"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[5904,7706],{35904:(e,t,n)=>{n.r(t),n.d(t,{default:()=>p});var r=n(46377),a=n(32595),s=n(99834),o=n(66885),i=n(99546),c=n(68584),l=n(7706),h=n(82727),d=n(72147),u=n(78054);function f(e){const[t,n]=e.reduce((([e,t],[n,r])=>[e+n*r,t+r]),[0,0]);return t/n}const{parseCigar:m}=h.aF;class p extends r.BaseFeatureDataAdapter{static capabilities=["getFeatures","getRefNames"];async setup(e){return this.setupP||(this.setupP=this.setupPre(e).catch((e=>{throw this.setupP=void 0,e}))),this.setupP}async setupPre(e){const t=this.pluginManager,n=(0,s.openLocation)(this.getConf("pafLocation"),t),r=await n.readFile(e),a=(0,i.isGzip)(r)?await(0,l.unzip)(r):r;return(0,u.PX)(a,u.xI)}async hasDataForRefName(){return!0}getAssemblyNames(){const e=this.getConf("assemblyNames");return 0===e.length?[this.getConf("queryAssembly"),this.getConf("targetAssembly")]:e}async getRefNames(e={}){const t=e.regions?.[0].assemblyName,n=await this.setup(e),r=this.getAssemblyNames().indexOf(t);if(-1!==r){const e=new Set;for(const t of n)e.add(0===r?t.qname:t.tname);return[...e]}return console.warn("Unable to do ref renaming on adapter"),[]}getFeatures(e,t={}){return(0,o.ObservableCreate)((async n=>{let r=await this.setup(t);const{config:s}=t;s&&"meanQueryIdentity"===(0,c.readConfObject)(s,"colorBy")&&(r=function(e){const t={};for(const n of e){const e=`${n.qname}-${n.tname}`;t[e]||(t[e]={quals:[],len:[]}),t[e].quals.push(n.extra.mappingQual),t[e].len.push(n.extra.blockLen||1)}const n=Object.fromEntries(Object.entries(t).map((([e,t])=>[e,f((0,u.yU)(t.quals,t.len))])));for(const t of e){const e=`${t.qname}-${t.tname}`;t.extra.meanScore=n[e]}let r=1e4,a=0;for(const t of e)r=Math.min(t.extra.meanScore||0,r),a=Math.max(t.extra.meanScore||0,a);for(const t of e){const e=t.extra.meanScore||0;t.extra.meanScore=(e-r)/(a-r)}return e}(r));const o=this.getAssemblyNames(),{start:i,end:l,refName:h,assemblyName:p}=e,g=o.indexOf(p),w=0===g;-1===g&&(console.warn(`${p} not found in this adapter`),n.complete());for(let e=0;e<r.length;e++){const t=r[e];let s=0,c=0,f="",g="",b=0,y=0;w?(s=t.qstart,c=t.qend,f=t.qname,g=t.tname,b=t.tstart,y=t.tend):(s=t.tstart,c=t.tend,f=t.tname,g=t.qname,b=t.qstart,y=t.qend);const{extra:x,strand:k}=t;if(f===h&&(0,a.R6)(i,l,s,c)){const{numMatches:t=0,blockLen:r=1,cg:a,...i}=x;let l=x.cg;x.cg&&(w&&-1===k?l=(0,u.qm)(m(x.cg)).join(""):w&&(l=(0,u.gJ)(x.cg))),n.next(new d.A({uniqueId:e+p,assemblyName:p,start:s,end:c,type:"match",refName:f,strand:k,...i,CIGAR:l,syntenyId:e,identity:t/r,numMatches:t,blockLen:r,mate:{start:b,end:y,refName:g,assemblyName:o[+w]}}))}}n.complete()}))}freeResources(){}}},72147:(e,t,n)=>{n.d(t,{A:()=>o});var r=n(99546),a=n(82727);const{getMismatches:s}=a.aF;class o extends 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Error("problem decompressing block: incorrect gzip header check");throw e}}async function i(e,t){try{let n;const{minv:a,maxv:o}=t;let i=a.blockPosition,c=a.dataPosition;const l=[],h=[],d=[];let u=0,f=0;do{const t=e.subarray(i-a.blockPosition),r=new s.Inflate;if(({strm:n}=r),r.push(t,s.Z_SYNC_FLUSH),r.err)throw new Error(r.msg);const m=r.result;l.push(m);let p=m.length;h.push(i),d.push(c),1===l.length&&a.dataPosition&&(l[0]=l[0].subarray(a.dataPosition),p=l[0].length);const g=i;if(i+=n.next_in,c+=p,g>=o.blockPosition){l[f]=l[f].subarray(0,o.blockPosition===a.blockPosition?o.dataPosition-a.dataPosition+1:o.dataPosition+1),h.push(i),d.push(c),u+=l[f].length;break}u+=l[f].length,f++}while(n.avail_in);const m=new Uint8Array(u);for(let e=0,t=0;e<l.length;e++)m.set(l[e],t),t+=l[e].length;return{buffer:r.hp.from(m),cpositions:h,dpositions:d}}catch(e){if(`${e}`.match(/incorrect header check/))throw new Error("problem decompressing block: incorrect gzip header check");throw e}}var c=n(59086),l=n.n(c);class h{constructor({filehandle:e,path:t}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new a.EY(t)}}_readLongWithOverflow(e,t=0,n=!0){const r=l().fromBytesLE(e.slice(t,t+8),n);if(r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new TypeError("integer overflow");return r.toNumber()}_getIndex(){return this.index||(this.index=this._readIndex()),this.index}async _readIndex(){let e=r.hp.allocUnsafe(8);await this.filehandle.read(e,0,8,0);const t=this._readLongWithOverflow(e,0,!0);if(!t)return[[0,0]];const n=new Array(t+1);n[0]=[0,0];const a=16*t;if(a>Number.MAX_SAFE_INTEGER)throw new TypeError("integer overflow");e=r.hp.allocUnsafe(a),await this.filehandle.read(e,0,a,8);for(let r=0;r<t;r+=1){const t=this._readLongWithOverflow(e,16*r),a=this._readLongWithOverflow(e,16*r+8);n[r+1]=[t,a]}return n}async getLastBlock(){const e=await this._getIndex();if(e.length)return e[e.length-1]}async getRelevantBlocksForRead(e,t){const n=t+e;if(0===e)return[];const r=await this._getIndex(),a=[],s=(e,n)=>{const r=e[1],a=n?n[1]:1/0;return r<=t&&a>t?0:r<t?-1:1};let o=0,i=r.length-1,c=Math.floor(r.length/2),l=s(r[c],r[c+1]);for(;0!==l;)l>0?i=c-1:l<0&&(o=c+1),c=Math.ceil((i-o)/2)+o,l=s(r[c],r[c+1]);a.push(r[c]);let h=c+1;for(;h<r.length&&(a.push(r[h]),!(r[h][1]>=n));h+=1);return a[a.length-1][1]<n&&a.push([]),a}}class d{constructor({filehandle:e,path:t,gziFilehandle:n,gziPath:r}){if(e)this.filehandle=e;else{if(!t)throw new TypeError("either filehandle or path must be defined");this.filehandle=new a.EY(t)}if(!n&&!r&&!t)throw new TypeError("either gziFilehandle or gziPath must be defined");this.gzi=new h({filehandle:n,path:n||r||!t?`${t}.gzi`:r})}async stat(){const e=await this.filehandle.stat();return Object.assign(e,{size:await this.getUncompressedFileSize(),blocks:void 0,blksize:void 0})}async getUncompressedFileSize(){const[,e]=await 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