igv 2.13.2 → 2.13.3

package/dist/igv.min.js

@@ -36,7 +36,7 @@ function(t){var e,n,r,i,o,s,a,l,c,h,u,f,d,p,g,m,v,b,w,y="sizzle"+1*new Date,x=t.
      *
      *  Copyright (c) 2014 Gliffy Inc.
      */
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r.setAttribute("id",i),r.setAttribute("width",t.width),r.setAttribute("height",t.height),"CANVAS"===t.nodeName||"IMG"===t.nodeName?(n=this.__createElement("image"),n.setAttribute("width",t.width),n.setAttribute("height",t.height),n.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===t.nodeName?t.toDataURL():t.getAttribute("src")),r.appendChild(n),this.__defs.appendChild(r)):t instanceof oa&&(r.appendChild(t.__root.childNodes[1]),this.__defs.appendChild(r)),new ia(r,this)}setLineDash(t){t&&t.length>0?this.lineDash=t.join(","):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}class sa{constructor(t,e,n){this.name=t,this.order=e,this.bpLength=n}}const aa=Ce,la=new Set(["fastaURL","indexURL","cytobandURL","indexed"]);class ca{constructor(t){this.fastaURL=t.fastaURL,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences=new Map;const e={};for(let n in t)t.hasOwnProperty(n)&&!la.has(n)&&(e[n]=t[n]);this.config=e}async init(){return this.loadAll()}async getSequence(t,e,n){if(!this.sequences.has(t))return;let r=this.sequences.get(t).find((t=>t.contains(e,n)));if(!r&&(r=this.sequences.get(t).find((t=>t.overlaps(e,n))),!r))return;e-=r.offset,n-=r.offset;let i="";if(e<0)for(let t=e;t<Math.min(n,0);t++)i+="*";if(n<=0)return Promise.resolve(i);const o=r.sequence,s=Math.min(n,o.length);return i+o.substring(e,s)}async loadAll(){let t;if(Ms(this.fastaURL)){let e=co(this.fastaURL);t="";for(let n of e)t+=String.fromCharCode(n)}else t=await Eo.load(this.fastaURL,Cs(this.config));const e=new Set,n=aa(t),r=n.length;let i,o=0,s=0,a={};for(;o<r;){if(i=n[o++].trim(),i.startsWith("#")||0===i.length);else if(i.startsWith(">")){a&&a.seq&&l.call(this,a,s++);const t=i.substr(1).split(/\s+/),e=t[0].split(":");if(a.chr=e[0],a.seq="",a.offset=0,e.length>1&&e[1].indexOf("-")>0){const n=e[1].split("-");2===n.length&&/^[0-9]+$/.test(n[0])&&/^[0-9]+$/.test(n[1]);const r=Number.parseInt(n[0]);if(Number.parseInt(n[1])>r&&(a.offset=r-1),t.length>1&&t[1].startsWith("@len="))try{a.length=parseInt(t[1].trim().substring(5))}catch(t){a.length=void 0,console.error(`Error parsing sequence length for ${i}`)}else a.length=void 0}}else a.seq+=i;a&&a.seq&&l.call(this,a,s)}function l(t,n){const r=t.length||t.offset+t.seq.length;if(e.has(t.chr)){const e=this.chromosomes[t.chr];e.bpLength=Math.max(e.bpLength,r)}else this.chromosomeNames.push(t.chr),this.sequences.set(t.chr,[]),this.chromosomes[t.chr]=new sa(t.chr,n,r),e.add(t.chr);this.sequences.get(t.chr).push(new ha(t.offset,t.seq))}}}class ha{constructor(t,e){this.offset=t,this.sequence=e}contains(t,e){return this.offset<=t&&this.end>=e}overlaps(t,e){return this.offset<e&&this.end>t}get end(){return this.offset+this.sequence.length}}const ua=function(t,e,n,r){this.chr=t,this.start=e,this.end=n,this.features=r};ua.prototype.contains=function(t,e,n){return this.chr===t&&this.start<=e&&this.end>=n},ua.prototype.containsRange=function(t){return this.chr===t.chr&&this.start<=t.start&&this.end>=t.end};const fa=Ce,da=new Set(["fastaURL","indexURL","compressedIndexURL","cytobandURL","indexed"]);class pa{constructor(t){this.file=t.fastaURL,this.indexFile=t.indexURL||t.indexFile||this.file+".fai",this.compressedIndexFile=t.compressedIndexURL||!1,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences={},this.offsets={};const e={};for(let n in t)t.hasOwnProperty(n)&&!da.has(n)&&(e[n]=t[n]);this.config=e}async init(){return this.getIndex()}async getSequence(t,e,n){if(!(this.interval&&this.interval.contains(t,e,n))){let r=e,i=n;if(n-e<5e4){const t=n-e,o=Math.round(e+t/2);r=Math.max(0,o-25e3),i=o+25e3}const o=await this.readSequence(t,r,i);this.interval=new ua(t,r,i,o)}const r=e-this.interval.start,i=n-e;return this.interval.features?this.interval.features.substr(r,i):null}async getIndex(){if(this.index)return this.index;{const t=await Eo.load(this.indexFile,Cs(this.config)),e=fa(t),n=e.length;let r=0,i=0;for(this.index={};r<n;){const t=e[r++].split("\t");if(5===t.length){const e=t[0],n=parseInt(t[1]),r={size:n,position:parseInt(t[2]),basesPerLine:parseInt(t[3]),bytesPerLine:parseInt(t[4])};this.chromosomeNames.push(e),this.index[e]=r,this.chromosomes[e]=new sa(e,i++,n)}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const t=await Eo.loadArrayBuffer(this.compressedIndexFile,Cs(this.config)),e=t.byteLength;if(e<8)return console.log("Cannot parse GZI index file: length ("+e+" bytes) is insufficient to determine content of index."),this.compressedIndex;const n=t.slice(0,8),r=Number(new DataView(n).getBigUint64(0,!0)),i=8+2*r*8;if(e!=i)return console.log("Incorrect file size of reference genome index. Expected : "+i+". Received : "+e),this.compressedIndex;this.compressedIndex.push([0,0]);for(let e=0;e<r;e++){const n=8+2*e*8,r=8+2*e*8+16,i=t.slice(n,r),o=new DataView(i),s=Number(o.getBigUint64(0,!0)),a=Number(o.getBigUint64(8,!0));this.compressedIndex.push([s,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(t,e){if(t<0||e<0||e<t)return console.log("Incompatible query positions for reference-genome. Start:"+t+" | End:"+e),[];await this.getCompressedIndex();let n=[];const r=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log("Compressed index does not contain any content"),[];if(t>this.compressedIndex[r][1])return[r];let i=0,o=r,s=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,l=!1;for(let e=0;e<a;e++){const e=this.compressedIndex[s][1],n=s<this.compressedIndex.length-1?this.compressedIndex[s+1][1]:1/0;if(e<=t&&n>t){l=!0;break}e<t?i=s+1:o=s-1,s=Math.ceil((o-i)/2)+i}if(!l)return console.log("No blocks within compressed index found that correspond with query positions "+t+","+e),console.log(this.compressedIndex),[];n.push(s);for(let t=s+1;t<this.compressedIndex.length;t++){n.push(t);if(this.compressedIndex[t][1]>=e)break}const c=n[n.length-1];return c===this.compressedIndex.length-1&&this.compressedIndex[c][1]<e&&n.push(-1),n}async loadAndUncompressBlocks(t,e){if(await this.getCompressedIndex(),0==t.length)return"";let n=Array(t.length-1);for(let e=0;e<t.length-1;e++){const r=t[e],i=this.compressedIndex[r][0],o=t[e+1];let s=[];if(-1!=o){const t=this.compressedIndex[o][0]-i;s=await Eo.loadArrayBuffer(this.file,Cs(this.config,{range:{start:i,size:t}}))}else s=await Eo.loadArrayBuffer(this.file,Cs(this.config,{range:{start:i}}));const a=await io(s);n[e]=a}let r="";for(let t=0;t<n.length;t++)for(let e=0;e<n[t].length;e++){r+=String.fromCharCode(n[t][e])}const i=e-this.compressedIndex[t[0]][1];return r=r.substring(i),r}async readSequence(t,e,n){await this.getIndex(),await this.getCompressedIndex();const r=this.index[t];if(!r)return console.log("No index entry for chr: "+t),this.interval=new ua(t,e,n,null),null;const i=Math.max(0,e),o=Math.min(r.size,n),s=r.bytesPerLine,a=r.basesPerLine,l=r.position,c=s-a,h=Math.floor(i/a),u=Math.floor(o/a),f=i-h*a,d=l+h*s+f,p=l+u*s+(o-u*a)-1,g=p-d+1;if(g<=0)return console.error("No sequence for "+t+":"+e+"-"+n),null;let m;if(this.compressedIndexFile){let t=await this.getRelevantCompressedBlockNumbers(d,p);if(0===t.length)return console.log("No blocks in the compressed index that correspond with the requested byte positions ("+d+","+p+")"),null;m=await this.loadAndUncompressBlocks(t,d)}else m=await Eo.load(this.file,Cs(this.config,{range:{start:d,size:g}}));if(!m)return null;let v,b="",w=0,y=m.length;for(f>0&&(v=Math.min(o-i,a-f),b+=m.substr(w,v),w+=v+c);w<y;)v=Math.min(a,y-w),b+=m.substr(w,v),w+=v+c;return b}}const ga=Ce;class ma{constructor(t){this.url=t,this.chromosomeNames=[],this.chromosomes={}}async init(){return this.loadAll()}async getSequence(t,e,n){}async loadAll(){let t;if(Ms(this.url)){let e=co(this.fastaURL);t="";for(let n of e)t+=String.fromCharCode(n)}else t=await Eo.load(this.url,{});this.chromosomeNames=[],this.chromosomes={};const e=ga(t);let n=0;for(let t of e){const e=t.split("\t");this.chromosomeNames.push(e[0]);const r=Number.parseInt(e[1]),i=new sa(e[0],n++,r);this.chromosomes[e[0]]=i}}}const va=function(t,e,n,r){this.start=t,this.end=e,this.name=n,this.stain=0,"acen"===r?this.type="c":(this.type=r.charAt(1),"p"===this.type&&(this.stain=parseInt(r.substring(4))))};function ba(){return"2.13.2"}const wa=Ce,ya={loadGenome:async function(t){const e=t.cytobandURL,n=t.aliasURL,r=await async function(t){let e;return e="chromsizes"===t.format?new ma(t.fastaURL):Ms(t.fastaURL)||!1===t.indexed?new ca(t):new pa(t),await e.init(),e}(t);let i;n&&(i=await function(t,e){return Eo.loadString(t,Cs(e)).then((function(t){var e=wa(t),n=[];return e.forEach((function(t){!t.startsWith("#")&&t.length>0&&n.push(t.split("\t"))})),n}))}(n,r.config));const o=new xa(t,r,i);return e&&(o.cytobands=await async function(t,e,n){let r;if(Ms(t)){const e=co(t);r="";const n=e.length;for(let t=0;t<n;t++)r+=String.fromCharCode(e[t])}else r=await Eo.loadString(t,Cs(e));const i={};let o,s=[];const a=wa(r);for(let t of a){var l=t.split("\t"),c=n.getChromosomeName(l[0]);if(o||(o=c),c!==o&&(i[o]=s,s=[],o=c),5===l.length){var h=parseInt(l[1]),u=parseInt(l[2]),f=l[3],d=l[4];s.push(new va(h,u,f,d))}}return i}(e,r.config,o)),o},initializeGenomes:async function(t){if(!ya.KNOWN_GENOMES){const e={};if(!1!==t.loadDefaultGenomes)try{const i=`https://igv.org/genomes/genomes.json?randomSeed=${Math.random().toString(36)}&version=2.13.2`;r(await Eo.loadJson(i,{timeout:5e3}))}catch(o){console.error(o);try{const s=`https://s3.amazonaws.com/igv.org.genomes/genomes.json?randomSeed=${Math.random().toString(36)}&version=2.13.2`;r(await Eo.loadJson(s,{}))}catch(a){console.error(a),console.warn("Errors loading default genome definitions.")}}const n=t.genomeList||t.genomes;if(n)if("string"==typeof n){r(await Eo.loadJson(n,{}))}else r(n);function r(t){return t.forEach((function(t){e[t.id]=t})),e}ya.KNOWN_GENOMES=e}},isWholeGenomeView:function(t){return"all"===t.toLowerCase()},expandReference:function(t,e){if(ke(e)&&e.startsWith("{"))try{e=JSON.parse(e)}catch(t){}let n;if(ke(e)?n=e:e.genome?n=e.genome:void 0!==e.id&&void 0===e.fastaURL&&(n=e.id),n){const e=ya.KNOWN_GENOMES[n];return e||t.present(new Error(`Unknown genome id: ${n}`),void 0),e}return e}};class xa{constructor(t,e,n){this.config=t,this.id=t.id||function(t){return void 0!==t.id?t.id:t.fastaURL&&ke(t.fastaURL)?t.fastaURL:t.fastaURL&&t.fastaURL.name?t.fastaURL.name:("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}(t),this.sequence=e,this.chromosomeNames=e.chromosomeNames,this.chromosomes=e.chromosomes,this.featureDB={},this.wholeGenomeView=void 0===t.wholeGenomeView||t.wholeGenomeView,this.wholeGenomeView&&Object.keys(e.chromosomes).length>1?function(t,e){let n;if(e.chromosomeOrder)Array.isArray(e.chromosomeOrder)?t.wgChromosomeNames=e.chromosomeOrder:t.wgChromosomeNames=e.chromosomeOrder.split(",").map((t=>t.trim())),n=t.wgChromosomeNames.map((e=>t.chromosomes[e])).filter((t=>void 0!==t));else{const e=Object.keys(t.chromosomes).map((e=>t.chromosomes[e].bpLength)).reduce(((t,e)=>Math.max(t,e)))/50;n=Object.values(t.chromosomes).filter((t=>t.bpLength>e));const r=n.filter((t=>i(t.name.replace("chr","")))),o=n.filter((t=>!i(t.name.replace("chr",""))));r.sort(((t,e)=>Number.parseInt(t.name.replace("chr",""))-Number.parseInt(e.name.replace("chr",""))));const s=r.map((t=>t.name));for(let t of o)s.push(t.name);t.wgChromosomeNames=s}const r=n.reduce(((t,e)=>t+e.bpLength),0);function i(t){return/^\d+$/.test(t)}t.chromosomes.all={name:"all",bpLength:r}}(this,t):this.wgChromosomeNames=e.chromosomeNames;var r={},i=this;r.all="all",this.chromosomeNames.forEach((function(t){var e=t.startsWith("chr")?t.substring(3):"chr"+t;r[e.toLowerCase()]=t,"chrM"===t&&(r.mt="chrM"),"MT"===t&&(r.chrm="MT"),r[t.toLowerCase()]=t})),n&&n.forEach((function(t){var e,n;for(n=0;n<t.length;n++)if(i.chromosomes[t[n]]){e=t[n];break}e&&t.forEach((function(t){t!==e&&(r[t.toLowerCase()]=e,r[t]=e)}))})),this.chrAliasTable=r}showWholeGenomeView(){return!1!==this.config.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}getInitialLocus(){}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.hasOwnProperty("all")?"all":this.chromosomeNames[0]}getChromosomeName(t){const e=t?this.chrAliasTable[t.toLowerCase()]:t;return e||t}getChromosome(t){return t=this.getChromosomeName(t),this.chromosomes[t]}getCytobands(t){return this.cytobands?this.cytobands[t]:null}getLongestChromosome(){var t,e=this.chromosomes;for(let r in e){if(e.hasOwnProperty(r)){var n=e[r];(void 0===t||n.bpLength>t.bpLength)&&(t=n)}return t}}getChromosomes(){return this.chromosomes}getGenomeCoordinate(t,e){var n=this.getCumulativeOffset(t);if(void 0!==n)return n+e}getChromosomeCoordinate(t){let e;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let n=0;for(let r of this.wgChromosomeNames){const i=this.cumulativeOffsets[r];if(i>t){return{chr:e,position:t-n}}e=r,n=i}return{chr:this.wgChromosomeNames[this.wgChromosomeNames.length-1],position:0}}getCumulativeOffset(t){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let t=this,e={},n=0;for(let r of t.wgChromosomeNames){e[r]=Math.floor(n);n+=t.getChromosome(r).bpLength}return e}.call(this));const e=this.getChromosomeName(t);return this.cumulativeOffsets[e]}getGenomeLength(){let t=this;if(!this.bpLength){let e=0;t.wgChromosomeNames.forEach((function(n){let r=t.chromosomes[n];e+=r.bpLength})),this.bpLength=e}return this.bpLength}async getSequence(t,e,n){return t=this.getChromosomeName(t),this.sequence.getSequence(t,e,n)}}let _a,ka=0,Sa=0;class Ca extends class{constructor(t,e,n,r){this.guid=be(),this.trackView=t,this.referenceFrame=n,this.browser=t.browser,this.$viewport=pe('<div class="igv-viewport">'),e.appendChild(this.$viewport.get(0)),t.track.height&&(this.$viewport.get(0).style.height=`${t.track.height}px`),t.track instanceof Ys&&(this.alert=new cs(this.$viewport.get(0))),this.$content=pe("<div>",{class:"igv-viewport-content"}),this.$viewport.append(this.$content),this.$content.height(this.$viewport.height()),this.contentDiv=this.$content.get(0),this.$viewport.width(r),this.initializationHelper()}initializationHelper(){}showMessage(t){this.messageDiv||(this.messageDiv=document.createElement("div"),this.messageDiv.className="igv-viewport-message",this.contentDiv.append(this.messageDiv)),this.messageDiv.textContent=t,this.messageDiv.style.display="inline-block"}hideMessage(t){this.messageDiv&&(this.messageDiv.style.display="none")}setTrackLabel(t){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(t){const e=-t,n=e+this.$viewport.height();this.$content.css("top",`${t}px`),(void 0===this.canvasVerticalRange||this.canvasVerticalRange.bottom<n||this.canvasVerticalRange.top>e)&&this.repaint()}async loadFeatures(){}clearCache(){}async repaint(){}draw(t,e,n){console.log("Viewport - draw(drawConfiguration, features, roiFeatures)")}checkContentHeight(t){let e=this.trackView.track;if(t=t||this.cachedFeatures,"FILL"===e.displayMode)this.setContentHeight(this.$viewport.height());else if("function"==typeof e.computePixelHeight&&t&&t.length>0){let n=e.computePixelHeight(t);n!==this.$content.height()&&this.setContentHeight(n)}}getContentHeight(){return this.$content.height()}setContentHeight(t){t=Math.min(t,32e3),this.$content.height(t)}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(t){this.$viewport.width(t)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentDiv.offsetTop}containsPosition(t,e){console.log("Viewport - containsPosition(chr, position)")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.popover&&this.popover.dispose(),this.$viewport.get(0).remove();for(let t of Object.keys(this))this[t]=void 0}}{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.$spinner=pe("<div>",{class:"igv-loading-spinner-container"}),this.$viewport.append(this.$spinner),this.$spinner.append(pe("<div>"));const t=this.trackView.track;"sequence"!==t.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$content)),t.name&&"sequence"!==t.id&&(this.$trackLabel=pe('<div class="igv-track-label">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(t.name),!1===this.browser.trackLabelsVisible&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(t){super.setContentHeight(t),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(t){this.$trackLabel.empty(),this.$trackLabel.html(t);const e=this.$trackLabel.text();this.$trackLabel.attr("title",e)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&"sequence"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>1)return pe(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if("all"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const t=this.trackView.track.visibilityWindow;return void 0!==t&&t>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>t}return!0})()){if(this.canvas&&(pe(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const t=this.trackView.minHeight||0;this.setContentHeight(t)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const t=this.referenceFrame;if(this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===t.bpPerPixel){const e=Math.round((this.canvas._data.bpStart-t.start)/t.bpPerPixel);this.canvas.style.left=e+"px"}}async loadFeatures(){const t=this.referenceFrame,e=t.chr,n=this.browser.genome.getChromosome(e).bpLength,r=this.$content.width()*t.bpPerPixel,i=Math.floor(Math.max(0,t.start-r)),o=Math.ceil(Math.min(n,t.start+r+r));if(!this.loading||this.loading.start!==i||this.loading.end!==o){this.loading={start:i,end:o},this.startSpinner();try{const n=this.trackView.track,r=await this.getFeatures(n,e,i,o,t.bpPerPixel);let s=[];if(n.roiSets&&n.roiSets.length>0)for(let r of n.roiSets){const n=await r.getFeatures(e,i,o,t.bpPerPixel);s.push({track:r,features:n})}const a=n&&("wig"===n.type||"merged"===n.type);return this.featureCache=new Ta(e,i,o,t.bpPerPixel,r,s,a),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}catch(t){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage("Error loading track data"),this.browser.alert.present(t),console.error(t))}finally{this.loading=!1,this.stopSpinner()}}}repaintDimensions(){const t=ya.isWholeGenomeView(this.referenceFrame.chr),e=t?this.$viewport.width():3*this.$viewport.width(),n=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(t?0:e/3*n),bpEnd:this.referenceFrame.end+(t?0:e/3*n),pixelWidth:e}}repaint(){if(void 0===this.featureCache)return;const{features:t,roiFeatures:e}=this.featureCache;ya.isWholeGenomeView(this.referenceFrame.chr);const{bpStart:n,bpEnd:r,pixelWidth:i}=this.repaintDimensions(),o=this.$viewport.height(),s=this.getContentHeight(),a=e?Math.max(s,o):s,l=Math.min(a,3*o);if(0===i||0===l)return void(this.canvas&&pe(this.canvas).remove());const c=Math.max(0,-this.$content.position().top-o),h=this.referenceFrame.bpPerPixel,u=Math.round((n-this.referenceFrame.start)/h),f=pe('<canvas class="igv-canvas">').get(0);f.style.width=i+"px",f.style.height=l+"px",f.style.left=u+"px",f.style.top=c+"px";const d="FILL"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=d*i,f.height=d*l;const p=f.getContext("2d");p.scale(d,d),p.translate(0,-c);const g={context:p,pixelXOffset:u,pixelWidth:i,pixelHeight:l,pixelTop:c,bpStart:n,bpEnd:r,bpPerPixel:h,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(g,t,e),this.canvas&&pe(this.canvas).remove(),f._data=g,this.canvas=f,this.$content.append(pe(f))}refresh(){if(!this.canvas||!this.featureCache)return;const t=this.canvas._data;t.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:e,roiFeatures:n}=this.featureCache;this.draw(t,e,n)}draw(t,e,n){if(e&&(t.features=e,this.trackView.track.draw(t)),n)for(let e of n)t.features=e.features,e.track.draw(t)}containsPosition(t,e){return this.referenceFrame.chr===t&&e>=this.referenceFrame.start&&e<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const t=this.featureCache,e=t?t.canvasTop:0,n=window.devicePixelRatio,r=this.$viewport.width()*n,i=this.$viewport.height()*n,o=-pe(this.canvas).position().left*n,s=(-this.$content.position().top-e)*n,a=this.canvas.getContext("2d").getImageData(o,s,r,i),l=document.createElement("canvas"),c=l.getContext("2d");l.width=a.width,l.height=a.height,c.putImageData(a,0,0);We((this.$trackLabel.text()?this.$trackLabel.text():"image")+".png",l.toDataURL("image/png"))}saveSVG(){const{width:t,height:e}=this.$viewport.get(0).getBoundingClientRect(),n={width:t,height:e,viewbox:{x:0,y:-this.$content.position().top,width:t,height:e}},r=new oa(n),i=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${be()}`;this.drawSVGWithContext(r,t,e,i,0,0,0);const o=r.getSerializedSvg(!0);We(`${i}.svg`,URL.createObjectURL(new Blob([o],{type:"application/octet-stream"})))}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;if(this.$zoomInNotice&&this.$zoomInNotice.is(":visible"))return;const i=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${be()}`,{top:o}=this.$content.position(),{width:s,height:a}=this.$viewport.get(0).getBoundingClientRect();if(this.drawSVGWithContext(t,s,a,i,n,r+o,-o),this.$trackLabel&&!0===this.browser.trackLabelsVisible){const{x:e,y:i,width:o,height:s}=((t,e)=>{const{x:n,y:r,width:i,height:o}=t.getBoundingClientRect(),{x:s,y:a,width:l,height:c}=e.getBoundingClientRect();return{x:s-n,y:a-r,width:l,height:c}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(t,n+e,r+i,o,s)}}renderTrackLabelSVG(t,e,n,r,i){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_track_label_guid_${be()}`;t.saveWithTranslationAndClipRect(o,e,n,r,i,0),t.fillStyle="white",t.fillRect(0,0,r,i),t.font="12px Arial",t.fillStyle="rgb(68, 68, 68)";const{width:s}=t.measureText(this.$trackLabel.text()),a=.25*(r-s),l=.7*(i-12);t.fillText(this.$trackLabel.text(),a,i-l),t.strokeStyle="rgb(68, 68, 68)",t.strokeRect(0,0,r,i),t.restore()}drawSVGWithContext(t,e,n,r,i,o,s){t.saveWithTranslationAndClipRect(r,i,o,e,n,s);let{start:a,bpPerPixel:l}=this.referenceFrame;const c={context:t,viewport:this,referenceFrame:this.referenceFrame,top:s,pixelTop:s,pixelWidth:e,pixelHeight:n,bpStart:a,bpEnd:a+e*l,bpPerPixel:l,viewportWidth:e,selection:this.selection},h=this.featureCache?this.featureCache.features:[],u=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(c,h,u),t.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(t,e,n,r,i){if(this.featureCache&&this.featureCache.containsRange(e,n,r,i))return this.featureCache.features;if("function"==typeof t.getFeatures){const o=await t.getFeatures(e,n,r,i,this);return this.checkContentHeight(o),o}}needsRepaint(){if(!this.canvas)return!0;const t=this.canvas._data;return!t||this.referenceFrame.start<t.bpStart||this.referenceFrame.end>t.bpEnd||this.referenceFrame.chr!==t.referenceFrame.chr||this.referenceFrame.bpPerPixel!=t.bpPerPixel}needsReload(){if(!this.featureCache)return!0;const{chr:t,bpPerPixel:e}=this.referenceFrame,{bpStart:n,bpEnd:r}=this.repaintDimensions();return!this.featureCache.containsRange(t,n,r,e)}createZoomInNotice(t){const e=pe("<div>",{class:"igv-zoom-in-notice-container"});t.append(e);const n=pe("<div>");return e.append(n),n.text("Zoom in to see features"),e.hide(),e}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const t=this.$viewport.get(0);this.addViewportContextMenuHandler(t);const e=t=>{this.enableClick=!0,this.browser.mouseDownOnViewport(t,this),ve(t)};t.addEventListener("mousedown",e),t.addEventListener("touchstart",e);const n=t=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};t.addEventListener("mouseup",n),t.addEventListener("touchend",n),"function"==typeof this.trackView.track._hoverText&&t.addEventListener("mousemove",(t=>{if(Date.now()-Sa>100){Sa=Date.now();const e=Ea(t,this);if(e){const t=this.trackView.track._hoverText(e);t?this.$viewport[0].setAttribute("title",t):this.$viewport[0].removeAttribute("title")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&"sequence"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(t){t.addEventListener("contextmenu",(t=>{if(this.browser.dragObject)return!1;const e=Ea(t,this);if(void 0===e)return!1;t.preventDefault();let n=[];if("function"==typeof this.trackView.track.contextMenuItemList){const t=this.trackView.track.contextMenuItemList(e);t&&(n=t)}n.length>0&&n.push({label:pe("<HR>")}),n.push({label:"Save Image (PNG)",click:()=>this.savePNG()}),n.push({label:"Save Image (SVG)",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(t,n)}))}addViewportClickHandler(t){t.addEventListener("click",(t=>{if(this.enableClick&&this.canvas){if(3===t.which||t.ctrlKey)return;if(pe(".igv-popover").hide(),this.browser.dragObject||this.browser.isScrolling)return;t.preventDefault();const e=we(t,this.$viewport.get(0)).x,n=we(t,this.canvas).x,r=this.referenceFrame,i=Math.floor(r.start+r.toBP(n)),o=Date.now();if(o-ka<this.browser.constants.doubleClickDelay){_a&&(window.clearTimeout(_a),_a=void 0);const t=Math.round(r.start+r.toBP(e));let n;if("all"===this.referenceFrame.chr.toLowerCase()){const e=this.browser.genome.getChromosomeCoordinate(t).chr;if(1===this.browser.referenceFrameList.length)n=e;else{const t=this.browser.referenceFrameList.map((t=>{let{locusSearchString:e}=t;return e}));t[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=e,n=t.join(" ")}this.browser.search(n)}else this.browser.zoomWithScaleFactor(.5,t,this.referenceFrame)}else t.shiftKey&&"function"==typeof this.trackView.track.shiftClick?this.trackView.track.shiftClick(i,t):"function"==typeof this.trackView.track.popupData&&(_a=setTimeout((()=>{const e=function(t,e){const n=Ea(t,e);if(void 0===n)return;let r=e.trackView.track;const i=r.popupData(n),o=e.browser.fireEvent("trackclick",[r,i]);let s;void 0===o||!0===o?i&&i.length>0&&(s=i.map((t=>{if(t.name){const e=`<span>${t.name}</span>&nbsp&nbsp&nbsp${t.value}`;return`<div title="${t.value}">${e}</div>`}return"<hr>"===t?t:t.html?t.html:`<div title="${t}">${t}</div>`})).join("")):"string"==typeof o&&(s=o);return s}(t,this);e&&(this.popover&&this.popover.dispose(),this.popover=new ms(this.browser.columnContainer),this.popover.presentContentWithEvent(t,e)),window.clearTimeout(_a),_a=void 0}),this.browser.constants.doubleClickDelay));ka=o}}))}addTrackLabelClickHandler(t){t.addEventListener("click",(t=>{t.stopPropagation();const{track:e}=this.trackView;let n;"function"==typeof e.description?n=e.description():e.description&&(n=`<div>${e.description}</div>`),n&&(this.popover&&this.popover.dispose(),this.popover=new ms(this.browser.columnContainer,e.name||""),this.popover.presentContentWithEvent(t,n))}))}}function Ea(t,e){if(!e.contentDiv||!e.canvas)return;const n=e.referenceFrame,r=we(t,e.contentDiv),i=we(t,e.canvas),o=n.start+n.toBP(r.x);return{event:t,viewport:e,referenceFrame:n,genomicLocation:o,x:r.x,y:r.y,canvasX:i.x,canvasY:i.y}}class Ta{constructor(t,e,n,r,i,o,s){this.chr=t,this.bpStart=e,this.bpEnd=n,this.bpPerPixel=r,this.features=i,this.roiFeatures=o,this.multiresolution=s}containsRange(t,e,n,r){const i=this.multiresolution?this.bpPerPixel/r:1;return e>=this.bpStart&&n<=this.bpEnd&&t===this.chr&&i>.5&&i<2}overlapsRange(t,e,n){return this.chr===t&&n>=this.bpStart&&e<=this.bpEnd}}function Aa(t,e){if(!(t.length<6))return{chr:t[0],start:t[1],end:t[2],chr1:t[8],start1:Number.parseInt(t[9]),end1:Number.parseInt(t[10]),chr2:t[13],start2:Number.parseInt(t[14]),end2:Number.parseInt(t[15]),name:t[3],score:Number(t[4]),value:Number(t[5]),color:"."===t[7]?void 0:"0"===t[7]?"rgb(0,0,0)":t[7]};console.log("Skipping line: "+t.join(" "))}const La=new Set(["transcript","primary_transcript","processed_transcript","mRNA","mrna","lnc_RNA","miRNA","ncRNA","rRNA","scRNA","snRNA","snoRNA","tRNA"]),Ma=new Set(["CDS","cds"]),Ra=new Set(["start_codon","stop_codon"]),Ia=new Set(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),Na=new Set(["exon","coding-exon"]),Oa=new Set;for(let dv of[Ma,Ra,Ia,Na])for(let pv of dv)Oa.add(pv);function Pa(t){return t.includes("intron")}function Fa(t){return Ma.has(t)||Ra.has(t)}function Da(t){return Ia.has(t)}function Ba(t){return La.has(t)||t.endsWith("RNA")||t.endsWith("transcript")}function za(t){return Oa.has(t)||t.endsWith("RNA")||Pa(t)}const Ha=new Set(["id","parent","name"]);class Va{constructor(t){Object.assign(this,t)}popupData(t){const e=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&e.push("<hr/>"),this.name&&e.push({name:"Name",value:this.name}),e.push({name:"Type",value:this.type}),e.push({name:"Source",value:this.source}),void 0!==this.score&&e.push({name:"Score",value:this.score}),this.attributeString){const t=$a(this.attributeString,this.delim);for(let[n,r]of t)void 0!==r&&r.length>0&&!Ha.has(n.toLowerCase())&&e.push({name:n+":",value:r})}return e.push({name:"Location",value:`${this.chr}:${Se(this.start+1)}-${Se(this.end)}`}),e}getAttributeValue(t){if(this.hasOwnProperty(t))return this[t];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(t))return this._attributeCache.get(t);{const e=$a(this.attributeString,this.delim);let n;for(let[r,i]of e)if(r===t){n=i;break}return this._attributeCache.set(t,n),n}}}class ja extends Va{constructor(t){super(t),this.exons=[],this.parts=[]}addExon(t){this.exons.push(t),this.start=Math.min(this.start,t.start),this.end=Math.max(this.end,t.end)}addPart(t){this.parts.push(t)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(t,e){return t.start-e.start}));let t=this.parts[0].start,e=this.parts[0].end;for(let n=1;n<this.parts.length;n++){const r=this.parts[n];if(!Pa(r.type))if(r.start<=e)e=Math.max(e,r.end);else{this.findExonContaining({start:t,end:e})||this.exons.push({start:t,end:e,psuedo:!0}),t=r.start,e=r.end}}this.findExonContaining({start:t,end:e})||(this.exons.push({start:t,end:e,psuedo:!0}),this.start=Math.min(this.start,t),this.end=Math.max(this.end,e));for(let t of this.parts){const e=t.type;Fa(e)?this.addCDS(t):Da(e)&&this.addUTR(t)}}findExonContaining(t){let{start:e,end:n}=t;for(let t of this.exons)if(t.end>=n&&t.start<=e)return t}addCDS(t){let e;const n=this.exons;for(let r of n)if(r.start<=t.start&&r.end>=t.end){e=r;break}e?(e.cdStart=e.cdStart?Math.min(t.start,e.cdStart):t.start,e.cdEnd=e.cdEnd?Math.max(t.end,e.cdEnd):t.end):console.error("No exon found spanning "+t.start+"-"+t.end),this.cdStart=this.cdStart?Math.min(t.start,this.cdStart):t.start,this.cdEnd=this.cdEnd?Math.max(t.end,this.cdEnd):t.end}addUTR(t){let e;const n=this.exons;for(let r=0;r<n.length;r++)if(n[r].start<=t.start&&n[r].end>=t.end){e=n[r];break}e?t.start===e.start&&t.end===e.end?e.utr=!0:(t.end<e.end&&(e.cdStart=t.end),t.start>e.start&&(e.cdEnd=t.start)):console.error("No exon found spanning "+cds.start+"-"+cds.end)}finish(){this.assembleParts();var t=this.cdStart,e=this.cdEnd;this.exons.sort((function(t,e){return t.start-e.start})),t&&this.exons.forEach((function(n){(n.end<t||n.start>e)&&(n.utr=!0)}))}popupData(t){const e=super.popupData(t);for(let n of this.exons)if(!n.pseudo&&t>=n.start&&t<n.end&&"function"==typeof n.popupData){e.push("<hr/>");const r=n.popupData(t);for(let t of r)e.push(t)}for(let n of this.parts)if(t>=n.start&&t<n.end&&"function"==typeof n.popupData){e.push("<hr/>");const r=n.popupData(t);for(let t of r)e.push(t)}return e}}function Ua(t,e){const n=e.format;if(t.length<9)return;const r="gff3"===n?"=":" ";return new Va({source:t[1],type:t[2],chr:t[0],start:parseInt(t[3])-1,end:parseInt(t[4]),score:"."===t[5]?void 0:Number(t[5]),strand:t[6],phase:"."===t[7]?0:parseInt(t[7]),attributeString:t[8],delim:r})}function qa(t,e){const n=Ua(t,e);if(!n)return;const r=$a(n.attributeString,n.delim);for(let[t,e]of r){const r=t.toLowerCase();"color"===r||"colour"===r?n.color=mo.createColorString(e):"ID"===t?n.id=e:"Parent"===t&&(n.parent=e)}return n}function Wa(t,e){const n=Ua(t,e);if(!n)return;const r=$a(n.attributeString,n.delim);let i,o;switch(n.type){case"gene":i="gene_id";break;case"transcript":i="transcript_id",o="gene_id";break;default:o="transcript_id"}for(let[t,e]of r){const r=t.toLowerCase();"color"===r||"colour"===r?n.color=mo.createColorString(e):t===i?n.id=e:t===o&&(n.parent=e)}return n}function $a(t,e){var n=[];for(let r of t.split(";")){r=r.trim();const t=r.indexOf(e);if(t>0&&t<r.length-1){const e=r.substring(0,t);let i=Ga(decodeURIComponent(r.substring(t+1).trim()));n.push([e,i])}}return n}function Ga(t){return t.startsWith('"')&&t.endsWith('"')&&(t=t.substr(1,t.length-2)),t}class Za{constructor(t){this.message=t}}function Xa(t,e){if(t.length<3)return;e&&e.gffTags;const n=t[0],r=parseInt(t[1]),i=t.length>2?parseInt(t[2]):r+1;if(isNaN(r)||isNaN(i))return new Za("Unparsable bed record.");const o=new ol({chr:n,start:r,end:i,score:1e3});try{if(t.length>3){if(t[3].indexOf(";")>0&&t[3].indexOf("=")>0){const e=$a(t[3],"=");o.attributes={};for(let t of e)o.attributes[t[0]]=t[1]}o.name||(o.name="."===t[3]?"":t[3])}if(t.length>4&&(o.score="."===t[4]?0:Number(t[4]),isNaN(o.score)))return o;if(t.length>5&&(o.strand=t[5],"."!==o.strand&&"+"!==o.strand&&"-"!==o.strand))return o;if(t.length>6&&(o.cdStart=parseInt(t[6]),isNaN(o.cdStart)))return o;if(t.length>7&&(o.cdEnd=parseInt(t[7]),isNaN(o.cdEnd)))return o;if(t.length>8&&"."!==t[8]&&"0"!==t[8]&&(o.color=mo.createColorString(t[8])),t.length>11){const e=parseInt(t[9]);if(e>1e3)return o;const n=t[10].replace(/,$/,"").split(","),i=t[11].replace(/,$/,"").split(",");if(n.length!==i.length||e!==n.length)return o;const s=[];for(let t=0;t<e;t++){const e=r+parseInt(i[t]),o=e+parseInt(n[t]);s.push({start:e,end:o})}tl(s,o.cdStart,o.cdEnd),o.exons=s}if(e){let n=e.thicknessColumn,r=e.colorColumn;r&&r<t.length&&(o.color=mo.createColorString(t[r])),n&&n<t.length&&(o.thickness=t[n])}}catch(t){}return o}function Ya(t,e){if(t.length<=15)return;return{swScore:Number.parseInt(t[1]),milliDiv:Number.parseInt(t[2]),milliDel:Number.parseInt(t[3]),milliIns:Number.parseInt(t[4]),chr:t[5],start:Number.parseInt(t[6]),end:Number.parseInt(t[7]),strand:t[9],repName:t[10],repClass:t[11],repFamily:t[12],repStart:Number.parseInt(t[13]),repEnd:Number.parseInt(t[14]),repLeft:Number.parseInt(t[15])}}function Ka(t,e){var n=void 0===e.shift?0:1;if(t.length<=9+n)return;const r=parseInt(t[5+n]),i=parseInt(t[6+n]);var o={name:t[0+n],chr:t[1+n],strand:t[2+n],start:parseInt(t[3+n]),end:parseInt(t[4+n]),cdStart:r,cdEnd:i,id:t[0+n]},s=parseInt(t[7+n]),a=t[8+n].split(","),l=t[9+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function Qa(t,e){var n=void 0===e.shift?0:1;if(t.length<=11+n)return;const r=parseInt(t[5+n]),i=parseInt(t[6+n]),o={name:t[11+n],chr:t[1+n],strand:t[2+n],start:parseInt(t[3+n]),end:parseInt(t[4+n]),cdStart:r,cdEnd:i,id:t[0+n]},s=parseInt(t[7+n]),a=t[8+n].split(","),l=t[9+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function Ja(t,e){var n=void 0===e.shift?0:1;if(t.length<=10+n)return;const r=parseInt(t[6+n]),i=parseInt(t[7+n]);var o={name:t[0+n],id:t[1+n],chr:t[2+n],strand:t[3+n],start:parseInt(t[4+n]),end:parseInt(t[5+n]),cdStart:r,cdEnd:i},s=parseInt(t[8+n]),a=t[9+n].split(","),l=t[10+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function tl(t,e,n){for(let r of t){const t=r.end,i=r.start;t<e||i>n?r.utr=!0:(e>=i&&e<=t&&(r.cdStart=e),n>=i&&n<=t&&(r.cdEnd=n))}}function el(t,e){var n,r,i,o,s,a,l;if(!(t.length<9))return n=t[0],r=parseInt(t[1]),i=parseInt(t[2]),s=t[3],a=Number(t[4]),o=t[5].trim(),l=Number(t[6]),0===a&&(a=l),{chr:n,start:r,end:i,name:s,score:a,strand:o,signal:l,pValue:Number(t[7]),qValue:Number(t[8])}}function nl(t,e){if(t.length<=3)return;const n={chr:t[0],start:parseInt(t[1]),end:parseInt(t[2]),value:Number(t[3])};if(e){let r=e.colorColumn;r&&r<t.length&&(n.color=mo.createColorString(t[r]))}return n}function rl(t,e){const n=e.wig;if(n&&"fixedStep"===n.format){const e=n.index*n.step+n.start,r=e+n.span,i=Number(t[0]);return++n.index,isNaN(i)?null:{chr:n.chrom,start:e,end:r,value:i}}if(n&&"variableStep"===n.format){if(t.length<2)return null;const e=parseInt(t[0],10)-1,r=e+n.span,i=Number(t[1]);return isNaN(i)?null:{chr:n.chrom,start:e,end:r,value:i}}return nl(t)}function il(t,e){if(t.length<6)return;const n=["bin","chr","start","end","name","score","strand","refNCBI","refUCSC","observed","molType","class","valid","avHet","avHetSE","func","locType","weight","exceptions","submitterCount","submitters","alleleFreqCount","alleles","alleleNs","alleleFreqs","bitfields"],r={chr:t[1],start:Number.parseInt(t[2]),end:Number.parseInt(t[3]),name:t[4],score:Number.parseInt(t[5])},i=Math.min(t.length,n.length);for(let e=6;e<i;e++)r[n[e]]=t[e];return r}class ol{constructor(t){Object.assign(this,t)}getAttributeValue(t){return this.hasOwnProperty(t)?this[t]:this.attributes?this.attributes[t]:void 0}}function sl(t,e){if(!(t.length<7)){var n=t[0],r=t[1],i=parseInt(t[2]),o=parseInt(t[3]),s=parseInt(t[4]),a=parseInt(t[5]),l=t[6],c={chr:n,name:r,junction_left:i,junction_right:o,num_junction_reads:s,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=i,u=o;if(a>0)for(var f=l.split(","),d=0;d<f.length;d++){var p=f[d].split("-"),g=p[0],m=p[1];g<h&&(h=g),m>u&&(u=m),c.spanning_frag_coords.push({left:g,right:m})}return c.start=h,c.end=u,c}}function al(t,e){if(t.length<7)return null;const n={chr:t[0],start:parseInt(t[1])-1,end:parseInt(t[2]),"Strongest SNP-risk allele":t[3],"Disease/Phenotype":t[4],"P-value":t[5],"Odds ratio or beta":t[6]};return t.length>6&&(n.PUBMEDID=`<a target = "blank" href = "https://www.ncbi.nlm.nih.gov/pubmed/${t[7]}">${t[7]}</a>`),n}function ll(t,e){const n=e.customFormat;if(t.length<n.fields.length)return;const r=n.coords||0,i=t[n.chr],o=parseInt(t[n.start])-r,s={chr:i,start:o,end:void 0!==n.end?parseInt(t[n.end]):o+1};return n.fields&&n.fields.forEach((function(e,r){r!==n.chr&&r!==n.start&&r!==n.end&&(s[e]=t[r])})),s}function cl(t,e){const n=e.columnNames;if(!n)throw Error("Sample names are not defined.   Missing column headers?");const r=n.length-3,i=t[0],o=parseInt(t[1]),s=parseInt(t[2]),a=t.slice(3).map(Number);return a.length==r?{chr:i,start:o,end:s,values:a}:void console.warn(`${i}:${o}-${s} row contains ${a.length} sample columns instead of the expected ${r} columns. Skipping...`)}class hl{constructor(t){this.config=t,this.header={},t.nameField&&(this.header.nameField=t.nameField),this.skipRows=0,t.decode?(this.decode=t.decode,this.delimiter=t.delimiter||"\t"):t.format&&(this.header.format=t.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter="\t")}async parseHeader(t){let e,n,r=this.header;for(;void 0!==(n=await t.nextLine());)if(n.startsWith("track")||n.startsWith("#track")){let t=ul(n);Object.assign(r,t)}else if(n.startsWith("browser"));else if(n.startsWith("#columns")){let t=fl(n);Object.assign(r,t)}else if(n.startsWith("##gff-version 3"))r.format="gff3";else if(n.startsWith("#gffTags"))r.gffTags=!0;else{if(n.startsWith("fixedStep")||n.startsWith("variableStep"))break;if(n.startsWith("#")){const t=n.split(this.delimiter||"\t");t.length>1&&(e=t)}else{this.setDecoder(r.format);const t=n.split(this.delimiter||"\t");try{const n=Object.assign({columnNames:e},r);if(this.decode(t,n))break;t.length>1&&(e=t)}catch(n){t.length>1&&(e=t)}}}if(e){r.columnNames=e;for(let t=0;t<e.length;t++)"color"===e[t]||"colour"===e[t]?r.colorColumn=t:"thickness"===e[t]&&(r.thicknessColumn=t)}return this.header=r,r}async parseFeatures(t){const e=[],n=this.decode,r=this.header.format,i=this.delimiter||"\t";let o,s=0,a=0;for(;void 0!==(o=await t.nextLine());){if(s++,s<=this.skipRows)continue;if(!o||o.startsWith("track")||o.startsWith("#")||o.startsWith("browser"))continue;if("wig"===r&&o.startsWith("fixedStep")){this.header.wig=dl(o);continue}if("wig"===r&&o.startsWith("variableStep")){this.header.wig=pl(o);continue}const t=o.split(i);if(t.length<1)continue;const l=n(t,this.header);l instanceof Za?(a++,a>0&&console.error(`Error parsing line '${o}': ${l.message}`)):l&&e.push(l)}return n===Ps&&function(t){if(0==t.length)return;const e=t[0];if(void 0===e.score&&void 0!==e.name){for(let e of t)if(!("number"==typeof(n=e.name)?n-n==0:"string"==typeof n&&""!==n.trim()&&(Number.isFinite?Number.isFinite(+n):isFinite(+n)))&&"."!==e.name)return;for(let e of t)e.score=Number(e.name),delete e.name}var n;const r=t.filter((t=>t.chr1!==t.chr2));for(let e of r){const n=Object.assign({},e);n.dup=!0,t.push(n),e.chr=e.chr1,e.start=e.start1,e.end=e.end1,n.chr=n.chr2,n.start=n.start2,n.end=n.end2}}(e),e}setDecoder(t){switch(t){case"narrowpeak":case"broadpeak":case"regionpeak":case"peaks":this.decode=el,this.delimiter=this.config.delimiter||/\s+/;break;case"bedgraph":this.decode=nl,this.delimiter=/\s+/;break;case"wig":this.decode=rl,this.delimiter=this.config.delimiter||/\s+/;break;case"gff3":case"gff":this.decode=qa,this.delimiter="\t";break;case"gtf":this.decode=Wa,this.delimiter="\t";break;case"fusionjuncspan":this.decode=sl,this.delimiter=this.config.delimiter||/\s+/;break;case"gtexgwas":this.skipRows=1,this.decode=al,this.delimiter="\t";break;case"refflat":this.decode=Ja,this.delimiter=this.config.delimiter||/\s+/;break;case"genepred":this.decode=Ka,this.delimiter=this.config.delimiter||/\s+/;break;case"genepredext":this.decode=Qa,this.delimiter=this.config.delimiter||/\s+/;break;case"ensgene":this.decode=Ka,this.header.shift=1,this.delimiter=this.config.delimiter||/\s+/;break;case"refgene":this.decode=Qa,this.delimiter=this.config.delimiter||/\s+/,this.header.shift=1;break;case"bed":this.decode=Xa,this.delimiter=this.config.delimiter||/\s+/;break;case"bedpe":case"hiccups":this.decode=Ps,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-domain":this.decode=Fs,this.headerLine=!0,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-loop":this.decode=Ps,this.delimiter=this.config.delimiter||"\t",this.header={colorColumn:7};break;case"interact":this.decode=Aa,this.delimiter=this.config.delimiter||/\s+/;break;case"snp":this.decode=il,this.delimiter="\t";break;case"rmsk":this.decode=Ya,this.delimiter="\t";break;case"gcnv":this.decode=cl,this.delimiter="\t";break;default:const e=function(t){return ks&&ks[t]?function(t){const e=t.fields,n=["chr","start","end"];for(let r=0;r<e.length;r++)for(let i of n)i===e[r]&&(t[i]=r);return t}(ks[t]):void 0}(t);void 0!==e?(this.decode=ll,this.header.customFormat=e,this.delimiter=e.delimiter||"\t"):(this.decode=Xa,this.delimiter=this.config.delimiter||/\s+/)}}}function ul(t){const e={},n=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let r;const i=[];for(let t of n)t&&0!==t.trim().length&&(t.endsWith("=")?r=t:r?(i.push(r+t),r=void 0):i.push(t));for(let t of i){if(!t)return;var o=t.split("=",2);if(2===o.length){const t=o[0].trim(),n=o[1].trim();if(e.hasOwnProperty(t)){let r=e[t];Array.isArray(r)?r.push(n):e[t]=[r,n]}else e[t]=n}}return"interact"==e.type?e.format="interact":"gcnv"===e.type&&(e.format="gcnv"),e}function fl(t){let e={},n=t.split(/\s+/);if(2===n.length){n[1].split(";").forEach((function(t){let n=t.split("=");"color"===n[0]?e.colorColumn=Number.parseInt(n[1])-1:"thickness"===n[0]&&(e.thicknessColumn=Number.parseInt(n[1])-1)}))}return e}function dl(t){const e=t.split(/\s+/);return{format:"fixedStep",chrom:e[1].split("=")[1],start:parseInt(e[2].split("=")[1],10)-1,step:parseInt(e[3].split("=")[1],10),span:e.length>4?parseInt(e[4].split("=")[1],10):1,index:0}}function pl(t){const e=t.split(/\s+/);return{format:"variableStep",chrom:e[1].split("=")[1],span:e.length>2?parseInt(e[2].split("=")[1],10):1}}const gl=t=>ke(t)&&t.indexOf(",")>0&&!t.startsWith("rgb(")?`rgb(${t})`:t;class ml{constructor(t,e){this.browser=e,this.init(t)}init(t){t.displayMode&&(t.displayMode=t.displayMode.toUpperCase()),this.config=t,this.url=t.url,this.type=t.type,this.supportHiDPI=void 0===t.supportHiDPI||t.supportHiDPI,t.name||t.label?this.name=t.name||t.label:Ue(t.url)?this.name=t.url.name:ke(t.url)&&!t.url.startsWith("data:")&&(this.name=je(t.url)),this.id=void 0===this.config.id?this.name:this.config.id,this.order=t.order,t.color&&(this.color=gl(t.color)),t.altColor&&(this.altColor=gl(t.altColor)),"civic-ws"===t.sourceType?this.defaultColor="rgb(155,20,20)":this.defaultColor="rgb(0,0,150)",this.autoscaleGroup=t.autoscaleGroup,this.removable=void 0===t.removable||t.removable,this.height=t.height||100,this.autoHeight=t.autoHeight,this.minHeight=t.minHeight||Math.min(25,this.height),this.maxHeight=t.maxHeight||Math.max(1e3,this.height),this.visibilityWindow=t.visibilityWindow,t.onclick&&(this.onclick=t.onclick,t.onclick=void 0),t.description&&("function"==typeof t.description?this.description=t.description:this.description=()=>t.description),t.hoverTextFields&&(this.hoverTextFields=t.hoverTextFields)}get name(){return this._name}set name(t){this._name=t,this.trackView&&this.trackView.setTrackLabelName(t)}updateConfig(t){this.init(t)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}getState(){const t={};for(let e of Object.keys(this.config))e.startsWith("_")||"function"==typeof this.config[e]||void 0===this.config[e]||(t[e]=this.config[e]);for(let e of Object.keys(t)){if(e.startsWith("_"))continue;const n=this[e];n&&(Ss(n)||"boolean"==typeof n||"metadata"===e)&&(t[e]=n)}this.color&&(t.color=this.color),this.altColor&&(t.altColor=this.altColor),!this.autoscale&&this.dataRange&&(t.min=this.dataRange.min,t.max=this.dataRange.max);for(let e of Object.keys(t)){const n=t[e];if("function"==typeof n)throw Error(`Property '${e}' of track '${this.name} is a function. Functions cannot be saved in sessions.`);if(n instanceof File){const t=`Track ${this.name} is a local file. Sessions cannot be saved with local file references.`;throw Error(t)}if(n instanceof Promise)throw Error(`Property '${e}' of track '${this.name} is a Promise. Promises cannot be saved in sessions.`)}return t}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(t){if(this.disposed)return;const e={};let n;for(let r of Object.keys(t))switch(r.toLowerCase()){case"usescore":e.useScore=1===t[r]||"1"===t[r]||"on"===t[r]||!0===t[r];break;case"visibility":switch(t[r]){case"2":case"3":case"pack":case"full":e.displayMode="EXPANDED";break;case"4":case"squish":e.displayMode="SQUISHED";break;case"1":case"dense":e.displayMode="COLLAPSED"}break;case"color":case"altcolor":e[r]=t[r].startsWith("rgb(")?t[r]:"rgb("+t[r]+")";break;case"featurevisiblitywindow":case"visibilitywindow":e.visibilityWindow=Number.parseInt(t[r]);break;case"maxheightpixels":n=t[r].split(":"),3===n.length&&(e.minHeight=Number.parseInt(n[2]),e.height=Number.parseInt(n[1]),e.maxHeight=Number.parseInt(n[0]));break;case"viewlimits":if(!this.config.autoscale){n=t[r].split(":");let i,o=0;1==n.length?i=Number(n[0]):2==n.length&&(o=Number(n[0]),i=Number(n[1])),e.autoscale=!1,e.dataRange={min:o,max:i}}case"name":e[r]=t[r];break;case"url":e.infoURL=t[r];break;case"type":const i=t[r];vl.has(i)?e[r]=vl.get(i):e[r]=i;break;case"graphtype":e.graphType=t[r];break;default:e[r]=t[r]}for(let t of Object.keys(e))if(!this.config.hasOwnProperty(t)||"name"===t&&this.config._derivedName){let n=e[t];if("true"===n&&(n=!0),"false"===n&&(n=!1),this[t]=n,"height"===t&&this.trackView)try{const t=Number.parseInt(n);this.trackView.setTrackHeight(t)}catch(t){console.error(t)}}}clickedFeatures(t,e){if(e||(e=t.viewport.cachedFeatures),!e||0===e.length)return[];const n=t.genomicLocation,r=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2;return Uo(e,n-r,n+r)}extractPopupData(t,e){const n=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),r=[];let i,o;for(let e in t)if(t.hasOwnProperty(e)&&!n.has(e)&&Ss(t[e])){let n=t[e];r.push({name:Te(e),value:n}),"alleles"===e?i=t[e]:"alleleFreqs"===e&&(o=t[e])}if(i&&o){i.endsWith(",")&&(i=i.substr(0,i.length-1)),o.endsWith(",")&&(o=o.substr(0,o.length-1));let n=i.split(","),s=o.split(",");if(s.length>1){let i=[];for(let t=0;t<s.length;t++)i.push({a:n[t],af:Number(s[t])});i.sort((function(t,e){return t.af-e.af}));let o=i[i.length-1].a;if(1===o.length)for(let n=i.length-2;n>=0;n--){let s=i[n].a;if(1===s.length){e||(e=this.getGenomeId());const n=ml.getCravatLink(t.chr,t.start+1,o,s,e);console.log(n),n&&(r.push("<hr/>"),r.push({html:n}),r.push("<hr/>"))}}}}if(t.attributes)for(let e of Object.keys(t.attributes))r.push({name:e,value:t.attributes[e]});let s=`${t.chr}:${Se(t.start+1)}-${Se(t.end)}`;return t.strand&&(s+=` (${t.strand})`),r.push({name:"Location",value:s}),r}_hoverText(t){const e=this.clickedFeatures(t);if(e&&e.length>0){let t="";for(let n=0;n<e.length;n++){if(10===n){t+="; ...";break}if(!e[n])continue;const r=e[n]._f||e[n];if(t.length>0&&(t+="\n"),this.hoverTextFields){t="";for(let e of this.hoverTextFields)t.length>0&&(t+="\n"),r.hasOwnProperty(e)?t+=r[e]:"function"==typeof r.getAttribute&&(t+=r.getAttribute(e))}else"function"==typeof this.config.hoverText?t+=this.config.hoverText(r):"function"==typeof r.hoverText?t+=r.hoverText():t+=this.hoverText(r)}return t}}hoverText(t){let e="";return t.name&&(e+=t.name,t.value&&(e+=": ")),t.value&&(e+=t.value),e}description(){const t=(t,e)=>`<div class="igv-track-label-popup-shim"><b>${t}: </b>${e}</div>`;let e='<div class="igv-track-label-popup">';if(this.url?Ue(this.url)?e+=t("Filename",this.url.name):e+=t("URL",this.url):e=this.name,this.config){if(this.config.metadata)for(let n of Object.keys(this.config.metadata)){e+=t(n,this.config.metadata[n])}for(let n of Object.keys(this.config)){if(n.startsWith("_"))continue;let r=n.substr(0,1);if(r!==r.toLowerCase()){const r=this.config[n];r&&Ss(r)&&(e+=t(n,r))}}}return e+="</div>",e}dispose(){this.disposed=!0;for(let t of Object.keys(this))this[t]=void 0}static getCravatLink(t,e,n,r,i){if("hg38"===i||"GRCh38"===i){return`<a target="_blank" href="https://run.opencravat.org/result/nocache/variant.html?chrom=${t.startsWith("chr")?t:"chr"+t}&pos=${e}&ref_base=${n}&alt_base=${r}"><b>Cravat ${n}->${r}</b></a>`}}}const vl=new Map([["wiggle_0","wig"],["bed","bed"],["bigBed","bigBed"],["bigWig","bigWig"]]);class bl{constructor(t){switch(this.type=t||"seg",this.type){case"mut":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case"maf":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(t){let e;for(;void 0!==(e=await t.nextLine());)if(!e.startsWith("#")){const t=e.split("\t");this.header={headings:t};break}return this.header}async parseFeatures(t){const e=[];let n;this.header||(this.header=await this.parseHeader(t)),"seg"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(n=this.extractExtraColumns(this.header.headings));const r=this.header.headings[this.dataColumn];let i;for(;void 0!==(i=await t.nextLine());){const t=i.split("\t"),o="seg"===this.type?Number(t[this.dataColumn]):t[this.dataColumn];if(t.length>this.dataColumn){const i=new wl({sample:t[this.sampleColumn],chr:t[this.chrColumn],start:parseInt(t[this.startColumn])-1,end:parseInt(t[this.endColumn]),value:o,valueColumnName:r});if(n){const e=this.extractExtraColumns(t);i.setAttributes({names:n,values:e})}e.push(i)}}return e}extractExtraColumns(t){const e=[];for(let n=0;n<t.length;n++)n!==this.chrColumn&&n!==this.startColumn&&n!==this.endColumn&&n!==this.sampleColumn&&e.push(t[n]);return e}}class wl{constructor(t){let{sample:e,chr:n,start:r,end:i,value:o,valueColumnName:s}=t;this.sample=e,this.chr=n,this.start=r,this.end=i,this.value=o,this.valueColumnName=s}setAttributes(t){let{names:e,values:n}=t;this.attributeNames=e,this.attributeValues=n}getAttribute(t){if(this.attributeNames){const e=this.attributeNames.indexOf(t);if(e>=0)return this.attributeValues[e]}}popupData(t,e){const n=new Set(["chr","start","end","sample","value","row","color","sampleKey","uniqueSampleKey","sampleId","chromosome","uniquePatientKey"]),r=this.chr+":"+Se(this.start+1)+"-"+Se(this.end),i=[{name:"Sample",value:this.sample},{name:"Location",value:r},{name:this.valueColumnName?Te(this.valueColumnName):"Value",value:this.value}];if("mut"===t&&"hg38"===e){const t=this.extractCravatLink(e);t&&(i.push("<hr/>"),i.push({html:t}),i.push("<hr/>"))}if(this.attributeNames&&this.attributeNames.length>0)for(let t=0;t<this.attributeNames.length;t++)!n.has(this.attributeNames[t])&this.valueColumnName!==this.attributeNames[t]&&i.push({name:Te(this.attributeNames[t]),value:this.attributeValues[t]});return i}hoverText(){return`${this.sample}: ${this.value}`}extractCravatLink(t){let e,n;if(this.attributeNames&&this.attributeNames.length>0)for(let r=0;r<this.attributeNames.length;r++)if(e||"Reference_Allele"!==this.attributeNames[r]||(e=this.attributeValues[r]),!n&&this.attributeNames[r].startsWith("Tumor_Seq_Allele")&&this.attributeValues[r]!==e&&(n=this.attributeValues[r]),e&&n)return ml.getCravatLink(this.chr,this.start+1,e,n,t)}}function yl(t){const e=new xl;e.chr=t[0],e.pos=parseInt(t[1]),e.names=t[2],e.referenceBases=t[3],e.alternateBases=t[4],e.quality=t[5],e.filter=t[6],e.info={};const n=t[7];if(n)for(let t of n.split(";")){var r=t.split("=");e.info[r[0]]=r[1]}return e.init(),e}class xl{init(){const t=this.referenceBases,e=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type="SV":this.info.PERIOD&&(this.type="STR")),void 0===this.type&&(this.type=function(t,e){const n=t.length;if(void 0===e)return"UNKNOWN";if(0===e.trim().length||"<NON_REF>"===e||"<*>"===e||"."===e)return"NONVARIANT";{const t=e.split(",").map((function(t){return 1===n&&1===t.length?"SNP":"<NON_REF>"===t?"NONVARIANT":"OTHER"}));let r=t[0];for(let e of t)if(e!==r)return"MIXED";return r}}(t,e)),"NONVARIANT"===this.type&&(this.heterozygosity=0),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if("NONVARIANT"===this.type)this.start=this.pos-1,this.end=this.start+t.length;else{const n=e.split(",").filter((t=>t.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let e of n)if(this.alleles.push(e),"SV"!==this.type&&kl(e)){let n=e.length,r=t.length;const i=Math.min(n,r);let o=0;for(;o<i&&t.charCodeAt(o)===e.charCodeAt(o);)o++,n--,r--;for(;n>0&&r>0;){const i=o+n-1,s=o+r-1;if(e.charCodeAt(i)!==t.charCodeAt(s))break;n--,r--}for(;n>0&&r>0;){const i=o,s=o;if(e.charCodeAt(i)!==t.charCodeAt(s))break;o++,n--,r--}const s=this.pos+o-1,a=s+r;this.start=void 0===this.start?s:Math.min(this.start,s),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos)}}popupData(t,e){const n=`${Se(this.pos)}`,r=this.start===this.end?`${Se(this.start)} | ${Se(this.start+1)}`:`${Se(this.start+1)}-${Se(this.end)}`,i=[{name:"Chr",value:this.chr},{name:"Pos",value:n},{name:"Loc",value:r},{name:"ID",value:this.names?this.names:""},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases.replace("<","&lt;")},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter}];if("SNP"===this.type){let t=this.referenceBases;if(1===t.length){let n=this.alternateBases.split(",");for(let r of n)if(1===r.length){let n=ml.getCravatLink(this.chr,this.pos,t,r,e);n&&(i.push("<hr/>"),i.push({html:n}))}}}if(this.hasOwnProperty("heterozygosity")&&i.push({name:"Heterozygosity",value:this.heterozygosity}),this.info){i.push({html:'<hr style="border-top: dotted 1px;border-color: #c9c3ba" />'});for(let t of Object.keys(this.info))i.push({name:t,value:Sl(decodeURIComponent(this.info[t]))})}return i}hoverText(){return`${this.names}  ${this.referenceBases}->${this.alternateBases}`}getInfo(t){return this.info?this.info[t]:void 0}isRefBlock(){return"NONVARIANT"===this.type}}const _l=new Set(["A","C","T","G"].map((t=>t.charCodeAt(0))));function kl(t){for(let e=0;e<t.length;e++)if(!_l.has(t.charCodeAt(e)))return!1;return!0}function Sl(t,e){return void 0===e&&(e=","),Array.isArray(t)?t.join(e):t}class Cl{construtor(){}async parseHeader(t,e){const n={};n.chrAliasTable=new Map;let r=await t.nextLine();if(!r.startsWith("##fileformat"))throw new Error("Invalid VCF file: missing fileformat line");for(n.version=r.substr(13);void 0!==(r=await t.nextLine())&&r.startsWith("#");){let t;const o={};if(r.startsWith("##")){if(r.startsWith("##INFO")||r.startsWith("##FILTER")||r.startsWith("##FORMAT")){const e=r.indexOf("<"),s=r.lastIndexOf(">");if(!(e>2&&s>0)){console.log("Malformed VCF header line: "+r);continue}const a=r.substring(2,e-1);n[a]||(n[a]={});const l=Ee(r.substring(e+1,s-1),",");for(let e of l){var i=e.split("=");i.length>1&&("ID"===i[0]?t=i[1]:o[i[0]]=i[1])}t&&(n[a][t]=o)}else if(r.startsWith("##contig")&&e){const t=r.indexOf("<ID=");let i=r.indexOf(",",t);-1==i&&(i=r.indexOf(">",t));const o=r.substring(t+4,i),s=e.getChromosomeName(o);n.chrAliasTable.set(s,o)}}else if(r.startsWith("#CHROM")){const t=r.split("\t");if(t.length>8){n.callSets=[];for(let e=9;e<t.length;e++)n.callSets.push({id:e,name:t[e]})}}}return this.header=n,n}async parseFeatures(t){const e=[],n=this.header.callSets,r=8+(n?n.length+1:0);let i;for(;void 0!==(i=await t.nextLine());)if(i&&!i.startsWith("#")){const t=i.split("\t");if(t.length===r){const r=yl(t);if(r.header=this.header,e.push(r),t.length>9){const e=El(t[8].split(":"));r.calls={};for(let i=9;i<t.length;i++){const o=t[i],s=n[i-9],a={callSetName:s.name,info:{}};r.calls[s.id]=a,o.split(":").forEach((function(t,n){if(n===e.genotypeIndex)a.genotype=[],t.split(/[\|\/]/).forEach((function(t){a.genotype.push("."===t?t:parseInt(t))}));else a.info[e.fields[n]]=t}))}}r.info&&r.info.CHR2&&r.info.END&&e.push(Tl(r))}}return e}}function El(t){const e={genotypeIndex:-1,fields:t};for(let n=0;n<t.length;n++)"GT"===t[n]&&(e.genotypeIndex=n);return e}function Tl(t){const e=t.info.CHR2,n=Number.parseInt(t.info.END);return{chr:e,start:n-1,end:n,_f:t}}class Al{constructor(t){if(this.config=t,t.columns){if(void 0===t.columns.chromosome||void 0===t.columns.position||void 0===t.columns.value)throw Error("columns property must define chrCol, posCol, and valueCol");this.posCol=t.columns.position-1,this.chrCol=t.columns.chromosome-1,this.valueCol=t.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(t){const e=await t.nextLine();return this.parseHeaderLine(e)}parseHeaderLine(t){if(this.columns=t.split(/\t/),!this.config.columns)for(let t=0;t<this.columns.length;t++){switch(this.columns[t].toLowerCase()){case"chr":case"chromosome":case"chr_id":this.chrCol=t;break;case"bp":case"pos":case"position":case"chr_pos":this.posCol=t;break;case"p":case"pval":case"pvalue":case"p-value":case"p.value":this.valueCol=t}}return this.columns}async parseFeatures(t){const e=[],n=t.nextLine();let r;for(this.columns||this.parseHeaderLine(n);void 0!==(r=t.nextLine());){const t=r.split(/\t/);if(t.length===this.columns.length){const n=t[this.chrCol],i=parseInt(t[this.posCol])-1,o=i+1,s=Number(t[this.valueCol]);e.push(new Ll({chr:n,start:i,end:o,value:s,line:r,columns:this.columns}))}}return e}}class Ll{constructor(t){let{chr:e,start:n,end:r,value:i,line:o,columns:s}=t;this.chr=e,this.start=n,this.end=r,this.value=i,this.line=o,this.columns=s}popupData(){const t=this.line.split(/\t/);return this.columns.map((function(e,n){return{name:e,value:t[n]}}))}getAttribute(t){const e=this.line.split(/\t/);for(let n=0;n<this.columns.length;n++)if(this.columns[n]===t)return e[n]}}var Ml=new RegExp("([^:]*)\\(([^)]*)\\)"),Rl=new RegExp("([^:]*):([^(]*)\\(([^)]*)\\)");class Il{constructor(t){const e=t?t.decode:void 0;this.nameField=t?t.nameField:void 0,this.skipRows=0,this.decode=e||Bl,this.delimiter="\t"}async parseHeader(t){let e,n;for(;(e=await t.nextLine())&&(e.startsWith("track")||e.startsWith("#")||e.startsWith("browser"));)if(e.startsWith("track")||e.startsWith("#track")){let t=Pl(e);n?Object.assign(n,t):n=t}else if(e.startsWith("#columns")){let t=Fl(e);n?Object.assign(n,t):n=t}else e.startsWith("##gff-version 3")&&(this.format="gff3",n||(n={}),n.format="gff3");return this.header=n,n}async parseFeatures(t){const e=[],n=this.decode,r=this.delimiter||"\t";let i,o=0;for(;void 0!==(i=t.nextLine());){if(o++,o<=this.skipRows||i.startsWith("track")||i.startsWith("#")||i.startsWith("browser"))continue;let t=s();if(t.length<1)continue;if(!this.aed){this.aed=Ol(t);continue}const r=n.call(this,t,undefined);r&&e.push(r)}return e;function s(){for(var t,e,n=[],o="",s=!1;i||""===i;){for(t=0;t<i.length;t++)(e=i.charAt(t))===r?s?o+=e:(n.push(o),o=""):'"'===e?t+1<i.length&&'"'===i.charAt(t+1)?(s&&(o+='"'),t++):s=!s:o+=e;if(!s)break;o+="\n",i=nextLine()}return n.push(o),n}}}function Nl(t){var e=Rl.exec(t);if(e)return{namespace:e[1],name:e[2],type:e[3]};if(e=Ml.exec(t))return{namespace:"?",name:e[1],type:e[2]};throw new Error("Error parsing the header row of AED file - column not in ns:name(ns:type) format")}function Ol(t){var e,n,r;for(e={columns:[],metadata:{}},n=0;n<t.length;n++)r=Nl(t[n]),e.columns.push(r);return e}function Pl(t){const e={},n=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let r;const i=[];for(let t of n)t&&0!==t.trim().length&&(t.endsWith("=")>0?r=t:r?(i.push(r+t),r=void 0):i.push(t));for(let t of i){if(!t)return;var o=t.split("=",2);if(2===o.length){const t=o[0].trim(),n=o[1].trim();e[t]=n}}return e}function Fl(t){let e={},n=t.split(/\s+/);if(2===n.length){n[1].split(";").forEach((function(t){let n=t.split("=");"color"===n[0]?e.colorColumn=Number.parseInt(n[1])-1:"thickness"===n[0]&&(e.thicknessColumn=Number.parseInt(n[1])-1)}))}return e}function Dl(t,e){var n,r,i=t.columns;this.aed=t,this.allColumns=e,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=".",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let t=0;t<e.length;t++)if(n=e[t]){"aed:Integer"===(r=i[t]).type&&(n=parseInt(n));var o=[];if(r.namespace.length>0)for(let t=0;t<r.namespace.length;t++)o.push(r.namespace.charCodeAt(t));"bio"===r.namespace.trim()?"sequence"===r.name?this.chr=n:"start"===r.name?this.start=n:"end"===r.name?this.end=n:"cdsMin"===r.name?this.cdStart=n:"cdsMax"===r.name?this.cdEnd=n:"strand"===r.name&&(this.strand=n):"aed"===r.namespace?"name"===r.name&&(this.name=n):"style"===r.namespace&&"color"===r.name&&(this.color=mo.createColorString(n))}}function Bl(t,e){var n,r,i,o,s,a,l=0,c=this.aed.columns;if(t.length===c.length){for(a=0;a<t.length;a++)o=c[a],""!==(i=t[a])&&l++,"name"===o.name&&"aed"===o.namespace?n=i:"value"===o.name&&"aed"===o.namespace&&(r=i);if(2===l&&n&&r)return s=Nl(n),this.aed.metadata[s.namespace]||(this.aed.metadata[s.namespace]={}),void(this.aed.metadata[s.namespace][s.name]||(this.aed.metadata[s.namespace][s.name]={type:s.type,value:r}));var h=new Dl(this.aed,t);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log("Cannot parse feature: "+t.join(","))}else console.log("Corrupted AED file row: "+t.join(","))}Dl.prototype.popupData=function(){for(var t=[],e=this.aed,n=0;n<this.allColumns.length;n++){var r=this.allColumns[n],i=e.columns[n].name;"sequence"!==i&&"color"!==i&&r&&t.push({name:i,value:r})}return t};class zl{constructor(t,e){this.littleEndian=void 0===e||e,this.position=0,this.view=t,this.length=t.byteLength}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){var t=this.view.getUint8(this.position,this.littleEndian);return this.position++,t}getShort(){var t=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,t}getUShort(){var t=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,t}getInt(){var t=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,t}getUInt(){var t=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,t}getLong(){var t=[];t[0]=this.view.getUint8(this.position),t[1]=this.view.getUint8(this.position+1),t[2]=this.view.getUint8(this.position+2),t[3]=this.view.getUint8(this.position+3),t[4]=this.view.getUint8(this.position+4),t[5]=this.view.getUint8(this.position+5),t[6]=this.view.getUint8(this.position+6),t[7]=this.view.getUint8(this.position+7);var e=0;if(this.littleEndian)for(let n=t.length-1;n>=0;n--)e=256*e+t[n];else for(let n=0;n<t.length;n++)e=256*e+t[n];return this.position+=8,e}getString(t){for(var e,n="";0!==(e=this.view.getUint8(this.position++))&&(n+=String.fromCharCode(e),!t||n.length!==t););return n}getFixedLengthString(t){var e,n,r="";for(e=0;e<t;e++)(n=this.view.getUint8(this.position++))>0&&(r+=String.fromCharCode(n));return r}getFixedLengthTrimmedString(t){var e,n,r="";for(e=0;e<t;e++)(n=this.view.getUint8(this.position++))>32&&(r+=String.fromCharCode(n));return r}getFloat(){var t=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,t}getDouble(){var t=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,t}skip(t){return this.position+=t,this.position}getVPointer(){var t=this.position,e=this.view.getUint8(t+1)<<8|this.view.getUint8(t),n=4294967296*(255&this.view.getUint8(t+6))+16777216*(255&this.view.getUint8(t+5))+65536*(255&this.view.getUint8(t+4))+256*(255&this.view.getUint8(t+3))+(255&this.view.getUint8(t+2));return this.position+=8,new Hl(n,e)}}class Hl{constructor(t,e){this.block=t,this.offset=e}isLessThan(t){return this.block<t.block||this.block===t.block&&this.offset<t.offset}isGreaterThan(t){return this.block>t.block||this.block===t.block&&this.offset>t.offset}print(){return this.block+":"+this.offset}}class Vl{constructor(t){this.tabix=!0}parse(t,e){const n=new zl(new DataView(t)),r=n.getInt();if(21582659!==r)throw 38359875===r?Error("CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js"):Error("Not a CSI index");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=n.getInt(),this.depth=n.getInt();const i=[];let o=0;if(n.getInt()>=28){n.getInt(),n.getInt(),n.getInt(),n.getInt(),n.getInt(),n.getInt();const t=n.getInt(),r=n.position+t;let o=0;for(;n.position<r;){let t=n.getString();e&&(t=e.getChromosomeName(t)),this.sequenceIndexMap[t]=o,i[o]=t,o++}}const s=this.bin_limit()+1,a=n.getInt();for(let t=0;t<a;t++){const e=[],r=[],i=n.getInt();for(let t=0;t<i;t++){const t=n.getInt();if(r[t]=n.getVPointer(),t>s)n.getInt(),n.getVPointer(),n.getVPointer(),n.getLong(),n.getLong();else{e[t]=[];const r=n.getInt();for(let i=0;i<r;i++){const r=n.getVPointer(),i=n.getVPointer();r&&i&&(r.block<this.blockMin&&(this.blockMin=r.block),i.block>o&&(o=i.block),e[t].push([r,i]))}}}i>0&&(this.indices[t]={binIndex:e,loffset:r})}this.lastBlockPosition=o}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}blocksForRange(t,e,n){const r=this.indices[t];if(r){const t=this.reg2bins(e,n);if(0==t.length)return[];const i=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(r.binIndex[t]){const e=r.binIndex[t],n=e.length;for(let r=0;r<n;++r){const n=e[r][0],o=e[r][1];i.push({minv:n,maxv:o,bin:t})}}return function(t,e){const n=[];let r=null;return 0===t.length?t:(t.sort((function(t,e){const n=t.minv.block-e.minv.block;return 0!==n?n:t.minv.offset-e.minv.offset})),t.forEach((function(t){var i,o;e&&!t.maxv.isGreaterThan(e)||(null===r?(n.push(t),r=t):(i=r,(o=t).minv.block-i.maxv.block<65e3&&o.maxv.block-i.minv.block<5e6?t.maxv.isGreaterThan(r.maxv)&&(r.maxv=t.maxv):(n.push(t),r=t)))})),n)}(i,r.loffset[t[0]])}return[]}reg2bins(t,e){(t-=1)<1&&(t=1),e>2**50&&(e=2**34),e-=1;let n=0,r=0,i=this.minShift+3*this.depth;const o=[];for(;n<=this.depth;i-=3,r+=1<<3*n,n+=1){const n=r+(t>>i),s=r+(e>>i);if(s-n+o.length>this.maxBinNumber)throw new Error(`query ${t}-${e} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);o.push([n,s])}return o}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}const jl=1e6;class Ul{constructor(){}async parse(t,e,n){const r=[];let i=Number.MAX_SAFE_INTEGER,o=0;const s=new zl(new DataView(t)),a=s.getInt(),l={};if(!(21578050===a||e&&21578324===a))throw new Error(indexURL+" is not a "+(e?"tabix":"bai")+" file");{const t=s.getInt();if(e){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let e=0;e<t;e++){let t=s.getString();n&&(t=n.getChromosomeName(t)),l[t]=e}}for(let e=0;e<t;e++){const t={},n=[],a=s.getInt();for(let e=0;e<a;e++){const e=s.getInt();if(37450===e)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{t[e]=[];const n=s.getInt();for(let r=0;r<n;r++){const n=s.getVPointer(),r=s.getVPointer();n&&r&&(n.block<i&&(i=n.block),r.block>o&&(o=r.block),t[e].push([n,r]))}}}const l=s.getInt();for(let t=0;t<l;t++){const t=s.getVPointer();n.push(t)}a>0&&(r[e]={binIndex:t,linearIndex:n})}this.firstBlockPosition=i,this.lastBlockPosition=o,this.indices=r,this.sequenceIndexMap=l,this.tabix=e}}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}blocksForRange(t,e,n){const r=this.indices[t];if(r){const t=function(t,e){const n=[];e>=1<<29&&(e=1<<29);return--e,n.push([0,0]),n.push([1+(t>>26),1+(e>>26)]),n.push([9+(t>>23),9+(e>>23)]),n.push([73+(t>>20),73+(e>>20)]),n.push([585+(t>>17),585+(e>>17)]),n.push([4681+(t>>14),4681+(e>>14)]),n}(e,n),i=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(r.binIndex[t]){const e=r.binIndex[t],n=e.length;for(let r=0;r<n;++r){const n=e[r][0],o=e[r][1];i.push({minv:n,maxv:o,bin:t})}}const o=r.linearIndex.length;let s=null;const a=Math.min(e>>14,o-1),l=Math.min(n>>14,o-1);for(let t=a;t<=l;++t){const e=r.linearIndex[t];e&&(s&&!e.isLessThan(s)||(s=e))}return function(t,e){const n=[];let r=null;return 0===t.length?t:(t.sort((function(t,e){const n=t.minv.block-e.minv.block;return 0!==n?n:t.minv.offset-e.minv.offset})),t.forEach((function(t){e&&!t.maxv.isGreaterThan(e)||(null!==r&&function(t,e){const n=e.minv.block-t.maxv.block,r=e.maxv.block-t.minv.block;return n<3e4&&r<10*jl}(r,t)?t.maxv.isGreaterThan(r.maxv)&&(r.maxv=t.maxv):(n.push(t),r=t))})),n)}(i,s)}return[]}}class ql{constructor(){}async parse(t,e){let n=0;this.chrIndex={},this.lastBlockPosition=[];const r=new zl(new DataView(t));!function(t){t.getInt(),t.getInt();const e=t.getInt();if(t.getString(),t.getLong(),t.getLong(),t.getString(),t.getInt(),e>=3){let e=t.getInt();for(;e-- >0;)t.getString(),t.getString()}}(r);let i=r.getInt();for(;i-- >0;){let t=r.getString();e&&(t=e.getChromosomeName(t));const i=r.getInt(),o=r.getInt(),s=r.getInt();r.getInt(),r.getInt();let a=r.getLong();const l=[];for(let t=0;t<o;t++){const t=r.getLong();l.push({min:a,max:t}),a=t,t>n&&(n=t)}this.chrIndex[t]={chr:t,blocks:l,longestFeature:s,binWidth:i}}this.lastBlockPosition=n}get chromosomeNames(){return Object.keys(this.chrIndex)}blocksForRange(t,e,n){const r=this.chrIndex[t];if(r){const t=r.blocks,i=r.longestFeature,o=r.binWidth,s=Math.max(e-i,0),a=Math.floor(s/o);if(a>=t.length)return[];{const e=Math.min(Math.floor((n-1)/o),t.length-1),r=t[a].min,i=t[e].max;if(0===i-r)return[];return[{minv:{block:r,offset:0},maxv:{block:i,offset:0}}]}}}}async function Wl(t,e,n){let r=await Eo.loadArrayBuffer(t,Cs(e)),i=new DataView(r);if(31===i.getUint8(0)&&139===i.getUint8(1)){r=io(r).buffer,i=new DataView(r)}switch(i.getInt32(0,!0)){case 21578050:return async function(t,e){const n=new Ul;return await n.parse(t,!1,e),n}(r,n);case 21578324:return async function(t,e){const n=new Ul;return await n.parse(t,!0,e),n}(r,n);case 21582659:return async function(t,e){const n=new Vl;return n.parse(t,e),n}(r,n);case 1480870228:return async function(t,e){const n=new ql;return n.parse(t,e),n}(r,n);case 38359875:throw Error("CSI version 2 is not supported.");default:throw Error(`Unrecognized index type: ${t}`)}}function $l(t){return"string"==typeof t||t instanceof String?new Gl(t):new Zl(t)}class Gl{constructor(t){this.data=t,this.ptr=0}nextLine(){var t=this.ptr,e=this.data.indexOf("\n",t),n=this.data;if(e>0)return this.ptr=e+1,e>t&&"\r"===n.charAt(e-1)?n.substring(t,e-1):n.substring(t,e);var r=n.length;return this.ptr=r,t>=r?void 0:n.substring(t)}}class Zl{constructor(t){this.data=t,this.length=this.data.length,this.ptr=0}nextLine(){var t,e;if(e="",!(this.ptr>=this.length)){for(var n=this.ptr;n<this.length;n++)if("\r"!==(t=String.fromCharCode(this.data[n]))){if("\n"===t)break;e+=t}return this.ptr=n+1,e}}}class Xl{constructor(t){this.config=t,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let t;try{for(;;){const e=this.buffer?this.buffer.length:0;for(;this.bufferPtr<e;){const e=String.fromCharCode(this.buffer[this.bufferPtr++]);if("\r"!==e){if("\n"===e)return t;t=t?t+e:e}}if(this.eof)return t;await this.readNextBlock()}}catch(e){return console.warn(e),this.eof=!0,t}}async readNextBlock(){const t=Cs(this.config,{range:{start:this.filePtr,size:26}}),e=oo(await Eo.loadArrayBuffer(this.config.url,t));if(0===e)this.eof=!0,this.buffer=void 0;else{const t=Cs(this.config,{range:{start:this.filePtr,size:e}}),n=await Eo.loadArrayBuffer(this.config.url,t);n.byteLength<e&&(this.eof=!0),this.buffer=io(n),this.bufferPtr=0,this.filePtr+=n.byteLength}}}class Yl{constructor(t,e){var n;this.config=t||{},this.genome=e,this.indexURL=t.indexURL,this.indexed=t.indexed,Ue(this.config.url)?this.filename=this.config.url.name:Ms(this.config.url)?(this.indexed=!1,this.dataURI=t.url):(n=He(this.config.url),this.filename=t.filename||n.file),this.parser=this.getParser(this.config),"vcf"!==this.config.format||this.config.indexURL||console.warn("Warning: index file not specified.  The entire vcf file will be loaded.")}async defaultVisibilityWindow(){if(this.config.indexURL){const t=await this.getIndex();if(t&&t.lastBlockPosition){let e=0;const n=1e4;for(let n of t.chromosomeNames){const t=this.genome.getChromosome(n);t&&(e+=t.bpLength)}return Math.round(e/t.lastBlockPosition*n)}}}async readFeatures(t,e,n){return await this.getIndex()?(this.indexed=!0,this.loadFeaturesWithIndex(t,e,n)):this.dataURI?(this.indexed=!1,this.loadFeaturesFromDataURI()):(this.indexed=!1,this.loadFeaturesNoIndex())}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const t=await this.getIndex();if(!t)throw new Error("Unable to load index: "+this.config.indexURL);let e;if(t.tabix)e=new Xl(this.config);else{const n=Object.values(t.chrIndex).flatMap((t=>t.blocks)).map((t=>t.max)).reduce(((t,e)=>Math.min(t,e)),Number.MAX_SAFE_INTEGER),r=Cs(this.config,{bgz:t.tabix,range:{start:0,size:n}});e=$l(await Eo.loadString(this.config.url,r))}return this.header=await this.parser.parseHeader(e),this.header}{const t=Cs(this.config),e=await Eo.loadString(this.config.url,t);let n=$l(e);return this.header=await this.parser.parseHeader(n),n=$l(e),this.features=await this.parser.parseFeatures(n),this.header}}getParser(t){switch(t.format){case"vcf":return new Cl(t);case"seg":return new bl("seg");case"mut":return new bl("mut");case"maf":return new bl("maf");case"gwas":return new Al(t);case"aed":return new Il(t);default:return new hl(t)}}async loadFeaturesNoIndex(){if(this.features){const t=this.features;return delete this.features,t}{const t=Cs(this.config),e=await Eo.loadString(this.config.url,t);if(!this.header){const t=$l(e);this.header=await this.parser.parseHeader(t)}const n=$l(e);return await this.parser.parseFeatures(n)}}async loadFeaturesWithIndex(t,e,n){const r=this.config,i=this.parser,o=this.index.tabix,s=o?this.index.sequenceIndexMap[t]:t;if(void 0===s)return[];const a=this.genome,l=this.index.blocksForRange(s,e,n);if(l&&0!==l.length){const s=[];for(let c of l){const l=c.minv.block,h=c.minv.offset,u=c.maxv.offset;let f;if(o){let t=0;if(u>0){const e=Cs(r,{range:{start:c.maxv.block,size:26}});t=oo(await Eo.loadArrayBuffer(r.url,e))}f=c.maxv.block+t}else f=c.maxv.block;const d=Cs(r,{range:{start:l,size:f-l+1}});let p;if(o){p=io(await Eo.loadArrayBuffer(r.url,d))}else p=await Eo.loadString(r.url,d);const g=$l(h?p.slice(h):p);let m=await i.parseFeatures(g);m=m.filter((t=>void 0===t._f));let v=!1;for(let r=0;r<m.length;r++){const i=m[r];if((a?a.getChromosomeName(i.chr):i.chr)!==t){if(0===s.length)continue;break}if(i.start>n){s.push(i);break}i.end>=e&&i.start<=n&&(v||(v=!0,r>0&&s.push(m[r-1])),s.push(i))}}return s.sort((function(t,e){return t.start-e.start})),s}return[]}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return Wl(this.config.indexURL,this.config,this.genome)}async loadFeaturesFromDataURI(){if(this.features){const t=this.features;return delete this.features,t}{const t=co(this.dataURI);let e=$l(t);return this.header=await this.parser.parseHeader(e),this.header instanceof String&&this.header.startsWith("##gff-version 3")&&(this.format="gff3"),e=$l(t),this.features=await this.parser.parseFeatures(e),this.features}}}const Kl=ke;class Ql{constructor(t){this.config=t}async readFeatures(t,e,n){let r;r="function"==typeof this.config.url?this.config.url({chr:t,start:e,end:n}):this.config.url.replace("$CHR",t).replace("$START",e).replace("$END",n);let i,o=Object.assign({},this.config);void 0!==this.config.body&&("function"==typeof this.config.body?o.body=this.config.body({chr:t,start:e,end:n}):o.body=this.config.body.replace("$CHR",t).replace("$START",e).replace("$END",n));const s=await Eo.load(r,o);if(s&&(i="function"==typeof this.config.parser?this.config.parser(s):Kl(s)?JSON.parse(s):s),this.config.mappings){let t=Object.keys(this.config.mappings);for(let e of i)for(let n of t)e[n]=e[this.config.mappings[n]]}return i}}const Jl=function(t,e){this.config=t,this.genome=e,this.expandQueryInterval=!1};Jl.prototype.readFeatures=function(t,e,n){const r=Math.max(0,Math.floor(e));let i=Math.ceil(n);if(this.genome){const e=this.genome.getChromosome(t);e&&i>e.bpLength&&(i=e.bpLength)}const o=this.config.url+"?db="+this.config.db+"&table="+this.config.tableName+"&chr="+t+"&start="+r+"&end="+i;return Eo.loadJson(o,this.config).then((function(t){return t?(t.forEach((function(t){t.hasOwnProperty("exonStarts")&&t.hasOwnProperty("exonEnds")&&t.hasOwnProperty("exonCount")&&t.hasOwnProperty("cdsStart")&&t.hasOwnProperty("cdsEnd")&&function(t){var e,n,r,i,o,s;e=t.exonCount,n=t.exonStarts.split(","),r=t.exonEnds.split(","),i=[];for(var a=0;a<e;a++){var l={start:o=parseInt(n[a]),end:s=parseInt(r[a])};(t.cdsStart>s||t.cdsEnd<t.cdsStart)&&(l.utr=!0),t.cdsStart>=o&&t.cdsStart<=s&&(l.cdStart=t.cdsStart),t.cdsEnd>=o&&t.cdsEnd<=s&&(l.cdEnd=t.cdsEnd),i.push(l)}t.exons=i}(t)})),t):null}))};const tc=["Name","gene_name","gene","gene_id","alias","locus","name"];class ec{constructor(t){this.format=t.format,this.nameField=t.nameField,this.filterTypes=void 0===t.filterTypes?new Set(["chromosome"]):new Set(t.filterTypes)}combineFeatures(t,e){let n;const r=this.filterTypes;if(t=t.filter((t=>void 0===r||!r.has(t.type))),"gff3"===this.format){const e=this.combineFeaturesById(t);n=this.combineFeaturesByType(e)}else n=this.combineFeaturesByType(t);return n.sort((function(t,e){return t.start-e.start})),this.numberExons(n,e),this.nameFeatures(n),n}combineFeaturesById(t){const e=new Map,n=[];for(let r of t)if(za(r.type)||Ba(r.type)||!r.id)n.push(r);else{let t=e.get(r.chr);t||(t=new Map,e.set(r.chr,t));let n=t.get(r.id);n?n.push(r):t.set(r.id,[r])}for(let t of e.values())for(let e of t.values())if(e.length>1){const t=e[0];t.exons=[];for(let n of e)t.start=Math.min(t.start,n.start),t.end=Math.max(t.end,n.end),t.exons.push({start:n.start,end:n.end});n.push(t)}else n.push(e[0]);return n}combineFeaturesByType(t){const e=t.filter((t=>"gene"===t.type||t.type.endsWith("_gene"))),n=Object.create(null);for(let t of e)n[t.id]=t;const r=Object.create(null),i=[],o=new Set,s=this.filterTypes;t=t.filter((t=>void 0===s||!s.has(t.type)));for(let e of t)if("biological_region"===e.type&&console.log(),Ba(e.type)){const t=e.id;if(void 0!==t){const s=new ja(e);r[t]=s,i.push(s),o.add(e);const a=n[e.parent];a&&(s.geneObject=a,o.add(a))}}for(let e of t)if(za(e.type)){const t=c(e);if(t)for(let n of t){let s=r[n];if(!s&&"gtf"===this.format){const t=Object.assign({},e);t.type="transcript",s=new ja(t),r[n]=s,i.push(s)}if(void 0!==s){if(a=e.type,Na.has(a))if(t.length>1){const t=new Va(e);s.addExon(t)}else s.addExon(e);else s.addPart(e);o.add(e)}}}var a;i.forEach((function(t){"function"==typeof t.finish&&t.finish()}));const l=t.filter((t=>!o.has(t)));for(let t of l)i.push(t);return i;function c(t){return t.parent&&""!==t.parent.trim()?t.parent.trim().split(","):null}}numberExons(t,e){for(let n of t)if(n.exons&&(!e||n.end<=e.end&&n.start>e.start))for(let t=0;t<n.exons.length;t++){n.exons[t].number="-"===n.strand?n.exons.length-t:t+1}}nameFeatures(t){for(let e of t)if(e.attributeString){const t="gff3"===this.format?"=":" ",n=$a(e.attributeString,t),r=new Map(n);if(this.nameField)e.name=r.get(this.nameField);else for(let t of tc)if(r.has(t)){e.name=r.get(t);break}}}}const nc=function(t){this.config=t,this.url=t.url,this.tissueId=t.tissueSiteDetailId,this.indexed=!0,this.datasetId=t.datasetId||"gtex_v8"};nc.prototype.readFeatures=async function(t,e,n){let r=t.startsWith("chr")?t:"chr"+t,i=Math.floor(e),o=Math.ceil(n),s=this.datasetId,a=this.url+"?chromosome="+r+"&start="+i+"&end="+o+"&tissueSiteDetailId="+this.tissueId+"&datasetId="+s;const l=await Eo.loadJson(a,{withCredentials:this.config.withCredentials});return l&&l.singleTissueEqtl?(l.singleTissueEqtl.forEach((function(t){t.chr=t.chromosome,t.position=t.pos,t.start=t.pos-1,t.end=t.start+1,t.snp=t.snpId,t.geneName=t.geneSymbol,t.geneId=t.gencodeId})),l.singleTissueEqtl):void 0};const rc=function(t){this.config=t,this.url=t.url,this.cellConditionId=t.cellConditionId,this.valueThreshold=t.valueThreshold?t.valueThreshold:.05};rc.prototype.readFeatures=function(t,e,n){var r=this,i=this.url+"?chromosome="+t+"&start="+e+"&end="+n+"&cell_condition_id="+this.cellConditionId;return new Promise((function(t,e){Eo.loadJson(i,{withCredentials:r.config.withCredentials}).then((function(e){e?(e.eqtls.forEach((function(t){t.chr=t.chromosome,t.start=t.position,t.end=t.position+1})),t(e.eqtls)):t(null)})).catch((function(t){e(t)}))}))};const ic=Eo.apiKey;function oc(t){var e=t.url+"/"+t.entity+"/"+t.entityId;return t.headers={"Cache-Control":"no-cache"},Eo.loadJson(e,t)}function sc(t){return new Promise((function(e,n){var r=t.results?t.results:[],i=t.url,o=t.body,s=t.decode,a="?",l=t.fields;return ic&&(i=i+a+"key="+ic,a="&"),l&&(i=i+a+"fields="+l),function t(a){a?o.pageToken=a:void 0!==o.pageToken&&delete o.pageToken;var l=JSON.stringify(o);Eo.loadJson(i,{sendData:l,contentType:"application/json",headers:{"Cache-Control":"no-cache"}}).then((function(n){var i,o;n?((o=s?s(n):n)&&o.forEach((function(t){r.push(t)})),(i=n.nextPageToken)?t(i):e(r)):e(r)})).catch((function(t){n(t)}))}()}))}const ac=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.variantSetId=t.variantSetId,this.callSetIds=t.callSetIds,this.includeCalls=void 0===t.includeCalls||t.includeCalls};ac.prototype.readHeader=function(){var t=this;return t.header?Promise.resolve(t.header):(t.header={},!1===t.includeCalls?Promise.resolve(t.header):sc({url:t.url+"/callsets/search",fields:"nextPageToken,callSets(id,name)",body:{variantSetIds:Array.isArray(t.variantSetId)?t.variantSetId:[t.variantSetId],pageSize:"10000"},decode:function(e){if(t.callSetIds){var n=[],r=new Set;return t.callSetIds.forEach((function(t){r.add(t)})),e.callSets.forEach((function(t){r.has(t.id)&&n.push(t)})),n}return e.callSets}}).then((function(e){return t.header.callSets=e,t.header})))},ac.prototype.readFeatures=function(t,e,n){const r=this,i=this.genome;return r.readHeader().then((function(t){return new Promise((function(t,e){r.chrAliasTable?t(r.chrAliasTable):r.readMetadata().then((function(e){r.metadata=e.metadata,r.chrAliasTable={},e.referenceBounds&&i&&e.referenceBounds.forEach((function(t){var e=t.referenceName,n=i.getChromosomeName(e);r.chrAliasTable[n]=e})),t(r.chrAliasTable)}))}))})).then((function(i){var o=i.hasOwnProperty(t)?i[t]:t;return sc({url:r.url+"/variants/search",fields:r.includeCalls?void 0:"nextPageToken,variants(id,variantSetId,names,referenceName,start,end,referenceBases,alternateBases,quality,filter,info)",body:{variantSetIds:Array.isArray(r.variantSetId)?r.variantSetId:[r.variantSetId],callSetIds:r.callSetIds?r.callSetIds:void 0,referenceName:o,start:e.toString(),end:n.toString(),pageSize:"10000"},decode:function(t){var e,n=[];return t.variants.forEach((function(t){e=function(t){var e,n=new xl;return n.chr=t.referenceName,n.start=parseInt(t.start),n.end=parseInt(t.end),n.pos=n.start+1,n.names=Sl(t.names,"; "),n.referenceBases=t.referenceBases,n.alternateBases=Sl(t.alternateBases),n.quality=t.quality,n.filter=Sl(t.filter),n.info={},t.info&&Object.keys(t.info).forEach((function(e){var r,i=t.info[e];r=Array.isArray(i)?i.join(","):i,n.info[e]=r})),n.calls={},t.calls&&t.calls.forEach((function(t){e=t.callSetId,n.calls[e]=t})),init(n),n}(t),e.isRefBlock()||n.push(e)})),n}})}))},ac.prototype.readMetadata=function(){return oc({url:this.url,entity:"variantsets",entityId:this.variantSetId})};class lc{constructor(t){this.config=t}async readFeatures(t,e,n){const r=(await Eo.loadJson(this.config.url+"/variants/?count=50000")).records,i=[];for(let t of r)if(t.coordinates){t.id;const e=t.coordinates;e.chromosome&&i.push(new cc(e.chromosome,e.start-1,e.stop,t)),e.chromosome2&&i.push(new cc(e.chromosome2,e.start2-1,e.stop2,t))}return i}}class cc{constructor(t,e,n,r){if(this.chr=t,this.start=e,this.end=n,this.id=r.id,this.entrezName=r.entrez_name,this.name=r.name,this.actionabilityScore=r.civic_actionability_score,r.coordinates.reference_bases&&(this.refBases=r.coordinates.reference_bases),r.coordinates.variant_bases&&(this.altBases=r.coordinates.variant_bases),r.variant_types&&(this.variant_types=r.variant_types),this.locationString=this.chr+":"+Se(this.start+1)+"-"+Se(this.end),void 0!==this.actionabilityScore){let t;if(this.actionabilityScore<=10)t=.2;else{const e=Math.min(30,this.actionabilityScore);t=.2+.8*Math.log10((e-10)/2)}this.alpha=t}}popupData(){const t=n("CIViC","https://civicdb.org/links/variants/"+this.id);this.refBases!==this.altBases&&this.refBases&&1===this.refBases.length&&this.altBases&&this.altBases.length;const e=[t];if(e.push({name:"Entrez",value:n(this.entrezName,"https://ghr.nlm.nih.gov/gene/"+this.entrezName)}),e.push({name:"Name",value:this.name}),this.variant_types&&this.variant_types.length>0){const t=1===this.variant_types.length?"Type":"Types";let n;for(let t of this.variant_types)n?n+=", "+t.display_name:n=t.display_name;e.push({name:t,value:n})}return e.push({name:"Actionability",value:this.actionabilityScore}),e.push({name:"Location",value:this.locationString}),e;function n(t,e){return"<a target='_blank' href='"+e+"'>"+t+"</a>"}}}class hc{constructor(t,e){if(this.config=t,this.genome=e,this.format=t.format?t.format.toUpperCase():"BAM","BAM"!==this.format&&"VCF"!==this.format)throw Error(`htsget format ${t.format} is not supported`)}async readHeaderData(){const t=`${uc(this.config)}?class=header&format=${this.format}`,e=await Eo.loadJson(t,Cs(this.config));return await this.loadUrls(e.htsget.urls)}async readData(t,e,n){const r=`${uc(this.config)}?format=${this.format}&referenceName=${t}&start=${Math.floor(e)}&end=${Math.ceil(n)}`,i=await Eo.loadJson(r,Cs(this.config));return this.loadUrls(i.htsget.urls)}async loadUrls(t){const e=[];for(let n of t)if(n.url.startsWith("data:"))e.push(Promise.resolve(fc(n.url)));else{const t=Cs(this.config||{});n.headers&&(t.headers=Object.assign(t.headers||{},n.headers)),e.push(Eo.loadArrayBuffer(n.url,t))}return function(t){let e=0;for(let n of t)e+=n.byteLength;let n=0;const r=new Uint8Array(e);for(let e of t){const t=new Uint8Array(e);r.set(t,n),n+=t.length}return r}(await Promise.all(e))}static async inferFormat(t){try{const e=uc(t),n=`${e}${e.includes("?")?"&":"?"}class=header`,r=await Eo.loadJson(n,Cs(t));if(r.htsget){const e=r.htsget.format;if("BAM"!==e&&"VCF"!==e)throw Error(`htsget format ${e} is not supported`);t.format=e.toLowerCase(),t.sourceType="htsget",t.name||(t.name=await As(t.url))}}catch(t){}}}function uc(t){if(t.url&&t.endpoint&&t.id)return t.url+t.endpoint+t.id;if(t.endpoint&&t.id)return t.endpoint+t.id;if(t.url)return t.url.startsWith("htsget://")?t.url.replace("htsget://","https://"):t.url;throw Error("Must specify either 'url', or 'endpoint' and 'id")}function fc(t){const e=t.split(","),n=e[0].split(":")[1];let r=e[1];r=n.indexOf("base64")>=0?atob(r):decodeURI(r);const i=new Uint8Array(r.length);for(var o=0;o<r.length;o++)i[o]=r.charCodeAt(o);return i}class dc extends hc{constructor(t,e){super(t,e),this.parser=new Cl}async readHeader(){if(!this.header){const t=$l(await this.readHeaderData());this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(t,e,n){if(this.config.format&&"VCF"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let r=this.chrAliasTable.has(t)?this.chrAliasTable.get(t):t;const i=$l(await this.readData(r,e,n));return this.parser.parseFeatures(i)}}function pc(t,e){e=e||Number.MAX_SAFE_INTEGER;const n=[];t.sort((function(t,e){return t.start-e.start})),n.push(-1e3);for(let r of t){let t=0;const i=Math.min(n.length,e);for(t=0;t<i;t++)if(r.start>=n[t]){r.row=t,n[t]=r.end;break}r.row=t,n[t]=r.end}}function gc(t,e,n){const r=n||1e4,i=t=>{const n=Object.assign({},t);return n.chr="all",n.start=e.getGenomeCoordinate(t.chr,t.start),n.end=e.getGenomeCoordinate(t.chr,t.end),n._f=t,n.exons&&delete n.exons,n},o=new Set(e.wgChromosomeNames),s=[];let a=0;for(let n of e.wgChromosomeNames){if(Array.isArray(t)){const n={};for(let r of t){const t=e.getChromosomeName(r.chr);n.hasOwnProperty(t)||(n[t]=[]),n[t].push(r)}t=n}const l=t[n];if(l)for(let t of l){let n=e.getChromosomeName(t.chr);if(o.has(n))if(s.length<r)s.push(i(t));else{const e=r/(a+1);if(Math.random()<e){s[Math.floor(Math.random()*(r-1))]=i(t)}}a++}}return s.sort((function(t,e){return t.start-e.start})),s}function mc(t,e){if(e=e||1e3,null==t||0===t.length)return;const n={},r=[];for(let e of t){const t=e.chr;let i=n[t];i||(i=[],n[t]=i,r.push(t)),i.push(e)}for(let t of r)pc(n[t],e)}class vc{constructor(t,e){this.config=t||{},this.genome=e,this.sourceType=void 0===t.sourceType?"file":t.sourceType,this.maxWGCount=t.maxWGCount||1e4;const n=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak","tdf"]);t.reader?(this.reader=t.reader,this.queryable=!1!==t.queryable):"ga4gh"===t.sourceType?(this.reader=new ac(t,e),this.queryable=!0):"immvar"===t.sourceType?(this.reader=new rc(t),this.queryable=!0):"eqtl"===t.type&&"gtex-ws"===t.sourceType?(this.reader=new nc(t),this.queryable=!0):"htsget"===t.sourceType?this.reader=new dc(t,e):"ucscservice"===t.sourceType?(this.reader=new Jl(t.source),this.queryable=!0):"custom"===t.sourceType?(this.reader=new Ql(t.source),this.queryable=!1!==t.source.queryable):"civic-ws"===t.sourceType?(this.reader=new lc(t),this.queryable=!1):(this.reader=new Yl(t,e),void 0!==t.queryable?this.queryable=t.queryable:(n.has(t.format)||this.reader.indexed)&&(this.queryable=!0))}async defaultVisibilityWindow(){if(this.reader&&"function"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const t=await this.getHeader();return t?t.type:void 0}async getHeader(){if(!this.header)if(this.reader&&"function"==typeof this.reader.readHeader){const t=await this.reader.readHeader();t?(this.header=t,t.format&&(this.config.format=t.format)):this.header={}}else this.header={};return this.header}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome,a=s?s.getChromosomeName(e):e,l="all"===a.toLowerCase();return(l&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new ua(a,n,r)))&&await this.loadFeatures(a,n,r,o),l?(this.wgFeatures||(this.supportsWholeGenome()?this.wgFeatures=gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.wgFeatures=[]),this.wgFeatures):this.featureCache.queryFeatures(a,n,r)}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(t,e,n,r){const i=this.reader;let o=e,s=n;if((!r||r<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(t):void 0;o=0,s=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,n)}else if(r>n-e&&!1!==this.config.expandQuery){const t=Math.min(4.1*(n-e),r);o=Math.max(0,(e+n)/2-t),s=e+t}let a=await i.readFeatures(t,o,s);void 0===this.queryable&&(this.queryable=i.indexed);const l=this.queryable?new ua(t,o,s):void 0;if(a){if(!1===this.config.assembleGFF||"gtf"!==this.config.format&&"gff3"!==this.config.format&&"gff"!==this.config.format||(a=new ec(this.config).combineFeatures(a,l)),"wig"!==this.config.format&&"junctions"!==this.config.type){mc(a,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Ho(a,this.genome,l),(this.config.searchable||this.config.searchableFields)&&this.addFeaturesToDB(a)}else this.featureCache=new Ho([],l)}addFeaturesToDB(t){for(let e of t)if(e.name&&(this.genome.featureDB[e.name.toUpperCase()]=e),e.gene&&e.gene.name&&(this.genome.featureDB[e.gene.name.toUpperCase()]=e),this.config.searchableFields)for(let t of this.config.searchableFields){const n=e.getAttributeValue(t);n&&(n.indexOf(" ")>0?(this.genome.featureDB[n.replaceAll(" ","+").toUpperCase()]=e,this.genome.featureDB[n.replaceAll(" ","%20").toUpperCase()]=e):this.genome.featureDB[n.toUpperCase()]=e)}}}class bc{constructor(t,e,n){this.path=t.url,this.bufferSize=n||512e3,this.range={start:-1,size:-1},this.config=t}async dataViewForRange(t,e){if(!(this.data&&this.range.start<=t.start&&this.range.start+this.range.size>=t.start+t.size)){let e;e=t.size?Math.max(this.bufferSize,t.size):this.bufferSize;const n={start:t.start,size:e},r=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:n}));this.data=r,this.range=n}const n=this.data.byteLength,r=t.start-this.range.start;return e?new Uint8Array(this.data,r,n-r):new DataView(this.data,r,n-r)}}let wc=512e3;class yc{constructor(t,e){this.path=t.url,this.format=t.format||"bigwig",this.genome=e,this.rpTreeCache={},this.config=t,this.loader=Ms(this.path)?new Rc(this.path):Eo}async readWGFeatures(t,e){await this.loadHeader();const n=this.chromTree.idToChrom.length-1,r=this.chromTree.idToChrom[0],i=this.chromTree.idToChrom[n];return this.readFeatures(r,0,i,Number.MAX_VALUE,t,e)}async readFeatures(t,e,n,r,i,o){await this.loadHeader();const s=this.chromTree.chromToID[t],a=this.chromTree.chromToID[n];if(void 0===s||void 0===a)return[];let l,c;if("bigwig"===this.type){const t=await this.getZoomHeaders();let e=i?function(t,e){let n;for(let r=0;r<e.length;r++){const i=e[r];if(i.reductionLevel<t){n=i;break}}return n}(i,t):void 0;e?(l=e.indexOffset,c=Mc):(l=this.header.fullIndexOffset,c=Ac)}else l=this.header.fullIndexOffset,c=Lc.call(this);const h=await this.loadRPTree(l),u=await h.findLeafItemsOverlapping(s,e,a,r);if(u&&0!==u.length){let t=Number.MAX_VALUE,n=0;for(let e of u)t=Math.min(t,e.dataOffset),n=Math.max(n,e.dataOffset+e.dataSize);const i=n-t,l=await this.loader.loadArrayBuffer(this.config.url,Cs(this.config,{range:{start:t,size:i}})),h=[];for(let n of u){const i=new Uint8Array(l,n.dataOffset-t,n.dataSize);let u;u=this.header.uncompressBuffSize>0?ro(i):i,c.call(this,new DataView(u.buffer),s,e,a,r,h,this.chromTree.idToChrom,o)}return h.sort((function(t,e){return t.start-e.start})),h}return[]}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let t,e=await this.loader.loadArrayBuffer(this.path,Cs(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;let n=new zl(new DataView(e)),r=n.getUInt();if(2291137574===r)this.type="bigwig";else if(2273964779===r)this.type="bigbed";else{this.littleEndian=!1,n.littleEndian=!1,n.position=0;let t=n.getUInt();654085990===t?this.type="bigwig":3958540679===t&&(this.type="bigbed")}t={bwVersion:n.getUShort(),nZoomLevels:n.getUShort(),chromTreeOffset:n.getLong(),fullDataOffset:n.getLong(),fullIndexOffset:n.getLong(),fieldCount:n.getUShort(),definedFieldCount:n.getUShort(),autoSqlOffset:n.getLong(),totalSummaryOffset:n.getLong(),uncompressBuffSize:n.getInt(),extensionOffset:n.getLong()};const i=64;let o={start:i,size:t.fullDataOffset-i+5};e=await this.loader.loadArrayBuffer(this.path,Cs(this.config,{range:o}));const s=t.nZoomLevels;n=new zl(new DataView(e)),this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let t=1;t<=s;t++){const e=s-t,r=new xc(e,n);this.firstZoomDataOffset=Math.min(r.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[e]=r}if(t.autoSqlOffset>0){n.position=t.autoSqlOffset-i;const e=n.getString();e&&(this.autoSql=function(t){let e;const n=[];let r=!1;const i=t.trim().split(/\s*[\r\n]+\s*/g);for(let t of i)if(t.startsWith("table"))e=t.split(/\s+/)[1].trim();else if(t.startsWith("("))r=!0;else if(t.startsWith(")"));else if(r&&t.length>0){const e=t.indexOf(";"),r=t.substr(0,e).split(/\s+/),i=t.substr(e+1).replace(/"/g,"").trim();n.push({type:r[0],name:r[1],description:i})}return{table:e,fields:n}}(e))}if(t.totalSummaryOffset>0&&(n.position=t.totalSummaryOffset-i,this.totalSummary=new Ec(n)),!(t.chromTreeOffset>0))throw"BigWig chromosome tree offset <= 0";return n.position=t.chromTreeOffset-i,this.chromTree=new Sc(n,i,this.genome),n.position=t.fullDataOffset-i,t.dataCount=n.getInt(),this.setDefaultVisibilityWindow(t),this.header=t,this.header}}async loadRPTree(t){let e=this.rpTreeCache[t];return e||(e=new _c(t,this.config,this.littleEndian,this.loader),await e.load(),this.rpTreeCache[t]=e,e)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),"bigwig"===this.type?"wig":this.autoSql&&"chromatinInteract"===this.autoSql.table?"interact":"annotation"}setDefaultVisibilityWindow(t){if("bigwig"===this.type)this.visibilityWindow=-1;else{let e=this.genome?this.genome.getGenomeLength():3088286401;this.visibilityWindow=t.dataCount<1e3?-1:e/t.dataCount*1e3}}}class xc{constructor(t,e){this.index=t,this.reductionLevel=e.getInt(),this.reserved=e.getInt(),this.dataOffset=e.getLong(),this.indexOffset=e.getLong()}}class _c{constructor(t,e,n,r){this.config=e,this.loader=r,this.fileOffset=t,this.path=e.url,this.littleEndian=n}async load(){const t=this.fileOffset+48,e=Ms(this.path)?this.loader:new bc(this.config,wc);return this.rootNode=await this.readNode(t,e),this}async readNode(t,e){let n=await e.dataViewForRange({start:t,size:4},!1),r=new zl(n,this.littleEndian);const i=1===r.getByte();r.getByte();const o=r.getUShort();let s={start:t+=4,size:o*(i?32:24)};n=await e.dataViewForRange(s,!1);const a=new Array(o);if(r=new zl(n),i){for(let t=0;t<o;t++){let e={isLeaf:!0,startChrom:r.getInt(),startBase:r.getInt(),endChrom:r.getInt(),endBase:r.getInt(),dataOffset:r.getLong(),dataSize:r.getLong()};a[t]=e}return new kc(a)}for(let t=0;t<o;t++){let e={isLeaf:!1,startChrom:r.getInt(),startBase:r.getInt(),endChrom:r.getInt(),endBase:r.getInt(),childOffset:r.getLong()};a[t]=e}return new kc(a)}async findLeafItemsOverlapping(t,e,n,r){let i=this;return new Promise((function(o,s){let a=[],l=new Set,c=Ms(i.path)?i.loader:new bc(i.config,wc);l.add(0),function h(u,f){if(Cc(u,t,e,n,r)){u.items.forEach((function(o){Cc(o,t,e,n,r)&&(o.isLeaf?a.push(o):o.childNode?h(o.childNode):(l.add(o.childOffset),i.readNode(o.childOffset,c).then((function(t){o.childNode=t,h(t,o.childOffset)})).catch(s)))}))}void 0!==f&&l.delete(f);0===l.size&&o(a)}(i.rootNode,0)}))}}class kc{constructor(t){this.items=t;let e,n,r=Number.MAX_SAFE_INTEGER,i=0,o=Number.MAX_SAFE_INTEGER,s=0;for(e=0;e<t.length;e++)n=t[e],r=Math.min(r,n.startChrom),i=Math.max(i,n.endChrom),o=Math.min(o,n.startBase),s=Math.max(s,n.endBase);this.startChrom=r,this.endChrom=i,this.startBase=o,this.endBase=s}}class Sc{constructor(t,e,n){let r=t.getInt(),i=t.getInt(),o=t.getInt(),s=t.getInt(),a=t.getLong(),l=t.getLong(),c={},h=[];this.header={magic:r,blockSize:i,keySize:o,valSize:s,itemCount:a,reserved:l},this.chromToID=c,this.idToChrom=h,function t(r,i){i>=0&&(r.position=i);let s=r.getByte();r.getByte();let a,l,u,f,d,p,g=r.getUShort();if(1===s)for(a=0;a<g;a++)l=r.getFixedLengthTrimmedString(o),u=r.getInt(),r.getInt(),n&&(l=n.getChromosomeName(l)),c[l]=u,h[u]=l;else for(a=0;a<g;a++)l=r.getFixedLengthTrimmedString(o),f=r.getLong(),d=f-e,p=r.position,t(r,d),r.position=p}(t,-1)}}function Cc(t,e,n,r,i){return t?(r>t.startChrom||r===t.startChrom&&i>=t.startBase)&&(e<t.endChrom||e===t.endChrom&&n<=t.endBase):(console.log("null item for "+e+" "+n+" "+i),!1)}class Ec{constructor(t){t?(this.basesCovered=t.getLong(),this.minVal=t.getDouble(),this.maxVal=t.getDouble(),this.sumData=t.getDouble(),this.sumSquares=t.getDouble(),Tc.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function Tc(){let t=this.basesCovered;if(t>0){this.mean=this.sumData/t,this.stddev=Math.sqrt(this.sumSquares/(t-1));let e=this.minVal<0?this.mean-2*this.stddev:0,n=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:e,max:n}}}function Ac(t,e,n,r,i,o,s){const a=new zl(t),l=a.getInt();let c=a.getInt(),h=a.getInt();const u=a.getInt(),f=a.getInt(),d=a.getByte();a.getByte();let p=a.getUShort();if(l>=e&&l<=r)for(;p-- >0;){let t;switch(d){case 1:c=a.getInt(),h=a.getInt(),t=a.getFloat();break;case 2:c=a.getInt(),t=a.getFloat(),h=c+f;break;case 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t=i.start+parseInt(n[o]),s=t+parseInt(e[o]);r.push({start:t,end:s})}!function(t,e,n){for(let r of t){const t=r.end,i=r.start;t<e||i>n?r.utr=!0:(e>=i&&e<=t&&(r.cdStart=e),n>=i&&n<=t&&(r.cdEnd=n))}}(r,i.cdStart,i.cdEnd),i.exons=r}if(n)for(let r=t;r<e;r++)if(r<n.fields.length){const t=n.fields[r].name,e=o[r-3];i[t]=e}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(e,n,r,i,o,s,a){const l=new zl(e);for(;l.remLength()>=13;){const e=l.getInt(),c=a[e],h=l.getInt(),u=l.getInt(),f=l.getString();if(!(e<n||e===n&&u<r)){if(e>i||e===i&&h>=o)break;if(u>0){const e={chr:c,start:h,end:u};s.push(e);const n=f.split("\t");t(e,n)}}}}}function Mc(t,e,n,r,i,o,s,a){const l=new zl(t);for(;l.remLength()>=32;){const t=l.getInt(),c=s[t],h=l.getInt(),u=l.getInt(),f=l.getInt(),d=l.getFloat(),p=l.getFloat(),g=l.getFloat();let 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t=xh(this),e="";return t.hasIndices&&(e+="d"),t.global&&(e+="g"),t.ignoreCase&&(e+="i"),t.multiline&&(e+="m"),t.dotAll&&(e+="s"),t.unicode&&(e+="u"),t.unicodeSets&&(e+="v"),t.sticky&&(e+="y"),e}});class Au{constructor(t,e){this.config=t,this.genome=e,this.path=t.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let t=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:0,size:64e3}})),e=new zl(new DataView(t));if(this.magic=e.getInt(),this.version=e.getInt(),this.indexPos=e.getLong(),this.indexSize=e.getInt(),e.getInt(),this.version>=2){let t=e.getInt();for(this.windowFunctions=[];t-- >0;)this.windowFunctions.push(e.getString())}this.trackType=e.getString(),this.trackLine=e.getString();let n=e.getInt();for(this.trackNames=[];n-- >0;)this.trackNames.push(e.getString());this.genomeID=e.getString(),this.flags=e.getInt(),this.compressed=0!=(1&this.flags),t=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:this.indexPos,size:this.indexSize}})),e=new zl(new DataView(t)),this.datasetIndex={};let r=e.getInt();for(;r-- >0;){const t=e.getString(),n=e.getLong(),r=e.getInt();this.datasetIndex[t]={position:n,size:r}}for(this.groupIndex={},r=e.getInt();r-- >0;){const t=e.getString(),n=e.getLong(),r=e.getInt();this.groupIndex[t]={position:n,size:r}}return this}async readDataset(t,e,n){const r=t+"_"+e+"_"+n;if(this.datasetCache[r])return this.datasetCache[r];{await this.readHeader();const i=this.version<2?"":"/"+e,o="all"===t.toLowerCase()||void 0===n?"0":n.toString();let s;s="raw"===e?"/"+t+"/raw":"/"+t+"/z"+o+i;const a=this.datasetIndex[s];if(void 0===a)return;const l=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:a.position,size:a.size}}));if(!l)return;const c=new zl(new DataView(l));let h=c.getInt();const u={};for(;h-- >0;)u[c.getString()]=c.getString();const f=c.getString(),d=c.getFloat();let p=c.getInt();const g=[];for(;p-- >0;)g.push({position:c.getLong(),size:c.getInt()});const m={name:s,attributes:u,dataType:f,tileWidth:d,tiles:g};return this.datasetCache[r]=m,m}}async readRootGroup(){const t=this.genome,e=this.groupCache["/"];if(e)return e;{const e=await this.readGroup("/"),n=e.chromosomes,r=e.maxZoom;r&&(this.maxZoom=Number(r));const i=e.totalCount;i&&(e.totalCount=Number(i));const o={};return n&&n.split(",").forEach((function(e){const n=t.getChromosomeName(e);o[n]=e})),this.chrAliasTable=o,this.groupCache["/"]=e,e}}async readGroup(t){const e=this.groupCache[t];if(e)return e;{await this.readHeader();const e=this.groupIndex[t];if(void 0===e)return;const n=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:e.position,size:e.size}}));if(!n)return;const r=new zl(new DataView(n)),i={name:t};let o=r.getInt();for(;o-- >0;){const t=r.getString(),e=r.getString();i[t]=e}return this.groupCache[t]=i,i}}async readTiles(t,e){if(t.sort((function(t,e){return t.position-e.position})),0===(t=t.filter((function(t){return t.size>0}))).length)return Promise.resolve([]);const n=t[0],r=t[t.length-1],i=n.position,o=r.position+r.size-i,s=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:i,size:o}})),a=[];for(let n of t){const t=n.position-i,r=n.size;if(r>0){let n;if(this.compressed){n=ro(s.slice(t,t+r)).buffer}else n=s.slice(t,t+r);const i=new zl(new DataView(n)),o=i.getString();let l;switch(o){case"fixedStep":l=Lu(i,e);break;case"variableStep":l=Mu(i,e);break;case"bed":case"bedWithName":l=Ru(i,e,o);break;default:throw"Unknown tile type: "+o}a.push(l)}}return a}async readTile(t,e){let n=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:t.position,size:t.size}}));if(this.compressed){n=ro(n).buffer}const r=new zl(new DataView(n)),i=r.getString();switch(i){case"fixedStep":return Lu(r,e);case"variableStep":return Mu(r,e);case"bed":case"bedWithName":return Ru(r,e,i);default:throw"Unknown tile type: "+i}}}function Lu(t,e){const n=t.getInt(),r=t.getInt(),i=t.getFloat(),o=[];let s=e;for(;s-- >0;){let e=n;const r=[];for(;e-- >0;)r.push(t.getFloat());o.push(r)}return{type:"fixedStep",start:r,span:i,data:o,nTracks:e,nPositions:n}}function Mu(t,e){const n=t.getInt(),r=t.getFloat(),i=t.getInt(),o=[];let s=i;for(;s-- >0;)o.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){s=i;const e=[];for(;s-- >0;)e.push(t.getFloat());a.push(e)}return{type:"variableStep",tileStart:n,span:r,start:o,data:a,nTracks:e,nPositions:i}}function Ru(t,e,n){const r=t.getInt();let i=r;const o=[];for(;i-- >0;)o.push(t.getInt());i=r;const s=[];for(;i-- >0;)s.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){let e=r;const n=[];for(;e-- >0;)n.push(t.getFloat());a.push(n)}if("bedWithName"===n){i=r;const e=[];for(;i-- >0;)e.push(t.getString())}return{type:n,start:o,end:s,data:a,nTracks:e,nPositions:r}}class Iu{constructor(t,e){this.genome=e,this.windowFunction=t.windowFunction||"mean",this.reader=new Au(t,e)}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i}=t;if("all"===e.toLowerCase()){const t=[],e=this.genome;if(this.genome.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n).bpLength;i=r/1e3;const o=await this._getFeatures(n,0,r,i);if(o)for(let n of o){const r=Object.assign({},n);r.chr="all",r.start=e.getGenomeCoordinate(n.chr,n.start),r.end=e.getGenomeCoordinate(n.chr,n.end),r._f=n,t.push(r)}}return t}return this._getFeatures(e,n,r,i)}async _getFeatures(t,e,n,r){const i=new ua(t,e,n),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const t=this.rootGroup.totalCount;t&&(this.normalizationFactor=1e6/t)}i.bpPerPixel=r;const s=function(t,e,n){var r=n.getChromosome(t).bpLength;return Math.ceil(Math.log(Math.max(0,r/(700*e)))/Fu)}(t,r,o);let a=this.reader.chrAliasTable[t],l=this.reader.maxZoom;void 0===a&&(a=t),void 0===l&&(l=-1);const c=s>l?"raw":this.windowFunction,h=await this.reader.readDataset(a,c,s);if(null==h)return[];const u=h.tileWidth,f=Math.floor(e/u),d=Math.floor(n/u),p=await this.reader.readTiles(h.tiles.slice(f,d+1),1),g=[];for(let i of p)switch(i.type){case"bed":Nu(i,t,e,n,r,g);break;case"variableStep":Ou(i,t,e,n,r,g);break;case"fixedStep":Pu(i,t,e,n,r,g);break;default:throw"Unknown tile type: "+i.type}return g.sort((function(t,e){return t.start-e.start})),g}get supportsWholeGenome(){return!0}}function Nu(t,e,n,r,i,o){const s=t.nPositions,a=t.start,l=t.end,c=t.data[0];for(let t=0;t<s;t++){const i=a[t],s=l[t];if(!(s<n)){if(i>r)break;o.push({chr:e,start:i,end:s,value:c[t]})}}}function Ou(t,e,n,r,i,o){const s=t.nPositions,a=t.start,l=t.span,c=t.data[0];for(let t=0;t<s;t++){const i=a[t],s=i+l;if(!(s<n)){if(i>r)break;o.push({chr:e,start:i,end:s,value:c[t]})}}}function Pu(t,e,n,r,i,o){const s=t.nPositions;let a=t.start;const l=t.span,c=t.data[0];for(let t=0;t<s;t++){const i=a+l;if(a>r)break;i>=n&&(Number.isNaN(c[t])||o.push({chr:e,start:a,end:i,value:c[t]})),a=i}}var Fu=Math.log(2);class Du{constructor(t,e){this.config=t,this.genome=e,this.queryable=!1,this.updateFeatures(t.features)}updateFeatures(t){mc(t=function(t,e){if(e)for(let n of t)n.chr=e.getChromosomeName(n.chr);return t}(t,this.genome)),this.config.mappings&&function(t,e){let n=Object.keys(e);t.forEach((function(t){n.forEach((function(n){t[n]=t[e[n]]}))}))}(t,this.config.mappings),this.featureCache=new Ho(t,this.genome)}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome,a=s?s.getChromosomeName(e):e;return"all"===a.toLowerCase()?gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(a,n,r)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}}const Bu=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak"]);function zu(t,e){const n=t.format?t.format.toLowerCase():void 0;return t.features?new Du(t,e):Bu.has(n)?new Ic(t,e):"tdf"===n?new Iu(t,e):new vc(t,e)}const Hu={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};const Vu={Set1:["rgb(228,26,28)","rgb(55,126,184)","rgb(77,175,74)","rgb(166,86,40)","rgb(152,78,163)","rgb(255,127,0)","rgb(247,129,191)","rgb(153,153,153)","rgb(255,255,51)"],Dark2:["rgb(27,158,119)","rgb(217,95,2)","rgb(117,112,179)","rgb(231,41,138)","rgb(102,166,30)","rgb(230,171,2)","rgb(166,118,29)","rgb(102,102,102)"],Set2:["rgb(102, 194,165)","rgb(252,141,98)","rgb(141,160,203)","rgb(231,138,195)","rgb(166,216,84)","rgb(255,217,47)","rgb(229,196,148)","rgb(179,179,179)"],Set3:["rgb(141,211,199)","rgb(255,255,179)","rgb(190,186,218)","rgb(251,128,114)","rgb(128,177,211)","rgb(253,180,98)","rgb(179,222,105)","rgb(252,205,229)","rgb(217,217,217)","rgb(188,128,189)","rgb(204,235,197)","rgb(255,237,111)"],Pastel1:["rgb(251,180,174)","rgb(179,205,227)","rgb(204,235,197)","rgb(222,203,228)","rgb(254,217,166)","rgb(255,255,204)","rgb(229,216,189)","rgb(253,218,236)"],Pastel2:["rgb(173,226,207)","rgb(253,205,172)","rgb(203,213,232)","rgb(244,202,228)","rgb(230,245,201)","rgb(255,242,174)","rgb(243,225,206)"],Accent:["rgb(127,201,127)","rgb(190,174,212)","rgb(253,192,134)","rgb(255,255,153)","rgb(56,108,176)","rgb(240,2,127)","rgb(191,91,23)"]};class ju{constructor(t){this.colors=Vu[t],Array.isArray(this.colors)||(this.colors=[]),this.colorTable={},this.nextIdx=0,this.colorGenerator=new qu}getColor(t){return this.colorTable.hasOwnProperty(t)||(this.nextIdx<this.colors.length?this.colorTable[t]=this.colors[this.nextIdx]:this.colorTable[t]=this.colorGenerator.get(),this.nextIdx++),this.colorTable[t]}}class Uu{constructor(t){this.colorTable=t||{},this.nextIdx=0,this.colorGenerator=new qu}getColor(t){if(!this.colorTable.hasOwnProperty(t)){if(this.colorTable.hasOwnProperty("*"))return this.colorTable["*"];this.colorTable[t]=this.colorGenerator.get()}return this.colorTable[t]}}function qu(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}qu.prototype.hsvToRgb=function(t,e,n){var r=Math.floor(6*t),i=6*t-r,o=n*(1-e),s=n*(1-i*e),a=n*(1-(1-i)*e),l=255,c=255,h=255;switch(r){case 0:l=n,c=a,h=o;break;case 1:l=s,c=n,h=o;break;case 2:l=o,c=n,h=a;break;case 3:l=o,c=s,h=n;break;case 4:l=a,c=o,h=n;break;case 5:l=n,c=o,h=s}return[Math.floor(256*l),Math.floor(256*c),Math.floor(256*h)]},qu.prototype.padHex=function(t){return t.length>this.hexwidth?t:new Array(this.hexwidth-t.length+1).join("0")+t},qu.prototype.get=function(t,e){this.hue+=this.goldenRatio,this.hue%=1,"number"!=typeof t&&(t=.5),"number"!=typeof e&&(e=.95);var n=this.hsvToRgb(this.hue,t,e);return"#"+this.padHex(n[0].toString(16))+this.padHex(n[1].toString(16))+this.padHex(n[2].toString(16))};const Wu=new qu;const $u=function(t,e){const{r:n,g:r,b:i}=Hu[t];return`rgba(${n},${r},${i},${e})`}("nickel",2/16),Gu=$u;class Zu{constructor(t,e){if(this.url=t.url,t.name?this.name=t.name:t.url&&Ue(t.url)?this.name=t.url.name:t.url&&ke(t.url)&&!t.url.startsWith("data:")&&(this.name=je(t.url)),this.isUserDefined=t.isUserDefined,t.features)this.featureSource=new Yu(t.features,e);else{if(t.format)t.format=t.format.toLowerCase();else{const e=je(t.url);t.format=zs(e)}this.featureSource=t.featureSource||zu(t,e)}!0===this.isUserDefined?(this.color=t.color||Gu,this.headerColor="rgba(155,185,129)"):(this.color=t.color||$u,this.headerColor="rgb(190,190,190)")}async getFeatures(t,e,n){return this.featureSource.getFeatures({chr:t,start:e,end:n})}async getAllFeatures(){return"function"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(t){this.isUserDefined?this.featureSource.addFeature(t):console.error("Attempt to add ROI to non user-defined set")}removeFeature(t){this.isUserDefined?this.featureSource.removeFeature(t):console.error("Attempt to remove ROI from non user-defined set")}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined};{const t=this.featureSource.getAllFeatures(),e=[];for(let n of Object.keys(t))for(let r of t[n])e.push(r);return{name:this.name,color:this.color,features:e,isUserDefined:this.isUserDefined}}}dispose(){for(let t of Object.keys(this))this[t]=void 0}}function Xu(t,e,n,r){let i=Math.round((t-n)/r);let o=Math.round((e-n)/r)-i;return o<3&&(o=3,i-=1),{x:i,width:o}}class Yu{constructor(t,e){this.featureMap={},this.genome=e;for(let e of t){let t=this.featureMap[e.chr];t||(t=[],this.featureMap[e.chr]=t),t.push(e)}for(let t of Object.keys(this.featureMap))this.featureMap[t].sort(((t,e)=>t.start-e.start))}getFeatures(t){let{chr:e,start:n,end:r}=t;if("all"===e.toLowerCase())return gc(this.featureMap,this.genome);{const t=this.featureMap[e];return t?t.filter((t=>t.end>n&&t.start<r)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(t){let e=this.featureMap[t.chr];e||(e=[],this.featureMap[t.chr]=e),e.push(t),e.sort(((t,e)=>t.start-e.start))}removeFeature(t){let{chr:e,start:n,end:r}=t;if(this.featureMap[e]){const t=`${e}-${n}-${r}`;this.featureMap[e]=this.featureMap[e].filter((e=>t!==`${e.chr}-${e.start}-${e.end}`))}}}class Ku{constructor(t,e,n,r){this.rulerViewport=t,this.rulerSweeper=ge({class:"igv-ruler-sweeper"}),e.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(ya.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on("locuschange",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off("locuschange",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let t,e,n,r,i,o;this.boundContentMouseDownHandler=function(o){t=!0,e=!0;const{x:s}=we(o,this.rulerViewport.contentDiv);r=n=s,i=1,this.rulerSweeper.style.display="block",this.rulerSweeper.style.backgroundColor=!0===o.shiftKey?Gu:"rgba(68, 134, 247, 0.25)",this.rulerSweeper.style.left=`${r}px`,this.rulerSweeper.style.width=`${i}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener("mousedown",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(s){let a;if(t&&e){const{x:t}=we(s,this.rulerViewport.contentDiv);a=Math.max(Math.min(t,this.rulerViewport.contentDiv.clientWidth),0),o=a-n,i=Math.abs(o),this.rulerSweeper.style.width=`${i}px`,o<0&&(r=n+o,this.rulerSweeper.style.left=`${r}px`)}}.bind(this),document.addEventListener("mousemove",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(n){let o;if(!0===t&&!0===e&&(t=e=void 0,this.rulerSweeper.style.display="none",i>1)){o={start:Math.floor(this.referenceFrame.calculateEnd(r)),end:Math.floor(this.referenceFrame.calculateEnd(r+i))};!0===n.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},o)):(Ts(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,o,this.browser.minimumBases()),function(t,e,n){t.start=Math.round(e.start),t.end=Math.round(e.end),t.bpPerPixel=(t.end-t.start)/n}(this.referenceFrame,o,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener("mousedown",this.boundContentMouseDownHandler),document.removeEventListener("mousemove",this.boundDocumentMouseMoveHandler),document.removeEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}class Qu{constructor(t){this.paired=!0,this.firstAlignment=t,this.chr=t.chr,this.readName=t.readName,t.start<t.mate.position?(this.start=t.start,this.scStart=t.scStart,this.connectingStart=t.start+t.lengthOnRef,this.connectingEnd=t.mate.position):(this.start=t.mate.position,this.scStart=this.start,this.connectingStart=t.mate.position,this.connectingEnd=t.start),this.end=Math.max(t.mate.position,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start;let e=Math.max(this.end,t.scStart+t.scLengthOnRef);this.scLengthOnRef=e-this.scStart}setSecondAlignment(t){this.secondAlignment=t;const e=this.firstAlignment;t.start>e.start?this.connectingEnd=t.start:this.connectingStart=t.start+t.lengthOnRef,this.start=Math.min(e.start,t.start),this.end=Math.max(e.start+e.lengthOnRef,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(e.scStart,t.scStart);const n=Math.max(e.scStart+e.scLengthOnRef,t.scStart+t.scLengthOnRef);this.scLengthOnRef=n-this.scStart}containsLocation(t,e){const n=e?this.scStart:this.start,r=e?this.scLengthOnRef:this.lengthOnRef;return t>=n&&t<=n+r}alignmentContaining(t,e){return this.firstAlignment.containsLocation(t,e)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(t,e)?this.secondAlignment:void 0}popupData(t){let e=this.firstAlignment.popupData(t);return this.secondAlignment&&(e.push("-------------------------------"),e=e.concat(this.secondAlignment.popupData(t))),e}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}firstOfPairStrand(){return this.firstAlignment.isFirstOfPair()?this.firstAlignment.strand:this.secondAlignment&&this.secondAlignment.isFirstOfPair()?this.secondAlignment.strand:this.firstAlignment.mate.strand}hasTag(t){return this.firstAlignment.hasTag(t)||this.secondAlignment&&this.secondAlignment.hasTag(t)}}const Ju=ke,tf=function(t){return t.split("").reduce((function(t,e){return(t=(t<<5)-t+e.charCodeAt(0))&t}),0)};class ef{constructor(){this.alignments=[],this.score=void 0}findAlignment(t){const e=(t,e)=>e>=t.start&&e<t.start+t.lengthOnRef;let n;for(let r=0;r<this.alignments.length;r++){const i=this.alignments[r];if(t>=i.start&&t<i.start+i.lengthOnRef){i.paired?i.firstAlignment&&e(i.firstAlignment,t)?n=i.firstAlignment:i.secondAlignment&&e(i.secondAlignment,t)&&(n=i.secondAlignment):n=i;break}}return n}updateScore(t,e){this.score=this.calculateScore(t,e)}calculateScore(t,e){let{position:n,option:r,direction:i,tag:o}=t;r||(r="BASE");const s=this.findAlignment(n);if(void 0===s)return Number.MAX_VALUE*(i?1:-1);let a;switch(r){case"NUCLEOTIDE":case"BASE":return function(t,e,n){let r;const i=Math.floor(n)-e.start;i<e.sequence.length&&(r=e.sequence.charAt(i));if(!r)return 0;const o=t.readBaseAt(n),s=t.readBaseQualityAt(n),a=e.coverageMap,l=Math.floor(n-a.bpStart),c=a.coverage[l];let h=0;if(t.insertions)for(let e of t.insertions)e.start===n&&(h=-c.ins);if(o)if(r=r.toUpperCase(),"N"===o&&0===h)h=2;else if(r!==o&&"="!==o||0!==h){if("X"===o||r!==o){h-=c["pos"+o]+c["neg"+o]+s/1e3}}else h=4-s/1e3;else{const t=c.del;t>0?h-=t:0===h&&(h=1)}return h}(s,e,n);case"STRAND":return s.strand?1:-1;case"START":return s.start;case"TAG":{const t=s.tags()[o];return void 0!==t?Ju(t)?tf(t):t:Number.MAX_VALUE}case"READ_NAME":return tf(s.readName);case"INSERT_SIZE":return-Math.abs(s.fragmentLength);case"GAP_SIZE":return-s.gapSizeAt(n);case"MATE_CHR":return a=s.mate,a?a.chr===s.chr?Number.MAX_VALUE-1:tf(a.chr):Number.MAX_VALUE;case"MQ":return void 0===s.mq?Number.MAX_VALUE:-s.mq;case"ALIGNED_READ_LENGTH":return-s.lengthOnRef;default:return Number.MAX_VALUE}}}function nf(t){return t.isPaired()&&t.mate&&t.isMateMapped()&&t.chr===t.mate.chr&&(t.isFirstOfPair()||t.isSecondOfPair())&&!(t.isSecondary()||t.isSupplementary())}function rf(t){const e=[];for(let n of t)for(let t of n.alignments)t instanceof Qu?(t.firstAlignment&&e.push(t.firstAlignment),t.secondAlignment&&e.push(t.secondAlignment)):e.push(t);return e}function of(t,e,n,r){if(t){if(0===t.length)return[];{t.sort((function(t,e){return r?t.scStart-e.scStart:t.start-e.start}));const i=t[0];let o=Math.max(e,r?i.scStart:i.start),s=o;const a=[];for(let e of t){const t=r?e.scStart:e.start,n=Math.max(0,t-o);void 0===a[n]&&(a[n]=[]),a[n].push(e)}let l=0,c=0;const h=[],u=2;try{for(;l<t.length;){const t=new ef;for(;s<=n;){let e,i;for(;!e&&s<=n;)i=s-o,void 0===a[i]?++s:e=a[i];if(!e)break;const c=e.pop();0===e.length&&(a[i]=void 0),t.alignments.push(c),s=r?c.scStart+c.scLengthOnRef+u:c.start+c.lengthOnRef+u,++l}if(t.alignments.length>0&&h.push(t),s=o,l===c)break;c=l}}catch(t){throw console.error(t),t}return h}}}class sf{constructor(t,e,n,r){let{samplingWindowSize:i,samplingDepth:o,pairsSupported:s,alleleFreqThreshold:a}=r;this.chr=t,this.start=Math.floor(e),this.end=Math.ceil(n),this.length=n-e,this.alleleFreqThreshold=void 0===a?.2:a,this.coverageMap=new lf(t,e,n,this.alleleFreqThreshold),this.alignments=[],this.downsampledIntervals=[],this.samplingWindowSize=void 0===i?100:i,this.samplingDepth=void 0===o?1e3:o,this.pairsSupported=void 0===s||s,this.paired=!1,this.pairsCache={},this.downsampledReads=new Set,this.currentBucket=new af(this.start,this.start+this.samplingWindowSize,this),this.filter=function(t){return t.isMapped()&&!t.isFailsVendorQualityCheck()}}push(t){!1!==this.filter(t)&&(this.coverageMap.incCounts(t),this.pairsSupported&&this.downsampledReads.has(t.readName)||(t.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new af(t.start,t.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(t)))}forEach(t){this.alignments.forEach(t)}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.alignments.sort((function(t,e){return t.start-e.start})),this.pairsCache=void 0,this.downsampledReads=void 0}contains(t,e,n){return this.chr===t&&this.start<=e&&this.end>=n}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new hf(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount)),this.paired=this.paired||this.currentBucket.paired}setViewAsPairs(t){let e;e=t?function(t){const e={},n=[];for(let r of t)for(let t of r.alignments)if(nf(t)){let r=e[t.readName];r?(r.setSecondAlignment(t),e[t.readName]=void 0):(r=new Qu(t),e[t.readName]=r,n.push(r))}else n.push(t);return n}(this.packedAlignmentRows):rf(this.packedAlignmentRows),this.packedAlignmentRows=of(e,this.start,this.end)}setShowSoftClips(t){const e=this.allAlignments();this.packedAlignmentRows=of(e,this.start,this.end,t)}repack(t,e){const n=this.allAlignments();this.packedAlignmentRows=of(n,this.start,this.end,e)}allAlignments(){const t=[];for(let e of this.packedAlignmentRows)for(let n of e.alignments)t.push(n);return t}getMax(t,e){return this.coverageMap.getMax(t,e)}}class af{constructor(t,e,n){this.start=t,this.end=e,this.alignments=[],this.downsampledCount=0,this.samplingDepth=n.samplingDepth,this.pairsSupported=n.pairsSupported,this.downsampledReads=n.downsampledReads,this.pairsCache=n.pairsCache}addAlignment(t){var e,n,r;if(this.pairsSupported&&nf(t)&&(r=this.pairsCache[t.readName]))return r.setSecondAlignment(t),void(this.pairsCache[t.readName]=void 0);this.alignments.length<this.samplingDepth?this.pairsSupported&&nf(t)?(r=new Qu(t),this.paired=!0,this.pairsCache[t.readName]=r,this.alignments.push(r)):this.alignments.push(t):((e=Math.floor(Math.random()*(this.samplingDepth+this.downsampledCount-1)))<this.samplingDepth?(n=this.alignments[e],this.pairsSupported&&nf(t)?(void 0!==this.pairsCache[n.readName]&&(this.pairsCache[n.readName]=void 0),r=new Qu(t),this.paired=!0,this.pairsCache[t.readName]=r,this.alignments[e]=r):this.alignments[e]=t,this.downsampledReads.add(n.readName)):this.downsampledReads.add(t.readName),this.downsampledCount++)}}class lf{constructor(t,e,n,r){this.chr=t,this.bpStart=e,this.length=n-e,this.coverage=new Array(this.length),this.maximum=0,this.threshold=r,this.qualityWeight=!0}getMax(t,e){let n=0;const r=this.coverage.length;for(let i=0;i<r;i++){const r=this.bpStart+i;if(r>e)break;const o=this.coverage[i];r>=t&&o&&(n=Math.max(n,o.total))}return n}incCounts(t){var e=this;if(void 0===t.blocks?n(t):t.blocks.forEach((function(t){n(t)})),t.gaps)for(let n of t.gaps)if("D"===n.type){const t=n.start-e.bpStart;for(let r=t;r<t+n.len;r++)r<0||(this.coverage[r]||(this.coverage[r]=new cf(e.threshold)),this.coverage[r].del++)}if(t.insertions)for(let n of t.insertions){const t=n.start-this.bpStart;t<0||(this.coverage[t]||(this.coverage[t]=new cf(e.threshold)),this.coverage[t].ins++)}function n(n){if("S"===n.type)return;const r=t.seq,i=t.qual,o=n.seqOffset;for(let s=n.start-e.bpStart,a=0;a<n.len;s++,a++){e.coverage[s]||(e.coverage[s]=new cf(e.threshold));const n=null==r?"N":r.charAt(o+a),l=t.strand?"pos"+n:"neg"+n,c=i&&o+a<i.length?i[o+a]:30;e.coverage[s][l]+=1,e.coverage[s]["qual"+n]+=c,e.coverage[s].total+=1,e.coverage[s].qual+=c,e.maximum=Math.max(e.coverage[s].total,e.maximum)}}}}class cf{constructor(t){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=t}hoverText(){const t=this.posA+this.posT+this.posC+this.posG+this.posN,e=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${t}+, ${e}-)`}isMismatch(t){const e=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let n=0;for(let e of["A","T","C","G"])e!==t&&(n+=this.qualityWeight&&this.qual?this["qual"+e]:this["pos"+e]+this["neg"+e]);return n>=e}}class hf{constructor(t,e,n){this.start=t,this.end=e,this.counts=n}popupData(t){return[{name:"start",value:this.start+1},{name:"end",value:this.end},{name:"# downsampled:",value:this.counts}]}}class uf{constructor(t){const e=t.split(",");this.chr=e[0],this.start=parseInt(e[1]),this.strand=e[2].charAt(0),this.mapQ=parseInt(e[4]),this.numMismatches=parseInt(e[5]),this.lenOnRef=Af.computeLengthOnReference(e[3])}printString(){return this.chr+":"+Se(this.start)+"-"+Se(this.start+this.lenOnRef)+" ("+this.strand+") = "+Se(this.lenOnRef)+"bp @MAPQ: "+this.mapQ+" NM: "+this.numMismatches}}function ff(t){return t.split(";").filter((t=>t.length>0)).map((t=>new uf(t)))}const df={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class pf{constructor(){this.hidden=!1}isMapped(){return 0==(4&this.flags)}isPaired(){return 0!=(1&this.flags)}isProperPair(){return 0!=(2&this.flags)}isFirstOfPair(){return 0!=(64&this.flags)}isSecondOfPair(){return 0!=(128&this.flags)}isSecondary(){return 0!=(256&this.flags)}isSupplementary(){return 0!=(2048&this.flags)}isFailsVendorQualityCheck(){return 0!=(512&this.flags)}isDuplicate(){return 0!=(1024&this.flags)}isMateMapped(){return 0==(8&this.flags)}isNegativeStrand(){return 0!=(16&this.flags)}isMateNegativeStrand(){return 0!=(32&this.flags)}hasTag(t){return(this.tagDict||mf(this.tagBA)).hasOwnProperty(t)}tags(){return this.tagDict||(this.tagBA?(this.tagDict=mf(this.tagBA),this.tagBA=void 0):this.tagDict={}),this.tagDict}containsLocation(t,e){const n=e?this.scStart:this.start,r=e?this.scLengthOnRef:this.lengthOnRef;return t>=n&&t<=n+r}hoverText(){return this.readName}popupData(t){const e=[];if(t=Math.floor(t),this.insertions){const r=this.seq;for(let i of this.insertions){var n=i.start;if(t===n||t===n-1)return e.push({name:"Insertion",value:r.substr(i.seqOffset,i.len)}),e.push({name:"Location",value:n}),e}}e.push({name:"Read Name",value:this.readName}),e.push("<hr/>"),e.push({name:"Alignment Start",value:Se(1+this.start),borderTop:!0}),e.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0});let r=this.cigar;if(r&&r.length>50){const t=25;r=`${r.substring(0,t-2)} ... ${r.substring(r.length-t+2)}`}e.push({name:"Cigar",value:r}),e.push({name:"Mapping Quality",value:this.mq}),e.push({name:"Secondary",value:s(this.isSecondary())}),e.push({name:"Supplementary",value:s(this.isSupplementary())}),e.push({name:"Duplicate",value:s(this.isDuplicate())}),e.push({name:"Failed QC",value:s(this.isFailsVendorQualityCheck())}),this.isPaired()&&(e.push("<hr/>"),e.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),e.push({name:"Mate is Mapped",value:s(this.isMateMapped())}),this.pairOrientation&&e.push({name:"Pair Orientation",value:this.pairOrientation}),this.isMateMapped()&&(e.push({name:"Mate Chromosome",value:this.mate.chr}),e.push({name:"Mate Start",value:this.mate.position+1}),e.push({name:"Mate Strand",value:!0===this.mate.strand?"(+)":"(-)"}),e.push({name:"Insert Size",value:this.fragmentLength})));const i=this.tags();if(i.hasOwnProperty("SA")){e.push("<hr/>"),e.push({name:"Supplementary Alignments",value:""});const t=ff(i.SA);if(t){e.push("<ul>");for(let n of t)e.push(`<li>${n.printString()}</li>`);e.push("</ul>")}}const o=new Set(["SA","MD"]);e.push("<hr/>");for(let t in i)o.has(t)||e.push({name:t,value:i[t]});return e.push({name:"Hidden Tags",value:"SA, MD"}),e.push("<hr/>"),e.push({name:"Genomic Location: ",value:Se(1+t)}),e.push({name:"Read Base:",value:this.readBaseAt(t)}),e.push({name:"Base Quality:",value:this.readBaseQualityAt(t)}),e;function s(t){return t?"Yes":"No"}}readBaseAt(t){const e=gf(this.blocks,t);if(e){if("*"===this.seq)return"*";{const n=e.seqIndexAt(t);return this.seq[n]}}}readBaseQualityAt(t){const e=gf(this.blocks,t);if(e){if("*"===this.qual)return 30;{const n=e.seqIndexAt(t);return n>=0&&this.qual&&n<this.qual.length?this.qual[n]:30}}}gapSizeAt(t){if(this.gaps)for(let e of this.gaps)if(t>=e.start&&t<e.start+e.len)return e.len;return 0}}function gf(t,e){for(let n=0;n<t.length;n++){const r=t[n];if(e>=r.start&&e<r.start+r.len)return r}}function mf(t){let e=0;const n=t.length,r={};for(;e<n;){const n=String.fromCharCode(t[e])+String.fromCharCode(t[e+1]);e+=2;const o=String.fromCharCode(t[e++]);let s;if("A"===o)s=String.fromCharCode(t[e]),e++;else if("i"===o||"I"===o)s=vf(t,e),e+=4;else if("c"===o)s=yf(t,e),e++;else if("C"===o)s=xf(t,e),e++;else if("s"===o||"S"===o)s=bf(t,e),e+=2;else if("f"===o)s=wf(t,e),e+=4;else if("Z"===o)for(s="";;){var i=t[e++];if(0===i)break;s+=String.fromCharCode(i)}else{if("B"!==o){s="Error unknown type: "+o,r[n]=s;break}{const i=String.fromCharCode(t[e++]);let o=df[i];if(void 0===o){r[n]=`Error: unknown element type '${i}'`;break}e+=4+vf(t,e)*o,s="[not shown]"}}r[n]=s}return r}function vf(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function bf(t,e){return t[e+1]<<8|t[e]}function wf(t,e){return new DataView(t.buffer).getFloat32(e)}function yf(t,e){return new DataView(t.buffer).getInt8(e)}function xf(t,e){return new DataView(t.buffer).getUint8(e)}class _f{constructor(t){t&&Object.assign(this,t)}seqIndexAt(t){return Math.floor(t)-this.start+this.seqOffset}}class kf{constructor(t){t||(t={}),this.vendorFailed=void 0===t.vendorFailed||t.vendorFailed,this.duplicates=void 0===t.duplicates||t.duplicates,this.secondary=t.secondary||!1,this.supplementary=t.supplementary||!1,this.mqThreshold=void 0===t.mqThreshold?0:t.mqThreshold,t.readgroups&&(this.readgroups=new Set(t.readgroups))}pass(t){if(this.vendorFailed&&t.isFailsVendorQualityCheck())return!1;if(this.duplicates&&t.isDuplicate())return!1;if(this.secondary&&t.isSecondary())return!1;if(this.supplementary&&t.isSupplementary())return!1;if(t.mq<this.mqThreshold)return!1;if(this.readgroups){var e=t.tags().RG;return this.readgroups.has(e)}return!0}}const Sf=["=","A","C","x","G","x","x","x","T","x","x","x","x","x","x","N"],Cf=["M","I","D","N","S","H","P","=","X","?","?","?","?","?","?","?"],Ef=Mf(new Uint8Array([66,65,77,1]),0),Tf=1e4,Af={readHeader:function(t,e,n){return Eo.loadArrayBuffer(t,e).then((function(t){var e;return e=io(t),Af.decodeBamHeader(e,n)}))},decodeBamHeader:function(t,e){var n,r,i,o,s;if((n=Mf(t,0))!==Ef)throw new Error("BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.");r=Mf(t,4);for(var a=0;a<r;++a)String.fromCharCode(t[a+8]);var l=Mf(t,r+8),c=r+12;for(i={},o=[],s={},a=0;a<l;++a){for(var h=Mf(t,c),u="",f=0;f<h-1;++f)u+=String.fromCharCode(t[c+4+f]);Mf(t,c+h+4),i[u]=a,o[a]=u,e&&(s[e.getChromosomeName(u)]=u),c=c+8+h}return{magicNumber:n,size:c,chrNames:o,chrToIndex:i,chrAliasTable:s}},bam_tag2cigar:function(t,e,n,r,i,o){function s(t){return"C"===t||"c"===t||"A"===t?1:"S"===t||"s"===t?2:"I"===t||"i"===t||"f"===t?4:0}if(1!==o.length||i.start<0)return!1;for(var a=n+(r+1>>1)+r;a+4<e;){if("CG"===String.fromCharCode(t[a])+String.fromCharCode(t[a+1]))break;var l=String.fromCharCode(t[a+2]);if("B"===l)a+=8+s(l=String.fromCharCode(t[a+3]))*Mf(t,a+4);else if("Z"===l||"H"===l)for(a+=3;0!==t[a++];);else a+=3+s(l)}if(a>=e)return!1;if("B"!==String.fromCharCode(t[a+2])||"I"!==String.fromCharCode(t[a+3]))return!1;var c=Mf(t,a+4),h=a+8;if(h+4*c>e)return!1;var u="",f=0;o.length=0,a=h;for(var d=0;d<c;++d,a+=4){var p=Mf(t,a),g=p>>4,m=Cf[15&p];"M"!==m&&"EQ"!==m&&"X"!==m&&"D"!==m&&"N"!==m&&"="!==m||(f+=g),u=u+g+m,o.push({len:g,ltr:m})}return i.cigar=u,i.lengthOnRef=f,!0},decodeBamRecords:function(t,e,n,r,i,o,s,a){for(;e<t.length;){const f=e+Mf(t,e)+4,d=new pf,p=Mf(t,e+4),g=Mf(t,e+8);if(f>t.length)return;if(p<0){e=f;continue}if(void 0!==i&&(p>i||g>s))return!0;if(void 0!==i&&p<i){e=f;continue}const m=Mf(t,e+12),v=(65280&m)>>8,b=255&m,w=Mf(t,e+16),y=(4294901760&w)>>16,x=65535&w,_=Mf(t,e+20),k=Mf(t,e+24),S=Mf(t,e+28),C=Mf(t,e+32);let E=[];for(let n=0;n<b-1;++n)E.push(String.fromCharCode(t[e+36+n]));E=E.join("");let T=0,A="",L=e+36+b;const M=[];let R;for(let e=0;e<x;++e){var l=Mf(t,L),c=l>>4,h=Cf[15&l];"M"!==h&&"EQ"!==h&&"X"!==h&&"D"!==h&&"N"!==h&&"="!==h||(T+=c),A=A+c+h,L+=4,R={len:c,ltr:h},M.push(R)}if(d.chr=r[p],d.start=g,d.flags=y,d.strand=!(16&y),d.readName=E,d.cigar=A,d.lengthOnRef=T,d.fragmentLength=C,d.mq=v,Af.bam_tag2cigar(t,f,L,_,d,M),d.end=d.start+d.lengthOnRef,d.end<o){e=f;continue}let I=[];const N=_+1>>1;for(let e=0;e<N;++e){var u=t[L+e];I.push(Sf[(240&u)>>4]),I.push(Sf[15&u])}I=I.slice(0,_).join(""),L+=N;const O=[];for(let e=0;e<_;++e)O.push(t[L+e]);L+=_,k>=0&&(d.mate={chr:r[k],position:S,strand:!(32&y)}),d.seq=I,d.qual=O,d.tagBA=new Uint8Array(t.buffer.slice(L,f)),this.setPairOrientation(d),(void 0===a||a.pass(d))&&(Lf(d,M),n.push(d)),e=f}},decodeSamRecords:function(t,e,n,r,i,o){var s,a,l,c,h,u,f,d,p,g;for(c=(s=Ce(t)).length,!1,a=0;a<c;a++)if(h=s[a].split("\t"),(p=new pf).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],"*"!==p.chr&&p.isMapped()&&p.chr===n){if(p.start>i)break;if(d=0,(g=Rf(p.cigar)).forEach((function(t){var e=t.len,n=t.ltr;"M"!==n&&"EQ"!==n&&"X"!==n&&"D"!==n&&"N"!==n&&"="!==n||(d+=e)})),p.lengthOnRef=d,!(p.start+d<r)){for(u=h[10],p.qual=[],l=0;l<u.length;l++)p.qual[l]=u.charCodeAt(l)-33;p.tagDict=h.length<11?{}:If(h.slice(11)),p.isMateMapped()&&(f=h[6],p.mate={chr:"="===f?p.chr:f,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===o||o.pass(p))&&(Lf(p,g),e.push(p))}}},setReaderDefaults:function(t,e){t.filter=new kf(e.filter),e.readgroup&&(t.filter.readgroups=new Set([e.readgroup])),t.alleleFreqThreshold=void 0===e.alleleFreqThreshold?.2:e.alleleFreqThreshold,t.samplingWindowSize=void 0===e.samplingWindowSize?100:e.samplingWindowSize,t.samplingDepth=void 0===e.samplingDepth?500:e.samplingDepth,t.samplingDepth>Tf&&(console.log("Warning: attempt to set sampling depth > maximum value of 10000"),t.samplingDepth=Tf),e.viewAsPairs?t.pairsSupported=!0:t.pairsSupported=void 0===e.pairsSupported||e.pairsSupported},setPairOrientation:function(t){if(t.isMapped()&&t.mate&&t.isMateMapped()&&t.mate.chr===t.chr){var e=t.strand?"F":"R",n=t.mate,r=n.strand?"F":"R",i=" ",o=" ";t.isFirstOfPair()?(i="1",o="2"):t.isSecondOfPair()&&(i="2",o="1");var s=[],a=t.fragmentLength,l=t.end-t.start;if(0===a)a=(t.start<n.position?n.position+l:n.position-l)-t.start;a>0?(s[0]=e,s[1]=i,s[2]=r,s[3]=o):(s[2]=e,s[3]=i,s[0]=r,s[1]=o),t.pairOrientation=s.join("")}},computeLengthOnReference:function(t){let e=0,n="";for(let r=0;r<t.length;r++){const i=t.charCodeAt(r);if(i>47&&i<58)n+=t.charAt(r);else{switch(i){case 78:case 68:case 77:case 61:case 88:e+=parseInt(n.toString())}n=""}}return e}};function 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"+e+")";if(p instanceof oa){if((a=p.getSvg().cloneNode(!0)).childNodes&&a.childNodes.length>1){for(l=a.childNodes[0];l.childNodes.length;)f=l.childNodes[0].getAttribute("id"),this.__ids[f]=f,this.__defs.appendChild(l.childNodes[0]);if(c=a.childNodes[1]){var b,w=c.getAttribute("transform");b=w?w+" "+v:v,c.setAttribute("transform",b),s.appendChild(c)}}}else"CANVAS"!==p.nodeName&&"IMG"!==p.nodeName||((h=this.__createElement("image")).setAttribute("width",n),h.setAttribute("height",r),h.setAttribute("preserveAspectRatio","none"),(g||m||i!==p.width||o!==p.height)&&((u=this.__document.createElement("canvas")).width=n,u.height=r,u.getContext("2d").drawImage(p,g,m,i,o,0,0,n,r),p=u),h.setAttribute("transform",v),h.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===p.nodeName?p.toDataURL():p.getAttribute("src")),s.appendChild(h))}createPattern(t,e){let n,r=this.__document.__createElement("pattern"),i=Qs(this.__ids);return r.setAttribute("id",i),r.setAttribute("width",t.width),r.setAttribute("height",t.height),"CANVAS"===t.nodeName||"IMG"===t.nodeName?(n=this.__createElement("image"),n.setAttribute("width",t.width),n.setAttribute("height",t.height),n.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===t.nodeName?t.toDataURL():t.getAttribute("src")),r.appendChild(n),this.__defs.appendChild(r)):t instanceof oa&&(r.appendChild(t.__root.childNodes[1]),this.__defs.appendChild(r)),new ia(r,this)}setLineDash(t){t&&t.length>0?this.lineDash=t.join(","):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}class sa{constructor(t,e,n){this.name=t,this.order=e,this.bpLength=n}}const aa=Ce,la=new Set(["fastaURL","indexURL","cytobandURL","indexed"]);class ca{constructor(t){this.fastaURL=t.fastaURL,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences=new Map;const e={};for(let n in t)t.hasOwnProperty(n)&&!la.has(n)&&(e[n]=t[n]);this.config=e}async init(){return this.loadAll()}async getSequence(t,e,n){if(!this.sequences.has(t))return;let r=this.sequences.get(t).find((t=>t.contains(e,n)));if(!r&&(r=this.sequences.get(t).find((t=>t.overlaps(e,n))),!r))return;e-=r.offset,n-=r.offset;let i="";if(e<0)for(let t=e;t<Math.min(n,0);t++)i+="*";if(n<=0)return Promise.resolve(i);const o=r.sequence,s=Math.min(n,o.length);return i+o.substring(e,s)}async loadAll(){let t;if(Ms(this.fastaURL)){let e=co(this.fastaURL);t="";for(let n of e)t+=String.fromCharCode(n)}else t=await Eo.load(this.fastaURL,Cs(this.config));const e=new Set,n=aa(t),r=n.length;let i,o=0,s=0,a={};for(;o<r;){if(i=n[o++].trim(),i.startsWith("#")||0===i.length);else if(i.startsWith(">")){a&&a.seq&&l.call(this,a,s++);const t=i.substr(1).split(/\s+/),e=t[0].split(":");if(a.chr=e[0],a.seq="",a.offset=0,e.length>1&&e[1].indexOf("-")>0){const n=e[1].split("-");2===n.length&&/^[0-9]+$/.test(n[0])&&/^[0-9]+$/.test(n[1]);const r=Number.parseInt(n[0]);if(Number.parseInt(n[1])>r&&(a.offset=r-1),t.length>1&&t[1].startsWith("@len="))try{a.length=parseInt(t[1].trim().substring(5))}catch(t){a.length=void 0,console.error(`Error parsing sequence length for ${i}`)}else a.length=void 0}}else a.seq+=i;a&&a.seq&&l.call(this,a,s)}function l(t,n){const r=t.length||t.offset+t.seq.length;if(e.has(t.chr)){const e=this.chromosomes[t.chr];e.bpLength=Math.max(e.bpLength,r)}else this.chromosomeNames.push(t.chr),this.sequences.set(t.chr,[]),this.chromosomes[t.chr]=new sa(t.chr,n,r),e.add(t.chr);this.sequences.get(t.chr).push(new ha(t.offset,t.seq))}}}class ha{constructor(t,e){this.offset=t,this.sequence=e}contains(t,e){return this.offset<=t&&this.end>=e}overlaps(t,e){return this.offset<e&&this.end>t}get end(){return this.offset+this.sequence.length}}const ua=function(t,e,n,r){this.chr=t,this.start=e,this.end=n,this.features=r};ua.prototype.contains=function(t,e,n){return this.chr===t&&this.start<=e&&this.end>=n},ua.prototype.containsRange=function(t){return this.chr===t.chr&&this.start<=t.start&&this.end>=t.end};const fa=Ce,da=new Set(["fastaURL","indexURL","compressedIndexURL","cytobandURL","indexed"]);class pa{constructor(t){this.file=t.fastaURL,this.indexFile=t.indexURL||t.indexFile||this.file+".fai",this.compressedIndexFile=t.compressedIndexURL||!1,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences={},this.offsets={};const e={};for(let n in t)t.hasOwnProperty(n)&&!da.has(n)&&(e[n]=t[n]);this.config=e}async init(){return this.getIndex()}async getSequence(t,e,n){if(!(this.interval&&this.interval.contains(t,e,n))){let r=e,i=n;if(n-e<5e4){const t=n-e,o=Math.round(e+t/2);r=Math.max(0,o-25e3),i=o+25e3}const o=await this.readSequence(t,r,i);this.interval=new ua(t,r,i,o)}const r=e-this.interval.start,i=n-e;return this.interval.features?this.interval.features.substr(r,i):null}async getIndex(){if(this.index)return this.index;{const t=await Eo.load(this.indexFile,Cs(this.config)),e=fa(t),n=e.length;let r=0,i=0;for(this.index={};r<n;){const t=e[r++].split("\t");if(5===t.length){const e=t[0],n=parseInt(t[1]),r={size:n,position:parseInt(t[2]),basesPerLine:parseInt(t[3]),bytesPerLine:parseInt(t[4])};this.chromosomeNames.push(e),this.index[e]=r,this.chromosomes[e]=new sa(e,i++,n)}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const t=await Eo.loadArrayBuffer(this.compressedIndexFile,Cs(this.config)),e=t.byteLength;if(e<8)return console.log("Cannot parse GZI index file: length ("+e+" bytes) is insufficient to determine content of index."),this.compressedIndex;const n=t.slice(0,8),r=Number(new DataView(n).getBigUint64(0,!0)),i=8+2*r*8;if(e!=i)return console.log("Incorrect file size of reference genome index. Expected : "+i+". Received : "+e),this.compressedIndex;this.compressedIndex.push([0,0]);for(let e=0;e<r;e++){const n=8+2*e*8,r=8+2*e*8+16,i=t.slice(n,r),o=new DataView(i),s=Number(o.getBigUint64(0,!0)),a=Number(o.getBigUint64(8,!0));this.compressedIndex.push([s,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(t,e){if(t<0||e<0||e<t)return console.log("Incompatible query positions for reference-genome. Start:"+t+" | End:"+e),[];await this.getCompressedIndex();let n=[];const r=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log("Compressed index does not contain any content"),[];if(t>this.compressedIndex[r][1])return[r];let i=0,o=r,s=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,l=!1;for(let e=0;e<a;e++){const e=this.compressedIndex[s][1],n=s<this.compressedIndex.length-1?this.compressedIndex[s+1][1]:1/0;if(e<=t&&n>t){l=!0;break}e<t?i=s+1:o=s-1,s=Math.ceil((o-i)/2)+i}if(!l)return console.log("No blocks within compressed index found that correspond with query positions "+t+","+e),console.log(this.compressedIndex),[];n.push(s);for(let t=s+1;t<this.compressedIndex.length;t++){n.push(t);if(this.compressedIndex[t][1]>=e)break}const c=n[n.length-1];return c===this.compressedIndex.length-1&&this.compressedIndex[c][1]<e&&n.push(-1),n}async loadAndUncompressBlocks(t,e){if(await this.getCompressedIndex(),0==t.length)return"";let n=Array(t.length-1);for(let e=0;e<t.length-1;e++){const r=t[e],i=this.compressedIndex[r][0],o=t[e+1];let s=[];if(-1!=o){const t=this.compressedIndex[o][0]-i;s=await Eo.loadArrayBuffer(this.file,Cs(this.config,{range:{start:i,size:t}}))}else s=await Eo.loadArrayBuffer(this.file,Cs(this.config,{range:{start:i}}));const a=await io(s);n[e]=a}let r="";for(let t=0;t<n.length;t++)for(let e=0;e<n[t].length;e++){r+=String.fromCharCode(n[t][e])}const i=e-this.compressedIndex[t[0]][1];return r=r.substring(i),r}async readSequence(t,e,n){await this.getIndex(),await this.getCompressedIndex();const r=this.index[t];if(!r)return console.log("No index entry for chr: "+t),this.interval=new ua(t,e,n,null),null;const i=Math.max(0,e),o=Math.min(r.size,n),s=r.bytesPerLine,a=r.basesPerLine,l=r.position,c=s-a,h=Math.floor(i/a),u=Math.floor(o/a),f=i-h*a,d=l+h*s+f,p=l+u*s+(o-u*a)-1,g=p-d+1;if(g<=0)return console.error("No sequence for "+t+":"+e+"-"+n),null;let m;if(this.compressedIndexFile){let t=await this.getRelevantCompressedBlockNumbers(d,p);if(0===t.length)return console.log("No blocks in the compressed index that correspond with the requested byte positions ("+d+","+p+")"),null;m=await this.loadAndUncompressBlocks(t,d)}else m=await Eo.load(this.file,Cs(this.config,{range:{start:d,size:g}}));if(!m)return null;let v,b="",w=0,y=m.length;for(f>0&&(v=Math.min(o-i,a-f),b+=m.substr(w,v),w+=v+c);w<y;)v=Math.min(a,y-w),b+=m.substr(w,v),w+=v+c;return b}}const ga=Ce;class ma{constructor(t){this.url=t,this.chromosomeNames=[],this.chromosomes={}}async init(){return this.loadAll()}async getSequence(t,e,n){}async loadAll(){let t;if(Ms(this.url)){let e=co(this.fastaURL);t="";for(let n of e)t+=String.fromCharCode(n)}else t=await Eo.load(this.url,{});this.chromosomeNames=[],this.chromosomes={};const e=ga(t);let n=0;for(let t of e){const e=t.split("\t");this.chromosomeNames.push(e[0]);const r=Number.parseInt(e[1]),i=new sa(e[0],n++,r);this.chromosomes[e[0]]=i}}}const va=function(t,e,n,r){this.start=t,this.end=e,this.name=n,this.stain=0,"acen"===r?this.type="c":(this.type=r.charAt(1),"p"===this.type&&(this.stain=parseInt(r.substring(4))))};function ba(){return"2.13.3"}const wa=Ce,ya={loadGenome:async function(t){const e=t.cytobandURL,n=t.aliasURL,r=await async function(t){let e;return e="chromsizes"===t.format?new ma(t.fastaURL):Ms(t.fastaURL)||!1===t.indexed?new ca(t):new pa(t),await e.init(),e}(t);let i;n&&(i=await function(t,e){return Eo.loadString(t,Cs(e)).then((function(t){var e=wa(t),n=[];return e.forEach((function(t){!t.startsWith("#")&&t.length>0&&n.push(t.split("\t"))})),n}))}(n,r.config));const o=new xa(t,r,i);return e&&(o.cytobands=await async function(t,e,n){let r;if(Ms(t)){const e=co(t);r="";const n=e.length;for(let t=0;t<n;t++)r+=String.fromCharCode(e[t])}else r=await Eo.loadString(t,Cs(e));const i={};let o,s=[];const a=wa(r);for(let t of a){var l=t.split("\t"),c=n.getChromosomeName(l[0]);if(o||(o=c),c!==o&&(i[o]=s,s=[],o=c),5===l.length){var h=parseInt(l[1]),u=parseInt(l[2]),f=l[3],d=l[4];s.push(new va(h,u,f,d))}}return i}(e,r.config,o)),o},initializeGenomes:async function(t){if(!ya.KNOWN_GENOMES){const e={};if(!1!==t.loadDefaultGenomes)try{const i=`https://igv.org/genomes/genomes.json?randomSeed=${Math.random().toString(36)}&version=2.13.3`;r(await Eo.loadJson(i,{timeout:5e3}))}catch(o){console.error(o);try{const s=`https://s3.amazonaws.com/igv.org.genomes/genomes.json?randomSeed=${Math.random().toString(36)}&version=2.13.3`;r(await Eo.loadJson(s,{}))}catch(a){console.error(a),console.warn("Errors loading default genome definitions.")}}const n=t.genomeList||t.genomes;if(n)if("string"==typeof n){r(await Eo.loadJson(n,{}))}else r(n);function r(t){return t.forEach((function(t){e[t.id]=t})),e}ya.KNOWN_GENOMES=e}},isWholeGenomeView:function(t){return"all"===t.toLowerCase()},expandReference:function(t,e){if(ke(e)&&e.startsWith("{"))try{e=JSON.parse(e)}catch(t){}let n;if(ke(e)?n=e:e.genome?n=e.genome:void 0!==e.id&&void 0===e.fastaURL&&(n=e.id),n){const e=ya.KNOWN_GENOMES[n];return e||t.present(new Error(`Unknown genome id: ${n}`),void 0),e}return e}};class xa{constructor(t,e,n){this.config=t,this.id=t.id||function(t){return void 0!==t.id?t.id:t.fastaURL&&ke(t.fastaURL)?t.fastaURL:t.fastaURL&&t.fastaURL.name?t.fastaURL.name:("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}(t),this.sequence=e,this.chromosomeNames=e.chromosomeNames,this.chromosomes=e.chromosomes,this.featureDB={},this.wholeGenomeView=void 0===t.wholeGenomeView||t.wholeGenomeView,this.wholeGenomeView&&Object.keys(e.chromosomes).length>1?function(t,e){let n;if(e.chromosomeOrder)Array.isArray(e.chromosomeOrder)?t.wgChromosomeNames=e.chromosomeOrder:t.wgChromosomeNames=e.chromosomeOrder.split(",").map((t=>t.trim())),n=t.wgChromosomeNames.map((e=>t.chromosomes[e])).filter((t=>void 0!==t));else{const e=Object.keys(t.chromosomes).map((e=>t.chromosomes[e].bpLength)).reduce(((t,e)=>Math.max(t,e)))/50;n=Object.values(t.chromosomes).filter((t=>t.bpLength>e));const r=n.filter((t=>i(t.name.replace("chr","")))),o=n.filter((t=>!i(t.name.replace("chr",""))));r.sort(((t,e)=>Number.parseInt(t.name.replace("chr",""))-Number.parseInt(e.name.replace("chr",""))));const s=r.map((t=>t.name));for(let t of o)s.push(t.name);t.wgChromosomeNames=s}const r=n.reduce(((t,e)=>t+e.bpLength),0);function i(t){return/^\d+$/.test(t)}t.chromosomes.all={name:"all",bpLength:r}}(this,t):this.wgChromosomeNames=e.chromosomeNames;var r={},i=this;r.all="all",this.chromosomeNames.forEach((function(t){var e=t.startsWith("chr")?t.substring(3):"chr"+t;r[e.toLowerCase()]=t,"chrM"===t&&(r.mt="chrM"),"MT"===t&&(r.chrm="MT"),r[t.toLowerCase()]=t})),n&&n.forEach((function(t){var e,n;for(n=0;n<t.length;n++)if(i.chromosomes[t[n]]){e=t[n];break}e&&t.forEach((function(t){t!==e&&(r[t.toLowerCase()]=e,r[t]=e)}))})),this.chrAliasTable=r}showWholeGenomeView(){return!1!==this.config.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}getInitialLocus(){}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.hasOwnProperty("all")?"all":this.chromosomeNames[0]}getChromosomeName(t){const e=t?this.chrAliasTable[t.toLowerCase()]:t;return e||t}getChromosome(t){return t=this.getChromosomeName(t),this.chromosomes[t]}getCytobands(t){return this.cytobands?this.cytobands[t]:null}getLongestChromosome(){var t,e=this.chromosomes;for(let r in e){if(e.hasOwnProperty(r)){var n=e[r];(void 0===t||n.bpLength>t.bpLength)&&(t=n)}return t}}getChromosomes(){return this.chromosomes}getGenomeCoordinate(t,e){var n=this.getCumulativeOffset(t);if(void 0!==n)return n+e}getChromosomeCoordinate(t){let e;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let n=0;for(let r of this.wgChromosomeNames){const i=this.cumulativeOffsets[r];if(i>t){return{chr:e,position:t-n}}e=r,n=i}return{chr:this.wgChromosomeNames[this.wgChromosomeNames.length-1],position:0}}getCumulativeOffset(t){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let t=this,e={},n=0;for(let r of t.wgChromosomeNames){e[r]=Math.floor(n);n+=t.getChromosome(r).bpLength}return e}.call(this));const e=this.getChromosomeName(t);return this.cumulativeOffsets[e]}getGenomeLength(){let t=this;if(!this.bpLength){let e=0;t.wgChromosomeNames.forEach((function(n){let r=t.chromosomes[n];e+=r.bpLength})),this.bpLength=e}return this.bpLength}async getSequence(t,e,n){return t=this.getChromosomeName(t),this.sequence.getSequence(t,e,n)}}let _a,ka=0,Sa=0;class Ca extends class{constructor(t,e,n,r){this.guid=be(),this.trackView=t,this.referenceFrame=n,this.browser=t.browser,this.$viewport=pe('<div class="igv-viewport">'),e.appendChild(this.$viewport.get(0)),t.track.height&&(this.$viewport.get(0).style.height=`${t.track.height}px`),t.track instanceof Ys&&(this.alert=new cs(this.$viewport.get(0))),this.$content=pe("<div>",{class:"igv-viewport-content"}),this.$viewport.append(this.$content),this.$content.height(this.$viewport.height()),this.contentDiv=this.$content.get(0),this.$viewport.width(r),this.initializationHelper()}initializationHelper(){}showMessage(t){this.messageDiv||(this.messageDiv=document.createElement("div"),this.messageDiv.className="igv-viewport-message",this.contentDiv.append(this.messageDiv)),this.messageDiv.textContent=t,this.messageDiv.style.display="inline-block"}hideMessage(t){this.messageDiv&&(this.messageDiv.style.display="none")}setTrackLabel(t){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(t){const e=-t,n=e+this.$viewport.height();this.$content.css("top",`${t}px`),(void 0===this.canvasVerticalRange||this.canvasVerticalRange.bottom<n||this.canvasVerticalRange.top>e)&&this.repaint()}async loadFeatures(){}clearCache(){}async repaint(){}draw(t,e,n){console.log("Viewport - draw(drawConfiguration, features, roiFeatures)")}checkContentHeight(t){let e=this.trackView.track;if(t=t||this.cachedFeatures,"FILL"===e.displayMode)this.setContentHeight(this.$viewport.height());else if("function"==typeof e.computePixelHeight&&t&&t.length>0){let n=e.computePixelHeight(t);n!==this.$content.height()&&this.setContentHeight(n)}}getContentHeight(){return this.$content.height()}setContentHeight(t){t=Math.min(t,32e3),this.$content.height(t)}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(t){this.$viewport.width(t)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentDiv.offsetTop}containsPosition(t,e){console.log("Viewport - containsPosition(chr, position)")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.popover&&this.popover.dispose(),this.$viewport.get(0).remove();for(let t of Object.keys(this))this[t]=void 0}}{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.$spinner=pe("<div>",{class:"igv-loading-spinner-container"}),this.$viewport.append(this.$spinner),this.$spinner.append(pe("<div>"));const t=this.trackView.track;"sequence"!==t.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$content)),t.name&&"sequence"!==t.id&&(this.$trackLabel=pe('<div class="igv-track-label">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(t.name),!1===this.browser.trackLabelsVisible&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(t){super.setContentHeight(t),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(t){this.$trackLabel.empty(),this.$trackLabel.html(t);const e=this.$trackLabel.text();this.$trackLabel.attr("title",e)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&"sequence"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>1)return pe(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if("all"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const t=this.trackView.track.visibilityWindow;return void 0!==t&&t>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>t}return!0})()){if(this.canvas&&(pe(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const t=this.trackView.minHeight||0;this.setContentHeight(t)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const t=this.referenceFrame;if(this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===t.bpPerPixel){const e=Math.round((this.canvas._data.bpStart-t.start)/t.bpPerPixel);this.canvas.style.left=e+"px"}}async loadFeatures(){const t=this.referenceFrame,e=t.chr,n=this.browser.genome.getChromosome(e).bpLength,r=this.$content.width()*t.bpPerPixel,i=Math.floor(Math.max(0,t.start-r)),o=Math.ceil(Math.min(n,t.start+r+r));if(!this.loading||this.loading.start!==i||this.loading.end!==o){this.loading={start:i,end:o},this.startSpinner();try{const n=this.trackView.track,r=await this.getFeatures(n,e,i,o,t.bpPerPixel);let s=[];if(n.roiSets&&n.roiSets.length>0)for(let r of n.roiSets){const n=await r.getFeatures(e,i,o,t.bpPerPixel);s.push({track:r,features:n})}const a=n&&("wig"===n.type||"merged"===n.type);return this.featureCache=new Ta(e,i,o,t.bpPerPixel,r,s,a),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}catch(t){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage("Error loading track data"),this.browser.alert.present(t),console.error(t))}finally{this.loading=!1,this.stopSpinner()}}}repaintDimensions(){const t=ya.isWholeGenomeView(this.referenceFrame.chr),e=t?this.$viewport.width():3*this.$viewport.width(),n=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(t?0:e/3*n),bpEnd:this.referenceFrame.end+(t?0:e/3*n),pixelWidth:e}}repaint(){if(void 0===this.featureCache)return;const{features:t,roiFeatures:e}=this.featureCache;ya.isWholeGenomeView(this.referenceFrame.chr);const{bpStart:n,bpEnd:r,pixelWidth:i}=this.repaintDimensions(),o=this.$viewport.height(),s=this.getContentHeight(),a=e?Math.max(s,o):s,l=Math.min(a,3*o);if(0===i||0===l)return void(this.canvas&&pe(this.canvas).remove());const c=Math.max(0,-this.$content.position().top-o),h=this.referenceFrame.bpPerPixel,u=Math.round((n-this.referenceFrame.start)/h),f=pe('<canvas class="igv-canvas">').get(0);f.style.width=i+"px",f.style.height=l+"px",f.style.left=u+"px",f.style.top=c+"px";const d="FILL"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=d*i,f.height=d*l;const p=f.getContext("2d");p.scale(d,d),p.translate(0,-c);const g={context:p,pixelXOffset:u,pixelWidth:i,pixelHeight:l,pixelTop:c,bpStart:n,bpEnd:r,bpPerPixel:h,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(g,t,e),this.canvas&&pe(this.canvas).remove(),f._data=g,this.canvas=f,this.$content.append(pe(f))}refresh(){if(!this.canvas||!this.featureCache)return;const t=this.canvas._data;t.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:e,roiFeatures:n}=this.featureCache;this.draw(t,e,n)}draw(t,e,n){if(e&&(t.features=e,this.trackView.track.draw(t)),n)for(let e of n)t.features=e.features,e.track.draw(t)}containsPosition(t,e){return this.referenceFrame.chr===t&&e>=this.referenceFrame.start&&e<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const t=this.featureCache,e=t?t.canvasTop:0,n=window.devicePixelRatio,r=this.$viewport.width()*n,i=this.$viewport.height()*n,o=-pe(this.canvas).position().left*n,s=(-this.$content.position().top-e)*n,a=this.canvas.getContext("2d").getImageData(o,s,r,i),l=document.createElement("canvas"),c=l.getContext("2d");l.width=a.width,l.height=a.height,c.putImageData(a,0,0);We((this.$trackLabel.text()?this.$trackLabel.text():"image")+".png",l.toDataURL("image/png"))}saveSVG(){const{width:t,height:e}=this.$viewport.get(0).getBoundingClientRect(),n={width:t,height:e,viewbox:{x:0,y:-this.$content.position().top,width:t,height:e}},r=new oa(n),i=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${be()}`;this.drawSVGWithContext(r,t,e,i,0,0,0);const o=r.getSerializedSvg(!0);We(`${i}.svg`,URL.createObjectURL(new Blob([o],{type:"application/octet-stream"})))}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;if(this.$zoomInNotice&&this.$zoomInNotice.is(":visible"))return;const i=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${be()}`,{top:o}=this.$content.position(),{width:s,height:a}=this.$viewport.get(0).getBoundingClientRect();if(this.drawSVGWithContext(t,s,a,i,n,r+o,-o),this.$trackLabel&&!0===this.browser.trackLabelsVisible){const{x:e,y:i,width:o,height:s}=((t,e)=>{const{x:n,y:r,width:i,height:o}=t.getBoundingClientRect(),{x:s,y:a,width:l,height:c}=e.getBoundingClientRect();return{x:s-n,y:a-r,width:l,height:c}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(t,n+e,r+i,o,s)}}renderTrackLabelSVG(t,e,n,r,i){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_track_label_guid_${be()}`;t.saveWithTranslationAndClipRect(o,e,n,r,i,0),t.fillStyle="white",t.fillRect(0,0,r,i),t.font="12px Arial",t.fillStyle="rgb(68, 68, 68)";const{width:s}=t.measureText(this.$trackLabel.text()),a=.25*(r-s),l=.7*(i-12);t.fillText(this.$trackLabel.text(),a,i-l),t.strokeStyle="rgb(68, 68, 68)",t.strokeRect(0,0,r,i),t.restore()}drawSVGWithContext(t,e,n,r,i,o,s){t.saveWithTranslationAndClipRect(r,i,o,e,n,s);let{start:a,bpPerPixel:l}=this.referenceFrame;const c={context:t,viewport:this,referenceFrame:this.referenceFrame,top:s,pixelTop:s,pixelWidth:e,pixelHeight:n,bpStart:a,bpEnd:a+e*l,bpPerPixel:l,viewportWidth:e,selection:this.selection},h=this.featureCache?this.featureCache.features:[],u=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(c,h,u),t.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(t,e,n,r,i){if(this.featureCache&&this.featureCache.containsRange(e,n,r,i))return this.featureCache.features;if("function"==typeof t.getFeatures){const o=await t.getFeatures(e,n,r,i,this);return this.checkContentHeight(o),o}}needsRepaint(){if(!this.canvas)return!0;const t=this.canvas._data;return!t||this.referenceFrame.start<t.bpStart||this.referenceFrame.end>t.bpEnd||this.referenceFrame.chr!==t.referenceFrame.chr||this.referenceFrame.bpPerPixel!=t.bpPerPixel}needsReload(){if(!this.featureCache)return!0;const{chr:t,bpPerPixel:e}=this.referenceFrame,{bpStart:n,bpEnd:r}=this.repaintDimensions();return!this.featureCache.containsRange(t,n,r,e)}createZoomInNotice(t){const e=pe("<div>",{class:"igv-zoom-in-notice-container"});t.append(e);const n=pe("<div>");return e.append(n),n.text("Zoom in to see features"),e.hide(),e}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const t=this.$viewport.get(0);this.addViewportContextMenuHandler(t);const e=t=>{this.enableClick=!0,this.browser.mouseDownOnViewport(t,this),ve(t)};t.addEventListener("mousedown",e),t.addEventListener("touchstart",e);const n=t=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};t.addEventListener("mouseup",n),t.addEventListener("touchend",n),"function"==typeof this.trackView.track._hoverText&&t.addEventListener("mousemove",(t=>{if(Date.now()-Sa>100){Sa=Date.now();const e=Ea(t,this);if(e){const t=this.trackView.track._hoverText(e);t?this.$viewport[0].setAttribute("title",t):this.$viewport[0].removeAttribute("title")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&"sequence"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(t){t.addEventListener("contextmenu",(t=>{if(this.browser.dragObject)return!1;const e=Ea(t,this);if(void 0===e)return!1;t.preventDefault();let n=[];if("function"==typeof this.trackView.track.contextMenuItemList){const t=this.trackView.track.contextMenuItemList(e);t&&(n=t)}n.length>0&&n.push({label:pe("<HR>")}),n.push({label:"Save Image (PNG)",click:()=>this.savePNG()}),n.push({label:"Save Image (SVG)",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(t,n)}))}addViewportClickHandler(t){t.addEventListener("click",(t=>{if(this.enableClick&&this.canvas){if(3===t.which||t.ctrlKey)return;if(pe(".igv-popover").hide(),this.browser.dragObject||this.browser.isScrolling)return;t.preventDefault();const e=we(t,this.$viewport.get(0)).x,n=we(t,this.canvas).x,r=this.referenceFrame,i=Math.floor(r.start+r.toBP(n)),o=Date.now();if(o-ka<this.browser.constants.doubleClickDelay){_a&&(window.clearTimeout(_a),_a=void 0);const t=Math.round(r.start+r.toBP(e));let n;if("all"===this.referenceFrame.chr.toLowerCase()){const e=this.browser.genome.getChromosomeCoordinate(t).chr;if(1===this.browser.referenceFrameList.length)n=e;else{const t=this.browser.referenceFrameList.map((t=>{let{locusSearchString:e}=t;return e}));t[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=e,n=t.join(" ")}this.browser.search(n)}else this.browser.zoomWithScaleFactor(.5,t,this.referenceFrame)}else t.shiftKey&&"function"==typeof this.trackView.track.shiftClick?this.trackView.track.shiftClick(i,t):"function"==typeof this.trackView.track.popupData&&(_a=setTimeout((()=>{const e=function(t,e){const n=Ea(t,e);if(void 0===n)return;let r=e.trackView.track;const i=r.popupData(n),o=e.browser.fireEvent("trackclick",[r,i]);let s;void 0===o||!0===o?i&&i.length>0&&(s=i.map((t=>{if(t.name){const e=`<span>${t.name}</span>&nbsp&nbsp&nbsp${t.value}`;return`<div title="${t.value}">${e}</div>`}return"<hr>"===t?t:t.html?t.html:`<div title="${t}">${t}</div>`})).join("")):"string"==typeof o&&(s=o);return s}(t,this);e&&(this.popover&&this.popover.dispose(),this.popover=new ms(this.browser.columnContainer),this.popover.presentContentWithEvent(t,e)),window.clearTimeout(_a),_a=void 0}),this.browser.constants.doubleClickDelay));ka=o}}))}addTrackLabelClickHandler(t){t.addEventListener("click",(t=>{t.stopPropagation();const{track:e}=this.trackView;let n;"function"==typeof e.description?n=e.description():e.description&&(n=`<div>${e.description}</div>`),n&&(this.popover&&this.popover.dispose(),this.popover=new ms(this.browser.columnContainer,e.name||""),this.popover.presentContentWithEvent(t,n))}))}}function Ea(t,e){if(!e.contentDiv||!e.canvas)return;const n=e.referenceFrame,r=we(t,e.contentDiv),i=we(t,e.canvas),o=n.start+n.toBP(r.x);return{event:t,viewport:e,referenceFrame:n,genomicLocation:o,x:r.x,y:r.y,canvasX:i.x,canvasY:i.y}}class Ta{constructor(t,e,n,r,i,o,s){this.chr=t,this.bpStart=e,this.bpEnd=n,this.bpPerPixel=r,this.features=i,this.roiFeatures=o,this.multiresolution=s}containsRange(t,e,n,r){const i=this.multiresolution?this.bpPerPixel/r:1;return e>=this.bpStart&&n<=this.bpEnd&&t===this.chr&&i>.5&&i<2}overlapsRange(t,e,n){return this.chr===t&&n>=this.bpStart&&e<=this.bpEnd}}function Aa(t,e){if(!(t.length<6))return{chr:t[0],start:t[1],end:t[2],chr1:t[8],start1:Number.parseInt(t[9]),end1:Number.parseInt(t[10]),chr2:t[13],start2:Number.parseInt(t[14]),end2:Number.parseInt(t[15]),name:t[3],score:Number(t[4]),value:Number(t[5]),color:"."===t[7]?void 0:"0"===t[7]?"rgb(0,0,0)":t[7]};console.log("Skipping line: "+t.join(" "))}const La=new Set(["transcript","primary_transcript","processed_transcript","mRNA","mrna","lnc_RNA","miRNA","ncRNA","rRNA","scRNA","snRNA","snoRNA","tRNA"]),Ma=new Set(["CDS","cds"]),Ra=new Set(["start_codon","stop_codon"]),Ia=new Set(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),Na=new Set(["exon","coding-exon"]),Oa=new Set;for(let dv of[Ma,Ra,Ia,Na])for(let pv of dv)Oa.add(pv);function Pa(t){return t.includes("intron")}function Fa(t){return Ma.has(t)||Ra.has(t)}function Da(t){return Ia.has(t)}function Ba(t){return La.has(t)||t.endsWith("RNA")||t.endsWith("transcript")}function za(t){return Oa.has(t)||t.endsWith("RNA")||Pa(t)}const Ha=new Set(["id","parent","name"]);class Va{constructor(t){Object.assign(this,t)}popupData(t){const e=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&e.push("<hr/>"),this.name&&e.push({name:"Name",value:this.name}),e.push({name:"Type",value:this.type}),e.push({name:"Source",value:this.source}),void 0!==this.score&&e.push({name:"Score",value:this.score}),this.attributeString){const t=$a(this.attributeString,this.delim);for(let[n,r]of t)void 0!==r&&r.length>0&&!Ha.has(n.toLowerCase())&&e.push({name:n+":",value:r})}return e.push({name:"Location",value:`${this.chr}:${Se(this.start+1)}-${Se(this.end)}`}),e}getAttributeValue(t){if(this.hasOwnProperty(t))return this[t];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(t))return this._attributeCache.get(t);{const e=$a(this.attributeString,this.delim);let n;for(let[r,i]of e)if(r===t){n=i;break}return this._attributeCache.set(t,n),n}}}class ja extends Va{constructor(t){super(t),this.exons=[],this.parts=[]}addExon(t){this.exons.push(t),this.start=Math.min(this.start,t.start),this.end=Math.max(this.end,t.end)}addPart(t){this.parts.push(t)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(t,e){return t.start-e.start}));let t=this.parts[0].start,e=this.parts[0].end;for(let n=1;n<this.parts.length;n++){const r=this.parts[n];if(!Pa(r.type))if(r.start<=e)e=Math.max(e,r.end);else{this.findExonContaining({start:t,end:e})||this.exons.push({start:t,end:e,psuedo:!0}),t=r.start,e=r.end}}this.findExonContaining({start:t,end:e})||(this.exons.push({start:t,end:e,psuedo:!0}),this.start=Math.min(this.start,t),this.end=Math.max(this.end,e));for(let t of this.parts){const e=t.type;Fa(e)?this.addCDS(t):Da(e)&&this.addUTR(t)}}findExonContaining(t){let{start:e,end:n}=t;for(let t of this.exons)if(t.end>=n&&t.start<=e)return t}addCDS(t){let e;const n=this.exons;for(let r of n)if(r.start<=t.start&&r.end>=t.end){e=r;break}e?(e.cdStart=e.cdStart?Math.min(t.start,e.cdStart):t.start,e.cdEnd=e.cdEnd?Math.max(t.end,e.cdEnd):t.end):console.error("No exon found spanning "+t.start+"-"+t.end),this.cdStart=this.cdStart?Math.min(t.start,this.cdStart):t.start,this.cdEnd=this.cdEnd?Math.max(t.end,this.cdEnd):t.end}addUTR(t){let e;const n=this.exons;for(let r=0;r<n.length;r++)if(n[r].start<=t.start&&n[r].end>=t.end){e=n[r];break}e?t.start===e.start&&t.end===e.end?e.utr=!0:(t.end<e.end&&(e.cdStart=t.end),t.start>e.start&&(e.cdEnd=t.start)):console.error("No exon found spanning "+cds.start+"-"+cds.end)}finish(){this.assembleParts();var t=this.cdStart,e=this.cdEnd;this.exons.sort((function(t,e){return t.start-e.start})),t&&this.exons.forEach((function(n){(n.end<t||n.start>e)&&(n.utr=!0)}))}popupData(t){const e=super.popupData(t);for(let n of this.exons)if(!n.pseudo&&t>=n.start&&t<n.end&&"function"==typeof n.popupData){e.push("<hr/>");const r=n.popupData(t);for(let t of r)e.push(t)}for(let n of this.parts)if(t>=n.start&&t<n.end&&"function"==typeof n.popupData){e.push("<hr/>");const r=n.popupData(t);for(let t of r)e.push(t)}return e}}function Ua(t,e){const n=e.format;if(t.length<9)return;const r="gff3"===n?"=":" ";return new Va({source:t[1],type:t[2],chr:t[0],start:parseInt(t[3])-1,end:parseInt(t[4]),score:"."===t[5]?void 0:Number(t[5]),strand:t[6],phase:"."===t[7]?0:parseInt(t[7]),attributeString:t[8],delim:r})}function qa(t,e){const n=Ua(t,e);if(!n)return;const r=$a(n.attributeString,n.delim);for(let[t,e]of r){const r=t.toLowerCase();"color"===r||"colour"===r?n.color=mo.createColorString(e):"ID"===t?n.id=e:"Parent"===t&&(n.parent=e)}return n}function Wa(t,e){const n=Ua(t,e);if(!n)return;const r=$a(n.attributeString,n.delim);let i,o;switch(n.type){case"gene":i="gene_id";break;case"transcript":i="transcript_id",o="gene_id";break;default:o="transcript_id"}for(let[t,e]of r){const r=t.toLowerCase();"color"===r||"colour"===r?n.color=mo.createColorString(e):t===i?n.id=e:t===o&&(n.parent=e)}return n}function $a(t,e){var n=[];for(let r of t.split(";")){r=r.trim();const t=r.indexOf(e);if(t>0&&t<r.length-1){const e=r.substring(0,t);let i=Ga(decodeURIComponent(r.substring(t+1).trim()));n.push([e,i])}}return n}function Ga(t){return t.startsWith('"')&&t.endsWith('"')&&(t=t.substr(1,t.length-2)),t}class Za{constructor(t){this.message=t}}function Xa(t,e){if(t.length<3)return;e&&e.gffTags;const n=t[0],r=parseInt(t[1]),i=t.length>2?parseInt(t[2]):r+1;if(isNaN(r)||isNaN(i))return new Za("Unparsable bed record.");const o=new ol({chr:n,start:r,end:i,score:1e3});try{if(t.length>3){if(t[3].indexOf(";")>0&&t[3].indexOf("=")>0){const e=$a(t[3],"=");o.attributes={};for(let t of e)o.attributes[t[0]]=t[1]}o.name||(o.name="."===t[3]?"":t[3])}if(t.length>4&&(o.score="."===t[4]?0:Number(t[4]),isNaN(o.score)))return o;if(t.length>5&&(o.strand=t[5],"."!==o.strand&&"+"!==o.strand&&"-"!==o.strand))return o;if(t.length>6&&(o.cdStart=parseInt(t[6]),isNaN(o.cdStart)))return o;if(t.length>7&&(o.cdEnd=parseInt(t[7]),isNaN(o.cdEnd)))return o;if(t.length>8&&"."!==t[8]&&"0"!==t[8]&&(o.color=mo.createColorString(t[8])),t.length>11){const e=parseInt(t[9]);if(e>1e3)return o;const n=t[10].replace(/,$/,"").split(","),i=t[11].replace(/,$/,"").split(",");if(n.length!==i.length||e!==n.length)return o;const s=[];for(let t=0;t<e;t++){const e=r+parseInt(i[t]),o=e+parseInt(n[t]);s.push({start:e,end:o})}tl(s,o.cdStart,o.cdEnd),o.exons=s}if(e){let n=e.thicknessColumn,r=e.colorColumn;r&&r<t.length&&(o.color=mo.createColorString(t[r])),n&&n<t.length&&(o.thickness=t[n])}}catch(t){}return o}function Ya(t,e){if(t.length<=15)return;return{swScore:Number.parseInt(t[1]),milliDiv:Number.parseInt(t[2]),milliDel:Number.parseInt(t[3]),milliIns:Number.parseInt(t[4]),chr:t[5],start:Number.parseInt(t[6]),end:Number.parseInt(t[7]),strand:t[9],repName:t[10],repClass:t[11],repFamily:t[12],repStart:Number.parseInt(t[13]),repEnd:Number.parseInt(t[14]),repLeft:Number.parseInt(t[15])}}function Ka(t,e){var n=void 0===e.shift?0:1;if(t.length<=9+n)return;const r=parseInt(t[5+n]),i=parseInt(t[6+n]);var o={name:t[0+n],chr:t[1+n],strand:t[2+n],start:parseInt(t[3+n]),end:parseInt(t[4+n]),cdStart:r,cdEnd:i,id:t[0+n]},s=parseInt(t[7+n]),a=t[8+n].split(","),l=t[9+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function Qa(t,e){var n=void 0===e.shift?0:1;if(t.length<=11+n)return;const r=parseInt(t[5+n]),i=parseInt(t[6+n]),o={name:t[11+n],chr:t[1+n],strand:t[2+n],start:parseInt(t[3+n]),end:parseInt(t[4+n]),cdStart:r,cdEnd:i,id:t[0+n]},s=parseInt(t[7+n]),a=t[8+n].split(","),l=t[9+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function Ja(t,e){var n=void 0===e.shift?0:1;if(t.length<=10+n)return;const r=parseInt(t[6+n]),i=parseInt(t[7+n]);var o={name:t[0+n],id:t[1+n],chr:t[2+n],strand:t[3+n],start:parseInt(t[4+n]),end:parseInt(t[5+n]),cdStart:r,cdEnd:i},s=parseInt(t[8+n]),a=t[9+n].split(","),l=t[10+n].split(","),c=[];for(let t=0;t<s;t++){const e=parseInt(a[t]),n=parseInt(l[t]);c.push({start:e,end:n})}return tl(c,r,i),o.exons=c,o}function tl(t,e,n){for(let r of t){const t=r.end,i=r.start;t<e||i>n?r.utr=!0:(e>=i&&e<=t&&(r.cdStart=e),n>=i&&n<=t&&(r.cdEnd=n))}}function el(t,e){var n,r,i,o,s,a,l;if(!(t.length<9))return n=t[0],r=parseInt(t[1]),i=parseInt(t[2]),s=t[3],a=Number(t[4]),o=t[5].trim(),l=Number(t[6]),0===a&&(a=l),{chr:n,start:r,end:i,name:s,score:a,strand:o,signal:l,pValue:Number(t[7]),qValue:Number(t[8])}}function nl(t,e){if(t.length<=3)return;const n={chr:t[0],start:parseInt(t[1]),end:parseInt(t[2]),value:Number(t[3])};if(e){let r=e.colorColumn;r&&r<t.length&&(n.color=mo.createColorString(t[r]))}return n}function rl(t,e){const n=e.wig;if(n&&"fixedStep"===n.format){const e=n.index*n.step+n.start,r=e+n.span,i=Number(t[0]);return++n.index,isNaN(i)?null:{chr:n.chrom,start:e,end:r,value:i}}if(n&&"variableStep"===n.format){if(t.length<2)return null;const e=parseInt(t[0],10)-1,r=e+n.span,i=Number(t[1]);return isNaN(i)?null:{chr:n.chrom,start:e,end:r,value:i}}return nl(t)}function il(t,e){if(t.length<6)return;const n=["bin","chr","start","end","name","score","strand","refNCBI","refUCSC","observed","molType","class","valid","avHet","avHetSE","func","locType","weight","exceptions","submitterCount","submitters","alleleFreqCount","alleles","alleleNs","alleleFreqs","bitfields"],r={chr:t[1],start:Number.parseInt(t[2]),end:Number.parseInt(t[3]),name:t[4],score:Number.parseInt(t[5])},i=Math.min(t.length,n.length);for(let e=6;e<i;e++)r[n[e]]=t[e];return r}class ol{constructor(t){Object.assign(this,t)}getAttributeValue(t){return this.hasOwnProperty(t)?this[t]:this.attributes?this.attributes[t]:void 0}}function sl(t,e){if(!(t.length<7)){var n=t[0],r=t[1],i=parseInt(t[2]),o=parseInt(t[3]),s=parseInt(t[4]),a=parseInt(t[5]),l=t[6],c={chr:n,name:r,junction_left:i,junction_right:o,num_junction_reads:s,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=i,u=o;if(a>0)for(var f=l.split(","),d=0;d<f.length;d++){var p=f[d].split("-"),g=p[0],m=p[1];g<h&&(h=g),m>u&&(u=m),c.spanning_frag_coords.push({left:g,right:m})}return c.start=h,c.end=u,c}}function al(t,e){if(t.length<7)return null;const n={chr:t[0],start:parseInt(t[1])-1,end:parseInt(t[2]),"Strongest SNP-risk allele":t[3],"Disease/Phenotype":t[4],"P-value":t[5],"Odds ratio or beta":t[6]};return t.length>6&&(n.PUBMEDID=`<a target = "blank" href = "https://www.ncbi.nlm.nih.gov/pubmed/${t[7]}">${t[7]}</a>`),n}function ll(t,e){const n=e.customFormat;if(t.length<n.fields.length)return;const r=n.coords||0,i=t[n.chr],o=parseInt(t[n.start])-r,s={chr:i,start:o,end:void 0!==n.end?parseInt(t[n.end]):o+1};return n.fields&&n.fields.forEach((function(e,r){r!==n.chr&&r!==n.start&&r!==n.end&&(s[e]=t[r])})),s}function cl(t,e){const n=e.columnNames;if(!n)throw Error("Sample names are not defined.   Missing column headers?");const r=n.length-3,i=t[0],o=parseInt(t[1]),s=parseInt(t[2]),a=t.slice(3).map(Number);return a.length==r?{chr:i,start:o,end:s,values:a}:void console.warn(`${i}:${o}-${s} row contains ${a.length} sample columns instead of the expected ${r} columns. Skipping...`)}class hl{constructor(t){this.config=t,this.header={},t.nameField&&(this.header.nameField=t.nameField),this.skipRows=0,t.decode?(this.decode=t.decode,this.delimiter=t.delimiter||"\t"):t.format&&(this.header.format=t.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter="\t")}async parseHeader(t){let e,n,r=this.header;for(;void 0!==(n=await t.nextLine());)if(n.startsWith("track")||n.startsWith("#track")){let t=ul(n);Object.assign(r,t)}else if(n.startsWith("browser"));else if(n.startsWith("#columns")){let t=fl(n);Object.assign(r,t)}else if(n.startsWith("##gff-version 3"))r.format="gff3";else if(n.startsWith("#gffTags"))r.gffTags=!0;else{if(n.startsWith("fixedStep")||n.startsWith("variableStep"))break;if(n.startsWith("#")){const t=n.split(this.delimiter||"\t");t.length>1&&(e=t)}else{this.setDecoder(r.format);const t=n.split(this.delimiter||"\t");try{const n=Object.assign({columnNames:e},r);if(this.decode(t,n))break;t.length>1&&(e=t)}catch(n){t.length>1&&(e=t)}}}if(e){r.columnNames=e;for(let t=0;t<e.length;t++)"color"===e[t]||"colour"===e[t]?r.colorColumn=t:"thickness"===e[t]&&(r.thicknessColumn=t)}return this.header=r,r}async parseFeatures(t){const e=[],n=this.decode,r=this.header.format,i=this.delimiter||"\t";let o,s=0,a=0;for(;void 0!==(o=await t.nextLine());){if(s++,s<=this.skipRows)continue;if(!o||o.startsWith("track")||o.startsWith("#")||o.startsWith("browser"))continue;if("wig"===r&&o.startsWith("fixedStep")){this.header.wig=dl(o);continue}if("wig"===r&&o.startsWith("variableStep")){this.header.wig=pl(o);continue}const t=o.split(i);if(t.length<1)continue;const l=n(t,this.header);l instanceof Za?(a++,a>0&&console.error(`Error parsing line '${o}': ${l.message}`)):l&&e.push(l)}return n===Ps&&function(t){if(0==t.length)return;const e=t[0];if(void 0===e.score&&void 0!==e.name){for(let e of t)if(!("number"==typeof(n=e.name)?n-n==0:"string"==typeof n&&""!==n.trim()&&(Number.isFinite?Number.isFinite(+n):isFinite(+n)))&&"."!==e.name)return;for(let e of t)e.score=Number(e.name),delete e.name}var n;const r=t.filter((t=>t.chr1!==t.chr2));for(let e of r){const n=Object.assign({},e);n.dup=!0,t.push(n),e.chr=e.chr1,e.start=e.start1,e.end=e.end1,n.chr=n.chr2,n.start=n.start2,n.end=n.end2}}(e),e}setDecoder(t){switch(t){case"narrowpeak":case"broadpeak":case"regionpeak":case"peaks":this.decode=el,this.delimiter=this.config.delimiter||/\s+/;break;case"bedgraph":this.decode=nl,this.delimiter=/\s+/;break;case"wig":this.decode=rl,this.delimiter=this.config.delimiter||/\s+/;break;case"gff3":case"gff":this.decode=qa,this.delimiter="\t";break;case"gtf":this.decode=Wa,this.delimiter="\t";break;case"fusionjuncspan":this.decode=sl,this.delimiter=this.config.delimiter||/\s+/;break;case"gtexgwas":this.skipRows=1,this.decode=al,this.delimiter="\t";break;case"refflat":this.decode=Ja,this.delimiter=this.config.delimiter||/\s+/;break;case"genepred":this.decode=Ka,this.delimiter=this.config.delimiter||/\s+/;break;case"genepredext":this.decode=Qa,this.delimiter=this.config.delimiter||/\s+/;break;case"ensgene":this.decode=Ka,this.header.shift=1,this.delimiter=this.config.delimiter||/\s+/;break;case"refgene":this.decode=Qa,this.delimiter=this.config.delimiter||/\s+/,this.header.shift=1;break;case"bed":this.decode=Xa,this.delimiter=this.config.delimiter||/\s+/;break;case"bedpe":case"hiccups":this.decode=Ps,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-domain":this.decode=Fs,this.headerLine=!0,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-loop":this.decode=Ps,this.delimiter=this.config.delimiter||"\t",this.header={colorColumn:7};break;case"interact":this.decode=Aa,this.delimiter=this.config.delimiter||/\s+/;break;case"snp":this.decode=il,this.delimiter="\t";break;case"rmsk":this.decode=Ya,this.delimiter="\t";break;case"gcnv":this.decode=cl,this.delimiter="\t";break;default:const e=function(t){return ks&&ks[t]?function(t){const e=t.fields,n=["chr","start","end"];for(let r=0;r<e.length;r++)for(let i of n)i===e[r]&&(t[i]=r);return t}(ks[t]):void 0}(t);void 0!==e?(this.decode=ll,this.header.customFormat=e,this.delimiter=e.delimiter||"\t"):(this.decode=Xa,this.delimiter=this.config.delimiter||/\s+/)}}}function ul(t){const e={},n=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let r;const i=[];for(let t of n)t&&0!==t.trim().length&&(t.endsWith("=")?r=t:r?(i.push(r+t),r=void 0):i.push(t));for(let t of i){if(!t)return;var o=t.split("=",2);if(2===o.length){const t=o[0].trim(),n=o[1].trim();if(e.hasOwnProperty(t)){let r=e[t];Array.isArray(r)?r.push(n):e[t]=[r,n]}else e[t]=n}}return"interact"==e.type?e.format="interact":"gcnv"===e.type&&(e.format="gcnv"),e}function fl(t){let e={},n=t.split(/\s+/);if(2===n.length){n[1].split(";").forEach((function(t){let n=t.split("=");"color"===n[0]?e.colorColumn=Number.parseInt(n[1])-1:"thickness"===n[0]&&(e.thicknessColumn=Number.parseInt(n[1])-1)}))}return e}function dl(t){const e=t.split(/\s+/);return{format:"fixedStep",chrom:e[1].split("=")[1],start:parseInt(e[2].split("=")[1],10)-1,step:parseInt(e[3].split("=")[1],10),span:e.length>4?parseInt(e[4].split("=")[1],10):1,index:0}}function pl(t){const e=t.split(/\s+/);return{format:"variableStep",chrom:e[1].split("=")[1],span:e.length>2?parseInt(e[2].split("=")[1],10):1}}const gl=t=>ke(t)&&t.indexOf(",")>0&&!t.startsWith("rgb(")&&!t.startsWith("rgba(")?`rgb(${t})`:t;class ml{constructor(t,e){this.browser=e,this.init(t)}init(t){t.displayMode&&(t.displayMode=t.displayMode.toUpperCase()),this.config=t,this.url=t.url,this.type=t.type,this.supportHiDPI=void 0===t.supportHiDPI||t.supportHiDPI,t.name||t.label?this.name=t.name||t.label:Ue(t.url)?this.name=t.url.name:ke(t.url)&&!t.url.startsWith("data:")&&(this.name=je(t.url)),this.id=void 0===this.config.id?this.name:this.config.id,this.order=t.order,t.color&&(this.color=gl(t.color)),t.altColor&&(this.altColor=gl(t.altColor)),"civic-ws"===t.sourceType?this.defaultColor="rgb(155,20,20)":this.defaultColor="rgb(0,0,150)",this.autoscaleGroup=t.autoscaleGroup,this.removable=void 0===t.removable||t.removable,this.height=t.height||100,this.autoHeight=t.autoHeight,this.minHeight=t.minHeight||Math.min(25,this.height),this.maxHeight=t.maxHeight||Math.max(1e3,this.height),this.visibilityWindow=t.visibilityWindow,t.onclick&&(this.onclick=t.onclick,t.onclick=void 0),t.description&&("function"==typeof t.description?this.description=t.description:this.description=()=>t.description),t.hoverTextFields&&(this.hoverTextFields=t.hoverTextFields)}get name(){return this._name}set name(t){this._name=t,this.trackView&&this.trackView.setTrackLabelName(t)}updateConfig(t){this.init(t)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}getState(){const t={};for(let e of Object.keys(this.config))e.startsWith("_")||"function"==typeof this.config[e]||void 0===this.config[e]||(t[e]=this.config[e]);for(let e of Object.keys(t)){if(e.startsWith("_"))continue;const n=this[e];n&&(Ss(n)||"boolean"==typeof n||"metadata"===e)&&(t[e]=n)}this.color&&(t.color=this.color),this.altColor&&(t.altColor=this.altColor),!this.autoscale&&this.dataRange&&(t.min=this.dataRange.min,t.max=this.dataRange.max);for(let e of Object.keys(t)){const n=t[e];if("function"==typeof n)throw Error(`Property '${e}' of track '${this.name} is a function. Functions cannot be saved in sessions.`);if(n instanceof File){const t=`Track ${this.name} is a local file. Sessions cannot be saved with local file references.`;throw Error(t)}if(n instanceof Promise)throw Error(`Property '${e}' of track '${this.name} is a Promise. Promises cannot be saved in sessions.`)}return t}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(t){if(this.disposed)return;const e={};let n;for(let r of Object.keys(t))switch(r.toLowerCase()){case"usescore":e.useScore=1===t[r]||"1"===t[r]||"on"===t[r]||!0===t[r];break;case"visibility":switch(t[r]){case"2":case"3":case"pack":case"full":e.displayMode="EXPANDED";break;case"4":case"squish":e.displayMode="SQUISHED";break;case"1":case"dense":e.displayMode="COLLAPSED"}break;case"color":case"altcolor":e[r]=t[r].startsWith("rgb(")?t[r]:"rgb("+t[r]+")";break;case"featurevisiblitywindow":case"visibilitywindow":e.visibilityWindow=Number.parseInt(t[r]);break;case"maxheightpixels":n=t[r].split(":"),3===n.length&&(e.minHeight=Number.parseInt(n[2]),e.height=Number.parseInt(n[1]),e.maxHeight=Number.parseInt(n[0]));break;case"viewlimits":if(!this.config.autoscale){n=t[r].split(":");let i,o=0;1==n.length?i=Number(n[0]):2==n.length&&(o=Number(n[0]),i=Number(n[1])),e.autoscale=!1,e.dataRange={min:o,max:i}}case"name":e[r]=t[r];break;case"url":e.infoURL=t[r];break;case"type":const i=t[r];vl.has(i)?e[r]=vl.get(i):e[r]=i;break;case"graphtype":e.graphType=t[r];break;default:e[r]=t[r]}for(let t of Object.keys(e))if(!this.config.hasOwnProperty(t)||"name"===t&&this.config._derivedName){let n=e[t];if("true"===n&&(n=!0),"false"===n&&(n=!1),this[t]=n,"height"===t&&this.trackView)try{const t=Number.parseInt(n);this.trackView.setTrackHeight(t)}catch(t){console.error(t)}}}clickedFeatures(t,e){if(e||(e=t.viewport.cachedFeatures),!e||0===e.length)return[];const n=t.genomicLocation,r=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2;return Uo(e,n-r,n+r)}extractPopupData(t,e){const n=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),r=[];let i,o;for(let e in t)if(t.hasOwnProperty(e)&&!n.has(e)&&Ss(t[e])){let n=t[e];r.push({name:Te(e),value:n}),"alleles"===e?i=t[e]:"alleleFreqs"===e&&(o=t[e])}if(i&&o){i.endsWith(",")&&(i=i.substr(0,i.length-1)),o.endsWith(",")&&(o=o.substr(0,o.length-1));let n=i.split(","),s=o.split(",");if(s.length>1){let i=[];for(let t=0;t<s.length;t++)i.push({a:n[t],af:Number(s[t])});i.sort((function(t,e){return t.af-e.af}));let o=i[i.length-1].a;if(1===o.length)for(let n=i.length-2;n>=0;n--){let s=i[n].a;if(1===s.length){e||(e=this.getGenomeId());const n=ml.getCravatLink(t.chr,t.start+1,o,s,e);console.log(n),n&&(r.push("<hr/>"),r.push({html:n}),r.push("<hr/>"))}}}}if(t.attributes)for(let e of Object.keys(t.attributes))r.push({name:e,value:t.attributes[e]});let s=`${t.chr}:${Se(t.start+1)}-${Se(t.end)}`;return t.strand&&(s+=` (${t.strand})`),r.push({name:"Location",value:s}),r}_hoverText(t){const e=this.clickedFeatures(t);if(e&&e.length>0){let t="";for(let n=0;n<e.length;n++){if(10===n){t+="; ...";break}if(!e[n])continue;const r=e[n]._f||e[n];if(t.length>0&&(t+="\n"),this.hoverTextFields){t="";for(let e of this.hoverTextFields)t.length>0&&(t+="\n"),r.hasOwnProperty(e)?t+=r[e]:"function"==typeof r.getAttribute&&(t+=r.getAttribute(e))}else"function"==typeof this.config.hoverText?t+=this.config.hoverText(r):"function"==typeof r.hoverText?t+=r.hoverText():t+=this.hoverText(r)}return t}}hoverText(t){let e="";return t.name&&(e+=t.name,t.value&&(e+=": ")),t.value&&(e+=t.value),e}description(){const t=(t,e)=>`<div class="igv-track-label-popup-shim"><b>${t}: </b>${e}</div>`;let e='<div class="igv-track-label-popup">';if(this.url?Ue(this.url)?e+=t("Filename",this.url.name):e+=t("URL",this.url):e=this.name,this.config){if(this.config.metadata)for(let n of Object.keys(this.config.metadata)){e+=t(n,this.config.metadata[n])}for(let n of Object.keys(this.config)){if(n.startsWith("_"))continue;let r=n.substr(0,1);if(r!==r.toLowerCase()){const r=this.config[n];r&&Ss(r)&&(e+=t(n,r))}}}return e+="</div>",e}dispose(){this.disposed=!0;for(let t of Object.keys(this))this[t]=void 0}static getCravatLink(t,e,n,r,i){if("hg38"===i||"GRCh38"===i){return`<a target="_blank" href="https://run.opencravat.org/result/nocache/variant.html?chrom=${t.startsWith("chr")?t:"chr"+t}&pos=${e}&ref_base=${n}&alt_base=${r}"><b>Cravat ${n}->${r}</b></a>`}}}const vl=new Map([["wiggle_0","wig"],["bed","bed"],["bigBed","bigBed"],["bigWig","bigWig"]]);class bl{constructor(t){switch(this.type=t||"seg",this.type){case"mut":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case"maf":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(t){let e;for(;void 0!==(e=await t.nextLine());)if(!e.startsWith("#")){const t=e.split("\t");this.header={headings:t};break}return this.header}async parseFeatures(t){const e=[];let n;this.header||(this.header=await this.parseHeader(t)),"seg"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(n=this.extractExtraColumns(this.header.headings));const r=this.header.headings[this.dataColumn];let i;for(;void 0!==(i=await t.nextLine());){const t=i.split("\t"),o="seg"===this.type?Number(t[this.dataColumn]):t[this.dataColumn];if(t.length>this.dataColumn){const i=new wl({sample:t[this.sampleColumn],chr:t[this.chrColumn],start:parseInt(t[this.startColumn])-1,end:parseInt(t[this.endColumn]),value:o,valueColumnName:r});if(n){const e=this.extractExtraColumns(t);i.setAttributes({names:n,values:e})}e.push(i)}}return e}extractExtraColumns(t){const e=[];for(let n=0;n<t.length;n++)n!==this.chrColumn&&n!==this.startColumn&&n!==this.endColumn&&n!==this.sampleColumn&&e.push(t[n]);return e}}class wl{constructor(t){let{sample:e,chr:n,start:r,end:i,value:o,valueColumnName:s}=t;this.sample=e,this.chr=n,this.start=r,this.end=i,this.value=o,this.valueColumnName=s}setAttributes(t){let{names:e,values:n}=t;this.attributeNames=e,this.attributeValues=n}getAttribute(t){if(this.attributeNames){const e=this.attributeNames.indexOf(t);if(e>=0)return this.attributeValues[e]}}popupData(t,e){const n=new Set(["chr","start","end","sample","value","row","color","sampleKey","uniqueSampleKey","sampleId","chromosome","uniquePatientKey"]),r=this.chr+":"+Se(this.start+1)+"-"+Se(this.end),i=[{name:"Sample",value:this.sample},{name:"Location",value:r},{name:this.valueColumnName?Te(this.valueColumnName):"Value",value:this.value}];if("mut"===t&&"hg38"===e){const t=this.extractCravatLink(e);t&&(i.push("<hr/>"),i.push({html:t}),i.push("<hr/>"))}if(this.attributeNames&&this.attributeNames.length>0)for(let t=0;t<this.attributeNames.length;t++)!n.has(this.attributeNames[t])&this.valueColumnName!==this.attributeNames[t]&&i.push({name:Te(this.attributeNames[t]),value:this.attributeValues[t]});return i}hoverText(){return`${this.sample}: ${this.value}`}extractCravatLink(t){let e,n;if(this.attributeNames&&this.attributeNames.length>0)for(let r=0;r<this.attributeNames.length;r++)if(e||"Reference_Allele"!==this.attributeNames[r]||(e=this.attributeValues[r]),!n&&this.attributeNames[r].startsWith("Tumor_Seq_Allele")&&this.attributeValues[r]!==e&&(n=this.attributeValues[r]),e&&n)return ml.getCravatLink(this.chr,this.start+1,e,n,t)}}function yl(t){const e=new xl;e.chr=t[0],e.pos=parseInt(t[1]),e.names=t[2],e.referenceBases=t[3],e.alternateBases=t[4],e.quality=t[5],e.filter=t[6],e.info={};const n=t[7];if(n)for(let t of n.split(";")){var r=t.split("=");e.info[r[0]]=r[1]}return e.init(),e}class xl{init(){const t=this.referenceBases,e=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type="SV":this.info.PERIOD&&(this.type="STR")),void 0===this.type&&(this.type=function(t,e){const n=t.length;if(void 0===e)return"UNKNOWN";if(0===e.trim().length||"<NON_REF>"===e||"<*>"===e||"."===e)return"NONVARIANT";{const t=e.split(",").map((function(t){return 1===n&&1===t.length?"SNP":"<NON_REF>"===t?"NONVARIANT":"OTHER"}));let r=t[0];for(let e of t)if(e!==r)return"MIXED";return r}}(t,e)),"NONVARIANT"===this.type&&(this.heterozygosity=0),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if("NONVARIANT"===this.type)this.start=this.pos-1,this.end=this.start+t.length;else{const n=e.split(",").filter((t=>t.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let e of n)if(this.alleles.push(e),"SV"!==this.type&&kl(e)){let n=e.length,r=t.length;const i=Math.min(n,r);let o=0;for(;o<i&&t.charCodeAt(o)===e.charCodeAt(o);)o++,n--,r--;for(;n>0&&r>0;){const i=o+n-1,s=o+r-1;if(e.charCodeAt(i)!==t.charCodeAt(s))break;n--,r--}for(;n>0&&r>0;){const i=o,s=o;if(e.charCodeAt(i)!==t.charCodeAt(s))break;o++,n--,r--}const s=this.pos+o-1,a=s+r;this.start=void 0===this.start?s:Math.min(this.start,s),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos)}}popupData(t,e){const n=`${Se(this.pos)}`,r=this.start===this.end?`${Se(this.start)} | ${Se(this.start+1)}`:`${Se(this.start+1)}-${Se(this.end)}`,i=[{name:"Chr",value:this.chr},{name:"Pos",value:n},{name:"Loc",value:r},{name:"ID",value:this.names?this.names:""},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases.replace("<","&lt;")},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter}];if("SNP"===this.type){let t=this.referenceBases;if(1===t.length){let n=this.alternateBases.split(",");for(let r of n)if(1===r.length){let n=ml.getCravatLink(this.chr,this.pos,t,r,e);n&&(i.push("<hr/>"),i.push({html:n}))}}}if(this.hasOwnProperty("heterozygosity")&&i.push({name:"Heterozygosity",value:this.heterozygosity}),this.info){i.push({html:'<hr style="border-top: dotted 1px;border-color: #c9c3ba" />'});for(let t of Object.keys(this.info))i.push({name:t,value:Sl(decodeURIComponent(this.info[t]))})}return i}hoverText(){return`${this.names}  ${this.referenceBases}->${this.alternateBases}`}getInfo(t){return this.info?this.info[t]:void 0}isRefBlock(){return"NONVARIANT"===this.type}}const _l=new Set(["A","C","T","G"].map((t=>t.charCodeAt(0))));function kl(t){for(let e=0;e<t.length;e++)if(!_l.has(t.charCodeAt(e)))return!1;return!0}function Sl(t,e){return void 0===e&&(e=","),Array.isArray(t)?t.join(e):t}class Cl{construtor(){}async parseHeader(t,e){const n={};n.chrAliasTable=new Map;let r=await t.nextLine();if(!r.startsWith("##fileformat"))throw new Error("Invalid VCF file: missing fileformat line");for(n.version=r.substr(13);void 0!==(r=await t.nextLine())&&r.startsWith("#");){let t;const o={};if(r.startsWith("##")){if(r.startsWith("##INFO")||r.startsWith("##FILTER")||r.startsWith("##FORMAT")){const e=r.indexOf("<"),s=r.lastIndexOf(">");if(!(e>2&&s>0)){console.log("Malformed VCF header line: "+r);continue}const a=r.substring(2,e-1);n[a]||(n[a]={});const l=Ee(r.substring(e+1,s-1),",");for(let e of l){var i=e.split("=");i.length>1&&("ID"===i[0]?t=i[1]:o[i[0]]=i[1])}t&&(n[a][t]=o)}else if(r.startsWith("##contig")&&e){const t=r.indexOf("<ID=");let i=r.indexOf(",",t);-1==i&&(i=r.indexOf(">",t));const o=r.substring(t+4,i),s=e.getChromosomeName(o);n.chrAliasTable.set(s,o)}}else if(r.startsWith("#CHROM")){const t=r.split("\t");if(t.length>8){n.callSets=[];for(let e=9;e<t.length;e++)n.callSets.push({id:e,name:t[e]})}}}return this.header=n,n}async parseFeatures(t){const e=[],n=this.header.callSets,r=8+(n?n.length+1:0);let i;for(;void 0!==(i=await t.nextLine());)if(i&&!i.startsWith("#")){const t=i.split("\t");if(t.length===r){const r=yl(t);if(r.header=this.header,e.push(r),t.length>9){const e=El(t[8].split(":"));r.calls={};for(let i=9;i<t.length;i++){const o=t[i],s=n[i-9],a={callSetName:s.name,info:{}};r.calls[s.id]=a,o.split(":").forEach((function(t,n){if(n===e.genotypeIndex)a.genotype=[],t.split(/[\|\/]/).forEach((function(t){a.genotype.push("."===t?t:parseInt(t))}));else a.info[e.fields[n]]=t}))}}r.info&&r.info.CHR2&&r.info.END&&e.push(Tl(r))}}return e}}function El(t){const e={genotypeIndex:-1,fields:t};for(let n=0;n<t.length;n++)"GT"===t[n]&&(e.genotypeIndex=n);return e}function Tl(t){const e=t.info.CHR2,n=Number.parseInt(t.info.END);return{chr:e,start:n-1,end:n,_f:t}}class Al{constructor(t){if(this.config=t,t.columns){if(void 0===t.columns.chromosome||void 0===t.columns.position||void 0===t.columns.value)throw Error("columns property must define chrCol, posCol, and valueCol");this.posCol=t.columns.position-1,this.chrCol=t.columns.chromosome-1,this.valueCol=t.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(t){const e=await t.nextLine();return this.parseHeaderLine(e)}parseHeaderLine(t){if(this.columns=t.split(/\t/),!this.config.columns)for(let t=0;t<this.columns.length;t++){switch(this.columns[t].toLowerCase()){case"chr":case"chromosome":case"chr_id":this.chrCol=t;break;case"bp":case"pos":case"position":case"chr_pos":this.posCol=t;break;case"p":case"pval":case"pvalue":case"p-value":case"p.value":this.valueCol=t}}return this.columns}async parseFeatures(t){const e=[],n=t.nextLine();let r;for(this.columns||this.parseHeaderLine(n);void 0!==(r=t.nextLine());){const t=r.split(/\t/);if(t.length===this.columns.length){const n=t[this.chrCol],i=parseInt(t[this.posCol])-1,o=i+1,s=Number(t[this.valueCol]);e.push(new Ll({chr:n,start:i,end:o,value:s,line:r,columns:this.columns}))}}return e}}class Ll{constructor(t){let{chr:e,start:n,end:r,value:i,line:o,columns:s}=t;this.chr=e,this.start=n,this.end=r,this.value=i,this.line=o,this.columns=s}popupData(){const t=this.line.split(/\t/);return this.columns.map((function(e,n){return{name:e,value:t[n]}}))}getAttribute(t){const e=this.line.split(/\t/);for(let n=0;n<this.columns.length;n++)if(this.columns[n]===t)return e[n]}}var Ml=new RegExp("([^:]*)\\(([^)]*)\\)"),Rl=new RegExp("([^:]*):([^(]*)\\(([^)]*)\\)");class Il{constructor(t){const e=t?t.decode:void 0;this.nameField=t?t.nameField:void 0,this.skipRows=0,this.decode=e||Bl,this.delimiter="\t"}async parseHeader(t){let e,n;for(;(e=await t.nextLine())&&(e.startsWith("track")||e.startsWith("#")||e.startsWith("browser"));)if(e.startsWith("track")||e.startsWith("#track")){let t=Pl(e);n?Object.assign(n,t):n=t}else if(e.startsWith("#columns")){let t=Fl(e);n?Object.assign(n,t):n=t}else e.startsWith("##gff-version 3")&&(this.format="gff3",n||(n={}),n.format="gff3");return this.header=n,n}async parseFeatures(t){const e=[],n=this.decode,r=this.delimiter||"\t";let i,o=0;for(;void 0!==(i=t.nextLine());){if(o++,o<=this.skipRows||i.startsWith("track")||i.startsWith("#")||i.startsWith("browser"))continue;let t=s();if(t.length<1)continue;if(!this.aed){this.aed=Ol(t);continue}const r=n.call(this,t,undefined);r&&e.push(r)}return e;function s(){for(var t,e,n=[],o="",s=!1;i||""===i;){for(t=0;t<i.length;t++)(e=i.charAt(t))===r?s?o+=e:(n.push(o),o=""):'"'===e?t+1<i.length&&'"'===i.charAt(t+1)?(s&&(o+='"'),t++):s=!s:o+=e;if(!s)break;o+="\n",i=nextLine()}return n.push(o),n}}}function Nl(t){var e=Rl.exec(t);if(e)return{namespace:e[1],name:e[2],type:e[3]};if(e=Ml.exec(t))return{namespace:"?",name:e[1],type:e[2]};throw new Error("Error parsing the header row of AED file - column not in ns:name(ns:type) format")}function Ol(t){var e,n,r;for(e={columns:[],metadata:{}},n=0;n<t.length;n++)r=Nl(t[n]),e.columns.push(r);return e}function Pl(t){const e={},n=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let r;const i=[];for(let t of n)t&&0!==t.trim().length&&(t.endsWith("=")>0?r=t:r?(i.push(r+t),r=void 0):i.push(t));for(let t of i){if(!t)return;var o=t.split("=",2);if(2===o.length){const t=o[0].trim(),n=o[1].trim();e[t]=n}}return e}function Fl(t){let e={},n=t.split(/\s+/);if(2===n.length){n[1].split(";").forEach((function(t){let n=t.split("=");"color"===n[0]?e.colorColumn=Number.parseInt(n[1])-1:"thickness"===n[0]&&(e.thicknessColumn=Number.parseInt(n[1])-1)}))}return e}function Dl(t,e){var n,r,i=t.columns;this.aed=t,this.allColumns=e,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=".",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let t=0;t<e.length;t++)if(n=e[t]){"aed:Integer"===(r=i[t]).type&&(n=parseInt(n));var o=[];if(r.namespace.length>0)for(let t=0;t<r.namespace.length;t++)o.push(r.namespace.charCodeAt(t));"bio"===r.namespace.trim()?"sequence"===r.name?this.chr=n:"start"===r.name?this.start=n:"end"===r.name?this.end=n:"cdsMin"===r.name?this.cdStart=n:"cdsMax"===r.name?this.cdEnd=n:"strand"===r.name&&(this.strand=n):"aed"===r.namespace?"name"===r.name&&(this.name=n):"style"===r.namespace&&"color"===r.name&&(this.color=mo.createColorString(n))}}function Bl(t,e){var n,r,i,o,s,a,l=0,c=this.aed.columns;if(t.length===c.length){for(a=0;a<t.length;a++)o=c[a],""!==(i=t[a])&&l++,"name"===o.name&&"aed"===o.namespace?n=i:"value"===o.name&&"aed"===o.namespace&&(r=i);if(2===l&&n&&r)return s=Nl(n),this.aed.metadata[s.namespace]||(this.aed.metadata[s.namespace]={}),void(this.aed.metadata[s.namespace][s.name]||(this.aed.metadata[s.namespace][s.name]={type:s.type,value:r}));var h=new Dl(this.aed,t);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log("Cannot parse feature: "+t.join(","))}else console.log("Corrupted AED file row: "+t.join(","))}Dl.prototype.popupData=function(){for(var t=[],e=this.aed,n=0;n<this.allColumns.length;n++){var r=this.allColumns[n],i=e.columns[n].name;"sequence"!==i&&"color"!==i&&r&&t.push({name:i,value:r})}return t};class zl{constructor(t,e){this.littleEndian=void 0===e||e,this.position=0,this.view=t,this.length=t.byteLength}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){var t=this.view.getUint8(this.position,this.littleEndian);return this.position++,t}getShort(){var t=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,t}getUShort(){var t=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,t}getInt(){var t=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,t}getUInt(){var t=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,t}getLong(){var t=[];t[0]=this.view.getUint8(this.position),t[1]=this.view.getUint8(this.position+1),t[2]=this.view.getUint8(this.position+2),t[3]=this.view.getUint8(this.position+3),t[4]=this.view.getUint8(this.position+4),t[5]=this.view.getUint8(this.position+5),t[6]=this.view.getUint8(this.position+6),t[7]=this.view.getUint8(this.position+7);var e=0;if(this.littleEndian)for(let n=t.length-1;n>=0;n--)e=256*e+t[n];else for(let n=0;n<t.length;n++)e=256*e+t[n];return this.position+=8,e}getString(t){for(var e,n="";0!==(e=this.view.getUint8(this.position++))&&(n+=String.fromCharCode(e),!t||n.length!==t););return n}getFixedLengthString(t){var e,n,r="";for(e=0;e<t;e++)(n=this.view.getUint8(this.position++))>0&&(r+=String.fromCharCode(n));return r}getFixedLengthTrimmedString(t){var e,n,r="";for(e=0;e<t;e++)(n=this.view.getUint8(this.position++))>32&&(r+=String.fromCharCode(n));return r}getFloat(){var t=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,t}getDouble(){var t=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,t}skip(t){return this.position+=t,this.position}getVPointer(){var t=this.position,e=this.view.getUint8(t+1)<<8|this.view.getUint8(t),n=4294967296*(255&this.view.getUint8(t+6))+16777216*(255&this.view.getUint8(t+5))+65536*(255&this.view.getUint8(t+4))+256*(255&this.view.getUint8(t+3))+(255&this.view.getUint8(t+2));return this.position+=8,new Hl(n,e)}}class Hl{constructor(t,e){this.block=t,this.offset=e}isLessThan(t){return this.block<t.block||this.block===t.block&&this.offset<t.offset}isGreaterThan(t){return this.block>t.block||this.block===t.block&&this.offset>t.offset}print(){return this.block+":"+this.offset}}class Vl{constructor(t){this.tabix=!0}parse(t,e){const n=new zl(new DataView(t)),r=n.getInt();if(21582659!==r)throw 38359875===r?Error("CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js"):Error("Not a CSI index");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=n.getInt(),this.depth=n.getInt();const i=[];let o=0;if(n.getInt()>=28){n.getInt(),n.getInt(),n.getInt(),n.getInt(),n.getInt(),n.getInt();const t=n.getInt(),r=n.position+t;let o=0;for(;n.position<r;){let t=n.getString();e&&(t=e.getChromosomeName(t)),this.sequenceIndexMap[t]=o,i[o]=t,o++}}const s=this.bin_limit()+1,a=n.getInt();for(let t=0;t<a;t++){const e=[],r=[],i=n.getInt();for(let t=0;t<i;t++){const t=n.getInt();if(r[t]=n.getVPointer(),t>s)n.getInt(),n.getVPointer(),n.getVPointer(),n.getLong(),n.getLong();else{e[t]=[];const r=n.getInt();for(let i=0;i<r;i++){const r=n.getVPointer(),i=n.getVPointer();r&&i&&(r.block<this.blockMin&&(this.blockMin=r.block),i.block>o&&(o=i.block),e[t].push([r,i]))}}}i>0&&(this.indices[t]={binIndex:e,loffset:r})}this.lastBlockPosition=o}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}blocksForRange(t,e,n){const r=this.indices[t];if(r){const t=this.reg2bins(e,n);if(0==t.length)return[];const i=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(r.binIndex[t]){const e=r.binIndex[t],n=e.length;for(let r=0;r<n;++r){const n=e[r][0],o=e[r][1];i.push({minv:n,maxv:o,bin:t})}}return function(t,e){const n=[];let r=null;return 0===t.length?t:(t.sort((function(t,e){const n=t.minv.block-e.minv.block;return 0!==n?n:t.minv.offset-e.minv.offset})),t.forEach((function(t){var i,o;e&&!t.maxv.isGreaterThan(e)||(null===r?(n.push(t),r=t):(i=r,(o=t).minv.block-i.maxv.block<65e3&&o.maxv.block-i.minv.block<5e6?t.maxv.isGreaterThan(r.maxv)&&(r.maxv=t.maxv):(n.push(t),r=t)))})),n)}(i,r.loffset[t[0]])}return[]}reg2bins(t,e){(t-=1)<1&&(t=1),e>2**50&&(e=2**34),e-=1;let n=0,r=0,i=this.minShift+3*this.depth;const o=[];for(;n<=this.depth;i-=3,r+=1<<3*n,n+=1){const n=r+(t>>i),s=r+(e>>i);if(s-n+o.length>this.maxBinNumber)throw new Error(`query ${t}-${e} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);o.push([n,s])}return o}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}const jl=1e6;class Ul{constructor(){}async parse(t,e,n){const r=[];let i=Number.MAX_SAFE_INTEGER,o=0;const s=new zl(new DataView(t)),a=s.getInt(),l={};if(!(21578050===a||e&&21578324===a))throw new Error(indexURL+" is not a "+(e?"tabix":"bai")+" file");{const t=s.getInt();if(e){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let e=0;e<t;e++){let t=s.getString();n&&(t=n.getChromosomeName(t)),l[t]=e}}for(let e=0;e<t;e++){const t={},n=[],a=s.getInt();for(let e=0;e<a;e++){const e=s.getInt();if(37450===e)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{t[e]=[];const n=s.getInt();for(let r=0;r<n;r++){const n=s.getVPointer(),r=s.getVPointer();n&&r&&(n.block<i&&(i=n.block),r.block>o&&(o=r.block),t[e].push([n,r]))}}}const l=s.getInt();for(let t=0;t<l;t++){const t=s.getVPointer();n.push(t)}a>0&&(r[e]={binIndex:t,linearIndex:n})}this.firstBlockPosition=i,this.lastBlockPosition=o,this.indices=r,this.sequenceIndexMap=l,this.tabix=e}}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}blocksForRange(t,e,n){const r=this.indices[t];if(r){const t=function(t,e){const n=[];e>=1<<29&&(e=1<<29);return--e,n.push([0,0]),n.push([1+(t>>26),1+(e>>26)]),n.push([9+(t>>23),9+(e>>23)]),n.push([73+(t>>20),73+(e>>20)]),n.push([585+(t>>17),585+(e>>17)]),n.push([4681+(t>>14),4681+(e>>14)]),n}(e,n),i=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(r.binIndex[t]){const e=r.binIndex[t],n=e.length;for(let r=0;r<n;++r){const n=e[r][0],o=e[r][1];i.push({minv:n,maxv:o,bin:t})}}const o=r.linearIndex.length;let s=null;const a=Math.min(e>>14,o-1),l=Math.min(n>>14,o-1);for(let t=a;t<=l;++t){const e=r.linearIndex[t];e&&(s&&!e.isLessThan(s)||(s=e))}return function(t,e){const n=[];let r=null;return 0===t.length?t:(t.sort((function(t,e){const n=t.minv.block-e.minv.block;return 0!==n?n:t.minv.offset-e.minv.offset})),t.forEach((function(t){e&&!t.maxv.isGreaterThan(e)||(null!==r&&function(t,e){const n=e.minv.block-t.maxv.block,r=e.maxv.block-t.minv.block;return n<3e4&&r<10*jl}(r,t)?t.maxv.isGreaterThan(r.maxv)&&(r.maxv=t.maxv):(n.push(t),r=t))})),n)}(i,s)}return[]}}class ql{constructor(){}async parse(t,e){let n=0;this.chrIndex={},this.lastBlockPosition=[];const r=new zl(new DataView(t));!function(t){t.getInt(),t.getInt();const e=t.getInt();if(t.getString(),t.getLong(),t.getLong(),t.getString(),t.getInt(),e>=3){let e=t.getInt();for(;e-- >0;)t.getString(),t.getString()}}(r);let i=r.getInt();for(;i-- >0;){let t=r.getString();e&&(t=e.getChromosomeName(t));const i=r.getInt(),o=r.getInt(),s=r.getInt();r.getInt(),r.getInt();let a=r.getLong();const l=[];for(let t=0;t<o;t++){const t=r.getLong();l.push({min:a,max:t}),a=t,t>n&&(n=t)}this.chrIndex[t]={chr:t,blocks:l,longestFeature:s,binWidth:i}}this.lastBlockPosition=n}get chromosomeNames(){return Object.keys(this.chrIndex)}blocksForRange(t,e,n){const r=this.chrIndex[t];if(r){const t=r.blocks,i=r.longestFeature,o=r.binWidth,s=Math.max(e-i,0),a=Math.floor(s/o);if(a>=t.length)return[];{const e=Math.min(Math.floor((n-1)/o),t.length-1),r=t[a].min,i=t[e].max;if(0===i-r)return[];return[{minv:{block:r,offset:0},maxv:{block:i,offset:0}}]}}}}async function Wl(t,e,n){let r=await Eo.loadArrayBuffer(t,Cs(e)),i=new DataView(r);if(31===i.getUint8(0)&&139===i.getUint8(1)){r=io(r).buffer,i=new DataView(r)}switch(i.getInt32(0,!0)){case 21578050:return async function(t,e){const n=new Ul;return await n.parse(t,!1,e),n}(r,n);case 21578324:return async function(t,e){const n=new Ul;return await n.parse(t,!0,e),n}(r,n);case 21582659:return async function(t,e){const n=new Vl;return n.parse(t,e),n}(r,n);case 1480870228:return async function(t,e){const n=new ql;return n.parse(t,e),n}(r,n);case 38359875:throw Error("CSI version 2 is not supported.");default:throw Error(`Unrecognized index type: ${t}`)}}function $l(t){return"string"==typeof t||t instanceof String?new Gl(t):new Zl(t)}class Gl{constructor(t){this.data=t,this.ptr=0}nextLine(){var t=this.ptr,e=this.data.indexOf("\n",t),n=this.data;if(e>0)return this.ptr=e+1,e>t&&"\r"===n.charAt(e-1)?n.substring(t,e-1):n.substring(t,e);var r=n.length;return this.ptr=r,t>=r?void 0:n.substring(t)}}class Zl{constructor(t){this.data=t,this.length=this.data.length,this.ptr=0}nextLine(){var t,e;if(e="",!(this.ptr>=this.length)){for(var n=this.ptr;n<this.length;n++)if("\r"!==(t=String.fromCharCode(this.data[n]))){if("\n"===t)break;e+=t}return this.ptr=n+1,e}}}class Xl{constructor(t){this.config=t,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let t;try{for(;;){const e=this.buffer?this.buffer.length:0;for(;this.bufferPtr<e;){const e=String.fromCharCode(this.buffer[this.bufferPtr++]);if("\r"!==e){if("\n"===e)return t;t=t?t+e:e}}if(this.eof)return t;await this.readNextBlock()}}catch(e){return console.warn(e),this.eof=!0,t}}async readNextBlock(){const t=Cs(this.config,{range:{start:this.filePtr,size:26}}),e=oo(await Eo.loadArrayBuffer(this.config.url,t));if(0===e)this.eof=!0,this.buffer=void 0;else{const t=Cs(this.config,{range:{start:this.filePtr,size:e}}),n=await Eo.loadArrayBuffer(this.config.url,t);n.byteLength<e&&(this.eof=!0),this.buffer=io(n),this.bufferPtr=0,this.filePtr+=n.byteLength}}}class Yl{constructor(t,e){var n;this.config=t||{},this.genome=e,this.indexURL=t.indexURL,this.indexed=t.indexed,Ue(this.config.url)?this.filename=this.config.url.name:Ms(this.config.url)?(this.indexed=!1,this.dataURI=t.url):(n=He(this.config.url),this.filename=t.filename||n.file),this.parser=this.getParser(this.config),"vcf"!==this.config.format||this.config.indexURL||console.warn("Warning: index file not specified.  The entire vcf file will be loaded.")}async defaultVisibilityWindow(){if(this.config.indexURL){const t=await this.getIndex();if(t&&t.lastBlockPosition){let e=0;const n=1e4;for(let n of t.chromosomeNames){const t=this.genome.getChromosome(n);t&&(e+=t.bpLength)}return Math.round(e/t.lastBlockPosition*n)}}}async readFeatures(t,e,n){return await this.getIndex()?(this.indexed=!0,this.loadFeaturesWithIndex(t,e,n)):this.dataURI?(this.indexed=!1,this.loadFeaturesFromDataURI()):(this.indexed=!1,this.loadFeaturesNoIndex())}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const t=await this.getIndex();if(!t)throw new Error("Unable to load index: "+this.config.indexURL);let e;if(t.tabix)e=new Xl(this.config);else{const n=Object.values(t.chrIndex).flatMap((t=>t.blocks)).map((t=>t.max)).reduce(((t,e)=>Math.min(t,e)),Number.MAX_SAFE_INTEGER),r=Cs(this.config,{bgz:t.tabix,range:{start:0,size:n}});e=$l(await Eo.loadString(this.config.url,r))}return this.header=await this.parser.parseHeader(e),this.header}{const t=Cs(this.config),e=await Eo.loadString(this.config.url,t);let n=$l(e);return this.header=await this.parser.parseHeader(n),n=$l(e),this.features=await this.parser.parseFeatures(n),this.header}}getParser(t){switch(t.format){case"vcf":return new Cl(t);case"seg":return new bl("seg");case"mut":return new bl("mut");case"maf":return new bl("maf");case"gwas":return new Al(t);case"aed":return new Il(t);default:return new hl(t)}}async loadFeaturesNoIndex(){if(this.features){const t=this.features;return delete this.features,t}{const t=Cs(this.config),e=await Eo.loadString(this.config.url,t);if(!this.header){const t=$l(e);this.header=await this.parser.parseHeader(t)}const n=$l(e);return await this.parser.parseFeatures(n)}}async loadFeaturesWithIndex(t,e,n){const r=this.config,i=this.parser,o=this.index.tabix,s=o?this.index.sequenceIndexMap[t]:t;if(void 0===s)return[];const a=this.genome,l=this.index.blocksForRange(s,e,n);if(l&&0!==l.length){const s=[];for(let c of l){const l=c.minv.block,h=c.minv.offset,u=c.maxv.offset;let f;if(o){let t=0;if(u>0){const e=Cs(r,{range:{start:c.maxv.block,size:26}});t=oo(await Eo.loadArrayBuffer(r.url,e))}f=c.maxv.block+t}else f=c.maxv.block;const d=Cs(r,{range:{start:l,size:f-l+1}});let p;if(o){p=io(await Eo.loadArrayBuffer(r.url,d))}else p=await Eo.loadString(r.url,d);const g=$l(h?p.slice(h):p);let m=await i.parseFeatures(g);m=m.filter((t=>void 0===t._f));let v=!1;for(let r=0;r<m.length;r++){const i=m[r];if((a?a.getChromosomeName(i.chr):i.chr)!==t){if(0===s.length)continue;break}if(i.start>n){s.push(i);break}i.end>=e&&i.start<=n&&(v||(v=!0,r>0&&s.push(m[r-1])),s.push(i))}}return s.sort((function(t,e){return t.start-e.start})),s}return[]}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return Wl(this.config.indexURL,this.config,this.genome)}async loadFeaturesFromDataURI(){if(this.features){const t=this.features;return delete this.features,t}{const t=co(this.dataURI);let e=$l(t);return this.header=await this.parser.parseHeader(e),this.header instanceof String&&this.header.startsWith("##gff-version 3")&&(this.format="gff3"),e=$l(t),this.features=await this.parser.parseFeatures(e),this.features}}}const Kl=ke;class Ql{constructor(t){this.config=t}async readFeatures(t,e,n){let r;r="function"==typeof this.config.url?this.config.url({chr:t,start:e,end:n}):this.config.url.replace("$CHR",t).replace("$START",e).replace("$END",n);let i,o=Object.assign({},this.config);void 0!==this.config.body&&("function"==typeof this.config.body?o.body=this.config.body({chr:t,start:e,end:n}):o.body=this.config.body.replace("$CHR",t).replace("$START",e).replace("$END",n));const s=await Eo.load(r,o);if(s&&(i="function"==typeof this.config.parser?this.config.parser(s):Kl(s)?JSON.parse(s):s),this.config.mappings){let t=Object.keys(this.config.mappings);for(let e of i)for(let n of t)e[n]=e[this.config.mappings[n]]}return i}}const Jl=function(t,e){this.config=t,this.genome=e,this.expandQueryInterval=!1};Jl.prototype.readFeatures=function(t,e,n){const r=Math.max(0,Math.floor(e));let i=Math.ceil(n);if(this.genome){const e=this.genome.getChromosome(t);e&&i>e.bpLength&&(i=e.bpLength)}const o=this.config.url+"?db="+this.config.db+"&table="+this.config.tableName+"&chr="+t+"&start="+r+"&end="+i;return Eo.loadJson(o,this.config).then((function(t){return t?(t.forEach((function(t){t.hasOwnProperty("exonStarts")&&t.hasOwnProperty("exonEnds")&&t.hasOwnProperty("exonCount")&&t.hasOwnProperty("cdsStart")&&t.hasOwnProperty("cdsEnd")&&function(t){var e,n,r,i,o,s;e=t.exonCount,n=t.exonStarts.split(","),r=t.exonEnds.split(","),i=[];for(var a=0;a<e;a++){var l={start:o=parseInt(n[a]),end:s=parseInt(r[a])};(t.cdsStart>s||t.cdsEnd<t.cdsStart)&&(l.utr=!0),t.cdsStart>=o&&t.cdsStart<=s&&(l.cdStart=t.cdsStart),t.cdsEnd>=o&&t.cdsEnd<=s&&(l.cdEnd=t.cdsEnd),i.push(l)}t.exons=i}(t)})),t):null}))};const tc=["Name","gene_name","gene","gene_id","alias","locus","name"];class ec{constructor(t){this.format=t.format,this.nameField=t.nameField,this.filterTypes=void 0===t.filterTypes?new Set(["chromosome"]):new Set(t.filterTypes)}combineFeatures(t,e){let n;const r=this.filterTypes;if(t=t.filter((t=>void 0===r||!r.has(t.type))),"gff3"===this.format){const e=this.combineFeaturesById(t);n=this.combineFeaturesByType(e)}else n=this.combineFeaturesByType(t);return n.sort((function(t,e){return t.start-e.start})),this.numberExons(n,e),this.nameFeatures(n),n}combineFeaturesById(t){const e=new Map,n=[];for(let r of t)if(za(r.type)||Ba(r.type)||!r.id)n.push(r);else{let t=e.get(r.chr);t||(t=new Map,e.set(r.chr,t));let n=t.get(r.id);n?n.push(r):t.set(r.id,[r])}for(let t of e.values())for(let e of t.values())if(e.length>1){const t=e[0];t.exons=[];for(let n of e)t.start=Math.min(t.start,n.start),t.end=Math.max(t.end,n.end),t.exons.push({start:n.start,end:n.end});n.push(t)}else n.push(e[0]);return n}combineFeaturesByType(t){const e=t.filter((t=>"gene"===t.type||t.type.endsWith("_gene"))),n=Object.create(null);for(let t of e)n[t.id]=t;const r=Object.create(null),i=[],o=new Set,s=this.filterTypes;t=t.filter((t=>void 0===s||!s.has(t.type)));for(let e of t)if("biological_region"===e.type&&console.log(),Ba(e.type)){const t=e.id;if(void 0!==t){const s=new ja(e);r[t]=s,i.push(s),o.add(e);const a=n[e.parent];a&&(s.geneObject=a,o.add(a))}}for(let e of t)if(za(e.type)){const t=c(e);if(t)for(let n of t){let s=r[n];if(!s&&"gtf"===this.format){const t=Object.assign({},e);t.type="transcript",s=new ja(t),r[n]=s,i.push(s)}if(void 0!==s){if(a=e.type,Na.has(a))if(t.length>1){const t=new Va(e);s.addExon(t)}else s.addExon(e);else s.addPart(e);o.add(e)}}}var a;i.forEach((function(t){"function"==typeof t.finish&&t.finish()}));const l=t.filter((t=>!o.has(t)));for(let t of l)i.push(t);return i;function c(t){return t.parent&&""!==t.parent.trim()?t.parent.trim().split(","):null}}numberExons(t,e){for(let n of t)if(n.exons&&(!e||n.end<=e.end&&n.start>e.start))for(let t=0;t<n.exons.length;t++){n.exons[t].number="-"===n.strand?n.exons.length-t:t+1}}nameFeatures(t){for(let e of t)if(e.attributeString){const t="gff3"===this.format?"=":" ",n=$a(e.attributeString,t),r=new Map(n);if(this.nameField)e.name=r.get(this.nameField);else for(let t of tc)if(r.has(t)){e.name=r.get(t);break}}}}const nc=function(t){this.config=t,this.url=t.url,this.tissueId=t.tissueSiteDetailId,this.indexed=!0,this.datasetId=t.datasetId||"gtex_v8"};nc.prototype.readFeatures=async function(t,e,n){let r=t.startsWith("chr")?t:"chr"+t,i=Math.floor(e),o=Math.ceil(n),s=this.datasetId,a=this.url+"?chromosome="+r+"&start="+i+"&end="+o+"&tissueSiteDetailId="+this.tissueId+"&datasetId="+s;const l=await Eo.loadJson(a,{withCredentials:this.config.withCredentials});return l&&l.singleTissueEqtl?(l.singleTissueEqtl.forEach((function(t){t.chr=t.chromosome,t.position=t.pos,t.start=t.pos-1,t.end=t.start+1,t.snp=t.snpId,t.geneName=t.geneSymbol,t.geneId=t.gencodeId})),l.singleTissueEqtl):void 0};const rc=function(t){this.config=t,this.url=t.url,this.cellConditionId=t.cellConditionId,this.valueThreshold=t.valueThreshold?t.valueThreshold:.05};rc.prototype.readFeatures=function(t,e,n){var r=this,i=this.url+"?chromosome="+t+"&start="+e+"&end="+n+"&cell_condition_id="+this.cellConditionId;return new Promise((function(t,e){Eo.loadJson(i,{withCredentials:r.config.withCredentials}).then((function(e){e?(e.eqtls.forEach((function(t){t.chr=t.chromosome,t.start=t.position,t.end=t.position+1})),t(e.eqtls)):t(null)})).catch((function(t){e(t)}))}))};const ic=Eo.apiKey;function oc(t){var e=t.url+"/"+t.entity+"/"+t.entityId;return t.headers={"Cache-Control":"no-cache"},Eo.loadJson(e,t)}function sc(t){return new Promise((function(e,n){var r=t.results?t.results:[],i=t.url,o=t.body,s=t.decode,a="?",l=t.fields;return ic&&(i=i+a+"key="+ic,a="&"),l&&(i=i+a+"fields="+l),function t(a){a?o.pageToken=a:void 0!==o.pageToken&&delete o.pageToken;var l=JSON.stringify(o);Eo.loadJson(i,{sendData:l,contentType:"application/json",headers:{"Cache-Control":"no-cache"}}).then((function(n){var i,o;n?((o=s?s(n):n)&&o.forEach((function(t){r.push(t)})),(i=n.nextPageToken)?t(i):e(r)):e(r)})).catch((function(t){n(t)}))}()}))}const ac=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.variantSetId=t.variantSetId,this.callSetIds=t.callSetIds,this.includeCalls=void 0===t.includeCalls||t.includeCalls};ac.prototype.readHeader=function(){var t=this;return t.header?Promise.resolve(t.header):(t.header={},!1===t.includeCalls?Promise.resolve(t.header):sc({url:t.url+"/callsets/search",fields:"nextPageToken,callSets(id,name)",body:{variantSetIds:Array.isArray(t.variantSetId)?t.variantSetId:[t.variantSetId],pageSize:"10000"},decode:function(e){if(t.callSetIds){var n=[],r=new Set;return t.callSetIds.forEach((function(t){r.add(t)})),e.callSets.forEach((function(t){r.has(t.id)&&n.push(t)})),n}return e.callSets}}).then((function(e){return t.header.callSets=e,t.header})))},ac.prototype.readFeatures=function(t,e,n){const r=this,i=this.genome;return r.readHeader().then((function(t){return new Promise((function(t,e){r.chrAliasTable?t(r.chrAliasTable):r.readMetadata().then((function(e){r.metadata=e.metadata,r.chrAliasTable={},e.referenceBounds&&i&&e.referenceBounds.forEach((function(t){var e=t.referenceName,n=i.getChromosomeName(e);r.chrAliasTable[n]=e})),t(r.chrAliasTable)}))}))})).then((function(i){var o=i.hasOwnProperty(t)?i[t]:t;return sc({url:r.url+"/variants/search",fields:r.includeCalls?void 0:"nextPageToken,variants(id,variantSetId,names,referenceName,start,end,referenceBases,alternateBases,quality,filter,info)",body:{variantSetIds:Array.isArray(r.variantSetId)?r.variantSetId:[r.variantSetId],callSetIds:r.callSetIds?r.callSetIds:void 0,referenceName:o,start:e.toString(),end:n.toString(),pageSize:"10000"},decode:function(t){var e,n=[];return t.variants.forEach((function(t){e=function(t){var e,n=new xl;return n.chr=t.referenceName,n.start=parseInt(t.start),n.end=parseInt(t.end),n.pos=n.start+1,n.names=Sl(t.names,"; "),n.referenceBases=t.referenceBases,n.alternateBases=Sl(t.alternateBases),n.quality=t.quality,n.filter=Sl(t.filter),n.info={},t.info&&Object.keys(t.info).forEach((function(e){var r,i=t.info[e];r=Array.isArray(i)?i.join(","):i,n.info[e]=r})),n.calls={},t.calls&&t.calls.forEach((function(t){e=t.callSetId,n.calls[e]=t})),init(n),n}(t),e.isRefBlock()||n.push(e)})),n}})}))},ac.prototype.readMetadata=function(){return oc({url:this.url,entity:"variantsets",entityId:this.variantSetId})};class lc{constructor(t){this.config=t}async readFeatures(t,e,n){const r=(await Eo.loadJson(this.config.url+"/variants/?count=50000")).records,i=[];for(let t of r)if(t.coordinates){t.id;const e=t.coordinates;e.chromosome&&i.push(new cc(e.chromosome,e.start-1,e.stop,t)),e.chromosome2&&i.push(new cc(e.chromosome2,e.start2-1,e.stop2,t))}return i}}class cc{constructor(t,e,n,r){if(this.chr=t,this.start=e,this.end=n,this.id=r.id,this.entrezName=r.entrez_name,this.name=r.name,this.actionabilityScore=r.civic_actionability_score,r.coordinates.reference_bases&&(this.refBases=r.coordinates.reference_bases),r.coordinates.variant_bases&&(this.altBases=r.coordinates.variant_bases),r.variant_types&&(this.variant_types=r.variant_types),this.locationString=this.chr+":"+Se(this.start+1)+"-"+Se(this.end),void 0!==this.actionabilityScore){let t;if(this.actionabilityScore<=10)t=.2;else{const e=Math.min(30,this.actionabilityScore);t=.2+.8*Math.log10((e-10)/2)}this.alpha=t}}popupData(){const t=n("CIViC","https://civicdb.org/links/variants/"+this.id);this.refBases!==this.altBases&&this.refBases&&1===this.refBases.length&&this.altBases&&this.altBases.length;const e=[t];if(e.push({name:"Entrez",value:n(this.entrezName,"https://ghr.nlm.nih.gov/gene/"+this.entrezName)}),e.push({name:"Name",value:this.name}),this.variant_types&&this.variant_types.length>0){const t=1===this.variant_types.length?"Type":"Types";let n;for(let t of this.variant_types)n?n+=", "+t.display_name:n=t.display_name;e.push({name:t,value:n})}return e.push({name:"Actionability",value:this.actionabilityScore}),e.push({name:"Location",value:this.locationString}),e;function n(t,e){return"<a target='_blank' href='"+e+"'>"+t+"</a>"}}}class hc{constructor(t,e){if(this.config=t,this.genome=e,this.format=t.format?t.format.toUpperCase():"BAM","BAM"!==this.format&&"VCF"!==this.format)throw Error(`htsget format ${t.format} is not supported`)}async readHeaderData(){const t=`${uc(this.config)}?class=header&format=${this.format}`,e=await Eo.loadJson(t,Cs(this.config));return await this.loadUrls(e.htsget.urls)}async readData(t,e,n){const r=`${uc(this.config)}?format=${this.format}&referenceName=${t}&start=${Math.floor(e)}&end=${Math.ceil(n)}`,i=await Eo.loadJson(r,Cs(this.config));return this.loadUrls(i.htsget.urls)}async loadUrls(t){const e=[];for(let n of t)if(n.url.startsWith("data:"))e.push(Promise.resolve(fc(n.url)));else{const t=Cs(this.config||{});n.headers&&(t.headers=Object.assign(t.headers||{},n.headers)),e.push(Eo.loadArrayBuffer(n.url,t))}return function(t){let e=0;for(let n of t)e+=n.byteLength;let n=0;const r=new Uint8Array(e);for(let e of t){const t=new Uint8Array(e);r.set(t,n),n+=t.length}return r}(await Promise.all(e))}static async inferFormat(t){try{const e=uc(t),n=`${e}${e.includes("?")?"&":"?"}class=header`,r=await Eo.loadJson(n,Cs(t));if(r.htsget){const e=r.htsget.format;if("BAM"!==e&&"VCF"!==e)throw Error(`htsget format ${e} is not supported`);t.format=e.toLowerCase(),t.sourceType="htsget",t.name||(t.name=await As(t.url))}}catch(t){}}}function uc(t){if(t.url&&t.endpoint&&t.id)return t.url+t.endpoint+t.id;if(t.endpoint&&t.id)return t.endpoint+t.id;if(t.url)return t.url.startsWith("htsget://")?t.url.replace("htsget://","https://"):t.url;throw Error("Must specify either 'url', or 'endpoint' and 'id")}function fc(t){const e=t.split(","),n=e[0].split(":")[1];let r=e[1];r=n.indexOf("base64")>=0?atob(r):decodeURI(r);const i=new Uint8Array(r.length);for(var o=0;o<r.length;o++)i[o]=r.charCodeAt(o);return i}class dc extends hc{constructor(t,e){super(t,e),this.parser=new Cl}async readHeader(){if(!this.header){const t=$l(await this.readHeaderData());this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(t,e,n){if(this.config.format&&"VCF"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let r=this.chrAliasTable.has(t)?this.chrAliasTable.get(t):t;const i=$l(await this.readData(r,e,n));return this.parser.parseFeatures(i)}}function pc(t,e){e=e||Number.MAX_SAFE_INTEGER;const n=[];t.sort((function(t,e){return t.start-e.start})),n.push(-1e3);for(let r of t){let t=0;const i=Math.min(n.length,e);for(t=0;t<i;t++)if(r.start>=n[t]){r.row=t,n[t]=r.end;break}r.row=t,n[t]=r.end}}function gc(t,e,n){const r=n||1e4,i=t=>{const n=Object.assign({},t);return n.chr="all",n.start=e.getGenomeCoordinate(t.chr,t.start),n.end=e.getGenomeCoordinate(t.chr,t.end),n._f=t,n.exons&&delete n.exons,n},o=new Set(e.wgChromosomeNames),s=[];let a=0;for(let n of e.wgChromosomeNames){if(Array.isArray(t)){const n={};for(let r of t){const t=e.getChromosomeName(r.chr);n.hasOwnProperty(t)||(n[t]=[]),n[t].push(r)}t=n}const l=t[n];if(l)for(let t of l){let n=e.getChromosomeName(t.chr);if(o.has(n))if(s.length<r)s.push(i(t));else{const e=r/(a+1);if(Math.random()<e){s[Math.floor(Math.random()*(r-1))]=i(t)}}a++}}return s.sort((function(t,e){return t.start-e.start})),s}function mc(t,e){if(e=e||1e3,null==t||0===t.length)return;const n={},r=[];for(let e of t){const t=e.chr;let i=n[t];i||(i=[],n[t]=i,r.push(t)),i.push(e)}for(let t of r)pc(n[t],e)}class vc{constructor(t,e){this.config=t||{},this.genome=e,this.sourceType=void 0===t.sourceType?"file":t.sourceType,this.maxWGCount=t.maxWGCount||1e4;const n=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak","tdf"]);t.reader?(this.reader=t.reader,this.queryable=!1!==t.queryable):"ga4gh"===t.sourceType?(this.reader=new ac(t,e),this.queryable=!0):"immvar"===t.sourceType?(this.reader=new rc(t),this.queryable=!0):"eqtl"===t.type&&"gtex-ws"===t.sourceType?(this.reader=new nc(t),this.queryable=!0):"htsget"===t.sourceType?this.reader=new dc(t,e):"ucscservice"===t.sourceType?(this.reader=new Jl(t.source),this.queryable=!0):"custom"===t.sourceType?(this.reader=new Ql(t.source),this.queryable=!1!==t.source.queryable):"civic-ws"===t.sourceType?(this.reader=new lc(t),this.queryable=!1):(this.reader=new Yl(t,e),void 0!==t.queryable?this.queryable=t.queryable:(n.has(t.format)||this.reader.indexed)&&(this.queryable=!0))}async defaultVisibilityWindow(){if(this.reader&&"function"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const t=await this.getHeader();return t?t.type:void 0}async getHeader(){if(!this.header)if(this.reader&&"function"==typeof this.reader.readHeader){const t=await this.reader.readHeader();t?(this.header=t,t.format&&(this.config.format=t.format)):this.header={}}else this.header={};return this.header}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome,a=s?s.getChromosomeName(e):e,l="all"===a.toLowerCase();return(l&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new ua(a,n,r)))&&await this.loadFeatures(a,n,r,o),l?(this.wgFeatures||(this.supportsWholeGenome()?this.wgFeatures=gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.wgFeatures=[]),this.wgFeatures):this.featureCache.queryFeatures(a,n,r)}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(t,e,n,r){const i=this.reader;let o=e,s=n;if((!r||r<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(t):void 0;o=0,s=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,n)}else if(r>n-e&&!1!==this.config.expandQuery){const t=Math.min(4.1*(n-e),r);o=Math.max(0,(e+n)/2-t),s=e+t}let a=await i.readFeatures(t,o,s);void 0===this.queryable&&(this.queryable=i.indexed);const l=this.queryable?new ua(t,o,s):void 0;if(a){if(!1===this.config.assembleGFF||"gtf"!==this.config.format&&"gff3"!==this.config.format&&"gff"!==this.config.format||(a=new ec(this.config).combineFeatures(a,l)),"wig"!==this.config.format&&"junctions"!==this.config.type){mc(a,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Ho(a,this.genome,l),(this.config.searchable||this.config.searchableFields)&&this.addFeaturesToDB(a)}else this.featureCache=new Ho([],l)}addFeaturesToDB(t){for(let e of t)if(e.name&&(this.genome.featureDB[e.name.toUpperCase()]=e),e.gene&&e.gene.name&&(this.genome.featureDB[e.gene.name.toUpperCase()]=e),this.config.searchableFields)for(let t of this.config.searchableFields){const n=e.getAttributeValue(t);n&&(n.indexOf(" ")>0?(this.genome.featureDB[n.replaceAll(" ","+").toUpperCase()]=e,this.genome.featureDB[n.replaceAll(" ","%20").toUpperCase()]=e):this.genome.featureDB[n.toUpperCase()]=e)}}}class bc{constructor(t,e,n){this.path=t.url,this.bufferSize=n||512e3,this.range={start:-1,size:-1},this.config=t}async dataViewForRange(t,e){if(!(this.data&&this.range.start<=t.start&&this.range.start+this.range.size>=t.start+t.size)){let e;e=t.size?Math.max(this.bufferSize,t.size):this.bufferSize;const n={start:t.start,size:e},r=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:n}));this.data=r,this.range=n}const n=this.data.byteLength,r=t.start-this.range.start;return e?new Uint8Array(this.data,r,n-r):new DataView(this.data,r,n-r)}}let wc=512e3;class yc{constructor(t,e){this.path=t.url,this.format=t.format||"bigwig",this.genome=e,this.rpTreeCache={},this.config=t,this.loader=Ms(this.path)?new Rc(this.path):Eo}async readWGFeatures(t,e){await this.loadHeader();const n=this.chromTree.idToChrom.length-1,r=this.chromTree.idToChrom[0],i=this.chromTree.idToChrom[n];return this.readFeatures(r,0,i,Number.MAX_VALUE,t,e)}async readFeatures(t,e,n,r,i,o){await this.loadHeader();const s=this.chromTree.chromToID[t],a=this.chromTree.chromToID[n];if(void 0===s||void 0===a)return[];let l,c;if("bigwig"===this.type){const t=await this.getZoomHeaders();let e=i?function(t,e){let n;for(let r=0;r<e.length;r++){const i=e[r];if(i.reductionLevel<t){n=i;break}}return n}(i,t):void 0;e?(l=e.indexOffset,c=Mc):(l=this.header.fullIndexOffset,c=Ac)}else l=this.header.fullIndexOffset,c=Lc.call(this);const h=await this.loadRPTree(l),u=await h.findLeafItemsOverlapping(s,e,a,r);if(u&&0!==u.length){let t=Number.MAX_VALUE,n=0;for(let e of u)t=Math.min(t,e.dataOffset),n=Math.max(n,e.dataOffset+e.dataSize);const i=n-t,l=await this.loader.loadArrayBuffer(this.config.url,Cs(this.config,{range:{start:t,size:i}})),h=[];for(let n of u){const i=new Uint8Array(l,n.dataOffset-t,n.dataSize);let u;u=this.header.uncompressBuffSize>0?ro(i):i,c.call(this,new DataView(u.buffer),s,e,a,r,h,this.chromTree.idToChrom,o)}return h.sort((function(t,e){return t.start-e.start})),h}return[]}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let t,e=await this.loader.loadArrayBuffer(this.path,Cs(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;let n=new zl(new DataView(e)),r=n.getUInt();if(2291137574===r)this.type="bigwig";else if(2273964779===r)this.type="bigbed";else{this.littleEndian=!1,n.littleEndian=!1,n.position=0;let t=n.getUInt();654085990===t?this.type="bigwig":3958540679===t&&(this.type="bigbed")}t={bwVersion:n.getUShort(),nZoomLevels:n.getUShort(),chromTreeOffset:n.getLong(),fullDataOffset:n.getLong(),fullIndexOffset:n.getLong(),fieldCount:n.getUShort(),definedFieldCount:n.getUShort(),autoSqlOffset:n.getLong(),totalSummaryOffset:n.getLong(),uncompressBuffSize:n.getInt(),extensionOffset:n.getLong()};const i=64;let o={start:i,size:t.fullDataOffset-i+5};e=await this.loader.loadArrayBuffer(this.path,Cs(this.config,{range:o}));const s=t.nZoomLevels;n=new zl(new DataView(e)),this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let t=1;t<=s;t++){const e=s-t,r=new xc(e,n);this.firstZoomDataOffset=Math.min(r.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[e]=r}if(t.autoSqlOffset>0){n.position=t.autoSqlOffset-i;const e=n.getString();e&&(this.autoSql=function(t){let e;const n=[];let r=!1;const i=t.trim().split(/\s*[\r\n]+\s*/g);for(let t of i)if(t.startsWith("table"))e=t.split(/\s+/)[1].trim();else if(t.startsWith("("))r=!0;else if(t.startsWith(")"));else if(r&&t.length>0){const e=t.indexOf(";"),r=t.substr(0,e).split(/\s+/),i=t.substr(e+1).replace(/"/g,"").trim();n.push({type:r[0],name:r[1],description:i})}return{table:e,fields:n}}(e))}if(t.totalSummaryOffset>0&&(n.position=t.totalSummaryOffset-i,this.totalSummary=new Ec(n)),!(t.chromTreeOffset>0))throw"BigWig chromosome tree offset <= 0";return n.position=t.chromTreeOffset-i,this.chromTree=new Sc(n,i,this.genome),n.position=t.fullDataOffset-i,t.dataCount=n.getInt(),this.setDefaultVisibilityWindow(t),this.header=t,this.header}}async loadRPTree(t){let e=this.rpTreeCache[t];return e||(e=new _c(t,this.config,this.littleEndian,this.loader),await e.load(),this.rpTreeCache[t]=e,e)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),"bigwig"===this.type?"wig":this.autoSql&&"chromatinInteract"===this.autoSql.table?"interact":"annotation"}setDefaultVisibilityWindow(t){if("bigwig"===this.type)this.visibilityWindow=-1;else{let e=this.genome?this.genome.getGenomeLength():3088286401;this.visibilityWindow=t.dataCount<1e3?-1:e/t.dataCount*1e3}}}class xc{constructor(t,e){this.index=t,this.reductionLevel=e.getInt(),this.reserved=e.getInt(),this.dataOffset=e.getLong(),this.indexOffset=e.getLong()}}class _c{constructor(t,e,n,r){this.config=e,this.loader=r,this.fileOffset=t,this.path=e.url,this.littleEndian=n}async load(){const t=this.fileOffset+48,e=Ms(this.path)?this.loader:new bc(this.config,wc);return this.rootNode=await this.readNode(t,e),this}async readNode(t,e){let n=await e.dataViewForRange({start:t,size:4},!1),r=new zl(n,this.littleEndian);const i=1===r.getByte();r.getByte();const o=r.getUShort();let s={start:t+=4,size:o*(i?32:24)};n=await e.dataViewForRange(s,!1);const a=new Array(o);if(r=new zl(n),i){for(let t=0;t<o;t++){let e={isLeaf:!0,startChrom:r.getInt(),startBase:r.getInt(),endChrom:r.getInt(),endBase:r.getInt(),dataOffset:r.getLong(),dataSize:r.getLong()};a[t]=e}return new kc(a)}for(let t=0;t<o;t++){let e={isLeaf:!1,startChrom:r.getInt(),startBase:r.getInt(),endChrom:r.getInt(),endBase:r.getInt(),childOffset:r.getLong()};a[t]=e}return new kc(a)}async findLeafItemsOverlapping(t,e,n,r){let i=this;return new Promise((function(o,s){let a=[],l=new Set,c=Ms(i.path)?i.loader:new bc(i.config,wc);l.add(0),function h(u,f){if(Cc(u,t,e,n,r)){u.items.forEach((function(o){Cc(o,t,e,n,r)&&(o.isLeaf?a.push(o):o.childNode?h(o.childNode):(l.add(o.childOffset),i.readNode(o.childOffset,c).then((function(t){o.childNode=t,h(t,o.childOffset)})).catch(s)))}))}void 0!==f&&l.delete(f);0===l.size&&o(a)}(i.rootNode,0)}))}}class kc{constructor(t){this.items=t;let e,n,r=Number.MAX_SAFE_INTEGER,i=0,o=Number.MAX_SAFE_INTEGER,s=0;for(e=0;e<t.length;e++)n=t[e],r=Math.min(r,n.startChrom),i=Math.max(i,n.endChrom),o=Math.min(o,n.startBase),s=Math.max(s,n.endBase);this.startChrom=r,this.endChrom=i,this.startBase=o,this.endBase=s}}class Sc{constructor(t,e,n){let r=t.getInt(),i=t.getInt(),o=t.getInt(),s=t.getInt(),a=t.getLong(),l=t.getLong(),c={},h=[];this.header={magic:r,blockSize:i,keySize:o,valSize:s,itemCount:a,reserved:l},this.chromToID=c,this.idToChrom=h,function t(r,i){i>=0&&(r.position=i);let s=r.getByte();r.getByte();let a,l,u,f,d,p,g=r.getUShort();if(1===s)for(a=0;a<g;a++)l=r.getFixedLengthTrimmedString(o),u=r.getInt(),r.getInt(),n&&(l=n.getChromosomeName(l)),c[l]=u,h[u]=l;else for(a=0;a<g;a++)l=r.getFixedLengthTrimmedString(o),f=r.getLong(),d=f-e,p=r.position,t(r,d),r.position=p}(t,-1)}}function Cc(t,e,n,r,i){return t?(r>t.startChrom||r===t.startChrom&&i>=t.startBase)&&(e<t.endChrom||e===t.endChrom&&n<=t.endBase):(console.log("null item for "+e+" "+n+" "+i),!1)}class Ec{constructor(t){t?(this.basesCovered=t.getLong(),this.minVal=t.getDouble(),this.maxVal=t.getDouble(),this.sumData=t.getDouble(),this.sumSquares=t.getDouble(),Tc.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function Tc(){let t=this.basesCovered;if(t>0){this.mean=this.sumData/t,this.stddev=Math.sqrt(this.sumSquares/(t-1));let e=this.minVal<0?this.mean-2*this.stddev:0,n=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:e,max:n}}}function Ac(t,e,n,r,i,o,s){const a=new zl(t),l=a.getInt();let c=a.getInt(),h=a.getInt();const u=a.getInt(),f=a.getInt(),d=a.getByte();a.getByte();let p=a.getUShort();if(l>=e&&l<=r)for(;p-- >0;){let t;switch(d){case 1:c=a.getInt(),h=a.getInt(),t=a.getFloat();break;case 2:c=a.getInt(),t=a.getFloat(),h=c+f;break;case 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t=i.start+parseInt(n[o]),s=t+parseInt(e[o]);r.push({start:t,end:s})}!function(t,e,n){for(let r of t){const t=r.end,i=r.start;t<e||i>n?r.utr=!0:(e>=i&&e<=t&&(r.cdStart=e),n>=i&&n<=t&&(r.cdEnd=n))}}(r,i.cdStart,i.cdEnd),i.exons=r}if(n)for(let r=t;r<e;r++)if(r<n.fields.length){const t=n.fields[r].name,e=o[r-3];i[t]=e}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(e,n,r,i,o,s,a){const l=new zl(e);for(;l.remLength()>=13;){const e=l.getInt(),c=a[e],h=l.getInt(),u=l.getInt(),f=l.getString();if(!(e<n||e===n&&u<r)){if(e>i||e===i&&h>=o)break;if(u>0){const e={chr:c,start:h,end:u};s.push(e);const n=f.split("\t");t(e,n)}}}}}function Mc(t,e,n,r,i,o,s,a){const l=new zl(t);for(;l.remLength()>=32;){const t=l.getInt(),c=s[t],h=l.getInt(),u=l.getInt(),f=l.getInt(),d=l.getFloat(),p=l.getFloat(),g=l.getFloat();let 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l=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:a.position,size:a.size}}));if(!l)return;const c=new zl(new DataView(l));let h=c.getInt();const u={};for(;h-- >0;)u[c.getString()]=c.getString();const f=c.getString(),d=c.getFloat();let p=c.getInt();const g=[];for(;p-- >0;)g.push({position:c.getLong(),size:c.getInt()});const m={name:s,attributes:u,dataType:f,tileWidth:d,tiles:g};return this.datasetCache[r]=m,m}}async readRootGroup(){const t=this.genome,e=this.groupCache["/"];if(e)return e;{const e=await this.readGroup("/"),n=e.chromosomes,r=e.maxZoom;r&&(this.maxZoom=Number(r));const i=e.totalCount;i&&(e.totalCount=Number(i));const o={};return n&&n.split(",").forEach((function(e){const n=t.getChromosomeName(e);o[n]=e})),this.chrAliasTable=o,this.groupCache["/"]=e,e}}async readGroup(t){const e=this.groupCache[t];if(e)return e;{await this.readHeader();const e=this.groupIndex[t];if(void 0===e)return;const n=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:e.position,size:e.size}}));if(!n)return;const r=new zl(new DataView(n)),i={name:t};let o=r.getInt();for(;o-- >0;){const t=r.getString(),e=r.getString();i[t]=e}return this.groupCache[t]=i,i}}async readTiles(t,e){if(t.sort((function(t,e){return t.position-e.position})),0===(t=t.filter((function(t){return t.size>0}))).length)return Promise.resolve([]);const n=t[0],r=t[t.length-1],i=n.position,o=r.position+r.size-i,s=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:i,size:o}})),a=[];for(let n of t){const t=n.position-i,r=n.size;if(r>0){let n;if(this.compressed){n=ro(s.slice(t,t+r)).buffer}else n=s.slice(t,t+r);const i=new zl(new DataView(n)),o=i.getString();let l;switch(o){case"fixedStep":l=Iu(i,e);break;case"variableStep":l=Nu(i,e);break;case"bed":case"bedWithName":l=Ou(i,e,o);break;default:throw"Unknown tile type: "+o}a.push(l)}}return a}async readTile(t,e){let n=await Eo.loadArrayBuffer(this.path,Cs(this.config,{range:{start:t.position,size:t.size}}));if(this.compressed){n=ro(n).buffer}const r=new zl(new DataView(n)),i=r.getString();switch(i){case"fixedStep":return Iu(r,e);case"variableStep":return Nu(r,e);case"bed":case"bedWithName":return Ou(r,e,i);default:throw"Unknown tile type: "+i}}}function Iu(t,e){const n=t.getInt(),r=t.getInt(),i=t.getFloat(),o=[];let s=e;for(;s-- >0;){let e=n;const r=[];for(;e-- >0;)r.push(t.getFloat());o.push(r)}return{type:"fixedStep",start:r,span:i,data:o,nTracks:e,nPositions:n}}function Nu(t,e){const n=t.getInt(),r=t.getFloat(),i=t.getInt(),o=[];let s=i;for(;s-- >0;)o.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){s=i;const e=[];for(;s-- >0;)e.push(t.getFloat());a.push(e)}return{type:"variableStep",tileStart:n,span:r,start:o,data:a,nTracks:e,nPositions:i}}function Ou(t,e,n){const r=t.getInt();let i=r;const o=[];for(;i-- >0;)o.push(t.getInt());i=r;const s=[];for(;i-- >0;)s.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){let e=r;const n=[];for(;e-- >0;)n.push(t.getFloat());a.push(n)}if("bedWithName"===n){i=r;const e=[];for(;i-- >0;)e.push(t.getString())}return{type:n,start:o,end:s,data:a,nTracks:e,nPositions:r}}class Pu{constructor(t,e){this.genome=e,this.windowFunction=t.windowFunction||"mean",this.reader=new Ru(t,e)}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i}=t;if("all"===e.toLowerCase()){const t=[],e=this.genome;if(this.genome.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n).bpLength;i=r/1e3;const o=await this._getFeatures(n,0,r,i);if(o)for(let n of o){const r=Object.assign({},n);r.chr="all",r.start=e.getGenomeCoordinate(n.chr,n.start),r.end=e.getGenomeCoordinate(n.chr,n.end),r._f=n,t.push(r)}}return t}return this._getFeatures(e,n,r,i)}async _getFeatures(t,e,n,r){const i=new ua(t,e,n),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const t=this.rootGroup.totalCount;t&&(this.normalizationFactor=1e6/t)}i.bpPerPixel=r;const s=function(t,e,n){var r=n.getChromosome(t).bpLength;return Math.ceil(Math.log(Math.max(0,r/(700*e)))/zu)}(t,r,o);let a=this.reader.chrAliasTable[t],l=this.reader.maxZoom;void 0===a&&(a=t),void 0===l&&(l=-1);const c=s>l?"raw":this.windowFunction,h=await this.reader.readDataset(a,c,s);if(null==h)return[];const u=h.tileWidth,f=Math.floor(e/u),d=Math.floor(n/u),p=await this.reader.readTiles(h.tiles.slice(f,d+1),1),g=[];for(let i of p)switch(i.type){case"bed":Fu(i,t,e,n,r,g);break;case"variableStep":Du(i,t,e,n,r,g);break;case"fixedStep":Bu(i,t,e,n,r,g);break;default:throw"Unknown tile type: "+i.type}return g.sort((function(t,e){return t.start-e.start})),g}get supportsWholeGenome(){return!0}}function Fu(t,e,n,r,i,o){const s=t.nPositions,a=t.start,l=t.end,c=t.data[0];for(let t=0;t<s;t++){const i=a[t],s=l[t];if(!(s<n)){if(i>r)break;o.push({chr:e,start:i,end:s,value:c[t]})}}}function Du(t,e,n,r,i,o){const s=t.nPositions,a=t.start,l=t.span,c=t.data[0];for(let t=0;t<s;t++){const i=a[t],s=i+l;if(!(s<n)){if(i>r)break;o.push({chr:e,start:i,end:s,value:c[t]})}}}function Bu(t,e,n,r,i,o){const s=t.nPositions;let a=t.start;const l=t.span,c=t.data[0];for(let t=0;t<s;t++){const i=a+l;if(a>r)break;i>=n&&(Number.isNaN(c[t])||o.push({chr:e,start:a,end:i,value:c[t]})),a=i}}var zu=Math.log(2);class Hu{constructor(t,e){this.config=t,this.genome=e,this.queryable=!1,this.updateFeatures(t.features)}updateFeatures(t){mc(t=function(t,e){if(e)for(let n of t)n.chr=e.getChromosomeName(n.chr);return t}(t,this.genome)),this.config.mappings&&function(t,e){let n=Object.keys(e);t.forEach((function(t){n.forEach((function(n){t[n]=t[e[n]]}))}))}(t,this.config.mappings),this.featureCache=new Ho(t,this.genome)}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome,a=s?s.getChromosomeName(e):e;return"all"===a.toLowerCase()?gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(a,n,r)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}}const Vu=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak"]);function ju(t,e){const n=t.format?t.format.toLowerCase():void 0;return t.features?new Hu(t,e):Vu.has(n)?new Ic(t,e):"tdf"===n?new Pu(t,e):new vc(t,e)}const Uu={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};const qu={Set1:["rgb(228,26,28)","rgb(55,126,184)","rgb(77,175,74)","rgb(166,86,40)","rgb(152,78,163)","rgb(255,127,0)","rgb(247,129,191)","rgb(153,153,153)","rgb(255,255,51)"],Dark2:["rgb(27,158,119)","rgb(217,95,2)","rgb(117,112,179)","rgb(231,41,138)","rgb(102,166,30)","rgb(230,171,2)","rgb(166,118,29)","rgb(102,102,102)"],Set2:["rgb(102, 194,165)","rgb(252,141,98)","rgb(141,160,203)","rgb(231,138,195)","rgb(166,216,84)","rgb(255,217,47)","rgb(229,196,148)","rgb(179,179,179)"],Set3:["rgb(141,211,199)","rgb(255,255,179)","rgb(190,186,218)","rgb(251,128,114)","rgb(128,177,211)","rgb(253,180,98)","rgb(179,222,105)","rgb(252,205,229)","rgb(217,217,217)","rgb(188,128,189)","rgb(204,235,197)","rgb(255,237,111)"],Pastel1:["rgb(251,180,174)","rgb(179,205,227)","rgb(204,235,197)","rgb(222,203,228)","rgb(254,217,166)","rgb(255,255,204)","rgb(229,216,189)","rgb(253,218,236)"],Pastel2:["rgb(173,226,207)","rgb(253,205,172)","rgb(203,213,232)","rgb(244,202,228)","rgb(230,245,201)","rgb(255,242,174)","rgb(243,225,206)"],Accent:["rgb(127,201,127)","rgb(190,174,212)","rgb(253,192,134)","rgb(255,255,153)","rgb(56,108,176)","rgb(240,2,127)","rgb(191,91,23)"]};class Wu{constructor(t){this.colors=qu[t],Array.isArray(this.colors)||(this.colors=[]),this.colorTable={},this.nextIdx=0,this.colorGenerator=new Gu}getColor(t){return this.colorTable.hasOwnProperty(t)||(this.nextIdx<this.colors.length?this.colorTable[t]=this.colors[this.nextIdx]:this.colorTable[t]=this.colorGenerator.get(),this.nextIdx++),this.colorTable[t]}}class $u{constructor(t){this.colorTable=t||{},this.nextIdx=0,this.colorGenerator=new Gu}getColor(t){if(!this.colorTable.hasOwnProperty(t)){if(this.colorTable.hasOwnProperty("*"))return this.colorTable["*"];this.colorTable[t]=this.colorGenerator.get()}return this.colorTable[t]}}function Gu(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}Gu.prototype.hsvToRgb=function(t,e,n){var r=Math.floor(6*t),i=6*t-r,o=n*(1-e),s=n*(1-i*e),a=n*(1-(1-i)*e),l=255,c=255,h=255;switch(r){case 0:l=n,c=a,h=o;break;case 1:l=s,c=n,h=o;break;case 2:l=o,c=n,h=a;break;case 3:l=o,c=s,h=n;break;case 4:l=a,c=o,h=n;break;case 5:l=n,c=o,h=s}return[Math.floor(256*l),Math.floor(256*c),Math.floor(256*h)]},Gu.prototype.padHex=function(t){return t.length>this.hexwidth?t:new Array(this.hexwidth-t.length+1).join("0")+t},Gu.prototype.get=function(t,e){this.hue+=this.goldenRatio,this.hue%=1,"number"!=typeof t&&(t=.5),"number"!=typeof e&&(e=.95);var n=this.hsvToRgb(this.hue,t,e);return"#"+this.padHex(n[0].toString(16))+this.padHex(n[1].toString(16))+this.padHex(n[2].toString(16))};const Zu=new Gu;const Xu=function(t,e){const{r:n,g:r,b:i}=Uu[t];return`rgba(${n},${r},${i},${e})`}("nickel",2/16),Yu=Xu;class Ku{constructor(t,e){if(this.url=t.url,t.name?this.name=t.name:t.url&&Ue(t.url)?this.name=t.url.name:t.url&&ke(t.url)&&!t.url.startsWith("data:")&&(this.name=je(t.url)),this.isUserDefined=t.isUserDefined,t.features)this.featureSource=new Ju(t.features,e);else{if(t.format)t.format=t.format.toLowerCase();else{const e=je(t.url);t.format=zs(e)}this.featureSource=t.featureSource||ju(t,e)}!0===this.isUserDefined?(this.color=t.color||Yu,this.headerColor="rgba(155,185,129)"):(this.color=t.color||Xu,this.headerColor="rgb(190,190,190)")}async getFeatures(t,e,n){return this.featureSource.getFeatures({chr:t,start:e,end:n})}async getAllFeatures(){return"function"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(t){this.isUserDefined?this.featureSource.addFeature(t):console.error("Attempt to add ROI to non user-defined set")}removeFeature(t){this.isUserDefined?this.featureSource.removeFeature(t):console.error("Attempt to remove ROI from non user-defined set")}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined};{const t=this.featureSource.getAllFeatures(),e=[];for(let n of Object.keys(t))for(let r of t[n])e.push(r);return{name:this.name,color:this.color,features:e,isUserDefined:this.isUserDefined}}}dispose(){for(let t of Object.keys(this))this[t]=void 0}}function Qu(t,e,n,r){let i=Math.round((t-n)/r);let o=Math.round((e-n)/r)-i;return o<3&&(o=3,i-=1),{x:i,width:o}}class Ju{constructor(t,e){this.featureMap={},this.genome=e;for(let n of t){const t=e?e.getChromosomeName(n.chr):n.chr;let r=this.featureMap[t];r||(r=[],this.featureMap[t]=r),r.push(n)}for(let t of Object.keys(this.featureMap))this.featureMap[t].sort(((t,e)=>t.start-e.start))}getFeatures(t){let{chr:e,start:n,end:r}=t;if("all"===e.toLowerCase())return gc(this.featureMap,this.genome);{const t=this.featureMap[e];return t?t.filter((t=>t.end>n&&t.start<r)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(t){let e=this.featureMap[t.chr];e||(e=[],this.featureMap[t.chr]=e),e.push(t),e.sort(((t,e)=>t.start-e.start))}removeFeature(t){let{chr:e,start:n,end:r}=t;if(this.featureMap[e]){const t=`${e}-${n}-${r}`;this.featureMap[e]=this.featureMap[e].filter((e=>t!==`${e.chr}-${e.start}-${e.end}`))}}}class tf{constructor(t,e,n,r){this.rulerViewport=t,this.rulerSweeper=ge({class:"igv-ruler-sweeper"}),e.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(ya.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on("locuschange",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off("locuschange",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let t,e,n,r,i,o;this.boundContentMouseDownHandler=function(o){t=!0,e=!0;const{x:s}=we(o,this.rulerViewport.contentDiv);r=n=s,i=1,this.rulerSweeper.style.display="block",this.rulerSweeper.style.backgroundColor=!0===o.shiftKey?Yu:"rgba(68, 134, 247, 0.25)",this.rulerSweeper.style.left=`${r}px`,this.rulerSweeper.style.width=`${i}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener("mousedown",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(s){let a;if(t&&e){const{x:t}=we(s,this.rulerViewport.contentDiv);a=Math.max(Math.min(t,this.rulerViewport.contentDiv.clientWidth),0),o=a-n,i=Math.abs(o),this.rulerSweeper.style.width=`${i}px`,o<0&&(r=n+o,this.rulerSweeper.style.left=`${r}px`)}}.bind(this),document.addEventListener("mousemove",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(n){let o;if(!0===t&&!0===e&&(t=e=void 0,this.rulerSweeper.style.display="none",i>1)){o={start:Math.floor(this.referenceFrame.calculateEnd(r)),end:Math.floor(this.referenceFrame.calculateEnd(r+i))};!0===n.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},o)):(Ts(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,o,this.browser.minimumBases()),function(t,e,n){t.start=Math.round(e.start),t.end=Math.round(e.end),t.bpPerPixel=(t.end-t.start)/n}(this.referenceFrame,o,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener("mousedown",this.boundContentMouseDownHandler),document.removeEventListener("mousemove",this.boundDocumentMouseMoveHandler),document.removeEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}class ef{constructor(t){this.paired=!0,this.firstAlignment=t,this.chr=t.chr,this.readName=t.readName,t.start<t.mate.position?(this.start=t.start,this.scStart=t.scStart,this.connectingStart=t.start+t.lengthOnRef,this.connectingEnd=t.mate.position):(this.start=t.mate.position,this.scStart=this.start,this.connectingStart=t.mate.position,this.connectingEnd=t.start),this.end=Math.max(t.mate.position,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start;let e=Math.max(this.end,t.scStart+t.scLengthOnRef);this.scLengthOnRef=e-this.scStart}setSecondAlignment(t){this.secondAlignment=t;const e=this.firstAlignment;t.start>e.start?this.connectingEnd=t.start:this.connectingStart=t.start+t.lengthOnRef,this.start=Math.min(e.start,t.start),this.end=Math.max(e.start+e.lengthOnRef,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(e.scStart,t.scStart);const n=Math.max(e.scStart+e.scLengthOnRef,t.scStart+t.scLengthOnRef);this.scLengthOnRef=n-this.scStart}containsLocation(t,e){const n=e?this.scStart:this.start,r=e?this.scLengthOnRef:this.lengthOnRef;return t>=n&&t<=n+r}alignmentContaining(t,e){return this.firstAlignment.containsLocation(t,e)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(t,e)?this.secondAlignment:void 0}popupData(t){let e=this.firstAlignment.popupData(t);return this.secondAlignment&&(e.push("-------------------------------"),e=e.concat(this.secondAlignment.popupData(t))),e}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}firstOfPairStrand(){return this.firstAlignment.isFirstOfPair()?this.firstAlignment.strand:this.secondAlignment&&this.secondAlignment.isFirstOfPair()?this.secondAlignment.strand:this.firstAlignment.mate.strand}hasTag(t){return this.firstAlignment.hasTag(t)||this.secondAlignment&&this.secondAlignment.hasTag(t)}}class nf{constructor(){this.alignments=[],this.score=void 0}findAlignment(t){const e=(t,e)=>e>=t.start&&e<t.start+t.lengthOnRef;let n;for(let r=0;r<this.alignments.length;r++){const i=this.alignments[r];if(t>=i.start&&t<i.start+i.lengthOnRef){i.paired?i.firstAlignment&&e(i.firstAlignment,t)?n=i.firstAlignment:i.secondAlignment&&e(i.secondAlignment,t)&&(n=i.secondAlignment):n=i;break}}return n}getSortValue(t,e){let{position:n,option:r,tag:i}=t;r||(r="BASE");const o=this.findAlignment(n);if(void 0===o)return Number.MAX_VALUE;switch(r){case"NUCLEOTIDE":case"BASE":return function(t,e,n){let r;const i=Math.floor(n)-e.start;i<e.sequence.length&&(r=e.sequence.charAt(i));if(!r)return 0;const o=t.readBaseAt(n),s=t.readBaseQualityAt(n),a=e.coverageMap,l=Math.floor(n-a.bpStart),c=a.coverage[l];let h=0;if(t.insertions)for(let e of t.insertions)e.start===n&&(h=-c.ins);if(o)if(r=r.toUpperCase(),"N"===o&&0===h)h=2;else if(r!==o&&"="!==o||0!==h){if("X"===o||r!==o){h-=c["pos"+o]+c["neg"+o]+s/1e3}}else h=4-s/1e3;else{const t=c.del;t>0?h-=t:0===h&&(h=1)}return h}(o,e,n);case"STRAND":return o.strand?1:-1;case"START":return o.start;case"TAG":return o.tags()[i];case"READ_NAME":return o.readName;case"INSERT_SIZE":return-Math.abs(o.fragmentLength);case"GAP_SIZE":return-o.gapSizeAt(n);case"MATE_CHR":return o.mate;case"MQ":return void 0===o.mq?Number.MAX_VALUE:-o.mq;case"ALIGNED_READ_LENGTH":return-o.lengthOnRef;default:return Number.MAX_VALUE}}}function rf(t){return t.isPaired()&&t.mate&&t.isMateMapped()&&t.chr===t.mate.chr&&(t.isFirstOfPair()||t.isSecondOfPair())&&!(t.isSecondary()||t.isSupplementary())}function of(t){const e=[];for(let n of t)for(let t of n.alignments)t instanceof ef?(t.firstAlignment&&e.push(t.firstAlignment),t.secondAlignment&&e.push(t.secondAlignment)):e.push(t);return e}function sf(t,e,n,r){if(t){if(0===t.length)return[];{t.sort((function(t,e){return r?t.scStart-e.scStart:t.start-e.start}));const i=t[0];let o=Math.max(e,r?i.scStart:i.start),s=o;const a=[];for(let e of t){const t=r?e.scStart:e.start,n=Math.max(0,t-o);void 0===a[n]&&(a[n]=[]),a[n].push(e)}let l=0,c=0;const h=[],u=2;try{for(;l<t.length;){const t=new nf;for(;s<=n;){let e,i;for(;!e&&s<=n;)i=s-o,void 0===a[i]?++s:e=a[i];if(!e)break;const c=e.pop();0===e.length&&(a[i]=void 0),t.alignments.push(c),s=r?c.scStart+c.scLengthOnRef+u:c.start+c.lengthOnRef+u,++l}if(t.alignments.length>0&&h.push(t),s=o,l===c)break;c=l}}catch(t){throw console.error(t),t}return h}}}class af{constructor(t,e,n,r){let{samplingWindowSize:i,samplingDepth:o,pairsSupported:s,alleleFreqThreshold:a}=r;this.chr=t,this.start=Math.floor(e),this.end=Math.ceil(n),this.length=n-e,this.alleleFreqThreshold=void 0===a?.2:a,this.coverageMap=new cf(t,e,n,this.alleleFreqThreshold),this.alignments=[],this.downsampledIntervals=[],this.samplingWindowSize=void 0===i?100:i,this.samplingDepth=void 0===o?1e3:o,this.pairsSupported=void 0===s||s,this.paired=!1,this.pairsCache={},this.downsampledReads=new Set,this.currentBucket=new lf(this.start,this.start+this.samplingWindowSize,this),this.filter=function(t){return t.isMapped()&&!t.isFailsVendorQualityCheck()}}push(t){!1!==this.filter(t)&&(this.coverageMap.incCounts(t),this.pairsSupported&&this.downsampledReads.has(t.readName)||(t.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new lf(t.start,t.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(t)))}forEach(t){this.alignments.forEach(t)}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.alignments.sort((function(t,e){return t.start-e.start})),this.pairsCache=void 0,this.downsampledReads=void 0}contains(t,e,n){return this.chr===t&&this.start<=e&&this.end>=n}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new uf(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount)),this.paired=this.paired||this.currentBucket.paired}setViewAsPairs(t){let e;e=t?function(t){const e={},n=[];for(let r of t)for(let t of r.alignments)if(rf(t)){let r=e[t.readName];r?(r.setSecondAlignment(t),e[t.readName]=void 0):(r=new ef(t),e[t.readName]=r,n.push(r))}else n.push(t);return n}(this.packedAlignmentRows):of(this.packedAlignmentRows),this.packedAlignmentRows=sf(e,this.start,this.end)}setShowSoftClips(t){const e=this.allAlignments();this.packedAlignmentRows=sf(e,this.start,this.end,t)}repack(t,e){const n=this.allAlignments();this.packedAlignmentRows=sf(n,this.start,this.end,e)}allAlignments(){const t=[];for(let e of this.packedAlignmentRows)for(let n of e.alignments)t.push(n);return t}getMax(t,e){return this.coverageMap.getMax(t,e)}sortRows(t){const e=[],n=[];for(let r of this.packedAlignmentRows){void 0!==r.findAlignment(t.position)?e.push(r):n.push(r)}e.sort(((e,n)=>{const r=t.direction,i=e.getSortValue(t,this),o=n.getSortValue(t,this);if(void 0===o&&void 0!==o)return 1;if(void 0!==i&&void 0===o)return-1;const s=i>o?1:i<o?-1:0;return!0===r?s:-s}));for(let t of n)e.push(t);this.packedAlignmentRows=e}}class lf{constructor(t,e,n){this.start=t,this.end=e,this.alignments=[],this.downsampledCount=0,this.samplingDepth=n.samplingDepth,this.pairsSupported=n.pairsSupported,this.downsampledReads=n.downsampledReads,this.pairsCache=n.pairsCache}addAlignment(t){var e,n,r;if(this.pairsSupported&&rf(t)&&(r=this.pairsCache[t.readName]))return r.setSecondAlignment(t),void(this.pairsCache[t.readName]=void 0);this.alignments.length<this.samplingDepth?this.pairsSupported&&rf(t)?(r=new ef(t),this.paired=!0,this.pairsCache[t.readName]=r,this.alignments.push(r)):this.alignments.push(t):((e=Math.floor(Math.random()*(this.samplingDepth+this.downsampledCount-1)))<this.samplingDepth?(n=this.alignments[e],this.pairsSupported&&rf(t)?(void 0!==this.pairsCache[n.readName]&&(this.pairsCache[n.readName]=void 0),r=new ef(t),this.paired=!0,this.pairsCache[t.readName]=r,this.alignments[e]=r):this.alignments[e]=t,this.downsampledReads.add(n.readName)):this.downsampledReads.add(t.readName),this.downsampledCount++)}}class cf{constructor(t,e,n,r){this.chr=t,this.bpStart=e,this.length=n-e,this.coverage=new Array(this.length),this.maximum=0,this.threshold=r,this.qualityWeight=!0}getMax(t,e){let n=0;const r=this.coverage.length;for(let i=0;i<r;i++){const r=this.bpStart+i;if(r>e)break;const o=this.coverage[i];r>=t&&o&&(n=Math.max(n,o.total))}return n}incCounts(t){var e=this;if(void 0===t.blocks?n(t):t.blocks.forEach((function(t){n(t)})),t.gaps)for(let n of t.gaps)if("D"===n.type){const t=n.start-e.bpStart;for(let r=t;r<t+n.len;r++)r<0||(this.coverage[r]||(this.coverage[r]=new hf(e.threshold)),this.coverage[r].del++)}if(t.insertions)for(let n of t.insertions){const t=n.start-this.bpStart;t<0||(this.coverage[t]||(this.coverage[t]=new hf(e.threshold)),this.coverage[t].ins++)}function n(n){if("S"===n.type)return;const r=t.seq,i=t.qual,o=n.seqOffset;for(let s=n.start-e.bpStart,a=0;a<n.len;s++,a++){e.coverage[s]||(e.coverage[s]=new hf(e.threshold));const n=null==r?"N":r.charAt(o+a),l=t.strand?"pos"+n:"neg"+n,c=i&&o+a<i.length?i[o+a]:30;e.coverage[s][l]+=1,e.coverage[s]["qual"+n]+=c,e.coverage[s].total+=1,e.coverage[s].qual+=c,e.maximum=Math.max(e.coverage[s].total,e.maximum)}}}}class hf{constructor(t){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=t}hoverText(){const t=this.posA+this.posT+this.posC+this.posG+this.posN,e=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${t}+, ${e}-)`}isMismatch(t){const e=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let n=0;for(let e of["A","T","C","G"])e!==t&&(n+=this.qualityWeight&&this.qual?this["qual"+e]:this["pos"+e]+this["neg"+e]);return n>=e}}class uf{constructor(t,e,n){this.start=t,this.end=e,this.counts=n}popupData(t){return[{name:"start",value:this.start+1},{name:"end",value:this.end},{name:"# downsampled:",value:this.counts}]}}class ff{constructor(t){const e=t.split(",");this.chr=e[0],this.start=parseInt(e[1]),this.strand=e[2].charAt(0),this.mapQ=parseInt(e[4]),this.numMismatches=parseInt(e[5]),this.lenOnRef=Lf.computeLengthOnReference(e[3])}printString(){return this.chr+":"+Se(this.start)+"-"+Se(this.start+this.lenOnRef)+" ("+this.strand+") = "+Se(this.lenOnRef)+"bp @MAPQ: "+this.mapQ+" NM: "+this.numMismatches}}function df(t){return t.split(";").filter((t=>t.length>0)).map((t=>new ff(t)))}const pf={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class gf{constructor(){this.hidden=!1}isMapped(){return 0==(4&this.flags)}isPaired(){return 0!=(1&this.flags)}isProperPair(){return 0!=(2&this.flags)}isFirstOfPair(){return 0!=(64&this.flags)}isSecondOfPair(){return 0!=(128&this.flags)}isSecondary(){return 0!=(256&this.flags)}isSupplementary(){return 0!=(2048&this.flags)}isFailsVendorQualityCheck(){return 0!=(512&this.flags)}isDuplicate(){return 0!=(1024&this.flags)}isMateMapped(){return 0==(8&this.flags)}isNegativeStrand(){return 0!=(16&this.flags)}isMateNegativeStrand(){return 0!=(32&this.flags)}hasTag(t){return(this.tagDict||vf(this.tagBA)).hasOwnProperty(t)}tags(){return this.tagDict||(this.tagBA?(this.tagDict=vf(this.tagBA),this.tagBA=void 0):this.tagDict={}),this.tagDict}containsLocation(t,e){const n=e?this.scStart:this.start,r=e?this.scLengthOnRef:this.lengthOnRef;return t>=n&&t<=n+r}hoverText(){return this.readName}popupData(t){const e=[];if(t=Math.floor(t),this.insertions){const r=this.seq;for(let i of this.insertions){var n=i.start;if(t===n||t===n-1)return e.push({name:"Insertion",value:r.substr(i.seqOffset,i.len)}),e.push({name:"Location",value:n}),e}}e.push({name:"Read Name",value:this.readName}),e.push("<hr/>"),e.push({name:"Alignment Start",value:Se(1+this.start),borderTop:!0}),e.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0});let r=this.cigar;if(r&&r.length>50){const t=25;r=`${r.substring(0,t-2)} ... ${r.substring(r.length-t+2)}`}e.push({name:"Cigar",value:r}),e.push({name:"Mapping Quality",value:this.mq}),e.push({name:"Secondary",value:s(this.isSecondary())}),e.push({name:"Supplementary",value:s(this.isSupplementary())}),e.push({name:"Duplicate",value:s(this.isDuplicate())}),e.push({name:"Failed QC",value:s(this.isFailsVendorQualityCheck())}),this.isPaired()&&(e.push("<hr/>"),e.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),e.push({name:"Mate is Mapped",value:s(this.isMateMapped())}),this.pairOrientation&&e.push({name:"Pair Orientation",value:this.pairOrientation}),this.isMateMapped()&&(e.push({name:"Mate Chromosome",value:this.mate.chr}),e.push({name:"Mate Start",value:this.mate.position+1}),e.push({name:"Mate Strand",value:!0===this.mate.strand?"(+)":"(-)"}),e.push({name:"Insert Size",value:this.fragmentLength})));const i=this.tags();if(i.hasOwnProperty("SA")){e.push("<hr/>"),e.push({name:"Supplementary Alignments",value:""});const t=df(i.SA);if(t){e.push("<ul>");for(let n of t)e.push(`<li>${n.printString()}</li>`);e.push("</ul>")}}const o=new Set(["SA","MD"]);e.push("<hr/>");for(let t in i)o.has(t)||e.push({name:t,value:i[t]});return e.push({name:"Hidden Tags",value:"SA, MD"}),e.push("<hr/>"),e.push({name:"Genomic Location: ",value:Se(1+t)}),e.push({name:"Read Base:",value:this.readBaseAt(t)}),e.push({name:"Base Quality:",value:this.readBaseQualityAt(t)}),e;function s(t){return t?"Yes":"No"}}readBaseAt(t){const e=mf(this.blocks,t);if(e){if("*"===this.seq)return"*";{const n=e.seqIndexAt(t);return this.seq[n]}}}readBaseQualityAt(t){const e=mf(this.blocks,t);if(e){if("*"===this.qual)return 30;{const n=e.seqIndexAt(t);return n>=0&&this.qual&&n<this.qual.length?this.qual[n]:30}}}gapSizeAt(t){if(this.gaps)for(let e of this.gaps)if(t>=e.start&&t<e.start+e.len)return e.len;return 0}}function mf(t,e){for(let n=0;n<t.length;n++){const r=t[n];if(e>=r.start&&e<r.start+r.len)return r}}function vf(t){let e=0;const n=t.length,r={};for(;e<n;){const n=String.fromCharCode(t[e])+String.fromCharCode(t[e+1]);e+=2;const o=String.fromCharCode(t[e++]);let s;if("A"===o)s=String.fromCharCode(t[e]),e++;else if("i"===o||"I"===o)s=bf(t,e),e+=4;else if("c"===o)s=xf(t,e),e++;else if("C"===o)s=_f(t,e),e++;else if("s"===o||"S"===o)s=wf(t,e),e+=2;else if("f"===o)s=yf(t,e),e+=4;else if("Z"===o)for(s="";;){var i=t[e++];if(0===i)break;s+=String.fromCharCode(i)}else{if("B"!==o){s="Error unknown type: "+o,r[n]=s;break}{const i=String.fromCharCode(t[e++]);let o=pf[i];if(void 0===o){r[n]=`Error: unknown element type '${i}'`;break}e+=4+bf(t,e)*o,s="[not shown]"}}r[n]=s}return r}function bf(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function wf(t,e){return t[e+1]<<8|t[e]}function yf(t,e){return new DataView(t.buffer).getFloat32(e)}function xf(t,e){return new DataView(t.buffer).getInt8(e)}function _f(t,e){return new DataView(t.buffer).getUint8(e)}class kf{constructor(t){t&&Object.assign(this,t)}seqIndexAt(t){return Math.floor(t)-this.start+this.seqOffset}}class Sf{constructor(t){t||(t={}),this.vendorFailed=void 0===t.vendorFailed||t.vendorFailed,this.duplicates=void 0===t.duplicates||t.duplicates,this.secondary=t.secondary||!1,this.supplementary=t.supplementary||!1,this.mqThreshold=void 0===t.mqThreshold?0:t.mqThreshold,t.readgroups&&(this.readgroups=new Set(t.readgroups))}pass(t){if(this.vendorFailed&&t.isFailsVendorQualityCheck())return!1;if(this.duplicates&&t.isDuplicate())return!1;if(this.secondary&&t.isSecondary())return!1;if(this.supplementary&&t.isSupplementary())return!1;if(t.mq<this.mqThreshold)return!1;if(this.readgroups){var e=t.tags().RG;return this.readgroups.has(e)}return!0}}const Cf=["=","A","C","x","G","x","x","x","T","x","x","x","x","x","x","N"],Ef=["M","I","D","N","S","H","P","=","X","?","?","?","?","?","?","?"],Tf=Rf(new Uint8Array([66,65,77,1]),0),Af=1e4,Lf={readHeader:function(t,e,n){return Eo.loadArrayBuffer(t,e).then((function(t){var e;return e=io(t),Lf.decodeBamHeader(e,n)}))},decodeBamHeader:function(t,e){var n,r,i,o,s;if((n=Rf(t,0))!==Tf)throw new Error("BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.");r=Rf(t,4);for(var a=0;a<r;++a)String.fromCharCode(t[a+8]);var l=Rf(t,r+8),c=r+12;for(i={},o=[],s={},a=0;a<l;++a){for(var h=Rf(t,c),u="",f=0;f<h-1;++f)u+=String.fromCharCode(t[c+4+f]);Rf(t,c+h+4),i[u]=a,o[a]=u,e&&(s[e.getChromosomeName(u)]=u),c=c+8+h}return{magicNumber:n,size:c,chrNames:o,chrToIndex:i,chrAliasTable:s}},bam_tag2cigar:function(t,e,n,r,i,o){function s(t){return"C"===t||"c"===t||"A"===t?1:"S"===t||"s"===t?2:"I"===t||"i"===t||"f"===t?4:0}if(1!==o.length||i.start<0)return!1;for(var a=n+(r+1>>1)+r;a+4<e;){if("CG"===String.fromCharCode(t[a])+String.fromCharCode(t[a+1]))break;var l=String.fromCharCode(t[a+2]);if("B"===l)a+=8+s(l=String.fromCharCode(t[a+3]))*Rf(t,a+4);else if("Z"===l||"H"===l)for(a+=3;0!==t[a++];);else a+=3+s(l)}if(a>=e)return!1;if("B"!==String.fromCharCode(t[a+2])||"I"!==String.fromCharCode(t[a+3]))return!1;var c=Rf(t,a+4),h=a+8;if(h+4*c>e)return!1;var u="",f=0;o.length=0,a=h;for(var d=0;d<c;++d,a+=4){var p=Rf(t,a),g=p>>4,m=Ef[15&p];"M"!==m&&"EQ"!==m&&"X"!==m&&"D"!==m&&"N"!==m&&"="!==m||(f+=g),u=u+g+m,o.push({len:g,ltr:m})}return i.cigar=u,i.lengthOnRef=f,!0},decodeBamRecords:function(t,e,n,r,i,o,s,a){for(;e<t.length;){const f=e+Rf(t,e)+4,d=new gf,p=Rf(t,e+4),g=Rf(t,e+8);if(f>t.length)return;if(p<0){e=f;continue}if(void 0!==i&&(p>i||g>s))return!0;if(void 0!==i&&p<i){e=f;continue}const m=Rf(t,e+12),v=(65280&m)>>8,b=255&m,w=Rf(t,e+16),y=(4294901760&w)>>16,x=65535&w,_=Rf(t,e+20),k=Rf(t,e+24),S=Rf(t,e+28),C=Rf(t,e+32);let E=[];for(let n=0;n<b-1;++n)E.push(String.fromCharCode(t[e+36+n]));E=E.join("");let T=0,A="",L=e+36+b;const M=[];let R;for(let e=0;e<x;++e){var l=Rf(t,L),c=l>>4,h=Ef[15&l];"M"!==h&&"EQ"!==h&&"X"!==h&&"D"!==h&&"N"!==h&&"="!==h||(T+=c),A=A+c+h,L+=4,R={len:c,ltr:h},M.push(R)}if(d.chr=r[p],d.start=g,d.flags=y,d.strand=!(16&y),d.readName=E,d.cigar=A,d.lengthOnRef=T,d.fragmentLength=C,d.mq=v,Lf.bam_tag2cigar(t,f,L,_,d,M),d.end=d.start+d.lengthOnRef,d.end<o){e=f;continue}let I=[];const N=_+1>>1;for(let e=0;e<N;++e){var u=t[L+e];I.push(Cf[(240&u)>>4]),I.push(Cf[15&u])}I=I.slice(0,_).join(""),L+=N;const O=[];for(let e=0;e<_;++e)O.push(t[L+e]);L+=_,k>=0&&(d.mate={chr:r[k],position:S,strand:!(32&y)}),d.seq=I,d.qual=O,d.tagBA=new Uint8Array(t.buffer.slice(L,f)),this.setPairOrientation(d),(void 0===a||a.pass(d))&&(Mf(d,M),n.push(d)),e=f}},decodeSamRecords:function(t,e,n,r,i,o){var s,a,l,c,h,u,f,d,p,g;for(c=(s=Ce(t)).length,!1,a=0;a<c;a++)if(h=s[a].split("\t"),(p=new gf).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],"*"!==p.chr&&p.isMapped()&&p.chr===n){if(p.start>i)break;if(d=0,(g=If(p.cigar)).forEach((function(t){var e=t.len,n=t.ltr;"M"!==n&&"EQ"!==n&&"X"!==n&&"D"!==n&&"N"!==n&&"="!==n||(d+=e)})),p.lengthOnRef=d,!(p.start+d<r)){for(u=h[10],p.qual=[],l=0;l<u.length;l++)p.qual[l]=u.charCodeAt(l)-33;p.tagDict=h.length<11?{}:Nf(h.slice(11)),p.isMateMapped()&&(f=h[6],p.mate={chr:"="===f?p.chr:f,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===o||o.pass(p))&&(Mf(p,g),e.push(p))}}},setReaderDefaults:function(t,e){t.filter=new Sf(e.filter),e.readgroup&&(t.filter.readgroups=new Set([e.readgroup])),t.alleleFreqThreshold=void 0===e.alleleFreqThreshold?.2:e.alleleFreqThreshold,t.samplingWindowSize=void 0===e.samplingWindowSize?100:e.samplingWindowSize,t.samplingDepth=void 0===e.samplingDepth?500:e.samplingDepth,t.samplingDepth>Af&&(console.log("Warning: attempt to set sampling depth > maximum value of 10000"),t.samplingDepth=Af),e.viewAsPairs?t.pairsSupported=!0:t.pairsSupported=void 0===e.pairsSupported||e.pairsSupported},setPairOrientation:function(t){if(t.isMapped()&&t.mate&&t.isMateMapped()&&t.mate.chr===t.chr){var e=t.strand?"F":"R",n=t.mate,r=n.strand?"F":"R",i=" ",o=" ";t.isFirstOfPair()?(i="1",o="2"):t.isSecondOfPair()&&(i="2",o="1");var s=[],a=t.fragmentLength,l=t.end-t.start;if(0===a)a=(t.start<n.position?n.position+l:n.position-l)-t.start;a>0?(s[0]=e,s[1]=i,s[2]=r,s[3]=o):(s[2]=e,s[3]=i,s[0]=r,s[1]=o),t.pairOrientation=s.join("")}},computeLengthOnReference:function(t){let e=0,n="";for(let r=0;r<t.length;r++){const i=t.charCodeAt(r);if(i>47&&i<58)n+=t.charAt(r);else{switch(i){case 78:case 68:case 77:case 61:case 88:e+=parseInt(n.toString())}n=""}}return e}};function 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Eo.loadArrayBuffer(this.bamPath,Cs(this.config)));return this.parseAlignments(r),this.fetchAlignments(t,e,n)}}parseAlignments(t){const e=[];this.header=Lf.decodeBamHeader(t),Lf.decodeBamRecords(t,this.header.size,e,this.header.chrNames),this.alignmentCache=new Ho(e,this.genome)}fetchAlignments(t,e,n){const r=this.header.chrAliasTable.hasOwnProperty(t)?this.header.chrAliasTable[t]:t,i=this.alignmentCache.queryFeatures(r,e,n),o=new af(t,e,n,this.config);for(let t of i)o.push(t);return o.finish(),o}}class Pf{constructor(t,e){this.config=t,this.genome=e,this.bamPath=t.url,this.baiPath=t.indexURL,Lf.setReaderDefaults(this,t)}async readAlignments(t,e,n){const r=(await this.getChrIndex())[this.chrAliasTable.hasOwnProperty(t)?this.chrAliasTable[t]:t],i=new af(t,e,n,this.config);if(void 0===r)return i;{const t=(await this.getIndex()).blocksForRange(r,e,n);if(!t||0===t.length)return i;for(let s of t){let t;if(0===s.maxv.offset)t=0;else{const 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this.chrToIndex=t.chrToIndex,this.indexToChr=t.chrNames,this.chrAliasTable=t.chrAliasTable,this.chrToIndex}}}class Ff{constructor(t,e){this.config=t,this.genome=e;const n={};t.sources.sequences.forEach((function(r){const i=e?e.getChromosomeName(r):r;n[i]=function(t,e,n){const r={url:t.sources.url.replace("$CHR",n)};t.sources.indexURL&&(r.indexURL=t.sources.indexURL.replace("$CHR",n));const i=Object.assign(t,r);return new Pf(i,e)}(t,e,r)})),this.bamReaders=n,Lf.setReaderDefaults(this,t)}async readAlignments(t,e,n){if(this.bamReaders.hasOwnProperty(t)){let r=this.bamReaders[t];return await r.readAlignments(t,e,n)}return new af(t,e,n,this.config)}}const Df=function(t,e){this.config=t,this.genome=e,Lf.setReaderDefaults(this,t)};function Bf(){const t=this,e=this.genome;if(this.header)return Promise.resolve(this.header);{const n=this.config.url+"?file="+this.config.alignmentFile+"&options=-b,-H",r=Cs(this.config);return Lf.readHeader(n,r,e).then((function(e){return 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i.status=73;if(73===i.status)if(i.gzhead.name){s=i.pending;do{if(i.pending===i.pending_buf_size&&(i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),b(t),s=i.pending,i.pending===i.pending_buf_size)){l=1;break}l=i.gzindex<i.gzhead.name.length?255&i.gzhead.name.charCodeAt(i.gzindex++):0,y(i,l)}while(0!==l);i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),0===l&&(i.gzindex=0,i.status=91)}else i.status=91;if(91===i.status)if(i.gzhead.comment){s=i.pending;do{if(i.pending===i.pending_buf_size&&(i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),b(t),s=i.pending,i.pending===i.pending_buf_size)){l=1;break}l=i.gzindex<i.gzhead.comment.length?255&i.gzhead.comment.charCodeAt(i.gzindex++):0,y(i,l)}while(0!==l);i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),0===l&&(i.status=f)}else i.status=f;if(i.status===f&&(i.gzhead.hcrc?(i.pending+2>i.pending_buf_size&&b(t),i.pending+2<=i.pending_buf_size&&(y(i,255&t.adler),y(i,t.adler>>8&255),t.adler=0,i.status=d)):i.status=d),0!==i.pending){if(b(t),0===t.avail_out)return i.last_flush=-1,0}else if(0===t.avail_in&&m(e)<=m(n)&&4!==e)return g(t,-5);if(i.status===p&&0!==t.avail_in)return g(t,-5);if(0!==t.avail_in||0!==i.lookahead||0!==e&&i.status!==p){var _=2===i.strategy?function(t,e){for(var n;;){if(0===t.lookahead&&(k(t),0===t.lookahead)){if(0===e)return 1;break}if(t.match_length=0,n=o._tr_tally(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++,n&&(w(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,4===e?(w(t,!0),0===t.strm.avail_out?3:4):t.last_lit&&(w(t,!1),0===t.strm.avail_out)?1:2}(i,e):3===i.strategy?function(t,e){for(var n,r,i,s,a=t.window;;){if(t.lookahead<=h){if(k(t),t.lookahead<=h&&0===e)return 1;if(0===t.lookahead)break}if(t.match_length=0,t.lookahead>=3&&t.strstart>0&&(r=a[i=t.strstart-1])===a[++i]&&r===a[++i]&&r===a[++i]){s=t.strstart+h;do{}while(r===a[++i]&&r===a[++i]&&r===a[++i]&&r===a[++i]&&r===a[++i]&&r===a[++i]&&r===a[++i]&&r===a[++i]&&i<s);t.match_length=h-(s-i),t.match_length>t.lookahead&&(t.match_length=t.lookahead)}if(t.match_length>=3?(n=o._tr_tally(t,1,t.match_length-3),t.lookahead-=t.match_length,t.strstart+=t.match_length,t.match_length=0):(n=o._tr_tally(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++),n&&(w(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,4===e?(w(t,!0),0===t.strm.avail_out?3:4):t.last_lit&&(w(t,!1),0===t.strm.avail_out)?1:2}(i,e):r[i.level].func(i,e);if(3!==_&&4!==_||(i.status=p),1===_||3===_)return 0===t.avail_out&&(i.last_flush=-1),0;if(2===_&&(1===e?o._tr_align(i):5!==e&&(o._tr_stored_block(i,0,0,!1),3===e&&(v(i.head),0===i.lookahead&&(i.strstart=0,i.block_start=0,i.insert=0))),b(t),0===t.avail_out))return i.last_flush=-1,0}return 4!==e?0:i.wrap<=0?1:(2===i.wrap?(y(i,255&t.adler),y(i,t.adler>>8&255),y(i,t.adler>>16&255),y(i,t.adler>>24&255),y(i,255&t.total_in),y(i,t.total_in>>8&255),y(i,t.total_in>>16&255),y(i,t.total_in>>24&255)):(x(i,t.adler>>>16),x(i,65535&t.adler)),b(t),i.wrap>0&&(i.wrap=-i.wrap),0!==i.pending?0:1)},e.deflateEnd=function(t){var e;return t&&t.state?42!==(e=t.state.status)&&69!==e&&73!==e&&91!==e&&e!==f&&e!==d&&e!==p?g(t,c):(t.state=null,e===d?g(t,-3):0):c},e.deflateSetDictionary=function(t,e){var n,r,o,a,l,h,u,f,d=e.length;if(!t||!t.state)return c;if(2===(a=(n=t.state).wrap)||1===a&&42!==n.status||n.lookahead)return c;for(1===a&&(t.adler=s(t.adler,e,d,0)),n.wrap=0,d>=n.w_size&&(0===a&&(v(n.head),n.strstart=0,n.block_start=0,n.insert=0),f=new i.Buf8(n.w_size),i.arraySet(f,e,d-n.w_size,n.w_size,0),e=f,d=n.w_size),l=t.avail_in,h=t.next_in,u=t.input,t.avail_in=d,t.next_in=0,t.input=e,k(n);n.lookahead>=3;){r=n.strstart,o=n.lookahead-2;do{n.ins_h=(n.ins_h<<n.hash_shift^n.window[r+3-1])&n.hash_mask,n.prev[r&n.w_mask]=n.head[n.ins_h],n.head[n.ins_h]=r,r++}while(--o);n.strstart=r,n.lookahead=2,k(n)}return n.strstart+=n.lookahead,n.block_start=n.strstart,n.insert=n.lookahead,n.lookahead=0,n.match_length=n.prev_length=2,n.match_available=0,t.next_in=h,t.input=u,t.avail_in=l,n.wrap=a,0},e.deflateInfo="pako deflate (from Nodeca project)"},function(t,e,n){var r=n(72);function i(t){for(var e=t.length;--e>=0;)t[e]=0}var o=256,s=286,a=30,l=15,c=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],h=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],u=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],f=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],d=new Array(576);i(d);var p=new Array(60);i(p);var g=new Array(512);i(g);var m=new Array(256);i(m);var v=new Array(29);i(v);var b,w,y,x=new Array(a);function _(t,e,n,r,i){this.static_tree=t,this.extra_bits=e,this.extra_base=n,this.elems=r,this.max_length=i,this.has_stree=t&&t.length}function k(t,e){this.dyn_tree=t,this.max_code=0,this.stat_desc=e}function S(t){return t<256?g[t]:g[256+(t>>>7)]}function C(t,e){t.pending_buf[t.pending++]=255&e,t.pending_buf[t.pending++]=e>>>8&255}function E(t,e,n){t.bi_valid>16-n?(t.bi_buf|=e<<t.bi_valid&65535,C(t,t.bi_buf),t.bi_buf=e>>16-t.bi_valid,t.bi_valid+=n-16):(t.bi_buf|=e<<t.bi_valid&65535,t.bi_valid+=n)}function T(t,e,n){E(t,n[2*e],n[2*e+1])}function A(t,e){var n=0;do{n|=1&t,t>>>=1,n<<=1}while(--e>0);return n>>>1}function L(t,e,n){var r,i,o=new Array(16),s=0;for(r=1;r<=l;r++)o[r]=s=s+n[r-1]<<1;for(i=0;i<=e;i++){var a=t[2*i+1];0!==a&&(t[2*i]=A(o[a]++,a))}}function M(t){var e;for(e=0;e<s;e++)t.dyn_ltree[2*e]=0;for(e=0;e<a;e++)t.dyn_dtree[2*e]=0;for(e=0;e<19;e++)t.bl_tree[2*e]=0;t.dyn_ltree[512]=1,t.opt_len=t.static_len=0,t.last_lit=t.matches=0}function R(t){t.bi_valid>8?C(t,t.bi_buf):t.bi_valid>0&&(t.pending_buf[t.pending++]=t.bi_buf),t.bi_buf=0,t.bi_valid=0}function I(t,e,n,r){var i=2*e,o=2*n;return t[i]<t[o]||t[i]===t[o]&&r[e]<=r[n]}function N(t,e,n){for(var r=t.heap[n],i=n<<1;i<=t.heap_len&&(i<t.heap_len&&I(e,t.heap[i+1],t.heap[i],t.depth)&&i++,!I(e,r,t.heap[i],t.depth));)t.heap[n]=t.heap[i],n=i,i<<=1;t.heap[n]=r}function O(t,e,n){var r,i,s,a,l=0;if(0!==t.last_lit)do{r=t.pending_buf[t.d_buf+2*l]<<8|t.pending_buf[t.d_buf+2*l+1],i=t.pending_buf[t.l_buf+l],l++,0===r?T(t,i,e):(T(t,(s=m[i])+o+1,e),0!==(a=c[s])&&E(t,i-=v[s],a),T(t,s=S(--r),n),0!==(a=h[s])&&E(t,r-=x[s],a))}while(l<t.last_lit);T(t,256,e)}function P(t,e){var n,r,i,o=e.dyn_tree,s=e.stat_desc.static_tree,a=e.stat_desc.has_stree,c=e.stat_desc.elems,h=-1;for(t.heap_len=0,t.heap_max=573,n=0;n<c;n++)0!==o[2*n]?(t.heap[++t.heap_len]=h=n,t.depth[n]=0):o[2*n+1]=0;for(;t.heap_len<2;)o[2*(i=t.heap[++t.heap_len]=h<2?++h:0)]=1,t.depth[i]=0,t.opt_len--,a&&(t.static_len-=s[2*i+1]);for(e.max_code=h,n=t.heap_len>>1;n>=1;n--)N(t,o,n);i=c;do{n=t.heap[1],t.heap[1]=t.heap[t.heap_len--],N(t,o,1),r=t.heap[1],t.heap[--t.heap_max]=n,t.heap[--t.heap_max]=r,o[2*i]=o[2*n]+o[2*r],t.depth[i]=(t.depth[n]>=t.depth[r]?t.depth[n]:t.depth[r])+1,o[2*n+1]=o[2*r+1]=i,t.heap[1]=i++,N(t,o,1)}while(t.heap_len>=2);t.heap[--t.heap_max]=t.heap[1],function(t,e){var n,r,i,o,s,a,c=e.dyn_tree,h=e.max_code,u=e.stat_desc.static_tree,f=e.stat_desc.has_stree,d=e.stat_desc.extra_bits,p=e.stat_desc.extra_base,g=e.stat_desc.max_length,m=0;for(o=0;o<=l;o++)t.bl_count[o]=0;for(c[2*t.heap[t.heap_max]+1]=0,n=t.heap_max+1;n<573;n++)(o=c[2*c[2*(r=t.heap[n])+1]+1]+1)>g&&(o=g,m++),c[2*r+1]=o,r>h||(t.bl_count[o]++,s=0,r>=p&&(s=d[r-p]),a=c[2*r],t.opt_len+=a*(o+s),f&&(t.static_len+=a*(u[2*r+1]+s)));if(0!==m){do{for(o=g-1;0===t.bl_count[o];)o--;t.bl_count[o]--,t.bl_count[o+1]+=2,t.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(r=t.bl_count[o];0!==r;)(i=t.heap[--n])>h||(c[2*i+1]!==o&&(t.opt_len+=(o-c[2*i+1])*c[2*i],c[2*i+1]=o),r--)}}(t,e),L(o,h,t.bl_count)}function F(t,e,n){var r,i,o=-1,s=e[1],a=0,l=7,c=4;for(0===s&&(l=138,c=3),e[2*(n+1)+1]=65535,r=0;r<=n;r++)i=s,s=e[2*(r+1)+1],++a<l&&i===s||(a<c?t.bl_tree[2*i]+=a:0!==i?(i!==o&&t.bl_tree[2*i]++,t.bl_tree[32]++):a<=10?t.bl_tree[34]++:t.bl_tree[36]++,a=0,o=i,0===s?(l=138,c=3):i===s?(l=6,c=3):(l=7,c=4))}function D(t,e,n){var r,i,o=-1,s=e[1],a=0,l=7,c=4;for(0===s&&(l=138,c=3),r=0;r<=n;r++)if(i=s,s=e[2*(r+1)+1],!(++a<l&&i===s)){if(a<c)do{T(t,i,t.bl_tree)}while(0!=--a);else 0!==i?(i!==o&&(T(t,i,t.bl_tree),a--),T(t,16,t.bl_tree),E(t,a-3,2)):a<=10?(T(t,17,t.bl_tree),E(t,a-3,3)):(T(t,18,t.bl_tree),E(t,a-11,7));a=0,o=i,0===s?(l=138,c=3):i===s?(l=6,c=3):(l=7,c=4)}}i(x);var B=!1;function z(t,e,n,i){E(t,0+(i?1:0),3),function(t,e,n,i){R(t),C(t,n),C(t,~n),r.arraySet(t.pending_buf,t.window,e,n,t.pending),t.pending+=n}(t,e,n)}e._tr_init=function(t){B||(function(){var t,e,n,r,i,o=new Array(16);for(n=0,r=0;r<28;r++)for(v[r]=n,t=0;t<1<<c[r];t++)m[n++]=r;for(m[n-1]=r,i=0,r=0;r<16;r++)for(x[r]=i,t=0;t<1<<h[r];t++)g[i++]=r;for(i>>=7;r<a;r++)for(x[r]=i<<7,t=0;t<1<<h[r]-7;t++)g[256+i++]=r;for(e=0;e<=l;e++)o[e]=0;for(t=0;t<=143;)d[2*t+1]=8,t++,o[8]++;for(;t<=255;)d[2*t+1]=9,t++,o[9]++;for(;t<=279;)d[2*t+1]=7,t++,o[7]++;for(;t<=287;)d[2*t+1]=8,t++,o[8]++;for(L(d,287,o),t=0;t<a;t++)p[2*t+1]=5,p[2*t]=A(t,5);b=new _(d,c,257,s,l),w=new _(p,h,0,a,l),y=new _(new Array(0),u,0,19,7)}(),B=!0),t.l_desc=new k(t.dyn_ltree,b),t.d_desc=new k(t.dyn_dtree,w),t.bl_desc=new k(t.bl_tree,y),t.bi_buf=0,t.bi_valid=0,M(t)},e._tr_stored_block=z,e._tr_flush_block=function(t,e,n,r){var i,s,a=0;t.level>0?(2===t.strm.data_type&&(t.strm.data_type=function(t){var e,n=4093624447;for(e=0;e<=31;e++,n>>>=1)if(1&n&&0!==t.dyn_ltree[2*e])return 0;if(0!==t.dyn_ltree[18]||0!==t.dyn_ltree[20]||0!==t.dyn_ltree[26])return 1;for(e=32;e<o;e++)if(0!==t.dyn_ltree[2*e])return 1;return 0}(t)),P(t,t.l_desc),P(t,t.d_desc),a=function(t){var e;for(F(t,t.dyn_ltree,t.l_desc.max_code),F(t,t.dyn_dtree,t.d_desc.max_code),P(t,t.bl_desc),e=18;e>=3&&0===t.bl_tree[2*f[e]+1];e--);return t.opt_len+=3*(e+1)+5+5+4,e}(t),i=t.opt_len+3+7>>>3,(s=t.static_len+3+7>>>3)<=i&&(i=s)):i=s=n+5,n+4<=i&&-1!==e?z(t,e,n,r):4===t.strategy||s===i?(E(t,2+(r?1:0),3),O(t,d,p)):(E(t,4+(r?1:0),3),function(t,e,n,r){var i;for(E(t,e-257,5),E(t,n-1,5),E(t,r-4,4),i=0;i<r;i++)E(t,t.bl_tree[2*f[i]+1],3);D(t,t.dyn_ltree,e-1),D(t,t.dyn_dtree,n-1)}(t,t.l_desc.max_code+1,t.d_desc.max_code+1,a+1),O(t,t.dyn_ltree,t.dyn_dtree)),M(t),r&&R(t)},e._tr_tally=function(t,e,n){return t.pending_buf[t.d_buf+2*t.last_lit]=e>>>8&255,t.pending_buf[t.d_buf+2*t.last_lit+1]=255&e,t.pending_buf[t.l_buf+t.last_lit]=255&n,t.last_lit++,0===e?t.dyn_ltree[2*n]++:(t.matches++,e--,t.dyn_ltree[2*(m[n]+o+1)]++,t.dyn_dtree[2*S(e)]++),t.last_lit===t.lit_bufsize-1},e._tr_align=function(t){E(t,2,3),T(t,256,d),function(t){16===t.bi_valid?(C(t,t.bi_buf),t.bi_buf=0,t.bi_valid=0):t.bi_valid>=8&&(t.pending_buf[t.pending++]=255&t.bi_buf,t.bi_buf>>=8,t.bi_valid-=8)}(t)}},function(t,e,n){t.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"}},function(t,e,n){var r=n(72),i=n(134),o=n(135),s=n(221),a=n(222),l=-2,c=12,h=30;function u(t){return(t>>>24&255)+(t>>>8&65280)+((65280&t)<<8)+((255&t)<<24)}function f(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new r.Buf16(320),this.work=new r.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function d(t){var e;return t&&t.state?(e=t.state,t.total_in=t.total_out=e.total=0,t.msg="",e.wrap&&(t.adler=1&e.wrap),e.mode=1,e.last=0,e.havedict=0,e.dmax=32768,e.head=null,e.hold=0,e.bits=0,e.lencode=e.lendyn=new r.Buf32(852),e.distcode=e.distdyn=new r.Buf32(592),e.sane=1,e.back=-1,0):l}function p(t){var e;return t&&t.state?((e=t.state).wsize=0,e.whave=0,e.wnext=0,d(t)):l}function g(t,e){var n,r;return t&&t.state?(r=t.state,e<0?(n=0,e=-e):(n=1+(e>>4),e<48&&(e&=15)),e&&(e<8||e>15)?l:(null!==r.window&&r.wbits!==e&&(r.window=null),r.wrap=n,r.wbits=e,p(t))):l}function m(t,e){var n,r;return t?(r=new f,t.state=r,r.window=null,0!==(n=g(t,e))&&(t.state=null),n):l}var v,b,w=!0;function y(t){if(w){var e;for(v=new r.Buf32(512),b=new r.Buf32(32),e=0;e<144;)t.lens[e++]=8;for(;e<256;)t.lens[e++]=9;for(;e<280;)t.lens[e++]=7;for(;e<288;)t.lens[e++]=8;for(a(1,t.lens,0,288,v,0,t.work,{bits:9}),e=0;e<32;)t.lens[e++]=5;a(2,t.lens,0,32,b,0,t.work,{bits:5}),w=!1}t.lencode=v,t.lenbits=9,t.distcode=b,t.distbits=5}function x(t,e,n,i){var o,s=t.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new 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t;m--,b+=f[p++]<<w,w+=8}n.head&&(n.head.time=b),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,B[2]=b>>>16&255,B[3]=b>>>24&255,n.check=o(n.check,B,4,0)),b=0,w=0,n.mode=4;case 4:for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.head&&(n.head.xflags=255&b,n.head.os=b>>8),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0)),b=0,w=0,n.mode=5;case 5:if(1024&n.flags){for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.length=b,n.head&&(n.head.extra_len=b),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0)),b=0,w=0}else n.head&&(n.head.extra=null);n.mode=6;case 6:if(1024&n.flags&&((S=n.length)>m&&(S=m),S&&(n.head&&(N=n.head.extra_len-n.length,n.head.extra||(n.head.extra=new Array(n.head.extra_len)),r.arraySet(n.head.extra,f,p,S,N)),512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,n.length-=S),n.length))break t;n.length=0,n.mode=7;case 7:if(2048&n.flags){if(0===m)break t;S=0;do{N=f[p+S++],n.head&&N&&n.length<65536&&(n.head.name+=String.fromCharCode(N))}while(N&&S<m);if(512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,N)break t}else n.head&&(n.head.name=null);n.length=0,n.mode=8;case 8:if(4096&n.flags){if(0===m)break t;S=0;do{N=f[p+S++],n.head&&N&&n.length<65536&&(n.head.comment+=String.fromCharCode(N))}while(N&&S<m);if(512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,N)break t}else n.head&&(n.head.comment=null);n.mode=9;case 9:if(512&n.flags){for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b!==(65535&n.check)){t.msg="header crc mismatch",n.mode=h;break}b=0,w=0}n.head&&(n.head.hcrc=n.flags>>9&1,n.head.done=!0),t.adler=n.check=0,n.mode=c;break;case 10:for(;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}t.adler=n.check=u(b),b=0,w=0,n.mode=11;case 11:if(0===n.havedict)return t.next_out=g,t.avail_out=v,t.next_in=p,t.avail_in=m,n.hold=b,n.bits=w,2;t.adler=n.check=1,n.mode=c;case c:if(5===e||6===e)break t;case 13:if(n.last){b>>>=7&w,w-=7&w,n.mode=27;break}for(;w<3;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}switch(n.last=1&b,w-=1,3&(b>>>=1)){case 0:n.mode=14;break;case 1:if(y(n),n.mode=20,6===e){b>>>=2,w-=2;break t}break;case 2:n.mode=17;break;case 3:t.msg="invalid block type",n.mode=h}b>>>=2,w-=2;break;case 14:for(b>>>=7&w,w-=7&w;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if((65535&b)!=(b>>>16^65535)){t.msg="invalid stored block lengths",n.mode=h;break}if(n.length=65535&b,b=0,w=0,n.mode=15,6===e)break t;case 15:n.mode=16;case 16:if(S=n.length){if(S>m&&(S=m),S>v&&(S=v),0===S)break t;r.arraySet(d,f,p,S,g),m-=S,p+=S,v-=S,g+=S,n.length-=S;break}n.mode=c;break;case 17:for(;w<14;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(n.nlen=257+(31&b),b>>>=5,w-=5,n.ndist=1+(31&b),b>>>=5,w-=5,n.ncode=4+(15&b),b>>>=4,w-=4,n.nlen>286||n.ndist>30){t.msg="too many length or distance symbols",n.mode=h;break}n.have=0,n.mode=18;case 18:for(;n.have<n.ncode;){for(;w<3;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.lens[z[n.have++]]=7&b,b>>>=3,w-=3}for(;n.have<19;)n.lens[z[n.have++]]=0;if(n.lencode=n.lendyn,n.lenbits=7,P={bits:n.lenbits},O=a(0,n.lens,0,19,n.lencode,0,n.work,P),n.lenbits=P.bits,O){t.msg="invalid code lengths set",n.mode=h;break}n.have=0,n.mode=19;case 19:for(;n.have<n.nlen+n.ndist;){for(;A=(D=n.lencode[b&(1<<n.lenbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(L<16)b>>>=T,w-=T,n.lens[n.have++]=L;else{if(16===L){for(F=T+2;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b>>>=T,w-=T,0===n.have){t.msg="invalid bit length repeat",n.mode=h;break}N=n.lens[n.have-1],S=3+(3&b),b>>>=2,w-=2}else if(17===L){for(F=T+3;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}w-=T,N=0,S=3+(7&(b>>>=T)),b>>>=3,w-=3}else{for(F=T+7;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}w-=T,N=0,S=11+(127&(b>>>=T)),b>>>=7,w-=7}if(n.have+S>n.nlen+n.ndist){t.msg="invalid bit length repeat",n.mode=h;break}for(;S--;)n.lens[n.have++]=N}}if(n.mode===h)break;if(0===n.lens[256]){t.msg="invalid code -- missing end-of-block",n.mode=h;break}if(n.lenbits=9,P={bits:n.lenbits},O=a(1,n.lens,0,n.nlen,n.lencode,0,n.work,P),n.lenbits=P.bits,O){t.msg="invalid literal/lengths set",n.mode=h;break}if(n.distbits=6,n.distcode=n.distdyn,P={bits:n.distbits},O=a(2,n.lens,n.nlen,n.ndist,n.distcode,0,n.work,P),n.distbits=P.bits,O){t.msg="invalid distances set",n.mode=h;break}if(n.mode=20,6===e)break t;case 20:n.mode=21;case 21:if(m>=6&&v>=258){t.next_out=g,t.avail_out=v,t.next_in=p,t.avail_in=m,n.hold=b,n.bits=w,s(t,k),g=t.next_out,d=t.output,v=t.avail_out,p=t.next_in,f=t.input,m=t.avail_in,b=n.hold,w=n.bits,n.mode===c&&(n.back=-1);break}for(n.back=0;A=(D=n.lencode[b&(1<<n.lenbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(A&&0==(240&A)){for(M=T,R=A,I=L;A=(D=n.lencode[I+((b&(1<<M+R)-1)>>M)])>>>16&255,L=65535&D,!(M+(T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}b>>>=M,w-=M,n.back+=M}if(b>>>=T,w-=T,n.back+=T,n.length=L,0===A){n.mode=26;break}if(32&A){n.back=-1,n.mode=c;break}if(64&A){t.msg="invalid literal/length code",n.mode=h;break}n.extra=15&A,n.mode=22;case 22:if(n.extra){for(F=n.extra;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.length+=b&(1<<n.extra)-1,b>>>=n.extra,w-=n.extra,n.back+=n.extra}n.was=n.length,n.mode=23;case 23:for(;A=(D=n.distcode[b&(1<<n.distbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(0==(240&A)){for(M=T,R=A,I=L;A=(D=n.distcode[I+((b&(1<<M+R)-1)>>M)])>>>16&255,L=65535&D,!(M+(T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}b>>>=M,w-=M,n.back+=M}if(b>>>=T,w-=T,n.back+=T,64&A){t.msg="invalid distance code",n.mode=h;break}n.offset=L,n.extra=15&A,n.mode=24;case 24:if(n.extra){for(F=n.extra;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.offset+=b&(1<<n.extra)-1,b>>>=n.extra,w-=n.extra,n.back+=n.extra}if(n.offset>n.dmax){t.msg="invalid distance too far back",n.mode=h;break}n.mode=25;case 25:if(0===v)break t;if(S=k-v,n.offset>S){if((S=n.offset-S)>n.whave&&n.sane){t.msg="invalid distance too far back",n.mode=h;break}S>n.wnext?(S-=n.wnext,C=n.wsize-S):C=n.wnext-S,S>n.length&&(S=n.length),E=n.window}else E=d,C=g-n.offset,S=n.length;S>v&&(S=v),v-=S,n.length-=S;do{d[g++]=E[C++]}while(--S);0===n.length&&(n.mode=21);break;case 26:if(0===v)break t;d[g++]=n.length,v--,n.mode=21;break;case 27:if(n.wrap){for(;w<32;){if(0===m)break t;m--,b|=f[p++]<<w,w+=8}if(k-=v,t.total_out+=k,n.total+=k,k&&(t.adler=n.check=n.flags?o(n.check,d,k,g-k):i(n.check,d,k,g-k)),k=v,(n.flags?b:u(b))!==n.check){t.msg="incorrect data check",n.mode=h;break}b=0,w=0}n.mode=28;case 28:if(n.wrap&&n.flags){for(;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b!==(4294967295&n.total)){t.msg="incorrect length check",n.mode=h;break}b=0,w=0}n.mode=29;case 29:O=1;break t;case h:O=-3;break t;case 31:return-4;default:return l}return t.next_out=g,t.avail_out=v,t.next_in=p,t.avail_in=m,n.hold=b,n.bits=w,(n.wsize||k!==t.avail_out&&n.mode<h&&(n.mode<27||4!==e))&&x(t,t.output,t.next_out,k-t.avail_out)?(n.mode=31,-4):(_-=t.avail_in,k-=t.avail_out,t.total_in+=_,t.total_out+=k,n.total+=k,n.wrap&&k&&(t.adler=n.check=n.flags?o(n.check,d,k,t.next_out-k):i(n.check,d,k,t.next_out-k)),t.data_type=n.bits+(n.last?64:0)+(n.mode===c?128:0)+(20===n.mode||15===n.mode?256:0),(0===_&&0===k||4===e)&&0===O&&(O=-5),O)},e.inflateEnd=function(t){if(!t||!t.state)return l;var e=t.state;return e.window&&(e.window=null),t.state=null,0},e.inflateGetHeader=function(t,e){var n;return t&&t.state?0==(2&(n=t.state).wrap)?l:(n.head=e,e.done=!1,0):l},e.inflateSetDictionary=function(t,e){var n,r=e.length;return t&&t.state?0!==(n=t.state).wrap&&11!==n.mode?l:11===n.mode&&i(1,e,r,0)!==n.check?-3:x(t,e,r,r)?(n.mode=31,-4):(n.havedict=1,0):l},e.inflateInfo="pako inflate (from Nodeca project)"},function(t,e,n){t.exports=function(t,e){var n,r,i,o,s,a,l,c,h,u,f,d,p,g,m,v,b,w,y,x,_,k,S,C,E;n=t.state,r=t.next_in,C=t.input,i=r+(t.avail_in-5),o=t.next_out,E=t.output,s=o-(e-t.avail_out),a=o+(t.avail_out-257),l=n.dmax,c=n.wsize,h=n.whave,u=n.wnext,f=n.window,d=n.hold,p=n.bits,g=n.lencode,m=n.distcode,v=(1<<n.lenbits)-1,b=(1<<n.distbits)-1;t:do{p<15&&(d+=C[r++]<<p,p+=8,d+=C[r++]<<p,p+=8),w=g[d&v];e:for(;;){if(d>>>=y=w>>>24,p-=y,0==(y=w>>>16&255))E[o++]=65535&w;else{if(!(16&y)){if(0==(64&y)){w=g[(65535&w)+(d&(1<<y)-1)];continue e}if(32&y){n.mode=12;break t}t.msg="invalid literal/length code",n.mode=30;break t}x=65535&w,(y&=15)&&(p<y&&(d+=C[r++]<<p,p+=8),x+=d&(1<<y)-1,d>>>=y,p-=y),p<15&&(d+=C[r++]<<p,p+=8,d+=C[r++]<<p,p+=8),w=m[d&b];n:for(;;){if(d>>>=y=w>>>24,p-=y,!(16&(y=w>>>16&255))){if(0==(64&y)){w=m[(65535&w)+(d&(1<<y)-1)];continue n}t.msg="invalid distance code",n.mode=30;break t}if(_=65535&w,p<(y&=15)&&(d+=C[r++]<<p,(p+=8)<y&&(d+=C[r++]<<p,p+=8)),(_+=d&(1<<y)-1)>l){t.msg="invalid distance too far back",n.mode=30;break 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e=(new a).itf8("refSeqId").itf8("refSeqStart").itf8("refSeqSpan").itf8("numRecords"),n=20;return t>=3?(e=e.ltf8("recordCounter"),n+=9):2===t&&(e=e.itf8("recordCounter"),n+=5),e=e.itf8("numBlocks").itf8("numContentIds").array("contentIds",{type:l,length:"numContentIds"}).itf8("refBaseBlockId"),n+=15,t>=2&&(e=e.array("md5",{type:"uint8",length:16}),n+=16),{parser:e,maxLength:function(t){return n+5*t}}},cramEncoding:function(t){return{parser:(new a).namely("cramEncoding").itf8("codecId").itf8("parametersBytes").choice("parameters",{tag:"codecId",choices:{0:new a,1:(new a).itf8("blockContentId"),2:(new a).itf8("offset").itf8("M"),3:a.start().itf8("numCodes").array("symbols",{length:"numCodes",type:l}).itf8("numLengths").array("bitLengths",{length:"numLengths",type:l}),4:a.start().nest("lengthsEncoding",{type:"cramEncoding"}).nest("valuesEncoding",{type:"cramEncoding"}),5:(new a).uint8("stopByte")[t>1?"itf8":"int"]("blockContentId"),6:(new a).itf8("offset").itf8("length"),7:(new a).itf8("offset").itf8("K"),8:(new a).itf8("offset").itf8("log2m"),9:(new a).itf8("offset")}})}},cramDataSeriesEncodingMap:function(t){return(new a).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new a).string("key",{length:2,stripNull:!1}).nest("value",{type:this.cramEncoding(t).parser})})},cramTagEncodingMap:function(t){return(new a).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new a).itf8("key",{formatter:function(t){return String.fromCharCode(t>>16&255)+String.fromCharCode(t>>8&255)+String.fromCharCode(255&t)}}).nest("value",{type:this.cramEncoding(t).parser})})},cramCompressionHeader:function(t){var e=new a;return{parser:e=e.nest("preservation",{type:p,formatter:g}).nest("dataSeriesEncoding",{type:this.cramDataSeriesEncodingMap(t),formatter:g}).nest("tagEncoding",{type:this.cramTagEncodingMap(t),formatter:g})}},cramContainerHeader1:function(t){var e=(new a).int32("length").itf8("refSeqId").itf8("refSeqStart").itf8("alignmentSpan").itf8("numRecords"),n=24;return t>=3?(e=e.ltf8("recordCounter"),n+=9):2===t&&(e=e.itf8("recordCounter"),n+=5),t>1&&(e=e.ltf8("numBases"),n+=9),{parser:e=e.itf8("numBlocks").itf8("numLandmarks"),maxLength:n+=10}},cramContainerHeader2:function(t){var e=(new a).itf8("numLandmarks").array("landmarks",{type:(new a).itf8(),length:"numLandmarks"}),n=0;return t>=3&&(e=e.uint32("crc32"),n=4),{parser:e,maxLength:function(t){return 5+5*t+n}}}};t.exports={cramFileDefinition:c,getSectionParsers:function(t){var e,n=(0,s.default)({},m);return(0,o.default)(e=(0,i.default)(v)).call(e,(function(e){n[e]=v[e](t)})),n}}},function(t,e,n){t.exports=n(320)},function(t,e,n){n(321);var r=n(3);t.exports=r.Object.keys},function(t,e,n){var r=n(0),i=n(22),o=n(51);r({target:"Object",stat:!0,forced:n(12)((function(){o(1)}))},{keys:function(t){return o(i(t))}})},function(t,e,n){t.exports=n(323)},function(t,e,n){n(324);var r=n(3);t.exports=r.Object.assign},function(t,e,n){var r=n(0),i=n(325);r({target:"Object",stat:!0,forced:Object.assign!==i},{assign:i})},function(t,e,n){var r=n(17),i=n(12),o=n(51),s=n(138),a=n(65),l=n(22),c=n(60),h=Object.assign;t.exports=!h||i((function(){var t={},e={},n=Symbol();return t[n]=7,"abcdefghijklmnopqrst".split("").forEach((function(t){e[t]=t})),7!=h({},t)[n]||"abcdefghijklmnopqrst"!=o(h({},e)).join("")}))?function(t,e){for(var n=l(t),i=arguments.length,h=1,u=s.f,f=a.f;i>h;)for(var d,p=c(arguments[h++]),g=u?o(p).concat(u(p)):o(p),m=g.length,v=0;m>v;)d=g[v++],r&&!f.call(p,d)||(n[d]=p[d]);return n}:h},function(t,e,n){(function(t){function r(t){return(r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var i=n(327),o=n(328).Context,s=n(146);"undefined"!=typeof window&&(window.Buffer=t),"undefined"!=typeof self&&(self.Buffer=t);var a={UInt8:1,UInt16LE:2,UInt16BE:2,UInt32LE:4,UInt32BE:4,Int8:1,Int16LE:2,Int16BE:2,Int32LE:4,Int32BE:4,FloatLE:4,FloatBE:4,DoubleLE:8,DoubleBE:8,UInt64:8,Int64:8},l={},c=[];!function(){var t;for(t=1;t<=32;t++)c.push(t)}();var h={};Object.keys(a).concat(Object.keys({String:null,Buffer:null,Array:null,Skip:null,Choice:null,Nest:null,Bit:null,Itf8:null,Ltf8:null})).forEach((function(t){h[t.toLowerCase()]=t}));var u=function(){this.varName="",this.type="",this.options={},this.next=null,this.head=null,this.compiled=null,this.endian="le",this.constructorFn=null,this.alias=null};u.start=function(){return new u},Object.keys(a).forEach((function(t){u.prototype[t.toLowerCase()]=function(e,n){return this.setNextParser(t.toLowerCase(),e,n)};var e=t.replace(/BE|LE/,"").toLowerCase();e in u.prototype||(u.prototype[e]=function(t,n){return this[e+this.endian](t,n)})})),c.forEach((function(t){u.prototype["bit".concat(t.toString())]=function(e,n){return 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t="(function(buffer, constructorFn, Long) { ".concat(this.getCode()," })");this.compiled=i.runInThisContext(t)},u.prototype.sizeOf=function(){var t=NaN;if(Object.keys(a).indexOf(this.type)>=0)t=a[this.type];else if("String"===this.type&&"number"==typeof this.options.length)t=this.options.length;else if("Buffer"===this.type&&"number"==typeof this.options.length)t=this.options.length;else if("Array"===this.type&&"number"==typeof this.options.length){var e=NaN;"string"==typeof this.options.type?e=a[h[this.options.type]]:this.options.type instanceof u&&(e=this.options.type.sizeOf()),t=this.options.length*e}else"Skip"===this.type?t=this.options.length:"Nest"===this.type?t=this.options.type.sizeOf():this.type||(t=0);return this.next&&(t+=this.next.sizeOf()),t},u.prototype.parse=function(t){return this.compiled||this.compile(),this.compiled(t,this.constructorFn,s)},u.prototype.setNextParser=function(t,e,n){var r=new u;return 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this.next&&(t=this.next.generate(t)),t},Object.keys(a).forEach((function(t){u.prototype["generate".concat(t)]=function(e){"UInt64"===t?e.pushCode("{0} = Long.fromBytes(buffer.slice(offset,offset+8), true, this.endian === 'le').toNumber();",e.generateVariable(this.varName),t):"Int64"===t?e.pushCode("{0} = Long.fromBytes(buffer.slice(offset,offset+8), false, this.endian === 'le').toNumber();",e.generateVariable(this.varName),t):e.pushCode("{0} = buffer.read{1}(offset);",e.generateVariable(this.varName),t),e.pushCode("offset += {0};",a[t])}})),u.prototype.generateBit=function(t){var e=JSON.parse(JSON.stringify(this));if(e.varName=t.generateVariable(e.varName),t.bitFields.push(e),!this.next||this.next&&["Bit","Nest"].indexOf(this.next.type)<0){var n=0;t.bitFields.forEach((function(t){n+=t.options.length}));var r=t.generateTmpVariable();if(n<=8)t.pushCode("var {0} = buffer.readUInt8(offset);",r),n=8;else if(n<=16)t.pushCode("var {0} = buffer.readUInt16BE(offset);",r),n=16;else if(n<=24){var i=t.generateTmpVariable(),o=t.generateTmpVariable();t.pushCode("var {0} = buffer.readUInt16BE(offset);",i),t.pushCode("var {0} = buffer.readUInt8(offset + 2);",o),t.pushCode("var {2} = ({0} << 8) | {1};",i,o,r),n=24}else{if(!(n<=32))throw new Error("Currently, bit field sequence longer than 4-bytes is not supported.");t.pushCode("var {0} = buffer.readUInt32BE(offset);",r),n=32}t.pushCode("offset += {0};",n/8);var s=0,a="be"===this.endian;t.bitFields.forEach((function(e){t.pushCode("{0} = {1} >> {2} & {3};",e.varName,r,a?n-s-e.options.length:s,(1<<e.options.length)-1),s+=e.options.length})),t.bitFields=[]}},u.prototype.generateSkip=function(t){var e=t.generateOption(this.options.length);t.pushCode("offset += {0};",e)},u.prototype.generateString=function(t){var e=t.generateVariable(this.varName),n=t.generateTmpVariable();this.options.length&&this.options.zeroTerminated?(t.pushCode("var {0} = offset;",n),t.pushCode("while(buffer.readUInt8(offset++) !== 0 && offset - {0}  < 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buffer.slice(offset);",t.generateVariable(this.varName)):(t.pushCode("{0} = buffer.slice(offset, offset + {1});",t.generateVariable(this.varName),t.generateOption(this.options.length)),t.pushCode("offset += {0};",t.generateOption(this.options.length))),this.options.clone&&t.pushCode("{0} = Buffer.from({0});",t.generateVariable(this.varName))},u.prototype.generateArray=function(t){var e=t.generateOption(this.options.length),n=t.generateOption(this.options.lengthInBytes),r=this.options.type,i=t.generateTmpVariable(),o=t.generateVariable(this.varName),s=t.generateTmpVariable(),c=this.options.key,f="string"==typeof c;if(f?t.pushCode("{0} = {};",o):t.pushCode("{0} = [];",o),"function"==typeof this.options.readUntil?t.pushCode("do {"):"eof"===this.options.readUntil?t.pushCode("for (var {0} = 0; offset < buffer.length; {0}++) {",i):void 0!==n?t.pushCode("for (var {0} = offset; offset - {0} < {1}; ) {",i,n):t.pushCode("for (var {0} = 0; {0} < {1}; {0}++) {",i,e),"string"==typeof r)if(l[r]){var 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n,r,i=t.max_chain_length,o=t.strstart,s=t.prev_length,a=t.nice_match,l=t.strstart>t.w_size-u?t.strstart-(t.w_size-u):0,c=t.window,f=t.w_mask,d=t.prev,p=t.strstart+h,g=c[o+s-1],m=c[o+s];t.prev_length>=t.good_match&&(i>>=2),a>t.lookahead&&(a=t.lookahead);do{if(c[(n=e)+s]===m&&c[n+s-1]===g&&c[n]===c[o]&&c[++n]===c[o+1]){o+=2,n++;do{}while(c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&c[++o]===c[++n]&&o<p);if(r=h-(p-o),o=p-h,r>s){if(t.match_start=e,s=r,r>=a)break;g=c[o+s-1],m=c[o+s]}}}while((e=d[e&f])>l&&0!=--i);return s<=t.lookahead?s:t.lookahead}function k(t){var 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t.insert=t.strstart<2?t.strstart:2,4===e?(w(t,!0),0===t.strm.avail_out?3:4):t.last_lit&&(w(t,!1),0===t.strm.avail_out)?1:2}function C(t,e){for(var n,r,i;;){if(t.lookahead<u){if(k(t),t.lookahead<u&&0===e)return 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if(t.match_available){if((r=o._tr_tally(t,0,t.window[t.strstart-1]))&&w(t,!1),t.strstart++,t.lookahead--,0===t.strm.avail_out)return 1}else t.match_available=1,t.strstart++,t.lookahead--}return t.match_available&&(r=o._tr_tally(t,0,t.window[t.strstart-1]),t.match_available=0),t.insert=t.strstart<2?t.strstart:2,4===e?(w(t,!0),0===t.strm.avail_out?3:4):t.last_lit&&(w(t,!1),0===t.strm.avail_out)?1:2}function E(t,e,n,r,i){this.good_length=t,this.max_lazy=e,this.nice_length=n,this.max_chain=r,this.func=i}function 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i.Buf16(573),v(this.depth),this.l_buf=0,this.lit_bufsize=0,this.last_lit=0,this.d_buf=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}function A(t){var e;return t&&t.state?(t.total_in=t.total_out=0,t.data_type=2,(e=t.state).pending=0,e.pending_out=0,e.wrap<0&&(e.wrap=-e.wrap),e.status=e.wrap?42:d,t.adler=2===e.wrap?0:1,e.last_flush=0,o._tr_init(e),0):g(t,c)}function L(t){var e,n=A(t);return 0===n&&((e=t.state).window_size=2*e.w_size,v(e.head),e.max_lazy_match=r[e.level].max_lazy,e.good_match=r[e.level].good_length,e.nice_match=r[e.level].nice_length,e.max_chain_length=r[e.level].max_chain,e.strstart=0,e.block_start=0,e.lookahead=0,e.insert=0,e.match_length=e.prev_length=2,e.match_available=0,e.ins_h=0),n}function M(t,e,n,r,o,s){if(!t)return c;var a=1;if(-1===e&&(e=6),r<0?(a=0,r=-r):r>15&&(a=2,r-=16),o<1||o>9||8!==n||r<8||r>15||e<0||e>9||s<0||s>4)return g(t,c);8===r&&(r=9);var l=new T;return t.state=l,l.strm=t,l.wrap=a,l.gzhead=null,l.w_bits=r,l.w_size=1<<l.w_bits,l.w_mask=l.w_size-1,l.hash_bits=o+7,l.hash_size=1<<l.hash_bits,l.hash_mask=l.hash_size-1,l.hash_shift=~~((l.hash_bits+3-1)/3),l.window=new i.Buf8(2*l.w_size),l.head=new i.Buf16(l.hash_size),l.prev=new i.Buf16(l.w_size),l.lit_bufsize=1<<o+6,l.pending_buf_size=4*l.lit_bufsize,l.pending_buf=new i.Buf8(l.pending_buf_size),l.d_buf=1*l.lit_bufsize,l.l_buf=3*l.lit_bufsize,l.level=e,l.strategy=s,l.method=n,L(t)}r=[new E(0,0,0,0,(function(t,e){var n=65535;for(n>t.pending_buf_size-5&&(n=t.pending_buf_size-5);;){if(t.lookahead<=1){if(k(t),0===t.lookahead&&0===e)return 1;if(0===t.lookahead)break}t.strstart+=t.lookahead,t.lookahead=0;var r=t.block_start+n;if((0===t.strstart||t.strstart>=r)&&(t.lookahead=t.strstart-r,t.strstart=r,w(t,!1),0===t.strm.avail_out))return 1;if(t.strstart-t.block_start>=t.w_size-u&&(w(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,4===e?(w(t,!0),0===t.strm.avail_out?3:4):(t.strstart>t.block_start&&(w(t,!1),t.strm.avail_out),1)})),new E(4,4,8,4,S),new E(4,5,16,8,S),new E(4,6,32,32,S),new E(4,4,16,16,C),new E(8,16,32,32,C),new E(8,16,128,128,C),new E(8,32,128,256,C),new E(32,128,258,1024,C),new E(32,258,258,4096,C)],e.deflateInit=function(t,e){return M(t,e,8,15,8,0)},e.deflateInit2=M,e.deflateReset=L,e.deflateResetKeep=A,e.deflateSetHeader=function(t,e){return t&&t.state?2!==t.state.wrap?c:(t.state.gzhead=e,0):c},e.deflate=function(t,e){var n,i,s,l;if(!t||!t.state||e>5||e<0)return t?g(t,c):c;if(i=t.state,!t.output||!t.input&&0!==t.avail_in||i.status===p&&4!==e)return g(t,0===t.avail_out?-5:c);if(i.strm=t,n=i.last_flush,i.last_flush=e,42===i.status)if(2===i.wrap)t.adler=0,y(i,31),y(i,139),y(i,8),i.gzhead?(y(i,(i.gzhead.text?1:0)+(i.gzhead.hcrc?2:0)+(i.gzhead.extra?4:0)+(i.gzhead.name?8:0)+(i.gzhead.comment?16:0)),y(i,255&i.gzhead.time),y(i,i.gzhead.time>>8&255),y(i,i.gzhead.time>>16&255),y(i,i.gzhead.time>>24&255),y(i,9===i.level?2:i.strategy>=2||i.level<2?4:0),y(i,255&i.gzhead.os),i.gzhead.extra&&i.gzhead.extra.length&&(y(i,255&i.gzhead.extra.length),y(i,i.gzhead.extra.length>>8&255)),i.gzhead.hcrc&&(t.adler=a(t.adler,i.pending_buf,i.pending,0)),i.gzindex=0,i.status=69):(y(i,0),y(i,0),y(i,0),y(i,0),y(i,0),y(i,9===i.level?2:i.strategy>=2||i.level<2?4:0),y(i,3),i.status=d);else{var 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i.status=73;if(73===i.status)if(i.gzhead.name){s=i.pending;do{if(i.pending===i.pending_buf_size&&(i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),b(t),s=i.pending,i.pending===i.pending_buf_size)){l=1;break}l=i.gzindex<i.gzhead.name.length?255&i.gzhead.name.charCodeAt(i.gzindex++):0,y(i,l)}while(0!==l);i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),0===l&&(i.gzindex=0,i.status=91)}else i.status=91;if(91===i.status)if(i.gzhead.comment){s=i.pending;do{if(i.pending===i.pending_buf_size&&(i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),b(t),s=i.pending,i.pending===i.pending_buf_size)){l=1;break}l=i.gzindex<i.gzhead.comment.length?255&i.gzhead.comment.charCodeAt(i.gzindex++):0,y(i,l)}while(0!==l);i.gzhead.hcrc&&i.pending>s&&(t.adler=a(t.adler,i.pending_buf,i.pending-s,s)),0===l&&(i.status=f)}else 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e;for(e=0;e<s;e++)t.dyn_ltree[2*e]=0;for(e=0;e<a;e++)t.dyn_dtree[2*e]=0;for(e=0;e<19;e++)t.bl_tree[2*e]=0;t.dyn_ltree[512]=1,t.opt_len=t.static_len=0,t.last_lit=t.matches=0}function R(t){t.bi_valid>8?C(t,t.bi_buf):t.bi_valid>0&&(t.pending_buf[t.pending++]=t.bi_buf),t.bi_buf=0,t.bi_valid=0}function I(t,e,n,r){var i=2*e,o=2*n;return t[i]<t[o]||t[i]===t[o]&&r[e]<=r[n]}function N(t,e,n){for(var r=t.heap[n],i=n<<1;i<=t.heap_len&&(i<t.heap_len&&I(e,t.heap[i+1],t.heap[i],t.depth)&&i++,!I(e,r,t.heap[i],t.depth));)t.heap[n]=t.heap[i],n=i,i<<=1;t.heap[n]=r}function O(t,e,n){var r,i,s,a,l=0;if(0!==t.last_lit)do{r=t.pending_buf[t.d_buf+2*l]<<8|t.pending_buf[t.d_buf+2*l+1],i=t.pending_buf[t.l_buf+l],l++,0===r?T(t,i,e):(T(t,(s=m[i])+o+1,e),0!==(a=c[s])&&E(t,i-=v[s],a),T(t,s=S(--r),n),0!==(a=h[s])&&E(t,r-=x[s],a))}while(l<t.last_lit);T(t,256,e)}function P(t,e){var n,r,i,o=e.dyn_tree,s=e.stat_desc.static_tree,a=e.stat_desc.has_stree,c=e.stat_desc.elems,h=-1;for(t.heap_len=0,t.heap_max=573,n=0;n<c;n++)0!==o[2*n]?(t.heap[++t.heap_len]=h=n,t.depth[n]=0):o[2*n+1]=0;for(;t.heap_len<2;)o[2*(i=t.heap[++t.heap_len]=h<2?++h:0)]=1,t.depth[i]=0,t.opt_len--,a&&(t.static_len-=s[2*i+1]);for(e.max_code=h,n=t.heap_len>>1;n>=1;n--)N(t,o,n);i=c;do{n=t.heap[1],t.heap[1]=t.heap[t.heap_len--],N(t,o,1),r=t.heap[1],t.heap[--t.heap_max]=n,t.heap[--t.heap_max]=r,o[2*i]=o[2*n]+o[2*r],t.depth[i]=(t.depth[n]>=t.depth[r]?t.depth[n]:t.depth[r])+1,o[2*n+1]=o[2*r+1]=i,t.heap[1]=i++,N(t,o,1)}while(t.heap_len>=2);t.heap[--t.heap_max]=t.heap[1],function(t,e){var n,r,i,o,s,a,c=e.dyn_tree,h=e.max_code,u=e.stat_desc.static_tree,f=e.stat_desc.has_stree,d=e.stat_desc.extra_bits,p=e.stat_desc.extra_base,g=e.stat_desc.max_length,m=0;for(o=0;o<=l;o++)t.bl_count[o]=0;for(c[2*t.heap[t.heap_max]+1]=0,n=t.heap_max+1;n<573;n++)(o=c[2*c[2*(r=t.heap[n])+1]+1]+1)>g&&(o=g,m++),c[2*r+1]=o,r>h||(t.bl_count[o]++,s=0,r>=p&&(s=d[r-p]),a=c[2*r],t.opt_len+=a*(o+s),f&&(t.static_len+=a*(u[2*r+1]+s)));if(0!==m){do{for(o=g-1;0===t.bl_count[o];)o--;t.bl_count[o]--,t.bl_count[o+1]+=2,t.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(r=t.bl_count[o];0!==r;)(i=t.heap[--n])>h||(c[2*i+1]!==o&&(t.opt_len+=(o-c[2*i+1])*c[2*i],c[2*i+1]=o),r--)}}(t,e),L(o,h,t.bl_count)}function F(t,e,n){var r,i,o=-1,s=e[1],a=0,l=7,c=4;for(0===s&&(l=138,c=3),e[2*(n+1)+1]=65535,r=0;r<=n;r++)i=s,s=e[2*(r+1)+1],++a<l&&i===s||(a<c?t.bl_tree[2*i]+=a:0!==i?(i!==o&&t.bl_tree[2*i]++,t.bl_tree[32]++):a<=10?t.bl_tree[34]++:t.bl_tree[36]++,a=0,o=i,0===s?(l=138,c=3):i===s?(l=6,c=3):(l=7,c=4))}function D(t,e,n){var r,i,o=-1,s=e[1],a=0,l=7,c=4;for(0===s&&(l=138,c=3),r=0;r<=n;r++)if(i=s,s=e[2*(r+1)+1],!(++a<l&&i===s)){if(a<c)do{T(t,i,t.bl_tree)}while(0!=--a);else 0!==i?(i!==o&&(T(t,i,t.bl_tree),a--),T(t,16,t.bl_tree),E(t,a-3,2)):a<=10?(T(t,17,t.bl_tree),E(t,a-3,3)):(T(t,18,t.bl_tree),E(t,a-11,7));a=0,o=i,0===s?(l=138,c=3):i===s?(l=6,c=3):(l=7,c=4)}}i(x);var B=!1;function z(t,e,n,i){E(t,0+(i?1:0),3),function(t,e,n,i){R(t),C(t,n),C(t,~n),r.arraySet(t.pending_buf,t.window,e,n,t.pending),t.pending+=n}(t,e,n)}e._tr_init=function(t){B||(function(){var t,e,n,r,i,o=new Array(16);for(n=0,r=0;r<28;r++)for(v[r]=n,t=0;t<1<<c[r];t++)m[n++]=r;for(m[n-1]=r,i=0,r=0;r<16;r++)for(x[r]=i,t=0;t<1<<h[r];t++)g[i++]=r;for(i>>=7;r<a;r++)for(x[r]=i<<7,t=0;t<1<<h[r]-7;t++)g[256+i++]=r;for(e=0;e<=l;e++)o[e]=0;for(t=0;t<=143;)d[2*t+1]=8,t++,o[8]++;for(;t<=255;)d[2*t+1]=9,t++,o[9]++;for(;t<=279;)d[2*t+1]=7,t++,o[7]++;for(;t<=287;)d[2*t+1]=8,t++,o[8]++;for(L(d,287,o),t=0;t<a;t++)p[2*t+1]=5,p[2*t]=A(t,5);b=new _(d,c,257,s,l),w=new _(p,h,0,a,l),y=new _(new Array(0),u,0,19,7)}(),B=!0),t.l_desc=new k(t.dyn_ltree,b),t.d_desc=new k(t.dyn_dtree,w),t.bl_desc=new k(t.bl_tree,y),t.bi_buf=0,t.bi_valid=0,M(t)},e._tr_stored_block=z,e._tr_flush_block=function(t,e,n,r){var i,s,a=0;t.level>0?(2===t.strm.data_type&&(t.strm.data_type=function(t){var e,n=4093624447;for(e=0;e<=31;e++,n>>>=1)if(1&n&&0!==t.dyn_ltree[2*e])return 0;if(0!==t.dyn_ltree[18]||0!==t.dyn_ltree[20]||0!==t.dyn_ltree[26])return 1;for(e=32;e<o;e++)if(0!==t.dyn_ltree[2*e])return 1;return 0}(t)),P(t,t.l_desc),P(t,t.d_desc),a=function(t){var e;for(F(t,t.dyn_ltree,t.l_desc.max_code),F(t,t.dyn_dtree,t.d_desc.max_code),P(t,t.bl_desc),e=18;e>=3&&0===t.bl_tree[2*f[e]+1];e--);return t.opt_len+=3*(e+1)+5+5+4,e}(t),i=t.opt_len+3+7>>>3,(s=t.static_len+3+7>>>3)<=i&&(i=s)):i=s=n+5,n+4<=i&&-1!==e?z(t,e,n,r):4===t.strategy||s===i?(E(t,2+(r?1:0),3),O(t,d,p)):(E(t,4+(r?1:0),3),function(t,e,n,r){var i;for(E(t,e-257,5),E(t,n-1,5),E(t,r-4,4),i=0;i<r;i++)E(t,t.bl_tree[2*f[i]+1],3);D(t,t.dyn_ltree,e-1),D(t,t.dyn_dtree,n-1)}(t,t.l_desc.max_code+1,t.d_desc.max_code+1,a+1),O(t,t.dyn_ltree,t.dyn_dtree)),M(t),r&&R(t)},e._tr_tally=function(t,e,n){return t.pending_buf[t.d_buf+2*t.last_lit]=e>>>8&255,t.pending_buf[t.d_buf+2*t.last_lit+1]=255&e,t.pending_buf[t.l_buf+t.last_lit]=255&n,t.last_lit++,0===e?t.dyn_ltree[2*n]++:(t.matches++,e--,t.dyn_ltree[2*(m[n]+o+1)]++,t.dyn_dtree[2*S(e)]++),t.last_lit===t.lit_bufsize-1},e._tr_align=function(t){E(t,2,3),T(t,256,d),function(t){16===t.bi_valid?(C(t,t.bi_buf),t.bi_buf=0,t.bi_valid=0):t.bi_valid>=8&&(t.pending_buf[t.pending++]=255&t.bi_buf,t.bi_buf>>=8,t.bi_valid-=8)}(t)}},function(t,e,n){t.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"}},function(t,e,n){var r=n(72),i=n(134),o=n(135),s=n(221),a=n(222),l=-2,c=12,h=30;function u(t){return(t>>>24&255)+(t>>>8&65280)+((65280&t)<<8)+((255&t)<<24)}function f(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new r.Buf16(320),this.work=new r.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function d(t){var e;return t&&t.state?(e=t.state,t.total_in=t.total_out=e.total=0,t.msg="",e.wrap&&(t.adler=1&e.wrap),e.mode=1,e.last=0,e.havedict=0,e.dmax=32768,e.head=null,e.hold=0,e.bits=0,e.lencode=e.lendyn=new r.Buf32(852),e.distcode=e.distdyn=new r.Buf32(592),e.sane=1,e.back=-1,0):l}function p(t){var e;return t&&t.state?((e=t.state).wsize=0,e.whave=0,e.wnext=0,d(t)):l}function g(t,e){var n,r;return t&&t.state?(r=t.state,e<0?(n=0,e=-e):(n=1+(e>>4),e<48&&(e&=15)),e&&(e<8||e>15)?l:(null!==r.window&&r.wbits!==e&&(r.window=null),r.wrap=n,r.wbits=e,p(t))):l}function m(t,e){var n,r;return t?(r=new f,t.state=r,r.window=null,0!==(n=g(t,e))&&(t.state=null),n):l}var v,b,w=!0;function y(t){if(w){var e;for(v=new r.Buf32(512),b=new r.Buf32(32),e=0;e<144;)t.lens[e++]=8;for(;e<256;)t.lens[e++]=9;for(;e<280;)t.lens[e++]=7;for(;e<288;)t.lens[e++]=8;for(a(1,t.lens,0,288,v,0,t.work,{bits:9}),e=0;e<32;)t.lens[e++]=5;a(2,t.lens,0,32,b,0,t.work,{bits:5}),w=!1}t.lencode=v,t.lenbits=9,t.distcode=b,t.distbits=5}function x(t,e,n,i){var o,s=t.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new 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t;m--,b+=f[p++]<<w,w+=8}if(2&n.wrap&&35615===b){n.check=0,B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0),b=0,w=0,n.mode=2;break}if(n.flags=0,n.head&&(n.head.done=!1),!(1&n.wrap)||(((255&b)<<8)+(b>>8))%31){t.msg="incorrect header check",n.mode=h;break}if(8!=(15&b)){t.msg="unknown compression method",n.mode=h;break}if(w-=4,N=8+(15&(b>>>=4)),0===n.wbits)n.wbits=N;else if(N>n.wbits){t.msg="invalid window size",n.mode=h;break}n.dmax=1<<N,t.adler=n.check=1,n.mode=512&b?10:c,b=0,w=0;break;case 2:for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(n.flags=b,8!=(255&n.flags)){t.msg="unknown compression method",n.mode=h;break}if(57344&n.flags){t.msg="unknown header flags set",n.mode=h;break}n.head&&(n.head.text=b>>8&1),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0)),b=0,w=0,n.mode=3;case 3:for(;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.head&&(n.head.time=b),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,B[2]=b>>>16&255,B[3]=b>>>24&255,n.check=o(n.check,B,4,0)),b=0,w=0,n.mode=4;case 4:for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.head&&(n.head.xflags=255&b,n.head.os=b>>8),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0)),b=0,w=0,n.mode=5;case 5:if(1024&n.flags){for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.length=b,n.head&&(n.head.extra_len=b),512&n.flags&&(B[0]=255&b,B[1]=b>>>8&255,n.check=o(n.check,B,2,0)),b=0,w=0}else n.head&&(n.head.extra=null);n.mode=6;case 6:if(1024&n.flags&&((S=n.length)>m&&(S=m),S&&(n.head&&(N=n.head.extra_len-n.length,n.head.extra||(n.head.extra=new Array(n.head.extra_len)),r.arraySet(n.head.extra,f,p,S,N)),512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,n.length-=S),n.length))break t;n.length=0,n.mode=7;case 7:if(2048&n.flags){if(0===m)break t;S=0;do{N=f[p+S++],n.head&&N&&n.length<65536&&(n.head.name+=String.fromCharCode(N))}while(N&&S<m);if(512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,N)break t}else n.head&&(n.head.name=null);n.length=0,n.mode=8;case 8:if(4096&n.flags){if(0===m)break t;S=0;do{N=f[p+S++],n.head&&N&&n.length<65536&&(n.head.comment+=String.fromCharCode(N))}while(N&&S<m);if(512&n.flags&&(n.check=o(n.check,f,S,p)),m-=S,p+=S,N)break t}else n.head&&(n.head.comment=null);n.mode=9;case 9:if(512&n.flags){for(;w<16;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b!==(65535&n.check)){t.msg="header crc mismatch",n.mode=h;break}b=0,w=0}n.head&&(n.head.hcrc=n.flags>>9&1,n.head.done=!0),t.adler=n.check=0,n.mode=c;break;case 10:for(;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}t.adler=n.check=u(b),b=0,w=0,n.mode=11;case 11:if(0===n.havedict)return t.next_out=g,t.avail_out=v,t.next_in=p,t.avail_in=m,n.hold=b,n.bits=w,2;t.adler=n.check=1,n.mode=c;case c:if(5===e||6===e)break t;case 13:if(n.last){b>>>=7&w,w-=7&w,n.mode=27;break}for(;w<3;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}switch(n.last=1&b,w-=1,3&(b>>>=1)){case 0:n.mode=14;break;case 1:if(y(n),n.mode=20,6===e){b>>>=2,w-=2;break t}break;case 2:n.mode=17;break;case 3:t.msg="invalid block type",n.mode=h}b>>>=2,w-=2;break;case 14:for(b>>>=7&w,w-=7&w;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if((65535&b)!=(b>>>16^65535)){t.msg="invalid stored block lengths",n.mode=h;break}if(n.length=65535&b,b=0,w=0,n.mode=15,6===e)break t;case 15:n.mode=16;case 16:if(S=n.length){if(S>m&&(S=m),S>v&&(S=v),0===S)break t;r.arraySet(d,f,p,S,g),m-=S,p+=S,v-=S,g+=S,n.length-=S;break}n.mode=c;break;case 17:for(;w<14;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(n.nlen=257+(31&b),b>>>=5,w-=5,n.ndist=1+(31&b),b>>>=5,w-=5,n.ncode=4+(15&b),b>>>=4,w-=4,n.nlen>286||n.ndist>30){t.msg="too many length or distance symbols",n.mode=h;break}n.have=0,n.mode=18;case 18:for(;n.have<n.ncode;){for(;w<3;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.lens[z[n.have++]]=7&b,b>>>=3,w-=3}for(;n.have<19;)n.lens[z[n.have++]]=0;if(n.lencode=n.lendyn,n.lenbits=7,P={bits:n.lenbits},O=a(0,n.lens,0,19,n.lencode,0,n.work,P),n.lenbits=P.bits,O){t.msg="invalid code lengths set",n.mode=h;break}n.have=0,n.mode=19;case 19:for(;n.have<n.nlen+n.ndist;){for(;A=(D=n.lencode[b&(1<<n.lenbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(L<16)b>>>=T,w-=T,n.lens[n.have++]=L;else{if(16===L){for(F=T+2;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b>>>=T,w-=T,0===n.have){t.msg="invalid bit length repeat",n.mode=h;break}N=n.lens[n.have-1],S=3+(3&b),b>>>=2,w-=2}else if(17===L){for(F=T+3;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}w-=T,N=0,S=3+(7&(b>>>=T)),b>>>=3,w-=3}else{for(F=T+7;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}w-=T,N=0,S=11+(127&(b>>>=T)),b>>>=7,w-=7}if(n.have+S>n.nlen+n.ndist){t.msg="invalid bit length repeat",n.mode=h;break}for(;S--;)n.lens[n.have++]=N}}if(n.mode===h)break;if(0===n.lens[256]){t.msg="invalid code -- missing end-of-block",n.mode=h;break}if(n.lenbits=9,P={bits:n.lenbits},O=a(1,n.lens,0,n.nlen,n.lencode,0,n.work,P),n.lenbits=P.bits,O){t.msg="invalid literal/lengths set",n.mode=h;break}if(n.distbits=6,n.distcode=n.distdyn,P={bits:n.distbits},O=a(2,n.lens,n.nlen,n.ndist,n.distcode,0,n.work,P),n.distbits=P.bits,O){t.msg="invalid distances set",n.mode=h;break}if(n.mode=20,6===e)break t;case 20:n.mode=21;case 21:if(m>=6&&v>=258){t.next_out=g,t.avail_out=v,t.next_in=p,t.avail_in=m,n.hold=b,n.bits=w,s(t,k),g=t.next_out,d=t.output,v=t.avail_out,p=t.next_in,f=t.input,m=t.avail_in,b=n.hold,w=n.bits,n.mode===c&&(n.back=-1);break}for(n.back=0;A=(D=n.lencode[b&(1<<n.lenbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(A&&0==(240&A)){for(M=T,R=A,I=L;A=(D=n.lencode[I+((b&(1<<M+R)-1)>>M)])>>>16&255,L=65535&D,!(M+(T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}b>>>=M,w-=M,n.back+=M}if(b>>>=T,w-=T,n.back+=T,n.length=L,0===A){n.mode=26;break}if(32&A){n.back=-1,n.mode=c;break}if(64&A){t.msg="invalid literal/length code",n.mode=h;break}n.extra=15&A,n.mode=22;case 22:if(n.extra){for(F=n.extra;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.length+=b&(1<<n.extra)-1,b>>>=n.extra,w-=n.extra,n.back+=n.extra}n.was=n.length,n.mode=23;case 23:for(;A=(D=n.distcode[b&(1<<n.distbits)-1])>>>16&255,L=65535&D,!((T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(0==(240&A)){for(M=T,R=A,I=L;A=(D=n.distcode[I+((b&(1<<M+R)-1)>>M)])>>>16&255,L=65535&D,!(M+(T=D>>>24)<=w);){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}b>>>=M,w-=M,n.back+=M}if(b>>>=T,w-=T,n.back+=T,64&A){t.msg="invalid distance code",n.mode=h;break}n.offset=L,n.extra=15&A,n.mode=24;case 24:if(n.extra){for(F=n.extra;w<F;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}n.offset+=b&(1<<n.extra)-1,b>>>=n.extra,w-=n.extra,n.back+=n.extra}if(n.offset>n.dmax){t.msg="invalid distance too far back",n.mode=h;break}n.mode=25;case 25:if(0===v)break t;if(S=k-v,n.offset>S){if((S=n.offset-S)>n.whave&&n.sane){t.msg="invalid distance too far back",n.mode=h;break}S>n.wnext?(S-=n.wnext,C=n.wsize-S):C=n.wnext-S,S>n.length&&(S=n.length),E=n.window}else E=d,C=g-n.offset,S=n.length;S>v&&(S=v),v-=S,n.length-=S;do{d[g++]=E[C++]}while(--S);0===n.length&&(n.mode=21);break;case 26:if(0===v)break t;d[g++]=n.length,v--,n.mode=21;break;case 27:if(n.wrap){for(;w<32;){if(0===m)break t;m--,b|=f[p++]<<w,w+=8}if(k-=v,t.total_out+=k,n.total+=k,k&&(t.adler=n.check=n.flags?o(n.check,d,k,g-k):i(n.check,d,k,g-k)),k=v,(n.flags?b:u(b))!==n.check){t.msg="incorrect data check",n.mode=h;break}b=0,w=0}n.mode=28;case 28:if(n.wrap&&n.flags){for(;w<32;){if(0===m)break t;m--,b+=f[p++]<<w,w+=8}if(b!==(4294967295&n.total)){t.msg="incorrect length check",n.mode=h;break}b=0,w=0}n.mode=29;case 29:O=1;break t;case h:O=-3;break t;case 31:return-4;default:return l}return 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i=t.generateTmpVariable(),o=t.generateTmpVariable();t.pushCode("var {0} = buffer.readUInt16BE(offset);",i),t.pushCode("var {0} = buffer.readUInt8(offset + 2);",o),t.pushCode("var {2} = ({0} << 8) | {1};",i,o,r),n=24}else{if(!(n<=32))throw new Error("Currently, bit field sequence longer than 4-bytes is not supported.");t.pushCode("var {0} = buffer.readUInt32BE(offset);",r),n=32}t.pushCode("offset += {0};",n/8);var s=0,a="be"===this.endian;t.bitFields.forEach((function(e){t.pushCode("{0} = {1} >> {2} & {3};",e.varName,r,a?n-s-e.options.length:s,(1<<e.options.length)-1),s+=e.options.length})),t.bitFields=[]}},u.prototype.generateSkip=function(t){var e=t.generateOption(this.options.length);t.pushCode("offset += {0};",e)},u.prototype.generateString=function(t){var e=t.generateVariable(this.varName),n=t.generateTmpVariable();this.options.length&&this.options.zeroTerminated?(t.pushCode("var {0} = offset;",n),t.pushCode("while(buffer.readUInt8(offset++) !== 0 && offset - {0}  < 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d=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",d,"___parser_"+r),t.pushCode("var {0} = {1}.result; offset = {1}.offset;",s,d),r!==this.alias&&t.addReference(r)}else t.pushCode("var {0} = buffer.read{1}(offset);",s,h[r]),t.pushCode("offset += {0};",a[h[r]]);else r instanceof u&&(t.pushCode("var {0} = {};",s),t.pushScope(s),r.generate(t),t.popScope());f?t.pushCode("{0}[{2}.{1}] = {2};",o,c,s):t.pushCode("{0}.push({1});",o,s),t.pushCode("}"),"function"==typeof this.options.readUntil&&t.pushCode(" while (!({0}).call(this, {1}, buffer.slice(offset)));",this.options.readUntil,s)},u.prototype.generateChoiceCase=function(t,e,n){if("string"==typeof n)if(l[n]){var r=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",r,"___parser_"+n),t.pushCode("{0} = {1}.result; offset = {1}.offset;",t.generateVariable(this.varName),r),n!==this.alias&&t.addReference(n)}else t.pushCode("{0} = buffer.read{1}(offset);",t.generateVariable(this.varName),h[n]),t.pushCode("offset += 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n=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",n,"___parser_"+this.options.type),t.pushCode("{0} = {1}.result; offset = {1}.offset;",e,n),this.options.type!==this.alias&&t.addReference(this.options.type)}},u.prototype.generateFormatter=function(t,e,n){"function"==typeof n&&t.pushCode("{0} = ({1}).call(this, {0});",e,n)},u.prototype.isInteger=function(){return!!this.type.match(/U?Int[8|16|32][BE|LE]?|Bit\d+/)},u.prototype.itf8=function(t,e){return this.setNextParser("itf8",t,e)},u.prototype.itf8=function(t,e){return this.setNextParser("itf8",t,e)},u.prototype.generateItf8=function(t){var e=t.generateVariable(this.varName),n=t.generateTmpVariable();t.pushCode("\n    var ".concat(n," = buffer[offset];\n    if (").concat(n," < 0x80) {\n      ").concat(e," = ").concat(n,";\n      offset += 1;\n    } else if (").concat(n," < 0xc0) {\n      ").concat(e," = ((").concat(n,"<<8) | buffer[offset+1]) & 0x3fff;\n      offset += 2;\n    } else if (").concat(n," < 0xe0) {\n      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(").concat(n," < 0xc0) {\n    ").concat(e," = ((buffer[offset]<<8) | buffer[offset+1]) & 0x3fff;\n    offset += 2;\n  } else if (").concat(n," < 0xe0) {\n    ").concat(e," = ((buffer[offset]<<16) | (buffer[offset+1]<<8) | buffer[offset+2]) & 0x1fffff;\n    ").concat(e," = (((").concat(n," & 63) << 16) | buffer.readUInt16LE(offset + 1));\n    offset += 3;\n  } else if (").concat(n," < 0xf0) {\n    ").concat(e," = ((buffer[offset]<<24) | (buffer[offset+1]<<16) | (buffer[offset+2]<<8) | buffer[offset+3]) & 0x0fffffff;\n    offset += 4;\n  } else if (").concat(n," < 0xf8) {\n    ").concat(e," = (((buffer[offset] & 15) * Math.pow(2,32))) +\n      (buffer[offset+1]<<24) | (buffer[offset+2]<<16 | buffer[offset+3]<<8 | buffer[offset+4])\n    // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;\n    offset += 5;\n  } else if (").concat(n," < 0xfc) {\n    ").concat(e," = ((((buffer[offset] & 7) << 8) | buffer[offset+1] )) * Math.pow(2,32) +\n      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b=c,w=h,y=u,x=f;c=p(c,h,u,f,n[d+0],7,-680876936),f=p(f,c,h,u,n[d+1],12,-389564586),u=p(u,f,c,h,n[d+2],17,606105819),h=p(h,u,f,c,n[d+3],22,-1044525330),c=p(c,h,u,f,n[d+4],7,-176418897),f=p(f,c,h,u,n[d+5],12,1200080426),u=p(u,f,c,h,n[d+6],17,-1473231341),h=p(h,u,f,c,n[d+7],22,-45705983),c=p(c,h,u,f,n[d+8],7,1770035416),f=p(f,c,h,u,n[d+9],12,-1958414417),u=p(u,f,c,h,n[d+10],17,-42063),h=p(h,u,f,c,n[d+11],22,-1990404162),c=p(c,h,u,f,n[d+12],7,1804603682),f=p(f,c,h,u,n[d+13],12,-40341101),u=p(u,f,c,h,n[d+14],17,-1502002290),c=g(c,h=p(h,u,f,c,n[d+15],22,1236535329),u,f,n[d+1],5,-165796510),f=g(f,c,h,u,n[d+6],9,-1069501632),u=g(u,f,c,h,n[d+11],14,643717713),h=g(h,u,f,c,n[d+0],20,-373897302),c=g(c,h,u,f,n[d+5],5,-701558691),f=g(f,c,h,u,n[d+10],9,38016083),u=g(u,f,c,h,n[d+15],14,-660478335),h=g(h,u,f,c,n[d+4],20,-405537848),c=g(c,h,u,f,n[d+9],5,568446438),f=g(f,c,h,u,n[d+14],9,-1019803690),u=g(u,f,c,h,n[d+3],14,-187363961),h=g(h,u,f,c,n[d+8],20,1163531501),c=g(c,h,u,f,n[d+13],5,-1444681467),f=g(f,c,h,u,n[d+2],9,-51403784),u=g(u,f,c,h,n[d+7],14,1735328473),c=m(c,h=g(h,u,f,c,n[d+12],20,-1926607734),u,f,n[d+5],4,-378558),f=m(f,c,h,u,n[d+8],11,-2022574463),u=m(u,f,c,h,n[d+11],16,1839030562),h=m(h,u,f,c,n[d+14],23,-35309556),c=m(c,h,u,f,n[d+1],4,-1530992060),f=m(f,c,h,u,n[d+4],11,1272893353),u=m(u,f,c,h,n[d+7],16,-155497632),h=m(h,u,f,c,n[d+10],23,-1094730640),c=m(c,h,u,f,n[d+13],4,681279174),f=m(f,c,h,u,n[d+0],11,-358537222),u=m(u,f,c,h,n[d+3],16,-722521979),h=m(h,u,f,c,n[d+6],23,76029189),c=m(c,h,u,f,n[d+9],4,-640364487),f=m(f,c,h,u,n[d+12],11,-421815835),u=m(u,f,c,h,n[d+15],16,530742520),c=v(c,h=m(h,u,f,c,n[d+2],23,-995338651),u,f,n[d+0],6,-198630844),f=v(f,c,h,u,n[d+7],10,1126891415),u=v(u,f,c,h,n[d+14],15,-1416354905),h=v(h,u,f,c,n[d+5],21,-57434055),c=v(c,h,u,f,n[d+12],6,1700485571),f=v(f,c,h,u,n[d+3],10,-1894986606),u=v(u,f,c,h,n[d+10],15,-1051523),h=v(h,u,f,c,n[d+1],21,-2054922799),c=v(c,h,u,f,n[d+8],6,1873313359),f=v(f,c,h,u,n[d+15],10,-30611744),u=v(u,f,c,h,n[d+6],15,-1560198380),h=v(h,u,f,c,n[d+13],21,1309151649),c=v(c,h,u,f,n[d+4],6,-145523070),f=v(f,c,h,u,n[d+11],10,-1120210379),u=v(u,f,c,h,n[d+2],15,718787259),h=v(h,u,f,c,n[d+9],21,-343485551),c=c+b>>>0,h=h+w>>>0,u=u+y>>>0,f=f+x>>>0}return r.endian([c,h,u,f])})._ff=function(t,e,n,r,i,o,s){var a=t+(e&n|~e&r)+(i>>>0)+s;return(a<<o|a>>>32-o)+e},a._gg=function(t,e,n,r,i,o,s){var a=t+(e&r|n&~r)+(i>>>0)+s;return(a<<o|a>>>32-o)+e},a._hh=function(t,e,n,r,i,o,s){var a=t+(e^n^r)+(i>>>0)+s;return(a<<o|a>>>32-o)+e},a._ii=function(t,e,n,r,i,o,s){var a=t+(n^(e|~r))+(i>>>0)+s;return(a<<o|a>>>32-o)+e},a._blocksize=16,a._digestsize=16,t.exports=function(t,e){if(null==t)throw new Error("Illegal argument "+t);var n=r.wordsToBytes(a(t,e));return e&&e.asBytes?n:e&&e.asString?s.bytesToString(n):r.bytesToHex(n)}},function(t,e){var n,r;n="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/",r={rotl:function(t,e){return t<<e|t>>>32-e},rotr:function(t,e){return t<<32-e|t>>>e},endian:function(t){if(t.constructor==Number)return 16711935&r.rotl(t,8)|4278255360&r.rotl(t,24);for(var e=0;e<t.length;e++)t[e]=r.endian(t[e]);return t},randomBytes:function(t){for(var e=[];t>0;t--)e.push(Math.floor(256*Math.random()));return e},bytesToWords:function(t){for(var e=[],n=0,r=0;n<t.length;n++,r+=8)e[r>>>5]|=t[n]<<24-r%32;return e},wordsToBytes:function(t){for(var e=[],n=0;n<32*t.length;n+=8)e.push(t[n>>>5]>>>24-n%32&255);return e},bytesToHex:function(t){for(var e=[],n=0;n<t.length;n++)e.push((t[n]>>>4).toString(16)),e.push((15&t[n]).toString(16));return e.join("")},hexToBytes:function(t){for(var e=[],n=0;n<t.length;n+=2)e.push(parseInt(t.substr(n,2),16));return e},bytesToBase64:function(t){for(var e=[],r=0;r<t.length;r+=3)for(var i=t[r]<<16|t[r+1]<<8|t[r+2],o=0;o<4;o++)8*r+6*o<=8*t.length?e.push(n.charAt(i>>>6*(3-o)&63)):e.push("=");return e.join("")},base64ToBytes:function(t){t=t.replace(/[^A-Z0-9+\/]/gi,"");for(var e=[],r=0,i=0;r<t.length;i=++r%4)0!=i&&e.push((n.indexOf(t.charAt(r-1))&Math.pow(2,-2*i+8)-1)<<2*i|n.indexOf(t.charAt(r))>>>6-2*i);return e}},t.exports=r},function(t,e){function n(t){return!!t.constructor&&"function"==typeof t.constructor.isBuffer&&t.constructor.isBuffer(t)}
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        * Determine if an object is a Buffer
        *
        * @author   Feross Aboukhadijeh <https://feross.org>
        * @license  MIT
        */t.exports=function(t){return null!=t&&(n(t)||function(t){return"function"==typeof t.readFloatLE&&"function"==typeof t.slice&&n(t.slice(0,0))}(t)||!!t._isBuffer)}},function(t,e,n){var r,i=n(1),o=i(n(148)),s=i(n(76)),a=i(n(150)),l=i(n(37)),c=i(n(30)),h=i(n(31)),u=i(n(7)),f=i(n(10)),d=i(n(99)),p=i(n(16)),g=i(n(77)),m=i(n(59)),v=n(9),b=v.CramMalformedError,w=v.CramBufferOverrunError,y=v.CramArgumentError,x=n(58),_=x.parseItem,k=x.tinyMemoize,S=x.sequenceMD5,C=n(100),E=n(363);function T(t,e,n,r){if(!r)throw new b("could not resolve intra-slice mate pairs, file seems truncated or malformed");var i=!!(r.mate||void 0!==r.mateRecordNumber&&r.mateRecordNumber!==e);n.readName||(n.readName=String(n.uniqueId),r.readName=n.readName),n.mate={sequenceId:r.sequenceId,alignmentStart:r.alignmentStart,uniqueId:r.uniqueId},r.readName&&(n.mate.readName=r.readName),r.mate||void 0!==r.mateRecordNumber||(r.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(r.mate.readName=n.readName)),n.flags|=C.BAM_FPAIRED,(0,d.default)(r)&C.BAM_FUNMAP&&(n.flags|=C.BAM_FMUNMAP),(0,d.default)(n)&C.BAM_FUNMAP&&(r.flags|=C.BAM_FMUNMAP),(0,d.default)(r)&C.BAM_FREVERSE&&(n.flags|=C.BAM_FMREVERSE),(0,d.default)(n)&C.BAM_FREVERSE&&(r.flags|=C.BAM_FMREVERSE),void 0===n.templateLength&&(i?function(t,e,n){var r=function e(n){var r=[n];if(n.mateRecordNumber>=0){var i=t[n.mateRecordNumber];if(!i)throw new b("intra-slice mate record not found, this file seems malformed");r.push.apply(r,(0,m.default)(e(i)))}return r}(n),i=(0,g.default)(r).call(r,(function(t){return t.alignmentStart})),o=(0,g.default)(r).call(r,(function(t){return t.alignmentStart+t.readLength-1})),s=Math.max.apply(Math,(0,m.default)(o))-Math.min.apply(Math,(0,m.default)(i))+1;s>=0&&(0,p.default)(r).call(r,(function(t){if(void 0!==t.templateLength)throw new b("mate pair group has some members that have template lengths already, this file seems malformed");t.templateLength=s}))}(t,0,n):function(t,e){var n=Math.min(t.alignmentStart,e.alignmentStart),r=Math.max(t.alignmentStart+t.readLength-1,e.alignmentStart+e.readLength-1)-n+1;t.templateLength=r,e.templateLength=r}(n,r)),delete n.mateRecordNumber}var A=function(){function t(e,n){(0,u.default)(this,t),this.container=e,this.file=e.file,this.containerPosition=n}var e,n,r,i,d,m,v,x;return(0,f.default)(t,[{key:"getHeader",value:(x=(0,h.default)(c.default.mark((function t(){var e,n,r;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.file.getSectionParsers();case 2:return e=t.sent,t.next=5,this.container.getHeader();case 5:return n=t.sent,t.next=8,this.file.readBlock(n._endPosition+this.containerPosition);case 8:if("MAPPED_SLICE_HEADER"!==(r=t.sent).contentType){t.next=13;break}r.content=_(r.content,e.cramMappedSliceHeader.parser,0,n._endPosition),t.next=18;break;case 13:if("UNMAPPED_SLICE_HEADER"!==r.contentType){t.next=17;break}r.content=_(r.content,e.cramUnmappedSliceHeader.parser,0,n._endPosition),t.next=18;break;case 17:throw new b("error reading slice header block, invalid content type ".concat(r._contentType));case 18:return t.abrupt("return",r);case 19:case"end":return t.stop()}}),t,this)}))),function(){return x.apply(this,arguments)})},{key:"getBlocks",value:(v=(0,h.default)(c.default.mark((function t(){var e,n,r,i;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.getHeader();case 2:e=t.sent,n=e._endPosition,r=new Array(e.content.numBlocks),i=0;case 6:if(!(i<r.length)){t.next=14;break}return t.next=9,this.file.readBlock(n);case 9:r[i]=t.sent,n=r[i]._endPosition;case 11:i+=1,t.next=6;break;case 14:return t.abrupt("return",r);case 15:case"end":return t.stop()}}),t,this)}))),function(){return v.apply(this,arguments)})},{key:"getCoreDataBlock",value:(m=(0,h.default)(c.default.mark((function t(){var e;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.getBlocks();case 2:return e=t.sent,t.abrupt("return",e[0]);case 4:case"end":return t.stop()}}),t,this)}))),function(){return m.apply(this,arguments)})},{key:"_getBlocksContentIdIndex",value:(d=(0,h.default)(c.default.mark((function t(){var e,n;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.getBlocks();case 2:return e=t.sent,n={},(0,p.default)(e).call(e,(function(t){"EXTERNAL_DATA"===t.contentType&&(n[t.contentId]=t)})),t.abrupt("return",n);case 6:case"end":return t.stop()}}),t,this)}))),function(){return d.apply(this,arguments)})},{key:"getBlockByContentId",value:(i=(0,h.default)(c.default.mark((function t(e){var n;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this._getBlocksContentIdIndex();case 2:return n=t.sent,t.abrupt("return",n[e]);case 4:case"end":return t.stop()}}),t,this)}))),function(t){return i.apply(this,arguments)})},{key:"getReferenceRegion",value:(r=(0,h.default)(c.default.mark((function t(){var e,n,r,i;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.getHeader();case 2:if(!((e=t.sent.content).refSeqId<0)){t.next=5;break}return t.abrupt("return",void 0);case 5:return t.next=7,this.container.getCompressionScheme();case 7:if(n=t.sent,!(e.refBaseBlockId>=0)){t.next=15;break}if(r=this.getBlockByContentId(e.refBaseBlockId)){t.next=12;break}throw new b("embedded reference specified, but reference block does not exist");case 12:if(!(e.span>r.uncompressedSize)){t.next=14;break}throw new b("Embedded reference is too small");case 14:return t.abrupt("return",{seq:r.data.toString("utf8"),start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan});case 15:if(!n.referenceRequired&&!this.file.fetchReferenceSequenceCallback){t.next=24;break}if(this.file.fetchReferenceSequenceCallback){t.next=18;break}throw new Error("reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence");case 18:return t.next=20,this.file.fetchReferenceSequenceCallback(e.refSeqId,e.refSeqStart,e.refSeqStart+e.refSeqSpan-1);case 20:if((i=t.sent).length===e.refSeqSpan){t.next=23;break}throw new y("seqFetch callback returned a reference sequence of the wrong length");case 23:return t.abrupt("return",{seq:i,start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan});case 24:return t.abrupt("return",void 0);case 25:case"end":return t.stop()}}),t,this)}))),function(){return r.apply(this,arguments)})},{key:"getAllRecords",value:function(){return this.getRecords((function(){return!0}))}},{key:"_fetchRecords",value:(n=(0,h.default)(c.default.mark((function t(){var e,n,r,i,o,s,h,u,f,d,p,m,v,y,x,_,k,C,A,L,M,R,I,N=this;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return t.next=2,this.file.getDefinition();case 2:return e=t.sent,n=e.majorVersion,t.next=6,this.container.getCompressionScheme();case 6:return r=t.sent,t.next=9,this.getHeader();case 9:return i=t.sent,t.next=12,this._getBlocksContentIdIndex();case 12:if(o=t.sent,!(n>1&&this.file.options.checkSequenceMD5&&i.content.refSeqId>=0&&"0000000000000000"!==i.content.md5.join(""))){t.next=23;break}return t.next=16,this.getReferenceRegion();case 16:if(!(s=t.sent)){t.next=23;break}if(m=s.seq,v=s.start,y=s.end,x=S(m),_=(0,g.default)(h=i.content.md5).call(h,(function(t){return(t<16?"0":"")+t.toString(16)})).join(""),x===_){t.next=23;break}throw new b((0,l.default)(u=(0,l.default)(f=(0,l.default)(d=(0,l.default)(p="MD5 checksum reference mismatch for ref ".concat(i.content.refSeqId," pos ")).call(p,v,"..")).call(d,y,". recorded MD5: ")).call(f,_,", calculated MD5: ")).call(u,x));case 23:return t.next=25,this.getCoreDataBlock();case 25:k=t.sent,C={lastAlignmentStart:i.content.refSeqStart||0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{getCursor:function(t){return this[t]||(this[t]={bitPosition:7,bytePosition:0}),this[t]}}},A=function(t){var e=r.getCodecForDataSeries(t);if(!e)throw new b("no codec defined for ".concat(t," data series"));return e.decode(N,k,o,C)},L=new Array(i.content.numRecords),M=0;case 30:if(!(M<L.length)){t.next=48;break}t.prev=31,L[M]=E(this,A,r,i,k,o,C,n,M),L[M].uniqueId=i.contentPosition+i.content.recordCounter+M+1,t.next=45;break;case 36:if(t.prev=36,t.t0=t.catch(31),!(t.t0 instanceof w)){t.next=44;break}return console.warn("read attempted beyond end of buffer, file seems truncated."),L=(0,a.default)(L).call(L,(function(t){return!!t})),t.abrupt("break",48);case 44:throw t.t0;case 45:M+=1,t.next=30;break;case 48:for(R=0;R<L.length;R+=1)(I=L[R].mateRecordNumber)>=0&&T(L,R,L[R],L[I]);return t.abrupt("return",L);case 50:case"end":return t.stop()}}),t,this,[[31,36]])}))),function(){return n.apply(this,arguments)})},{key:"getRecords",value:(e=(0,h.default)(c.default.mark((function t(e){var n,r,i,l,u,f,d,p,m,v,b,w,y,x,_,k,S=this;return c.default.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:return r=this.container.filePosition+this.containerPosition,(i=this.file.featureCache.get(r))||(i=this._fetchRecords(),this.file.featureCache.set(r,i)),t.t0=a.default,t.next=6,i;case 6:if(t.t1=n=t.sent,t.t2=n,t.t3=e,!(l=(0,t.t0)(t.t1).call(t.t2,t.t3)).length||!this.file.fetchReferenceSequenceCallback){t.next=24;break}return t.next=13,this.getHeader();case 13:if(!((u=t.sent).content.refSeqId>=0||-2===u.content.refSeqId)){t.next=24;break}return d=u.content.refSeqId>=0?u.content.refSeqId:void 0,t.next=18,this.container.getCompressionScheme();case 18:for(p=t.sent,m={},v=0;v<l.length;v+=1)b=void 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n=t.alignmentStart-e.start;if(!t.readFeatures)return e.seq.substr(n,t.lengthOnRef).toUpperCase();for(var r="",i=n,o=0;r.length<t.readLength;)if(o<t.readFeatures.length){var s=t.readFeatures[o];if("Q"===s.code||"q"===s.code)o+=1;else if(s.pos===r.length+1)if(o+=1,"b"===s.code){var a=s.data.split(","),l=String.fromCharCode.apply(String,(0,c.default)(a));r+=l,i+=l.length}else"B"===s.code?(r+=s.data[0],i+=1):"X"===s.code?(r+=s.sub,i+=1):"I"===s.code?r+=s.data:"D"===s.code?i+=s.data:"i"===s.code?r+=s.data:"N"===s.code?i+=s.data:"S"===s.code?r+=s.data:"P"===s.code||s.code;else if(o<t.readFeatures.length){var h=e.seq.substr(i,t.readFeatures[o].pos-r.length-1);r+=h,i+=h.length}}else{var u=e.seq.substr(i,t.readLength-r.length);r+=u,i+=u.length}return r.toUpperCase()}}(this,this._refRegion)),this.readBases}},{key:"getPairOrientation",value:function(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){var t=this.isReverseComplemented()?"R":"F",e=this.isMateReverseComplemented()?"R":"F",n=" ",r=" ";this.isRead1()?(n="1",r="2"):this.isRead2()&&(n="2",r="1");var i=[],o=this.templateLength||this.templateSize;return this.alignmentStart>this.mate.alignmentStart&&o>0&&(o=-o),o>0?(i[0]=t,i[1]=n,i[2]=e,i[3]=r):(i[2]=t,i[3]=n,i[0]=e,i[1]=r),i.join("")}return null}},{key:"addReferenceSequence",value:function(t,e){var n;this.readFeatures&&(0,o.default)(n=this.readFeatures).call(n,(function(n){"X"===n.code&&function(t,e,n,r){if(e){var i=r.refPos-e.start,o=e.seq.charAt(i);o&&(r.ref=o);var s=u[o];void 0===s&&(s=4);var a=n.substitutionMatrix[s][r.data];a&&(r.sub=a)}}(0,t,e,n)})),!this.readBases&&t.start<=this.alignmentStart&&t.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=t)}},{key:"toJSON",value:function(){var t,e=this,n={};return(0,o.default)(t=(0,i.default)(this)).call(t,(function(t){"_"!==t.charAt(0)&&(n[t]=e[t])})),n.readBases=this.getReadBases(),n}}]),t}();t.exports=f},function(t,e,n){var r=n(1),i=r(n(98)),o=r(n(16)),s=r(n(75)),a=r(n(7)),l=r(n(10)),c=n(9).CramMalformedError,h=n(391).instantiateCodec,u={BF:"int",CF:"int",RI:"int",RL:"int",AP:"int",RG:"int",MF:"int",NS:"int",NP:"int",TS:"int",NF:"int",TC:"byte",TN:"int",FN:"int",FC:"byte",FP:"int",BS:"byte",IN:"byteArray",SC:"byteArray",DL:"int",BA:"byte",BB:"byteArray",RS:"int",PD:"int",HC:"int",MQ:"int",RN:"byteArray",QS:"byte",QQ:"byteArray",TL:"int",TM:"ignore",TV:"ignore"},f=function(){function t(e){(0,a.default)(this,t),(0,s.default)(this,e),this.readNamesIncluded=e.preservation.RN,this.APdelta=e.preservation.AP,this.referenceRequired=!!e.preservation.RR,this.tagIdsDictionary=e.preservation.TD,this.substitutionMatrix=function(t){for(var e=new Array(5),n=0;n<5;n+=1)e[n]=new Array(4);return e[0][t[0]>>6&3]="C",e[0][t[0]>>4&3]="G",e[0][t[0]>>2&3]="T",e[0][t[0]>>0&3]="N",e[1][t[1]>>6&3]="A",e[1][t[1]>>4&3]="G",e[1][t[1]>>2&3]="T",e[1][t[1]>>0&3]="N",e[2][t[2]>>6&3]="A",e[2][t[2]>>4&3]="C",e[2][t[2]>>2&3]="T",e[2][t[2]>>0&3]="N",e[3][t[3]>>6&3]="A",e[3][t[3]>>4&3]="C",e[3][t[3]>>2&3]="G",e[3][t[3]>>0&3]="N",e[4][t[4]>>6&3]="A",e[4][t[4]>>4&3]="C",e[4][t[4]>>2&3]="G",e[4][t[4]>>0&3]="T",e}(e.preservation.SM),this.dataSeriesCodecCache={},this.tagCodecCache={}}return(0,l.default)(t,[{key:"getCodecForTag",value:function(t){if(!this.tagCodecCache[t]){var e=this.tagEncoding[t];e&&(this.tagCodecCache[t]=h(e,"byteArray"))}return this.tagCodecCache[t]}},{key:"getTagNames",value:function(t){return this.tagIdsDictionary[t]}},{key:"getCodecForDataSeries",value:function(t){if(!this.dataSeriesCodecCache[t]){var e=this.dataSeriesEncoding[t];if(e){var n=u[t];if(!n)throw new c("data series name ".concat(t," not defined in file compression header"));this.dataSeriesCodecCache[t]=h(e,n)}}return this.dataSeriesCodecCache[t]}},{key:"toJSON",value:function(){var t,e=this,n={};return(0,o.default)(t=(0,i.default)(this)).call(t,(function(t){/Cache$/.test(t)||(n[t]=e[t])})),n}}]),t}();t.exports=f},function(t,e,n){var r=n(9).CramUnimplementedError,i=n(392),o=n(413),s=n(414),a=n(415),l=n(416),c=n(417),h={1:o,3:i,4:a,5:s,6:l,7:n(418),9:c};function u(t){return h[t]}t.exports={getCodecClassWithId:u,instantiateCodec:function t(e,n){var i=u("ignore"===n?0:e.codecId);if(!i)throw new r("no codec implemented for codec ID ".concat(e.codecId));return new i(e.parameters,n,t)}}},function(t,e,n){var r=n(1),i=r(n(97)),o=r(n(59)),s=r(n(77)),a=r(n(148)),l=r(n(159)),c=r(n(48)),h=r(n(102)),u=r(n(16)),f=r(n(103)),d=r(n(403)),p=r(n(7)),g=r(n(10)),m=r(n(32)),v=r(n(27)),b=r(n(33)),w=n(9).CramMalformedError,y=function(t){function e(){var t,n,r=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},i=arguments.length>1?arguments[1]:void 0;if((0,p.default)(this,e),n=(0,m.default)(this,(0,v.default)(e).call(this,r,i)),!(0,d.default)(t=["byte","int"]).call(t,n.dataType))throw new TypeError("".concat(n.dataType," decoding not yet implemented by HUFFMAN_INT codec"));return n.buildCodeBook(),n.buildCodes(),n.buildCaches(),0===n.sortedCodes[0].bitLength&&(n._decode=n._decodeZeroLengthCode),n}return(0,b.default)(e,t),(0,g.default)(e,[{key:"buildCodeBook",value:function(){for(var t=this,e=new Array(this.parameters.numCodes),n=0;n<this.parameters.numCodes;n+=1)e[n]={symbol:this.parameters.symbols[n],bitLength:this.parameters.bitLengths[n]};e=(0,f.default)(e).call(e,(function(t,e){return t.bitLength-e.bitLength||t.symbol-e.symbol})),this.codeBook={},(0,u.default)(e).call(e,(function(e){t.codeBook[e.bitLength]||(t.codeBook[e.bitLength]=[]),t.codeBook[e.bitLength].push(e.symbol)}))}},{key:"buildCodes",value:function(){var t,e=this;this.codes={};var n=0,r=-1;(0,u.default)(t=(0,h.default)(this.codeBook)).call(t,(function(t){var i=(0,c.default)(t,2),o=i[0],s=i[1];o=(0,l.default)(o,10),(0,u.default)(s).call(s,(function(t){var i={bitLength:o,value:t};r+=1;var s,a,l=o-n;if(r<<=l,i.bitCode=r,n+=l,16843009*((a=(858993459&(a=(s=r)-(s>>1)&1431655765))+(a>>2&858993459))+(a>>4)&252645135)>>24>o)throw new w("Symbol out of range");e.codes[t]=i}))}))}},{key:"buildCaches",value:function(){var t,e,n,r,l,c;this.sortedCodes=(0,f.default)(t=(0,a.default)(this.codes)).call(t,(function(t,e){return t.bitLength-e.bitLength||t.bitCode-e.bitCode})),this.sortedByValue=(0,f.default)(e=(0,a.default)(this.codes)).call(e,(function(t,e){return t.value-e.value})),this.sortedValuesByBitCode=(0,s.default)(n=this.sortedCodes).call(n,(function(t){return t.value})),this.sortedBitCodes=(0,s.default)(r=this.sortedCodes).call(r,(function(t){return t.bitCode})),this.sortedBitLengthsByBitCode=(0,s.default)(l=this.sortedCodes).call(l,(function(t){return t.bitLength}));var h=Math.max.apply(Math,(0,o.default)(this.sortedBitCodes));this.bitCodeToValue=(0,i.default)(c=new Array(h+1)).call(c,-1);for(var u=0;u<this.sortedBitCodes.length;u+=1)this.bitCodeToValue[this.sortedCodes[u].bitCode]=u}},{key:"decode",value:function(t,e,n,r){return this._decode(t,e,r.coreBlock)}},{key:"_decodeZeroLengthCode",value:function(){return this.sortedCodes[0].value}},{key:"_decode",value:function(t,e,n){for(var r=e.content,i=0,o=0,s=0;s<this.sortedCodes.length;s+=1){var a=this.sortedCodes[s].bitLength;o<<=a-i,o|=this._getBits(r,n,a-i),i=a;var l=this.bitCodeToValue[o];if(l>-1&&this.sortedBitLengthsByBitCode[l]===a)return this.sortedValuesByBitCode[l];for(var c=s;this.sortedCodes[c+1].bitLength===a&&c<this.sortedCodes.length;c+=1)s+=1}throw new w("Huffman symbol not found.")}}]),e}(n(40));t.exports=y},function(t,e,n){t.exports=n(394)},function(t,e,n){n(395);var r=n(3);t.exports=r.parseInt},function(t,e,n){var r=n(0),i=n(155);r({global:!0,forced:parseInt!=i},{parseInt:i})},function(t,e,n){t.exports=n(397)},function(t,e,n){n(398);var r=n(3);t.exports=r.Object.entries},function(t,e,n){var r=n(0),i=n(149).entries;r({target:"Object",stat:!0},{entries:function(t){return i(t)}})},function(t,e,n){t.exports=n(400)},function(t,e,n){var r=n(401),i=Array.prototype;t.exports=function(t){var e=t.sort;return t===i||t instanceof Array&&e===i.sort?r:e}},function(t,e,n){n(402);var r=n(18);t.exports=r("Array").sort},function(t,e,n){var r=n(0),i=n(5),o=n(22),s=n(12),a=n(54),l=[].sort,c=[1,2,3],h=s((function(){c.sort(void 0)})),u=s((function(){c.sort(null)})),f=a("sort");r({target:"Array",proto:!0,forced:h||!u||f},{sort:function(t){return void 0===t?l.call(o(this)):l.call(o(this),i(t))}})},function(t,e,n){t.exports=n(404)},function(t,e,n){t.exports=n(405)},function(t,e,n){var r=n(406),i=n(408),o=Array.prototype,s=String.prototype;t.exports=function(t){var e=t.includes;return t===o||t instanceof Array&&e===o.includes?r:"string"==typeof t||t===s||t instanceof String&&e===s.includes?i:e}},function(t,e,n){n(407);var r=n(18);t.exports=r("Array").includes},function(t,e,n){var r=n(0),i=n(82).includes,o=n(78);r({target:"Array",proto:!0},{includes:function(t){return i(this,t,arguments.length>1?arguments[1]:void 0)}}),o("includes")},function(t,e,n){n(409);var r=n(18);t.exports=r("String").includes},function(t,e,n){var r=n(0),i=n(410),o=n(49);r({target:"String",proto:!0,forced:!n(412)("includes")},{includes:function(t){return!!~String(o(this)).indexOf(i(t),arguments.length>1?arguments[1]:void 0)}})},function(t,e,n){var r=n(411);t.exports=function(t){if(r(t))throw TypeError("The method doesn't accept regular expressions");return t}},function(t,e,n){var r=n(14),i=n(34),o=n(6)("match");t.exports=function(t){var e;return r(t)&&(void 0!==(e=t[o])?!!e:"RegExp"==i(t))}},function(t,e,n){var r=n(6)("match");t.exports=function(t){var e=/./;try{"/./"[t](e)}catch(n){try{return e[r]=!1,"/./"[t](e)}catch(t){}}return!1}},function(t,e,n){var r=n(1),i=r(n(48)),o=r(n(7)),s=r(n(10)),a=r(n(32)),l=r(n(27)),c=r(n(33)),h=n(9),u=h.CramUnimplementedError,f=h.CramMalformedError,d=h.CramBufferOverrunError,p=n(40),g=n(58).parseItf8,m=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0;if((0,o.default)(this,e),"int"===(t=(0,a.default)(this,(0,l.default)(e).call(this,n,r))).dataType)t._decodeData=t._decodeInt;else{if("byte"!==t.dataType)throw new u("".concat(t.dataType," decoding not yet implemented by EXTERNAL codec"));t._decodeData=t._decodeByte}return t}return(0,c.default)(e,t),(0,s.default)(e,[{key:"decode",value:function(t,e,n,r){var i=this.parameters.blockContentId,o=n[i];if(!o)throw new f("no block found with content ID ".concat(i));var s=r.externalBlocks.getCursor(i);return this._decodeData(o,s)}},{key:"_decodeInt",value:function(t,e){var n=g(t.content,e.bytePosition),r=(0,i.default)(n,2),o=r[0],s=r[1];return e.bytePosition+=s,o}},{key:"_decodeByte",value:function(t,e){if(e.bytePosition>=t.content.length)throw new d("attempted to read beyond end of block. this file seems truncated.");var n=t.content[e.bytePosition];return e.bytePosition+=1,n}}]),e}(p);t.exports=m},function(t,e,n){var r=n(1),i=r(n(101)),o=r(n(7)),s=r(n(10)),a=r(n(32)),l=r(n(27)),c=r(n(33)),h=n(9),u=h.CramBufferOverrunError,f=h.CramMalformedError,d=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0;if((0,o.default)(this,e),t=(0,a.default)(this,(0,l.default)(e).call(this,n,r)),"byteArray"!==r)throw new TypeError("byteArrayStop codec does not support data type ".concat(r));return t._decode=t._decodeByteArray,t}return(0,c.default)(e,t),(0,s.default)(e,[{key:"decode",value:function(t,e,n,r){var i=this.parameters.blockContentId,o=n[i];if(!o)throw new f("no block found with content ID ".concat(i));var s=r.externalBlocks.getCursor(i);return this._decode(o,s)}},{key:"_decodeByteArray",value:function(t,e){for(var n=t.content,r=this.parameters.stopByte,o=e.bytePosition,s=e.bytePosition;n[s]!==r&&s<n.length;){if(s===n.length)throw new u("byteArrayStop reading beyond length of data buffer?");s+=1}return e.bytePosition=s+1,(0,i.default)(n).call(n,o,s)}}]),e}(n(40));t.exports=d},function(t,e,n){var r,i=n(1),o=i(n(16)),s=i(n(7)),a=i(n(10)),l=i(n(32)),c=i(n(27)),h=i(n(33)),u=n(58).tinyMemoize,f=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0,i=arguments.length>2?arguments[2]:void 0;if((0,s.default)(this,e),(t=(0,l.default)(this,(0,c.default)(e).call(this,n,r))).instantiateCodec=i,"byteArray"!==r)throw new TypeError("byteArrayLength does not support data type ".concat(r));return t}return(0,h.default)(e,t),(0,a.default)(e,[{key:"decode",value:function(t,e,n,r){for(var i=this._getLengthCodec().decode(t,e,n,r),o=this._getDataCodec(),s=new Array(i),a=0;a<i;a+=1)s[a]=o.decode(t,e,n,r);return s}},{key:"_getLengthCodec",value:function(){var t=this.parameters.lengthsEncoding;return this.instantiateCodec(t,"int")}},{key:"_getDataCodec",value:function(){var t=this.parameters.valuesEncoding;return this.instantiateCodec(t,"byte")}}]),e}(n(40));(0,o.default)(r="_getLengthCodec _getDataCodec".split(" ")).call(r,(function(t){return u(f,t)})),t.exports=f},function(t,e,n){var r=n(1),i=r(n(7)),o=r(n(10)),s=r(n(32)),a=r(n(27)),l=r(n(33)),c=n(9).CramUnimplementedError,h=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0;if((0,i.default)(this,e),"int"!==(t=(0,s.default)(this,(0,a.default)(e).call(this,n,r))).dataType)throw new c("".concat(t.dataType," decoding not yet implemented by BETA codec"));return t}return(0,l.default)(e,t),(0,o.default)(e,[{key:"decode",value:function(t,e,n,r){return this._getBits(e.content,r.coreBlock,this.parameters.length)-this.parameters.offset}}]),e}(n(40));t.exports=h},function(t,e,n){var r=n(1),i=r(n(7)),o=r(n(10)),s=r(n(32)),a=r(n(27)),l=r(n(33)),c=n(9).CramUnimplementedError,h=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0;if((0,i.default)(this,e),"int"!==(t=(0,s.default)(this,(0,a.default)(e).call(this,n,r))).dataType)throw new c("".concat(t.dataType," decoding not yet implemented by GAMMA codec"));return t}return(0,l.default)(e,t),(0,o.default)(e,[{key:"decode",value:function(t,e,n,r){for(var i=1;0===this._getBits(e.content,r.coreBlock,1);)i+=1;return(this._getBits(e.content,r.coreBlock,i-1)|1<<i-1)-this.parameters.offset}}]),e}(n(40));t.exports=h},function(t,e,n){var r=n(1),i=r(n(7)),o=r(n(10)),s=r(n(32)),a=r(n(27)),l=r(n(33)),c=n(9).CramUnimplementedError,h=function(t){function e(){var t,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},r=arguments.length>1?arguments[1]:void 0;if((0,i.default)(this,e),"int"!==(t=(0,s.default)(this,(0,a.default)(e).call(this,n,r))).dataType)throw new c("".concat(t.dataType," decoding not yet implemented by SUBEXP codec"));return t}return(0,l.default)(e,t),(0,o.default)(e,[{key:"decode",value:function(t,e,n,r){for(var i,o,s=0;this._getBits(e.content,r.coreBlock,1);)s+=1;return 0===s?(i=this.parameters.K,o=this._getBits(e.content,r.coreBlock,i)):o=1<<(i=s+this.parameters.K-1)|this._getBits(e.content,r.coreBlock,i),o-this.parameters.offset}}]),e}(n(40));t.exports=h},function(t,e,n){var r=n(420),i=n(422);function o(){this.protocol=null,this.slashes=null,this.auth=null,this.host=null,this.port=null,this.hostname=null,this.hash=null,this.search=null,this.query=null,this.pathname=null,this.path=null,this.href=null}e.parse=w,e.resolve=function(t,e){return w(t,!1,!0).resolve(e)},e.resolveObject=function(t,e){return t?w(t,!1,!0).resolveObject(e):e},e.format=function(t){return i.isString(t)&&(t=w(t)),t instanceof o?t.format():o.prototype.format.call(t)},e.Url=o;var s=/^([a-z0-9.+-]+:)/i,a=/:[0-9]*$/,l=/^(\/\/?(?!\/)[^\?\s]*)(\?[^\s]*)?$/,c=["{","}","|","\\","^","`"].concat(["<",">",'"',"`"," ","\r","\n","\t"]),h=["'"].concat(c),u=["%","/","?",";","#"].concat(h),f=["/","?","#"],d=/^[+a-z0-9A-Z_-]{0,63}$/,p=/^([+a-z0-9A-Z_-]{0,63})(.*)$/,g={javascript:!0,"javascript:":!0},m={javascript:!0,"javascript:":!0},v={http:!0,https:!0,ftp:!0,gopher:!0,file:!0,"http:":!0,"https:":!0,"ftp:":!0,"gopher:":!0,"file:":!0},b=n(423);function w(t,e,n){if(t&&i.isObject(t)&&t instanceof o)return t;var r=new o;return r.parse(t,e,n),r}o.prototype.parse=function(t,e,n){if(!i.isString(t))throw new TypeError("Parameter 'url' must be a string, not "+typeof t);var o=t.indexOf("?"),a=-1!==o&&o<t.indexOf("#")?"?":"#",c=t.split(a);c[0]=c[0].replace(/\\/g,"/");var w=t=c.join(a);if(w=w.trim(),!n&&1===t.split("#").length){var y=l.exec(w);if(y)return this.path=w,this.href=w,this.pathname=y[1],y[2]?(this.search=y[2],this.query=e?b.parse(this.search.substr(1)):this.search.substr(1)):e&&(this.search="",this.query={}),this}var x=s.exec(w);if(x){var _=(x=x[0]).toLowerCase();this.protocol=_,w=w.substr(x.length)}if(n||x||w.match(/^\/\/[^@\/]+@[^@\/]+/)){var k="//"===w.substr(0,2);!k||x&&m[x]||(w=w.substr(2),this.slashes=!0)}if(!m[x]&&(k||x&&!v[x])){for(var S,C,E=-1,T=0;T<f.length;T++)-1!==(A=w.indexOf(f[T]))&&(-1===E||A<E)&&(E=A);for(-1!==(C=-1===E?w.lastIndexOf("@"):w.lastIndexOf("@",E))&&(S=w.slice(0,C),w=w.slice(C+1),this.auth=decodeURIComponent(S)),E=-1,T=0;T<u.length;T++){var 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e&&e.signal&&delete e.signal,Promise.race([i,c(t,e)])}return c(t,e)},Request:l}}},function(t,e,n){Object.defineProperty(e,"__esModule",{value:!0});var r=n(162),i=function(){},o=function(){function t(){this.signals=new Set,this.abortController=new r.AbortController}return t.prototype.addSignal=function(t){var e=this;if(void 0===t&&(t=new i),this.signal.aborted)throw new Error("cannot add a signal, already aborted!");this.signals.add(t),t.aborted?this.handleAborted(t):"function"==typeof t.addEventListener&&t.addEventListener("abort",(function(){e.handleAborted(t)}))},t.prototype.handleAborted=function(t){this.signals.delete(t),0===this.signals.size&&this.abortController.abort()},Object.defineProperty(t.prototype,"signal",{get:function(){return this.abortController.signal},enumerable:!0,configurable:!0}),t.prototype.abort=function(){this.abortController.abort()},t}();e.default=o}]);class ap{constructor(t,e,n){this.config=t,this.browser=n,this.genome=e,this.cramFile=new sp.CramFile({filehandle:new lp(t.url,t),seqFetch:t.seqFetch||function(t,e,n){const r=this.genome.sequence,i=this.genome;return this.getHeader().then((function(o){const s=i.getChromosomeName(o.chrNames[t]);return r.getSequence(s,e-1,n)}))}.bind(this),checkSequenceMD5:void 0===t.checkSequenceMD5||t.checkSequenceMD5});const r=new lp(t.indexURL,t);this.indexedCramFile=new sp.IndexedCramFile({cram:this.cramFile,index:new sp.CraiIndex({filehandle:r}),fetchSizeLimit:3e7}),Af.setReaderDefaults(this,t)}async getHeader(){if(!this.header){const t=this.genome,e=await this.cramFile.getSamHeader(),n={},r=[],i={},o=[];for(let s of e)if("SQ"===s.tag){for(let e of s.data)if("SN"===e.tag){const o=e.value;if(n[o]=r.length,r.push(o),t){i[t.getChromosomeName(o)]=o}break}}else"RG"===s.tag&&o.push(s.data);this.header={chrNames:r,chrToIndex:n,chrAliasTable:i,readGroups:o}}return this.header}async readAlignments(t,e,n){this.browser;const r=await this.getHeader(),i=r.chrAliasTable.hasOwnProperty(t)?r.chrAliasTable[t]:t,o=r.chrToIndex[i],s=new sf(t,e,n,this.config);if(void 0===o)return s;try{const t=await this.indexedCramFile.getRecordsForRange(o,e,n);for(let i of t){const t=i.sequenceId,l=i.alignmentStart,c=l+i.lengthOnRef;if(t<0)continue;if(t>o||l>n)return;if(t<o)continue;if(c<e)continue;const h=a(i,r.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(t){let e=t.message;throw e&&e.indexOf("MD5")>=0&&(e="Sequence mismatch. Is this the correct genome for the loaded CRAM?"),this.browser.alert.present(new Error(e)),t}function a(t,e){const n=new pf;if(n.chr=e[t.sequenceId],n.start=t.alignmentStart-1,n.lengthOnRef=t.lengthOnRef,n.flags=t.flags,n.strand=!(16&t.flags),n.fragmentLength=t.templateLength||t.templateSize,n.mq=t.mappingQuality,n.end=t.alignmentStart+t.lengthOnRef,n.readGroupId=t.readGroupId,t.mate&&void 0!==t.mate.sequenceId){const r=void 0!==t.mate.flags?!(1&t.mate.flags):!(32&t.flags);n.mate={chr:e[t.mate.sequenceId],position:t.mate.alignmentStart,strand:r}}return n.seq=t.getReadBases(),n.qual=t.qualityScores,n.tagDict=t.tags,n.readName=t.readName,function(t,e){const n=[];let r,i,o=0,s="";if(e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef,t.readFeatures)for(let a of t.readFeatures){const t=a.code,l=a.data,c=a.pos-1,h=a.refPos-1;switch(t){case"S":case"I":case"i":case"N":case"D":if(c>o){const t=c-o;n.push(new _f({start:h-t,seqOffset:o,len:t,type:"M"})),o+=t,s+=t+"M"}if("S"===t){let r=h;e.scLengthOnRef+=l.length,0===c&&(e.scStart-=l.length,r-=l.length);const i=l.length;n.push(new _f({start:r,seqOffset:o,len:i,type:"S"})),o+=i,s+=i+t}else if("I"===t||"i"===t){void 0===r&&(r=[]);const e="i"===t?1:l.length;r.push(new _f({start:h,len:e,seqOffset:o,type:"I"})),o+=e,s+=e+t}else"D"!==t&&"N"!==t||(i||(i=[]),i.push({start:h,len:l,type:t}),s+=l+t);break;case"H":case"P":s+=l+t}}const a=t.readLength-o;a>0&&(n.push(new _f({start:t.alignmentStart+t.lengthOnRef-a-1,seqOffset:o,len:a,type:"M"})),s+=a+"M");e.blocks=n,e.insertions=r,e.gaps=i,e.cigar=s}(t,n),n.mate&&n.start>n.mate.position&&n.fragmentLength>0&&(n.fragmentLength=-n.fragmentLength),Af.setPairOrientation(n),n}}}class lp{constructor(t,e){this.position=0,this.url=t,this.config=e,this.cache=new cp({fetch:(t,e)=>this._fetch(t,e)})}async _fetch(t,e){const n={start:t,size:e};this._stat={size:void 0};const r=await Eo.loadArrayBuffer(this.url,Cs(this.config,{range:n}));return Buffer.from(r)}async read(t){let e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:0,n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:1/0,r=arguments.length>3&&void 0!==arguments[3]?arguments[3]:0,i=r;return null===r&&(i=this.position,this.position+=n),this.cache.get(t,e,n,r)}async readFile(){const t=await Eo.loadArrayBuffer(this.url,Cs(this.config));return Buffer.from(t)}async stat(){if(!this._stat){const t=Buffer.allocUnsafe(10);if(await this.read(t,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class cp{constructor(t){let{fetch:e,size:n=1e7,chunkSize:r=32768}=t;this.fetch=e,this.chunkSize=r,this.lruCache=new hp({maxSize:Math.floor(n/r)})}async get(t,e,n,r){if(t.length<e+n)throw new Error("output buffer not big enough for request");const i=Math.floor(r/this.chunkSize),o=Math.floor((r+n)/this.chunkSize),s=new Array(o-i+1);for(let t=i;t<=o;t+=1)s[t-i]=this._getChunk(t).then((e=>({data:e,chunkNumber:t})));const a=await Promise.all(s),l=r-a[0].chunkNumber*this.chunkSize;a.forEach((s=>{let{data:a,chunkNumber:c}=s;const h=c*this.chunkSize;let u=0,f=this.chunkSize,d=e+(c-i)*this.chunkSize-l;c===i&&(d=e,u=l),c===o&&(f=r+n-h),a.copy(t,d,u,f)}))}_getChunk(t){const e=this.lruCache.get(t);if(e)return e;const n=this.fetch(t*this.chunkSize,this.chunkSize);return this.lruCache.set(t,n),n}}class hp{constructor(){let t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};if(!(t.maxSize&&t.maxSize>0))throw new TypeError("`maxSize` must be a number greater than 0");this.maxSize=t.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(t,e){this.cache.set(t,e),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(t){if(this.cache.has(t))return this.cache.get(t);if(this.oldCache.has(t)){const e=this.oldCache.get(t);return this._set(t,e),e}}set(t,e){return this.cache.has(t)?this.cache.set(t,e):this._set(t,e),this}has(t){return this.cache.has(t)||this.oldCache.has(t)}peek(t){return this.cache.has(t)?this.cache.get(t):this.oldCache.has(t)?this.oldCache.get(t):void 0}delete(t){const e=this.cache.delete(t);return e&&this._size--,this.oldCache.delete(t)||e}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[t]of this)yield t}*values(){for(const[,t]of this)yield t}*[Symbol.iterator](){for(const t of this.cache)yield t;for(const t of this.oldCache){const[e]=t;this.cache.has(e)||(yield t)}}get size(){let t=0;for(const e of this.oldCache.keys())this.cache.has(e)||t++;return this._size+t}}var up={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};const fp=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.filter=new kf(t.filter),this.readGroupSetIds=t.readGroupSetIds,this.authKey=t.authKey,this.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,this.samplingDepth=void 0===t.samplingDepth?1e3:t.samplingDepth,t.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===t.pairsSupported||t.pairsSupported};fp.prototype.readAlignments=function(t,e,n){const r=this.genome,i=this;return(i.chrAliasTable?Promise.resolve(i.chrAliasTable):i.readMetadata().then((function(t){if(i.chrAliasTable={},r&&t.readGroups&&t.readGroups.length>0){var e=t.readGroups[0].referenceSetId;return e?sc({url:i.url+"/references/search",body:{referenceSetId:e},decode:function(t){return t.references}}).then((function(t){return t.forEach((function(t){var e=t.name,n=r.getChromosomeName(e);i.chrAliasTable[n]=e})),i.chrAliasTable})):(function(t,e){var n;if("461916304629"===e||"337315832689"===e){for(n=1;n<23;n++)t["chr"+n]=n;t.chrX="X",t.chrY="Y",t.chrM="MT"}}(i.chrAliasTable,i.config.datasetId),i.chrAliasTable)}return i.chrAliasTable}))).then((function(r){var s=r.hasOwnProperty(t)?r[t]:t;return sc({url:i.url+"/reads/search",body:{readGroupSetIds:[i.readGroupSetIds],referenceName:s,start:e,end:n,pageSize:"10000"},decode:o,results:new sf(t,e,n,i.config)})}));function o(t){var e,n,o,s,a,l=t.alignments,c=l.length,h=[];for(e=0;e<c;e++){let t=l[e];(n=new pf).readName=t.fragmentName,n.properPlacement=t.properPlacement,n.duplicateFragment=t.duplicateFragment,n.numberReads=t.numberReads,n.fragmentLength=t.fragmentLength,n.readNumber=t.readNumber,n.failedVendorQualityChecks=t.failedVendorQualityChecks,n.secondaryAlignment=t.secondaryAlignment,n.supplementaryAlignment=t.supplementaryAlignment,n.seq=t.alignedSequence,n.qual=t.alignedQuality,n.matePos=t.nextMatePosition,n.tagDict=t.info,n.flags=0,t.alignment?(n.mapped=!0,n.chr=t.alignment.position.referenceName,r&&(n.chr=r.getChromosomeName(n.chr)),n.start=parseInt(t.alignment.position.position),n.strand=!t.alignment.position.reverseStrand,n.mq=t.alignment.mappingQuality,n.cigar=u(t.alignment.cigar),o=f(t.alignment.cigar),n.lengthOnRef=o.lengthOnRef,a=d(n,o.array),n.blocks=a.blocks,n.insertions=a.insertions):n.mapped=!1,(s=t.nextMatePosition)&&(n.mate={chr:s.referenceFrame,position:parseInt(s.position),strand:!s.reverseStrand}),i.filter.pass(n)&&h.push(n)}return h;function u(t){var e="";return t.forEach((function(t){var n=up[t.operation],r=t.operationLength;e+=r+n})),e}function f(t){var e,n,r,i,o=0,s=[];for(i=0;i<t.length;i++)e=t[i],r=up[e.operation],n=parseInt(e.operationLength),"M"!==r&&"EQ"!==r&&"X"!==r&&"D"!==r&&"N"!==r&&"="!==r||(o+=n),s.push({len:n,ltr:r});return{lengthOnRef:o,array:s}}function d(t,e){for(var n,r,i,o=[],s=0,a=t.start,l=e.length,c=0;c<l;c++){var h=e[c];switch(h.ltr){case"H":case"P":break;case"S":s+=h.len,i="S";break;case"N":case"D":void 0===n&&(n=[]),n.push({start:a,len:h.len,type:h.ltr}),a+=h.len;break;case"I":void 0===r&&(r=[]),r.push(new _f({start:a,len:h.len,seqOffset:s})),s+=h.len;break;case"M":case"EQ":case"=":case"X":o.push(new _f({start:a,len:h.len,seqOffset:s,gapType:i})),s+=h.len,a+=h.len;break;default:console.log("Error processing cigar element: "+h.len+h.ltr)}}return{blocks:o,insertions:r,gaps:n}}}},fp.prototype.readMetadata=function(){return oc({url:this.url,entity:"readgroupsets",entityId:this.readGroupSetIds})};class dp{constructor(t,e){const n=e.genome;if(this.config=t,this.genome=n,Ms(t.url)){if("cram"===t.format)throw"CRAM data uris are not supported";this.config.indexed=!1}if("ga4gh"===t.sourceType)this.bamReader=new fp(t,n);else if("pysam"===t.sourceType)this.bamReader=new Ff(t,n);else if("htsget"===t.sourceType)this.bamReader=new Bf(t,n);else if("shardedBam"===t.sourceType)this.bamReader=new Pf(t,n);else if("cram"===t.format)this.bamReader=new ap(t,n,e);else{if(!this.config.indexURL&&!1!==t.indexed)if(ke(this.config.url)){const t=function(t,e){if(ke(t)){if(t.includes("?")){const n=t.indexOf("?");return t.substring(0,n)+"."+e+t.substring(n)}return t+"."+e}}(this.config.url,"bai");t?(console.error(`Warning: no indexURL specified for ${this.config.url}.  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0!==s&&s;if(!function(t){return t.__FORCE_INSTALL_ABORTCONTROLLER_POLYFILL?(console.log("__FORCE_INSTALL_ABORTCONTROLLER_POLYFILL=true is set, will force install polyfill"),!0):"function"==typeof t.Request&&!t.Request.prototype.hasOwnProperty("signal")||!t.AbortController}({fetch:n,Request:i,AbortController:o,__FORCE_INSTALL_ABORTCONTROLLER_POLYFILL:a}))return{fetch:n,Request:l};var l=i;(l&&!l.prototype.hasOwnProperty("signal")||a)&&((l=function(t,e){var n;e&&e.signal&&(n=e.signal,delete e.signal);var r=new i(t,e);return n&&Object.defineProperty(r,"signal",{writable:!1,enumerable:!1,configurable:!0,value:n}),r}).prototype=i.prototype);var c=n;return{fetch:function(t,e){var n=l&&l.prototype.isPrototypeOf(t)?t.signal:e?e.signal:void 0;if(n){var r;try{r=new DOMException("Aborted","AbortError")}catch(t){(r=new Error("Aborted")).name="AbortError"}if(n.aborted)return Promise.reject(r);var i=new Promise((function(t,e){n.addEventListener("abort",(function(){return e(r)}),{once:!0})}));return e&&e.signal&&delete e.signal,Promise.race([i,c(t,e)])}return c(t,e)},Request:l}}},function(t,e,n){Object.defineProperty(e,"__esModule",{value:!0});var r=n(162),i=function(){},o=function(){function t(){this.signals=new Set,this.abortController=new r.AbortController}return t.prototype.addSignal=function(t){var e=this;if(void 0===t&&(t=new i),this.signal.aborted)throw new Error("cannot add a signal, already aborted!");this.signals.add(t),t.aborted?this.handleAborted(t):"function"==typeof t.addEventListener&&t.addEventListener("abort",(function(){e.handleAborted(t)}))},t.prototype.handleAborted=function(t){this.signals.delete(t),0===this.signals.size&&this.abortController.abort()},Object.defineProperty(t.prototype,"signal",{get:function(){return this.abortController.signal},enumerable:!0,configurable:!0}),t.prototype.abort=function(){this.abortController.abort()},t}();e.default=o}]);class lp{constructor(t,e,n){this.config=t,this.browser=n,this.genome=e,this.cramFile=new ap.CramFile({filehandle:new cp(t.url,t),seqFetch:t.seqFetch||function(t,e,n){const r=this.genome.sequence,i=this.genome;return this.getHeader().then((function(o){const s=i.getChromosomeName(o.chrNames[t]);return r.getSequence(s,e-1,n)}))}.bind(this),checkSequenceMD5:void 0===t.checkSequenceMD5||t.checkSequenceMD5});const r=new cp(t.indexURL,t);this.indexedCramFile=new ap.IndexedCramFile({cram:this.cramFile,index:new ap.CraiIndex({filehandle:r}),fetchSizeLimit:3e7}),Lf.setReaderDefaults(this,t)}async getHeader(){if(!this.header){const t=this.genome,e=await this.cramFile.getSamHeader(),n={},r=[],i={},o=[];for(let s of e)if("SQ"===s.tag){for(let e of s.data)if("SN"===e.tag){const o=e.value;if(n[o]=r.length,r.push(o),t){i[t.getChromosomeName(o)]=o}break}}else"RG"===s.tag&&o.push(s.data);this.header={chrNames:r,chrToIndex:n,chrAliasTable:i,readGroups:o}}return this.header}async readAlignments(t,e,n){this.browser;const r=await this.getHeader(),i=r.chrAliasTable.hasOwnProperty(t)?r.chrAliasTable[t]:t,o=r.chrToIndex[i],s=new af(t,e,n,this.config);if(void 0===o)return s;try{const t=await this.indexedCramFile.getRecordsForRange(o,e,n);for(let i of t){const t=i.sequenceId,l=i.alignmentStart,c=l+i.lengthOnRef;if(t<0)continue;if(t>o||l>n)return;if(t<o)continue;if(c<e)continue;const h=a(i,r.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(t){let e=t.message;throw e&&e.indexOf("MD5")>=0&&(e="Sequence mismatch. Is this the correct genome for the loaded CRAM?"),this.browser.alert.present(new Error(e)),t}function a(t,e){const n=new gf;if(n.chr=e[t.sequenceId],n.start=t.alignmentStart-1,n.lengthOnRef=t.lengthOnRef,n.flags=t.flags,n.strand=!(16&t.flags),n.fragmentLength=t.templateLength||t.templateSize,n.mq=t.mappingQuality,n.end=t.alignmentStart+t.lengthOnRef,n.readGroupId=t.readGroupId,t.mate&&void 0!==t.mate.sequenceId){const r=void 0!==t.mate.flags?!(1&t.mate.flags):!(32&t.flags);n.mate={chr:e[t.mate.sequenceId],position:t.mate.alignmentStart,strand:r}}return n.seq=t.getReadBases(),n.qual=t.qualityScores,n.tagDict=t.tags,n.readName=t.readName,function(t,e){const n=[];let r,i,o=0,s="";if(e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef,t.readFeatures)for(let a of t.readFeatures){const t=a.code,l=a.data,c=a.pos-1,h=a.refPos-1;switch(t){case"S":case"I":case"i":case"N":case"D":if(c>o){const t=c-o;n.push(new kf({start:h-t,seqOffset:o,len:t,type:"M"})),o+=t,s+=t+"M"}if("S"===t){let r=h;e.scLengthOnRef+=l.length,0===c&&(e.scStart-=l.length,r-=l.length);const i=l.length;n.push(new kf({start:r,seqOffset:o,len:i,type:"S"})),o+=i,s+=i+t}else if("I"===t||"i"===t){void 0===r&&(r=[]);const e="i"===t?1:l.length;r.push(new kf({start:h,len:e,seqOffset:o,type:"I"})),o+=e,s+=e+t}else"D"!==t&&"N"!==t||(i||(i=[]),i.push({start:h,len:l,type:t}),s+=l+t);break;case"H":case"P":s+=l+t}}const a=t.readLength-o;a>0&&(n.push(new kf({start:t.alignmentStart+t.lengthOnRef-a-1,seqOffset:o,len:a,type:"M"})),s+=a+"M");e.blocks=n,e.insertions=r,e.gaps=i,e.cigar=s}(t,n),n.mate&&n.start>n.mate.position&&n.fragmentLength>0&&(n.fragmentLength=-n.fragmentLength),Lf.setPairOrientation(n),n}}}class cp{constructor(t,e){this.position=0,this.url=t,this.config=e,this.cache=new hp({fetch:(t,e)=>this._fetch(t,e)})}async _fetch(t,e){const n={start:t,size:e};this._stat={size:void 0};const r=await Eo.loadArrayBuffer(this.url,Cs(this.config,{range:n}));return Buffer.from(r)}async read(t){let e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:0,n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:1/0,r=arguments.length>3&&void 0!==arguments[3]?arguments[3]:0,i=r;return null===r&&(i=this.position,this.position+=n),this.cache.get(t,e,n,r)}async readFile(){const t=await Eo.loadArrayBuffer(this.url,Cs(this.config));return Buffer.from(t)}async stat(){if(!this._stat){const t=Buffer.allocUnsafe(10);if(await this.read(t,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class hp{constructor(t){let{fetch:e,size:n=1e7,chunkSize:r=32768}=t;this.fetch=e,this.chunkSize=r,this.lruCache=new up({maxSize:Math.floor(n/r)})}async get(t,e,n,r){if(t.length<e+n)throw new Error("output buffer not big enough for request");const i=Math.floor(r/this.chunkSize),o=Math.floor((r+n)/this.chunkSize),s=new Array(o-i+1);for(let t=i;t<=o;t+=1)s[t-i]=this._getChunk(t).then((e=>({data:e,chunkNumber:t})));const a=await Promise.all(s),l=r-a[0].chunkNumber*this.chunkSize;a.forEach((s=>{let{data:a,chunkNumber:c}=s;const h=c*this.chunkSize;let u=0,f=this.chunkSize,d=e+(c-i)*this.chunkSize-l;c===i&&(d=e,u=l),c===o&&(f=r+n-h),a.copy(t,d,u,f)}))}_getChunk(t){const e=this.lruCache.get(t);if(e)return e;const n=this.fetch(t*this.chunkSize,this.chunkSize);return this.lruCache.set(t,n),n}}class up{constructor(){let t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};if(!(t.maxSize&&t.maxSize>0))throw new TypeError("`maxSize` must be a number greater than 0");this.maxSize=t.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(t,e){this.cache.set(t,e),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(t){if(this.cache.has(t))return this.cache.get(t);if(this.oldCache.has(t)){const e=this.oldCache.get(t);return this._set(t,e),e}}set(t,e){return this.cache.has(t)?this.cache.set(t,e):this._set(t,e),this}has(t){return this.cache.has(t)||this.oldCache.has(t)}peek(t){return this.cache.has(t)?this.cache.get(t):this.oldCache.has(t)?this.oldCache.get(t):void 0}delete(t){const e=this.cache.delete(t);return e&&this._size--,this.oldCache.delete(t)||e}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[t]of this)yield t}*values(){for(const[,t]of this)yield t}*[Symbol.iterator](){for(const t of this.cache)yield t;for(const t of this.oldCache){const[e]=t;this.cache.has(e)||(yield t)}}get size(){let t=0;for(const e of this.oldCache.keys())this.cache.has(e)||t++;return this._size+t}}var fp={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};const dp=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.filter=new Sf(t.filter),this.readGroupSetIds=t.readGroupSetIds,this.authKey=t.authKey,this.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,this.samplingDepth=void 0===t.samplingDepth?1e3:t.samplingDepth,t.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===t.pairsSupported||t.pairsSupported};dp.prototype.readAlignments=function(t,e,n){const r=this.genome,i=this;return(i.chrAliasTable?Promise.resolve(i.chrAliasTable):i.readMetadata().then((function(t){if(i.chrAliasTable={},r&&t.readGroups&&t.readGroups.length>0){var e=t.readGroups[0].referenceSetId;return e?sc({url:i.url+"/references/search",body:{referenceSetId:e},decode:function(t){return t.references}}).then((function(t){return t.forEach((function(t){var e=t.name,n=r.getChromosomeName(e);i.chrAliasTable[n]=e})),i.chrAliasTable})):(function(t,e){var n;if("461916304629"===e||"337315832689"===e){for(n=1;n<23;n++)t["chr"+n]=n;t.chrX="X",t.chrY="Y",t.chrM="MT"}}(i.chrAliasTable,i.config.datasetId),i.chrAliasTable)}return i.chrAliasTable}))).then((function(r){var s=r.hasOwnProperty(t)?r[t]:t;return sc({url:i.url+"/reads/search",body:{readGroupSetIds:[i.readGroupSetIds],referenceName:s,start:e,end:n,pageSize:"10000"},decode:o,results:new af(t,e,n,i.config)})}));function o(t){var e,n,o,s,a,l=t.alignments,c=l.length,h=[];for(e=0;e<c;e++){let t=l[e];(n=new gf).readName=t.fragmentName,n.properPlacement=t.properPlacement,n.duplicateFragment=t.duplicateFragment,n.numberReads=t.numberReads,n.fragmentLength=t.fragmentLength,n.readNumber=t.readNumber,n.failedVendorQualityChecks=t.failedVendorQualityChecks,n.secondaryAlignment=t.secondaryAlignment,n.supplementaryAlignment=t.supplementaryAlignment,n.seq=t.alignedSequence,n.qual=t.alignedQuality,n.matePos=t.nextMatePosition,n.tagDict=t.info,n.flags=0,t.alignment?(n.mapped=!0,n.chr=t.alignment.position.referenceName,r&&(n.chr=r.getChromosomeName(n.chr)),n.start=parseInt(t.alignment.position.position),n.strand=!t.alignment.position.reverseStrand,n.mq=t.alignment.mappingQuality,n.cigar=u(t.alignment.cigar),o=f(t.alignment.cigar),n.lengthOnRef=o.lengthOnRef,a=d(n,o.array),n.blocks=a.blocks,n.insertions=a.insertions):n.mapped=!1,(s=t.nextMatePosition)&&(n.mate={chr:s.referenceFrame,position:parseInt(s.position),strand:!s.reverseStrand}),i.filter.pass(n)&&h.push(n)}return h;function u(t){var e="";return t.forEach((function(t){var n=fp[t.operation],r=t.operationLength;e+=r+n})),e}function f(t){var e,n,r,i,o=0,s=[];for(i=0;i<t.length;i++)e=t[i],r=fp[e.operation],n=parseInt(e.operationLength),"M"!==r&&"EQ"!==r&&"X"!==r&&"D"!==r&&"N"!==r&&"="!==r||(o+=n),s.push({len:n,ltr:r});return{lengthOnRef:o,array:s}}function d(t,e){for(var n,r,i,o=[],s=0,a=t.start,l=e.length,c=0;c<l;c++){var h=e[c];switch(h.ltr){case"H":case"P":break;case"S":s+=h.len,i="S";break;case"N":case"D":void 0===n&&(n=[]),n.push({start:a,len:h.len,type:h.ltr}),a+=h.len;break;case"I":void 0===r&&(r=[]),r.push(new kf({start:a,len:h.len,seqOffset:s})),s+=h.len;break;case"M":case"EQ":case"=":case"X":o.push(new kf({start:a,len:h.len,seqOffset:s,gapType:i})),s+=h.len,a+=h.len;break;default:console.log("Error processing cigar element: "+h.len+h.ltr)}}return{blocks:o,insertions:r,gaps:n}}}},dp.prototype.readMetadata=function(){return oc({url:this.url,entity:"readgroupsets",entityId:this.readGroupSetIds})};class pp{constructor(t,e){const n=e.genome;if(this.config=t,this.genome=n,Ms(t.url)&&(this.config.indexed=!1),"ga4gh"===t.sourceType)this.bamReader=new dp(t,n);else if("pysam"===t.sourceType)this.bamReader=new Df(t,n);else if("htsget"===t.sourceType)this.bamReader=new zf(t,n);else if("shardedBam"===t.sourceType)this.bamReader=new Ff(t,n);else if("cram"===t.format)this.bamReader=new lp(t,n,e);else{if(!this.config.indexURL&&!1!==t.indexed)if(ke(this.config.url)){const t=function(t,e){if(ke(t)){if(t.includes("?")){const n=t.indexOf("?");return t.substring(0,n)+"."+e+t.substring(n)}return t+"."+e}}(this.config.url,"bai");t?(console.error(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${this.baiPath}`),this.config.indexURL=t):(console.error(`Warning: no indexURL specified for ${this.config.url}.`),this.config.indexed=!1)}else console.error(`Warning: no indexURL specified for ${this.config.name}.`),this.config.indexed=!1;!1!==this.config.indexed?this.bamReader=new Pf(t,n):this.bamReader=new Of(t,n)}this.viewAsPairs=t.viewAsPairs,this.showSoftClips=t.showSoftClips}setViewAsPairs(t){this.viewAsPairs=t}setShowSoftClips(t){this.showSoftClips=t}async getAlignments(t,e,n){const r=this.genome,i=this.showSoftClips,o=await this.bamReader.readAlignments(t,e,n);let s=o.alignments;this.viewAsPairs||(s=of([{alignments:s}]));const a=s.length>0;if(o.packedAlignmentRows=sf(s,o.start,o.end,i),this.alignmentContainer=o,a){const e=await r.sequence.getSequence(t,o.start,o.end);if(e)return o.coverageMap.refSeq=e,o.sequence=e,o;console.error("No sequence for: "+t+":"+o.start+"-"+o.end)}return o}}function gp(t,e,n){var r,i,o,s,a,l,c,h={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;let u=void 0!==this.flipAxis&&this.flipAxis;function f(t){return 0===t?"0":Math.abs(t)>=10?t.toFixed():Math.abs(t)>=1?t.toFixed(1):t.toFixed(2)}Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"}),r=(c=.95*e)-8,a={x:i=c,y:o=s=.01*n},Xo.strokeLine(t,r,o,i,s,h),Xo.fillText(t,f(u?this.dataRange.min:this.dataRange.max),r+4,o+12,h),l={x:i,y:o=s=.99*n},Xo.strokeLine(t,r,o,i,s,h),Xo.fillText(t,f(u?this.dataRange.max:this.dataRange.min),r+4,o-4,h),Xo.strokeLine(t,a.x,a.y,l.x,l.y,h)}class mp{constructor(t){let{chr:e,start:n,end:r}=t;this.chr=e,this.start=n,this.end=r}contains(t){return t.chr===this.chr&&t.start>=this.start&&t.end<=this.end}overlaps(t){return t.chr===this.chr&&!(t.end<this.start||t.start>this.end)}extend(t){t.chr===this.chr&&(this.start=Math.min(t.start,this.start),this.end=Math.max(t.end,this.end))}getLocusString(){if("all"===this.chr)return"all";{const t=Se(Math.floor(this.start)+1),e=Se(Math.round(this.end));return`${this.chr}:${t}-${e}`}}static fromLocusString(t){if("all"===t)return new mp({chr:"all"});const e=t.split(":"),n=e[0],r=e[1].split("-"),i=Number.parseInt(r[0].replace(/,/g,""))-1,o=Number.parseInt(r[1].replace(/,/g,""));return new mp({chr:n,start:i,end:o})}}
 /*!
      * vanilla-picker v2.12.1
      * https://vanilla-picker.js.org
      *
      * Copyright 2017-2021 Andreas Borgen (https://github.com/Sphinxxxx), Adam Brooks (https://github.com/dissimulate)
      * Released under the ISC license.
-     */var mp=function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")},vp=function(){function t(t,e){for(var n=0;n<e.length;n++){var r=e[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(t,r.key,r)}}return function(e,n,r){return n&&t(e.prototype,n),r&&t(e,r),e}}(),bp=function(t,e){if(Array.isArray(t))return t;if(Symbol.iterator in Object(t))return function(t,e){var n=[],r=!0,i=!1,o=void 0;try{for(var s,a=t[Symbol.iterator]();!(r=(s=a.next()).done)&&(n.push(s.value),!e||n.length!==e);r=!0);}catch(t){i=!0,o=t}finally{try{!r&&a.return&&a.return()}finally{if(i)throw o}}return n}(t,e);throw new TypeError("Invalid attempt to destructure non-iterable instance")};String.prototype.startsWith=String.prototype.startsWith||function(t){return 0===this.indexOf(t)},String.prototype.padStart=String.prototype.padStart||function(t,e){for(var n=this;n.length<t;)n=e+n;return n};var wp={cb:"0f8ff",tqw:"aebd7",q:"-ffff",qmrn:"7fffd4",zr:"0ffff",bg:"5f5dc",bsq:"e4c4",bck:"---",nch:"ebcd",b:"--ff",bvt:"8a2be2",brwn:"a52a2a",brw:"deb887",ctb:"5f9ea0",hrt:"7fff-",chcT:"d2691e",cr:"7f50",rnw:"6495ed",crns:"8dc",crms:"dc143c",cn:"-ffff",Db:"--8b",Dcn:"-8b8b",Dgnr:"b8860b",Dgr:"a9a9a9",Dgrn:"-64-",Dkhk:"bdb76b",Dmgn:"8b-8b",Dvgr:"556b2f",Drng:"8c-",Drch:"9932cc",Dr:"8b--",Dsmn:"e9967a",Dsgr:"8fbc8f",DsTb:"483d8b",DsTg:"2f4f4f",Dtrq:"-ced1",Dvt:"94-d3",ppnk:"1493",pskb:"-bfff",mgr:"696969",grb:"1e90ff",rbrc:"b22222",rwht:"af0",stg:"228b22",chs:"-ff",gnsb:"dcdcdc",st:"8f8ff",g:"d7-",gnr:"daa520",gr:"808080",grn:"-8-0",grnw:"adff2f",hnw:"0fff0",htpn:"69b4",nnr:"cd5c5c",ng:"4b-82",vr:"0",khk:"0e68c",vnr:"e6e6fa",nrb:"0f5",wngr:"7cfc-",mnch:"acd",Lb:"add8e6",Lcr:"08080",Lcn:"e0ffff",Lgnr:"afad2",Lgr:"d3d3d3",Lgrn:"90ee90",Lpnk:"b6c1",Lsmn:"a07a",Lsgr:"20b2aa",Lskb:"87cefa",LsTg:"778899",Lstb:"b0c4de",Lw:"e0",m:"-ff-",mgrn:"32cd32",nn:"af0e6",mgnt:"-ff",mrn:"8--0",mqm:"66cdaa",mmb:"--cd",mmrc:"ba55d3",mmpr:"9370db",msg:"3cb371",mmsT:"7b68ee","":"-fa9a",mtr:"48d1cc",mmvt:"c71585",mnLb:"191970",ntc:"5fffa",mstr:"e4e1",mccs:"e4b5",vjw:"dead",nv:"--80",c:"df5e6",v:"808-0",vrb:"6b8e23",rng:"a5-",rngr:"45-",rch:"da70d6",pgnr:"eee8aa",pgrn:"98fb98",ptrq:"afeeee",pvtr:"db7093",ppwh:"efd5",pchp:"dab9",pr:"cd853f",pnk:"c0cb",pm:"dda0dd",pwrb:"b0e0e6",prp:"8-080",cc:"663399",r:"--",sbr:"bc8f8f",rb:"4169e1",sbrw:"8b4513",smn:"a8072",nbr:"4a460",sgrn:"2e8b57",ssh:"5ee",snn:"a0522d",svr:"c0c0c0",skb:"87ceeb",sTb:"6a5acd",sTgr:"708090",snw:"afa",n:"-ff7f",stb:"4682b4",tn:"d2b48c",t:"-8080",thst:"d8bfd8",tmT:"6347",trqs:"40e0d0",vt:"ee82ee",whT:"5deb3",wht:"",hts:"5f5f5",w:"-",wgrn:"9acd32"};function yp(t){var e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:1,n=e>0?t.toFixed(e).replace(/0+$/,"").replace(/\.$/,""):t.toString();return n||"0"}var xp=function(){function t(e,n,r,i){mp(this,t);var o=this;if(void 0===e);else if(Array.isArray(e))this.rgba=e;else if(void 0===r){var s=e&&""+e;s&&function(e){if(e.startsWith("hsl")){var n=e.match(/([\-\d\.e]+)/g).map(Number),r=bp(n,4),i=r[0],s=r[1],a=r[2],l=r[3];void 0===l&&(l=1),i/=360,s/=100,a/=100,o.hsla=[i,s,a,l]}else if(e.startsWith("rgb")){var c=e.match(/([\-\d\.e]+)/g).map(Number),h=bp(c,4),u=h[0],f=h[1],d=h[2],p=h[3];void 0===p&&(p=1),o.rgba=[u,f,d,p]}else e.startsWith("#")?o.rgba=t.hexToRgb(e):o.rgba=t.nameToRgb(e)||t.hexToRgb(e)}(s.toLowerCase())}else this.rgba=[e,n,r,void 0===i?1:i]}return vp(t,[{key:"printRGB",value:function(t){var e=(t?this.rgba:this.rgba.slice(0,3)).map((function(t,e){return yp(t,3===e?3:0)}));return t?"rgba("+e+")":"rgb("+e+")"}},{key:"printHSL",value:function(t){var e=[360,100,100,1],n=["","%","%",""],r=(t?this.hsla:this.hsla.slice(0,3)).map((function(t,r){return yp(t*e[r],3===r?3:1)+n[r]}));return t?"hsla("+r+")":"hsl("+r+")"}},{key:"printHex",value:function(t){var e=this.hex;return t?e:e.substring(0,7)}},{key:"rgba",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error("No color is set");return this._rgba=t.hslToRgb(this._hsla)},set:function(t){3===t.length&&(t[3]=1),this._rgba=t,this._hsla=null}},{key:"rgbString",get:function(){return this.printRGB()}},{key:"rgbaString",get:function(){return this.printRGB(!0)}},{key:"hsla",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error("No color is set");return this._hsla=t.rgbToHsl(this._rgba)},set:function(t){3===t.length&&(t[3]=1),this._hsla=t,this._rgba=null}},{key:"hslString",get:function(){return this.printHSL()}},{key:"hslaString",get:function(){return this.printHSL(!0)}},{key:"hex",get:function(){return"#"+this.rgba.map((function(t,e){return e<3?t.toString(16):Math.round(255*t).toString(16)})).map((function(t){return t.padStart(2,"0")})).join("")},set:function(e){this.rgba=t.hexToRgb(e)}}],[{key:"hexToRgb",value:function(t){var e=(t.startsWith("#")?t.slice(1):t).replace(/^(\w{3})$/,"$1F").replace(/^(\w)(\w)(\w)(\w)$/,"$1$1$2$2$3$3$4$4").replace(/^(\w{6})$/,"$1FF");if(!e.match(/^([0-9a-fA-F]{8})$/))throw new Error("Unknown hex color; "+t);var n=e.match(/^(\w\w)(\w\w)(\w\w)(\w\w)$/).slice(1).map((function(t){return parseInt(t,16)}));return n[3]=n[3]/255,n}},{key:"nameToRgb",value:function(e){var n=e.toLowerCase().replace("at","T").replace(/[aeiouyldf]/g,"").replace("ght","L").replace("rk","D").slice(-5,4),r=wp[n];return void 0===r?r:t.hexToRgb(r.replace(/\-/g,"00").padStart(6,"f"))}},{key:"rgbToHsl",value:function(t){var e=bp(t,4),n=e[0],r=e[1],i=e[2],o=e[3];n/=255,r/=255,i/=255;var s=Math.max(n,r,i),a=Math.min(n,r,i),l=void 0,c=void 0,h=(s+a)/2;if(s===a)l=c=0;else{var u=s-a;switch(c=h>.5?u/(2-s-a):u/(s+a),s){case 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t._doRemove(e.target,e.type,e.handler)})),this._events=[]}}],[{key:"_doRemove",value:function(t,e,n){t.removeEventListener(e,n,!1)}}]),t}();function kp(t,e,n){var r=!1;function i(t,e,n){return Math.max(e,Math.min(t,n))}function o(t,o,s){if(s&&(r=!0),r){t.preventDefault();var a=e.getBoundingClientRect(),l=a.width,c=a.height,h=o.clientX,u=o.clientY,f=i(h-a.left,0,l),d=i(u-a.top,0,c);n(f/l,d/c)}}function s(t,e){1===(void 0===t.buttons?t.which:t.buttons)?o(t,t,e):r=!1}function a(t,e){1===t.touches.length?o(t,t.touches[0],e):r=!1}t.add(e,"mousedown",(function(t){s(t,!0)})),t.add(e,"touchstart",(function(t){a(t,!0)})),t.add(window,"mousemove",s),t.add(e,"touchmove",a),t.add(window,"mouseup",(function(t){r=!1})),t.add(e,"touchend",(function(t){r=!1})),t.add(e,"touchcancel",(function(t){r=!1}))}var Sp="keydown",Cp="mousedown",Ep="focusin";function Tp(t,e){return(e||document).querySelector(t)}function Ap(t){t.preventDefault(),t.stopPropagation()}function Lp(t,e,n,r,i){t.add(e,Sp,(function(t){n.indexOf(t.key)>=0&&(i&&Ap(t),r(t))}))}var Mp=function(){function t(e){mp(this,t),this.settings={popup:"right",layout:"default",alpha:!0,editor:!0,editorFormat:"hex",cancelButton:!1,defaultColor:"#0cf"},this._events=new _p,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(e)}return vp(t,[{key:"setOptions",value:function(t){var e=this;if(t){var n=this.settings;if(t instanceof HTMLElement)n.parent=t;else{n.parent&&t.parent&&n.parent!==t.parent&&(this._events.remove(n.parent),this._popupInited=!1),function(t,e,n){for(var r in t)n&&n.indexOf(r)>=0||(e[r]=t[r])}(t,n),t.onChange&&(this.onChange=t.onChange),t.onDone&&(this.onDone=t.onDone),t.onOpen&&(this.onOpen=t.onOpen),t.onClose&&(this.onClose=t.onClose);var r=t.color||t.colour;r&&this._setColor(r)}var i=n.parent;if(i&&n.popup&&!this._popupInited){var o=function(t){return e.openHandler(t)};this._events.add(i,"click",o),Lp(this._events,i,[" ","Spacebar","Enter"],o),this._popupInited=!0}else t.parent&&!n.popup&&this.show()}}},{key:"openHandler",value:function(t){if(this.show()){t&&t.preventDefault(),this.settings.parent.style.pointerEvents="none";var e=t&&t.type===Sp?this._domEdit:this.domElement;setTimeout((function(){return e.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:"closeHandler",value:function(t){var e=t&&t.type,n=!1;if(t)if(e===Cp||e===Ep){var r=(this.__containedEvent||0)+100;t.timeStamp>r&&(n=!0)}else Ap(t),n=!0;else n=!0;n&&this.hide()&&(this.settings.parent.style.pointerEvents="",e!==Cp&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:"movePopup",value:function(t,e){this.closeHandler(),this.setOptions(t),e&&this.openHandler()}},{key:"setColor",value:function(t,e){this._setColor(t,{silent:e})}},{key:"_setColor",value:function(t,e){if("string"==typeof t&&(t=t.trim()),t){e=e||{};var n=void 0;try{n=new xp(t)}catch(t){if(e.failSilently)return;throw t}if(!this.settings.alpha){var r=n.hsla;r[3]=1,n.hsla=r}this.colour=this.color=n,this._setHSLA(null,null,null,null,e)}}},{key:"setColour",value:function(t,e){this.setColor(t,e)}},{key:"show",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var t=this._toggleDOM(!0);return this._setPosition(),t}var e=function(t){var e=document.createElement("div");return e.innerHTML=t,e.firstElementChild}(this.settings.template||'<div class="picker_wrapper" tabindex="-1"><div class="picker_arrow"></div><div class="picker_hue picker_slider"><div class="picker_selector"></div></div><div class="picker_sl"><div class="picker_selector"></div></div><div class="picker_alpha picker_slider"><div class="picker_selector"></div></div><div class="picker_editor"><input aria-label="Type a color name or hex value"/></div><div class="picker_sample"></div><div class="picker_done"><button>Ok</button></div><div class="picker_cancel"><button>Cancel</button></div></div>');return this.domElement=e,this._domH=Tp(".picker_hue",e),this._domSL=Tp(".picker_sl",e),this._domA=Tp(".picker_alpha",e),this._domEdit=Tp(".picker_editor input",e),this._domSample=Tp(".picker_sample",e),this._domOkay=Tp(".picker_done button",e),this._domCancel=Tp(".picker_cancel button",e),e.classList.add("layout_"+this.settings.layout),this.settings.alpha||e.classList.add("no_alpha"),this.settings.editor||e.classList.add("no_editor"),this.settings.cancelButton||e.classList.add("no_cancel"),this._ifPopup((function(){return e.classList.add("popup")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:"hide",value:function(){return this._toggleDOM(!1)}},{key:"destroy",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:"_bindEvents",value:function(){var t=this,e=this,n=this.domElement,r=this._events;function i(t,e,n){r.add(t,e,n)}i(n,"click",(function(t){return t.preventDefault()})),kp(r,this._domH,(function(t,n){return e._setHSLA(t)})),kp(r,this._domSL,(function(t,n){return e._setHSLA(null,t,1-n)})),this.settings.alpha&&kp(r,this._domA,(function(t,n){return e._setHSLA(null,null,null,1-n)}));var o=this._domEdit;i(o,"input",(function(t){e._setColor(this.value,{fromEditor:!0,failSilently:!0})})),i(o,"focus",(function(t){var e=this;e.selectionStart===e.selectionEnd&&e.select()})),this._ifPopup((function(){var e=function(e){return t.closeHandler(e)};i(window,Cp,e),i(window,Ep,e),Lp(r,n,["Esc","Escape"],e);var o=function(e){t.__containedEvent=e.timeStamp};i(n,Cp,o),i(n,Ep,o),i(t._domCancel,"click",e)}));var s=function(e){t._ifPopup((function(){return t.closeHandler(e)})),t.onDone&&t.onDone(t.colour)};i(this._domOkay,"click",s),Lp(r,n,["Enter"],s)}},{key:"_setPosition",value:function(){var t=this.settings.parent,e=this.domElement;t!==e.parentNode&&t.appendChild(e),this._ifPopup((function(n){"static"===getComputedStyle(t).position&&(t.style.position="relative");var r=!0===n?"popup_right":"popup_"+n;["popup_top","popup_bottom","popup_left","popup_right"].forEach((function(t){t===r?e.classList.add(t):e.classList.remove(t)})),e.classList.add(r)}))}},{key:"_setHSLA",value:function(t,e,n,r,i){i=i||{};var o=this.colour,s=o.hsla;[t,e,n,r].forEach((function(t,e){(t||0===t)&&(s[e]=t)})),o.hsla=s,this._updateUI(i),this.onChange&&!i.silent&&this.onChange(o)}},{key:"_updateUI",value:function(t){if(this.domElement){t=t||{};var e=this.colour,n=e.hsla,r="hsl("+360*n[0]+", 100%, 50%)",i=e.hslString,o=e.hslaString,s=this._domH,a=this._domSL,l=this._domA,c=Tp(".picker_selector",s),h=Tp(".picker_selector",a),u=Tp(".picker_selector",l);b(0,c,n[0]),this._domSL.style.backgroundColor=this._domH.style.color=r,b(0,h,n[1]),w(0,h,1-n[2]),a.style.color=i,w(0,u,1-n[3]);var f=i,d=f.replace("hsl","hsla").replace(")",", 0)"),p="linear-gradient("+[f,d]+")";if(this._domA.style.background=p+", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em",!t.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,v=void 0;switch(g){case"rgb":v=e.printRGB(m);break;case"hsl":v=e.printHSL(m);break;default:v=e.printHex(m)}this._domEdit.value=v}this._domSample.style.color=o}function b(t,e,n){e.style.left=100*n+"%"}function w(t,e,n){e.style.top=100*n+"%"}}},{key:"_ifPopup",value:function(t,e){this.settings.parent&&this.settings.popup?t&&t(this.settings.popup):e&&e()}},{key:"_toggleDOM",value:function(t){var e=this.domElement;if(!e)return!1;var n=t?"":"none",r=e.style.display!==n;return r&&(e.style.display=n),r}}]),t}(),Rp=document.createElement("style");function Ip(t){if(Np[t])return Np[t];if(Np["chr"+t]){const e=Np["chr"+t];return Np[t]=e,e}{const i=(e=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),r=Math.round(255*Math.random()).toString(10),"rgb("+e+","+n+","+r+")");return Np[t]=i,i}var e,n,r}Rp.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:"";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 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gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:"";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:"";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(Rp),Mp.StyleElement=Rp;const Np={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};class Op{constructor(t){this.tracks=[],this.chordSets=[]}addChordSet(t){this.chordSets=this.chordSets.filter((e=>e.name!==t.name)),this.chordSets.push(t);let e=this.tracks.find((e=>t.trackName===e.name));e&&(e.chordSets=e.chordSets.filter((e=>e.name!==t.name)),e.chordSets.push(t)),e||(e=new Pp(t),this.tracks.push(e))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(t){return this.tracks.find((e=>t===e.name))}getChordSet(t){return this.chordSets.find((e=>t===e.name))}}class Pp{constructor(t){this.name=t.trackName,this.color=t.trackColor,this.visible=!0,this.chordSets=[t],this.id=("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const t=[];for(let e of this.chordSets)for(let n of e.chords)t.push(n);return t}}const Fp=Math.exp(5);class Dp{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(t,e){if(e=e||{},this.config=e,Dp.isInstalled()){this.parent=t,this.groupByTrack=!0===e.groupByTrack,this.chordManager=new Op(e);const n=document.createElement("div");n.className="igv-circview-container",t.appendChild(n),this.createControls(n),this.resetControlPanel();const r=document.createElement("div");r.className="igv-circview-circular-genome-view",n.appendChild(r),this.container=r,e.assembly&&this.setAssembly(e.assembly),this.width=e.width||500,this.height=e.height||500,this.setSize(this.width,this.height)}else console.error("JBrowse circular view is not installed")}createControls(t){const e=document.createElement("div");e.className="igv-circview-toolbar",t.appendChild(e),this.toolbar=e;const n=document.createElement("div");n.className="igv-circview-track-panel",t.appendChild(n),this.controlPanel=n,this.controlPanel.style.display="none";const r=document.createElement("div");r.className="igv-circview-toolbar-button-container",this.toolbar.appendChild(r),this.showControlsButton=document.createElement("div"),this.showControlsButton.className="igv-circview-button",r.appendChild(this.showControlsButton),this.showControlsButton.innerText="none"===this.controlPanel.style.display?"Show Controls":"Hide Controls",this.showControlsButton.addEventListener("click",(t=>{this.controlPanel.querySelectorAll("div").length>0&&("none"===this.controlPanel.style.display?(this.controlPanel.style.display="flex",t.target.innerText="Hide Controls"):(this.controlPanel.style.display="none",t.target.innerText="Show Controls"))}));let i=document.createElement("div");i.className="igv-circview-button",r.appendChild(i),i.innerText="Clear All",i.addEventListener("click",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(i=document.createElement("div"),i.className="igv-circview-button",r.appendChild(i),i.innerText="Close",i.addEventListener("click",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML="",this.controlPanel.appendChild(this.createGroupByCB());const t=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let e of t)this.addToControlPanel(e)}createGroupByCB(){const t=document.createElement("input");t.type="checkbox",t.id="groupByCB",t.style.width="1.4em",t.style.height="1.4em",t.checked=this.groupByTrack,t.onclick=t=>{this.groupByTrack=t.target.checked,this.resetControlPanel(),this.render()};const e=document.createElement("label");e.for="groupByCB",e.innerText="Group by track",e.style.color="black",e.style.paddingLeft="10px";const n=document.createElement("div");return n.style.width="100%",n.style.paddingTop="5px",n.style.paddingBottom="5px",n.style.background="rgb(216, 230, 234)",n.appendChild(t),n.appendChild(e),n}addToControlPanel(t){const e=document.createElement("div");this.controlPanel.appendChild(e);const n=document.createElement("div");n.className="igv-circview-button",e.appendChild(n),n.innerText=!0===t.visible?"Hide":"Show",n.addEventListener("click",(e=>{!0===t.visible?(this.hideChordSet(t.name),e.target.innerText="Show"):(this.showChordSet(t.name),e.target.innerText="Hide")}));const r=document.createElement("input"),i=t=>200*Math.log(t*Fp),o=document.createElement("div");o.className="igv-circview-button",o.innerHTML="&nbsp;&nbsp;&nbsp;&nbsp;",e.appendChild(o),o.style.backgroundColor=Bp(t.color,1);const s={parent:o,popup:"right",editorFormat:"rgb",color:t.color,onChange:({rgbaString:e})=>{o.style.backgroundColor=Bp(e,1),this.setColor(t.name,e),r.value=i(zp(t.color))}},a=new Mp(s);r.setAttribute("title","Adjust transparency of arcs"),r.type="range",r.style.width="100px",r.style.marginRight="10px",r.setAttribute("class","range"),r.setAttribute("min","0"),r.setAttribute("max","1000"),r.value=i(zp(t.color)),r.oninput=()=>{const e=(n=r.value,Math.exp(n/200)/Fp);var n;this.setColor(t.name,Bp(t.color,e)),a.setColor(t.color)},e.appendChild(r);const l=document.createElement("div");l.style.color="black",e.appendChild(l),l.innerText=l.title=t.name}setAssembly(t){const e=this.genomeId||jp();if(this.genomeId===e)return;this.chordManager.clearChords(),this.genomeId=e,this.chrNames=new Set(t.chromosomes.map((t=>Hp(t.name))));const n=[],r=[];for(let e of t.chromosomes){const t=Hp(e.name);r.push(e.color||Ip(t)),n.push({refName:t,uniqueId:t,start:0,end:e.bpLength})}this.assembly={name:t.name,sequence:{trackId:e,type:"ReferenceSequenceTrack",adapter:{type:"FromConfigSequenceAdapter",features:n}},refNameColors:r},this.render()}addChords(t,e={}){const n=e.name||e.track||"*",r=n.split(" ")[0].replaceAll("%20"," "),i={name:n.replaceAll("%20"," "),trackName:r,chords:t,color:e.color||"black",trackColor:e.trackColor||e.color||"black",visible:!0,id:e.id||jp()};this.chordManager.addChordSet(i),this.resetControlPanel(),this.render()}setSize(t,e){if(e=e||t,this.width=t,this.height=e,this.viewState){const n=this.viewState.session.view;n.setWidth(t),n.setHeight(e),n.setBpPerPx(n.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display="block"}hide(){this.parent.style.display="none"}get visible(){return"none"!==this.parent.style.display}set visible(t){this.parent.style.display=t?"block":"none"}hideChordSet(t){let e=this.getChordSet(t);e?(e.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(t){let e=this.getChordSet(t);e?(e.visible=!0,this.render()):console.warn(`No track with name: ${t}`)}deleteTrack(t){let e=this.tracks.findIndex((e=>t===e.name));e>=0&&this.tracks.splice(e,1),this.render()}getChordSet(t){return this.groupByTrack?this.chordManager.getTrack(t):this.chordManager.getChordSet(t)}setColor(t,e){const n=this.getChordSet(t);if(n){n.color=e;const t=n.id;for(let n of this.viewState.config.tracks)if(t===n.trackId){n.displays[0].renderer.strokeColor.set(e);break}}}render(){const{createViewState:t,JBrowseCircularGenomeView:e}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const n=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((t=>t.visible)),r=[],i=[];for(let t of n)r.push({trackId:t.id,name:t.name,assemblyNames:["forIGV"],type:"VariantTrack",adapter:{type:"FromConfigAdapter",features:t.chords}}),i.push(t.color);this.viewState=t({assembly:this.assembly,tracks:r});for(let t=0;t<n.length;t++)this.viewState.config.tracks[t].displays[0].renderer.strokeColor.set(i[t]);this.element=React.createElement(e,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const o=this.config.onChordClick||Vp;for(let t=0;t<n.length;t++)this.viewState.session.view.showTrack(this.viewState.config.tracks[t].trackId),o&&(this.viewState.pluginManager.jexl.addFunction("onChordClick",o),this.viewState.config.tracks[t].displays[0].onChordClick.set("jexl:onChordClick(feature, track, pluginManager)"))}}function Bp(t,e){const[n,r,i,o]=t.split(",");return`${n},${r},${i},${e})`}function zp(t){return t.startsWith("rgba(")?Number(t.split(",")[3].replace(")","")):1}function Hp(t){return t.startsWith("chr")?t.substring(3):t}function Vp(t,e,n){console.log(t)}function jp(){return("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}if("undefined"!=typeof document){function mv(t){for(let e of document.styleSheets)if(e=e.href?e.href.replace(/^.*[\\\/]/,""):"",e===t)return!0;return!1}mv("circular-view.css")||function(){const t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-circview-container {\n  z-index: 2048;\n  width: fit-content;\n  height: fit-content;\n  box-sizing: content-box;\n  color: dimgray;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  background-color: white;\n  border-color: dimgray;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n}\n\n.igv-circview-toolbar {\n  position: relative;\n  width: 100%;\n  height: 32px;\n  background-color: lightgrey;\n  border-bottom-style: solid;\n  border-bottom-color: dimgray;\n  border-bottom-width: thin;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n\n.igv-circview-toolbar-button-container {\n  height: 100%;\n  width: fit-content;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-circview-toolbar-button-container > div {\n  margin: 4px;\n}\n\n.igv-circview-track-panel {\n  z-index: 1024;\n  position: absolute;\n  top: 33px;\n  left: 0;\n  width: 100%;\n  height: fit-content;\n  border-bottom-style: solid;\n  border-bottom-color: dimgray;\n  border-bottom-width: thin;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n}\n.igv-circview-track-panel > div {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-circview-track-panel > div > div {\n  margin: 4px;\n}\n\n.igv-circview-swatch-button {\n  cursor: pointer;\n  padding: 5px;\n  width: 8px;\n  height: 8px;\n  border: 1px solid #8d8b8b;\n  border-radius: 16px;\n}\n\n.igv-circview-button {\n  cursor: pointer;\n  padding: 5px;\n  color: #444;\n  vertical-align: middle;\n  text-align: center;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  border: 1px solid #8d8b8b;\n  border-radius: 4px;\n  background: #efefef;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\n}\n\n.igv-circview-button:hover {\n  background: #efefef;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n.igv-circview-button:active {\n  color: #007bff;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n/*# sourceMappingURL=circular-view.css.map */\n',document.head.insertBefore(t,document.head.childNodes[document.head.childNodes.length-1])}()}const Up=t=>t.startsWith("chr")?t.substring(3):t;function qp(t){const e=[],n=[];for(let r of t.wgChromosomeNames){const i=t.getChromosome(r);n.push(tg(i.name)),e.push({name:i.name,bpLength:i.bpLength})}return e}function Wp(t,e,n,r){const i=mo.addAlpha("all"===n.chr?e.color:tg(n.chr),r),o=mo.addAlpha(e.color||"rgb(0,0,255)",r),s=e.name.replaceAll(" ","%20"),a="all"===n.chr?s:`${s}  ${n.chr}:${n.start}-${n.end}`;e.browser.circularView.addChords(t,{track:a,color:i,trackColor:o}),e.browser.circularViewVisible||(e.browser.circularViewVisible=!0)}class $p{constructor(t,e){let{minTLENPercentile:n,maxTLENPercentile:r}=e;this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===n?.1:n,this.up=void 0===r?99.5:r,this.isizes=[],this.compute(t)}compute(t){for(let r of t)if(r.isProperPair()){var e=Math.abs(r.fragmentLength);this.sumF+=e,this.sumF2+=e*e,this.isizes.push(e);var n=r.pairOrientation;if("string"==typeof n&&4===n.length)switch(""+n.charAt(0)+n.charAt(2)){case"FF":case"RR":this.ffCount++;break;case"FR":this.frCount++;break;case"RF":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation="ff":this.frCount/this.totalCount>.9?this.orienation="fr":this.rfCount/this.totalCount>.9&&(this.orienation="rf"),this.minTLEN=0===this.lp?0:Gp(this.isizes,this.lp),this.maxTLEN=Gp(this.isizes,this.up)}}function Gp(t,e){if(0!==t.length){var n=Math.floor(t.length*(e/100));return t.sort((function(t,e){return t-e})),t[n]}}class Zp extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type="alignment",void 0===t.alleleFreqThreshold&&(t.alleleFreqThreshold=.2),this.featureSource=new dp(t,this.browser),this.showCoverage=void 0===t.showCoverage||t.showCoverage,this.showAlignments=void 0===t.showAlignments||t.showAlignments,this.coverageTrack=new Xp(t,this),this.alignmentTrack=new Yp(t,this),this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.visibilityWindow=t.visibilityWindow||3e4,this.viewAsPairs=t.viewAsPairs,this.pairsSupported=!1!==t.pairsSupported,this.showSoftClips=t.showSoftClips,this.showAllBases=t.showAllBases,this.showInsertions=!1!==t.showInsertions,this.showMismatches=!1!==t.showMismatches,this.color=t.color,this.coverageColor=t.coverageColor,t.sort&&(Array.isArray(t.sort)?this.assignSort(t.sort[0]):this.assignSort(t.sort)),this.height=void 0!==t.height?t.height:300}set height(t){this._height=t,this.coverageTrack&&this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?t-this.coverageTrack.height:t)}get height(){return this._height}get minTemplateLength(){const t=void 0!==this.config.minTLEN?this.config.minTLEN:this.config.minFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.minTLEN:0}get maxTemplateLength(){const t=void 0!==this.config.maxTLEN?this.config.maxTLEN:this.config.maxFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.maxTLEN:1e3}sort(t){t=this.assignSort(t);for(let e of this.trackView.viewports)if(e.containsPosition(t.chr,t.position)){const n=e.cachedFeatures;n&&(Kp(t,n),e.repaint())}}assignSort(t){if(t.locus){const e=function(t){const e=t.split(":"),n=e[1].split("-"),r={chr:e[0],start:Number.parseInt(n[0].replace(/,/g,""))-1};return n.length>1?r.end=Number.parseInt(n[1].replace(/,/g,"")):r.end=r.start+1,r}(t.locus);t.chr=e.chr,t.position=e.start}else t.position--;return t.direction="ASC"===t.direction||!0===t.direction,t.chr=this.browser.genome.getChromosomeName(t.chr),this.sortObject=t,this.sortObject}async getFeatures(t,e,n,r,i){const o=await this.featureSource.getAlignments(t,e,n);if(o.paired&&!this._pairedEndStats&&!this.config.maxFragmentLength){const t=new $p(o.alignments,this.config);t.totalCount>99&&(this._pairedEndStats=t)}o.alignments=void 0;const s=this.sortObject;return s&&s.chr===t&&s.position>=e&&s.position<=n&&Kp(s,o),o}computePixelHeight(t){return(this.showCoverage?this.coverageTrack.height:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(t):0)+15}draw(t){Xo.fillRect(t.context,0,t.pixelTop,t.pixelWidth,t.pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),!0===this.showCoverage&&this.coverageTrack.height>0?(this.trackView.axisCanvas.style.display="block",this.coverageTrack.draw(t)):this.trackView.axisCanvas.style.display="none",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(t))}paintAxis(t,e,n){this.coverageTrack.paintAxis(t,e,this.coverageTrack.height)}contextMenuItemList(t){return this.alignmentTrack.contextMenuItemList(t)}popupData(t){return!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y<this.coverageTrack.height?this.coverageTrack.popupData(t):this.alignmentTrack.popupData(t)}clickedFeatures(t){let e;return e=!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y<this.coverageTrack.height?this.coverageTrack.getClickedObject(t):this.alignmentTrack.getClickedObject(t),e?[e]:void 0}menuItemList(){let t=[];t=t.concat(Wo.numericDataMenuItems(this.trackView)),t.push("<hr/>");const e=pe('<div class="igv-track-menu-category">');e.text("Color by:"),t.push({name:void 0,object:e,click:void 0,init:void 0});const n=[{key:"strand",label:"read strand"}];this.alignmentTrack.hasPairs&&(n.push({key:"firstOfPairStrand",label:"first-of-pair strand"}),n.push({key:"pairOrientation",label:"pair orientation"}),n.push({key:"tlen",label:"insert size (TLEN)"}),n.push({key:"unexpectedPair",label:"pair orientation & insert size (TLEN)"}));const r="tag"+(this.alignmentTrack.colorByTag?" ("+this.alignmentTrack.colorByTag+")":"");n.push({key:"tag",label:r});for(let e of n){const n=this.alignmentTrack.colorBy===e.key;t.push(this.colorByCB(e,n))}const i=()=>{if(!this.autoHeight){const t=15+(this.showCoverage?this.coverageTrack.height:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(t)}};t.push("<hr/>"),t.push({object:pe(qo("Show Coverage",this.showCoverage)),click:()=>{this.showCoverage=!this.showCoverage,i(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:pe(qo("Show Alignments",this.showAlignments)),click:()=>{this.showAlignments=!this.showAlignments,i(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push("<hr/>"),t.push({object:pe(qo("Show all bases",this.showAllBases)),click:()=>{this.showAllBases=!this.showAllBases,this.config.showAllBases=this.showAllBases,this.trackView.repaintViews()}}),t.push("<hr/>"),t.push({object:pe(qo("Show mismatches",this.showMismatches)),click:()=>{this.showMismatches=!this.showMismatches,this.config.showMismatches=this.showMismatches,this.trackView.repaintViews()}}),t.push({object:pe(qo("Show insertions",this.showInsertions)),click:()=>{this.showInsertions=!this.showInsertions,this.config.showInsertions=this.showInsertions,this.getCachedAlignmentContainers(),this.trackView.repaintViews()}}),t.push({object:pe(qo("Show soft clips",this.showSoftClips)),click:()=>{this.showSoftClips=!this.showSoftClips,this.config.showSoftClips=this.showSoftClips,this.featureSource.setShowSoftClips(this.showSoftClips);const t=this.getCachedAlignmentContainers();for(let e of t)e.setShowSoftClips(this.showSoftClips);this.trackView.repaintViews()}}),this.pairsSupported&&this.alignmentTrack.hasPairs&&(t.push("<hr/>"),t.push({object:pe(qo("View as pairs",this.viewAsPairs)),click:()=>{this.viewAsPairs=!this.viewAsPairs,this.config.viewAsPairs=this.viewAsPairs,this.featureSource.setViewAsPairs(this.viewAsPairs);const t=this.getCachedAlignmentContainers();for(let e of t)e.setViewAsPairs(this.viewAsPairs);this.trackView.repaintViews()}})),this.browser.circularView&&(this.alignmentTrack.hasPairs||this.alignmentTrack.hasSupplemental)&&(t.push("<hr/>"),this.alignmentTrack.hasPairs&&t.push({label:"Add discordant pairs to circular view",click:()=>{for(let t of this.trackView.viewports)this.addPairedChordsForViewport(t)}}),this.alignmentTrack.hasSupplemental&&t.push({label:"Add split reads to circular view",click:()=>{for(let t of this.trackView.viewports)this.addSplitChordsForViewport(t)}})),t.push("<hr/>");const o=pe('<div class="igv-track-menu-category">');return o.text("Display mode:"),t.push({name:void 0,object:o,click:void 0,init:void 0}),t.push({object:pe(qo("expand","EXPANDED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="EXPANDED",this.config.displayMode="EXPANDED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:pe(qo("squish","SQUISHED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="SQUISHED",this.config.displayMode="SQUISHED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t}colorByCB(t,e){return{name:void 0,object:pe(qo(t.label,e)),click:e=>{"tag"!==t.key?t.key===this.alignmentTrack.colorBy?(this.alignmentTrack.colorBy="none",this.config.colorBy="none",this.trackView.repaintViews()):(this.alignmentTrack.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews()):this.browser.inputDialog.present({label:"Tag Name",value:this.alignmentTrack.colorByTag?this.alignmentTrack.colorByTag:"",callback:t=>{t?(this.alignmentTrack.colorBy="tag",this.alignmentTrack.colorByTag=t,this.alignmentTrack.tagColors||(this.alignmentTrack.tagColors=new ju("Set1"))):(this.alignmentTrack.colorBy="none",this.alignmentTrack.colorByTag=""),this.trackView.repaintViews()}},e)},init:void 0}}getState(){const t=super.getState();return this.sortObject&&(t.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?"ASC":"DESC"}),t}getCachedAlignmentContainers(){return this.trackView.viewports.map((t=>t.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(t){this.coverageTrack.dataRange=t}get logScale(){return this.coverageTrack.logScale}set logScale(t){this.coverageTrack.logScale=t}get autoscale(){return this.coverageTrack.autoscale}set autoscale(t){this.coverageTrack.autoscale=t}addPairedChordsForViewport(t){const e=this.maxTemplateLength,n=[],r=t.referenceFrame;for(let i of t.cachedFeatures.allAlignments())i.end>=r.start&&i.start<=r.end&&(i.paired?i.end-i.start>e&&n.push(i):i.mate&&i.mate.chr&&(i.mate.chr!==i.chr||Math.max(i.fragmentLength)>e)&&n.push(i));Wp((t=>{const e=[];for(let n of t)if(n.paired)n.firstAlignment&&n.secondAlignment&&e.push({uniqueId:n.readName,refName:Up(n.firstAlignment.chr),start:n.firstAlignment.start,end:n.firstAlignment.end,mate:{refName:Up(n.secondAlignment.chr),start:n.secondAlignment.start,end:n.secondAlignment.end}});else{const t=n.mate;t&&t.chr&&t.position&&e.push({uniqueId:n.readName,refName:Up(n.chr),start:n.start,end:n.end,mate:{refName:Up(t.chr),start:t.position-1,end:t.position}})}return e})(n),this,r,.02)}addSplitChordsForViewport(t){const e=[],n=t.referenceFrame;for(let r of t.cachedFeatures.allAlignments()){const t=r.hasTag("SA");r.end>=n.start&&r.start<=n.end&&t&&e.push(r)}Wp((t=>{const e=t=>{const e=ff(t.tags().SA);let r=0;for(let i of e)i.start!==t.start&&n.push({uniqueId:`${t.readName}_${r++}`,refName:Up(t.chr),start:t.start,end:t.end,mate:{refName:Up(i.chr),start:i.start,end:i.start+i.lenOnRef}})},n=[];for(let n of t)n.paired?(e(n.firstAlignment),n.secondAlignment&&e(n.secondAlignment)):e(n);return n})(e),this,n,.02)}}class Xp{constructor(t,e){this.parent=e,this.featureSource=e.featureSource,this.height=void 0!==t.coverageTrackHeight?t.coverageTrackHeight:50,this.paintAxis=pp,this.top=0,this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max})}draw(t){const e=t.pixelTop;t.pixelHeight;const n=this.parent.browser.nucleotideColors;if(e>this.height)return;const r=t.context,i=t.features.coverageMap;let o;i.refSeq&&(o=i.refSeq.toUpperCase());const s=t.bpPerPixel,a=t.bpStart,l=a+t.pixelWidth*s+1;let c;c=this.parent.coverageColor?this.parent.coverageColor:void 0!==this.parent.color&&"function"!=typeof this.parent.color?mo.darkenLighten(this.parent.color,-35):"rgb(150, 150, 150)",Xo.setProperties(r,{fillStyle:c,strokeStyle:c});const h=Math.max(1,Math.ceil(1/s));for(let t=0,e=i.coverage.length;t<e;t++){const e=i.bpStart+t;if(e<a)continue;if(e>l)break;const n=i.coverage[t];if(!n)continue;const o=Math.round(n.total/this.dataRange.max*this.height),c=this.height-o,u=Math.floor((e-a)/s);Xo.fillRect(r,u,c,h,o)}if(o)for(let t=0,e=i.coverage.length;t<e;t++){const e=i.bpStart+t;if(e<a)continue;if(e>l)break;const c=i.coverage[t];if(!c)continue;const u=c.total/this.dataRange.max*this.height;let f=this.height-u;const d=Math.floor((e-a)/s),p=o[t];if(c.isMismatch(p)){Xo.setProperties(r,{fillStyle:n[p]}),Xo.fillRect(r,d,f,h,u);let t=0;for(let e of["A","C","T","G"]){const i=(c["pos"+e]+c["neg"+e])/this.dataRange.max*this.height;f=this.height-i-t,t+=i,Xo.setProperties(r,{fillStyle:n[e]}),Xo.fillRect(r,d,f,h,i)}}}}getClickedObject(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return;const n=Math.floor(t.genomicLocation),r=e.coverageMap,i=Math.floor(n-r.bpStart);return r.coverage[i]}popupData(t){const e=[],n=this.getClickedObject(t);if(n){const r=Math.floor(t.genomicLocation),i=t.viewport.referenceFrame;e.push(i.chr+":"+Se(1+r)),e.push({name:"Total Count",value:n.total});let o=n.posA+n.negA;o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posA+"+, "+n.negA+"- )"),e.push({name:"A",value:o}),o=n.posC+n.negC,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posC+"+, "+n.negC+"- )"),e.push({name:"C",value:o}),o=n.posG+n.negG,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posG+"+, "+n.negG+"- )"),e.push({name:"G",value:o}),o=n.posT+n.negT,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posT+"+, "+n.negT+"- )"),e.push({name:"T",value:o}),o=n.posN+n.negN,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posN+"+, "+n.negN+"- )"),e.push({name:"N",value:o}),e.push("<HR/>"),e.push({name:"DEL",value:n.del.toString()}),e.push({name:"INS",value:n.ins.toString()})}return e}}class Yp{constructor(t,e){this.parent=e,this.browser=e.browser,this.featureSource=e.featureSource,this.top=0===t.coverageTrackHeight?0:t.coverageTrackHeight+5,this.displayMode=t.displayMode||"EXPANDED",this.alignmentRowHeight=t.alignmentRowHeight||14,this.squishedRowHeight=t.squishedRowHeight||3,this.negStrandColor=t.negStrandColor||"rgba(150, 150, 230, 0.75)",this.posStrandColor=t.posStrandColor||"rgba(230, 150, 150, 0.75)",this.insertionColor=t.insertionColor||"rgb(138, 94, 161)",this.insertionTextColor=t.insertionTextColor||"white",this.showInsertionText=void 0!==t.showInsertionText&&!!t.showInsertionText,this.deletionColor=t.deletionColor||"black",this.deletionTextColor=t.deletionTextColor||"black",this.showDeletionText=void 0!==t.showDeletionText&&!!t.showDeletionText,this.skippedColor=t.skippedColor||"rgb(150, 170, 170)",this.pairConnectorColor=t.pairConnectorColor,this.smallTLENColor=t.smallTLENColor||t.smallFragmentLengthColor||"rgb(0, 0, 150)",this.largeTLENColor=t.largeTLENColor||t.largeFragmentLengthColor||"rgb(200, 0, 0)",this.pairOrientation=t.pairOrienation||"fr",this.pairColors={},this.pairColors.RL=t.rlColor||"rgb(0, 150, 0)",this.pairColors.RR=t.rrColor||"rgb(20, 50, 200)",this.pairColors.LL=t.llColor||"rgb(0, 150, 150)",this.colorBy=t.colorBy||"unexpectedPair",this.colorByTag=t.colorByTag?t.colorByTag.toUpperCase():void 0,this.bamColorTag=void 0===t.bamColorTag?"YC":t.bamColorTag,this.hideSmallIndels=t.hideSmallIndels,this.indelSizeThreshold=t.indelSizeThreshold||1,this.hasPairs=!1,this.hasSupplemental=!1}setTop(t,e){this.top=0===t.height||!1===e?0:5+t.height}computePixelHeight(t){if(t.packedAlignmentRows){return(t.hasDownsampledIntervals()?10:0)+("SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight)*t.packedAlignmentRows.length+5}return 0}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=i+o*r+1,a=this.parent.showSoftClips,l=this.parent.showAllBases,c=this.browser.nucleotideColors,h=e.packedAlignmentRows;n.save();let u=e.sequence;u&&(u=u.toUpperCase());let f=0,d=t.pixelTop;this.top&&n.translate(0,this.top);const p=d+t.pixelHeight;e.hasDownsampledIntervals()?(f=10,e.downsampledIntervals.forEach((function(t){var e=(t.start-i)/r,o=(t.end-i)/r;o-e>5&&(e+=1,o-=1),Xo.fillRect(n,e,2,o-e,3,{fillStyle:"black"})}))):f=0,this.alignmentsYOffset=f;const g="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;if(h){const t=h.length;for(let e=0;e<t;e++){const t=h[e],n=f+g*e,r=g<=4?g:g-2;if(n>p)break;if(!(n+r<d))for(let e of t.alignments)if(this.hasPairs=this.hasPairs||e.isPaired(),this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag("SA")),!(e.start+e.lengthOnRef<i)){if(e.start>s)break;!0!==e.hidden&&(e instanceof Qu?(m.call(this,e,n,r),v.call(this,e.firstAlignment,n,r),e.secondAlignment&&v.call(this,e.secondAlignment,n,r)):v.call(this,e,n,r))}}}function m(t,e,o){var a=this.getConnectorColor(t.firstAlignment),l=(t.connectingStart-i)/r,c=(t.connectingEnd-i)/r,h=e+o/2;t.connectingEnd<i||t.connectingStart>s||(t.mq<=0&&(a=mo.addAlpha(a,.15)),Xo.setProperties(n,{fillStyle:a,strokeStyle:a}),Xo.strokeLine(n,l,h,c,h))}function v(t,h,f){if(t.start+t.lengthOnRef<i||t.start>s)return;const d=a?t.blocks:t.blocks.filter((t=>"S"!==t.type));let p=this.getAlignmentColor(t);const m=p;t.mq<=0&&(p=mo.addAlpha(p,.15)),Xo.setProperties(n,{fillStyle:p,strokeStyle:m});const v=[];for(let t=0;t<d.length;t++){const e=d[t];if(!(t!==d.length-1&&d[t+1].start<i)&&(v.push(...b.call(this,e,t)),e.start+e.len>s))break}if(t.gaps){const e=h+f/2;for(let o of t.gaps){const t=(o.start-i)/r,s=(o.start+o.len-i)/r,a=s-t,l=o.len.toString(),c=6*l.length,u=t+a/2,f="D"===o.type?this.deletionColor:this.skippedColor;if(Xo.strokeLine(n,t,e,s,e,{strokeStyle:f,lineWidth:2}),this.showDeletionText&&o.len>1&&a>=c+8){const t=u-c/2;Xo.fillRect(n,t-1,h-1,c+2,12,{fillStyle:"white"}),Xo.fillText(n,l,t,h+10,{font:"normal 10px monospace",fillStyle:this.deletionTextColor})}}}if(t.insertions&&this.parent.showInsertions){let e=-1;for(let o of t.insertions){if(this.hideSmallIndels&&o.len<=this.indelSizeThreshold)continue;if(o.start<i)continue;if(o.start>s)break;const t=o.start-i,a=o.len.toString(),l=2+6*a.length,c=this.showInsertionText&&1!==o.len?Math.round(o.len/r):2,u=Math.max(Math.min(l,c),2),d=t/r-u/2;if(d-e>2){const t={fillStyle:this.insertionColor};Xo.fillRect(n,d-2,h,u+4,2,t),Xo.fillRect(n,d,h+2,u,f-4,t),Xo.fillRect(n,d-2,h+f-2,u+4,2,t),this.showInsertionText&&o.len>1&&c>l&&Xo.fillText(n,a,d+1,h+10,{font:"normal 10px monospace",fillStyle:this.insertionTextColor}),e=d}}}function b(s,a){const v=[],b=s.start-e.start,w=(s.start-i)/r,y=(s.start+s.len-i)/r,x=Math.max(1,y-w),_=100/r,k=Math.min(g/2,_/6),S="S"===s.type,C=t.mq<=0||this.highlightedAlignmentReadNamed===t.readName||S;let E=m;this.highlightedAlignmentReadNamed===t.readName?E="red":S&&(E="rgb(50,50,50)");const T=!0===t.strand&&a===d.length-1,A=!1===t.strand&&0===a;if(T|A){let t,e;T?(t=[w,y,y+k,y,w,w],e=[h,h,h+f/2,h+f,h+f,h]):A&&(t=[y,w,w-k,w,y,y],e=[h,h,h+f/2,h+f,h+f,h]),Xo.fillPolygon(n,t,e,{fillStyle:p}),C&&Xo.strokePolygon(n,t,e,{strokeStyle:E})}else Xo.fillRect(n,w,h,x,f,{fillStyle:p}),C&&(n.save(),n.strokeStyle=E,n.strokeRect(w,h,x,f),n.restore());if(S||l||this.parent.showMismatches&&u&&t.seq&&"*"!==t.seq){const e=t.seq?t.seq.toUpperCase():void 0,n=t.qual,a=s.seqOffset,d=Math.max(1,1/r);for(let t=0,p=s.len;t<p;t++){const p=(s.start+t-i)/r;if(p+d<0)continue;if(p>o)break;let g=e?e.charAt(a+t):"";const m=b+t>=0?u.charAt(b+t):"";if("="===g&&(g=m),"X"===g||m!==g||S||l){let e;if(!S&&void 0!==n&&n.length>a+t){e=Qp(n[a+t],c[g])}else e=c[g];e&&v.push({bbox:{x:p,y:h,width:d,height:f},baseColor:e,readChar:g})}}}return v}v.forEach((t=>{let{bbox:e,baseColor:i,readChar:o}=t;!function(t,e,n,r,i){var o;if(e<=.1&&n.height>=8){const e=Math.min(10,n.height);t.font=e+"px sans-serif",o=n.x+n.width/2,Xo.strokeText(t,i,o-t.measureText(i).width/2,e-1+n.y,{strokeStyle:r})}else Xo.fillRect(t,n.x,n.y,n.width,n.height,{fillStyle:r})}(n,r,e,i,o)}))}n.restore()}popupData(t){const e=this.getClickedObject(t);return e?e.popupData(t.genomicLocation):void 0}contextMenuItemList(t){const e=t.viewport,n=[],r=n=>{const r=this.parent.sortObject,i=!r||r.position!==Math.floor(t.genomicLocation)||!r.direction,o={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:n,direction:i};this.parent.sortObject=o,Kp(o,e.cachedFeatures),e.repaint()};n.push("<b>Sort by...</b>"),n.push({label:"&nbsp; base",click:()=>r("BASE")}),n.push({label:"&nbsp; read strand",click:()=>r("STRAND")}),n.push({label:"&nbsp; insert size",click:()=>r("INSERT_SIZE")}),n.push({label:"&nbsp; gap size",click:()=>r("GAP_SIZE")}),n.push({label:"&nbsp; chromosome of mate",click:()=>r("MATE_CHR")}),n.push({label:"&nbsp; mapping quality",click:()=>r("MQ")}),n.push({label:"&nbsp; read name",click:()=>r("READ_NAME")}),n.push({label:"&nbsp; aligned read length",click:()=>r("ALIGNED_READ_LENGTH")}),n.push({label:"&nbsp; tag",click:()=>{const n=this.parent.sortObject,r=!n||n.position!==Math.floor(t.genomicLocation)||!n.direction,i={label:"Tag Name",value:this.sortByTag?this.sortByTag:"",callback:n=>{if(n){const i={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:"TAG",tag:n,direction:r};this.sortByTag=n,this.parent.sortObject=i,Kp(i,e.cachedFeatures),e.repaint()}}};this.browser.inputDialog.present(i,t.event)}}),n.push("<hr/>");const i=this.getClickedObject(t);if(i){const e=this.parent.showSoftClips,r="function"==typeof i.alignmentContaining?i.alignmentContaining(t.genomicLocation,e):i;r&&(r.isPaired()&&r.isMateMapped()&&n.push({label:"View mate in split screen",click:()=>{if(r.mate){const e=t.viewport.referenceFrame;if(this.browser.genome.getChromosome(r.mate.chr)){this.highlightedAlignmentReadNamed=r.readName;const t=e.end-e.start,n=r.mate.position-t/2,i=r.mate.position+t/2;this.browser.addMultiLocusPanel(r.mate.chr,n,i,e)}else this.browser.alert.present(`Reference does not contain chromosome: ${r.mate.chr}`)}},init:void 0}),n.push({label:"View read sequence",click:()=>{const t=r.seq;t&&"*"!==t?this.browser.alert.present(t):this.browser.alert.present("Read sequence: *")}}),Os()&&n.push({label:"Copy read sequence",click:async()=>{const t=r.seq;try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),n.push("<hr/>"))}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&n.push({label:"Add discordant pairs to circular view",click:()=>{this.parent.addPairedChordsForViewport(e)}}),this.hasSupplemental&&n.push({label:"Add split reads to circular view",click:()=>{this.parent.addSplitChordsForViewport(e)}}),n.push("<hr/>")),n}getClickedObject(t){const e=t.viewport,n=t.y,r=t.genomicLocation,i=this.parent.showSoftClips;let o=e.cachedFeatures;if(!o||0===o.length)return;let s=o.packedAlignmentRows,a=o.downsampledIntervals;const l="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let c=Math.floor((n-this.top-this.alignmentsYOffset)/l);if(c<0){for(let t=0;t<a.length;t++)if(a[t].start<=r&&a[t].end>=r)return a[t]}else if(c<s.length){const t=s[c].alignments.filter((t=>t.containsLocation(r,i)));if(t.length>0)return t[0]}}getConnectorColor(t){if(this.pairConnectorColor)return this.pairConnectorColor;switch(this.colorBy){case"strand":case"firstOfPairStrand":case"pairOrientation":case"tag":return this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:"rgb(200, 200, 200)";default:return this.getAlignmentColor(t)}}getAlignmentColor(t){let e="rgb(185, 185, 185)";this.parent.color&&(e="function"==typeof this.parent.color?this.parent.color(t):this.parent.color);const n=this.colorBy;switch(n){case"strand":e=t.strand?this.posStrandColor:this.negStrandColor;break;case"firstOfPairStrand":t instanceof Qu?e=t.firstOfPairStrand()?this.posStrandColor:this.negStrandColor:t.isPaired()&&(t.isFirstOfPair()?e=t.strand?this.posStrandColor:this.negStrandColor:t.isSecondOfPair()?e=t.strand?this.negStrandColor:this.posStrandColor:console.error("ERROR. Paired alignments are either first or second."));break;case"unexpectedPair":case"pairOrientation":if(this.pairOrientation&&t.pairOrientation){const n=Jp[this.pairOrientation];if(n){const r=this.pairColors[n[t.pairOrientation]];if(r){e=r;break}}}if("pairOrientation"===n)break;case"tlen":case"fragmentLength":t.mate&&t.isMateMapped()&&(t.mate.chr!==t.chr?e=tg(t.mate.chr):this.parent.minTemplateLength&&Math.abs(t.fragmentLength)<this.parent.minTemplateLength?e=this.smallTLENColor:this.parent.maxTemplateLength&&Math.abs(t.fragmentLength)>this.parent.maxTemplateLength&&(e=this.largeTLENColor));break;case"tag":const r=t.tags()[this.colorByTag];void 0!==r&&(this.bamColorTag===this.colorByTag?e="rgb("+r+")":(this.tagColors||(this.tagColors=new ju("Set1")),e=this.tagColors.getColor(r)))}return e}}function Kp(t,e){const n=t.direction;for(let n of e.packedAlignmentRows)n.updateScore(t,e);e.packedAlignmentRows.sort((function(t,e){const r=t.score>e.score?1:t.score<e.score?-1:0;return!0===n?r:-r}))}function Qp(t,e){let n;return n=t<5?.1:Math.max(.1,Math.min(1,.1+.9*(t-5)/15)),n=Math.round(10*n)/10,n<1&&(e=mo.addAlpha(e,n)),e}const Jp={fr:{F1R2:"LR",F2R1:"LR",F1F2:"LL",F2F1:"LL",R1R2:"RR",R2R1:"RR",R1F2:"RL",R2F1:"RL"},rf:{R1F2:"LR",R2F1:"LR",R1R2:"LL",R2R1:"LL",F1F2:"RR",F2F1:"RR",F1R2:"RL",F2R1:"RL"},ff:{F2F1:"LR",R1R2:"LR",F2R1:"LL",R1F2:"LL",R2F1:"RR",F1R2:"RR",R2R1:"RL",F1F2:"RL"}};function tg(t){if(eg[t])return eg[t];if(eg["chr"+t]){const e=eg["chr"+t];return eg[t]=e,e}{const e=mo.randomRGB(0,255);return eg[t]=e,e}}const eg={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0)",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};let ng,rg;class ig extends Ca{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.$multiLocusCloseButton=pe("<div>",{class:"igv-multi-locus-close-button"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(ye("times-circle")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=pe("<div>",{class:"igv-multi-locus-ruler-label"}),this.$viewport.append(this.$rulerLabel),this.$rulerLabel.click((async()=>{await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=pe("<div>",{class:"igv-ruler-tooltip"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=pe("<div>"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Ku(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(ya.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(t){this.$rulerLabel.get(0).innerHTML="",this.$rulerLabel.get(0).style.backgroundColor=tg(this.referenceFrame.chr),this.$rulerLabel.get(0).appendChild((()=>{const e=`<div>${this.referenceFrame.getMultiLocusLabel(t)}</div>`;return document.createRange().createContextualFragment(e).firstChild})()),this.$rulerLabel.show(),this.$multiLocusCloseButton.show()}presentLocusLabel_Square_Dot(t){this.$rulerLabel.get(0).innerHTML="",this.$rulerLabel.get(0).appendChild((()=>{const t=`<div>\n                                <?xml version="1.0" encoding="UTF-8"?>\n                                <svg width="14px" height="14px" viewBox="0 0 89 89" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n                                    <g>\n                                        <circle id="Oval" fill="${tg(this.referenceFrame.chr)}" cx="44.5" cy="44.5" r="44.5"></circle>\n                                    </g>\n                                </svg>\n                            </div>`;return document.createRange().createContextualFragment(t).firstChild})()),this.$rulerLabel.get(0).appendChild((()=>{const e=`<div>${this.referenceFrame.getMultiLocusLabel(t)}</div>`;return document.createRange().createContextualFragment(e).firstChild})()),this.$rulerLabel.show(),this.$multiLocusCloseButton.show()}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(t){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===t){const t=this.browser.referenceFrameList.indexOf(this.referenceFrame),e=`click${this.namespace}`;this.$viewport.on(e,(e=>{const{x:n}=we(e,this.$viewport.get(0)),r=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(n));let i;const{chr:o}=this.browser.genome.getChromosomeCoordinate(r);if(1===this.browser.referenceFrameList.length)i=o;else{let e=this.browser.referenceFrameList.map((t=>{let{locusSearchString:e}=t;return e}));e[t]=o,i=e.join(" ")}this.browser.search(i)})),this.$viewport.get(0).style.cursor="pointer"}else this.$viewport.get(0).style.cursor="default"}mouseMove(t){if(!0===this.browser.cursorGuideVisible){void 0===rg?(rg=this,this.$tooltip.show()):rg.guid!==this.guid?(rg.$tooltip&&rg.$tooltip.hide(),this.$tooltip.show(),rg=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:e}=we(t,this.$viewport.get(0)),{start:n,bpPerPixel:r}=this.referenceFrame,i=Math.round(.5+n+Math.max(0,e)*r);this.$tooltipContent.text(Se(i));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:s}=this.$viewport.get(0).getBoundingClientRect();this.$tooltip.css({left:`${uo(e,0,s-o)}px`}),clearTimeout(ng),ng=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4)}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class og extends Ca{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.canvas=document.createElement("canvas"),this.canvas.className="igv-ideogram-canvas",this.$content.append(pe(this.canvas)),this.ideogram_ctx=this.canvas.getContext("2d"),this.addMouseHandlers()}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(t){this.boundClickHandler=function(t){const{xNormalized:e,width:n}=we(t,this.ideogram_ctx.canvas),{bpLength:r}=this.browser.genome.getChromosome(this.referenceFrame.chr),i=this.referenceFrame.bpPerPixel*n/r;let o=e;o-i/2<0&&(o=i/2);o+i/2>1&&(o=1-i/2);const s=Math.round((o-i/2)*r),a=Math.round((o+i/2)*r);this.referenceFrame.start=s,this.referenceFrame.end=a,this.referenceFrame.bpPerPixel=(a-s)/n,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),t.addEventListener("click",this.boundClickHandler)}setWidth(t){this.$viewport.width(t)}drawSVGWithContext(t,e,n,r,i,o,s){t.saveWithTranslationAndClipRect(r,i,o,e,n,s),this.trackView.track.draw({context:t,referenceFrame:this.referenceFrame,pixelWidth:e,pixelHeight:n}),t.restore()}repaint(){this.draw({referenceFrame:this.referenceFrame})}draw(t){let{referenceFrame:e}=t;Xo.configureHighDPICanvas(this.ideogram_ctx,this.$viewport.width(),this.$viewport.height()),this.trackView.track.draw({context:this.ideogram_ctx,referenceFrame:e,pixelWidth:this.$viewport.width(),pixelHeight:this.$viewport.height()})}startSpinner(){}stopSpinner(){}}function sg(t,e,n,r){if("ruler"===t.track.type)return new ig(t,e,n,r);if("ideogram"===t.track.id)return new og(t,e,n,r);return new Ca(t,e,n,r)}const ag={textAlign:"start",textBaseline:"bottom",strokeStyle:"black",fillStyle:"black"};class lg{constructor(t,e,n,r){this.guid=be(),this.trackView=t,this.browser=t.browser,this.viewport=ge({class:"igv-viewport"}),e.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement("canvas"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext("2d"),this.trackScrollDelta=0,this.contentTop=0,this.setWidth(r),!1===this.browser.showSampleNames&&this.hide(),this.addMouseHandlers()}checkCanvas(){const t=window.devicePixelRatio,e=this.viewport.clientHeight,n=this.browser.sampleNameViewportWidth;if(this.canvas.width!==n*t||this.canvas.height!==e*t){const r=this.canvas;r.width=n*t,r.height=e*t,r.style.width=`${n}px`,r.style.height=`${e}px`,this.ctx=this.canvas.getContext("2d"),this.ctx.scale(t,t)}}setTop(t){if("function"==typeof this.trackView.track.getSamples){this.contentTop=t;const e=this.trackView.track.getSamples();this.repaint(e)}}setWidth(t){this.viewport.innerWidth=t,this.checkCanvas()}show(){this.viewport.style.display="block"}hide(){this.viewport.style.display="none"}async repaint(t){this.checkCanvas(),this.draw({context:this.ctx,samples:t})}draw(t){let{context:e,samples:n}=t;if(!n||0===n.names.length)return;!function(t,e,n){let{textAlign:r,textBaseline:i,strokeStyle:o,fillStyle:s}=e;const a=Math.min(n,10);t.font=`${a}px sans-serif`,t.textAlign=r,t.textBaseline=i,t.fillStyle=s}(e,ag,n.height);e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=function(t){const{r:e,g:n,b:r}=Hu[t];return`rgb(${e},${n},${r})`}("lead");const r=this.viewport.getBoundingClientRect().height;let i=(n.yOffset||0)+this.contentTop;for(let t of n.names){if(i>r)break;if(i+n.height>0){const r=t,o=cg(e,r,i,n.height);e.fillText(r,4,o)}i+=n.height}}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;if("function"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples(),i=0,{width:o,height:s}=this.viewport.getBoundingClientRect(),a=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_sample_names_guid_${be()}`;t.saveWithTranslationAndClipRect(a,n,r+i,o,s,-i),this.draw({context:t,samples:e}),t.restore()}}addMouseHandlers(){this.addViewportContextMenuHandler(this.viewport)}removeMouseHandlers(){this.removeViewportContextMenuHandler(this.viewport)}addViewportContextMenuHandler(t){this.boundContextMenuHandler=function(t){t.preventDefault(),t.stopPropagation();const e={label:"Name Panel Width",value:this.browser.sampleNameViewportWidth,callback:t=>{this.browser.sampleNameViewportWidth=parseInt(t);for(let{sampleNameViewport:t}of this.browser.trackViews)t.setWidth(this.browser.sampleNameViewportWidth);this.browser.layoutChange()}};this.browser.inputDialog.present(e,t)}.bind(this),t.addEventListener("contextmenu",this.boundContextMenuHandler)}removeViewportContextMenuHandler(t){t.removeEventListener("contextmenu",this.boundContextMenuHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function cg(t,e,n,r){return n+r-function(t,e,n){const{actualBoundingBoxAscent:r,actualBoundingBoxDescent:i}=t.measureText(e);return(n-(r+i))/2}(t,e,r)}const hg=function(t){this.popover=ge({class:"igv-menu-popup"}),t.appendChild(this.popover);const e=ge({class:"igv-menu-popup-header"});this.popover.appendChild(e),_e(e,(()=>this.hide())),this.popoverContent=ge(),this.popover.appendChild(this.popoverContent),bo(this.popover,e),e.addEventListener("click",(t=>{t.stopPropagation(),t.preventDefault()})),this.hide()};hg.prototype.hide=function(){this.popover.style.display="none"},hg.prototype.presentMenuList=function(t){if(ug(),t.length>0){this.popoverContent.innerHTML="",t=Wo.trackMenuItemListHelper(t,this);for(let e of t){e.init&&e.init();let n=e.object;0===t.indexOf(e)&&n.removeClass("igv-track-menu-border-top"),n.hasClass("igv-track-menu-border-top")||n.hasClass("igv-menu-popup-check-container")||n.is("div")&&n.addClass("igv-menu-popup-shim"),this.popoverContent.appendChild(n.get(0))}this.popover.style.display="flex";const{width:e}=this.popover.getBoundingClientRect();this.popover.style.left=-e+"px",this.popover.style.top="0px"}},hg.prototype.presentTrackContextMenu=function(t,e){this.popoverContent.innerHTML="";const n=(r=e,i=this.popover,r.map((t=>{let e;if("string"==typeof t&&"<hr/>"===t)e=document.createElement("hr");else if("string"==typeof t)e=ge({class:"context-menu"}),e.innerHTML=t;else if("Node"==typeof t)e=t;else{if("function"==typeof t.init&&t.init(),"checkbox"===t.type)e=qo("Show all bases",t.value);else if("color"===t.type){const n=new xs({parent:i.parentElement,width:364});n.configure(void 0,{color:e=>t.click(e)}),e=ge({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);const r=t=>{n.show(),me(i),t.preventDefault(),t.stopPropagation()};e.addEventListener("click",r),e.addEventListener("touchend",r),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}else e=ge({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);if(t.click&&"color"!==t.type){function o(e){t.click(),me(i),e.preventDefault(),e.stopPropagation()}e.addEventListener("click",o),e.addEventListener("touchend",o),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}}return{el:e,init:t.init}})));var r,i;for(let{el:t}of n)this.popoverContent.appendChild(t);!function(t,e){e.style.display="flex";const{x:n,y:r}=we(t,e.parentNode),{width:i}=e.getBoundingClientRect(),o=n+i,{width:s}=e.parentNode.getBoundingClientRect();e.style.left=`${o>s?n-(o-s):n}px`,e.style.top=`${r}px`}(t,this.popover)},hg.prototype.dispose=function(){this.popoverContent.innerHTML="",this.popover.innerHTML="",Object.keys(this).forEach((function(t){this[t]=void 0}))};const ug=()=>{const t=document.querySelectorAll(".igv-menu-popup");for(let e=0;e<t.length;e++)t[e].style.display="none"},fg=new Set(["ruler","sequence","ideogram"]),dg=new Set(["ruler","sequence","ideogram"]);class pg{constructor(t,e,n){this.browser=t,this.track=n,n.trackView=this,this.addDOMToColumnContainer(t,e,t.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(t,e,n){this.axis=this.createAxis(t,this.track),this.viewports=[];const r=t.calculateViewportWidth(n.length),i=e.querySelectorAll(".igv-column");for(let t=0;t<i.length;t++){const e=sg(this,i[t],n[t],r);this.viewports.push(e)}this.sampleNameViewport=new lg(this,t.columnContainer.querySelector(".igv-sample-name-column"),void 0,t.sampleNameViewportWidth),this.createTrackScrollbar(t),this.createTrackDragHandle(t),this.createTrackGearPopup(t)}createAxis(t,e){const n=ge();if(t.columnContainer.querySelector(".igv-axis-column").appendChild(n),n.style.height=`${e.height}px`,"function"==typeof e.paintAxis){e.dataRange&&n.addEventListener("click",(()=>{t.dataRangeDialog.configure(this),t.dataRangeDialog.present(pe(t.columnContainer))}));const{width:r,height:i}=n.getBoundingClientRect();this.axisCanvas=document.createElement("canvas"),this.axisCanvas.style.width=`${r}px`,this.axisCanvas.style.height=`${i}px`,n.appendChild(this.axisCanvas)}return n}resizeAxisCanvas(t,e){this.axis.style.width=`${t}px`,this.axis.style.height=`${e}px`,"function"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${t}px`,this.axisCanvas.style.height=`${e}px`)}removeDOMFromColumnContainer(){this.boundAxisClickHander&&this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.$viewport.remove();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;!function(t,e,n,r,i){if("function"==typeof e.paintAxis){const{y:o,width:s,height:a}=n.getBoundingClientRect(),l=`${(e.name||e.id).replace(/\W/g,"")}_axis_guid_${be()}`;t.saveWithTranslationAndClipRect(l,r,o+i,s,a,0),e.paintAxis(t,s,a),t.restore()}}(t,this.track,this.axisCanvas,n,r);const{width:i}=this.axis.getBoundingClientRect(),{y:o}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let s={deltaX:i+n,deltaY:o+r};for(let e of this.viewports){e.renderSVGContext(t,s);const{width:n}=e.$viewport.get(0).getBoundingClientRect();s.deltaX+=n}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(t,s)}dataRange(){return this.track.dataRange?this.track.dataRange:void 0}setDataRange(t,e){void 0!==t&&(this.track.dataRange.min=t),void 0!==e&&(this.track.dataRange.max=e),this.track.autoscale=!1,this.repaintViews()}presentColorPicker(t){if(!1===dg.has(this.track.type)){const e=[],n=this.track.color||this.track.defaultColor;ke(n)&&e.push(n),this.track.altColor&&ke(this.track.altColor)&&e.push(this.track.altColor);const r=e.map((t=>t.startsWith("#")?t:t.startsWith("rgb(")?mo.rgbToHex(t):mo.colorNameToHex(t))),i={color:t=>{this.track.color=t,this.repaintViews()},altColor:t=>{this.track.altColor=t,this.repaintViews()}};this.browser.genericColorPicker.configure(r,i),this.browser.genericColorPicker.setActiveColorHandler(t),this.browser.genericColorPicker.show()}}setTrackHeight(t,e){e||(this.track.minHeight&&(t=Math.max(this.track.minHeight,t)),this.track.maxHeight&&(t=Math.min(this.track.maxHeight,t))),this.track.height=t,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),"function"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:e}of this.viewports)e.height(t);if(this.sampleNameViewport.viewport.style.height=`${t}px`,"function"!=typeof this.track.computePixelHeight)for(let e of this.viewports)e.setContentHeight(t);this.repaintViews(),!1===fg.has(this.track.type)&&this.updateScrollbar(),this.dragHandle.style.height=`${t}px`,this.gearContainer.style.height=`${t}px`}updateScrollbar(){const t=this.viewports[0].$viewport.height();this.outerScroll.style.height=`${t}px`;const e=gg(this.viewports),n=Math.round(t/e*t);e>t?(this.innerScroll.style.display="block",this.innerScroll.style.height=`${n}px`):this.innerScroll.style.display="none"}moveScroller(t){const e=pe(this.innerScroll).position().top+t,n=Math.min(Math.max(0,e),this.outerScroll.clientHeight-this.innerScroll.clientHeight);pe(this.innerScroll).css("top",`${n}px`);const r=gg(this.viewports),i=-Math.round(n*(r/this.viewports[0].$viewport.height()));for(let t of this.viewports)t.setTop(i);this.sampleNameViewport.trackScrollDelta=t,this.sampleNameViewport.setTop(i)}isLoading(){for(let t of this.viewports)if(t.isLoading())return!0}repaintViews(){for(let t of this.viewports)t.isVisible()&&t.repaint();"function"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSamples()}repaintSamples(){if("function"==typeof this.track.getSamples){const t=this.track.getSamples();this.sampleNameViewport.repaint(t)}}setTrackLabelName(t){this.viewports.forEach((e=>e.setTrackLabel(t)))}resize(t){for(let e of this.viewports)e.setWidth(t)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const t=this.viewports.filter((t=>t.isVisible()));if(t.forEach((t=>t.shift())),this.browser.dragObject)return;const e=t.filter((t=>t.needsRepaint())).filter((t=>t.checkZoomIn())),n=e.filter((t=>t.needsReload()));for(let t of n)await t.loadFeatures();if(this.disposed)return;if(this.track&&"function"==typeof this.track.variantRowCount&&n.length>0){let t=0;for(let e of this.viewports)e.featureCache&&e.featureCache.features&&(t=Math.max(t,e.featureCache.features.reduce(((t,e)=>Math.max(t,e.row||0)),0)));if(this.track.nVariantRows!==t+1){this.track.variantRowCount(t+1);for(let t of this.viewports)t.checkContentHeight()}}if(this.track.autoscale){let e=[];for(let n of t){const t=n.referenceFrame,r=t.start,i=r+t.toBP(pe(n.contentDiv).width());if(n.featureCache&&n.featureCache.features)if("function"==typeof n.featureCache.features.getMax){const t=n.featureCache.features.getMax(r,i);e.push({value:t})}else e=e.concat(Uo(n.featureCache.features,r,i))}"function"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(e):this.track.dataRange=Es(e)}const r=this.track.autoscale||this.track.autoscaleGroup||"ruler"===this.track.type;for(let n of t)e.includes(n)?n.repaint():r&&n.refresh();this.adjustTrackHeight(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let t of this.viewports)t.clearCache()}updateRulerViewportLabels(){const t=this.browser.calculateViewportWidth(this.viewports.length);for(let e of this.viewports)"ruler"===this.track.type&&(this.viewports.length>1?e.presentLocusLabel(t):e.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let t=[];const e=this.viewports.filter((t=>t.isVisible()));for(let n of e){const e=n.referenceFrame,{chr:r,start:i,bpPerPixel:o}=n.referenceFrame,s=i+e.toBP(pe(n.contentDiv).width());if((!n.featureCache||!n.featureCache.containsRange(r,i,s,o))&&await n.loadFeatures(),n.featureCache&&n.featureCache.features)if("function"==typeof n.featureCache.features.getMax){const e=n.featureCache.features.getMax(i,s);t.push({value:e})}else{const e="function"==typeof n.featureCache.queryFeatures?n.featureCache.queryFeatures(r,i,s):Uo(n.featureCache.features,i,s);t=t.concat(e)}}return t}checkContentHeight(){for(let t of this.viewports)t.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var t=gg(this.viewports);if(this.track.autoHeight?this.setTrackHeight(t,!1):this.track.paintAxis&&this.paintAxis(),!1===fg.has(this.track.type)){const t=this.viewports[0].getContentTop(),e=this.viewports.map((t=>t.getContentHeight())),n=Math.min(...e),r=Math.min(0,this.viewports[0].$viewport.height()-n);if(t<r)for(let t of this.viewports)t.$content.css("top",`${r}px`);this.updateScrollbar()}}createTrackScrollbar(t){const e=ge();if(t.columnContainer.querySelector(".igv-scrollbar-column").appendChild(e),e.style.height=`${this.track.height}px`,this.outerScroll=e,!1===fg.has(this.track.type)){const n=ge();e.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){const e="ideogram"===this.track.type||"ruler"===this.track.type?"igv-track-drag-shim":"igv-track-drag-handle";this.dragHandle=ge({class:e}),t.columnContainer.querySelector(".igv-track-drag-column").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){this.gearContainer=ge(),t.columnContainer.querySelector(".igv-gear-menu-column").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu||(this.gear=ge(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(ye("cog")),this.trackGearPopup=new hg(this.gear),this.addTrackGearMouseHandlers())}addAxisEventListener(t){this.boundAxisClickHander=function(t){this.browser.dataRangeDialog.configure(this),this.browser.dataRangeDialog.present(pe(this.browser.columnContainer))}.bind(this),t.addEventListener("click",this.boundAxisClickHander)}removeAxisEventListener(t){t.removeEventListener("click",this.boundAxisClickHander)}addTrackScrollMouseHandlers(t){this.boundTrackScrollMouseDownHandler=function(e){e.stopPropagation();const{y:n}=ve(e);pe(this.innerScroll).data("yDown",n.toString()),this.boundColumnContainerMouseMoveHandler=function(t){t.stopPropagation();const{y:e}=ve(t);this.moveScroller(e-parseInt(pe(this.innerScroll).data("yDown"))),pe(this.innerScroll).data("yDown",e.toString())}.bind(this),t.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener("mousedown",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(e){t.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler)}.bind(this),t.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===fg.has(this.track.type)&&(this.innerScroll.removeEventListener("mousedown",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(t){if("ideogram"===this.track.id||"ruler"===this.track.id);else{let e;function n(n){n.preventDefault(),e=n.target,e.classList.add("igv-track-drag-handle-hover"),t.startTrackDrag(this)}function r(n){t.endTrackDrag(),e&&n.target!==e&&e.classList.remove("igv-track-drag-handle-hover"),e=void 0}function i(n){n.preventDefault(),void 0===e&&n.target.classList.add("igv-track-drag-handle-hover"),t.updateTrackDrag(this)}function o(t){t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")}this.boundTrackDragMouseDownHandler=n.bind(this),this.dragHandle.addEventListener("mousedown",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=r.bind(this),document.addEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=i.bind(this),this.dragHandle.addEventListener("mouseenter",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener("mouseout",(t=>{t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")})),this.boundTrackDragMouseOutHandler=o.bind(this),this.dragHandle.addEventListener("mouseout",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){"ideogram"===this.track.id||"ruler"===this.track.id||(this.dragHandle.removeEventListener("mousedown",this.boundTrackDragMouseDownHandler),document.removeEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener("mouseup",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener("mouseout",this.boundTrackDragMouseOutHandler))}addTrackGearMouseHandlers(){if(!0===this.track.ignoreTrackMenu);else{function t(t){t.preventDefault(),t.stopPropagation(),this.trackGearPopup.presentMenuList(Wo.trackMenuItemList(this))}this.boundTrackGearClickHandler=t.bind(this),this.gear.addEventListener("click",this.boundTrackGearClickHandler)}}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener("click",this.boundTrackGearClickHandler)}dispose(){this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.dispose();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),"function"==typeof this.track.dispose&&this.track.dispose();for(let t of Object.keys(this))this[t]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if("function"==typeof this.track.paintAxis){const{width:t,height:e}=this.axisCanvas.getBoundingClientRect(),n=window.devicePixelRatio||1;this.axisCanvas.height=n*e,this.axisCanvas.width=n*t;const r=this.axisCanvas.getContext("2d");r.scale(n,n),this.track.paintAxis(r,t,e)}}}function gg(t){const e=t.map((t=>t.getContentHeight()));return Math.max(...e)}const mg={getTissueInfo:function(t,e){let n=(e=e||"https://gtexportal.org/rest/v1")+"/dataset/tissueInfo?datasetId="+(t=t||"gtex_v8");return Eo.loadJson(n,{})},trackConfiguration:function(t,e){return{type:"eqtl",sourceType:"gtex-ws",url:(e=e||"https://gtexportal.org/rest/v1")+"/association/singleTissueEqtlByLocation",tissueSiteDetailId:t.tissueSiteDetailId,name:t.tissueSiteDetailId.split("_").join(" "),visibilityWindow:25e4}}};function vg(t,e,n){let r=(t.start-e)/n,i=(t.end-e)/n,o=i-r;return o<3&&(o=3,r-=1.5),{px:r,px1:i,pw:o}}function bg(t,e,n,r,i,o){try{i.save(),i.fillStyle=this.defaultColor,i.strokeStyle=this.defaultColor;const r=yg.call(this,t);let s,a;i.fillStyle=r,i.strokeStyle=r,"SQUISHED"===this.displayMode&&void 0!==t.row?(s=this.featureHeight/2,a=this.margin+this.squishedRowHeight*t.row):"EXPANDED"===this.displayMode&&void 0!==t.row?(s=this.featureHeight,a=this.margin+this.expandedRowHeight*t.row):(s=this.featureHeight,a=this.margin);const l=o.pixelWidth,c=a+s/2,h=s/2,u=c-h/2,f=t.exons?t.exons.length:0,d=vg(t,e,n),p=this.arrowSpacing,g="+"===t.strand?1:"-"===t.strand?-1:0;if(0===f){const t=Math.max(0,d.px),e=Math.min(l,d.px1),n=e-t;if(i.fillRect(t,a,n,s),0!==g){i.fillStyle="white",i.strokeStyle="white";for(let n=t+p/2;n<e;n+=p)Xo.strokeLine(i,n-2*g,c-2,n,c),Xo.strokeLine(i,n-2*g,c+2,n,c);i.fillStyle=r,i.strokeStyle=r}}else{Xo.strokeLine(i,d.px+1,c,d.px1-1,c);const o=Math.max(0,d.px)+p/2,m=Math.min(l,d.px1);for(let t=o;t<m;t+=p)Xo.strokeLine(i,t-2*g,c-2,t,c),Xo.strokeLine(i,t-2*g,c+2,t,c);for(let o=0;o<f;o++){const f=t.exons[o];let d,m=Math.round((f.start-e)/n),v=Math.round((f.end-e)/n),b=Math.max(1,v-m);if(!(m+b<0)){if(m>l)break;if(f.utr)i.fillRect(m,u,b,h);else if(f.cdStart&&(d=Math.round((f.cdStart-e)/n),i.fillRect(m,u,d-m,h),b-=d-m,m=d),f.cdEnd&&(d=Math.round((f.cdEnd-e)/n),i.fillRect(d,u,v-d,h),b-=v-d,v=d),b=Math.max(b,1),i.fillRect(m,a,b,s),b>p+5&&0!==g){i.fillStyle="white",i.strokeStyle="white";for(let t=m+p/2;t<v;t+=p)Xo.strokeLine(i,t-2*g,c-2,t,c),Xo.strokeLine(i,t-2*g,c+2,t,c);i.fillStyle=r,i.strokeStyle=r}}}}o.drawLabel&&"SQUISHED"!==this.displayMode&&wg.call(this,i,t,d.px,d.px1,a,o.referenceFrame,o)}finally{i.restore()}}function wg(t,e,n,r,i,o,s){try{t.save();let a=e.name;if(void 0===a&&e.gene&&(a=e.gene.name),void 0===a&&(a=e.id||e.ID),!a||"."===a)return;let l=s.pixelXOffset||0;const c=Math.max(n,-l);let h,u=(c+Math.min(r,-l+s.viewportWidth))/2;"COLLAPSED"===this.displayMode&&"SLANT"===this.labelDisplayMode&&(h={rotate:{angle:45}});const f=function(t,e){return e?t+20:t+25}(i,h);let d,p=yg.call(this,e),g=!1;o.selection&&mg.gtexLoaded&&(g=!0,d=o.selection.colorForGene(a));const m={textAlign:"SLANT"===this.labelDisplayMode?void 0:"center",fillStyle:d||p,strokeStyle:d||p},v=t.measureText(a),b=u-v.width/2,w=u+v.width/2,y=s.rowLastLabelX[e.row]||-Number.MAX_SAFE_INTEGER;(s.labelAllFeatures||b>y||g)&&(s.rowLastLabelX[e.row]=w,Xo.fillText(t,a,u,f,m,h))}finally{t.restore()}}function yg(t){let e;if(this.altColor&&"-"===t.strand)e="function"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)e="function"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const n=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];e=this.colorTable.getColor(n)}else e=t.color?t.color:this.defaultColor;if(t.alpha&&1!==t.alpha)e=mo.addAlpha(e,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const n=function(t,e,n){const r=(e-t)/9,i=Math.floor((n-t)/r);return Math.min(1,.2+.8*i/9)}(this.config.min?this.config.min:0,this.config.max?this.config.max:1e3,t.score);t.alpha=n,e=mo.addAlpha(e,n)}return e}const xg=new Set(["nonsense","missense","stop-loss","frameshift","cds-indel"]),_g=new Set(["coding-synon"]),kg=new Set(["splice-3","splice-5"]),Sg=new Set(["untranslated-5","untranslated-3"]);function Cg(t,e,n,r,i){var o,s,a,l,c=vg(t,e,n),h=this.margin,u=this.snpColors.length;switch(o="squished"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case"function":l=t.func,s=l.split(",").map((function(t){return xg.has(t)||kg.has(t)?u-1:_g.has(t)?u-2:Sg.has(t)?u-3:0})).reduce((function(t,e){return Math.max(t,e)}));break;case"class":s="deletion"===(a=t.class)?u-1:"mnp"===a?u-2:"microsatellite"===a||"named"===a?u-3:0}i.fillStyle=this.snpColors[s],i.fillRect(c.px,h,c.pw,o)}function Eg(t,e,n,r,i){const o="EXPANDED"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let s=this.margin;"COLLAPSED"!==this.displayMode&&void 0!==t.row&&(s+=t.row*o);const a=s+.5*o,l=a-.5*o,c=a+.5*o,h=Math.round((t.junction_left-e)/n),u=Math.round((t.junction_right-e)/n);i.beginPath(),i.moveTo(h,a),i.bezierCurveTo(h,l,u,l,u,a),i.lineWidth=1+Math.log(t.num_junction_reads)/Math.log(2),i.strokeStyle="blue",i.stroke();const f=t.spanning_frag_coords;for(let t=0;t<f.length;t++){const r=f[t],o=Math.round((r.left-e)/n),s=Math.round((r.right-e)/n);i.beginPath(),i.moveTo(o,a),i.bezierCurveTo(o,c,s,c,s,a),i.lineWidth=1,i.strokeStyle="purple",i.stroke()}}class Tg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"annotation",this.maxRows=void 0===t.maxRows?1e3:t.maxRows,this.displayMode=t.displayMode||"EXPANDED",this.labelDisplayMode=t.labelDisplayMode,t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:zu(t,this.browser.genome),this.autoHeight=t.autoHeight,this.margin=void 0===t.margin?10:t.margin,this.featureHeight=t.featureHeight||14,"FusionJuncSpan"===t.type?(this.render=t.render||Eg,this.squishedRowHeight=t.squishedRowHeight||50,this.expandedRowHeight=t.expandedRowHeight||50,this.height=t.height||this.margin+2*this.expandedRowHeight):"snp"===t.type?(this.render=t.render||Cg,this.snpColors=["rgb(0,0,0)","rgb(0,0,255)","rgb(0,255,0)","rgb(255,0,0)"],this.colorBy="function",this.expandedRowHeight=t.expandedRowHeight||10,this.squishedRowHeight=t.squishedRowHeight||5,this.height=t.height||30):(this.render=t.render||bg,this.arrowSpacing=30,function(t){t.browser.on&&(t.browser.on("trackdragend",e),t.browser.on("trackremoved",n));function e(){t.trackView&&"SQUISHED"!==t.displayMode&&t.trackView.repaintViews()}function n(r){t.browser.un&&t===r&&(t.browser.un("trackdragend",e),t.browser.un("trackremoved",n))}}(this),this.squishedRowHeight=t.squishedRowHeight||15,this.expandedRowHeight=t.expandedRowHeight||30,this.height=t.height||this.margin+2*this.expandedRowHeight,t.colorBy&&(t.colorBy.field&&(t.colorTable=t.colorBy.pallete||t.colorBy.palette,t.colorBy=t.colorBy.field),this.colorBy=t.colorBy,t.colorTable?this.colorTable=new Uu(t.colorTable):this.colorTable=new ju("Set1"))),this.useScore=t.useScore}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&"function"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(t,e,n,r){const i=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:i})}computePixelHeight(t){if("COLLAPSED"===this.displayMode)return this.margin+this.expandedRowHeight;{let e=0;if(t&&"function"==typeof t.forEach)for(let n of t)n.row&&n.row>e&&(e=n.row);return this.margin+(e+1)*("SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=t.pixelHeight,a=i+o*r+1;if(this.config.isMergedTrack||Xo.fillRect(n,0,t.pixelTop,o,s,{fillStyle:"rgb(255, 255, 255)"}),e){const l=[];t.rowLastX=[],t.rowLastLabelX=[];for(let n of e)if(n.start>i&&n.end<a){const e="COLLAPSED"===this.displayMode?0:n.row||0;void 0===l[e]?l[e]=1:l[e]++,t.rowLastX[e]=-Number.MAX_SAFE_INTEGER,t.rowLastLabelX[e]=-Number.MAX_SAFE_INTEGER}const c=o/Math.max(1,Math.max(...l));let h=[];for(let o of e){if(o.end<i)continue;if(o.start>a)break;const e="COLLAPSED"===this.displayMode?0:o.row;t.drawLabel=t.labelAllFeatures||c>10;const l=Math.ceil((o.end-i)/r),u=h[e];if(!u||l>u){this.render.call(this,o,i,r,s,n,t);const a=Math.floor((o.start-i)/r);u&&a-u<=0&&(n.globalAlpha=.5,Xo.strokeLine(n,a,0,a,s,{strokeStyle:"rgb(255, 255, 255)"}),n.globalAlpha=1),h[e]=l}}}else console.log("No feature list")}clickedFeatures(t,e){const n=t.y-this.margin,r=super.clickedFeatures(t,e);let i;switch(this.displayMode){case"SQUISHED":i=Math.floor(n/this.squishedRowHeight);break;case"EXPANDED":i=Math.floor(n/this.expandedRowHeight);break;default:i=void 0}return r.filter((function(t){return void 0===i||void 0===t.row||i===t.row}))}popupData(t,e){e=this.clickedFeatures(t,e);const n=t.genomicLocation,r=[];for(let t of e){const e=t._f||t,i="function"==typeof e.popupData?e.popupData(n):this.extractPopupData(e);if(i){r.length>0&&r.push("<hr/><hr/>");const o=this.infoURL||this.config.infoURL;for(let e of i)if(r.push(e),o&&e.name&&"name"===e.name.toLowerCase()&&e.value&&ke(e.value)&&!e.value.startsWith("<")){const n=o.replace("$$",t.name);e.value=`<a target=_blank href=${n}>${e.value}</a>`}const s="gff"===this.config.format||"gff3"===this.config.format||"gtf"===this.config.format;if(e.exons)for(let t=0;t<e.exons.length;t++){const i=e.exons[t];if(n>=i.start&&n<=i.end){const n=s?i.number:"-"===e.strand?e.exons.length-t:t+1;n&&(r.push("<hr/>"),r.push({name:"Exon Number",value:n}));break}}}}return r}menuItemList(){const t=[];if(this.render===Cg){t.push("<hr/>");for(let e of["function","class"])t.push({object:pe(qo("Color by "+e,e===this.colorBy)),click:()=>{this.colorBy=e,this.trackView.repaintViews()}})}t.push("<hr/>");for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){const n={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};t.push({object:pe(qo(n[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.config.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return t}contextMenuItemList(t){const e=this.clickedFeatures(t);if(void 0===e||0===e.length)return;e.length>1&&e.sort(((t,e)=>e.end-e.start-(t.end-t.start)));const n=e[0];if(n.end-n.start<=1e6){const t=[{label:"View feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(n.chr,n.start,n.end);t?"-"===n.strand&&(t=Us(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return Os()&&void 0!==navigator.clipboard&&t.push({label:"Copy feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(n.chr,n.start,n.end);t?"-"===n.strand&&(t=Us(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),t.push("<hr/>"),t}}description(){if(Cg===this.render){let t="<html>"+this.name+"<hr/>";return t+="<em>Color By Function:</em><br>",t+='<span style="color:red">Red</span>: Coding-Non-Synonymous, Splice Site<br>',t+='<span style="color:green">Green</span>: Coding-Synonymous<br>',t+='<span style="color:blue">Blue</span>: Untranslated<br>',t+='<span style="color:black">Black</span>: Intron, Locus, Unknown<br><br>',t+="<em>Color By Class:</em><br>",t+='<span style="color:red">Red</span>: Deletion<br>',t+='<span style="color:green">Green</span>: MNP<br>',t+='<span style="color:blue">Blue</span>: Microsatellite, Named<br>',t+='<span style="color:black">Black</span>: Indel, Insertion, SNP',t+="</html>",t}return super.description()}dispose(){this.trackView=void 0}}class Ag extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type="wig",this.height=t.height||50,this.featureType="numeric",this.paintAxis=pp;const e=t.format?t.format.toLowerCase():t.format;this.flipAxis=!!t.flipAxis&&t.flipAxis,this.logScale=!!t.logScale&&t.logScale,t.featureSource?(this.featureSource=t.featureSource,delete t.featureSource):this.featureSource="bigwig"===e?new Ic(t,this.browser.genome):"tdf"===e?new Iu(t,this.browser.genome):zu(t,this.browser.genome),this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max}),this.windowFunction=t.windowFunction||"mean",this.graphType=t.graphType||"bar",this.normalize=t.normalize,this.scaleFactor=t.scaleFactor}async postInit(){const t=await this.getHeader();this.disposed||t&&this.setTrackProperties(t)}async getFeatures(t,e,n,r){const i=await this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:this.visibilityWindow,windowFunction:this.windowFunction});if(this.normalize&&this.featureSource.normalizationFactor){const t=this.featureSource.normalizationFactor;for(let e of i)e.value*=t}if(this.scaleFactor){const t=this.scaleFactor;for(let e of i)e.value*=t}return i}menuItemList(){let t=[];return void 0!==this.flipAxis&&(t.push("<hr>"),t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}})),t=t.concat(Wo.numericDataMenuItems(this.trackView)),t}async getHeader(){return"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(t,e,n,r){return r?n/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):n/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let n=this.dataRange.max,r=this.dataRange.min;return n<=0?0:(r<=-1&&(r=0),r=r<=0?0:Math.log10(r+1),n=Math.log10(n+1),t=Math.log10(t+1),(this.flipAxis?t-r:n-t)*e)}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth;t.pixelHeight;const s=i+o*r+1;let a=-1,l=-1;const c=this.color||"rgb(150,150,150)";let h;"string"==typeof c&&c.startsWith("rgb(")&&(h=mo.addAlpha(c,.1));const u=this.getScaleFactor(this.dataRange.min,this.dataRange.max,t.pixelHeight,this.logScale),f=t=>this.logScale?this.computeYPixelValueInLogScale(t,u):this.computeYPixelValue(t,u);if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const o=f(0);for(let t of e){if(t.end<i)continue;if(t.start>s)break;const e=Math.floor((t.start-i)/r);if(isNaN(e))continue;let h=f(t.value);const u=Math.ceil((t.end-i)/r),d=Math.max(1,u-e);let p=t.value<0&&this.altColor?this.altColor:c;const g="function"==typeof p?p(t.value):p;if("points"===this.graphType){const t=this.config.pointSize||3,r=e+d/2;Xo.fillCircle(n,r,h,t/2,{fillStyle:g,strokeStyle:g})}else{let r=h-o;const i=e+d;(i>a||t.value>=0&&t.value>l||t.value<0&&t.value<1)&&Xo.fillRect(n,e,o,d,r,{fillStyle:g}),l=t.value,a=i}}if(this.dataRange.min<0){const e=this.dataRange.max/(this.dataRange.max-this.dataRange.min)*t.pixelHeight;Xo.strokeLine(n,0,e,t.pixelWidth,e,{strokeStyle:h})}}if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let n=f(e.y),r={strokeStyle:e.color,strokeWidth:2};e.dotted?Xo.dashedLine(t.context,0,n,t.pixelWidth,n,5,r):Xo.strokeLine(t.context,0,n,t.pixelWidth,n,r)}}popupData(t,e){if((e=this.clickedFeatures(t,e))&&e.length>0){const n=t.genomicLocation,r=[];e.sort((function(t,e){return Math.abs((t.start+t.end)/2-n)-Math.abs((e.start+e.end)/2-n)}));const i=e.length>10?e.slice(0,10):e;i.sort((function(t,e){return t.start-e.start}));for(let t of i)if(t){r.length>0&&r.push("<hr/>");let e=t.end-t.start==1?Se(t.start+1):Se(t.start+1)+"-"+Se(t.end);r.push({name:"Position:",value:e}),r.push({name:"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;",value:Se(t.value)})}return i.length<e.length&&r.push("<hr/>..."),r}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}dispose(){this.trackView=void 0}getState(){const t=super.getState();return void 0!==this.flipAxis&&(t.flipAxis=this.flipAxis),void 0!==this.logScale&&(t.logScale=this.logScale),t}}function Lg(t){this.thresholds=t.thresholds,this.colors=t.colors}function Mg(t){this.scale=t,this.lowColor="rgb("+t.lowR+","+t.lowG+","+t.lowB+")",this.highColor="rgb("+t.highR+","+t.highG+","+t.highB+")",this.diff=t.high-t.low}Lg.prototype.getColor=function(t){for(let e of this.thresholds)if(t<e)return this.colors[this.thresholds.indexOf(e)];return this.colors[this.colors.length-1]},Mg.prototype.getColor=function(t){var e,n=this.scale;return t<=n.low?this.lowColor:t>=n.high?this.highColor:(e=(t-n.low)/this.diff,"rgb("+Math.floor(n.lowR+e*(n.highR-n.lowR))+","+Math.floor(n.lowG+e*(n.highG-n.lowG))+","+Math.floor(n.lowB+e*(n.highB-n.lowB))+")")};class Rg{constructor(t){this.color=t}getColor(){return this.color}}class Ig extends ml{constructor(t,e){super(t,e)}init(t){if(super.init(t),this.type=t.type||"seg","maf"===this.type&&(this.type="mut"),this.isLog=t.isLog,this.displayMode=t.displayMode||"EXPANDED",this.height=t.height||300,this.maxHeight=t.maxHeight||500,this.squishedRowHeight=t.sampleSquishHeight||t.squishedRowHeight||2,this.expandedRowHeight=t.sampleExpandHeight||t.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,t.color?this.color=t.color:(this.posColorScale=t.posColorScale||new Mg({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=t.negColorScale||new Mg({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),"mut"===this.type&&(this.colorTable=new Uu(t.colorTable||Ng))),this.sampleKeys=[],this.sampleNames=new Map,t.samples){for(let e of t.samples)this.sampleKeys.push(e),this.sampleNames.set(e,e);this.explicitSamples=!0}const e=Object.assign({},this.config);e.maxWGCount=e.maxWGCount||Number.MAX_SAFE_INTEGER,this.featureSource=zu(e,this.browser.genome),this.initialSort=t.sort}async postInit(){"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const t=[],e={SQUISHED:"Squish",EXPANDED:"Expand",FILL:"Fill"};t.push("<hr/>"),t.push("DisplayMode:");const n="seg"===this.type?["SQUISHED","EXPANDED","FILL"]:["SQUISHED","EXPANDED"];for(let r of n){const n=qo(e[r],r===this.displayMode);t.push({object:pe(n),click:()=>{this.displayMode=r,this.config.displayMode=r,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return t}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys.map((t=>this.sampleNames.get(t))),height:this.sampleHeight,yOffset:0}}async getFeatures(t,e,n){const r=await this.featureSource.getFeatures({chr:t,start:e,end:n});if(this.initialSort){const t=this.initialSort;this.sortSamples(t.chr,t.start,t.end,t.direction,r),this.initialSort=void 0}return r}draw(t){let{context:e,renderSVG:n,pixelTop:r,pixelWidth:i,pixelHeight:o,features:s,bpPerPixel:a,bpStart:l}=t;if(Xo.fillRect(e,0,0,i,o,{fillStyle:"rgb(255, 255, 255)"}),s&&s.length>0){this.checkForLog(s),this.updateSampleKeys(s);const t={};let n;switch(this.sampleKeys.forEach((function(e,n){t[e]=n})),this.displayMode){case"FILL":this.sampleHeight=o/this.sampleKeys.length,n=0;break;case"SQUISHED":this.sampleHeight=this.squishedRowHeight,n=0;break;default:this.sampleHeight=this.expandedRowHeight,n=1}const c=this.sampleHeight;for(let t of s)t.pixelRect=void 0;const h=r+o,u=l+i*a+1,f=a;this.sampleYStart=void 0;for(let i of s){if(i.end<l)continue;if(i.start>u)break;const o=i.sampleKey||i.sample;i.row=t[o];const s=i.row*c+n;void 0===this.sampleYStart&&(this.sampleYStart=s);if(s+c<r||s>h)continue;const a=Math.max(i.start,l);let d=Math.round((a-l)/f);const p=Math.min(i.end,u),g=Math.round((p-l)/f);let m,v,b=Math.max(1,g-d);if(this.color?m="function"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),"mut"===this.type)v=c-2*n,b<3&&(b=3,d-=1);else{let t=i.value;this.isLog||(t=fo(t/2)),m=t<-.1?this.negColorScale.getColor(t):t>.1?this.posColorScale.getColor(t):"white";let e=c;if(c<.25){const n=.1+2*Math.abs(t);e=Math.min(1,n*c)}v=e-2*n}i.pixelRect={x:d,y:s,w:b,h:v},e.fillStyle=m,e.fillRect(d,s,b,v)}}}checkForLog(t){if(void 0===this.isLog){this.isLog=!1;for(let e of t)if(e.value<0)return void(this.isLog=!0)}}computePixelHeight(t){if(!t)return 0;const e="SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(t),this.sampleKeys.length*e}async sortSamples(t,e,n,r,i){if(i||(i=await this.featureSource.getFeatures({chr:t,start:e,end:n})),!i)return;this.updateSampleKeys(i);const o={},s="ASC"===r?1:-1,a=()=>{const t=n-e+1;for(let r of i){if(r.end<e)continue;if(r.start>n)break;const i=Math.max(e,r.start),s=(Math.min(n,r.end)-i)/t,a=r.sampleKey||r.sample,l=o[a]||0;o[a]=l+s*r.value}this.sampleKeys.sort((function(t,e){let n=o[t],r=o[e];return n||(n=s*Number.MAX_VALUE),r||(r=s*Number.MAX_VALUE),n===r?0:n>r?s:-1*s}))},l=()=>{for(let t of i){if(t.end<e)continue;if(t.start>n)break;const r=t.sampleKey||t.sample;(!o.hasOwnProperty(r)||t.value.localeCompare(o[r])>0)&&(o[r]=t.value)}this.sampleKeys.sort((function(t,e){let n=o[t]||"",r=o[e]||"";return s*n.localeCompare(r)}))};"mut"===this.type?l():a(),this.trackView.repaintViews()}clickedFeatures(t,e){const n=super.clickedFeatures(t,e),r=t.y;return n.filter((function(t){const e=t.pixelRect;return e&&r>=e.y&&r<=e.y+e.h}))}hoverText(t){return`${t.sample}: ${t.value}`}popupData(t,e){e=this.clickedFeatures(t);const n=[];for(let t of e){n.length>0&&(n.push("<hr/>"),n.push("<hr/>"));const e=t._f||t,r="function"==typeof e.popupData?e.popupData(this.type,this.browser.genome.id):this.extractPopupData(e);Array.prototype.push.apply(n,r)}return n}contextMenuItemList(t){const e=t.viewport.referenceFrame,n=t.genomicLocation,r=this.config.sort?"ASC"===this.config.sort.direction?"DESC":"ASC":"DESC",i=e.toBP(2.5),o=e=>{const n=t.viewport.cachedFeatures;this.sortSamples(e.chr,e.start,e.end,e.direction,n)};return[{label:"seg"===this.type?"Sort by value":"Sort by type",click:e=>{const s={direction:r,chr:t.viewport.referenceFrame.chr,start:n-i,end:n+i};o(s),this.config.sort=s}}]}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(t){if(!this.explicitSamples)for(let e of t){const t=e.sampleKey||e.sample;this.sampleNames.has(t)||(this.sampleNames.set(t,e.sample),this.sampleKeys.push(t))}}}const Ng={indel:"rgb(0,200,0)","targeted region":"rgb(236,155,43)",truncating:"rgb(\t150,0,0)","non-coding transcript":"rgb(0,0,150)",synonymous:"rgb(109,165,95)",silent:"rgb(109,135,80)",missense_mutation:"rgb(72,130,187)",missense:"rgb(72,130,187)","splice site":"rgb(143,83,155)",splice_region:"rgb(143,83,155)",nonsense:"rgb(216, 57,81)",nonsense_mutation:"rgb(216, 57,81)",frame_shift_del:"rgb(226,135,65)",frame_shift_ins:"rgb(226,135,65)",in_frame_del:"rgb(247,235,94)",in_frame_ins:"rgb(247,235,94)","*other*":"rgb(159,91,50)"};class Og extends ml{constructor(t,e){super(t,e),this.type="merged",this.featureType="numeric",this.paintAxis=pp}init(t){if(!t.tracks)throw Error("Error: no tracks defined for merged track"+t);super.init(t)}async postInit(){this.tracks=[];const t=[];for(let e of this.config.tracks){e.isMergedTrack=!0;const n=await this.browser.createTrack(e);n?(n.autoscale=!1,this.tracks.push(n)):console.warn("Could not create track "+e),"function"==typeof n.postInit&&t.push(n.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale||void 0===this.config.max,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return this.height=this.config.height||50,Promise.all(t)}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];return void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Wo.numericDataMenuItems(this.trackView)),t}async getFeatures(t,e,n,r){const i=this.tracks.map((i=>i.getFeatures(t,e,n,r)));return Promise.all(i)}draw(t){const e=t.features;this.autoscale&&(this.dataRange=function(t,e){let n=0,r=-Number.MAX_VALUE;for(let t of e)for(let e of t)void 0===e.value||Number.isNaN(e.value)||(n=Math.min(n,e.value),r=Math.max(r,e.value));return{min:n,max:r}}(t.referenceFrame.chr,e));for(let n=0,r=this.tracks.length;n<r;n++){const r=Object.assign({},t);r.features=e[n],this.tracks[n].dataRange=this.dataRange,this.tracks[n].flipAxis=this.flipAxis,this.tracks[n].logScale=this.logScale,this.tracks[n].graphType=this.graphType,this.tracks[n].draw(r)}}popupData(t,e){const n=e||t.viewport.cachedFeatures;if(n&&n.length===this.tracks.length){const e=[];for(let r=0;r<this.tracks.length;r++){r>0&&e.push("<hr/>"),e.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[r].name}</div>`);const i=this.tracks[r].popupData(t,n[r]);e.push(...i)}return e}}get supportsWholeGenome(){return this.tracks.every((t=>t.supportsWholeGenome()))}}class Pg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.theta=t.theta||Math.PI/4,this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.height=t.height||250,this.arcType=function(t){if(!t.arcType)return"nested";switch(t.arcType){case"chiapet":return"inView";case"chiapetoutbound":return"partialInView";default:return t.arcType}}(t),this.arcOrientation=void 0===t.arcOrientation||t.arcOrientation,this.showBlocks=void 0===t.showBlocks||t.showBlocks,this.blockHeight=t.blockHeight||3,this.thickness=t.thickness||1,this.color=t.color,this.alpha=t.alpha||.02,this.painter={flipAxis:!this.arcOrientation,dataRange:this.dataRange,paintAxis:pp},t.valueColumn?(this.valueColumn=t.valueColumn,this.hasValue=!0):t.useScore&&(this.hasValue=!0,this.valueColumn="score"),this.logScale=!1!==t.logScale,t.max?(this.dataRange={min:t.min||0,max:t.max},this.autoscale=!1):this.autoscale=!0,t.featureSource?(this.featureSource=t.featureSource,delete t._featureSource):(this.featureSource=zu(t,this.browser.genome),this.featureSource.getWGFeatures=Hg)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,n){const r=this.visibilityWindow,i=await this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r});return void 0===this.hasValue&&i&&i.length>0&&(this.hasValue=void 0!==i[0].score),i}draw(t){"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?this.drawProportional(t):this.drawNested(t)}drawNested(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight,i=t.viewportWidth,o=t.bpPerPixel,s=t.bpStart,a=o;Xo.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const l=t.features;if(l){(function(){let t=0;for(let e of l){let r=(e.start-s)/a,i=(e.end-s)/a;r>=0&&i<=n&&(t=Math.max(t,i-r))}let e=Math.min(i,t)/2;if(t>0){let t=(r-10)/e;this.theta=function(t){let e,n=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],r=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(e=0;e<n.length&&!(n[e]>t);e++);let i=0===e?0:n[e-1],o=e<n.length?n[e]:1,s=(t-i)/(o-i),a=0===e?0:r[e-1],l=e<r.length?r[e]:Math.PI/2;return Math.min(Math.PI/2,a+s*(l-a))}(t),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const o=this.arcOrientation?t.pixelHeight:0,h=this.arcOrientation;e.font="8px sans-serif",e.textAlign="center";for(let t of l){let r;if(t.drawState=void 0,"function"==typeof this.color?r=this.color(t):(r=this.color||t.color||"rgb(180,25,137)",r&&this.config.useScore&&(r=zg(r,(c=t.score,Math.min(1,.11+c/779*.89).toString())))),e.lineWidth=t.thickness||this.thickness||1,t.chr1===t.chr2||"all"===t.chr){const{m1:l,m2:c}=Fg(t,this.browser.genome);let u=Math.round((l-s)/a),f=Math.round((c-s)/a);if(f<0||u>n)continue;let d=f-u;d<3&&(d=3,u--);const p=d/2,g=p/this.sinTheta,m=this.cosTheta*g,v=u+p;let b,w,y;if(h?(b=this.height+m,w=Math.PI+Math.PI/2-this.theta,y=Math.PI+Math.PI/2+this.theta):(b=-m,w=Math.PI/2-this.theta,y=Math.PI/2+this.theta),this.showBlocks&&"all"!==t.chr){const n=(t.start1-s)/a,r=(t.end1-s)/a,i=(t.start2-s)/a,l=(t.end2-s)/a,c=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(n,o,r-n,c),e.fillRect(i,o,l-i,c)}r&&!this.config.useScore&&d>i&&(r=zg(r,this.alpha)),e.strokeStyle=r,e.fillStyle=r,e.beginPath(),e.arc(v,b,g,w,y,!1),e.stroke(),t.drawState={xc:v,yc:b,r:g}}else{let i=Math.round((t.start-s)/a),o=Math.round((t.end-s)/a);if(o<0||i>n)continue;let l=o-i;l<3&&(l=3,i--);const c=t.chr===t.chr1?t.chr2:t.chr1;e.strokeStyle=r,e.fillStyle=zg(tg(c),.5),h?(e.fillRect(i,this.height/2,l,this.height/2),e.fillText(c,i+l/2,this.height/2-5),t.drawState={x:i,y:this.height/2,w:l,h:this.height/2}):(e.fillRect(i,0,l,this.height/2),e.fillText(c,i+l/2,this.height/2+13),t.drawState={x:i,y:0,w:l,h:this.height/2})}}}var c}getScaleFactor(t,e,n,r){return r?n/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):n/(e-t)}drawProportional(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight,i=t.bpPerPixel,o=t.bpStart,s=i,a=t.referenceFrame.start,l=t.referenceFrame.end;Xo.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const c=t.features;if(c&&c.length>0){const r=0,i=this.getScaleFactor(r,this.dataRange.max,t.pixelHeight-1,this.logScale),h=this.arcOrientation?t.pixelHeight:0;for(let t of c){t.drawState=void 0;const r=this.valueColumn?t[this.valueColumn]:t.score;if(void 0===r||Number.isNaN(r))continue;const c=Math.round((this.logScale?Math.log10(r+1):r)*i);if(t.chr1===t.chr2||"all"===t.chr){const{m1:n,m2:i}=Fg(t,this.browser.genome);let u=Math.round((n-o)/s),f=Math.round((i-o)/s)-u;if(f<3&&(f=3,u--),r<this.dataRange.min||r>this.dataRange.max)continue;if("proportional"!==this.arcType){const t="partialInView"===this.arcType,e=n>=a&&i<=l;let r=!1,o=!1;if(!e&&t&&(r=a<=n&&n<=l,r||(o=a<=i&&i<=l)),!(e||r||o))continue}const d=f/2,p=u+f/2;t.drawState={xc:p,yc:h,radiusX:d,radiusY:c};const g=!!this.arcOrientation,m=t.color||this.color;if(e.strokeStyle=m,e.lineWidth=t.thickness||this.thickness||1,!0===e.isSVG?e.strokeEllipse(p,h,d,c,0,0,Math.PI,g):(e.beginPath(),e.ellipse(p,h,d,c,0,0,Math.PI,g),e.stroke()),this.alpha&&(e.fillStyle=zg(m,this.alpha),!0===e.isSVG?e.fillEllipse(p,h,d,c,0,0,Math.PI,g):e.fill()),this.showBlocks&&"all"!==t.chr){e.fillStyle=m;const n=(t.start1-o)/s,r=(t.end1-o)/s,i=(t.start2-o)/s,a=(t.end2-o)/s,l=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(n,h,r-n,l),e.fillRect(i,h,a-i,l)}}else{let i=Math.round((t.start-o)/s),a=Math.round((t.end-o)/s);if(a<0||i>n||r<this.dataRange.min||r>this.dataRange.max)continue;const l=Math.min(c,this.height-13);let h=a-i;h<3&&(h=3,i--);const u=t.chr===t.chr1?t.chr2:t.chr1;if(e.font="8px sans-serif",e.textAlign="center",e.fillStyle=zg(tg(u),.5),this.arcOrientation){const n=this.height-l;e.fillRect(i,n,h,l),e.fillText(u,i+h/2,n-5),t.drawState={x:i,y:n,w:h,h:l}}else e.fillRect(i,0,h,l),e.fillText(u,i+h/2,l+13),t.drawState={x:i,y:0,w:h,h:l}}}}}clearAxis(t,e,n){Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"})}paintAxis(t,e,n){const r={min:0,max:this.dataRange.max};"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?(this.painter.flipAxis=!this.arcOrientation,this.painter.dataRange=r,this.painter.paintAxis(t,e,n)):this.clearAxis(t,e,n)}menuItemList(){let t=[];if(this.hasValue){t.push("<hr/>");const e={nested:"Nested",proportional:"Proportional - All",inView:"Proportional - Both Ends in View",partialInView:"Proportional - One End in View"};t.push("<b>Arc Type</b>");for(let n of["nested","proportional","inView","partialInView"])t.push({object:pe(qo(e[n],n===this.arcType)),click:()=>{this.arcType=n,this.trackView.repaintViews()}})}return t.push("<hr/>"),t.push({name:"Toggle arc direction",click:()=>{this.arcOrientation=!this.arcOrientation,this.trackView.repaintViews()}}),t.push({name:this.showBlocks?"Hide Blocks":"Show Blocks",click:()=>{this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),"proportional"!==this.arcType&&"inView"!==this.arcType&&"partialInView"!==this.arcType||(t=t.concat(Wo.numericDataMenuItems(this.trackView))),this.browser.circularView&&(t.push("<hr/>"),t.push({label:"Add interactions to circular view",click:()=>{for(let t of this.trackView.viewports)this.addChordsForViewport(t.referenceFrame)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,n=[];return n.push({label:"Add interactions to circular view",click:()=>{const t=e.referenceFrame;this.addChordsForViewport(t)}}),n.push("<hr/>"),n}}addChordsForViewport(t){const e=("all"===t.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end)).filter((t=>t.drawState));if(0===e.length)return;const n=e.map((t=>{const e=t._f||t;return{uniqueId:`${e.chr1}:${e.start1}-${e.end1}_${e.chr2}:${e.start2}-${e.end2}`,refName:Up(e.chr1),start:e.start1,end:e.end1,mate:{refName:Up(e.chr2),start:e.start2,end:e.end2}}}));Wp(n,this,t,.5)}doAutoscale(t){let e=0;if(t)for(let n of t){const t=this.valueColumn?n[this.valueColumn]:n.score;Number.isNaN(t)||(e=Math.max(e,t))}return{min:0,max:e}}popupData(t,e){e=this.clickedFeatures(t);const n=[];for(let t of e){const e=t._||t;if(n.push({name:"Region 1",value:Dg(e.chr1,e.start1,e.end1,e.strand1)}),n.push({name:"Region 2",value:Dg(e.chr2,e.start2,e.end2,e.strand2)}),e.name&&n.push({name:"Name",value:e.name}),void 0!==e.value&&n.push({name:"Value",value:e.value}),void 0!==e.score&&n.push({name:"Score",value:e.score}),e.extras&&this.header&&this.header.columnNames){const t=this.header.columnNames,r=this.header.hiccups?6:10;for(let i=r;i<t.length;i++)this.header.colorColumn!==i&&("info"===t[i]?Vg(n,e.extras[i-r]):n.push({name:t[i],value:e.extras[i-r]}))}break}return n}clickedFeatures(t,e){const n=e||t.viewport.cachedFeatures,r=[];if(n){const e="proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType;for(let i of n)if(i.drawState)if(i.chr1===i.chr2||"all"===i.chr)if(e){const{xc:e,yc:n,radiusX:o,radiusY:s}=i.drawState,a=t.canvasX-e,l=t.canvasY-n,c=a/o*(a/o)+l/s*(l/s);c<=1&&r.push({score:1/c,feature:i})}else{const{xc:e,yc:n,r:o}=i.drawState,s=t.canvasX-e,a=t.canvasY-n,l=Math.abs(Math.sqrt(s*s+a*a)-o);l<5&&r.push({score:l,feature:i})}else{const{x:e,y:n,w:o,h:s}=i.drawState,a=5;if(t.canvasX>=e-a&&t.canvasX<=e+o+a&&t.canvasY>=n&&t.canvasY<=n+s){const n=-Math.abs(t.canvasX-(e+o/2));r.push({score:n,feature:i});break}}}return r.length>1&&r.sort(((t,e)=>t.score-e.score)),r.map((t=>t.feature))}getState(){const t=super.getState();return void 0!==this.arcType&&(t.arcType=this.arcType),void 0!==this.arcOrientation&&(t.arcOrientation=this.arcOrientation),void 0!==this.showBlocks&&(t.showBlocks=this.showBlocks),void 0!==this.blockHeight&&(t.blockHeight=this.blockHeight),void 0!==this.thickness&&(t.thickness=this.thickness),void 0!==this.alpha&&(t.alpha=this.alpha),t}}function Fg(t,e){let n=(t.start1+t.end1)/2,r=(t.start2+t.end2)/2;if("all"===t.chr&&(n=e.getGenomeCoordinate(t.chr1,n),r=e.getGenomeCoordinate(t.chr2,r)),n>r){const t=n;n=r,r=t}return{m1:n,m2:r}}function Dg(t,e,n,r){return r&&"."!==r?`${t}:${Se(e+1)}-${Se(n)} (${r})`:`${t}:${Se(e+1)}-${Se(n)}`}const Bg=new Map;function zg(t,e){const n=`${t}_${e}`;let r=Bg.get(n);return r||(r=mo.addAlpha(t,e),Bg.set(n,r)),r}function Hg(t){const e=t=>{const e=Object.assign({},t);return e.chr="all",e.start=n.getGenomeCoordinate(t.chr1,t.start1),e.end=n.getGenomeCoordinate(t.chr2,t.end2),e},n=this.genome;let r,i=0;for(let e of n.wgChromosomeNames){let n=t[e];if(n)for(let t of n)t.dup||(i++,t.score&&(!r||t.score>r.score)&&(r=t))}const o=this.maxWGCount,s=r&&r.score>0&&i>o?5:1,a=Math.floor(o/s),l=r&&r.score>0?Math.log(r.score)/s:Number.MAX_SAFE_INTEGER;let c,h=[],u=[];for(let t=0;t<s;t++)u.push([0]),h.push([]);for(let r of n.wgChromosomeNames){let n=t[r];if(n)for(let t of n)if(!t.dup){const n=t.score?Math.max(0,Math.min(s-1,Math.floor(Math.log(t.score)/l))):0;if(h[n].length<a)h[n].push(e(t));else{const r=a/(u[n]+1);if(Math.random()<r){const r=Math.floor(Math.random()*(a-1));h[n][r]=e(t)}}u[n]++}}if(1===s)c=h[0];else{c=[];for(let t of h)for(let e of t)c.push(e);r&&c.push(e(r)),c.sort((function(t,e){return t.start-e.start})),console.log(c.length)}return c}function Vg(t,e){const n=e.split(";");for(let e of n){const n=e.split("=");2===n.length&&t.push({name:n[0],value:n[1]})}}const jg=ke,Ug=new Map([["REF","referenceBases"],["ALT","alternateBases"],["QUAL","quality"],["FILTER","filter"]]);class qg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.visibilityWindow=t.visibilityWindow,this.displayMode=t.displayMode||"EXPANDED",this.labelDisplayMode=t.labelDisplayMode,this.expandedVariantHeight=t.expandedVariantHeight||t.variantHeight||10,this.squishedVariantHeight=t.squishedVariantHeight||2,this.squishedCallHeight=t.squishedCallHeight||1,this.expandedCallHeight=t.expandedCallHeight||10,this.expandedVGap=void 0!==t.expandedVGap?t.expandedVGap:2,this.squishedVGap=void 0!==t.squishedVGap?t.squishedVGap:1,this.expandedGroupGap=t.expandedGroupGap||10,this.squishedGroupGap=t.squishedGroupGap||5,this.featureHeight=t.featureHeight||14,this.visibilityWindow=t.visibilityWindow,this.featureSource=zu(t,this.browser.genome),this.noGenotypeColor=t.noGenotypeColor||"rgb(200,180,180)",this.noCallColor=t.noCallColor||"rgb(225, 225, 225)",this.nonRefColor=t.nonRefColor||"rgb(200, 200, 215)",this.mixedColor=t.mixedColor||"rgb(200, 220, 200)",this.homrefColor=t.homrefColor||"rgb(200, 200, 200)",this.homvarColor=t.homvarColor||"rgb(17,248,254)",this.hetvarColor=t.hetvarColor||"rgb(34,12,253)",this.sortDirection="ASC",this.type=t.type||"variant",this.colorBy=t.colorBy,this._initColorBy=t.colorBy,t.colorTable&&(this.colorTables=new Map,this.colorTables.set(t.colorBy,new Uu(t.colorTable))),this._strokecolor=t.strokecolor,this._context_hook=t.context_hook,this.showGenotypes=void 0===t.showGenotypes||t.showGenotypes,this.variantRowCount(1)}async postInit(){if(this.header=await this.getHeader(),!this.disposed){if(void 0===this.visibilityWindow&&!1!==this.config.indexed){const t=Ue(this.config.url)?this.config.url.name:this.config.url;jg(t)&&t.toLowerCase().includes("gnomad")?this.visibilityWindow=1e3:"function"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!1===this.config.indexed||!0===this.config.supportsWholeGenome}get color(){return this._color}set color(t){this._color=t,this.colorBy=void 0}async getHeader(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const t=await this.featureSource.getHeader();t&&(this.callSets=t.callSets||[]),this.header=t}this.sampleNames=this.callSets?this.callSets.map((t=>t.name)):[]}return this.header}getCallsetsLength(){return this.callSets?this.callSets.length:0}async getFeatures(t,e,n,r){return void 0===this.header&&(this.header=await this.getHeader()),this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:this.visibilityWindow})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(t){if(!t||0==t.length)return 10;const e="COLLAPSED"===this.displayMode?1:this.nVariantRows,n="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,r="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,i="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+e*(r+n)+n+((!1===this.showGenotypes?0:this.getCallsetsLength()*e)+1)*(i+n)}variantRowCount(t){this.nVariantRows=t}draw(t){let{context:e,pixelWidth:n,pixelHeight:r,bpPerPixel:i,bpStart:o,pixelTop:s,features:a}=t;Xo.fillRect(e,0,s,n,r,{fillStyle:"rgb(255, 255, 255)"});const l="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,c="COLLAPSED"===this.displayMode?1:this.nVariantRows,h="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+c*(h+l);let u=this.callSets;!u&&this._f&&(u=this._f.callSets);const f=this.getCallsetsLength();if(u&&f>0&&!1!==this.showGenotypes&&Xo.strokeLine(e,0,this.variantBandHeight,n,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),a){const t="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,r="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,s=o+n*i+1;for(let n of a){if(n.end<o)continue;if(n.start>s)break;const a="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,l=10+("COLLAPSED"===this.displayMode?0:n.row*(a+r)),c=a;let h=Math.round((n.start-o)/i),d=Math.round((n.end-o)/i),p=Math.max(1,d-h);p<3?(p=3,h-=1):p>5&&(h+=1,p-=2),e.fillStyle=this.getVariantColor(n),e.fillRect(h,l,p,c);let g=this.getVariantStrokecolor(n);if(g&&(e.strokeStyle=g,e.strokeRect(h,l,p,c)),this.callContextHook(n,e,h,l,p,c),n.pixelRect={x:h,y:l,w:p,h:c},f>0&&!1!==this.showGenotypes){const i="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+r,this.sampleHeight=i*(t+r);let o=0;if(u&&n.calls)for(let i of u){const s=n.calls[i.id];if(s){const a="COLLAPSED"===this.displayMode?0:n.row,l=this.sampleYOffset+o*this.sampleHeight+a*(t+r);let c=!0,u=!0,f=!1;if(s.genotype)for(let t of s.genotype){if("."===t){f=!0;break}0!==t&&(u=!1),0===t&&(c=!1)}s.genotype?e.fillStyle=f?this.noCallColor:u?this.homrefColor:c?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,l,p,t),i.pixelRect={x:h,y:l,w:p,h:t}}o++}}}}else console.log("No feature list")}getVariantColor(t){const e=t._f||t;let n;if(this.colorBy){const t=this.colorBy;let r;if(e.info.hasOwnProperty(t))r=e.info[t];else if(Ug.has(t)){r=e[Ug.get(t)]}n=this.getVariantColorTable(t).getColor(r),n||(n="gray")}else n=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===e.type?this.nonRefColor:"MIXED"===e.type?this.mixedColor:this.defaultColor;return n}getVariantStrokecolor(t){const e=t._f||t;let n;return n=this._strokecolor?"function"==typeof this._strokecolor?this._strokecolor(e):this._strokecolor:void 0,n}callContextHook(t,e,n,r,i,o){if(this._context_hook&&"function"==typeof this._context_hook){const s=t._f||t;e.save(),this._context_hook(s,e,n,r,i,o),e.restore()}}clickedFeatures(t,e){let n=super.clickedFeatures(t,e);const r="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,i=r+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),o=t.y;if(o<=this.variantBandHeight){const t="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,e=Math.floor((o-10)/(t+r));"COLLAPSED"!==this.displayMode&&(n=n.filter((t=>t.row===e)))}else if(this.callSets){const t=this.callSets,e=o-this.variantBandHeight,r=Math.floor(e/this.sampleHeight);if(r>=0&&r<t.length){const o=Math.floor((e-r*this.sampleHeight)/i),s="COLLAPSED"===this.displayMode?n:n.filter((t=>t.row===o)),a=t[r];n=s.map((t=>{const e=t.calls[a.id];return function(t,e){if(t.genotype){let n="";if("."===e.alternateBases)n="No Call";else{const r=e.alternateBases.split(",");for(let i of t.genotype)if(n.length>0&&(n+="|"),"."===i)n+=".";else if(0===i)n+=e.referenceBases;else{n+=r[i-1].replace("<","&lt;")}}t.genotypeName=n}}(e,t),e}))}}return n}popupData(t,e){const n=this.clickedFeatures(t,e),r=t.genomicLocation,i=this.browser.genome.id,o=this.browser.sampleInformation;let s=[];for(let t of n){const e=t._f||t;if(s.length>0&&s.push({html:'<hr style="border-top-width:2px ;border-color: #c9c3ba" />'}),"function"==typeof e.popupData){const t=e.popupData(r,i);Array.prototype.push.apply(s,t)}else{const t=e;if(void 0!==t.callSetName&&s.push({name:"Name",value:t.callSetName}),t.genotypeName&&s.push({name:"Genotype",value:t.genotypeName}),void 0!==t.phaseset&&s.push({name:"Phase set",value:t.phaseset}),void 0!==t.genotypeLikelihood&&s.push({name:"genotypeLikelihood",value:t.genotypeLikelihood.toString()}),o){var a=o.getAttributes(t.callSetName);a&&Object.keys(a).forEach((function(t){var e=t.replace(/([A-Z])/g," $1");e=e.charAt(0).toUpperCase()+e.slice(1),s.push({name:e,value:a[t]})}))}var l=Object.keys(t.info);l.length&&s.push("<hr/>"),l.forEach((function(e){s.push({name:e,value:decodeURIComponent(t.info[e])})}))}}return s}menuItemList(){const t=[];if(this.header.INFO&&this.header.INFO){const e=this.header.INFO.SVTYPE?["SVTYPE"]:[];if(this._initColorBy&&"SVTYPE"!==this._initColorBy&&e.push(this._initColorBy),e.length>0){t.push("<hr/>");const n=pe('<div class="igv-track-menu-category igv-track-menu-border-top">');n.text("Color by:"),t.push({name:void 0,object:n,click:void 0,init:void 0}),e.sort();for(let n of e){const e=this.colorBy===n,r=n||"None";t.push(this.colorByCB({key:n,label:r},e))}t.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),t.push("<hr/>")}}this.getCallsetsLength()>0&&(t.push({object:pe('<div class="igv-track-menu-border-top">')}),t.push({object:pe(qo("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),t.push({object:pe('<div class="igv-track-menu-border-top">')});for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){t.push({object:pe(qo({COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"}[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(t.push("<hr>"),t.push({label:"Add SVs to circular view",click:()=>{for(let t of this.trackView.viewports)this.sendChordsForViewport(t)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,n=[];return n.push({label:"Add SVs to Circular View",click:()=>{this.sendChordsForViewport(e)}}),n.push("<hr/>"),n}}sendChordsForViewport(t){const e=t.referenceFrame,n=(t=>{const e=t.filter((t=>{const e=t._f||t;return e.info&&e.info.CHR2&&e.info.END&&(e.info.CHR2!==e.chr||Math.abs(Number.parseInt(e.info.END)-e.pos)>1e6)}));return e.map((t=>{const e=t._f||t,n=Number.parseInt(e.info.END),r=n-100,i=n+100;return{uniqueId:`${e.chr}:${e.start}-${e.end}_${e.info.CHR2}:${e.info.END}`,refName:Up(e.chr),start:e.start,end:e.end,mate:{refName:Up(e.info.CHR2),start:r,end:i}}}))})("all"===e.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end));Wp(n,this,e,.5)}colorByCB(t,e){return{name:void 0,object:pe(qo(t.label,e)),click:()=>{t.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews())},init:void 0}}getState(){const t=super.getState();return this._color&&"function"!=typeof this._color&&(t.color=this._color),t}getVariantColorTable(t){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(t)){let e;if("SVTYPE"===t)e=Wg;else e=new ju("Set1");this.colorTables.set(t,e)}return this.colorTables.get(t)}}const Wg=new Uu({DEL:"#ff2101",INS:"#001888",DUP:"#028401",INV:"#008688",CNV:"#8931ff",BND:"#891100","*":"#002eff"});class $g extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.name=t.name,this.pValueField=t.pValueField||"pValue",this.geneField=t.geneField||"geneSymbol",this.snpField=t.snpField||"snp";const e=t.minLogP||t.min,n=t.maxLogP||t.max;this.dataRange={min:e||3.5,max:n||25},this.autoscale=!n||t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||2,this.height=t.height||100,this.autoHeight=!1,this.disableButtons=t.disableButtons,this.visibilityWindow=void 0===t.visibilityWindow?2e6:t.visibilityWindow>=0?Math.min(2e6,t.visibilityWindow):2e6,this.featureSource=zu(t,this.browser.genome),mg.gtexLoaded=!0}paintAxis(t,e,n){const r=(this.dataRange.max-this.dataRange.min)/n,i={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"});const o=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/n);for(let s=4;s<=this.dataRange.max;s+=o){const o=.85*e,a=o-5,l=o,c=n-(s-this.dataRange.min)/r;Xo.strokeLine(t,a,c,l,c,i),c>8&&Xo.fillText(t,s,a-1,c+2,i)}i.textAlign="center",Xo.fillText(t,"-log10(pvalue)",e/4,n/2,i,{rotate:{angle:-90}})}async getFeatures(t,e,n){const r=this.pValueField,i=this.visibilityWindow,o=await this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:i});return o.forEach((function(t){t.value=t[r]})),o}draw(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight;this.background&&Xo.fillRect(e,0,0,n,r,{fillStyle:this.background}),Xo.strokeLine(e,0,r-1,n,r-1,{strokeStyle:this.divider});const i=i=>{const o=i?2*this.dotSize:this.dotSize,s=t.bpStart,a=(this.dataRange.max-this.dataRange.min)/r,l=t.referenceFrame.selection;for(let h of t.features){const u=(h.start-s+.5)/t.bpPerPixel;if(u<0)continue;if(u>n)break;const f=h.snp.toUpperCase(),d=h[this.geneField].toUpperCase(),p=l&&(l.snp===f||l.gene===d);if(!i||p){l&&l.snp===f&&l.addGene(d);var c=-Math.log(h[this.pValueField])/Math.LN10;if(c>=this.dataRange.min){let t;c>this.dataRange.max?(c=this.dataRange.max,t=!0):t=!1;const n=Math.max(0+o,r-Math.round((c-this.dataRange.min)/a));let s;h.px=u,h.py=n,h.radius=o,i&&l?(s=l.colorForGene(d),Xo.setProperties(e,{fillStyle:s,strokeStyle:"black"})):(s=t?"rgb(150, 150, 150)":"rgb(180, 180, 180)",Xo.setProperties(e,{fillStyle:s,strokeStyle:s})),Xo.fillCircle(e,u,n,o),Xo.strokeCircle(e,u,n,o)}}}};i(!1),i(!0)}popupData(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return[];const n=this.name,r=[];for(let i of e)Math.abs(i.px-t.canvasX)<i.radius+3&&Math.abs(i.py-t.canvasY)<i.radius+3&&(r.length>0&&r.push("<hr/>"),r.push({name:"snp id",value:i.snp},{name:"gene id",value:i.geneId},{name:"gene name",value:i.geneName},{name:"p value",value:i.pValue},{name:"tissue",value:n}));return r}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){var e=t.map((function(t){return-Math.log(t.value)/Math.LN10}));this.dataRange.max=ho(e,this.autoscalePercentile)}else{const t=this.config.maxLogP||this.config.max;this.dataRange.max=t||25}return this.dataRange}}const Gg={X:"rgb(204, 153, 0)",Y:"rgb(153, 204, 0)",Un:"darkGray)",1:"rgb(80, 80, 255)",I:"rgb(139, 155, 187)",2:"rgb(206, 61, 50)",II:"rgb(206, 61, 50)","2a":"rgb(210, 65, 55)","2b":"rgb(215, 70, 60)",3:"rgb(116, 155, 88)",III:"rgb(116, 155, 88)",4:"rgb(240, 230, 133)",IV:"rgb(240, 230, 133)",5:"rgb(70, 105, 131)",6:"rgb(186, 99, 56)",7:"rgb(93, 177, 221)",8:"rgb(128, 34, 104)",9:"rgb(107, 215, 107)",10:"rgb(213, 149, 167)",11:"rgb(146, 72, 34)",12:"rgb(131, 123, 141)",13:"rgb(199, 81, 39)",14:"rgb(213, 143, 92)",15:"rgb(122, 101, 165)",16:"rgb(228, 175, 105)",17:"rgb(59, 27, 83)",18:"rgb(205, 222, 183)",19:"rgb(97, 42, 121)",20:"rgb(174, 31, 99)",21:"rgb(231, 199, 111)",22:"rgb(90, 101, 94)",23:"rgb(204, 153, 0)",24:"rgb(153, 204, 0)",25:"rgb(51, 204, 0)",26:"rgb(0, 204, 51)",27:"rgb(0, 204, 153)",28:"rgb(0, 153, 204)",29:"rgb(10, 71, 255)",30:"rgb(71, 117, 255)",31:"rgb(255, 194, 10)",32:"rgb(255, 209, 71)",33:"rgb(153, 0, 51)",34:"rgb(153, 26, 0)",35:"rgb(153, 102, 0)",36:"rgb(128, 153, 0)",37:"rgb(51, 153, 0)",38:"rgb(0, 153, 26)",39:"rgb(0, 153, 102)",40:"rgb(0, 128, 153)",41:"rgb(0, 51, 153)",42:"rgb(26, 0, 153)",43:"rgb(102, 0, 153)",44:"rgb(153, 0, 128)",45:"rgb(214, 0, 71)",46:"rgb(255, 20, 99)",47:"rgb(0, 214, 143)",48:"rgb(20, 255, 177)"};for(let vv of Object.keys(Gg)){Gg["chr"+vv]=Gg[vv]}class Zg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=void 0===t.useChrColors||t.useChrColors,this.trait=t.trait,this.posteriorProbability=t.posteriorProbability,this.valueProperty="bed"===t.format?"score":"value",this.height=t.height||100,this.autoscale=t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.colorScales=t.color?new Rg(t.color):{"*":new Lg(t.colorScale||{thresholds:[5e-8,5e-4,.5],colors:["rgb(255,50,50)","rgb(251,100,100)","rgb(251,170,170)","rgb(227,238,249)"]})},this.featureSource=zu(t,this.browser.genome)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r})}draw(t){const e=t.features,n=t.context,r=t.pixelWidth,i=t.pixelHeight;if(this.background&&Xo.fillRect(n,0,0,r,i,{fillStyle:this.background}),Xo.strokeLine(n,0,i-1,r,i-1,{strokeStyle:this.divider}),e){const o=t.bpPerPixel,s=t.bpStart,a=s+r*o+1;for(let t of e){const e=t.start;if(e<s)continue;if(e>a)break;const r=this.getColorScale(t._f?t._f.chr:t.chr);let l,c;if(this.posteriorProbability)c=t[this.valueProperty],l=r.getColor(c);else{const e=t[this.valueProperty];if(!e)continue;c=-Math.log10(e),l=r.getColor(c)}const h=(this.dataRange.max-this.dataRange.min)/i,u=Math.round((e-s)/o),f=Math.max(this.dotSize,i-Math.round((c-this.dataRange.min)/h));l&&Xo.setProperties(n,{fillStyle:l,strokeStyle:"black"}),Xo.fillCircle(n,u,f,this.dotSize),t.px=u,t.py=f}}}getColorScale(t){if(this.useChrColors){let e=this.colorScales[t];if(!e){const n=Gg[t]||Wu.get();e=new Rg(n),this.colorScales[t]=e}return e}return this.colorScales("*")}paintAxis(t,e,n){Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"});var r={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};const i=(this.dataRange.max-this.dataRange.min)/n;if(this.posteriorProbability){const e=.1;for(let o=this.dataRange.min;o<this.dataRange.max;o+=e){const e=n-Math.round((o-this.dataRange.min)/i);Xo.strokeLine(t,45,e-2,50,e-2,r),Xo.fillText(t,o.toFixed(1),44,e+2,r)}}else{const e=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/n);for(let o=this.dataRange.min;o<this.dataRange.max;o+=e){const e=n-Math.round((o-this.dataRange.min)/i);Xo.strokeLine(t,45,e,50,e,r),Xo.fillText(t,Math.floor(o),44,e+4,r)}}r.textAlign="center",this.posteriorProbability?Xo.fillText(t,"PPA",e/2,n/2,r,{rotate:{angle:-90}}):Xo.fillText(t,"-log10(pvalue)",e/2,n/2,r,{rotate:{angle:-90}})}popupData(t){let e=[];const n=t.viewport.trackView.track,r=t.viewport.cachedFeatures;if(r){let i=0;for(let o of r){const r=Math.abs(t.canvasX-o.px),s=Math.abs(t.canvasY-o.py),a=o[this.valueProperty];if(r<this.dotSize&&s<this.dotSize){if(i>0&&e.push("<HR/>"),5==i){e.push("...");break}if("function"==typeof o.popupData)e=e.concat(o.popupData());else{const t=o.realChr||o.chr,r=(o.realStart||o.start)+1;e.push({name:"chromosome",value:t}),e.push({name:"position",value:r}),e.push({name:"name",value:o.name}),n.posteriorProbability?e.push({name:"posterior probability",value:a}):e.push({name:"pValue",value:a})}i++}}}return e}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){const e=this.valueProperty,n=this.posteriorProbability,r=t.map((function(t){const r=t[e];return{value:n?r:-Math.log(r)/Math.LN10}}));this.dataRange=Es(r)}else this.posteriorProbability?(this.dataRange.min=this.config.min||0,this.dataRange.max=this.config.max||1):(this.dataRange.max=this.config.max||25,this.dataRange.min=this.config.min||0);return this.dataRange}}class Xg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.autoscale=t.autoscale||void 0===t.max,this.dataRange={min:t.min||0,max:t.max},this.windowFunction=t.windowFunction||"mean",this.paintAxis=pp,this.graphType=t.graphType||"bar",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=zu(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if("function"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleNames=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty("clickToHighlight")){let t=this.header.clickToHighlight;this.config.clickToHighlight=t,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty("highlight")){this.config.highlightSamples={};let t=this.header.highlight;Array.isArray(t)||(t=[t]);for(let e of t){const t=e.split(";");2===t.length&&(this.config.highlightSamples[t[0]]=t[1])}}}}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}async getFeatures(t,e,n){const r=await this.featureSource.getFeatures({chr:t,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let i,o;for(let t=1;t<r.length-1;t++)if(void 0===i&&r[t].end>e&&(i=t-1),void 0===o&&r[t].start>n){o=t+1;break}return void 0===i&&(i=0),void 0===o&&(o=r.length),r.slice(i,o)}draw(t){const{features:e,context:n,bpPerPixel:r,bpStart:i,pixelWidth:o,pixelHeight:s}=t,a=t=>(this.dataRange.max-t)/(this.dataRange.max-this.dataRange.min)*s,l=function(t){let e=Math.floor((t-i)/r);return isNaN(e)&&console.warn("isNaN(x). feature start "+Se(t)+" bp start "+Se(i)),e};if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const t=this.config.highlightSamples,r=this.config.onlyHandleClicksForHighlightedSamples,i=this.config.clickToHighlight;let o=-1,s={},c=[],h=[];this.clickDetectorCache={};for(let u of e){const e=l(u.start),f=l(u.end),d=o>=0?l(o):e;if(!isNaN(e)&&!isNaN(f)){this.clickDetectorCache[e]=[],this.clickDetectorCache[f]=[];for(let o=0;o<u.values.length;o++){const l=this.sampleNames[o],p=u.values[o],g=a(p);if(e-d>=1){const o=s[l],h=a(o),u=t&&t[l];u?c.push([d,h,e,g,u]):i&&l in this.config.samplesClickedToHighlight?c.push([d,h,e,g,this.config.samplesClickedToHighlight[l]]):Xo.strokeLine(n,d,h,e,g,{strokeStyle:"#D9D9D9"}),r&&!(l in t)||this.clickDetectorCache[e].push([d,h,e,g,l,u||"gray"])}if(f-e>=1){const o=t&&t[l];o?h.push([e,g,f,g,o]):i&&l in this.config.samplesClickedToHighlight?h.push([e,g,f,g,this.config.samplesClickedToHighlight[l]]):Xo.strokeLine(n,e,g,f,g,{strokeStyle:"gray"}),r&&!(l in t)||this.clickDetectorCache[f].push([e,g,f,g,l,o||"gray"])}s[l]=p}o=u.end}}for(let t of c)Xo.strokeLine(n,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:1.3});for(let t of h)Xo.strokeLine(n,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:2})}(t=>{if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let n=a(e.y),r={strokeStyle:e.color,strokeWidth:2};e.dotted?Xo.dashedLine(t.context,0,n,t.pixelWidth,n,5,r):Xo.strokeLine(t.context,0,n,t.pixelWidth,n,r)}})(t)}doAutoscale(t){let e,n;return t.length>0?(e=Number.MAX_VALUE,n=-Number.MAX_VALUE,t.forEach((function(t){e=Math.min(e,...t.values),n=Math.max(n,...t.values)})),e-=.01,n+=.01):(e=0,n=100),{min:e,max:n}}clickedFeatures(t){const e=t.canvasX,n=t.canvasY;let r=null;for(r of Object.keys(this.clickDetectorCache))if(r=parseInt(r),r>=e)break;if(r){let t=Number.MAX_VALUE,s=[];const a=this.clickDetectorCache[r];for(let r of a){const i=r[0],o=r[2];if(e<i||e>o)return[];const a=r[1],l=r[3];if(n<Math.min(a,l)-10||n>Math.max(a,l)+10)continue;const c=Yg(e,n,i,a,o,l);c<t&&(s=[{name:r[4],color:r[5]}],t=c)}if(t<5){if(this.config.clickToHighlight){if(s[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[s[0].name];else if("any"===this.config.clickToHighlight){var i=["red","darkblue","green","teal","olivedrab","orange","maroon","purple","blue","gold"],o=i[Math.floor(Math.random()*(i.length+1))];this.config.samplesClickedToHighlight[s[0].name]=o}else this.config.samplesClickedToHighlight[s[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return s}}return[]}popupData(t,e){e=this.clickedFeatures(t,e);const n=[];return e.forEach((function(t){for(let e of Object.keys(t))Ss(t[e])&&n.push({name:e,value:t[e]})})),n}get supportsWholeGenome(){return!1}}function Yg(t,e,n,r,i,o){const s=i-n,a=o-r,l=Math.abs(s*(r-e)-(n-t)*a),c=Math.sqrt(s*s+a*a);return c>0?l/c:0}class Kg extends ml{constructor(t,e){super(t,e),t.height||(this.height=300),this.arcOrientation=!1,this.theta=Math.PI/2,"bp"===t.format?this.featureSource=new Jg(t,e.genome):this.featureSource=new vc(t,e.genome)}async getFeatures(t,e,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r})}draw(t){const e=t.context,n=Math.PI/2,r=t.pixelWidth,i=t.pixelHeight;t.viewportWidth;const o=t.bpPerPixel,s=t.bpStart,a=o,l=this.arcOrientation;Xo.fillRect(e,0,t.pixelTop,r,i,{fillStyle:"rgb(255, 255, 255)"});const c=t.features;if(c){Qg(c,1);for(let t of c)if(t.startLeft){let r=Math.round((t.startLeft-s)/a),i=Math.round((t.startRight-s)/a),o=Math.round((t.endLeft-s)/a),c=Math.round((t.endRight-s)/a);e.fillStyle=t.color,e.strokeStyle=t.color,e.beginPath();let h=(r+c)/2,u=(c-r)/2,f=this.height,d=Math.PI+(Math.PI/2-n),p=2*Math.PI-(Math.PI/2-n);l?(f=0,e.arc(h,f,u,p,d),e.lineTo(c,f)):(e.arc(h,f,u,d,p),e.lineTo(o,f));const g=(i+o)/2,m=(o-i)/2,v=f;l?(e.arc(g,v,m,d,p,!0),e.lineTo(o,v)):(e.arc(g,v,m,p,d,!0),e.lineTo(r,v)),e.stroke(),e.fill(),t.drawState={x1:h,y1:f,r1:u,x2:g,y2:v,r2:m,sa:d,ea:p}}else{let r=Math.round((t.start-s)/a),i=Math.round((t.end-s)/a);e.strokeStyle=t.color,e.beginPath();let o=(r+i)/2,c=(i-r)/2,h=this.height,u=Math.PI+(Math.PI/2-n),f=2*Math.PI-(Math.PI/2-n);l?(h=0,e.arc(o,h,c,f,u)):e.arc(o,h,c,u,f),e.stroke(),t.drawState={x1:o,y1:h,r1:c,sa:u,ea:f}}}}clickedFeatures(t,e){const n=[];Qg(e=super.clickedFeatures(t,e),-1);for(let r of e){const e=r.drawState,i=t.canvasX-e.x1,o=t.canvasY-e.y1,s=Math.sqrt(i*i+o*o),a=e.r1+3;let l,c;if(void 0===e.x2)l=s,c=e.r1-3;else{const n=t.canvasX-e.x2,r=t.canvasY-e.y2;l=Math.sqrt(n*n+r*r),c=e.r2-3}if(s<a&&l>c){n.push(r);break}}return n}popupData(t,e){if((e=this.clickedFeatures(t,e))&&e.length>0)return this.extractPopupData(e[0],this.getGenomeId())}menuItemList(){var t=this;return[{name:"Toggle arc direction",click:function(){t.arcOrientation=!t.arcOrientation,t.trackView.repaintViews()}}]}}function Qg(t,e){t.sort((function(t,n){const r=void 0===t.score?-Number.MAX_VALUE:t.score,i=void 0===n.score?-Number.MAX_VALUE:n.score;return(void 0===e?1:e)*(r-i)}))}class Jg{constructor(t,e){this.config=t,this.genome=e}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,n,r);{const t=Cs(this.config),i=await Eo.loadString(this.config.url,t);return this.featureCache=new Ho(function(t){if(!t)return null;const e=$l(t);let n,r=!0;const i=[],o=[],s=[];for(;void 0!==(n=e.nextLine());){const t=n.split("\t");if(r&&n.startsWith("color:")){const e="rgb("+t[1]+","+t[2]+","+t[3]+")";i.push(e),t.length>4&&o.push(t[4])}else{r=!1;const e=t[0],n=Number.parseInt(t[1])-1,l=Number.parseInt(t[2])-1,c=Number.parseInt(t[3]),h=Number.parseInt(t[4]);var a=Number.parseInt(t[5]);const u=i[a];let f;f=n<=h?{chr:e,startLeft:Math.min(n,l),startRight:Math.max(n,l),endLeft:Math.min(c,h),endRight:Math.max(c,h),color:u,score:a}:{chr:e,startLeft:Math.min(c,h),startRight:Math.max(c,h),endLeft:Math.min(n,l),endRight:Math.max(n,l),color:u,score:a},f.start=f.startLeft,f.end=f.endRight,o.length>a&&(f.description=o[a]),s.push(f)}}return s}(i),s),this.featureCache.queryFeatures(e,n,r)}}}class tm{constructor(t){this.browser=t,this.type="ideogram",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}async getFeatures(t,e,n){return[]}computePixelHeight(t){return this.height}draw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i}=t;const o=n.chr,s=n.genome.getChromosome(o);if(void 0===s||r<=0||i<=0||"all"===o.toLowerCase())return;!function(t){let{ctx:e,chr:n,referenceFrame:r,genome:i,width:o,height:s,stainColors:a}=t;const l=1,c=.5*l,h=0;if(void 0===i)return;Xo.fillRect(e,0,0,o,s,{fillStyle:mo.greyScale(255)});const u=i.getCytobands(n);if(u){const t=h+s/2,n=[],r=[];if(0===u.length)return;const i=o/u[u.length-1].end;e.beginPath(),Xo.roundRect(e,c,c+h,o-2*c,s-2*c,(s-2*c)/2,0,1),e.clip();for(let o=0;o<u.length;o++){const c=u[o],f=i*c.start,d=i*c.end;"c"===c.type?("p"===c.name.charAt(0)?(n[0]=f,r[0]=s+h,n[1]=f,r[1]=h,n[2]=d,r[2]=t):(n[0]=d,r[0]=s+h,n[1]=d,r[1]=h,n[2]=f,r[2]=t),e.fillStyle="rgb(150, 0, 0)",e.strokeStyle="rgb(150, 0, 0)",Xo.polygon(e,n,r,1,0)):(e.fillStyle=em(a,c),Xo.fillRect(e,f,l+h,d-f,s-2*l))}}e.strokeStyle=mo.greyScale(41),Xo.roundRect(e,c,c+h,o-2*c,s-2*c,(s-2*c)/2,0,1)}({ctx:e,chr:o,referenceFrame:n,genome:n.genome,width:r,height:i,stainColors:[]});const a=Math.round(n.bpPerPixel*r),l=n.start;let c=s.bpLength;const h=n.genome.getCytobands(o);if(h&&h.length>0&&h[h.length-1].end&&(c=Math.max(c,h[h.length-1].end),s.bpLength=c),a<c){const t=a/c,n=l/c;let o=Math.floor(n*r),s=Math.floor(t*r);o=Math.max(0,o),o=Math.min(r-s,o),e.save(),e.strokeStyle="red",e.lineWidth=s<2?1:2;const h=o+e.lineWidth/2;s=s<2?1:s-e.lineWidth;const u=e.lineWidth/2,f=i-e.lineWidth;e.strokeRect(h,u,s,f),e.restore()}}dispose(){this.trackView=void 0}}function em(t,e){if("c"===e.type)return"rgb(150, 10, 10)";var n=e.stain,r=230;"p"===e.type&&(r=Math.floor(230-n/100*230));var i=t[r];return i||(i="rgb("+r+","+r+","+r+")",t[r]=i),i}let nm=new ju("Dark2");["GT/AG","CT/AC","GC/AG","CT/GC","AT/AC","GT/AT","non-canonical"].forEach((t=>{nm.getColor(t)}));const rm={};class im extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"junctions",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:zu(t,this.browser.genome),this.margin=void 0===t.margin?10:t.margin,this.height||(this.height=100),void 0===t.colorByNumReadsThreshold&&(t.colorByNumReadsThreshold=5)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(t,e,n,r){const i=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:i})}computePixelHeight(t){return this.height}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=t.pixelHeight,a=i+o*r+1;if(this.config.isMergedTrack||Xo.fillRect(n,0,t.pixelTop,o,s,{fillStyle:"rgb(255, 255, 255)"}),e){rm.referenceFrame=t.viewport.referenceFrame,rm.referenceFrameStart=rm.referenceFrame.start,rm.referenceFrameEnd=rm.referenceFrameStart+rm.referenceFrame.toBP(pe(t.viewport.contentDiv).width()),rm.featureZoomOutTracker={};for(let t of e)if(!(t.end<i)){if(t.start>a)break;this.renderJunction(t,i,r,s,n)}}else console.log("No feature list")}renderJunction(t,e,n,r,i){t.isVisible=!1;const o=Math.round((t.start-e)/n),s=Math.round((t.end-e)/n),a=(o+s)/2;if(s-o<=3){if(a in rm.featureZoomOutTracker)return;rm.featureZoomOutTracker[a]=!0}if(this.config.hideAnnotatedJunctions&&"true"===t.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&"false"===t.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(t.attributes.motif))return;if(this.config.hideStrand===t.strand)return;if(this.config.minJunctionEndsVisible){let e=0;if(t.start>=rm.referenceFrameStart&&t.start<=rm.referenceFrameEnd&&(e+=1),t.end>=rm.referenceFrameStart&&t.end<=rm.referenceFrameEnd&&(e+=1),e<this.config.minJunctionEndsVisible)return}let l,c,h,u;if(t.attributes.uniquely_mapped){if(l=parseInt(t.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(c=parseInt(t.attributes.multi_mapped),h=l+c,h<this.config.minTotalReads)return;if(h>0&&c/h>this.config.maxFractionMultiMappedReads)return;if(t.attributes.maximum_spliced_alignment_overhang&&parseInt(t.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(t.attributes.num_samples_with_this_junction){if(u=parseInt(t.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(t.attributes.num_samples_total&&(t.attributes.percent_samples_with_this_junction=100*u/Number(t.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(t.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||t.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,d=this.height,p=f+.5*d;let g=f;const m=f+d-10,v=(o+a)/2,b=(a+s)/2;let w,y,x=1;t.attributes.line_width?x=Number(t.attributes.line_width):(void 0===this.config.thicknessBasedOn||"numUniqueReads"===this.config.thicknessBasedOn?x=l:"numReads"===this.config.thicknessBasedOn?x=h:"numSamplesWithThisJunction"===this.config.thicknessBasedOn&&void 0!==u&&(x=u),x=1+Math.log(x+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||"random"===this.config.bounceHeightBasedOn?w=(t.start+t.end)%7:"distance"===this.config.bounceHeightBasedOn?w=6*(t.end-t.start)/(rm.referenceFrameEnd-rm.referenceFrameStart):"thickness"===this.config.bounceHeightBasedOn&&(w=2*x),g+=d*Math.max(7-w,0)/10,y=t.attributes.color?t.attributes.color:void 0===this.config.colorBy||"numUniqueReads"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"numReads"===this.config.colorBy?h>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"isAnnotatedJunction"===this.config.colorBy?"true"===t.attributes.annotated_junction?"#b0b0ec":"orange":"strand"===this.config.colorBy?"+"===t.strand?"#b0b0ec":"#ecb0b0":"motif"===this.config.colorBy?nm.getColor(t.attributes.motif):"#AAAAAA";let _="";t.attributes.label?_=t.attributes.label.replace(/_/g," "):void 0===this.config.labelWith||"uniqueReadCount"===this.config.labelWith?_=l:"totalReadCount"===this.config.labelWith?_=h:"numSamplesWithThisJunction"===this.config.labelWith?void 0!==u&&(_=u):"percentSamplesWithThisJunction"===this.config.labelWith?void 0!==t.attributes.percent_samples_with_this_junction&&(_=t.attributes.percent_samples_with_this_junction.toFixed(0)+"%"):"motif"===this.config.labelWith&&void 0!==t.attributes.motif&&(_+=t.attributes.motif),"uniqueReadCount"===this.config.labelWithInParen?_+=" ("+l+")":"totalReadCount"===this.config.labelWithInParen?_+=" ("+h+")":"multiMappedReadCount"===this.config.labelWithInParen?c>0&&(_+=" (+"+c+")"):"numSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==u&&(_+=" ("+u+")"):"percentSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==t.attributes.percent_samples_with_this_junction&&(_+=" ("+t.attributes.percent_samples_with_this_junction.toFixed(0)+"%)"):"motif"===this.config.labelWithInParen&&void 0!==t.attributes.motif&&(_+=` ${t.attributes.motif}`),t.isVisible=!0,i.beginPath(),i.moveTo(o,m),i.bezierCurveTo(v,g,b,g,s,m),i.lineWidth=x,i.strokeStyle=y,i.stroke();const k=(t,e,n,r)=>{t.beginPath(),t.moveTo(e,n),t.lineTo(e-r/2,n-r),t.lineTo(e+r/2,n-r),t.lineTo(e,n),t.closePath(),t.fill()};if(t.attributes.left_shape||t.attributes.right_shape){i.fillStyle=y;const e=i.lineWidth>2?10:7;t.attributes.left_shape&&k(i,o,m,e),t.attributes.right_shape&&k(i,s,m,e)}i.fillText(_,a-i.measureText(_).width/2,(7*g+p)/8)}clickedFeatures(t,e){return super.clickedFeatures(t,e).filter((function(t){return t.isVisible&&t.attributes}))}popupData(t,e){e=this.clickedFeatures(t,e);const n=t.genomicLocation,r=[];for(let t of e){const e="function"==typeof t.popupData?t.popupData(n):this.extractPopupData(t._f||t,this.getGenomeId());e&&(r.length>0&&r.push("<hr/><hr/>"),Array.prototype.push.apply(r,e))}return r}dispose(){this.trackView=void 0}}const om=new Map([["ideogram",(t,e)=>new tm(t,e)],["sequence",(t,e)=>new Ys(t,e)],["feature",(t,e)=>new Tg(t,e)],["seg",(t,e)=>new Ig(t,e)],["mut",(t,e)=>new Ig(t,e)],["maf",(t,e)=>new Ig(t,e)],["wig",(t,e)=>new Ag(t,e)],["merged",(t,e)=>new Og(t,e)],["alignment",(t,e)=>new Zp(t,e)],["interaction",(t,e)=>new Pg(t,e)],["interact",(t,e)=>new Pg(t,e)],["variant",(t,e)=>new qg(t,e)],["eqtl",(t,e)=>new $g(t,e)],["gwas",(t,e)=>new Zg(t,e)],["arc",(t,e)=>new Kg(t,e)],["gcnv",(t,e)=>new Xg(t,e)],["junction",(t,e)=>new im(t,e)]]);var sm=function(t,e){om.set(t,e)},am=function(t,e,n){let r;switch(t){case"annotation":case"genes":case"fusionjuncspan":case"snp":r="feature";break;case"seg":case"maf":case"mut":r="seg";break;case"junctions":case"splicejunctions":r="junction";break;default:r=t}return om.has(r)?om.get(r)(e,n):void 0};class lm{constructor(t,e){const n=(new DOMParser).parseFromString(t,"text/xml");this.processRootNode(n,e);const r=n.getElementsByTagName("Resource"),i=n.getElementsByTagName("Track"),o=i&&i.length>0,s=[];this.tracks=s;const a=new Map;Array.from(r).forEach((function(t,e){var n={url:t.getAttribute("path"),indexURL:t.getAttribute("index"),order:e};a.set(n.url,n),o||s.push(n)})),o&&Array.from(i).forEach((function(t){const e=t.getElementsByTagName("Track");if(e&&e.length>0){const n={type:"merged",tracks:[]};cm(t,n),s.push(n),Array.from(e).forEach((function(t){t.processed=!0;const e=t.getAttribute("id"),r=a.get(e);r&&(n.tracks.push(r),cm(t,r),r.autoscale=!1,n.height=r.height)}))}else if(!t.processed){const e=t.getAttribute("id"),n=a.get(e);n&&(s.push(n),cm(t,n))}}))}processRootNode(t,e){const n=t.getElementsByTagName("Session");!n||n.length;const r=n.item(0),i=r.getAttribute("genome"),o=r.getAttribute("locus"),s=r.getAttribute("ucscID");e&&e.hasOwnProperty(i)?this.genome=i:(this.reference={fastaURL:i},s&&(this.reference.id=s)),o&&(this.locus=o)}}function cm(t,e){e.name=t.getAttribute("name");const n=t.getAttribute("color");n&&(e.color="rgb("+n+")");const r=t.getAttribute("altColor");n&&(e.altColor="rgb("+r+")");const i=t.getAttribute("height");i&&(e.height=parseInt(i));const o=t.getAttribute("autoScale");o&&(e.autoscale="true"===o);const s=t.getAttribute("autoscaleGroup");s&&(e.autoscaleGroup=s);const a=t.getAttribute("windowFunction");a&&(e.windowFunction=a);const l=t.getAttribute("visibilityWindow")||t.getAttribute("featureVisibilityWindow");l&&(e.visibilityWindow=l);const c=t.getAttribute("indexed");c&&(e.indexed="true"===c);const h=t.getAttribute("normalize");h&&(e.normalize="true"===h);const u=t.getElementsByTagName("DataRange");if(u.length>0){const t=u.item(0);e.min=Number(t.getAttribute("minimum")),e.max=Number(t.getAttribute("maximum")),e.logScale="LOG"===t.getAttribute("type")}}const hm=Ce;class um{constructor(){this.attributes={},this.plinkLoaded=!1}async loadPlinkFile(t,e){e||(e={});var n=Cs(e);const r=await Eo.loadString(t,n);var i=hm(r);for(let t of i){var o=t.split(" ");this.attributes[o[1]]={familyId:o[0],fatherId:o[2],motherId:o[3],sex:o[4],phenotype:o[5]}}return this.plinkLoaded=!0,this}getAttributes(t){return this.attributes[t]}getAttributeNames(){return this.hasAttributes()?Object.keys(this.attributes[Object.keys(this.attributes)[0]]):[]}hasAttributes(){return Object.keys(this.attributes).length>0}}class fm{constructor(t,e){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,t&&(this.gene=t.toUpperCase(),this.geneColors[this.gene]=dm[this.genesCount++]),e&&(this.snp=e.toUpperCase())}addGene(t){this.geneColors[t.toUpperCase()]||(this.geneColors[t.toUpperCase()]=dm[this.genesCount++])}colorForGene(t){return this.geneColors[t.toUpperCase()]}}var dm=[];dm.push("rgb(228,26,28)"),dm.push("rgb(55,126,184)"),dm.push("rgb(77,175,74)"),dm.push("rgb(166,86,40)"),dm.push("rgb(152,78,163)"),dm.push("rgb(255,127,0)"),dm.push("rgb(247,129,191)"),dm.push("rgb(153,153,153)"),dm.push("rgb(255,255,51)"),dm.push("rgb(102, 194, 165"),dm.push("rgb(252, 141, 98"),dm.push("rgb(141, 160, 203"),dm.push("rgb(231, 138, 195"),dm.push("rgb(166, 216, 84"),dm.push("rgb(255, 217, 47"),dm.push("rgb(229, 196, 148"),dm.push("rgb(179, 179, 179"),dm.push("rgb( 141, 211, 199"),dm.push("rgb(255, 255, 179"),dm.push("rgb(190, 186, 218"),dm.push("rgb(251, 128, 114"),dm.push("rgb(128, 177, 211"),dm.push("rgb(253, 180, 98"),dm.push("rgb(179, 222, 105"),dm.push("rgb(252, 205, 229"),dm.push("rgb(217, 217, 217"),dm.push("rgb(188, 128, 189"),dm.push("rgb(204, 235, 197"),dm.push("rgb(255, 237, 111");class pm{constructor(t,e,n,r,i){this.genome=t,this.chr=e,this.start=n,this.end=r,this.bpPerPixel=i,this.id=be()}extend(t){const e=Math.min(t.start,this.start),n=Math.max(t.end,this.end),r=(n-e)/(this.end-this.start);this.start=e,this.end=n,this.bpPerPixel*=r}calculateEnd(t){return this.start+this.bpPerPixel*t}calculateBPP(t,e){return(t-this.start)/e}set(t){this.chr=t.chr,this.start=t.start,this.bpPerPixel=t.bpPerPixel}toPixels(t){return t/this.bpPerPixel}toBP(t){return this.bpPerPixel*t}shiftPixels(t,e,n){const r=this.start,i=t*this.bpPerPixel;return this.start+=i,n&&this.clampStart(e),this.end=this.start+e*this.bpPerPixel,r!==this.start}clampStart(t){const e=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(e,this.start),t){const{bpLength:e}=this.genome.getChromosome(this.chr),n=e-t*this.bpPerPixel;this.start>n&&(this.start=n)}}async zoomWithScaleFactor(t,e,n,r){const i=void 0===r?this.start+this.toBP(n/2):r,{start:o,bpPerPixel:s}=this.start,{bpLength:a}=this.getChromosome(),l=e<1?t.minimumBases()/n:a/n;this.bpPerPixel=e<1?Math.max(this.bpPerPixel*e,l):Math.min(this.bpPerPixel*e,l);const c=this.bpPerPixel*n;this.start=i-.5*c,this.clampStart(n),this.end=this.start+c;(o!==this.start||s!==this.bpPerPixel)&&await t.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabel(t){const e=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*t);return`&nbsp${this.chr}&nbsp &nbsp &nbsp${Ls(n-e)}&nbsp`}getPresentationLocusComponents(t){if("all"===this.chr)return{chr:this.chr};{const e=Se(Math.floor(this.start)+1),n=Se(Math.round(this.start+this.bpPerPixel*t));return{chr:this.chr,start:e,end:n}}}getLocusString(){if("all"===this.chr)return"all";{const t=Se(Math.floor(this.start)+1),e=Se(Math.round(this.end));return`${this.chr}:${t}-${e}`}}description(t){console.log(` ${t||""} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Se(Math.round(this.start))} end ${Se(Math.round(this.end))} `)}}const gm={A:"rgb(  0, 200,   0)",C:"rgb(  0,0,200)",T:"rgb(255,0,0)",G:"rgb(209,113,  5)",N:"rgb(80,80,80)"},mm={timeout:5e3,type:"plain",url:"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$",coords:0,chromosomeField:"chromosome",startField:"start",endField:"end",geneField:"gene",snpField:"snp"};async function vm(t,e){if(void 0===e||""===e.trim())return;(e&&"all"===e.trim().toLowerCase()||"*"===e)&&(e="all");const n=e.split(" ");let r=t.searchConfig||mm,i=[];const o=async n=>{let i=function(t,e){const n=e.split("\t");if(n.length>=3)try{const e=t.genome.getChromosomeName(n[0]),r=parseInt(n[1].replace(/,/g,""),10)-1,i=parseInt(n[2].replace(/,/g,""),10);if(!isNaN(r)&&!isNaN(i))return{chr:e,start:r,end:i}}catch(t){}const r=e.split(":"),i=r[0];if("all"===i&&t.genome.getChromosome(i))return{chr:i,start:0,end:t.genome.getChromosome(i).bpLength};if(void 0===t.genome.getChromosome(i))return;{const e={chr:t.genome.getChromosomeName(i),start:0,end:t.genome.getChromosome(i).bpLength};if(r.length>1){let n,i=r[1].split("-");if(i.length>2){if(!r[1].startsWith("-"))return;{const t=r[1].indexOf("-",1);if(t>0){i=[r[1].substring(0,t),r[1].substring(t+1)]}}}if(n=i[0].replace(/,/g,""),isNaN(n))return;if(e.start=parseInt(n,10)-1,e.end=e.start+1,1===i.length&&(e.start-=20,e.end+=20),2===i.length){if(n=i[1].replace(/,/g,""),isNaN(n))return;if(e.end=parseInt(n,10),e.start<0&&!t.isSoftclipped()){const t=-e.start;e.start+=t,e.end+=t}}}return e}}(t,n);if(!i){const r=t.genome.featureDB[n.toUpperCase()];r&&(i={chr:r.chr,start:r.start,end:r.end,gene:r.name,locusSearchString:e})}if(!i&&t.config&&!1!==t.config.search)try{i=await async function(t,e,n){let r=n.url.replace("$FEATURE$",e.toUpperCase());r.indexOf("$GENOME$")>-1&&(r=r.replace("$GENOME$",t.genome.id?t.genome.id:"hg19"));const i=n.timeout?{timeout:n.timeout}:void 0,o=await Eo.loadString(r,i),s=function(t,e,n){let r;r="plain"===n.type?function(t,e){const n=[],r=[];return Ce(e).forEach((function(t){""===t||n.push(t)})),n.forEach((function(e){var n,i,o,s,a=e.split("\t");a.length>=3&&(o=(i=a[1].split(":"))[1].split("-"),n=a[2].trim(),s={gene:a[0],chromosome:t.genome.getChromosomeName(i[0].trim()),start:parseInt(o[0].replace(/,/g,"")),end:parseInt(o[1].replace(/,/g,"")),type:"gtex"===n?"snp":"gene"},r.push(s))})),r}(t,e):JSON.parse(e);n.resultsField&&(r=r[n.resultsField]);if(r&&0!==r.length){const e=n.chromosomeField||"chromosome",i=n.startField||"start",o=n.endField||"end",s=n.coords||1;let a;a=Array.isArray(r)?r[0]:r,a.hasOwnProperty(e)&&a.hasOwnProperty(i)||console.error("Search service results must include chromosome and start fields: "+a);const l=a[e],c=t.genome.getChromosome(l);if(!c)return;const h=c.name;let u=a[i]-s,f=a[o];void 0===f&&(f=u+1);const d={chr:h,start:u,end:f},p=a.type?a.type:"gene";return n.geneField&&"gene"===p&&(d.gene=a[n.geneField]),n.snpField&&"snp"===p&&(d.snp=a[n.snpField]),d}return}(t,o,n);s&&(s.locusSearchString=e);return s}(t,n,r)}catch(t){throw console.error(t),Error("Search service currently unavailable.")}return i};for(let t of n){const e=await o(t);e&&(e.locusSearchString=t,i.push(e))}if(0===i.length){const t=await o(e);t&&(t.locusSearchString=e,i.push(t))}return 0===i.length?void 0:i}class bm{constructor(t){this.browser=t}navbarDidResize(t,e){this.updateNavbar(this.createResponsiveClassSchedule(t,e))}updateNavbar(t){this.browser.$toggle_button_container.removeClass(),this.browser.$toggle_button_container.addClass(t.$toggle_button_container),pe(this.browser.zoomWidget.zoomContainer).removeClass(),pe(this.browser.zoomWidget.zoomContainer).addClass(t.zoomContainer)}createResponsiveClassSchedule(t,e){let n={};return e?this.browser.windowSizePanel.hide():this.browser.windowSizePanel.show(),t>990?(n.$toggle_button_container="igv-navbar-toggle-button-container",n.zoomContainer="igv-zoom-widget"):t>860?(n.$toggle_button_container="igv-navbar-toggle-button-container",n.zoomContainer="igv-zoom-widget-900"):t>540?(n.$toggle_button_container="igv-navbar-toggle-button-container-750",n.zoomContainer="igv-zoom-widget-900"):(n.$toggle_button_container="igv-navbar-toggle-button-container-750",n.zoomContainer="igv-zoom-widget-900",this.browser.windowSizePanel.hide()),e&&(n.zoomContainer="igv-zoom-widget-hidden"),n}}const wm=function(t,e){this.container=ge({class:"igv-chromosome-select-widget-container"}),e.appendChild(this.container),this.select=document.createElement("select"),this.select.setAttribute("name","chromosome-select-widget"),this.container.appendChild(this.select),this.select.addEventListener("change",(()=>{this.select.blur(),""!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes};wm.prototype.show=function(){this.container.style.display="flex"},wm.prototype.hide=function(){this.container.style.display="none"},wm.prototype.update=function(t){const e=this.showAllChromosomes?t.chromosomeNames.slice():t.wgChromosomeNames.slice();t.showWholeGenomeView()&&(e.unshift("all"),e.unshift("")),this.select.innerHTML="";for(let t of e){const e=document.createElement("option");e.setAttribute("value",t),e.innerText=t,this.select.appendChild(e)}};class ym{constructor(t,e){this.container=ge({class:"igv-windowsize-panel-container"}),t.appendChild(this.container),e.on("locuschange",(t=>{this.updatePanel(t)})),this.browser=e}show(){this.container.style.display="block"}hide(){this.container.style.display="none"}updatePanel(t){const e=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===t.length?Ls(Math.round(e*t[0].bpPerPixel)):""}}class xm{constructor(t,e){this.browser=e,this.columnContainer=t,this.horizontalGuide=ge({class:"igv-cursor-guide-horizontal"}),t.appendChild(this.horizontalGuide),this.verticalGuide=ge({class:"igv-cursor-guide-vertical"}),t.appendChild(this.verticalGuide),this.addMouseHandler(e),this.setVisibility(e.config.showCursorGuide)}addMouseHandler(t){this.boundMouseMoveHandler=function(e){const{x:n,y:r}=we(e,this.columnContainer);this.horizontalGuide.style.top=`${r}px`;const i=document.elementFromPoint(e.clientX,e.clientY);let o;if(i.parentElement&&(i.parentElement.classList.contains("igv-viewport-content")?o=i.parentElement.parentElement:i.parentElement.classList.contains("igv-viewport")&&i.classList.contains("igv-viewport-content")&&(o=i.parentElement),o&&t.getRulerTrackView())){this.verticalGuide.style.left=`${n}px`;const r=t.root.querySelectorAll(".igv-column");let i;const s=o.parentElement;for(let t=0;t<r.length;t++)void 0===i&&s===r[t]&&(i=t);const a=t.getRulerTrackView().viewports[i].mouseMove(e);if(a){const{start:t,bp:e,end:n}=a,r=(e-t)/(n-t);this.customMouseHandler&&this.customMouseHandler({start:t,bp:e,end:n,interpolant:r})}}}.bind(this),this.columnContainer.addEventListener("mousemove",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener("mousemove",this.boundMouseMoveHandler)}setVisibility(t){!0===t?this.show():this.hide()}show(){this.verticalGuide.style.display="block",this.horizontalGuide.style.display="block"}hide(){if(this.verticalGuide.style.display="none",this.horizontalGuide.style.display="none",this.browser.getRulerTrackView())for(let t of this.browser.getRulerTrackView().viewports)t.$tooltip.hide()}}class _m{constructor(t,e){this.browser=t,this.button=ge({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="cursor guide",this.button.addEventListener("click",(()=>{t.cursorGuideVisible=!t.cursorGuideVisible,t.setCursorGuideVisibility(t.cursorGuideVisible),this.setButtonState(t.cursorGuideVisible)})),this.setButtonState(t.cursorGuideVisible),t.config.showCursorTrackingGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setButtonState(this.browser.cursorGuideVisible)}hide(){this.button.style.display="none"}}class km{constructor(t,e){this.browser=t,this.button=ge({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="center line",this.button.addEventListener("click",(()=>{t.isCenterLineVisible=!t.isCenterLineVisible,t.setCenterLineVisibility(t.isCenterLineVisible),this.setButtonState(t.isCenterLineVisible)})),this.setButtonState(t.isCenterLineVisible),t.config.showCenterGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.isVisible=!0,this.button.style.display="block",this.setButtonState(this.browser.isCenterLineVisible)}hide(){this.isVisible=!1,this.button.style.display="none"}}class Sm{constructor(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="track labels",this.button.addEventListener("click",(()=>{e.trackLabelsVisible=!e.trackLabelsVisible,this.setState(e.trackLabelsVisible),e.setTrackLabelVisibility(e.trackLabelsVisible)})),this.browser=e,this.setVisibility(e.config.showTrackLabelButton),this.setState(e.trackLabelsVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.trackLabelsVisible)}hide(){this.button.style.display="none"}}class Cm{constructor(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.innerText="Sample Names",this.setState(e.showSampleNames),this.setVisibility(e.showSampleNameButton),this.button.addEventListener("click",(()=>{e.showSampleNames=!e.showSampleNames,this.setState(e.showSampleNames);for(let{sampleNameViewport:t}of e.trackViews)!1===e.showSampleNames?t.hide():t.show();e.layoutChange()}))}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}hide(){this.button.style.display="none"}show(){this.button.style.display="block"}}let Em=23,Tm=0;const Am=function(t,e){this.browser=t,this.zoomContainer=ge({class:"igv-zoom-widget"}),e.appendChild(this.zoomContainer),this.zoomOutButton=ge(),this.zoomContainer.appendChild(this.zoomOutButton),this.zoomOutButton.appendChild(ye("minus-circle")),this.zoomOutButton.addEventListener("click",(()=>{t.zoomOut()}));const n=ge();this.zoomContainer.appendChild(n),this.slider=document.createElement("input"),this.slider.type="range",this.slider.min="0",this.slider.max=`${Em}`,n.appendChild(this.slider),this.slider.addEventListener("change",(e=>{e.preventDefault(),e.stopPropagation();const n=t.referenceFrameList[0],{bpLength:r}=n.genome.getChromosome(n.chr),{end:i,start:o}=n,s=i-o,a=r/Math.pow(2,e.target.valueAsNumber);t.zoomWithScaleFactor(a/s)})),this.zoomInButton=ge(),this.zoomContainer.appendChild(this.zoomInButton),this.zoomInButton.appendChild(ye("plus-circle")),this.zoomInButton.addEventListener("click",(()=>{t.zoomIn()})),t.on("locuschange",(t=>{this.browser.isMultiLocusMode()?this.disable():(this.enable(),this.update(t))}))};Am.prototype.update=function(t){const e=t[0],{bpLength:n}=e.genome.getChromosome(e.chr),{start:r,end:i}=e;Em=Math.ceil(Math.log2(n/this.browser.minimumBases())),this.slider.max=`${Em}`;const o=n/(i-r);Tm=Math.log2(o),this.slider.value=`${Math.round(Tm)}`},Am.prototype.enable=function(){this.slider.disabled=!1},Am.prototype.disable=function(){this.slider.disabled=!0},Am.prototype.hide=function(){this.zoomContainer.style.display="none"},Am.prototype.show=function(){this.zoomContainer.style.display="block"},Am.prototype.hideSlider=function(){this.slider.style.display="none"},Am.prototype.showSlider=function(){this.slider.style.display="block"};const Lm=function(t,e){const n=ge({class:"igv-navbar-button"});t.append(n),n.textContent="Save SVG",n.addEventListener("click",(()=>e.saveSVGtoFile({})))},Mm=(t,e)=>{const n=0===t?e.nextElementSibling:e.previousElementSibling;e.remove(),n.remove()},Rm=t=>{const e=ge({class:"igv-column-shim"});Ns(e,t);const n=ge({class:"igv-column"});return Ns(n,e),n},Im=(t,e)=>{for(let n=0;n<e;n++){const r=ge({class:"igv-column"});if(Is(r,t),e>1&&n>0){Is(ge({class:"igv-column-shim"}),r)}}};class Nm{constructor(t,e,n){this.browser=t,this.referenceFrame=e,this.column=n,this.container=ge({class:"igv-center-line"}),n.appendChild(this.container),t.isCenterLineVisible?this.show():this.hide()}repaint(){if(this.referenceFrame){if(1/this.referenceFrame.bpPerPixel>1){const t=Math.floor(this.referenceFrame.toPixels(1));this.container.style.width=`${t}px`,this.container.classList.remove("igv-center-line-thin"),this.container.classList.add("igv-center-line-wide")}else this.container.style.width="1px",this.container.classList.remove("igv-center-line-wide"),this.container.classList.add("igv-center-line-thin")}}show(){this.isVisible=!0,this.container.style.display="block",this.repaint()}hide(){this.isVisible=!1,this.container.style.display="none"}resize(){this.repaint()}}const Om=Se;class Pm{constructor(t){this.browser=t,this.height=40,this.name="",this.id="ruler",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type="ruler"}async getFeatures(t,e,n){return[]}computePixelHeight(t){return this.height}draw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpPerPixel:o,bpStart:s}=t;ya.isWholeGenomeView(n.chr)?this.drawWholeGenome({context:e,pixelWidth:r,pixelHeight:i,bpPerPixel:o}):this.doDraw({context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpStart:s})}drawWholeGenome(t){let{context:e,pixelWidth:n,pixelHeight:r,bpPerPixel:i}=t;e.save(),Xo.fillRect(e,0,0,n,r,{fillStyle:"white"});for(let t of this.browser.genome.wgChromosomeNames){let n=this.browser.genome.getCumulativeOffset(t),o=this.browser.genome.getChromosome(t).bpLength,s=Math.round(n/i),a=Math.round(o/i);this.renderChromosomeRect(e,s,0,a,r,t)}e.restore()}doDraw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpStart:o}=t;e.clearRect(0,0,r,i);const s=function(t,e){if(t<10)return new Fm(1,"bp",1);const n=Math.floor(Math.log10(t));let r="bp",i=1;n>9?(r="gb",i=1e9):n>6?(r="mb",i=1e6):n>3&&(r="kb",i=1e3);const o=Math.pow(10,n-1),s=t/o,a=75,l=Math.pow(10,n-1),c=Math.pow(10,n)/2;return new Fm(s<a&&!0!==e?l:c,r,i)}(Math.floor(n.toBP(r)),e.isSVG);let a=Math.floor(o/s.majorTick)-1;const{tickDelta:l,labelLength:c}=function(t,e,n,r,i){const o=c(e,l(1+r,i),n)-c(e,l(r,i),n),s=`${Se(Math.floor(l(r,i)/i.unitMultiplier))} ${i.majorUnit}`,a=Math.floor(t.measureText(s).width);return{tickDelta:o,labelLength:a};function l(t,e){return Math.floor(t*e.majorTick)}function c(t,e,n){return Math.round(t.toPixels(e-1-n+.5))}}(e,n,o,a,s);let h,u;this.browser.referenceFrameList.indexOf(n);let f=l;const d=.25*c;do{u=Math.floor(a*s.majorTick);const t=`${Se(Math.floor(u/s.unitMultiplier))} ${s.majorUnit}`;h=Math.round(n.toPixels(u-1-o+.5));const r=Math.round(h-e.measureText(t).width/2);r>0&&d+c<=f&&(Xo.fillText(e,t,r,this.height-8),f=0),h>0&&Xo.strokeLine(e,h,this.height-6,h,this.height-2),u=Math.floor((1+a)*s.majorTick);let i=h+(Math.round(n.toPixels(u-1-o+.5))-h)/2;i>0&&Xo.strokeLine(e,i,this.height-6,i,this.height-2),++a,f+=l}while(h<r);Xo.strokeLine(e,0,this.height-2,r,this.height-2)}renderChromosomeRect(t,e,n,r,i,o){t.textAlign="center",t.textBaseline="middle",t.font="12px sans-serif",Xo.strokeLine(t,e+r,n,e+r,n+i,{strokeStyle:mo.greyScale(191)});const s=o.startsWith("chr")?o.substring(3):o;r>t.measureText(s).width&&Xo.fillText(t,s,e+r/2,n+i/2,{fillStyle:mo.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Fm{constructor(t,e,n){this.majorTick=t,this.minorTick=t/10,this.majorUnit=e,this.unitMultiplier=n}description(t){console.log((t||"")+" tick "+Om(this.majorTick)+" label width "+Om(this.labelWidthBP)+" multiplier "+this.unitMultiplier)}}const Dm=function(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="circular view",this.button.addEventListener("click",(()=>{e.circularViewVisible=!e.circularViewVisible})),this.browser=e,this.setVisibility(e.config.showCircularViewButton),this.setState(e.circularViewVisible)};Dm.prototype.setVisibility=function(t){!0===t?this.show():this.hide()},Dm.prototype.setState=function(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")},Dm.prototype.show=function(){this.button.style.display="block",this.setState(this.browser.circularViewVisible)},Dm.prototype.hide=function(){this.button.style.display="none"};const Bm=function(t,e,n){const r=ge({class:"igv-navbar-button"});t.append(r),r.textContent=n.label,r.addEventListener("click",(()=>n.callback(e)))};class zm{constructor(t,e,n,r,i){this.browser=t,this.roiMenu=e,this.roiTable=n,this.top=r,this.roiSets=i||[],this.boundLocusChangeHandler=Hm.bind(this),t.on("locuschange",this.boundLocusChangeHandler)}async initialize(){this.roiSets.length>0&&(this.browser.showROITableButton=!0,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton));const t=this.roiSets.map((t=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})));t.length>0&&await Promise.all(t);const e=await this.getTableRecords();this.roiTable.renderTable(e)}async loadROI(t,e){const n=Array.isArray(t)?t:[t];for(let t of n)this.roiSets.push(new Zu(t,e));await this.initialize()}clearROIs(){this.roiTable.clearTable();const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();for(let t of this.roiSets)t.dispose();this.roiSets=[]}async getTableRecords(){const t=[];for(let e of this.roiSets){const n=e.isUserDefined?"":e.name||"",r=await e.getAllFeatures();for(let e of Object.keys(r))for(let i of r[e])t.push({setName:n,feature:i})}return t}presentTable(){this.roiTable.present()}async repaintTable(){const t=await this.getTableRecords();this.roiTable.renderTable(t)}dismissTable(){this.roiTable.dismiss()}async updateUserDefinedROISet(t){let e=await this.getUserDefinedROISet();void 0===e&&(e=this.initializeUserDefinedROISet()),e.addFeature(t),!1===this.browser.showROITableButton&&this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e});const n=await this.getTableRecords();this.roiTable.renderTable(n)}setROITableButtonVisibility(t){this.browser.showROITableButton=t,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton)}async renderAllROISets(){for(let t of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})}async renderROISet(t){let{browser:e,pixelTop:n,roiSet:r}=t;const i=e.columnContainer.querySelectorAll(".igv-column");for(let t=0;t<i.length;t++){let{chr:o,start:s,end:a,bpPerPixel:l}=e.referenceFrameList[t];const c=i[t].querySelectorAll(".igv-roi-region");for(let t of c){const e=t.dataset.region,{chr:n,start:r,end:i}=Um(e);(n!==o||i<s||r>a)&&t.remove()}const h=await r.getFeatures(o,s,a);if(h)for(let c of h){const h=Vm(o,c.start,c.end),{x:u,width:f}=Xu(Math.max(s,c.start),Math.min(a,c.end),s,l),d=i[t].querySelector(jm(h));if(d)d.style.left=`${u}px`,d.style.width=`${f}px`;else{const o=this.createRegionElement(e.columnContainer,n,u,f,r,h,c.name);i[t].appendChild(o)}}}}createRegionElement(t,e,n,r,i,o,s){const a=ge({class:"igv-roi-region"});a.style.top=`${e}px`,a.style.left=`${n}px`,a.style.width=`${r}px`,a.style.backgroundColor=i.color,a.dataset.region=o;const l=ge();return a.appendChild(l),l.style.backgroundColor=i.headerColor,!0===i.isUserDefined?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation();const{x:n,y:r}=we(e,t);this.roiMenu.present(n,r,this,t,a)})):s?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation(),this.popover&&this.popover.dispose(),this.popover=new ms(t,i.name),this.popover.presentContentWithEvent(e,s)})):l.style.pointerEvents="none",a}async getUserDefinedROISet(){return this.roiSets.find((t=>!0===t.isUserDefined))}initializeUserDefinedROISet(){const t=new Zu({isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(t),t}async deleteUserDefinedRegionWithKey(t,e){e.querySelectorAll(jm(t)).forEach((t=>t.remove()));const n=await this.findUserDefinedRegionWithKey(t),r=await this.getUserDefinedROISet();r&&r.removeFeature(n);0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}async findUserDefinedRegionWithKey(t){const{chr:e,start:n,end:r}=Um(t),i=await this.getUserDefinedROISet();if(i){const t=await i.getFeatures(e,n,r);for(let i of t)if(i.chr===e&&i.start>=n&&i.end<=r)return i}}toJSON(){return this.roiSets.map((t=>t.toJSON()))}dispose(){this.browser.off("locuschange",this.boundLocusChangeHandler);const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let t of this.roiSets)t.dispose();for(let t of Object.keys(this))this[t]=void 0}}function Hm(){this.renderAllROISets()}function Vm(t,e,n){return`${t}-${e}-${n}`}function jm(t){return`[data-region="${t}"]`}function Um(t){let[e,n,r]=t.split("-");return n=parseInt(n),r=parseInt(r),{chr:e,start:n,end:r,locus:`${e}:${n}-${r}`,bedRecord:`${e}\t${n}\t${r}`}}const qm=[];class Wm{constructor(t,e,n){this.browser=t,this.container=ge({class:n?"igv-roi-table":"igv-roi-table-four-column"}),e.appendChild(this.container),this.hasROISetNames=n;const r=this.createHeaderDOM(this.container);this.columnTitleDOM=function(t,e){const n=ge({class:"igv-roi-table-column-titles"});t.appendChild(n);let r=["Chr","Start","End","Description","ROI Set"];!1===e&&(r=r.slice(0,4));for(let t of r){const e=ge();e.innerText=t,n.appendChild(e)}return n}(this.container,n),this.tableRowContainerDOM=this.createTableRowContainerDOM(this.container),this.footerDOM=this.createFooterDOM(this.container);const{y:i}=t.root.getBoundingClientRect(),{y:o}=e.getBoundingClientRect(),s=-(o-i);bo(this.container,r,{minX:0,minY:s}),this.container.style.display="none"}clearTable(){const t=this.tableRowContainerDOM.querySelectorAll(".igv-roi-table-row");for(let e of t)e.remove()}present(){this.container.style.left="0px",this.container.style.top="0px",this.container.style.display="flex"}dismiss(){this.container.style.display="none"}renderTable(t){if(Array.from(this.tableRowContainerDOM.querySelectorAll(".igv-roi-table-row")).forEach((t=>t.remove())),t.length>0){const e=t.sort(((t,e)=>t.feature.chr.localeCompare(e.feature.chr)||t.feature.start-e.feature.start||t.feature.end-e.feature.end));for(let t of e){const e=this.createTableRowDOM(t);this.tableRowContainerDOM.appendChild(e)}}}createHeaderDOM(t){const e=ge();t.appendChild(e);const n=ge();e.appendChild(n),n.innerText="Regions of Interest";const r=ge();return e.appendChild(r),r.appendChild(ye("times")),r.addEventListener("click",(t=>{t.stopPropagation(),this.browser.roiTableControl.buttonHandler(!1)})),e}createTableRowContainerDOM(t){const e=ge({class:"igv-roi-table-row-container"});return t.appendChild(e),e}createTableRowDOM(t){const e=ge({class:"igv-roi-table-row"}),{setName:n,feature:r}=t;e.dataset.region=Vm(r.chr,r.start,r.end);let i=[r.chr,Se(r.start),Se(r.end),r.name||"",n];!1===this.hasROISetNames&&(i=i.slice(0,4));for(let t of i){const n=ge();n.innerText=t,e.appendChild(n)}return e.addEventListener("mousedown",(t=>{t.stopPropagation(),e.classList.toggle("igv-roi-table-row-selected"),e.classList.contains("igv-roi-table-row-selected")?e.classList.remove("igv-roi-table-row-hover"):e.classList.add("igv-roi-table-row-hover"),this.setButtonState(e.classList.contains("igv-roi-table-row-selected"))})),e.addEventListener("mouseover",(t=>{e.classList.contains("igv-roi-table-row-selected")?e.classList.remove("igv-roi-table-row-hover"):e.classList.add("igv-roi-table-row-hover")})),e.addEventListener("mouseout",(t=>{e.classList.remove("igv-roi-table-row-hover")})),e}createFooterDOM(t){const e=ge();t.appendChild(e);const n=ge({class:"igv-roi-table-button"});return e.appendChild(n),n.id="igv-roi-table-view-button",n.textContent="Go To",n.style.pointerEvents="none",n.addEventListener("click",(e=>{e.stopPropagation();const n=t.querySelectorAll(".igv-roi-table-row-selected"),r=[];for(let t of n){const{locus:e}=Um(t.dataset.region);r.push(e)}for(let e of t.querySelectorAll(".igv-roi-table-row"))e.classList.remove("igv-roi-table-row-selected");this.setButtonState(!1),r.length>0&&this.browser.search(r.join(" "))})),e}setButtonState(t){t?qm.push(1):qm.pop();this.footerDOM.querySelector("#igv-roi-table-view-button").style.pointerEvents=qm.length>0?"auto":"none"}dispose(){this.browser.roiTableControl.buttonHandler(!1),this.container.innerHTML="";for(let t of Object.keys(this))this[t]=void 0}}class $m{constructor(t,e){this.browser=t,this.container=ge({class:"igv-roi-menu-next-gen"}),e.appendChild(this.container);const n=ge();this.container.appendChild(n),_e(n,(()=>this.container.style.display="none")),this.body=ge(),this.container.appendChild(this.body),this.container.style.display="none"}async present(t,e,n,r,i){Gm(this.body);const o=await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region),s=ge();this.body.appendChild(s);const a="Description",l=o.name||a;s.innerText=l,s.setAttribute("title",l),a===l?s.classList.add("igv-roi-placeholder"):s.classList.remove("igv-roi-placeholder");const c=ge();this.body.appendChild(c),c.innerText="Set Description",c.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none";const e={label:"Description",value:o.name||"",callback:()=>{const t=this.browser.inputDialog.input.value||"";o.name=t.trim(),this.container.style.display="none",this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(e,t)}));const h=ge();this.body.appendChild(h),h.innerText="Delete Region",h.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(i.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex"}async __present(t,e,n,r,i){Gm(this.container);const o=await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region);let s;s=ge({class:"igv-roi-menu-row-edit-description"}),this.container.appendChild(s),s.addEventListener("click",(t=>{t.stopPropagation()}));const a="description-input",l=document.createElement("label");s.appendChild(l),l.setAttribute("for",a),l.innerText="Description:";const c=document.createElement("input");s.appendChild(c),c.setAttribute("type","text"),c.setAttribute("name",a),c.setAttribute("placeholder",""),c.value=o.name||"",c.addEventListener("change",(async t=>{t.stopPropagation();(await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region)).name=c.value,c.blur(),this.container.style.display="none",await this.browser.roiManager.repaintTable()})),s=ge({class:"igv-roi-menu-row"}),s.innerText="Delete region",this.container.appendChild(s),s.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(i.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex",r.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none"}))}dispose(){this.container.innerHTML=""}}function Gm(t){for(;t.firstChild;)t.removeChild(t.firstChild)}class Zm{constructor(t,e){this.name=t.name,this.featureSource=t.featureSource||zu(t,e),this.color=t.color||$u}async getFeatures(t,e,n){return this.featureSource.getFeatures({chr:t,start:e,end:n})}draw(t){const{context:e,bpPerPixel:n,bpStart:r,pixelTop:i,pixelHeight:o,pixelWidth:s,features:a}=t;if(!a)return;const l=r+s*n+1;for(let{start:t,end:s}of a){if(s<r)continue;if(t>l)break;const{x:a,width:c}=Xu(t,s,r,n);Xo.fillRect(e,a,i,c,o,{fillStyle:this.color})}}}class Xm{constructor(t,e){this.browser=e,this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="ROI Table",this.button.addEventListener("click",(()=>{this.buttonHandler(!e.roiTableVisible)})),this.browser=e,this.setVisibility(e.showROITableButton),this.setState(e.roiTableVisible)}buttonHandler(t){this.browser.roiTableVisible=t,this.setState(this.browser.roiTableVisible),this.browser.setROITableVisibility(this.browser.roiTableVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.roiTableVisible)}hide(){this.button.style.display="none"}}class Ym{constructor(t,e){this.config=t,this.guid=be(),this.namespace=".browser_"+this.guid,this.parent=e,this.root=ge({class:"igv-container"}),e.appendChild(this.root),this.alert=new _s(this.root),this.columnContainer=ge({class:"igv-column-container"}),this.root.appendChild(this.columnContainer),this.menuPopup=new hg(this.columnContainer),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:"rgb(0,0,150)",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},this.addMouseHandlers(),this.setControls(t)}initialize(t){t.gtex&&(mg.gtexLoaded=!0),this.flanking=t.flanking,this.crossDomainProxy=t.crossDomainProxy,this.formats=t.formats,this.trackDefaults=t.trackDefaults,this.nucleotideColors=t.nucleotideColors||gm;for(let t of Object.keys(this.nucleotideColors))this.nucleotideColors[t.toLowerCase()]=this.nucleotideColors[t];this.trackLabelsVisible=t.showTrackLabels,this.roiTableVisible=t.showROITable,this.showROITableButton=t.showROITableButton,this.isCenterLineVisible=t.showCenterGuide,this.cursorGuideVisible=t.showCursorGuide,this.showSampleNames=t.showSampleNames,this.showSampleNameButton=t.showSampleNameButton,this.sampleNameViewportWidth=t.sampleNameViewportWidth||200,t.search&&(this.searchConfig={type:"json",url:t.search.url,coords:void 0===t.search.coords?1:t.search.coords,chromosomeField:t.search.chromosomeField||"chromosome",startField:t.search.startField||"start",endField:t.search.endField||"end",geneField:t.search.geneField||"gene",snpField:t.search.snpField||"snp",resultsField:t.search.resultsField})}setControls(t){const e=this.createStandardControls(t);e.insertBefore(pe(this.columnContainer)),this.$navigation=e,!1===t.showControls&&e.hide()}createStandardControls(t){this.navbarManager=new 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a=pe("<div>",{class:"igv-search-container"});s.append(a),this.$searchInput=pe("<input>",{class:"igv-search-input",type:"text",placeholder:"Locus Search"}),a.append(this.$searchInput),this.$searchInput.change((()=>this.doSearch(this.$searchInput.val())));const l=ge({class:"igv-search-icon-container"});a.append(pe(l)),l.appendChild(ye("search")),l.addEventListener("click",(()=>this.doSearch(this.$searchInput.val()))),this.windowSizePanel=new ym(s.get(0),this);const c=pe("<div>",{class:"igv-navbar-right-container"});e.append(c);const h=pe('<div class="igv-navbar-toggle-button-container">');if(c.append(h),this.$toggle_button_container=h,this.cursorGuide=new xm(this.columnContainer,this),this.cursorGuideButton=new _m(this,h.get(0)),this.centerLineButton=new km(this,h.get(0)),this.setTrackLabelVisibility(t.showTrackLabels),this.trackLabelControl=new Sm(h.get(0),this),this.roiTableControl=new Xm(h.get(0),this),this.sampleNameControl=new Cm(h.get(0),this),!0===t.showSVGButton&&(this.svgSaveControl=new Lm(h.get(0),this)),t.customButtons)for(let e of t.customButtons)new Bm(h.get(0),this,e);return this.zoomWidget=new Am(this,c.get(0)),!1===t.showNavigation&&this.$navigation.hide(),this.inputDialog=new hs(this.root),this.inputDialog.container.id=`igv-input-dialog-${be()}`,this.dataRangeDialog=new Zo(this,pe(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${be()}`,this.genericColorPicker=new xs({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${be()}`,e}getSampleNameViewportWidth(){return!1===this.showSampleNames?0:this.sampleNameViewportWidth}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}addTrackToFactory(t,e){sm(t,e)}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let t of this.referenceFrameList)if("all"===t.chr.toLowerCase())return!0;return!1}currentLoci(){const t=t=>`${t.chr}:${t.start+1}-${t.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?"":1===this.referenceFrameList.length?t(this.referenceFrameList[0]):this.referenceFrameList.map((e=>t(e)))}toSVG(){let{x:t,y:e,width:n,height:r}=this.columnContainer.getBoundingClientRect();let i=new oa({width:n,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:n,height:8e3}});for(let t of this.trackViews)t.renderSVGContext(i,{deltaX:0,deltaY:-e});return i.setHeight(r),i.getSerializedSvg(!0)}renderSVG(t){const e=this.toSVG();return t.empty(),t.append(e),e}saveSVGtoFile(t){let e=this.toSVG();t.$container&&(t.$container.empty(),t.$container.append(e));We(t.filename||"igvjs.svg",URL.createObjectURL(new Blob([e],{type:"application/octet-stream"})))}async loadSession(t){let e;return this.roiSets=[],e=t.url||t.file?await async function(t){const e=t.url||t.file;if(t.url&&(t.url.startsWith("blob:")||t.url.startsWith("data:"))){const e=Ym.uncompressSession(t.url);return JSON.parse(e)}{let n=t.filename;if(n||(n=t.url?await As(t.url):t.file.name),n.endsWith(".xml")){const t=ya.KNOWN_GENOMES,n=await Eo.loadString(e);return new lm(n,t)}return n.endsWith(".json")?Eo.loadJson(e):void 0}}(t):t,this.loadSessionObject(e)}async loadSessionObject(t){this.cleanHouseForSession(),this.showSampleNames=t.showSampleNames||!1,this.sampleNameControl.setState(!0===this.showSampleNames),t.sampleNameViewportWidth&&(this.sampleNameViewportWidth=t.sampleNameViewportWidth),Rs(this.columnContainer,"igv-axis-column"),Rs(this.columnContainer,"igv-sample-name-column"),Rs(this.columnContainer,"igv-scrollbar-column"),Rs(this.columnContainer,"igv-track-drag-column"),Rs(this.columnContainer,"igv-gear-menu-column");const e=await ya.expandReference(this.alert,t.reference||t.genome);await this.loadReference(e,t.locus),this.centerLineList=this.createCenterLineList(this.columnContainer);let n=0;if(!1!==t.showIdeogram){const t=new tm(this);t.id="ideogram";const e=new pg(this,this.columnContainer,t),{$viewport:r}=e.viewports[0];n=function(t){t="string"==typeof t?document.querySelector(t):t;const e=window.getComputedStyle(t),n=parseFloat(e.marginTop)+parseFloat(e.marginBottom),r=t.offsetHeight;return Math.ceil(n+r)}(r.get(0)),this.trackViews.push(e)}if(!1!==t.showRuler&&this.trackViews.push(new pg(this,this.columnContainer,new Pm(this))),t.gtexSelections)for(let e of this.referenceFrameList)for(let n of Object.keys(t.gtexSelections)){const r=t.gtexSelections[n].gene,i=t.gtexSelections[n].snp;e.selection=new fm(r,i)}this.roiManager&&this.roiManager.dispose();const r=new $m(this,this.columnContainer);if(t.roi){const e=t.roi.map((t=>new Zu(t,this.genome))),i=e.filter((t=>{let{name:e}=t;return void 0!==e&&e.length>0})),o=new Wm(this,this.columnContainer,i.length>0);this.roiManager=new zm(this,r,o,n,e)}else{const t=new Wm(this,this.columnContainer,!1);this.roiManager=new zm(this,r,t,n,void 0)}await this.roiManager.initialize();const i=e.tracks||[],o=t.tracks?i.concat(t.tracks):i;0===o.filter((t=>"sequence"===t.type)).length&&o.push({type:"sequence",order:qs});let s=1;for(let t of o)void 0===t.order&&(t.order=s++);await this.loadTrackList(o);for(let t of this.trackViews.filter((t=>"ruler"===t.track.type||"ideogram"===t.track.type)))t.updateViews();this.updateUIWithReferenceFrameList()}createCenterLineList(t){const e=t.querySelectorAll(".igv-center-line");for(let t=0;t<e.length;t++)e[t].remove();const n=[],r=t.querySelectorAll(".igv-column");for(let t=0;t<r.length;t++)n.push(new Nm(this,this.referenceFrameList[t],r[t]));return n}async loadReference(t,e){const n=await ya.loadGenome(t),r=void 0===this.genome||this.genome.id!==n.id;this.genome=n,this.updateNavbarDOMWithGenome(n),r&&this.removeAllTracks();let i=function(t,e){return t?Array.isArray(t)?t.join(" "):t:e.getHomeChromosomeName()}(e,n);if(!await this.search(i,!0)){console.log("Initial locus not found: "+i),i=n.getHomeChromosomeName();if(!await this.search(i,!0))throw new Error("Cannot set initial locus")}r&&this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:qp(this.genome)})}cleanHouseForSession(){for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column").forEach((t=>t.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}updateNavbarDOMWithGenome(t){let e=t.id&&t.id.length<10?t.id:"";this.$current_genome.text(e),this.$current_genome.attr("title",t.id||""),this.chromosomeSelectWidget.update(t)}async loadGenome(t){const e=await ya.expandReference(this.alert,t);await this.loadReference(e,void 0);const n=e.tracks||[];return 0===n.filter((t=>"sequence"===t.type)).length&&n.push({type:"sequence",order:qs}),await this.loadTrackList(n),await this.updateViews(),this.genome}updateUIWithReferenceFrameList(){const t=this.referenceFrameList;this.updateLocusSearchWidget();const e=this.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(t[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),e),tv(this.trackViews,this.trackLabelsVisible),this.setCenterLineAndCenterLineButtonVisibility(!ya.isWholeGenomeView(t[0].chr))}setTrackLabelVisibility(t){tv(this.trackViews,t)}setROITableVisibility(t){!0===t?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(t){t?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(t){this.cursorGuide.customMouseHandler=t}setCenterLineVisibility(t){for(let e of this.centerLineList)!0===t?(e.show(),e.repaint()):e.hide()}setCenterLineAndCenterLineButtonVisibility(t){for(let e of this.centerLineList){t&&e.isVisible?e.show():e.container.style.display="none"}t&&this.centerLineButton.isVisible?this.centerLineButton.show():this.centerLineButton.button.style.display="none"}async loadTrackList(t){const e=[];for(let n of t)e.push(this._loadTrack(n));const n=await Promise.all(e);return this.trackViews.filter((function(t){return t.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(t){const e=this._loadTrack(t);return t.autoscaleGroup&&(await e,this.updateViews()),e}async _loadTrack(t){ke(t)&&(t=JSON.parse(t));try{const e=await this.createTrack(t);if(void 0===e)return;void 0===e.order&&(e.order=this.trackViews.length);const n=new pg(this,this.columnContainer,e);if(this.trackViews.push(n),tv(this.trackViews,this.trackLabelsVisible),this.reorderTracks(),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),"function"==typeof e.postInit)try{n.startSpinner(),await e.postInit()}finally{n.stopSpinner()}return e.autoscaleGroup||(t.sync?await n.updateViews():n.updateViews()),"function"==typeof e.hasSamples&&e.hasSamples()&&!1!==this.config.showSampleNameButton&&this.sampleNameControl.show(),e}catch(e){const n={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};console.error(e);let r=e.message||e.error||e.toString();n.hasOwnProperty(r)&&(r=n[r]),r+=": "+t.url,this.alert.present(new Error(r),void 0)}}async loadROI(t){await this.roiManager.loadROI(t,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const t=await this.roiManager.getUserDefinedROISet();if(void 0===t)return[];const e=await t.getAllFeatures(),n=[];for(let t of Object.values(e))n.push(...t);return n}return[]}getRulerTrackView(){const t=this.trackViews.filter((t=>{let{track:e}=t;return"ruler"===e.id}));return t.length>0?t[0]:void 0}async createTrack(t){let e=await async function(t){return"function"==typeof t?t():t}(t.url);if(ke(e)&&(e=e.trim()),e)if(t.format)t.format=t.format.toLowerCase();else{let n=t.filename;n||(n=await As(e));const r=zs(n);"tsv"===r?t.format=await async function(t){if(t.url){const e=await Eo.loadString(t.url,Cs(t,{range:{start:0,size:1e3}}));if(e&&Ds(e.split("\n")[0].split("\t")))return"hiccups"}}(t):r?t.format=r:void 0!==t.sourceType&&"htsget"!==t.sourceType||await hc.inferFormat(t)}let n=t.type?t.type.toLowerCase():void 0;if(!n){if(n=Hs(t),"bedtype"===n){const e=zu(t,this.genome);t._featureSource=e;const r=await e.trackType();n=r||"annotation"}t.type=n}if(this.trackDefaults&&n){const e=this.trackDefaults[n];if(e)for(let n in e)e.hasOwnProperty(n)&&void 0===t[n]&&(t[n]=e[n])}const r=am(n,t,this);if(void 0!==r)return t.roi&&t.roi.length>0&&(r.roiSets=t.roi.map((t=>new Zm(t,this.genome)))),r;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${t.url||t}`),void 0)}reorderTracks(){this.trackViews.sort((function(t,e){const n=t=>"ideogram"===t.track.id?1:"ruler"===t.track.id?2:3,r=n(t),i=n(e);if(r===i){return(t.track.order||0)-(e.track.order||0)}return r-i}));for(let{axis:t,viewports:e,sampleNameViewport:n,outerScroll:r,dragHandle:i,gearContainer:o}of this.trackViews){t.remove();for(let{$viewport:t}of e)t.detach();n.viewport.remove(),r.remove(),i.remove(),o.remove()}const t=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:e,viewports:n,sampleNameViewport:r,outerScroll:i,dragHandle:o,gearContainer:s}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(e);for(let e=0;e<t.length;e++){const{$viewport:r}=n[e];t[e].appendChild(r.get(0))}this.columnContainer.querySelector(".igv-sample-name-column").appendChild(r.viewport),this.columnContainer.querySelector(".igv-scrollbar-column").appendChild(i),this.columnContainer.querySelector(".igv-track-drag-column").appendChild(o),this.columnContainer.querySelector(".igv-gear-menu-column").appendChild(s)}}getTrackOrder(){return this.trackViews.filter((t=>t.track&&t.track.name)).map((t=>t.track.name))}removeTrackByName(t){const e=this.trackViews.slice();for(let n of e)t===n.track.name&&this.removeTrack(n.track)}removeTrack(t){for(let e of this.trackViews)if(t===e.track){this._removeTrack(e.track);break}}_removeTrack(t){t.disposed||(this.trackViews.splice(this.trackViews.indexOf(t.trackView),1),this.fireEvent("trackremoved",[t]),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),t.trackView&&t.trackView.dispose())}removeAllTracks(){const t=[];for(let e of this.trackViews)"ruler"!==e.track.id&&"ideogram"!==e.track.id?(this.fireEvent("trackremoved",[e.track]),e.dispose()):t.push(e);this.trackViews=t}findTracks(t,e){let n="function"==typeof t?e=>t(e.track):n=>e===n.track[t];return this.trackViews.filter(n).map((t=>t.track))}setTrackHeight(t){this.trackHeight=t,this.trackViews.forEach((function(e){e.setTrackHeight(t)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((t=>t.bpPerPixel<0))){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel=(e.end-e.start)/t}if(this.referenceFrameList){const t=this.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(this.referenceFrameList[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),t)}Km.call(this),await this.updateViews()}async updateViews(){const t=this.trackViews;this.updateLocusSearchWidget();for(let t of this.centerLineList)t.repaint();if(this.dragObject)for(let e of t)await e.updateViews();else{const i={},o=[];for(let n of t){const t=n.track.autoscaleGroup;if(t){var e=i[t];e||(e=[],i[t]=e),e.push(n)}else o.push(n)}if(Object.entries(i).length>0){const t=Object.keys(i);for(let e of t){const t=i[e],o=[];for(let e of t)o.push(e.getInViewFeatures());const s=await Promise.all(o);var n,r=[];for(let t of s)r=r.concat(t);n=Es(r);const a=[];for(let e of t)e.track.dataRange=n,e.track.autoscale=!1,a.push(e.updateViews());await Promise.all(a)}}await Promise.all(o.map((t=>t.updateViews())))}}repaintViews(){for(let t of this.trackViews)t.repaintViews()}updateLocusSearchWidget(){const t=this.referenceFrameList,e=this.calculateViewportWidth(this.referenceFrameList.length);for(let n of t)n.end=n.start+n.bpPerPixel*e;this.chromosomeSelectWidget.select.value=1===t.length?this.referenceFrameList[0].chr:"";const n=this.referenceFrameList.map((t=>t.getLocusString())).join(" ");this.$searchInput.val(n),this.fireEvent("locuschange",[this.referenceFrameList])}calculateViewportWidth(t){let{width:e}=this.columnContainer.getBoundingClientRect();return e-=50+this.getSampleNameViewportWidth()+14+12+28,e-=5*(t-1),Math.floor(e/t)}getCenterLineXOffset(){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleNameViewportWidth()+14+12+28,Math.floor(t/2+50)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(t,e,n){const r=this.calculateViewportWidth(this.referenceFrameList.length);let i=n?[n]:this.referenceFrameList;for(let n of i)n.zoomWithScaleFactor(this,t,r,e)}async addMultiLocusPanel(t,e,n,r){const i=this.calculateViewportWidth(1+this.referenceFrameList.length),o=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=o;const s=(n-e)/i,a=new pm(this.genome,t,e,n,s),l=r?this.referenceFrameList.indexOf(r):this.referenceFrameList.length-1,c=1+l,{$viewport:h}=this.trackViews[0].viewports[l],u=Rm(h.get(0).parentElement);if(c===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let t of this.trackViews){const e=sg(t,u,a);t.viewports.push(e)}}else{this.referenceFrameList.splice(c,0,a);for(let t of this.trackViews){const e=sg(t,u,a);t.viewports.splice(c,0,e)}}this.centerLineList=this.createCenterLineList(this.columnContainer),Km.call(this),await this.updateViews(!0)}async removeMultiLocusPanel(t){const e=this.referenceFrameList.indexOf(t),{$viewport:n}=this.trackViews[0].viewports[e];Mm(e,n.parent().get(0));for(let{viewports:t}of this.trackViews)t[e].dispose(),t.splice(e,1);if(this.referenceFrameList.splice(e,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let t of this.getRulerTrackView().viewports)t.dismissLocusLabel();const r=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(r)}async gotoMultilocusPanel(t){const e=this.referenceFrameList.indexOf(t);this.columnContainer.querySelectorAll(".igv-column").forEach(((t,n)=>{n===e||t.remove()})),this.columnContainer.querySelectorAll(".igv-column-shim").forEach((t=>t.remove()));for(let t of this.trackViews){const n=t.viewports[e];t.viewports.filter(((t,n)=>n!==e)).forEach((t=>t.dispose())),t.viewports=[n]}const n=this.calculateViewportWidth(1);t.bpPerPixel=(t.end-t.start)/n,this.referenceFrameList=[t],this.trackViews.forEach((t=>{let{viewports:e}=t;return e.forEach((t=>t.setWidth(n)))})),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(t){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=t;for(let{viewports:t}of this.trackViews)for(let n of t)n.setWidth(e);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(t,e,n){await this.search(t+":"+e+"-"+n)}async doSearch(t,e){const n=await this.search(t,e);return n||this.alert.present(new Error(`Unrecognized locus: <b> ${t} </b>`)),n}async search(t,e){const n=await vm(this,t);if(n&&n.length>0){this.referenceFrameList=function(t,e,n,r,i,o){return t.map((t=>{if(n&&t.gene&&(t.start=Math.max(0,t.start-n),t.end+=n),!o){const n=e.getChromosome(t.chr);Ts(n.bpLength,t,r)}const s=new pm(e,t.chr,t.start,t.end,(t.end-t.start)/i);return s.locusSearchString=t.locusSearchString,(t.gene||t.snp)&&(s.selection=new fm(t.gene,t.snp)),s}))}(n,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(n.length),this.isSoftclipped());for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-column-shim, .igv-column").forEach((t=>t.remove())),Im(this.columnContainer.querySelector(".igv-sample-name-column"),this.referenceFrameList.length),this.centerLineList=this.createCenterLineList(this.columnContainer);for(let t of this.trackViews)t.addDOMToColumnContainer(this,this.columnContainer,this.referenceFrameList);return this.updateUIWithReferenceFrameList(),e||await this.updateViews(),!0}return!1}async loadSampleInformation(t){var e=t;Ue(t)&&(e=t.name),"fam"===e.substr(e.lastIndexOf(".")+1)&&(this.sampleInformation=await function(t,e){return(new um).loadPlinkFile(t,e)}(t))}on(t,e){this.eventHandlers[t]||(this.eventHandlers[t]=[]),this.eventHandlers[t].push(e)}un(t,e){this.off(t,e)}off(t,e){if(t)if(e){const n=this.eventHandlers[t];if(n&&0!==n.length){const r=n.indexOf(e);-1!==r&&this.eventHandlers[t].splice(r,1)}else console.warn("No handlers to remove for event: "+t)}else this.eventHandlers[t]=[];else this.eventHandlers={}}fireEvent(t,e,n){const r=this.eventHandlers[t];if(void 0===r||0===r.length)return;const i=n||window;return r.map((function(t){return t.apply(i,e)}))[0]}dispose(){this.removeMouseHandlers();for(let t of this.trackViews)t.dispose()}toJSON(){const t={version:"2.13.2"};if(void 0!==this.showSampleNames&&(t.showSampleNames=this.showSampleNames),200!==this.sampleNameViewportWidth&&(t.sampleNameViewportWidth=this.sampleNameViewportWidth),t.reference=this.genome.toJSON(),qe(t.reference.fastaURL))throw new Error(`Error. Sessions cannot include local file references ${t.reference.fastaURL.name}.`);if(qe(t.reference.indexURL))throw new Error(`Error. Sessions cannot include local file references ${t.reference.indexURL.name}.`);const e=[],n={};let r=!1,i=this.trackViews[0];for(let{referenceFrame:t}of i.viewports){const i=t.getLocusString();if(e.push(i),t.selection){const e={gene:t.selection.gene,snp:t.selection.snp};n[i]=e,r=!0}}t.locus=1===e.length?e[0]:e,r&&(t.gtexSelections=n),t.roi=this.roiManager.toJSON();const o=[],s=[];for(let{track:t}of this.trackViews)try{let e;e="function"==typeof t.getState?t.getState():t.config,e&&(e.browser&&delete e.browser,e.order=t.order,o.push(e))}catch(e){console.error(`Track: ${t.name}: ${e}`),s.push(`Track: ${t.name}: ${e}`)}if(s.length>0){let t=1,e="Errors encountered saving session: </br>";for(let n of s)e+=` (${t++}) ${n.toString()} <br/>`;throw Error(e)}return t.tracks=o,t}compressedSession(){return function(t){const e=new Uint8Array(t.length);for(var n=0;n<t.length;n++)e[n]=t.charCodeAt(n);const r=new no.deflateRaw(e),i=String.fromCharCode.apply(null,r);return btoa(i).replace(/\+/g,".").replace(/\//g,"_").replace(/=/g,"-")}(JSON.stringify(this.toJSON()))}sessionURL(){const t=window.location.href.slice(),e=t.indexOf("?");return(e>0?t.substring(0,e):t)+"?sessionURL=blob:"+this.compressedSession()}mouseDownOnViewport(t,e){var n;n=ve(t),this.vpMouseDown={viewport:e,lastMouseX:n.x,mouseDownX:n.x,lastMouseY:n.y,mouseDownY:n.y,referenceFrame:e.referenceFrame}}cancelTrackPan(){const t=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,t&&t.viewport.referenceFrame.start!==t.start&&(this.updateViews(),this.fireEvent("trackdragend"))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((t=>!0===t.track.showSoftClips))}startTrackDrag(t){this.dragTrack=t}updateTrackDrag(t){if(t&&this.dragTrack){const e=this.dragTrack,n=this.trackViews.indexOf(t),r=this.trackViews.indexOf(e),i=this.trackViews;i[n]=e,i[r]=t;const o=this.trackViews[n].track.order;this.trackViews[r].track.order=o;const s=i.length;let a=o;if(n<r)for(let t=n+1;t<s;t++){const e=i[t].track;if(!(e.order<=a))break;e.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=e.order}else for(let t=n-1;t>0;t--){const e=i[t].track;if(!(e.order>=a))break;e.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=e.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addMouseHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers()}removeMouseHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers()}addWindowResizeHandler(){this.boundWindowResizeHandler=Km.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=Jm.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=Jm.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=Qm.bind(this),this.boundColumnContainerTouchMoveHandler=Qm.bind(this),this.boundColumnContainerMouseLeaveHandler=Jm.bind(this),this.boundColumnContainerMouseUpHandler=Jm.bind(this),this.boundColumnContainerTouchEndHandler=Jm.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}async getDriveFileInfo(t){const e="https://www.googleapis.com/drive/v3/files/"+Ne(t)+"?supportsTeamDrives=true";return Eo.loadJson(e,Cs({}))}static uncompressSession(t){let e;if(t.indexOf("/gzip;base64")>0){e=co(t);let n="";for(let t of e)n+=String.fromCharCode(t);return n}return function(t){t=t.replace(/\./g,"+").replace(/_/g,"/").replace(/-/g,"=");const e=atob(t),n=[];for(let t=0;t<e.length;t++)n.push(e.charCodeAt(t));const r=no.inflateRaw(n);let i="";for(let t of r)i+=String.fromCharCode(t);return i}(t.substring(5))}createCircularView(t,e){var n;return e=!0===e,this.circularView=(n=this,new Dp(t,{onChordClick:(t,e,r)=>{const i=t.data,o=i.mate;function s(t){t.chr=n.genome.getChromosomeName(t.refName);let e=!1;for(let r of n.referenceFrameList){const n=gp.fromLocusString(r.getLocusString());if(n.contains(t)){e=!0;break}if(n.overlaps(t)){r.extend(t),e=!0;break}}if(!e){const e=2e3,r=(t.start+t.end)/2;n.addMultiLocusPanel(t.chr,r-e,r+e)}}s(i),s(o)}})),this.circularViewControl=new Dm(this.$toggle_button_container.get(0),this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:qp(this.genome)}),this.circularViewVisible=e,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(t){this.circularView&&(this.circularView.visible=t,this.circularViewControl.setState(t))}}async function Km(){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList){const n=this.referenceFrameList.indexOf(e),{chr:r,genome:i}=e,{bpLength:o}=i.getChromosome(e.chr),s=e.toBP(t);ya.isWholeGenomeView(r)||s>o?e.bpPerPixel=o/t:e.end=e.start+e.toBP(t);for(let{viewports:e}of this.trackViews)e[n].setWidth(t)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function Qm(t){t.preventDefault();const{x:e,y:n}=ve(t);if(this.vpMouseDown){const{viewport:t,referenceFrame:r}=this.vpMouseDown,i=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(n-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(i)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:t,start:r.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(n-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const e=t.$viewport.height(),n=gg(t.trackView.viewports);this.vpMouseDown.r=e/n}if(this.dragObject){const n=!this.isSoftclipped();let i=this.vpMouseDown.lastMouseX-e;r.shiftPixels(i,t.$viewport.width(),n)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const e=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-n);t.trackView.moveScroller(e)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=n}}function Jm(t){this.cancelTrackPan(),this.endTrackDrag()}function tv(t,e){for(let{viewports:n}of t)for(let t of n)t.$trackLabel&&(0===n.indexOf(t)&&!0===e?t.$trackLabel.show():t.$trackLabel.hide())}let ev=[];const nv=Eo.setApiKey;!function(){var t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-navbar {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  box-sizing: border-box;\n  width: 100%;\n  color: #444;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  line-height: 32px;\n  padding-left: 8px;\n  padding-right: 8px;\n  margin-top: 2px;\n  margin-bottom: 6px;\n  height: 32px;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n  width: 34px;\n  height: 32px;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n  height: 32px;\n  margin-left: 4px;\n  margin-right: 4px;\n  user-select: none;\n  line-height: 32px;\n  vertical-align: middle;\n  text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n  height: 100%;\n  width: 125px;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n  display: block;\n  cursor: pointer;\n  width: 100px;\n  height: 75%;\n  outline: none;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  margin-left: 8px;\n  height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 210px;\n  height: 22px;\n  line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n  cursor: text;\n  width: 85%;\n  height: 22px;\n  line-height: 22px;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  text-align: left;\n  padding-left: 8px;\n  margin-right: 8px;\n  outline: none;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n  cursor: pointer;\n  height: 16px;\n  width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n  margin-left: 4px;\n  user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n  margin-left: 0;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n  margin-left: 0;\n  margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n  display: block;\n  height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n  display: block;\n  width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n  display: none;\n}\n\n.igv-navbar-button {\n  display: block;\n  box-sizing: unset;\n  padding-left: 6px;\n  padding-right: 6px;\n  height: 18px;\n  text-transform: capitalize;\n  user-select: none;\n  line-height: 18px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: "Open Sans", sans-serif;\n  font-size: 11px;\n  font-weight: 200;\n  color: #737373;\n  background-color: #f3f3f3;\n  border-color: #737373;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n  color: white;\n  background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n  cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n  z-index: 1024;\n  position: absolute;\n  top: 8px;\n  left: 50%;\n  transform: translate(-50%, 0%);\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n  background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-top: 2px;\n  padding-bottom: 2px;\n  width: 100%;\n  height: 100%;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n  position: absolute;\n  top: 10px;\n  left: 50%;\n}\n.igv-zoom-in-notice div {\n  position: relative;\n  left: -50%;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #3f3f3f;\n  background-color: rgba(255, 255, 255, 0.51);\n  z-index: 64;\n}\n\n.igv-container-spinner {\n  position: absolute;\n  top: 90%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  z-index: 1024;\n  width: 24px;\n  height: 24px;\n  pointer-events: none;\n  color: #737373;\n}\n\n.igv-multi-locus-close-button {\n  position: absolute;\n  top: 2px;\n  right: 0;\n  padding-left: 2px;\n  padding-right: 2px;\n  width: 18px;\n  height: 18px;\n  color: #666666;\n  background-color: white;\n  z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n  vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n  cursor: pointer;\n  color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n  z-index: 64;\n  position: absolute;\n  top: 2px;\n  left: 0;\n  width: 100%;\n  height: 14px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label div {\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n  background-color: white;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n  z-index: 64;\n  position: absolute;\n  left: 50%;\n  top: 5%;\n  transform: translate(-50%, 0%);\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n  width: 14px;\n  height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n  margin-left: 16px;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n}\n\n.igv-multi-locus-ruler-label:hover {\n  cursor: pointer;\n}\n\n.igv-ruler-sweeper {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 26px;\n  bottom: 0;\n  left: 0;\n  width: 0;\n  z-index: 99999;\n  background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n  pointer-events: none;\n  z-index: 128;\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 1px;\n  height: 32px;\n  background-color: transparent;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-ruler-tooltip > div {\n  pointer-events: none;\n  width: 128px;\n  height: auto;\n  padding: 1px;\n  color: #373737;\n  font-size: 10px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  background-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-color: #373737;\n}\n\n.igv-track-label {\n  position: absolute;\n  left: 8px;\n  top: 8px;\n  width: auto;\n  height: auto;\n  max-width: 200px;\n  padding-left: 4px;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  text-align: center;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-color: #444;\n  border-radius: 2px;\n  border-style: solid;\n  border-width: thin;\n  background-color: white;\n  z-index: 128;\n  cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n  background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-top: 4px;\n}\n\n.igv-center-line {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  transform: translateX(-50%);\n  z-index: 8;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-left-style: dashed;\n  border-left-width: thin;\n  border-right-style: dashed;\n  border-right-width: thin;\n}\n\n.igv-center-line-wide {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n  display: none;\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  left: 0;\n  right: 0;\n  top: 50%;\n  height: 1px;\n  z-index: 1;\n  margin-left: 50px;\n  margin-right: 54px;\n  border-top-style: dotted;\n  border-top-width: thin;\n  border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  width: 1px;\n  z-index: 1;\n  border-left-style: dotted;\n  border-left-width: thin;\n  border-left-color: rgba(127, 127, 127, 0.76);\n  display: none;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-generic-dialog-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 300px;\n  height: 200px;\n  border-color: #7F7F7F;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  z-index: 2048;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n  color: #373737;\n  width: 95%;\n  height: 24px;\n  line-height: 24px;\n  text-align: left;\n  margin-top: 8px;\n  padding-left: 8px;\n  overflow-wrap: break-word;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n  margin-top: 8px;\n  width: 95%;\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  padding-left: 8px;\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n  width: 30%;\n  height: 100%;\n  font-size: 16px;\n  text-align: right;\n  padding-right: 8px;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  width: 50%;\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n  margin-top: 8px;\n  width: calc(100% - 16px);\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n  width: 100%;\n  height: 28px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n  margin-top: 32px;\n  color: white;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  width: 75px;\n  height: 28px;\n  line-height: 28px;\n  text-align: center;\n  border-color: transparent;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n  margin-left: 32px;\n  margin-right: 0;\n  background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n  margin-left: 0;\n  margin-right: 32px;\n  background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n  cursor: pointer;\n  background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n  cursor: pointer;\n  background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n  width: 100%;\n  height: 36px;\n  margin-top: 32px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n  width: 98px;\n  height: 36px;\n  line-height: 36px;\n  text-align: center;\n  color: white;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  border-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 4px;\n  background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n  cursor: pointer;\n  background-color: #25597f;\n}\n\n.igv-generic-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  z-index: 2048;\n  background-color: white;\n  cursor: pointer;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: wrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-container div:first-child {\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  height: 24px;\n  width: 100%;\n  background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n  display: block;\n  color: #5f5f5f;\n  cursor: pointer;\n  width: 14px;\n  height: 14px;\n  margin-right: 8px;\n  margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: max-content;\n  z-index: 4096;\n  cursor: pointer;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background: white;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-end;\n  text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n  width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n  background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n  padding-left: 4px;\n  padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n  background: #efefef;\n}\n\n.igv-menu-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-bottom: 1px;\n  padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n  position: relative;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-menu-popup-header div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n.igv-menu-popup-check-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 100%;\n  height: 20px;\n  margin-right: 4px;\n  background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n  padding-top: 2px;\n  padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n  position: relative;\n  width: 12px;\n  height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n  position: absolute;\n  width: 12px;\n  height: 12px;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-loading-spinner-container {\n  z-index: 1024;\n  position: absolute;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 32px;\n  height: 32px;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-loading-spinner-container > div {\n  box-sizing: border-box;\n  width: 100%;\n  height: 100%;\n  border-radius: 50%;\n  border: 4px solid rgba(128, 128, 128, 0.5);\n  border-top-color: rgb(255, 255, 255);\n  animation: spin 1s ease-in-out infinite;\n  -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n@-webkit-keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n\n    transform: rotate(360deg); } }\n.igv-roi-menu-next-gen {\n  position: absolute;\n  z-index: 512;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background-color: white;\n  width: 192px;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch; }\n  .igv-roi-menu-next-gen > div:first-child {\n    height: 24px;\n    border-top-color: transparent;\n    border-top-left-radius: 4px;\n    border-top-right-radius: 4px;\n    border-bottom-color: #7F7F7F;\n    border-bottom-style: solid;\n    border-bottom-width: thin;\n    background-color: #eee;\n    display: flex;\n    flex-flow: row;\n    flex-wrap: nowrap;\n    justify-content: flex-end;\n    align-items: center; }\n    .igv-roi-menu-next-gen > div:first-child > div {\n      margin-right: 4px;\n      height: 12px;\n      width: 12px;\n      color: #7F7F7F; }\n    .igv-roi-menu-next-gen > div:first-child > div:hover {\n      cursor: pointer;\n      color: #444; }\n  .igv-roi-menu-next-gen > div:last-child {\n    background-color: white;\n    border-bottom-left-radius: 4px;\n    border-bottom-right-radius: 4px;\n    border-bottom-color: transparent;\n    border-bottom-style: solid;\n    border-bottom-width: 0;\n    display: flex;\n    flex-direction: column;\n    flex-wrap: nowrap;\n    justify-content: flex-start;\n    align-items: stretch;\n    text-align: start;\n    vertical-align: middle;\n    cursor: pointer; }\n    .igv-roi-menu-next-gen > div:last-child > div {\n      height: 24px;\n      padding-left: 4px;\n      border-bottom-style: solid;\n      border-bottom-width: thin;\n      border-bottom-color: #7f7f7f; }\n    .igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n      background-color: rgba(127, 127, 127, 0.1); }\n    .igv-roi-menu-next-gen > div:last-child div:first-child {\n      cursor: default;\n      font-style: italic;\n      text-align: center;\n      padding-right: 4px;\n      white-space: nowrap;\n      overflow: hidden;\n      text-overflow: ellipsis; }\n    .igv-roi-menu-next-gen > div:last-child > div:last-child {\n      border-bottom-width: 0;\n      border-bottom-color: transparent; }\n\n.igv-roi-placeholder {\n  font-style: normal;\n  color: rgba(75, 75, 75, 0.6); }\n\n\n.igv-roi-table {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(1) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(2) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(3) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(4) {\n  width: 30%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(5) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n  resize: both;\n  overflow: scroll;\n  min-width: 512px;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(1) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(2) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(3) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(4) {\n  width: 30%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(5) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-four-column {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table-four-column > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table-four-column > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table-four-column > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table-four-column > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table-four-column > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(1) {\n  width: 25%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(2) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(3) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(4) {\n  width: 35%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container {\n  resize: both;\n  overflow: scroll;\n  min-width: 512px;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(1) {\n  width: 25%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(2) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(3) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(4) {\n  width: 35%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table-four-column > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-row-selected {\n  background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n  height: 20px;\n  user-select: none;\n  line-height: 20px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: "Open Sans", sans-serif;\n  font-size: 13px;\n  font-weight: 400;\n  color: black;\n  padding-left: 6px;\n  padding-right: 6px;\n  background-color: rgb(239, 239, 239);\n  border-color: black;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n  cursor: pointer;\n  font-weight: 400;\n  background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n  z-index: 64;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  pointer-events: none;\n  overflow: visible;\n  margin-top: 44px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-region > div {\n  position: relative;\n  width: 100%;\n  height: 8px;\n  cursor: pointer;\n  pointer-events: auto;\n}\n\n.igv-roi-menu {\n  position: absolute;\n  z-index: 1024;\n  width: 144px;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n  border-bottom-color: rgba(128, 128, 128, 0.5);\n  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flex-start;\n  align-items: stretch;\n  width: 100%;\n}\n\n.igv-column-shim {\n  width: 1px;\n  margin-left: 2px;\n  margin-right: 2px;\n  background-color: #545453;\n}\n\n.igv-column {\n  position: relative;\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-axis-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 50px;\n}\n.igv-axis-column > div {\n  margin-top: 5px;\n  width: 100%;\n}\n\n.igv-sample-name-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-scrollbar-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 14px;\n}\n.igv-scrollbar-column > div {\n  position: relative;\n  margin-top: 5px;\n  width: 14px;\n}\n.igv-scrollbar-column > div > div {\n  cursor: pointer;\n  position: absolute;\n  top: 0;\n  left: 2px;\n  width: 8px;\n  border-width: 1px;\n  border-style: solid;\n  border-color: #c4c4c4;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n  background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 12px;\n  background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n  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e=[360,100,100,1],n=["","%","%",""],r=(t?this.hsla:this.hsla.slice(0,3)).map((function(t,r){return xp(t*e[r],3===r?3:1)+n[r]}));return t?"hsla("+r+")":"hsl("+r+")"}},{key:"printHex",value:function(t){var e=this.hex;return t?e:e.substring(0,7)}},{key:"rgba",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error("No color is set");return this._rgba=t.hslToRgb(this._hsla)},set:function(t){3===t.length&&(t[3]=1),this._rgba=t,this._hsla=null}},{key:"rgbString",get:function(){return this.printRGB()}},{key:"rgbaString",get:function(){return this.printRGB(!0)}},{key:"hsla",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error("No color is set");return this._hsla=t.rgbToHsl(this._rgba)},set:function(t){3===t.length&&(t[3]=1),this._hsla=t,this._rgba=null}},{key:"hslString",get:function(){return this.printHSL()}},{key:"hslaString",get:function(){return this.printHSL(!0)}},{key:"hex",get:function(){return"#"+this.rgba.map((function(t,e){return e<3?t.toString(16):Math.round(255*t).toString(16)})).map((function(t){return t.padStart(2,"0")})).join("")},set:function(e){this.rgba=t.hexToRgb(e)}}],[{key:"hexToRgb",value:function(t){var e=(t.startsWith("#")?t.slice(1):t).replace(/^(\w{3})$/,"$1F").replace(/^(\w)(\w)(\w)(\w)$/,"$1$1$2$2$3$3$4$4").replace(/^(\w{6})$/,"$1FF");if(!e.match(/^([0-9a-fA-F]{8})$/))throw new Error("Unknown hex color; "+t);var n=e.match(/^(\w\w)(\w\w)(\w\w)(\w\w)$/).slice(1).map((function(t){return parseInt(t,16)}));return n[3]=n[3]/255,n}},{key:"nameToRgb",value:function(e){var n=e.toLowerCase().replace("at","T").replace(/[aeiouyldf]/g,"").replace("ght","L").replace("rk","D").slice(-5,4),r=yp[n];return void 0===r?r:t.hexToRgb(r.replace(/\-/g,"00").padStart(6,"f"))}},{key:"rgbToHsl",value:function(t){var e=wp(t,4),n=e[0],r=e[1],i=e[2],o=e[3];n/=255,r/=255,i/=255;var s=Math.max(n,r,i),a=Math.min(n,r,i),l=void 0,c=void 0,h=(s+a)/2;if(s===a)l=c=0;else{var u=s-a;switch(c=h>.5?u/(2-s-a):u/(s+a),s){case n:l=(r-i)/u+(r<i?6:0);break;case r:l=(i-n)/u+2;break;case i:l=(n-r)/u+4}l/=6}return[l,c,h,o]}},{key:"hslToRgb",value:function(t){var e=wp(t,4),n=e[0],r=e[1],i=e[2],o=e[3],s=void 0,a=void 0,l=void 0;if(0===r)s=a=l=i;else{var c=function(t,e,n){return n<0&&(n+=1),n>1&&(n-=1),n<1/6?t+6*(e-t)*n:n<.5?e:n<2/3?t+(e-t)*(2/3-n)*6:t},h=i<.5?i*(1+r):i+r-i*r,u=2*i-h;s=c(u,h,n+1/3),a=c(u,h,n),l=c(u,h,n-1/3)}var f=[255*s,255*a,255*l].map(Math.round);return f[3]=o,f}}]),t}(),kp=function(){function t(){vp(this,t),this._events=[]}return bp(t,[{key:"add",value:function(t,e,n){t.addEventListener(e,n,!1),this._events.push({target:t,type:e,handler:n})}},{key:"remove",value:function(e,n,r){this._events=this._events.filter((function(i){var o=!0;return e&&e!==i.target&&(o=!1),n&&n!==i.type&&(o=!1),r&&r!==i.handler&&(o=!1),o&&t._doRemove(i.target,i.type,i.handler),!o}))}},{key:"destroy",value:function(){this._events.forEach((function(e){return t._doRemove(e.target,e.type,e.handler)})),this._events=[]}}],[{key:"_doRemove",value:function(t,e,n){t.removeEventListener(e,n,!1)}}]),t}();function Sp(t,e,n){var r=!1;function i(t,e,n){return Math.max(e,Math.min(t,n))}function o(t,o,s){if(s&&(r=!0),r){t.preventDefault();var a=e.getBoundingClientRect(),l=a.width,c=a.height,h=o.clientX,u=o.clientY,f=i(h-a.left,0,l),d=i(u-a.top,0,c);n(f/l,d/c)}}function s(t,e){1===(void 0===t.buttons?t.which:t.buttons)?o(t,t,e):r=!1}function a(t,e){1===t.touches.length?o(t,t.touches[0],e):r=!1}t.add(e,"mousedown",(function(t){s(t,!0)})),t.add(e,"touchstart",(function(t){a(t,!0)})),t.add(window,"mousemove",s),t.add(e,"touchmove",a),t.add(window,"mouseup",(function(t){r=!1})),t.add(e,"touchend",(function(t){r=!1})),t.add(e,"touchcancel",(function(t){r=!1}))}var Cp="keydown",Ep="mousedown",Tp="focusin";function Ap(t,e){return(e||document).querySelector(t)}function Lp(t){t.preventDefault(),t.stopPropagation()}function Mp(t,e,n,r,i){t.add(e,Cp,(function(t){n.indexOf(t.key)>=0&&(i&&Lp(t),r(t))}))}var Rp=function(){function t(e){vp(this,t),this.settings={popup:"right",layout:"default",alpha:!0,editor:!0,editorFormat:"hex",cancelButton:!1,defaultColor:"#0cf"},this._events=new kp,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(e)}return bp(t,[{key:"setOptions",value:function(t){var e=this;if(t){var n=this.settings;if(t instanceof HTMLElement)n.parent=t;else{n.parent&&t.parent&&n.parent!==t.parent&&(this._events.remove(n.parent),this._popupInited=!1),function(t,e,n){for(var r in t)n&&n.indexOf(r)>=0||(e[r]=t[r])}(t,n),t.onChange&&(this.onChange=t.onChange),t.onDone&&(this.onDone=t.onDone),t.onOpen&&(this.onOpen=t.onOpen),t.onClose&&(this.onClose=t.onClose);var r=t.color||t.colour;r&&this._setColor(r)}var i=n.parent;if(i&&n.popup&&!this._popupInited){var o=function(t){return e.openHandler(t)};this._events.add(i,"click",o),Mp(this._events,i,[" ","Spacebar","Enter"],o),this._popupInited=!0}else t.parent&&!n.popup&&this.show()}}},{key:"openHandler",value:function(t){if(this.show()){t&&t.preventDefault(),this.settings.parent.style.pointerEvents="none";var e=t&&t.type===Cp?this._domEdit:this.domElement;setTimeout((function(){return e.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:"closeHandler",value:function(t){var e=t&&t.type,n=!1;if(t)if(e===Ep||e===Tp){var r=(this.__containedEvent||0)+100;t.timeStamp>r&&(n=!0)}else Lp(t),n=!0;else n=!0;n&&this.hide()&&(this.settings.parent.style.pointerEvents="",e!==Ep&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:"movePopup",value:function(t,e){this.closeHandler(),this.setOptions(t),e&&this.openHandler()}},{key:"setColor",value:function(t,e){this._setColor(t,{silent:e})}},{key:"_setColor",value:function(t,e){if("string"==typeof t&&(t=t.trim()),t){e=e||{};var n=void 0;try{n=new _p(t)}catch(t){if(e.failSilently)return;throw t}if(!this.settings.alpha){var r=n.hsla;r[3]=1,n.hsla=r}this.colour=this.color=n,this._setHSLA(null,null,null,null,e)}}},{key:"setColour",value:function(t,e){this.setColor(t,e)}},{key:"show",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var t=this._toggleDOM(!0);return this._setPosition(),t}var e=function(t){var e=document.createElement("div");return e.innerHTML=t,e.firstElementChild}(this.settings.template||'<div class="picker_wrapper" tabindex="-1"><div class="picker_arrow"></div><div class="picker_hue picker_slider"><div class="picker_selector"></div></div><div class="picker_sl"><div class="picker_selector"></div></div><div class="picker_alpha picker_slider"><div class="picker_selector"></div></div><div class="picker_editor"><input aria-label="Type a color name or hex value"/></div><div class="picker_sample"></div><div class="picker_done"><button>Ok</button></div><div class="picker_cancel"><button>Cancel</button></div></div>');return this.domElement=e,this._domH=Ap(".picker_hue",e),this._domSL=Ap(".picker_sl",e),this._domA=Ap(".picker_alpha",e),this._domEdit=Ap(".picker_editor input",e),this._domSample=Ap(".picker_sample",e),this._domOkay=Ap(".picker_done button",e),this._domCancel=Ap(".picker_cancel button",e),e.classList.add("layout_"+this.settings.layout),this.settings.alpha||e.classList.add("no_alpha"),this.settings.editor||e.classList.add("no_editor"),this.settings.cancelButton||e.classList.add("no_cancel"),this._ifPopup((function(){return e.classList.add("popup")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:"hide",value:function(){return this._toggleDOM(!1)}},{key:"destroy",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:"_bindEvents",value:function(){var t=this,e=this,n=this.domElement,r=this._events;function i(t,e,n){r.add(t,e,n)}i(n,"click",(function(t){return t.preventDefault()})),Sp(r,this._domH,(function(t,n){return e._setHSLA(t)})),Sp(r,this._domSL,(function(t,n){return e._setHSLA(null,t,1-n)})),this.settings.alpha&&Sp(r,this._domA,(function(t,n){return e._setHSLA(null,null,null,1-n)}));var o=this._domEdit;i(o,"input",(function(t){e._setColor(this.value,{fromEditor:!0,failSilently:!0})})),i(o,"focus",(function(t){var e=this;e.selectionStart===e.selectionEnd&&e.select()})),this._ifPopup((function(){var e=function(e){return t.closeHandler(e)};i(window,Ep,e),i(window,Tp,e),Mp(r,n,["Esc","Escape"],e);var o=function(e){t.__containedEvent=e.timeStamp};i(n,Ep,o),i(n,Tp,o),i(t._domCancel,"click",e)}));var s=function(e){t._ifPopup((function(){return t.closeHandler(e)})),t.onDone&&t.onDone(t.colour)};i(this._domOkay,"click",s),Mp(r,n,["Enter"],s)}},{key:"_setPosition",value:function(){var t=this.settings.parent,e=this.domElement;t!==e.parentNode&&t.appendChild(e),this._ifPopup((function(n){"static"===getComputedStyle(t).position&&(t.style.position="relative");var r=!0===n?"popup_right":"popup_"+n;["popup_top","popup_bottom","popup_left","popup_right"].forEach((function(t){t===r?e.classList.add(t):e.classList.remove(t)})),e.classList.add(r)}))}},{key:"_setHSLA",value:function(t,e,n,r,i){i=i||{};var o=this.colour,s=o.hsla;[t,e,n,r].forEach((function(t,e){(t||0===t)&&(s[e]=t)})),o.hsla=s,this._updateUI(i),this.onChange&&!i.silent&&this.onChange(o)}},{key:"_updateUI",value:function(t){if(this.domElement){t=t||{};var e=this.colour,n=e.hsla,r="hsl("+360*n[0]+", 100%, 50%)",i=e.hslString,o=e.hslaString,s=this._domH,a=this._domSL,l=this._domA,c=Ap(".picker_selector",s),h=Ap(".picker_selector",a),u=Ap(".picker_selector",l);b(0,c,n[0]),this._domSL.style.backgroundColor=this._domH.style.color=r,b(0,h,n[1]),w(0,h,1-n[2]),a.style.color=i,w(0,u,1-n[3]);var f=i,d=f.replace("hsl","hsla").replace(")",", 0)"),p="linear-gradient("+[f,d]+")";if(this._domA.style.background=p+", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em",!t.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,v=void 0;switch(g){case"rgb":v=e.printRGB(m);break;case"hsl":v=e.printHSL(m);break;default:v=e.printHex(m)}this._domEdit.value=v}this._domSample.style.color=o}function b(t,e,n){e.style.left=100*n+"%"}function w(t,e,n){e.style.top=100*n+"%"}}},{key:"_ifPopup",value:function(t,e){this.settings.parent&&this.settings.popup?t&&t(this.settings.popup):e&&e()}},{key:"_toggleDOM",value:function(t){var e=this.domElement;if(!e)return!1;var n=t?"":"none",r=e.style.display!==n;return r&&(e.style.display=n),r}}]),t}(),Ip=document.createElement("style");function Np(t){if(Op[t])return Op[t];if(Op["chr"+t]){const e=Op["chr"+t];return Op[t]=e,e}{const i=(e=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),r=Math.round(255*Math.random()).toString(10),"rgb("+e+","+n+","+r+")");return Op[t]=i,i}var e,n,r}Ip.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:"";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 auto}.layout_default .picker_sl::before{content:"";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:"";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:"";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(Ip),Rp.StyleElement=Ip;const Op={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};class Pp{constructor(t){this.tracks=[],this.chordSets=[]}addChordSet(t){this.chordSets=this.chordSets.filter((e=>e.name!==t.name)),this.chordSets.push(t);let e=this.tracks.find((e=>t.trackName===e.name));e&&(e.chordSets=e.chordSets.filter((e=>e.name!==t.name)),e.chordSets.push(t)),e||(e=new Fp(t),this.tracks.push(e))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(t){return this.tracks.find((e=>t===e.name))}getChordSet(t){return this.chordSets.find((e=>t===e.name))}}class Fp{constructor(t){this.name=t.trackName,this.color=t.trackColor,this.visible=!0,this.chordSets=[t],this.id=("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const t=[];for(let e of this.chordSets)for(let n of e.chords)t.push(n);return t}}const Dp=Math.exp(5);class Bp{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(t,e){if(e=e||{},this.config=e,Bp.isInstalled()){this.parent=t,this.groupByTrack=!0===e.groupByTrack,this.chordManager=new Pp(e);const n=document.createElement("div");n.className="igv-circview-container",t.appendChild(n),this.createControls(n),this.resetControlPanel();const r=document.createElement("div");r.className="igv-circview-circular-genome-view",n.appendChild(r),this.container=r,e.assembly&&this.setAssembly(e.assembly),this.width=e.width||500,this.height=e.height||500,this.setSize(this.width,this.height)}else console.error("JBrowse circular view is not installed")}createControls(t){const e=document.createElement("div");e.className="igv-circview-toolbar",t.appendChild(e),this.toolbar=e;const n=document.createElement("div");n.className="igv-circview-track-panel",t.appendChild(n),this.controlPanel=n,this.controlPanel.style.display="none";const r=document.createElement("div");r.className="igv-circview-toolbar-button-container",this.toolbar.appendChild(r),this.showControlsButton=document.createElement("div"),this.showControlsButton.className="igv-circview-button",r.appendChild(this.showControlsButton),this.showControlsButton.innerText="none"===this.controlPanel.style.display?"Show Controls":"Hide Controls",this.showControlsButton.addEventListener("click",(t=>{this.controlPanel.querySelectorAll("div").length>0&&("none"===this.controlPanel.style.display?(this.controlPanel.style.display="flex",t.target.innerText="Hide Controls"):(this.controlPanel.style.display="none",t.target.innerText="Show Controls"))}));let i=document.createElement("div");i.className="igv-circview-button",r.appendChild(i),i.innerText="Clear All",i.addEventListener("click",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(i=document.createElement("div"),i.className="igv-circview-button",r.appendChild(i),i.innerText="Close",i.addEventListener("click",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML="",this.controlPanel.appendChild(this.createGroupByCB());const t=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let e of t)this.addToControlPanel(e)}createGroupByCB(){const t=document.createElement("input");t.type="checkbox",t.id="groupByCB",t.style.width="1.4em",t.style.height="1.4em",t.checked=this.groupByTrack,t.onclick=t=>{this.groupByTrack=t.target.checked,this.resetControlPanel(),this.render()};const e=document.createElement("label");e.for="groupByCB",e.innerText="Group by track",e.style.color="black",e.style.paddingLeft="10px";const n=document.createElement("div");return n.style.width="100%",n.style.paddingTop="5px",n.style.paddingBottom="5px",n.style.background="rgb(216, 230, 234)",n.appendChild(t),n.appendChild(e),n}addToControlPanel(t){const e=document.createElement("div");this.controlPanel.appendChild(e);const n=document.createElement("div");n.className="igv-circview-button",e.appendChild(n),n.innerText=!0===t.visible?"Hide":"Show",n.addEventListener("click",(e=>{!0===t.visible?(this.hideChordSet(t.name),e.target.innerText="Show"):(this.showChordSet(t.name),e.target.innerText="Hide")}));const r=document.createElement("input"),i=t=>200*Math.log(t*Dp),o=document.createElement("div");o.className="igv-circview-button",o.innerHTML="&nbsp;&nbsp;&nbsp;&nbsp;",e.appendChild(o),o.style.backgroundColor=zp(t.color,1);const s={parent:o,popup:"right",editorFormat:"rgb",color:t.color,onChange:({rgbaString:e})=>{o.style.backgroundColor=zp(e,1),this.setColor(t.name,e),r.value=i(Hp(t.color))}},a=new Rp(s);r.setAttribute("title","Adjust transparency of arcs"),r.type="range",r.style.width="100px",r.style.marginRight="10px",r.setAttribute("class","range"),r.setAttribute("min","0"),r.setAttribute("max","1000"),r.value=i(Hp(t.color)),r.oninput=()=>{const e=(n=r.value,Math.exp(n/200)/Dp);var n;this.setColor(t.name,zp(t.color,e)),a.setColor(t.color)},e.appendChild(r);const l=document.createElement("div");l.style.color="black",e.appendChild(l),l.innerText=l.title=t.name}setAssembly(t){const e=this.genomeId||Up();if(this.genomeId===e)return;this.chordManager.clearChords(),this.genomeId=e,this.chrNames=new Set(t.chromosomes.map((t=>Vp(t.name))));const n=[],r=[];for(let e of t.chromosomes){const t=Vp(e.name);r.push(e.color||Np(t)),n.push({refName:t,uniqueId:t,start:0,end:e.bpLength})}this.assembly={name:t.name,sequence:{trackId:e,type:"ReferenceSequenceTrack",adapter:{type:"FromConfigSequenceAdapter",features:n}},refNameColors:r},this.render()}addChords(t,e={}){const n=e.name||e.track||"*",r=n.split(" ")[0].replaceAll("%20"," "),i={name:n.replaceAll("%20"," "),trackName:r,chords:t,color:e.color||"black",trackColor:e.trackColor||e.color||"black",visible:!0,id:e.id||Up()};this.chordManager.addChordSet(i),this.resetControlPanel(),this.render()}setSize(t,e){if(e=e||t,this.width=t,this.height=e,this.viewState){const n=this.viewState.session.view;n.setWidth(t),n.setHeight(e),n.setBpPerPx(n.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display="block"}hide(){this.parent.style.display="none"}get visible(){return"none"!==this.parent.style.display}set visible(t){this.parent.style.display=t?"block":"none"}hideChordSet(t){let e=this.getChordSet(t);e?(e.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(t){let e=this.getChordSet(t);e?(e.visible=!0,this.render()):console.warn(`No track with name: ${t}`)}deleteTrack(t){let e=this.tracks.findIndex((e=>t===e.name));e>=0&&this.tracks.splice(e,1),this.render()}getChordSet(t){return this.groupByTrack?this.chordManager.getTrack(t):this.chordManager.getChordSet(t)}setColor(t,e){const n=this.getChordSet(t);if(n){n.color=e;const t=n.id;for(let n of this.viewState.config.tracks)if(t===n.trackId){n.displays[0].renderer.strokeColor.set(e);break}}}render(){const{createViewState:t,JBrowseCircularGenomeView:e}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const n=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((t=>t.visible)),r=[],i=[];for(let t of n)r.push({trackId:t.id,name:t.name,assemblyNames:["forIGV"],type:"VariantTrack",adapter:{type:"FromConfigAdapter",features:t.chords}}),i.push(t.color);this.viewState=t({assembly:this.assembly,tracks:r});for(let t=0;t<n.length;t++)this.viewState.config.tracks[t].displays[0].renderer.strokeColor.set(i[t]);this.element=React.createElement(e,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const o=this.config.onChordClick||jp;for(let t=0;t<n.length;t++)this.viewState.session.view.showTrack(this.viewState.config.tracks[t].trackId),o&&(this.viewState.pluginManager.jexl.addFunction("onChordClick",o),this.viewState.config.tracks[t].displays[0].onChordClick.set("jexl:onChordClick(feature, track, pluginManager)"))}}function zp(t,e){const[n,r,i,o]=t.split(",");return`${n},${r},${i},${e})`}function Hp(t){return t.startsWith("rgba(")?Number(t.split(",")[3].replace(")","")):1}function Vp(t){return t.startsWith("chr")?t.substring(3):t}function jp(t,e,n){console.log(t)}function Up(){return("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}if("undefined"!=typeof document){function mv(t){for(let e of document.styleSheets)if(e=e.href?e.href.replace(/^.*[\\\/]/,""):"",e===t)return!0;return!1}mv("circular-view.css")||function(){const t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-circview-container {\n  z-index: 2048;\n  width: fit-content;\n  height: fit-content;\n  box-sizing: content-box;\n  color: dimgray;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  background-color: white;\n  border-color: dimgray;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n}\n\n.igv-circview-toolbar {\n  position: relative;\n  width: 100%;\n  height: 32px;\n  background-color: lightgrey;\n  border-bottom-style: solid;\n  border-bottom-color: dimgray;\n  border-bottom-width: thin;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n\n.igv-circview-toolbar-button-container {\n  height: 100%;\n  width: fit-content;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-circview-toolbar-button-container > div {\n  margin: 4px;\n}\n\n.igv-circview-track-panel {\n  z-index: 1024;\n  position: absolute;\n  top: 33px;\n  left: 0;\n  width: 100%;\n  height: fit-content;\n  border-bottom-style: solid;\n  border-bottom-color: dimgray;\n  border-bottom-width: thin;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n}\n.igv-circview-track-panel > div {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-circview-track-panel > div > div {\n  margin: 4px;\n}\n\n.igv-circview-swatch-button {\n  cursor: pointer;\n  padding: 5px;\n  width: 8px;\n  height: 8px;\n  border: 1px solid #8d8b8b;\n  border-radius: 16px;\n}\n\n.igv-circview-button {\n  cursor: pointer;\n  padding: 5px;\n  color: #444;\n  vertical-align: middle;\n  text-align: center;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  border: 1px solid #8d8b8b;\n  border-radius: 4px;\n  background: #efefef;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\n}\n\n.igv-circview-button:hover {\n  background: #efefef;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n.igv-circview-button:active {\n  color: #007bff;\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n/*# sourceMappingURL=circular-view.css.map */\n',document.head.insertBefore(t,document.head.childNodes[document.head.childNodes.length-1])}()}const qp=t=>t.startsWith("chr")?t.substring(3):t;function Wp(t){const e=[],n=[];for(let r of t.wgChromosomeNames){const i=t.getChromosome(r);n.push(tg(i.name)),e.push({name:i.name,bpLength:i.bpLength})}return e}function $p(t,e,n,r){const i=mo.addAlpha("all"===n.chr?e.color:tg(n.chr),r),o=mo.addAlpha(e.color||"rgb(0,0,255)",r),s=e.name.replaceAll(" ","%20"),a="all"===n.chr?s:`${s}  ${n.chr}:${n.start}-${n.end}`;e.browser.circularView.addChords(t,{track:a,color:i,trackColor:o}),e.browser.circularViewVisible||(e.browser.circularViewVisible=!0)}class Gp{constructor(t,e){let{minTLENPercentile:n,maxTLENPercentile:r}=e;this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===n?.1:n,this.up=void 0===r?99.5:r,this.isizes=[],this.compute(t)}compute(t){for(let r of t)if(r.isProperPair()){var e=Math.abs(r.fragmentLength);this.sumF+=e,this.sumF2+=e*e,this.isizes.push(e);var n=r.pairOrientation;if("string"==typeof n&&4===n.length)switch(""+n.charAt(0)+n.charAt(2)){case"FF":case"RR":this.ffCount++;break;case"FR":this.frCount++;break;case"RF":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation="ff":this.frCount/this.totalCount>.9?this.orienation="fr":this.rfCount/this.totalCount>.9&&(this.orienation="rf"),this.minTLEN=0===this.lp?0:Zp(this.isizes,this.lp),this.maxTLEN=Zp(this.isizes,this.up)}}function Zp(t,e){if(0!==t.length){var n=Math.floor(t.length*(e/100));return t.sort((function(t,e){return t-e})),t[n]}}class Xp extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type="alignment",void 0===t.alleleFreqThreshold&&(t.alleleFreqThreshold=.2),this.featureSource=new pp(t,this.browser),this.showCoverage=void 0===t.showCoverage||t.showCoverage,this.showAlignments=void 0===t.showAlignments||t.showAlignments,this.coverageTrack=new Yp(t,this),this.alignmentTrack=new Kp(t,this),this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.visibilityWindow=t.visibilityWindow||3e4,this.viewAsPairs=t.viewAsPairs,this.pairsSupported=!1!==t.pairsSupported,this.showSoftClips=t.showSoftClips,this.showAllBases=t.showAllBases,this.showInsertions=!1!==t.showInsertions,this.showMismatches=!1!==t.showMismatches,this.color=t.color,this.coverageColor=t.coverageColor,t.sort&&(Array.isArray(t.sort)?this.assignSort(t.sort[0]):this.assignSort(t.sort)),this.height=void 0!==t.height?t.height:300}set height(t){this._height=t,this.coverageTrack&&this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?t-this.coverageTrack.height:t)}get height(){return this._height}get minTemplateLength(){const t=void 0!==this.config.minTLEN?this.config.minTLEN:this.config.minFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.minTLEN:0}get maxTemplateLength(){const t=void 0!==this.config.maxTLEN?this.config.maxTLEN:this.config.maxFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.maxTLEN:1e3}sort(t){t=this.assignSort(t);for(let e of this.trackView.viewports)if(e.containsPosition(t.chr,t.position)){const n=e.cachedFeatures;n&&(n.sortRows(t),e.repaint())}}assignSort(t){if(t.locus){const e=function(t){const e=t.split(":"),n=e[1].split("-"),r={chr:e[0],start:Number.parseInt(n[0].replace(/,/g,""))-1};return n.length>1?r.end=Number.parseInt(n[1].replace(/,/g,"")):r.end=r.start+1,r}(t.locus);t.chr=e.chr,t.position=e.start}else t.position--;return t.direction="ASC"===t.direction||!0===t.direction,t.chr=this.browser.genome.getChromosomeName(t.chr),this.sortObject=t,this.sortObject}async getFeatures(t,e,n,r,i){const o=await this.featureSource.getAlignments(t,e,n);if(o.paired&&!this._pairedEndStats&&!this.config.maxFragmentLength){const t=new Gp(o.alignments,this.config);t.totalCount>99&&(this._pairedEndStats=t)}o.alignments=void 0;const s=this.sortObject;return s&&s.chr===t&&s.position>=e&&s.position<=n&&o.sortRows(s),o}computePixelHeight(t){return(this.showCoverage?this.coverageTrack.height:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(t):0)+15}draw(t){Xo.fillRect(t.context,0,t.pixelTop,t.pixelWidth,t.pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),!0===this.showCoverage&&this.coverageTrack.height>0?(this.trackView.axisCanvas.style.display="block",this.coverageTrack.draw(t)):this.trackView.axisCanvas.style.display="none",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(t))}paintAxis(t,e,n){this.coverageTrack.paintAxis(t,e,this.coverageTrack.height)}contextMenuItemList(t){return this.alignmentTrack.contextMenuItemList(t)}popupData(t){return!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y<this.coverageTrack.height?this.coverageTrack.popupData(t):this.alignmentTrack.popupData(t)}clickedFeatures(t){let e;return e=!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y<this.coverageTrack.height?this.coverageTrack.getClickedObject(t):this.alignmentTrack.getClickedObject(t),e?[e]:void 0}menuItemList(){let t=[];t=t.concat(Wo.numericDataMenuItems(this.trackView)),t.push("<hr/>");const e=pe('<div class="igv-track-menu-category">');e.text("Color by:"),t.push({name:void 0,object:e,click:void 0,init:void 0});const n=[{key:"strand",label:"read strand"}];this.alignmentTrack.hasPairs&&(n.push({key:"firstOfPairStrand",label:"first-of-pair strand"}),n.push({key:"pairOrientation",label:"pair orientation"}),n.push({key:"tlen",label:"insert size (TLEN)"}),n.push({key:"unexpectedPair",label:"pair orientation & insert size (TLEN)"}));const r="tag"+(this.alignmentTrack.colorByTag?" ("+this.alignmentTrack.colorByTag+")":"");n.push({key:"tag",label:r});for(let e of n){const n=this.alignmentTrack.colorBy===e.key;t.push(this.colorByCB(e,n))}const i=()=>{if(!this.autoHeight){const t=15+(this.showCoverage?this.coverageTrack.height:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(t)}};t.push("<hr/>"),t.push({object:pe(qo("Show Coverage",this.showCoverage)),click:()=>{this.showCoverage=!this.showCoverage,i(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:pe(qo("Show Alignments",this.showAlignments)),click:()=>{this.showAlignments=!this.showAlignments,i(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push("<hr/>"),t.push({object:pe(qo("Show all bases",this.showAllBases)),click:()=>{this.showAllBases=!this.showAllBases,this.config.showAllBases=this.showAllBases,this.trackView.repaintViews()}}),t.push("<hr/>"),t.push({object:pe(qo("Show mismatches",this.showMismatches)),click:()=>{this.showMismatches=!this.showMismatches,this.config.showMismatches=this.showMismatches,this.trackView.repaintViews()}}),t.push({object:pe(qo("Show insertions",this.showInsertions)),click:()=>{this.showInsertions=!this.showInsertions,this.config.showInsertions=this.showInsertions,this.getCachedAlignmentContainers(),this.trackView.repaintViews()}}),t.push({object:pe(qo("Show soft clips",this.showSoftClips)),click:()=>{this.showSoftClips=!this.showSoftClips,this.config.showSoftClips=this.showSoftClips,this.featureSource.setShowSoftClips(this.showSoftClips);const t=this.getCachedAlignmentContainers();for(let e of t)e.setShowSoftClips(this.showSoftClips);this.trackView.repaintViews()}}),this.pairsSupported&&this.alignmentTrack.hasPairs&&(t.push("<hr/>"),t.push({object:pe(qo("View as pairs",this.viewAsPairs)),click:()=>{this.viewAsPairs=!this.viewAsPairs,this.config.viewAsPairs=this.viewAsPairs,this.featureSource.setViewAsPairs(this.viewAsPairs);const t=this.getCachedAlignmentContainers();for(let e of t)e.setViewAsPairs(this.viewAsPairs);this.trackView.repaintViews()}})),this.browser.circularView&&(this.alignmentTrack.hasPairs||this.alignmentTrack.hasSupplemental)&&(t.push("<hr/>"),this.alignmentTrack.hasPairs&&t.push({label:"Add discordant pairs to circular view",click:()=>{for(let t of this.trackView.viewports)this.addPairedChordsForViewport(t)}}),this.alignmentTrack.hasSupplemental&&t.push({label:"Add split reads to circular view",click:()=>{for(let t of this.trackView.viewports)this.addSplitChordsForViewport(t)}})),t.push("<hr/>");const o=pe('<div class="igv-track-menu-category">');return o.text("Display mode:"),t.push({name:void 0,object:o,click:void 0,init:void 0}),t.push({object:pe(qo("expand","EXPANDED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="EXPANDED",this.config.displayMode="EXPANDED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:pe(qo("squish","SQUISHED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="SQUISHED",this.config.displayMode="SQUISHED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t}colorByCB(t,e){return{name:void 0,object:pe(qo(t.label,e)),click:e=>{"tag"!==t.key?t.key===this.alignmentTrack.colorBy?(this.alignmentTrack.colorBy="none",this.config.colorBy="none",this.trackView.repaintViews()):(this.alignmentTrack.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews()):this.browser.inputDialog.present({label:"Tag Name",value:this.alignmentTrack.colorByTag?this.alignmentTrack.colorByTag:"",callback:t=>{t?(this.alignmentTrack.colorBy="tag",this.alignmentTrack.colorByTag=t,this.alignmentTrack.tagColors||(this.alignmentTrack.tagColors=new Wu("Set1"))):(this.alignmentTrack.colorBy="none",this.alignmentTrack.colorByTag=""),this.trackView.repaintViews()}},e)},init:void 0}}getState(){const t=super.getState();return this.sortObject&&(t.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?"ASC":"DESC"}),t}getCachedAlignmentContainers(){return this.trackView.viewports.map((t=>t.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(t){this.coverageTrack.dataRange=t}get logScale(){return this.coverageTrack.logScale}set logScale(t){this.coverageTrack.logScale=t}get autoscale(){return this.coverageTrack.autoscale}set autoscale(t){this.coverageTrack.autoscale=t}addPairedChordsForViewport(t){const e=this.maxTemplateLength,n=[],r=t.referenceFrame;for(let i of t.cachedFeatures.allAlignments())i.end>=r.start&&i.start<=r.end&&(i.paired?i.end-i.start>e&&n.push(i):i.mate&&i.mate.chr&&(i.mate.chr!==i.chr||Math.max(i.fragmentLength)>e)&&n.push(i));$p((t=>{const e=[];for(let n of t)if(n.paired)n.firstAlignment&&n.secondAlignment&&e.push({uniqueId:n.readName,refName:qp(n.firstAlignment.chr),start:n.firstAlignment.start,end:n.firstAlignment.end,mate:{refName:qp(n.secondAlignment.chr),start:n.secondAlignment.start,end:n.secondAlignment.end}});else{const t=n.mate;t&&t.chr&&t.position&&e.push({uniqueId:n.readName,refName:qp(n.chr),start:n.start,end:n.end,mate:{refName:qp(t.chr),start:t.position-1,end:t.position}})}return e})(n),this,r,.02)}addSplitChordsForViewport(t){const e=[],n=t.referenceFrame;for(let r of t.cachedFeatures.allAlignments()){const t=r.hasTag("SA");r.end>=n.start&&r.start<=n.end&&t&&e.push(r)}$p((t=>{const e=t=>{const e=df(t.tags().SA);let r=0;for(let i of e)i.start!==t.start&&n.push({uniqueId:`${t.readName}_${r++}`,refName:qp(t.chr),start:t.start,end:t.end,mate:{refName:qp(i.chr),start:i.start,end:i.start+i.lenOnRef}})},n=[];for(let n of t)n.paired?(e(n.firstAlignment),n.secondAlignment&&e(n.secondAlignment)):e(n);return n})(e),this,n,.02)}}class Yp{constructor(t,e){this.parent=e,this.featureSource=e.featureSource,this.height=void 0!==t.coverageTrackHeight?t.coverageTrackHeight:50,this.paintAxis=gp,this.top=0,this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max})}draw(t){const e=t.pixelTop;t.pixelHeight;const n=this.parent.browser.nucleotideColors;if(e>this.height)return;const r=t.context,i=t.features.coverageMap;let o;i.refSeq&&(o=i.refSeq.toUpperCase());const s=t.bpPerPixel,a=t.bpStart,l=a+t.pixelWidth*s+1;let c;c=this.parent.coverageColor?this.parent.coverageColor:void 0!==this.parent.color&&"function"!=typeof this.parent.color?mo.darkenLighten(this.parent.color,-35):"rgb(150, 150, 150)",Xo.setProperties(r,{fillStyle:c,strokeStyle:c});const h=Math.max(1,Math.ceil(1/s));for(let t=0,e=i.coverage.length;t<e;t++){const e=i.bpStart+t;if(e<a)continue;if(e>l)break;const n=i.coverage[t];if(!n)continue;const o=Math.round(n.total/this.dataRange.max*this.height),c=this.height-o,u=Math.floor((e-a)/s);Xo.fillRect(r,u,c,h,o)}if(o)for(let t=0,e=i.coverage.length;t<e;t++){const e=i.bpStart+t;if(e<a)continue;if(e>l)break;const c=i.coverage[t];if(!c)continue;const u=c.total/this.dataRange.max*this.height;let f=this.height-u;const d=Math.floor((e-a)/s),p=o[t];if(c.isMismatch(p)){Xo.setProperties(r,{fillStyle:n[p]}),Xo.fillRect(r,d,f,h,u);let t=0;for(let e of["A","C","T","G"]){const i=(c["pos"+e]+c["neg"+e])/this.dataRange.max*this.height;f=this.height-i-t,t+=i,Xo.setProperties(r,{fillStyle:n[e]}),Xo.fillRect(r,d,f,h,i)}}}}getClickedObject(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return;const n=Math.floor(t.genomicLocation),r=e.coverageMap,i=Math.floor(n-r.bpStart);return r.coverage[i]}popupData(t){const e=[],n=this.getClickedObject(t);if(n){const r=Math.floor(t.genomicLocation),i=t.viewport.referenceFrame;e.push(i.chr+":"+Se(1+r)),e.push({name:"Total Count",value:n.total});let o=n.posA+n.negA;o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posA+"+, "+n.negA+"- )"),e.push({name:"A",value:o}),o=n.posC+n.negC,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posC+"+, "+n.negC+"- )"),e.push({name:"C",value:o}),o=n.posG+n.negG,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posG+"+, "+n.negG+"- )"),e.push({name:"G",value:o}),o=n.posT+n.negT,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posT+"+, "+n.negT+"- )"),e.push({name:"T",value:o}),o=n.posN+n.negN,o>0&&(o=o.toString()+" ("+Math.round(o/n.total*100)+"%, "+n.posN+"+, "+n.negN+"- )"),e.push({name:"N",value:o}),e.push("<HR/>"),e.push({name:"DEL",value:n.del.toString()}),e.push({name:"INS",value:n.ins.toString()})}return e}}class Kp{constructor(t,e){this.parent=e,this.browser=e.browser,this.featureSource=e.featureSource,this.top=0===t.coverageTrackHeight?0:t.coverageTrackHeight+5,this.displayMode=t.displayMode||"EXPANDED",this.alignmentRowHeight=t.alignmentRowHeight||14,this.squishedRowHeight=t.squishedRowHeight||3,this.negStrandColor=t.negStrandColor||"rgba(150, 150, 230, 0.75)",this.posStrandColor=t.posStrandColor||"rgba(230, 150, 150, 0.75)",this.insertionColor=t.insertionColor||"rgb(138, 94, 161)",this.insertionTextColor=t.insertionTextColor||"white",this.showInsertionText=void 0!==t.showInsertionText&&!!t.showInsertionText,this.deletionColor=t.deletionColor||"black",this.deletionTextColor=t.deletionTextColor||"black",this.showDeletionText=void 0!==t.showDeletionText&&!!t.showDeletionText,this.skippedColor=t.skippedColor||"rgb(150, 170, 170)",this.pairConnectorColor=t.pairConnectorColor,this.smallTLENColor=t.smallTLENColor||t.smallFragmentLengthColor||"rgb(0, 0, 150)",this.largeTLENColor=t.largeTLENColor||t.largeFragmentLengthColor||"rgb(200, 0, 0)",this.pairOrientation=t.pairOrienation||"fr",this.pairColors={},this.pairColors.RL=t.rlColor||"rgb(0, 150, 0)",this.pairColors.RR=t.rrColor||"rgb(20, 50, 200)",this.pairColors.LL=t.llColor||"rgb(0, 150, 150)",this.colorBy=t.colorBy||"unexpectedPair",this.colorByTag=t.colorByTag?t.colorByTag.toUpperCase():void 0,this.bamColorTag=void 0===t.bamColorTag?"YC":t.bamColorTag,this.hideSmallIndels=t.hideSmallIndels,this.indelSizeThreshold=t.indelSizeThreshold||1,this.hasPairs=!1,this.hasSupplemental=!1}setTop(t,e){this.top=0===t.height||!1===e?0:5+t.height}computePixelHeight(t){if(t.packedAlignmentRows){return(t.hasDownsampledIntervals()?10:0)+("SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight)*t.packedAlignmentRows.length+5}return 0}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=i+o*r+1,a=this.parent.showSoftClips,l=this.parent.showAllBases,c=this.browser.nucleotideColors,h=e.packedAlignmentRows;n.save();let u=e.sequence;u&&(u=u.toUpperCase());let f=0,d=t.pixelTop;this.top&&n.translate(0,this.top);const p=d+t.pixelHeight;e.hasDownsampledIntervals()?(f=10,e.downsampledIntervals.forEach((function(t){var e=(t.start-i)/r,o=(t.end-i)/r;o-e>5&&(e+=1,o-=1),Xo.fillRect(n,e,2,o-e,3,{fillStyle:"black"})}))):f=0,this.alignmentsYOffset=f;const g="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;if(h){const t=h.length;for(let e=0;e<t;e++){const t=h[e],n=f+g*e,r=g<=4?g:g-2;if(n>p)break;if(!(n+r<d))for(let e of t.alignments)if(this.hasPairs=this.hasPairs||e.isPaired(),this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag("SA")),!(e.start+e.lengthOnRef<i)){if(e.start>s)break;!0!==e.hidden&&(e instanceof ef?(m.call(this,e,n,r),v.call(this,e.firstAlignment,n,r),e.secondAlignment&&v.call(this,e.secondAlignment,n,r)):v.call(this,e,n,r))}}}function m(t,e,o){var a=this.getConnectorColor(t.firstAlignment),l=(t.connectingStart-i)/r,c=(t.connectingEnd-i)/r,h=e+o/2;t.connectingEnd<i||t.connectingStart>s||(t.mq<=0&&(a=mo.addAlpha(a,.15)),Xo.setProperties(n,{fillStyle:a,strokeStyle:a}),Xo.strokeLine(n,l,h,c,h))}function v(t,h,f){if(t.start+t.lengthOnRef<i||t.start>s)return;const d=a?t.blocks:t.blocks.filter((t=>"S"!==t.type));let p=this.getAlignmentColor(t);const m=p;t.mq<=0&&(p=mo.addAlpha(p,.15)),Xo.setProperties(n,{fillStyle:p,strokeStyle:m});const v=[];for(let t=0;t<d.length;t++){const e=d[t];if(!(t!==d.length-1&&d[t+1].start<i)&&(v.push(...b.call(this,e,t)),e.start+e.len>s))break}if(t.gaps){const e=h+f/2;for(let o of t.gaps){const t=(o.start-i)/r,s=(o.start+o.len-i)/r,a=s-t,l=o.len.toString(),c=6*l.length,u=t+a/2,f="D"===o.type?this.deletionColor:this.skippedColor;if(Xo.strokeLine(n,t,e,s,e,{strokeStyle:f,lineWidth:2}),this.showDeletionText&&o.len>1&&a>=c+8){const t=u-c/2;Xo.fillRect(n,t-1,h-1,c+2,12,{fillStyle:"white"}),Xo.fillText(n,l,t,h+10,{font:"normal 10px monospace",fillStyle:this.deletionTextColor})}}}if(t.insertions&&this.parent.showInsertions){let e=-1;for(let o of t.insertions){if(this.hideSmallIndels&&o.len<=this.indelSizeThreshold)continue;if(o.start<i)continue;if(o.start>s)break;const t=o.start-i,a=o.len.toString(),l=2+6*a.length,c=this.showInsertionText&&1!==o.len?Math.round(o.len/r):2,u=Math.max(Math.min(l,c),2),d=t/r-u/2;if(d-e>2){const t={fillStyle:this.insertionColor};Xo.fillRect(n,d-2,h,u+4,2,t),Xo.fillRect(n,d,h+2,u,f-4,t),Xo.fillRect(n,d-2,h+f-2,u+4,2,t),this.showInsertionText&&o.len>1&&c>l&&Xo.fillText(n,a,d+1,h+10,{font:"normal 10px monospace",fillStyle:this.insertionTextColor}),e=d}}}function b(s,a){const v=[],b=s.start-e.start,w=(s.start-i)/r,y=(s.start+s.len-i)/r,x=Math.max(1,y-w),_=100/r,k=Math.min(g/2,_/6),S="S"===s.type,C=t.mq<=0||this.highlightedAlignmentReadNamed===t.readName||S;let E=m;this.highlightedAlignmentReadNamed===t.readName?E="red":S&&(E="rgb(50,50,50)");const T=!0===t.strand&&a===d.length-1,A=!1===t.strand&&0===a;if(T|A){let t,e;T?(t=[w,y,y+k,y,w,w],e=[h,h,h+f/2,h+f,h+f,h]):A&&(t=[y,w,w-k,w,y,y],e=[h,h,h+f/2,h+f,h+f,h]),Xo.fillPolygon(n,t,e,{fillStyle:p}),C&&Xo.strokePolygon(n,t,e,{strokeStyle:E})}else Xo.fillRect(n,w,h,x,f,{fillStyle:p}),C&&(n.save(),n.strokeStyle=E,n.strokeRect(w,h,x,f),n.restore());if(S||l||this.parent.showMismatches&&u&&t.seq&&"*"!==t.seq){const e=t.seq?t.seq.toUpperCase():void 0,n=t.qual,a=s.seqOffset,d=Math.max(1,1/r);for(let t=0,p=s.len;t<p;t++){const p=(s.start+t-i)/r;if(p+d<0)continue;if(p>o)break;let g=e?e.charAt(a+t):"";const m=b+t>=0?u.charAt(b+t):"";if("="===g&&(g=m),"X"===g||m!==g||S||l){let e;if(!S&&void 0!==n&&n.length>a+t){e=Qp(n[a+t],c[g])}else e=c[g];e&&v.push({bbox:{x:p,y:h,width:d,height:f},baseColor:e,readChar:g})}}}return v}v.forEach((t=>{let{bbox:e,baseColor:i,readChar:o}=t;!function(t,e,n,r,i){var o;if(e<=.1&&n.height>=8){const e=Math.min(10,n.height);t.font=e+"px sans-serif",o=n.x+n.width/2,Xo.strokeText(t,i,o-t.measureText(i).width/2,e-1+n.y,{strokeStyle:r})}else Xo.fillRect(t,n.x,n.y,n.width,n.height,{fillStyle:r})}(n,r,e,i,o)}))}n.restore()}popupData(t){const e=this.getClickedObject(t);return e?e.popupData(t.genomicLocation):void 0}contextMenuItemList(t){const e=t.viewport,n=[],r=n=>{const r=this.parent.sortObject,i=!r||r.position!==Math.floor(t.genomicLocation)||!r.direction,o={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:n,direction:i};this.parent.sortObject=o,e.cachedFeatures.sortRows(o),e.repaint()};n.push("<b>Sort by...</b>"),n.push({label:"&nbsp; base",click:()=>r("BASE")}),n.push({label:"&nbsp; read strand",click:()=>r("STRAND")}),n.push({label:"&nbsp; insert size",click:()=>r("INSERT_SIZE")}),n.push({label:"&nbsp; gap size",click:()=>r("GAP_SIZE")}),n.push({label:"&nbsp; chromosome of mate",click:()=>r("MATE_CHR")}),n.push({label:"&nbsp; mapping quality",click:()=>r("MQ")}),n.push({label:"&nbsp; read name",click:()=>r("READ_NAME")}),n.push({label:"&nbsp; aligned read length",click:()=>r("ALIGNED_READ_LENGTH")}),n.push({label:"&nbsp; tag",click:()=>{const n=this.parent.sortObject,r=!n||n.position!==Math.floor(t.genomicLocation)||!n.direction,i={label:"Tag Name",value:this.sortByTag?this.sortByTag:"",callback:n=>{if(n){const i={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:"TAG",tag:n,direction:r};this.sortByTag=n,this.parent.sortObject=i,e.cachedFeatures.sortRows(i),e.repaint()}}};this.browser.inputDialog.present(i,t.event)}}),n.push("<hr/>");const i=this.getClickedObject(t);if(i){const e=this.parent.showSoftClips,r="function"==typeof i.alignmentContaining?i.alignmentContaining(t.genomicLocation,e):i;r&&(r.isPaired()&&r.isMateMapped()&&n.push({label:"View mate in split screen",click:()=>{if(r.mate){const e=t.viewport.referenceFrame;if(this.browser.genome.getChromosome(r.mate.chr)){this.highlightedAlignmentReadNamed=r.readName;const t=e.end-e.start,n=r.mate.position-t/2,i=r.mate.position+t/2;this.browser.addMultiLocusPanel(r.mate.chr,n,i,e)}else this.browser.alert.present(`Reference does not contain chromosome: ${r.mate.chr}`)}},init:void 0}),n.push({label:"View read sequence",click:()=>{const t=r.seq;t&&"*"!==t?this.browser.alert.present(t):this.browser.alert.present("Read sequence: *")}}),Os()&&n.push({label:"Copy read sequence",click:async()=>{const t=r.seq;try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),n.push("<hr/>"))}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&n.push({label:"Add discordant pairs to circular view",click:()=>{this.parent.addPairedChordsForViewport(e)}}),this.hasSupplemental&&n.push({label:"Add split reads to circular view",click:()=>{this.parent.addSplitChordsForViewport(e)}}),n.push("<hr/>")),n}getClickedObject(t){const e=t.viewport,n=t.y,r=t.genomicLocation,i=this.parent.showSoftClips;let o=e.cachedFeatures;if(!o||0===o.length)return;let s=o.packedAlignmentRows,a=o.downsampledIntervals;const l="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let c=Math.floor((n-this.top-this.alignmentsYOffset)/l);if(c<0){for(let t=0;t<a.length;t++)if(a[t].start<=r&&a[t].end>=r)return a[t]}else if(c<s.length){const t=s[c].alignments.filter((t=>t.containsLocation(r,i)));if(t.length>0)return t[0]}}getConnectorColor(t){if(this.pairConnectorColor)return this.pairConnectorColor;switch(this.colorBy){case"strand":case"firstOfPairStrand":case"pairOrientation":case"tag":return this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:"rgb(200, 200, 200)";default:return this.getAlignmentColor(t)}}getAlignmentColor(t){let e="rgb(185, 185, 185)";this.parent.color&&(e="function"==typeof this.parent.color?this.parent.color(t):this.parent.color);const n=this.colorBy;switch(n){case"strand":e=t.strand?this.posStrandColor:this.negStrandColor;break;case"firstOfPairStrand":t instanceof ef?e=t.firstOfPairStrand()?this.posStrandColor:this.negStrandColor:t.isPaired()&&(t.isFirstOfPair()?e=t.strand?this.posStrandColor:this.negStrandColor:t.isSecondOfPair()?e=t.strand?this.negStrandColor:this.posStrandColor:console.error("ERROR. Paired alignments are either first or second."));break;case"unexpectedPair":case"pairOrientation":if(this.pairOrientation&&t.pairOrientation){const n=Jp[this.pairOrientation];if(n){const r=this.pairColors[n[t.pairOrientation]];if(r){e=r;break}}}if("pairOrientation"===n)break;case"tlen":case"fragmentLength":t.mate&&t.isMateMapped()&&(t.mate.chr!==t.chr?e=tg(t.mate.chr):this.parent.minTemplateLength&&Math.abs(t.fragmentLength)<this.parent.minTemplateLength?e=this.smallTLENColor:this.parent.maxTemplateLength&&Math.abs(t.fragmentLength)>this.parent.maxTemplateLength&&(e=this.largeTLENColor));break;case"tag":const r=t.tags()[this.colorByTag];void 0!==r&&(this.bamColorTag===this.colorByTag?e="rgb("+r+")":(this.tagColors||(this.tagColors=new Wu("Set1")),e=this.tagColors.getColor(r)))}return e}}function Qp(t,e){let n;return n=t<5?.1:Math.max(.1,Math.min(1,.1+.9*(t-5)/15)),n=Math.round(10*n)/10,n<1&&(e=mo.addAlpha(e,n)),e}const Jp={fr:{F1R2:"LR",F2R1:"LR",F1F2:"LL",F2F1:"LL",R1R2:"RR",R2R1:"RR",R1F2:"RL",R2F1:"RL"},rf:{R1F2:"LR",R2F1:"LR",R1R2:"LL",R2R1:"LL",F1F2:"RR",F2F1:"RR",F1R2:"RL",F2R1:"RL"},ff:{F2F1:"LR",R1R2:"LR",F2R1:"LL",R1F2:"LL",R2F1:"RR",F1R2:"RR",R2R1:"RL",F1F2:"RL"}};function tg(t){if(eg[t])return eg[t];if(eg["chr"+t]){const e=eg["chr"+t];return eg[t]=e,e}{const e=mo.randomRGB(0,255);return eg[t]=e,e}}const eg={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0)",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};let ng,rg;class ig extends Ca{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.$multiLocusCloseButton=pe("<div>",{class:"igv-multi-locus-close-button"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(ye("times-circle")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=pe("<div>",{class:"igv-multi-locus-ruler-label"}),this.$viewport.append(this.$rulerLabel),this.$rulerLabel.click((async()=>{await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=pe("<div>",{class:"igv-ruler-tooltip"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=pe("<div>"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new tf(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(ya.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(t){this.$rulerLabel.get(0).innerHTML="",this.$rulerLabel.get(0).style.backgroundColor=tg(this.referenceFrame.chr),this.$rulerLabel.get(0).appendChild((()=>{const e=`<div>${this.referenceFrame.getMultiLocusLabel(t)}</div>`;return document.createRange().createContextualFragment(e).firstChild})()),this.$rulerLabel.show(),this.$multiLocusCloseButton.show()}presentLocusLabel_Square_Dot(t){this.$rulerLabel.get(0).innerHTML="",this.$rulerLabel.get(0).appendChild((()=>{const t=`<div>\n                                <?xml version="1.0" encoding="UTF-8"?>\n                                <svg width="14px" height="14px" viewBox="0 0 89 89" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n                                    <g>\n                                        <circle id="Oval" fill="${tg(this.referenceFrame.chr)}" cx="44.5" cy="44.5" r="44.5"></circle>\n                                    </g>\n                                </svg>\n                            </div>`;return document.createRange().createContextualFragment(t).firstChild})()),this.$rulerLabel.get(0).appendChild((()=>{const e=`<div>${this.referenceFrame.getMultiLocusLabel(t)}</div>`;return document.createRange().createContextualFragment(e).firstChild})()),this.$rulerLabel.show(),this.$multiLocusCloseButton.show()}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(t){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===t){const t=this.browser.referenceFrameList.indexOf(this.referenceFrame),e=`click${this.namespace}`;this.$viewport.on(e,(e=>{const{x:n}=we(e,this.$viewport.get(0)),r=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(n));let i;const{chr:o}=this.browser.genome.getChromosomeCoordinate(r);if(1===this.browser.referenceFrameList.length)i=o;else{let e=this.browser.referenceFrameList.map((t=>{let{locusSearchString:e}=t;return e}));e[t]=o,i=e.join(" ")}this.browser.search(i)})),this.$viewport.get(0).style.cursor="pointer"}else this.$viewport.get(0).style.cursor="default"}mouseMove(t){if(!0===this.browser.cursorGuideVisible){void 0===rg?(rg=this,this.$tooltip.show()):rg.guid!==this.guid?(rg.$tooltip&&rg.$tooltip.hide(),this.$tooltip.show(),rg=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:e}=we(t,this.$viewport.get(0)),{start:n,bpPerPixel:r}=this.referenceFrame,i=Math.round(.5+n+Math.max(0,e)*r);this.$tooltipContent.text(Se(i));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:s}=this.$viewport.get(0).getBoundingClientRect();this.$tooltip.css({left:`${uo(e,0,s-o)}px`}),clearTimeout(ng),ng=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4)}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class og extends Ca{constructor(t,e,n,r){super(t,e,n,r)}initializationHelper(){this.canvas=document.createElement("canvas"),this.canvas.className="igv-ideogram-canvas",this.$content.append(pe(this.canvas)),this.ideogram_ctx=this.canvas.getContext("2d"),this.addMouseHandlers()}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(t){this.boundClickHandler=function(t){const{xNormalized:e,width:n}=we(t,this.ideogram_ctx.canvas),{bpLength:r}=this.browser.genome.getChromosome(this.referenceFrame.chr),i=this.referenceFrame.bpPerPixel*n/r;let o=e;o-i/2<0&&(o=i/2);o+i/2>1&&(o=1-i/2);const s=Math.round((o-i/2)*r),a=Math.round((o+i/2)*r);this.referenceFrame.start=s,this.referenceFrame.end=a,this.referenceFrame.bpPerPixel=(a-s)/n,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),t.addEventListener("click",this.boundClickHandler)}setWidth(t){this.$viewport.width(t)}drawSVGWithContext(t,e,n,r,i,o,s){t.saveWithTranslationAndClipRect(r,i,o,e,n,s),this.trackView.track.draw({context:t,referenceFrame:this.referenceFrame,pixelWidth:e,pixelHeight:n}),t.restore()}repaint(){this.draw({referenceFrame:this.referenceFrame})}draw(t){let{referenceFrame:e}=t;Xo.configureHighDPICanvas(this.ideogram_ctx,this.$viewport.width(),this.$viewport.height()),this.trackView.track.draw({context:this.ideogram_ctx,referenceFrame:e,pixelWidth:this.$viewport.width(),pixelHeight:this.$viewport.height()})}startSpinner(){}stopSpinner(){}}function sg(t,e,n,r){if("ruler"===t.track.type)return new ig(t,e,n,r);if("ideogram"===t.track.id)return new og(t,e,n,r);return new Ca(t,e,n,r)}const ag={textAlign:"start",textBaseline:"bottom",strokeStyle:"black",fillStyle:"black"};class lg{constructor(t,e,n,r){this.guid=be(),this.trackView=t,this.browser=t.browser,this.viewport=ge({class:"igv-viewport"}),e.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement("canvas"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext("2d"),this.trackScrollDelta=0,this.contentTop=0,this.setWidth(r),!1===this.browser.showSampleNames&&this.hide(),this.addMouseHandlers()}checkCanvas(){const t=window.devicePixelRatio,e=this.viewport.clientHeight,n=this.browser.sampleNameViewportWidth;if(this.canvas.width!==n*t||this.canvas.height!==e*t){const r=this.canvas;r.width=n*t,r.height=e*t,r.style.width=`${n}px`,r.style.height=`${e}px`,this.ctx=this.canvas.getContext("2d"),this.ctx.scale(t,t)}}setTop(t){if("function"==typeof this.trackView.track.getSamples){this.contentTop=t;const e=this.trackView.track.getSamples();this.repaint(e)}}setWidth(t){this.viewport.innerWidth=t,this.checkCanvas()}show(){this.viewport.style.display="block"}hide(){this.viewport.style.display="none"}async repaint(t){this.checkCanvas(),this.draw({context:this.ctx,samples:t})}draw(t){let{context:e,samples:n}=t;if(!n||0===n.names.length)return;!function(t,e,n){let{textAlign:r,textBaseline:i,strokeStyle:o,fillStyle:s}=e;const a=Math.min(n,10);t.font=`${a}px sans-serif`,t.textAlign=r,t.textBaseline=i,t.fillStyle=s}(e,ag,n.height);e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=function(t){const{r:e,g:n,b:r}=Uu[t];return`rgb(${e},${n},${r})`}("lead");const r=this.viewport.getBoundingClientRect().height;let i=(n.yOffset||0)+this.contentTop;for(let t of n.names){if(i>r)break;if(i+n.height>0){const r=t,o=cg(e,r,i,n.height);e.fillText(r,4,o)}i+=n.height}}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;if("function"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples(),i=0,{width:o,height:s}=this.viewport.getBoundingClientRect(),a=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_sample_names_guid_${be()}`;t.saveWithTranslationAndClipRect(a,n,r+i,o,s,-i),this.draw({context:t,samples:e}),t.restore()}}addMouseHandlers(){this.addViewportContextMenuHandler(this.viewport)}removeMouseHandlers(){this.removeViewportContextMenuHandler(this.viewport)}addViewportContextMenuHandler(t){this.boundContextMenuHandler=function(t){t.preventDefault(),t.stopPropagation();const e={label:"Name Panel Width",value:this.browser.sampleNameViewportWidth,callback:t=>{this.browser.sampleNameViewportWidth=parseInt(t);for(let{sampleNameViewport:t}of this.browser.trackViews)t.setWidth(this.browser.sampleNameViewportWidth);this.browser.layoutChange()}};this.browser.inputDialog.present(e,t)}.bind(this),t.addEventListener("contextmenu",this.boundContextMenuHandler)}removeViewportContextMenuHandler(t){t.removeEventListener("contextmenu",this.boundContextMenuHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function cg(t,e,n,r){return n+r-function(t,e,n){const{actualBoundingBoxAscent:r,actualBoundingBoxDescent:i}=t.measureText(e);return(n-(r+i))/2}(t,e,r)}const hg=function(t){this.popover=ge({class:"igv-menu-popup"}),t.appendChild(this.popover);const e=ge({class:"igv-menu-popup-header"});this.popover.appendChild(e),_e(e,(()=>this.hide())),this.popoverContent=ge(),this.popover.appendChild(this.popoverContent),bo(this.popover,e),e.addEventListener("click",(t=>{t.stopPropagation(),t.preventDefault()})),this.hide()};hg.prototype.hide=function(){this.popover.style.display="none"},hg.prototype.presentMenuList=function(t){if(ug(),t.length>0){this.popoverContent.innerHTML="",t=Wo.trackMenuItemListHelper(t,this);for(let e of t){e.init&&e.init();let n=e.object;0===t.indexOf(e)&&n.removeClass("igv-track-menu-border-top"),n.hasClass("igv-track-menu-border-top")||n.hasClass("igv-menu-popup-check-container")||n.is("div")&&n.addClass("igv-menu-popup-shim"),this.popoverContent.appendChild(n.get(0))}this.popover.style.display="flex";const{width:e}=this.popover.getBoundingClientRect();this.popover.style.left=-e+"px",this.popover.style.top="0px"}},hg.prototype.presentTrackContextMenu=function(t,e){this.popoverContent.innerHTML="";const n=(r=e,i=this.popover,r.map((t=>{let e;if("string"==typeof t&&"<hr/>"===t)e=document.createElement("hr");else if("string"==typeof t)e=ge({class:"context-menu"}),e.innerHTML=t;else if("Node"==typeof t)e=t;else{if("function"==typeof t.init&&t.init(),"checkbox"===t.type)e=qo("Show all bases",t.value);else if("color"===t.type){const n=new xs({parent:i.parentElement,width:364});n.configure(void 0,{color:e=>t.click(e)}),e=ge({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);const r=t=>{n.show(),me(i),t.preventDefault(),t.stopPropagation()};e.addEventListener("click",r),e.addEventListener("touchend",r),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}else e=ge({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);if(t.click&&"color"!==t.type){function o(e){t.click(),me(i),e.preventDefault(),e.stopPropagation()}e.addEventListener("click",o),e.addEventListener("touchend",o),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}}return{el:e,init:t.init}})));var r,i;for(let{el:t}of n)this.popoverContent.appendChild(t);!function(t,e){e.style.display="flex";const{x:n,y:r}=we(t,e.parentNode),{width:i}=e.getBoundingClientRect(),o=n+i,{width:s}=e.parentNode.getBoundingClientRect();e.style.left=`${o>s?n-(o-s):n}px`,e.style.top=`${r}px`}(t,this.popover)},hg.prototype.dispose=function(){this.popoverContent.innerHTML="",this.popover.innerHTML="",Object.keys(this).forEach((function(t){this[t]=void 0}))};const ug=()=>{const t=document.querySelectorAll(".igv-menu-popup");for(let e=0;e<t.length;e++)t[e].style.display="none"},fg=new Set(["ruler","sequence","ideogram"]),dg=new Set(["ruler","sequence","ideogram"]);class pg{constructor(t,e,n){this.browser=t,this.track=n,n.trackView=this,this.addDOMToColumnContainer(t,e,t.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(t,e,n){this.axis=this.createAxis(t,this.track),this.viewports=[];const r=t.calculateViewportWidth(n.length),i=e.querySelectorAll(".igv-column");for(let t=0;t<i.length;t++){const e=sg(this,i[t],n[t],r);this.viewports.push(e)}this.sampleNameViewport=new lg(this,t.columnContainer.querySelector(".igv-sample-name-column"),void 0,t.sampleNameViewportWidth),this.createTrackScrollbar(t),this.createTrackDragHandle(t),this.createTrackGearPopup(t)}createAxis(t,e){const n=ge();if(t.columnContainer.querySelector(".igv-axis-column").appendChild(n),n.style.height=`${e.height}px`,"function"==typeof e.paintAxis){e.dataRange&&n.addEventListener("click",(()=>{t.dataRangeDialog.configure(this),t.dataRangeDialog.present(pe(t.columnContainer))}));const{width:r,height:i}=n.getBoundingClientRect();this.axisCanvas=document.createElement("canvas"),this.axisCanvas.style.width=`${r}px`,this.axisCanvas.style.height=`${i}px`,n.appendChild(this.axisCanvas)}return n}resizeAxisCanvas(t,e){this.axis.style.width=`${t}px`,this.axis.style.height=`${e}px`,"function"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${t}px`,this.axisCanvas.style.height=`${e}px`)}removeDOMFromColumnContainer(){this.boundAxisClickHander&&this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.$viewport.remove();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}renderSVGContext(t,e){let{deltaX:n,deltaY:r}=e;!function(t,e,n,r,i){if("function"==typeof e.paintAxis){const{y:o,width:s,height:a}=n.getBoundingClientRect(),l=`${(e.name||e.id).replace(/\W/g,"")}_axis_guid_${be()}`;t.saveWithTranslationAndClipRect(l,r,o+i,s,a,0),e.paintAxis(t,s,a),t.restore()}}(t,this.track,this.axisCanvas,n,r);const{width:i}=this.axis.getBoundingClientRect(),{y:o}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let s={deltaX:i+n,deltaY:o+r};for(let e of this.viewports){e.renderSVGContext(t,s);const{width:n}=e.$viewport.get(0).getBoundingClientRect();s.deltaX+=n}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(t,s)}dataRange(){return this.track.dataRange?this.track.dataRange:void 0}setDataRange(t,e){void 0!==t&&(this.track.dataRange.min=t),void 0!==e&&(this.track.dataRange.max=e),this.track.autoscale=!1,this.repaintViews()}presentColorPicker(t){if(!1===dg.has(this.track.type)){const e=[],n=this.track.color||this.track.defaultColor;ke(n)&&e.push(n),this.track.altColor&&ke(this.track.altColor)&&e.push(this.track.altColor);const r=e.map((t=>t.startsWith("#")?t:t.startsWith("rgb(")?mo.rgbToHex(t):mo.colorNameToHex(t))),i={color:t=>{this.track.color=t,this.repaintViews()},altColor:t=>{this.track.altColor=t,this.repaintViews()}};this.browser.genericColorPicker.configure(r,i),this.browser.genericColorPicker.setActiveColorHandler(t),this.browser.genericColorPicker.show()}}setTrackHeight(t,e){e||(this.track.minHeight&&(t=Math.max(this.track.minHeight,t)),this.track.maxHeight&&(t=Math.min(this.track.maxHeight,t))),this.track.height=t,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),"function"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:e}of this.viewports)e.height(t);if(this.sampleNameViewport.viewport.style.height=`${t}px`,"function"!=typeof this.track.computePixelHeight)for(let e of this.viewports)e.setContentHeight(t);this.repaintViews(),!1===fg.has(this.track.type)&&this.updateScrollbar(),this.dragHandle.style.height=`${t}px`,this.gearContainer.style.height=`${t}px`}updateScrollbar(){const t=this.viewports[0].$viewport.height();this.outerScroll.style.height=`${t}px`;const e=gg(this.viewports),n=Math.round(t/e*t);e>t?(this.innerScroll.style.display="block",this.innerScroll.style.height=`${n}px`):this.innerScroll.style.display="none"}moveScroller(t){const e=pe(this.innerScroll).position().top+t,n=Math.min(Math.max(0,e),this.outerScroll.clientHeight-this.innerScroll.clientHeight);pe(this.innerScroll).css("top",`${n}px`);const r=gg(this.viewports),i=-Math.round(n*(r/this.viewports[0].$viewport.height()));for(let t of this.viewports)t.setTop(i);this.sampleNameViewport.trackScrollDelta=t,this.sampleNameViewport.setTop(i)}isLoading(){for(let t of this.viewports)if(t.isLoading())return!0}repaintViews(){for(let t of this.viewports)t.isVisible()&&t.repaint();"function"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSamples()}repaintSamples(){if("function"==typeof this.track.getSamples){const t=this.track.getSamples();this.sampleNameViewport.repaint(t)}}setTrackLabelName(t){this.viewports.forEach((e=>e.setTrackLabel(t)))}resize(t){for(let e of this.viewports)e.setWidth(t)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const t=this.viewports.filter((t=>t.isVisible()));if(t.forEach((t=>t.shift())),this.browser.dragObject)return;const e=t.filter((t=>t.needsRepaint())).filter((t=>t.checkZoomIn())),n=e.filter((t=>t.needsReload()));for(let t of n)await t.loadFeatures();if(this.disposed)return;if(this.track&&"function"==typeof this.track.variantRowCount&&n.length>0){let t=0;for(let e of this.viewports)e.featureCache&&e.featureCache.features&&(t=Math.max(t,e.featureCache.features.reduce(((t,e)=>Math.max(t,e.row||0)),0)));if(this.track.nVariantRows!==t+1){this.track.variantRowCount(t+1);for(let t of this.viewports)t.checkContentHeight()}}if(this.track.autoscale){let e=[];for(let n of t){const t=n.referenceFrame,r=t.start,i=r+t.toBP(pe(n.contentDiv).width());if(n.featureCache&&n.featureCache.features)if("function"==typeof n.featureCache.features.getMax){const t=n.featureCache.features.getMax(r,i);e.push({value:t})}else e=e.concat(Uo(n.featureCache.features,r,i))}"function"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(e):this.track.dataRange=Es(e)}const r=this.track.autoscale||this.track.autoscaleGroup||"ruler"===this.track.type;for(let n of t)e.includes(n)?n.repaint():r&&n.refresh();this.adjustTrackHeight(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let t of this.viewports)t.clearCache()}updateRulerViewportLabels(){const t=this.browser.calculateViewportWidth(this.viewports.length);for(let e of this.viewports)"ruler"===this.track.type&&(this.viewports.length>1?e.presentLocusLabel(t):e.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let t=[];const e=this.viewports.filter((t=>t.isVisible()));for(let n of e){const e=n.referenceFrame,{chr:r,start:i,bpPerPixel:o}=n.referenceFrame,s=i+e.toBP(pe(n.contentDiv).width());if((!n.featureCache||!n.featureCache.containsRange(r,i,s,o))&&await n.loadFeatures(),n.featureCache&&n.featureCache.features)if("function"==typeof n.featureCache.features.getMax){const e=n.featureCache.features.getMax(i,s);t.push({value:e})}else{const e="function"==typeof n.featureCache.queryFeatures?n.featureCache.queryFeatures(r,i,s):Uo(n.featureCache.features,i,s);t=t.concat(e)}}return t}checkContentHeight(){for(let t of this.viewports)t.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var t=gg(this.viewports);if(this.track.autoHeight?this.setTrackHeight(t,!1):this.track.paintAxis&&this.paintAxis(),!1===fg.has(this.track.type)){const t=this.viewports[0].getContentTop(),e=this.viewports.map((t=>t.getContentHeight())),n=Math.min(...e),r=Math.min(0,this.viewports[0].$viewport.height()-n);if(t<r)for(let t of this.viewports)t.$content.css("top",`${r}px`);this.updateScrollbar()}}createTrackScrollbar(t){const e=ge();if(t.columnContainer.querySelector(".igv-scrollbar-column").appendChild(e),e.style.height=`${this.track.height}px`,this.outerScroll=e,!1===fg.has(this.track.type)){const n=ge();e.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){const e="ideogram"===this.track.type||"ruler"===this.track.type?"igv-track-drag-shim":"igv-track-drag-handle";this.dragHandle=ge({class:e}),t.columnContainer.querySelector(".igv-track-drag-column").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){this.gearContainer=ge(),t.columnContainer.querySelector(".igv-gear-menu-column").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu||(this.gear=ge(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(ye("cog")),this.trackGearPopup=new hg(this.gear),this.addTrackGearMouseHandlers())}addAxisEventListener(t){this.boundAxisClickHander=function(t){this.browser.dataRangeDialog.configure(this),this.browser.dataRangeDialog.present(pe(this.browser.columnContainer))}.bind(this),t.addEventListener("click",this.boundAxisClickHander)}removeAxisEventListener(t){t.removeEventListener("click",this.boundAxisClickHander)}addTrackScrollMouseHandlers(t){this.boundTrackScrollMouseDownHandler=function(e){e.stopPropagation();const{y:n}=ve(e);pe(this.innerScroll).data("yDown",n.toString()),this.boundColumnContainerMouseMoveHandler=function(t){t.stopPropagation();const{y:e}=ve(t);this.moveScroller(e-parseInt(pe(this.innerScroll).data("yDown"))),pe(this.innerScroll).data("yDown",e.toString())}.bind(this),t.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener("mousedown",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(e){t.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler)}.bind(this),t.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===fg.has(this.track.type)&&(this.innerScroll.removeEventListener("mousedown",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(t){if("ideogram"===this.track.id||"ruler"===this.track.id);else{let e;function n(n){n.preventDefault(),e=n.target,e.classList.add("igv-track-drag-handle-hover"),t.startTrackDrag(this)}function r(n){t.endTrackDrag(),e&&n.target!==e&&e.classList.remove("igv-track-drag-handle-hover"),e=void 0}function i(n){n.preventDefault(),void 0===e&&n.target.classList.add("igv-track-drag-handle-hover"),t.updateTrackDrag(this)}function o(t){t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")}this.boundTrackDragMouseDownHandler=n.bind(this),this.dragHandle.addEventListener("mousedown",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=r.bind(this),document.addEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=i.bind(this),this.dragHandle.addEventListener("mouseenter",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener("mouseout",(t=>{t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")})),this.boundTrackDragMouseOutHandler=o.bind(this),this.dragHandle.addEventListener("mouseout",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){"ideogram"===this.track.id||"ruler"===this.track.id||(this.dragHandle.removeEventListener("mousedown",this.boundTrackDragMouseDownHandler),document.removeEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener("mouseup",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener("mouseout",this.boundTrackDragMouseOutHandler))}addTrackGearMouseHandlers(){if(!0===this.track.ignoreTrackMenu);else{function t(t){t.preventDefault(),t.stopPropagation(),this.trackGearPopup.presentMenuList(Wo.trackMenuItemList(this))}this.boundTrackGearClickHandler=t.bind(this),this.gear.addEventListener("click",this.boundTrackGearClickHandler)}}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener("click",this.boundTrackGearClickHandler)}dispose(){this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.dispose();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),"function"==typeof this.track.dispose&&this.track.dispose();for(let t of Object.keys(this))this[t]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if("function"==typeof this.track.paintAxis){const{width:t,height:e}=this.axisCanvas.getBoundingClientRect(),n=window.devicePixelRatio||1;this.axisCanvas.height=n*e,this.axisCanvas.width=n*t;const r=this.axisCanvas.getContext("2d");r.scale(n,n),this.track.paintAxis(r,t,e)}}}function gg(t){const e=t.map((t=>t.getContentHeight()));return Math.max(...e)}const mg={getTissueInfo:function(t,e){let n=(e=e||"https://gtexportal.org/rest/v1")+"/dataset/tissueInfo?datasetId="+(t=t||"gtex_v8");return Eo.loadJson(n,{})},trackConfiguration:function(t,e){return{type:"eqtl",sourceType:"gtex-ws",url:(e=e||"https://gtexportal.org/rest/v1")+"/association/singleTissueEqtlByLocation",tissueSiteDetailId:t.tissueSiteDetailId,name:t.tissueSiteDetailId.split("_").join(" "),visibilityWindow:25e4}}};function vg(t,e,n){let r=(t.start-e)/n,i=(t.end-e)/n,o=i-r;return o<3&&(o=3,r-=1.5),{px:r,px1:i,pw:o}}function bg(t,e,n,r,i,o){try{i.save(),i.fillStyle=this.defaultColor,i.strokeStyle=this.defaultColor;const r=yg.call(this,t);let s,a;i.fillStyle=r,i.strokeStyle=r,"SQUISHED"===this.displayMode&&void 0!==t.row?(s=this.featureHeight/2,a=this.margin+this.squishedRowHeight*t.row):"EXPANDED"===this.displayMode&&void 0!==t.row?(s=this.featureHeight,a=this.margin+this.expandedRowHeight*t.row):(s=this.featureHeight,a=this.margin);const l=o.pixelWidth,c=a+s/2,h=s/2,u=c-h/2,f=t.exons?t.exons.length:0,d=vg(t,e,n),p=this.arrowSpacing,g="+"===t.strand?1:"-"===t.strand?-1:0;if(0===f){const t=Math.max(0,d.px),e=Math.min(l,d.px1),n=e-t;if(i.fillRect(t,a,n,s),0!==g){i.fillStyle="white",i.strokeStyle="white";for(let n=t+p/2;n<e;n+=p)Xo.strokeLine(i,n-2*g,c-2,n,c),Xo.strokeLine(i,n-2*g,c+2,n,c);i.fillStyle=r,i.strokeStyle=r}}else{Xo.strokeLine(i,d.px+1,c,d.px1-1,c);const o=Math.max(0,d.px)+p/2,m=Math.min(l,d.px1);for(let t=o;t<m;t+=p)Xo.strokeLine(i,t-2*g,c-2,t,c),Xo.strokeLine(i,t-2*g,c+2,t,c);for(let o=0;o<f;o++){const f=t.exons[o];let d,m=Math.round((f.start-e)/n),v=Math.round((f.end-e)/n),b=Math.max(1,v-m);if(!(m+b<0)){if(m>l)break;if(f.utr)i.fillRect(m,u,b,h);else if(f.cdStart&&(d=Math.round((f.cdStart-e)/n),i.fillRect(m,u,d-m,h),b-=d-m,m=d),f.cdEnd&&(d=Math.round((f.cdEnd-e)/n),i.fillRect(d,u,v-d,h),b-=v-d,v=d),b=Math.max(b,1),i.fillRect(m,a,b,s),b>p+5&&0!==g){i.fillStyle="white",i.strokeStyle="white";for(let t=m+p/2;t<v;t+=p)Xo.strokeLine(i,t-2*g,c-2,t,c),Xo.strokeLine(i,t-2*g,c+2,t,c);i.fillStyle=r,i.strokeStyle=r}}}}o.drawLabel&&"SQUISHED"!==this.displayMode&&wg.call(this,i,t,d.px,d.px1,a,o.referenceFrame,o)}finally{i.restore()}}function wg(t,e,n,r,i,o,s){try{t.save();let a=e.name;if(void 0===a&&e.gene&&(a=e.gene.name),void 0===a&&(a=e.id||e.ID),!a||"."===a)return;let l=s.pixelXOffset||0;const c=Math.max(n,-l);let h,u=(c+Math.min(r,-l+s.viewportWidth))/2;"COLLAPSED"===this.displayMode&&"SLANT"===this.labelDisplayMode&&(h={rotate:{angle:45}});const f=function(t,e){return e?t+20:t+25}(i,h);let d,p=yg.call(this,e),g=!1;o.selection&&mg.gtexLoaded&&(g=!0,d=o.selection.colorForGene(a));const m={textAlign:"SLANT"===this.labelDisplayMode?void 0:"center",fillStyle:d||p,strokeStyle:d||p},v=t.measureText(a),b=u-v.width/2,w=u+v.width/2,y=s.rowLastLabelX[e.row]||-Number.MAX_SAFE_INTEGER;(s.labelAllFeatures||b>y||g)&&(s.rowLastLabelX[e.row]=w,Xo.fillText(t,a,u,f,m,h))}finally{t.restore()}}function yg(t){let e;if(this.altColor&&"-"===t.strand)e="function"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)e="function"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const n=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];e=this.colorTable.getColor(n)}else e=t.color?t.color:this.defaultColor;if(t.alpha&&1!==t.alpha)e=mo.addAlpha(e,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const n=function(t,e,n){const r=(e-t)/9,i=Math.floor((n-t)/r);return Math.min(1,.2+.8*i/9)}(this.config.min?this.config.min:0,this.config.max?this.config.max:1e3,t.score);t.alpha=n,e=mo.addAlpha(e,n)}return e}const xg=new Set(["nonsense","missense","stop-loss","frameshift","cds-indel"]),_g=new Set(["coding-synon"]),kg=new Set(["splice-3","splice-5"]),Sg=new Set(["untranslated-5","untranslated-3"]);function Cg(t,e,n,r,i){var o,s,a,l,c=vg(t,e,n),h=this.margin,u=this.snpColors.length;switch(o="squished"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case"function":l=t.func,s=l.split(",").map((function(t){return xg.has(t)||kg.has(t)?u-1:_g.has(t)?u-2:Sg.has(t)?u-3:0})).reduce((function(t,e){return Math.max(t,e)}));break;case"class":s="deletion"===(a=t.class)?u-1:"mnp"===a?u-2:"microsatellite"===a||"named"===a?u-3:0}i.fillStyle=this.snpColors[s],i.fillRect(c.px,h,c.pw,o)}function Eg(t,e,n,r,i){const o="EXPANDED"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let s=this.margin;"COLLAPSED"!==this.displayMode&&void 0!==t.row&&(s+=t.row*o);const a=s+.5*o,l=a-.5*o,c=a+.5*o,h=Math.round((t.junction_left-e)/n),u=Math.round((t.junction_right-e)/n);i.beginPath(),i.moveTo(h,a),i.bezierCurveTo(h,l,u,l,u,a),i.lineWidth=1+Math.log(t.num_junction_reads)/Math.log(2),i.strokeStyle="blue",i.stroke();const f=t.spanning_frag_coords;for(let t=0;t<f.length;t++){const r=f[t],o=Math.round((r.left-e)/n),s=Math.round((r.right-e)/n);i.beginPath(),i.moveTo(o,a),i.bezierCurveTo(o,c,s,c,s,a),i.lineWidth=1,i.strokeStyle="purple",i.stroke()}}class Tg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"annotation",this.maxRows=void 0===t.maxRows?1e3:t.maxRows,this.displayMode=t.displayMode||"EXPANDED",this.labelDisplayMode=t.labelDisplayMode,t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:ju(t,this.browser.genome),this.autoHeight=t.autoHeight,this.margin=void 0===t.margin?10:t.margin,this.featureHeight=t.featureHeight||14,"FusionJuncSpan"===t.type?(this.render=t.render||Eg,this.squishedRowHeight=t.squishedRowHeight||50,this.expandedRowHeight=t.expandedRowHeight||50,this.height=t.height||this.margin+2*this.expandedRowHeight):"snp"===t.type?(this.render=t.render||Cg,this.snpColors=["rgb(0,0,0)","rgb(0,0,255)","rgb(0,255,0)","rgb(255,0,0)"],this.colorBy="function",this.expandedRowHeight=t.expandedRowHeight||10,this.squishedRowHeight=t.squishedRowHeight||5,this.height=t.height||30):(this.render=t.render||bg,this.arrowSpacing=30,function(t){t.browser.on&&(t.browser.on("trackdragend",e),t.browser.on("trackremoved",n));function e(){t.trackView&&"SQUISHED"!==t.displayMode&&t.trackView.repaintViews()}function n(r){t.browser.un&&t===r&&(t.browser.un("trackdragend",e),t.browser.un("trackremoved",n))}}(this),this.squishedRowHeight=t.squishedRowHeight||15,this.expandedRowHeight=t.expandedRowHeight||30,this.height=t.height||this.margin+2*this.expandedRowHeight,t.colorBy&&(t.colorBy.field&&(t.colorTable=t.colorBy.pallete||t.colorBy.palette,t.colorBy=t.colorBy.field),this.colorBy=t.colorBy,t.colorTable?this.colorTable=new $u(t.colorTable):this.colorTable=new Wu("Set1"))),this.useScore=t.useScore}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&"function"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(t,e,n,r){const i=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:i})}computePixelHeight(t){if("COLLAPSED"===this.displayMode)return this.margin+this.expandedRowHeight;{let e=0;if(t&&"function"==typeof t.forEach)for(let n of t)n.row&&n.row>e&&(e=n.row);return this.margin+(e+1)*("SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=t.pixelHeight,a=i+o*r+1;if(this.config.isMergedTrack||Xo.fillRect(n,0,t.pixelTop,o,s,{fillStyle:"rgb(255, 255, 255)"}),e){const l=[];t.rowLastX=[],t.rowLastLabelX=[];for(let n of e)if(n.start>i&&n.end<a){const e="COLLAPSED"===this.displayMode?0:n.row||0;void 0===l[e]?l[e]=1:l[e]++,t.rowLastX[e]=-Number.MAX_SAFE_INTEGER,t.rowLastLabelX[e]=-Number.MAX_SAFE_INTEGER}const c=o/Math.max(1,Math.max(...l));let h=[];for(let o of e){if(o.end<i)continue;if(o.start>a)break;const e="COLLAPSED"===this.displayMode?0:o.row;t.drawLabel=t.labelAllFeatures||c>10;const l=Math.ceil((o.end-i)/r),u=h[e];if(!u||l>u){this.render.call(this,o,i,r,s,n,t);const a=Math.floor((o.start-i)/r);u&&a-u<=0&&(n.globalAlpha=.5,Xo.strokeLine(n,a,0,a,s,{strokeStyle:"rgb(255, 255, 255)"}),n.globalAlpha=1),h[e]=l}}}else console.log("No feature list")}clickedFeatures(t,e){const n=t.y-this.margin,r=super.clickedFeatures(t,e);let i;switch(this.displayMode){case"SQUISHED":i=Math.floor(n/this.squishedRowHeight);break;case"EXPANDED":i=Math.floor(n/this.expandedRowHeight);break;default:i=void 0}return r.filter((function(t){return void 0===i||void 0===t.row||i===t.row}))}popupData(t,e){e=this.clickedFeatures(t,e);const n=t.genomicLocation,r=[];for(let t of e){const e=t._f||t,i="function"==typeof e.popupData?e.popupData(n):this.extractPopupData(e);if(i){r.length>0&&r.push("<hr/><hr/>");const o=this.infoURL||this.config.infoURL;for(let e of i)if(r.push(e),o&&e.name&&"name"===e.name.toLowerCase()&&e.value&&ke(e.value)&&!e.value.startsWith("<")){const n=o.replace("$$",t.name);e.value=`<a target=_blank href=${n}>${e.value}</a>`}const s="gff"===this.config.format||"gff3"===this.config.format||"gtf"===this.config.format;if(e.exons)for(let t=0;t<e.exons.length;t++){const i=e.exons[t];if(n>=i.start&&n<=i.end){const n=s?i.number:"-"===e.strand?e.exons.length-t:t+1;n&&(r.push("<hr/>"),r.push({name:"Exon Number",value:n}));break}}}}return r}menuItemList(){const t=[];if(this.render===Cg){t.push("<hr/>");for(let e of["function","class"])t.push({object:pe(qo("Color by "+e,e===this.colorBy)),click:()=>{this.colorBy=e,this.trackView.repaintViews()}})}t.push("<hr/>");for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){const n={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};t.push({object:pe(qo(n[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.config.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return t}contextMenuItemList(t){const e=this.clickedFeatures(t);if(void 0===e||0===e.length)return;e.length>1&&e.sort(((t,e)=>e.end-e.start-(t.end-t.start)));const n=e[0];if(n.end-n.start<=1e6){const t=[{label:"View feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(n.chr,n.start,n.end);t?"-"===n.strand&&(t=Us(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return Os()&&void 0!==navigator.clipboard&&t.push({label:"Copy feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(n.chr,n.start,n.end);t?"-"===n.strand&&(t=Us(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),t.push("<hr/>"),t}}description(){if(Cg===this.render){let t="<html>"+this.name+"<hr/>";return t+="<em>Color By Function:</em><br>",t+='<span style="color:red">Red</span>: Coding-Non-Synonymous, Splice Site<br>',t+='<span style="color:green">Green</span>: Coding-Synonymous<br>',t+='<span style="color:blue">Blue</span>: Untranslated<br>',t+='<span style="color:black">Black</span>: Intron, Locus, Unknown<br><br>',t+="<em>Color By Class:</em><br>",t+='<span style="color:red">Red</span>: Deletion<br>',t+='<span style="color:green">Green</span>: MNP<br>',t+='<span style="color:blue">Blue</span>: Microsatellite, Named<br>',t+='<span style="color:black">Black</span>: Indel, Insertion, SNP',t+="</html>",t}return super.description()}dispose(){this.trackView=void 0}}class Ag extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type="wig",this.height=t.height||50,this.featureType="numeric",this.paintAxis=gp;const e=t.format?t.format.toLowerCase():t.format;this.flipAxis=!!t.flipAxis&&t.flipAxis,this.logScale=!!t.logScale&&t.logScale,t.featureSource?(this.featureSource=t.featureSource,delete t.featureSource):this.featureSource="bigwig"===e?new Ic(t,this.browser.genome):"tdf"===e?new Pu(t,this.browser.genome):ju(t,this.browser.genome),this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max}),this.windowFunction=t.windowFunction||"mean",this.graphType=t.graphType||"bar",this.normalize=t.normalize,this.scaleFactor=t.scaleFactor}async postInit(){const t=await this.getHeader();this.disposed||t&&this.setTrackProperties(t)}async getFeatures(t,e,n,r){const i=await this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:this.visibilityWindow,windowFunction:this.windowFunction});if(this.normalize&&this.featureSource.normalizationFactor){const t=this.featureSource.normalizationFactor;for(let e of i)e.value*=t}if(this.scaleFactor){const t=this.scaleFactor;for(let e of i)e.value*=t}return i}menuItemList(){let t=[];return void 0!==this.flipAxis&&(t.push("<hr>"),t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}})),t=t.concat(Wo.numericDataMenuItems(this.trackView)),t}async getHeader(){return"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(t,e,n,r){return r?n/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):n/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let n=this.dataRange.max,r=this.dataRange.min;return n<=0?0:(r<=-1&&(r=0),r=r<=0?0:Math.log10(r+1),n=Math.log10(n+1),t=Math.log10(t+1),(this.flipAxis?t-r:n-t)*e)}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth;t.pixelHeight;const s=i+o*r+1;let a=-1,l=-1;const c=this.color||"rgb(150,150,150)";let h;"string"==typeof c&&c.startsWith("rgb(")&&(h=mo.addAlpha(c,.1));const u=this.getScaleFactor(this.dataRange.min,this.dataRange.max,t.pixelHeight,this.logScale),f=t=>this.logScale?this.computeYPixelValueInLogScale(t,u):this.computeYPixelValue(t,u);if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const o=f(0);for(let t of e){if(t.end<i)continue;if(t.start>s)break;const e=Math.floor((t.start-i)/r);if(isNaN(e))continue;let h=f(t.value);const u=Math.ceil((t.end-i)/r),d=Math.max(1,u-e);let p=t.value<0&&this.altColor?this.altColor:c;const g="function"==typeof p?p(t.value):p;if("points"===this.graphType){const t=this.config.pointSize||3,r=e+d/2;Xo.fillCircle(n,r,h,t/2,{fillStyle:g,strokeStyle:g})}else{let r=h-o;const i=e+d;(i>a||t.value>=0&&t.value>l||t.value<0&&t.value<1)&&Xo.fillRect(n,e,o,d,r,{fillStyle:g}),l=t.value,a=i}}if(this.dataRange.min<0){const e=this.dataRange.max/(this.dataRange.max-this.dataRange.min)*t.pixelHeight;Xo.strokeLine(n,0,e,t.pixelWidth,e,{strokeStyle:h})}}if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let n=f(e.y),r={strokeStyle:e.color,strokeWidth:2};e.dotted?Xo.dashedLine(t.context,0,n,t.pixelWidth,n,5,r):Xo.strokeLine(t.context,0,n,t.pixelWidth,n,r)}}popupData(t,e){if((e=this.clickedFeatures(t,e))&&e.length>0){const n=t.genomicLocation,r=[];e.sort((function(t,e){return Math.abs((t.start+t.end)/2-n)-Math.abs((e.start+e.end)/2-n)}));const i=e.length>10?e.slice(0,10):e;i.sort((function(t,e){return t.start-e.start}));for(let t of i)if(t){r.length>0&&r.push("<hr/>");let e=t.end-t.start==1?Se(t.start+1):Se(t.start+1)+"-"+Se(t.end);r.push({name:"Position:",value:e}),r.push({name:"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;",value:Se(t.value)})}return i.length<e.length&&r.push("<hr/>..."),r}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}dispose(){this.trackView=void 0}getState(){const t=super.getState();return void 0!==this.flipAxis&&(t.flipAxis=this.flipAxis),void 0!==this.logScale&&(t.logScale=this.logScale),t}}function Lg(t){this.thresholds=t.thresholds,this.colors=t.colors}function Mg(t){this.scale=t,this.lowColor="rgb("+t.lowR+","+t.lowG+","+t.lowB+")",this.highColor="rgb("+t.highR+","+t.highG+","+t.highB+")",this.diff=t.high-t.low}Lg.prototype.getColor=function(t){for(let e of this.thresholds)if(t<e)return this.colors[this.thresholds.indexOf(e)];return this.colors[this.colors.length-1]},Mg.prototype.getColor=function(t){var e,n=this.scale;return t<=n.low?this.lowColor:t>=n.high?this.highColor:(e=(t-n.low)/this.diff,"rgb("+Math.floor(n.lowR+e*(n.highR-n.lowR))+","+Math.floor(n.lowG+e*(n.highG-n.lowG))+","+Math.floor(n.lowB+e*(n.highB-n.lowB))+")")};class Rg{constructor(t){this.color=t}getColor(){return this.color}}class Ig extends ml{constructor(t,e){super(t,e)}init(t){if(super.init(t),this.type=t.type||"seg","maf"===this.type&&(this.type="mut"),this.isLog=t.isLog,this.displayMode=t.displayMode||"EXPANDED",this.height=t.height||300,this.maxHeight=t.maxHeight||500,this.squishedRowHeight=t.sampleSquishHeight||t.squishedRowHeight||2,this.expandedRowHeight=t.sampleExpandHeight||t.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,t.color?this.color=t.color:(this.posColorScale=t.posColorScale||new Mg({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=t.negColorScale||new Mg({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),"mut"===this.type&&(this.colorTable=new $u(t.colorTable||Ng))),this.sampleKeys=[],this.sampleNames=new Map,t.samples){for(let e of t.samples)this.sampleKeys.push(e),this.sampleNames.set(e,e);this.explicitSamples=!0}const e=Object.assign({},this.config);e.maxWGCount=e.maxWGCount||Number.MAX_SAFE_INTEGER,this.featureSource=ju(e,this.browser.genome),this.initialSort=t.sort}async postInit(){"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const t=[],e={SQUISHED:"Squish",EXPANDED:"Expand",FILL:"Fill"};t.push("<hr/>"),t.push("DisplayMode:");const n="seg"===this.type?["SQUISHED","EXPANDED","FILL"]:["SQUISHED","EXPANDED"];for(let r of n){const n=qo(e[r],r===this.displayMode);t.push({object:pe(n),click:()=>{this.displayMode=r,this.config.displayMode=r,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return t}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys.map((t=>this.sampleNames.get(t))),height:this.sampleHeight,yOffset:0}}async getFeatures(t,e,n){const r=await this.featureSource.getFeatures({chr:t,start:e,end:n});if(this.initialSort){const t=this.initialSort;this.sortSamples(t.chr,t.start,t.end,t.direction,r),this.initialSort=void 0}return r}draw(t){let{context:e,renderSVG:n,pixelTop:r,pixelWidth:i,pixelHeight:o,features:s,bpPerPixel:a,bpStart:l}=t;if(Xo.fillRect(e,0,0,i,o,{fillStyle:"rgb(255, 255, 255)"}),s&&s.length>0){this.checkForLog(s),this.updateSampleKeys(s);const t={};let n;switch(this.sampleKeys.forEach((function(e,n){t[e]=n})),this.displayMode){case"FILL":this.sampleHeight=o/this.sampleKeys.length,n=0;break;case"SQUISHED":this.sampleHeight=this.squishedRowHeight,n=0;break;default:this.sampleHeight=this.expandedRowHeight,n=1}const c=this.sampleHeight;for(let t of s)t.pixelRect=void 0;const h=r+o,u=l+i*a+1,f=a;this.sampleYStart=void 0;for(let i of s){if(i.end<l)continue;if(i.start>u)break;const o=i.sampleKey||i.sample;i.row=t[o];const s=i.row*c+n;void 0===this.sampleYStart&&(this.sampleYStart=s);if(s+c<r||s>h)continue;const a=Math.max(i.start,l);let d=Math.round((a-l)/f);const p=Math.min(i.end,u),g=Math.round((p-l)/f);let m,v,b=Math.max(1,g-d);if(this.color?m="function"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),"mut"===this.type)v=c-2*n,b<3&&(b=3,d-=1);else{let t=i.value;this.isLog||(t=fo(t/2)),m=t<-.1?this.negColorScale.getColor(t):t>.1?this.posColorScale.getColor(t):"white";let e=c;if(c<.25){const n=.1+2*Math.abs(t);e=Math.min(1,n*c)}v=e-2*n}i.pixelRect={x:d,y:s,w:b,h:v},e.fillStyle=m,e.fillRect(d,s,b,v)}}}checkForLog(t){if(void 0===this.isLog){this.isLog=!1;for(let e of t)if(e.value<0)return void(this.isLog=!0)}}computePixelHeight(t){if(!t)return 0;const e="SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(t),this.sampleKeys.length*e}async sortSamples(t,e,n,r,i){if(i||(i=await this.featureSource.getFeatures({chr:t,start:e,end:n})),!i)return;this.updateSampleKeys(i);const o={},s="ASC"===r?1:-1,a=()=>{const t=n-e+1;for(let r of i){if(r.end<e)continue;if(r.start>n)break;const i=Math.max(e,r.start),s=(Math.min(n,r.end)-i)/t,a=r.sampleKey||r.sample,l=o[a]||0;o[a]=l+s*r.value}this.sampleKeys.sort((function(t,e){let n=o[t],r=o[e];return n||(n=s*Number.MAX_VALUE),r||(r=s*Number.MAX_VALUE),n===r?0:n>r?s:-1*s}))},l=()=>{for(let t of i){if(t.end<e)continue;if(t.start>n)break;const r=t.sampleKey||t.sample;(!o.hasOwnProperty(r)||t.value.localeCompare(o[r])>0)&&(o[r]=t.value)}this.sampleKeys.sort((function(t,e){let n=o[t]||"",r=o[e]||"";return s*n.localeCompare(r)}))};"mut"===this.type?l():a(),this.trackView.repaintViews()}clickedFeatures(t,e){const n=super.clickedFeatures(t,e),r=t.y;return n.filter((function(t){const e=t.pixelRect;return e&&r>=e.y&&r<=e.y+e.h}))}hoverText(t){return`${t.sample}: ${t.value}`}popupData(t,e){e=this.clickedFeatures(t);const n=[];for(let t of e){n.length>0&&(n.push("<hr/>"),n.push("<hr/>"));const e=t._f||t,r="function"==typeof e.popupData?e.popupData(this.type,this.browser.genome.id):this.extractPopupData(e);Array.prototype.push.apply(n,r)}return n}contextMenuItemList(t){const e=t.viewport.referenceFrame,n=t.genomicLocation,r=this.config.sort?"ASC"===this.config.sort.direction?"DESC":"ASC":"DESC",i=e.toBP(2.5),o=e=>{const n=t.viewport.cachedFeatures;this.sortSamples(e.chr,e.start,e.end,e.direction,n)};return[{label:"seg"===this.type?"Sort by value":"Sort by type",click:e=>{const s={direction:r,chr:t.viewport.referenceFrame.chr,start:n-i,end:n+i};o(s),this.config.sort=s}}]}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(t){if(!this.explicitSamples)for(let e of t){const t=e.sampleKey||e.sample;this.sampleNames.has(t)||(this.sampleNames.set(t,e.sample),this.sampleKeys.push(t))}}}const Ng={indel:"rgb(0,200,0)","targeted region":"rgb(236,155,43)",truncating:"rgb(\t150,0,0)","non-coding transcript":"rgb(0,0,150)",synonymous:"rgb(109,165,95)",silent:"rgb(109,135,80)",missense_mutation:"rgb(72,130,187)",missense:"rgb(72,130,187)","splice site":"rgb(143,83,155)",splice_region:"rgb(143,83,155)",nonsense:"rgb(216, 57,81)",nonsense_mutation:"rgb(216, 57,81)",frame_shift_del:"rgb(226,135,65)",frame_shift_ins:"rgb(226,135,65)",in_frame_del:"rgb(247,235,94)",in_frame_ins:"rgb(247,235,94)","*other*":"rgb(159,91,50)"};class Og extends ml{constructor(t,e){super(t,e),this.type="merged",this.featureType="numeric",this.paintAxis=gp,this.graphType=t.graphType}init(t){if(!t.tracks)throw Error("Error: no tracks defined for merged track"+t);super.init(t)}async postInit(){this.tracks=[];const t=[];for(let e of this.config.tracks){e.isMergedTrack=!0;const n=await this.browser.createTrack(e);n?(n.autoscale=!1,this.tracks.push(n)):console.warn("Could not create track "+e),"function"==typeof n.postInit&&t.push(n.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale||void 0===this.config.max,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return this.height=this.config.height||50,Promise.all(t)}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];return void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Wo.numericDataMenuItems(this.trackView)),t}async getFeatures(t,e,n,r){const i=this.tracks.map((i=>i.getFeatures(t,e,n,r)));return Promise.all(i)}draw(t){const e=t.features;this.autoscale&&(this.dataRange=function(t,e){let n=0,r=-Number.MAX_VALUE;for(let t of e)for(let e of t)void 0===e.value||Number.isNaN(e.value)||(n=Math.min(n,e.value),r=Math.max(r,e.value));return{min:n,max:r}}(t.referenceFrame.chr,e));for(let n=0,r=this.tracks.length;n<r;n++){const r=Object.assign({},t);r.features=e[n],this.tracks[n].dataRange=this.dataRange,this.tracks[n].flipAxis=this.flipAxis,this.tracks[n].logScale=this.logScale,this.graphType&&(this.tracks[n].graphType=this.graphType),this.tracks[n].draw(r)}}popupData(t,e){const n=e||t.viewport.cachedFeatures;if(n&&n.length===this.tracks.length){const e=[];for(let r=0;r<this.tracks.length;r++){r>0&&e.push("<hr/>"),e.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[r].name}</div>`);const i=this.tracks[r].popupData(t,n[r]);e.push(...i)}return e}}get supportsWholeGenome(){return this.tracks.every((t=>t.supportsWholeGenome))}}class Pg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.theta=t.theta||Math.PI/4,this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.height=t.height||250,this.arcType=function(t){if(!t.arcType)return"nested";switch(t.arcType){case"chiapet":return"inView";case"chiapetoutbound":return"partialInView";default:return t.arcType}}(t),this.arcOrientation=void 0===t.arcOrientation||t.arcOrientation,this.showBlocks=void 0===t.showBlocks||t.showBlocks,this.blockHeight=t.blockHeight||3,this.thickness=t.thickness||1,this.color=t.color,this.alpha=t.alpha||.02,this.painter={flipAxis:!this.arcOrientation,dataRange:this.dataRange,paintAxis:gp},t.valueColumn?(this.valueColumn=t.valueColumn,this.hasValue=!0):t.useScore&&(this.hasValue=!0,this.valueColumn="score"),this.logScale=!1!==t.logScale,t.max?(this.dataRange={min:t.min||0,max:t.max},this.autoscale=!1):this.autoscale=!0,t.featureSource?(this.featureSource=t.featureSource,delete t._featureSource):(this.featureSource=ju(t,this.browser.genome),this.featureSource.getWGFeatures=Hg)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,n){const r=this.visibilityWindow,i=await this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r});return void 0===this.hasValue&&i&&i.length>0&&(this.hasValue=void 0!==i[0].score),i}draw(t){"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?this.drawProportional(t):this.drawNested(t)}drawNested(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight,i=t.viewportWidth,o=t.bpPerPixel,s=t.bpStart,a=o;Xo.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const l=t.features;if(l){(function(){let t=0;for(let e of l){let r=(e.start-s)/a,i=(e.end-s)/a;r>=0&&i<=n&&(t=Math.max(t,i-r))}let e=Math.min(i,t)/2;if(t>0){let t=(r-10)/e;this.theta=function(t){let e,n=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],r=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(e=0;e<n.length&&!(n[e]>t);e++);let i=0===e?0:n[e-1],o=e<n.length?n[e]:1,s=(t-i)/(o-i),a=0===e?0:r[e-1],l=e<r.length?r[e]:Math.PI/2;return Math.min(Math.PI/2,a+s*(l-a))}(t),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const o=this.arcOrientation?t.pixelHeight:0,h=this.arcOrientation;e.font="8px sans-serif",e.textAlign="center";for(let t of l){let r;if(t.drawState=void 0,"function"==typeof this.color?r=this.color(t):(r=this.color||t.color||"rgb(180,25,137)",r&&this.config.useScore&&(r=zg(r,(c=t.score,Math.min(1,.11+c/779*.89).toString())))),e.lineWidth=t.thickness||this.thickness||1,t.chr1===t.chr2||"all"===t.chr){const{m1:l,m2:c}=Fg(t,this.browser.genome);let u=Math.round((l-s)/a),f=Math.round((c-s)/a);if(f<0||u>n)continue;let d=f-u;d<3&&(d=3,u--);const p=d/2,g=p/this.sinTheta,m=this.cosTheta*g,v=u+p;let b,w,y;if(h?(b=this.height+m,w=Math.PI+Math.PI/2-this.theta,y=Math.PI+Math.PI/2+this.theta):(b=-m,w=Math.PI/2-this.theta,y=Math.PI/2+this.theta),this.showBlocks&&"all"!==t.chr){const n=(t.start1-s)/a,r=(t.end1-s)/a,i=(t.start2-s)/a,l=(t.end2-s)/a,c=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(n,o,r-n,c),e.fillRect(i,o,l-i,c)}r&&!this.config.useScore&&d>i&&(r=zg(r,this.alpha)),e.strokeStyle=r,e.fillStyle=r,e.beginPath(),e.arc(v,b,g,w,y,!1),e.stroke(),t.drawState={xc:v,yc:b,r:g}}else{let i=Math.round((t.start-s)/a),o=Math.round((t.end-s)/a);if(o<0||i>n)continue;let l=o-i;l<3&&(l=3,i--);const c=t.chr===t.chr1?t.chr2:t.chr1;e.strokeStyle=r,e.fillStyle=zg(tg(c),.5),h?(e.fillRect(i,this.height/2,l,this.height/2),e.fillText(c,i+l/2,this.height/2-5),t.drawState={x:i,y:this.height/2,w:l,h:this.height/2}):(e.fillRect(i,0,l,this.height/2),e.fillText(c,i+l/2,this.height/2+13),t.drawState={x:i,y:0,w:l,h:this.height/2})}}}var c}getScaleFactor(t,e,n,r){return r?n/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):n/(e-t)}drawProportional(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight,i=t.bpPerPixel,o=t.bpStart,s=i,a=t.referenceFrame.start,l=t.referenceFrame.end;Xo.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const c=t.features;if(c&&c.length>0){const r=0,i=this.getScaleFactor(r,this.dataRange.max,t.pixelHeight-1,this.logScale),h=this.arcOrientation?t.pixelHeight:0;for(let t of c){t.drawState=void 0;const r=this.valueColumn?t[this.valueColumn]:t.score;if(void 0===r||Number.isNaN(r))continue;const c=Math.round((this.logScale?Math.log10(r+1):r)*i);if(t.chr1===t.chr2||"all"===t.chr){const{m1:n,m2:i}=Fg(t,this.browser.genome);let u=Math.round((n-o)/s),f=Math.round((i-o)/s)-u;if(f<3&&(f=3,u--),r<this.dataRange.min||r>this.dataRange.max)continue;if("proportional"!==this.arcType){const t="partialInView"===this.arcType,e=n>=a&&i<=l;let r=!1,o=!1;if(!e&&t&&(r=a<=n&&n<=l,r||(o=a<=i&&i<=l)),!(e||r||o))continue}const d=f/2,p=u+f/2;t.drawState={xc:p,yc:h,radiusX:d,radiusY:c};const g=!!this.arcOrientation,m=t.color||this.color;if(e.strokeStyle=m,e.lineWidth=t.thickness||this.thickness||1,!0===e.isSVG?e.strokeEllipse(p,h,d,c,0,0,Math.PI,g):(e.beginPath(),e.ellipse(p,h,d,c,0,0,Math.PI,g),e.stroke()),this.alpha&&(e.fillStyle=zg(m,this.alpha),!0===e.isSVG?e.fillEllipse(p,h,d,c,0,0,Math.PI,g):e.fill()),this.showBlocks&&"all"!==t.chr){e.fillStyle=m;const n=(t.start1-o)/s,r=(t.end1-o)/s,i=(t.start2-o)/s,a=(t.end2-o)/s,l=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(n,h,r-n,l),e.fillRect(i,h,a-i,l)}}else{let i=Math.round((t.start-o)/s),a=Math.round((t.end-o)/s);if(a<0||i>n||r<this.dataRange.min||r>this.dataRange.max)continue;const l=Math.min(c,this.height-13);let h=a-i;h<3&&(h=3,i--);const u=t.chr===t.chr1?t.chr2:t.chr1;if(e.font="8px sans-serif",e.textAlign="center",e.fillStyle=zg(tg(u),.5),this.arcOrientation){const n=this.height-l;e.fillRect(i,n,h,l),e.fillText(u,i+h/2,n-5),t.drawState={x:i,y:n,w:h,h:l}}else e.fillRect(i,0,h,l),e.fillText(u,i+h/2,l+13),t.drawState={x:i,y:0,w:h,h:l}}}}}clearAxis(t,e,n){Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"})}paintAxis(t,e,n){const r={min:0,max:this.dataRange.max};"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?(this.painter.flipAxis=!this.arcOrientation,this.painter.dataRange=r,this.painter.paintAxis(t,e,n)):this.clearAxis(t,e,n)}menuItemList(){let t=[];if(this.hasValue){t.push("<hr/>");const e={nested:"Nested",proportional:"Proportional - All",inView:"Proportional - Both Ends in View",partialInView:"Proportional - One End in View"};t.push("<b>Arc Type</b>");for(let n of["nested","proportional","inView","partialInView"])t.push({object:pe(qo(e[n],n===this.arcType)),click:()=>{this.arcType=n,this.trackView.repaintViews()}})}return t.push("<hr/>"),t.push({name:"Toggle arc direction",click:()=>{this.arcOrientation=!this.arcOrientation,this.trackView.repaintViews()}}),t.push({name:this.showBlocks?"Hide Blocks":"Show Blocks",click:()=>{this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),"proportional"!==this.arcType&&"inView"!==this.arcType&&"partialInView"!==this.arcType||(t=t.concat(Wo.numericDataMenuItems(this.trackView))),this.browser.circularView&&(t.push("<hr/>"),t.push({label:"Add interactions to circular view",click:()=>{for(let t of this.trackView.viewports)this.addChordsForViewport(t.referenceFrame)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,n=[];return n.push({label:"Add interactions to circular view",click:()=>{const t=e.referenceFrame;this.addChordsForViewport(t)}}),n.push("<hr/>"),n}}addChordsForViewport(t){const e=("all"===t.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end)).filter((t=>t.drawState));if(0===e.length)return;const n=e.map((t=>{const e=t._f||t;return{uniqueId:`${e.chr1}:${e.start1}-${e.end1}_${e.chr2}:${e.start2}-${e.end2}`,refName:qp(e.chr1),start:e.start1,end:e.end1,mate:{refName:qp(e.chr2),start:e.start2,end:e.end2}}}));$p(n,this,t,.5)}doAutoscale(t){let e=0;if(t)for(let n of t){const t=this.valueColumn?n[this.valueColumn]:n.score;Number.isNaN(t)||(e=Math.max(e,t))}return{min:0,max:e}}popupData(t,e){e=this.clickedFeatures(t);const n=[];for(let t of e){const e=t._||t;if(n.push({name:"Region 1",value:Dg(e.chr1,e.start1,e.end1,e.strand1)}),n.push({name:"Region 2",value:Dg(e.chr2,e.start2,e.end2,e.strand2)}),e.name&&n.push({name:"Name",value:e.name}),void 0!==e.value&&n.push({name:"Value",value:e.value}),void 0!==e.score&&n.push({name:"Score",value:e.score}),e.extras&&this.header&&this.header.columnNames){const t=this.header.columnNames,r=this.header.hiccups?6:10;for(let i=r;i<t.length;i++)this.header.colorColumn!==i&&("info"===t[i]?Vg(n,e.extras[i-r]):n.push({name:t[i],value:e.extras[i-r]}))}break}return n}clickedFeatures(t,e){const n=e||t.viewport.cachedFeatures,r=[];if(n){const e="proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType;for(let i of n)if(i.drawState)if(i.chr1===i.chr2||"all"===i.chr)if(e){const{xc:e,yc:n,radiusX:o,radiusY:s}=i.drawState,a=t.canvasX-e,l=t.canvasY-n,c=a/o*(a/o)+l/s*(l/s);c<=1&&r.push({score:1/c,feature:i})}else{const{xc:e,yc:n,r:o}=i.drawState,s=t.canvasX-e,a=t.canvasY-n,l=Math.abs(Math.sqrt(s*s+a*a)-o);l<5&&r.push({score:l,feature:i})}else{const{x:e,y:n,w:o,h:s}=i.drawState,a=5;if(t.canvasX>=e-a&&t.canvasX<=e+o+a&&t.canvasY>=n&&t.canvasY<=n+s){const n=-Math.abs(t.canvasX-(e+o/2));r.push({score:n,feature:i});break}}}return r.length>1&&r.sort(((t,e)=>t.score-e.score)),r.map((t=>t.feature))}getState(){const t=super.getState();return void 0!==this.arcType&&(t.arcType=this.arcType),void 0!==this.arcOrientation&&(t.arcOrientation=this.arcOrientation),void 0!==this.showBlocks&&(t.showBlocks=this.showBlocks),void 0!==this.blockHeight&&(t.blockHeight=this.blockHeight),void 0!==this.thickness&&(t.thickness=this.thickness),void 0!==this.alpha&&(t.alpha=this.alpha),t}}function Fg(t,e){let n=(t.start1+t.end1)/2,r=(t.start2+t.end2)/2;if("all"===t.chr&&(n=e.getGenomeCoordinate(t.chr1,n),r=e.getGenomeCoordinate(t.chr2,r)),n>r){const t=n;n=r,r=t}return{m1:n,m2:r}}function Dg(t,e,n,r){return r&&"."!==r?`${t}:${Se(e+1)}-${Se(n)} (${r})`:`${t}:${Se(e+1)}-${Se(n)}`}const Bg=new Map;function zg(t,e){const n=`${t}_${e}`;let r=Bg.get(n);return r||(r=mo.addAlpha(t,e),Bg.set(n,r)),r}function Hg(t){const e=t=>{const e=Object.assign({},t);return e.chr="all",e.start=n.getGenomeCoordinate(t.chr1,t.start1),e.end=n.getGenomeCoordinate(t.chr2,t.end2),e},n=this.genome;let r,i=0;for(let e of n.wgChromosomeNames){let n=t[e];if(n)for(let t of n)t.dup||(i++,t.score&&(!r||t.score>r.score)&&(r=t))}const o=this.maxWGCount,s=r&&r.score>0&&i>o?5:1,a=Math.floor(o/s),l=r&&r.score>0?Math.log(r.score)/s:Number.MAX_SAFE_INTEGER;let c,h=[],u=[];for(let t=0;t<s;t++)u.push([0]),h.push([]);for(let r of n.wgChromosomeNames){let n=t[r];if(n)for(let t of n)if(!t.dup){const n=t.score?Math.max(0,Math.min(s-1,Math.floor(Math.log(t.score)/l))):0;if(h[n].length<a)h[n].push(e(t));else{const r=a/(u[n]+1);if(Math.random()<r){const r=Math.floor(Math.random()*(a-1));h[n][r]=e(t)}}u[n]++}}if(1===s)c=h[0];else{c=[];for(let t of h)for(let e of t)c.push(e);r&&c.push(e(r)),c.sort((function(t,e){return t.start-e.start})),console.log(c.length)}return c}function Vg(t,e){const n=e.split(";");for(let e of n){const n=e.split("=");2===n.length&&t.push({name:n[0],value:n[1]})}}const jg=ke,Ug=new Map([["REF","referenceBases"],["ALT","alternateBases"],["QUAL","quality"],["FILTER","filter"]]);class qg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.visibilityWindow=t.visibilityWindow,this.displayMode=t.displayMode||"EXPANDED",this.labelDisplayMode=t.labelDisplayMode,this.expandedVariantHeight=t.expandedVariantHeight||t.variantHeight||10,this.squishedVariantHeight=t.squishedVariantHeight||2,this.squishedCallHeight=t.squishedCallHeight||1,this.expandedCallHeight=t.expandedCallHeight||10,this.expandedVGap=void 0!==t.expandedVGap?t.expandedVGap:2,this.squishedVGap=void 0!==t.squishedVGap?t.squishedVGap:1,this.expandedGroupGap=t.expandedGroupGap||10,this.squishedGroupGap=t.squishedGroupGap||5,this.featureHeight=t.featureHeight||14,this.visibilityWindow=t.visibilityWindow,this.featureSource=ju(t,this.browser.genome),this.noGenotypeColor=t.noGenotypeColor||"rgb(200,180,180)",this.noCallColor=t.noCallColor||"rgb(225, 225, 225)",this.nonRefColor=t.nonRefColor||"rgb(200, 200, 215)",this.mixedColor=t.mixedColor||"rgb(200, 220, 200)",this.homrefColor=t.homrefColor||"rgb(200, 200, 200)",this.homvarColor=t.homvarColor||"rgb(17,248,254)",this.hetvarColor=t.hetvarColor||"rgb(34,12,253)",this.sortDirection="ASC",this.type=t.type||"variant",this.colorBy=t.colorBy,this._initColorBy=t.colorBy,t.colorTable&&(this.colorTables=new Map,this.colorTables.set(t.colorBy,new $u(t.colorTable))),this._strokecolor=t.strokecolor,this._context_hook=t.context_hook,this.showGenotypes=void 0===t.showGenotypes||t.showGenotypes,this.variantRowCount(1)}async postInit(){if(this.header=await this.getHeader(),!this.disposed){if(void 0===this.visibilityWindow&&!1!==this.config.indexed){const t=Ue(this.config.url)?this.config.url.name:this.config.url;jg(t)&&t.toLowerCase().includes("gnomad")?this.visibilityWindow=1e3:"function"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!1===this.config.indexed||!0===this.config.supportsWholeGenome}get color(){return this._color}set color(t){this._color=t,this.colorBy=void 0}async getHeader(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const t=await this.featureSource.getHeader();t&&(this.callSets=t.callSets||[]),this.header=t}this.sampleNames=this.callSets?this.callSets.map((t=>t.name)):[]}return this.header}getCallsetsLength(){return this.callSets?this.callSets.length:0}async getFeatures(t,e,n,r){return void 0===this.header&&(this.header=await this.getHeader()),this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:this.visibilityWindow})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(t){if(!t||0==t.length)return 10;const e="COLLAPSED"===this.displayMode?1:this.nVariantRows,n="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,r="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,i="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+e*(r+n)+n+((!1===this.showGenotypes?0:this.getCallsetsLength()*e)+1)*(i+n)}variantRowCount(t){this.nVariantRows=t}draw(t){let{context:e,pixelWidth:n,pixelHeight:r,bpPerPixel:i,bpStart:o,pixelTop:s,features:a}=t;Xo.fillRect(e,0,s,n,r,{fillStyle:"rgb(255, 255, 255)"});const l="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,c="COLLAPSED"===this.displayMode?1:this.nVariantRows,h="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+c*(h+l);let u=this.callSets;!u&&this._f&&(u=this._f.callSets);const f=this.getCallsetsLength();if(u&&f>0&&!1!==this.showGenotypes&&Xo.strokeLine(e,0,this.variantBandHeight,n,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),a){const t="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,r="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,s=o+n*i+1;for(let n of a){if(n.end<o)continue;if(n.start>s)break;const a="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,l=10+("COLLAPSED"===this.displayMode?0:n.row*(a+r)),c=a;let h=Math.round((n.start-o)/i),d=Math.round((n.end-o)/i),p=Math.max(1,d-h);p<3?(p=3,h-=1):p>5&&(h+=1,p-=2),e.fillStyle=this.getVariantColor(n),e.fillRect(h,l,p,c);let g=this.getVariantStrokecolor(n);if(g&&(e.strokeStyle=g,e.strokeRect(h,l,p,c)),this.callContextHook(n,e,h,l,p,c),n.pixelRect={x:h,y:l,w:p,h:c},f>0&&!1!==this.showGenotypes){const i="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+r,this.sampleHeight=i*(t+r);let o=0;if(u&&n.calls)for(let i of u){const s=n.calls[i.id];if(s){const a="COLLAPSED"===this.displayMode?0:n.row,l=this.sampleYOffset+o*this.sampleHeight+a*(t+r);let c=!0,u=!0,f=!1;if(s.genotype)for(let t of s.genotype){if("."===t){f=!0;break}0!==t&&(u=!1),0===t&&(c=!1)}s.genotype?e.fillStyle=f?this.noCallColor:u?this.homrefColor:c?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,l,p,t),i.pixelRect={x:h,y:l,w:p,h:t}}o++}}}}else console.log("No feature list")}getVariantColor(t){const e=t._f||t;let n;if(this.colorBy){const t=this.colorBy;let r;if(e.info.hasOwnProperty(t))r=e.info[t];else if(Ug.has(t)){r=e[Ug.get(t)]}n=this.getVariantColorTable(t).getColor(r),n||(n="gray")}else n=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===e.type?this.nonRefColor:"MIXED"===e.type?this.mixedColor:this.defaultColor;return n}getVariantStrokecolor(t){const e=t._f||t;let n;return n=this._strokecolor?"function"==typeof this._strokecolor?this._strokecolor(e):this._strokecolor:void 0,n}callContextHook(t,e,n,r,i,o){if(this._context_hook&&"function"==typeof this._context_hook){const s=t._f||t;e.save(),this._context_hook(s,e,n,r,i,o),e.restore()}}clickedFeatures(t,e){let n=super.clickedFeatures(t,e);const r="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,i=r+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),o=t.y;if(o<=this.variantBandHeight){const t="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,e=Math.floor((o-10)/(t+r));"COLLAPSED"!==this.displayMode&&(n=n.filter((t=>t.row===e)))}else if(this.callSets){const t=this.callSets,e=o-this.variantBandHeight,r=Math.floor(e/this.sampleHeight);if(r>=0&&r<t.length){const o=Math.floor((e-r*this.sampleHeight)/i),s="COLLAPSED"===this.displayMode?n:n.filter((t=>t.row===o)),a=t[r];n=s.map((t=>{const e=t.calls[a.id];return function(t,e){if(t.genotype){let n="";if("."===e.alternateBases)n="No Call";else{const r=e.alternateBases.split(",");for(let i of t.genotype)if(n.length>0&&(n+="|"),"."===i)n+=".";else if(0===i)n+=e.referenceBases;else{n+=r[i-1].replace("<","&lt;")}}t.genotypeName=n}}(e,t),e}))}}return n}popupData(t,e){const n=this.clickedFeatures(t,e),r=t.genomicLocation,i=this.browser.genome.id,o=this.browser.sampleInformation;let s=[];for(let t of n){const e=t._f||t;if(s.length>0&&s.push({html:'<hr style="border-top-width:2px ;border-color: #c9c3ba" />'}),"function"==typeof e.popupData){const t=e.popupData(r,i);Array.prototype.push.apply(s,t)}else{const t=e;if(void 0!==t.callSetName&&s.push({name:"Name",value:t.callSetName}),t.genotypeName&&s.push({name:"Genotype",value:t.genotypeName}),void 0!==t.phaseset&&s.push({name:"Phase set",value:t.phaseset}),void 0!==t.genotypeLikelihood&&s.push({name:"genotypeLikelihood",value:t.genotypeLikelihood.toString()}),o){var a=o.getAttributes(t.callSetName);a&&Object.keys(a).forEach((function(t){var e=t.replace(/([A-Z])/g," $1");e=e.charAt(0).toUpperCase()+e.slice(1),s.push({name:e,value:a[t]})}))}var l=Object.keys(t.info);l.length&&s.push("<hr/>"),l.forEach((function(e){s.push({name:e,value:decodeURIComponent(t.info[e])})}))}}return s}menuItemList(){const t=[];if(this.header.INFO&&this.header.INFO){const e=this.header.INFO.SVTYPE?["SVTYPE"]:[];if(this._initColorBy&&"SVTYPE"!==this._initColorBy&&e.push(this._initColorBy),e.length>0){t.push("<hr/>");const n=pe('<div class="igv-track-menu-category igv-track-menu-border-top">');n.text("Color by:"),t.push({name:void 0,object:n,click:void 0,init:void 0}),e.sort();for(let n of e){const e=this.colorBy===n,r=n||"None";t.push(this.colorByCB({key:n,label:r},e))}t.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),t.push("<hr/>")}}this.getCallsetsLength()>0&&(t.push({object:pe('<div class="igv-track-menu-border-top">')}),t.push({object:pe(qo("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),t.push({object:pe('<div class="igv-track-menu-border-top">')});for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){t.push({object:pe(qo({COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"}[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(t.push("<hr>"),t.push({label:"Add SVs to circular view",click:()=>{for(let t of this.trackView.viewports)this.sendChordsForViewport(t)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,n=[];return n.push({label:"Add SVs to Circular View",click:()=>{this.sendChordsForViewport(e)}}),n.push("<hr/>"),n}}sendChordsForViewport(t){const e=t.referenceFrame,n=(t=>{const e=t.filter((t=>{const e=t._f||t;return e.info&&e.info.CHR2&&e.info.END&&(e.info.CHR2!==e.chr||Math.abs(Number.parseInt(e.info.END)-e.pos)>1e6)}));return e.map((t=>{const e=t._f||t,n=Number.parseInt(e.info.END),r=n-100,i=n+100;return{uniqueId:`${e.chr}:${e.start}-${e.end}_${e.info.CHR2}:${e.info.END}`,refName:qp(e.chr),start:e.start,end:e.end,mate:{refName:qp(e.info.CHR2),start:r,end:i}}}))})("all"===e.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end));$p(n,this,e,.5)}colorByCB(t,e){return{name:void 0,object:pe(qo(t.label,e)),click:()=>{t.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews())},init:void 0}}getState(){const t=super.getState();return this._color&&"function"!=typeof this._color&&(t.color=this._color),t}getVariantColorTable(t){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(t)){let e;if("SVTYPE"===t)e=Wg;else e=new Wu("Set1");this.colorTables.set(t,e)}return this.colorTables.get(t)}}const Wg=new $u({DEL:"#ff2101",INS:"#001888",DUP:"#028401",INV:"#008688",CNV:"#8931ff",BND:"#891100","*":"#002eff"});class $g extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.name=t.name,this.pValueField=t.pValueField||"pValue",this.geneField=t.geneField||"geneSymbol",this.snpField=t.snpField||"snp";const e=t.minLogP||t.min,n=t.maxLogP||t.max;this.dataRange={min:e||3.5,max:n||25},this.autoscale=!n||t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||2,this.height=t.height||100,this.autoHeight=!1,this.disableButtons=t.disableButtons,this.visibilityWindow=void 0===t.visibilityWindow?2e6:t.visibilityWindow>=0?Math.min(2e6,t.visibilityWindow):2e6,this.featureSource=ju(t,this.browser.genome),mg.gtexLoaded=!0}paintAxis(t,e,n){const r=(this.dataRange.max-this.dataRange.min)/n,i={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"});const o=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/n);for(let s=4;s<=this.dataRange.max;s+=o){const o=.85*e,a=o-5,l=o,c=n-(s-this.dataRange.min)/r;Xo.strokeLine(t,a,c,l,c,i),c>8&&Xo.fillText(t,s,a-1,c+2,i)}i.textAlign="center",Xo.fillText(t,"-log10(pvalue)",e/4,n/2,i,{rotate:{angle:-90}})}async getFeatures(t,e,n){const r=this.pValueField,i=this.visibilityWindow,o=await this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:i});return o.forEach((function(t){t.value=t[r]})),o}draw(t){const e=t.context,n=t.pixelWidth,r=t.pixelHeight;this.background&&Xo.fillRect(e,0,0,n,r,{fillStyle:this.background}),Xo.strokeLine(e,0,r-1,n,r-1,{strokeStyle:this.divider});const i=i=>{const o=i?2*this.dotSize:this.dotSize,s=t.bpStart,a=(this.dataRange.max-this.dataRange.min)/r,l=t.referenceFrame.selection;for(let h of t.features){const u=(h.start-s+.5)/t.bpPerPixel;if(u<0)continue;if(u>n)break;const f=h.snp.toUpperCase(),d=h[this.geneField].toUpperCase(),p=l&&(l.snp===f||l.gene===d);if(!i||p){l&&l.snp===f&&l.addGene(d);var c=-Math.log(h[this.pValueField])/Math.LN10;if(c>=this.dataRange.min){let t;c>this.dataRange.max?(c=this.dataRange.max,t=!0):t=!1;const n=Math.max(0+o,r-Math.round((c-this.dataRange.min)/a));let s;h.px=u,h.py=n,h.radius=o,i&&l?(s=l.colorForGene(d),Xo.setProperties(e,{fillStyle:s,strokeStyle:"black"})):(s=t?"rgb(150, 150, 150)":"rgb(180, 180, 180)",Xo.setProperties(e,{fillStyle:s,strokeStyle:s})),Xo.fillCircle(e,u,n,o),Xo.strokeCircle(e,u,n,o)}}}};i(!1),i(!0)}popupData(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return[];const n=this.name,r=[];for(let i of e)Math.abs(i.px-t.canvasX)<i.radius+3&&Math.abs(i.py-t.canvasY)<i.radius+3&&(r.length>0&&r.push("<hr/>"),r.push({name:"snp id",value:i.snp},{name:"gene id",value:i.geneId},{name:"gene name",value:i.geneName},{name:"p value",value:i.pValue},{name:"tissue",value:n}));return r}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){var e=t.map((function(t){return-Math.log(t.value)/Math.LN10}));this.dataRange.max=ho(e,this.autoscalePercentile)}else{const t=this.config.maxLogP||this.config.max;this.dataRange.max=t||25}return this.dataRange}}const Gg={X:"rgb(204, 153, 0)",Y:"rgb(153, 204, 0)",Un:"darkGray)",1:"rgb(80, 80, 255)",I:"rgb(139, 155, 187)",2:"rgb(206, 61, 50)",II:"rgb(206, 61, 50)","2a":"rgb(210, 65, 55)","2b":"rgb(215, 70, 60)",3:"rgb(116, 155, 88)",III:"rgb(116, 155, 88)",4:"rgb(240, 230, 133)",IV:"rgb(240, 230, 133)",5:"rgb(70, 105, 131)",6:"rgb(186, 99, 56)",7:"rgb(93, 177, 221)",8:"rgb(128, 34, 104)",9:"rgb(107, 215, 107)",10:"rgb(213, 149, 167)",11:"rgb(146, 72, 34)",12:"rgb(131, 123, 141)",13:"rgb(199, 81, 39)",14:"rgb(213, 143, 92)",15:"rgb(122, 101, 165)",16:"rgb(228, 175, 105)",17:"rgb(59, 27, 83)",18:"rgb(205, 222, 183)",19:"rgb(97, 42, 121)",20:"rgb(174, 31, 99)",21:"rgb(231, 199, 111)",22:"rgb(90, 101, 94)",23:"rgb(204, 153, 0)",24:"rgb(153, 204, 0)",25:"rgb(51, 204, 0)",26:"rgb(0, 204, 51)",27:"rgb(0, 204, 153)",28:"rgb(0, 153, 204)",29:"rgb(10, 71, 255)",30:"rgb(71, 117, 255)",31:"rgb(255, 194, 10)",32:"rgb(255, 209, 71)",33:"rgb(153, 0, 51)",34:"rgb(153, 26, 0)",35:"rgb(153, 102, 0)",36:"rgb(128, 153, 0)",37:"rgb(51, 153, 0)",38:"rgb(0, 153, 26)",39:"rgb(0, 153, 102)",40:"rgb(0, 128, 153)",41:"rgb(0, 51, 153)",42:"rgb(26, 0, 153)",43:"rgb(102, 0, 153)",44:"rgb(153, 0, 128)",45:"rgb(214, 0, 71)",46:"rgb(255, 20, 99)",47:"rgb(0, 214, 143)",48:"rgb(20, 255, 177)"};for(let vv of Object.keys(Gg)){Gg["chr"+vv]=Gg[vv]}class Zg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=void 0===t.useChrColors||t.useChrColors,this.trait=t.trait,this.posteriorProbability=t.posteriorProbability,this.valueProperty="bed"===t.format?"score":"value",this.height=t.height||100,this.autoscale=t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.colorScales=t.color?new Rg(t.color):{"*":new Lg(t.colorScale||{thresholds:[5e-8,5e-4,.5],colors:["rgb(255,50,50)","rgb(251,100,100)","rgb(251,170,170)","rgb(227,238,249)"]})},this.featureSource=ju(t,this.browser.genome)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r})}draw(t){const e=t.features,n=t.context,r=t.pixelWidth,i=t.pixelHeight;if(this.background&&Xo.fillRect(n,0,0,r,i,{fillStyle:this.background}),Xo.strokeLine(n,0,i-1,r,i-1,{strokeStyle:this.divider}),e){const o=t.bpPerPixel,s=t.bpStart,a=s+r*o+1;for(let t of e){const e=t.start;if(e<s)continue;if(e>a)break;const r=this.getColorScale(t._f?t._f.chr:t.chr);let l,c;if(this.posteriorProbability)c=t[this.valueProperty],l=r.getColor(c);else{const e=t[this.valueProperty];if(!e)continue;c=-Math.log10(e),l=r.getColor(c)}const h=(this.dataRange.max-this.dataRange.min)/i,u=Math.round((e-s)/o),f=Math.max(this.dotSize,i-Math.round((c-this.dataRange.min)/h));l&&Xo.setProperties(n,{fillStyle:l,strokeStyle:"black"}),Xo.fillCircle(n,u,f,this.dotSize),t.px=u,t.py=f}}}getColorScale(t){if(this.useChrColors){let e=this.colorScales[t];if(!e){const n=Gg[t]||Zu.get();e=new Rg(n),this.colorScales[t]=e}return e}return this.colorScales("*")}paintAxis(t,e,n){Xo.fillRect(t,0,0,e,n,{fillStyle:"rgb(255, 255, 255)"});var r={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};const i=(this.dataRange.max-this.dataRange.min)/n;if(this.posteriorProbability){const e=.1;for(let o=this.dataRange.min;o<this.dataRange.max;o+=e){const e=n-Math.round((o-this.dataRange.min)/i);Xo.strokeLine(t,45,e-2,50,e-2,r),Xo.fillText(t,o.toFixed(1),44,e+2,r)}}else{const e=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/n);for(let o=this.dataRange.min;o<this.dataRange.max;o+=e){const e=n-Math.round((o-this.dataRange.min)/i);Xo.strokeLine(t,45,e,50,e,r),Xo.fillText(t,Math.floor(o),44,e+4,r)}}r.textAlign="center",this.posteriorProbability?Xo.fillText(t,"PPA",e/2,n/2,r,{rotate:{angle:-90}}):Xo.fillText(t,"-log10(pvalue)",e/2,n/2,r,{rotate:{angle:-90}})}popupData(t){let e=[];const n=t.viewport.trackView.track,r=t.viewport.cachedFeatures;if(r){let i=0;for(let o of r){const r=Math.abs(t.canvasX-o.px),s=Math.abs(t.canvasY-o.py),a=o[this.valueProperty];if(r<this.dotSize&&s<this.dotSize){if(i>0&&e.push("<HR/>"),5==i){e.push("...");break}if("function"==typeof o.popupData)e=e.concat(o.popupData());else{const t=o.realChr||o.chr,r=(o.realStart||o.start)+1;e.push({name:"chromosome",value:t}),e.push({name:"position",value:r}),e.push({name:"name",value:o.name}),n.posteriorProbability?e.push({name:"posterior probability",value:a}):e.push({name:"pValue",value:a})}i++}}}return e}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){const e=this.valueProperty,n=this.posteriorProbability,r=t.map((function(t){const r=t[e];return{value:n?r:-Math.log(r)/Math.LN10}}));this.dataRange=Es(r)}else this.posteriorProbability?(this.dataRange.min=this.config.min||0,this.dataRange.max=this.config.max||1):(this.dataRange.max=this.config.max||25,this.dataRange.min=this.config.min||0);return this.dataRange}}class Xg extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.autoscale=t.autoscale||void 0===t.max,this.dataRange={min:t.min||0,max:t.max},this.windowFunction=t.windowFunction||"mean",this.paintAxis=gp,this.graphType=t.graphType||"bar",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=ju(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if("function"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleNames=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty("clickToHighlight")){let t=this.header.clickToHighlight;this.config.clickToHighlight=t,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty("highlight")){this.config.highlightSamples={};let t=this.header.highlight;Array.isArray(t)||(t=[t]);for(let e of t){const t=e.split(";");2===t.length&&(this.config.highlightSamples[t[0]]=t[1])}}}}menuItemList(){return Wo.numericDataMenuItems(this.trackView)}async getFeatures(t,e,n){const r=await this.featureSource.getFeatures({chr:t,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let i,o;for(let t=1;t<r.length-1;t++)if(void 0===i&&r[t].end>e&&(i=t-1),void 0===o&&r[t].start>n){o=t+1;break}return void 0===i&&(i=0),void 0===o&&(o=r.length),r.slice(i,o)}draw(t){const{features:e,context:n,bpPerPixel:r,bpStart:i,pixelWidth:o,pixelHeight:s}=t,a=t=>(this.dataRange.max-t)/(this.dataRange.max-this.dataRange.min)*s,l=function(t){let e=Math.floor((t-i)/r);return isNaN(e)&&console.warn("isNaN(x). feature start "+Se(t)+" bp start "+Se(i)),e};if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const t=this.config.highlightSamples,r=this.config.onlyHandleClicksForHighlightedSamples,i=this.config.clickToHighlight;let o=-1,s={},c=[],h=[];this.clickDetectorCache={};for(let u of e){const e=l(u.start),f=l(u.end),d=o>=0?l(o):e;if(!isNaN(e)&&!isNaN(f)){this.clickDetectorCache[e]=[],this.clickDetectorCache[f]=[];for(let o=0;o<u.values.length;o++){const l=this.sampleNames[o],p=u.values[o],g=a(p);if(e-d>=1){const o=s[l],h=a(o),u=t&&t[l];u?c.push([d,h,e,g,u]):i&&l in this.config.samplesClickedToHighlight?c.push([d,h,e,g,this.config.samplesClickedToHighlight[l]]):Xo.strokeLine(n,d,h,e,g,{strokeStyle:"#D9D9D9"}),r&&!(l in t)||this.clickDetectorCache[e].push([d,h,e,g,l,u||"gray"])}if(f-e>=1){const o=t&&t[l];o?h.push([e,g,f,g,o]):i&&l in this.config.samplesClickedToHighlight?h.push([e,g,f,g,this.config.samplesClickedToHighlight[l]]):Xo.strokeLine(n,e,g,f,g,{strokeStyle:"gray"}),r&&!(l in t)||this.clickDetectorCache[f].push([e,g,f,g,l,o||"gray"])}s[l]=p}o=u.end}}for(let t of c)Xo.strokeLine(n,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:1.3});for(let t of h)Xo.strokeLine(n,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:2})}(t=>{if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let n=a(e.y),r={strokeStyle:e.color,strokeWidth:2};e.dotted?Xo.dashedLine(t.context,0,n,t.pixelWidth,n,5,r):Xo.strokeLine(t.context,0,n,t.pixelWidth,n,r)}})(t)}doAutoscale(t){let e,n;return t.length>0?(e=Number.MAX_VALUE,n=-Number.MAX_VALUE,t.forEach((function(t){e=Math.min(e,...t.values),n=Math.max(n,...t.values)})),e-=.01,n+=.01):(e=0,n=100),{min:e,max:n}}clickedFeatures(t){const e=t.canvasX,n=t.canvasY;let r=null;for(r of Object.keys(this.clickDetectorCache))if(r=parseInt(r),r>=e)break;if(r){let t=Number.MAX_VALUE,s=[];const a=this.clickDetectorCache[r];for(let r of a){const i=r[0],o=r[2];if(e<i||e>o)return[];const a=r[1],l=r[3];if(n<Math.min(a,l)-10||n>Math.max(a,l)+10)continue;const c=Yg(e,n,i,a,o,l);c<t&&(s=[{name:r[4],color:r[5]}],t=c)}if(t<5){if(this.config.clickToHighlight){if(s[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[s[0].name];else if("any"===this.config.clickToHighlight){var i=["red","darkblue","green","teal","olivedrab","orange","maroon","purple","blue","gold"],o=i[Math.floor(Math.random()*(i.length+1))];this.config.samplesClickedToHighlight[s[0].name]=o}else this.config.samplesClickedToHighlight[s[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return s}}return[]}popupData(t,e){e=this.clickedFeatures(t,e);const n=[];return e.forEach((function(t){for(let e of Object.keys(t))Ss(t[e])&&n.push({name:e,value:t[e]})})),n}get supportsWholeGenome(){return!1}}function Yg(t,e,n,r,i,o){const s=i-n,a=o-r,l=Math.abs(s*(r-e)-(n-t)*a),c=Math.sqrt(s*s+a*a);return c>0?l/c:0}class Kg extends ml{constructor(t,e){super(t,e),t.height||(this.height=300),this.arcOrientation=!1,this.theta=Math.PI/2,"bp"===t.format?this.featureSource=new Jg(t,e.genome):this.featureSource=new vc(t,e.genome)}async getFeatures(t,e,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,visibilityWindow:r})}draw(t){const e=t.context,n=Math.PI/2,r=t.pixelWidth,i=t.pixelHeight;t.viewportWidth;const o=t.bpPerPixel,s=t.bpStart,a=o,l=this.arcOrientation;Xo.fillRect(e,0,t.pixelTop,r,i,{fillStyle:"rgb(255, 255, 255)"});const c=t.features;if(c){Qg(c,1);for(let t of c)if(t.startLeft){let r=Math.round((t.startLeft-s)/a),i=Math.round((t.startRight-s)/a),o=Math.round((t.endLeft-s)/a),c=Math.round((t.endRight-s)/a);e.fillStyle=t.color,e.strokeStyle=t.color,e.beginPath();let h=(r+c)/2,u=(c-r)/2,f=this.height,d=Math.PI+(Math.PI/2-n),p=2*Math.PI-(Math.PI/2-n);l?(f=0,e.arc(h,f,u,p,d),e.lineTo(c,f)):(e.arc(h,f,u,d,p),e.lineTo(o,f));const g=(i+o)/2,m=(o-i)/2,v=f;l?(e.arc(g,v,m,d,p,!0),e.lineTo(o,v)):(e.arc(g,v,m,p,d,!0),e.lineTo(r,v)),e.stroke(),e.fill(),t.drawState={x1:h,y1:f,r1:u,x2:g,y2:v,r2:m,sa:d,ea:p}}else{let r=Math.round((t.start-s)/a),i=Math.round((t.end-s)/a);e.strokeStyle=t.color,e.beginPath();let o=(r+i)/2,c=(i-r)/2,h=this.height,u=Math.PI+(Math.PI/2-n),f=2*Math.PI-(Math.PI/2-n);l?(h=0,e.arc(o,h,c,f,u)):e.arc(o,h,c,u,f),e.stroke(),t.drawState={x1:o,y1:h,r1:c,sa:u,ea:f}}}}clickedFeatures(t,e){const n=[];Qg(e=super.clickedFeatures(t,e),-1);for(let r of e){const e=r.drawState,i=t.canvasX-e.x1,o=t.canvasY-e.y1,s=Math.sqrt(i*i+o*o),a=e.r1+3;let l,c;if(void 0===e.x2)l=s,c=e.r1-3;else{const n=t.canvasX-e.x2,r=t.canvasY-e.y2;l=Math.sqrt(n*n+r*r),c=e.r2-3}if(s<a&&l>c){n.push(r);break}}return n}popupData(t,e){if((e=this.clickedFeatures(t,e))&&e.length>0)return this.extractPopupData(e[0],this.getGenomeId())}menuItemList(){var t=this;return[{name:"Toggle arc direction",click:function(){t.arcOrientation=!t.arcOrientation,t.trackView.repaintViews()}}]}}function Qg(t,e){t.sort((function(t,n){const r=void 0===t.score?-Number.MAX_VALUE:t.score,i=void 0===n.score?-Number.MAX_VALUE:n.score;return(void 0===e?1:e)*(r-i)}))}class Jg{constructor(t,e){this.config=t,this.genome=e}async getFeatures(t){let{chr:e,start:n,end:r,bpPerPixel:i,visibilityWindow:o}=t;const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,n,r);{const t=Cs(this.config),i=await Eo.loadString(this.config.url,t);return this.featureCache=new Ho(function(t){if(!t)return null;const e=$l(t);let n,r=!0;const i=[],o=[],s=[];for(;void 0!==(n=e.nextLine());){const t=n.split("\t");if(r&&n.startsWith("color:")){const e="rgb("+t[1]+","+t[2]+","+t[3]+")";i.push(e),t.length>4&&o.push(t[4])}else{r=!1;const e=t[0],n=Number.parseInt(t[1])-1,l=Number.parseInt(t[2])-1,c=Number.parseInt(t[3]),h=Number.parseInt(t[4]);var a=Number.parseInt(t[5]);const u=i[a];let f;f=n<=h?{chr:e,startLeft:Math.min(n,l),startRight:Math.max(n,l),endLeft:Math.min(c,h),endRight:Math.max(c,h),color:u,score:a}:{chr:e,startLeft:Math.min(c,h),startRight:Math.max(c,h),endLeft:Math.min(n,l),endRight:Math.max(n,l),color:u,score:a},f.start=f.startLeft,f.end=f.endRight,o.length>a&&(f.description=o[a]),s.push(f)}}return s}(i),s),this.featureCache.queryFeatures(e,n,r)}}}class tm{constructor(t){this.browser=t,this.type="ideogram",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}async getFeatures(t,e,n){return[]}computePixelHeight(t){return this.height}draw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i}=t;const o=n.chr,s=n.genome.getChromosome(o);if(void 0===s||r<=0||i<=0||"all"===o.toLowerCase())return;!function(t){let{ctx:e,chr:n,referenceFrame:r,genome:i,width:o,height:s,stainColors:a}=t;const l=1,c=.5*l,h=0;if(void 0===i)return;Xo.fillRect(e,0,0,o,s,{fillStyle:mo.greyScale(255)});const u=i.getCytobands(n);if(u){const t=h+s/2,n=[],r=[];if(0===u.length)return;const i=o/u[u.length-1].end;e.beginPath(),Xo.roundRect(e,c,c+h,o-2*c,s-2*c,(s-2*c)/2,0,1),e.clip();for(let o=0;o<u.length;o++){const c=u[o],f=i*c.start,d=i*c.end;"c"===c.type?("p"===c.name.charAt(0)?(n[0]=f,r[0]=s+h,n[1]=f,r[1]=h,n[2]=d,r[2]=t):(n[0]=d,r[0]=s+h,n[1]=d,r[1]=h,n[2]=f,r[2]=t),e.fillStyle="rgb(150, 0, 0)",e.strokeStyle="rgb(150, 0, 0)",Xo.polygon(e,n,r,1,0)):(e.fillStyle=em(a,c),Xo.fillRect(e,f,l+h,d-f,s-2*l))}}e.strokeStyle=mo.greyScale(41),Xo.roundRect(e,c,c+h,o-2*c,s-2*c,(s-2*c)/2,0,1)}({ctx:e,chr:o,referenceFrame:n,genome:n.genome,width:r,height:i,stainColors:[]});const a=Math.round(n.bpPerPixel*r),l=n.start;let c=s.bpLength;const h=n.genome.getCytobands(o);if(h&&h.length>0&&h[h.length-1].end&&(c=Math.max(c,h[h.length-1].end),s.bpLength=c),a<c){const t=a/c,n=l/c;let o=Math.floor(n*r),s=Math.floor(t*r);o=Math.max(0,o),o=Math.min(r-s,o),e.save(),e.strokeStyle="red",e.lineWidth=s<2?1:2;const h=o+e.lineWidth/2;s=s<2?1:s-e.lineWidth;const u=e.lineWidth/2,f=i-e.lineWidth;e.strokeRect(h,u,s,f),e.restore()}}dispose(){this.trackView=void 0}}function em(t,e){if("c"===e.type)return"rgb(150, 10, 10)";var n=e.stain,r=230;"p"===e.type&&(r=Math.floor(230-n/100*230));var i=t[r];return i||(i="rgb("+r+","+r+","+r+")",t[r]=i),i}let nm=new Wu("Dark2");["GT/AG","CT/AC","GC/AG","CT/GC","AT/AC","GT/AT","non-canonical"].forEach((t=>{nm.getColor(t)}));const rm={};class im extends ml{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"junctions",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:ju(t,this.browser.genome),this.margin=void 0===t.margin?10:t.margin,this.height||(this.height=100),void 0===t.colorByNumReadsThreshold&&(t.colorByNumReadsThreshold=5)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(t,e,n,r){const i=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:n,bpPerPixel:r,visibilityWindow:i})}computePixelHeight(t){return this.height}draw(t){const e=t.features,n=t.context,r=t.bpPerPixel,i=t.bpStart,o=t.pixelWidth,s=t.pixelHeight,a=i+o*r+1;if(this.config.isMergedTrack||Xo.fillRect(n,0,t.pixelTop,o,s,{fillStyle:"rgb(255, 255, 255)"}),e){rm.referenceFrame=t.viewport.referenceFrame,rm.referenceFrameStart=rm.referenceFrame.start,rm.referenceFrameEnd=rm.referenceFrameStart+rm.referenceFrame.toBP(pe(t.viewport.contentDiv).width()),rm.featureZoomOutTracker={};for(let t of e)if(!(t.end<i)){if(t.start>a)break;this.renderJunction(t,i,r,s,n)}}else console.log("No feature list")}renderJunction(t,e,n,r,i){t.isVisible=!1;const o=Math.round((t.start-e)/n),s=Math.round((t.end-e)/n),a=(o+s)/2;if(s-o<=3){if(a in rm.featureZoomOutTracker)return;rm.featureZoomOutTracker[a]=!0}if(this.config.hideAnnotatedJunctions&&"true"===t.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&"false"===t.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(t.attributes.motif))return;if(this.config.hideStrand===t.strand)return;if(this.config.minJunctionEndsVisible){let e=0;if(t.start>=rm.referenceFrameStart&&t.start<=rm.referenceFrameEnd&&(e+=1),t.end>=rm.referenceFrameStart&&t.end<=rm.referenceFrameEnd&&(e+=1),e<this.config.minJunctionEndsVisible)return}let l,c,h,u;if(t.attributes.uniquely_mapped){if(l=parseInt(t.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(c=parseInt(t.attributes.multi_mapped),h=l+c,h<this.config.minTotalReads)return;if(h>0&&c/h>this.config.maxFractionMultiMappedReads)return;if(t.attributes.maximum_spliced_alignment_overhang&&parseInt(t.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(t.attributes.num_samples_with_this_junction){if(u=parseInt(t.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(t.attributes.num_samples_total&&(t.attributes.percent_samples_with_this_junction=100*u/Number(t.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(t.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||t.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,d=this.height,p=f+.5*d;let g=f;const m=f+d-10,v=(o+a)/2,b=(a+s)/2;let w,y,x=1;t.attributes.line_width?x=Number(t.attributes.line_width):(void 0===this.config.thicknessBasedOn||"numUniqueReads"===this.config.thicknessBasedOn?x=l:"numReads"===this.config.thicknessBasedOn?x=h:"numSamplesWithThisJunction"===this.config.thicknessBasedOn&&void 0!==u&&(x=u),x=1+Math.log(x+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||"random"===this.config.bounceHeightBasedOn?w=(t.start+t.end)%7:"distance"===this.config.bounceHeightBasedOn?w=6*(t.end-t.start)/(rm.referenceFrameEnd-rm.referenceFrameStart):"thickness"===this.config.bounceHeightBasedOn&&(w=2*x),g+=d*Math.max(7-w,0)/10,y=t.attributes.color?t.attributes.color:void 0===this.config.colorBy||"numUniqueReads"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"numReads"===this.config.colorBy?h>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"isAnnotatedJunction"===this.config.colorBy?"true"===t.attributes.annotated_junction?"#b0b0ec":"orange":"strand"===this.config.colorBy?"+"===t.strand?"#b0b0ec":"#ecb0b0":"motif"===this.config.colorBy?nm.getColor(t.attributes.motif):"#AAAAAA";let _="";t.attributes.label?_=t.attributes.label.replace(/_/g," "):void 0===this.config.labelWith||"uniqueReadCount"===this.config.labelWith?_=l:"totalReadCount"===this.config.labelWith?_=h:"numSamplesWithThisJunction"===this.config.labelWith?void 0!==u&&(_=u):"percentSamplesWithThisJunction"===this.config.labelWith?void 0!==t.attributes.percent_samples_with_this_junction&&(_=t.attributes.percent_samples_with_this_junction.toFixed(0)+"%"):"motif"===this.config.labelWith&&void 0!==t.attributes.motif&&(_+=t.attributes.motif),"uniqueReadCount"===this.config.labelWithInParen?_+=" ("+l+")":"totalReadCount"===this.config.labelWithInParen?_+=" ("+h+")":"multiMappedReadCount"===this.config.labelWithInParen?c>0&&(_+=" (+"+c+")"):"numSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==u&&(_+=" ("+u+")"):"percentSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==t.attributes.percent_samples_with_this_junction&&(_+=" ("+t.attributes.percent_samples_with_this_junction.toFixed(0)+"%)"):"motif"===this.config.labelWithInParen&&void 0!==t.attributes.motif&&(_+=` ${t.attributes.motif}`),t.isVisible=!0,i.beginPath(),i.moveTo(o,m),i.bezierCurveTo(v,g,b,g,s,m),i.lineWidth=x,i.strokeStyle=y,i.stroke();const k=(t,e,n,r)=>{t.beginPath(),t.moveTo(e,n),t.lineTo(e-r/2,n-r),t.lineTo(e+r/2,n-r),t.lineTo(e,n),t.closePath(),t.fill()};if(t.attributes.left_shape||t.attributes.right_shape){i.fillStyle=y;const e=i.lineWidth>2?10:7;t.attributes.left_shape&&k(i,o,m,e),t.attributes.right_shape&&k(i,s,m,e)}i.fillText(_,a-i.measureText(_).width/2,(7*g+p)/8)}clickedFeatures(t,e){return super.clickedFeatures(t,e).filter((function(t){return t.isVisible&&t.attributes}))}popupData(t,e){e=this.clickedFeatures(t,e);const n=t.genomicLocation,r=[];for(let t of e){const e="function"==typeof t.popupData?t.popupData(n):this.extractPopupData(t._f||t,this.getGenomeId());e&&(r.length>0&&r.push("<hr/><hr/>"),Array.prototype.push.apply(r,e))}return r}dispose(){this.trackView=void 0}}const om=new Map([["ideogram",(t,e)=>new tm(t,e)],["sequence",(t,e)=>new Ys(t,e)],["feature",(t,e)=>new Tg(t,e)],["seg",(t,e)=>new Ig(t,e)],["mut",(t,e)=>new Ig(t,e)],["maf",(t,e)=>new Ig(t,e)],["wig",(t,e)=>new Ag(t,e)],["merged",(t,e)=>new Og(t,e)],["alignment",(t,e)=>new Xp(t,e)],["interaction",(t,e)=>new Pg(t,e)],["interact",(t,e)=>new Pg(t,e)],["variant",(t,e)=>new qg(t,e)],["eqtl",(t,e)=>new $g(t,e)],["gwas",(t,e)=>new Zg(t,e)],["arc",(t,e)=>new Kg(t,e)],["gcnv",(t,e)=>new Xg(t,e)],["junction",(t,e)=>new im(t,e)]]);var sm=function(t,e){om.set(t,e)},am=function(t,e,n){let r;switch(t){case"annotation":case"genes":case"fusionjuncspan":case"snp":r="feature";break;case"seg":case"maf":case"mut":r="seg";break;case"junctions":case"splicejunctions":r="junction";break;default:r=t}return om.has(r)?om.get(r)(e,n):void 0};class lm{constructor(t,e){const n=(new DOMParser).parseFromString(t,"text/xml");this.processRootNode(n,e);const r=n.getElementsByTagName("Resource"),i=n.getElementsByTagName("Track"),o=i&&i.length>0,s=[];this.tracks=s;const a=new Map;Array.from(r).forEach((function(t,e){var n={url:t.getAttribute("path"),indexURL:t.getAttribute("index"),order:e};a.set(n.url,n),o||s.push(n)})),o&&Array.from(i).forEach((function(t){const e=t.getElementsByTagName("Track");if(e&&e.length>0){const n={type:"merged",tracks:[]};cm(t,n),s.push(n),Array.from(e).forEach((function(t){t.processed=!0;const e=t.getAttribute("id"),r=a.get(e);r&&(n.tracks.push(r),cm(t,r),r.autoscale=!1,n.height=r.height)}))}else if(!t.processed){const e=t.getAttribute("id"),n=a.get(e);n&&(s.push(n),cm(t,n))}}))}processRootNode(t,e){const n=t.getElementsByTagName("Session");!n||n.length;const r=n.item(0),i=r.getAttribute("genome"),o=r.getAttribute("locus"),s=r.getAttribute("ucscID");e&&e.hasOwnProperty(i)?this.genome=i:(this.reference={fastaURL:i},s&&(this.reference.id=s)),o&&(this.locus=o)}}function cm(t,e){e.name=t.getAttribute("name");const n=t.getAttribute("color");n&&(e.color="rgb("+n+")");const r=t.getAttribute("altColor");n&&(e.altColor="rgb("+r+")");const i=t.getAttribute("height");i&&(e.height=parseInt(i));const o=t.getAttribute("autoScale");o&&(e.autoscale="true"===o);const s=t.getAttribute("autoscaleGroup");s&&(e.autoscaleGroup=s);const a=t.getAttribute("windowFunction");a&&(e.windowFunction=a);const l=t.getAttribute("visibilityWindow")||t.getAttribute("featureVisibilityWindow");l&&(e.visibilityWindow=l);const c=t.getAttribute("indexed");c&&(e.indexed="true"===c);const h=t.getAttribute("normalize");h&&(e.normalize="true"===h);const u=t.getElementsByTagName("DataRange");if(u.length>0){const t=u.item(0);e.min=Number(t.getAttribute("minimum")),e.max=Number(t.getAttribute("maximum")),e.logScale="LOG"===t.getAttribute("type")}}const hm=Ce;class um{constructor(){this.attributes={},this.plinkLoaded=!1}async loadPlinkFile(t,e){e||(e={});var n=Cs(e);const r=await Eo.loadString(t,n);var i=hm(r);for(let t of i){var o=t.split(" ");this.attributes[o[1]]={familyId:o[0],fatherId:o[2],motherId:o[3],sex:o[4],phenotype:o[5]}}return this.plinkLoaded=!0,this}getAttributes(t){return this.attributes[t]}getAttributeNames(){return this.hasAttributes()?Object.keys(this.attributes[Object.keys(this.attributes)[0]]):[]}hasAttributes(){return Object.keys(this.attributes).length>0}}class fm{constructor(t,e){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,t&&(this.gene=t.toUpperCase(),this.geneColors[this.gene]=dm[this.genesCount++]),e&&(this.snp=e.toUpperCase())}addGene(t){this.geneColors[t.toUpperCase()]||(this.geneColors[t.toUpperCase()]=dm[this.genesCount++])}colorForGene(t){return this.geneColors[t.toUpperCase()]}}var dm=[];dm.push("rgb(228,26,28)"),dm.push("rgb(55,126,184)"),dm.push("rgb(77,175,74)"),dm.push("rgb(166,86,40)"),dm.push("rgb(152,78,163)"),dm.push("rgb(255,127,0)"),dm.push("rgb(247,129,191)"),dm.push("rgb(153,153,153)"),dm.push("rgb(255,255,51)"),dm.push("rgb(102, 194, 165"),dm.push("rgb(252, 141, 98"),dm.push("rgb(141, 160, 203"),dm.push("rgb(231, 138, 195"),dm.push("rgb(166, 216, 84"),dm.push("rgb(255, 217, 47"),dm.push("rgb(229, 196, 148"),dm.push("rgb(179, 179, 179"),dm.push("rgb( 141, 211, 199"),dm.push("rgb(255, 255, 179"),dm.push("rgb(190, 186, 218"),dm.push("rgb(251, 128, 114"),dm.push("rgb(128, 177, 211"),dm.push("rgb(253, 180, 98"),dm.push("rgb(179, 222, 105"),dm.push("rgb(252, 205, 229"),dm.push("rgb(217, 217, 217"),dm.push("rgb(188, 128, 189"),dm.push("rgb(204, 235, 197"),dm.push("rgb(255, 237, 111");class pm{constructor(t,e,n,r,i){this.genome=t,this.chr=e,this.start=n,this.end=r,this.bpPerPixel=i,this.id=be()}extend(t){const e=Math.min(t.start,this.start),n=Math.max(t.end,this.end),r=(n-e)/(this.end-this.start);this.start=e,this.end=n,this.bpPerPixel*=r}calculateEnd(t){return this.start+this.bpPerPixel*t}calculateBPP(t,e){return(t-this.start)/e}set(t){this.chr=t.chr,this.start=t.start,this.bpPerPixel=t.bpPerPixel}toPixels(t){return t/this.bpPerPixel}toBP(t){return this.bpPerPixel*t}shiftPixels(t,e,n){const r=this.start,i=t*this.bpPerPixel;return this.start+=i,n&&this.clampStart(e),this.end=this.start+e*this.bpPerPixel,r!==this.start}clampStart(t){const e=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(e,this.start),t){const{bpLength:e}=this.genome.getChromosome(this.chr),n=e-t*this.bpPerPixel;this.start>n&&(this.start=n)}}async zoomWithScaleFactor(t,e,n,r){const i=void 0===r?this.start+this.toBP(n/2):r,{start:o,bpPerPixel:s}=this.start,{bpLength:a}=this.getChromosome(),l=e<1?t.minimumBases()/n:a/n;this.bpPerPixel=e<1?Math.max(this.bpPerPixel*e,l):Math.min(this.bpPerPixel*e,l);const c=this.bpPerPixel*n;this.start=i-.5*c,this.clampStart(n),this.end=this.start+c;(o!==this.start||s!==this.bpPerPixel)&&await t.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabel(t){const e=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*t);return`&nbsp${this.chr}&nbsp &nbsp &nbsp${Ls(n-e)}&nbsp`}getPresentationLocusComponents(t){if("all"===this.chr)return{chr:this.chr};{const e=Se(Math.floor(this.start)+1),n=Se(Math.round(this.start+this.bpPerPixel*t));return{chr:this.chr,start:e,end:n}}}getLocusString(){if("all"===this.chr)return"all";{const t=Se(Math.floor(this.start)+1),e=Se(Math.round(this.end));return`${this.chr}:${t}-${e}`}}description(t){console.log(` ${t||""} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Se(Math.round(this.start))} end ${Se(Math.round(this.end))} `)}}const gm={A:"rgb(  0, 200,   0)",C:"rgb(  0,0,200)",T:"rgb(255,0,0)",G:"rgb(209,113,  5)",N:"rgb(80,80,80)"},mm={timeout:5e3,type:"plain",url:"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$",coords:0,chromosomeField:"chromosome",startField:"start",endField:"end",geneField:"gene",snpField:"snp"};async function vm(t,e){if(void 0===e||""===e.trim())return;(e&&"all"===e.trim().toLowerCase()||"*"===e)&&(e="all");const n=e.split(" ");let r=t.searchConfig||mm,i=[];const o=async n=>{let i=function(t,e){const n=e.split("\t");if(n.length>=3)try{const e=t.genome.getChromosomeName(n[0]),r=parseInt(n[1].replace(/,/g,""),10)-1,i=parseInt(n[2].replace(/,/g,""),10);if(!isNaN(r)&&!isNaN(i))return{chr:e,start:r,end:i}}catch(t){}const r=e.split(":"),i=r[0];if("all"===i&&t.genome.getChromosome(i))return{chr:i,start:0,end:t.genome.getChromosome(i).bpLength};if(void 0===t.genome.getChromosome(i))return;{const e={chr:t.genome.getChromosomeName(i),start:0,end:t.genome.getChromosome(i).bpLength};if(r.length>1){let n,i=r[1].split("-");if(i.length>2){if(!r[1].startsWith("-"))return;{const t=r[1].indexOf("-",1);if(t>0){i=[r[1].substring(0,t),r[1].substring(t+1)]}}}if(n=i[0].replace(/,/g,""),isNaN(n))return;if(e.start=parseInt(n,10)-1,e.end=e.start+1,1===i.length&&(e.start-=20,e.end+=20),2===i.length){if(n=i[1].replace(/,/g,""),isNaN(n))return;if(e.end=parseInt(n,10),e.start<0&&!t.isSoftclipped()){const t=-e.start;e.start+=t,e.end+=t}}}return e}}(t,n);if(!i){const r=t.genome.featureDB[n.toUpperCase()];r&&(i={chr:r.chr,start:r.start,end:r.end,gene:r.name,locusSearchString:e})}if(!i&&t.config&&!1!==t.config.search)try{i=await async function(t,e,n){let r=n.url.replace("$FEATURE$",e.toUpperCase());r.indexOf("$GENOME$")>-1&&(r=r.replace("$GENOME$",t.genome.id?t.genome.id:"hg19"));const i=n.timeout?{timeout:n.timeout}:void 0,o=await Eo.loadString(r,i),s=function(t,e,n){let r;r="plain"===n.type?function(t,e){const n=[],r=[];return Ce(e).forEach((function(t){""===t||n.push(t)})),n.forEach((function(e){var n,i,o,s,a=e.split("\t");a.length>=3&&(o=(i=a[1].split(":"))[1].split("-"),n=a[2].trim(),s={gene:a[0],chromosome:t.genome.getChromosomeName(i[0].trim()),start:parseInt(o[0].replace(/,/g,"")),end:parseInt(o[1].replace(/,/g,"")),type:"gtex"===n?"snp":"gene"},r.push(s))})),r}(t,e):JSON.parse(e);n.resultsField&&(r=r[n.resultsField]);if(r&&0!==r.length){const e=n.chromosomeField||"chromosome",i=n.startField||"start",o=n.endField||"end",s=n.coords||1;let a;a=Array.isArray(r)?r[0]:r,a.hasOwnProperty(e)&&a.hasOwnProperty(i)||console.error("Search service results must include chromosome and start fields: "+a);const l=a[e],c=t.genome.getChromosome(l);if(!c)return;const h=c.name;let u=a[i]-s,f=a[o];void 0===f&&(f=u+1);const d={chr:h,start:u,end:f},p=a.type?a.type:"gene";return n.geneField&&"gene"===p&&(d.gene=a[n.geneField]),n.snpField&&"snp"===p&&(d.snp=a[n.snpField]),d}return}(t,o,n);s&&(s.locusSearchString=e);return s}(t,n,r)}catch(t){throw console.error(t),Error("Search service currently unavailable.")}return i};for(let t of n){const e=await o(t);e&&(e.locusSearchString=t,i.push(e))}if(0===i.length){const t=await o(e);t&&(t.locusSearchString=e,i.push(t))}return 0===i.length?void 0:i}class bm{constructor(t){this.browser=t}navbarDidResize(t,e){this.updateNavbar(this.createResponsiveClassSchedule(t,e))}updateNavbar(t){this.browser.$toggle_button_container.removeClass(),this.browser.$toggle_button_container.addClass(t.$toggle_button_container),pe(this.browser.zoomWidget.zoomContainer).removeClass(),pe(this.browser.zoomWidget.zoomContainer).addClass(t.zoomContainer)}createResponsiveClassSchedule(t,e){let n={};return e?this.browser.windowSizePanel.hide():this.browser.windowSizePanel.show(),t>990?(n.$toggle_button_container="igv-navbar-toggle-button-container",n.zoomContainer="igv-zoom-widget"):t>860?(n.$toggle_button_container="igv-navbar-toggle-button-container",n.zoomContainer="igv-zoom-widget-900"):t>540?(n.$toggle_button_container="igv-navbar-toggle-button-container-750",n.zoomContainer="igv-zoom-widget-900"):(n.$toggle_button_container="igv-navbar-toggle-button-container-750",n.zoomContainer="igv-zoom-widget-900",this.browser.windowSizePanel.hide()),e&&(n.zoomContainer="igv-zoom-widget-hidden"),n}}const wm=function(t,e){this.container=ge({class:"igv-chromosome-select-widget-container"}),e.appendChild(this.container),this.select=document.createElement("select"),this.select.setAttribute("name","chromosome-select-widget"),this.container.appendChild(this.select),this.select.addEventListener("change",(()=>{this.select.blur(),""!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes};wm.prototype.show=function(){this.container.style.display="flex"},wm.prototype.hide=function(){this.container.style.display="none"},wm.prototype.update=function(t){const e=this.showAllChromosomes?t.chromosomeNames.slice():t.wgChromosomeNames.slice();t.showWholeGenomeView()&&(e.unshift("all"),e.unshift("")),this.select.innerHTML="";for(let t of e){const e=document.createElement("option");e.setAttribute("value",t),e.innerText=t,this.select.appendChild(e)}};class ym{constructor(t,e){this.container=ge({class:"igv-windowsize-panel-container"}),t.appendChild(this.container),e.on("locuschange",(t=>{this.updatePanel(t)})),this.browser=e}show(){this.container.style.display="block"}hide(){this.container.style.display="none"}updatePanel(t){const e=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===t.length?Ls(Math.round(e*t[0].bpPerPixel)):""}}class xm{constructor(t,e){this.browser=e,this.columnContainer=t,this.horizontalGuide=ge({class:"igv-cursor-guide-horizontal"}),t.appendChild(this.horizontalGuide),this.verticalGuide=ge({class:"igv-cursor-guide-vertical"}),t.appendChild(this.verticalGuide),this.addMouseHandler(e),this.setVisibility(e.config.showCursorGuide)}addMouseHandler(t){this.boundMouseMoveHandler=function(e){const{x:n,y:r}=we(e,this.columnContainer);this.horizontalGuide.style.top=`${r}px`;const i=document.elementFromPoint(e.clientX,e.clientY);let o;if(i.parentElement&&(i.parentElement.classList.contains("igv-viewport-content")?o=i.parentElement.parentElement:i.parentElement.classList.contains("igv-viewport")&&i.classList.contains("igv-viewport-content")&&(o=i.parentElement),o&&t.getRulerTrackView())){this.verticalGuide.style.left=`${n}px`;const r=t.root.querySelectorAll(".igv-column");let i;const s=o.parentElement;for(let t=0;t<r.length;t++)void 0===i&&s===r[t]&&(i=t);const a=t.getRulerTrackView().viewports[i].mouseMove(e);if(a){const{start:t,bp:e,end:n}=a,r=(e-t)/(n-t);this.customMouseHandler&&this.customMouseHandler({start:t,bp:e,end:n,interpolant:r})}}}.bind(this),this.columnContainer.addEventListener("mousemove",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener("mousemove",this.boundMouseMoveHandler)}setVisibility(t){!0===t?this.show():this.hide()}show(){this.verticalGuide.style.display="block",this.horizontalGuide.style.display="block"}hide(){if(this.verticalGuide.style.display="none",this.horizontalGuide.style.display="none",this.browser.getRulerTrackView())for(let t of this.browser.getRulerTrackView().viewports)t.$tooltip.hide()}}class _m{constructor(t,e){this.browser=t,this.button=ge({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="cursor guide",this.button.addEventListener("click",(()=>{t.cursorGuideVisible=!t.cursorGuideVisible,t.setCursorGuideVisibility(t.cursorGuideVisible),this.setButtonState(t.cursorGuideVisible)})),this.setButtonState(t.cursorGuideVisible),t.config.showCursorTrackingGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setButtonState(this.browser.cursorGuideVisible)}hide(){this.button.style.display="none"}}class km{constructor(t,e){this.browser=t,this.button=ge({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="center line",this.button.addEventListener("click",(()=>{t.isCenterLineVisible=!t.isCenterLineVisible,t.setCenterLineVisibility(t.isCenterLineVisible),this.setButtonState(t.isCenterLineVisible)})),this.setButtonState(t.isCenterLineVisible),t.config.showCenterGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.isVisible=!0,this.button.style.display="block",this.setButtonState(this.browser.isCenterLineVisible)}hide(){this.isVisible=!1,this.button.style.display="none"}}class Sm{constructor(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="track labels",this.button.addEventListener("click",(()=>{e.trackLabelsVisible=!e.trackLabelsVisible,this.setState(e.trackLabelsVisible),e.setTrackLabelVisibility(e.trackLabelsVisible)})),this.browser=e,this.setVisibility(e.config.showTrackLabelButton),this.setState(e.trackLabelsVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.trackLabelsVisible)}hide(){this.button.style.display="none"}}class Cm{constructor(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.innerText="Sample Names",this.setState(e.showSampleNames),this.setVisibility(e.showSampleNameButton),this.button.addEventListener("click",(()=>{e.showSampleNames=!e.showSampleNames,this.setState(e.showSampleNames);for(let{sampleNameViewport:t}of e.trackViews)!1===e.showSampleNames?t.hide():t.show();e.layoutChange()}))}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}hide(){this.button.style.display="none"}show(){this.button.style.display="block"}}let Em=23,Tm=0;const Am=function(t,e){this.browser=t,this.zoomContainer=ge({class:"igv-zoom-widget"}),e.appendChild(this.zoomContainer),this.zoomOutButton=ge(),this.zoomContainer.appendChild(this.zoomOutButton),this.zoomOutButton.appendChild(ye("minus-circle")),this.zoomOutButton.addEventListener("click",(()=>{t.zoomOut()}));const n=ge();this.zoomContainer.appendChild(n),this.slider=document.createElement("input"),this.slider.type="range",this.slider.min="0",this.slider.max=`${Em}`,n.appendChild(this.slider),this.slider.addEventListener("change",(e=>{e.preventDefault(),e.stopPropagation();const n=t.referenceFrameList[0],{bpLength:r}=n.genome.getChromosome(n.chr),{end:i,start:o}=n,s=i-o,a=r/Math.pow(2,e.target.valueAsNumber);t.zoomWithScaleFactor(a/s)})),this.zoomInButton=ge(),this.zoomContainer.appendChild(this.zoomInButton),this.zoomInButton.appendChild(ye("plus-circle")),this.zoomInButton.addEventListener("click",(()=>{t.zoomIn()})),t.on("locuschange",(t=>{this.browser.isMultiLocusMode()?this.disable():(this.enable(),this.update(t))}))};Am.prototype.update=function(t){const e=t[0],{bpLength:n}=e.genome.getChromosome(e.chr),{start:r,end:i}=e;Em=Math.ceil(Math.log2(n/this.browser.minimumBases())),this.slider.max=`${Em}`;const o=n/(i-r);Tm=Math.log2(o),this.slider.value=`${Math.round(Tm)}`},Am.prototype.enable=function(){this.slider.disabled=!1},Am.prototype.disable=function(){this.slider.disabled=!0},Am.prototype.hide=function(){this.zoomContainer.style.display="none"},Am.prototype.show=function(){this.zoomContainer.style.display="block"},Am.prototype.hideSlider=function(){this.slider.style.display="none"},Am.prototype.showSlider=function(){this.slider.style.display="block"};const Lm=function(t,e){const n=ge({class:"igv-navbar-button"});t.append(n),n.textContent="Save SVG",n.addEventListener("click",(()=>e.saveSVGtoFile({})))},Mm=(t,e)=>{const n=0===t?e.nextElementSibling:e.previousElementSibling;e.remove(),n.remove()},Rm=t=>{const e=ge({class:"igv-column-shim"});Ns(e,t);const n=ge({class:"igv-column"});return Ns(n,e),n},Im=(t,e)=>{for(let n=0;n<e;n++){const r=ge({class:"igv-column"});if(Is(r,t),e>1&&n>0){Is(ge({class:"igv-column-shim"}),r)}}};class Nm{constructor(t,e,n){this.browser=t,this.referenceFrame=e,this.column=n,this.container=ge({class:"igv-center-line"}),n.appendChild(this.container),t.isCenterLineVisible?this.show():this.hide()}repaint(){if(this.referenceFrame){if(1/this.referenceFrame.bpPerPixel>1){const t=Math.floor(this.referenceFrame.toPixels(1));this.container.style.width=`${t}px`,this.container.classList.remove("igv-center-line-thin"),this.container.classList.add("igv-center-line-wide")}else this.container.style.width="1px",this.container.classList.remove("igv-center-line-wide"),this.container.classList.add("igv-center-line-thin")}}show(){this.isVisible=!0,this.container.style.display="block",this.repaint()}hide(){this.isVisible=!1,this.container.style.display="none"}resize(){this.repaint()}}const Om=Se;class Pm{constructor(t){this.browser=t,this.height=40,this.name="",this.id="ruler",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type="ruler"}async getFeatures(t,e,n){return[]}computePixelHeight(t){return this.height}draw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpPerPixel:o,bpStart:s}=t;ya.isWholeGenomeView(n.chr)?this.drawWholeGenome({context:e,pixelWidth:r,pixelHeight:i,bpPerPixel:o}):this.doDraw({context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpStart:s})}drawWholeGenome(t){let{context:e,pixelWidth:n,pixelHeight:r,bpPerPixel:i}=t;e.save(),Xo.fillRect(e,0,0,n,r,{fillStyle:"white"});for(let t of this.browser.genome.wgChromosomeNames){let n=this.browser.genome.getCumulativeOffset(t),o=this.browser.genome.getChromosome(t).bpLength,s=Math.round(n/i),a=Math.round(o/i);this.renderChromosomeRect(e,s,0,a,r,t)}e.restore()}doDraw(t){let{context:e,referenceFrame:n,pixelWidth:r,pixelHeight:i,bpStart:o}=t;e.clearRect(0,0,r,i);const s=function(t,e){if(t<10)return new Fm(1,"bp",1);const n=Math.floor(Math.log10(t));let r="bp",i=1;n>9?(r="gb",i=1e9):n>6?(r="mb",i=1e6):n>3&&(r="kb",i=1e3);const o=Math.pow(10,n-1),s=t/o,a=75,l=Math.pow(10,n-1),c=Math.pow(10,n)/2;return new Fm(s<a&&!0!==e?l:c,r,i)}(Math.floor(n.toBP(r)),e.isSVG);let a=Math.floor(o/s.majorTick)-1;const{tickDelta:l,labelLength:c}=function(t,e,n,r,i){const o=c(e,l(1+r,i),n)-c(e,l(r,i),n),s=`${Se(Math.floor(l(r,i)/i.unitMultiplier))} ${i.majorUnit}`,a=Math.floor(t.measureText(s).width);return{tickDelta:o,labelLength:a};function l(t,e){return Math.floor(t*e.majorTick)}function c(t,e,n){return Math.round(t.toPixels(e-1-n+.5))}}(e,n,o,a,s);let h,u;this.browser.referenceFrameList.indexOf(n);let f=l;const d=.25*c;do{u=Math.floor(a*s.majorTick);const t=`${Se(Math.floor(u/s.unitMultiplier))} ${s.majorUnit}`;h=Math.round(n.toPixels(u-1-o+.5));const r=Math.round(h-e.measureText(t).width/2);r>0&&d+c<=f&&(Xo.fillText(e,t,r,this.height-8),f=0),h>0&&Xo.strokeLine(e,h,this.height-6,h,this.height-2),u=Math.floor((1+a)*s.majorTick);let i=h+(Math.round(n.toPixels(u-1-o+.5))-h)/2;i>0&&Xo.strokeLine(e,i,this.height-6,i,this.height-2),++a,f+=l}while(h<r);Xo.strokeLine(e,0,this.height-2,r,this.height-2)}renderChromosomeRect(t,e,n,r,i,o){t.textAlign="center",t.textBaseline="middle",t.font="12px sans-serif",Xo.strokeLine(t,e+r,n,e+r,n+i,{strokeStyle:mo.greyScale(191)});const s=o.startsWith("chr")?o.substring(3):o;r>t.measureText(s).width&&Xo.fillText(t,s,e+r/2,n+i/2,{fillStyle:mo.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Fm{constructor(t,e,n){this.majorTick=t,this.minorTick=t/10,this.majorUnit=e,this.unitMultiplier=n}description(t){console.log((t||"")+" tick "+Om(this.majorTick)+" label width "+Om(this.labelWidthBP)+" multiplier "+this.unitMultiplier)}}const Dm=function(t,e){this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="circular view",this.button.addEventListener("click",(()=>{e.circularViewVisible=!e.circularViewVisible})),this.browser=e,this.setVisibility(e.config.showCircularViewButton),this.setState(e.circularViewVisible)};Dm.prototype.setVisibility=function(t){!0===t?this.show():this.hide()},Dm.prototype.setState=function(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")},Dm.prototype.show=function(){this.button.style.display="block",this.setState(this.browser.circularViewVisible)},Dm.prototype.hide=function(){this.button.style.display="none"};const Bm=function(t,e,n){const r=ge({class:"igv-navbar-button"});t.append(r),r.textContent=n.label,r.addEventListener("click",(()=>n.callback(e)))};class zm{constructor(t,e,n,r,i){this.browser=t,this.roiMenu=e,this.roiTable=n,this.top=r,this.roiSets=i||[],this.boundLocusChangeHandler=Hm.bind(this),t.on("locuschange",this.boundLocusChangeHandler)}async initialize(){this.roiSets.length>0&&(this.browser.showROITableButton=!0,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton));const t=this.roiSets.map((t=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})));t.length>0&&await Promise.all(t);const e=await this.getTableRecords();this.roiTable.renderTable(e)}async loadROI(t,e){const n=Array.isArray(t)?t:[t];for(let t of n)this.roiSets.push(new Ku(t,e));await this.initialize()}clearROIs(){this.roiTable.clearTable();const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();for(let t of this.roiSets)t.dispose();this.roiSets=[]}async getTableRecords(){const t=[];for(let e of this.roiSets){const n=e.isUserDefined?"":e.name||"",r=await e.getAllFeatures();for(let e of Object.keys(r))for(let i of r[e])t.push({setName:n,feature:i})}return t}presentTable(){this.roiTable.present()}async repaintTable(){const t=await this.getTableRecords();this.roiTable.renderTable(t)}dismissTable(){this.roiTable.dismiss()}async updateUserDefinedROISet(t){let e=await this.getUserDefinedROISet();void 0===e&&(e=this.initializeUserDefinedROISet()),e.addFeature(t),!1===this.browser.showROITableButton&&this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e});const n=await this.getTableRecords();this.roiTable.renderTable(n)}setROITableButtonVisibility(t){this.browser.showROITableButton=t,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton)}async renderAllROISets(){for(let t of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})}async renderROISet(t){let{browser:e,pixelTop:n,roiSet:r}=t;const i=e.columnContainer.querySelectorAll(".igv-column");for(let t=0;t<i.length;t++){let{chr:o,start:s,end:a,bpPerPixel:l}=e.referenceFrameList[t];const c=i[t].querySelectorAll(".igv-roi-region");for(let t of c){const e=t.dataset.region,{chr:n,start:r,end:i}=Um(e);(n!==o||i<s||r>a)&&t.remove()}const h=await r.getFeatures(o,s,a);if(h)for(let c of h){const h=Vm(o,c.start,c.end),{x:u,width:f}=Qu(Math.max(s,c.start),Math.min(a,c.end),s,l),d=i[t].querySelector(jm(h));if(d)d.style.left=`${u}px`,d.style.width=`${f}px`;else{const o=this.createRegionElement(e.columnContainer,n,u,f,r,h,c.name);i[t].appendChild(o)}}}}createRegionElement(t,e,n,r,i,o,s){const a=ge({class:"igv-roi-region"});a.style.top=`${e}px`,a.style.left=`${n}px`,a.style.width=`${r}px`,a.style.backgroundColor=i.color,a.dataset.region=o;const l=ge();return a.appendChild(l),l.style.backgroundColor=i.headerColor,!0===i.isUserDefined?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation();const{x:n,y:r}=we(e,t);this.roiMenu.present(n,r,this,t,a)})):s?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation(),this.popover&&this.popover.dispose(),this.popover=new ms(t,i.name),this.popover.presentContentWithEvent(e,s)})):l.style.pointerEvents="none",a}async getUserDefinedROISet(){return this.roiSets.find((t=>!0===t.isUserDefined))}initializeUserDefinedROISet(){const t=new Ku({isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(t),t}async deleteUserDefinedRegionWithKey(t,e){e.querySelectorAll(jm(t)).forEach((t=>t.remove()));const n=await this.findUserDefinedRegionWithKey(t),r=await this.getUserDefinedROISet();r&&r.removeFeature(n);0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}async findUserDefinedRegionWithKey(t){const{chr:e,start:n,end:r}=Um(t),i=await this.getUserDefinedROISet();if(i){const t=await i.getFeatures(e,n,r);for(let i of t)if(i.chr===e&&i.start>=n&&i.end<=r)return i}}toJSON(){return this.roiSets.map((t=>t.toJSON()))}dispose(){this.browser.off("locuschange",this.boundLocusChangeHandler);const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let t of this.roiSets)t.dispose();for(let t of Object.keys(this))this[t]=void 0}}function Hm(){this.renderAllROISets()}function Vm(t,e,n){return`${t}-${e}-${n}`}function jm(t){return`[data-region="${t}"]`}function Um(t){let[e,n,r]=t.split("-");return n=parseInt(n),r=parseInt(r),{chr:e,start:n,end:r,locus:`${e}:${n}-${r}`,bedRecord:`${e}\t${n}\t${r}`}}const qm=[];class Wm{constructor(t,e,n){this.browser=t,this.container=ge({class:n?"igv-roi-table":"igv-roi-table-four-column"}),e.appendChild(this.container),this.hasROISetNames=n;const r=this.createHeaderDOM(this.container);this.columnTitleDOM=function(t,e){const n=ge({class:"igv-roi-table-column-titles"});t.appendChild(n);let r=["Chr","Start","End","Description","ROI Set"];!1===e&&(r=r.slice(0,4));for(let t of r){const e=ge();e.innerText=t,n.appendChild(e)}return n}(this.container,n),this.tableRowContainerDOM=this.createTableRowContainerDOM(this.container),this.footerDOM=this.createFooterDOM(this.container);const{y:i}=t.root.getBoundingClientRect(),{y:o}=e.getBoundingClientRect(),s=-(o-i);bo(this.container,r,{minX:0,minY:s}),this.container.style.display="none"}clearTable(){const t=this.tableRowContainerDOM.querySelectorAll(".igv-roi-table-row");for(let e of t)e.remove()}present(){this.container.style.left="0px",this.container.style.top="0px",this.container.style.display="flex"}dismiss(){this.container.style.display="none"}renderTable(t){if(Array.from(this.tableRowContainerDOM.querySelectorAll(".igv-roi-table-row")).forEach((t=>t.remove())),t.length>0){const e=t.sort(((t,e)=>t.feature.chr.localeCompare(e.feature.chr)||t.feature.start-e.feature.start||t.feature.end-e.feature.end));for(let t of e){const e=this.createTableRowDOM(t);this.tableRowContainerDOM.appendChild(e)}}}createHeaderDOM(t){const e=ge();t.appendChild(e);const n=ge();e.appendChild(n),n.innerText="Regions of Interest";const r=ge();return e.appendChild(r),r.appendChild(ye("times")),r.addEventListener("click",(t=>{t.stopPropagation(),this.browser.roiTableControl.buttonHandler(!1)})),e}createTableRowContainerDOM(t){const e=ge({class:"igv-roi-table-row-container"});return t.appendChild(e),e}createTableRowDOM(t){const e=ge({class:"igv-roi-table-row"}),{setName:n,feature:r}=t;e.dataset.region=Vm(r.chr,r.start,r.end);let i=[r.chr,Se(r.start),Se(r.end),r.name||"",n];!1===this.hasROISetNames&&(i=i.slice(0,4));for(let t of i){const n=ge();n.innerText=t,e.appendChild(n)}return e.addEventListener("mousedown",(t=>{t.stopPropagation(),e.classList.toggle("igv-roi-table-row-selected"),e.classList.contains("igv-roi-table-row-selected")?e.classList.remove("igv-roi-table-row-hover"):e.classList.add("igv-roi-table-row-hover"),this.setButtonState(e.classList.contains("igv-roi-table-row-selected"))})),e.addEventListener("mouseover",(t=>{e.classList.contains("igv-roi-table-row-selected")?e.classList.remove("igv-roi-table-row-hover"):e.classList.add("igv-roi-table-row-hover")})),e.addEventListener("mouseout",(t=>{e.classList.remove("igv-roi-table-row-hover")})),e}createFooterDOM(t){const e=ge();t.appendChild(e);const n=ge({class:"igv-roi-table-button"});return e.appendChild(n),n.id="igv-roi-table-view-button",n.textContent="Go To",n.style.pointerEvents="none",n.addEventListener("click",(e=>{e.stopPropagation();const n=t.querySelectorAll(".igv-roi-table-row-selected"),r=[];for(let t of n){const{locus:e}=Um(t.dataset.region);r.push(e)}for(let e of t.querySelectorAll(".igv-roi-table-row"))e.classList.remove("igv-roi-table-row-selected");this.setButtonState(!1),r.length>0&&this.browser.search(r.join(" "))})),e}setButtonState(t){t?qm.push(1):qm.pop();this.footerDOM.querySelector("#igv-roi-table-view-button").style.pointerEvents=qm.length>0?"auto":"none"}dispose(){this.browser.roiTableControl.buttonHandler(!1),this.container.innerHTML="";for(let t of Object.keys(this))this[t]=void 0}}class $m{constructor(t,e){this.browser=t,this.container=ge({class:"igv-roi-menu-next-gen"}),e.appendChild(this.container);const n=ge();this.container.appendChild(n),_e(n,(()=>this.container.style.display="none")),this.body=ge(),this.container.appendChild(this.body),this.container.style.display="none"}async present(t,e,n,r,i){Gm(this.body);const o=await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region),s=ge();this.body.appendChild(s);const a="Description",l=o.name||a;s.innerText=l,s.setAttribute("title",l),a===l?s.classList.add("igv-roi-placeholder"):s.classList.remove("igv-roi-placeholder");const c=ge();this.body.appendChild(c),c.innerText="Set Description",c.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none";const e={label:"Description",value:o.name||"",callback:()=>{const t=this.browser.inputDialog.input.value||"";o.name=t.trim(),this.container.style.display="none",this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(e,t)}));const h=ge();this.body.appendChild(h),h.innerText="Delete Region",h.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(i.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex"}async __present(t,e,n,r,i){Gm(this.container);const o=await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region);let s;s=ge({class:"igv-roi-menu-row-edit-description"}),this.container.appendChild(s),s.addEventListener("click",(t=>{t.stopPropagation()}));const a="description-input",l=document.createElement("label");s.appendChild(l),l.setAttribute("for",a),l.innerText="Description:";const c=document.createElement("input");s.appendChild(c),c.setAttribute("type","text"),c.setAttribute("name",a),c.setAttribute("placeholder",""),c.value=o.name||"",c.addEventListener("change",(async t=>{t.stopPropagation();(await this.browser.roiManager.findUserDefinedRegionWithKey(i.dataset.region)).name=c.value,c.blur(),this.container.style.display="none",await this.browser.roiManager.repaintTable()})),s=ge({class:"igv-roi-menu-row"}),s.innerText="Delete region",this.container.appendChild(s),s.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(i.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex",r.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none"}))}dispose(){this.container.innerHTML=""}}function Gm(t){for(;t.firstChild;)t.removeChild(t.firstChild)}class Zm{constructor(t,e){this.name=t.name,this.featureSource=t.featureSource||ju(t,e),this.color=t.color||Xu}async getFeatures(t,e,n){return this.featureSource.getFeatures({chr:t,start:e,end:n})}draw(t){const{context:e,bpPerPixel:n,bpStart:r,pixelTop:i,pixelHeight:o,pixelWidth:s,features:a}=t;if(!a)return;const l=r+s*n+1;for(let{start:t,end:s}of a){if(s<r)continue;if(t>l)break;const{x:a,width:c}=Qu(t,s,r,n);Xo.fillRect(e,a,i,c,o,{fillStyle:this.color})}}}class Xm{constructor(t,e){this.browser=e,this.button=ge({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="ROI Table",this.button.addEventListener("click",(()=>{this.buttonHandler(!e.roiTableVisible)})),this.browser=e,this.setVisibility(e.showROITableButton),this.setState(e.roiTableVisible)}buttonHandler(t){this.browser.roiTableVisible=t,this.setState(this.browser.roiTableVisible),this.browser.setROITableVisibility(this.browser.roiTableVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.roiTableVisible)}hide(){this.button.style.display="none"}}class Ym{constructor(t,e){this.config=t,this.guid=be(),this.namespace=".browser_"+this.guid,this.parent=e,this.root=ge({class:"igv-container"}),e.appendChild(this.root),this.alert=new _s(this.root),this.columnContainer=ge({class:"igv-column-container"}),this.root.appendChild(this.columnContainer),this.menuPopup=new hg(this.columnContainer),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:"rgb(0,0,150)",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},this.addMouseHandlers(),this.setControls(t)}initialize(t){t.gtex&&(mg.gtexLoaded=!0),this.flanking=t.flanking,this.crossDomainProxy=t.crossDomainProxy,this.formats=t.formats,this.trackDefaults=t.trackDefaults,this.nucleotideColors=t.nucleotideColors||gm;for(let t of Object.keys(this.nucleotideColors))this.nucleotideColors[t.toLowerCase()]=this.nucleotideColors[t];this.trackLabelsVisible=t.showTrackLabels,this.roiTableVisible=t.showROITable,this.showROITableButton=t.showROITableButton,this.isCenterLineVisible=t.showCenterGuide,this.cursorGuideVisible=t.showCursorGuide,this.showSampleNames=t.showSampleNames,this.showSampleNameButton=t.showSampleNameButton,this.sampleNameViewportWidth=t.sampleNameViewportWidth||200,t.search&&(this.searchConfig={type:"json",url:t.search.url,coords:void 0===t.search.coords?1:t.search.coords,chromosomeField:t.search.chromosomeField||"chromosome",startField:t.search.startField||"start",endField:t.search.endField||"end",geneField:t.search.geneField||"gene",snpField:t.search.snpField||"snp",resultsField:t.search.resultsField})}setControls(t){const e=this.createStandardControls(t);e.insertBefore(pe(this.columnContainer)),this.$navigation=e,!1===t.showControls&&e.hide()}createStandardControls(t){this.navbarManager=new bm(this);const e=pe("<div>",{class:"igv-navbar"});this.$navigation=e;const n=pe("<div>",{class:"igv-navbar-left-container"});e.append(n);const r=pe("<div>",{class:"igv-logo"});n.append(r);const i=pe('<svg width="690px" height="324px" viewBox="0 0 690 324" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><title>IGV</title><g id="Page-1" stroke="none" stroke-width="1" fill="none" fill-rule="evenodd"><g id="IGV" fill="#666666"><polygon id="Path" points="379.54574 8.00169252 455.581247 8.00169252 515.564813 188.87244 532.884012 253.529506 537.108207 253.529506 554.849825 188.87244 614.833392 8.00169252 689.60164 8.00169252 582.729511 320.722144 486.840288 320.722144"></polygon><path d="M261.482414,323.793286 C207.975678,323.793286 168.339046,310.552102 142.571329,284.069337 C116.803612,257.586572 103.919946,217.158702 103.919946,162.784513 C103.919946,108.410325 117.437235,67.8415913 144.472217,41.0770945 C171.507199,14.3125977 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a=pe("<div>",{class:"igv-search-container"});s.append(a),this.$searchInput=pe("<input>",{class:"igv-search-input",type:"text",placeholder:"Locus Search"}),a.append(this.$searchInput),this.$searchInput.change((()=>this.doSearch(this.$searchInput.val())));const l=ge({class:"igv-search-icon-container"});a.append(pe(l)),l.appendChild(ye("search")),l.addEventListener("click",(()=>this.doSearch(this.$searchInput.val()))),this.windowSizePanel=new ym(s.get(0),this);const c=pe("<div>",{class:"igv-navbar-right-container"});e.append(c);const h=pe('<div class="igv-navbar-toggle-button-container">');if(c.append(h),this.$toggle_button_container=h,this.cursorGuide=new xm(this.columnContainer,this),this.cursorGuideButton=new _m(this,h.get(0)),this.centerLineButton=new km(this,h.get(0)),this.setTrackLabelVisibility(t.showTrackLabels),this.trackLabelControl=new Sm(h.get(0),this),this.roiTableControl=new Xm(h.get(0),this),this.sampleNameControl=new Cm(h.get(0),this),!0===t.showSVGButton&&(this.svgSaveControl=new Lm(h.get(0),this)),t.customButtons)for(let e of t.customButtons)new Bm(h.get(0),this,e);return this.zoomWidget=new Am(this,c.get(0)),!1===t.showNavigation&&this.$navigation.hide(),this.inputDialog=new hs(this.root),this.inputDialog.container.id=`igv-input-dialog-${be()}`,this.dataRangeDialog=new Zo(this,pe(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${be()}`,this.genericColorPicker=new xs({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${be()}`,e}getSampleNameViewportWidth(){return!1===this.showSampleNames?0:this.sampleNameViewportWidth}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}addTrackToFactory(t,e){sm(t,e)}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let t of this.referenceFrameList)if("all"===t.chr.toLowerCase())return!0;return!1}currentLoci(){const t=t=>`${t.chr}:${t.start+1}-${t.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?"":1===this.referenceFrameList.length?t(this.referenceFrameList[0]):this.referenceFrameList.map((e=>t(e)))}toSVG(){let{x:t,y:e,width:n,height:r}=this.columnContainer.getBoundingClientRect();let i=new oa({width:n,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:n,height:8e3}});for(let t of this.trackViews)t.renderSVGContext(i,{deltaX:0,deltaY:-e});return i.setHeight(r),i.getSerializedSvg(!0)}renderSVG(t){const e=this.toSVG();return t.empty(),t.append(e),e}saveSVGtoFile(t){let e=this.toSVG();t.$container&&(t.$container.empty(),t.$container.append(e));We(t.filename||"igvjs.svg",URL.createObjectURL(new Blob([e],{type:"application/octet-stream"})))}async loadSession(t){let e;return this.roiSets=[],e=t.url||t.file?await async function(t){const e=t.url||t.file;if(t.url&&(t.url.startsWith("blob:")||t.url.startsWith("data:"))){const e=Ym.uncompressSession(t.url);return JSON.parse(e)}{let n=t.filename;if(n||(n=t.url?await As(t.url):t.file.name),n.endsWith(".xml")){const t=ya.KNOWN_GENOMES,n=await Eo.loadString(e);return new lm(n,t)}return n.endsWith(".json")?Eo.loadJson(e):void 0}}(t):t,this.loadSessionObject(e)}async loadSessionObject(t){this.cleanHouseForSession(),this.showSampleNames=t.showSampleNames||!1,this.sampleNameControl.setState(!0===this.showSampleNames),t.sampleNameViewportWidth&&(this.sampleNameViewportWidth=t.sampleNameViewportWidth),Rs(this.columnContainer,"igv-axis-column"),Rs(this.columnContainer,"igv-sample-name-column"),Rs(this.columnContainer,"igv-scrollbar-column"),Rs(this.columnContainer,"igv-track-drag-column"),Rs(this.columnContainer,"igv-gear-menu-column");const e=await ya.expandReference(this.alert,t.reference||t.genome);await this.loadReference(e,t.locus),this.centerLineList=this.createCenterLineList(this.columnContainer);let n=0;if(!1!==t.showIdeogram){const t=new tm(this);t.id="ideogram";const e=new pg(this,this.columnContainer,t),{$viewport:r}=e.viewports[0];n=function(t){t="string"==typeof t?document.querySelector(t):t;const e=window.getComputedStyle(t),n=parseFloat(e.marginTop)+parseFloat(e.marginBottom),r=t.offsetHeight;return Math.ceil(n+r)}(r.get(0)),this.trackViews.push(e)}if(!1!==t.showRuler&&this.trackViews.push(new pg(this,this.columnContainer,new Pm(this))),t.gtexSelections)for(let e of this.referenceFrameList)for(let n of Object.keys(t.gtexSelections)){const r=t.gtexSelections[n].gene,i=t.gtexSelections[n].snp;e.selection=new fm(r,i)}this.roiManager&&this.roiManager.dispose();const r=new $m(this,this.columnContainer);if(t.roi){const e=t.roi.map((t=>new Ku(t,this.genome))),i=e.filter((t=>{let{name:e}=t;return void 0!==e&&e.length>0})),o=new Wm(this,this.columnContainer,i.length>0);this.roiManager=new zm(this,r,o,n,e)}else{const t=new Wm(this,this.columnContainer,!1);this.roiManager=new zm(this,r,t,n,void 0)}await this.roiManager.initialize();const i=e.tracks||[],o=t.tracks?i.concat(t.tracks):i;0===o.filter((t=>"sequence"===t.type)).length&&o.push({type:"sequence",order:qs});let s=1;for(let t of o)void 0===t.order&&(t.order=s++);await this.loadTrackList(o);for(let t of this.trackViews.filter((t=>"ruler"===t.track.type||"ideogram"===t.track.type)))t.updateViews();this.updateUIWithReferenceFrameList()}createCenterLineList(t){const e=t.querySelectorAll(".igv-center-line");for(let t=0;t<e.length;t++)e[t].remove();const n=[],r=t.querySelectorAll(".igv-column");for(let t=0;t<r.length;t++)n.push(new Nm(this,this.referenceFrameList[t],r[t]));return n}async loadReference(t,e){const n=await ya.loadGenome(t),r=void 0===this.genome||this.genome.id!==n.id;this.genome=n,this.updateNavbarDOMWithGenome(n),r&&this.removeAllTracks();let i=function(t,e){return t?Array.isArray(t)?t.join(" "):t:e.getHomeChromosomeName()}(e,n);if(!await this.search(i,!0)){console.log("Initial locus not found: "+i),i=n.getHomeChromosomeName();if(!await this.search(i,!0))throw new Error("Cannot set initial locus")}r&&this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Wp(this.genome)})}cleanHouseForSession(){for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column").forEach((t=>t.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}updateNavbarDOMWithGenome(t){let e=t.id&&t.id.length<10?t.id:"";this.$current_genome.text(e),this.$current_genome.attr("title",t.id||""),this.chromosomeSelectWidget.update(t)}async loadGenome(t){const e=await ya.expandReference(this.alert,t);await this.loadReference(e,void 0);const n=e.tracks||[];return 0===n.filter((t=>"sequence"===t.type)).length&&n.push({type:"sequence",order:qs}),await this.loadTrackList(n),await this.updateViews(),this.genome}updateUIWithReferenceFrameList(){const t=this.referenceFrameList;this.updateLocusSearchWidget();const e=this.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(t[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),e),tv(this.trackViews,this.trackLabelsVisible),this.setCenterLineAndCenterLineButtonVisibility(!ya.isWholeGenomeView(t[0].chr))}setTrackLabelVisibility(t){tv(this.trackViews,t)}setROITableVisibility(t){!0===t?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(t){t?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(t){this.cursorGuide.customMouseHandler=t}setCenterLineVisibility(t){for(let e of this.centerLineList)!0===t?(e.show(),e.repaint()):e.hide()}setCenterLineAndCenterLineButtonVisibility(t){for(let e of this.centerLineList){t&&e.isVisible?e.show():e.container.style.display="none"}t&&this.centerLineButton.isVisible?this.centerLineButton.show():this.centerLineButton.button.style.display="none"}async loadTrackList(t){const e=[];for(let n of t)e.push(this._loadTrack(n));const n=await Promise.all(e);return this.trackViews.filter((function(t){return t.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(t){const e=this._loadTrack(t);return t.autoscaleGroup&&(await e,this.updateViews()),e}async _loadTrack(t){ke(t)&&(t=JSON.parse(t));try{const e=await this.createTrack(t);if(void 0===e)return;void 0===e.order&&(e.order=this.trackViews.length);const n=new pg(this,this.columnContainer,e);if(this.trackViews.push(n),tv(this.trackViews,this.trackLabelsVisible),this.reorderTracks(),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),"function"==typeof e.postInit)try{n.startSpinner(),await e.postInit()}finally{n.stopSpinner()}return e.autoscaleGroup||(t.sync?await n.updateViews():n.updateViews()),"function"==typeof e.hasSamples&&e.hasSamples()&&!1!==this.config.showSampleNameButton&&this.sampleNameControl.show(),e}catch(e){const n={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};console.error(e);let r=e.message||e.error||e.toString();n.hasOwnProperty(r)&&(r=n[r]),r+=": "+t.url,this.alert.present(new Error(r),void 0)}}async loadROI(t){await this.roiManager.loadROI(t,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const t=await this.roiManager.getUserDefinedROISet();if(void 0===t)return[];const e=await t.getAllFeatures(),n=[];for(let t of Object.values(e))n.push(...t);return n}return[]}getRulerTrackView(){const t=this.trackViews.filter((t=>{let{track:e}=t;return"ruler"===e.id}));return t.length>0?t[0]:void 0}async createTrack(t){let e=await async function(t){return"function"==typeof t?t():t}(t.url);if(ke(e)&&(e=e.trim()),e)if(t.format)t.format=t.format.toLowerCase();else{let n=t.filename;n||(n=await As(e));const r=zs(n);"tsv"===r?t.format=await async function(t){if(t.url){const e=await Eo.loadString(t.url,Cs(t,{range:{start:0,size:1e3}}));if(e&&Ds(e.split("\n")[0].split("\t")))return"hiccups"}}(t):r?t.format=r:void 0!==t.sourceType&&"htsget"!==t.sourceType||await hc.inferFormat(t)}let n=t.type?t.type.toLowerCase():void 0;if(!n){if(n=Hs(t),"bedtype"===n){const e=ju(t,this.genome);t._featureSource=e;const r=await e.trackType();n=r||"annotation"}t.type=n}if(this.trackDefaults&&n){const e=this.trackDefaults[n];if(e)for(let n in e)e.hasOwnProperty(n)&&void 0===t[n]&&(t[n]=e[n])}const r=am(n,t,this);if(void 0!==r)return t.roi&&t.roi.length>0&&(r.roiSets=t.roi.map((t=>new Zm(t,this.genome)))),r;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${t.url||t}`),void 0)}reorderTracks(){this.trackViews.sort((function(t,e){const n=t=>"ideogram"===t.track.id?1:"ruler"===t.track.id?2:3,r=n(t),i=n(e);if(r===i){return(t.track.order||0)-(e.track.order||0)}return r-i}));for(let{axis:t,viewports:e,sampleNameViewport:n,outerScroll:r,dragHandle:i,gearContainer:o}of this.trackViews){t.remove();for(let{$viewport:t}of e)t.detach();n.viewport.remove(),r.remove(),i.remove(),o.remove()}const t=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:e,viewports:n,sampleNameViewport:r,outerScroll:i,dragHandle:o,gearContainer:s}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(e);for(let e=0;e<t.length;e++){const{$viewport:r}=n[e];t[e].appendChild(r.get(0))}this.columnContainer.querySelector(".igv-sample-name-column").appendChild(r.viewport),this.columnContainer.querySelector(".igv-scrollbar-column").appendChild(i),this.columnContainer.querySelector(".igv-track-drag-column").appendChild(o),this.columnContainer.querySelector(".igv-gear-menu-column").appendChild(s)}}getTrackOrder(){return this.trackViews.filter((t=>t.track&&t.track.name)).map((t=>t.track.name))}removeTrackByName(t){const e=this.trackViews.slice();for(let n of e)t===n.track.name&&this.removeTrack(n.track)}removeTrack(t){for(let e of this.trackViews)if(t===e.track){this._removeTrack(e.track);break}}_removeTrack(t){t.disposed||(this.trackViews.splice(this.trackViews.indexOf(t.trackView),1),this.fireEvent("trackremoved",[t]),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),t.trackView&&t.trackView.dispose())}removeAllTracks(){const t=[];for(let e of this.trackViews)"ruler"!==e.track.id&&"ideogram"!==e.track.id?(this.fireEvent("trackremoved",[e.track]),e.dispose()):t.push(e);this.trackViews=t}findTracks(t,e){let n="function"==typeof t?e=>t(e.track):n=>e===n.track[t];return this.trackViews.filter(n).map((t=>t.track))}setTrackHeight(t){this.trackHeight=t,this.trackViews.forEach((function(e){e.setTrackHeight(t)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((t=>t.bpPerPixel<0))){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel=(e.end-e.start)/t}if(this.referenceFrameList){const t=this.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(this.referenceFrameList[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),t)}Km.call(this),await this.updateViews()}async updateViews(){const t=this.trackViews;this.updateLocusSearchWidget();for(let t of this.centerLineList)t.repaint();if(this.dragObject)for(let e of t)await e.updateViews();else{const i={},o=[];for(let n of t){const t=n.track.autoscaleGroup;if(t){var e=i[t];e||(e=[],i[t]=e),e.push(n)}else o.push(n)}if(Object.entries(i).length>0){const t=Object.keys(i);for(let e of t){const t=i[e],o=[];for(let e of t)o.push(e.getInViewFeatures());const s=await Promise.all(o);var n,r=[];for(let t of s)r=r.concat(t);n=Es(r);const a=[];for(let e of t)e.track.dataRange=n,e.track.autoscale=!1,a.push(e.updateViews());await Promise.all(a)}}await Promise.all(o.map((t=>t.updateViews())))}}repaintViews(){for(let t of this.trackViews)t.repaintViews()}updateLocusSearchWidget(){const t=this.referenceFrameList,e=this.calculateViewportWidth(this.referenceFrameList.length);for(let n of t)n.end=n.start+n.bpPerPixel*e;this.chromosomeSelectWidget.select.value=1===t.length?this.referenceFrameList[0].chr:"";const n=this.referenceFrameList.map((t=>t.getLocusString())).join(" ");this.$searchInput.val(n),this.fireEvent("locuschange",[this.referenceFrameList])}calculateViewportWidth(t){let{width:e}=this.columnContainer.getBoundingClientRect();return e-=50+this.getSampleNameViewportWidth()+14+12+28,e-=5*(t-1),Math.floor(e/t)}getCenterLineXOffset(){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleNameViewportWidth()+14+12+28,Math.floor(t/2+50)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(t,e,n){const r=this.calculateViewportWidth(this.referenceFrameList.length);let i=n?[n]:this.referenceFrameList;for(let n of i)n.zoomWithScaleFactor(this,t,r,e)}async addMultiLocusPanel(t,e,n,r){const i=this.calculateViewportWidth(1+this.referenceFrameList.length),o=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=o;const s=(n-e)/i,a=new pm(this.genome,t,e,n,s),l=r?this.referenceFrameList.indexOf(r):this.referenceFrameList.length-1,c=1+l,{$viewport:h}=this.trackViews[0].viewports[l],u=Rm(h.get(0).parentElement);if(c===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let t of this.trackViews){const e=sg(t,u,a);t.viewports.push(e)}}else{this.referenceFrameList.splice(c,0,a);for(let t of this.trackViews){const e=sg(t,u,a);t.viewports.splice(c,0,e)}}this.centerLineList=this.createCenterLineList(this.columnContainer),Km.call(this),await this.updateViews(!0)}async removeMultiLocusPanel(t){const e=this.referenceFrameList.indexOf(t),{$viewport:n}=this.trackViews[0].viewports[e];Mm(e,n.parent().get(0));for(let{viewports:t}of this.trackViews)t[e].dispose(),t.splice(e,1);if(this.referenceFrameList.splice(e,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let t of this.getRulerTrackView().viewports)t.dismissLocusLabel();const r=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(r)}async gotoMultilocusPanel(t){const e=this.referenceFrameList.indexOf(t);this.columnContainer.querySelectorAll(".igv-column").forEach(((t,n)=>{n===e||t.remove()})),this.columnContainer.querySelectorAll(".igv-column-shim").forEach((t=>t.remove()));for(let t of this.trackViews){const n=t.viewports[e];t.viewports.filter(((t,n)=>n!==e)).forEach((t=>t.dispose())),t.viewports=[n]}const n=this.calculateViewportWidth(1);t.bpPerPixel=(t.end-t.start)/n,this.referenceFrameList=[t],this.trackViews.forEach((t=>{let{viewports:e}=t;return e.forEach((t=>t.setWidth(n)))})),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(t){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=t;for(let{viewports:t}of this.trackViews)for(let n of t)n.setWidth(e);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(t,e,n){await this.search(t+":"+e+"-"+n)}async doSearch(t,e){const n=await this.search(t,e);return n||this.alert.present(new Error(`Unrecognized locus: <b> ${t} </b>`)),n}async search(t,e){const n=await vm(this,t);if(n&&n.length>0){this.referenceFrameList=function(t,e,n,r,i,o){return t.map((t=>{if(n&&t.gene&&(t.start=Math.max(0,t.start-n),t.end+=n),!o){const n=e.getChromosome(t.chr);Ts(n.bpLength,t,r)}const s=new pm(e,t.chr,t.start,t.end,(t.end-t.start)/i);return s.locusSearchString=t.locusSearchString,(t.gene||t.snp)&&(s.selection=new fm(t.gene,t.snp)),s}))}(n,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(n.length),this.isSoftclipped());for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-column-shim, .igv-column").forEach((t=>t.remove())),Im(this.columnContainer.querySelector(".igv-sample-name-column"),this.referenceFrameList.length),this.centerLineList=this.createCenterLineList(this.columnContainer);for(let t of this.trackViews)t.addDOMToColumnContainer(this,this.columnContainer,this.referenceFrameList);return this.updateUIWithReferenceFrameList(),e||await this.updateViews(),!0}return!1}async loadSampleInformation(t){var e=t;Ue(t)&&(e=t.name),"fam"===e.substr(e.lastIndexOf(".")+1)&&(this.sampleInformation=await function(t,e){return(new um).loadPlinkFile(t,e)}(t))}on(t,e){this.eventHandlers[t]||(this.eventHandlers[t]=[]),this.eventHandlers[t].push(e)}un(t,e){this.off(t,e)}off(t,e){if(t)if(e){const n=this.eventHandlers[t];if(n&&0!==n.length){const r=n.indexOf(e);-1!==r&&this.eventHandlers[t].splice(r,1)}else console.warn("No handlers to remove for event: "+t)}else this.eventHandlers[t]=[];else this.eventHandlers={}}fireEvent(t,e,n){const r=this.eventHandlers[t];if(void 0===r||0===r.length)return;const i=n||window;return r.map((function(t){return t.apply(i,e)}))[0]}dispose(){this.removeMouseHandlers();for(let t of this.trackViews)t.dispose()}toJSON(){const t={version:"2.13.3"};if(void 0!==this.showSampleNames&&(t.showSampleNames=this.showSampleNames),200!==this.sampleNameViewportWidth&&(t.sampleNameViewportWidth=this.sampleNameViewportWidth),t.reference=this.genome.toJSON(),qe(t.reference.fastaURL))throw new Error(`Error. Sessions cannot include local file references ${t.reference.fastaURL.name}.`);if(qe(t.reference.indexURL))throw new Error(`Error. Sessions cannot include local file references ${t.reference.indexURL.name}.`);const e=[],n={};let r=!1,i=this.trackViews[0];for(let{referenceFrame:t}of i.viewports){const i=t.getLocusString();if(e.push(i),t.selection){const e={gene:t.selection.gene,snp:t.selection.snp};n[i]=e,r=!0}}t.locus=1===e.length?e[0]:e,r&&(t.gtexSelections=n),t.roi=this.roiManager.toJSON();const o=[],s=[];for(let{track:t}of this.trackViews)try{let e;e="function"==typeof t.getState?t.getState():t.config,e&&(e.browser&&delete e.browser,e.order=t.order,o.push(e))}catch(e){console.error(`Track: ${t.name}: ${e}`),s.push(`Track: ${t.name}: ${e}`)}if(s.length>0){let t=1,e="Errors encountered saving session: </br>";for(let n of s)e+=` (${t++}) ${n.toString()} <br/>`;throw Error(e)}return t.tracks=o,t}compressedSession(){return function(t){const e=new Uint8Array(t.length);for(var n=0;n<t.length;n++)e[n]=t.charCodeAt(n);const r=new no.deflateRaw(e),i=String.fromCharCode.apply(null,r);return btoa(i).replace(/\+/g,".").replace(/\//g,"_").replace(/=/g,"-")}(JSON.stringify(this.toJSON()))}sessionURL(){const t=window.location.href.slice(),e=t.indexOf("?");return(e>0?t.substring(0,e):t)+"?sessionURL=blob:"+this.compressedSession()}mouseDownOnViewport(t,e){var n;n=ve(t),this.vpMouseDown={viewport:e,lastMouseX:n.x,mouseDownX:n.x,lastMouseY:n.y,mouseDownY:n.y,referenceFrame:e.referenceFrame}}cancelTrackPan(){const t=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,t&&t.viewport.referenceFrame.start!==t.start&&(this.updateViews(),this.fireEvent("trackdragend"))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((t=>!0===t.track.showSoftClips))}startTrackDrag(t){this.dragTrack=t}updateTrackDrag(t){if(t&&this.dragTrack){const e=this.dragTrack,n=this.trackViews.indexOf(t),r=this.trackViews.indexOf(e),i=this.trackViews;i[n]=e,i[r]=t;const o=this.trackViews[n].track.order;this.trackViews[r].track.order=o;const s=i.length;let a=o;if(n<r)for(let t=n+1;t<s;t++){const e=i[t].track;if(!(e.order<=a))break;e.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=e.order}else for(let t=n-1;t>0;t--){const e=i[t].track;if(!(e.order>=a))break;e.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=e.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addMouseHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers()}removeMouseHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers()}addWindowResizeHandler(){this.boundWindowResizeHandler=Km.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=Jm.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=Jm.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=Qm.bind(this),this.boundColumnContainerTouchMoveHandler=Qm.bind(this),this.boundColumnContainerMouseLeaveHandler=Jm.bind(this),this.boundColumnContainerMouseUpHandler=Jm.bind(this),this.boundColumnContainerTouchEndHandler=Jm.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}async getDriveFileInfo(t){const e="https://www.googleapis.com/drive/v3/files/"+Ne(t)+"?supportsTeamDrives=true";return Eo.loadJson(e,Cs({}))}static uncompressSession(t){let e;if(t.indexOf("/gzip;base64")>0){e=co(t);let n="";for(let t of e)n+=String.fromCharCode(t);return n}return function(t){t=t.replace(/\./g,"+").replace(/_/g,"/").replace(/-/g,"=");const e=atob(t),n=[];for(let t=0;t<e.length;t++)n.push(e.charCodeAt(t));const r=no.inflateRaw(n);let i="";for(let t of r)i+=String.fromCharCode(t);return i}(t.substring(5))}createCircularView(t,e){var n;return e=!0===e,this.circularView=(n=this,new Bp(t,{onChordClick:(t,e,r)=>{const i=t.data,o=i.mate;function s(t){t.chr=n.genome.getChromosomeName(t.refName);let e=!1;for(let r of n.referenceFrameList){const n=mp.fromLocusString(r.getLocusString());if(n.contains(t)){e=!0;break}if(n.overlaps(t)){r.extend(t),e=!0;break}}if(!e){const e=2e3,r=(t.start+t.end)/2;n.addMultiLocusPanel(t.chr,r-e,r+e)}}s(i),s(o)}})),this.circularViewControl=new Dm(this.$toggle_button_container.get(0),this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Wp(this.genome)}),this.circularViewVisible=e,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(t){this.circularView&&(this.circularView.visible=t,this.circularViewControl.setState(t))}}async function Km(){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList){const n=this.referenceFrameList.indexOf(e),{chr:r,genome:i}=e,{bpLength:o}=i.getChromosome(e.chr),s=e.toBP(t);ya.isWholeGenomeView(r)||s>o?e.bpPerPixel=o/t:e.end=e.start+e.toBP(t);for(let{viewports:e}of this.trackViews)e[n].setWidth(t)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function Qm(t){t.preventDefault();const{x:e,y:n}=ve(t);if(this.vpMouseDown){const{viewport:t,referenceFrame:r}=this.vpMouseDown,i=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(n-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(i)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:t,start:r.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(n-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const e=t.$viewport.height(),n=gg(t.trackView.viewports);this.vpMouseDown.r=e/n}if(this.dragObject){const n=!this.isSoftclipped();let i=this.vpMouseDown.lastMouseX-e;r.shiftPixels(i,t.$viewport.width(),n)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const e=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-n);t.trackView.moveScroller(e)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=n}}function Jm(t){this.cancelTrackPan(),this.endTrackDrag()}function tv(t,e){for(let{viewports:n}of t)for(let t of n)t.$trackLabel&&(0===n.indexOf(t)&&!0===e?t.$trackLabel.show():t.$trackLabel.hide())}let ev=[];const nv=Eo.setApiKey;!function(){var t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-navbar {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  box-sizing: border-box;\n  width: 100%;\n  color: #444;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  line-height: 32px;\n  padding-left: 8px;\n  padding-right: 8px;\n  margin-top: 2px;\n  margin-bottom: 6px;\n  height: 32px;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n  width: 34px;\n  height: 32px;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n  height: 32px;\n  margin-left: 4px;\n  margin-right: 4px;\n  user-select: none;\n  line-height: 32px;\n  vertical-align: middle;\n  text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n  height: 100%;\n  width: 125px;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n  display: block;\n  cursor: pointer;\n  width: 100px;\n  height: 75%;\n  outline: none;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  margin-left: 8px;\n  height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 210px;\n  height: 22px;\n  line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n  cursor: text;\n  width: 85%;\n  height: 22px;\n  line-height: 22px;\n  font-size: 12px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  text-align: left;\n  padding-left: 8px;\n  margin-right: 8px;\n  outline: none;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n  cursor: pointer;\n  height: 16px;\n  width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n  margin-left: 4px;\n  user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n  margin-left: 0;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n  margin-left: 0;\n  margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n  display: block;\n  height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n  display: block;\n  width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n  display: none;\n}\n\n.igv-navbar-button {\n  display: block;\n  box-sizing: unset;\n  padding-left: 6px;\n  padding-right: 6px;\n  height: 18px;\n  text-transform: capitalize;\n  user-select: none;\n  line-height: 18px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: "Open Sans", sans-serif;\n  font-size: 11px;\n  font-weight: 200;\n  color: #737373;\n  background-color: #f3f3f3;\n  border-color: #737373;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n  color: white;\n  background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n  cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n  z-index: 1024;\n  position: absolute;\n  top: 8px;\n  left: 50%;\n  transform: translate(-50%, 0%);\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n  background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-top: 2px;\n  padding-bottom: 2px;\n  width: 100%;\n  height: 100%;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n  position: absolute;\n  top: 10px;\n  left: 50%;\n}\n.igv-zoom-in-notice div {\n  position: relative;\n  left: -50%;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #3f3f3f;\n  background-color: rgba(255, 255, 255, 0.51);\n  z-index: 64;\n}\n\n.igv-container-spinner {\n  position: absolute;\n  top: 90%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  z-index: 1024;\n  width: 24px;\n  height: 24px;\n  pointer-events: none;\n  color: #737373;\n}\n\n.igv-multi-locus-close-button {\n  position: absolute;\n  top: 2px;\n  right: 0;\n  padding-left: 2px;\n  padding-right: 2px;\n  width: 18px;\n  height: 18px;\n  color: #666666;\n  background-color: white;\n  z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n  vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n  cursor: pointer;\n  color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n  z-index: 64;\n  position: absolute;\n  top: 2px;\n  left: 0;\n  width: 100%;\n  height: 14px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label div {\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n  background-color: white;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n  z-index: 64;\n  position: absolute;\n  left: 50%;\n  top: 5%;\n  transform: translate(-50%, 0%);\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n  width: 14px;\n  height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n  margin-left: 16px;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n}\n\n.igv-multi-locus-ruler-label:hover {\n  cursor: pointer;\n}\n\n.igv-ruler-sweeper {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 26px;\n  bottom: 0;\n  left: 0;\n  width: 0;\n  z-index: 99999;\n  background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n  pointer-events: none;\n  z-index: 128;\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 1px;\n  height: 32px;\n  background-color: transparent;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-ruler-tooltip > div {\n  pointer-events: none;\n  width: 128px;\n  height: auto;\n  padding: 1px;\n  color: #373737;\n  font-size: 10px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  background-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-color: #373737;\n}\n\n.igv-track-label {\n  position: absolute;\n  left: 8px;\n  top: 8px;\n  width: auto;\n  height: auto;\n  max-width: 200px;\n  padding-left: 4px;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  text-align: center;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-color: #444;\n  border-radius: 2px;\n  border-style: solid;\n  border-width: thin;\n  background-color: white;\n  z-index: 128;\n  cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n  background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-top: 4px;\n}\n\n.igv-center-line {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  transform: translateX(-50%);\n  z-index: 8;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-left-style: dashed;\n  border-left-width: thin;\n  border-right-style: dashed;\n  border-right-width: thin;\n}\n\n.igv-center-line-wide {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n  display: none;\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  left: 0;\n  right: 0;\n  top: 50%;\n  height: 1px;\n  z-index: 1;\n  margin-left: 50px;\n  margin-right: 54px;\n  border-top-style: dotted;\n  border-top-width: thin;\n  border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  width: 1px;\n  z-index: 1;\n  border-left-style: dotted;\n  border-left-width: thin;\n  border-left-color: rgba(127, 127, 127, 0.76);\n  display: none;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-generic-dialog-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 300px;\n  height: 200px;\n  border-color: #7F7F7F;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  z-index: 2048;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n  color: #373737;\n  width: 95%;\n  height: 24px;\n  line-height: 24px;\n  text-align: left;\n  margin-top: 8px;\n  padding-left: 8px;\n  overflow-wrap: break-word;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n  margin-top: 8px;\n  width: 95%;\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  padding-left: 8px;\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n  width: 30%;\n  height: 100%;\n  font-size: 16px;\n  text-align: right;\n  padding-right: 8px;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  width: 50%;\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n  margin-top: 8px;\n  width: calc(100% - 16px);\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: "Open Sans", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n  width: 100%;\n  height: 28px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n  margin-top: 32px;\n  color: white;\n  font-family: "Open Sans", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  width: 75px;\n  height: 28px;\n  line-height: 28px;\n  text-align: center;\n  border-color: transparent;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n  margin-left: 32px;\n  margin-right: 0;\n  background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n  margin-left: 0;\n  margin-right: 32px;\n  background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n  cursor: pointer;\n  background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n  cursor: pointer;\n  background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n  width: 100%;\n  height: 36px;\n  margin-top: 32px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n  width: 98px;\n  height: 36px;\n  line-height: 36px;\n  text-align: center;\n  color: white;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  border-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 4px;\n  background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n  cursor: pointer;\n  background-color: #25597f;\n}\n\n.igv-generic-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  z-index: 2048;\n  background-color: white;\n  cursor: pointer;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: wrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-container div:first-child {\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  height: 24px;\n  width: 100%;\n  background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n  display: block;\n  color: #5f5f5f;\n  cursor: pointer;\n  width: 14px;\n  height: 14px;\n  margin-right: 8px;\n  margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: max-content;\n  z-index: 4096;\n  cursor: pointer;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background: white;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-end;\n  text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n  width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n  background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n  padding-left: 4px;\n  padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n  background: #efefef;\n}\n\n.igv-menu-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-bottom: 1px;\n  padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n  position: relative;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-menu-popup-header div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n.igv-menu-popup-check-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 100%;\n  height: 20px;\n  margin-right: 4px;\n  background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n  padding-top: 2px;\n  padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n  position: relative;\n  width: 12px;\n  height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n  position: absolute;\n  width: 12px;\n  height: 12px;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-loading-spinner-container {\n  z-index: 1024;\n  position: absolute;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 32px;\n  height: 32px;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-loading-spinner-container > div {\n  box-sizing: border-box;\n  width: 100%;\n  height: 100%;\n  border-radius: 50%;\n  border: 4px solid rgba(128, 128, 128, 0.5);\n  border-top-color: rgb(255, 255, 255);\n  animation: spin 1s ease-in-out infinite;\n  -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n@-webkit-keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n.igv-roi-menu-next-gen {\n  position: absolute;\n  z-index: 512;\n  font-family: "Open Sans", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background-color: white;\n  width: 192px;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu-next-gen > div:first-child {\n  height: 24px;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-roi-menu-next-gen > div:first-child > div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-roi-menu-next-gen > div:first-child > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-menu-next-gen > div:last-child {\n  background-color: white;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  text-align: start;\n  vertical-align: middle;\n  cursor: pointer;\n}\n.igv-roi-menu-next-gen > div:last-child > div {\n  height: 24px;\n  padding-left: 4px;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  border-bottom-color: #7f7f7f;\n}\n.igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n  background-color: rgba(127, 127, 127, 0.1);\n}\n.igv-roi-menu-next-gen > div:last-child div:first-child {\n  cursor: default;\n  font-style: italic;\n  text-align: center;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-menu-next-gen > div:last-child > div:last-child {\n  border-bottom-width: 0;\n  border-bottom-color: transparent;\n}\n\n.igv-roi-placeholder {\n  font-style: normal;\n  color: rgba(75, 75, 75, 0.6);\n}\n\n.igv-roi-table {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(1) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(2) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(3) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(4) {\n  width: 30%;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:nth-child(5) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n  resize: both;\n  overflow: scroll;\n  min-width: 512px;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(1) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(2) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(3) {\n  width: 15%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(4) {\n  width: 30%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(5) {\n  width: 20%;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-four-column {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table-four-column > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table-four-column > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table-four-column > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table-four-column > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table-four-column > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(1) {\n  width: 25%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(2) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(3) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-column-titles > div:nth-child(4) {\n  width: 35%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container {\n  resize: both;\n  overflow: scroll;\n  min-width: 512px;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: center;\n  margin-left: 4px;\n  margin-right: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(1) {\n  width: 25%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(2) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(3) {\n  width: 20%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row > div:nth-child(4) {\n  width: 35%;\n}\n.igv-roi-table-four-column > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table-four-column > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-row-selected {\n  background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n  height: 20px;\n  user-select: none;\n  line-height: 20px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: "Open Sans", sans-serif;\n  font-size: 13px;\n  font-weight: 400;\n  color: black;\n  padding-left: 6px;\n  padding-right: 6px;\n  background-color: rgb(239, 239, 239);\n  border-color: black;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n  cursor: pointer;\n  font-weight: 400;\n  background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n  z-index: 64;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  pointer-events: none;\n  overflow: visible;\n  margin-top: 44px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-region > div {\n  position: relative;\n  width: 100%;\n  height: 8px;\n  cursor: pointer;\n  pointer-events: auto;\n}\n\n.igv-roi-menu {\n  position: absolute;\n  z-index: 1024;\n  width: 144px;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: "Open Sans", sans-serif;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n  border-bottom-color: rgba(128, 128, 128, 0.5);\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-menu > div:first-child {\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-color: transparent;\n  border-top-style: solid;\n  border-top-width: 0;\n}\n.igv-roi-menu > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n}\n\n.igv-roi-menu-row {\n  height: 24px;\n  padding-left: 8px;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n  background-color: white;\n}\n\n.igv-roi-menu-row-edit-description {\n  width: -webkit-fill-available;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  background-color: white;\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-bottom: 4px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-menu-row-edit-description > label {\n  margin-left: 2px;\n  margin-bottom: 0;\n  display: block;\n  width: -webkit-fill-available;\n}\n.igv-roi-menu-row-edit-description > input {\n  display: block;\n  margin-left: 2px;\n  margin-right: 2px;\n  margin-bottom: 1px;\n  width: -webkit-fill-available;\n}\n\n.igv-container {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  padding-top: 4px;\n  user-select: none;\n  -webkit-user-select: none;\n  -ms-user-select: none;\n}\n\n.igv-viewport {\n  position: relative;\n  margin-top: 5px;\n  overflow-x: hidden;\n  overflow-y: hidden;\n}\n\n.igv-viewport-content {\n  position: relative;\n  width: 100%;\n}\n.igv-viewport-content > canvas {\n  position: relative;\n  display: block;\n}\n\n.igv-column-container {\n  position: relative;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  width: 100%;\n}\n\n.igv-column-shim {\n  width: 1px;\n  margin-left: 2px;\n  margin-right: 2px;\n  background-color: #545453;\n}\n\n.igv-column {\n  position: relative;\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-axis-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 50px;\n}\n.igv-axis-column > div {\n  margin-top: 5px;\n  width: 100%;\n}\n\n.igv-sample-name-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-scrollbar-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 14px;\n}\n.igv-scrollbar-column > div {\n  position: relative;\n  margin-top: 5px;\n  width: 14px;\n}\n.igv-scrollbar-column > div > div {\n  cursor: pointer;\n  position: absolute;\n  top: 0;\n  left: 2px;\n  width: 8px;\n  border-width: 1px;\n  border-style: solid;\n  border-color: #c4c4c4;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n  background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 12px;\n  background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n  z-index: 512;\n  position: relative;\n  cursor: pointer;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n  border-top-right-radius: 6px;\n  border-bottom-right-radius: 6px;\n  background-color: #c4c4c4;\n}\n.igv-track-drag-column .igv-track-drag-handle-hover {\n  background-color: #787878;\n}\n.igv-track-drag-column > .igv-track-drag-shim {\n  position: relative;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n}\n\n.igv-gear-menu-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 28px;\n}\n.igv-gear-menu-column > div {\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  margin-top: 5px;\n  width: 100%;\n  background: white;\n}\n.igv-gear-menu-column > div > div {\n  position: relative;\n  margin-top: 4px;\n  width: 16px;\n  height: 16px;\n  color: #7F7F7F;\n}\n.igv-gear-menu-column > div > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n/*# sourceMappingURL=dom.css.map */\n',document.head.insertBefore(t,document.head.childNodes[document.head.childNodes.length-1])}();var rv={IGVGraphics:Xo,MenuUtils:Wo,DataRangeDialog:Zo,createTrack:async function(t,e){return await Ym.prototype.createTrack.call(e,t)},createBrowser:async function(t,e){void 0===e&&(e={}),ya.KNOWN_GENOMES||await ya.initializeGenomes(e),function(t){void 0===t.minimumBases&&(t.minimumBases=40);void 0===t.showIdeogram&&(t.showIdeogram=!0);void 0===t.showCircularView&&(t.showCircularView=!1);void 0===t.showCircularViewButton&&(t.showCircularViewButton=!1);void 0===t.showTrackLabelButton&&(t.showTrackLabelButton=!0);void 0===t.showTrackLabels&&(t.showTrackLabels=!0);void 0===t.showROITableButton&&(t.showROITableButton=!1);void 0===t.showROITable&&(t.showROITable=!1);void 0===t.showCursorTrackingGuideButton&&(t.showCursorTrackingGuideButton=!0);void 0===t.showCursorGuide&&(t.showCursorGuide=t.showCursorTrackingGuide||!1);void 0===t.showCenterGuideButton&&(t.showCenterGuideButton=!0);void 0===t.showCenterGuide&&(t.showCenterGuide=!1);void 0===t.showSampleNames&&(t.showSampleNames=!1);void 0===t.showSVGButton&&(t.showSVGButton=!0);void 0===t.showControls&&(t.showControls=!0);void 0===t.showNavigation&&(t.showNavigation=!0);void 0===t.showRuler&&(t.showRuler=!0);void 0===t.flanking&&(t.flanking=1e3);void 0===t.pairsSupported&&(t.pairsSupported=!0);t.tracks||(t.tracks=[])}(e),e.queryParametersSupported&&function(t){var e,n,r,i,o,s,a,l,c;let h,u,f;if(a=window.location.href,o={},e=a.indexOf("?"),n=a.lastIndexOf("#"),e>=0)for(n<0&&(n=a.length),r=e+1;r<n;)(i=a.indexOf("&",r))<0&&(i=n),2===(s=a.substring(r,i).split("=",2)).length?(l=s[0],c=decodeURIComponent(s[1]),"file"===l?h=c.split(","):"index"===l?u=c.split(","):"name"===l?f=c.split(","):"genome"!==l||!c.startsWith("https://")&&!c.startsWith("http://")||c.endsWith(".json")?t[l]=c:t.reference={fastaURL:c,indexURL:c+".fai"},r=i+1):r++;if(h){t.tracks||(t.tracks=[]);for(let e=0;e<h.length;e++){if(h[e].endsWith(".xml")||h[e].endsWith(".json")){t.sessionURL=h[e];break}const n={url:h[e]};u&&u.length>e&&(n.indexURL=u[e]),f&&f.length>e&&(n.name=f[e]),t.tracks.push(n)}}}(e),e.apiKey&&Eo.setApiKey(e.apiKey),e.oauthToken&&_o.setToken(e.oauthToken),e.clientId&&!Fe()&&await Pe({clientId:e.clientId,apiKey:e.apiKey,scope:"https://www.googleapis.com/auth/userinfo.profile"});const n=new Ym(e,t);ev.push(n),e.sessionURL?await n.loadSession({url:e.sessionURL}):await n.loadSessionObject(e);const r=n.isMultiLocusWholeGenomeView()||ya.isWholeGenomeView(n.referenceFrameList[0].chr);return n.navbarManager.navbarDidResize(n.$navigation.width(),r),n},removeBrowser:function(t){t.dispose(),t.root.remove(),ev=ev.filter((e=>e!==t))},removeAllBrowsers:function(){for(let t of ev)t.dispose(),t.root.remove();ev=[]},visibilityChange:async function(){for(let t of ev)await t.visibilityChange()},setGoogleOauthToken:function(t){return _o.setToken(t)},setOauthToken:function(t,e){return _o.setToken(t,e)},oauth:_o,version:ba,setApiKey:nv,doAutoscale:Es,TrackView:pg};return rv}));
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