixels","pixels/count","bins"].includes(r)},keys(r){return r===""||r==="/"?["chroms","bins","pixels","indexes"]:r==="chroms"||r==="contigs"?["name","length"]:r==="pixels"?["bin1_id","bin2_id","count"]:r==="indexes"?["chrom_offset"]:r==="bins"?[]:[]},isSoftLink:()=>!1,datasetLength(r){return r==="chroms/name"||r==="chroms/length"?n.contigs.length:r==="indexes/chrom_offset"?n.contigs.length+1:r.startsWith("pixels/")?n.nnz:0},dtype(r){return r==="pixels/count"||r==="pixels/bin1_id"||r==="pixels/bin2_id"||r==="chroms/length"?"<i":r==="chroms/name"?"S":"<d"},readNumeric(r,i=0,a){if(r==="indexes/chrom_offset")return n.chromOffset.slice();if(r==="chroms/length"){const c=a??n.contigs.length;return Float64Array.from(n.contigs.slice(i,c),l=>l.length)}throw r==="bins/weight"?new C("unsupported","A map binned from a .pairs file carries raw counts and no balancing weights: nothing has been balanced. Export the .mcool and run `cooler balance` on it, or open a cooler that was written with weights.",{}):((r==="indexes/bin1_offset"||r.startsWith("pixels/"))&&Mr(r),new C("unsupported",`An imported .pairs map has no ${r}.`,{path:r}))},readInt32(r){throw r.startsWith("pixels/")&&Mr(r),new C("unsupported",`An imported .pairs map has no ${r}.`,{path:r})},readStrings(r,i=0,a){if(r==="chroms/name")return n.contigs.slice(i,a??n.contigs.length).map(c=>c.name);throw new C("unsupported",`An imported .pairs map has no ${r}.`,{path:r})},readTable(r){if(r==="chroms"||r==="contigs")return s();throw new C("unsupported",`An imported .pairs map has no /${r} table.`,{path:r})},at(r){throw new C("unsupported",`An imported .pairs has no /${r} group to open.`,{path:r})},close:()=>{}}}function Yh(e){const t=/v?(\d+)(?:\.(\d+))?/.exec(e);return t===null?null:Number(t[1])}const xr=1<<20;class Vh{constructor(t){this.pixels=t}offsets=null;get nnz(){return this.pixels.nnz}countKind="i";scoreColumns(){return["count"]}binOffsets(){if(this.offsets!==null)return this.offsets;const{bin1:t,nnz:n,nBins:s}=this.pixels,o=new Float64Array(s+1);let r=0;for(let i=0;i<s;i++){for(;r<n&&t[r]===i;)r++;o[i+1]=r}return this.offsets=o,o}async forEachWindow(t,n,s,o,r={}){this.refuseOtherColumns(r.value);const i=this.pixelRange(s.span[0],s.span[1]);return this.emit(i[0],i[1],o,r)}async forEachBands(t,n,s={}){this.refuseOtherColumns(s.value);for(const[o,r]of this.mergedBands(t))if(!await this.emit(o,r,n,s))return!1;return!0}async scanAll(t){const n=Math.max(1,Math.trunc(t.chunkSize??xr)),s=this.pixels.nnz;for(let o=0;o<s;o+=n){const r=Math.min(o+n,s);if(t.onChunk(this.chunk(o,r))===!1)return;t.onProgress?.(r,s),await St()}}pixelRange(t,n){const s=this.binOffsets(),o=this.pixels.nBins,r=s[Math.max(0,Math.min(o,t))],i=s[Math.max(0,Math.min(o,n))];return[r,Math.max(r,i)]}mergedBands(t){const n=[];for(const[o,r]of t){if(r<=o)continue;const[i,a]=this.pixelRange(o,r);a>i&&n.push([i,a])}n.sort((o,r)=>o[0]-r[0]);const s=[];for(const o of n){const r=s[s.length-1];r!==void 0&&o[0]<=r[1]+Ti?r[1]=Math.max(r[1],o[1]):s.push([o[0],o[1]])}return s}async emit(t,n,s,o){const r=Math.max(1,Math.trunc(o.chunkSize??xr)),i=n-t;for(let a=t;a<n;a+=r){if(o.cancelled?.()===!0)return!1;const c=Math.min(a+r,n);s(this.chunk(a,c)),o.onProgress?.(c-t,i),await St()}return!0}chunk(t,n){const{bin1:s,bin2:o,count:r}=this.pixels;return{bin1:s.slice(t,n),bin2:o.slice(t,n),count:Float64Array.from(r.subarray(t,n)),length:n-t}}refuseOtherColumns(t){if(!(t===void 0||t==="count"))throw new C("unsupported",`A map binned from a .pairs file stores one value per pixel — the number of contacts — so there is no '${t}' column to draw. Extra per-pixel columns come from a cooler that was written with them.`,{value:t})}}function en(e,t,n){const s=Math.max(0,Math.min(Math.trunc(t),e)),o=Math.max(s,Math.min(Math.trunc(n??e),e));return[s,o]}function Kh(e,t){const{bins:n,pixels:s}=t,o=()=>De(n.names.length,["name","length"],{name:[...n.names],length:n.lengths.slice()}),r={format:"HiC-Pro","format-url":"https://github.com/nservant/HiC-Pro","bin-size":n.binsize,"bin-type":"fixed",ordering:"genome-then-length","storage-mode":"symmetric-upper",nbins:n.nBins,ncontigs:n.names.length,nnz:s.nnz,sum:s.sum,ngenomes:null,"hicpro-matrix":t.matrixName,"hicpro-bins":t.binsName,"hicpro-stored":s.observed};return{uri:e,group:"/",rootEntries:[],rootEntryGroup:"",attrs:()=>({...r}),attrsAt:i=>i===""||i==="/"?{...r}:{},has(i){return["chroms","chroms/name","chroms/length","bins","pixels","pixels/bin1_id","pixels/bin2_id","pixels/count","indexes","indexes/bin1_offset","indexes/chrom_offset"].includes(i)},keys(i){return i===""||i==="/"?["chroms","bins","pixels","indexes"]:i==="chroms"?["name","length"]:i==="pixels"?["bin1_id","bin2_id","count"]:i==="indexes"?["bin1_offset","chrom_offset"]:i==="bins"?[]:[]},isSoftLink:()=>!1,datasetLength(i){return i==="chroms/name"||i==="chroms/length"?n.names.length:i.startsWith("pixels/")?s.nnz:i==="indexes/bin1_offset"?n.nBins+1:i==="indexes/chrom_offset"?n.names.length+1:0},dtype(i){return i==="pixels/count"?"<f":i==="pixels/bin1_id"||i==="pixels/bin2_id"||i==="chroms/length"?"<i":i==="chroms/name"?"S":"<d"},readNumeric(i,a=0,c){if(i==="indexes/chrom_offset")return n.chromOffset.slice();if(i==="indexes/bin1_offset"){const[l,u]=en(n.nBins+1,a,c);return s.binOffset.slice(l,u)}if(i==="chroms/length"){const[l,u]=en(n.names.length,a,c);return n.lengths.slice(l,u)}if(i==="pixels/count"){const[l,u]=en(s.nnz,a,c);return Float64Array.from(s.count.subarray(l,u))}throw i==="bins/weight"?new C("unsupported","A HiC-Pro matrix carries no balancing weights. Its `iced/` matrix is already normalised — open that one instead of balancing this one — and its `.biases` file belongs to the raw matrix, so applying it here would normalise twice.",{path:i}):new C("unsupported",`A HiC-Pro matrix has no ${i}.`,{path:i})},readInt32(i,a=0,c){const[l,u]=en(s.nnz,a,c);if(i==="pixels/bin1_id")return s.bin1.subarray(l,u);if(i==="pixels/bin2_id")return s.bin2.subarray(l,u);throw new C("unsupported",`A HiC-Pro matrix has no ${i}.`,{path:i})},readStrings(i,a=0,c){if(i==="chroms/name"){const[l,u]=en(n.names.length,a,c);return n.names.slice(l,u)}throw new C("unsupported",`A HiC-Pro matrix has no ${i}.`,{path:i})},readTable(i){if(i==="chroms"||i==="contigs")return o();throw new C("unsupported",`A HiC-Pro matrix has no /${i} table.`,{path:i})},at(i){throw new C("unsupported",`A HiC-Pro matrix has no /${i} group.`,{path:i})},close:()=>{}}}const Xh={K:1e3,KB:1e3,M:1e6,MB:1e6,G:1e9,GB:1e9};function Wt(e,t={}){throw new C("bad-range",e,t)}function Sr(e){const t=e.replace(/,/g,"").split(/([0-9.]+)/);(t.length!==3||t[0]!=="")&&Wt(`Unexpected token "${e}"`,{token:e});const[,n,s]=t;if(s.length===0)return/^[0-9]+$/.test(n)||Wt(`Unexpected token "${e}"`,{token:e}),Number(n);const o=Number.parseFloat(n);Number.isFinite(o)||Wt(`Unexpected token "${e}"`,{token:e});const r=s.toUpperCase().trim(),i=Xh[r];return i===void 0&&Wt(`Unknown unit '${r}'`,{unit:r}),Math.trunc(o*i)}function Zh(e){const t=/\s*(-)|\s*([0-9,]+(?:\.[0-9]*)?(?:[a-z]+)?)|\s*(.+)/gi,n=[];for(const s of e.matchAll(t)){const o=s[1],r=s[2],i=s[3];o!==void 0?n.push({kind:"HYPHEN",text:o}):r!==void 0?n.push({kind:"COORD",text:r}):n.push({kind:"OTHER",text:i??""})}return n}function Aa(e,t={}){const n=e.split(":"),s=n[0].trim();if(s.length===0&&Wt("Chromosome name cannot be empty",{region:e}),n.length<2)return[s,null,null];const o=Zh(n[1]);let r=0;const i=()=>o[r++],a=(h,f)=>(h===void 0&&Wt(`Expected ${f.join(" or ")} token missing`,{region:e}),f.includes(h.kind)||Wt(`Unexpected token "${h.text}"`,{region:e}),h),c=Sr(a(i(),["COORD"]).text);a(i(),["HYPHEN"]);const l=i();if(l===void 0)return[s,c,null];const u=Sr(a(l,["COORD"]).text);return u<c&&t.reversed!==!0&&Wt("End coordinate less than start — unless the sequence joins its own ends, which is a tick in the circular column of the Chromosomes table",{region:e,start:c,end:u}),[s,c,u]}function Jh(e,t){const[n,s,o]=Aa(e),r=t.get(n);if(r===void 0)throw new C("unknown-label",`Unknown sequence label: ${n}`,{label:n});const i=s===null?0:s,a=o===null?r:o;return a<i&&Wt("End cannot be less than start",{region:e,start:i,end:a}),(i<0||a>r)&&Wt(`Genomic region out of bounds: [${i}, ${a})`,{region:e,start:i,end:a,length:r}),[n,i,a]}function tf(e,t,n,s){const o=t.split(":")[0],r=e.genomes===null?[]:e.genomes.strings("name"),i=e.contigs.strings("name");if(r.includes(o)){if(o===ke)throw new C("unbinned-not-displayable",`Range ${V(t)}: ${V(ke)} holds every contig that binning failed to assign. It is a bookkeeping row, not a genome — there is no coherent contact map to draw for it — so it cannot be displayed. Its share of the file is reported as a QC statistic in the file info panel.`,{label:o});if(t.includes(":"))throw new C("genome-coordinate-suffix",`Range ${V(t)}: ${V(o)} is a genome name — coordinate suffixes are not allowed for genome ranges. Use just ${V(o)}.`,{label:o,region:t});return{kind:"genome",label:o,extent:e.genomeExtent(o)}}if(i.includes(o))return{kind:"contig",label:o,extent:Ir(e,o,t,s)};const a=(e.names??ef(e)).find(o,{from:n});if(a!==null){const c=t.slice(o.length);return{kind:"contig",label:a.name,extent:Ir(e,a.name,`${a.name}${c}`,s),matched:a}}throw e.genomes===null?new C("unknown-label",`Range ${V(t)}: ${V(o)} is not a sequence of this file.
+  Sequences: ${_e(i)}`,{label:o,region:t}):new C("unknown-label",`Range ${V(t)}: ${V(o)} is not a known genome or contig.
+  Genomes: ${_e(e.displayGenomes().map(c=>r[c]))}
+  Contigs: ${_e(i)}`,{label:o,region:t})}function Ir(e,t,n,s){if(s===void 0||!s.includes(t))return e.extent(n);const[,o,r]=Aa(n,{reversed:!0});if(o===null||r===null||r>=o)return e.extent(n);const i=e.extent(t),a=e.extent(`${t}:${o}-`),c=e.extent(`${t}:0-${r}`);return[a[0],i[1]+(c[1]-i[0])]}function ef(e){const t=e.contigs.strings("name"),n=e.contigs.numbers("length");return ie.of(t.map((s,o)=>({name:s,length:n[o]})))}function nf(e,t,n,s,o){const r=e[t],i=e[t+1]??r,a=Math.min(r+Math.floor(n/o),i),c=Math.min(r+Math.ceil(s/o),i);return[a,Math.max(a,c)]}const sf=["name","length","n_contigs","n_bins"],of=["name","length"],Es=["name","length","genome_id"],rf=["name","length","n_contigs","n_bins"],af=["bin-size","bin-type","storage-mode"],vs=["nnz","sum"];class et{uri;layout;entries;entryGroup;tables;info;metadata;genomes;contigs;binsize;unlensed;storageMode;countKind;coords;chromnames;get chromsizes(){return this.chromsizeCache??=new Map(this.chromnames.map((t,n)=>[t,this.contigLengths[n]])),this.chromsizeCache}get contigIds(){return this.contigIdCache??=new Map(this.chromnames.map((t,n)=>[t,n])),this.contigIdCache}get names(){return this.nameIndexCache??=ie.of(this.chromnames.map((t,n)=>({name:t,length:this.contigLengths[n]}))),this.nameIndexCache}genomeNames;contigGenomeIds;rawHandle;get handle(){const t=this.resampled?.weightScale??1;return t===1?this.rawHandle:(this.weighted?.scale!==t&&(this.weighted={scale:t,handle:cf(this.rawHandle,t)}),this.weighted.handle)}weighted=null;pixelStore;get store(){return this.resampled??this.pixelStore}get storedPixels(){return this.pixelStore}resampled=null;census=null;censusWanted=!1;chromOffset;genomeOffset;genomeIds;closed=!1;fullContigTable=null;fullGenomeTable=null;contigIdCache=null;chromsizeCache=null;nameIndexCache=null;contigLengths;static async open(t,n,s={}){if(await n.mount(),da(n.readBytes(0,4)))return et.fromHic(t,n);if(await qh(n)){const i=await ba(n);throw new C("pairs-binning-needed","This is a .pairs file: a list of contacts with no resolution of its own. Choose a bin size to build a map at.",{contigs:i.contigs.length,assembly:i.assembly,sorted:i.sorted})}const o=s.metacool===!1?".cool, .mcool or .scool":".cool, .mcool, .scool or .metacool";if(ma(n.readBytes(0,2)))throw new C("not-hdf5",`This file is gzip-compressed. HDF5 is read in place and cannot be decompressed on the fly, so a ${o} must be decompressed first. A .pairs.gz is read compressed — but this one carries no \`## pairs format\` line, so it is not one.`,{});if(!df(n))throw new C("not-hdf5",`${Mt(t).path} does not start with the HDF5 signature, so it is not a ${o} whatever its name says. A download that stopped short, an HTML page saved under the file’s name, or a text matrix look like this.`,{});const r=await Sl(t,n,Mt(t).group);try{return s.listingAgreed!==!0&&hf(r,n),et.fromHandle(r,s)}catch(i){if(r.close(),!(i instanceof C)&&i instanceof Error){const a=Mt(t).group;throw new C("format",`${Mt(t).path}${a===""?"":`::${a}`} could not be read as a cooler container. HDF5 said: ${i.message}. The file opens as HDF5, so this is a group, dataset or attribute the reader expected and did not find.`,{hdf5:i.message})}throw i}}static fromHic(t,n){const{group:s}=Mt(t),o=/^\/resolutions\/(\d+)$/.exec(s),r=So.open(n,o===null?{}:{binSize:Number(o[1])});if(!r.hasAnyMatrix())throw new C("unsupported",`This .hic carries no base-pair matrix at ${r.binSize} bp. Its resolutions are ${r.resolutions.join(", ")}.`,{binSize:r.binSize,resolutions:r.resolutions});const i=Oh(t,r),a=i.attrs();return new et({uri:t,handle:i,layout:{kind:"hic",group:s,entries:r.resolutions.map(c=>String(c))},attrs:a,contigs:i.readTable("chroms"),chromOffset:i.readNumeric("indexes/chrom_offset"),store:new _h(r)})}static fromPairs(t){const n=Qh({uri:t.uri,header:t.header,pixels:t.pixels,rungs:t.rungs,indexed:t.indexed,declaredRecords:t.declaredRecords??null});return new et({uri:t.uri,handle:n,layout:{kind:"pairs",group:`/resolutions/${t.pixels.binSize}`,entries:t.rungs.map(s=>String(s))},attrs:n.attrs(),contigs:n.readTable("chroms"),chromOffset:n.readNumeric("indexes/chrom_offset"),store:new Vh(t.pixels)})}static fromScool(t,n,s,o){const r=rr(n.entries??[],o),i=t.at(ts(n,(n.entries??[])[0])),a=Ui(t,n,s).attrs,c={...s};for(const f of af)c[f]===void 0&&a[f]!==void 0&&(c[f]=a[f]);const l=i.readNumeric("indexes/chrom_offset"),u=Ho(i.dtype("pixels/count")),h=Number(l[l.length-1]??0);return new et({uri:t.uri,handle:t,tables:i,layout:n,attrs:c,contigs:i.readTable("chroms",void 0,void 0,Es),chromOffset:l,store:new rn(t,n,r,h,u)})}static fromHicPro(t,n){if(!n.bins.fixed||n.bins.binsize===null)throw new C("variable-bins",`The viewer supports fixed-bin files only, and ${n.binsName} is not one: its intervals are of differing widths, which is what a fragment-level map (\`GENOME_FRAGMENT\` in HiC-Pro's config) looks like. Re-run HiC-Pro with a \`BIN_SIZE\`, or open the fixed-bin matrix beside this one.`,{"bin-type":"variable","bin-size":null,bins:n.binsName});const s=Kh(t,n);return new et({uri:t,handle:s,layout:{kind:"hicpro",group:"/"},attrs:s.attrs(),contigs:s.readTable("chroms"),chromOffset:n.bins.chromOffset})}static fromHandle(t,n={}){const s=t.attrs(),o=n.metacool===void 0?{}:{metacool:n.metacool},r=fl(t,s,o);if(bl(t,r,s,o),r.kind==="scool")return et.fromScool(t,r,s,null);if(r.kind!=="metacool")return new et({uri:t.uri,handle:t,layout:r,attrs:s,contigs:t.readTable("chroms",void 0,void 0,Es),chromOffset:t.readNumeric("indexes/chrom_offset")});if(!t.has("indexes/genome_offset"))throw new st("indexes/genome_offset is missing");return new et({uri:t.uri,handle:t,layout:r,attrs:s,genomes:t.readTable("genomes",void 0,void 0,rf),contigs:t.readTable("contigs",void 0,void 0,Es),chromOffset:t.readNumeric("indexes/chrom_offset"),genomeOffset:t.readNumeric("indexes/genome_offset")})}fullContigs(){return this.fullContigTable??=this.tables.readTable(this.layout.kind==="metacool"?"contigs":"chroms"),this.fullContigTable}fullGenomes(){return this.genomes===null?null:(this.fullGenomeTable??=this.handle.readTable("genomes"),this.fullGenomeTable)}constructor(t){this.uri=t.uri,this.unlensed=t.unlensed??null,this.rawHandle=t.handle,this.tables=t.tables??t.handle,this.layout=t.layout,this.entries=t.handle.rootEntries,this.entryGroup=t.handle.rootEntryGroup,this.genomes=t.genomes??null,this.contigs=t.contigs,this.chromOffset=t.chromOffset,this.genomeOffset=t.genomeOffset??new Float64Array(0),this.info=Al(t.attrs),this.metadata=Ml(t.attrs),this.storageMode=this.info["storage-mode"];const n=this.info["bin-size"];if(n===null||n<=0)throw new st(`attrs['bin-size'] must be positive, got ${V(n)}`,{"bin-size":n});this.binsize=n,this.chromnames=this.contigs.strings("name"),this.genomeNames=this.genomes===null?[]:this.genomes.strings("name");const s=lf(this.contigs,"length");this.contigGenomeIds=this.genomes===null?new Int32Array(0):uf(this.contigs,"genome_id"),this.coords=new Tl(this.binsize,this.chromOffset,s),this.contigLengths=s,this.genomeIds=new Map;for(let o=0;o<this.genomeNames.length;o++)this.genomeIds.set(this.genomeNames[o],o);this.countKind=Ho(this.tables.dtype("pixels/count")),this.pixelStore=t.store??new Vi(this.rawHandle,this.nBins,this.countKind),this.validateLight()}get hasGenomes(){return this.genomes!==null}get hasWeights(){return this.handle.has(`bins/${Ne}`)}get scoreColumns(){return this.store.scoreColumns()}get nGenomes(){return this.genomes?.length??0}get nContigs(){return this.contigs.length}get nBins(){return this.coords.nBins}get shape(){return[this.nBins,this.nBins]}hasGenome(t){return this.genomeIds.has(t)}hasContig(t){return this.contigIds.has(t)}genomeId(t){const n=this.genomeIds.get(t);if(n===void 0)throw new C("unknown-label",`Genome ${V(t)} not found. Available: ${_e(this.displayGenomes().map(s=>this.genomeNames[s]))}`,{label:t});return n}contigId(t){const n=this.contigIds.get(t);if(n===void 0)throw new C("unknown-label",`Contig ${V(t)} not found. Available: ${_e(this.chromnames)}`,{label:t});return n}extent(t){const[n,s,o]=Jh(t,this.chromsizes);return nf(this.chromOffset,this.contigId(n),s,o,this.binsize)}offset(t){return this.extent(t)[0]}genomeContigExtent(t){const n=typeof t=="number"?t:this.genomeId(t);return[this.genomeOffset[n],this.genomeOffset[n+1]]}genomeExtent(t){const n=typeof t=="number"?t:this.genomeId(t),[s,o]=this.genomeContigExtent(n);if(o<=s)return[0,0];this.assertContiguous(n,s,o);const r=this.chromOffset[s],i=this.chromOffset[o];return i<=r?[0,0]:[r,i]}assertContiguous(t,n,s){const o=this.contigGenomeIds;if(o[n]!==t||o[s-1]!==t||n>0&&o[n-1]===t||s<o.length&&o[s]===t)throw new C("bad-ordering",`Genome ${V(this.genomeNames[t])} is not contiguous in bin space under contig-ordering ${V(this.info.ordering)}; a single bin range cannot represent it, so the file's ordering attribute does not describe its actual contig layout. Re-create the file with a genome-grouped ordering.`,{genome:this.genomeNames[t],genomeId:t,contigs:[n,s]})}contigExtent(t){const n=typeof t=="number"?t:this.contigId(t),[s,o]=this.coords.contigBinExtent(n);return o<=s?[0,0]:[s,o]}displayGenomes(){const t=[];for(let n=0;n<this.genomeNames.length;n++)this.genomeNames[n]!==ke&&t.push(n);return t}displayBinExtent(){const t=[0,this.nBins],n=this.genomeIds.get(ke);if(n===void 0)return t;const[s,o]=this.genomeExtent(n);return o<=s?t:s===0?[o,this.nBins]:o===this.nBins?[0,s]:t}unassignedStats(){const t=this.nContigs,n=this.nBins,s=this.genomeIds.get(ke);if(s===void 0||this.genomes===null)return null;const o=Number(this.genomes.get("n_contigs",s)??0),r=Number(this.genomes.get("n_bins",s)??0);return{genomeIndex:s,contigs:o,bins:r,totalContigs:t,totalBins:n,contigFraction:t>0?o/t:0,binFraction:n>0?r/n:0}}genomeDensity(t){const[n,s]=this.genomeExtent(t);if(s<=n)return 0;const o=this.binOffsets();return o[s]-o[n]}binOffsets(){return this.store.binOffsets()}genomeDensities(){const t=new Float64Array(this.nGenomes);if(this.genomes===null)return t;const n=this.binOffsets();for(const s of this.displayGenomes()){const[o,r]=this.genomeExtent(s);r>o&&(t[s]=n[r]-n[o])}return t}async matrix(t,n=un.range){return Kc(this,t,n)}async genomeMatrix(t){const n=this.genomeExtent(t);return this.matrix({rows:n},un.binSelection)}async genomePairMatrix(t,n){return this.matrix({rows:this.genomeExtent(t),cols:this.genomeExtent(n)},un.binSelection)}async aggregateSparse(t,n,s={}){const o=On(t.rows,this.nBins),r=On(t.cols??t.rows,this.nBins),i=Te(o,r,this.storageMode),a=Ol(o,r,this.coords,this.contigGenomeIds,n,i.mode,this.storageMode==="symmetric-upper",qt),c=t.balance===!0?this.weightSlices(o,r):null;return await this.store.forEachWindow(o,r,i,l=>{for(let u=0;u<l.length;u++){const h=l.bin1[u],f=l.bin2[u],d=c===null?l.count[u]:l.count[u]*kn(c,o,r,h)*kn(c,o,r,f);a.place(h,f,d)}},vr(s,t.value)),{...a.finish(),contigsPerCell:a.perCell}}async pooledMatrix(t,n,s={}){const o=On(t.rows,this.nBins),r=On(t.cols??t.rows,this.nBins),i=Te(o,r,this.storageMode),a=o[0]===r[0]&&o[1]===r[1],c=this.contigGenomeIds,l=Qo(this.coords,o[0],o[1],n,qt,c),u=a?l:Qo(this.coords,r[0],r[1],n,qt,c),h=Vs(o,r,l,u,i.mode,this.storageMode==="symmetric-upper",!0),f=t.balance===!0?this.weightSlices(o,r):null;return await this.store.forEachWindow(o,r,i,d=>{for(let m=0;m<d.length;m++){const g=d.bin1[m],w=d.bin2[m],p=f===null?d.count[m]:d.count[m]*kn(f,o,r,g)*kn(f,o,r,w);h.place(g,w,p)}},vr(s,t.value)),{...h.finish(),binsPerCell:l.stride,contigsPerCell:Math.max(l.contigsPerCell,u.contigsPerCell),rowMembers:l,colMembers:u}}async selectionMatrix(t,n,s={}){const o=s.byGenome===!0?this.contigGenomeIds:void 0,r=Nl(this.nBins,t,n,s.cellCap===void 0?qt:s.cellCap,o),i=[0,this.nBins],a=Vs(i,i,r,r,Te(i,i,this.storageMode).mode,this.storageMode==="symmetric-upper"),c=s.balance===!0?this.weightSlices(i,i):null;return await this.store.forEachBands(t.map(({extent:u})=>[u[0],u[1]]),u=>{for(let h=0;h<u.length;h++){const f=u.bin1[h],d=u.bin2[h],m=c===null?u.count[h]:u.count[h]*c.rows[f]*c.cols[d];a.place(f,d,m)}},s),{...a.finish(),binsPerCell:r.stride,contigsPerCell:r.contigsPerCell,ids:r.ids,pooling:r}}static withLens(t,n){const s=n.original.genome!==void 0;if(t.hasGenomes&&!s)return{map:t,refusal:"An edit is not yet drawn on a map of several genomes."};if(t.layout.kind==="scool")return{map:t,refusal:"An edit is not yet drawn on a single-cell file."};const o=du(n,t.chromnames,t.contigLengths,{always:s});if(o===null)return{map:t,refusal:null};if("refusal"in o)return{map:t,refusal:o.refusal};const r=bo.of(t.coords,t.chromnames,o.assembly),i=fu(r),a={...t.rawHandle.attrs(),nchroms:r.names.length,nbins:r.nBins};return{map:new et({uri:t.uri,handle:hu(t.rawHandle,r,i,a),layout:t.layout,attrs:a,contigs:i,chromOffset:r.chromOffset,store:new uu(t.store,r,t.storageMode==="symmetric-upper"),unlensed:t}),refusal:null}}static coarsened(t,n){if(!Number.isInteger(n)||n<1)return{map:t,refusal:`A resolution is a whole number of this map's bins, not ${n} of them.`};if(n===1)return{map:t,refusal:null};if(t.layout.kind==="scool")return{map:t,refusal:"A single-cell file is not yet measured at a resolution you added; measure it at one it stores."};const s=yo.of(t.chromOffset,n),{nnz:o,...r}=t.handle.attrs(),i={...r,"bin-size":t.binsize*n,nbins:s.nBins};return{map:new et({uri:t.uri,handle:bu(t.handle,s,i),layout:t.layout,attrs:i,contigs:t.contigs,chromOffset:s.chromOffset,...t.genomes===null?{}:{genomes:t.genomes,genomeOffset:t.genomeOffset},store:new wu(t.store,s,t.storageMode),...t.unlensed===null?{}:{unlensed:t.unlensed}}),refusal:null}}async picture(t,n={}){const s=[0,this.nBins],o=n.balance===!0?this.weightSlices(s,s).rows:null,r=await Yl({store:this.store,coords:this.coords,layout:t,weights:o,...n.value===void 0?{}:{value:n.value},...n.gather===void 0?{}:{gather:n.gather},...n.cancelled===void 0?{}:{cancelled:n.cancelled},...n.onProgress===void 0?{}:{onProgress:n.onProgress}});return r===null?null:{levels:Xl({n:t.n,cells:r.cells},r.quantizer),quantizer:r.quantizer,histogram:r.histogram,pixels:r.pixels,...r.contacts===void 0?{}:{contacts:r.contacts}}}binColumns(){if(!this.tables.has("bins"))return[];const t=[];for(const n of this.tables.keys("bins")){const s=Er(this.tables.dtype(`bins/${n}`));s!==null&&t.push({name:n,text:s})}return t}binColumn(t,n,s){const o=`bins/${t}`;if(!this.tables.has(o))throw new C("unsupported",`This file has no /${o} column.`,{column:t});const r=Math.max(0,Math.min(n,this.nBins)),i=Math.max(r,Math.min(s,this.nBins));return t===Ne&&this.tables===this.rawHandle?this.handle.readNumeric(o,r,i):Er(this.tables.dtype(o))===!0?this.tables.readStrings(o,r,i):this.tables.readNumeric(o,r,i)}weightSlices(t,n){const s=`bins/${Ne}`;if(!this.handle.has(s))throw new C("unsupported",`This file has no /${s} column, so there are no weights to balance with. Run \`cooler balance\` on it, or view the raw counts.`,{column:Ne});const o=this.handle.readNumeric(s,t[0],t[1]),r=n[0]===t[0]&&n[1]===t[1]?o:this.handle.readNumeric(s,n[0],n[1]);return{rows:o,cols:r}}aggregate(t,n){return kl(t,this.coords,this.contigGenomeIds,n,this.storageMode==="symmetric-upper")}get cells(){return this.layout.kind==="scool"?this.layout.entries??[]:[]}get activeCells(){return this.pixelStore instanceof rn?this.pixelStore.names:[]}selectCells(t){if(this.layout.kind!=="scool")throw new C("unsupported",`${this.uri} is not a single-cell container, so it has no cells to choose.`,{layout:this.layout.kind});const n=rr(this.cells,t);this.pixelStore=new rn(this.handle,this.layout,n,this.nBins,this.countKind)}async scanCells(t){if(!(this.pixelStore instanceof rn))throw new C("unsupported",`${this.uri} is not a single-cell container, so it has no cells to walk.`,{layout:this.layout.kind});await this.pixelStore.scanPerCell(t)}cellTable(){const t=this.cells,n=t.map(a=>this.handle.attrsAt(ts(this.layout,a))),s=["name"],o={name:t},r=new Set;for(const a of n)for(const c of Object.keys(a))r.add(c);const i=[...r].filter(a=>!vs.includes(a)&&a!=="metadata").sort();for(const a of[...vs,...i]){if(!r.has(a))continue;const c=n.map(u=>u[a]);if(!vs.includes(a)&&c.every(u=>u===c[0]))continue;c.every(u=>typeof u=="number"||typeof u=="boolean")?o[a]=Float64Array.from(c,u=>Number(u)):o[a]=c.map(u=>u==null?"":String(u)),s.push(a)}return De(t.length,s,o)}get nnz(){return this.store.nnz??0}async scanPixels(t){await this.store.scanAll(t)}async validateDeep(t){const n=[],s=new Set,o=(b,y)=>{s.has(b)||(s.add(b),n.push(y))},r=this.nBins,i=this.storageMode==="square",a=this.binOffsets(),c=this.nnz;a.length!==r+1?n.push(`bin1_offset length (${a.length}) != ${r+1}`):(a[0]!==0||a[r]!==c)&&n.push(`bin1_offset endpoints (${a[0]}, ${a[r]}) do not bracket the table (0, ${c})`);for(let b=1;b<a.length;b++)if(a[b]<a[b-1]){o("monotone",`bin1_offset is not non-decreasing: bin1_offset[${b-1}]=${a[b-1]} > bin1_offset[${b}]=${a[b]}`);break}let l=0;const u=this.countKind!=="f";let h=-1,f=-1;const d=a.length===r+1;let m=0,g=0;const w=t?.cancelled;if(await this.pixelStore.scanAll({onProgress:t?.onProgress,storedRows:!0,onChunk:b=>{if(w?.()===!0)return!1;for(let y=0;y<b.length;y++,g++){const A=b.bin1[y],x=b.bin2[y],E=b.count[y];if(u&&(l+=E),(A<0||x<0||A>=r||x>=r)&&o("range",`pixel bin ids out of range [0, ${r}) at row ${g}`),!i&&A>x&&o("triangle",`pixels are not upper-triangular (bin1_id <= bin2_id): row ${g} is (${A}, ${x})`),h>=0&&!(h<A||h===A&&f<=x)&&o("order",`pixels are not sorted by (bin1_id, bin2_id) at row ${g}`),d){for(;m<r&&a[m+1]<=g;)m++;m!==A&&o("index",`bin1_offset disagrees with pixels/bin1_id at row ${g}: the index places it in bin ${m}, the pixel says ${A}`)}h=A,f=x}return!0}}),w?.()===!0){const b=new Error("cancelled");throw b.name="AbortError",b}const p=this.info.sum;return u&&p!==null&&p!==l&&n.push(`attrs['sum'] (${p}) != the sum of pixels/count (${l})`),{ok:n.length===0,problems:n,note:`Scanned ${c} pixels for range, upper-triangle, sort order and bin1_offset agreement${u?", and reconciled attrs['sum']":" (float counts: sum not reconciled)"}. The /bins geometry checks of the Python validate() are not run — this reader never reads /bins.`}}validateLight(){const t=(s,o={})=>{throw new st(s,o)};this.nContigs===0&&t("/contigs table is empty");for(const s of of)this.contigs.columns.includes(s)||t(`Missing column in /contigs: ${s}`);if(this.chromOffset.length!==this.nContigs+1&&t(`chrom_offset length (${this.chromOffset.length}) != ${this.nContigs+1}`),this.chromOffset[0]!==0&&t(`chrom_offset endpoints (${this.chromOffset[0]}, ${this.nBins}) do not bracket the table`),this.genomes!==null){this.nGenomes===0&&t("/genomes table is empty");for(const s of sf)this.genomes.columns.includes(s)||t(`Missing column in /genomes: ${s}`);this.contigs.columns.includes("genome_id")||t("Missing column in /contigs: genome_id"),this.handle.isSoftLink("chroms")||t("/chroms must be a soft link to /contigs for cooler compatibility"),this.genomeOffset.length!==this.nGenomes+1&&t(`genome_offset length (${this.genomeOffset.length}) != ${this.nGenomes+1}`),(this.genomeOffset[0]!==0||this.genomeOffset[this.nGenomes]!==this.nContigs)&&t(`genome_offset endpoints (${this.genomeOffset[0]}, ${this.genomeOffset[this.nGenomes]}) do not bracket the table (0, ${this.nContigs})`)}const n=[["nchroms",this.info.ncontigs,this.nContigs,"len(/contigs)"],...this.genomes===null?[]:[["ngenomes",this.info.ngenomes,this.nGenomes,"len(/genomes)"]],["nbins",this.info.nbins,this.nBins,"len(/bins)"],["nnz",this.info.nnz,this.tables.datasetLength("pixels/bin1_id"),"len(/pixels)"]];for(const[s,o,r,i]of n)o!==null&&o!==r&&t(`attrs[${V(s)}] (${o}) != ${i} (${r})`)}async resample(t,n={}){if(t===null)return this.resampled=null,null;const s=this.resampleRefusal();this.censusWanted=!0,n.census!==void 0&&(this.census=Promise.resolve(n.census));let o;s!==null?o=Promise.reject(s):(this.census??=sr(this.pixelStore,this.chromOffset,{...n.onProgress===void 0?{}:{onProgress:n.onProgress},cancelled:()=>this.closed||n.cancelled?.()===!0}),o=this.census,o.catch(i=>{i instanceof DOMException&&i.name==="AbortError"&&this.census===o&&(this.census=null)}));const r=new oh(this.pixelStore,{starts:this.chromOffset,names:this.chromnames},t,o);return this.resampled=r,r.ready()}get declaredContacts(){const t=this.info.sum;return typeof t=="number"&&Number.isFinite(t)&&t>=0?t:null}async countContacts(t={}){const n=this.declaredContacts;if(n!==null)return n;if(this.resampleRefusal()!==null)return null;const s=t.pause;this.census??=sr(this.pixelStore,this.chromOffset,{...t.onProgress===void 0?{}:{onProgress:t.onProgress},...s===void 0?{}:{pause:()=>s(()=>this.censusWanted)},cancelled:()=>this.closed});try{return(await this.census).total}catch{return null}}async takenCensus(){if(this.census===null)return null;try{return await this.census}catch{return null}}resampleRefusal(){return this.layout.kind==="scool"?new C("unsupported","A single-cell container’s map is a sum of its cells rather than one library, so it is not resampled as one. Open one cell, or a pseudo-bulk written as a cooler, to resample it.",{resample:!0,layout:"scool"}):this.storageMode!=="symmetric-upper"?new C("unsupported","This map stores both triangles, so each contact would be drawn twice. Resampling reads upper-triangular files — cooler’s default.",{resample:!0,storageMode:this.storageMode}):null}close(){this.closed||(this.closed=!0,this.rawHandle.close())}}function cf(e,t){const n=`bins/${Ne}`;return new Proxy(e,{get(s,o){if(o==="readNumeric")return(i,a,c)=>{const l=s.readNumeric(i,a,c);if(i!==n)return l;const u=new Float64Array(l.length);for(let h=0;h<l.length;h++)u[h]=l[h]*t;return u};const r=Reflect.get(s,o,s);return typeof r=="function"?r.bind(s):r}})}function lf(e,t){const n=e.data[t];return n instanceof Float64Array?n:Float64Array.from(e.numbers(t))}function Er(e){try{return"SOU".includes(Oi(e))}catch{return null}}function uf(e,t){const n=e.data[t];if(ArrayBuffer.isView(n)&&!(n instanceof DataView)&&!(n instanceof BigInt64Array)){const s=new Int32Array(n.length);return s.set(n),s}return Int32Array.from(e.numbers(t))}function vr(e,t){return t===void 0?e:{...e,value:t}}function On(e,t){const n=Math.min(Math.max(Math.trunc(e[0]),0),t),s=Math.min(Math.max(Math.trunc(e[1]),n),t);return[n,s]}function kn(e,t,n,s){return s>=t[0]&&s<t[1]?e.rows[s-t[0]]:s>=n[0]&&s<n[1]?e.cols[s-n[0]]:1}function hf(e,t){if(!t.isRemote||!ul(e,e.attrs()))return;const{path:n}=Mt(e.uri);throw new C("scool-listing-cost",`${n} is a single-cell container, and listing its cells is not a bounded read: the names live in HDF5 link records spread across the whole object. Reading them over the network costs either one download of ${At.bytes(t.size)} or a few percent of that in about a thousand separate requests. Choose which to pay, or open a local copy, where neither cost applies.`,{path:n,size:t.size})}const ff=[137,72,68,70,13,10,26,10];function df(e){for(const t of[0,512,1024,2048,4096,8192]){if(t+8>e.size)return!1;const n=e.readBytes(t,8);if(n.length===8&&ff.every((s,o)=>n[o]===s))return!0}return!1}const Le=16,mf=4,gf=64,wf=2048,pf=160,bf={width:gf,coarseCells:wf,endDepth:pf},Cr=48,yf=8,Af=[0,1,2,4,8,16,32,64,128,256,512,1024,2048],Ma=.01,Mf=.1;function Cs(e){if(e.length===0)return Number.NaN;e.sort();const t=Math.max(1,Math.floor(e.length*(1-Ma)));let n=0;for(let s=0;s<t;s++)n+=e[s];return n/t}function $r(e){if(e.length===0)return Number.NaN;e.sort();const t=e.length>>1;return e.length%2===1?e[t]:(e[t-1]+e[t])/2}class nn{data=new Float64Array(64);length=0;push(t){if(this.length===this.data.length){const n=new Float64Array(this.data.length*2);n.set(this.data),this.data=n}this.data[this.length++]=t}view(){return this.data.subarray(0,this.length)}}function xf(e,t){const{n,width:s,band:o,coarse:r,marginal:i,kept:a,sequenceOf:c}=e,l=new Float64Array(n).fill(1);if(!t){const k=new nn;for(let H=0;H<n;H++)i[H]>0&&k.push(i[H]);const G=$r(k.view());for(let H=0;H<n;H++)l[H]=i[H]>=Mf*G&&G>0?i[H]/G:Number.NaN}for(let k=0;k<n;k++)a[k]===0&&(l[k]=Number.NaN);let u=1;for(let k=0;k<n;k++)a[k]>u&&(u=a[k]);const h=new Float64Array(n);for(let k=0;k<n;k++)h[k]=a[k]/u;const f=new Float64Array(s).fill(Number.NaN),d=new nn;for(let k=0;k<s;k++){if(!t){let lt=0,U=0,q=0;for(let K=0;K+k<n;K++){const bt=h[K]*h[K+k],wt=o[K*s+k]*bt,yt=l[K]*l[K+k]*bt;!(wt>=0)||!(yt>0)||(lt+=wt,U+=yt,q++)}if(q<8||!(U>0))continue;const tt=lt/U;if(f[k]=tt,k===0||!(tt>0))continue;let nt=0;for(let K=0;K+k<n;K++){const bt=h[K]*h[K+k],wt=o[K*s+k]*bt,yt=l[K]*l[K+k]*bt;!(wt>=0)||!(yt>0)||(nt+=(wt-yt*tt)**2/(yt*tt))}d.push(nt/Math.max(1,q-1));continue}const G=new nn;for(let lt=0;lt+k<n;lt++){const U=o[lt*s+k]/(l[lt]*l[lt+k]);U>=0&&G.push(U)}if(G.length<8)continue;const H=G.view();if(f[k]=Cs(H),k===0)continue;const mt=Math.max(1,Math.floor(H.length*(1-Ma)));let gt=0,ct=0;for(let lt=0;lt<mt;lt++)gt+=H[lt],ct+=H[lt]*H[lt];const _t=gt/mt,ge=Math.max(0,ct/mt-_t*_t);_t>0&&d.push(ge/_t)}const m=r.factor,g=r.n,w=new Int32Array(g).fill(-1),p=new Float64Array(g),b=new Float64Array(g);for(let k=0;k<n;k++){const G=r.of[k];w[G]=c[k],l[k]>0&&(p[G]+=l[k],b[G]++)}for(let k=0;k<g;k++)p[k]=b[k]>0?p[k]/b[k]:Number.NaN;const y=[],A=new nn,x=new Float64Array(g),E=new Float64Array(g),S=new Int32Array(g);let v=0,I=0;for(let k=0;k<g;k++){let G=vt(k,k,g);for(let H=k;H<g;H++,G++){const mt=p[k]*p[H],gt=r.values[G]/mt;if(gt>=0)if(w[k]===w[H]){const ct=H-k;if(ct===0)continue;(y[ct]??=new nn).push(gt),x[ct]+=r.values[G],E[ct]+=mt,S[ct]++}else A.push(gt),v+=r.values[G],I+=mt}}const N=new Float64Array(y.length).fill(Number.NaN);for(let k=1;k<y.length;k++){const G=y[k];G===void 0||G.length<4||(N[k]=t?Cs(G.view()):E[k]>0?x[k]/E[k]:Number.NaN)}const B=new Float64Array(n+1).fill(Number.NaN),z=k=>{const G=k/m,H=Math.floor(G),mt=H+1,gt=N[H],ct=N[mt];return H>=1&&gt>0&&ct>0?Math.exp(Math.log(gt)+(Math.log(ct)-Math.log(gt))*(G-H)):H>=1&&gt>0?gt:ct>0&&H<1?ct:Number.NaN};let R=0;for(let k=0;k<=n;k++){const G=k<s&&f[k]>0?f[k]:k>=1?z(k):Number.NaN;G>0&&(B[k]=G,R=k)}for(let k=1;k<=R;k++)B[k]>0||(B[k]=B[k-1]);for(let k=1;k<=R;k++)B[k]>B[k-1]&&(B[k]=B[k-1]);const P=Sf(B,R);for(let k=R+1;k<=n;k++)B[k]=B[R]*Math.pow(k/Math.max(1,R),P);B[0]>0||(B[0]=B[1]>0?B[1]:1);let L=t?Cs(A.view()):I>0?v/I:Number.NaN;L>0||(L=.5*B[Math.max(1,R)]),L=Math.max(L,B[1]*1e-9);const j=Math.max($r(d.view())||1,1e-12);let W=1;for(;W<2*Le&&W<n&&B[W]>=8*L;)W++;const J=Math.max(mf,Math.min(Le,Math.ceil(W/2)));let Z=0;for(let k=0;k<J;k++)for(let G=0;G<J;G++)Z+=B[Math.min(n,k+G+1)];Z/=J*J;const It=Math.max(L,Z);let pt=0;for(let k=0;k<J;k++)for(let G=0;G<J;G++){const H=B[Math.min(n,k+G+1)];pt+=H*Math.log(H/It)-(H-It)}pt=Math.max(pt/j,1e-9);let Ut=1;for(;Ut<3*Cr&&Ut<n&&B[Ut]>=8*L;)Ut++;const Qt=Math.max(yf,Math.min(Cr,Math.ceil(Ut/3)));let Et=0;for(let k=0;k<Qt;k++)for(let G=0;G<Qt;G++){const H=B[Math.min(n,k+G+1)];Et+=H*Math.log((H+L)/L)-H}return Et=Math.max(Et/j,1e-9),{law:B,trans:L,dispersion:j,bias:l,share:h,window:J,unit:pt,reach:Qt,meetUnit:Et}}function Sf(e,t){const n=Math.max(1,Math.floor(t/10));let s=0,o=0,r=0,i=0,a=0;for(let u=n;u<=t;u++){if(!(e[u]>0))continue;const h=Math.log(u),f=Math.log(e[u]);s++,o+=h,r+=f,i+=h*h,a+=h*f}const c=s*i-o*o,l=s>=2&&c!==0?(s*a-o*r)/c:-1;return Math.max(-3,Math.min(-.3,l))}class xa{constructor(t,n,s){this.cellMap=s,this.law=n.law,this.trans=n.trans,this.dispersion=n.dispersion,this.window=n.window,this.unit=n.unit,this.reach=n.reach,this.meetUnit=n.meetUnit,this.band=t.band,this.width=t.width,this.sequenceOf=t.sequenceOf,this.coarseOf=t.coarse.of,this.coarseValues=t.coarse.values,this.coarseN=t.coarse.n,this.bias=n.bias,this.share=n.share,this.ends=t.ends??null,this.near=new Float64Array(2*this.window+2),this.logNear=new Float64Array(this.near.length);for(let o=0;o<this.near.length;o++)this.near[o]=this.law[Math.min(this.law.length-1,o)],this.logNear[o]=Math.log(this.near[o])}law;trans;dispersion;window;unit;reach;meetUnit;near;logNear;band;width;sequenceOf;coarseOf;coarseValues;coarseN;bias;share;ends;get n(){return this.cellMap.length}value(t,n){const s=this.cellMap[t],o=this.cellMap[n];return s<0||o<0?Number.NaN:this.original(s,o)}original(t,n){const s=t<n?t:n,o=t<n?n:t,r=o-s;let i;if(r<this.width&&this.sequenceOf[s]===this.sequenceOf[o])i=this.band[s*this.width+r];else{const a=this.ends,c=a!==null&&a.zone[s]>=0&&a.zone[o]>=0,l=c?Wl(a,s,o):void 0;l!==void 0?i=l:c&&a.complete?i=0:i=this.coarseValues[vt(this.coarseOf[s],this.coarseOf[o],this.coarseN)]}return i/(this.bias[t]*this.bias[n])}weight(t,n){const s=this.cellMap[t],o=this.cellMap[n];if(s<0||o<0)return 0;const r=this.bias[s]*this.bias[o]*this.share[s]*this.share[o];return r>0?r:0}coarseCell(t){const n=this.cellMap[t];return n<0?-1:this.coarseOf[n]}coarseValue(t,n){return this.coarseValues[t<=n?vt(t,n,this.coarseN):vt(n,t,this.coarseN)]}holds(t){const n=this.cellMap[t];return n>=0&&this.bias[n]>0}expectedAt(t){return this.law[Math.min(this.law.length-1,Math.max(0,t))]}}const Nr=new Float64Array(Le*Le),$s=new Float64Array(Le*Le);function Sa(e,t,n,s="trans"){const o=e.near,r=e.logNear,i=e.trans,a=e.window;let c=0,l=0,u=0,h=0;for(let p=0;p<a;p++){const b=t.cell+t.dir*p,y=b>=t.lo&&b<t.hi;for(let A=0;A<a;A++){const x=n.cell+n.dir*A;let E=Number.NaN,S=0;y&&x>=n.lo&&x<n.hi&&(l++,E=e.value(b,x),S=e.weight(b,x),E>=0&&S>0?(c++,u+=S*E,h+=S):E=Number.NaN),Nr[p*a+A]=E,$s[p*a+A]=S}}const f=s==="local"&&h>0?Math.max(i,u/h):i;let d=0,m=0;const g=Math.log(f);for(let p=0;p<a;p++)for(let b=0;b<a;b++){const y=Nr[p*a+b];if(Number.isNaN(y))continue;const A=p+b+1;d+=$s[p*a+b]*(y*(r[A]-g)-(o[A]-f)),m+=$s[p*a+b]*o[A]}const w=e.dispersion;return{score:d/w,seen:c,reached:l,contacts:Math.max(0,u-h*i)/w,expected:m/w}}function Br(e,t,n){const s=t.hi-t.lo,o=Math.max(1,Math.min(n,Math.floor(s/2))),r=new Int32Array(o),i=new Int32Array(o);let a=0;for(let c=0;c<3*o&&a<o;c++){const l=t.cell+t.dir*c;if(l<t.lo||l>=t.hi)break;e.holds(l)&&(r[a]=l,i[a]=c,a++)}return{cells:r,distance:i,length:a}}function If(e,t,n){const s=new Set,o=new Set;for(let a=0;a<t.length;a++)s.add(e.coarseCell(t.cells[a]));for(let a=0;a<n.length;a++)o.add(e.coarseCell(n.cells[a]));let r=0,i=0;for(const a of s)if(!(a<0))for(const c of o){if(c<0)continue;const l=e.coarseValue(a,c);l>=0&&(r+=l,i++)}return i===0||r>2*i*e.trans}function Ef(e,t,n){const s=e.reach,o=Br(e,t,s),r=Br(e,n,s),i=o.length*r.length,a={score:0,gap:0,amplitude:0,brightness:0,level:0,ideal:0,seen:0,reached:i,contacts:0};if(i===0||!If(e,o,r))return a;const c=new Float64Array(i),l=new Float64Array(i),u=new Int32Array(i);let h=0,f=0,d=0;for(let b=0;b<o.length;b++)for(let y=0;y<r.length;y++){const A=e.value(o.cells[b],r.cells[y]),x=e.weight(o.cells[b],r.cells[y]);!(A>=0)||!(x>0)||(c[h]=A,l[h]=x,u[h]=o.distance[b]+r.distance[y]+1,f+=x*A,d+=x,h++)}if(h===0)return a;const m=e.trans;if(f<1.5*d*m)return{...a,level:f/d/m,seen:h};let g=0,w=0;for(let b=0;b<h;b++){const y=e.expectedAt(u[b]);g+=l[b]*(y*Math.log((y+m)/m)-y),w+=l[b]*y}let p={score:Number.NEGATIVE_INFINITY,gap:0,amplitude:0};for(const b of Af){let y=0;for(let E=0;E<h;E++)y+=l[E]*e.expectedAt(u[E]+b);if(!(y>0))continue;const A=Math.min(1,Math.max(1e-6,(f-d*m)/y));let x=0;for(let E=0;E<h;E++){const S=A*e.expectedAt(u[E]+b)+m;x+=l[E]*(c[E]*Math.log(S/m)-(S-m))}if(x>p.score&&(p={score:x,gap:b,amplitude:A}),e.expectedAt(b)<m)break}return{score:p.score/e.dispersion,gap:p.gap,amplitude:p.amplitude,brightness:w>0?Math.max(0,f-d*m)/w:0,level:f/d/m,ideal:g/e.dispersion,seen:h,reached:i,contacts:Math.max(0,f-d*m)/e.dispersion}}function Ia(e,t){const n=new Float64Array(e.n+1).fill(Number.NaN),s=new Float64Array(e.n+1);for(const o of t)for(let r=o.from+1;r<o.to;r++){const i=Sa(e,{cell:r-1,dir:-1,lo:o.from,hi:r},{cell:r,dir:1,lo:r,hi:o.to});s[r]=i.reached===0?0:i.seen/i.reached,i.seen>=Math.max(4,i.reached/4)&&(n[r]=i.score)}return{score:n,seen:s}}const Ea=3;function vf(e,t,n,s,o=.2){const r=[],i=Math.max(1,s>>1),a=Math.max(o*n,Ea);for(const c of t)for(let l=c.from+1;l<c.to;l++){const u=e[l];if(!(u<-a))continue;let h=!0;for(let f=Math.max(c.from+1,l-i);f<=Math.min(c.to-1,l+i);f++){const d=e[f];if(f!==l&&d<u){h=!1;break}if(f<l&&d===u){h=!1;break}}h&&r.push(l)}return r}const Cf=4,Ns=1,$f=.45;function Nf(e,t){const{coarse:n,sequenceOf:s,n:o}=e,r=n.n,i=new Int32Array(r).fill(-1),a=new Int32Array(r+1).fill(o),c=new Float64Array(r),l=new Float64Array(r),u=new Float64Array(r);for(let y=o-1;y>=0;y--){const A=n.of[y];i[A]=s[y],a[A]=y,u[A]++,t.bias[y]>0&&(c[A]+=t.bias[y],l[A]++)}for(let y=0;y<r;y++)c[y]=l[y]>=.6*u[y]?c[y]/l[y]:Number.NaN;const h=[];for(let y=0;y<r;y++){const A=i[y];if(A<0)continue;const x=h[A];x===void 0?h[A]=[y,y+1]:x[1]=y+1}const f=[];if(h.forEach((y,A)=>{y!==void 0&&y[1]-y[0]>=Cf&&f.push(A)}),f.length<3)return[];const d=(y,A)=>{const x=n.values[y<=A?vt(y,A,r):vt(A,y,r)]/(c[y]*c[A]);return x>=0?x:Number.NaN},m=f.map(()=>new Int32Array(f.length).fill(-1));for(let y=0;y<f.length;y++){const[A,x]=h[f[y]];for(let E=y+1;E<f.length;E++){const[S,v]=h[f[E]];let I=0,N=-1,B=-1;for(let z=A;z<x;z++)for(let R=S;R<v;R++){let P=0,L=0;for(let W=-1;W<=1;W++)for(let J=-1;J<=1;J++){const Z=z+W,It=R+J;if(Z<A||Z>=x||It<S||It>=v)continue;const pt=d(Z,It);Number.isNaN(pt)||(P+=pt,L++)}const j=L>0?P/L:0;j>I&&(I=j,N=z,B=R)}N<0||I<4*t.trans||(m[y][E]=N,m[E][y]=B)}}const g=(y,A)=>{const x=[];for(const I of A)I!==y&&m[y][I]>=0&&x.push(m[y][I]);const E=A.filter(I=>I!==y).length;if(x.length<3||E===0)return{mode:-1,agreement:0};let S=-1,v=0;for(const I of x){let N=0;for(const B of x)Math.abs(B-I)<=Ns&&N++;N>v&&(v=N,S=I)}return{mode:S,agreement:v/E}},w=f.map((y,A)=>A),p=w.filter(y=>g(y,w).agreement>=1/3);if(p.length<3)return[];const b=[];return f.forEach((y,A)=>{const{mode:x,agreement:E}=g(A,p);if(x<0||E<$f)return;const S=Math.max(h[y][0],x-Ns),v=Math.min(h[y][1],x+Ns+1);b.push({sequence:y,from:a[S],to:a[v],agreement:E})}),b}const Or=4,kr=Math.log(3),Bf=240;function Of(e,t){const{coarse:n,n:s,sequenceOf:o}=e,r=n.n,i=n.factor;if(r<2*Or+1)return[];const a=new Int32Array(r+1).fill(s),c=new Int32Array(r),l=new Float64Array(r),u=new Float64Array(r);for(let I=s-1;I>=0;I--){const N=n.of[I];a[N]=I,c[N]=o[I];const B=t.bias[I];B>0&&(l[N]+=B,u[N]++)}a[r]=s;for(let I=0;I<r;I++)l[I]=u[I]>0?l[I]/u[I]:Number.NaN;const h=r+1,f=new Float64Array(h*h),d=new Int32Array(h*h);for(let I=0;I<r;I++){let N=0,B=0;for(let z=0;z<r;z++){const R=I<z?I:z,P=I<z?z:I,L=n.values[vt(R,P,r)]/(l[R]*l[P]);if(L>=0&&R!==P){const W=c[R]===c[P]?t.law[Math.min(s,(P-R)*i)]:t.trans;N+=Math.log((L+.5*W)/(1.5*W)),B++}const j=(I+1)*h+(z+1);f[j]=f[j-h]+N,d[j]=d[j-h]+B}}const m=(I,N,B,z)=>{if(I<0||B<0||N>r||z>r||N<=I||z<=B)return Number.NaN;const R=d[N*h+z]-d[I*h+z]-d[N*h+B]+d[I*h+B];return R<4?Number.NaN:(f[N*h+z]-f[I*h+z]-f[N*h+B]+f[I*h+B])/R},g=Or,w=[],p=I=>Number.isNaN(I)?0:I;for(let I=1;I<r;I++)for(let N=I+1;N<r;N++){if(c[I]===c[N-1]&&N-I<2*g)continue;const B=m(I-g,I,N-g,N),z=m(I,I+g,N,N+g),R=m(I-g,I,N,N+g),P=m(I,I+g,N-g,N),L=[[B,R,P,-1,-1],[z,R,P,1,1],[R,B,z,-1,1],[P,B,z,1,-1]];for(const[j,W,J,Z,It]of L){if(!(j>kr))continue;const pt=j-Math.max(p(W),p(J));pt>kr&&w.push({p:I,q:N,rowSide:Z,colSide:It,strength:pt})}}w.sort((I,N)=>N.strength-I.strength);const b=[];for(const I of w)if(b.some(B=>B.rowSide===I.rowSide&&B.colSide===I.colSide&&Math.abs(B.p-I.p)<=g&&Math.abs(B.q-I.q)<=g)||b.push(I),b.length>=Bf)break;const y=[];for(let I=0;I<s;I++)(I===0||o[I]!==o[I-1])&&y.push(I);y.push(s);const A=y.slice(0,-1).map((I,N)=>({from:I,to:y[N+1]})),x=new Int32Array(s);for(let I=0;I<s;I++)x[I]=I;const E=Ia(new xa(e,t,x),A),S=new Set(y),v=I=>{const N=a[I];let B=N,z=-.2*t.unit;for(let R=Math.max(1,N-i);R<=Math.min(s-1,N+i);R++){const P=E.score[R];P<z&&(B=R,z=P)}if(B!==N)return B;for(let R=Math.max(0,N-i);R<=Math.min(s,N+i);R++)if(S.has(R))return R;return N};return b.map(I=>{const N=v(I.p),B=v(I.q);return N<=B?{row:N,col:B,rowSide:I.rowSide,colSide:I.colSide,strength:I.strength}:{row:B,col:N,rowSide:I.colSide,colSide:I.rowSide,strength:I.strength}})}class Bo{binsize;n;parts;sequences;cellMap;pictureCells;axisHeld;constructor(t){this.binsize=t.binsize,this.n=t.n,this.parts=t.parts,this.sequences=t.sequences,this.cellMap=t.cellMap,this.pictureCells=t.pictureCells}static of(t,n){const s=n.binsize,o=new Map(n.sequences.map((u,h)=>[u.name,{...u,index:h}])),r=n.sequences.reduce((u,h)=>Math.max(u,h.firstCell+h.cells),0),i=(u,h,f)=>f>=h?u:Math.max(0,Math.min(u,Math.round(f/s))),a=[],c=[],l=[];for(const u of t.sequences){const h=l.length,f=a.length;let d=0;u.parts.forEach((m,g)=>{const w=l.length;if(at(m)){const v=Math.round(m.gap/s);for(let I=0;I<v;I++)l.push(-1);a.push({sequence:u.name,index:g,offset:d,length:m.gap,from:w,to:l.length,piece:null,original:-1,segment:null}),d+=m.gap;return}const p=o.get(m.sequence),b=m.end-m.start;if(p===void 0){a.push({sequence:u.name,index:g,offset:d,length:b,from:w,to:w,piece:m,original:-1,segment:null}),d+=b;return}const y=i(p.cells,p.length,m.start),A=i(p.cells,p.length,m.end),x=Math.max(0,A-y);for(let v=0;v<x;v++)l.push(m.strand===1?p.firstCell+y+v:p.firstCell+A-1-v);const E=l.length,S=x===0?null:{contig:m.sequence,unitStart:w,unitEnd:E,bpStart:(m.strand===1?y:A)*s,bpPerUnit:s,contigLength:p.length,strand:m.strand,bpFrom:m.start,bpTo:m.end};a.push({sequence:u.name,index:g,offset:d,length:b,from:w,to:E,piece:m,original:p.index,segment:S}),d+=b}),c.push({name:u.name,length:d,from:h,to:l.length,partFrom:f,partTo:a.length})}return new Bo({binsize:s,n:l.length,parts:a,sequences:c,cellMap:Int32Array.from(l),pictureCells:r})}get axis(){if(this.axisHeld===void 0){const t=this.parts.flatMap(n=>n.segment===null?[]:[n.segment]);this.axisHeld=t.length===0?null:new Tc(t)}return this.axisHeld}partAt(t){if(!(t>=0&&t<this.n))return null;let n=0,s=this.parts.length-1;for(;n<=s;){const o=n+s>>1,r=this.parts[o];if(t<r.from)s=o-1;else if(t>=r.to)n=o+1;else return r}return null}sequenceAt(t){if(!(t>=0&&t<this.n))return null;let n=0,s=this.sequences.length-1;for(;n<=s;){const o=n+s>>1,r=this.sequences[o];if(t<r.from)s=o-1;else if(t>=r.to)n=o+1;else return r}return null}sequence(t){return this.sequences.find(n=>n.name===t)??null}place(t){const n=this.partAt(t);if(n===null)return null;const s=n.piece;if(s===null||n.segment===null){const i=n.to>n.from?(t-n.from)/(n.to-n.from):0;return{sequence:n.sequence,bp:n.offset+i*n.length,part:n}}const o=Math.max(s.start,Math.min(s.end,Hn(n.segment,t))),r=s.strand===1?o-s.start:s.end-o;return{sequence:n.sequence,bp:n.offset+r,part:n}}unitOf(t,n){const s=this.sequence(t);if(s===null)return null;if(n<=0)return s.from;if(n>=s.length)return s.to;for(let o=s.partFrom;o<s.partTo;o++){const r=this.parts[o];if(n<r.offset||n>=r.offset+r.length)continue;if(n===r.offset)return r.from;const i=r.piece;if(i===null||r.segment===null){const l=(n-r.offset)/r.length;return r.from+l*(r.to-r.from)}const a=n-r.offset,c=i.strand===1?i.start+a:i.end-a;return Math.max(r.from,Math.min(r.to,qs(r.segment,c)))}return s.to}junctions(){const t=[];for(const n of this.sequences)for(let s=n.partFrom+1;s<n.partTo;s++){const o=this.parts[s].from;o>n.from&&o<n.to&&t[t.length-1]!==o&&t.push(o)}return t}boundaries(){const t=[0];for(const n of this.sequences)t[t.length-1]!==n.to&&t.push(n.to);return t}}function kf(e){return`${e.contig}:${(e.start+1).toLocaleString("en-US")}-${e.end.toLocaleString("en-US")}`}function _r(e,t){return`${e}:${_f(t)}`}function _f(e){return(e+1).toLocaleString("en-US")}function Ie(e,t,n){return kf({contig:e,start:t,end:n})}const Tf={debris:"debris",contaminant:"a contaminant",haplotig:"a haplotig",unplaced:"unplaced"};function Ff(e){switch(e.op){case"cut":return`cut ${e.sequence} before ${(e.at+1).toLocaleString("en-US")}`;case"invert":return`turn ${Ie(e.sequence,e.from,e.to)}`;case"move":case"duplicate":{const t=e.op==="move"?"move":"copy",n=e.at===0?`before ${_r(e.into,0)}`:`after ${_r(e.into,e.at-1)}`;return`${t} ${Ie(e.sequence,e.from,e.to)} ${n}${e.strand===-1?", turned":""}`}case"join":return`join ${e.a}’s ${e.aEnd} to ${e.b}’s ${e.bEnd}${e.gap>0?`, ${e.gap.toLocaleString("en-US")} N between`:""}`;case"split":return`split ${e.sequence} before ${(e.at+1).toLocaleString("en-US")}`;case"aside":return e.genome!==void 0&&e.genome!==""?`send ${Ie(e.sequence,e.from,e.to)} to ${e.genome}`:`set aside ${Ie(e.sequence,e.from,e.to)} as ${Tf[e.why]}`;case"bring":return`bring in ${e.sequence}`;case"rotate":return`start ${e.sequence} at ${(e.at+1).toLocaleString("en-US")}`;case"rename":return`rename ${e.sequence} to ${e.name}`;case"reorder":return"reorder the sequences";case"restore":return`put back ${Ie(e.sequence,e.start,e.end)}`;case"place":{const t=e.before===null?"last":`before ${e.before}`,n=e.strand===-1?", turned":"";return e.whole===!0?`put ${e.sequence} ${t}${n}`:`make ${Ie(e.sequence,e.from,e.to)} a sequence of its own, ${t}${n}`}case"layout":{const t=e.sequences.length;return`lay out as in ${e.from} · ${t.toLocaleString("en-US")} sequence${t===1?"":"s"}`}}}const Oo=16,va=1.5,zf=16,Rf=.5,Pf=.25,Lf=4;function Df(e,t,n){const s=[...new Set(e)].filter(i=>i>0&&i>=n).sort((i,a)=>i-a),o=[];let r=t;for(;;){const i=s.filter(c=>c*2<=r);if(i.length===0)break;const a=i.find(c=>r/c<=zf)??i[i.length-1];o.push(a),r=a}return o}function Uf(e){if(e.length<Lf)return Number.NaN;e.sort((o,r)=>o-r);const t=e.length>>1,n=e.length%2===1?e[t]:(e[t-1]+e[t])/2;if(n>0)return n;const s=e.reduce((o,r)=>o+r,0)/e.length;return s>0?s:Number.NaN}function Gf(e,t,n,s=Oo){const o=e.n,r=e.values,i=2*s-1,a=new Float64Array(i+1).fill(Number.NaN);for(let u=1;u<=i;u++){const h=[];for(let f=0;f+u<o;f++){const d=f+u;if(!(d<t||f>=n))continue;const m=r[f*o+d];Number.isNaN(m)||h.push(m)}a[u]=Uf(h)}const c=(t+n)/2;let l=null;for(let u=Math.max(1,t);u<=Math.min(o-1,n);u++){let h=0,f=0,d=0;for(let w=Math.max(0,u-s);w<u;w++)for(let p=u;p<Math.min(o,u+s);p++){const b=a[p-w],y=r[w*o+p];Number.isNaN(y)||!(b>0)||(h+=y,f+=b,d++)}if(d<Pf*s*s||!(f>0))continue;const m=h/f;(l===null||m<l.support-1e-9||m<=l.support+1e-9&&Math.abs(u-c)<Math.abs(l.cut-c))&&(l={cut:u,support:m})}return l}async function Hf(e,t,n,s,o){let r=e.bp,i=n,a=null;const c=Oo;for(const l of s){const u=Math.ceil(t/l),h=Math.round(r/l),f=Math.ceil(va*i/l),d=Math.max(1,h-f),m=Math.min(u-1,h+f);if(m<d)break;const g=Math.max(0,d-3*c),w=Math.min(u,m+3*c),p=await o(e.sequence,g,w,l);if(p===null||p.n!==w-g)break;const b=Gf(p,d-g,m-g);if(b===null||!(b.support<Rf))break;const y=(g+b.cut)*l;if(!(y>0&&y<t))break;r=y,i=l,a={bp:y,binsize:l,support:b.support}}return a}const _n=100,no=[-1.5,2,1.5,2,2.5,1.5,5,4,1,2],Tr=16,Fr=Math.log2(2.5),qf=Math.log2(1.6),Wf=1.2,zr=.1,jf=64;function Qf(e){return 1/(1+Math.exp(-e))}function Yf(e,t=no){let n=t[0]??0;for(let s=0;s<e.length;s++)n+=(t[s+1]??0)*e[s];return Qf(n)}const Rr=new WeakMap;function Vf(e){const{grid:t,expected:n}=e,s=new xa(e.contacts,n,t.cellMap),o=s.unit,r=t.sequences,i=r.map(M=>({from:M.from,to:M.to})),a=Ia(s,i),c=vf(a.score,i,o,s.window),l=t.n,u=new Int8Array(l);for(const M of t.parts)M.piece!==null&&u.fill(M.piece.strand,M.from,M.to);const h=e.contacts.n,f=new Int32Array(h+1);for(let M=0;M<l;M++){const $=t.cellMap[M];$>=0&&f[$+1]++}for(let M=0;M<h;M++)f[M+1]+=f[M];const d=new Int32Array(f[h]),m=f.slice(0,h);for(let M=0;M<l;M++){const $=t.cellMap[M];$>=0&&(d[m[$]++]=M)}const g=M=>{let $=0,O=r.length-1;for(;$<=O;){const _=$+O>>1;if(M<r[_].from)O=_-1;else if(M>=r[_].to)$=_+1;else return _}return-1},w=Math.max(2,Math.round(s.window/4)),p=r.map(M=>new Set([M.from,M.to])),b=r.map(()=>new Set),y=(M,$)=>{let O=-1,_=w+1;for(const T of p[M]){const F=Math.abs(T-$);F<_&&(O=T,_=F)}return O>=0?O:(p[M].add($),$)};for(const M of[...t.junctions(),...c]){const $=g(M);$>=0&&M>r[$].from&&y($,M)}const A=(M,$)=>{if(M<0||M>=h)return[];const O=[];for(let _=f[M];_<f[M+1];_++){const T=d[_],F=$*u[T],D=g(T);if(D<0)continue;const Y=y(D,F<0?T+1:T);b[D].add(Y),O.push(`${D}:${Y}`)}return O},x=new Map,E=(M,$)=>{let O=x.get(M);O===void 0&&(O=new Set,x.set(M,O)),O.add($)};for(const M of e.corners){const $=A(M.rowSide<0?M.row-1:M.row,M.rowSide),O=A(M.colSide<0?M.col-1:M.col,M.colSide);for(const _ of $)for(const T of O)E(_,T),E(T,_)}const S=(M,$)=>x.get(`${M.sequence}:${M.x}`)?.has(`${$.sequence}:${$.x}`)===!0,v=new Set(t.junctions()),I=r.map((M,$)=>[...p[$]].filter(O=>O>=M.from&&O<=M.to).sort((O,_)=>O-_).map(O=>{const _=O>M.from&&O<M.to,T=_&&a.score[O]<-Ea,F=T||_&&v.has(O)&&!(a.score[O]>=0);return{sequence:$,x:O,inside:_,refused:T,open:F,cornered:b[$].has(O)}})),N=(M,$,O)=>{const _=r[M.sequence];if($<0?M.x<=_.from:M.x>=_.to)return null;let T=_.from,F=_.to;for(const D of O)D.sequence===M.sequence&&(D.x<M.x&&D.x>T&&(T=D.x),D.x>M.x&&D.x<F&&(F=D.x));return $<0?{cell:M.x-1,dir:-1,lo:T,hi:M.x}:{cell:M.x,dir:1,lo:M.x,hi:F}},B=new Map,z=M=>`${M.cell}:${M.dir}:${M.lo}:${M.hi}`,R=(M,$,O)=>{const _=z(M),T=z($),F=_<T?`${_}|${T}|${O}`:`${T}|${_}|${O}`;let D=B.get(F);return D===void 0&&(D=Sa(s,M,$,O),B.set(F,D)),D},P=(M,$)=>M===null||$===null?0:R(M,$,"local").score/o,L=P,j=new Map,W=(M,$)=>{const O=z(M),_=z($),T=O<_?`${O}|${_}`:`${_}|${O}`;let F=j.get(T);return F===void 0&&(F=Ef(s,M,$),j.set(T,F)),F};let J=Rr.get(e.contacts);J===void 0&&(J=Nf(e.contacts,n),Rr.set(e.contacts,J));const Z=r.map(()=>[]);for(const M of J){const $=new Map;for(let O=M.from;O<M.to;O++)for(let _=f[O];_<f[O+1];_++){const T=d[_],F=g(T);if(F<0)continue;const D=$.get(F)??[];D.push(T),$.set(F,D)}for(const[O,_]of $)Z[O].push([Math.min(..._),Math.max(..._)+1])}const It=4*e.contacts.coarse.factor,pt=(M,$,O,_,T)=>{if($===_)return!1;for(const[F,D]of Z[$]){const Y=M.dir<0?M.cell+1-D:F-M.cell;for(const[Q,it]of Z[_]){const ot=O.dir<0?O.cell+1-it:Q-O.cell;if(Math.max(0,Y)+Math.max(0,ot)+T>It)return!0}}return!1},Ut=(M,$)=>{let O=0;for(let _=0;_<2;_++)for(let T=0;T<2;T++){const F=M.cell+M.dir*_,D=$.cell+$.dir*T;if(F<M.lo||F>=M.hi||D<$.lo||D>=$.hi)continue;const Y=s.value(F,D);Y>0&&(O=Math.max(O,Y/s.expectedAt(_+T+1)))}return O>0?Math.log2(O):0},Qt=[],Et=e.evidence?.facts,k=M=>{if(Et===void 0)return null;const $=t.partAt(M.cell),O=$?.piece;if($==null||O==null)return null;const _=M.dir===1;if(_?M.cell!==$.from:M.cell!==$.to-1)return null;const T=Et.get(O.sequence);return T===void 0?null:_===(O.strand===1)?O.start===0?T.start:null:O.end===T.length?T.end:null},G=M=>M.some(([$,O])=>k($)!==null||k(O)!==null),H=(M,$)=>{if(Et===void 0||$<=M.from||$>=M.to)return null;const O=t.place($),_=O?.part.piece;if(O==null||_==null||O.sequence!==M.name)return null;const T=Et.get(_.sequence);if(T===void 0||T.gaps.length===0)return null;const F=O.bp-O.part.offset,D=_.strand===1?_.start+F:_.end-F,Y=t.binsize;for(const[Q,it]of T.gaps){if(it+Y<D||Q-Y>D)continue;const ot=Math.max(_.start,Math.min(_.end,Math.round((Q+it)/2)));return O.part.offset+(_.strand===1?ot-_.start:_.end-ot)}return null},mt=(M,$)=>H(M,$)??Zf(t,M,$),gt=M=>M.some($=>$.inside&&H(r[$.sequence],$.x)!==null),ct=M=>{if(!(M.kind==="join"&&(M.exclusivity??0)>=1||M.gain>zr)||!(M.gain>0))return;let O=0,_=0,T=0;for(const[Q,it]of M.made){const ot=M.kind==="join"?W(Q,it):R(Q,it,"local");O+=ot.seen,_+=ot.reached,T+=ot.contacts}let F=0;for(const[Q,it]of M.taken){const ot=R(Q,it,"local");O+=ot.seen,_+=ot.reached,F+=R(Q,it,"trans").expected}M.made.length===0&&(T=F);const D=M.made.reduce((Q,[it,ot])=>Math.max(Q,M.kind==="join"?Math.log2(Math.max(1e-9,W(it,ot).brightness))-qf+Fr:Ut(it,ot)),0),Y=M.kind==="move"?M.points.slice(0,2):M.kind==="join"?[]:M.points;Qt.push({...M,seen:_===0?0:O/_,excess:D,atGap:gt(Y),buried:G(M.made),contacts:T})},_t=(M,$)=>{if(!M.inside)return null;const O=N(M,-1,$),_=N(M,1,$);return O===null||_===null?null:[O,_]};for(const M of I)for(const $ of M){if(!$.refused)continue;const O=r[$.sequence],_=_t($,[]);_!==null&&ct({kind:"split",gain:-L(..._),points:[$],made:[],taken:[_],step:{op:"split",sequence:O.name,at:mt(O,$.x)},stretch:null,target:null,cells:Number.POSITIVE_INFINITY})}const ge=I.flat(),lt=r.length<=jf;for(const M of I){if(M.length===0)continue;const $=r[M[0].sequence];for(let O=0;O<M.length;O++)for(let _=O+1;_<M.length;_++){const T=M[O],F=M[_],D=F.x-T.x,Y=!T.inside&&!F.inside,Q=[T,F],it=_t(T,Q),ot=_t(F,Q),ft=[it,ot].filter(X=>X!==null),Ft=ft.reduce((X,[zt,Bt])=>X+L(zt,Bt),0);if(!Y&&(T.open||F.open||T.cornered&&F.cornered)){const X=[],zt=N(T,-1,Q),Bt=N(F,-1,Q),se=N(T,1,Q),Qe=N(F,1,Q);zt!==null&&Bt!==null&&X.push([zt,Bt]),se!==null&&Qe!==null&&X.push([se,Qe]),ct({kind:"turn",gain:X.reduce((Ae,[Me,xe])=>Ae+P(Me,xe),0)-Ft,points:[T,F],made:X,taken:ft,step:{op:"invert",sequence:$.name,from:mt($,T.x),to:mt($,F.x)},stretch:[T.x,F.x],target:null,cells:D})}if(!((T.open||F.open)&&(T.open||!T.inside)&&(F.open||!F.inside)||Y&&(T.cornered||F.cornered)))continue;let ut=null;for(const X of ge){if(X.sequence===T.sequence&&X.x>=T.x&&X.x<=F.x||Y&&(!X.inside||!(S(T,X)||S(F,X))))continue;const zt=X.sequence===T.sequence?[T,F,X]:[X],Bt=X.sequence===T.sequence?[T,F,X]:Q,se=N(T,-1,Bt),Qe=N(F,1,Bt),Ae=N(T,1,Bt),Me=N(F,-1,Bt),xe=N(X,-1,zt),yn=N(X,1,zt),An=_t(X,zt),nc=An===null?0:L(...An),Mn=se!==null&&Qe!==null&&T.inside&&F.inside?[[se,Qe]]:[],sc=Mn.reduce((xn,[Kt,Ye])=>xn+P(Kt,Ye),0);for(const xn of[1,-1]){const Kt=[...Mn];if(xn===1?(xe!==null&&Ae!==null&&Kt.push([xe,Ae]),Me!==null&&yn!==null&&Kt.push([Me,yn])):(xe!==null&&Me!==null&&Kt.push([xe,Me]),Ae!==null&&yn!==null&&Kt.push([Ae,yn])),Kt.length===Mn.length)continue;let Ye=sc-Ft-nc;for(const[oc,rc]of Kt.slice(Mn.length))Ye+=P(oc,rc);(ut===null||Ye>ut.gain)&&(ut={gain:Ye,z:X,strand:xn,made:Kt,taken:An===null?ft:[...ft,An]})}}if(ut!==null){const X=r[ut.z.sequence],zt=mt($,T.x),Bt=mt($,F.x),se=mt(X,ut.z.x);ct({kind:"move",gain:ut.gain,points:[T,F,ut.z],made:ut.made,taken:ut.taken,step:{op:"move",sequence:$.name,from:zt,to:Bt,into:X.name,at:ut.z.sequence===T.sequence&&ut.z.x>F.x?se-(Bt-zt):se,strand:ut.strand},stretch:[T.x,F.x],target:ut.z.x,cells:D})}}}const U=new Map,q=[],tt=new Set,nt=(M,$)=>`${M.sequence}:${M.x}:${$}`;if(!lt){const M=[],$=new Map;for(const F of I){const D=F[0],Y=F[F.length-1];if(!(D===void 0||Y===void 0))for(const[Q,it]of[[D,1],[Y,-1]]){const ot=N(Q,it,[]);if(ot===null)continue;const ft=new Set;for(let Vt=0;Vt<s.reach;Vt++){const ut=ot.cell+ot.dir*Vt;if(ut<ot.lo||ut>=ot.hi)break;const X=s.coarseCell(ut);X>=0&&ft.add(X)}const Ft=q.length;U.set(nt(Q,it),Ft),q.push(Q.sequence),M.push([...ft]);for(const Vt of ft){const ut=$.get(Vt);ut===void 0?$.set(Vt,[Ft]):ut.push(Ft)}}}const O=q.length,_=2*s.trans,T=[...$.keys()];for(let F=0;F<O;F++)for(const D of M[F])for(const Y of T)if(s.coarseValue(D,Y)>_)for(const Q of $.get(Y)??[])q[Q]!==q[F]&&tt.add(F*O+Q)}const K=(M,$,O,_)=>{if(S(M,O))return!0;const T=U.get(nt(M,$.dir)),F=U.get(nt(O,_.dir));return T!==void 0&&F!==void 0&&tt.has(T*q.length+F)},bt=[];if(lt)for(let M=0;M<r.length;M++)for(let $=M+1;$<r.length;$++)bt.push([M,$]);else{const M=new Set,$=(_,T)=>{if(_===T||_<0||T<0)return;const F=Math.min(_,T),D=Math.max(_,T),Y=F*r.length+D;M.has(Y)||(M.add(Y),bt.push([F,D]))},O=q.length;for(const _ of tt)$(q[Math.floor(_/O)],q[_%O]);for(const[_,T]of x){const F=Number(_.slice(0,_.indexOf(":")));for(const D of T)$(F,Number(D.slice(0,D.indexOf(":"))))}}const wt=[];for(const[M,$]of bt){const O=I[M],_=I[$],T=O[0],F=O[O.length-1],D=_[0],Y=_[_.length-1];if(T===void 0||F===void 0||D===void 0||Y===void 0)continue;const Q=r[M].name,it=r[$].name,ot=[{e:N(F,-1,[]),f:N(D,1,[]),pa:F,pb:D,step:{op:"join",a:Q,aEnd:"end",b:it,bEnd:"start",gap:_n}},{e:N(F,-1,[]),f:N(Y,-1,[]),pa:F,pb:Y,step:{op:"join",a:Q,aEnd:"end",b:it,bEnd:"end",gap:_n}},{e:N(T,1,[]),f:N(D,1,[]),pa:T,pb:D,step:{op:"join",a:Q,aEnd:"start",b:it,bEnd:"start",gap:_n}},{e:N(T,1,[]),f:N(Y,-1,[]),pa:T,pb:Y,step:{op:"join",a:it,aEnd:"end",b:Q,bEnd:"start",gap:_n}}];for(const ft of ot){if(ft.e===null||ft.f===null||!lt&&!K(ft.pa,ft.e,ft.pb,ft.f))continue;const Ft=W(ft.e,ft.f),Vt=Ft.ideal>0?Math.min(Wf,Ft.score/Ft.ideal):0;wt.push({...ft,e:ft.e,f:ft.f,a:M,b:$,meeting:Ft,gain:Vt})}}const yt=new Map,Yt=(M,$)=>`${M.sequence}:${M.x}:${$.dir}`,we=M=>Math.max(0,M.score)/s.meetUnit,qe=new Set(wt.filter(M=>!G([[M.e,M.f]])&&!pt(M.e,M.a,M.f,M.b,M.meeting.gap)));for(const M of wt)if(qe.has(M))for(const $ of[Yt(M.pa,M.e),Yt(M.pb,M.f)]){const O=yt.get($)??[];O.push(we(M.meeting)),yt.set($,O)}for(const M of yt.values())M.sort(($,O)=>O-$);const pe=(M,$)=>{const O=yt.get(M)??[];return O[0]===$?O[1]??0:O[0]??0},be=.01;for(const M of wt){const $=we(M.meeting),O=Math.max(pe(Yt(M.pa,M.e),$),pe(Yt(M.pb,M.f),$)),_=Math.max(-2,Math.min(2,Math.log2(Math.max($,be)/Math.max(O,be)))),T=M.meeting.gap>s.window?M.meeting.gap*t.binsize:0,F=T>0&&M.step.op==="join"?{...M.step,gap:T}:M.step;ct({kind:"join",gain:M.gain,points:[M.pa,M.pb],made:[[M.e,M.f]],taken:[],step:F,stretch:null,target:null,cells:Number.POSITIVE_INFINITY,exclusivity:_,dicentric:pt(M.e,M.a,M.f,M.b,M.meeting.gap),gapCells:M.meeting.gap})}const We=e.weights!==void 0&&e.weights.length===no.length?e.weights:no,ye=Qt.map(M=>{const $=[Math.log2(1+Math.min(Math.max(0,M.gain),M.contacts/Tr)),Number.isFinite(M.cells)?Math.min(0,Math.log10(M.cells/4)):0,M.seen-1,-Math.max(0,M.excess-Fr)*(M.kind==="join"?1-Math.max(0,Math.min(1,M.exclusivity??0)):1),M.exclusivity??0,M.dicentric===!0?-1:0,M.buried===!0?-1:0,M.atGap===!0?1:0,Math.min(0,Math.log2(Math.max(.001,M.contacts)/Tr))];return{trade:M,features:$,confidence:Yf($,We)}});ye.sort((M,$)=>$.confidence-M.confidence||$.trade.gain-M.trade.gain);const je=[],Tt=M=>je.some($=>$.sequence===M.sequence&&Math.abs($.x-M.x)<=w),Nt=[];for(const{trade:M,features:$,confidence:O}of ye)M.points.some(Tt)||(je.push(...M.points),Nt.push(Kf(M,$,O,t,o,(_,T)=>M.kind==="join"?{score:W(_,T).score/s.meetUnit*o,seen:0,reached:0,contacts:0,expected:0}:R(_,T,"local"))));return{list:Nt,along:a.score,breakpoints:c,unit:o}}function Pr(e){return e.dir<0?{x:e.cell+1,side:-1}:{x:e.cell,side:1}}function Kf(e,t,n,s,o,r){const i=e.made.map(([d,m])=>{const g=Pr(d),w=Pr(m),p=r(d,m).score/o;return g.x<=w.x?{row:g.x,col:w.x,rowSide:g.side,colSide:w.side,score:p}:{row:w.x,col:g.x,rowSide:w.side,colSide:g.side,score:p}}),c=(e.kind==="move"?e.points.slice(0,2):e.points).filter(d=>d.inside&&e.kind!=="join").map(d=>d.x),l=[...e.points.map(d=>d.x)],u=[Math.min(...l),Math.max(...l)],h=e.made.flat().map(d=>{const m=s.cellMap[d.cell]??-1,w=(s.partAt(d.cell)?.piece?.strand??1)*d.dir;return`${m}${w<0?"<":">"}`}).concat(e.points.filter(d=>d.inside&&e.made.length===0).map(d=>{const m=s.cellMap[d.x-1]??-1,g=s.cellMap[d.x]??-1;return`${m}|${g}`})).sort().join(","),f=["map"];return t[2]<-.25&&f.push("sparse"),t[3]<0&&f.push("brighter than an adjacency"),e.kind==="join"&&(e.gapCells??0)>0&&f.push(`a gap of about ${Xf((e.gapCells??0)*s.binsize)}`),t[4]<-.5&&f.push("an end with a better offer"),e.dicentric===!0&&f.push("two centromeres"),e.buried===!0&&f.push("a telomere"),e.atGap===!0&&f.push("at a gap of N"),t[8]<-.5&&f.push("few contacts"),{key:`${e.kind}:${h}`,kind:e.kind,step:e.step,words:Ff(e.step),gain:e.gain,confidence:n,features:t,breaks:c,corners:i,extent:u,stretch:e.stretch,target:e.target,evidence:f}}function Xf(e){return e>=1e6?`${(e/1e6).toPrecision(2)} Mb`:e>=1e3?`${Math.round(e/1e3)} kb`:`${Math.round(e)} bp`}function Zf(e,t,n){if(n<=t.from)return 0;if(n>=t.to)return t.length;const s=e.place(n);return s===null||s.sequence!==t.name?0:Math.max(0,Math.min(t.length,Math.round(s.bp)))}function bn(e,t,n,s,o){const r=[];if(e.length===0)return r;let i=0;for(let a=1;a<=e.length;a++)if(a===e.length||e[a]!==e[i]){const c=e[i];r.push({label:t(c),start:i,end:a,...n===void 0?{}:{unitStart:n(c)},...s===void 0?{}:{unitLength:s(c)},...o===void 0?{}:{unitBin:o(c)}}),i=a}return r}function Lr(e,t){const n=e.coords.contigsOfBins(t[0],t[1]);return bn(n,s=>e.chromnames[s]??String(s),s=>e.coords.contigStartBin(s),s=>e.coords.contigLengths[s],s=>e.coords.contigStartBin(s))}function Dr(e,t){const n=e.coords.contigsOfBins(t[0],t[1]),s=new Int32Array(n.length);for(let o=0;o<n.length;o++)s[o]=e.contigGenomeIds[n[o]];return bn(s,o=>e.genomeNames[o]??String(o),o=>e.genomeExtent(o)[0])}function dn(e,t){const n=new Int32Array(t.length);for(let s=0;s<t.length;s++)n[s]=e.contigGenomeIds[t[s]];return bn(n,s=>e.genomeNames[s]??String(s))}function Jf(e,t){return e==="genome"&&t!==void 0&&t.length>1}function Ur(e,t,n){const s=n==="contig"?e.chromnames:e.genomeNames,o=new Array(t.length);for(let r=0;r<t.length;r++)o[r]={label:s[t[r]]??String(t[r]),start:r,end:r+1};return o}function td(e,t){return{rows:Ur(e,t.rowIds,t.level),cols:Ur(e,t.colIds,t.level)}}const Gr=new WeakMap;function Ca(e){let t=Gr.get(e);return t===void 0&&(t={},Gr.set(e,t)),t}function ed(e){const t=Ca(e);return t.contig??=e.coords.contigsOfBins(0,e.nBins),t.contig}function nd(e){const t=Ca(e);if(t.genome===void 0){const n=e.coords.contigsOfBins(0,e.nBins),s=e.contigGenomeIds;for(let o=0;o<n.length;o++)n[o]=s[n[o]];t.genome=n}return t.genome}const so=qt,sd=8,od=12*so*so;function rd(e){const t=Math.max(0,e-od),n=Math.floor(Math.sqrt(t/sd));return Math.max(256,Math.min(so,n))}function id(e,t,n){const s=new Int32Array(e);if(e<=t){for(let c=0;c<e;c++)s[c]=c;return{slotOf:s,slots:e,pooled:!1}}const o=n===void 0?null:ad(e,n);if(o===null||o.length>t){for(let c=0;c<e;c++)s[c]=Math.floor(c*t/e);return{slotOf:s,slots:t,pooled:!0}}const r=cd(o,t);let i=0,a=0;for(let c=0;c<o.length;c++){const l=o[c],u=r[c];for(let h=0;h<l;h++,i++)s[i]=a+Math.min(u-1,Math.floor(h*u/l));a+=u}return{slotOf:s,slots:a,pooled:!0}}function ad(e,t){const n=[];let s=0;for(let o=1;o<=e;o++)o<e&&t(o)===t(s)||(n.push(o-s),s=o);return n}function cd(e,t){const n=e.length,s=new Int32Array(n);if(n===0)return s;const o=e.reduce((c,l)=>c+l,0),r=t-n,i=[];let a=0;for(let c=0;c<n;c++){const l=o===0?0:e[c]*r/o,u=Math.floor(l);s[c]=1+u,a+=u,i.push({index:c,fraction:l-u})}i.sort((c,l)=>l.fraction-c.fraction||c.index-l.index);for(let c=0;a<r;c++,a++)s[i[c%n].index]+=1;return s}class ld{n;values;constructor(t){this.n=t,this.values=new Float64Array(t*(t+1)/2)}add(t,n,s){const o=t<n?t:n,r=t<n?n:t;this.values[o*this.n-o*(o-1)/2+(r-o)]+=s}get(t,n){const s=t<n?t:n,o=t<n?n:t;return this.values[s*this.n-s*(s-1)/2+(o-s)]}toSquare(){const{n:t,values:n}=this,s=new Float32Array(t*t);let o=0;for(let r=0;r<t;r++)for(let i=r;i<t;i++,o++){const a=n[o];s[r*t+i]=a,s[i*t+r]=a}return s}}function $a(e,t){const n=t[1]-t[0];if(!(n>0))return[];const s=Math.min(n,Math.max(0,Math.round(e[1])-Math.round(e[0])));if(s<=0)return[];const o=Math.round(e[0]),r=Math.floor((o-t[0])/n);let i=o-r*n,a=r*n,c=0,l=s;const u=[];for(;l>0;){const h=Math.min(l,t[1]-i);u.push({from:i,to:i+h,at:c,shift:a}),c+=h,l-=h,i=t[0],a+=n}return u}function Hr(e,t){const n=$a(e,t);return n.length>1||n.length===1&&n[0].shift!==0}function ud(e){const t=e.map(a=>a[0]?.nrows??0),n=(e[0]??[]).map(a=>a.ncols),s=t.reduce((a,c)=>a+c,0),o=n.reduce((a,c)=>a+c,0),r=new Float32Array(s*o);let i=0;for(let a=0;a<e.length;a++){let c=0;for(let l=0;l<e[a].length;l++){const u=e[a][l];for(let h=0;h<u.nrows;h++)r.set(u.values.subarray(h*u.ncols,h*u.ncols+u.ncols),(i+h)*o+c);c+=n[l]}i+=t[a]}return{nrows:s,ncols:o,values:r}}function hd(e){const t=Math.max(1,e.binsPerCell),n=[];let s=0;for(let o=0;o<e.starts.length;o++){const r=Math.round((e.starts[o]-e.contigStart)/t);n.push(e.blockStart+s-r),s+=e.cells[o]??0}return n}async function fd(e,t,n,s,o,r){const i=e.coords.contigOfBin(o[0]),[a,c]=e.coords.contigBinExtent(i);if(a!==o[0]||c!==o[1])throw new C("unsupported","A circular window must be a whole sequence: it is the sequence that joins its own ends.",{wrap:o,contig:e.chromnames[i]});const l={binsPerCell:Math.max(1,Math.trunc(t.binsPerCell??1)),contigsPerCell:Math.max(1,Math.trunc(t.contigsPerCell??1))},u=l.binsPerCell>1||l.contigsPerCell>1?l:r.planFor(o,n[1]-n[0],s[1]-s[0])??{binsPerCell:1,contigsPerCell:1};if(u.contigsPerCell>1)throw new C("unsupported","A circular sequence cannot be read at whole-sequence resolution: there is only one of it.",{wrap:o});const h=Math.max(1,u.binsPerCell),f=qr(r,n,o,u),d=qr(r,s,o,u);if(f.length===0||d.length===0)throw new C("unsupported","A circular window with nothing in it cannot be read.",{rows:n,cols:s,wrap:o});const m=async(S,v)=>{const I={rows:S.read,cols:v.read,...t.balance===!0?{balance:!0}:{},...t.value===void 0?{}:{value:t.value},...t.budgetBytes===void 0?{}:{budgetBytes:t.budgetBytes}};if(h<=1){const z=await e.matrix(I,r.hint(S.read,v.read));return{nrows:z.nrows,ncols:z.ncols,values:z.values}}const N=await e.pooledMatrix(I,u,r.hooks??{});r.throwIfCancelled();const B=N.values instanceof Float32Array?N.values:Float32Array.from(N.values);return{nrows:N.nrows,ncols:N.ncols,values:B}},g=[];for(const S of f){const v=[];for(const I of d)v.push(await m(S,I));g.push(v)}const w=g.map(S=>S[0].nrows),p=g[0].map(S=>S.ncols),{nrows:b,ncols:y,values:A}=ud(g),x=Wr(f),E=Wr(d);return{nrows:b,ncols:y,values:A,rowExtent:x,colExtent:E,rowGroups:jr(e,i,f,w,x[0],h),colGroups:jr(e,i,d,p,E[0],h),...t.genomes===!0&&e.hasGenomes?{rowGenomes:Qr(e,i,f,w),colGenomes:Qr(e,i,d,p)}:{},level:"bin",wrapped:o,...h>1?{binsPerCell:h}:{}}}function qr(e,t,n,s){const o=[];for(const r of $a(t,n)){const i=s.binsPerCell>1?e.snap([r.from,r.to],s):[r.from,r.to];i[1]>i[0]&&o.push({read:i,unwrapped:i[0]+r.shift})}return o}function Wr(e){const t=e.reduce((n,s)=>n+(s.read[1]-s.read[0]),0);return[e[0].unwrapped,e[0].unwrapped+t]}function jr(e,t,n,s,o,r){const[i]=e.coords.contigBinExtent(t),a=e.chromnames[t]??String(t),c=e.coords.contigLengths[t],l=hd({starts:n.map(f=>f.read[0]),cells:s,blockStart:o,contigStart:i,binsPerCell:r}),u=[];let h=0;for(let f=0;f<n.length;f++)u.push({label:a,start:h,end:h+s[f],unitStart:l[f],...c===void 0?{}:{unitLength:c}}),h+=s[f];return u}function Qr(e,t,n,s){const o=e.contigGenomeIds[t],r=e.genomeNames[o]??String(o),i=s.reduce((a,c)=>a+c,0);return i>0?[{label:r,start:0,end:i}]:[]}function dd(e){return Array.isArray(e)&&(e.length===0||typeof e[0]=="string")}function ko(e){const t={};for(const n of e.columns){const s=e.data[n];s!==void 0&&(dd(s)?t[n]=s:s instanceof BigInt64Array?t[n]=Float64Array.from(s,Number):t[n]=Float64Array.from(s))}return{length:e.length,columns:[...e.columns],data:t}}function Qn(e){if(e==null)return null;switch(typeof e){case"string":case"number":case"boolean":return e;case"bigint":return Number(e);case"object":{if(Array.isArray(e))return e.map(Qn);if(ArrayBuffer.isView(e))return Array.from(e);if(e instanceof Map){const n={};for(const[s,o]of e)n[String(s)]=Qn(o);return n}const t={};for(const[n,s]of Object.entries(e))t[n]=Qn(s);return t}default:return String(e)}}function md(e){return e instanceof C?{name:e.name,code:e.code,message:e.message,detail:Qn(e.detail),stack:e.stack}:e instanceof Error?{name:e.name,code:null,message:e.message,detail:{},stack:e.stack}:{name:"Error",code:null,message:String(e),detail:{}}}function gd(e){const t=[],n=new Set,s=o=>{if(!(o===null||typeof o!="object")){if(ArrayBuffer.isView(o)){const r=o.buffer;r instanceof ArrayBuffer&&!n.has(r)&&(n.add(r),t.push(r));return}if(Array.isArray(o)){if(o.length===0||typeof o[0]!="object")return;for(const r of o)s(r);return}for(const r of Object.values(o))s(r)}};return s(e),t}const Ee=1<<20,wd=64<<20;let Yr=0;class te{id;size;isRemote=!1;bytes;blob;existingPath;tempDir;mountPath=null;ownsMount=!1;requests=0;bytesRead=0;cache=new Map;cachedBytes=0;syncReader=null;module=null;readExact;constructor(t,n={}){if(this.tempDir=n.tempDir,this.bytes=null,this.blob=null,this.existingPath=null,pd(t)){const o=typeof File<"u"&&t instanceof File?t.name:null;this.blob=t,this.size=t.size,this.id=n.name??o??`blob-${Bs()}`,this.readExact=(r,i)=>this.readBlobExact(t,r,i);return}if(bd(t)){this.existingPath=t.path,this.size=t.size,this.id=n.name??t.path;return}const s=yd(t);this.bytes=s,this.size=s.byteLength,this.id=n.name??`bytes-${Bs()}`}static async fromPath(t,n={}){if(!Re())throw new C("bad-uri",`cannot open the filesystem path ${t} in a browser; pass the File object instead`,{path:t});const s=await ae();let o;try{o=s.FS.stat(t).size}catch(r){throw new C("not-hdf5",`cannot stat ${t}: ${r instanceof Error?r.message:String(r)}`,{path:t})}return new te({path:t,size:o},{name:n.name??t,...n})}static async open(t,n={}){return typeof t=="string"?te.fromPath(t,n):new te(t,n)}async mount(){if(this.mountPath!==null)return this.mountPath;const t=await ae();if(this.module=t,this.existingPath!==null)return this.mountPath=this.existingPath,this.ownsMount=!1,this.mountPath;if(this.blob!==null&&typeof FileReaderSync<"u")return this.mountPath=this.mountLazy(t,this.blob),this.ownsMount=!0,this.mountPath;const n=this.bytes??new Uint8Array(await this.blob.arrayBuffer()),s=this.mountTarget();return t.FS.writeFile(s,n),this.mountPath=s,this.ownsMount=!0,this.requests+=1,this.bytesRead+=n.byteLength,s}mountLazy(t,n){const s=this.mountTarget().replace(/^\//,""),o=t.FS.createFile("/",s,{},!0,!1),r={length:this.size};return o.contents=r,Object.defineProperty(o,"usedBytes",{get:()=>r.length}),o.stream_ops={...o.stream_ops,read:(i,a,c,l,u)=>{if(u>=this.size)return 0;const h=Math.min(this.size-u,l);return this.copyInto(n,a,c,u,h),h},mmap:(i,a,c)=>{const l=t.Module._malloc(a);if(l===0)throw new Error("mmap allocation failed");const u=Math.max(0,Math.min(this.size-c,a));return u>0&&this.copyInto(n,t.Module.HEAPU8,l,c,u),{ptr:l,allocated:!0}}},`/${s}`}readBytes(t,n){const s=Math.max(0,Math.min(this.size-t,n));if(s<=0)return new Uint8Array(0);if(this.bytes!==null)return this.bytes.subarray(t,t+s).slice();if(this.blob!==null){const a=new Uint8Array(s);return this.copyInto(this.blob,a,0,t,s),a}const o=this.module;if(this.existingPath===null||o===null)throw new C("unsupported",`${this.id} cannot be read directly before it has been mounted.`,{id:this.id});const r=new Uint8Array(s),i=o.FS.open(this.existingPath,"r");try{let a=0;for(;a<s;){const c=o.FS.read(i,r,a,s-a,t+a);if(c<=0)break;a+=c}return this.requests+=1,this.bytesRead+=a,a===s?r:r.subarray(0,a)}finally{o.FS.close(i)}}async readBlobExact(t,n,s){const o=Math.max(0,Math.min(this.size-n,s));if(o===0)return new Uint8Array(0);const r=Math.floor(n/Ee),i=Math.floor((n+o-1)/Ee);let a=!0;for(let l=r;l<=i&&a;l++)a=this.cache.has(l);if(a)return this.readBytes(n,o);const c=new Uint8Array(await t.slice(n,n+o).arrayBuffer());return this.requests+=1,this.bytesRead+=c.byteLength,c}copyInto(t,n,s,o,r){let i=0;for(;i<r;){const a=o+i,c=Math.floor(a/Ee);let l=this.cache.get(c);if(l===void 0){const f=c*Ee,d=Math.min(f+Ee,this.size);l=new Uint8Array(this.reader().readAsArrayBuffer(t.slice(f,d))),this.store(c,l),this.requests+=1,this.bytesRead+=l.byteLength}else this.cache.delete(c),this.cache.set(c,l);const u=a-c*Ee,h=Math.min(l.length-u,r-i);if(h<=0)throw new Error(`short read of ${this.id} at ${a}`);n.set(l.subarray(u,u+h),s+i),i+=h}}store(t,n){this.cache.set(t,n),this.cachedBytes+=n.byteLength;for(const s of this.cache.keys()){if(this.cachedBytes<=wd)break;if(s===t)continue;const o=this.cache.get(s);o&&(this.cachedBytes-=o.byteLength),this.cache.delete(s)}}reader(){return this.syncReader??=new FileReaderSync,this.syncReader}close(){if(this.cache.clear(),this.cachedBytes=0,this.mountPath===null)return;const 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s=`${e}|${t}|${n}`;if(Tn!==null&&Tn.id===s)return Tn.key;const o=an(he(`AWS4${e}`),he(t)),r=an(o,he(n)),i=an(r,he(Ba)),a=an(i,he(Oa));return Tn={id:s,key:a},a}function kd(e){const t=new URL(e.url),n=e.now??new Date,s=$d(n),o=s.slice(0,8),r=e.payloadHash??Cd,{credential:i}=e,a=[["host",t.host],["x-amz-content-sha256",r],["x-amz-date",s]];i.sessionToken!==void 0&&i.sessionToken!==""&&a.push(["x-amz-security-token",i.sessionToken]);const c=a.map(([g,w])=>`${g}:${w.trim()}
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+`),d=Xr(an(Od(i.secretAccessKey,o,i.region),he(f))),m={Authorization:`${Zr} Credential=${i.accessKeyId}/${h}, SignedHeaders=${l}, Signature=${d}`,"x-amz-content-sha256":r,"x-amz-date":s};return i.sessionToken!==void 0&&i.sessionToken!==""&&(m["x-amz-security-token"]=i.sessionToken),m}function me(e){const t={...e.headers};return e.credential===void 0?t:{...t,...kd({method:(e.method??"GET").toUpperCase(),url:e.url,credential:e.credential})}}function _o(e){const t=_d(e);return t.has("x-amz-signature")||t.has("x-goog-signature")?!0:t.has("sig")&&t.has("sv")}function _d(e){const t=new Set;if(typeof e!="string")return t;const n=e.indexOf("#"),s=n<0?e:e.slice(0,n),o=s.indexOf("?");if(o<0)return t;const r=s.slice(o+1);for(const i of r.split("&")){const a=i.indexOf("=");a<=0||t.add(i.slice(0,a).toLowerCase())}return t}const Td=1<<20,Fd=64<<20,zd=4<<20,Rd=16<<20,Pd=8;function Ld(e,t){const n=new XMLHttpRequest;n.open("GET",e,!1);for(const[s,o]of Object.entries(t))n.setRequestHeader(s,o);return n.responseType="arraybuffer",n.send(null),{status:n.status,body:new Uint8Array(n.response??new ArrayBuffer(0)),contentRange:n.getResponseHeader("content-range")}}class de{id;size;isRemote=!0;url;chunkSize;onRead;maxCacheBytes;cache=new Map;cachedBytes=0;readAhead;recent=[];requests;bytesRead;mountPath=null;credential;headers;fetchImpl;syncFetch;constructor(t,n,s,o){this.url=t,this.id=t,this.size=n,this.credential=s.credential,this.headers=s.headers,this.fetchImpl=s.fetchImpl??((i,a)=>globalThis.fetch(i,a)),this.syncFetch=s.syncFetch??null,this.chunkSize=Math.max(1,Math.trunc(s.chunkSize??Td)),this.readAhead=s.readAhead??!0,this.onRead=s.onRead;const r=Math.trunc(s.maxCacheBytes??Fd);this.maxCacheBytes=Math.max(this.chunkSize,r),this.requests=o.requests,this.bytesRead=o.bytes}static async open(t,n={}){const s=n.fetchImpl??globalThis.fetch,o=m=>me({url:t,method:m,...n.headers===void 0?{}:{headers:n.headers},...n.credential===void 0?{}:{credential:n.credential}});if(typeof s!="function")throw new C("remote-cors","this runtime has no fetch(); remote files need one",{url:t});const r=sn(t),i={requests:0,bytes:0};let a=null;if(!_o(t))try{i.requests+=1,a=await s(t,{method:"HEAD",headers:o("HEAD")})}catch(m){await ti(t,r,m,s,i)}if(a&&!a.ok)throw new C("bad-uri",n.credential===void 0?`${r} answered ${a.status} ${a.statusText} to a HEAD of ${t}; the viewer needs a publicly readable object, or a bucket entry holding a key for it (Open a file → Private buckets). A presigned link is read without this probe and does not reach here, so a URL carrying a signature in its query that fails has expired rather than been rejected for its method.`:`${r} answered ${a.status} ${a.statusText} to a signed HEAD of ${t}. The key reached the bucket and was rejected: check that the region on the bucket entry matches the bucket, that the key is allowed \`s3:GetObject\` on this prefix, and — for a temporary credential — that the session token has not expired.`,{url:t,host:r,status:a.status,signed:n.credential!==void 0});const c=ei(a);if(c!==null){const m=await Dd(t,s,o,i),g=ni(m?.headers.get("content-range")??null)??Fn(m,"content-length");if(m!==null&&m.status===206&&ei(m)===null&&g!==null)return new de(t,g,n,i);throw new C("remote-compressed",`${r} is serving ${t} with “Content-Encoding: ${c}”, so byte ranges address the compressed stream rather than the file.`,{url:t,host:r,encoding:c,encodedLength:Fn(a,"content-length")})}const l=Fn(a,"content-length"),u=l===0?null:l;if((a?.headers.get("accept-ranges")??"").toLowerCase().includes("bytes")&&u!==null)return new de(t,u,n,i);let f;try{i.requests+=1,f=await s(t,{method:"GET",headers:{...o("GET"),Range:"bytes=0-0"}})}catch(m){throw await ti(t,r,m,s,i),new Error("unreachable")}if(i.bytes+=Fn(f,"content-length")??1,f.status!==206)throw new C("remote-no-ranges",`${r} does not serve HTTP range requests: a “Range: bytes=0-0” request for ${t} returned ${f.status}, not 206 Partial Content.`,{url:t,host:r,status:f.status});const d=ni(f.headers.get("content-range"))??u;if(d===null)throw new C("remote-cors",`${r} serves ranges for ${t} but does not expose its size to this page: neither “Content-Length” nor “Content-Range” was readable. Add both to the bucket’s CORS “Access-Control-Expose-Headers”.`,{url:t,host:r});return new de(t,d,n,i)}async mount(){if(this.mountPath!==null)return this.mountPath;if(this.syncFetch===null&&typeof XMLHttpRequest>"u")throw new C("remote-cors","remote files are read with synchronous XMLHttpRequest, which exists only in a browser worker; this runtime has none.",{url:this.url});const t=await ae(),n=`remote-${Math.abs(Gd(this.url)).toString(36)}`;return this.mountPath=xd(t,n,this.size,(s,o,r,i)=>this.copyInto(s,o,r,i)),this.mountPath}close(){if(this.cache.clear(),this.cachedBytes=0,this.mountPath===null)return;const t=this.mountPath;this.mountPath=null,ae().then(n=>Sd(n,t),()=>{})}stats(){return{requests:this.requests,bytes:this.bytesRead}}resetStats(){this.requests=0,this.bytesRead=0}cachedChunkCount(){return this.cache.size}readBytes(t,n){const s=Math.max(0,Math.min(this.size-t,n)),o=new Uint8Array(s);return s>0&&this.copyInto(o,0,t,s),o}async readExact(t,n){const s=Math.max(0,Math.min(this.size-t,n));if(s===0)return new Uint8Array(0);const o=Math.floor(t/this.chunkSize),r=Math.floor((t+s-1)/this.chunkSize);let i=!0;for(let d=o;d<=r&&i;d++)i=this.cache.has(d);if(i)return this.readBytes(t,s);const a=t,c=t+s-1,l=this.fetchImpl,u=await l(this.url,{method:"GET",headers:{...this.authorisation(),Range:`bytes=${a}-${c}`}});this.requests+=1,this.refuseStatus(u.status,a,c);const h=new Uint8Array(await u.arrayBuffer());this.bytesRead+=h.byteLength,this.onRead?.(this.requests,this.bytesRead);const f=this.windowOf(h,a,c,u.headers.get("content-range"));if(f.byteLength<s)throw new C("remote-no-ranges","a range request returned a short response",{wanted:s,available:f.byteLength});return f.byteLength===s&&f.buffer.byteLength===s?f:f.slice(0,s)}copyInto(t,n,s,o){let r=0;for(;r<o;){const i=s+r,a=Math.floor(i/this.chunkSize),c=this.cache.get(a);if(c){this.touch(a),r+=Jr(t,n+r,c,i-a*this.chunkSize,o-r);continue}const l=Math.floor((s+o-1)/this.chunkSize);let u=a;for(;u+1<=l&&!this.cache.has(u+1);)u+=1;const{ahead:h,streak:f}=this.aheadFor(a,u),d=Math.min(u+h,Math.ceil(this.size/this.chunkSize)-1);for(;u<d&&!this.cache.has(u+1);)u+=1;this.recent.push({from:a,to:u,streak:f}),this.recent.length>Pd&&this.recent.shift();const m=a*this.chunkSize,g=Math.min((u+1)*this.chunkSize,this.size)-1,w=this.fetchRange(m,g);r+=Jr(t,n+r,w,i-m,o-r);for(let p=a;p<=u;p++){const b=p*this.chunkSize-m;if(b>=w.length)break;this.store(p,w.subarray(b,Math.min(b+this.chunkSize,w.length)))}}}aheadFor(t,n){if(!this.readAhead)return{ahead:0,streak:0};const s=Math.max(1,Math.floor(zd/this.chunkSize));let o=0;for(const i of this.recent)t>=i.from-s&&t<=i.to+s&&(o=Math.max(o,i.streak+1));if(o<2)return{ahead:0,streak:o};const r=Math.max(0,Math.floor(Rd/this.chunkSize)-(n-t+1));return{ahead:Math.min(r,2**(o-2)),streak:o}}fetchRange(t,n){const s={...this.authorisation(),Range:`bytes=${t}-${n}`},o=(this.syncFetch??Ld)(this.url,s);return this.requests+=1,this.refuseStatus(o.status,t,n),this.bytesRead+=o.body.byteLength,this.onRead?.(this.requests,this.bytesRead),this.windowOf(o.body,t,n,o.contentRange)}authorisation(){return this.credential===void 0&&this.headers===void 0?{}:me({url:this.url,method:"GET",...this.headers===void 0?{}:{headers:this.headers},...this.credential===void 0?{}:{credential:this.credential}})}refuseStatus(t,n,s){if(t===403&&this.credential!==void 0)throw new C("bad-uri",`${sn(this.url)} refused a signed request for bytes ${n}-${s} of ${this.url}. The key reached the bucket and was rejected: check the region on the bucket entry matches the bucket, that the key is allowed \`s3:GetObject\` on this prefix, and — for a temporary credential — that the session token has not expired.`,{url:this.url,status:403,from:n,to:s,signed:!0});if(t!==206&&t!==200)throw new C("remote-no-ranges",`${sn(this.url)} returned ${t} for bytes ${n}-${s} of ${this.url}`,{url:this.url,status:t,from:n,to:s})}windowOf(t,n,s,o){const r=s-n+1,i=ka(o);if(i!==null&&i.end-i.start+1!==t.byteLength)throw new C("remote-compressed",`${sn(this.url)} answered a request for bytes ${n}-${s} of ${this.url} with “Content-Range: ${o}” — ${i.end-i.start+1} octets — but the body is ${t.byteLength}. The response was re-encoded in transit (transfer compression), so ranges do not address the file. Serve it without “Content-Encoding”, or download it and drop it here.`,{url:this.url,from:n,to:s,claimed:i.end-i.start+1,received:t.byteLength});const a=i?.start??Ud(o),c=a===null?t.byteLength>r?n:0:n-a;if(c===0&&t.byteLength<=r)return t;if(c<0||c>=t.byteLength)throw new C("remote-no-ranges",`${sn(this.url)} answered a request for bytes ${n}-${s} of ${this.url} with ${t.byteLength} bytes starting at ${a??"an unstated offset"}, which does not contain what was asked for.`,{url:this.url,from:n,to:s,start:a,length:t.byteLength});return t.subarray(c,Math.min(c+r,t.byteLength))}store(t,n){const s=new Uint8Array(n);this.cache.set(t,s),this.cachedBytes+=s.byteLength;for(const o of this.cache.keys()){if(this.cachedBytes<=this.maxCacheBytes)break;if(o===t)continue;const r=this.cache.get(o);r&&(this.cachedBytes-=r.byteLength),this.cache.delete(o)}}touch(t){const n=this.cache.get(t);n&&(this.cache.delete(t),this.cache.set(t,n))}}function Jr(e,t,n,s,o){const r=Math.min(n.length-s,o);if(r<=0)throw new C("remote-no-ranges","a range request returned a short response",{wanted:o,available:n.length-s});return e.set(n.subarray(s,s+r),t),r}async function ti(e,t,n,s,o){let r=!1;try{o.requests+=1,await s(e,{method:"GET",mode:"no-cors",headers:{Range:"bytes=0-0"}}),r=!0}catch{r=!1}const i=n instanceof Error?`${n.name}: ${n.message}`:String(n);throw r?new C("remote-cors",`${t} is reachable but refused a cross-origin read of ${e} (${i}). That is what a missing “Access-Control-Allow-Origin” looks like from a browser: the failure has no status and no headers. Configure the bucket to allow GET and HEAD and the “Range” request header, and to expose “Content-Length” and “Content-Range”.`,{url:e,host:t,cause:i,reachable:!0}):new C("remote-cors",`${t} could not be reached for ${e} (${i}). 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A=n*this.nContigs+r;if(this.densePairs!==null)this.densePairs[A]===0&&this.notePair(this.contigs[n].name,this.contigs[r].name),this.densePairs[A]++;else{const x=this.sparsePairs.get(A);x===void 0&&this.notePair(this.contigs[n].name,this.contigs[r].name),this.sparsePairs.set(A,(x??0)+1)}}else{const A=n>=0?this.contigs[n].name:this.decoder.decode(t.subarray(s,o)),x=r>=0?this.contigs[r].name:this.decoder.decode(t.subarray(i,a));p=A===x;const E=`${A}	${x}`;this.namedPairs.has(E)||this.notePair(A,x),this.namedPairs.set(E,(this.namedPairs.get(E)??0)+1)}if(!p){this.trans++;return}if(this.cis++,c<0||l<0)return;const b=Math.abs(l-c),y=im(u,h);if(y>=0){const A=this.edges;let x=0,E=A.length;for(;E-x>1;){const S=x+E>>1;A[S]<=b?x=S:E=S}this.distFreq[y][x]++}for(let A=0;A<zn.length;A++)b>=zn[A]*1e3&&this.cisAtLeast[A]++}notePair(t,n){const s=`${t}	${n}`;this.pairSeen.has(s)||this.pairSeen.set(s,this.pairSeen.size)}result(t){const n=c=>c.length===2&&this.longTypes.get(c)===void 0?this.shortTypes[c.charCodeAt(0)<<8|c.charCodeAt(1)]:this.longTypes.get(c)??0,s=this.typeOrder.map((c,l)=>({name:c,count:n(c),order:l})).sort((c,l)=>l.count-c.count||c.order-l.order).map(({name:c,count:l})=>[c,l]),o=[],r=this.nContigs;if(this.densePairs!==null)for(let c=0;c<this.densePairs.length;c++){const l=this.densePairs[c];l>0&&o.push({name1:this.contigs[Math.floor(c/r)].name,name2:this.contigs[c%r].name,count:l})}else for(const[c,l]of this.sparsePairs)o.push({name1:this.contigs[Math.floor(c/r)].name,name2:this.contigs[c%r].name,count:l});for(const[c,l]of this.namedPairs){const[u,h]=c.split("	");o.push({name1:u,name2:h,count:l})}const i=c=>this.pairSeen.get(`${c.name1}	${c.name2}`)??0;o.sort((c,l)=>l.count-c.count||i(c)-i(l));const a={};return li.forEach((c,l)=>{a[c]=Array.from(this.distFreq[l])}),{total:this.total,totalUnmapped:this.totalUnmapped,totalSingleSidedMapped:this.total-this.totalMapped-this.totalUnmapped,totalMapped:this.totalMapped,totalDups:this.totalDups,totalNodups:this.totalMapped-this.totalDups,cis:this.cis,trans:this.trans,pairTypes:s,cisAtLeast:zn.map((c,l)=>[c,this.cisAtLeast[l]]),chromFreq:o.map(({name1:c,name2:l,count:u})=>[c,l,u]),distEdges:[...this.edges],distFreq:a,chromsizes:this.contigs.map(c=>[c.name,c.length]),pairTypeColumn:this.pairTypeColumn&&this.pairTypeSeen,scoped:t}}}const lm=9,um=35,Ts=1<<20;class hm{unique=new Map;ambiguous=new Map;byName=new Map;decoder=new TextDecoder;constructor(t){for(let n=0;n<t.length;n++){const s=t[n].name;this.byName.set(s,n);const o=fm(s),r=this.unique.get(o);if(r===void 0&&!this.ambiguous.has(o)){this.unique.set(o,n);continue}const i=this.ambiguous.get(o)??[];r!==void 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Choose a coarser base resolution, or import fewer sequences.`,{binSize:n,nnz:N,limitBytes:t.maxPixelBytes}),Et;for(;N+E>S.length;)S=Rn(S),v=Rn(v),I=Rn(I);for(let q=0;q<E;q++){const tt=U[q];S[N]=B,v[N]=tt,I[N]=A[tt],N++,A[tt]=0}E=0},H=t.expectedRecords??0,mt=U=>{if(U.length===0||U[0]===um)return;let q=0,tt=0,nt=-1,K=-1,bt=-1,wt=-1,yt=-1,Yt=-1,we=0,qe=0,pe=0,be=0,We=-1,ye=-1;const je=U.length;for(let $=0;$<=je;$++)if(!($!==je&&U[$]!==lm)){if(q===o.chrom1?(nt=c.lookup(U,tt,$),we=tt,qe=$):q===o.chrom2?(K=c.lookup(U,tt,$),pe=tt,be=$):q===h?(We=tt,ye=$):q===o.pos1?bt=hi(U,tt,$):q===o.pos2?wt=hi(U,tt,$):u&&q===o.strand1?yt=$>tt?U[tt]:-1:u&&q===o.strand2&&(Yt=$>tt?U[tt]:-1),q++,q>f)break;tt=$+1}if(d.add(U,nt,we,qe,K,pe,be,bt,wt,yt,Yt,We,ye),m!==void 0&&m(U,nt,we,qe,K,pe,be,bt,wt,yt,Yt,We,ye),nt<0||K<0){P++;return}if(bt<0||wt<0){L++;return}if(p!==null&&w!==null&&nt===K){const $=gm(yt,Yt);if($>=0){const O=Math.abs(wt-bt);let _=0,T=w.length-1;for(;_+1<T;){const F=_+T>>1;w[F]<=O?_=F:T=F}p[$][_]++,b++}}let Tt=gt(bt),Nt=gt(wt);if(Tt>y[nt]&&(Tt=y[nt],j++),Nt>y[K]&&(Nt=y[K],j++),Tt+=i[nt],Nt+=i[K],Tt>Nt){const $=Tt;Tt=Nt,Nt=$}nt===K&&(Qt[nt]=1);let M=!1;if(!J){const $=nt<=K?nt*l+K:K*l+nt;$!==Z&&(M=!0,Z>=0&&It.add(Z),It.has($)&&(J=!0,It.clear()),Z=$)}Tt!==B&&(Tt<B&&(W=!0,M||(J=!0)),G(),B=Tt),A[Nt]===0&&(E===x.length&&(x=Rn(x)),x[E++]=Nt),A[Nt]++,z++,R++};function gt(U){const q=r?U-1:U;return q<0?0:Math.floor(q/n)}const ct=t.spans??[{from:0,to:e.size}],_t=ct.reduce((U,q)=>U+Math.max(0,q.to-q.from),0);let ge=0;try{for(const U of ct){const q={from:U.from,to:U.to,onProgress:nt=>{H>0?t.onProgress?.(z,H,"reading records"):t.onProgress?.(ge+nt,_t,"reading records")}};t.cancelled!==void 0&&(q.cancelled=t.cancelled),t.spans===void 0&&(q.onFraming=nt=>{Ut=!0,(nt.partialMember||!nt.endedOnEofMarker)&&(pt=!0)});const tt=await $o(Co(e,q),mt,t.cancelled);if(ge+=Math.max(0,U.to-U.from),!tt||t.cancelled?.()===!0)return null}G()}catch(U){throw Et!==null?Et:U}const lt={binSize:n,contigs:[...s],chromOffset:i,nBins:a,bin1:S.subarray(0,N),bin2:v.subarray(0,N),count:I.subarray(0,N),nnz:N,sum:R,skippedUnknownContig:P,skippedBadPosition:L,clampedPosition:j,wasUnsorted:J,truncated:Ut&&pt,contigsWithoutCisContacts:s.filter((U,q)=>Qt[q]===0).map(U=>U.name),orientation:w===null||p===null?null:{edges:w,counts:p,total:b},stats:d.result(t.spans!==void 0)};return W?La(lt):lt}function Rn(e){const t=new Int32Array(e.length*2);return t.set(e),t}function hi(e,t,n){if(n<=t)return-1;let s=0;for(let o=t;o<n;o++){const r=e[o]-48;if(r<0||r>9)return-1;s=s*10+r}return s}function La(e){const{nnz:t,nBins:n}=e,s=new Int32Array(n+1);for(let h=0;h<t;h++)s[e.bin1[h]+1]++;for(let h=0;h<n;h++)s[h+1]+=s[h];const o=s.slice(0,n),r=new Int32Array(t),i=new Int32Array(t);for(let h=0;h<t;h++){const f=o[e.bin1[h]]++;r[f]=e.bin2[h],i[f]=e.count[h]}const a=new Int32Array(t),c=new Int32Array(t),l=new Int32Array(t);let u=0;for(let h=0;h<n;h++){const f=s[h],d=s[h+1];if(d<=f)continue;let m=!0;for(let p=f+1;p<d;p++)if(r[p]<r[p-1]){m=!1;break}const g=m?null:Array.from({length:d-f},(p,b)=>f+b);g?.sort((p,b)=>r[p]-r[b]);let w=-1;for(let p=0;p<d-f;p++){const b=g===null?f+p:g[p],y=r[b];if(y===w){l[u-1]+=i[b];continue}a[u]=h,c[u]=y,l[u]=i[b],u++,w=y}}return{...e,bin1:a.subarray(0,u),bin2:c.subarray(0,u),count:l.subarray(0,u),nnz:u}}const Da=[1,2,5,10,20,50,100,200,500,1e3,2e3,5e3,1e4],pm=Da.length;function bm(e,t){const n=Math.max(1,Math.min(t,pm));return Da.slice(0,n).map(s=>e*s)}function ym(e,t){const n=new Int32Array(t);for(let s=0;s+1<e.length;s++){const o=e[s],r=e[s+1];for(let i=o;i<r&&i<t;i++)n[i]=s}return n}async function Am(e,t,n={}){if(t===e.binSize)return e;if(t%e.binSize!==0)throw new Error(`A ladder rung must be a whole multiple of the base: ${t} is not a multiple of ${e.binSize}.`);const s=t/e.binSize,o=e.contigs,r=No(o,t),i=ya(o,t),a=ym(e.chromOffset,e.nBins),c=A=>{const x=a[A];return r[x]+Math.floor((A-e.chromOffset[x])/s)},l=new Int32Array(i);let u=new Int32Array(Math.min(i,65536)),h=0,f=new Int32Array(Math.min(e.nnz,1<<20)||1),d=new Int32Array(f.length),m=new Int32Array(f.length),g=0,w=-1,p=0;const b=()=>{if(h===0)return;const A=u.subarray(0,h);for(A.sort();g+h>f.length;)f=Pn(f),d=Pn(d),m=Pn(m);for(let x=0;x<h;x++){const E=A[x];f[g]=w,d[g]=E,m[g]=l[E],g++,l[E]=0}h=0},y=1<<20;for(let A=0;A<e.nnz;A+=y){if(n.cancelled?.()===!0)return null;const x=Math.min(A+y,e.nnz);for(let E=A;E<x;E++){const S=c(e.bin1[E]),v=c(e.bin2[E]);S!==w&&(b(),w=S),l[v]===0&&(h===u.length&&(u=Pn(u)),u[h++]=v),l[v]+=e.count[E],p+=e.count[E]}n.onProgress?.(x,e.nnz,`aggregating to ${t} bp`),await St()}return b(),{binSize:t,contigs:[...o],chromOffset:r,nBins:i,bin1:f.subarray(0,g),bin2:d.subarray(0,g),count:m.subarray(0,g),nnz:g,sum:p,skippedUnknownContig:e.skippedUnknownContig,skippedBadPosition:e.skippedBadPosition,clampedPosition:e.clampedPosition,wasUnsorted:e.wasUnsorted,truncated:e.truncated,contigsWithoutCisContacts:[...e.contigsWithoutCisContacts]}}function Pn(e){const t=new Int32Array(Math.max(1,e.length*2));return t.set(e),t}const Mm=[{magic:"PX2.004
",wideLinecount:!0},{magic:"PX2.003
",wideLinecount:!1},{magic:"PX2.002
",wideLinecount:!1}],fi=[36,40,44];function xm(e){if(e.length<20)throw new C("format","This .px2 index is too short to hold a header.",{bytes:e.length});const t=new DataView(e.buffer,e.byteOffset,e.byteLength),n=String.fromCharCode(...e.subarray(0,8)),s=Mm.find(p=>p.magic===n);if(s===void 0)throw new C("format","This is not a pairix index: the magic bytes are not PX2. A `.tbi` cannot be used for a pairs file — build one with `pairix <file>.pairs.gz`.",{magic:n.replace(/[^\x20-\x7e]/g,"?")});const o=t.getInt32(8,!0);let r=12,i;s.wideLinecount?(i=Number(t.getBigUint64(r,!0)),r+=8):(i=t.getUint32(r,!0),r+=4);const a=Sm(t,e,r,o),{splitChar:c,metaChar:l,lineSkip:u,namesAt:h,nameBytes:f}=a,d=[],m=new TextDecoder().decode(e.subarray(h,h+f));for(const p of m.split("\0"))p!==""&&d.push(p);let g=h+f;const w=new Map;for(let p=0;p<o&&!(g+4>e.length);p++){const b=t.getInt32(g,!0);g+=4;let y=Number.POSITIVE_INFINITY,A=Number.NEGATIVE_INFINITY;for(let E=0;E<b&&!(g+8>e.length);E++){g+=4;const S=t.getInt32(g,!0);g+=4;for(let v=0;v<S&&!(g+16>e.length);v++){const I=Number(t.getBigUint64(g,!0)>>16n),N=Number(t.getBigUint64(g+8,!0)>>16n);g+=16,I<y&&(y=I),N>A&&(A=N)}}if(g+4>e.length)break;const x=t.getInt32(g,!0);g+=4;for(let E=0;E<x&&!(g+8>e.length);E++){const S=Number(t.getBigUint64(g,!0)>>16n);g+=8,S>0&&S<y&&(y=S)}Number.isFinite(y)&&Number.isFinite(A)&&p<d.length&&w.set(d[p],{from:y,to:A})}return{keys:d,spans:w,linecount:i,splitChar:c,metaChar:l,lineSkip:u}}function Sm(e,t,n,s){const o=[];for(const r of fi){const i=n+r;if(i+4>t.length)continue;const a=e.getInt32(i,!0),c=i+4;if(o.push(a),a<=0||c+a>t.length||new TextDecoder().decode(t.subarray(c,c+a)).split("\0").filter(h=>h!=="").length!==s)continue;const u=n+28;return{splitChar:String.fromCharCode(t[u+1]||124),metaChar:String.fromCharCode(t[u+2]||35),lineSkip:e.getInt32(n+32,!0),namesAt:c,nameBytes:a}}throw new C("format",`This .px2 index has a header this reader cannot lay out: no candidate config size produced a coherent name block for ${s} references. Rebuild it with \`pairix <file>.pairs.gz\`, or open the file without an index.`,{nRef:s,candidates:fi,sawNameBytes:o})}async function Im(e){const t=await e();if(t===null)return null;try{const n=t.readBytes(0,t.size);return xm(await _a(n))}finally{t.close()}}function Em(e,t,n){const s=[];for(const r of t){const i=e.spans.get(r);i!==void 0&&s.push({from:i.from,to:vm(n,i.to)})}s.sort((r,i)=>r.from-i.from);const o=[];for(const r of s){const i=o[o.length-1];i!==void 0&&r.from<=i.to+(1<<20)?i.to=Math.max(i.to,r.to):o.push({...r})}return o}function vm(e,t){if(t>=e.size)return e.size;const n=e.readBytes(t,Math.min(si,e.size-t)),s=Fo(n);return s===null?Math.min(e.size,t+si):Math.min(e.size,t+s)}const Cm=12;async function Ua(e,t){const n=await ba(e);let s=null;try{s=await Im(t)}catch(r){if(!(r instanceof C))throw r;s=null}let o=0;for(const r of n.contigs)o+=r.length;return{header:n,index:s,records:s?.linecount??null,genomeLength:o,sourceBytes:e.size}}function $m(e,t=wn()){const n=e.records??Nm(e),s=Math.max(1,Math.floor(t/Cm)),o=Math.max(1e3,Math.min(Math.sqrt(s*2),2e5)),r=Math.max(1,e.genomeLength/o),i=Math.max(r,e.genomeLength/Math.max(1,Math.sqrt(n)));return Bm(i)}function Nm(e){return Math.max(1,Math.round(e.sourceBytes*4.5/55))}function Bm(e){if(!Number.isFinite(e)||e<=1)return 1;const t=10**Math.floor(Math.log10(e));for(const n of[1,2,5,10])if(e<=n*t)return n*t;return 10*t}async function Ga(e,t,n){const s=bm(n.base,n.rungs),o=n.maxPixelBytes??wn(),r=.85,i=(h,f)=>{n.onProgress?.(Math.round(h*1e3),1e3,f)},a=n.keys===void 0?void 0:Om(t,n.keys,e),c={binSize:n.base,contigs:t.header.contigs,columns:t.header.columns,oneBased:n.oneBased??!0,maxPixelBytes:o,onProgress:(h,f,d)=>{i(f>0?h/f*r:0,d??"reading records")}};a!==void 0&&(c.spans=a),t.records!==null&&(c.expectedRecords=t.records),n.cancelled!==void 0&&(c.cancelled=n.cancelled);const l=await wm(e,c);if(l===null)return null;const u=new Map([[n.base,l]]);for(let h=1;h<s.length;h++){const f=s[h],d=await Am(l,f,{onProgress:(m,g)=>{const w=g>0?m/g:1,p=(h-1+w)/Math.max(1,s.length-1);i(r+p*(1-r),`building the ${Ha(f)} rung`)},...n.cancelled===void 0?{}:{cancelled:n.cancelled}});if(d===null)return null;u.set(f,d)}return i(1,"done"),{header:t.header,rungs:s,tables:u,indexed:t.index!==null,declaredRecords:t.records}}function Om(e,t,n){if(e.index===null)return;const s=Em(e.index,t,n);return s.length===0?void 0:s}function km(e,t,n){if(Mt(n).path!==Mt(t).path)return null;const s=/^\/resolutions\/(\d+)$/.exec(Mt(n).group);if(s===null)return null;const o=Number(s[1]);return e.tables.has(o)?o:null}function Ha(e){return e>=1e6&&e%1e6===0?`${e/1e6} Mb`:e>=1e3&&e%1e3===0?`${e/1e3} kb`:`${e} bp`}function _m(e){return`${(e.split(/[\\/]/).pop()??"pairs").replace(/\.px2$/i,"").replace(/\.b?gz$/i,"").replace(/\.pairs$/i,"")||"pairs"}.mcool`}const os="0.17.0",Rs=1<<20;function Tm(){if(!Re())return"";const e=globalThis.process?.env;return(e?.TMPDIR??e?.TMP??e?.TEMP??"/tmp").replace(/\/+$/,"")}const rs="<q",cn="<i",Fm="HDF5::Cooler",zm="HDF5::MCOOL",Rm=3,Pm=2,Lm="https://github.com/open2c/cooler";async function qa(e,t={}){const n=await ae(),s=`${Tm()}/pairs-export-${Date.now()}.mcool`;n.FS.analyzePath(s).exists&&n.FS.unlink(s);try{return await Dm(n,s,e,t)}finally{n.FS.analyzePath(s).exists&&n.FS.unlink(s)}}async function Dm(e,t,n,s){const o=new e.File(t,"w");try{o.create_attribute("format",zm),o.create_attribute("format-version",Pm);const i=o.create_group("resolutions"),a=n.rungs.reduce((l,u)=>l+(n.tables.get(u)?.nnz??0),0);let c=0;for(const l of n.rungs){const u=n.tables.get(l);if(u===void 0)continue;const h=i.create_group(String(l));if(Um(h,u,n,l,s.about),c=await Hm(h,u,c,a,s),s.cancelled?.()===!0)return null;s.onProgress?.(c,a,`writing the ${Ha(l)} rung`)}}finally{o.close()}const r=e.FS.readFile(t);return r instanceof Uint8Array?r:new Uint8Array(r)}function Um(e,t,n,s,o){const r=t.contigs.length;e.create_attribute("format",Fm),e.create_attribute("format-version",Rm),e.create_attribute("format-url",Lm),e.create_attribute("bin-type","fixed"),e.create_attribute("bin-size",s),e.create_attribute("storage-mode","symmetric-upper"),e.create_attribute("nchroms",r),e.create_attribute("nbins",t.nBins),e.create_attribute("nnz",t.nnz),e.create_attribute("sum",t.sum),e.create_attribute("generated-by",o?.generatedBy??`chromosomix ${os} (pairs import; unbalanced)`),e.create_attribute("creation-date",new Date().toISOString()),n.header.assembly!==null&&e.create_attribute("genome-assembly",n.header.assembly),e.create_attribute("metadata",JSON.stringify(o===void 0?qm(n,t):o.metadata(t)));const i=e.create_group("chroms");i.create_dataset({name:"name",data:t.contigs.map(f=>f.name)}),i.create_dataset({name:"length",data:Int32Array.from(t.contigs,f=>f.length),dtype:cn});const a=e.create_group("bins"),c=new Int32Array(t.nBins),l=new Int32Array(t.nBins),u=new Int32Array(t.nBins);for(let f=0;f<r;f++){const d=t.chromOffset[f],m=t.chromOffset[f+1],g=t.contigs[f].length;for(let w=d;w<m;w++){const p=(w-d)*s;c[w]=f,l[w]=p,u[w]=Math.min(p+s,g)}}a.create_dataset({name:"chrom",data:c,dtype:cn}),a.create_dataset({name:"start",data:l,dtype:cn}),a.create_dataset({name:"end",data:u,dtype:cn});const h=e.create_group("indexes");h.create_dataset({name:"chrom_offset",data:BigInt64Array.from(t.chromOffset,f=>BigInt(f)),dtype:rs}),h.create_dataset({name:"bin1_offset",data:Gm(t),dtype:rs})}function Gm(e){const t=new BigInt64Array(e.nBins+1);let n=0;for(let s=0;s<e.nBins;s++){for(;n<e.nnz&&e.bin1[n]===s;)n++;t[s+1]=BigInt(n)}return t}async function Hm(e,t,n,s,o){const r=e.create_group("pixels"),i=t.nnz,a=Math.min(Rs,Math.max(1,i)),c=r.create_dataset({name:"bin1_id",data:Ln(t.bin1,0,Math.min(a,i)),shape:[Math.min(a,i)],maxshape:[null],chunks:[a],dtype:rs,compression:"gzip"}),l=r.create_dataset({name:"bin2_id",data:Ln(t.bin2,0,Math.min(a,i)),shape:[Math.min(a,i)],maxshape:[null],chunks:[a],dtype:rs,compression:"gzip"}),u=r.create_dataset({name:"count",data:t.count.slice(0,Math.min(a,i)),shape:[Math.min(a,i)],maxshape:[null],chunks:[a],dtype:cn,compression:"gzip"});if(i>a){c.resize([i]),l.resize([i]),u.resize([i]);for(let h=a;h<i;h+=Rs){if(o.cancelled?.()===!0)return n+h;const f=Math.min(h+Rs,i);c.write_slice([[h,f]],Ln(t.bin1,h,f)),l.write_slice([[h,f]],Ln(t.bin2,h,f)),u.write_slice([[h,f]],t.count.slice(h,f)),o.onProgress?.(n+f,s,"writing pixels"),await new Promise(d=>setTimeout(d,0))}}return n+i}function Ln(e,t,n){const s=new BigInt64Array(Math.max(0,n-t));for(let o=0;o<s.length;o++)s[o]=BigInt(e[t+o]);return s}function qm(e,t){const n=e.header;return{"generated-by":`chromosomix ${os}`,"imported-from":"pairs","pairs-format":n.version,"pairs-sorted":n.sorted,"pairs-shape":n.shape,"pairs-indexed":e.indexed,"pairs-header":n.text,"records-binned":t.sum,...e.declaredRecords==null?{}:{"records-declared-by-index":e.declaredRecords},...t.skippedUnknownContig===0?{}:{"records-skipped-unknown-contig":t.skippedUnknownContig},...t.skippedBadPosition===0?{}:{"records-skipped-bad-position":t.skippedBadPosition},...t.clampedPosition===0?{}:{"positions-clamped":t.clampedPosition},...t.wasUnsorted?{"required-merge-pass":!0}:{},...t.truncated?{"source-truncated":!0}:{},...t.contigsWithoutCisContacts.length===0?{}:{"sequences-without-cis-contacts":t.contigsWithoutCisContacts},balanced:!1,note:"Raw counts, unbalanced. Run `cooler balance` to add a bins/weight column."}}class Ps{data=new Int32Array(65536);length=0;push(t){if(this.length===this.data.length){const n=new Int32Array(this.data.length*2);n.set(this.data),this.data=n}this.data[this.length++]=t}view(){return this.data.subarray(0,this.length)}}async function Wm(e,t={}){const n=[...e.chromnames],s=Array.from(e.coords.contigLengths),o=e.binsize,r=n.map((g,w)=>({name:g,length:s[w]})),i=No(r,o),a=i[i.length-1],c=new Ps,l=new Ps,u=new Ps;let h=!1;if(await e.storedPixels.scanAll({onChunk:g=>{if(t.cancelled?.()===!0)return h=!0,!1;for(let w=0;w<g.length;w++){const p=g.bin1[w],b=g.bin2[w],y=Math.round(g.count[w]);y<=0||p<0||b<0||p>=a||b>=a||(c.push(p<=b?p:b),l.push(p<=b?b:p),u.push(y))}return!0},...t.onProgress===void 0?{}:{onProgress:t.onProgress}}),h)return null;const f={binSize:o,contigs:r,chromOffset:i,nBins:a,bin1:c.view().slice(),bin2:l.view().slice(),count:u.view().slice(),nnz:u.length,sum:0,skippedUnknownContig:0,skippedBadPosition:0,clampedPosition:0,wasUnsorted:!0,truncated:!1,contigsWithoutCisContacts:[]},d=La(f);let m=0;for(let g=0;g<d.nnz;g++)m+=d.count[g];return{...d,sum:m}}function jm(e){return/\.matrix(\.gz)?$/i.test(e)}function is(e){const t=e.replace(/\.matrix(\.gz)?$/i,"").replace(/_iced$/i,"");return[`${t}_abs.bed`,`${t}_abs.bed.gz`]}const fn=9,Lt=10,Wa=13,ja=35,Qm=43,io=45,Ym=46,Ot=48,$e=57,Vm=69,Km=101;function Xm(e,t){const n=[],s=[],o=[0];let r=0,i=0,a=null,c=0,l=!1;const u=new TextDecoder,h=e.length;let f=0;for(;f<h;){if(e[f]===Lt||e[f]===Wa){f++;continue}if(e[f]===ja||Jm(e,f)){for(;f<h&&e[f]!==Lt;)f++;continue}const g=f;for(;f<h&&e[f]!==fn&&e[f]!==Lt;)f++;const w=u.decode(e.subarray(g,f));if(f<h&&e[f]===Lt)throw ve(t,i+1,"a row with one column");f++;const p=Ls(e,f);if(f=p.at,e[f]!==fn)throw ve(t,i+1,"a row with two columns");f++;const b=Ls(e,f);f=b.at;let y=null;if(e[f]===fn){f++;const x=Ls(e,f);if(f=x.at,!x.saw)throw new C("format",`${t} is a BED whose fourth column holds names rather than bin ids, so it describes features rather than a bin grid — drop it as a track instead. A HiC-Pro bin file numbers its bins 1…n, and is written as \`<prefix>_<res>_abs.bed\`.`,{label:t,row:i+1});y=x.value}for(;f<h&&e[f]!==Lt;)f++;f++;const A=b.value-p.value;if(A<=0)throw ve(t,i+1,`an interval of width ${A}`);if(A>r&&(r=A),i++,y!==null&&(l||(a=y),l=!0,c=y),n.length===0||n[n.length-1]!==w){if(n.includes(w))throw ve(t,i,`${JSON.stringify(w)} in two separate runs of rows`);n.push(w),s.push(b.value),o.push(i-1)}else s[s.length-1]=b.value}if(i===0)throw ve(t,0,"no rows at all");const d=Float64Array.from([...o.slice(1),i]);if(d.length!==n.length+1)throw ve(t,i,`${n.length} sequences but ${d.length} offsets`);const m=Zm(n.length,d,s,r);if(a!==null&&(a!==1||c!==i))throw new C("format",`${t} is not a HiC-Pro bin file: its bin ids run ${a}…${c} over ${i} rows, and HiC-Pro numbers them 1…n in row order. If this is an ordinary BED, it describes features rather than a bin grid — drop it as a track instead.`,{label:t,firstId:a,lastId:c,rows:i});return{names:n,lengths:Float64Array.from(s),chromOffset:d,nBins:i,binsize:m?r:null,fixed:m}}function Zm(e,t,n,s){if(s<=0)return!1;for(let o=0;o<e;o++){const r=t[o+1]-t[o],i=(r-1)*s;if(n[o]<=i||n[o]>r*s)return!1}return!0}function Jm(e,t){const n="track";if(t+n.length>e.length)return!1;for(let s=0;s<n.length;s++)if(e[t+s]!==n.charCodeAt(s))return!1;return!0}function ve(e,t,n){return new C("format",`${e} is not a HiC-Pro bin file: ${n}${t>0?` at row ${t}`:""}. The file beside a \`.matrix\` is \`chrom  start  end  binID\`, one row per bin of the whole genome, and HiC-Pro writes it as \`<prefix>_<res>_abs.bed\`.`,{label:e,row:t})}const tg=()=>{},eg=()=>!1;async function ng(e,t,n,s={}){const o=e.length;let r=0;for(let B=0;B<o;B++)e[B]===Lt&&r++;if(o>0&&e[o-1]!==Lt&&r++,r===0)throw new C("format",`${n} holds no pixels. A HiC-Pro matrix is \`binA  binB  count\`, one row per non-zero pixel.`,{label:n});const i=new Int32Array(r),a=new Int32Array(r),c=new Float32Array(r),l=new Uint8Array(r),u={out:0,line:0,sawUpper:!1,sawLower:!1};let h=0,f=0;const d=s.onProgress??tg,m=s.cancelled??eg;for(;f<o;){const B=og(e,Math.min(o,f+sg));if(f=rg(e,f,B,t,n,i,a,c,l,u),await St(),m())throw lg();d(u.out,r)}const g=u.out,{sawUpper:w,sawLower:p}=u,b=w&&p?"mixed":p?"lower":"upper",y=ag(a,g,t),{order:A,offsets:x}=cg(i,y,g,t),E=new Int32Array(g),S=new Int32Array(g),v=new Float32Array(g),I=new Uint8Array(g);for(let B=0;B<g;B++){const z=A[B];E[B]=i[z],S[B]=a[z],v[B]=c[z],I[B]=l[z]}const N=ig(E,S,v,I,x,t);for(let B=0;B<N.nnz;B++)h+=v[B];return{bin1:E.subarray(0,N.nnz),bin2:S.subarray(0,N.nnz),count:v.subarray(0,N.nnz),binOffset:N.binOffset,nnz:N.nnz,sum:h,observed:b==="mixed"&&N.mirrored>0?"complete":b}}const sg=1<<23;function og(e,t){let n=t;for(;n<e.length&&e[n]!==Lt;)n++;return Math.min(e.length,n+1)}function rg(e,t,n,s,o,r,i,a,c,l){let u=t,h=l.out,f=l.line,d=l.sawUpper,m=l.sawLower;for(;u<n;){if(e[u]===Lt||e[u]===Wa){u++;continue}if(e[u]===ja){for(;u<n&&e[u]!==Lt;)u++;continue}f++;let g=0,w=!1;for(;u<n;){const v=e[u];if(v<Ot||v>$e)break;g=g*10+(v-Ot),w=!0,u++}if(!w||e[u]!==fn)throw Ds(o,f,s);u++;let p=0,b=!1;for(;u<n;){const v=e[u];if(v<Ot||v>$e)break;p=p*10+(v-Ot),b=!0,u++}if(!b||e[u]!==fn)throw Ds(o,f,s);u++;let y=0,A=!1,x=!1;for(e[u]===io&&(x=!0,u++);u<n;){const v=e[u];if(v<Ot||v>$e)break;y=y*10+(v-Ot),A=!0,u++}if(e[u]===Ym){u++;let v=.1;for(;u<n;){const I=e[u];if(I<Ot||I>$e)break;y+=(I-Ot)*v,v/=10,A=!0,u++}}if(e[u]===Km||e[u]===Vm){const v=u;u++;let I=1;e[u]===io?(I=-1,u++):e[u]===Qm&&u++;let N=0,B=!1;for(;u<n;){const z=e[u];if(z<Ot||z>$e)break;N=N*10+(z-Ot),B=!0,u++}B?y*=10**(N*I):u=v}if(!A)throw Ds(o,f,s);for(x&&(y=-y);u<n&&e[u]!==Lt;)u++;u++;const E=g-1,S=p-1;if(E<0||S<0||E>=s||S>=s)throw new C("format",`${o} names bin ${g} × ${p} on line ${f}, and the bin file has ${s} bins numbered 1…${s}. The two halves of the pair are for different resolutions, or for different genomes.`,{label:o,line:f,bin1:g,bin2:p,nBins:s});E<S&&(d=!0),E>S&&(m=!0),r[h]=E<=S?E:S,i[h]=E<=S?S:E,a[h]=y,c[h]=E<=S?0:1,h++}return l.out=h,l.line=f,l.sawUpper=d,l.sawLower=m,u}function ig(e,t,n,s,o,r){let i=0,a=0;const c=new Float64Array(r+1);for(let l=0;l<r;l++){const u=o[l],h=o[l+1];c[l]=i;let f=-1;for(let d=u;d<h;d++){if(d>u&&t[d]===t[d-1]){if(s[d]!==f){a++,f=-2;continue}n[i-1]+=n[d];continue}f=s[d],e[i]=l,t[i]=t[d],n[i]=n[d],i++}}return c[r]=i,{nnz:i,binOffset:c,mirrored:a}}function ag(e,t,n){const s=new Int32Array(n+1);for(let r=0;r<t;r++)s[e[r]+1]++;for(let r=0;r<n;r++)s[r+1]+=s[r];const o=new Int32Array(t);for(let r=0;r<t;r++)o[s[e[r]]++]=r;return o}function cg(e,t,n,s){const o=new Float64Array(s+1);for(let a=0;a<n;a++)o[e[a]+1]++;for(let a=0;a<s;a++)o[a+1]+=o[a];const r=Float64Array.from(o),i=new Int32Array(n);for(let a=0;a<n;a++){const c=t[a];i[r[e[c]]++]=c}return{order:i,offsets:o}}function Ls(e,t){let n=0,s=!1,o=1;for(e[t]===io&&(o=-1,t++);t<e.length;){const r=e[t];if(r<Ot||r>$e)break;n=n*10+(r-Ot),s=!0,t++}return{value:n*o,at:t,saw:s}}function Ds(e,t,n){return new C("format",`${e} is not a HiC-Pro matrix: line ${t} is not \`binA  binB  count\`. The bin file beside it has ${n} bins, and the matrix names pairs of them, tab-separated, one pixel per line.`,{label:e,line:t,nBins:n})}function lg(){const e=new Error("cancelled");return e.name="AbortError",e}async function ug(e,t,n={}){const s=await wg(t);return s===null?await hg(e,t,n):await mg(e,t,s,n)}async function hg(e,t,n){const s=n.detached===!0?await Qd(t):await ro(t,{...n.report===void 0?{}:{onProgress:(r,i)=>n.report?.(r,i,"downloading")},...n.cancelled===void 0?{}:{cancelled:n.cancelled},...n.report===void 0||!di(e)?{}:{onRead:(r,i)=>n.report?.(i,0,`listing cells · ${r.toLocaleString()} reads`)}}),o=t.kind==="remote"&&t.reading!==void 0;di(e)&&n.report?.(0,0,"listing cells");try{return{mc:await et.open(e,s,{...o?{listingAgreed:!0}:{},...n.metacool===void 0?{}:{metacool:n.metacool}}),source:s}}catch(r){const i=n.binning;if(i===void 0||!(r instanceof C)||r.code!=="pairs-binning-needed")throw r;return{mc:await fg(e,t,s,i,n),source:s}}}async function fg(e,t,n,s,o){const r=await Ua(n,()=>Ta(t)),i=await Ga(n,r,{base:s.base,rungs:s.rungs,oneBased:s.oneBased??!0,...o.report===void 0?{}:{onProgress:(c,l,u)=>o.report?.(c,l,u??"binning records")},...o.cancelled===void 0?{}:{cancelled:o.cancelled}});if(i===null)throw dg();const a=i.tables.get(i.rungs[0]);if(a===void 0)throw new C("format",`${e} imported no pixel table.`);return et.fromPairs({uri:e,header:i.header,pixels:a,rungs:i.rungs,indexed:i.indexed,declaredRecords:i.declaredRecords})}function dg(){const e=new Error("open cancelled");return e.name="AbortError",e}async function mg(e,t,n,s){const o=ao(n),r=ao(t),i=u=>({...s.report===void 0?{}:{onProgress:(h,f)=>s.report?.(h,f,u)},...s.cancelled===void 0?{}:{cancelled:s.cancelled}}),a=await ai(n,i("reading the bins")),c=Xm(a,o);await yg(t,r,c.nBins);const l=await ai(t,i("downloading the matrix"));return gg(e,{bytes:l,name:r},c,o,a.length,s)}async function gg(e,t,n,s,o,r={}){const i=await ng(t.bytes,n.nBins,t.name,{...r.cancelled===void 0?{}:{cancelled:r.cancelled},...r.report===void 0?{}:{onProgress:(c,l)=>r.report?.(c,l,"reading pixels")}});return{mc:et.fromHicPro(e,{bins:n,pixels:i,matrixName:t.name,binsName:s}),source:Mg(t.name,o+t.bytes.length)}}async function wg(e){const t=ao(e);if(!jm(t))return null;if(e.bins!==void 0)return e.bins;if(e.kind==="remote"){const n=await pg(e.url,e.credential,e.headers);if(n!==null)return n}throw new C("hicpro-no-bins",`${t} is a HiC-Pro matrix, which is half of a contact map: the bin file beside it — ${is(t).join(" or ")} — is what says which genomic interval each bin id means, and there are no coordinates without it. Drop the two together, pick the matrix out of a connected folder so its bin file comes with it, or name the bin file on the URL as \`<matrix>#bins=<url>\`.`,{matrix:t,wanted:is(t)})}async function pg(e,t,n){if(_o(e))return null;const s=e.lastIndexOf("/"),o=s<0?"":e.slice(0,s+1),r=e.slice(s+1),i=is(r).map(c=>`${o}${c}`);if(o.includes("/iced/"))for(const c of is(r))i.push(`${o.replace("/iced/","/raw/")}${c}`);const a={...t===void 0?{}:{credential:t},...n===void 0?{}:{headers:n}};for(const c of i)try{if((await fetch(c,{method:"HEAD",headers:me({url:c,method:"HEAD",...a})})).ok)return{kind:"remote",url:c,...a}}catch{}return null}function di(e){return/\.scool(\.gz)?(\?|#|$)/i.test(e)}const bg=200<<20;async function yg(e,t,n){if(e.reading!==void 0)return;const s=await Ag(e);if(s===null||s<=bg)return;const o=Math.round(s/15);throw new C("hicpro-load-cost",`${t} is ${Math.round(s/(1<<20))} MB of text, and a HiC-Pro matrix has no index — so the whole of it is read and turned into about ${o.toLocaleString()} pixels over ${n.toLocaleString()} bins before anything can be drawn. That is the only cost: afterwards every region is instant and panning is free.`,{matrix:t,bytes:s,pixels:o,nBins:n})}async function Ag(e){if(e.kind==="local")return e.file.size;if(_o(e.url))return null;try{const t=await fetch(e.url,{method:"HEAD",headers:me({url:e.url,method:"HEAD",...e.credential===void 0?{}:{credential:e.credential},...e.headers===void 0?{}:{headers:e.headers}})}),n=Number(t.headers.get("Content-Length")??Number.NaN);return Number.isFinite(n)?n:null}catch{return null}}function ao(e){const t=e.kind==="local"?e.file.name:e.url;return t.split(/[\\/]/).pop()?.split(/[?#]/)[0]??t}function Mg(e,t){return{id:e,size:t,isRemote:!1,mount:()=>Promise.resolve(e),readBytes(){throw new C("unsupported",`${e} was read whole and parsed at open; there are no bytes left to read from it. A read reaching here is a code path that bypassed the parsed arrays.`,{id:e})},stats:()=>({requests:1,bytes:t}),close:()=>{}}}const xg=200,Sg=3e3,Ig=3e4,Eg=1e3;function vg(e=xg,t=Sg){const n=[];let s=performance.now();const o=setInterval(()=>{const r=performance.now(),i=r-s;for(s=r,i<Ig?n.push({at:r,span:i,late:Math.max(0,i-e)}):n.length=0;n.length>0&&r-n[0].at>t;)n.shift()},e);return{busy(){if(n.length<3)return 0;let r=0,i=0;for(const a of n)r+=a.span,i+=a.late;return r<=0?0:Math.min(1,i/r)},reset(){n.length=0,s=performance.now()},stop(){clearInterval(o)}}}const Cg=250,$g=50;class Ng{constructor(t=()=>performance.now(),n=s=>new Promise(o=>setTimeout(o,s))){this.now=t,this.sleep=n}reading=0;quietSince=Number.NEGATIVE_INFINITY;begin(){this.reading+=1;let t=!1;return()=>{t||(t=!0,this.reading-=1,this.quietSince=this.now())}}async quiet(t){for(await St();t?.()!==!0&&(this.reading>0||this.now()-this.quietSince<Cg);)await this.sleep($g)}}const Qa=self;ae().catch(()=>{});const Bg=1e6,mi=3;let Ct=null,Ya=0,Va={requests:0,bytes:0};const dt=new Set,co=new Ng;function rt(){if(Ct===null)throw new Error("no file is open in the reader worker");return Ct}async function He(e){const t=rt();if(e===void 0||e===""||!t.mc.entries.includes(e))return t.mc;const n=t.rungs.get(e);if(n!==void 0)return Us(t,e),n;if(t.pairs!==null){const i=t.pairs.tables.get(Number(e));if(i===void 0)return t.mc;const a=et.fromPairs({uri:t.mc.uri,header:t.pairs.header,pixels:i,rungs:t.pairs.rungs,indexed:t.pairs.indexed,declaredRecords:t.pairs.declaredRecords}),c=gi(t,a);for(wi(t,c),t.rungs.set(e,c),Us(t,e);t.recent.length>mi;){const l=t.recent.pop();if(l===void 0)break;t.rungs.get(l)?.close(),t.rungs.delete(l)}return c}const s=t.mc.entryGroup===""?"entries":t.mc.entryGroup,{path:o}=Mt(t.mc.uri);let r;try{r=await et.open(`${o}::${s}/${e}`,t.source,t.metacool===void 0?{}:{metacool:t.metacool})}catch{return t.mc}for(r=gi(t,r),wi(t,r),t.rungs.set(e,r),Us(t,e);t.recent.length>mi;){const i=t.recent.pop();if(i===void 0)break;t.rungs.get(i)?.close(),t.rungs.delete(i)}return r}function gi(e,t){if(e.lens===null)return t;const{map:n,refusal:s}=et.withLens(t,e.lens);return s===null?n:(t.close(),e.mc)}function wi(e,t){e.resample!==null&&t.resample(e.resample).catch(()=>{})}function Us(e,t){e.recent=[t,...e.recent.filter(n=>n!==t)]}function Ka(e){if(e!==null){for(const t of e.rungs.values())t.close();e.rungs.clear(),e.recent=[]}}function Gs(e,t,n){return e===t?n:Fl(e.coords,t.coords,n)}function ce(e,t=[]){Qa.postMessage(e,t)}function ne(e){return{cancelled:()=>dt.has(e),onProgress:(t,n,s)=>ce(s===void 0?{type:"progress",id:e,done:t,total:n}:{type:"progress",id:e,done:t,total:n,note:s})}}function $t(){const e=new Error("cancelled");return e.name="AbortError",e}async function Og(e,t){const n=await Ua(t,()=>Ta(e.source)),s=e.binning;if(s===void 0){const o={contigs:n.header.contigs.map(r=>({...r})),genomeLength:n.genomeLength,records:n.records,indexed:n.index!==null,assembly:n.header.assembly,sorted:n.header.sorted,sourceBytes:n.sourceBytes,suggestedBase:$m(n)};throw new C("pairs-binning-needed","This is a .pairs file: a list of contacts with no resolution of its own. Choose a bin size to build a map at.",o)}return Ga(t,n,{base:s.base,rungs:s.rungs,oneBased:s.oneBased??!0,...ne(e.id)})}function kg(e,t,n){const s=e.tables.get(e.rungs[0]),o=s.orientation??null;return{binning:n,orientation:o===null?null:{edges:o.edges,counts:o.counts,total:o.total},stats:s.stats??null,base:e.rungs[0],rungs:e.rungs,records:s.sum,nnz:s.nnz,indexed:e.indexed,skippedUnknownContig:s.skippedUnknownContig,skippedBadPosition:s.skippedBadPosition,clampedPosition:s.clampedPosition,requiredMerge:s.wasUnsorted,truncated:s.truncated,sequencesWithoutCisContacts:s.contigsWithoutCisContacts,download:t}}async function _g(e){const t=rt();if(t.pairs===null)throw new C("unsupported","This map was not imported from a .pairs file, so there is nothing to write: it is already a file on disk or on a bucket.",{layout:t.mc.layout.kind});const n=await qa(t.pairs,ne(e));if(n===null)throw $t();return{bytes:n,filename:_m(t.mc.uri),rungs:t.pairs.rungs}}const pi=6e7;async function Tg(e,t){const n=rt(),s=n.mc.unlensed??n.mc,o=ne(e),i=(s.entries.length>0?[...s.entries]:[""]).map(w=>({name:w,size:w===""?s.binsize:Number(w)})).sort((w,p)=>w.size-p.size),a=new Map,c=[];let l=0;for(const{name:w,size:p}of[...i].reverse()){const b=w===""?s:await Fg(n,w);if(b===null){c.push({rung:p,why:"it would not open"});continue}try{const y=b.nnz??0;if(l+y>pi){c.push({rung:p,why:`${y.toLocaleString("en-US")} pixels would pass the budget of ${pi.toLocaleString("en-US")}`});continue}const{map:A,refusal:x}=et.withLens(b,t);if(x!==null)throw new C("unsupported",x,{});const E=await Wm(A,{cancelled:o.cancelled,onProgress:(S,v)=>o.onProgress(S,v,`lifting the ${p.toLocaleString("en-US")} bp rung`)});if(E===null)throw $t();a.set(p,E),l+=E.nnz}finally{b!==s&&b.close()}}const u=[...a.keys()].sort((w,p)=>w-p);if(u.length===0)throw new C("unsupported","No rung of this map could be lifted within the budget.",{});const h=a.get(u[0]),f={version:"",assembly:null,sorted:null,shape:"upper triangle",contigs:h.contigs,columns:{chrom1:1,pos1:2,chrom2:3,pos2:4,strand1:-1,strand2:-1},text:""},d=await qa({header:f,rungs:u,tables:a,indexed:!1,declaredRecords:null},{...o,about:{generatedBy:`chromosomix ${os} (lifted through an edit of the reference; unbalanced)`,metadata:w=>({"generated-by":`chromosomix ${os}`,"lifted-from":n.mc.uri,"lifted-through":t.history.slice(0,t.cursor).map(p=>p.step),"contacts-written":w.sum,balanced:!1,note:"Raw counts through an edit of the reference: bins moved whole, a stretch set aside left out, a duplicated one written at each copy. Run `cooler balance` to add a bins/weight column."})}});if(d===null)throw $t();const m=(Mt(n.mc.uri).path.split("/").pop()??"map").replace(/\.(m?m?(meta)?cool|hic|pairs(\.b?gz)?)$/i,""),g=t.original.genome===void 0?"":`.${t.original.genome}`;return{bytes:d,filename:`${m}${g}.edited.mcool`,rungs:u,contacts:h.sum,skipped:c}}async function Fg(e,t){if(e.pairs!==null){const r=e.pairs.tables.get(Number(t));return r===void 0?null:et.fromPairs({uri:e.mc.uri,header:e.pairs.header,pixels:r,rungs:e.pairs.rungs,indexed:e.pairs.indexed,declaredRecords:e.pairs.declaredRecords})}const n=e.mc.unlensed??e.mc,s=n.entryGroup===""?"entries":n.entryGroup,{path:o}=Mt(n.uri);try{return await et.open(`${o}::${s}/${t}`,e.source,e.metacool===void 0?{}:{metacool:e.metacool})}catch{return null}}function zg(e,t){if(e?.pairs==null)return null;const n=km(e.pairs,e.mc.uri,t);return n===null?null:{pairs:e.pairs,size:n}}function gs(e){let t=0;return(n,s,o)=>{const r=Date.now();r-t<50&&n<s||(t=r,ce({type:"progress",id:e,done:n,total:s,note:o}))}}async function Rg(e){const t=zg(Ct,e.uri);Ka(Ct),t===null&&Ct?.mc.close(),Ct=null,dt.clear();const s={report:gs(e.id),cancelled:()=>dt.has(e.id),...e.metacool===void 0?{}:{metacool:e.metacool}};let o,r,i=t?.pairs??null;if(t!==null)r=await ro(e.source),o=et.fromPairs({uri:e.uri,header:t.pairs.header,pixels:t.pairs.tables.get(t.size),rungs:t.pairs.rungs,indexed:t.pairs.indexed,declaredRecords:t.pairs.declaredRecords});else try{({mc:o,source:r}=await ug(e.uri,e.source,s))}catch(l){if(!(l instanceof C)||l.code!=="pairs-binning-needed")throw l;if(r=await ro(e.source),i=await Og(e,r),i===null)throw $t();o=et.fromPairs({uri:e.uri,header:i.header,pixels:i.tables.get(i.rungs[0]),rungs:i.rungs,indexed:i.indexed,declaredRecords:i.declaredRecords})}let a=null,c=null;if(e.edit!==void 0){const l=et.withLens(o,e.edit);o=l.map,c=l.refusal,l.refusal===null&&(a=e.edit)}return Ct={mc:o,source:r,sourceKind:e.source.kind,rungs:new Map,recent:[],pairs:i,resample:null,lens:a,...e.metacool===void 0?{}:{metacool:e.metacool}},{...i===null||e.binning===void 0?{}:{pairs:kg(i,e.binning.download===!0,e.binning)},...e.edit===void 0?{}:{edit:{refusal:c}},uri:o.uri,layout:o.layout,info:o.info,metadata:o.metadata,binsize:o.binsize,shape:o.shape,nGenomes:o.nGenomes,nContigs:o.nContigs,nBins:o.nBins,unassigned:o.unassignedStats(),displayExtent:o.displayBinExtent(),entries:o.entries,entryGroup:o.entryGroup,cells:o.cells,activeCells:o.activeCells,cellNnz:o.cells.length>0&&!(e.source.kind==="remote"&&e.source.reading==="fine")?o.nnz:null,hasGenomes:o.hasGenomes,hasWeights:o.hasWeights,scoreColumns:o.scoreColumns,sourceBytes:r.size,contacts:o.declaredContacts,sourceKind:e.source.kind}}function Pg(){const{mc:e}=rt(),t=e.fullGenomes();if(t===null)return{table:{columns:[],length:0,data:{}},display:new Int32Array(0),density:new Float64Array(0)};const n=Int32Array.from(e.displayGenomes()),s=e.genomeDensities();return{table:ko(t),display:n,density:s}}function Lg(){return{table:ko(rt().mc.fullContigs())}}function Dg(){const{mc:e}=rt(),t=e.cellTable(),n=new Set(e.activeCells),s=e.cells,o=[];for(let r=0;r<s.length;r++)n.has(s[r])&&o.push(r);return{table:ko(t),selected:Int32Array.from(o)}}function Ug(e){const{mc:t}=rt();return t.selectCells(e.names),{names:t.activeCells,nnz:t.nnz??0,scoreColumns:t.scoreColumns}}function Gg(){return{columns:rt().mc.binColumns()}}function Hg(e){const{mc:t}=rt(),n=Math.max(0,Math.min(Math.trunc(e.from),t.nBins)),s=Math.max(n,Math.min(Math.trunc(e.to),t.nBins)),o=t.binColumn(e.column,n,s);return{column:e.column,from:n,to:s,...Array.isArray(o)?{text:o}:{values:o}}}function qg(e,t,n=!1){const s=n&&e.hasGenomes;return{nrows:t.nrows,ncols:t.ncols,values:t.values,rowExtent:t.rowExtent,colExtent:t.colExtent,rowGroups:Lr(e,t.rowExtent),colGroups:Lr(e,t.colExtent),...s?{rowGenomes:Dr(e,t.rowExtent),colGenomes:Dr(e,t.colExtent)}:{},level:"bin"}}function Xa(e,t){return e[0]===t[0]&&e[1]===t[1]?un.binSelection:un.range}async function Wg(e){const t=rt().mc,n=Math.max(256,Math.min(Ks,Math.trunc(e.cells??Ks))),s=t.unlensed??t;let o;if(e.contigs!==void 0){const S=new Map(s.chromnames.map((v,I)=>[v,I]));if(o=[...new Set(e.contigs.map(v=>S.get(v)).filter(v=>v!==void 0))].sort((v,I)=>v-I),o.length===0)throw new C("unsupported","None of the sequences the stage asked for are in this file.")}const r=Jg(s,n,o),i=await He(r),a=i.unlensed??i,c=Dl(a.coords,n,o);let l=null;try{l=a.store.binOffsets()}catch{l=null}const u=Ul(a.coords,l,o),h=c===null?null:Math.max(c,u);if(h===null)throw new C("unsupported",`The stage draws the whole assembly at ${n.toLocaleString("en-US")} cells a side, each inside one sequence, and this one has ${(o?.length??a.coords.nContigs).toLocaleString("en-US")} sequences.`);const f=Pl(a.coords,h,o),d=e.balance===!0&&a.hasWeights,m=Zg(a,l,o);ce({type:"progress",id:e.id,done:0,total:1,note:`${m===null?"every stored pixel":`${m.toLocaleString("en-US")} stored pixels`} at ${fc(a.binsize)}`+(h>1?`, ${h} bins a cell`:"")});const g=await a.picture(f,{balance:d,...e.value===void 0?{}:{value:e.value},...e.method===!0?{gather:bf}:{},...ne(e.id)});if(g===null||dt.has(e.id))throw $t();const{vmin:w,vmax:p}=Zl(g.histogram,g.quantizer),b=g.contacts,y=b===void 0?null:xf(b,d),A=b===void 0||y===null?void 0:{contacts:b,expected:y,corners:Of(b,y)},x=e.keep===!0&&A!==void 0,E=rt();return x&&(E.stageMethod={picture:e.id,...A}),{rung:i===t?null:r??null,binsize:a.binsize*h,stride:h,n:f.n,sequences:(o??a.chromnames.map((S,v)=>v)).map((S,v)=>({name:a.chromnames[S],length:a.coords.contigLengths[S],firstCell:f.offsets[v],cells:f.offsets[v+1]-f.offsets[v]})),levels:g.levels,low:g.quantizer.low,high:g.quantizer.high,vmin:w,vmax:p,balanced:d,pixels:g.pixels,least:Gl(a.coords,l,a.binsize,o),...A===void 0?{}:x?{methodKept:e.id}:{method:A}}}const jg=4e6;async function Qg(e){const t=rt(),n=t.mc.unlensed??t.mc,s=Za(n),o=s.filter(w=>w.size<=e.binsize),r=o.length>0?o[o.length-1]:s[0];if(r===void 0||!(r.size<e.coarser))return null;const i=`${r.name}|${e.key}`;if(t.stageWindowMap?.key!==i){const w=r.size===n.binsize?n:await He(r.name),p=w.unlensed??w,{map:b,refusal:y}=et.withLens(p,e.edit);if(y!==null)throw new C("unsupported",y);t.stageWindowMap={key:i,map:b}}const a=t.stageWindowMap.map,c=new Map(a.chromnames.map((w,p)=>[w,p])),l=a.coords.chromOffset,u=a.binsize,h=w=>{const p=c.get(w.from.sequence),b=c.get(w.to.sequence);if(p===void 0||b===void 0)return null;const y=Math.min(l[p+1]-1,l[p]+Math.floor(Math.max(0,w.from.bp)/u)),A=Math.min(l[b+1],l[b]+Math.ceil(Math.max(0,w.to.bp)/u));return A>y?[y,A]:null},f=h(e.rows),d=h(e.cols);if(f===null||d===null||(f[1]-f[0])*(d[1]-d[0])>jg)return null;const m=await a.matrix({rows:f,cols:d,balance:e.balance&&a.hasWeights}),g=([w,p])=>{const b=[];for(let y=0;y<a.chromnames.length;y++){const A=Math.max(w,l[y]),x=Math.min(p,l[y+1]);x>A&&b.push({sequence:a.chromnames[y],firstBin:A-l[y],count:x-A,at:A-w})}return b};return{binsize:u,rows:g(m.rowExtent),cols:g(m.colExtent),values:m.values,ncols:m.ncols}}function Za(e){return e.entryGroup==="resolutions"?e.entries.map(t=>({name:t,size:Number(t)})).filter(t=>Number.isInteger(t.size)&&t.size>0).sort((t,n)=>t.size-n.size):[{name:"",size:e.binsize}]}const Yg=4096;async function Vg(e){const t=rt(),n=t.mc.unlensed??t.mc,s=Za(n),o=Df(s.map(d=>d.size),e.cell,e.least);if(o.length===0)return e.points.map(()=>null);const r=au(e.edit);t.refineMaps?.fingerprint!==r&&(t.refineMaps={fingerprint:r,maps:new Map});const i=t.refineMaps.maps,a=t.refinePlaced??=new Map;a.size>Yg&&a.clear();const c=pn.of(e.edit),l=async d=>{const m=s.find(w=>w.size===d);if(m===void 0)return null;let g=i.get(m.name);if(g===void 0){const w=m.size===n.binsize?n:await He(m.name),{map:p,refusal:b}=et.withLens(w.unlensed??w,e.edit);if(b!==null)throw new C("unsupported",b);g=p,i.set(m.name,g)}return g},u=async(d,m,g,w)=>{if(dt.has(e.id))throw $t();const p=await l(w),b=p===null?-1:p.chromnames.indexOf(d);if(p===null||b<0)return null;const y=p.coords.chromOffset[b],A=[y+m,y+g],x=await p.matrix({rows:A,cols:A,balance:e.balance&&p.hasWeights});return x.nrows===g-m&&x.ncols===g-m?{n:g-m,values:x.values}:null},h=(Math.ceil(va*e.cell/o[0])+3*Oo+1)*o[0],f=[];for(const d of e.points){if(dt.has(e.id))throw $t();const m=c.lengthOf(d.sequence);if(m===null){f.push(null);continue}const g=d.bp,w=Math.max(0,g-h),p=Math.min(m,g+h),b=c.piecesIn(d.sequence,w,p).map(({offset:x,piece:E})=>`${x-g}:${E.sequence}:${E.start}:${E.end}:${E.strand}`).join(";"),y=[e.balance,e.cell,o.join(","),o.map(x=>g%x).join(","),w-g,p-g,b].join("|");let A=a.get(y);if(A===void 0){const x=await Hf(d,m,e.cell,o,u);A=x===null?null:{delta:x.bp-g,binsize:x.binsize,support:x.support},a.set(y,A)}f.push(A===null?null:{bp:g+A.delta,binsize:A.binsize,support:A.support})}return f}function Kg(e){const t=rt().stageMethod;if(t===void 0||t.picture!==e.picture)throw new C("unsupported","The picture these suggestions were asked of has been read again; they are counted against the new one.");const n=Bo.of(pn.of(e.edit),e.layout);return Vf({contacts:t.contacts,expected:t.expected,corners:t.corners,grid:n,...e.weights===void 0?{}:{weights:e.weights},...e.evidence===void 0?{}:{evidence:e.evidence}})}async function Xg(e){const t=rt().mc,n=t.unlensed??t;if(!n.hasGenomes)throw new C("unsupported","Only a metagenome has genomes a contig could belong to.");const s=n.coords.nContigs,o=new Map(n.chromnames.map((w,p)=>[w,p])),r=new Uint8Array(s);for(const w of e.contigs){const p=o.get(w);p!==void 0&&(r[p]=1)}const i=new Int32Array(n.nBins);for(let w=0;w<s;w++){const[p,b]=n.coords.contigBinExtent(w);i.fill(w,p,b)}const a=n.contigGenomeIds,c=n.genomeNames,l=new Float64Array(s),u=new Float64Array(s),h=new Map;for(let w=0;w<s;w++)r[w]===1&&h.set(w,new Float64Array(c.length));const f=ne(e.id);let d=0;if(await n.store.scanAll({onChunk:w=>{if(f.cancelled())return!1;for(let p=0;p<w.length;p++){const b=i[w.bin1[p]],y=i[w.bin2[p]];if(b===y)continue;const A=w.count[p];if(A>0){if(l[b]+=A,l[y]+=A,r[y]===1&&(u[b]+=A),r[b]===1){u[y]+=A;const x=h.get(b);x!==void 0&&a[y]>=0&&(x[a[y]]+=A)}if(r[y]===1){const x=h.get(y);x!==void 0&&a[b]>=0&&(x[a[b]]+=A)}}}return d+=w.length,!0},onProgress:(w,p)=>f.onProgress(w,p,"reading every contact for where the contigs belong")}),f.cancelled())throw $t();const m=[];for(const[w,p]of h){const b=[...p].map((y,A)=>({genome:c[A],contacts:y})).filter(y=>y.contacts>0).sort((y,A)=>A.contacts-y.contacts).slice(0,6);m.push({contig:n.chromnames[w],total:l[w],own:u[w],partners:b})}const g=[];for(let w=0;w<s;w++){if(r[w]===1||u[w]<3)continue;const p=a[w];g.push({contig:n.chromnames[w],genome:p>=0?c[p]:"__unbinned__",length:n.coords.contigLengths[w],contacts:u[w],total:l[w]})}return g.sort((w,p)=>p.contacts/p.total-w.contacts/w.total||p.contacts-w.contacts),{inside:m,outside:g.slice(0,100),pixels:d}}function Zg(e,t,n){if(n===void 0)return e.nnz??(t===null?null:t[t.length-1]);if(t===null)return null;let s=0;for(const o of n){const[r,i]=e.coords.contigBinExtent(o);s+=t[i]-t[r]}return s}function Jg(e,t,n){if(e.entryGroup!=="resolutions")return;const s=e.coords.contigLengths,o=n??Array.from({length:s.length},(c,l)=>l),r=c=>{let l=0;for(const u of o)l+=Math.ceil(s[u]/c);return l},i=e.entries.map(c=>({name:c,size:Number(c)})).filter(c=>Number.isInteger(c.size)&&c.size>0).sort((c,l)=>c.size-l.size);if(i.length===0)return;const a=i.find(c=>r(c.size)<=t)??i[i.length-1];return a.size===e.binsize?void 0:a.name}async function t0(e){const t=rt().mc,n=await He(e.rung),s=Gs(t,n,e.cols??e.rows),o=Gs(t,n,e.rows),r=tc(e.binsPerCell,e.contigsPerCell),i={rows:e.rows,cols:e.cols??e.rows};if(e.wrap!==void 0){const l=Gs(t,n,e.wrap);if(Hr(o,l)||Hr(s,l))return Dn(n,t,i,await fd(n,e,o,s,l,e0(n,e.id,e.budgetBytes)))}if(r.binsPerCell>1||r.contigsPerCell>1)return Dn(n,t,i,await bi(n,e,Oe(n,o,r),Oe(n,s,r),r));const a=Ja(n,o,s,e.budgetBytes);if(a!==null)return Dn(n,t,i,await bi(n,e,Oe(n,o,a),Oe(n,s,a),a));const c=await n.matrix({rows:o,cols:s,...e.balance===!0?{balance:!0}:{},...e.value===void 0?{}:{value:e.value},...e.budgetBytes===void 0?{}:{budgetBytes:e.budgetBytes}},Xa(o,s));return Dn(n,t,i,qg(n,c,e.genomes===!0))}function e0(e,t,n){return{planFor:(s,o,r)=>{const i=a=>{const c=Math.max(1,Math.min(a,s[1]-s[0]));return[s[0],s[0]+c]};return Ja(e,i(o),i(r),n)},snap:(s,o)=>Oe(e,s,o),hint:(s,o)=>Xa(s,o),throwIfCancelled:()=>{if(dt.has(t))throw $t()},hooks:ne(t)}}function Dn(e,t,n,s){return e===t?s:{...s,binsize:e.binsize,source:{rows:n.rows,cols:n.cols}}}async function bi(e,t,n,s,o){const r=t.id,i=await e.pooledMatrix({rows:n,cols:s,...t.balance===!0?{balance:!0}:{},...t.value===void 0?{}:{value:t.value}},o,ne(r));if(dt.has(r))throw $t();const a=l=>bn(l,u=>e.chromnames[u]??String(u),void 0,u=>e.coords.contigLengths[u],u=>e.coords.contigStartBin(u)),c=t.genomes===!0&&e.hasGenomes;return{nrows:i.nrows,ncols:i.ncols,values:i.values instanceof Float32Array?i.values:Float32Array.from(i.values),rowExtent:n,colExtent:s,rowGroups:lo(e,yi(e,a(i.rowIds),n,i.binsPerCell),i.rowMembers),colGroups:lo(e,yi(e,a(i.colIds),s,i.binsPerCell),i.colMembers),...c?{rowGenomes:dn(e,i.rowIds),colGenomes:dn(e,i.colIds)}:{},level:"bin",binsPerCell:i.binsPerCell,contigsPerCell:i.contigsPerCell,rowContigs:as(e,n),colContigs:as(e,s)}}function lo(e,t,n){return n.contigsPerCell<=1?t:t.map(s=>{const o=n.memberStart[s.start],r=n.memberStart[s.end],i=[];for(let a=o;a<r;a++){const c=n.members[a];a>o&&c===n.members[a-1]||i.push({label:e.chromnames[c]??String(c),unitLength:e.coords.contigLengths[c]??0})}return i.length>1?{...s,merged:i}:s})}function yi(e,t,[n],s){if(t.length===0||s<=1)return t;const[o]=e.coords.contigBinExtent(e.coords.contigOfBin(n)),r=Math.floor((n-o)/s);return r<=0?t:[{...t[0],unitStart:n+t[0].start-r},...t.slice(1)]}function as(e,[t,n]){return n<=t?0:e.coords.contigOfBin(n-1)-e.coords.contigOfBin(t)+1}function Ja(e,t,n,s){const o=t[0]===n[0]&&t[1]===n[1]?[t]:[t,n],r=Hc(s);if(o.every(([l,u])=>u-l<=r))return null;for(const[l,u]of o){const h=e.coords.contigOfBin(u-1)-e.coords.contigOfBin(l)+1;if(h>qt)return{binsPerCell:1,contigsPerCell:Math.ceil(h/qt)}}let i=2,a=2;const c=l=>o.every(u=>n0(e,Oe(e,u,{binsPerCell:l,contigsPerCell:1}),l));for(;!c(a);)a*=2;for(;i<a;){const l=i+a>>1;c(l)?a=l:i=l+1}return{binsPerCell:i,contigsPerCell:1}}function n0(e,[t,n],s){return s0(e,[t,n],s)<=qt}function s0(e,[t,n],s){if(n<=t)return 0;let o=0;const r=e.coords.contigOfBin(n-1);for(let i=e.coords.contigOfBin(t);i<=r;i++){const[a,c]=e.coords.contigBinExtent(i);o+=Math.ceil((Math.min(n,c)-Math.max(t,a))/s)}return o}function Oe(e,[t,n],s){if(n<=t)return[t,n];const[o]=e.coords.contigBinExtent(e.coords.contigOfBin(t)),[r,i]=e.coords.contigBinExtent(e.coords.contigOfBin(n-1));if(s.contigsPerCell>1)return[o,i];const a=s.binsPerCell;return a<=1?[t,n]:[o+Math.floor((t-o)/a)*a,Math.min(i,r+Math.ceil((n-r)/a)*a)]}function tc(e,t){return{binsPerCell:Math.max(1,Math.trunc(e??1)),contigsPerCell:Math.max(1,Math.trunc(t??1))}}async function o0(e){const{mc:t}=rt(),n=e.cols??e.rows,s=await t.aggregateSparse({rows:e.rows,cols:n,...e.balance===!0?{balance:!0}:{},...e.value===void 0?{}:{value:e.value}},e.level,ne(e.id));if(dt.has(e.id))throw $t();const o=td(t,s),r=e.genomes===!0&&t.hasGenomes&&e.level==="contig";return{nrows:s.nrows,ncols:s.ncols,values:Float32Array.from(s.values),rowExtent:e.rows,colExtent:n,rowGroups:o.rows,colGroups:o.cols,...r?{rowGenomes:dn(t,s.rowIds),colGenomes:dn(t,s.colIds)}:{},level:e.level,contigsPerCell:s.contigsPerCell,rowContigs:as(t,e.rows),colContigs:as(t,n)}}async function r0(e){const{mc:t}=rt(),n=e.id,s=[],o=i0(t,e.unit,e.names,e.naming,s);if(o.length===0)throw new C("unknown-label",`None of the ${e.unit==="genome"?"genomes":"sequences"} named are in this file, so there is nothing to draw. They may belong to another map.`,{unit:e.unit,names:e.names});const r=tc(e.binsPerCell,e.contigsPerCell),i={binsPerCell:Math.max(1,r.binsPerCell),contigsPerCell:1},a=e.unit==="genome"&&t.hasGenomes,c=await t.selectionMatrix(o,i,{...ne(n),...e.balance===!0?{balance:!0}:{},...e.value===void 0?{}:{value:e.value},...a?{byGenome:!0}:{},...e.budgetBytes===void 0?{}:{cellCap:Math.max(1,Math.floor(Math.sqrt(e.budgetBytes/4)))}});if(dt.has(n))throw $t();const l=bn(c.ids,d=>t.chromnames[d]??String(d),void 0,d=>t.coords.contigLengths[d]),u=t.hasGenomes?dn(t,c.ids):void 0,h=Jf(e.unit,u),f=lo(t,l,c.pooling);return{nrows:c.nrows,ncols:c.ncols,values:Float32Array.from(c.values),rowExtent:[0,c.nrows],colExtent:[0,c.ncols],rowGroups:f,colGroups:f,...u===void 0?{}:{rowGenomes:u,colGenomes:u},...h?{genomeBoundaries:!0}:{},level:"bin",binsPerCell:c.binsPerCell,contigsPerCell:c.contigsPerCell,rowContigs:o.length,colContigs:o.length,...s.length===0?{}:{matched:s}}}function i0(e,t,n,s,o){const r=new Set;for(const i of n){if(t==="contig"){const c=e.chromnames.indexOf(i);if(c>=0){r.add(c);continue}const l=e.names.find(i,s===void 0?{}:{from:s});if(l!==null){const u=e.chromnames.indexOf(l.name);u>=0&&(r.add(u),o?.push(l))}continue}const a=e.genomeNames.indexOf(i);if(!(a<0))for(let c=0;c<e.nContigs;c++)e.contigGenomeIds[c]===a&&r.add(c)}return[...r].map(i=>({id:i,extent:e.contigExtent(i)})).sort((i,a)=>i.extent[0]-a.extent[0])}async function ec(e){const{mc:t}=rt(),n=e.id,s=e.level??"genome";if(s==="genome"&&!t.hasGenomes)throw new C("unsupported","This file is a plain cooler and has no genomes, so there is no genome × genome view of it. The contig level is the same scan over the axes this file does have.",{level:s});const o=s==="genome"?t.displayGenomes():a0(t),r=Math.max(1,Math.trunc(e.maxUnits??rd(wn()))),i=s==="contig"&&t.hasGenomes?p=>t.contigGenomeIds[o[p]]:void 0,a=id(o.length,r,i),c=a.slots,l=s==="genome"?t.nGenomes:t.nContigs,u=new Int32Array(l).fill(-1);for(let p=0;p<o.length;p++)u[o[p]]=a.slotOf[p];const h=s==="genome"?nd(t):ed(t),f=t.storageMode==="symmetric-upper",d=f?new ld(c):null,m=f?null:new Float64Array(c*c);if(await t.scanPixels({chunkSize:Bg,onChunk:p=>{if(dt.has(n))return!1;if(d!==null)for(let b=0;b<p.length;b++){const y=u[h[p.bin1[b]]];if(y<0)continue;const A=u[h[p.bin2[b]]];A<0||d.add(y,A,p.count[b])}else for(let b=0;b<p.length;b++){const y=u[h[p.bin1[b]]];if(y<0)continue;const A=u[h[p.bin2[b]]];A<0||(m[y*c+A]+=p.count[b])}return!0},onProgress:(p,b)=>ce({type:"progress",id:n,done:p,total:b})}),dt.has(n))throw $t();const g=s==="genome"?t.genomeNames:t.chromnames,w=Ai(o,a,p=>g[p]);return{level:s,labels:w.labels,unitNames:w.unitNames,...s==="contig"&&t.hasGenomes?{groups:Ai(o,a,p=>t.genomeNames[t.contigGenomeIds[p]]).unitNames}:{},values:d!==null?d.toSquare():Float32Array.from(m),n:c,source:"scan",pooled:a.pooled,unitsPerSlot:a.pooled?o.length/c:1,totalUnits:o.length}}function Ai(e,t,n){const s=new Array(t.slots),o=new Int32Array(t.slots);for(let i=0;i<e.length;i++){const a=t.slotOf[i];o[a]===0&&(s[a]=e[i]),o[a]+=1}const r=Array.from({length:t.slots},(i,a)=>n(s[a])??String(s[a]));return{labels:r.map((i,a)=>o[a]>1?`${i} +${o[a]-1}`:i),unitNames:r}}function a0(e){const t=e.genomeNames.indexOf(ke),n=[];for(let s=0;s<e.nContigs;s++)(!e.hasGenomes||e.contigGenomeIds[s]!==t)&&n.push(s);return n}async function c0(e){const{mc:t,resample:n}=rt();if(n!==null)return ec({id:e.id,level:"genome"});const s=await fetch(e.url);if(!s.ok)throw new C("remote-cors",`The genome edge list at ${e.url} could not be read (HTTP ${s.status}).`,{url:e.url,status:s.status});const o=await s.text(),r=new Set(t.displayGenomes().map(f=>t.genomeNames[f])),i=[],a=new Set,c=[];for(const f of o.split(`
+`)){const d=f.trim();if(d===""||d.startsWith("#"))continue;const m=d.split("	");if(m.length<3)continue;const g=Number(m[2]);if(!Number.isFinite(g))continue;const[w,p]=m;if(!(!r.has(w)||!r.has(p))){for(const b of[w,p])a.has(b)||(a.add(b),i.push(b));c.push([w,p,g])}}i.sort();const l=new Map(i.map((f,d)=>[f,d])),u=i.length,h=new Float32Array(u*u);for(const[f,d,m]of c){const g=l.get(f),w=l.get(d);g===void 0||w===void 0||(h[g*u+w]=m,h[w*u+g]=m)}return{level:"genome",labels:i,unitNames:i,values:h,n:u,source:"edge-list",pooled:!1,unitsPerSlot:1,totalUnits:r.size}}async function l0(e){const t=e.id,n=await rt().mc.validateDeep({cancelled:()=>dt.has(t),onProgress:(s,o)=>ce({type:"progress",id:t,done:s,total:o})});if(dt.has(t))throw $t();return n}async function u0(e){const t=rt(),n=e.contacts===null?null:{contacts:e.contacts,...e.seed===void 0?{}:{seed:e.seed},...e.alpha===void 0?{}:{alpha:e.alpha}};t.resample=n;for(const i of t.rungs.values())i.resample(n).catch(()=>{});const s=gs(e.id),o=await t.mc.resample(n,{onProgress:(i,a)=>s(i,a,"counting contacts"),cancelled:()=>dt.has(e.id)}),r=await t.mc.takenCensus();return{mode:o?.mode??"none",contacts:n?.contacts??null,total:r?.total??null,census:r===null?null:{...r,a:r.a.slice(),b:r.b.slice(),sum:r.sum.slice()}}}async function h0(e){const t=rt(),n=t.mc.declaredContacts;if(n!==null)return{total:n};const s=t.mc.entries.filter(i=>/^\d+$/.test(i)).sort((i,a)=>Number(a)-Number(i)),o=s.length>0?await He(s[0]):t.mc,r=gs(e.id);return{total:await o.countContacts({onProgress:(i,a)=>r(i,a,"counting contacts"),pause:i=>co.quiet(i)})}}function f0(){const{source:e}=rt();return{total:e.stats(),lastOp:{...Va},calls:Ya}}function d0(e){return e==="matrix"||e==="aggregate"||e==="overview"||e==="selection"}async function m0(e){switch(e.kind){case"open":return Rg(e);case"exportMcool":return _g(e.id);case"exportLifted":return Tg(e.id,e.edit);case"genomes":return Pg();case"contigs":return Lg();case"cells":return Dg();case"selectCells":return Ug(e);case"binColumns":return Gg();case"binColumn":return Hg(e);case"range":return tf(await He(e.rung),e.range,e.naming,e.circular);case"matrix":return t0(e);case"aggregate":return o0(e);case"selection":return r0(e);case"overview":return ec(e);case"overviewSidecar":return c0(e);case"validateDeep":return l0(e);case"resample":return u0(e);case"contacts":return h0(e);case"stats":return f0();case"picture":return Wg(e);case"suggest":return Kg(e);case"stageWindow":return Qg(e);case"refine":return Vg(e);case"genomeLinks":return Xg(e);case"cancel":return dt.add(e.target),null;case"close":return Ka(Ct),Ct?.mc.close(),Ct=null,dt.clear(),gn(),null}}async function g0(e){Ya++;const t=e.kind==="contacts"||e.kind==="matrix"&&e.background===!0;t&&e.kind==="matrix"&&await co.quiet(()=>dt.has(e.id));const n=t?null:co.begin(),s=Ct?.source.stats(),o=w0(e.id);try{const r=await m0(e);if(d0(e.kind)&&s&&Ct){const i=Ct.source.stats();Va={requests:i.requests-s.requests,bytes:i.bytes-s.bytes}}ce({type:"result",id:e.id,kind:e.kind,payload:r},gd(r))}catch(r){ce({type:"error",id:e.id,error:md(r)})}finally{n?.(),o(),dt.delete(e.id)}}function w0(e){const t=Ct?.mc.store;if(!(t instanceof rn)||t.names.length<2)return()=>{};const n=gs(e),s=(o,r)=>n(o,r,"summing cells");return t.onCells=s,()=>{t.onCells===s&&(t.onCells=null)}}Qa.onmessage=e=>{g0(e.data)};const p0=vg();setInterval(()=>ce({type:"busy",fraction:p0.busy()}),Eg);