index.js

//see https://github.com/umdjs/umd/blob/master/templates/returnExports.js

// if the module has no dependencies, the above pattern can be simplified to
(function (root, factory) {
    if (typeof define === 'function' && define.amd) {
        // AMD. Register as an anonymous module.
        define(['jquery'], factory);
    } else if (typeof module === 'object' && module.exports) {
        // Node. Does not work with strict CommonJS, but
        // only CommonJS-like environments that support module.exports,
        // like Node.
        module.exports = factory(require('jquery'));
    } else {
        // Browser globals (root is window)
        root.igv = factory(root.jQuery);
  }
}(this, function (jQuery) {
   var windowBak = window.jQuery;
   window.jQuery = jQuery;
   var $ = jQuery;

function testOauth(){$.ajax("https://accounts.google.com/o/oauth2/auth?scope=https://www.googleapis.com/auth/genomics&state=%2Fprofile&redirect_uri=http%3A%2F%2Flocalhost%2Figv-web%2FemptyPage.html&response_type=token&client_id=661332306814-8nt29308rppg325bkq372vli8nm3na14.apps.googleusercontent.com",{success:function(data,status,xhr){console.log(status)},error:function(xhr,options,e){xhr.statusCode(),console.log(xhr.getResponseHeader("location"))},complete:function(xhr,status){console.log(status)}})}function ZStream(){}function Inflate(){this.was=[0]}function InfBlocks(z,checkfn,w){this.hufts=new Int32Array(3*MANY),this.window=new Uint8Array(w),this.end=w,this.checkfn=checkfn,this.mode=IB_TYPE,this.reset(z,null),this.left=0,this.table=0,this.index=0,this.blens=null,this.bb=new Int32Array(1),this.tb=new Int32Array(1),this.codes=new InfCodes,this.last=0,this.bitk=0,this.bitb=0,this.read=0,this.write=0,this.check=0,this.inftree=new InfTree}function InfCodes(){}function InfTree(){}function inflate_trees_fixed(bl,bd,tl,td,z){return bl[0]=fixed_bl,bd[0]=fixed_bd,tl[0]=fixed_tl,td[0]=fixed_td,Z_OK}function arrayCopy(src,srcOffset,dest,destOffset,count){if(0!=count){if(!src)throw"Undef src";if(!dest)throw"Undef dest";0==srcOffset&&count==src.length?arrayCopy_fast(src,dest,destOffset):hasSubarray?arrayCopy_fast(src.subarray(srcOffset,srcOffset+count),dest,destOffset):1==src.BYTES_PER_ELEMENT&&count>100?arrayCopy_fast(new Uint8Array(src.buffer,src.byteOffset+srcOffset,count),dest,destOffset):arrayCopy_slow(src,srcOffset,dest,destOffset,count)}}function arrayCopy_slow(src,srcOffset,dest,destOffset,count){for(var i=0;i<count;++i)dest[destOffset+i]=src[srcOffset+i]}function arrayCopy_fast(src,dest,destOffset){dest.set(src,destOffset)}function adler32(adler,buf,index,len){if(null==buf)return 1;for(var k,s1=65535&adler,s2=adler>>16&65535;len>0;){for(k=len<ADLER_NMAX?len:ADLER_NMAX,len-=k;k>=16;)s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,s1+=255&buf[index++],s2+=s1,k-=16;if(0!=k)do{s1+=255&buf[index++],s2+=s1}while(0!=--k);s1%=ADLER_BASE,s2%=ADLER_BASE}return s2<<16|s1}function jszlib_inflate_buffer(buffer,start,length,afterUncOffset){buffer=start?new Uint8Array(buffer,start,length):new Uint8Array(buffer);var z=new ZStream;z.inflateInit(DEF_WBITS,!0),z.next_in=buffer,z.next_in_index=0,z.avail_in=buffer.length;for(var oBlockList=[],totalSize=0;;){var obuf=new Uint8Array(32e3);z.next_out=obuf,z.next_out_index=0,z.avail_out=obuf.length;var status=z.inflate(Z_NO_FLUSH);if(status!=Z_OK&&status!=Z_STREAM_END)throw z.msg;if(0!=z.avail_out){var newob=new Uint8Array(obuf.length-z.avail_out);arrayCopy(obuf,0,newob,0,obuf.length-z.avail_out),obuf=newob}if(oBlockList.push(obuf),totalSize+=obuf.length,status==Z_STREAM_END)break}if(afterUncOffset&&(afterUncOffset[0]=(start||0)+z.next_in_index),1==oBlockList.length)return oBlockList[0].buffer;for(var out=new Uint8Array(totalSize),cursor=0,i=0;i<oBlockList.length;++i){var b=oBlockList[i];arrayCopy(b,0,out,cursor,b.length),cursor+=b.length}return out.buffer}var igv=function(igv){function canBePaired(alignment){return alignment.isPaired()&&alignment.mate&&alignment.isMateMapped()&&alignment.chr===alignment.mate.chr&&(alignment.isFirstOfPair()||alignment.isSecondOfPair())&&!(alignment.isSecondary()||alignment.isSupplementary())}function finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new DownsampledInterval(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount)),this.paired=this.paired||this.currentBucket.paired}function DownsampleBucket(start,end,alignmentContainer){this.start=start,this.end=end,this.alignments=[],this.downsampledCount=0,this.samplingDepth=alignmentContainer.samplingDepth,this.pairsSupported=alignmentContainer.pairsSupported,this.downsampledReads=alignmentContainer.downsampledReads,this.pairsCache=alignmentContainer.pairsCache}function CoverageMap(chr,start,end){this.chr=chr,this.bpStart=start,this.length=end-start,this.coverage=new Array(this.length),this.maximum=0,this.threshold=.2,this.qualityWeight=!0}function Coverage(){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}return igv.AlignmentContainer=function(chr,start,end,samplingWindowSize,samplingDepth,pairsSupported){this.chr=chr,this.start=start,this.end=end,this.length=end-start,this.coverageMap=new CoverageMap(chr,start,end),this.alignments=[],this.downsampledIntervals=[],this.samplingWindowSize=void 0===samplingWindowSize?100:samplingWindowSize,this.samplingDepth=void 0===samplingDepth?50:samplingDepth,this.pairsSupported=pairsSupported,this.paired=!1,this.pairsCache={},this.downsampledReads=new Set,this.currentBucket=new DownsampleBucket(this.start,this.start+this.samplingWindowSize,this),this.filter=function(alignment){return alignment.isMapped()&&!alignment.isFailsVendorQualityCheck()}},igv.AlignmentContainer.prototype.push=function(alignment){!1!==this.filter(alignment)&&(this.coverageMap.incCounts(alignment),this.pairsSupported&&this.downsampledReads.has(alignment.readName)||(alignment.start>=this.currentBucket.end&&(finishBucket.call(this),this.currentBucket=new DownsampleBucket(alignment.start,alignment.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(alignment)))},igv.AlignmentContainer.prototype.forEach=function(callback){this.alignments.forEach(callback)},igv.AlignmentContainer.prototype.finish=function(){if(void 0!==this.currentBucket&&finishBucket.call(this),this.pairsSupported){var tmp=[],ds=this.downsampledReads;this.alignments.forEach(function(a){ds.has(a.readName)||tmp.push(a)}),this.alignments=tmp}this.alignments.sort(function(a,b){return a.start-b.start}),this.pairsCache=void 0,this.downsampledReads=void 0},igv.AlignmentContainer.prototype.contains=function(chr,start,end){return this.chr==chr&&this.start<=start&&this.end>=end},igv.AlignmentContainer.prototype.hasDownsampledIntervals=function(){return this.downsampledIntervals&&this.downsampledIntervals.length>0},DownsampleBucket.prototype.addAlignment=function(alignment){var samplingProb,idx,replacedAlignment,pairedAlignment;this.alignments.length<this.samplingDepth?this.pairsSupported&&canBePaired(alignment)?(pairedAlignment=this.pairsCache[alignment.readName],pairedAlignment?(pairedAlignment.setSecondAlignment(alignment),this.pairsCache[alignment.readName]=void 0):(pairedAlignment=new igv.PairedAlignment(alignment),this.paired=!0,this.pairsCache[alignment.readName]=pairedAlignment,this.alignments.push(pairedAlignment))):this.alignments.push(alignment):(samplingProb=this.samplingDepth/(this.samplingDepth+this.downsampledCount+1),Math.random()<samplingProb?(idx=Math.floor(Math.random()*(this.alignments.length-1)),replacedAlignment=this.alignments[idx],this.pairsSupported&&canBePaired(alignment)?(void 0!==this.pairsCache[replacedAlignment.readName]&&(this.pairsCache[replacedAlignment.readName]=void 0),pairedAlignment=new igv.PairedAlignment(alignment),this.paired=!0,this.pairsCache[alignment.readName]=pairedAlignment,this.alignments[idx]=pairedAlignment):this.alignments[idx]=alignment,this.downsampledReads.add(replacedAlignment.readName)):this.downsampledReads.add(alignment.readName),this.downsampledCount++)},CoverageMap.prototype.incCounts=function(alignment){function incBlockCount(block){var key,base,i,j,q;for(i=block.start-self.bpStart,j=0;j<block.len;i++,j++)self.coverage[i]||(self.coverage[i]=new Coverage),base=block.seq.charAt(j),key=alignment.strand?"pos"+base:"neg"+base,q=block.qual[j],self.coverage[i][key]+=1,self.coverage[i]["qual"+base]+=q,self.coverage[i].total+=1,self.coverage[i].qual+=q,self.maximum=Math.max(self.coverage[i].total,self.maximum)}var self=this;void 0===alignment.blocks?incBlockCount(alignment):alignment.blocks.forEach(function(block){incBlockCount(block)})},Coverage.prototype.isMismatch=function(refBase){var mismatchQualitySum,myself=this,threshold=igv.CoverageMap.threshold*(igv.CoverageMap.qualityWeight&&this.qual?this.qual:this.total);return mismatchQualitySum=0,["A","T","C","G"].forEach(function(base){base!==refBase&&(mismatchQualitySum+=igv.CoverageMap.qualityWeight&&myself.qual?myself["qual"+base]:myself["pos"+base]+myself["neg"+base])}),mismatchQualitySum>=threshold},DownsampledInterval=function(start,end,counts){this.start=start,this.end=end,this.counts=counts},DownsampledInterval.prototype.popupData=function(genomicLocation){return[{name:"start",value:this.start+1},{name:"end",value:this.end},{name:"# downsampled:",value:this.counts}]},igv}(igv||{}),igv=function(igv){function readInt(ba,offset){return ba[offset+3]<<24|ba[offset+2]<<16|ba[offset+1]<<8|ba[offset]}function readShort(ba,offset){return ba[offset+1]<<8|ba[offset]}function readFloat(ba,offset){return new DataView(ba.buffer).getFloat32(offset,!0)}return igv.BamAlignment=function(){this.hidden=!1},igv.BamAlignment.prototype.isMapped=function(){return 0==(4&this.flags)},igv.BamAlignment.prototype.isPaired=function(){return 0!=(1&this.flags)},igv.BamAlignment.prototype.isProperPair=function(){return 0!=(2&this.flags)},igv.BamAlignment.prototype.isFirstOfPair=function(){return 0!=(64&this.flags)},igv.BamAlignment.prototype.isSecondOfPair=function(){return 0!=(128&this.flags)},igv.BamAlignment.prototype.isSecondary=function(){return 0!=(256&this.flags)},igv.BamAlignment.prototype.isSupplementary=function(){return 0!=(2048&this.flags)},igv.BamAlignment.prototype.isFailsVendorQualityCheck=function(){return 0!=(512&this.flags)},igv.BamAlignment.prototype.isDuplicate=function(){return 0!=(1024&this.flags)},igv.BamAlignment.prototype.isMateMapped=function(){return 0==(8&this.flags)},igv.BamAlignment.prototype.isNegativeStrand=function(){return 0!=(16&this.flags)},igv.BamAlignment.prototype.isMateNegativeStrand=function(){return 0!=(32&this.flags)},igv.BamAlignment.prototype.tags=function(){function decodeTags(ba){for(var p=0,len=ba.length,tags={};p<len;){var value,tag=String.fromCharCode(ba[p])+String.fromCharCode(ba[p+1]),type=String.fromCharCode(ba[p+2]);if("A"==type)value=String.fromCharCode(ba[p+3]),p+=4;else if("i"===type||"I"===type)value=readInt(ba,p+3),p+=7;else if("c"===type||"C"===type)value=ba[p+3],p+=4;else if("s"===type||"S"===type)value=readShort(ba,p+3),p+=5;else if("f"===type)value=readFloat(ba,p+3),p+=7;else{if("Z"!==type){value="Error unknown type: "+type,tags[tag]=value;break}for(p+=3,value="";;){var cc=ba[p++];if(0===cc)break;value+=String.fromCharCode(cc)}}tags[tag]=value}return tags}return this.tagDict||(this.tagBA?(this.tagDict=decodeTags(this.tagBA),this.tagBA=void 0):this.tagDict={}),this.tagDict},igv.BamAlignment.prototype.popupData=function(genomicLocation){function yesNo(bool){return bool?"Yes":"No"}var isFirst,tagDict,nameValues=[];if(this.insertions)for(var i=0;i<this.insertions.length;i+=1){var ins_start=this.insertions[i].start;if(genomicLocation==ins_start||genomicLocation==ins_start-1)return nameValues.push({name:"Insertion",value:this.insertions[i].seq}),nameValues.push({name:"Location",value:ins_start}),nameValues}nameValues.push({name:"Read Name",value:this.readName}),nameValues.push("<hr>"),nameValues.push({name:"Alignment Start",value:igv.numberFormatter(1+this.start),borderTop:!0}),nameValues.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0}),nameValues.push({name:"Cigar",value:this.cigar}),nameValues.push({name:"Mapped",value:yesNo(this.isMapped())}),nameValues.push({name:"Mapping Quality",value:this.mq}),nameValues.push({name:"Secondary",value:yesNo(this.isSecondary())}),nameValues.push({name:"Supplementary",value:yesNo(this.isSupplementary())}),nameValues.push({name:"Duplicate",value:yesNo(this.isDuplicate())}),nameValues.push({name:"Failed QC",value:yesNo(this.isFailsVendorQualityCheck())}),this.isPaired()&&(nameValues.push("<hr>"),nameValues.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),nameValues.push({name:"Mate is Mapped",value:yesNo(this.isMateMapped())}),this.isMateMapped()&&(nameValues.push({name:"Mate Chromosome",value:this.mate.chr}),nameValues.push({name:"Mate Start",value:this.mate.position+1}),nameValues.push({name:"Mate Strand",value:!0===this.mate.strand?"(+)":"(-)"}),nameValues.push({name:"Insert Size",value:this.fragmentLength}))),nameValues.push("<hr>"),tagDict=this.tags(),isFirst=!0;for(var key in tagDict)tagDict.hasOwnProperty(key)&&(isFirst?(nameValues.push({name:key,value:tagDict[key],borderTop:!0}),isFirst=!1):nameValues.push({name:key,value:tagDict[key]}));return nameValues},igv.BamFilter=function(options){options||(options={}),this.vendorFailed=void 0===options.vendorFailed||options.vendorFailed,this.duplicates=void 0===options.duplicates||options.duplicates,this.secondary=options.secondary||!1,this.supplementary=options.supplementary||!1,this.mqThreshold=void 0===options.mqThreshold?0:options.mqThreshold},igv.BamFilter.prototype.pass=function(alignment){return!(this.vendorFailed&&alignment.isFailsVendorQualityCheck()||this.duplicates&&alignment.isDuplicate()||this.secondary&&alignment.isSecondary()||this.supplementary&&alignment.isSupplementary()||alignment.mq<this.mqThreshold)},igv}(igv||{}),igv=function(igv){return igv.BamAlignmentRow=function(){this.alignments=[],this.score=void 0},igv.BamAlignmentRow.prototype.findCenterAlignment=function(bpStart,bpEnd){var centerAlignment=void 0;return this.alignments.forEach(function(a){void 0===centerAlignment&&(a.start+a.lengthOnRef<bpStart||a.start>bpEnd||(centerAlignment=a))}),centerAlignment},igv.BamAlignmentRow.prototype.updateScore=function(genomicLocation,genomicInterval,sortOption){this.score=this.caculateScore(genomicLocation,1+genomicLocation,genomicInterval,sortOption)},igv.BamAlignmentRow.prototype.caculateScore=function(bpStart,bpEnd,genomicInterval,sortOption){var baseScore,alignment;return alignment=this.findCenterAlignment(bpStart,bpEnd),void 0===alignment?Number.MAX_VALUE:"NUCLEOTIDE"===sortOption.sort?(baseScore=void 0,alignment.blocks.forEach(function(block){var reference,base,coverage,count,phred,sequence=genomicInterval.sequence,coverageMap=genomicInterval.coverageMap;if("*"!==block.seq)for(var i=0,indexReferenceSequence=block.start-genomicInterval.start,bpBlockSequence=block.start,lengthBlockSequence=block.seq.length;i<lengthBlockSequence;i++,indexReferenceSequence++,bpBlockSequence++)bpStart===bpBlockSequence&&(reference=sequence.charAt(indexReferenceSequence),base=block.seq.charAt(i),"="===base&&(base=reference),"N"===base?baseScore=2:base===reference?baseScore=3:"X"===base||base!==reference?(coverage=coverageMap.coverage[bpBlockSequence-coverageMap.bpStart],count=coverage["pos"+base]+coverage["neg"+base],phred=coverage.qual?coverage.qual:0,baseScore=-(count+phred/1e3)):console.log("BamAlignmentRow.caculateScore - huh?"));else baseScore=3}),void 0===baseScore?Number.MAX_VALUE:baseScore):"STRAND"===sortOption.sort?alignment.strand?1:-1:"START"===sortOption.sort?alignment.start:Number.MAX_VALUE},igv}(igv||{}),igv=function(igv){function reg2bins(beg,end){var k,list=[];for(end>=1<<29&&(end=1<<29),--end,list.push(0),k=1+(beg>>26);k<=1+(end>>26);++k)list.push(k);for(k=9+(beg>>23);k<=9+(end>>23);++k)list.push(k);for(k=73+(beg>>20);k<=73+(end>>20);++k)list.push(k);for(k=585+(beg>>17);k<=585+(end>>17);++k)list.push(k);for(k=4681+(beg>>14);k<=4681+(end>>14);++k)list.push(k);return list}return igv.loadBamIndex=function(indexURL,config,tabix){return new Promise(function(fulfill,reject){var genome=igv.browser?igv.browser.genome:null;igvxhr.loadArrayBuffer(indexURL,{headers:config.headers,withCredentials:config.withCredentials}).then(function(arrayBuffer){var magic,nbin,nintv,nref,parser,binIndex,linearIndex,binNumber,cs,ce,b,i,ref,sequenceIndexMap,indices=[],blockMin=Number.MAX_VALUE,blockMax=0;if(!arrayBuffer)return void fulfill(null);if(tabix&&(arrayBuffer=new Zlib.Gunzip(new Uint8Array(arrayBuffer)).decompress().buffer),parser=new igv.BinaryParser(new DataView(arrayBuffer)),!(21578050===(magic=parser.getInt())||tabix&&21578324===magic))throw new Error(indexURL+" is not a "+(tabix?"tabix":"bai")+" file");if(nref=parser.getInt(),tabix)for(parser.getInt(),parser.getInt(),parser.getInt(),parser.getInt(),parser.getInt(),parser.getInt(),parser.getInt(),sequenceIndexMap={},i=0;i<nref;i++){var seq_name=parser.getString();genome&&(seq_name=genome.getChromosomeName(seq_name)),sequenceIndexMap[seq_name]=i}for(ref=0;ref<nref;++ref){for(binIndex={},linearIndex=[],nbin=parser.getInt(),b=0;b<nbin;++b)if(37450==(binNumber=parser.getInt()))nchnk=parser.getInt(),cs=parser.getVPointer(),ce=parser.getVPointer(),parser.getLong(),parser.getLong();else{binIndex[binNumber]=[];var nchnk=parser.getInt();for(i=0;i<nchnk;i++)cs=parser.getVPointer(),ce=parser.getVPointer(),cs&&ce&&(cs.block<blockMin&&(blockMin=cs.block),ce.block>blockMax&&(blockMax=ce.block),binIndex[binNumber].push([cs,ce]))}for(nintv=parser.getInt(),i=0;i<nintv;i++)cs=parser.getVPointer(),linearIndex.push(cs);nbin>0&&(indices[ref]={binIndex:binIndex,linearIndex:linearIndex})}fulfill(new igv.BamIndex(indices,blockMin,sequenceIndexMap,tabix))}).catch(reject)})},igv.BamIndex=function(indices,blockMin,sequenceIndexMap,tabix){this.firstAlignmentBlock=blockMin,this.indices=indices,this.sequenceIndexMap=sequenceIndexMap,this.tabix=tabix},igv.BamIndex.prototype.blocksForRange=function(refId,min,max){var overlappingBins,leafChunks,otherChunks,nintv,lowest,minLin,lb,prunedOtherChunks,i,chnk,dif,intChunks,mergedChunks,bam=this,ba=bam.indices[refId];if(ba){for(overlappingBins=reg2bins(min,max),leafChunks=[],otherChunks=[],overlappingBins.forEach(function(bin){if(ba.binIndex[bin])for(var chunks=ba.binIndex[bin],nchnk=chunks.length,c=0;c<nchnk;++c){var cs=chunks[c][0],ce=chunks[c][1];(bin<4681?otherChunks:leafChunks).push({minv:cs,maxv:ce,bin:bin})}}),nintv=ba.linearIndex.length,lowest=null,minLin=Math.min(min>>14,nintv-1),maxLin=Math.min(max>>14,nintv-1),i=minLin;i<=maxLin;++i)(lb=ba.linearIndex[i])&&(!lowest||lb.block<lowest.block||lb.offset<lowest.offset)&&(lowest=lb);if(prunedOtherChunks=[],null!=lowest)for(i=0;i<otherChunks.length;++i)chnk=otherChunks[i],(chnk.maxv.block>lowest.block||chnk.maxv.block==lowest.block&&chnk.maxv.offset>=lowest.offset)&&prunedOtherChunks.push(chnk);for(intChunks=[],i=0;i<prunedOtherChunks.length;++i)intChunks.push(prunedOtherChunks[i]);for(i=0;i<leafChunks.length;++i)intChunks.push(leafChunks[i]);if(intChunks.sort(function(c0,c1){return dif=c0.minv.block-c1.minv.block,0!=dif?dif:c0.minv.offset-c1.minv.offset}),mergedChunks=[],intChunks.length>0){for(var cur=intChunks[0],i=1;i<intChunks.length;++i){var nc=intChunks[i];nc.minv.block-cur.maxv.block<65e3?cur={minv:cur.minv,maxv:nc.maxv}:(mergedChunks.push(cur),cur=nc)}mergedChunks.push(cur)}return mergedChunks}return[]},igv}(igv||{}),igv=function(igv){function getIndex(bam){return new Promise(function(fulfill,reject){bam.index?fulfill(bam.index):igv.loadBamIndex(bam.baiPath,bam.config).then(function(index){bam.index=index,fulfill(bam.index)}).catch(reject)})}function getChrIndex(bam){return new Promise(function(fulfill,reject){bam.chrToIndex?fulfill(bam.chrToIndex):bam.readHeader().then(function(){fulfill(bam.chrToIndex)}).catch(reject)})}function readInt(ba,offset){return ba[offset+3]<<24|ba[offset+2]<<16|ba[offset+1]<<8|ba[offset]}var SECRET_DECODER=["=","A","C","x","G","x","x","x","T","x","x","x","x","x","x","N"],CIGAR_DECODER=["M","I","D","N","S","H","P","=","X","?","?","?","?","?","?","?"],READ_STRAND_FLAG=16,MATE_STRAND_FLAG=32;const MAX_GZIP_BLOCK_SIZE=65536,MAXIMUM_SAMPLING_DEPTH=2500;return igv.BamReader=function(config){this.config=config,this.filter=config.filter||new igv.BamFilter,this.bamPath=config.url,this.baiPath=config.indexURL||this.bamPath+".bai",this.headPath=config.headURL||this.bamPath,this.samplingWindowSize=void 0===config.samplingWindowSize?100:config.samplingWindowSize,this.samplingDepth=void 0===config.samplingDepth?50:config.samplingDepth,this.samplingDepth>MAXIMUM_SAMPLING_DEPTH&&(igv.log("Warning: attempt to set sampling depth > maximum value of 2500"),this.samplingDepth=MAXIMUM_SAMPLING_DEPTH),config.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===config.pairsSupported||config.pairsSupported},igv.BamReader.prototype.readAlignments=function(chr,bpStart,bpEnd){function decodeBamRecords(ba,offset,alignmentContainer,min,max,chrId,filter){for(var blockSize,blockEnd,alignment,blocks,refID,pos,bmn,mq,nl,flag_nc,flag,nc,lseq,mateRefID,matePos,readName,j,p,lengthOnRef,cigar,c,cigarArray,seq,seqBytes;;){if(blockSize=readInt(ba,offset),(blockEnd=offset+blockSize+4)>ba.length)return;if(alignment=new igv.BamAlignment,refID=readInt(ba,offset+4),pos=readInt(ba,offset+8),refID<0)return;if(refID>chrId||pos>max)return;if(!(refID<chrId)){for(bmn=readInt(ba,offset+12),mq=(65280&bmn)>>8,nl=255&bmn,flag_nc=readInt(ba,offset+16),flag=(4294901760&flag_nc)>>16,nc=65535&flag_nc,alignment.flags=flag,alignment.strand=!(flag&READ_STRAND_FLAG),lseq=readInt(ba,offset+20),mateRefID=readInt(ba,offset+24),matePos=readInt(ba,offset+28),alignment.fragmentLength=readInt(ba,offset+32),readName="",j=0;j<nl-1;++j)readName+=String.fromCharCode(ba[offset+36+j]);for(p=offset+36+nl,lengthOnRef=0,cigar="",cigarArray=[],c=0;c<nc;++c){var cigop=readInt(ba,p),opLen=cigop>>4,opLtr=CIGAR_DECODER[15&cigop];"M"!=opLtr&&"EQ"!=opLtr&&"X"!=opLtr&&"D"!=opLtr&&"N"!=opLtr&&"="!=opLtr||(lengthOnRef+=opLen),cigar=cigar+opLen+opLtr,p+=4,cigarArray.push({len:opLen,ltr:opLtr})}if(alignment.cigar=cigar,alignment.lengthOnRef=lengthOnRef,!(alignment.start+alignment.lengthOnRef<min)){for(seq="",seqBytes=lseq+1>>1,j=0;j<seqBytes;++j){var sb=ba[p+j];seq+=SECRET_DECODER[(240&sb)>>4],seq+=SECRET_DECODER[15&sb]}if(seq=seq.substring(0,lseq),p+=seqBytes,alignment.seq=seq,1===lseq&&"*"===String.fromCharCode(ba[p+j]+33));else for(alignment.qual=[],j=0;j<lseq;++j)alignment.qual.push(ba[p+j]);p+=lseq,alignment.start=pos,alignment.mq=mq,alignment.readName=readName,alignment.chr=self.indexToChr[refID],mateRefID>=0&&(alignment.mate={chr:self.indexToChr[mateRefID],position:matePos,strand:!(flag&MATE_STRAND_FLAG)}),alignment.tagBA=new Uint8Array(ba.buffer.slice(p,blockEnd)),p+=blockEnd,(!min||alignment.start<=max&&alignment.start+alignment.lengthOnRef>=min&&filter.pass(alignment))&&(void 0!==chrId&&refID!=chrId||(blocks=makeBlocks(alignment,cigarArray),alignment.blocks=blocks.blocks,alignment.insertions=blocks.insertions,alignmentContainer.push(alignment))),offset=blockEnd}}}}function makeBlocks(record,cigarArray){for(var insertions,blockSeq,blockQuals,gapType,blocks=[],seqOffset=0,pos=record.start,len=cigarArray.length,i=0;i<len;i++){var c=cigarArray[i];switch(c.ltr){case"H":case"P":break;case"S":seqOffset+=c.len,gapType="S";break;case"N":pos+=c.len,gapType="N";break;case"D":pos+=c.len,gapType="D";break;case"I":blockSeq="*"===record.seq?"*":record.seq.substr(seqOffset,c.len),blockQuals=record.qual?record.qual.slice(seqOffset,c.len):void 0,void 0===insertions&&(insertions=[]),insertions.push({start:pos,len:c.len,seq:blockSeq,qual:blockQuals}),seqOffset+=c.len;break;case"M":case"EQ":case"=":case"X":blockSeq="*"===record.seq?"*":record.seq.substr(seqOffset,c.len),blockQuals=record.qual?record.qual.slice(seqOffset,c.len):void 0,blocks.push({start:pos,len:c.len,seq:blockSeq,qual:blockQuals,gapType:gapType}),seqOffset+=c.len,pos+=c.len;break;default:console.log("Error processing cigar element: "+c.len+c.ltr)}}return{blocks:blocks,insertions:insertions}}var self=this;return new Promise(function(fulfill,reject){getChrIndex(self).then(function(chrToIndex){var chrId=chrToIndex[chr],alignmentContainer=new igv.AlignmentContainer(chr,bpStart,bpEnd,self.samplingWindowSize,self.samplingDepth,self.pairsSupported);void 0===chrId?fulfill(alignmentContainer):getIndex(self).then(function(bamIndex){var chunks=bamIndex.blocksForRange(chrId,bpStart,bpEnd),promises=[];return chunks?0===chunks.length?void fulfill(alignmentContainer):(chunks.forEach(function(c){promises.push(new Promise(function(fulfill,reject){var fetchMin=c.minv.block,fetchMax=c.maxv.block+MAX_GZIP_BLOCK_SIZE,range={start:fetchMin,size:fetchMax-fetchMin+1};igvxhr.loadArrayBuffer(self.bamPath,{headers:self.config.headers,range:range,withCredentials:self.config.withCredentials}).then(function(compressed){decodeBamRecords(new Uint8Array(igv.unbgzf(compressed)),c.minv.offset,alignmentContainer,bpStart,bpEnd,chrId,self.filter),fulfill(alignmentContainer)}).catch(function(obj){reject(obj)})}))}),void Promise.all(promises).then(function(ignored){alignmentContainer.finish(),fulfill(alignmentContainer)}).catch(function(obj){reject(obj)})):(fulfill(null),void reject("Error reading bam index"))}).catch(reject)}).catch(reject)})},igv.BamReader.prototype.readHeader=function(){var self=this;return new Promise(function(fulfill,reject){getIndex(self).then(function(index){var len=index.firstAlignmentBlock+MAX_GZIP_BLOCK_SIZE;igvxhr.loadArrayBuffer(self.bamPath,{headers:self.config.headers,range:{start:0,size:len},withCredentials:self.config.withCredentials}).then(function(compressedBuffer){for(var unc=igv.unbgzf(compressedBuffer,len),uncba=new Uint8Array(unc),samHeaderLen=(readInt(uncba,0),readInt(uncba,4)),samHeader="",genome=igv.browser?igv.browser.genome:null,i=0;i<samHeaderLen;++i)samHeader+=String.fromCharCode(uncba[i+8]);var nRef=readInt(uncba,samHeaderLen+8),p=samHeaderLen+12;self.chrToIndex={},self.indexToChr=[];for(var i=0;i<nRef;++i){for(var lName=readInt(uncba,p),name="",j=0;j<lName-1;++j)name+=String.fromCharCode(uncba[p+4+j]);readInt(uncba,p+lName+4),genome&&genome.getChromosomeName&&(name=genome.getChromosomeName(name)),self.chrToIndex[name]=i,self.indexToChr.push(name),p=p+8+lName}fulfill()}).catch(reject)}).catch(reject)})},igv}(igv||{}),igv=function(igv){function pairAlignments(rows){var pairCache={},result=[];return rows.forEach(function(row){row.alignments.forEach(function(alignment){var pairedAlignment;canBePaired(alignment)?(pairedAlignment=pairCache[alignment.readName],pairedAlignment?(pairedAlignment.setSecondAlignment(alignment),pairCache[alignment.readName]=void 0):(pairedAlignment=new igv.PairedAlignment(alignment),pairCache[alignment.readName]=pairedAlignment,result.push(pairedAlignment))):result.push(alignment)})}),result}function unpairAlignments(rows){var result=[];return rows.forEach(function(row){row.alignments.forEach(function(alignment){alignment instanceof igv.PairedAlignment?(alignment.firstAlignment&&result.push(alignment.firstAlignment),alignment.secondAlignment&&result.push(alignment.secondAlignment)):result.push(alignment)})}),result}function canBePaired(alignment){return alignment.isPaired()&&alignment.isMateMapped()&&alignment.chr===alignment.mate.chr&&(alignment.isFirstOfPair()||alignment.isSecondOfPair())&&!(alignment.isSecondary()||alignment.isSupplementary())}function packAlignmentRows(alignments,start,end,maxRows){if(alignments){if(alignments.sort(function(a,b){return a.start-b.start}),0===alignments.length)return[];var alignmentRow,index,bucket,alignment,bucketList=[],allocatedCount=0,lastAllocatedCount=0,nextStart=start,packedAlignmentRows=[],bucketStart=Math.max(start,alignments[0].start);for(alignments.forEach(function(alignment){var buckListIndex=Math.max(0,alignment.start-bucketStart);void 0===bucketList[buckListIndex]&&(bucketList[buckListIndex]=[]),bucketList[buckListIndex].push(alignment)});allocatedCount<alignments.length&&packedAlignmentRows.length<maxRows;){for(alignmentRow=new igv.BamAlignmentRow;nextStart<=end;){for(bucket=void 0;!bucket&&nextStart<=end;)index=nextStart-bucketStart,void 0===bucketList[index]?++nextStart:bucket=bucketList[index];if(!bucket)break;alignment=bucket.pop(),0===bucket.length&&(bucketList[index]=void 0),alignmentRow.alignments.push(alignment),nextStart=alignment.start+alignment.lengthOnRef+8,++allocatedCount}if(alignmentRow.alignments.length>0&&packedAlignmentRows.push(alignmentRow),nextStart=bucketStart,allocatedCount===lastAllocatedCount)break;lastAllocatedCount=allocatedCount}return packedAlignmentRows}}return igv.BamSource=function(config){this.config=config,this.alignmentContainer=void 0,this.maxRows=config.maxRows||1e3,"ga4gh"===config.sourceType?this.bamReader=new igv.Ga4ghAlignmentReader(config):this.bamReader=new igv.BamReader(config),this.viewAsPairs=config.viewAsPairs},igv.BamSource.prototype.setViewAsPairs=function(bool){var self=this;if(this.viewAsPairs!==bool&&(this.viewAsPairs=bool,this.alignmentContainer)){var alignments,alignmentContainer=this.alignmentContainer;alignments=bool?pairAlignments(alignmentContainer.packedAlignmentRows):unpairAlignments(alignmentContainer.packedAlignmentRows),alignmentContainer.packedAlignmentRows=packAlignmentRows(alignments,alignmentContainer.start,alignmentContainer.end,self.maxRows)}},igv.BamSource.prototype.getAlignments=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){self.alignmentContainer&&self.alignmentContainer.contains(chr,bpStart,bpEnd)?fulfill(self.alignmentContainer):self.bamReader.readAlignments(chr,bpStart,bpEnd).then(function(alignmentContainer){var maxRows=self.config.maxRows||500,alignments=alignmentContainer.alignments;self.viewAsPairs||(alignments=unpairAlignments([{alignments:alignments}])),alignmentContainer.packedAlignmentRows=packAlignmentRows(alignments,alignmentContainer.start,alignmentContainer.end,maxRows),alignmentContainer.alignments=void 0,self.alignmentContainer=alignmentContainer,igv.browser.genome.sequence.getSequence(alignmentContainer.chr,alignmentContainer.start,alignmentContainer.end).then(function(sequence){sequence&&(alignmentContainer.coverageMap.refSeq=sequence,alignmentContainer.sequence=sequence,fulfill(alignmentContainer))}).catch(reject)}).catch(reject)})},igv}(igv||{}),igv=function(igv){function shadedBaseColor(qual,nucleotide,genomicLocation){var alpha,minQ=5,foregroundColor=igv.nucleotideColorComponents[nucleotide];if(foregroundColor)return alpha=qual<minQ?.1:Math.max(.1,Math.min(1,.1+.9*(qual-minQ)/(20-minQ))),alpha=Math.round(10*alpha)/10,alpha>=1?igv.nucleotideColors[nucleotide]:"rgba("+foregroundColor[0]+","+foregroundColor[1]+","+foregroundColor[2]+","+alpha+")"}function getAlignmentColor(alignment){var tagValue,color,alignmentTrack=this,option=alignmentTrack.colorBy;switch(color=alignmentTrack.parent.color,option){case"strand":color=alignment.strand?alignmentTrack.posStrandColor:alignmentTrack.negStrandColor;break;case"firstOfPairStrand":alignment instanceof igv.PairedAlignment?color=alignment.firstOfPairStrand()?alignmentTrack.posStrandColor:alignmentTrack.negStrandColor:alignment.isPaired()&&(alignment.isFirstOfPair()?color=alignment.strand?alignmentTrack.posStrandColor:alignmentTrack.negStrandColor:alignment.isSecondOfPair()?color=alignment.strand?alignmentTrack.negStrandColor:alignmentTrack.posStrandColor:console.log("ERROR. Paired alignments are either first or second."));break;case"tag":tagValue=alignment.tags()[alignmentTrack.colorByTag],void 0!==tagValue&&(color=alignmentTrack.bamColorTag===alignmentTrack.colorByTag?"rgb("+tagValue+")":alignmentTrack.tagColors.getColor(tagValue));break;default:color=alignmentTrack.parent.color}return color}var alignmentRowYInset=0,alignmentStartGap=5,downsampleRowHeight=5;return igv.BAMTrack=function(config){this.featureSource=new igv.BamSource(config),igv.configTrack(this,config),void 0===config.coverageTrackHeight&&(config.coverageTrackHeight=50),this.coverageTrack=new CoverageTrack(config,this),this.alignmentTrack=new AlignmentTrack(config,this),this.visibilityWindow=config.visibilityWindow||3e4,this.viewAsPairs=config.viewAsPairs,this.pairsSupported=void 0===config.pairsSupported,this.color=config.color||"rgb(185, 185, 185)",this.sortOption=config.sortOption||{sort:"NUCLEOTIDE"},this.sortDirection=!0,this.filterOption=config.filterOption||{name:"mappingQuality",params:[30,void 0]}},igv.BAMTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){return this.featureSource.getAlignments(chr,bpStart,bpEnd)},igv.BAMTrack.filters={noop:function(){return function(alignment){return!1}},strand:function(strand){return function(alignment){return alignment.strand===strand}},mappingQuality:function(lower,upper){return function(alignment){return!!(lower&&alignment.mq<lower)||!!(upper&&alignment.mq>upper)}}},igv.BAMTrack.prototype.altClick=function(genomicLocation,event){this.alignmentTrack.sortAlignmentRows(genomicLocation,this.sortOption),this.trackView.redrawTile(this.featureSource.alignmentContainer),$(this.trackView.viewportDiv).scrollTop(0),this.sortDirection=!this.sortDirection},igv.BAMTrack.prototype.computePixelHeight=function(alignmentContainer){return this.coverageTrack.computePixelHeight(alignmentContainer)+this.alignmentTrack.computePixelHeight(alignmentContainer)},igv.BAMTrack.prototype.draw=function(options){this.coverageTrack.height>0&&this.coverageTrack.draw(options),this.alignmentTrack.draw(options)},igv.BAMTrack.prototype.paintAxis=function(ctx,pixelWidth,pixelHeight){this.coverageTrack.paintAxis(ctx,pixelWidth,this.coverageTrackHeight)},igv.BAMTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){return yOffset>=this.coverageTrack.top&&yOffset<this.coverageTrack.height?this.coverageTrack.popupData(genomicLocation,xOffset,this.coverageTrack.top):this.alignmentTrack.popupData(genomicLocation,xOffset,yOffset-this.alignmentTrack.top)},igv.BAMTrack.prototype.popupMenuItems=function(popover){function colorByMarkup(menuItem,showCheck,index){var parts=[],item={};return parts.push('<div class="igv-track-menu-item">'),parts.push(showCheck?'<i class="fa fa-check fa-check-shim"></i>':'<i class="fa fa-check fa-check-shim fa-check-hidden"></i>'),"tag"===menuItem.key?parts.push('<span id="color-by-tag">'):parts.push("<span>"),parts.push(menuItem.label),parts.push("</span>"),parts.push("</div>"),item.object=$(parts.join("")),item.click=function(){igv.popover.hide(),"tag"===menuItem.key?(igv.dialog.configure(function(){return"Tag Name"},self.alignmentTrack.colorByTag?self.alignmentTrack.colorByTag:"",function(){var tag=igv.dialog.$dialogInput.val().trim();self.alignmentTrack.colorBy="tag",tag!==self.alignmentTrack.colorByTag&&(self.alignmentTrack.colorByTag=igv.dialog.$dialogInput.val().trim(),self.alignmentTrack.tagColors=new igv.PaletteColorTable("Set1"),$("#color-by-tag").text(self.alignmentTrack.colorByTag)),self.trackView.update()}),igv.dialog.show($(self.trackView.trackDiv))):(self.alignmentTrack.colorBy=menuItem.key,self.trackView.update())},item}var html,selected,self=this,menuItems=[],colorByMenuItems=[],tagLabel="tag"+(self.alignmentTrack.colorByTag?" ("+self.alignmentTrack.colorByTag+")":"");return colorByMenuItems.push({key:"none",label:"track color"}),self.viewAsPairs||colorByMenuItems.push({key:"strand",label:"read strand"}),self.pairsSupported&&self.alignmentTrack.hasPairs&&colorByMenuItems.push({key:"firstOfPairStrand",label:"first-of-pair strand"}),colorByMenuItems.push({key:"tag",label:tagLabel}),menuItems.push(igv.colorPickerMenuItem(popover,this.trackView)),menuItems.push('<div class="igv-track-menu-category igv-track-menu-border-top">Color by</div>'),colorByMenuItems.forEach(function(item){selected=self.alignmentTrack.colorBy===item.key,menuItems.push(colorByMarkup(item,selected))}),html=[],self.pairsSupported&&self.alignmentTrack.hasPairs&&(html.push('<div class="igv-track-menu-item igv-track-menu-border-top">'),html.push(!0===self.viewAsPairs?'<i class="fa fa-check fa-check-shim">':'<i class="fa fa-check fa-check-shim fa-check-hidden">'),html.push("</i>"),html.push("View as pairs"),html.push("</div>"),menuItems.push({object:$(html.join("")),click:function(){var $fa=$(this).find("i");popover.hide(),self.viewAsPairs=!self.viewAsPairs,!0===self.viewAsPairs?$fa.removeClass("fa-check-hidden"):$fa.addClass("fa-check-hidden"),self.featureSource.setViewAsPairs(self.viewAsPairs),self.trackView.update()}})),menuItems},CoverageTrack=function(config,parent){this.parent=parent,this.featureSource=parent.featureSource,this.top=0,this.height=config.coverageTrackHeight,this.dataRange={min:0},this.paintAxis=igv.paintAxis},CoverageTrack.prototype.computePixelHeight=function(alignmentContainer){return this.height},CoverageTrack.prototype.draw=function(options){var bp,x,y,w,h,refBase,i,len,item,accumulatedHeight,sequence,self=this,alignmentContainer=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,bpEnd=bpStart+pixelWidth*bpPerPixel+1,coverageMap=alignmentContainer.coverageMap;for(this.top&&ctx.translate(0,top),coverageMap.refSeq&&(sequence=coverageMap.refSeq.toUpperCase()),this.dataRange.max=coverageMap.maximum,w=Math.max(1,Math.ceil(1/bpPerPixel)),i=0,len=coverageMap.coverage.length;i<len;i++)if(!((bp=coverageMap.bpStart+i)<bpStart)){if(bp>bpEnd)break;(item=coverageMap.coverage[i])&&(h=Math.round(item.total/this.dataRange.max*this.height),y=this.height-h,x=Math.floor((bp-bpStart)/bpPerPixel),igv.graphics.setProperties(ctx,{fillStyle:this.parent.color,strokeStyle:this.color}),igv.graphics.fillRect(ctx,x,y,w,h))}if(sequence)for(i=0,len=coverageMap.coverage.length;i<len;i++)if(!((bp=coverageMap.bpStart+i)<bpStart)){if(bp>bpEnd)break;(item=coverageMap.coverage[i])&&(h=item.total/this.dataRange.max*this.height,y=this.height-h,x=Math.floor((bp-bpStart)/bpPerPixel),refBase=sequence[i],item.isMismatch(refBase)&&(igv.graphics.setProperties(ctx,{fillStyle:igv.nucleotideColors[refBase]}),igv.graphics.fillRect(ctx,x,y,w,h),accumulatedHeight=0,["A","C","T","G"].forEach(function(nucleotide){var count,hh;count=item["pos"+nucleotide]+item["neg"+nucleotide],hh=count/self.dataRange.max*self.height,y=self.height-hh-accumulatedHeight,accumulatedHeight+=hh,igv.graphics.setProperties(ctx,{fillStyle:igv.nucleotideColors[nucleotide]}),igv.graphics.fillRect(ctx,x,y,w,hh)})))}},CoverageTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){var coverageMapIndex,coverage,coverageMap=this.featureSource.alignmentContainer.coverageMap,nameValues=[];return coverageMapIndex=genomicLocation-coverageMap.bpStart,coverage=coverageMap.coverage[coverageMapIndex],coverage&&(nameValues.push(igv.browser.referenceFrame.chr+":"+igv.numberFormatter(1+genomicLocation)),nameValues.push({name:"Total Count",value:coverage.total}),tmp=coverage.posA+coverage.negA,tmp>0&&(tmp=tmp.toString()+" ("+Math.floor((coverage.posA+coverage.negA)/coverage.total*100)+"%)"),nameValues.push({name:"A",value:tmp}),tmp=coverage.posC+coverage.negC,tmp>0&&(tmp=tmp.toString()+" ("+Math.floor(tmp/coverage.total*100)+"%)"),nameValues.push({name:"C",value:tmp}),tmp=coverage.posG+coverage.negG,tmp>0&&(tmp=tmp.toString()+" ("+Math.floor(tmp/coverage.total*100)+"%)"),nameValues.push({name:"G",value:tmp}),tmp=coverage.posT+coverage.negT,tmp>0&&(tmp=tmp.toString()+" ("+Math.floor(tmp/coverage.total*100)+"%)"),nameValues.push({name:"T",value:tmp}),tmp=coverage.posN+coverage.negN,tmp>0&&(tmp=tmp.toString()+" ("+Math.floor(tmp/coverage.total*100)+"%)"),nameValues.push({name:"N",value:tmp})),nameValues},AlignmentTrack=function(config,parent){this.parent=parent,this.featureSource=parent.featureSource,this.top=0==config.coverageTrackHeight?0:config.coverageTrackHeight+5,this.alignmentRowHeight=config.alignmentRowHeight||14,this.negStrandColor=config.negStrandColor||"rgba(150, 150, 230, 0.75)",this.posStrandColor=config.posStrandColor||"rgba(230, 150, 150, 0.75)",this.insertionColor=config.insertionColor||"rgb(138, 94, 161)",this.deletionColor=config.deletionColor||"black",this.skippedColor=config.skippedColor||"rgb(150, 170, 170)",this.colorBy=config.colorBy||"none",this.colorByTag=config.colorByTag,this.bamColorTag=void 0===config.bamColorTag?"YC":config.bamColorTag,this.sortOption=config.sortOption||{sort:"NUCLEOTIDE"},this.sortDirection=!0,this.hasPairs=!1},AlignmentTrack.prototype.computePixelHeight=function(alignmentContainer){if(alignmentContainer.packedAlignmentRows){var h=0;return alignmentContainer.hasDownsampledIntervals()&&(h+=downsampleRowHeight+alignmentStartGap),h+this.alignmentRowHeight*alignmentContainer.packedAlignmentRows.length+5}return this.height},AlignmentTrack.prototype.draw=function(options){function drawPairConnector(alignment,yRect,alignmentHeight){var alignmentColor=getAlignmentColor.call(self,alignment.firstAlignment),outlineColor=alignmentColor,xBlockStart=(alignment.connectingStart-bpStart)/bpPerPixel,xBlockEnd=(alignment.connectingEnd-bpStart)/bpPerPixel,yStrokedLine=yRect+alignmentHeight/2;alignment.connectingEnd<bpStart||alignment.connectingStart>bpEnd||(alignment.mq<=0&&(alignmentColor=igv.addAlphaToRGB(alignmentColor,"0.15")),igv.graphics.setProperties(ctx,{fillStyle:alignmentColor,strokeStyle:outlineColor}),igv.graphics.strokeLine(ctx,xBlockStart,yStrokedLine,xBlockEnd,yStrokedLine))}function drawSingleAlignment(alignment,yRect,alignmentHeight){function drawBlock(block){var refChar,readChar,readQual,xBase,widthBase,colorBase,x,y,i,seqOffset=block.start-alignmentContainer.start,xBlockStart=(block.start-bpStart)/bpPerPixel,xBlockEnd=(block.start+block.len-bpStart)/bpPerPixel,widthBlock=Math.max(1,xBlockEnd-xBlockStart),widthArrowHead=self.alignmentRowHeight/2,blockSeq=block.seq.toUpperCase(),skippedColor=self.skippedColor,deletionColor=self.deletionColor,yStrokedLine=yRect+alignmentHeight/2;if(void 0!==block.gapType&&void 0!==xBlockEnd&&void 0!==lastBlockEnd&&("D"===block.gapType?igv.graphics.strokeLine(ctx,lastBlockEnd,yStrokedLine,xBlockStart,yStrokedLine,{strokeStyle:deletionColor}):igv.graphics.strokeLine(ctx,lastBlockEnd,yStrokedLine,xBlockStart,yStrokedLine,{strokeStyle:skippedColor})),lastBlockEnd=xBlockEnd,!0===alignment.strand&&b===blocks.length-1?(x=[xBlockStart,xBlockEnd,xBlockEnd+widthArrowHead,xBlockEnd,xBlockStart,xBlockStart],y=[yRect,yRect,yRect+alignmentHeight/2,yRect+alignmentHeight,yRect+alignmentHeight,yRect],igv.graphics.fillPolygon(ctx,x,y,{fillStyle:alignmentColor}),alignment.mq<=0&&igv.graphics.strokePolygon(ctx,x,y,{strokeStyle:outlineColor})):!1===alignment.strand&&0===b?(x=[xBlockEnd,xBlockStart,xBlockStart-widthArrowHead,xBlockStart,xBlockEnd,xBlockEnd],y=[yRect,yRect,yRect+alignmentHeight/2,yRect+alignmentHeight,yRect+alignmentHeight,yRect],igv.graphics.fillPolygon(ctx,x,y,{fillStyle:alignmentColor}),alignment.mq<=0&&igv.graphics.strokePolygon(ctx,x,y,{strokeStyle:outlineColor})):(igv.graphics.fillRect(ctx,xBlockStart,yRect,widthBlock,alignmentHeight,{fillStyle:alignmentColor}),alignment.mq<=0&&(ctx.save(),ctx.strokeStyle=outlineColor,ctx.strokeRect(xBlockStart,yRect,widthBlock,alignmentHeight),ctx.restore())),sequence&&"*"!==blockSeq)for(i=0,len=blockSeq.length;i<len;i++)readChar=blockSeq.charAt(i),refChar=sequence.charAt(seqOffset+i),"="===readChar&&(readChar=refChar),"X"!==readChar&&refChar===readChar||(block.qual&&block.qual.length>i?(readQual=block.qual[i],colorBase=shadedBaseColor(readQual,readChar,i+block.start)):colorBase=igv.nucleotideColors[readChar],colorBase&&(xBase=(block.start+i-bpStart)/bpPerPixel,widthBase=Math.max(1,1/bpPerPixel),igv.graphics.fillRect(ctx,xBase,yRect,widthBase,alignmentHeight,{fillStyle:colorBase})))}var lastBlockEnd,block,b,alignmentColor=getAlignmentColor.call(self,alignment),outlineColor=alignmentColor,blocks=alignment.blocks;if(!(alignment.start+alignment.lengthOnRef<bpStart||alignment.start>bpEnd))for(alignment.mq<=0&&(alignmentColor=igv.addAlphaToRGB(alignmentColor,"0.15")),igv.graphics.setProperties(ctx,{fillStyle:alignmentColor,strokeStyle:outlineColor}),b=0;b<blocks.length;b++)if(block=blocks[b],!(block.start+block.len<bpStart)){if(drawBlock(block),block.start+block.len>bpEnd)break;alignment.insertions&&alignment.insertions.forEach(function(block){var refOffset=block.start-bpStart,xBlockStart=refOffset/bpPerPixel-1;igv.graphics.fillRect(ctx,xBlockStart,yRect-1,3,alignmentHeight+2,{fillStyle:self.insertionColor})})}}var self=this,alignmentContainer=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,bpEnd=bpStart+pixelWidth*bpPerPixel+1,packedAlignmentRows=alignmentContainer.packedAlignmentRows,sequence=alignmentContainer.sequence;this.top&&ctx.translate(0,this.top),sequence&&(sequence=sequence.toUpperCase()),alignmentContainer.hasDownsampledIntervals()?(alignmentRowYInset=downsampleRowHeight+alignmentStartGap,alignmentContainer.downsampledIntervals.forEach(function(interval){var xBlockStart=(interval.start-bpStart)/bpPerPixel,xBlockEnd=(interval.end-bpStart)/bpPerPixel;xBlockEnd-xBlockStart>5&&(xBlockStart+=1,xBlockEnd-=1),igv.graphics.fillRect(ctx,xBlockStart,2,xBlockEnd-xBlockStart,downsampleRowHeight-2,{fillStyle:"black"})})):alignmentRowYInset=0,packedAlignmentRows&&packedAlignmentRows.forEach(function(alignmentRow,i){var i,alignment,yRect=alignmentRowYInset+self.alignmentRowHeight*i,alignmentHeight=self.alignmentRowHeight-2;for(i=0;i<alignmentRow.alignments.length;i++)if(alignment=alignmentRow.alignments[i],self.hasPairs=self.hasPairs||alignment.isPaired(),!(alignment.start+alignment.lengthOnRef<bpStart)){if(alignment.start>bpEnd)break;!0!==alignment.hidden&&(alignment instanceof igv.PairedAlignment?(drawPairConnector(alignment,yRect,alignmentHeight),drawSingleAlignment(alignment.firstAlignment,yRect,alignmentHeight),alignment.secondAlignment&&drawSingleAlignment(alignment.secondAlignment,yRect,alignmentHeight)):drawSingleAlignment(alignment,yRect,alignmentHeight))}})},AlignmentTrack.prototype.sortAlignmentRows=function(genomicLocation,sortOption){var self=this,alignmentContainer=this.featureSource.alignmentContainer,alignmentRows=alignmentContainer.packedAlignmentRows;alignmentRows.forEach(function(alignmentRow){alignmentRow.updateScore(genomicLocation,alignmentContainer,sortOption)}),alignmentRows.sort(function(a,b){return self.sortDirection?a.score-b.score:b.score-a.score})},AlignmentTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){var packedAlignmentsIndex,alignmentRow,clickedObject,i,len,tmp,packedAlignmentRows=this.featureSource.alignmentContainer.packedAlignmentRows,downsampledIntervals=this.featureSource.alignmentContainer.downsampledIntervals;if((packedAlignmentsIndex=Math.floor((yOffset-alignmentRowYInset)/this.alignmentRowHeight))<0){for(i=0,len=downsampledIntervals.length;i<len;i++)if(downsampledIntervals[i].start<=genomicLocation&&downsampledIntervals[i].end>=genomicLocation){clickedObject=downsampledIntervals[i];break}}else if(packedAlignmentsIndex<packedAlignmentRows.length)for(alignmentRow=packedAlignmentRows[packedAlignmentsIndex],clickedObject=void 0,i=0,len=alignmentRow.alignments.length,tmp;i<len;i++)if(tmp=alignmentRow.alignments[i],tmp.start<=genomicLocation&&tmp.start+tmp.lengthOnRef>=genomicLocation){clickedObject=tmp;break}return clickedObject?clickedObject.popupData(genomicLocation):[]},igv}(igv||{}),igv=function(igv){var BLOCK_HEADER_LENGTH=18;return igv.unbgzf=function(data,lim){var oBlockList=[],ptr=[0],totalSize=0;for(lim=lim||data.byteLength-18;ptr[0]<lim;){var ba=new Uint8Array(data,ptr[0],18),xlen=ba[11]<<8|ba[10],bsize=(ba[12],ba[13],ba[15],ba[14],ba[17]<<8|ba[16]+1),start=12+xlen+ptr[0],length=data.byteLength-start;if(length<bsize+8)break;var unc=jszlib_inflate_buffer(data,start,length,ptr);ptr[0]+=8,totalSize+=unc.byteLength,oBlockList.push(unc)}if(1==oBlockList.length)return oBlockList[0];for(var out=new Uint8Array(totalSize),cursor=0,i=0;i<oBlockList.length;++i){var b=new Uint8Array(oBlockList[i]);arrayCopy(b,0,out,cursor,b.length),cursor+=b.length}return out.buffer},igv.BGZFile=function(config){this.filePosition=0,this.config=config},igv.BGZFile.prototype.nextBlock=function(){var self=this;return new Promise(function(fulfill,reject){igvxhr.loadArrayBuffer(self.path,{headers:self.config.headers,range:{start:self.filePosition,size:BLOCK_HEADER_LENGTH},withCredentials:self.config.withCredentials}).then(function(arrayBuffer){var ba=new Uint8Array(arrayBuffer),bsize=(ba[11],ba[10],ba[12],ba[13],ba[15],ba[14],ba[17]<<8|ba[16]+1);self.filePosition+=BLOCK_HEADER_LENGTH,igvxhr.loadArrayBuffer(self.path,{headers:self.config.headers,range:{start:self.filePosition,size:bsize},withCredentials:self.config.withCredentials}).then(function(arrayBuffer){var unc=jszlib_inflate_buffer(arrayBuffer);self.filePosition+=bsize+8,fulfill(unc)}).catch(reject)}).catch(reject)})},igv}(igv||{}),igv=function(igv){function Coverage(){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}return igv.CoverageMap=function(chr,start,end,alignments,refSeq){var myself=this;this.refSeq=refSeq,this.chr=chr,this.bpStart=start,this.length=end-start,this.coverage=new Array(this.length),this.maximum=0,alignments.forEach(function(alignment){alignment.blocks.forEach(function(block){var key,base,i,j,q;for(i=block.start-myself.bpStart,j=0;j<block.len;i++,j++)myself.coverage[i]||(myself.coverage[i]=new Coverage),base=block.seq.charAt(j),key=alignment.strand?"pos"+base:"neg"+base,q=block.qual[j],myself.coverage[i][key]+=1,myself.coverage[i]["qual"+base]+=q,myself.coverage[i].total+=1,myself.coverage[i].qual+=q,myself.maximum=Math.max(myself.coverage[i].total,myself.maximum)})})},igv.CoverageMap.threshold=.2,igv.CoverageMap.qualityWeight=!0,Coverage.prototype.isMismatch=function(refBase){var mismatchQualitySum,myself=this,threshold=igv.CoverageMap.threshold*(igv.CoverageMap.qualityWeight&&this.qual?this.qual:this.total);return mismatchQualitySum=0,["A","T","C","G"].forEach(function(base){base!==refBase&&(mismatchQualitySum+=igv.CoverageMap.qualityWeight&&myself.qual?myself["qual"+base]:myself["pos"+base]+myself["neg"+base])}),mismatchQualitySum>=threshold},igv}(igv||{}),igv=function(igv){return igv.PairedAlignment=function(firstAlignment){this.firstAlignment=firstAlignment,this.chr=firstAlignment.chr,this.readName=firstAlignment.readName,firstAlignment.start<firstAlignment.mate.position?(this.start=firstAlignment.start,this.end=Math.max(firstAlignment.mate.position,firstAlignment.start+firstAlignment.lengthOnRef),this.connectingStart=firstAlignment.start+firstAlignment.lengthOnRef,this.connectingEnd=firstAlignment.mate.position):(this.start=firstAlignment.mate.position,this.end=firstAlignment.start+firstAlignment.lengthOnRef,this.connectingStart=firstAlignment.mate.position,this.connectingEnd=firstAlignment.start),this.lengthOnRef=this.end-this.start},igv.PairedAlignment.prototype.setSecondAlignment=function(alignment){this.secondAlignment=alignment,alignment.start>this.firstAlignment.start?(this.end=alignment.start+alignment.lengthOnRef,this.connectingEnd=alignment.start):(this.start=alignment.start,this.connectingStart=alignment.start+alignment.lengthOnRef),this.lengthOnRef=this.end-this.start},igv.PairedAlignment.prototype.popupData=function(genomicLocation){var nameValues=[];return nameValues=nameValues.concat(this.firstAlignment.popupData(genomicLocation)),this.secondAlignment&&(nameValues.push("-------------------------------"),nameValues=nameValues.concat(this.secondAlignment.popupData(genomicLocation))),nameValues},igv.PairedAlignment.prototype.isPaired=function(){return!0},igv.PairedAlignment.prototype.firstOfPairStrand=function(){return this.firstAlignment.isFirstOfPair()?this.firstAlignment.strand:this.secondAlignment?this.secondAlignment.strand:this.firstAlignment.strand},igv}(igv||{}),igv=function(igv){return igv.isb={querySegByStudy:function(study,limit){var q='SELECT * FROM [isb-cgc:tcga_201510_alpha.Copy_Number_segments] WHERE ParticipantBarcode IN (SELECT ParticipantBarcode FROM [isb-cgc:tcga_201510_alpha.Clinical_data] WHERE Study = "'+study+'")';return limit&&(q+=" limit "+limit),q},decodeSeg:function(row){var seg={};return seg.ParticipantBarcode=row.f[0].v,seg.Study=row.f[4].v,seg.Chromosome=row.f[6].v,seg.Start=row.f[7].v,seg.End=row.f[8].v,seg.Num_Probes=row.f[9].v,seg.Segment_mean=row.f[10].v,seg}},igv}(igv||{}),igv=function(igv){return igv.BufferedReader=function(config,contentLength,bufferSize){this.path=config.url,this.contentLength=contentLength,this.bufferSize=bufferSize||512e3,this.range={start:-1,size:-1},this.config=config},igv.BufferedReader.prototype.dataViewForRange=function(requestedRange,asUint8){var self=this;return new Promise(function(fulfill,reject){function subbuffer(bufferedReader,requestedRange,asUint8){var len=bufferedReader.data.byteLength,bufferStart=requestedRange.start-bufferedReader.range.start,result=asUint8?new Uint8Array(bufferedReader.data,bufferStart,len-bufferStart):new DataView(bufferedReader.data,bufferStart,len-bufferStart);fulfill(result)}var bufferSize,loadRange,hasData=self.data&&self.range.start<=requestedRange.start&&self.range.start+self.range.size>=requestedRange.start+requestedRange.size;hasData?subbuffer(self,requestedRange,asUint8):(bufferSize=Math.max(self.bufferSize,requestedRange.size),loadRange=self.contentLength>0&&requestedRange.start+bufferSize>self.contentLength?{start:requestedRange.start}:{start:requestedRange.start,size:bufferSize},igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:loadRange})).then(function(arrayBuffer){self.data=arrayBuffer,self.range=loadRange,subbuffer(self,requestedRange,asUint8)}).catch(reject))})},igv}(igv||{}),igv=function(igv){return igv.BPTree=function(binaryParser,startOffset){function readTreeNode(byteBuffer,offset,keySize,dictionary){offset>=0&&(byteBuffer.position=offset);var i,key,chromId,childOffset,bufferOffset,currOffset,type=byteBuffer.getByte(),count=(byteBuffer.getByte(),byteBuffer.getUShort());if(1==type)for(i=0;i<count;i++)key=byteBuffer.getFixedLengthTrimmedString(keySize),chromId=byteBuffer.getInt(),byteBuffer.getInt(),genome&&(key=genome.getChromosomeName(key)),dictionary[key]=chromId;else for(i=0;i<count;i++)key=byteBuffer.getFixedLengthTrimmedString(keySize),childOffset=byteBuffer.getLong(),bufferOffset=childOffset-startOffset,currOffset=byteBuffer.position,readTreeNode(byteBuffer,bufferOffset,keySize,dictionary),byteBuffer.position=currOffset}var genome=igv.browser?igv.browser.genome:null;this.header={},this.header.magic=binaryParser.getInt(),this.header.blockSize=binaryParser.getInt(),this.header.keySize=binaryParser.getInt(),this.header.valSize=binaryParser.getInt(),this.header.itemCount=binaryParser.getLong(),this.header.reserved=binaryParser.getLong(),this.dictionary={},readTreeNode(binaryParser,-1,this.header.keySize,this.dictionary);this.header.keySize},igv}(igv||{}),igv=function(igv){function RPTreeNode(items){this.items=items;var i,item,minChromId=Number.MAX_VALUE,maxChromId=0,minStartBase=Number.MAX_VALUE,maxEndBase=0;for(i=0;i<items.length;i++)item=items[i],minChromId=Math.min(minChromId,item.startChrom),maxChromId=Math.max(maxChromId,item.endChrom),minStartBase=Math.min(minStartBase,item.startBase),maxEndBase=Math.max(maxEndBase,item.endBase);this.startChrom=minChromId,this.endChrom=maxChromId,this.startBase=minStartBase,this.endBase=maxEndBase}function overlaps(item,chrIdx,startBase,endBase){return item?(chrIdx>item.startChrom||chrIdx==item.startChrom&&endBase>=item.startBase)&&(chrIdx<item.endChrom||chrIdx==item.endChrom&&startBase<item.endBase):(console.log("null item"),!1)}var RPTREE_HEADER_SIZE=48,RPTREE_NODE_LEAF_ITEM_SIZE=32;RPTREE_NODE_CHILD_ITEM_SIZE=24;var BUFFER_SIZE=512e3;return igv.RPTree=function(fileOffset,contentLength,config,littleEndian){this.config=config,this.filesize=contentLength,this.fileOffset=fileOffset,this.path=config.url,this.littleEndian=littleEndian},igv.RPTree.prototype.load=function(){var self=this;return new Promise(function(fulfill,reject){var rootNodeOffset=self.fileOffset+RPTREE_HEADER_SIZE,bufferedReader=new igv.BufferedReader(self.config,self.filesize,BUFFER_SIZE);self.readNode(rootNodeOffset,bufferedReader).then(function(node){self.rootNode=node,fulfill(self)}).catch(reject)})},igv.RPTree.prototype.readNode=function(filePosition,bufferedReader){var self=this;return new Promise(function(fulfill,reject){bufferedReader.dataViewForRange({start:filePosition,size:4},!1).then(function(dataView){var binaryParser=new igv.BinaryParser(dataView,self.littleEndian),type=binaryParser.getByte(),isLeaf=1===type,count=(binaryParser.getByte(),binaryParser.getUShort());filePosition+=4;var bytesRequired=count*(isLeaf?RPTREE_NODE_LEAF_ITEM_SIZE:RPTREE_NODE_CHILD_ITEM_SIZE),range2={start:filePosition,size:bytesRequired};bufferedReader.dataViewForRange(range2,!1).then(function(dataView){var i,items=new Array(count),binaryParser=new igv.BinaryParser(dataView);if(isLeaf){for(i=0;i<count;i++){var item={isLeaf:!0,startChrom:binaryParser.getInt(),startBase:binaryParser.getInt(),endChrom:binaryParser.getInt(),endBase:binaryParser.getInt(),dataOffset:binaryParser.getLong(),dataSize:binaryParser.getLong()};items[i]=item}fulfill(new RPTreeNode(items))}else{for(i=0;i<count;i++){var item={isLeaf:!1,startChrom:binaryParser.getInt(),startBase:binaryParser.getInt(),endChrom:binaryParser.getInt(),endBase:binaryParser.getInt(),childOffset:binaryParser.getLong()};items[i]=item}fulfill(new RPTreeNode(items))}}).catch(reject)}).catch(reject)})},igv.RPTree.prototype.findLeafItemsOverlapping=function(chrIdx,startBase,endBase){var self=this;return new Promise(function(fulfill,reject){function findLeafItems(node,nodeId){if(overlaps(node,chrIdx,startBase,endBase)){node.items.forEach(function(item){overlaps(item,chrIdx,startBase,endBase)&&(item.isLeaf?leafItems.push(item):item.childNode?findLeafItems(item.childNode):(processing.add(item.childOffset),self.readNode(item.childOffset,bufferedReader).then(function(node){item.childNode=node,findLeafItems(node,item.childOffset)}).catch(reject)))})}void 0!=nodeId&&processing.delete(nodeId),processing.isEmpty()&&fulfill(leafItems)}var leafItems=[],processing=new Set,bufferedReader=new igv.BufferedReader(self.config,self.filesize,BUFFER_SIZE);processing.add(0),findLeafItems(self.rootNode,0)})},igv}(igv||{}),igv=function(igv){function loadZoomHeadersAndChrTree(){var startOffset=BBFILE_HEADER_SIZE,self=this;return new Promise(function(fulfill,reject){var range={start:startOffset,size:self.header.fullDataOffset-startOffset+5};igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:range})).then(function(data){var i,zoomNumber,zlh,nZooms=self.header.nZoomLevels,binaryParser=new igv.BinaryParser(new DataView(data));for(self.zoomLevelHeaders=[],self.firstZoomDataOffset=Number.MAX_VALUE,i=0;i<nZooms;i++)zoomNumber=nZooms-i,zlh=new ZoomLevelHeader(zoomNumber,binaryParser),self.firstZoomDataOffset=Math.min(zlh.dataOffset,self.firstZoomDataOffset),self.zoomLevelHeaders.push(zlh);self.header.autoSqlOffset>0&&(binaryParser.position=self.header.autoSqlOffset-startOffset,self.autoSql=binaryParser.getString()),self.header.totalSummaryOffset>0&&(binaryParser.position=self.header.totalSummaryOffset-startOffset,self.totalSummary=new igv.BWTotalSummary(binaryParser)),self.header.chromTreeOffset>0&&(binaryParser.position=self.header.chromTreeOffset-startOffset,self.chromTree=new igv.BPTree(binaryParser,startOffset)),binaryParser.position=self.header.fullDataOffset-startOffset,self.dataCount=binaryParser.getInt(),fulfill()}).catch(reject)})}var BBFILE_HEADER_SIZE=64;igv.BWReader=function(config){this.path=config.url,this.headPath=config.headURL||this.path,this.rpTreeCache={},this.config=config},igv.BWReader.prototype.getZoomHeaders=function(){var self=this;return new Promise(function(fulfill,reject){self.zoomLevelHeaders?fulfill(self.zoomLevelHeaders):self.loadHeader().then(function(){fulfill(self.zoomLevelHeaders)}).catch(function(error){reject(error)})})},igv.BWReader.prototype.loadHeader=function(){var self=this;return new Promise(function(fulfill,reject){igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:0,size:BBFILE_HEADER_SIZE}})).then(function(data){if(data){self.littleEndian=!0;var binaryParser=new igv.BinaryParser(new DataView(data)),magic=binaryParser.getUInt();if(2291137574===magic)self.type="BigWig";else if(2273964779==magic)self.type="BigBed";else{self.littleEndian=!1,binaryParser.littleEndian=!1,binaryParser.position=0;var magic=binaryParser.getUInt();654085990===magic?self.type="BigWig":3958540679==magic&&(self.type="BigBed")}self.header={},self.header.bwVersion=binaryParser.getUShort(),self.header.nZoomLevels=binaryParser.getUShort(),self.header.chromTreeOffset=binaryParser.getLong(),self.header.fullDataOffset=binaryParser.getLong(),self.header.fullIndexOffset=binaryParser.getLong(),self.header.fieldCount=binaryParser.getUShort(),self.header.definedFieldCount=binaryParser.getUShort(),self.header.autoSqlOffset=binaryParser.getLong(),self.header.totalSummaryOffset=binaryParser.getLong(),self.header.uncompressBuffSize=binaryParser.getInt(),self.header.reserved=binaryParser.getLong(),loadZoomHeadersAndChrTree.call(self).then(fulfill).catch(reject)}}).catch(function(error){reject(error)})})},igv.BWReader.prototype.loadRPTree=function(offset){var self=this;return new Promise(function(fulfill,reject){var rpTree=self.rpTreeCache[offset];rpTree?fulfill(rpTree):(rpTree=new igv.RPTree(offset,self.contentLength,self.config,self.littleEndian),self.rpTreeCache[offset]=rpTree,rpTree.load().then(function(){fulfill(rpTree)}).catch(reject))})};var ZoomLevelHeader=function(index,byteBuffer){this.index=index,this.reductionLevel=byteBuffer.getInt(),this.reserved=byteBuffer.getInt(),this.dataOffset=byteBuffer.getLong(),this.indexOffset=byteBuffer.getLong()};return igv}(igv||{}),igv=function(igv){function zoomLevelForScale(bpPerPixel,zoomLevelHeaders){var i,zl,level=null;for(i=0;i<zoomLevelHeaders.length;i++)if(zl=zoomLevelHeaders[i],zl.reductionLevel>bpPerPixel){level=zl;break}return null==level&&(level=zoomLevelHeaders[zoomLevelHeaders.length-1]),level&&level.reductionLevel<4*bpPerPixel?level:null}function decodeWigData(data,chr,chrIdx,bpStart,bpEnd,featureArray){var value,binaryParser=new igv.BinaryParser(data),chromId=binaryParser.getInt(),chromStart=binaryParser.getInt(),chromEnd=binaryParser.getInt(),itemStep=binaryParser.getInt(),itemSpan=binaryParser.getInt(),type=binaryParser.getByte(),itemCount=(binaryParser.getByte(),binaryParser.getUShort());if(chromId===chrIdx)for(;itemCount-- >0;){switch(type){case 1:chromStart=binaryParser.getInt(),chromEnd=binaryParser.getInt(),value=binaryParser.getFloat();break;case 2:chromStart=binaryParser.getInt(),value=binaryParser.getFloat(),chromEnd=chromStart+itemSpan;break;case 3:value=binaryParser.getFloat(),chromEnd=chromStart+itemSpan,chromStart+=itemStep}if(chromStart>=bpEnd)break;chromEnd>bpStart&&Number.isFinite(value)&&featureArray.push({chr:chr,start:chromStart,end:chromEnd,value:value})}}function decodeZoomData(data,chr,chrIdx,bpStart,bpEnd,featureArray){for(var chromStart,chromEnd,validCount,sumData,value,binaryParser=new igv.BinaryParser(data),minSize=32;binaryParser.remLength()>=minSize;)if(binaryParser.getInt()===chrIdx){if(chromStart=binaryParser.getInt(),chromEnd=binaryParser.getInt(),validCount=binaryParser.getInt(),binaryParser.getFloat(),binaryParser.getFloat(),sumData=binaryParser.getFloat(),binaryParser.getFloat(),value=0==validCount?0:sumData/validCount,chromStart>=bpEnd)break;chromEnd>bpStart&&Number.isFinite(value)&&featureArray.push({chr:chr,start:chromStart,end:chromEnd,value:value})}}function decodeBedData(data,chr,chrIdx,bpStart,bpEnd,featureArray){for(var chromStart,chromEnd,rest,tokens,feature,exonCount,exonSizes,exonStarts,exons,eStart,eEnd,binaryParser=new igv.BinaryParser(data),minSize=13;binaryParser.remLength()>=minSize;)if(binaryParser.getInt()==chrIdx&&(chromStart=binaryParser.getInt(),chromEnd=binaryParser.getInt(),rest=binaryParser.getString(),feature={chr:chr,start:chromStart,end:chromEnd},chromStart<bpEnd&&chromEnd>=bpStart&&(featureArray.push(feature),tokens=rest.split("\t"),tokens.length>0&&(feature.name=tokens[0]),tokens.length>1&&(feature.score=parseFloat(tokens[1])),tokens.length>2&&(feature.strand=tokens[2]),tokens.length>3&&(feature.cdStart=parseInt(tokens[3])),tokens.length>4&&(feature.cdEnd=parseInt(tokens[4])),tokens.length>5&&"."!==tokens[5]&&"0"!==tokens[5]&&(feature.color=igv.createColorString(tokens[5])),tokens.length>8))){exonCount=parseInt(tokens[6]),exonSizes=tokens[7].split(","),exonStarts=tokens[8].split(","),exons=[];for(var i=0;i<exonCount;i++)eStart=start+parseInt(exonStarts[i]),eEnd=eStart+parseInt(exonSizes[i]),exons.push({start:eStart,end:eEnd});feature.exons=exons}}return igv.BWSource=function(config){this.reader=new igv.BWReader(config),this.bufferedReader=new igv.BufferedReader(config)},igv.BWSource.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){self.reader.getZoomHeaders().then(function(zoomLevelHeaders){var treeOffset,decodeFunction,bwReader=self.reader,bufferedReader=self.bufferedReader,bpPerPixel=igv.browser.referenceFrame.bpPerPixel,zoomLevelHeader=zoomLevelForScale(bpPerPixel,zoomLevelHeaders);zoomLevelHeader?(treeOffset=zoomLevelHeader.indexOffset,decodeFunction=decodeZoomData):(treeOffset=bwReader.header.fullIndexOffset,decodeFunction="BigWig"===bwReader.type?decodeWigData:decodeBedData),bwReader.loadRPTree(treeOffset).then(function(rpTree){var chrIdx=self.reader.chromTree.dictionary[chr];void 0===chrIdx?fulfill(null):rpTree.findLeafItemsOverlapping(chrIdx,bpStart,bpEnd).then(function(leafItems){var promises=[];leafItems&&0!=leafItems.length||fulfill([]),leafItems.forEach(function(item){promises.push(new Promise(function(fulfill,reject){var features=[];bufferedReader.dataViewForRange({start:item.dataOffset,size:item.dataSize},!0).then(function(uint8Array){var inflate=new Zlib.Inflate(uint8Array),plain=inflate.decompress();decodeFunction(new DataView(plain.buffer),chr,chrIdx,bpStart,bpEnd,features),fulfill(features)}).catch(reject)}))}),Promise.all(promises).then(function(featureArrays){var i,allFeatures=featureArrays[0];if(featureArrays.length>1)for(i=1;i<featureArrays.length;i++)allFeatures=allFeatures.concat(featureArrays[i]);allFeatures.sort(function(a,b){return a.start-b.start}),fulfill(allFeatures)}).catch(reject)}).catch(reject)}).catch(reject)}).catch(reject)})},igv.BWSource.prototype.getDefaultRange=function(){return void 0!=this.reader.totalSummary?this.reader.totalSummary.defaultRange:void 0},igv}(igv||{}),igv=function(igv){function computeStats(){var n=this.basesCovered;if(n>0){this.mean=this.sumData/n,this.stddev=Math.sqrt(this.sumSquares/(n-1));this.minVal<0&&(this.mean,this.stddev),this.maxVal>0&&(this.mean,this.stddev);this.defaultRange={min:0,max:this.mean+3*this.stddev}}}return igv.BWTotalSummary=function(byteBuffer){byteBuffer?(this.basesCovered=byteBuffer.getLong(),this.minVal=byteBuffer.getDouble(),this.maxVal=byteBuffer.getDouble(),this.sumData=byteBuffer.getDouble(),this.sumSquares=byteBuffer.getDouble(),computeStats.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)},igv.BWTotalSummary.prototype.updateStats=function(stats){this.basesCovered+=stats.count,this.sumData+=status.sumData,this.sumSquares+=sumSquares,this.minVal=MIN(_minVal,min),this.maxVal=MAX(_maxVal,max),computeStats.call(this)},igv}(igv||{}),igv=function(igv){function VPointer(block,offset){this.block=block,this.offset=offset}return igv.BinaryParser=function(dataView,littleEndian){this.littleEndian=littleEndian||!0,this.position=0,this.view=dataView,this.length=dataView.byteLength},igv.BinaryParser.prototype.available=function(){return this.length-this.position},igv.BinaryParser.prototype.remLength=function(){return this.length-this.position},igv.BinaryParser.prototype.hasNext=function(){return this.position<this.length-1},igv.BinaryParser.prototype.getByte=function(){var retValue=this.view.getUint8(this.position,this.littleEndian);return this.position++,retValue},igv.BinaryParser.prototype.getShort=function(){var retValue=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,retValue},igv.BinaryParser.prototype.getUShort=function(){var retValue=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,retValue},igv.BinaryParser.prototype.getInt=function(){var retValue=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,retValue},igv.BinaryParser.prototype.getUInt=function(){var retValue=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,retValue},igv.BinaryParser.prototype.getLong=function(){var b=[];b[0]=this.view.getUint8(this.position),b[1]=this.view.getUint8(this.position+1),b[2]=this.view.getUint8(this.position+2),b[3]=this.view.getUint8(this.position+3),b[4]=this.view.getUint8(this.position+4),b[5]=this.view.getUint8(this.position+5),b[6]=this.view.getUint8(this.position+6),b[7]=this.view.getUint8(this.position+7);var value=0;if(this.littleEndian)for(var i=b.length-1;i>=0;i--)value=256*value+b[i];else for(var i=0;i<b.length;i++)value=256*value+b[i];return this.position+=8,value},igv.BinaryParser.prototype.getString=function(len){for(var c,s="";0!=(c=this.view.getUint8(this.position++))&&(s+=String.fromCharCode(c),!len||s.length!=len););return s},igv.BinaryParser.prototype.getFixedLengthString=function(len){var i,c,s="";for(i=0;i<len;i++)(c=this.view.getUint8(this.position++))>0&&(s+=String.fromCharCode(c));return s},igv.BinaryParser.prototype.getFixedLengthTrimmedString=function(len){var i,c,s="";for(i=0;i<len;i++)(c=this.view.getUint8(this.position++))>32&&(s+=String.fromCharCode(c));return s},igv.BinaryParser.prototype.getFloat=function(){var retValue=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,retValue},igv.BinaryParser.prototype.getDouble=function(){var retValue=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,retValue},igv.BinaryParser.prototype.skip=function(n){return this.position+=n,this.position},igv.BinaryParser.prototype.getVPointer=function(){var position=this.position,offset=this.view.getUint8(position+1)<<8|this.view.getUint8(position),byte6=4294967296*(255&this.view.getUint8(position+6)),byte5=16777216*(255&this.view.getUint8(position+5)),byte4=65536*(255&this.view.getUint8(position+4)),byte3=256*(255&this.view.getUint8(position+3)),byte2=255&this.view.getUint8(position+2),block=byte6+byte5+byte4+byte3+byte2;return this.position+=8,new VPointer(block,offset)},VPointer.prototype.isLessThan=function(vp){return this.block<vp.block||this.block===vp.block&&this.offset<vp.offset},VPointer.prototype.isGreaterThan=function(vp){return this.block>vp.block||this.block===vp.block&&this.offset>vp.offset},VPointer.prototype.print=function(){return this.block+":"+this.offset},igv}(igv||{}),igv=function(igv){function initialize(options){var genomeId;this.flanking=options.flanking,this.type=options.type||"IGV",this.crossDomainProxy=options.crossDomainProxy,this.formats=options.formats,this.trackDefaults=options.trackDefaults,options.search?this.searchConfig={type:"json",url:options.search.url,coords:void 0===options.search.coords?1:options.search.coords,chromosomeField:options.search.chromosomeField||"chromosome",startField:options.search.startField||"start",endField:options.search.endField||"end",resultsField:options.search.resultsField}:(genomeId=options.reference&&options.reference.id?options.reference.id:options.genome?options.genome:"hg19",this.searchConfig={type:"plain",url:"https://portals.broadinstitute.org/webservices/igv/locus?genome="+genomeId+"&name=$FEATURE$",coords:0,chromosomeField:"chromosome",startField:"start",endField:"end"})}function gotoLocusFeature(locusFeature,genome,browser){function validateLocusExtent(browser,chromosome,extent){var ss=extent.start,ee=extent.end;void 0===ee?(ss-=igv.browser.minimumBasesExtent()/2,ee=ss+igv.browser.minimumBasesExtent(),ee>chromosome.bpLength?(ee=chromosome.bpLength,ss=ee-igv.browser.minimumBasesExtent()):ss<0&&(ss=0,ee=igv.browser.minimumBasesExtent())):ee-ss<igv.browser.minimumBasesExtent()&&(center=(ee+ss)/2,center-igv.browser.minimumBasesExtent()/2<0?(ss=0,ee=ss+igv.browser.minimumBasesExtent()):center+igv.browser.minimumBasesExtent()/2>chromosome.bpLength?(ee=chromosome.bpLength,ss=ee-igv.browser.minimumBasesExtent()):(ss=center-igv.browser.minimumBasesExtent()/2,ee=ss+igv.browser.minimumBasesExtent())),extent.start=Math.ceil(ss),extent.end=Math.floor(ee)}var type,tokens,chr,start,end,chrName,startEnd,center,obj;return type="locus",tokens=locusFeature.split(":"),chrName=genome.getChromosomeName(tokens[0]),chrName&&(chr=genome.getChromosome(chrName)),chr&&(start=end=void 0,1===tokens.length?(start=0,end=chr.bpLength):(startEnd=tokens[1].split("-"),start=Math.max(0,parseInt(startEnd[0].replace(/,/g,""))-1),2===startEnd.length&&(end=Math.min(chr.bpLength,parseInt(startEnd[1].replace(/,/g,""))))<0&&(end=chr.bpLength)),obj={start:start,end:end},validateLocusExtent(igv.browser,chr,obj),start=obj.start,end=obj.end),void 0===chr||isNaN(start)||start>end?(igv.presentAlert("Unrecognized feature or locus: "+locusFeature),!1):(browser.goto(chrName,start,end),fireOnsearch.call(igv.browser,locusFeature,type),!0)}function parseSearchResults(data){var lines=data.splitLines(),linesTrimmed=[],results=[];return lines.forEach(function(item){""===item||linesTrimmed.push(item)}),linesTrimmed.forEach(function(line){var source,locusTokens,rangeTokens,tokens=line.split("\t");tokens.length>=3&&(locusTokens=tokens[1].split(":"),rangeTokens=locusTokens[1].split("-"),source=tokens[2].trim(),results.push({chromosome:igv.browser.genome.getChromosomeName(locusTokens[0].trim()),start:parseInt(rangeTokens[0].replace(/,/g,"")),end:parseInt(rangeTokens[1].replace(/,/g,"")),type:"gtex"===source?"snp":"gene"}))}),results}function handleSearchResult(name,chr,start,end,type){igv.browser.selection=new igv.GtexSelection("gtex"===type||"snp"===type?{snp:name}:{gene:name}),void 0===end&&(end=start+1),igv.browser.flanking&&(start=Math.max(0,start-igv.browser.flanking),end+=igv.browser.flanking),igv.browser.goto(chr,start,end),fireOnsearch.call(igv.browser,name,type)}function fireOnsearch(feature,type){this.trackViews.forEach(function(tp){var track=tp.track;track.onsearch&&track.onsearch(feature,type)})}function addTrackContainerHandlers(trackContainerDiv){function mouseUpOrOut(e){igv.browser.$cursorTrackingGuide.get(0);isRulerTrack||igv.browser.$cursorTrackingGuide&&e.toElement===igv.browser.$cursorTrackingGuide.get(0)&&"mouseleave"===e.type||(isDragging&&(igv.browser.fireEvent("trackdragend"),isDragging=!1),mouseDownX=void 0,isMouseDown=!1,lastMouseX=void 0)}var isRulerTrack=!1,isMouseDown=!1,isDragging=!1,lastMouseX=void 0,mouseDownX=void 0;$(trackContainerDiv).mousedown(function(e){var coords=igv.translateMouseCoordinates(e,trackContainerDiv);igv.popover&&igv.popover.hide(),(isRulerTrack=!!$(e.target).parent().parent().parent()[0].dataset.rulerTrack)||(isMouseDown=!0,lastMouseX=coords.x,mouseDownX=lastMouseX)}),$(trackContainerDiv).mousemove(function(e){var xy,_left,$element=igv.browser.$cursorTrackingGuide;xy=igv.translateMouseCoordinates(e,trackContainerDiv),_left=Math.max(50,xy.x-5),_left=Math.min(igv.browser.trackContainerDiv.clientWidth-65,_left),$element.css({left:_left+"px"})}),$(trackContainerDiv).mousemove(igv.throttle(function(e){var maxEnd,maxStart,coords=igv.translateMouseCoordinates(e,trackContainerDiv),referenceFrame=igv.browser.referenceFrame;if(!isRulerTrack&&referenceFrame&&isMouseDown){if(mouseDownX&&Math.abs(coords.x-mouseDownX)>igv.browser.constants.dragThreshold){if(igv.browser.loadInProgress())return;isDragging=!0,referenceFrame.shiftPixels(lastMouseX-coords.x),referenceFrame.start=Math.max(0,referenceFrame.start);maxEnd=igv.browser.genome.getChromosome(referenceFrame.chr).bpLength,maxStart=maxEnd-igv.browser.trackViewportWidth()*referenceFrame.bpPerPixel,referenceFrame.start>maxStart&&(referenceFrame.start=maxStart),igv.browser.updateLocusSearch(referenceFrame),igv.browser.repaint(),igv.browser.fireEvent("trackdrag")}lastMouseX=coords.x}},10)),$(trackContainerDiv).mouseup(mouseUpOrOut),$(trackContainerDiv).mouseleave(mouseUpOrOut)}function inferTypes(config){function translateDeprecatedTypes(config){config.featureType&&(config.type=config.type||config.featureType,config.featureType=void 0),"bed"===config.type?(config.type="annotation",config.format=config.format||"bed"):"bam"===config.type?(config.type="alignment",config.format="bam"):"vcf"===config.type?(config.type="variant",config.format="vcf"):"t2d"===config.type?config.type="gwas":"FusionJuncSpan"===config.type&&(config.format="fusionjuncspan")}function inferFileFormat(config){if(config.format)return void(config.format=config.format.toLowerCase());var idx,ext,path=config.url||config.localFile.name,fn=path.toLowerCase();switch(idx=fn.indexOf("?"),idx>0&&(fn=fn.substr(0,idx)),fn.endsWith(".gz")?fn=fn.substr(0,fn.length-3):(fn.endsWith(".txt")||fn.endsWith(".tab"))&&(fn=fn.substr(0,fn.length-4)),idx=fn.lastIndexOf("."),ext=idx<0?fn:fn.substr(idx+1),ext.toLowerCase()){case"bw":config.format="bigwig";break;case"bb":config.format="bigbed";default:knownFileTypes.has(ext)&&(config.format=ext)}}function inferTrackType(config){if(!config.type&&void 0!==config.format)switch(config.format.toLowerCase()){case"bw":case"bigwig":case"wig":case"bedgraph":case"tdf":config.type="wig";break;case"vcf":config.type="variant";break;case"seg":config.type="seg";break;case"bam":config.type="alignment";break;default:config.type="annotation"}}translateDeprecatedTypes(config),void 0===config.sourceType&&(config.url||config.localFile)&&(config.sourceType="file"),"file"===config.sourceType&&void 0===config.format&&inferFileFormat(config),void 0===config.type&&inferTrackType(config)}var knownFileTypes=new Set(["narrowpeak","broadpeak","peaks","bedgraph","wig","gff3","gff","gtf","aneu","fusionjuncspan","refflat","seg","bed","vcf","bb","bigbed","bw","bigwig","bam","tdf"]);return igv.Browser=function(options,trackContainer){igv.browser=this,this.config=options,this.div=$('<div id="igvRootDiv" class="igv-root-div">')[0],initialize.call(this,options),$("input[id='trackHeightInput']").val(this.trackHeight),this.trackContainerDiv=trackContainer,addTrackContainerHandlers(trackContainer),this.trackViews=[],this.trackLabelsVisible=!0,this.featureDB={},this.constants={dragThreshold:3,defaultColor:"rgb(0,0,150)",doubleClickDelay:options.doubleClickDelay||500},this.eventHandlers={},window.onresize=igv.throttle(function(){igv.browser.resize()},10)},igv.Browser.prototype.getFormat=function(name){if(void 0!==this.formats)return this.formats[name]},igv.Browser.prototype.loadTracksWithConfigList=function(configList){var self=this,loadedTracks=[];return configList.forEach(function(config){loadedTracks.push(self.loadTrack(config))}),this.trackViews.forEach(function(trackView){trackView.resize()}),loadedTracks},igv.Browser.prototype.loadTrack=function(config){var settings,property,newTrack,featureSource,self=this;if(inferTypes(config),this.trackDefaults&&config.type&&(settings=this.trackDefaults[config.type]))for(property in settings)settings.hasOwnProperty(property)&&void 0===config[property]&&(config[property]=settings[property]);switch(void 0===config.type?"":config.type.toLowerCase()){case"gwas":newTrack=new igv.GWASTrack(config);break;case"annotation":case"genes":case"fusionjuncspan":newTrack=new igv.FeatureTrack(config);break;case"variant":newTrack=new igv.VariantTrack(config);break;case"alignment":newTrack=new igv.BAMTrack(config,featureSource);break;case"data":case"wig":newTrack=new igv.WIGTrack(config);break;case"sequence":newTrack=new igv.SequenceTrack(config);break;case"eqtl":newTrack=new igv.EqtlTrack(config);break;case"seg":newTrack=new igv.SegTrack(config);break;case"aneu":newTrack=new igv.AneuTrack(config);break;default:return igv.presentAlert("Unknown file type: "+config.url),null}return void 0===newTrack.order&&(newTrack.order=this.trackViews.length),"function"==typeof newTrack.getFileHeader?newTrack.getFileHeader().then(function(header){self.addTrack(newTrack)}).catch(function(error){igv.presentAlert(error)}):self.addTrack(newTrack),newTrack},igv.Browser.prototype.addTrack=function(track){var trackView=new igv.TrackView(track,this);void 0!==igv.popover&&igv.popover.hide(),track.trackView=trackView,this.trackViews.push(trackView),this.reorderTracks(),trackView.resize()},igv.Browser.prototype.reorderTracks=function(){var myself=this;this.trackViews.sort(function(a,b){return(a.track.order||0)-(b.track.order||0)}),$(this.trackContainerDiv).children("igv-track-div").detach(),this.trackViews.forEach(function(trackView,index,trackViews){myself.trackContainerDiv.appendChild(trackView.trackDiv)})},igv.Browser.prototype.removeTrack=function(track){for(var trackPanelRemoved,i=0;i<this.trackViews.length;i++)if(track===this.trackViews[i].track){trackPanelRemoved=this.trackViews[i];break}trackPanelRemoved&&(this.trackViews.splice(i,1),this.trackContainerDiv.removeChild(trackPanelRemoved.trackDiv),this.fireEvent("trackremoved",[trackPanelRemoved.track]))},igv.Browser.prototype.reduceTrackOrder=function(trackView){var raisable,raiseableOrder,indices=[];1!==this.trackViews.length&&(this.trackViews.forEach(function(tv,i,tvs){indices.push({trackView:tv,index:i}),trackView===tv&&(raisable=indices[i])}),0!==raisable.index&&(raiseableOrder=raisable.trackView.track.order,raisable.trackView.track.order=indices[raisable.index-1].trackView.track.order,indices[raisable.index-1].trackView.track.order=raiseableOrder,this.reorderTracks()))},igv.Browser.prototype.increaseTrackOrder=function(trackView){var raisable,raiseableOrder,indices=[];1!==this.trackViews.length&&(this.trackViews.forEach(function(tv,i,tvs){indices.push({trackView:tv,index:i}),trackView===tv&&(raisable=indices[i])}),this.trackViews.length-1!==raisable.index&&(raiseableOrder=raisable.trackView.track.order,raisable.trackView.track.order=indices[1+raisable.index].trackView.track.order,indices[1+raisable.index].trackView.track.order=raiseableOrder,this.reorderTracks()))},igv.Browser.prototype.setTrackHeight=function(newHeight){this.trackHeight=newHeight,this.trackViews.forEach(function(panel){panel.setTrackHeight(newHeight)})},igv.Browser.prototype.resize=function(){this.ideoPanel&&this.ideoPanel.resize(),this.karyoPanel&&this.karyoPanel.resize(),this.trackViews.forEach(function(panel){panel.resize()})},igv.Browser.prototype.repaint=function(){this.ideoPanel&&this.ideoPanel.repaint(),this.karyoPanel&&this.karyoPanel.repaint(),this.trackViews.forEach(function(trackView){trackView.repaint()})},igv.Browser.prototype.update=function(){this.updateLocusSearch(this.referenceFrame),this.centerGuide&&this.centerGuide.repaint(),this.ideoPanel&&this.ideoPanel.repaint(),this.karyoPanel&&this.karyoPanel.repaint(),this.trackViews.forEach(function(trackPanel){trackPanel.update()})},igv.Browser.prototype.loadInProgress=function(){var i;for(i=0;i<this.trackViews.length;i++)if(this.trackViews[i].loading)return!0;return!1},igv.Browser.prototype.updateLocusSearch=function(referenceFrame){var chr,ss,ee,str,end,chromosome;this.$searchInput&&(chr=referenceFrame.chr,ss=igv.numberFormatter(Math.floor(referenceFrame.start+1)),end=referenceFrame.start+this.trackViewportWidthBP(),this.genome&&(chromosome=this.genome.getChromosome(chr))&&(end=Math.min(end,chromosome.bpLength)),ee=igv.numberFormatter(Math.floor(end)),str=chr+":"+ss+"-"+ee,this.$searchInput.val(str),this.windowSizePanel.update(Math.floor(end-referenceFrame.start))),this.fireEvent("locuschange",[referenceFrame,str])},igv.Browser.prototype.trackViewportWidth=function(){return this.trackViews&&this.trackViews.length>0?this.trackViews[0].viewportDiv.clientWidth:this.trackContainerDiv.clientWidth-100},igv.Browser.prototype.trackViewportWidthBP=function(){return this.referenceFrame.bpPerPixel*this.trackViewportWidth()},igv.Browser.prototype.minimumBasesExtent=function(){return 40},igv.Browser.prototype.removeAllTracks=function(){for(var tracks=this.trackViews,i=0;i<tracks.length;i++){var track=this.trackViews[i].track;this.removeTrack(track)}},igv.Browser.prototype.setGotoCallback=function(gotocallback){this.gotocallback=gotocallback},igv.Browser.prototype.goto=function(chr,start,end){void 0!==this.gotocallback&&this.gotocallback(chr,start,end);var w,chromosome,viewportWidth=this.trackViewportWidth();if(igv.popover&&igv.popover.hide(),this.genome&&(chr=this.genome.getChromosomeName(chr)),this.referenceFrame.chr=chr,end?this.referenceFrame.bpPerPixel=(end-start)/viewportWidth:(w=Math.round(viewportWidth*this.referenceFrame.bpPerPixel/2),start=Math.max(0,start-w)),this.genome)if(chromosome=this.genome.getChromosome(this.referenceFrame.chr)){chromosome.bpLength||(chromosome.bpLength=1);var maxBpPerPixel=chromosome.bpLength/viewportWidth;this.referenceFrame.bpPerPixel>maxBpPerPixel&&(this.referenceFrame.bpPerPixel=maxBpPerPixel),end||(end=start+viewportWidth*this.referenceFrame.bpPerPixel),chromosome&&end>chromosome.bpLength&&(start-=end-chromosome.bpLength)}else console&&console.log&&console.log("Could not find chromsome "+this.referenceFrame.chr);this.referenceFrame.start=start,this.update()},igv.Browser.prototype.zoomIn=function(){function basesExtent(width,bpp){return Math.floor(width*bpp)}if(!this.loadInProgress()){var centerBP;if(console.log("browser.zoomIn - src extent "+basesExtent(this.trackViewportWidth(),this.referenceFrame.bpPerPixel)),this.minimumBasesExtent()>basesExtent(this.trackViewportWidth(),this.referenceFrame.bpPerPixel/2))return void console.log("browser.zoomIn - dst extent "+basesExtent(this.trackViewportWidth(),this.referenceFrame.bpPerPixel/2)+" bailing ...");console.log("browser.zoomIn - dst extent "+basesExtent(this.trackViewportWidth(),this.referenceFrame.bpPerPixel/2)),centerBP=this.referenceFrame.start+this.referenceFrame.bpPerPixel*(this.trackViewportWidth()/2),this.referenceFrame.start=centerBP-this.trackViewportWidth()/2*(this.referenceFrame.bpPerPixel/2),this.referenceFrame.bpPerPixel/=2,this.update()}},igv.Browser.prototype.zoomOut=function(){if(!this.loadInProgress()){var newScale,maxScale,center,chrLength,widthBP,viewportWidth;if(viewportWidth=this.trackViewportWidth(),newScale=2*this.referenceFrame.bpPerPixel,chrLength=25e7,this.genome){var chromosome=this.genome.getChromosome(this.referenceFrame.chr);chromosome&&(chrLength=chromosome.bpLength)}maxScale=chrLength/viewportWidth,newScale>maxScale&&(newScale=maxScale),center=this.referenceFrame.start+this.referenceFrame.bpPerPixel*viewportWidth/2,widthBP=newScale*viewportWidth,this.referenceFrame.start=Math.round(center-widthBP/2),this.referenceFrame.start<0?this.referenceFrame.start=0:this.referenceFrame.start>chrLength-widthBP&&(this.referenceFrame.start=chrLength-widthBP),this.referenceFrame.bpPerPixel=newScale,this.update()}},igv.Browser.prototype.search=function(feature,callback,force){function isLocusFeature(f,genome){return 2===f.split(":").length||!!genome.getChromosome(f)}var type,chr,start,end,searchConfig,url,result;if(void 0===igv.browser||void 0===igv.browser.genome)return igv.browser.initialLocus=feature,void(callback&&callback());if(isLocusFeature(feature,this.genome,force)){var success=gotoLocusFeature(feature,this.genome,this);(force||!0===success)&&callback&&callback()}else if(result=this.featureDB[feature.toUpperCase()])handleSearchResult(result.name,result.chr,result.start,result.end,"");else if(this.searchConfig){if(url=this.searchConfig.url.replace("$FEATURE$",feature),searchConfig=this.searchConfig,url.indexOf("$GENOME$")>-1){var genomeId=this.genome.id?this.genome.id:"hg19";url.replace("$GENOME$",genomeId)}igvxhr.loadString(url).then(function(data){var results="plain"===searchConfig.type?parseSearchResults(data):JSON.parse(data);searchConfig.resultsField&&(results=results[searchConfig.resultsField]),0==results.length?igv.presentAlert('No feature found with name "'+feature+'"'):(r=results[0],chr=r[searchConfig.chromosomeField],start=r[searchConfig.startField]-searchConfig.coords,end=r[searchConfig.endField],type=r.featureType||r.type,handleSearchResult(feature,chr,start,end,type)),callback&&callback()})}},igv.Browser.prototype.on=function(eventName,fn){this.eventHandlers[eventName]||(this.eventHandlers[eventName]=[]),this.eventHandlers[eventName].push(fn)},igv.Browser.prototype.un=function(eventName,fn){if(this.eventHandlers[eventName]){var callbackIndex=this.eventHandlers[eventName].indexOf(fn);-1!==callbackIndex&&this.eventHandlers[eventName].splice(callbackIndex,1)}},igv.Browser.prototype.fireEvent=function(eventName,args,thisObj){if(this.eventHandlers[eventName])for(var scope=thisObj||window,i=0,l=this.eventHandlers[eventName].length;i<l;i++){var item=this.eventHandlers[eventName][i],result=item.apply(scope,args);if(void 0!==result)return result}},igv}(igv||{}),igv=function(igv){function encodeAntibodyColor(antibody){var key;return antibody&&""!==antibody?(key=antibody.toUpperCase(),antibodyColors[key]?antibodyColors[key]:defaultColor):defaultColor}var antibodyColors={H3K27AC:"rgb(200, 0, 0)",H3K27ME3:"rgb(130, 0, 4)",H3K36ME3:"rgb(0, 0, 150)",H3K4ME1:"rgb(0, 150, 0)",H3K4ME2:"rgb(0, 150, 0)",H3K4ME3:"rgb(0, 150, 0)",H3K9AC:"rgb(100, 0, 0)",H3K9ME1:"rgb(100, 0, 0)"},defaultColor="rgb(3, 116, 178)";return igv.EncodeTable=function(parentModalBodyObject,continuation){var spinnerFA,self=this;this.encodeModalTableObject=$('<table id="encodeModalTable" cellpadding="0" cellspacing="0" border="0" class="display"></table>'),parentModalBodyObject.append(this.encodeModalTableObject[0]),this.initialized=!1,spinnerFA=$('<i class="fa fa-lg fa-spinner fa-spin"></i>'),this.spinner=$('<div class="igv-encode-spinner-container"></div>'),this.spinner.append(spinnerFA[0]),$("#encodeModalTable").append(this.spinner[0]),$("#igvEncodeModal").on("shown.bs.modal",function(e){!0!==self.initialized&&(self.initialized=!0,continuation())}),$("#encodeModalTopCloseButton").on("click",function(){$("tr.selected").removeClass("selected")}),$("#encodeModalBottomCloseButton").on("click",function(){$("tr.selected").removeClass("selected")}),$("#encodeModalGoButton").on("click",function(){var tableRows,dataSourceJSONRow,configList=[],encodeModalTable=$("#encodeModalTable"),dataTableAPIInstance=encodeModalTable.DataTable();(tableRows=self.dataTablesObject.$("tr.selected"))&&(tableRows.removeClass("selected"),tableRows.each(function(){var index;index=dataTableAPIInstance.row(this).data()[0],dataSourceJSONRow=self.dataSource.jSON.rows[index],configList.push({type:dataSourceJSONRow.Format,url:dataSourceJSONRow.url,color:encodeAntibodyColor(dataSourceJSONRow.Target),format:dataSourceJSONRow.Format,name:dataSourceJSONRow.Name})}),void 0===igv.browser.designatedTrack&&(configList[0].designatedTrack=!0),igv.browser.loadTracksWithConfigList(configList))})},igv.EncodeTable.prototype.loadWithDataSource=function(dataSource){var self=this,dataSet=dataSource.dataTablesData(),columns=dataSource.columnHeadings();this.dataSource=dataSource,this.dataTablesObject=self.encodeModalTableObject.dataTable({data:dataSet,scrollX:!0,scrollY:"400px",scrollCollapse:!0,paging:!1,columnDefs:[{targets:0,visible:!1}],autoWidth:!0,columns:columns}),self.encodeModalTableObject.find("tbody").on("click","tr",function(){$(this).hasClass("selected")?$(this).removeClass("selected"):$(this).addClass("selected")})},igv.EncodeTable.prototype.encodeTrackLabel=function(record){return record.antibody?record.antibody+" "+record.cell+" "+record.replicate:record.cell+record.dataType+" "+record.view+" "+record.replicate},igv.EncodeDataSource=function(config){this.config=config},igv.EncodeDataSource.prototype.loadJSON=function(continuation){this.jSON={},this.config.filePath?this.ingestFile(this.config.filePath,continuation):this.config.jSON&&this.ingestJSON(this.config.jSON,continuation)},igv.EncodeDataSource.prototype.ingestJSON=function(json,continuation){var self=this;self.jSON=json,json.rows.forEach(function(row,i){Object.keys(row).forEach(function(key){var item=row[key];self.jSON.rows[i][key]=void 0===item||""===item?"-":item})}),continuation()},igv.EncodeDataSource.prototype.ingestFile=function(file,continuation){var self=this;igvxhr.loadString(file).then(function(data){var item,lines=data.splitLines();self.jSON.columns=lines[0].split("\t"),self.jSON.columns.pop(),item=self.jSON.columns.shift(),self.jSON.columns.push(item),self.jSON.rows=[],lines.slice(1,lines.length-1).forEach(function(line){var tokens,row;tokens=line.split("\t"),tokens.pop(),item=tokens.shift(),tokens.push(item),row={},tokens.forEach(function(t,i,ts){var key=self.jSON.columns[i];row[key]=void 0===t||""===t?"-":t}),self.jSON.rows.push(row)}),continuation()})},igv.EncodeDataSource.prototype.dataTablesData=function(){var self=this,result=[];return this.jSON.rows.forEach(function(row,index){var rr=[];rr.push(index),self.jSON.columns.forEach(function(key){rr.push(row[key])}),result.push(rr)}),result},igv.EncodeDataSource.prototype.columnHeadings=function(){var columnHeadings=(this.jSON.columnWidths,[]);return columnHeadings.push({title:"index"}),this.jSON.columns.forEach(function(heading,i){columnHeadings.push({title:heading})}),columnHeadings},igv}(igv||{}),igv=function(igv){return igv.encodeSearch=function(continuation){igvxhr.loadJson("https://www.encodeproject.org/search/?type=experiment&files.output_type=peaks&files.file_format=bed&format=json&field=lab.title&field=biosample_term_name&field=assay_term_name&field=target.label&field=files.file_format&field=files.output_type&field=files.href&field=files.replicate.technical_replicate_number&field=files.replicate.biological_replicate_number&field=files.assembly&limit=all",{}).then(function(json){var columns=["Assembly","Cell Type","Target","Assay Type","Bio Rep","Tech Rep","Lab"],columnWidths=[8,20,10,10,8,8,40],rows=[];json["@graph"].forEach(function(record){var assayType=record.assay_term_name,experimentId=record["@id"],cellType=record.biosample_term_name||"",target=record.target?record.target.label:"",lab=record.lab?record.lab.title:"";record.files.forEach(function(file){if("bed"===file.file_format){var format=file.file_format,type=file.output_type,bioRep=file.replicate?file.replicate.bioligcal_replicate_number:void 0,techRep=file.replicate?file.replicate.technical_replicate_number:void 0,name=cellType+" "+target,assembly=file.assembly;bioRep&&(name+=" "+bioRep),techRep&&(name+=(bioRep?":":"0:")+techRep),rows.push({Assembly:assembly,ExperimentID:experimentId,"Cell Type":cellType,"Assay Type":assayType,Target:target,Lab:lab,Format:format,Type:type,url:"https://www.encodeproject.org"+file.href,"Bio Rep":bioRep,"Tech Rep":techRep,Name:name})}})}),rows.sort(function(a,b){var a1=a.Assembly,a2=b.Assembly,ct1=a["Cell Type"],ct2=b["Cell Type"],t1=a.Target,t2=b.Target;return a1===a2?ct1===ct2?t1===t2?0:t1<t2?-1:1:ct1<ct2?-1:1:a1<a2?-1:1}),continuation({columns:columns,columnWidths:columnWidths,rows:rows})})},igv}(igv||{}),igv=function(igv){function getSequenceIndexed(chr,start,end){var self=this;return new Promise(function(fulfill,reject){function getSequenceFromInterval(interval,start,end){var offset=start-interval.start,n=end-start;return interval.features?interval.features.substr(offset,n):null}var interval=self.interval;if(interval&&interval.contains(chr,start,end))fulfill(getSequenceFromInterval(interval,start,end));else{var qstart=start,qend=end;if(end-start<1e5){var w=end-start,center=Math.round(start+w/2);qstart=Math.max(0,center-5e4),qend=center+5e4}self.readSequence(chr,qstart,qend).then(function(seqBytes){self.interval=new igv.GenomicInterval(chr,qstart,qend,seqBytes),fulfill(getSequenceFromInterval(self.interval,start,end))}).catch(reject)}})}function getSequenceNonIndexed(chr,start,end){var self=this;return new Promise(function(fulfill,reject){var seq=self.sequences[chr];seq&&seq.length>end&&fulfill(seq.substring(start,end))})}return igv.FastaSequence=function(reference){this.file=reference.fastaURL,this.indexed=!1!==reference.indexed,this.indexed&&(this.indexFile=reference.indexURL||reference.indexFile||this.file+".fai"),this.withCredentials=reference.withCredentials},igv.FastaSequence.prototype.init=function(){var self=this;return self.indexed?new Promise(function(fulfill,reject){self.getIndex().then(function(index){var order=0;self.chromosomes={},self.chromosomeNames.forEach(function(chrName){var bpLength=self.index[chrName].size;self.chromosomes[chrName]=new igv.Chromosome(chrName,order++,bpLength)}),fulfill()}).catch(reject)}):self.loadAll()},igv.FastaSequence.prototype.getSequence=function(chr,start,end){return this.indexed?getSequenceIndexed.call(this,chr,start,end):getSequenceNonIndexed.call(this,chr,start,end)},igv.FastaSequence.prototype.getIndex=function(){var self=this;return new Promise(function(fulfill,reject){self.index?fulfill(self.index):igvxhr.load(self.indexFile,{withCredentials:self.withCredentials}).then(function(data){var lines=data.splitLines(),len=lines.length,lineNo=0;for(self.chromosomeNames=[],self.index={};lineNo<len;){var tokens=lines[lineNo++].split("\t");if(5==tokens.length){var chr=tokens[0],size=parseInt(tokens[1]),position=parseInt(tokens[2]),basesPerLine=parseInt(tokens[3]),bytesPerLine=parseInt(tokens[4]),indexEntry={size:size,position:position,basesPerLine:basesPerLine,bytesPerLine:bytesPerLine};self.chromosomeNames.push(chr),self.index[chr]=indexEntry}}fulfill&&fulfill(self.index)}).catch(reject)})},igv.FastaSequence.prototype.loadAll=function(){var self=this;return new Promise(function(fulfill,reject){self.chromosomeNames=[],self.chromosomes={},self.sequences={},igvxhr.load(self.file,{withCredentials:self.withCredentials}).then(function(data){for(var nextLine,currentChr,lines=data.splitLines(),len=lines.length,lineNo=0,currentSeq="",order=0;lineNo<len;)nextLine=lines[lineNo++].trim(),nextLine.startsWith("#")||0===nextLine.length||(nextLine.startsWith(">")?(currentSeq&&(self.chromosomeNames.push(currentChr),self.sequences[currentChr]=currentSeq,self.chromosomes[currentChr]=new igv.Chromosome(currentChr,order++,currentSeq.length)),currentChr=nextLine.substr(1).split("\\s+")[0],currentSeq=""):currentSeq+=nextLine);fulfill()})})},igv.FastaSequence.prototype.readSequence=function(chr,qstart,qend){var self=this;return new Promise(function(fulfill,reject){self.getIndex().then(function(){var idxEntry=self.index[chr];if(idxEntry){var start=Math.max(0,qstart),end=Math.min(idxEntry.size,qend),bytesPerLine=idxEntry.bytesPerLine,basesPerLine=idxEntry.basesPerLine,position=idxEntry.position,nEndBytes=bytesPerLine-basesPerLine,startLine=Math.floor(start/basesPerLine),endLine=Math.floor(end/basesPerLine),base0=startLine*basesPerLine,offset=start-base0,startByte=position+startLine*bytesPerLine+offset,base1=endLine*basesPerLine,offset1=end-base1,endByte=position+endLine*bytesPerLine+offset1-1,byteCount=endByte-startByte+1;byteCount<=0&&fulfill(null),igvxhr.load(self.file,{range:{start:startByte,size:byteCount}}).then(function(allBytes){var nBases,seqBytes="",srcPos=0,desPos=0,allBytesLength=allBytes.length;for(offset>0&&(nBases=Math.min(end-start,basesPerLine-offset),seqBytes+=allBytes.substr(srcPos,nBases),srcPos+=nBases+nEndBytes,desPos+=nBases);srcPos<allBytesLength;)nBases=Math.min(basesPerLine,allBytesLength-srcPos),seqBytes+=allBytes.substr(srcPos,nBases),srcPos+=nBases+nEndBytes,desPos+=nBases;fulfill(seqBytes)}).catch(reject)}else console.log("No index entry for chr: "+chr),self.interval=new igv.GenomicInterval(chr,qstart,qend,null),fulfill(null)}).catch(reject)})},igv}(igv||{}),igv=function(igv){function getParser(format){return new igv.FeatureParser(format)}return igv.AneuFeatureSource=function(config,thefilename){this.config=config||{};var getPath=function(urlorfile){var last=urlorfile.lastIndexOf("/");return urlorfile.substring(0,last+1)};if(config.localFile){var path=getPath(config.localFile.name);this.localFile=config.localFile,this.filename=path+thefilename}else{var path=getPath(config.url);this.url=path+thefilename,this.filename=thefilename,this.headURL=config.headURL||this.filename}this.parser=getParser("aneu")},igv.AneuFeatureSource.prototype.getFeatures=function(chr,bpStart,bpEnd,success){var myself=this,range=new igv.GenomicInterval(chr,bpStart,bpEnd),featureCache=this.featureCache;if(featureCache&&(void 0===featureCache.range||featureCache.range.containsRange(range))){var features=this.featureCache.queryFeatures(chr,bpStart,bpEnd);success(features)}else this.loadFeatures(function(featureList){myself.featureCache=new igv.FeatureCache(featureList);var features=myself.featureCache.queryFeatures(chr,bpStart,bpEnd);success(features)},range)},igv.AneuFeatureSource.prototype.getFeatureCache=function(success){var myself=this;this.featureCache?success(this.featureCache):this.loadFeatures(function(featureList){myself.featureCache=new igv.FeatureCache(featureList),success(myself.featureCache)})},igv.AneuFeatureSource.prototype.loadFeatures=function(continuation,range){var self=this,parser=self.parser,options={headers:self.config.headers,tokens:self.config.tokens,withCredentials:self.config.withCredentials},success=function(data){self.header=parser.parseHeader(data);var features=parser.parseFeatures(data);continuation(features)};self.localFile?igvxhr.loadStringFromFile(self.localFile,options).then(success):igvxhr.loadString(self.url,options).then(success)},igv}(igv||{}),igv=function(igv){function loadJson(){var self=this;return new Promise(function(fulfill,reject){if(self.featureSourceRed)fulfill();else{var afterJsonLoaded=function(json){json=JSON.parse(json),log("Got json: "+json+", diff :"+json.diff),self.featureSource=new igv.AneuFeatureSource(config,json.diff),self.featureSourceRed=new igv.AneuFeatureSource(config,json.redline),fulfill()},afterload={headers:self.config.headers,tokens:self.config.tokens,withCredentials:self.config.withCredentials},config=self.config;config.localFile?igvxhr.loadStringFromFile(config.localFile,afterload).then(afterJsonLoaded):igvxhr.loadString(config.url,afterload).then(afterJsonLoaded)}})}var debug=!1,log=function(msg){if(debug){var d=new Date,time=d.getHours()+":"+d.getMinutes()+":"+d.getSeconds();"undefined"!=typeof copy&&copy(msg),"undefined"!=typeof console&&console.log("AneuTrack: "+time+" "+msg)}},sortDirection=1;return igv.AneuTrack=function(config){igv.configTrack(this,config),this.maxHeight=config.maxHeight-2||500,this.sampleSquishHeight=config.sampleSquishHeight||20,this.sampleExpandHeight=config.sampleExpandHeight||125,this.sampleHeight=this.sampleExpandHeight,this.highColor=config.highColor||"rgb(30,30,255)",this.lowColor=config.lowColor||"rgb(220,0,0)",this.midColor=config.midColor||"rgb(150,150,150)",this.posColorScale=config.posColorScale||new igv.GradientColorScale({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=config.negColorScale||new igv.GradientColorScale({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),this.sampleCount=0,this.samples={},this.sampleNames=[],log("AneuTrack: config: "+JSON.stringify(config)),this.config=config},igv.AneuTrack.prototype.popupMenuItems=function(popover){return[]},igv.AneuTrack.prototype.getSummary=function(chr,bpStart,bpEnd,continuation){var filtersummary=function(redlinedata){var summarydata=[];for(i=0,len=redlinedata.length;i<len;i++){var feature=redlinedata[i];Math.abs(feature.score-2)>.5&&feature.end-feature.start>5e6&&summarydata.push(feature)}continuation(summarydata)};this.featureSourceRed?this.featureSourceRed.getFeatures(chr,bpStart,bpEnd,filtersummary):(log("Aneu track has no summary data yet"),continuation(null))},igv.AneuTrack.prototype.loadSummary=function(chr,bpStart,bpEnd,continuation){var self=this;if(!this.featureSourceRed){var afterJsonLoaded=function(json){json&&(json=JSON.parse(json),self.featureSourceRed=new igv.AneuFeatureSource(config,json.redline),self.getSummary(chr,bpStart,bpEnd,continuation))};afterload={headers:self.config.headers,tokens:self.config.tokens,success:afterJsonLoaded,withCredentials:self.config.withCredentials};var config=self.config;return config.localFile?igvxhr.loadStringFromFile(config.localFile,afterload):igvxhr.loadString(config.url,afterload),null}this.featureSourceRed.getFeatures(chr,bpStart,bpEnd,continuation)},igv.AneuTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){loadJson.call(self).then(function(){var loadsecondfile=function(redlinedata){self.redlinedata=redlinedata,self.featureSource.getFeatures(chr,bpStart,bpEnd,fulfill)};self.featureSourceRed.getFeatures(chr,bpStart,bpEnd,loadsecondfile)})})},igv.AneuTrack.prototype.getColor=function(value){var expected=2;return color=value<expected?this.lowColor:value>expected?this.highColor:this.midColor,color},igv.AneuTrack.prototype.paintAxis=function(ctx,pixelWidth,pixelHeight){function computeH(min,max,value,maxpixels){return maxpixels-Math.round((value-min)/max*maxpixels)}var track=this,font=(track.maxLogP,track.minLogP,{font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"});igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"});var max=track.max;max||(max=8);var min=0,x=49;igv.graphics.strokeLine(ctx,x,computeH(min,max,0,track.maxheight),x,computeH(min,max,max,track.maxheight),font),x-=5;for(var p=0;p<=max;p+=1){var h=computeH(min,max,p,track.maxheight);igv.graphics.strokeLine(ctx,x,h,x+5,h,font),p>0&&p<max&&igv.graphics.fillText(ctx,p,x-4,h+3,font)}font.textAlign="center",igv.graphics.fillText(ctx,"ploidy",x-15,pixelHeight/2,font,{rotate:{angle:-90}})},igv.AneuTrack.prototype.draw=function(options){function computeH(min,max,value,maxpixels){return maxpixels-Math.round((value-min)/max*maxpixels)}function checkForLog(featureList){var i;if(void 0===myself.isLog)for(myself.isLog=!1,i=0;i<featureList.length;i++)if(featureList[i].value<0)return void(myself.isLog=!0)}var ctx,bpPerPixel,bpStart,pixelWidth,pixelHeight,bpEnd,segment,len,sample,i,y,color,value,px,px1,pw,xScale,myself=this;ctx=options.context,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight;var max=4,min=0,PLOIDYMAX=10;igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"});var track=this;window.track=track;var computeMinMax=function(featureList){for(i=0,len=featureList.length;i<len;i++){sample=featureList[i].sample;var value=featureList[i].value;value>max&&(max=value),value<min&&(min=value)}max>PLOIDYMAX&&(max=PLOIDYMAX),min=Math.max(min,0),track.max=max},drawFeatureList=function(ctx,featureList,debug){for(bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,bpEnd=bpStart+pixelWidth*bpPerPixel+1,xScale=bpPerPixel,i=0,len=featureList.length;i<len;i++)(sample=featureList[i].sample)&&this.samples&&this.samples.hasOwnProperty(sample)&&(this.samples[sample]=myself.sampleCount,this.sampleNames.push(sample),this.sampleCount++);checkForLog(featureList);var expected=2;myself.isLog&&(min=0,expected=0);var maxheight=myself.height-4;myself.maxheight=maxheight;var len=featureList.length;for(i=0;i<len;i++)if(segment=featureList[i],!(segment.end<bpStart)){if(segment.start>bpEnd)break;if(segment.sample?(y=myself.samples[segment.sample]*myself.sampleHeight,log("Got sample y="+y)):y=0,value=segment.score,color=myself.midColor,myself.isLog?(value=Math.log2(value/2),value<expected-.1?color=myself.negColorScale.getColor(value):value>expected+.1&&(color=myself.posColorScale.getColor(value))):value<expected-.2?color=myself.lowColor:value>expected+.2&&(color=myself.highColor),px=Math.round((segment.start-bpStart)/xScale),px1=Math.round((segment.end-bpStart)/xScale),pw=Math.max(2,px1-px),value<=max){var h=computeH(min,max,value,maxheight);1==debug&&log("       Got value "+value+", h="+h+", y+h="+(y+h)+", px="+px+", px1="+px1+", pw="+pw+", color="+color+", maxh="+maxheight),igv.graphics.fillRect(ctx,px,y+h,pw,2,{fillStyle:color})}}},maxheight=myself.height-4,font={font:"normal 10px Arial",textAlign:"right",strokeStyle:"rgb(150,150,150)",fillStyle:"rgb(150,150,150)"};if(options.features&&computeMinMax(options.features),this.redlinedata&&computeMinMax(this.redlinedata),min<2&&2<max){var mid=computeH(min,max,2,maxheight);console.log("drawing dashed line and solid line at "+mid+" to "+pixelWidth),igv.graphics.dashedLine(ctx,20,mid,pixelWidth,mid,4,font);var zero=computeH(min,max,0,maxheight);igv.graphics.strokeLine(ctx,20,zero,pixelWidth,zero,font)}else log("NOT drawing line at 2");options.features?drawFeatureList(ctx,options.features,!1):console.log("No diff feature list. options="+JSON.stringify(options)),this.redlinedata?drawFeatureList(ctx,this.redlinedata,!1):console.log("No redline feature list")},igv.AneuTrack.prototype.computePixelHeight=function(features){for(i=0,len=features.length;i<len;i++)sample=features[i].sample,this.samples&&!this.samples.hasOwnProperty(sample)&&(this.samples[sample]=this.sampleCount,this.sampleNames.push(sample),this.sampleCount++);this.sampleCount=Math.max(1,this.sampleCount);var h=Math.max(30,this.sampleCount*this.sampleHeight);return this.height=h,h},igv.AneuTrack.prototype.sortSamples=function(chr,bpStart,bpEnd,direction,callback){var segment,min,max,f,i,s,sampleNames,myself=this,len=bpEnd-bpStart,scores={};this.featureSource.getFeatures(chr,bpStart,bpEnd,function(featureList){for(i=0,len=featureList.length;i<len;i++)if(segment=featureList[i],!(segment.end<bpStart)){if(segment.start>bpEnd)break;min=Math.max(bpStart,segment.start),max=Math.min(bpEnd,segment.end),f=(max-min)/len,s=scores[segment.sample],s||(s=0),scores[segment.sample]=s+f*segment.value}for(sampleNames=Object.keys(myself.samples),sampleNames.sort(function(a,b){var s1=scores[a],s2=scores[b];return s1||(s1=Number.MAX_VALUE),s2||(s2=Number.MAX_VALUE),s1==s2?0:s1>s2?direction:-1*direction}),i=0;i<sampleNames.length;i++)myself.samples[sampleNames[i]]=i;myself.sampleNames=sampleNames,callback()})},igv.AneuTrack.prototype.altClick=function(genomicLocation,event){var refFrame=igv.browser.referenceFrame,bpWidth=refFrame.toBP(2.5),bpStart=genomicLocation-bpWidth,bpEnd=genomicLocation+bpWidth,chr=refFrame.chr,track=this;this.sortSamples(chr,bpStart,bpEnd,sortDirection,function(){track.trackView.update()}),sortDirection*=-1},igv.AneuTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){var sampleName,items,row=Math.floor(yOffset/this.sampleHeight);if(log("popupData for row "+row+", sampleNames="+JSON.stringify(this.sampleNames)),row<this.sampleNames.length){if(sampleName=this.sampleNames[row],items=sampleName?[{name:"Sample",value:sampleName}]:[],this.featureSource.featureCache){var chr=igv.browser.referenceFrame.chr,featureList=this.featureSource.featureCache.queryFeatures(chr,genomicLocation,genomicLocation);featureList.forEach(function(f){f.sample===sampleName&&(items.push({name:"Value",value:f.value}),items.push({name:"Start",value:f.start}),items.push({name:"End",value:f.end}))})}if(this.featureSourceRed.featureCache){var chr=igv.browser.referenceFrame.chr,featureList=this.featureSourceRed.featureCache.queryFeatures(chr,genomicLocation,genomicLocation);featureList.forEach(function(f){f.sample===sampleName&&(items.push({name:"Value",value:f.value}),items.push({name:"Start",value:f.start}),items.push({name:"End",value:f.end}))})}return items}return null},igv}(igv||{}),igv=function(igv){function buildTreeMap(featureList){var featureCache={},chromosomes=[],treeMap={},genome=igv.browser?igv.browser.genome:null;if(featureList)for(featureList.forEach(function(feature){var geneList,chr=feature.chr;genome&&(chr=genome.getChromosomeName(chr)),geneList=featureCache[chr],geneList||(chromosomes.push(chr),geneList=[],featureCache[chr]=geneList),geneList.push(feature)}),i=0;i<chromosomes.length;i++)chr=chromosomes[i],treeMap[chr]=buildIntervalTree(featureCache[chr]);return treeMap}function buildIntervalTree(featureList){var i,e,iStart,iEnd,tree,chunkSize,len,subArray;for(tree=new igv.IntervalTree,len=featureList.length,chunkSize=Math.max(10,Math.round(len/100)),featureList.sort(function(f1,f2){return f1.start===f2.start?0:f1.start>f2.start?1:-1}),i=0;i<len;i+=chunkSize)e=Math.min(len,i+chunkSize),subArray=featureList.slice(i,e),iStart=subArray[0].start,iEnd=iStart,subArray.forEach(function(feature){iEnd=Math.max(iEnd,feature.end)}),tree.insert(iStart,iEnd,subArray);return tree}return igv.FeatureCache=function(featureList,range){this.treeMap=buildTreeMap(featureList),this.range=range},igv.FeatureCache.prototype.queryFeatures=function(chr,start,end){var featureList,intervalFeatures,feature,len,i,tree,intervals;return(tree=this.treeMap[chr])?(intervals=tree.findOverlapping(start,end),0==intervals.length?[]:(featureList=[],intervals.forEach(function(interval){for(intervalFeatures=interval.value,len=intervalFeatures.length,i=0;i<len&&(feature=intervalFeatures[i],!(feature.start>end));i++)feature.end>=start&&featureList.push(feature)}),featureList)):[]},igv.FeatureCache.prototype.allFeatures=function(){var allFeatures=[],treeMap=this.treeMap;if(treeMap)for(var key in treeMap)if(treeMap.hasOwnProperty(key)){var tree=treeMap[key];tree.mapIntervals(function(interval){allFeatures=allFeatures.concat(interval.value)})}return allFeatures},igv}(igv||{}),igv=function(igv){function getParser(format,decode){switch(format){case"vcf":return new igv.VcfParser;case"seg":return new igv.SegParser;default:return new igv.FeatureParser(format,decode,this.config)}}function isIndexable(){var configIndexURL=this.config.indexURL,type=this.type,configIndexed=this.config.indexed;return configIndexURL||"wig"!=type&&0!=configIndexed}function loadIndex(){var idxFile=this.indexURL;return this.filename.endsWith(".gz")?(idxFile||(idxFile=this.url+".tbi"),igv.loadBamIndex(idxFile,this.config,!0)):(idxFile||(idxFile=this.url+".idx"),igv.loadTribbleIndex(idxFile,this.config))}function loadFeaturesNoIndex(){var self=this;return new Promise(function(fulfill,reject){function parseData(data){self.header=parser.parseHeader(data),self.header instanceof String&&self.header.startsWith("##gff-version 3")&&(self.format="gff3"),fulfill(parser.parseFeatures(data))}var parser=self.parser,options={headers:self.config.headers,withCredentials:self.config.withCredentials};self.localFile?igvxhr.loadStringFromFile(self.localFile,options).then(parseData).catch(reject):igvxhr.loadString(self.url,options).then(parseData).catch(reject)})}function loadFeaturesWithIndex(chr,start,end){var self=this;return new Promise(function(fulfill,reject){var blocks,index=self.index,tabix=index&&index.tabix,refId=tabix?index.sequenceIndexMap[chr]:chr,promises=[];blocks=index.blocksForRange(refId,start,end),blocks&&0!==blocks.length?(blocks.forEach(function(block){promises.push(new Promise(function(fulfill,reject){var success,startPos=block.minv.block,startOffset=block.minv.offset,endPos=block.maxv.block+(index.tabix?MAX_GZIP_BLOCK_SIZE:0),options={headers:self.config.headers,range:{start:startPos,size:endPos-startPos+1},withCredentials:self.config.withCredentials};success=function(data){var inflated,slicedData;inflated=index.tabix?igvxhr.arrayBufferToString(igv.unbgzf(data)):data,slicedData=startOffset?inflated.slice(startOffset):inflated;var f=self.parser.parseFeatures(slicedData);fulfill(f)},self.localFile?igvxhr.loadStringFromFile(self.localFile,options).then(success).catch(reject):index.tabix?igvxhr.loadArrayBuffer(self.url,options).then(success).catch(reject):igvxhr.loadString(self.url,options).then(success).catch(reject)}))}),Promise.all(promises).then(function(featureArrays){var i,allFeatures;if(1===featureArrays.length)allFeatures=featureArrays[0];else{for(allFeatures=featureArrays[0],i=1;i<featureArrays.length;i++)allFeatures=allFeatures.concat(featureArrays[i]);allFeatures.sort(function(a,b){return a.start-b.start})}fulfill(allFeatures)}).catch(reject)):fulfill(null)})}function getIndex(){var self=this,isIndeedIndexible=isIndexable.call(this);return new Promise(function(fulfill,reject){void 0===self.indexed&&isIndeedIndexible?loadIndex.call(self).then(function(index){index?(self.index=index,self.indexed=!0):self.indexed=!1,fulfill(self.index)}):fulfill(self.index)})}const MAX_GZIP_BLOCK_SIZE=65536;return igv.FeatureFileReader=function(config){if(this.config=config||{},config.localFile)this.localFile=config.localFile,this.filename=config.localFile.name;else{this.url=config.url,this.indexURL=config.indexURL,this.headURL=config.headURL||this.filename;var uriParts=igv.parseUri(config.url);this.filename=uriParts.file,this.path=uriParts.path}this.format=config.format,this.parser=getParser.call(this,this.format,config.decode)},igv.FeatureFileReader.prototype.readHeader=function(){var self=this;return new Promise(function(fulfill,reject){self.header?fulfill(self.header):getIndex.call(self).then(function(index){if(index){var options={headers:self.config.headers,bgz:index.tabix,range:{start:0,size:65e3},withCredentials:self.config.withCredentials},success=function(data){self.header=self.parser.parseHeader(data),fulfill(self.header)};self.localFile?igvxhr.loadStringFromFile(self.localFile,options).then(success):igvxhr.loadString(self.url,options).then(success).catch(reject)}else loadFeaturesNoIndex.call(self,void 0).then(function(features){var header=self.header||{};header.features=features,fulfill(header)}).catch(reject)})})},igv.FeatureFileReader.prototype.readFeatures=function(chr,start,end){var self=this;return new Promise(function(fulfill,reject){function packFeatures(features){fulfill(features)}self.index?loadFeaturesWithIndex.call(self,chr,start,end).then(packFeatures):loadFeaturesNoIndex.call(self).then(packFeatures)})},igv}(igv||{}),igv=function(igv){function parseFixedStep(line){var tokens=line.split(/\s+/);return{format:"fixedStep",chrom:tokens[1].split("=")[1],start:parseInt(tokens[2].split("=")[1],10),step:parseInt(tokens[3].split("=")[1],10),span:tokens.length>4?parseInt(tokens[4].split("=")[1],10):1,index:0}}function parseVariableStep(line){var tokens=line.split(/\s+/);return{format:"variableStep",chrom:tokens[1].split("=")[1],span:tokens.length>2?parseInt(tokens[2].split("=")[1],10):1}}function parseTrackLine(line){var i,tk,curr,properties={},tokens=line.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g),tmp=[];for(i=1;i<tokens.length;i++)tokens[i]&&0!==tokens[i].trim().length&&(tk=tokens[i].trim(),tk.endsWith("=")>0?curr=tk:curr?(tmp.push(curr+tk),curr=void 0):tmp.push(tk));return tmp.forEach(function(str){if(str){var kv=str.split("=",2);2==kv.length&&(properties[kv[0]]=kv[1])}}),properties}function decodeBed(tokens,ignore){var chr,start,end,id,name,tmp,idName,exonCount,exonSizes,exonStarts,exons,exon,feature,eStart,eEnd;if(tokens.length<3)return null;if(chr=tokens[0],start=parseInt(tokens[1]),end=tokens.length>2?parseInt(tokens[2]):start+1,feature={chr:chr,start:start,end:end,score:1e3},tokens.length>3){tmp=tokens[3].replace(/"/g,""),idName=tmp.split(";");for(var i=0;i<idName.length;i++){var kv=idName[i].split("=");"gene_id"==kv[0]&&(id=kv[1]),"gene_name"==kv[0]&&(name=kv[1])}feature.id=id||tmp,feature.name=name||tmp}if(tokens.length>4&&(feature.score=parseFloat(tokens[4])),tokens.length>5&&(feature.strand=tokens[5]),tokens.length>6&&(feature.cdStart=parseInt(tokens[6])),tokens.length>7&&(feature.cdEnd=parseInt(tokens[7])),tokens.length>8&&"."!==tokens[8]&&"0"!==tokens[8]&&(feature.color=igv.createColorString(tokens[8])),tokens.length>11){exonCount=parseInt(tokens[9]),exonSizes=tokens[10].split(","),exonStarts=tokens[11].split(","),exons=[];for(var i=0;i<exonCount;i++){eStart=start+parseInt(exonStarts[i]),eEnd=eStart+parseInt(exonSizes[i]);var exon={start:eStart,end:eEnd};(feature.cdStart>eEnd||feature.cdEnd<feature.cdStart)&&(exon.utr=!0),feature.cdStart>=eStart&&feature.cdStart<=eEnd&&(exon.cdStart=feature.cdStart),feature.cdEnd>=eStart&&feature.cdEnd<=eEnd&&(exon.cdEnd=feature.cdEnd),exons.push(exon)}feature.exons=exons}return feature.popupData=function(){var data=[];return feature.name&&data.push({name:"Name",value:feature.name}),"+"!==feature.strand&&"-"!==feature.strand||data.push({name:"Strand",value:feature.strand}),data},feature}function decodeRefflat(tokens,ignore){if(tokens.length<10)return null;for(var feature={chr:tokens[2],start:parseInt(tokens[4]),end:parseInt(tokens[5]),id:tokens[1],name:tokens[0],strand:tokens[3],cdStart:parseInt(tokens[6]),cdEnd:parseInt(tokens[7])},exonCount=parseInt(tokens[8]),exonStarts=tokens[9].split(","),exonEnds=tokens[10].split(","),exons=[],i=0;i<exonCount;i++)exons.push({start:parseInt(exonStarts[i]),end:parseInt(exonEnds[i])});return feature.exons=exons,feature.popupData=function(){return[{name:"Name",value:feature.name}]},feature}function decodePeak(tokens,ignore){var chr,start,end,strand,name,score,qValue,signal,pValue;return tokens.length<9?null:(chr=tokens[0],start=parseInt(tokens[1]),end=parseInt(tokens[2]),name=tokens[3],score=parseFloat(tokens[4]),strand=tokens[5].trim(),signal=parseFloat(tokens[6]),pValue=parseFloat(tokens[7]),qValue=parseFloat(tokens[8]),0===score&&(score=signal),{chr:chr,start:start,end:end,name:name,score:score,strand:strand,signal:signal,pValue:pValue,qValue:qValue})}function decodeBedGraph(tokens,ignore){var chr,start,end,value;return tokens.length<3?null:(chr=tokens[0],start=parseInt(tokens[1]),end=parseInt(tokens[2]),value=parseFloat(tokens[3]),{chr:chr,start:start,end:end,value:value})}function decodeWig(tokens,wig){var ss,ee,value;return"fixedStep"===wig.format?(ss=wig.index*wig.step+wig.start,ee=ss+wig.span,value=parseFloat(tokens[0]),++wig.index,isNaN(value)?null:{chr:wig.chrom,start:ss,end:ee,value:value}):"variableStep"===wig.format?tokens.length<2?null:(ss=parseInt(tokens[0],10),ee=ss+wig.span,value=parseFloat(tokens[1]),isNaN(value)?null:{chr:wig.chrom,start:ss,end:ee,value:value}):decodeBedGraph(tokens)}function decodeAneu(tokens,ignore){var chr,start,end,feature;return tokens.length<4?null:(chr=tokens[1],start=parseInt(tokens[2]),end=tokens.length>3?parseInt(tokens[3]):start+1,feature={chr:chr,start:start,end:end},tokens.length>4&&(feature.score=parseFloat(tokens[4]),feature.value=feature.score),feature.popupData=function(){return[{name:"Name",value:feature.name}]},feature)}function decodeFusionJuncSpan(tokens,ignore){var chr=tokens[0],fusion_name=tokens[1],junction_left=parseInt(tokens[2]),junction_right=parseInt(tokens[3]),num_junction_reads=parseInt(tokens[4]),num_spanning_frags=parseInt(tokens[5]),spanning_frag_coords_text=tokens[6],feature={chr:chr,name:fusion_name,junction_left:junction_left,junction_right:junction_right,num_junction_reads:num_junction_reads,num_spanning_frags:num_spanning_frags,spanning_frag_coords:[],start:-1,end:-1},min_coord=junction_left,max_coord=junction_right;if(num_spanning_frags>0)for(var coord_pairs=spanning_frag_coords_text.split(","),i=0;i<coord_pairs.length;i++){var split_coords=coord_pairs[i].split("-"),span_left=split_coords[0],span_right=split_coords[1];span_left<min_coord&&(min_coord=span_left),span_right>max_coord&&(max_coord=span_right),feature.spanning_frag_coords.push({left:span_left,right:span_right})}return feature.start=min_coord,feature.end=max_coord,feature.popupData=function(){return[{name:"Name",value:feature.name}]},feature}function decodeGtexGWAS(tokens,ignore){var chr,start,end,pValue;return tokens.length<8?null:(chr=tokens[0],start=parseInt(tokens[1])-1,end=parseInt(tokens[3].split(":")[1]),pValue=parseFloat(tokens[5]),{chr:chr,start:start,end:end,pvalue:pValue})}function decodeGFF(tokens,ignore){var chr,start,end,strand,type,score,attributeString,id,parent,color,name,i,format=this.format;if(tokens.length<9)return null;chr=tokens[0],type=tokens[2],start=parseInt(tokens[3])-1,end=parseInt(tokens[4]),score="."===tokens[5]?0:parseFloat(tokens[5]),strand=tokens[6],"."===tokens[7]||parseInt(tokens[7]),attributeString=tokens[8];var delim="gff3"===format?"=":/\s+/,attributes={};if(attributeString.split(";").forEach(function(kv){var key,value,t=kv.trim().split(delim,2);2==t.length&&(key=t[0].trim(),value=t[1].trim(),value.startsWith('"')&&value.endsWith('"')&&(value=value.substr(1,value.length-2)),"ID"===t[0]?id=t[1]:"Parent"===t[0]?parent=t[1]:"color"===t[0].toLowerCase()?color=igv.createColorString(t[1]):"transcript_id"===t[0]&&(id=t[1]),attributes[key]=value)}),this.nameField)name=attributes[this.nameField];else for(i=0;i<gffNameFields.length;i++)if(attributes.hasOwnProperty(gffNameFields[i])){this.nameField=gffNameFields[i],name=attributes[this.nameField];break}return{id:id,parent:parent,name:name,type:type,chr:chr,start:start,end:end,score:score,strand:strand,color:color,attributeString:attributeString,popupData:function(){var key,value,kvs=this.attributeString.split(";"),pd=[];return kvs.forEach(function(kv){var t=kv.trim().split(delim,2);2===t.length&&void 0!==t[1]&&(key=t[0].trim(),value=t[1].trim(),value.startsWith('"')&&value.endsWith('"')&&(value=value.substr(1,value.length-2)),pd.push({name:key,value:value}))}),pd}}}function decodeCustom(tokens,ignore){var feature,chr,start,end,format=this.format,coords=format.coords||0;return tokens.length<3?null:(chr=tokens[format.chr],start=parseInt(tokens[format.start])-coords,end=void 0!==format.end?parseInt(tokens[format.end]):start+1,feature={chr:chr,start:start,end:end},format.fields&&format.fields.forEach(function(field,index){index!=format.chr&&index!=format.start&&index!=format.end&&(feature[field]=tokens[index])}),feature)}var maxFeatureCount=Number.MAX_VALUE,gffNameFields=["Name","gene_name","gene","gene_id","alias","locus"];return igv.FeatureParser=function(format,decode,config){var customFormat;switch(this.format=format,this.nameField=config?config.nameField:void 0,this.skipRows=0,decode&&(this.decode=decode),format){case"narrowpeak":case"broadpeak":case"peaks":this.decode=decodePeak,this.delimiter=/\s+/;break;case"bedgraph":this.decode=decodeBedGraph,this.delimiter=/\s+/;break;case"wig":this.decode=decodeWig,this.delimiter=/\s+/;break;case"gff3":case"gff":case"gtf":this.decode=decodeGFF,this.delimiter="\t";break;case"aneu":this.decode=decodeAneu,this.delimiter="\t";break;case"fusionjuncspan":this.decode=decodeFusionJuncSpan,this.delimiter=/\s+/;break;case"gtexgwas":this.skipRows=1,this.decode=decodeGtexGWAS,this.delimiter="\t";break;case"refflat":this.decode=decodeRefflat,this.delimiter="\t";break;default:customFormat=igv.browser.getFormat(format),void 0!==customFormat?(this.decode=decodeCustom,this.format=customFormat,this.delimiter=customFormat.delimiter||"\t"):(this.decode=decodeBed,this.delimiter=/\s+/)}},igv.FeatureParser.prototype.parseHeader=function(data){var line,i,header,lines=data.splitLines(),len=lines.length;for(i=0;i<len&&(line=lines[i],line.startsWith("track")||line.startsWith("#")||line.startsWith("browser"));i++)line.startsWith("track")?header=parseTrackLine(line):line.startsWith("##gff-version 3")&&(this.format="gff3",header||(header={}),header.format="gff3");return header},igv.FeatureParser.prototype.parseFeatures=function(data){if(!data)return null;var wig,feature,tokens,line,i,j,lines=data.splitLines(),len=lines.length,allFeatures=[],cnt=0,decode=this.decode,format=this.format,delimiter=this.delimiter||"\t";for(i=this.skipRows;i<len;i++)line=lines[i],line.startsWith("track")||line.startsWith("#")||line.startsWith("browser")||("wig"===format&&line.startsWith("fixedStep")?wig=parseFixedStep(line):"wig"===format&&line.startsWith("variableStep")?wig=parseVariableStep(line):(tokens=lines[i].split(delimiter),tokens.length<1||(feature=decode.call(this,tokens,wig))&&(allFeatures.length<maxFeatureCount?allFeatures.push(feature):(j=Math.floor(Math.random()*cnt))<maxFeatureCount&&(allFeatures[j]=feature),cnt++)));return allFeatures},igv}(igv||{}),igv=function(igv){function addFeaturesToDB(featureList){featureList.forEach(function(feature){feature.name&&(igv.browser.featureDB[feature.name.toUpperCase()]=feature)})}function packFeatures(features,maxRows){function pack(featureList,maxRows){var rows=[];featureList.sort(function(a,b){return a.start-b.start}),rows.push(-1e3),featureList.forEach(function(feature){var r,len=Math.min(rows.length,maxRows),start=feature.start;for(r=0;r<len;r++)if(start>=rows[r])return feature.row=r,void(rows[r]=feature.end);feature.row=r,rows[r]=feature.end})}if(null!=features&&0!==features.length){var chrFeatureMap={},chrs=[];features.forEach(function(feature){var chr=feature.chr,flist=chrFeatureMap[chr];flist||(flist=[],chrFeatureMap[chr]=flist,chrs.push(chr)),flist.push(feature)}),chrs.forEach(function(chr){pack(chrFeatureMap[chr],maxRows)})}}return igv.FeatureSource=function(config){this.config=config||{},this.sourceType=void 0===config.sourceType?"file":config.sourceType,"ga4gh"===config.sourceType?this.reader=new igv.Ga4ghVariantReader(config):"immvar"===config.sourceType?this.reader=new igv.ImmVarReader(config):"eqtl"===config.type?"gtex-ws"===config.sourceType?this.reader=new igv.GtexReader(config):this.reader=new igv.GtexFileReader(config):"bigquery"===config.sourceType?this.reader=new igv.BigQueryFeatureReader(config):this.reader=new igv.FeatureFileReader(config),this.visibilityWindow=config.visibilityWindow},igv.FeatureSource.prototype.getFileHeader=function(){var self=this,maxRows=this.config.maxRows||500;return new Promise(function(fulfill,reject){self.header?fulfill(self.header):"function"==typeof self.reader.readHeader?self.reader.readHeader().then(function(header){if(header){var features=header.features;features&&("gtf"!==self.config.format&&"gff3"!==self.config.format&&"gff"!==self.config.format||(features=new igv.GFFHelper(self.config.format).combineFeatures(features)),packFeatures(features,maxRows),self.featureCache=new igv.FeatureCache(features),self.config.searchable&&addFeaturesToDB(features))}header&&header.format&&(self.config.format=header.format),fulfill(header)}).catch(reject):fulfill(null)})},igv.FeatureSource.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){var genomicInterval=new igv.GenomicInterval(chr,bpStart,bpEnd),featureCache=self.featureCache,maxRows=self.config.maxRows||500;if(featureCache&&(void 0===featureCache.range||featureCache.range.containsRange(genomicInterval)))fulfill(self.featureCache.queryFeatures(chr,bpStart,bpEnd));else{if("file"===self.sourceType&&(void 0===self.visibilityWindow||self.visibilityWindow<=0)){genomicInterval.start=0;var chromosome=igv.browser.genome.getChromosome(chr);genomicInterval.end=void 0===chromosome?Number.MAX_VALUE:chromosome.bpLength}self.reader.readFeatures(chr,genomicInterval.start,genomicInterval.end).then(function(featureList){if(featureList&&"function"==typeof featureList.forEach){var isIndexed=self.reader.indexed||"ga4gh"===self.config.sourceType||"immvar"===self.config.sourceType||"gtex"===self.config.sourceType||"bigquery"===self.config.sourceType;"gtf"!==self.config.format&&"gff3"!==self.config.format&&"gff"!==self.config.format||(featureList=new igv.GFFHelper(self.config.format).combineFeatures(featureList)),self.featureCache=isIndexed?new igv.FeatureCache(featureList,genomicInterval):new igv.FeatureCache(featureList),packFeatures(featureList,maxRows),self.config.searchable&&addFeaturesToDB(featureList),fulfill(self.featureCache.queryFeatures(chr,bpStart,bpEnd))}else fulfill(null)}).catch(reject)}})},igv}(igv||{}),igv=function(igv){function extractPopupData(feature){var data=[];for(var property in feature)feature.hasOwnProperty(property)&&"chr"!==property&&"start"!==property&&"end"!==property&&"row"!==property&&igv.isStringOrNumber(feature[property])&&data.push({name:property,value:feature[property]});return data}function calculateFeatureCoordinates(feature,bpStart,xScale){var px=Math.round((feature.start-bpStart)/xScale),px1=Math.round((feature.end-bpStart)/xScale),pw=px1-px;return pw<3&&(pw=3,px-=1),{px:px,px1:px1,pw:pw}}function renderFeature(feature,bpStart,xScale,pixelHeight,ctx){var x,e,exonCount,cy,direction,exon,ePx,ePx1,ePxU,ePw,py2,h2,py,windowX,windowX1,coord=calculateFeatureCoordinates(feature,bpStart,xScale),h=this.featureHeight,step=this.arrowSpacing,color=this.color;if(this.config.colorBy){var colorByValue=feature[this.config.colorBy.field];colorByValue&&(color=this.config.colorBy.pallete[colorByValue])}else feature.color&&(color=feature.color);if(ctx.fillStyle=color,ctx.strokeStyle=color,"SQUISHED"===this.displayMode&&void 0!=feature.row?(h=this.featureHeight/2,py=this.expandedCallHeight*feature.row+2):py="EXPANDED"===this.displayMode&&void 0!=feature.row?this.squishedCallHeight*feature.row+5:5,cy=py+h/2,h2=h/2,py2=cy-h2/2,0==(exonCount=feature.exons?feature.exons.length:0))ctx.fillRect(coord.px,py,coord.pw,h);else{for(igv.graphics.strokeLine(ctx,coord.px+1,cy,coord.px1-1,cy),direction="+"==feature.strand?1:-1,x=coord.px+step/2;x<coord.px1;x+=step)igv.graphics.strokeLine(ctx,x-2*direction,cy-2,x,cy),igv.graphics.strokeLine(ctx,x-2*direction,cy+2,x,cy);for(e=0;e<exonCount;e++)if(exon=feature.exons[e],ePx=Math.round((exon.start-bpStart)/xScale),ePx1=Math.round((exon.end-bpStart)/xScale),ePw=Math.max(1,ePx1-ePx),exon.utr)ctx.fillRect(ePx,py2,ePw,h2);else if(exon.cdStart&&(ePxU=Math.round((exon.cdStart-bpStart)/xScale),ctx.fillRect(ePx,py2,ePxU-ePx,h2),ePw-=ePxU-ePx,ePx=ePxU),exon.cdEnd&&(ePxU=Math.round((exon.cdEnd-bpStart)/xScale),ctx.fillRect(ePxU,py2,ePx1-ePxU,h2),ePw-=ePx1-ePxU,ePx1=ePxU),ctx.fillRect(ePx,py,ePw,h),ePw>step+5){for(ctx.fillStyle="white",ctx.strokeStyle="white",x=ePx+step/2;x<ePx1;x+=step)igv.graphics.strokeLine(ctx,x-2*direction,cy-2,x,cy),igv.graphics.strokeLine(ctx,x-2*direction,cy+2,x,cy);ctx.fillStyle=color,ctx.strokeStyle=color}}windowX=Math.round(igv.browser.referenceFrame.toPixels(igv.browser.referenceFrame.start-bpStart)),windowX1=windowX+igv.browser.trackViewportWidth(),renderFeatureLabels.call(this,ctx,feature,coord.px,coord.px1,py,windowX,windowX1)}function renderFeatureLabels(ctx,feature,featureX,featureX1,featureY,windowX,windowX1){var geneColor,geneFontStyle,transform,boxX,boxX1,labelX,labelY,textFitsInBox;featureX1<windowX||featureX>windowX1?(boxX=featureX,boxX1=featureX1):(boxX=Math.max(featureX,windowX),boxX1=Math.min(featureX1,windowX1)),igv.browser.selection&&"genes"===this.config.type&&void 0!==feature.name&&(geneColor=igv.browser.selection.colorForGene(feature.name)),((textFitsInBox=boxX1-boxX>ctx.measureText(feature.name).width)||geneColor)&&"SQUISHED"!=this.displayMode&&void 0!==feature.name&&(geneFontStyle={font:"10px PT Sans",textAlign:"center",fillStyle:geneColor||this.color,strokeStyle:geneColor||this.color},"COLLAPSED"===this.displayMode&&"SLANT"===this.labelDisplayMode&&(transform={rotate:{angle:45}},delete geneFontStyle.textAlign),labelX=boxX+(boxX1-boxX)/2,labelY=getFeatureLabelY(featureY,transform),igv.graphics.fillText(ctx,feature.name,labelX,labelY,geneFontStyle,transform))}function getFeatureLabelY(featureY,transform){return transform?featureY+20:featureY+25}function monitorTrackDrag(track){var onDragEnd=function(){track.trackView&&track.trackView.tile&&"SQUISHED"!==track.displayMode&&track.trackView.update()},unSubscribe=function(removedTrack){track===removedTrack&&(igv.browser.un("trackdrag",onDragEnd),igv.browser.un("trackremoved",unSubscribe))};igv.browser.on("trackdragend",onDragEnd),igv.browser.on("trackremoved",unSubscribe)}function renderVariant(variant,bpStart,xScale,pixelHeight,ctx){var style,coord=calculateFeatureCoordinates(variant,bpStart,xScale),py=20,h=10;switch(variant.genotype){case"HOMVAR":style=this.homvarColor;break;case"HETVAR":style=this.hetvarColor;break;default:style=this.color}ctx.fillStyle=style,ctx.fillRect(coord.px,py,coord.pw,h)}function renderFusionJuncSpan(feature,bpStart,xScale,pixelHeight,ctx){var py=(calculateFeatureCoordinates(feature,bpStart,xScale),5),rowHeight="EXPANDED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;"SQUISHED"===this.displayMode&&void 0!=feature.row?py=rowHeight*feature.row:"EXPANDED"===this.displayMode&&void 0!=feature.row&&(py=rowHeight*feature.row);var cy=py+.5*rowHeight,top_y=cy-.5*rowHeight,bottom_y=cy+.5*rowHeight,junction_left_px=Math.round((feature.junction_left-bpStart)/xScale),junction_right_px=Math.round((feature.junction_right-bpStart)/xScale);ctx.beginPath(),ctx.moveTo(junction_left_px,cy),ctx.bezierCurveTo(junction_left_px,top_y,junction_right_px,top_y,junction_right_px,cy),ctx.lineWidth=1+Math.log(feature.num_junction_reads)/Math.log(2),ctx.strokeStyle="blue",ctx.stroke();for(var spanning_coords=feature.spanning_frag_coords,i=0;i<spanning_coords.length;i++){var spanning_info=spanning_coords[i],span_left_px=Math.round((spanning_info.left-bpStart)/xScale),span_right_px=Math.round((spanning_info.right-bpStart)/xScale);ctx.beginPath(),ctx.moveTo(span_left_px,cy),ctx.bezierCurveTo(span_left_px,bottom_y,span_right_px,bottom_y,span_right_px,cy),ctx.lineWidth=1,ctx.strokeStyle="purple",ctx.stroke()}}return igv.FeatureTrack=function(config){igv.configTrack(this,config),this.displayMode=config.displayMode||"COLLAPSED",this.labelDisplayMode=config.labelDisplayMode,this.variantHeight=config.variantHeight||this.height,this.squishedCallHeight=config.squishedCallHeight||30,this.expandedCallHeight=config.expandedCallHeight||15,this.featureHeight=config.featureHeight||14,void 0===config.maxRows&&(config.maxRows=500),this.maxRows=config.maxRows,config.url&&(config.url.toLowerCase().endsWith(".bigbed")||config.url.toLowerCase().endsWith(".bb"))?this.featureSource=new igv.BWSource(config):this.featureSource=new igv.FeatureSource(config),config.render?this.render=config.render:"variant"===config.type?(this.render=renderVariant,this.homvarColor="rgb(17,248,254)",this.hetvarColor="rgb(34,12,253)"):"FusionJuncSpan"===config.type?(this.render=renderFusionJuncSpan,this.height=config.height||50,this.autoHeight=!1):(this.render=renderFeature,this.arrowSpacing=30,monitorTrackDrag(this))},igv.FeatureTrack.prototype.getFileHeader=function(){var self=this;return new Promise(function(fulfill,reject){"function"==typeof self.featureSource.getFileHeader?self.featureSource.getFileHeader().then(function(header){header&&(header.name&&!self.config.name&&(self.name=header.name),header.color&&!self.config.color&&(self.color="rgb("+header.color+")")),fulfill(header)}).catch(reject):fulfill(null)})},igv.FeatureTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){self.featureSource.getFeatures(chr,bpStart,bpEnd).then(fulfill).catch(reject)})},igv.FeatureTrack.prototype.computePixelHeight=function(features){if("COLLAPSED"===this.displayMode)return this.variantHeight;var maxRow=0;return features&&"function"==typeof features.forEach&&features.forEach(function(feature){feature.row&&feature.row>maxRow&&(maxRow=feature.row)}),Math.max(this.variantHeight,(maxRow+1)*("SQUISHED"===this.displayMode?this.expandedCallHeight:this.squishedCallHeight))},igv.FeatureTrack.prototype.draw=function(options){var track=this,featureList=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,bpEnd=bpStart+pixelWidth*bpPerPixel+1;if(igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),featureList){for(var gene,i=0,len=featureList.length;i<len;i++)if(gene=featureList[i],!(gene.end<bpStart)){if(gene.start>bpEnd)break;track.render.call(this,gene,bpStart,bpPerPixel,pixelHeight,ctx)}}else console.log("No feature list")},igv.FeatureTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){if(this.featureSource.featureCache){var row,chr=igv.browser.referenceFrame.chr,tolerance=2*igv.browser.referenceFrame.bpPerPixel,featureList=this.featureSource.featureCache.queryFeatures(chr,genomicLocation-tolerance,genomicLocation+tolerance);if("COLLAPSED"!=this.displayMode&&(row=Math.floor("SQUISHED"===this.displayMode?yOffset/this.expandedCallHeight:yOffset/this.squishedCallHeight)),featureList&&featureList.length>0){var popupData=[];return featureList.forEach(function(feature){if(feature.end>=genomicLocation-tolerance&&feature.start<=genomicLocation+tolerance&&(void 0===row||void 0===feature.row||row===feature.row)){var featureData;featureData=feature.popupData?feature.popupData(genomicLocation):extractPopupData(feature),featureData&&(popupData.length>0&&popupData.push("<HR>"),Array.prototype.push.apply(popupData,featureData))}}),popupData}}return null},igv.FeatureTrack.prototype.popupMenuItems=function(popover){var myself=this,menuItems=[],lut={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};return menuItems.push(igv.colorPickerMenuItem(popover,this.trackView)),["COLLAPSED","SQUISHED","EXPANDED"].forEach(function(displayMode,index){var chosen,str;chosen=0===index?'<div class="igv-track-menu-item igv-track-menu-border-top">':'<div class="igv-track-menu-item">',str=displayMode===myself.displayMode?chosen+'<i class="fa fa-check fa-check-shim"></i>'+lut[displayMode]+"</div>":chosen+'<i class="fa fa-check fa-check-shim fa-check-hidden"></i>'+lut[displayMode]+"</div>",menuItems.push({object:$(str),click:function(){popover.hide(),myself.displayMode=displayMode,myself.trackView.update()}})}),menuItems},igv}(igv||{}),igv=function(igv){function setTypes(){transcriptTypes=new Set,cdsTypes=new Set,utrTypes=new Set,exonTypes=new Set,transcriptTypes.addAll(["transcript","primary_transcript","processed_transcript","mRNA","mrna"]),cdsTypes.addAll(["CDS","cds","start_codon","stop_codon"]),utrTypes.addAll(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),exonTypes.addAll(["exon","coding-exon"])}function combineFeaturesGTF(features){var transcripts={},combinedFeatures=[];return features.forEach(function(f){var transcriptId,gffTranscript;transcriptTypes.has(f.type)&&(transcriptId=f.id,transcriptId?(gffTranscript=new GFFTranscript(f),transcripts[transcriptId]=gffTranscript,combinedFeatures.push(gffTranscript)):combinedFeatures.push(f))}),features.forEach(function(f){var id,transcript;exonTypes.has(f.type)&&(id=f.id)&&(transcript=transcripts[id],void 0===transcript&&(transcript=new GFFTranscript(f),transcripts[id]=transcript,combinedFeatures.push(transcript)),transcript.addExon(f))}),features.forEach(function(f){var id,transcript;(cdsTypes.has(f.type)||utrTypes.has(f.type))&&(id=f.id)&&(transcript=transcripts[id],void 0===transcript&&(transcript=new GFFTranscript(f),transcripts[id]=transcript,combinedFeatures.push(transcript)),utrTypes.has(f.type)?transcript.addUTR(f):transcript.addCDS(f))}),combinedFeatures.forEach(function(f){f instanceof GFFTranscript&&f.finish()}),combinedFeatures.sort(function(a,b){return a.start-b.start}),combinedFeatures}function combineFeaturesGFF(features){function getParents(f){return f.parent&&""!==f.parent.trim()?f.parent.trim().split(","):null}var parents,transcripts={},combinedFeatures=[];return features.forEach(function(f){var transcriptId,gffTranscript;transcriptTypes.has(f.type)&&(transcriptId=f.id,transcriptId?(gffTranscript=new GFFTranscript(f),transcripts[transcriptId]=gffTranscript,combinedFeatures.push(gffTranscript)):combinedFeatures.push(f))}),features.forEach(function(f){var transcript;exonTypes.has(f.type)&&(parents=getParents(f),parents?parents.forEach(function(id){transcript=transcripts[id],void 0===transcript&&(transcript=new GFFTranscript(f),transcripts[id]=transcript,combinedFeatures.push(transcript)),transcript.addExon(f)}):combinedFeatures.push(f))}),features.forEach(function(f){var transcript;(cdsTypes.has(f.type)||utrTypes.has(f.type))&&(parents=getParents(f),parents?parents.forEach(function(id){transcript=transcripts[id],void 0===transcript&&(transcript=new GFFTranscript(f),transcripts[id]=transcript,combinedFeatures.push(transcript)),utrTypes.has(f.type)?transcript.addUTR(f):transcript.addCDS(f)}):combinedFeatures.push(f))}),combinedFeatures.forEach(function(f){f instanceof GFFTranscript&&f.finish()}),combinedFeatures.sort(function(a,b){return a.start-b.start}),combinedFeatures}var transcriptTypes,cdsTypes,utrTypes,exonTypes;return igv.GFFHelper=function(format){this.format=format},igv.GFFHelper.prototype.combineFeatures=function(features){return void 0===transcriptTypes&&setTypes(),"gff3"===this.format?combineFeaturesGFF.call(this,features):combineFeaturesGTF.call(this,features)},GFFTranscript=function(feature){Object.assign(this,feature),this.exons=[],this.attributeString=feature.attributeString},GFFTranscript.prototype.addExon=function(feature){this.exons.push({start:feature.start,end:feature.end}),this.start=Math.min(this.start,feature.start),this.end=Math.max(this.end,feature.end)},GFFTranscript.prototype.addCDS=function(cds){var i,exon,exons=this.exons;for(i=0;i<exons.length;i++)if(exons[i].start<=cds.start&&exons[i].end>=cds.end){exon=exons[i];break}exon?(exon.cdStart=exon.cdStart?Math.min(cds.start,exon.cdStart):cds.start,exon.cdEnd=exon.cdEnd?Math.max(cds.end,exon.cdEnd):cds.end):exons.push({start:cds.start,end:cds.end,cdStart:cds.start,cdEnd:cds.end}),this.start=Math.min(this.start,cds.start),this.end=Math.max(this.end,cds.end),this.cdStart=this.cdStart?Math.min(cds.start,this.cdStart):cds.start,this.cdEnd=this.cdEnd?Math.max(cds.end,this.cdEnd):cds.end},GFFTranscript.prototype.addUTR=function(utr){var i,exon,exons=this.exons;for(i=0;i<exons.length;i++)if(exons[i].start<=utr.start&&exons[i].end>=utr.end){exon=exons[i];break}exon?utr.start===exon.start&&utr.end===exon.end&&(exon.utr=!0):exons.push({start:utr.start,end:utr.end,utr:!0}),this.start=Math.min(this.start,utr.start),this.end=Math.max(this.end,utr.end)},GFFTranscript.prototype.finish=function(){var cdStart=this.cdStart,cdEnd=this.cdEnd;this.exons.sort(function(a,b){return a.start-b.start}),cdStart&&this.exons.forEach(function(exon){(exon.end<cdStart||exon.start>cdEnd)&&(exon.utr=!0)})},igv}(igv||{}),igv=function(igv){Number.MAX_VALUE;return igv.SegParser=function(){},igv.SegParser.prototype.parseHeader=function(data){var line,i,tokens,lines=data.splitLines(),len=lines.length;for(i=0;i<len;i++)if(line=lines[i],!line.startsWith("#"))return tokens=line.split("\t"),this.header={headings:tokens,lineCount:i+1},this.header;return this.header},igv.SegParser.prototype.parseFeatures=function(data){var tokens,i,dataColumn,lines=data?data.splitLines():[],len=lines.length,allFeatures=[];for(this.header||(this.header=this.parseHeader(data)),dataColumn=this.header.headings.length-1,i=this.header.lineCount;i<len;i++)lines[i],tokens=lines[i].split("\t"),tokens.length>dataColumn&&allFeatures.push({sample:tokens[0],chr:tokens[1],start:parseInt(tokens[2]),end:parseInt(tokens[3]),value:parseFloat(tokens[dataColumn])});return allFeatures},igv}(igv||{}),igv=function(igv){var sortDirection=1;return igv.SegTrack=function(config){igv.configTrack(this,config),this.displayMode=config.displayMode||"SQUISHED",this.maxHeight=config.maxHeight||500,this.sampleSquishHeight=config.sampleSquishHeight||2,this.sampleExpandHeight=config.sampleExpandHeight||12,this.posColorScale=config.posColorScale||new igv.GradientColorScale({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=config.negColorScale||new igv.GradientColorScale({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),this.sampleCount=0,this.samples={},this.sampleNames=[],this.featureSource=new igv.FeatureSource(this.config)},igv.SegTrack.prototype.popupMenuItems=function(popover){var myself=this;return[{name:"SQUISHED"===this.displayMode?"Expand sample hgt":"Squish sample hgt",click:function(){popover.hide(),myself.toggleSampleHeight()}}]},igv.SegTrack.prototype.toggleSampleHeight=function(){this.displayMode="SQUISHED"===this.displayMode?"EXPANDED":"SQUISHED",this.trackView.update()},igv.SegTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){0===self.sampleCount&&self.featureSource.reader.allSamples?self.featureSource.reader.allSamples().then(function(samples){samples.forEach(function(sample){self.samples[sample]=self.sampleCount,self.sampleNames.push(sample),self.sampleCount++}),self.featureSource.getFeatures(chr,bpStart,bpEnd).then(fulfill).catch(reject)}).catch(reject):self.featureSource.getFeatures(chr,bpStart,bpEnd).then(fulfill).catch(reject)})},igv.SegTrack.prototype.draw=function(options){function checkForLog(featureList){var i;if(void 0===myself.isLog)for(myself.isLog=!1,i=0;i<featureList.length;i++)if(featureList[i].value<0)return void(myself.isLog=!0)}var featureList,ctx,bpPerPixel,bpStart,pixelWidth,pixelHeight,bpEnd,segment,len,sample,i,y,color,value,px,px1,pw,xScale,sampleHeight,border,myself=this;if(sampleHeight="SQUISHED"===this.displayMode?this.sampleSquishHeight:this.sampleExpandHeight,border="SQUISHED"===this.displayMode?0:1,ctx=options.context,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),featureList=options.features){for(bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,bpEnd=bpStart+pixelWidth*bpPerPixel+1,xScale=bpPerPixel,i=0,len=featureList.length;i<len;i++)sample=featureList[i].sample,this.samples.hasOwnProperty(sample)||(this.samples[sample]=myself.sampleCount,this.sampleNames.push(sample),this.sampleCount++);for(checkForLog(featureList),i=0,len=featureList.length;i<len;i++)if(segment=featureList[i],!(segment.end<bpStart)){if(segment.start>bpEnd)break;y=myself.samples[segment.sample]*sampleHeight+border,value=segment.value,myself.isLog||(value=Math.log2(value/2)),color=value<-.1?myself.negColorScale.getColor(value):value>.1?myself.posColorScale.getColor(value):"white",px=Math.round((segment.start-bpStart)/xScale),px1=Math.round((segment.end-bpStart)/xScale),pw=Math.max(1,px1-px),igv.graphics.fillRect(ctx,px,y,pw,sampleHeight-2*border,{fillStyle:color})}}else console.log("No feature list")},igv.SegTrack.prototype.computePixelHeight=function(features){var sampleHeight="SQUISHED"===this.displayMode?this.sampleSquishHeight:this.sampleExpandHeight;for(i=0,len=features.length;i<len;i++)sample=features[i].sample,this.samples.hasOwnProperty(sample)||(this.samples[sample]=this.sampleCount,this.sampleNames.push(sample),this.sampleCount++);return this.sampleCount*sampleHeight},igv.SegTrack.prototype.sortSamples=function(chr,bpStart,bpEnd,direction,callback){var segment,min,max,f,i,s,sampleNames,myself=this,len=bpEnd-bpStart,scores={};this.featureSource.getFeatures(chr,bpStart,bpEnd).then(function(featureList){for(i=0,len=featureList.length;i<len;i++)if(segment=featureList[i],!(segment.end<bpStart)){if(segment.start>bpEnd)break;min=Math.max(bpStart,segment.start),max=Math.min(bpEnd,segment.end),f=(max-min)/len,s=scores[segment.sample],s||(s=0),scores[segment.sample]=s+f*segment.value}for(sampleNames=Object.keys(myself.samples),sampleNames.sort(function(a,b){var s1=scores[a],s2=scores[b];return s1||(s1=Number.MAX_VALUE),s2||(s2=Number.MAX_VALUE),s1==s2?0:s1>s2?direction:-1*direction}),i=0;i<sampleNames.length;i++)myself.samples[sampleNames[i]]=i;myself.sampleNames=sampleNames,callback()})},igv.SegTrack.prototype.altClick=function(genomicLocation,event){var refFrame=igv.browser.referenceFrame,bpWidth=refFrame.toBP(2.5),bpStart=genomicLocation-bpWidth,bpEnd=genomicLocation+bpWidth,chr=refFrame.chr,myself=this;this.sortSamples(chr,bpStart,bpEnd,sortDirection,function(){myself.trackView.update(),$(myself.trackView.viewportDiv).scrollTop(0)}),sortDirection*=-1},igv.SegTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){var sampleName,row,items,sampleHeight="SQUISHED"===this.displayMode?this.sampleSquishHeight:this.sampleExpandHeight;if((row=Math.floor(yOffset/sampleHeight))<this.sampleNames.length){if(sampleName=this.sampleNames[row],items=[{name:"Sample",value:sampleName}],this.featureSource.featureCache){var chr=igv.browser.referenceFrame.chr;this.featureSource.featureCache.queryFeatures(chr,genomicLocation,genomicLocation).forEach(function(f){f.sample===sampleName&&items.push({name:"Value",value:f.value})})}return items}return null},igv}(igv||{}),igv=function(igv){return igv.loadTribbleIndex=function(indexFile,config){var genome=igv.browser?igv.browser.genome:null;return new Promise(function(fulfill,reject){function readHeader(parser){var version=(parser.getInt(),parser.getInt(),parser.getInt());parser.getString(),parser.getLong(),parser.getLong(),parser.getString();if(flags=parser.getInt(),version<3&&(flags,SEQUENCE_DICTIONARY_FLAG,SEQUENCE_DICTIONARY_FLAG),version>=3)for(var nProperties=parser.getInt();nProperties-- >0;){parser.getString(),parser.getString()}}function readLinear(parser){var chr=parser.getString(),blockMax=0;genome&&(chr=genome.getChromosomeName(chr));for(var nBins=(parser.getInt(),parser.getInt()),blocks=(parser.getInt(),parser.getInt(),parser.getInt(),new Array),pos=parser.getLong(),blocks=new Array,binNumber=0;binNumber<nBins;binNumber++){var nextPos=parser.getLong();blocks.push({min:pos,max:nextPos}),pos=nextPos,nextPos>blockMax&&(blockMax=nextPos)}return{chr:chr,blocks:blocks}}igvxhr.loadArrayBuffer(indexFile,{headers:config.headers,withCredentials:config.withCredentials}).then(function(arrayBuffer){if(arrayBuffer){var index={},parser=new igv.BinaryParser(new DataView(arrayBuffer));readHeader(parser);for(var nChrs=parser.getInt();nChrs-- >0;){var chrIdx=readLinear(parser);index[chrIdx.chr]=chrIdx}fulfill(new igv.TribbleIndex(index))}else fulfill(null)}).catch(function(error){console.log(error),fulfill(null)})})},igv.TribbleIndex=function(chrIndexTable){this.chrIndex=chrIndexTable},igv.TribbleIndex.prototype.blocksForRange=function(queryChr,min,max){var chrIdx=this.chrIndex[queryChr];if(chrIdx){var blocks=chrIdx.blocks,lastBlock=blocks[blocks.length-1];return[{minv:{block:blocks[0].min,offset:0},maxv:{block:lastBlock.max,offset:0}}]}return null},igv}(igv||{}),igv=function(igv){function autoscale(features){var min=0,max=-Number.MAX_VALUE;return features.forEach(function(f){min=Math.min(min,f.value),max=Math.max(max,f.value)}),{min:min,max:max}}function signsDiffer(a,b){return a>0&&b<0||a<0&&b>0}return igv.WIGTrack=function(config){this.config=config,this.url=config.url,void 0===config.color&&(config.color="rgb(150,150,150)"),igv.configTrack(this,config),"bigwig"===config.format?this.featureSource=new igv.BWSource(config):"tdf"===config.format?this.featureSource=new igv.TDFSource(config):this.featureSource=new igv.FeatureSource(config),this.dataRange={min:config.min,max:config.max},this.paintAxis=igv.paintAxis},igv.WIGTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){self.featureSource.getFeatures(chr,bpStart,bpEnd).then(fulfill).catch(reject)})},igv.WIGTrack.prototype.popupMenuItems=function(popover){var self=this,menuItems=[],html=[];return menuItems.push(igv.colorPickerMenuItem(popover,this.trackView)),menuItems.push(igv.dataRangeMenuItem(popover,this.trackView)),html.push('<div class="igv-track-menu-item">'),html.push(!0===self.autoScale?'<i class="fa fa-check fa-check-shim">':'<i class="fa fa-check fa-check-shim fa-check-hidden">'),html.push("</i>"),html.push("Autoscale"),html.push("</div>"),menuItems.push({object:$(html.join("")),click:function(){var $fa=$(this).find("i");popover.hide(),self.autoScale=!self.autoScale,!0===self.autoScale?$fa.removeClass("fa-check-hidden"):$fa.addClass("fa-check-hidden"),self.trackView.update()}}),menuItems},igv.WIGTrack.prototype.draw=function(options){function renderFeature(feature,index,featureList){var yUnitless,heightUnitLess,x,width,rectEnd;feature.end<bpStart||feature.start>bpEnd||(x=Math.floor((feature.start-bpStart)/bpPerPixel),rectEnd=Math.ceil((feature.end-bpStart)/bpPerPixel),width=Math.max(1,rectEnd-x),signsDiffer(featureValueMinimum,featureValueMaximum)?feature.value<0?(yUnitless=featureValueMaximum/featureValueRange,heightUnitLess=-feature.value/featureValueRange):(yUnitless=(featureValueMaximum-feature.value)/featureValueRange,heightUnitLess=feature.value/featureValueRange):featureValueMinimum<0?(yUnitless=0,heightUnitLess=-feature.value/featureValueRange):(yUnitless=1-feature.value/featureValueRange,heightUnitLess=feature.value/featureValueRange),igv.graphics.fillRect(ctx,x,yUnitless*pixelHeight,width,heightUnitLess*pixelHeight,{fillStyle:self.color}))}var featureValueMinimum,featureValueMaximum,featureValueRange,self=this,features=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,bpEnd=bpStart+pixelWidth*bpPerPixel+1;if(features&&features.length>0){if(self.autoScale||void 0===self.dataRange.max){var s=autoscale(features);featureValueMinimum=s.min,featureValueMaximum=s.max}else featureValueMinimum=void 0===self.dataRange.min?0:self.dataRange.min,featureValueMaximum=self.dataRange.max;self.dataRange.min=featureValueMinimum,self.dataRange.max=featureValueMaximum,featureValueRange=featureValueMaximum-featureValueMinimum,features.forEach(renderFeature)}},igv}(igv||{}),igv=function(igv){function translateCigar(cigar){var cigarUnit,opLen,opLtr,lengthOnRef=0,cigarArray=[];for(i=0;i<cigar.length;i++)cigarUnit=cigar[i],opLtr=CigarOperationTable[cigarUnit.operation],opLen=parseInt(cigarUnit.operationLength),"M"!=opLtr&&"EQ"!=opLtr&&"X"!=opLtr&&"D"!=opLtr&&"N"!=opLtr&&"="!=opLtr||(lengthOnRef+=opLen),cigarArray.push({len:opLen,ltr:opLtr});return{lengthOnRef:lengthOnRef,array:cigarArray}}function translateCigar(cigar){var cigarUnit,opLen,opLtr,lengthOnRef=0,cigarArray=[];for(i=0;i<cigar.length;i++)cigarUnit=cigar[i],opLtr=CigarOperationTable[cigarUnit.operation],opLen=parseInt(cigarUnit.operationLength),"M"!=opLtr&&"EQ"!=opLtr&&"X"!=opLtr&&"D"!=opLtr&&"N"!=opLtr&&"="!=opLtr||(lengthOnRef+=opLen),cigarArray.push({len:opLen,ltr:opLtr});return{lengthOnRef:lengthOnRef,array:cigarArray}}function makeBlocks(record,cigarArray){for(var blockSeq,blockQuals,gapType,blocks=[],seqOffset=0,pos=record.start,len=cigarArray.length,i=0;i<len;i++){var c=cigarArray[i];switch(c.ltr){case"H":case"P":break;case"S":seqOffset+=c.len,gapType="S";break;case"N":pos+=c.len,gapType="N";break;case"D":pos+=c.len,gapType="D";break;case"I":seqOffset+=c.len;break;case"M":case"EQ":case"=":case"X":blockSeq="*"===record.seq?"*":record.seq.substr(seqOffset,c.len),blockQuals="*"===record.qual?"*":record.qual.slice(seqOffset,c.len),blocks.push({start:pos,len:c.len,seq:blockSeq,qual:blockQuals,gapType:gapType}),seqOffset+=c.len,pos+=c.len;break;default:console.log("Error processing cigar element: "+c.len+c.ltr)}}return blocks}var CigarOperationTable={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};return igv.Ga4ghAlignment=function(json,genome){this.readName=json.fragmentName,this.properPlacement=json.properPlacement,this.duplicateFragment=json.duplicateFragment,this.numberReads=json.numberReads,this.fragmentLength=json.fragmentLength,this.readNumber=json.readNumber,this.failedVendorQualityChecks=json.failedVendorQualityChecks,this.secondaryAlignment=json.secondaryAlignment,this.supplementaryAlignment=json.supplementaryAlignment,this.seq=json.alignedSequence,this.qual=json.alignedQuality,this.tagDict=json.info,alignment=json.alignment,alignment?(this.mapped=!0,this.chr=json.alignment.position.referenceName,genome&&(this.chr=genome.getChromosomeName(this.chr)),this.start=parseInt(json.alignment.position.position),this.strand=!json.alignment.position.reverseStrand,this.mq=json.alignment.mappingQuality,cigarDecoded=translateCigar(json.alignment.cigar),this.lengthOnRef=cigarDecoded.lengthOnRef,this.blocks=makeBlocks(this,cigarDecoded.array)):this.mapped=!1,json.nextMatePosition&&(this.mate={chr:json.nextMatePosition.referenceFrame,position:parseInt(json.nextMatePosition.position),strand:!json.nextMatePosition.reverseStrand},this.info=json.info)},igv.Ga4ghAlignment.prototype.isMapped=function(){return this.mapped},igv.Ga4ghAlignment.prototype.isPaired=function(){return this.numberReads&&this.numberReads>1},igv.Ga4ghAlignment.prototype.isProperPair=function(){return void 0===this.properPlacement||this.properPlacement},igv.Ga4ghAlignment.prototype.isFirstOfPair=function(){return this.readNumber&&0===this.readNumber},igv.Ga4ghAlignment.prototype.isSecondOfPair=function(){return this.readNumber&&1===this.readNumber},igv.Ga4ghAlignment.prototype.isSecondary=function(){return this.secondaryAlignment},igv.Ga4ghAlignment.prototype.isSupplementary=function(){return this.supplementaryAlignment},igv.Ga4ghAlignment.prototype.isFailsVendorQualityCheck=function(){return this.failedVendorQualityChecks},igv.Ga4ghAlignment.prototype.isDuplicate=function(){return this.duplicateFragment},igv.Ga4ghAlignment.prototype.isMateMapped=function(){return this.mate},igv.Ga4ghAlignment.prototype.mateStrand=function(){return this.mate&&this.mate.strand},igv.Ga4ghAlignment.prototype.tags=function(){return this.info},igv.Ga4ghAlignment.prototype.popupData=function(genomicLocation){function yesNo(bool){return bool?"Yes":"No"}var isFirst;nameValues=[],nameValues.push({name:"Read Name",value:this.readName}),nameValues.push("<hr>"),nameValues.push({name:"Alignment Start",value:igv.numberFormatter(1+this.start),borderTop:!0}),nameValues.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0}),nameValues.push({name:"Cigar",value:this.cigar}),nameValues.push({name:"Mapped",value:yesNo(this.isMapped())}),nameValues.push({name:"Mapping Quality",value:this.mq}),nameValues.push({name:"Secondary",value:yesNo(this.isSecondary())}),nameValues.push({name:"Supplementary",value:yesNo(this.isSupplementary())}),nameValues.push({name:"Duplicate",value:yesNo(this.isDuplicate())}),nameValues.push({name:"Failed QC",value:yesNo(this.isFailsVendorQualityCheck())}),this.isPaired()&&(nameValues.push("<hr>"),nameValues.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),nameValues.push({name:"Mate is Mapped",value:yesNo(this.isMateMapped())}),this.isMapped()&&(nameValues.push({name:"Mate Start",value:this.matePos}),nameValues.push({name:"Mate Strand",value:this.mateStrand()?"(-)":"(+)"}),nameValues.push({name:"Insert Size",value:this.fragmentLength}))),nameValues.push("<hr>"),this.tags(),isFirst=!0;for(var key in this.tagDict)this.tagDict.hasOwnProperty(key)&&(isFirst?(nameValues.push({name:key,value:this.tagDict[key],borderTop:!0}),isFirst=!1):nameValues.push({name:key,value:this.tagDict[key]}));return nameValues},igv}(igv||{}),igv=function(igv){function populateChrNameMap(chrNameMap,datasetId){var i;if("461916304629"===datasetId||"337315832689"===datasetId){for(i=1;i<23;i++)chrNameMap["chr"+i]=i;chrNameMap.chrX="X",chrNameMap.chrY="Y",chrNameMap.chrM="MT"}}var CigarOperationTable={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};return igv.Ga4ghAlignmentReader=function(config){this.config=config,this.url=config.url,this.filter=config.filter||new igv.BamFilter,this.readGroupSetIds=config.readGroupSetIds,this.authKey=config.authKey,this.samplingWindowSize=void 0===config.samplingWindowSize?100:config.samplingWindowSize,this.samplingDepth=void 0===config.samplingDepth?100:config.samplingDepth,config.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===config.pairsSupported||config.pairsSupported},igv.Ga4ghAlignmentReader.prototype.readAlignments=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){function getChrNameMap(){return new Promise(function(fulfill,reject){self.chrNameMap?fulfill(self.chrNameMap):self.readMetadata().then(function(json){if(self.chrNameMap={},igv.browser&&json.readGroups&&json.readGroups.length>0){var referenceSetId=json.readGroups[0].referenceSetId;if(console.log("No reference set specified"),referenceSetId){var readURL=self.url+"/references/search";igv.ga4ghSearch({url:readURL,body:{referenceSetId:referenceSetId},decode:function(j){return j.references}}).then(function(references){references.forEach(function(ref){var refName=ref.name,alias=igv.browser.genome.getChromosomeName(refName);self.chrNameMap[alias]=refName}),fulfill(self.chrNameMap)}).catch(reject)}else populateChrNameMap(self.chrNameMap,self.config.datasetId),fulfill(self.chrNameMap)}else fulfill(self.chrNameMap)}).catch(reject)})}function decodeGa4ghReads(json){function encodeCigar(cigarArray){var cigarString="";return cigarArray.forEach(function(cigarUnit){var op=CigarOperationTable[cigarUnit.operation],len=cigarUnit.operationLength;cigarString+=len+op}),cigarString}function encodeFlags(json){return 0}function translateCigar(cigar){var cigarUnit,opLen,opLtr,i,lengthOnRef=0,cigarArray=[];for(i=0;i<cigar.length;i++)cigarUnit=cigar[i],opLtr=CigarOperationTable[cigarUnit.operation],opLen=parseInt(cigarUnit.operationLength),"M"!==opLtr&&"EQ"!==opLtr&&"X"!==opLtr&&"D"!==opLtr&&"N"!==opLtr&&"="!==opLtr||(lengthOnRef+=opLen),cigarArray.push({len:opLen,ltr:opLtr});return{lengthOnRef:lengthOnRef,array:cigarArray}}function makeBlocks(record,cigarArray){for(var insertions,blockSeq,gapType,blockQuals,blocks=[],seqOffset=0,pos=record.start,len=cigarArray.length,i=0;i<len;i++){var c=cigarArray[i];switch(c.ltr){case"H":case"P":break;case"S":seqOffset+=c.len,gapType="S";break;case"N":pos+=c.len,gapType="N";break;case"D":pos+=c.len,gapType="D";break;case"I":blockSeq="*"===record.seq?"*":record.seq.substr(seqOffset,c.len),blockQuals=record.qual?record.qual.slice(seqOffset,c.len):void 0,void 0===insertions&&(insertions=[]),insertions.push({start:pos,len:c.len,seq:blockSeq,qual:blockQuals}),seqOffset+=c.len;break;case"M":case"EQ":case"=":case"X":blockSeq="*"===record.seq?"*":record.seq.substr(seqOffset,c.len),blockQuals=record.qual?record.qual.slice(seqOffset,c.len):void 0,blocks.push({start:pos,len:c.len,seq:blockSeq,qual:blockQuals,gapType:gapType}),seqOffset+=c.len,pos+=c.len;break;default:console.log("Error processing cigar element: "+c.len+c.ltr)}}return{blocks:blocks,insertions:insertions}}var i,json,alignment,jsonAlignment,cigarDecoded,mate,jsonRecords=json.alignments,len=jsonRecords.length,alignments=[],genome=igv.browser.genome;for(i=0;i<len;i++)json=jsonRecords[i],alignment=new igv.BamAlignment,alignment.readName=json.fragmentName,alignment.properPlacement=json.properPlacement,alignment.duplicateFragment=json.duplicateFragment,alignment.numberReads=json.numberReads,alignment.fragmentLength=json.fragmentLength,alignment.readNumber=json.readNumber,alignment.failedVendorQualityChecks=json.failedVendorQualityChecks,alignment.secondaryAlignment=json.secondaryAlignment,alignment.supplementaryAlignment=json.supplementaryAlignment,alignment.seq=json.alignedSequence,alignment.qual=json.alignedQuality,alignment.matePos=json.nextMatePosition,alignment.tagDict=json.info,alignment.flags=encodeFlags(json),jsonAlignment=json.alignment,jsonAlignment?(alignment.mapped=!0,alignment.chr=json.alignment.position.referenceName,genome&&(alignment.chr=genome.getChromosomeName(alignment.chr)),alignment.start=parseInt(json.alignment.position.position),alignment.strand=!json.alignment.position.reverseStrand,alignment.mq=json.alignment.mappingQuality,alignment.cigar=encodeCigar(json.alignment.cigar),cigarDecoded=translateCigar(json.alignment.cigar),alignment.lengthOnRef=cigarDecoded.lengthOnRef,blocks=makeBlocks(alignment,cigarDecoded.array),alignment.blocks=blocks.blocks,alignment.insertions=blocks.insertions):alignment.mapped=!1,mate=json.nextMatePosition,mate&&(alignment.mate={chr:mate.referenceFrame,position:parseInt(mate.position),strand:!mate.reverseStrand}),self.filter.pass(alignment)&&alignments.push(alignment);return alignments}getChrNameMap().then(function(chrNameMap){var queryChr=chrNameMap.hasOwnProperty(chr)?chrNameMap[chr]:chr,readURL=self.url+"/reads/search";igv.ga4ghSearch({url:readURL,body:{readGroupSetIds:[self.readGroupSetIds],referenceName:queryChr,start:bpStart,end:bpEnd,pageSize:"10000"},decode:decodeGa4ghReads,results:new igv.AlignmentContainer(chr,bpStart,bpEnd,self.samplingWindowSize,self.samplingDepth,self.pairsSupported)}).then(fulfill).catch(reject)}).catch(reject)})},igv.Ga4ghAlignmentReader.prototype.readMetadata=function(){return igv.ga4ghGet({url:this.url,entity:"readgroupsets",entityId:this.readGroupSetIds})},igv.decodeGa4ghReadset=function(json){var sequenceNames=[];return json.fileData.forEach(function(fileObject){fileObject.refSequences.forEach(function(refSequence){sequenceNames.push(refSequence.name)})}),sequenceNames},igv}(igv||{}),igv=function(igv){function ga4ghHeaders(){var headers={},acToken=oauth.google.access_token;return headers["Cache-Control"]="no-cache",acToken&&(headers.Authorization="Bearer "+acToken),headers}return igv.ga4ghGet=function(options){var url=options.url+"/"+options.entity+"/"+options.entityId;return igvxhr.loadJson(url,options)},igv.ga4ghSearch=function(options){return new Promise(function(fulfill,reject){function loadChunk(pageToken){pageToken?body.pageToken=pageToken:void 0!=body.pageToken&&delete body.pageToken;var sendData=JSON.stringify(body);igvxhr.loadJson(url,{sendData:sendData,contentType:"application/json",headers:ga4ghHeaders()}).then(function(json){var nextPageToken,tmp;json?(tmp=decode?decode(json):json,tmp&&tmp.forEach(function(a){results.push(a)}),nextPageToken=json.nextPageToken,nextPageToken?loadChunk(nextPageToken):fulfill(results)):fulfill(results)}).catch(function(error){reject(error)})}var results=options.results?options.results:[],url=options.url,body=options.body,decode=options.decode,apiKey=oauth.google.apiKey,paramSeparator="?",fields=options.fields;apiKey&&(url=url+paramSeparator+"key="+apiKey,paramSeparator="&"),fields&&(url=url+paramSeparator+"fields="+fields),loadChunk()})},igv.ga4ghSearchReadGroupSets=function(options){igv.ga4ghSearch({url:options.url+"/readgroupsets/search",body:{datasetIds:[options.datasetId],pageSize:"10000"},decode:function(json){return json.readGroupSets}}).then(function(results){options.success(results)}).catch(function(error){console.log(error)})},igv.ga4ghSearchVariantSets=function(options){igv.ga4ghSearch({url:options.url+"/variantsets/search",body:{datasetIds:[options.datasetId],pageSize:"10000"},decode:function(json){return json.variantSets}}).then(function(results){options.success(results)}).catch(function(error){console.log(error)})},igv.ga4ghSearchCallSets=function(options){options.datasetId?igv.ga4ghSearchVariantSets({url:options.url,datasetId:options.datasetId,success:function(results){var variantSetIds=[];results.forEach(function(vs){variantSetIds.push(vs.id)}),options.datasetId=void 0,options.variantSetIds=variantSetIds,igv.ga4ghSearchCallSets(options)}}):igv.ga4ghSearch({url:options.url+"/callsets/search",body:{variantSetIds:options.variantSetIds,pageSize:"10000"},decode:function(json){return json.callSets&&json.callSets.forEach(function(cs){cs.variantSetIds=options.variantSetIds}),json.callSets}}).then(function(results){options.success(results)}).catch(function(error){console.log(error)})},igv.ga4ghSearchReadAndCallSets=function(options){igv.ga4ghSearchReadGroupSets({url:options.url,datasetId:options.datasetId,success:function(readGroupSets){igv.ga4ghSearchCallSets({url:options.url,datasetId:options.datasetId,success:function(callSets){var csHash={};callSets.forEach(function(cs){csHash[cs.name]=cs});var mergedResults=[];readGroupSets.forEach(function(rg){var m={readGroupSetId:rg.id,name:rg.name,datasetId:options.datasetId},cs=csHash[rg.name];cs&&(m.callSetId=cs.id,m.variantSetIds=cs.variantSetIds),mergedResults.push(m)}),options.success(mergedResults)}})}})},igv}(igv||{}),igv=function(igv){return igv.Ga4ghVariantReader=function(config){this.config=config,this.url=config.url,this.variantSetId=config.variantSetId,this.callSetIds=config.callSetIds,this.includeCalls=void 0===config.includeCalls||config.includeCalls},igv.Ga4ghVariantReader.prototype.readHeader=function(){var self=this;return new Promise(function(fulfill,reject){if(self.header)fulfill(self.header);else if(self.header={},!1===self.includeCalls)fulfill(self.header);else{var readURL=self.url+"/callsets/search";igv.ga4ghSearch({url:readURL,fields:"nextPageToken,callSets(id,name)",body:{variantSetIds:Array.isArray(self.variantSetId)?self.variantSetId:[self.variantSetId],pageSize:"10000"},decode:function(json){if(self.callSetIds){var filteredCallSets=[],csIdSet=new Set;return csIdSet.addAll(self.callSetIds),json.callSets.forEach(function(cs){csIdSet.has(cs.id)&&filteredCallSets.push(cs)}),filteredCallSets}return json.callSets}}).then(function(callSets){self.header.callSets=callSets,fulfill(self.header)}).catch(reject)}})},igv.Ga4ghVariantReader.prototype.readFeatures=function(chr,bpStart,bpEnd){function getChrNameMap(){return new Promise(function(fulfill,reject){self.chrNameMap?fulfill(self.chrNameMap):self.readMetadata().then(function(json){self.metadata=json.metadata,self.chrNameMap={},json.referenceBounds&&igv.browser&&json.referenceBounds.forEach(function(rb){var refName=rb.referenceName,alias=igv.browser.genome.getChromosomeName(refName);self.chrNameMap[alias]=refName}),fulfill(self.chrNameMap)})})}var self=this;return new Promise(function(fulfill,reject){self.readHeader().then(function(header){getChrNameMap().then(function(chrNameMap){var queryChr=chrNameMap.hasOwnProperty(chr)?chrNameMap[chr]:chr,readURL=self.url+"/variants/search";igv.ga4ghSearch({url:readURL,fields:self.includeCalls?void 0:"nextPageToken,variants(id,variantSetId,names,referenceName,start,end,referenceBases,alternateBases,quality, filter, info)",body:{variantSetIds:Array.isArray(self.variantSetId)?self.variantSetId:[self.variantSetId],callSetIds:self.callSetIds?self.callSetIds:void 0,referenceName:queryChr,start:bpStart.toString(),end:bpEnd.toString(),pageSize:"10000"},decode:function(json){var variants=[];return json.variants.forEach(function(json){variants.push(igv.createGAVariant(json))}),variants}}).then(fulfill).catch(reject)}).catch(reject)}).catch(reject)})},igv.Ga4ghVariantReader.prototype.readMetadata=function(){return igv.ga4ghGet({url:this.url,entity:"variantsets",entityId:this.variantSetId})},igv}(igv||{}),igv=function(igv){return igv.Google={isGoogleURL:function(url){return url.contains("googleapis")},translateGoogleCloudURL:function(gsUrl){var i=gsUrl.indexOf("/",5);return i<0?(console.log("Invalid gs url: "+gsUrl),gsUrl):"https://www.googleapis.com/storage/v1/b/"+gsUrl.substring(5,i)+"/o/"+encodeURIComponent(gsUrl.substring(i+1))+"?alt=media"},addGoogleHeaders:function(headers){headers["Cache-Control"]="no-cache";var acToken=oauth.google.access_token;return acToken&&!headers.hasOwnProperty("Authorization")&&(headers.Authorization="Bearer "+acToken),headers},addApiKey:function(url){var apiKey=oauth.google.apiKey,paramSeparator=url.contains("?")?"&":"?";return void 0===apiKey||url.contains("key=")||apiKey&&(url=url+paramSeparator+"key="+apiKey),url}},igv}(igv||{}),igv=function(igv){function loadCytobands(cytobandUrl,withCredentials,continuation){igvxhr.loadString(cytobandUrl,{withCredentials:withCredentials}).then(function(data){for(var lastChr,bands=[],n=0,c=1,lines=data.splitLines(),len=lines.length,cytobands={},i=0;i<len;i++){var tokens=lines[i].split("\t"),chr=tokens[0];if(lastChr||(lastChr=chr),chr!=lastChr&&(cytobands[lastChr]=bands,bands=[],lastChr=chr,n=0,c++),5==tokens.length){var chr=tokens[0],start=parseInt(tokens[1]),end=parseInt(tokens[2]),name=tokens[3],stain=tokens[4];bands[n++]=new igv.Cytoband(start,end,name,stain)}}continuation(cytobands)})}function loadAliases(aliasURL,withCredentials,continuation){igvxhr.loadString(aliasURL,{withCredentials:withCredentials}).then(function(data){var lines=data.splitLines(),aliases=[];lines.forEach(function(line){!line.startsWith("#")&line.length>0&&aliases.push(line.split("\t"))}),continuation(aliases)})}return igv.Genome=function(sequence,ideograms,aliases){this.sequence=sequence,this.chromosomeNames=sequence.chromosomeNames,this.chromosomes=sequence.chromosomes,this.ideograms=ideograms;var chrAliasTable={},self=this;this.chromosomeNames.forEach(function(name){var alias=name.startsWith("chr")?name.substring(3):"chr"+name;chrAliasTable[alias]=name,"chrM"===name&&(chrAliasTable.MT="chrM"),"MT"===name&&(chrAliasTable.chrmM="MT")}),aliases&&aliases.forEach(function(array){var defName;for(i=0;i<array.length;i++)if(self.chromosomes[array[i]]){defName=array[i];break}defName&&array.forEach(function(alias){alias!==defName&&(chrAliasTable[alias]=defName)})}),this.chrAliasTable=chrAliasTable},igv.Genome.prototype.getChromosomeName=function(str){var chr=this.chrAliasTable[str];return chr||str},igv.Genome.prototype.getChromosome=function(chr){return chr=this.getChromosomeName(chr),this.chromosomes[chr]},igv.Genome.prototype.getCytobands=function(chr){return this.ideograms?this.ideograms[chr]:null},igv.Genome.prototype.getLongestChromosome=function(){var longestChr,key,chromosomes=this.chromosomes;for(key in chromosomes){if(chromosomes.hasOwnProperty(key)){var chr=chromosomes[key];(void 0===longestChr||chr.bpLength>longestChr.bpLength)&&(longestChr=chr)}return longestChr}},igv.Genome.prototype.getChromosomes=function(){return this.chromosomes},igv.Chromosome=function(name,order,bpLength){this.name=name,this.order=order,this.bpLength=bpLength},igv.Cytoband=function(start,end,name,typestain){this.start=start,this.end=end,this.name=name,this.stain=0,"acen"==typestain?this.type="c":(this.type=typestain.charAt(1),"p"==this.type&&(this.stain=parseInt(typestain.substring(4))))},igv.GenomicInterval=function(chr,start,end,features){this.chr=chr,this.start=start,this.end=end,this.features=features},igv.GenomicInterval.prototype.contains=function(chr,start,end){return this.chr==chr&&this.start<=start&&this.end>=end},igv.GenomicInterval.prototype.containsRange=function(range){return this.chr===range.chr&&this.start<=range.start&&this.end>=range.end},igv.loadGenome=function(reference){return new Promise(function(fulfill,reject){function checkReady(){!(void 0!==cytobandUrl&&void 0===cytobands||void 0!==aliasURL&&void 0===aliases)&&fulfill(new igv.Genome(sequence,cytobands,aliases))}var cytobands,aliases,chrNames,sequence,cytobandUrl=reference.cytobandURL,aliasURL=reference.aliasURL,chromosomes={};sequence=new igv.FastaSequence(reference),sequence.init().then(function(){chrNames=sequence.chromosomeNames,chromosomes=sequence.chromosomes,cytobandUrl&&loadCytobands(cytobandUrl,reference.withCredentials,function(result){cytobands=result,checkReady()}),aliasURL&&loadAliases(aliasURL,reference.withCredentials,function(result){aliases=result,checkReady()}),checkReady()}).catch(function(err){reject(err)})})},igv}(igv||{}),igv=function(igv){function selectedFeature(feature,source){console.log(feature+" "+source);var type="gtex"===source?"snp":"gene";this.selection=new GtexSelection("gene"==type?{gene:feature}:{snp:feature}),igv.browser.update()}igv.EqtlTrack=function(config){var url=config.url,label=config.name;this.config=config,this.url=url,this.name=label,this.pValueField=config.pValueField||"pValue",this.geneField=config.geneField||"geneName",this.minLogP=config.minLogP||3.5,this.maxLogP=config.maxLogP||25,this.background=config.background,this.divider=config.divider||"rgb(225,225,225)",this.dotSize=config.dotSize||2,this.height=config.height||100,this.autoHeight=!1,this.disableButtons=config.disableButtons,this.featureSource=new igv.FeatureSource(config),this.onsearch=function(feature,source){selectedFeature.call(this,feature,source)}},igv.EqtlTrack.prototype.paintAxis=function(ctx,pixelWidth,pixelHeight){var track=this,yScale=(track.maxLogP-track.minLogP)/pixelHeight,font={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"});for(var p=4;p<=track.maxLogP;p+=2){var x1,x2,y1,y2,ref;ref=.85*pixelWidth,x1=ref-5,x2=ref,y1=y2=pixelHeight-Math.round((p-track.minLogP)/yScale),igv.graphics.strokeLine(ctx,x1,y1,x2,y2,font),igv.graphics.fillText(ctx,p,x1-1,y1+2,font)}font.textAlign="center",igv.graphics.fillText(ctx,"-log10(pvalue)",pixelWidth/4,pixelHeight/2,font,{rotate:{angle:-90}})},igv.EqtlTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){return this.featureSource.getFeatures(chr,bpStart,bpEnd)},igv.EqtlTrack.prototype.draw=function(options){function drawEqtls(drawSelected){var eqtl,i,px,py,color,isSelected,snp,geneName,selection,radius=drawSelected?2*track.dotSize:track.dotSize;for(igv.graphics.setProperties(ctx,{fillStyle:"rgb(180, 180, 180)",strokeStyle:"rgb(180, 180, 180)"}),i=0;i<len;i++)if(eqtl=featureList[i],snp=eqtl.snp.toUpperCase(),geneName=eqtl[track.geneField].toUpperCase(),selection=igv.browser.selection,isSelected=selection&&(selection.snp===snp||selection.gene===geneName),(!drawSelected||isSelected)&&(selection&&selection.snp===snp&&selection.addGene(geneName),drawSelected&&selection&&(color=selection.colorForGene(geneName)),!(drawSelected&&void 0===color||(px=Math.round(eqtl.position-bpStart+.5)/bpPerPixel)<0))){if(px>pixelWidth)break;var mLogP=-Math.log(eqtl[track.pValueField])/Math.LN10;mLogP<track.minLogP||(py=Math.max(0+radius,pixelHeight-Math.round((mLogP-track.minLogP)/yScale)),eqtl.px=px,eqtl.py=py,color&&igv.graphics.setProperties(ctx,{fillStyle:color,strokeStyle:"black"}),igv.graphics.fillCircle(ctx,px,py,radius),igv.graphics.strokeCircle(ctx,px,py,radius))}}var track=this,featureList=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,yScale=(track.maxLogP-track.minLogP)/pixelHeight;if(this.background&&igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:this.background}),igv.graphics.strokeLine(ctx,0,pixelHeight-1,pixelWidth,pixelHeight-1,{strokeStyle:this.divider}),ctx){var len=featureList.length;ctx.save(),drawEqtls(!1),drawEqtls(!0),ctx.restore()}},igv.EqtlTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){if(this.featureSource.featureCache){var chr=igv.browser.referenceFrame.chr,tolerance=2*this.dotSize*igv.browser.referenceFrame.bpPerPixel,featureList=this.featureSource.featureCache.queryFeatures(chr,genomicLocation-tolerance,genomicLocation+tolerance),dotSize=this.dotSize,tissue=this.name;if(featureList&&featureList.length>0){var popupData=[];return featureList.forEach(function(feature){feature.end>=genomicLocation-tolerance&&feature.start<=genomicLocation+tolerance&&feature.py-yOffset<2*dotSize&&(popupData.length>0&&popupData.push("<hr>"),popupData.push({name:"snp id",value:feature.snp},{name:"gene id",value:feature.geneId},{name:"gene name",value:feature.geneName},{name:"p value",value:feature.pValue},{name:"tissue",value:tissue}))}),popupData}}},GtexSelection=function(selection){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,selection.gene&&(this.gene=selection.gene.toUpperCase(),this.geneColors[this.gene]=brewer[this.genesCount++]),selection.snp&&(this.snp=selection.snp.toUpperCase())},GtexSelection.prototype.addGene=function(geneName){this.geneColors[geneName.toUpperCase()]||(this.geneColors[geneName.toUpperCase()]=brewer[this.genesCount++])},GtexSelection.prototype.colorForGene=function(geneName){return this.geneColors[geneName.toUpperCase()]};var brewer=new Array;return brewer.push("rgb(228,26,28)"),brewer.push("rgb(55,126,184)"),brewer.push("rgb(77,175,74)"),brewer.push("rgb(166,86,40)"),brewer.push("rgb(152,78,163)"),brewer.push("rgb(255,127,0)"),brewer.push("rgb(247,129,191)"),brewer.push("rgb(153,153,153)"),brewer.push("rgb(255,255,51)"),brewer.push("rgb(102, 194, 165"),brewer.push("rgb(252, 141, 98"),brewer.push("rgb(141, 160, 203"),brewer.push("rgb(231, 138, 195"),brewer.push("rgb(166, 216, 84"),brewer.push("rgb(255, 217, 47"),brewer.push("rgb(229, 196, 148"),brewer.push("rgb(179, 179, 179"),brewer.push("rgb( 141, 211, 199"),brewer.push("rgb(255, 255, 179"),brewer.push("rgb(190, 186, 218"),brewer.push("rgb(251, 128, 114"),brewer.push("rgb(128, 177, 211"),brewer.push("rgb(253, 180, 98"),brewer.push("rgb(179, 222, 105"),brewer.push("rgb(252, 205, 229"),brewer.push("rgb(217, 217, 217"),brewer.push("rgb(188, 128, 189"),brewer.push("rgb(204, 235, 197"),brewer.push("rgb(255, 237, 111"),igv}(igv||{}),igv=function(igv){igv.GtexSelection=function(selection){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,selection.gene&&(this.gene=selection.gene.toUpperCase(),this.geneColors[this.gene]=brewer[this.genesCount++]),selection.snp&&(this.snp=selection.snp.toUpperCase())},igv.GtexSelection.prototype.addGene=function(geneName){this.geneColors[geneName.toUpperCase()]||(this.geneColors[geneName.toUpperCase()]=brewer[this.genesCount++])},igv.GtexSelection.prototype.colorForGene=function(geneName){return this.geneColors[geneName.toUpperCase()]};var brewer=new Array;return brewer.push("rgb(228,26,28)"),brewer.push("rgb(55,126,184)"),brewer.push("rgb(77,175,74)"),brewer.push("rgb(166,86,40)"),brewer.push("rgb(152,78,163)"),brewer.push("rgb(255,127,0)"),brewer.push("rgb(247,129,191)"),brewer.push("rgb(153,153,153)"),brewer.push("rgb(255,255,51)"),brewer.push("rgb(102, 194, 165"),brewer.push("rgb(252, 141, 98"),brewer.push("rgb(141, 160, 203"),brewer.push("rgb(231, 138, 195"),brewer.push("rgb(166, 216, 84"),brewer.push("rgb(255, 217, 47"),brewer.push("rgb(229, 196, 148"),brewer.push("rgb(179, 179, 179"),brewer.push("rgb( 141, 211, 199"),brewer.push("rgb(255, 255, 179"),brewer.push("rgb(190, 186, 218"),brewer.push("rgb(251, 128, 114"),brewer.push("rgb(128, 177, 211"),brewer.push("rgb(253, 180, 98"),brewer.push("rgb(179, 222, 105"),brewer.push("rgb(252, 205, 229"),brewer.push("rgb(217, 217, 217"),brewer.push("rgb(188, 128, 189"),brewer.push("rgb(204, 235, 197"),brewer.push("rgb(255, 237, 111"),igv}(igv||{}),igv=function(igv){igv.GtexFileReader=function(config){this.config=config,this.file=config.url,this.codec=this.file.endsWith(".bin")?createEqtlBinary:createEQTL,this.cache={},this.binary=this.file.endsWith(".bin"),this.compressed=this.file.endsWith(".compressed.bin")},igv.GtexFileReader.prototype.readFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){function loadWithIndex(index,chr,fulfill){var chrIdx=index[chr];if(chrIdx){var blocks=chrIdx.blocks,lastBlock=blocks[blocks.length-1],endPos=lastBlock.startPos+lastBlock.size,len=endPos-blocks[0].startPos,range={start:blocks[0].startPos,size:len};igvxhr.loadArrayBuffer(file,{range:range,withCredentials:self.config.withCredentials}).then(function(arrayBuffer){if(arrayBuffer){var data=new DataView(arrayBuffer),parser=new igv.BinaryParser(data),featureList=[];for(parser.offset;parser.hasNext();){var feature=createEqtlBinary(parser);featureList.push(feature)}fulfill(featureList)}else fulfill(null)}).catch(reject)}else fulfill([]);var createEqtlBinary=function(parser){return new Eqtl(parser.getString(),parser.getString(),parser.getInt(),parser.getString(),parser.getString(),parser.getFloat())}}function loadIndex(url,fulfill){var genome=igv.browser?igv.browser.genome:null;igvxhr.loadArrayBuffer(url,{range:{start:0,size:200},withCredentials:self.config.withCredentials}).then(function(arrayBuffer){var data=new DataView(arrayBuffer),parser=new igv.BinaryParser(data),indexPosition=(parser.getInt(),parser.getInt(),parser.getLong()),indexSize=parser.getInt();igvxhr.loadArrayBuffer(url,{range:{start:indexPosition,size:indexSize},withCredentials:self.config.withCredentials}).then(function(arrayBuffer2){for(var data2=new DataView(arrayBuffer2),index=null,parser=new igv.BinaryParser(data2),index={},nChrs=parser.getInt();nChrs-- >0;){var chr=parser.getString();genome&&(chr=genome.getChromosomeName(chr));var position=parser.getLong(),size=parser.getInt(),blocks=new Array;blocks.push(new Block(position,size)),index[chr]=new ChrIdx(chr,blocks)}fulfill(index)})})}function Eqtl(snp,chr,position,geneId,geneName,pValue){this.snp=snp,this.chr=chr,this.position=position,this.start=position,this.end=position+1,this.geneId=geneId,this.geneName=geneName,this.pValue=pValue}var file=self.file,index=self.index;index?loadWithIndex(index,chr,fulfill):loadIndex(self.file,function(index){self.index=index,loadWithIndex(index,chr,fulfill)}),Eqtl.prototype.description=function(){return"<b>snp</b>:&nbsp"+this.snp+"<br/><b>location</b>:&nbsp"+this.chr+":"+formatNumber(this.position+1)+"<br/><b>gene</b>:&nbsp"+this.geneName+"<br/><b>pValue</b>:&nbsp"+this.pValue+"<br/><b>mLogP</b>:&nbsp"+this.mLogP},Block=function(startPos,size){this.startPos=startPos,this.size=size},ChrIdx=function(chr,blocks){this.chr=chr,this.blocks=blocks}})};var createEQTL=function(tokens){var snp=tokens[0],chr=tokens[1],position=parseInt(tokens[2])-1,geneId=tokens[3],geneName=tokens[4],genePosition=tokens[5],fStat=parseFloat(tokens[6]),pValue=parseFloat(tokens[7]);return new Eqtl(snp,chr,position,geneId,geneName,genePosition,fStat,pValue)},createEqtlBinary=function(parser){var snp=parser.getString(),chr=parser.getString(),position=parser.getInt(),geneId=parser.getString(),geneName=parser.getString(),pValue=parser.getFloat();return new Eqtl(snp,chr,position,geneId,geneName,pValue)};return igv}(igv||{}),igv=function(igv){return igv.GtexReader=function(config){this.config=config,this.url=config.url,this.tissueName=config.tissueName,this.indexed=!0},igv.GtexReader.prototype.readFeatures=function(chr,bpStart,bpEnd){var self=this,queryChr=chr.startsWith("chr")?chr.substr(3):chr,queryStart=bpStart,queryEnd=bpEnd,queryURL=this.url+"?chromosome="+queryChr+"&start="+queryStart+"&end="+queryEnd+"&tissueName="+this.tissueName;return new Promise(function(fulfill,reject){igvxhr.loadJson(queryURL,{withCredentials:self.config.withCredentials}).then(function(json){json&&json.singleTissueEqtl?(json.singleTissueEqtl.forEach(function(eqtl){eqtl.chr="chr"+eqtl.chromosome,eqtl.position=eqtl.start,eqtl.start=eqtl.start-1,eqtl.snp=eqtl.snpId,eqtl.geneName=eqtl.geneSymbol,eqtl.geneId=eqtl.gencodeId,eqtl.end=eqtl.start}),fulfill(json.singleTissueEqtl)):fulfill(null)}).catch(reject)})},igv}(igv||{}),igv=function(igv){return igv.ImmVarReader=function(config){this.config=config,this.url=config.url,this.cellConditionId=config.cellConditionId,this.valueThreshold=config.valueThreshold?config.valueThreshold:.05},igv.ImmVarReader.prototype.readFeatures=function(queryChr,queryStart,queryEnd){var self=this,queryURL=this.url+"?chromosome="+queryChr+"&start="+queryStart+"&end="+queryEnd+"&cell_condition_id="+this.cellConditionId;return new Promise(function(fulfill,reject){igvxhr.loadJson(queryURL,{withCredentials:self.config.withCredentials}).then(function(json){json?(json.eqtls.forEach(function(eqtl){eqtl.chr=eqtl.chromosome,eqtl.start=eqtl.position,eqtl.end=eqtl.position+1}),fulfill(json.eqtls)):fulfill(null)}).catch(function(error){reject(error)})})},igv}(igv||{}),igv=function(igv){const DEFAULT_POPOVER_WINDOW=1e8;return igv.GWASTrack=function(config){this.config=config,this.url=config.url,this.name=config.name,this.trait=config.trait,this.height=config.height||100,this.minLogP=config.minLogP||0,this.maxLogP=config.maxLogP||15,this.background=config.background,this.divider=config.divider||"rgb(225,225,225)",this.dotSize=config.dotSize||4,this.popoverWindow=void 0===config.popoverWindow?DEFAULT_POPOVER_WINDOW:config.popoverWindow,this.description=config.description,this.proxy=config.proxy,this.portalURL=config.portalURL?config.portalURL:window.location.origin,this.variantURL=config.variantURL||"http://www.type2diabetesgenetics.org/variant/variantInfo/",this.traitURL=config.traitURL||"http://www.type2diabetesgenetics.org/trait/traitInfo/";var cs=config.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.pvalue=config.pvalue?config.pvalue:"PVALUE",this.colorScale=new igv.BinnedColorScale(cs),config.format&&"gtexGWAS"===config.format?this.featureSource=new igv.FeatureSource(config):this.featureSource=new igv.T2DVariantSource(config)},igv.GWASTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){return this.featureSource.getFeatures(chr,bpStart,bpEnd)},igv.GWASTrack.prototype.draw=function(options){var track=this,featureList=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,bpEnd=bpStart+pixelWidth*bpPerPixel+1,yScale=(track.maxLogP-track.minLogP)/pixelHeight,enablePopover=bpEnd-bpStart<DEFAULT_POPOVER_WINDOW;this.po=enablePopover?[]:void 0,this.background&&igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:this.background}),igv.graphics.strokeLine(ctx,0,pixelHeight-1,pixelWidth,pixelHeight-1,{strokeStyle:this.divider});var variant,pos,len,xScale,px,py,color,pvalue,val;if(featureList){len=featureList.length;for(var i=0;i<len;i++)if(variant=featureList[i],!((pos=variant.start)<bpStart)){if(pos>bpEnd)break;pvalue=variant.pvalue||variant[track.pvalue],pvalue&&(color=track.colorScale.getColor(pvalue),val=-Math.log(pvalue)/2.302585092994046,xScale=bpPerPixel,px=Math.round((pos-bpStart)/xScale),py=Math.max(track.dotSize,pixelHeight-Math.round((val-track.minLogP)/yScale)),color&&igv.graphics.setProperties(ctx,{fillStyle:color,strokeStyle:"black"}),igv.graphics.fillCircle(ctx,px,py,track.dotSize),enablePopover&&track.po.push({x:px,y:py,feature:variant}))}}},igv.GWASTrack.prototype.paintAxis=function(ctx,pixelWidth,pixelHeight){var track=this,yScale=(track.maxLogP-track.minLogP)/pixelHeight,font={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"});for(var p=2;p<track.maxLogP;p+=2){var yp=pixelHeight-Math.round((p-track.minLogP)/yScale);igv.graphics.strokeLine(ctx,45,yp-2,50,yp-2,font),igv.graphics.fillText(ctx,p,44,yp+2,font)}font.textAlign="center",igv.graphics.fillText(ctx,"-log10(pvalue)",pixelWidth/2,pixelHeight/2,font,{rotate:{angle:-90}})},igv.GWASTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){var i,len,p,dbSnp,url,chr,pos,pvalue,data=[];if(this.po)for(i=0,len=this.po.length;i<len;i++)p=this.po[i],Math.abs(xOffset-p.x)<this.dotSize&&Math.abs(yOffset-p.y)<=this.dotSize&&(chr=p.feature.CHROM||p.feature.chr,pos=p.feature.POS||p.feature.start,pvalue=p.feature[this.pvalue]||p.feature.pvalue,dbSnp=p.feature.DBSNP_ID,dbSnp&&(url=this.variantURL.startsWith("http")?this.variantURL:this.portalURL+"/"+this.variantURL,data.push("<a target='_blank' href='"+url+(url.endsWith("/")?"":"/")+dbSnp+"' >"+dbSnp+"</a>")),data.push(chr+":"+pos.toString()),data.push({name:"p-value",value:pvalue}),p.feature.ZSCORE&&data.push({name:"z-score",value:p.feature.ZSCORE}),dbSnp&&(url=this.traitURL.startsWith("http")?this.traitURL:this.portalURL+"/"+this.traitURL,data.push("<a target='_blank' href='"+url+(url.endsWith("/")?"":"/")+dbSnp+"'>see all available statistics for this variant</a>")),i<len-1&&data.push("<p/>"));else data.push("Popover not available at this resolution.");return data},igv}(igv||{}),igv=function(igv){function jsonToVariantsV2(json,config){return variants=[],json.variants.forEach(function(record){var variant={};record.forEach(function(object){for(var property in object)object.hasOwnProperty(property)&&("POS"===property&&(variant.start=object[property]-1),variant[property]=object[property])}),variant.pvalue=variant[config.pvalue][config.dataset][config.trait],variant[config.pvalue]=void 0,variants.push(variant)}),variants}function queryJsonV2(queryChr,queryStart,queryEnd,config){var phenotype=config.trait,pvalue=config.pvalue,dataset=config.dataset,properties={cproperty:["VAR_ID","DBSNP_ID","CHROM","POS"],orderBy:["CHROM"],dproperty:{},pproperty:JSON.parse('{"'+pvalue+'": {"'+dataset+'": ["'+phenotype+'"]}}')},filters=[{dataset_id:"x",phenotype:"x",operand:"CHROM",operator:"EQ",value:queryChr,operand_type:"STRING"},{dataset_id:"x",phenotype:"x",operand:"POS",operator:"GTE",value:queryStart,operand_type:"INTEGER"},{dataset_id:"x",phenotype:"x",operand:"POS",operator:"LTE",value:queryEnd,operand_type:"INTEGER"},{dataset_id:dataset,phenotype:phenotype,operand:pvalue,operator:"LT",value:config.valueThreshold,operand_type:"FLOAT"}],data={passback:"x",entity:"variant",properties:properties,filters:filters};return JSON.stringify(data)}function queryJsonV1(queryChr,queryStart,queryEnd,config){var type=config.url.contains("variant")?VARIANT:TRAIT,pvalue=config.pvalue?config.pvalue:"PVALUE",filters=[{operand:"CHROM",operator:"EQ",value:queryChr,filter_type:"STRING"},{operand:"POS",operator:"GT",value:queryStart,filter_type:"FLOAT"},{operand:"POS",operator:"LT",value:queryEnd,filter_type:"FLOAT"},{operand:pvalue,operator:"LTE",value:config.valueThreshold,filter_type:"FLOAT"}],columns=type===TRAIT?["CHROM","POS","DBSNP_ID","PVALUE","ZSCORE"]:["CHROM","POS",pvalue,"DBSNP_ID"],data={user_group:"ui",filters:filters,columns:columns};return type===TRAIT&&(data.trait=config.trait),config.proxy?"url="+config.url+"&data="+JSON.stringify(data):JSON.stringify(data)}function jsonToVariantsV1(json,config){return json.variants.forEach(function(variant){variant.chr=variant.CHROM,variant.start=variant.POS-1}),json.variants}const VARIANT="VARIANT",TRAIT="TRAIT";igv.T2DVariantSource=function(config){this.config=config,this.url=config.url,this.trait=config.trait,this.dataset=config.dataset,this.pvalue=config.pvalue,void 0===config.valueThreshold&&(config.valueThreshold=.05),void 0===config.dataset?(this.queryJson=config.queryJson||queryJsonV1,this.jsonToVariants=config.jsonToVariants||jsonToVariantsV1):(this.queryJson=config.queryJson||queryJsonV2,this.jsonToVariants=config.jsonToVariants||jsonToVariantsV2)},igv.T2DVariantSource.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){if(self.cache&&self.cache.chr===chr&&self.cache.end>bpEnd&&self.cache.start<bpStart)fulfill(self.cache.featuresBetween(bpStart,bpEnd));else{var window=Math.max(bpEnd-bpStart,1e7)/2,center=(bpEnd+bpStart)/2,queryChr=chr.startsWith("chr")?chr.substring(3):chr,queryStart=Math.max(0,center-window),queryEnd=center+window,queryURL=self.config.proxy?self.config.proxy:self.url,body=self.queryJson(queryChr,queryStart,queryEnd,self.config);igvxhr.loadJson(queryURL,{sendData:body,withCredentials:self.config.withCredentials}).then(function(json){var variants;json?json.error_code?(igv.presentAlert("Error querying trait "+self.trait+"  (error_code="+json.error_code+")"),fulfill(null)):(variants=self.jsonToVariants(json,self.config),variants.sort(function(a,b){return a.POS-b.POS}),self.cache=new FeatureCache(chr,queryStart,queryEnd,variants),fulfill(variants)):fulfill(null)}).catch(reject)}})};var FeatureCache=function(chr,start,end,features){var i,bin,lastBin;for(this.chr=chr,this.start=start,this.end=end,this.binSize=(end-start)/100,this.binIndeces=[0],this.features=features,lastBin=0,i=0;i<features.length;i++)(bin=Math.max(0,Math.floor((features[i].POS-this.start)/this.binSize)))>lastBin&&(this.binIndeces.push(i),lastBin=bin)};return FeatureCache.prototype.featuresBetween=function(start,end){var startBin=Math.max(0,Math.min(Math.floor((start-this.start)/this.binSize)-1,this.binIndeces.length-1)),endBin=Math.max(0,Math.min(Math.floor((end-this.start)/this.binSize),this.binIndeces.length-1));this.binIndeces[startBin],this.binIndeces[endBin];return this.features},igv}(igv||{}),igv=function(igv){return igv.IdeoPanel=function(parentElement){this.ideograms={},this.contentDiv=$('<div class="igv-ideogram-content-div"></div>'),$(parentElement).append(this.contentDiv[0]);var myself=this;this.contentDiv.click(function(e){var xy,xPercentage,chr,chrLength,locusLength,chrCoveragePercentage,locus;xy=igv.translateMouseCoordinates(e,myself.contentDiv),xPercentage=xy.x/myself.contentDiv.width(),locusLength=igv.browser.trackViewportWidthBP(),chr=igv.browser.genome.getChromosome(igv.browser.referenceFrame.chr),chrLength=chr.bpLength,chrCoveragePercentage=locusLength/chrLength,xPercentage-chrCoveragePercentage/2<0&&(xPercentage=chrCoveragePercentage/2),xPercentage+chrCoveragePercentage/2>1&&(xPercentage=1-chrCoveragePercentage/2),locus=igv.browser.referenceFrame.chr+":"+igv.numberFormatter(1+Math.floor((xPercentage-chrCoveragePercentage/2)*chrLength))+"-"+igv.numberFormatter(Math.floor((xPercentage+chrCoveragePercentage/2)*chrLength)),igv.browser.search(locus,void 0)}),this.canvas=$('<canvas class="igv-ideogram-canvas"></canvas>')[0],$(this.contentDiv).append(this.canvas),this.canvas.setAttribute("width",this.contentDiv.width()),this.canvas.setAttribute("height",this.contentDiv.height()),this.ctx=this.canvas.getContext("2d")},igv.IdeoPanel.prototype.resize=function(){this.canvas.setAttribute("width",this.contentDiv.width()),this.canvas.setAttribute("height",this.contentDiv.height()),this.ideograms={},this.repaint()},igv.IdeoPanel.prototype.repaint=function(){function drawIdeogram(bufferCtx,ideogramWidth,ideogramHeight){var ideogramTop=0;if(genome){var cytobands=genome.getCytobands(referenceFrame.chr);if(cytobands){var center=ideogramTop+ideogramHeight/2,xC=[],yC=[],len=cytobands.length;if(0==len)return;for(var chrLength=cytobands[len-1].end,scale=ideogramWidth/chrLength,lastPX=-1,i=0;i<cytobands.length;i++){var cytoband=cytobands[i],start=scale*cytoband.start,end=scale*cytoband.end;end>lastPX&&("c"==cytoband.type?("p"==cytoband.name.charAt(0)?(xC[0]=start,yC[0]=ideogramHeight+ideogramTop,xC[1]=start,yC[1]=ideogramTop,xC[2]=end,yC[2]=center):(xC[0]=end,yC[0]=ideogramHeight+ideogramTop,xC[1]=end,yC[1]=ideogramTop,xC[2]=start,yC[2]=center),bufferCtx.fillStyle="rgb(150, 0, 0)",bufferCtx.strokeStyle="rgb(150, 0, 0)",bufferCtx.polygon(xC,yC,1,0)):(bufferCtx.fillStyle=getCytobandColor(cytoband),bufferCtx.fillRect(start,ideogramTop,end-start,ideogramHeight)))}}bufferCtx.strokeStyle="black",bufferCtx.roundRect(0,ideogramTop,ideogramWidth,ideogramHeight,ideogramHeight/2,0,1),lastPX=end}}function getCytobandColor(data){if("c"==data.type)return"rgb(150, 10, 10)";var stain=data.stain,shade=230;"p"==data.type&&(shade=Math.floor(230-stain/100*230));var c=stainColors[shade];return null==c&&(c="rgb("+shade+","+shade+","+shade+")",stainColors[shade]=c),c}try{var y,image,bufferCtx,chromosome,widthPercentage,xPercentage,width,widthBP,x,xBP,genome=igv.browser.genome,referenceFrame=igv.browser.referenceFrame,stainColors=[];if(this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height),!(genome&&referenceFrame&&genome.getChromosome(referenceFrame.chr)))return;image=this.ideograms[igv.browser.referenceFrame.chr],image||(image=document.createElement("canvas"),image.width=this.canvas.width,image.height=13,bufferCtx=image.getContext("2d"),drawIdeogram(bufferCtx,this.canvas.width,image.height),this.ideograms[igv.browser.referenceFrame.chr]=image),y=(this.canvas.height-image.height)/2,this.ctx.drawImage(image,0,y),this.ctx.save(),chromosome=igv.browser.genome.getChromosome(igv.browser.referenceFrame.chr),widthBP=Math.floor(igv.browser.trackViewportWidthBP()),xBP=igv.browser.referenceFrame.start,widthBP<chromosome.bpLength&&(widthPercentage=widthBP/chromosome.bpLength,xPercentage=xBP/chromosome.bpLength,x=Math.floor(xPercentage*this.canvas.width),width=Math.floor(widthPercentage*this.canvas.width),x=Math.max(0,x),x=Math.min(this.canvas.width-width,x),this.ctx.strokeStyle="red",this.ctx.lineWidth=2,this.ctx.strokeRect(x,y,width,image.height+this.ctx.lineWidth-1),this.ctx.restore())}catch(e){console.log("Error painting ideogram: "+e.message)}},igv}(igv||{}),igv=function(igv){function doPath(ctx,x,y){var i,len=x.length;for(i=0;i<len;i++)x[i]=Math.round(x[i]),y[i]=Math.round(y[i]);for(ctx.beginPath(),ctx.moveTo(x[0],y[0]),i=1;i<len;i++)ctx.lineTo(x[i],y[i]);ctx.closePath()}var debug=!1,log=function(msg){if(debug){var d=new Date,time=d.getHours()+":"+d.getMinutes()+":"+d.getSeconds();"undefined"!=typeof copy&&copy(msg),"undefined"!=typeof console&&console.log("igv-canvas: "+time+" "+msg)}};return igv.graphics={setProperties:function(ctx,properties){for(var key in properties)if(properties.hasOwnProperty(key)){var value=properties[key];ctx[key]=value}},strokeLine:function(ctx,x1,y1,x2,y2,properties){x1=Math.floor(x1)+.5,y1=Math.floor(y1)+.5,x2=Math.floor(x2)+.5,y2=Math.floor(y2)+.5,log("stroke line, prop: "+properties),ctx.save(),properties&&igv.graphics.setProperties(ctx,properties),ctx.beginPath(),ctx.moveTo(x1,y1),ctx.lineTo(x2,y2),ctx.stroke(),ctx.restore()},fillRect:function(ctx,x,y,w,h,properties){x=Math.round(x),y=Math.round(y),properties&&(ctx.save(),igv.graphics.setProperties(ctx,properties)),ctx.fillRect(x,y,w,h),properties&&ctx.restore()},fillPolygon:function(ctx,x,y,properties){ctx.save(),properties&&igv.graphics.setProperties(ctx,properties),doPath(ctx,x,y),ctx.fill(),ctx.restore()},strokePolygon:function(ctx,x,y,properties){ctx.save(),properties&&igv.graphics.setProperties(ctx,properties),doPath(ctx,x,y),ctx.stroke(),ctx.restore()},fillText:function(ctx,text,x,y,properties,transforms){if(properties&&(ctx.save(),igv.graphics.setProperties(ctx,properties)),ctx.save(),ctx.translate(x,y),transforms)for(var transform in transforms){var value=transforms[transform];"translate"==transform&&ctx.translate(value.x,value.y),"rotate"==transform&&ctx.rotate(value.angle*Math.PI/180)}ctx.fillText(text,0,0),ctx.restore(),properties&&ctx.restore()},strokeText:function(ctx,text,x,y,properties,transforms){if(ctx.save(),properties&&igv.graphics.setProperties(ctx,properties),ctx.translate(x,y),transforms)for(var transform in transforms){var value=transforms[transform];"translate"==transform&&ctx.translate(value.x,value.y),"rotate"==transform&&ctx.rotate(value.angle*Math.PI/180)}ctx.strokeText(text,0,0),ctx.restore()},strokeCircle:function(ctx,x,y,radius){ctx.beginPath(),ctx.arc(x,y,radius,0,2*Math.PI),ctx.stroke()},fillCircle:function(ctx,x,y,radius){ctx.beginPath(),ctx.arc(x,y,radius,0,2*Math.PI),ctx.fill()},drawArrowhead:function(ctx,x,y,size,lineWidth){ctx.save(),size||(size=5),lineWidth&&(ctx.lineWidth=lineWidth),ctx.beginPath(),ctx.moveTo(x,y-size/2),ctx.lineTo(x,y+size/2),ctx.lineTo(x+size,y),ctx.lineTo(x,y-size/2),ctx.closePath(),ctx.fill(),ctx.restore()},dashedLine:function(ctx,x1,y1,x2,y2,dashLen,properties){ctx.save(),x1=Math.round(x1),y1=Math.round(y1),x2=Math.round(x2),y2=Math.round(y2),dashLen=Math.round(dashLen),log("dashedLine"),properties&&igv.graphics.setProperties(ctx,properties),void 0==dashLen&&(dashLen=2),ctx.moveTo(x1,y1);for(var dX=x2-x1,dY=y2-y1,dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen),dashX=dX/dashes,dashY=dY/dashes,q=0;q++<dashes;)x1+=dashX,y1+=dashY,ctx[q%2==0?"moveTo":"lineTo"](x1,y1);ctx[q%2==0?"moveTo":"lineTo"](x2,y2),ctx.restore()}},igv}(igv||{}),igv=function(igv){function clamp(value,min,max){return Math.min(Math.max(value,min),max)}igv.hex2Color=function(hex){var cooked=/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);if(null!==cooked)return"rgb("+parseInt(cooked[1],16)+","+parseInt(cooked[2],16)+","+parseInt(cooked[3],16)+")"},igv.rgbaColor=function(r,g,b,a){return r=clamp(r,0,255),g=clamp(g,0,255),b=clamp(b,0,255),a=clamp(a,0,1),"rgba("+r+","+g+","+b+","+a+")"},igv.rgbColor=function(r,g,b){return r=clamp(r,0,255),g=clamp(g,0,255),b=clamp(b,0,255),"rgb("+r+","+g+","+b+")"},igv.addAlphaToRGB=function(rgbString,alpha){return rgbString.startsWith("rgb")?rgbString.replace("rgb","rgba").replace(")",", "+alpha+")"):(console.log(rgbString+" is not an rgb style string"),rgbString)},igv.greyScale=function(value){var grey=clamp(value,0,255);return"rgb("+grey+","+grey+","+grey+")"},igv.randomGrey=function(min,max){min=clamp(min,0,255),max=clamp(max,0,255);var g=Math.round(igv.random(min,max)).toString(10);return"rgb("+g+","+g+","+g+")"},igv.randomRGB=function(min,max){return min=clamp(min,0,255),max=clamp(max,0,255),"rgb("+Math.round(igv.random(min,max)).toString(10)+","+Math.round(igv.random(min,max)).toString(10)+","+Math.round(igv.random(min,max)).toString(10)+")"},igv.nucleotideColorComponents={A:[0,200,0],C:[0,0,200],T:[255,0,0],G:[209,113,5],a:[0,200,0],c:[0,0,200],t:[255,0,0],g:[209,113,5]},igv.nucleotideColors={A:"rgb(  0, 200,   0)",C:"rgb(  0,   0, 200)",T:"rgb(255,   0,   0)",G:"rgb(209, 113,   5)",a:"rgb(  0, 200,   0)",c:"rgb(  0,   0, 200)",t:"rgb(255,   0,   0)",g:"rgb(209, 113,   5)"},igv.getCompositeColor=function(dest,src,alpha){return"rgb("+Math.floor(alpha*src[0]+(1-alpha)*dest[0])+","+Math.floor(alpha*src[1]+(1-alpha)*dest[1])+","+Math.floor(alpha*src[2]+(1-alpha)*dest[2])+")"},igv.createColorString=function(token){return token.includes(",")?token.startsWith("rgb")?token:"rgb("+token+")":token},igv.BinnedColorScale=function(cs){this.thresholds=cs.thresholds,this.colors=cs.colors},igv.BinnedColorScale.prototype.getColor=function(value){var i,len=this.thresholds.length;for(i=0;i<len;i++)if(value<this.thresholds[i])return this.colors[i];return this.colors[this.colors.length-1]},igv.GradientColorScale=function(scale){this.scale=scale,this.lowColor="rgb("+scale.lowR+","+scale.lowG+","+scale.lowB+")",this.highColor="rgb("+scale.highR+","+scale.highG+","+scale.highB+")",this.diff=scale.high-scale.low},igv.GradientColorScale.prototype.getColor=function(value){var r,g,b,frac,scale=this.scale;return value<=scale.low?this.lowColor:value>=scale.high?this.highColor:(frac=(value-scale.low)/this.diff,r=Math.floor(scale.lowR+frac*(scale.highR-scale.lowR)),g=Math.floor(scale.lowG+frac*(scale.highG-scale.lowG)),b=Math.floor(scale.lowB+frac*(scale.highB-scale.lowB)),"rgb("+r+","+g+","+b+")")};var colorPalettes={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)"]};return igv.PaletteColorTable=function(palette){this.colors=colorPalettes[palette],Array.isArray(this.colors)||(this.colors=[]),this.colorTable={},this.nextIdx=0,this.colorGenerator=new RColor},igv.PaletteColorTable.prototype.getColor=function(key){return this.colorTable.hasOwnProperty(key)||(this.nextIdx<this.colors.length?this.colorTable[key]=this.colors[this.nextIdx]:this.colorTable[key]=this.colorGenerator.get(),this.nextIdx++),this.colorTable[key]},RColor=function(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2},RColor.prototype.hsvToRgb=function(h,s,v){var h_i=Math.floor(6*h),f=6*h-h_i,p=v*(1-s),q=v*(1-f*s),t=v*(1-(1-f)*s),r=255,g=255,b=255;switch(h_i){case 0:r=v,g=t,b=p;break;case 1:r=q,g=v,b=p;break;case 2:r=p,g=v,b=t;break;case 3:r=p,g=q,b=v;break;case 4:r=t,g=p,b=v;break;case 5:r=v,g=p,b=q}return[Math.floor(256*r),Math.floor(256*g),Math.floor(256*b)]},RColor.prototype.padHex=function(str){return str.length>this.hexwidth?str:new Array(this.hexwidth-str.length+1).join("0")+str},RColor.prototype.get=function(saturation,value){this.hue+=this.goldenRatio,this.hue%=1,"number"!=typeof saturation&&(saturation=.5),"number"!=typeof value&&(value=.95);var rgb=this.hsvToRgb(this.hue,saturation,value);return"#"+this.padHex(rgb[0].toString(16))+this.padHex(rgb[1].toString(16))+this.padHex(rgb[2].toString(16))},igv}(igv||{}),igv=function(igv){function createStandardControls(browser,config){var $igvLogo,$controls,contentKaryo,$navigation,$searchContainer,$faZoom,$trackLabelToggle,$cursorTrackingGuideToggle,$zoomContainer,$faZoomIn,$faZoomOut,$karyoPanelToggle,display;return $controls=$('<div id="igvControlDiv">'),config.showNavigation&&($navigation=$('<div class="igvNavigation">'),$controls.append($navigation[0]),$igvLogo=$('<div class="igv-logo">'),$searchContainer=$('<div class="igvNavigationSearch">'),browser.$searchInput=$('<input class="igvNavigationSearchInput" type="text" placeholder="Locus Search">'),browser.$searchInput.change(function(){browser.search($(this).val())}),$faZoom=$('<i class="igv-app-icon fa fa-search fa-18px shim-left-6">'),$faZoom.click(function(){browser.search(browser.$searchInput.val())}),$searchContainer.append(browser.$searchInput[0]),$searchContainer.append($faZoom[0]),$navigation.append($igvLogo[0]),$navigation.append($searchContainer[0]),browser.$searchResults=$('<div class="igvNavigationSearchResults">'),browser.$searchResultsTable=$('<table class="igvNavigationSearchResultsTable">'),browser.$searchResults.append(browser.$searchResultsTable[0]),$searchContainer.append(browser.$searchResults[0]),browser.$searchResults.hide(),browser.windowSizePanel=new igv.WindowSizePanel($navigation),$faZoomOut=$('<i class="fa fa-minus-circle igv-app-icon fa-24px" style="padding-right: 4px;">'),$faZoomOut.click(function(){igv.browser.zoomOut()}),$faZoomIn=$('<i class="fa fa-plus-circle igv-app-icon fa-24px">'),$faZoomIn.click(function(){igv.browser.zoomIn()}),$zoomContainer=$('<div class="igvNavigationZoom">'),$zoomContainer.append($faZoomOut[0]),$zoomContainer.append($faZoomIn[0]),$navigation.append($zoomContainer[0]),$trackLabelToggle=$('<div class="igv-toggle-track-labels">'),$trackLabelToggle.text("hide labels"),$trackLabelToggle.click(function(){browser.trackLabelsVisible=!browser.trackLabelsVisible,$(this).text(!0===browser.trackLabelsVisible?"hide labels":"show labels"),$(browser.trackContainerDiv).find(".igv-track-label").toggle()}),browser.centerGuide=new igv.CenterGuide($(browser.trackContainerDiv),config),browser.$cursorTrackingGuide=$('<div class="igv-cursor-tracking-guide">'),$(browser.trackContainerDiv).append(browser.$cursorTrackingGuide),browser.$cursorTrackingGuide.css("display",config.showCursorTrackingGuide&&1==config.showCursorTrackingGuide?"block":"none"),$cursorTrackingGuideToggle=$('<div class="igv-toggle-track-labels">'),display=browser.$cursorTrackingGuide.css("display"),$cursorTrackingGuideToggle.text("none"===display?"show cursor guide":"hide cursor guide"),$cursorTrackingGuideToggle.click(function(){display=browser.$cursorTrackingGuide.css("display"),"none"===display?(browser.$cursorTrackingGuide.css("display","block"),$cursorTrackingGuideToggle.text("hide cursor guide")):(browser.$cursorTrackingGuide.css("display","none"),$cursorTrackingGuideToggle.text("show cursor guide"))}),void 0!==config.showCursorTrackingGuide&&0!=config.showCursorTrackingGuide||$cursorTrackingGuideToggle.css("display","none"),$navigation.append($cursorTrackingGuideToggle),$navigation.append(browser.centerGuide.$centerGuideToggle),$navigation.append($trackLabelToggle)),config.showKaryo&&(contentKaryo=$("#igvKaryoDiv")[0],contentKaryo||(contentKaryo=$('<div id="igvKaryoDiv" class="igv-karyo-div">')[0],$controls.append(contentKaryo)),browser.karyoPanel=new igv.KaryoPanel(contentKaryo),$karyoPanelToggle=$('<div class="igv-toggle-track-labels">'),"hide"===config.showKaryo?($karyoPanelToggle.text("Show Karyotype"),$(contentKaryo).addClass("igv-karyo-hide")):$karyoPanelToggle.text("Hide Karyotype"),$karyoPanelToggle.click(function(){$(".igv-karyo-div").hasClass("igv-karyo-hide")?($karyoPanelToggle.text("Hide Karyotype"),$(".igv-karyo-div").removeClass("igv-karyo-hide")):($karyoPanelToggle.text("Show Karyotype"),$(".igv-karyo-div").addClass("igv-karyo-hide"))}),$navigation.append($karyoPanelToggle[0])),$controls[0]}function expandGenome(genomeId){var reference={id:genomeId};switch(genomeId){case"hg18":reference.fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta",reference.cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/cytoBand.txt.gz";break;case"hg19":case"GRCh37":default:reference.fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",reference.cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"}return reference}function setDefaults(config){config.showKaryo=config.showKaryo||!1,void 0===config.showControls&&(config.showControls=!0),void 0===config.showNavigation&&(config.showNavigation=!0),void 0===config.showRuler&&(config.showRuler=!0),void 0===config.showSequence&&(config.showSequence=!0),void 0===config.showIdeogram&&(config.showIdoegram=!0),void 0===config.flanking&&(config.flanking=1e3),void 0===config.pairsSupported&&(config.pairsSupported=!0),void 0===config.type&&(config.type="IGV"),config.tracks||(config.tracks=[]),config.showSequence&&config.tracks.push({type:"sequence",order:-9999})}function phoneHome(){var url="https://data.broadinstitute.org/igv/projects/current/counter_igvjs.php?version="+igvjs_version;igvxhr.load(url).then(function(ignore){console.log(ignore)}).catch(function(error){console.log(error)})}var igvjs_version="beta";return igv.version=igvjs_version,igv.createBrowser=function(parentDiv,config){var igvLogo,contentDiv,headerDiv,trackContainerDiv,browser,rootDiv,controlDiv,trackOrder=1;if(igv.browser&&igv.removeBrowser(),config||(config={}),setDefaults(config),oauth.google.apiKey=config.apiKey,oauth.google.access_token=config.oauthToken,config.genome?config.reference=expandGenome(config.genome):config.fastaURL?config.reference={fastaURL:config.fastaURL,cytobandURL:config.cytobandURL}:config.reference&&void 0!==config.reference.id&&void 0===config.reference.fastaURL&&(config.reference=expandGenome(config.reference.id)),!config.reference||!config.reference.fastaURL)throw igv.presentAlert("Fatal error:  reference must be defined"),new Error("Fatal error:  reference must be defined");return config.tracks&&config.tracks.forEach(function(track){void 0===track.order&&(track.order=trackOrder++)}),trackContainerDiv=$('<div class="igv-track-container-div">')[0],browser=new igv.Browser(config,trackContainerDiv),rootDiv=browser.div,$(document).mousedown(function(e){browser.isMouseDown=!0}),$(document).mouseup(function(e){browser.isMouseDown=void 0,browser.dragTrackView&&$(browser.dragTrackView.igvTrackDragScrim).hide(),browser.dragTrackView=void 0}),$(document).click(function(e){var target=e.target;igv.browser.div.contains(target)||igv.popover.hide()}),$(parentDiv).append($(rootDiv)),!1!==config.showCommandBar&&!1!==config.showControls&&(controlDiv=config.createControls?config.createControls(browser,config):createStandardControls(browser,config),$(rootDiv).append($(controlDiv))),contentDiv=$('<div class="igv-content-div">')[0],$(rootDiv).append(contentDiv),headerDiv=$("<div>")[0],$(contentDiv).append(headerDiv),$(contentDiv).append(trackContainerDiv),browser.userFeedback=new igv.UserFeedback($(contentDiv)),browser.userFeedback.hide(),igv.popover=new igv.Popover($(contentDiv),"igv-popover"),igv.colorPicker=new igv.ColorPicker($(rootDiv),config.palette,"igv-color-picker"),igv.colorPicker.hide(),igv.alert=new igv.AlertDialog($(rootDiv),"igv-alert"),igv.alert.hide(),igv.dialog=new igv.Dialog($(rootDiv),igv.Dialog.dialogConstructor,"igv-dialog"),igv.dialog.hide(),igv.dataRangeDialog=new igv.DataRangeDialog($(rootDiv),"igv-data-range-dialog"),igv.dataRangeDialog.hide(),config.showNavigation||(igvLogo=$('<div class="igv-logo-nonav">'),$(headerDiv).append(igvLogo[0])),config.hideIdeogram&&!0===config.hideIdeogram||(browser.ideoPanel=new igv.IdeoPanel(headerDiv),browser.ideoPanel.resize()),phoneHome(),igv.loadGenome(config.reference).then(function(genome){genome.id=config.reference.genomeId,browser.genome=genome,config.showRuler&&browser.addTrack(new igv.RulerTrack);var viewportWidth=browser.trackViewportWidth();0===viewportWidth&&(viewportWidth=500);var firstChrName=browser.genome.chromosomeNames[0],firstChr=browser.genome.chromosomes[firstChrName];if(browser.referenceFrame=new igv.ReferenceFrame(firstChrName,0,firstChr.bpLength/viewportWidth),browser.controlPanelWidth=50,browser.updateLocusSearch(browser.referenceFrame),browser.ideoPanel&&browser.ideoPanel.repaint(),browser.karyoPanel&&browser.karyoPanel.resize(),browser.initialLocus||config.locus){var locus=browser.initialLocus?browser.initialLocus:config.locus;igv.startSpinnerAtParentElement(parentDiv),browser.search(locus,function(){igv.stopSpinnerAtParentElement(parentDiv);var refFrame=browser.referenceFrame,start=refFrame.start;browser.trackViewportWidth(),refFrame.bpPerPixel;config.tracks&&browser.loadTracksWithConfigList(config.tracks)},!0)}else config.tracks&&browser.loadTracksWithConfigList(config.tracks)}).catch(function(error){igv.presentAlert(error),console.log(error)}),browser},igv.removeBrowser=function(){$(igv.browser.div).remove(),$(".igv-grid-container-colorpicker").remove(),$(".igv-grid-container-dialog").remove(),$(".igv-grid-container-dialog").remove()},igv}(igv||{});CanvasRenderingContext2D.prototype.strokeLine=function(x1,y1,x2,y2,lineWidth){this.save(),this.beginPath(),lineWidth&&(this.lineWidth=lineWidth),this.moveTo(x1,y1),this.lineTo(x2,y2),this.stroke(),this.restore()},CanvasRenderingContext2D.prototype.drawArrowhead=function(x,y,size,lineWidth){this.save(),size||(size=5),lineWidth&&(this.lineWidth=lineWidth),this.beginPath(),this.moveTo(x,y-size/2),this.lineTo(x,y+size/2),this.lineTo(x+size,y),this.lineTo(x,y-size/2),this.closePath(),this.fill(),this.restore()},CanvasRenderingContext2D.prototype.roundRect=function(x,y,width,height,radius,fill,stroke){this.save(),void 0===stroke&&(stroke=!0),void 0===radius&&(radius=5),this.beginPath(),this.moveTo(x+radius,y),this.lineTo(x+width-radius,y),this.quadraticCurveTo(x+width,y,x+width,y+radius),this.lineTo(x+width,y+height-radius),this.quadraticCurveTo(x+width,y+height,x+width-radius,y+height),this.lineTo(x+radius,y+height),this.quadraticCurveTo(x,y+height,x,y+height-radius),this.lineTo(x,y+radius),this.quadraticCurveTo(x,y,x+radius,y),this.closePath(),stroke&&this.stroke(),fill&&this.fill(),this.restore()},CanvasRenderingContext2D.prototype.polygon=function(x,y,fill,stroke){this.save(),void 0===stroke&&(stroke=!0),this.beginPath();var len=x.length;this.moveTo(x[0],y[0]);for(var i=1;i<len;i++)this.lineTo(x[i],y[i]);this.closePath(),stroke&&this.stroke(),fill&&this.fill(),this.restore()},CanvasRenderingContext2D.prototype.eqTriangle=function(side,cx,cy){this.save();var h=side*(Math.sqrt(3)/2);this.beginPath(),this.moveTo(cx,cy-h/2),this.lineTo(cx-side/2,cy+h/2),this.lineTo(cx+side/2,cy+h/2),this.lineTo(cx,cy-h/2),this.closePath(),this.stroke(),this.fill(),this.restore()},void 0===String.prototype.startsWith&&(String.prototype.startsWith=function(aString){return!(this.length<aString.length)&&this.substr(0,aString.length)==aString}),void 0===String.prototype.endsWith&&(String.prototype.endsWith=function(aString){return!(this.length<aString.length)&&this.substr(this.length-aString.length,aString.length)==aString}),void 0===String.prototype.contains&&(String.prototype.contains=function(it){return-1!=this.indexOf(it)}),void 0===String.prototype.includes&&(String.prototype.includes=function(it){return-1!=this.indexOf(it)}),void 0===String.prototype.splitLines&&(String.prototype.splitLines=function(){return this.split(/\r\n|\n|\r/gm)}),void 0===Uint8Array.prototype.toText&&(Uint8Array.prototype.toText=function(){var i,len,str;for(str="",i=0,len=this.byteLength;i<len;i++)str+=String.fromCharCode(this[i]);return str});var log2=Math.log(2);void 0===Math.log2&&(Math.log2=function(x){return Math.log(x)/log2}),void 0===Function.prototype.bind&&(Function.prototype.bind=function(){var fn=this,args=Array.prototype.slice.call(arguments),object=args.shift();return function(){return fn.apply(object,args.concat(Array.prototype.slice.call(arguments)))}}),Date.now||(Date.now=function(){return(new Date).getTime()}),Object.keys||(Object.keys=function(){"use strict";var hasOwnProperty=Object.prototype.hasOwnProperty,hasDontEnumBug=!{toString:null}.propertyIsEnumerable("toString"),dontEnums=["toString","toLocaleString","valueOf","hasOwnProperty","isPrototypeOf","propertyIsEnumerable","constructor"],dontEnumsLength=dontEnums.length;return function(obj){if("object"!=typeof obj&&("function"!=typeof obj||null===obj))throw new TypeError("Object.keys called on non-object");var prop,i,result=[];for(prop in obj)hasOwnProperty.call(obj,prop)&&result.push(prop);if(hasDontEnumBug)for(i=0;i<dontEnumsLength;i++)hasOwnProperty.call(obj,dontEnums[i])&&result.push(dontEnums[i]);return result}}()),Array.isArray||(Array.isArray=function(arg){return"[object Array]"===Object.prototype.toString.call(arg)});var igv=function(igv){return igv.presentAlert=function(string){igv.alert.$dialogLabel.text(string),igv.alert.show(void 0),igv.popover.hide()},igv.trackMenuItems=function(popover,trackView){var trackItems,menuItems=[];return menuItems.push(igv.dialogMenuItem(popover,trackView,"Set track name",function(){return"Track Name"},trackView.track.name,function(){function parseAlphanumeric(value){var alphanumeric_re=/(?=.*[a-zA-Z].*)([a-zA-Z0-9 ]+)/,alphanumeric=alphanumeric_re.exec(value);return null!==alphanumeric?alphanumeric[0]:"untitled"}var alphanumeric=parseAlphanumeric(igv.dialog.$dialogInput.val());void 0!==alphanumeric&&(igv.setTrackLabel(trackView.track,alphanumeric),trackView.update())},void 0)),menuItems.push(igv.dialogMenuItem(popover,trackView,"Set track height",function(){return"Track Height"},trackView.trackDiv.clientHeight,function(){var number=parseFloat(igv.dialog.$dialogInput.val(),10);void 0!==number&&(void 0!==trackView.track.minHeight&&trackView.track.minHeight>number&&(trackView.track.minHeight=number),void 0!==trackView.track.maxHeight&&trackView.track.maxHeight<number&&(trackView.track.minHeight=number),trackView.setTrackHeight(number),trackView.track.autoHeight=!1)},void 0)),trackView.track.popupMenuItems&&(trackItems=trackView.track.popupMenuItems(popover))&&trackItems.length>0&&trackItems.forEach(function(trackItem,i){var str;trackItem.name?(str=0===i?'<div class="igv-track-menu-item igv-track-menu-border-top">':'<div class="igv-track-menu-item">',str=str+trackItem.name+"</div>",menuItems.push({object:$(str),click:trackItem.click,init:trackItem.init})):0===i?(trackItem.object.addClass("igv-track-menu-border-top"),menuItems.push(trackItem)):menuItems.push(trackItem)}),!1!==trackView.track.removable&&menuItems.push(igv.dialogMenuItem(popover,trackView,"Remove track",function(){return'<div class="igv-dialog-label-centered">Remove '+trackView.track.name+"</div>"},void 0,function(){popover.hide(),trackView.browser.removeTrack(trackView.track)},!0)),menuItems},igv.dialogMenuItem=function(popover,trackView,gearMenuLabel,labelHTMLFunction,inputValue,clickFunction,doDrawBorderOrUndefined){var _div=!0===doDrawBorderOrUndefined?'<div class="igv-track-menu-item igv-track-menu-border-top">':'<div class="igv-track-menu-item">';return{object:$(_div+gearMenuLabel+"</div>"),click:function(){igv.dialog.configure(labelHTMLFunction,inputValue,clickFunction),igv.dialog.show($(trackView.trackDiv)),popover.hide()}}},igv.dataRangeMenuItem=function(popover,trackView){return{object:$('<div class="igv-track-menu-item">Set data range</div>'),click:function(){igv.dataRangeDialog.configureWithTrackView(trackView),igv.dataRangeDialog.show(),popover.hide()}}},igv.colorPickerMenuItem=function(popover,trackView){return{object:$('<div class="igv-track-menu-item">Set track color</div>'),click:function(){igv.colorPicker.configure(trackView),igv.colorPicker.show(),popover.hide()}}},igv.attachDialogCloseHandlerWithParent=function($parent,closeHandler){var $container=$('<div class="igv-dialog-close-container">'),$fa=$('<i class="fa fa-times igv-dialog-close-fa">');$container.append($fa[0]),$parent.append($container[0]),$fa.hover(function(){$fa.removeClass("fa-times"),$fa.addClass("fa-times-circle"),$fa.css({color:"#222"})},function(){$fa.removeClass("fa-times-circle"),$fa.addClass("fa-times"),$fa.css({color:"#444"})}),$fa.click(closeHandler)},igv.spinner=function(size){var $container,$spinner;return $spinner=$('<i class="fa fa-spinner fa-spin">'),size&&$spinner.css("font-size",size),$container=$('<div class="igv-spinner-container">'),$container.append($spinner[0]),$container[0]},igv.getSpinnerObjectWithParentElement=function(parentElement){return $(parentElement).find("div.igv-spinner-container")},igv.startSpinnerAtParentElement=function(parentElement){var spinnerObject=igv.getSpinnerObjectWithParentElement(parentElement);spinnerObject&&spinnerObject.show()},igv.stopSpinnerAtParentElement=function(parentElement){var spinnerObject=igv.getSpinnerObjectWithParentElement(parentElement);spinnerObject&&spinnerObject.hide()},igv.parseUri=function(str){for(var o=igv.parseUri.options,m=o.parser[o.strictMode?"strict":"loose"].exec(str),uri={},i=14;i--;)uri[o.key[i]]=m[i]||"";return uri[o.q.name]={},uri[o.key[12]].replace(o.q.parser,function($0,$1,$2){$1&&(uri[o.q.name][$1]=$2)}),uri},igv.parseUri.options={strictMode:!1,key:["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],q:{name:"queryKey",parser:/(?:^|&)([^&=]*)=?([^&]*)/g},parser:{strict:/^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,loose:/^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/}},igv.domElementRectAsString=function(element){return" x "+element.clientLeft+" y "+element.clientTop+" w "+element.clientWidth+" h "+element.clientHeight},igv.isNumber=function(n){return""!==n&&(void 0!==n&&(!isNaN(parseFloat(n))&&isFinite(n)))},igv.guid=function(){return("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)},igv.random=function(min,max){return Math.random()*(max-min)+min},igv.numberFormatter=function(rawNumber){var dec=String(rawNumber).split(/[.,]/);return dec[0].split("").reverse().reduce(function(prev,now,i){return i%3==0?prev+","+now:prev+now}).split("").reverse().join("")+(dec[1]?"."+dec[1]:"")},igv.numberUnFormatter=function(formatedNumber){return formatedNumber.split(",").join().replace(",","","g")},igv.translateMouseCoordinates=function(e,target){var eFixed=$.event.fix(e);return{x:eFixed.pageX-$(target).offset().left,y:eFixed.pageY-$(target).offset().top}},igv.formatPopoverText=function(nameValueArray){var markup='<table class="igv-popover-table">';return nameValueArray.forEach(function(nameValue){nameValue.name?markup+='<tr><td class="igv-popover-td"><div class="igv-popoverNameValue"><span class="igv-popoverName">'+nameValue.name+'</span><span class="igv-popoverValue">'+nameValue.value+"</span></div></td></tr>":markup+="<tr><td>"+nameValue.toString()+"</td></tr>"}),markup+="</table>"},igv.throttle=function(fn,threshhold,scope){threshhold||(threshhold=200);var last,deferTimer;return function(){var context=scope||this,now=+new Date,args=arguments;last&&now<last+threshhold?(clearTimeout(deferTimer),deferTimer=setTimeout(function(){last=now,fn.apply(context,args)},threshhold)):(last=now,fn.apply(context,args))}},igv.splitStringRespectingQuotes=function(string,delim){var i,c,tokens=[],len=string.length,n=0,quote=!1;if(len>0)for(tokens[n]=string.charAt(0),i=1;i<len;i++)c=string.charAt(i),'"'===c?quote=!quote:quote||c!==delim?tokens[n]+=c:(n++,tokens[n]="");return tokens},igv.addAjaxExtensions=function(){$.ajaxTransport("+binary",function(options,originalOptions,jqXHR){return{send:function(_,callback){var xhr=new XMLHttpRequest,url=options.url,type=options.type;options.data;if(xhr.addEventListener("load",function(){var data={};data[options.dataType]=xhr.response,callback(xhr.status,xhr.statusText,data,xhr.getAllResponseHeaders())}),xhr.open(type,url),xhr.responseType="arraybuffer",options.headers)for(var prop in options.headers)options.headers.hasOwnProperty(prop)&&xhr.setRequestHeader(prop,options.headers[prop])},abort:function(){jqXHR.abort()}}})},igv.isStringOrNumber=function(value){return!(!value.substring&&!value.toFixed)},igv.constrainBBox=function($child,$parent){var delta,topLeft,bboxChild={},bboxParent={};return bboxParent.left=bboxParent.top=0,bboxParent.right=$parent.outerWidth(),bboxParent.bottom=$parent.outerHeight(),topLeft=$child.offset(),bboxChild.left=topLeft.left-$parent.offset().left,bboxChild.top=topLeft.top-$parent.offset().top,bboxChild.right=bboxChild.left+$child.outerWidth(),bboxChild.bottom=bboxChild.top+$child.outerHeight(),delta=bboxChild.bottom-bboxParent.bottom,delta>0&&(topLeft.top-=delta,bboxChild.top-=delta,bboxChild.bottom-=delta,(delta=bboxChild.top-bboxParent.top)<0&&(topLeft.top-=delta)),topLeft},igv.log=function(message){igv.enableLogging&&console&&console.log&&console.log(message)},igv}(igv||{}),igvxhr=function(igvxhr){function isCrossDomain(url){var origin=window.location.origin;return!url.startsWith(origin)}const NONE=0,GZIP=1,BGZF=2;return igvxhr.load=function(url,options){return options||(options={}),new Promise(function(fulfill,reject){function handleError(message){if(!reject)throw Error(message);reject(message)}var header_keys,key,value,i,xhr=new XMLHttpRequest,sendData=options.sendData,method=options.method||(sendData?"POST":"GET"),range=options.range,responseType=options.responseType,contentType=options.contentType,mimeType=options.mimeType,headers=options.headers,withCredentials=(0==navigator.vendor.indexOf("Apple")&&/\sSafari\//.test(navigator.userAgent),options.withCredentials);if(url=url.startsWith("gs://")?igv.Google.translateGoogleCloudURL(url):url,igv.Google.isGoogleURL(url)&&(url=igv.Google.addApiKey(url),headers=headers||{},igv.Google.addGoogleHeaders(headers),range&&(url+=url.includes("?")?"&":"?",url+="someRandomSeed="+Math.random().toString(36))),xhr.open(method,url),range){var rangeEnd=range.size?range.start+range.size-1:"";xhr.setRequestHeader("Range","bytes="+range.start+"-"+rangeEnd)}if(contentType&&xhr.setRequestHeader("Content-Type",contentType),mimeType&&xhr.overrideMimeType(mimeType),responseType&&(xhr.responseType=responseType),headers)for(header_keys=Object.keys(headers),i=0;i<header_keys.length;i++)key=header_keys[i],value=headers[key],xhr.setRequestHeader(key,value);!0===withCredentials&&(xhr.withCredentials=!0),xhr.onload=function(event){0==xhr.status||xhr.status>=200&&xhr.status<=300?range&&206!=xhr.status?handleError("ERROR: range-byte header was ignored for url: "+url):fulfill(xhr.response,xhr):handleError(416===xhr.status?"Unsatisfiable range":"Error accessing resource: "+xhr.status)},xhr.onerror=function(event){isCrossDomain(url)&&url&&!options.crossDomainRetried&&igv.browser.crossDomainProxy&&url!=igv.browser.crossDomainProxy?(options.sendData="url="+url,options.crossDomainRetried=!0,igvxhr.load(igv.browser.crossDomainProxy,options).then(fulfill)):handleError("Error accessing resource: "+url+" Status: "+xhr.status)},xhr.ontimeout=function(event){handleError("Timed out")},xhr.onabort=function(event){console.log("Aborted"),reject(new igv.AbortLoad)};try{xhr.send(sendData)}catch(e){console.log(e)}})},igvxhr.loadArrayBuffer=function(url,options){return void 0===options&&(options={}),options.responseType="arraybuffer",igvxhr.load(url,options)},igvxhr.loadJson=function(url,options){return"POST"==(options.method||(options.sendData?"POST":"GET"))&&(options.contentType="application/json"),new Promise(function(fulfill,reject){igvxhr.load(url,options).then(function(result){fulfill(result?JSON.parse(result):result)}).catch(reject)})},igvxhr.loadString=function(url,options){var compression,fn,idx;return void 0===options&&(options={}),idx=url.indexOf("?"),fn=idx>0?url.substring(0,idx):url,compression=options.bgz?BGZF:fn.endsWith(".gz")?GZIP:NONE,compression===NONE?(options.mimeType="text/plain; charset=x-user-defined",igvxhr.load(url,options)):(options.responseType="arraybuffer",new Promise(function(fulfill,reject){igvxhr.load(url,options).then(function(data){var result=igvxhr.arrayBufferToString(data,compression);fulfill(result)}).catch(reject)}))},igvxhr.loadStringFromFile=function(localfile,options){return new Promise(function(fulfill,reject){var fileReader=new FileReader;options.range;fileReader.onload=function(e){var compression,result;compression=options.bgz?BGZF:localfile.name.endsWith(".gz")?GZIP:NONE,result=igvxhr.arrayBufferToString(fileReader.result,compression),fulfill(result,localfile)},fileReader.onerror=function(e){console.log("reject uploading local file "+localfile.name),reject(null,fileReader)},fileReader.readAsArrayBuffer(localfile)})},igvxhr.arrayBufferToString=function(arraybuffer,compression){var plain,inflate;compression===GZIP?(inflate=new Zlib.Gunzip(new Uint8Array(arraybuffer)),plain=inflate.decompress()):plain=compression===BGZF?new Uint8Array(igv.unbgzf(arraybuffer)):new Uint8Array(arraybuffer);for(var result="",i=0,len=plain.length;i<len;i++)result+=String.fromCharCode(plain[i]);return result},igv.AbortLoad=function(){},igvxhr}(igvxhr||{}),igv=function(igv){function searchAll(interval,node,results){return node.interval.overlaps(interval)&&results.push(node.interval),node.left!=NIL&&node.left.max>=interval.low&&searchAll.call(this,interval,node.left,results),node.right!=NIL&&node.right.min<=interval.high&&searchAll.call(this,interval,node.right,results),results}function leftRotate(x){var y=x.right;x.right=y.left,y.left!=NIL&&(y.left.parent=x),y.parent=x.parent,x.parent==NIL?this.root=y:x.parent.left==x?x.parent.left=y:x.parent.right=y,y.left=x,x.parent=y,applyUpdate.call(this,x)}function rightRotate(x){var y=x.left;x.left=y.right,y.right!=NIL&&(y.right.parent=x),y.parent=x.parent,x.parent==NIL?this.root=y:x.parent.right==x?x.parent.right=y:x.parent.left=y,y.right=x,x.parent=y,applyUpdate.call(this,x)}function applyUpdate(node){for(;node!=NIL;){var nodeMax=node.left.max>node.right.max?node.left.max:node.right.max,intervalHigh=node.interval.high;node.max=nodeMax>intervalHigh?nodeMax:intervalHigh;var nodeMin=node.left.min<node.right.min?node.left.min:node.right.min,intervalLow=node.interval.low;node.min=nodeMin<intervalLow?nodeMin:intervalLow,node=node.parent}}function Interval(low,high,value){this.low=low,this.high=high,this.value=value}function Node(interval){this.parent=NIL,this.left=NIL,this.right=NIL,this.interval=interval,this.color=RED}var BLACK=1,RED=2,NIL={};return NIL.color=BLACK,NIL.parent=NIL,NIL.left=NIL,NIL.right=NIL,igv.IntervalTree=function(){this.root=NIL},igv.IntervalTree.prototype.insert=function(start,end,value){var interval=new Interval(start,end,value),x=new Node(interval);for(this.treeInsert(x),x.color=RED;x!=this.root&&x.parent.color==RED;)if(x.parent==x.parent.parent.left){var y=x.parent.parent.right;y.color==RED?(x.parent.color=BLACK,y.color=BLACK,x.parent.parent.color=RED,x=x.parent.parent):(x==x.parent.right&&(x=x.parent,leftRotate.call(this,x)),x.parent.color=BLACK,x.parent.parent.color=RED,rightRotate.call(this,x.parent.parent))}else{var y=x.parent.parent.left;y.color==RED?(x.parent.color=BLACK,y.color=BLACK,x.parent.parent.color=RED,x=x.parent.parent):(x==x.parent.left&&(x=x.parent,rightRotate.call(this,x)),x.parent.color=BLACK,x.parent.parent.color=RED,leftRotate.call(this,x.parent.parent))}this.root.color=BLACK},igv.IntervalTree.prototype.findOverlapping=function(start,end){var searchInterval=new Interval(start,end,0);if(this.root===NIL)return[];var intervals=searchAll.call(this,searchInterval,this.root,[]);return intervals.length>1&&intervals.sort(function(i1,i2){return i1.low-i2.low}),intervals},igv.IntervalTree.prototype.logIntervals=function(){function logNode(node,indent){for(var space="",i=0;i<indent;i++)space+=" ";console.log(space+node.interval.low+" "+node.interval.high),indent+=5,node.left!=NIL&&logNode(node.left,indent),node.right!=NIL&&logNode(node.right,indent)}logNode(this.root,0)},igv.IntervalTree.prototype.mapIntervals=function(func){function applyInterval(node){func(node.interval),node.left!=NIL&&applyInterval(node.left),node.right!=NIL&&applyInterval(node.right)}applyInterval(this.root)},igv.IntervalTree.prototype.treeInsert=function(x){for(var node=this.root,y=NIL;node!=NIL;)y=node,node=x.interval.low<=node.interval.low?node.left:node.right;x.parent=y,y==NIL?(this.root=x,x.left=x.right=NIL):x.interval.low<=y.interval.low?y.left=x:y.right=x,applyUpdate.call(this,x)},Interval.prototype.equals=function(other){return!!other&&(this==other||this.low==otherInterval.low&&this.high==otherInterval.high)},Interval.prototype.compareTo=function(other){return this.low<other.low?-1:this.low>other.low?1:this.high<other.high?-1:this.high>other.high?1:0},Interval.prototype.overlaps=function(other){try{return this.low<=other.high&&other.low<=this.high}catch(e){igv.presentAlert(e)}},igv}(igv||{}),igv=function(igv){var log=function(txt){};return igv.KaryoPanel=function(parentElement){this.ideograms=null,igv.guichromosomes=[],this.div=$('<div class="igv-karyo-div"></div>')[0],$(parentElement).append(this.div);var contentDiv=$('<div class="igv-karyo-content-div"></div>')[0];$(this.div).append(contentDiv);var canvas=$('<canvas class="igv-karyo-canvas"></canvas>')[0];$(contentDiv).append(canvas),canvas.setAttribute("width",contentDiv.offsetWidth),canvas.setAttribute("height",contentDiv.offsetHeight),this.canvas=canvas,this.ctx=canvas.getContext("2d");var tipCanvas=document.createElement("canvas");tipCanvas.style.position="absolute",tipCanvas.style.width="100px",tipCanvas.style.height="20px",tipCanvas.style.left="-2000px",tipCanvas.setAttribute("width","100px"),tipCanvas.setAttribute("height","20px");var tipCtx=tipCanvas.getContext("2d");contentDiv.appendChild(tipCanvas),this.canvas.onmousemove=function(e){for(var mouseCoords=igv.translateMouseCoordinates(e,canvas),mouseX=mouseCoords.x,mouseY=mouseCoords.y,hit=!1,i=0;i<igv.guichromosomes.length;i++){var g=igv.guichromosomes[i];if(g.x<mouseX&&g.right>mouseX&&g.y<mouseY&&g.bottom>mouseY){var dy=mouseY-g.y,bp=Math.round(g.size*dy/g.h);tipCanvas.style.left=Math.round(mouseX+20)+"px",tipCanvas.style.top=Math.round(mouseY-5)+"px",tipCtx.clearRect(0,0,tipCanvas.width,tipCanvas.height),tipCtx.fillStyle="rgb(255,255,220)",tipCtx.fillRect(0,0,tipCanvas.width,tipCanvas.height),tipCtx.fillStyle="rgb(0,0,0)";var mb=Math.round(bp/1e6);tipCtx.fillText(g.name+" @ "+mb+" MB",3,12),hit=!0;break}}hit||(tipCanvas.style.left="-2000px")},this.canvas.onclick=function(e){var mouseCoords=igv.translateMouseCoordinates(e,canvas),mouseX=mouseCoords.x,mouseY=mouseCoords.y;igv.navigateKaryo(mouseX,mouseY)}},igv.navigateKaryo=function(mouseX,mouseY){for(var i=0;i<igv.guichromosomes.length;i++){var g=igv.guichromosomes[i];if(g.x<mouseX&&g.right>mouseX&&g.y<mouseY&&g.bottom>mouseY){var dy=mouseY-g.y,center=Math.round(g.size*dy/g.h);log("Going to position "+center),igv.browser.goto(g.name,center,void 0);break}}igv.browser.update()},igv.KaryoPanel.prototype.resize=function(){var canvas=this.canvas;canvas.setAttribute("width",canvas.clientWidth),canvas.setAttribute("height",canvas.clientHeight),log("Resize called: width="+canvas.clientWidth+"/"+canvas.clientHeight),this.ideograms=void 0,this.repaint()},igv.KaryoPanel.prototype.repaint=function(){function drawImage(){image=document.createElement("canvas"),image.width=w,image.height=h;var bufferCtx=image.getContext("2d"),nr=0,col=0,row=1,y=top;igv.guichromosomes=[];for(chr in chromosomes){if(nr>nrchr)break;1==row&&2==nrrows&&nr+1>nrchr/2&&(row=2,col=0,y=y+chrheight+top),nr++,col++;var chromosome=genome.getChromosome(chr);"chrM"!=chr||chromosome.bpLength||(chromosome.bpLength=16e3),chromosome.x=col*totalchrwidth,chromosome.y=y;var guichrom=new Object;guichrom.name=chr,igv.guichromosomes.push(guichrom),drawIdeogram(guichrom,chromosome.x,chromosome.y,chromosome,bufferCtx,chrwidth,chrheight,maxLen)}this.ideograms=image,log("============= PROCESSING "+igv.browser.trackViews.length+" TRACKS");for(var tracknr=0,i=0;i<igv.browser.trackViews.length;i++){var trackPanel=igv.browser.trackViews[i],track=trackPanel.track;if(track.getSummary&&track.loadSummary){log("Found track with summary: "+track.name);var source=track;window.source=track,source.loadSummary("chr1",0,1e6,function(featureList){if(featureList){nr=0;for(chr in chromosomes){var guichrom=igv.guichromosomes[nr];nr++,guichrom&&guichrom.size&&loadfeatures(source,chr,0,guichrom.size,guichrom,bufferCtx,tracknr)}}}),tracknr++}}}function drawFeatures(source,featurelist,guichrom,ideogramLeft,top,bufferCtx,ideogramWidth,ideogramHeight,longestChr,tracknr){if(genome&&guichrom&&featurelist){if(0!=featurelist.length)for(var scale=ideogramHeight/longestChr,dx=1,i=0;i<featurelist.length;i++){var feature=featurelist[i],color="rgb(0,0,150)",value=feature.score;source.getColor&&(color=source.getColor(value));var starty=scale*feature.start+top,endy=scale*feature.end+top,dy=Math.max(.01,endy-starty);bufferCtx.fillStyle=color,bufferCtx.fillRect(ideogramLeft+ideogramWidth+2*tracknr+1,starty,dx,dy)}}}function drawIdeogram(guichrom,ideogramLeft,top,chromosome,bufferCtx,ideogramWidth,ideogramHeight,longestChr){if(genome&&chromosome){var cytobands=genome.getCytobands(chromosome.name);if(cytobands){var centerx=ideogramLeft+ideogramWidth/2,xC=[],yC=[],len=cytobands.length,scale=ideogramHeight/longestChr;guichrom.x=ideogramLeft,guichrom.y=top,guichrom.w=ideogramWidth,guichrom.right=ideogramLeft+ideogramWidth;var last=0,lastPY=-1;if(len>0)last=cytobands[len-1].end,guichrom.h=scale*last,guichrom.size=last;else{var MINH=5;lastPY=top+MINH,guichrom.h=MINH,guichrom.size=MINH/scale}if(guichrom.longest=longestChr,guichrom.bottom=top+guichrom.h,len>0)for(var i=0;i<cytobands.length;i++){var cytoband=cytobands[i],starty=scale*cytoband.start+top,endy=scale*cytoband.end+top;if(endy>lastPY)if("c"==cytoband.type)"p"==cytoband.name.charAt(0)?(yC[0]=starty,xC[0]=ideogramWidth+ideogramLeft,yC[1]=starty,xC[1]=ideogramLeft,yC[2]=endy,xC[2]=centerx):(yC[0]=endy,xC[0]=ideogramWidth+ideogramLeft,yC[1]=endy,xC[1]=ideogramLeft,yC[2]=starty,xC[2]=centerx),bufferCtx.fillStyle="rgb(220, 150, 100)",bufferCtx.strokeStyle="rgb(150, 0, 0)",bufferCtx.polygon(xC,yC,1,0);else{var dy=endy-starty;bufferCtx.fillStyle=getCytobandColor(cytoband),bufferCtx.fillRect(ideogramLeft,starty,ideogramWidth,dy)}lastPY=endy}}bufferCtx.fillStyle=null,bufferCtx.lineWidth=1,bufferCtx.strokeStyle="darkgray";var r=ideogramWidth/2;bufferCtx.roundRect(ideogramLeft,top-r/2,ideogramWidth,lastPY-top+r,ideogramWidth/2,0,1),bufferCtx.font="bold 10px Arial",bufferCtx.fillStyle="rgb(0, 0, 0)";var name=chromosome.name;name.length>3&&(name=name.substring(3)),bufferCtx.fillText(name,ideogramLeft+ideogramWidth/2-3*name.length,top-10)}}function getCytobandColor(data){if("c"==data.type)return"rgb(150, 10, 10)";var stain=data.stain,shade=230;"p"==data.type&&(shade=Math.floor(230-stain/100*230));var c=stainColors[shade];return null==c&&(c="rgb("+shade+","+shade+","+shade+")",stainColors[shade]=c),c}function loadfeatures(source,chr,start,end,guichrom,bufferCtx,tracknr){source.getSummary(chr,start,end,function(featureList){featureList&&(len=featureList.length,drawFeatures(source,featureList,guichrom,guichrom.x,guichrom.y,bufferCtx,chrwidth,chrheight,maxLen,tracknr),me.repaint())})}var genome=igv.browser.genome,referenceFrame=igv.browser.referenceFrame,stainColors=[],w=this.canvas.width,h=this.canvas.height;if(this.ctx.clearRect(0,0,w,h),genome&&referenceFrame&&genome.chromosomes&&referenceFrame.chr){var chromosomes=genome.getChromosomes(),image=this.ideograms;if(chromosomes.length<1)return void log("No chromosomes yet, returning");var nrchr=24,nrrows=1;w<300&&(nrrows=2);var totalchrwidth=Math.min(50,(w-20)/(nrchr+2)*nrrows),chrwidth=Math.min(20,totalchrwidth/2),top=25,chrheight=(h-25)/nrrows-top,longestChr=genome.getLongestChromosome(),cytobands=genome.getCytobands(longestChr.name),me=this,maxLen=cytobands[cytobands.length-1].end;image&&null!=image||drawImage.call(this),this.ctx.drawImage(image,0,0),this.ctx.save();var chr=referenceFrame.chr;this.genome&&(chr=this.genome.getChromosomeName(chr));var chromosome=igv.browser.genome.getChromosome(chr);if(chromosome){var ideoScale=longestChr.bpLength/chrheight,boxPY1=chromosome.y-3+Math.round(referenceFrame.start/ideoScale),boxHeight=Math.max(3,igv.browser.trackViewportWidth()*referenceFrame.bpPerPixel/ideoScale);this.ctx.strokeStyle="rgb(150, 0, 0)",this.ctx.lineWidth=2,this.ctx.strokeRect(chromosome.x-3,boxPY1,chrwidth+6,boxHeight+6),this.ctx.restore()}else log("Could not find chromosome "+chr)}},igv}(igv||{}),oauth=function(oauth){if(!oauth.google){var tokenType,expiresIn,user,OAUTHURL="https://accounts.google.com/o/oauth2/auth?",VALIDURL="https://www.googleapis.com/oauth2/v1/tokeninfo?access_token=",REDIRECT="http://localhost/igv-web/emptyPage.html",_url=OAUTHURL+"scope=https://www.googleapis.com/auth/cloud-platform https://www.googleapis.com/auth/genomics https://www.googleapis.com/auth/devstorage.read_only https://www.googleapis.com/auth/userinfo.profile&state=%2Fprofile&redirect_uri=http%3A%2F%2Flocalhost%2Figv-web%2FemptyPage.html&response_type=token&client_id=661332306814-8nt29308rppg325bkq372vli8nm3na14.apps.googleusercontent.com",loggedIn=!1;oauth.google={login:function(callback){var win=window.open(_url,"windowname1","width=800, height=600"),pollTimer=window.setInterval(function(){try{if(console.log(win.document.URL),-1!=win.document.URL.indexOf(REDIRECT)){window.clearInterval(pollTimer);var url=win.document.URL;oauth.google.access_token=oauth.google.gup(url,"access_token"),tokenType=oauth.google.gup(url,"token_type"),expiresIn=oauth.google.gup(url,"expires_in"),win.close(),oauth.google.validateToken(oauth.google.access_token),callback&&callback()}}catch(e){}},500)},validateToken:function(token){$.ajax({url:VALIDURL+token,data:null,success:function(responseText){oauth.google.getUserInfo(),loggedIn=!0},dataType:"jsonp"})},getUserInfo:function(){$.ajax({url:"https://www.googleapis.com/oauth2/v1/userinfo?access_token="+oauth.google.access_token,data:null,success:function(resp){user=resp,console.log(user)},dataType:"jsonp"})},gup:function(url,name){name=name.replace(/[\[]/,"\\[").replace(/[\]]/,"\\]");var regexS="[\\#&]"+name+"=([^&#]*)",regex=new RegExp(regexS),results=regex.exec(url);return null==results?"":results[1]}}}return oauth}(oauth||{}),igv=function(igv){return igv.oauth=oauth,igv}(igv||{}),igv=function(igv){return igv.isBlank=function(line){return!line.match(/\S+/g)},igv.isComment=function(line){return 0==line.indexOf("#")},igv.getQueryValue=function(name){name=name.replace(/[\[]/,"\\[").replace(/[\]]/,"\\]");var regexS="[\\?&]"+name+"=([^&#]*)",regex=new RegExp(regexS),results=regex.exec(window.location.href);return null==results?void 0:results[1]},igv}(igv||{}),igv=function(igv){return igv.ReferenceFrame=function(chr,start,bpPerPixel){this.chr=chr,this.start=start,this.bpPerPixel=bpPerPixel},igv.ReferenceFrame.prototype.toPixels=function(bp){return bp/this.bpPerPixel},igv.ReferenceFrame.prototype.toBP=function(pixels){return this.bpPerPixel*pixels},igv.ReferenceFrame.prototype.shiftPixels=function(pixels){this.start+=pixels*this.bpPerPixel},igv.ReferenceFrame.prototype.description=function(){return"ReferenceFrame "+this.chr+" "+igv.numberFormatter(Math.floor(this.start))+" bpp "+this.bpPerPixel},igv}(igv||{}),igv=function(igv){function TickSpacing(majorTick,majorUnit,unitMultiplier){this.majorTick=majorTick,this.majorUnit=majorUnit,this.unitMultiplier=unitMultiplier}function findSpacing(maxValue){function log10(x){var dn=Math.log(10);return Math.log(x)/dn}if(maxValue<10)return new TickSpacing(1,"",1);var nZeroes=Math.floor(log10(maxValue)),majorUnit="",unitMultiplier=1;return nZeroes>9&&(majorUnit="gb",unitMultiplier=1e9),nZeroes>6?(majorUnit="mb",unitMultiplier=1e6):nZeroes>3&&(majorUnit="kb",unitMultiplier=1e3),maxValue/Math.pow(10,nZeroes-1)<25?new TickSpacing(Math.pow(10,nZeroes-1),majorUnit,unitMultiplier):new TickSpacing(Math.pow(10,nZeroes)/2,majorUnit,unitMultiplier)}return igv.RulerTrack=function(){this.height=50,this.name="",this.id="ruler",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=-Number.MAX_VALUE},igv.RulerTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){return new Promise(function(fulfill,reject){fulfill([])})},igv.RulerTrack.prototype.draw=function(options){function formatNumber(anynum,decimal){var divider=10;switch(decimal){case 0:divider=1;break;case 1:divider=10;break;case 2:divider=100;break;default:divider=1e3}var workNum=Math.abs(Math.round(anynum*divider)/divider),workStr=""+workNum;-1==workStr.indexOf(".")&&(workStr+=".");for(var dStr=workStr.substr(0,workStr.indexOf(".")),dNum=dStr-0,pStr=workStr.substr(workStr.indexOf("."));pStr.length-1<decimal;)pStr+="0";if("."==pStr&&(pStr=""),dNum>=1e3){var dLen=dStr.length;dStr=parseInt(""+dNum/1e3)+","+dStr.substring(dLen-3,dLen)}dNum>=1e6&&(dLen=dStr.length,dStr=parseInt(""+dNum/1e6)+","+dStr.substring(dLen-7,dLen));var retval=dStr+pStr;return anynum<0&&(retval="("+retval+")"),retval}var fontStyle,range,ts,spacing,nTick,x,ctx=options.context;for(fontStyle={textAlign:"center",font:"10px PT Sans",fillStyle:"rgba(64, 64, 64, 1)",strokeStyle:"rgba(64, 64, 64, 1)"},range=Math.floor(1100*options.bpPerPixel),ts=findSpacing(range),spacing=ts.majorTick,nTick=Math.floor(options.bpStart/spacing)-1,x=0,igv.graphics.setProperties(ctx,fontStyle);x<options.pixelWidth;){var l=Math.floor(nTick*spacing),shim=2;x=Math.round((l-1-options.bpStart+.5)/options.bpPerPixel);var chrPosition=formatNumber(l/ts.unitMultiplier,0)+" "+ts.majorUnit;nTick%1==0&&igv.graphics.fillText(ctx,chrPosition,x,this.height-15),igv.graphics.strokeLine(ctx,x,this.height-10,x,this.height-shim),nTick++}igv.graphics.strokeLine(ctx,0,this.height-shim,options.pixelWidth,this.height-shim)},igv}(igv||{}),igv=function(igv){return igv.SequenceTrack=function(config){this.name="",this.id="sequence",this.sequenceType=config.sequenceType||"dna",this.height=15,this.disableButtons=!0,this.order=config.order||9999,this.ignoreTrackMenu=!0},igv.SequenceTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){return new Promise(function(fulfill,reject){igv.browser.referenceFrame.bpPerPixel>1?fulfill(null):igv.browser.genome.sequence.getSequence(chr,bpStart,bpEnd).then(fulfill).catch(reject)})},igv.SequenceTrack.prototype.draw=function(options){var len,w,y,pos,offset,b,p0,p1,pc,c,sequence=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,bpEnd=bpStart+pixelWidth*bpPerPixel+1;if(sequence)for(len=sequence.length,w=1/bpPerPixel,y=this.height/2,pos=bpStart;pos<=bpEnd;pos++)(offset=pos-bpStart)<len&&(b=sequence[offset],p0=Math.floor(offset*w),p1=Math.floor((offset+1)*w),pc=Math.round((p0+p1)/2),c=this.color?this.color:"dna"===this.sequenceType?igv.nucleotideColors[b]:"rgb(0, 0, 150)",c||(c="gray"),bpPerPixel>.1?igv.graphics.fillRect(ctx,p0,0,p1-p0,10,{fillStyle:c}):igv.graphics.strokeText(ctx,b,pc,y,{strokeStyle:c,font:"normal 10px Arial",textAlign:"center"}))},igv}(igv||{});Array.isArray||(Array.isArray=function(vArg){return"[object Array]"===Object.prototype.toString.call(vArg)}),"undefined"!=typeof Set?(Set.prototype.isEmpty=function(){return 0===this.size},Set.prototype.addAll=function(arrayOrSet){if(Array.isArray(arrayOrSet)||this._isPseudoArray(arrayOrSet))for(var j=0;j<arrayOrSet.length;j++)this.add(arrayOrSet[j]);else if(arrayOrSet instanceof Set){var self=this;arrayOrSet.each(function(val,key){self.add(key,val)})}}):(Set=function(){this.data={},this.add.apply(this,arguments)},Set.prototype={add:function(){for(var key,i=0;i<arguments.length;i++)if(key=arguments[i],Array.isArray(key)||this._isPseudoArray(key))for(var j=0;j<key.length;j++)this._add(key[j]);else if(key instanceof Set){var self=this;key.each(function(val,key){self._add(key,val)})}else this._add(key);return this},addAll:function(arrayOrSet){if(Array.isArray(arrayOrSet)||this._isPseudoArray(arrayOrSet))for(var j=0;j<arrayOrSet.length;j++)this._add(arrayOrSet[j]);else if(arrayOrSet instanceof Set){var self=this;arrayOrSet.each(function(val,key){self._add(key,val)})}return this},_add:function(key,val){return void 0===val&&(val=key),this.data[this._makeKey(key)]=val,this},_getKey:function(arg){return arg},_makeKey:function(arg){return arg},_removeItem:function(key){delete this.data[this._getKey(key)]},_isPseudoArray:function(item){return!1},delete:function(key){for(var item,j=0;j<arguments.length;j++)if(item=arguments[j],Array.isArray(item)||this._isPseudoArray(item))for(var i=0;i<item.length;i++)this._removeItem(item[i]);else this._removeItem(item);return this},has:function(key){return key=this._makeKey(key),Object.prototype.hasOwnProperty.call(this.data,key)},hasAll:function(args){var self=this;return this.makeNew.apply(this,arguments).every(function(data,key){return self.has(key)})},makeSet:function(args){return args instanceof Set?args:this.makeNew.apply(this,arguments)},equals:function(otherSet){return otherSet=this.makeSet(otherSet),this.isSubset(otherSet)&&this.isSuperset(otherSet)},isEmpty:function(){for(var key in this.data)if(this.has(key))return!1;return!0},size:function(){var size=0;for(var key in this.data)this.has(key)&&size++;return size},keys:function(){var results=[];return this.each(function(data){results.push(data)}),results},clear:function(){return this.data={},this},makeNew:function(){var newSet=new this.constructor;return arguments.length&&newSet.add.apply(newSet,arguments),newSet},union:function(otherSet){otherSet=this.makeSet(otherSet);var newSet=this.makeNew(this);return newSet.add(otherSet),newSet},intersection:function(otherSet){otherSet=this.makeSet(otherSet);var newSet=this.makeNew();return this.each(function(data,key){otherSet.has(key)&&newSet._add(key,data)}),newSet},difference:function(otherSet){otherSet=this.makeSet(otherSet);var newSet=this.makeNew();return this.each(function(data,key){otherSet.has(key)||newSet._add(key,data)}),newSet},notInBoth:function(otherSet){return otherSet=this.makeSet(otherSet),this.difference(otherSet).add(otherSet.difference(this))},isSubset:function(otherSet){return otherSet=this.makeSet(otherSet),this.eachReturn(function(data,key){if(!otherSet.has(key))return!1})},isSuperset:function(otherSet){otherSet=this.makeSet(otherSet);var self=this;return otherSet.eachReturn(function(data,key){if(!self.has(key))return!1})},each:function(fn){return this.eachReturn(fn),this},eachReturn:function(fn){for(var key in this.data)if(this.has(key)&&!1===fn.call(this,this.data[key],key))return!1;return!0},filter:function(fn){var newSet=this.makeNew();return this.each(function(data,key){!0===fn.call(this,key)&&newSet._add(key,data)}),newSet},map:function(fn){var newSet=this.makeNew();return this.each(function(data,key){void 0!==fn.call(this,key)&&newSet._add(key,data)}),newSet},some:function(fn){var found=!1;return this.eachReturn(function(key){if(!0===fn.call(this,key))return found=!0,!1}),found},every:function(fn){return this.eachReturn(fn)}},Set.prototype.constructor=Set);var igv=function(igv){var transformations;return igv.SVG=function(){this.svg="",this.contents=[],transformations=[]},igv.SVG.prototype.setProperties=function(properties){var str="";for(var key in properties)if(properties.hasOwnProperty(key)){var value=properties[key];"font-family"===key?str+="font-family:"+value+";":"font-size"===key?str+="font-size:"+value+";":"fillStyle"==key?str+="fill:"+value+";":"fill"===key?str+="fill:"+value+";":"strokeStyle"==key?str+="stroke:"+value+";":"stroke"===key?str+="stroke:"+value+";":"stroke-width"===key?str+="stroke-width:"+value+";":console.log("Unknown property: "+key)}return str},igv.SVG.prototype.setTransforms=function(transforms,x,y){var str="";for(var key in transforms){if(transforms.hasOwnProperty(key)){var value=transforms[key];"rotate"===key?(str+="rotate("+value.angle,str+=","+x,str+=","+y,str+=")"):"translate"===key?(str+="translate("+value[x],"y"in value&&(str+=","+value.y),str+=")"):console.log("Unknown transform: "+key)}str+=" "}return str},igv.SVG.prototype.clearRect=function(x,y,w,h){},igv.SVG.prototype.strokeLine=function(x1,y1,x2,y2,properties,transforms){var str="";str+='<line x1="'+x1+'" y1="'+y1+'" x2="'+x2+'" y2="'+y2+'"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,x1,y1)+'"'),str+="/>",this.contents.push(str)},igv.SVG.prototype.fillRect=function(x,y,w,h,properties,transforms){var str="";str+='<rect x="'+x+'" y="'+y,str+='" width="'+w+'" height="'+h+'"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,x,y)+'"'),str+="/>",this.contents.push(str)},igv.SVG.prototype.fillRectWithCenter=function(centerX,centerY,width,height,properties,transforms){var str="";str+='<rect x="'+(centerX-width/2)+'" y="'+(centerY-height/2),str+='" width="'+width+'" height="'+height+'"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,centerX,centerY)+'"'),str+="/>",this.contents.push(str)},igv.SVG.prototype.fillPolygon=function(x,y,properties,transforms){var str="";str+='<polygon points="';for(var index=0;index<x.length;index++)str+=" "+x[index]+","+y[index];str+='"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,x,y)+'"'),str+="/>",this.contents.push(str)},igv.SVG.prototype.fillText=function(text,x,y,properties,transforms){var str="";str+='<text x="'+x+'" y="'+y+'"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,x,y)+'"'),str+=">",str+=text,str+="</text>",this.contents.push(str)},igv.SVG.prototype.strokeText=function(text,x,y,properties,transforms){var str="";str+='<text x="'+x+'" y="'+y+'"',properties&&(str+=' style="'+this.setProperties(properties)+'"'),transforms&&(str+=' transform="'+this.setTransforms(transforms,x,y)+'"'),str+=">",str+=text,str+="</text>",this.contents.push(str)},igv.SVG.prototype.strokeCircle=function(x,y,radius,properties,transforms){var str="";str+='<circle cx="'+x+'" cy="'+y+'" r="'+radius+'" stroke="black" fill-opacity="0.0"/>',this.contents.push(str)},igv.SVG.prototype.string=function(){var string="";string+='<svg width="100%" height="100%" version="1.1" xmlns="http://www.w3.org/2000/svg">';for(var index=0;index<this.contents.length;index++)string+="\n"+this.contents[index];return string+="</svg>"},igv.SVG.prototype.innerString=function(){for(var string="",index=0;index<this.contents.length;index++)string+="\n"+this.contents[index];return string},igv}(igv||{}),igv=function(igv){function createFixedStep(binaryParser,nTracks){var data,dtrack,nPositions=binaryParser.getInt(),start=binaryParser.getInt(),span=binaryParser.getFloat(),np=nPositions,nt=nTracks;for(data=[];nt-- >0;){for(np=nPositions,dtrack=[];np-- >0;)dtrack.push(binaryParser.getFloat());data.push(dtrack)}return{type:"fixedStep",start:start,span:span,data:data,nTracks:nTracks,nPositions:nPositions}}function createVariableStep(binaryParser,nTracks){for(var data,dtrack,tileStart=binaryParser.getInt(),span=binaryParser.getFloat(),nPositions=binaryParser.getInt(),np=nPositions,nt=nTracks,start=[];np-- >0;)start.push(binaryParser.getInt());binaryParser.getInt();for(data=[];nt-- >0;){for(np=nPositions,dtrack=[];np-- >0;)dtrack.push(binaryParser.getFloat());data.push(dtrack)}return{type:"variableStep",tileStart:tileStart,span:span,start:start,data:data,nTracks:nTracks,nPositions:nPositions}}function createBed(binaryParser,nTracks,type){var nPositions,start,end,data,name,n,nt;for(nPositions=binaryParser.getInt(),n=nPositions,start=[];n-- >0;)start.push(binaryParser.getInt());for(n=nPositions,end=[];n-- >0;)end.push(binaryParser.getInt());binaryParser.getInt();for(data=[],nt=nTracks;nt-- >0;){for(np=nPositions,dtrack=[];np-- >0;)dtrack.push(binaryParser.getFloat());data.push(dtrack)}if("bedWithName"===type)for(n=nPositions,name=[];n-- >0;)name.push(binaryParser.getString());return{type:type,start:start,end:end,data:data,name:name,nTracks:nTracks,nPositions:nPositions}}return igv.TDFReader=function(config){this.config=config||{},this.path=config.url,this.groupCache={}},igv.TDFReader.prototype.readHeader=function(){var self=this;return void 0!==this.magic?Promise.resolve(this):new Promise(function(fulfill,reject){igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:0,size:64e3}})).then(function(data){if(!data)return void reject("no data");var binaryParser=new igv.BinaryParser(new DataView(data));if(self.magic=binaryParser.getInt(),self.version=binaryParser.getInt(),self.indexPos=binaryParser.getLong(),self.indexSize=binaryParser.getInt(),binaryParser.getInt(),self.version>=2){var nWindowFunctions=binaryParser.getInt();for(self.windowFunctions=[];nWindowFunctions-- >0;)self.windowFunctions.push(binaryParser.getString())}self.trackType=binaryParser.getString(),self.trackLine=binaryParser.getString();var nTracks=binaryParser.getInt();for(self.trackNames=[];nTracks-- >0;)self.trackNames.push(binaryParser.getString());self.genomeID=binaryParser.getString(),self.flags=binaryParser.getInt(),self.compressed=0!=(1&self.flags),igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:self.indexPos,size:self.indexSize}})).then(function(data){if(!data)return void reject("no data");binaryParser=new igv.BinaryParser(new DataView(data)),self.datasetIndex={};for(var nEntries=binaryParser.getInt();nEntries-- >0;){var name=binaryParser.getString(),pos=binaryParser.getLong(),size=binaryParser.getInt();self.datasetIndex[name]={position:pos,size:size}}for(self.groupIndex={},nEntries=binaryParser.getInt();nEntries-- >0;)name=binaryParser.getString(),pos=binaryParser.getLong(),size=binaryParser.getInt(),self.groupIndex[name]={position:pos,size:size};fulfill(self)}).catch(reject)}).catch(reject)})},igv.TDFReader.prototype.readDataset=function(chr,windowFunction,zoom){var self=this;return new Promise(function(fulfill,reject){self.readHeader().then(function(reader){var dsName,indexEntry,wf=self.version<2?"":"/"+windowFunction,zoomString="all"===chr||void 0===zoom?"0":zoom.toString();dsName="raw"===windowFunction?"/"+chr+"/raw":"/"+chr+"/z"+zoomString+wf,indexEntry=self.datasetIndex[dsName],void 0===indexEntry?fulfill(null):igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:indexEntry.position,size:indexEntry.size}})).then(function(data){if(!data)return void reject("no data");for(var binaryParser=new igv.BinaryParser(new DataView(data)),nAttributes=binaryParser.getInt(),attributes={};nAttributes-- >0;)attributes[binaryParser.getString()]=binaryParser.getString();for(var dataType=binaryParser.getString(),tileWidth=binaryParser.getFloat(),nTiles=binaryParser.getInt(),tiles=[];nTiles-- >0;)tiles.push({position:binaryParser.getLong(),size:binaryParser.getInt()});fulfill({name:dsName,attributes:attributes,dataType:dataType,tileWidth:tileWidth,tiles:tiles})}).catch(reject)}).catch(reject)})},igv.TDFReader.prototype.readRootGroup=function(){var self=this,rootGroup=this.groupCache["/"];return rootGroup?Promise.resolve(rootGroup):new Promise(function(fulfill,reject){self.readGroup("/").then(function(group){var genome=igv.browser.genome,names=group.chromosomes,maxZoomString=group.maxZoom;maxZoomString&&(self.maxZoom=Number(maxZoomString)),self.chrNameMap={},names&&names.split(",").forEach(function(chr){var canonicalName=genome.getChromosomeName(chr);self.chrNameMap[canonicalName]=chr}),fulfill(group)}).catch(reject)})},igv.TDFReader.prototype.readGroup=function(name){var self=this;return new Promise(function(fulfill,reject){self.readHeader().then(function(reader){var group=self.groupCache[name],indexEntry=self.groupIndex[name];if(group)fulfill(group);else{if(void 0===indexEntry)return fulfill(null);igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:indexEntry.position,size:indexEntry.size}})).then(function(data){if(!data)return void reject("no data");for(var binaryParser=new igv.BinaryParser(new DataView(data)),nAttributes=binaryParser.getInt(),group={name:name};nAttributes-- >0;)group[binaryParser.getString()]=binaryParser.getString();self.groupCache[name]=group,fulfill(group)}).catch(reject)}}).catch(reject)})},igv.TDFReader.prototype.readTile=function(indexEntry,nTracks){var self=this;return new Promise(function(fulfill,reject){igvxhr.loadArrayBuffer(self.path,Object.assign(self.config,{range:{start:indexEntry.position,size:indexEntry.size}})).then(function(data){if(!data)return void reject("no data");self.compressed&&(data=new Zlib.Inflate(new Uint8Array(data)).decompress().buffer);var binaryParser=new igv.BinaryParser(new DataView(data)),type=binaryParser.getString();switch(type){case"fixedStep":fulfill(createFixedStep(binaryParser,nTracks));break;case"variableStep":fulfill(createVariableStep(binaryParser,nTracks));break;case"bed":case"bedWithName":fulfill(createBed(binaryParser,nTracks,type));break;default:reject("Unknown tile type: "+type)}}).catch(reject)})},igv}(igv||{}),igv=function(igv){function decodeBedTile(tile,chr,bpStart,bpEnd,bpPerPixel,features){var i,nPositions=tile.nPositions,starts=tile.start,ends=tile.end,data=tile.data[0];for(i=0;i<nPositions;i++){var s=starts[i],e=ends[i];if(!(e<bpStart)){if(s>bpEnd)break;features.push({start:s,end:e,value:data[i]})}}}function decodeVaryTile(tile,chr,bpStart,bpEnd,bpPerPixel,features){var i,nPositions=tile.nPositions,starts=tile.start,span=tile.span,data=tile.data[0];for(i=0;i<nPositions;i++){var s=starts[i],e=s+span;if(!(e<bpStart)){if(s>bpEnd)break;features.push({start:s,end:e,value:data[i]})}}}function decodeFixedTile(tile,chr,bpStart,bpEnd,bpPerPixel,features){var i,nPositions=tile.nPositions,s=tile.start,span=tile.span,data=tile.data[0];for(i=0;i<nPositions;i++){var e=s+span;if(!(e<bpStart)){if(s>bpEnd)break;Number.isNaN(data[i])||features.push({start:s,end:e,value:data[i]}),s=e}}}function zoomLevelForScale(chr,bpPerPixel){var chrSize=igv.browser.genome.getChromosome(chr).bpLength;return Math.ceil(Math.log(Math.max(0,chrSize/(700*bpPerPixel)))/log2)}igv.TDFSource=function(config){this.windowFunction=config.windowFunction||"mean",this.reader=new igv.TDFReader(config)},igv.TDFSource.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this,bpPerPixel=igv.browser.referenceFrame.bpPerPixel;return new Promise(function(fulfill,reject){self.reader.readRootGroup().then(function(group){var wf,zoom=zoomLevelForScale(chr,bpPerPixel),queryChr=self.reader.chrNameMap[chr],maxZoom=self.reader.maxZoom;void 0===queryChr&&(queryChr=chr),void 0===maxZoom&&(maxZoom=-1),wf=zoom>maxZoom?"raw":self.windowFunction,self.reader.readDataset(queryChr,wf,zoom).then(function(dataset){if(null==dataset)return void fulfill(null);var i,tileWidth=dataset.tileWidth,startTile=Math.floor(bpStart/tileWidth),endTile=Math.floor(bpEnd/tileWidth),p=[];for(i=startTile;i<=endTile;i++)void 0!==dataset.tiles[i]&&p.push(self.reader.readTile(dataset.tiles[i],1));Promise.all(p).then(function(tiles){var features=[];tiles.forEach(function(tile){switch(tile.type){case"bed":decodeBedTile(tile,chr,bpStart,bpEnd,bpPerPixel,features);break;case"variableStep":decodeVaryTile(tile,chr,bpStart,bpEnd,bpPerPixel,features);break;case"fixedStep":decodeFixedTile(tile,chr,bpStart,bpEnd,bpPerPixel,features);break;default:return void reject("Unknown tile type: "+tile.type)}}),fulfill(features)}).catch(reject)}).catch(reject)})})};var log2=Math.log(2);return igv}(igv||{}),igv=function(igv){return igv.configTrack=function(track,config){track.config=config,track.url=config.url,config.name=config.name||config.label,config.name?track.name=config.name:config.localFile?track.name=config.localFile.name:track.name=config.url,track.id=config.id||track.name,track.order=config.order,track.color=config.color||igv.browser.constants.defaultColor,track.removable=void 0===config.removable||config.removable,track.height=config.height||("wig"===config.type?50:100),void 0===config.autoHeight&&(config.autoHeight=config.autoheight),track.autoHeight=void 0===config.autoHeight?void 0===config.height:config.autoHeight,track.minHeight=config.minHeight||Math.min(50,track.height),track.maxHeight=config.maxHeight||Math.max(500,track.height),config.visibilityWindow&&(track.visibilityWindow=config.visibilityWindow)},igv.setTrackLabel=function(track,label){track.name=label,$(track.trackView.viewportDiv).find(".igv-track-label").html(track.name),track.trackView&&track.trackView.repaint()},igv.setTrackColor=function(track,color){track.color=color,track.trackView&&track.trackView.repaint()},igv.paintAxis=function(ctx,pixelWidth,pixelHeight){function prettyPrint(number){return 0===number?"0":Math.abs(number)>=10?number.toFixed():Math.abs(number)>=1?number.toFixed(1):number.toFixed(2)}var x1,x2,y1,y2,a,b,reference,shim,font={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};void 0!==this.dataRange&&void 0!==this.dataRange.max&&void 0!==this.dataRange.min&&(igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),reference=.95*pixelWidth,x1=reference-8,x2=reference,shim=.01,y1=y2=shim*pixelHeight,a={x:x2,y:y1},igv.graphics.strokeLine(ctx,x1,y1,x2,y2,font),igv.graphics.fillText(ctx,prettyPrint(this.dataRange.max),x1+4,y1+12,font),y1=y2=(1-shim)*pixelHeight,b={x:x2,y:y1},igv.graphics.strokeLine(ctx,x1,y1,x2,y2,font),igv.graphics.fillText(ctx,prettyPrint(this.dataRange.min),x1+4,y1-4,font),igv.graphics.strokeLine(ctx,a.x,a.y,b.x,b.y,font))},igv}(igv||{}),igv=function(igv){function setTrackHeight_(newHeight,update){var trackHeightStr;this.track.minHeight&&(newHeight=Math.max(this.track.minHeight,newHeight)),this.track.maxHeight&&(newHeight=Math.min(this.track.maxHeight,newHeight)),trackHeightStr=newHeight+"px",this.track.height=newHeight,this.trackDiv.style.height=trackHeightStr,this.track.paintAxis&&(this.controlCanvas.style.height=trackHeightStr,this.controlCanvas.setAttribute("height",newHeight)),this.viewportDiv.style.height=trackHeightStr,void 0!==update&&!0!==update||this.update()}function Tile(chr,tileStart,tileEnd,scale,image){this.chr=chr,this.startBP=tileStart,this.endBP=tileEnd,this.scale=scale,this.image=image}function addRulerTrackHandlers(trackView){var left,rulerSweepWidth,dx,isMouseDown=void 0,isMouseIn=void 0,mouseDownXY=void 0,mouseMoveXY=void 0,rulerSweepThreshold=1;$(document).mousedown(function(e){mouseDownXY=igv.translateMouseCoordinates(e,trackView.contentDiv),left=mouseDownXY.x,rulerSweepWidth=0,trackView.rulerSweeper.css({display:"inline",left:left+"px",width:rulerSweepWidth+"px"}),isMouseIn=!0}),$(trackView.contentDiv).mousedown(function(e){isMouseDown=!0}),$(document).mousemove(function(e){isMouseDown&&isMouseIn&&(mouseMoveXY=igv.translateMouseCoordinates(e,trackView.contentDiv),dx=mouseMoveXY.x-mouseDownXY.x,(rulerSweepWidth=Math.abs(dx))>rulerSweepThreshold&&(trackView.rulerSweeper.css({width:rulerSweepWidth+"px"}),dx<0&&(left=mouseDownXY.x+dx,trackView.rulerSweeper.css({left:left+"px"}))))}),$(document).mouseup(function(e){var locus,ss,ee;isMouseDown&&(isMouseDown=!1,isMouseIn=!1,trackView.rulerSweeper.css({display:"none",left:"0px",width:"0px"}),ss=igv.browser.referenceFrame.start+left*igv.browser.referenceFrame.bpPerPixel,ee=ss+rulerSweepWidth*igv.browser.referenceFrame.bpPerPixel,rulerSweepWidth>rulerSweepThreshold&&(locus=igv.browser.referenceFrame.chr+":"+igv.numberFormatter(Math.floor(ss))+"-"+igv.numberFormatter(Math.floor(ee)),igv.browser.search(locus)))})}function addTrackHandlers(trackView){var popupTimer,isMouseDown=!1,lastMouseX=void 0,mouseDownX=void 0,lastClickTime=0,doubleClickDelay=igv.browser.constants.doubleClickDelay;$(trackView.canvas).mousedown(function(e){var canvasCoords=igv.translateMouseCoordinates(e,trackView.canvas);isMouseDown=!0,lastMouseX=canvasCoords.x,mouseDownX=lastMouseX}),$(trackView.canvas).click(function(e){e=$.event.fix(e),e.stopPropagation();var canvasCoords=igv.translateMouseCoordinates(e,trackView.canvas),referenceFrame=trackView.browser.referenceFrame,genomicLocation=Math.floor(referenceFrame.start+referenceFrame.toBP(canvasCoords.x)),time=Date.now();if(referenceFrame){if(time-lastClickTime<doubleClickDelay){popupTimer&&(window.clearTimeout(popupTimer),popupTimer=void 0);var newCenter=Math.round(referenceFrame.start+canvasCoords.x*referenceFrame.bpPerPixel);referenceFrame.bpPerPixel/=2,igv.browser.goto(referenceFrame.chr,newCenter)}else e.shiftKey?trackView.track.shiftClick&&trackView.tile&&trackView.track.shiftClick(genomicLocation,e):e.altKey?trackView.track.altClick&&trackView.tile&&trackView.track.altClick(genomicLocation,e):Math.abs(canvasCoords.x-mouseDownX)<=igv.browser.constants.dragThreshold&&trackView.track.popupData&&(popupTimer=window.setTimeout(function(){var popupData,xOrigin;if(void 0!==genomicLocation&&null!==trackView.tile){xOrigin=Math.round(referenceFrame.toPixels(trackView.tile.startBP-referenceFrame.start)),popupData=trackView.track.popupData(genomicLocation,canvasCoords.x-xOrigin,canvasCoords.y);var handlerResult=igv.browser.fireEvent("trackclick",[trackView.track,popupData]);void 0===handlerResult?popupData&&popupData.length>0&&igv.popover.presentTrackPopup(e.pageX,e.pageY,igv.formatPopoverText(popupData),!1):"string"==typeof handlerResult&&igv.popover.presentTrackPopup(e.pageX,e.pageY,handlerResult,!1),mouseDownX=void 0,popupTimer=void 0}},doubleClickDelay));mouseDownX=void 0,isMouseDown=!1,lastMouseX=void 0,lastClickTime=time}})}return igv.TrackView=function(track,browser){function makeTrackDraggable(track){self.igvTrackDragScrim=$('<div class="igv-track-drag-scrim">')[0],$(self.viewportDiv).append(self.igvTrackDragScrim),$(self.igvTrackDragScrim).hide(),self.igvTrackManipulationHandle=$('<div class="igv-track-manipulation-handle">')[0],$(self.trackDiv).append(self.igvTrackManipulationHandle),$(self.igvTrackManipulationHandle).mousedown(function(e){self.isMouseDown=!0,igv.browser.dragTrackView=self}),$(self.igvTrackManipulationHandle).mouseup(function(e){self.isMouseDown=void 0}),$(self.igvTrackManipulationHandle).mouseenter(function(e){self.isMouseIn=!0,igv.browser.dragTargetTrackView=self,void 0===igv.browser.dragTrackView?$(self.igvTrackDragScrim).show():self===igv.browser.dragTrackView&&$(self.igvTrackDragScrim).show(),igv.browser.dragTargetTrackView&&igv.browser.dragTrackView&&igv.browser.dragTargetTrackView!==igv.browser.dragTrackView&&(igv.browser.dragTargetTrackView.track.order<igv.browser.dragTrackView.track.order?(igv.browser.dragTrackView.track.order=igv.browser.dragTargetTrackView.track.order,igv.browser.dragTargetTrackView.track.order=1+igv.browser.dragTrackView.track.order):(igv.browser.dragTrackView.track.order=igv.browser.dragTargetTrackView.track.order,igv.browser.dragTargetTrackView.track.order=igv.browser.dragTrackView.track.order-1),igv.browser.reorderTracks())}),$(self.igvTrackManipulationHandle).mouseleave(function(e){self.isMouseIn=void 0,igv.browser.dragTargetTrackView=void 0,self!==igv.browser.dragTrackView&&$(self.igvTrackDragScrim).hide()})}var element,self=this;this.track=track,this.browser=browser,this.trackDiv=$('<div class="igv-track-div">')[0],$(browser.trackContainerDiv).append(this.trackDiv),track.height&&(this.trackDiv.style.height=track.height+"px"),this.appendLeftHandGutterDivToTrackDiv($(this.trackDiv)),this.appendViewportDivToTrackDiv($(this.trackDiv)),element=this.createRightHandGutter(),element&&$(this.trackDiv).append(element),this.trackDiv.appendChild(igv.spinner()),makeTrackDraggable(this.track),this.track instanceof igv.RulerTrack?(this.trackDiv.dataset.rulerTrack="rulerTrack",this.rulerSweeper=$('<div class="igv-ruler-sweeper-div">'),$(this.contentDiv).append(this.rulerSweeper[0]),addRulerTrackHandlers(this)):addTrackHandlers(this),$(".igv-ideogram-content-div").addClass("igv-ideogram-gutter-shim"),$(".igv-viewport-div").addClass("igv-gutter-shim")},igv.TrackView.prototype.appendViewportDivToTrackDiv=function($track){var description,$trackLabel,self=this;this.viewportDiv=$('<div class="igv-viewport-div">')[0],$track.append(this.viewportDiv),this.contentDiv=$('<div class="igv-content-div">')[0],$(this.viewportDiv).append(this.contentDiv),this.canvas=$('<canvas class = "igv-content-canvas">')[0],$(this.contentDiv).append(this.canvas),this.canvas.setAttribute("width",this.contentDiv.clientWidth),this.canvas.setAttribute("height",this.contentDiv.clientHeight),this.ctx=this.canvas.getContext("2d"),void 0!==this.track.visibilityWindow&&(self.$zoomInNotice=$('<div class="zoom-in-notice">'),self.$zoomInNotice.text("Zoom in to see features"),$(this.contentDiv).append(self.$zoomInNotice[0]),self.$zoomInNotice.hide()),"hidden"===$(this.viewportDiv).css("overflow-y")&&(this.scrollbar=new TrackScrollbar(this.viewportDiv,this.contentDiv),this.scrollbar.update(),$(this.viewportDiv).append(this.scrollbar.outerScrollDiv)),this.track.name&&(description=this.track.description||this.track.name,$trackLabel=$('<div class="igv-track-label">'),$trackLabel.html(this.track.name),$trackLabel.click(function(e){igv.popover.presentTrackPopup(e.pageX,e.pageY,description,!1)}),$(this.viewportDiv).append($trackLabel[0]))},igv.TrackView.prototype.appendLeftHandGutterDivToTrackDiv=function($track){var $leftHandGutter,$canvas,w,h,self=this;this.track.paintAxis&&($leftHandGutter=$('<div class="igv-left-hand-gutter">'),$track.append($leftHandGutter[0]),$canvas=$('<canvas class ="igv-track-control-canvas">'),w=$leftHandGutter.outerWidth(),h=$leftHandGutter.outerHeight(),$canvas.attr("width",w),$canvas.attr("height",h),$leftHandGutter.append($canvas[0]),this.controlCanvas=$canvas[0],this.controlCtx=this.controlCanvas.getContext("2d"),this.track.dataRange&&($leftHandGutter.click(function(e){igv.dataRangeDialog.configureWithTrackView(self),igv.dataRangeDialog.show()}),$leftHandGutter.addClass("igv-clickable")),this.leftHandGutter=$leftHandGutter[0])},igv.TrackView.prototype.createRightHandGutter=function(){var gearButton,self=this;if(!this.track.ignoreTrackMenu)return gearButton=$('<i class="fa fa-gear fa-20px igv-track-menu-gear igv-app-icon">'),$(gearButton).click(function(e){igv.popover.presentTrackMenu(e.pageX,e.pageY,self)}),this.rightHandGutter=$('<div class="igv-right-hand-gutter">')[0],$(this.rightHandGutter).append(gearButton[0]),this.rightHandGutter},igv.TrackView.prototype.resize=function(){var canvas=this.canvas,contentDiv=this.contentDiv,contentWidth=this.viewportDiv.clientWidth;contentWidth>0&&(contentDiv.style.width=contentWidth+"px",canvas.style.width=contentWidth+"px",canvas.setAttribute("width",contentWidth),this.update())},igv.TrackView.prototype.setTrackHeight=function(newHeight,update){setTrackHeight_.call(this,newHeight,update||!0)},igv.TrackView.prototype.setContentHeight=function(newHeight){newHeight=Math.min(newHeight,32e3),this.track.minHeight&&(newHeight=Math.max(this.track.minHeight,newHeight));var contentHeightStr=newHeight+"px";this.track.autoHeight&&setTrackHeight_.call(this,newHeight,!1),this.contentDiv.style.height=contentHeightStr,this.canvas.setAttribute("height",this.canvas.clientHeight),this.track.paintAxis&&(this.controlCanvas.style.height=contentHeightStr,this.controlCanvas.setAttribute("height",newHeight)),this.scrollbar&&this.scrollbar.update()},igv.TrackView.prototype.update=function(){this.tile=null,this.scrollbar&&this.scrollbar.update(),this.repaint()},igv.TrackView.prototype.repaint=function(){function viewIsReady(){return this.track&&this.browser&&this.browser.referenceFrame}var pixelWidth,bpWidth,bpStart,bpEnd,ctx,referenceFrame,chr,refFrameStart,refFrameEnd,self=this;if(viewIsReady.call(this)){if(void 0!==this.track.visibilityWindow&&this.track.visibilityWindow>0){if(igv.browser.trackViewportWidthBP()>this.track.visibilityWindow)return this.tile=null,this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height),igv.stopSpinnerAtParentElement(this.trackDiv),void this.$zoomInNotice.show();this.$zoomInNotice.hide()}if(referenceFrame=this.browser.referenceFrame,chr=referenceFrame.chr,refFrameStart=referenceFrame.start,refFrameEnd=refFrameStart+referenceFrame.toBP(this.canvas.width),this.tile&&this.tile.containsRange(chr,refFrameStart,refFrameEnd,referenceFrame.bpPerPixel))this.paintImage();else{if(pixelWidth=3*this.canvas.width,bpWidth=Math.round(referenceFrame.toBP(pixelWidth)),bpStart=Math.max(0,Math.round(referenceFrame.start-bpWidth/3)),bpEnd=bpStart+bpWidth,self.loading&&self.loading.start===bpStart&&self.loading.end===bpEnd)return;self.loading={start:bpStart,end:bpEnd},igv.startSpinnerAtParentElement(self.trackDiv),this.track.getFeatures(referenceFrame.chr,bpStart,bpEnd).then(function(features){if(self.loading=!1,igv.stopSpinnerAtParentElement(self.trackDiv),features){if("function"==typeof self.track.computePixelHeight){var requiredHeight=self.track.computePixelHeight(features);requiredHeight!=self.contentDiv.clientHeight&&self.setContentHeight(requiredHeight)}var buffer=document.createElement("canvas");if(buffer.width=pixelWidth,buffer.height=self.canvas.height,ctx=buffer.getContext("2d"),self.track.draw({features:features,context:ctx,bpStart:bpStart,bpPerPixel:referenceFrame.bpPerPixel,pixelWidth:buffer.width,pixelHeight:buffer.height}),self.track.paintAxis&&self.controlCanvas.width>0&&self.controlCanvas.height>0){var buffer2=document.createElement("canvas");buffer2.width=self.controlCanvas.width,buffer2.height=self.controlCanvas.height;var ctx2=buffer2.getContext("2d");self.track.paintAxis(ctx2,buffer2.width,buffer2.height),self.controlCtx.drawImage(buffer2,0,0)}self.tile=new Tile(referenceFrame.chr,bpStart,bpEnd,referenceFrame.bpPerPixel,buffer),self.paintImage()}else self.ctx.clearRect(0,0,self.canvas.width,self.canvas.height)}).catch(function(error){self.loading=!1,error instanceof igv.AbortLoad?console.log("Aborted ---"):(igv.stopSpinnerAtParentElement(self.trackDiv),console.log(error),igv.presentAlert(error))})}}},Tile.prototype.containsRange=function(chr,start,end,scale){return this.scale===scale&&start>=this.startBP&&end<=this.endBP&&chr===this.chr},Tile.prototype.overlapsRange=function(chr,start,end){return this.chr===chr&&this.endBP>=start&&this.startBP<=end},igv.TrackView.prototype.paintImage=function(){this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height),this.tile&&(this.xOffset=Math.round(this.browser.referenceFrame.toPixels(this.tile.startBP-this.browser.referenceFrame.start)),this.ctx.drawImage(this.tile.image,this.xOffset,0),this.ctx.save(),this.ctx.restore())},TrackScrollbar=function(viewportDiv,contentDiv){function mouseMove(event){moveScrollerTo(event.pageY-offY),event.stopPropagation()}function mouseUp(event){$(window).off("mousemove .igv",null,mouseMove),$(window).off("mouseup .igv",null,mouseUp)}function moveScrollerTo(y){var H=$(outerScrollDiv).height(),h=$(innerScrollDiv).height();newTop=Math.min(Math.max(0,y),H-h),contentTop=-Math.round(newTop*($(contentDiv).height()/$(viewportDiv).height())),$(innerScrollDiv).css("top",newTop+"px"),$(contentDiv).css("top",contentTop+"px")}var offY,outerScrollDiv=$('<div class="igv-scrollbar-outer-div">')[0],innerScrollDiv=$('<div class="igv-scrollbar-inner-div">')[0];$(outerScrollDiv).append(innerScrollDiv),this.viewportDiv=viewportDiv,this.contentDiv=contentDiv,this.outerScrollDiv=outerScrollDiv,this.innerScrollDiv=innerScrollDiv,$(this.innerScrollDiv).mousedown(function(event){offY=event.pageY-$(innerScrollDiv).position().top,$(window).on("mousemove .igv",null,null,mouseMove),$(window).on("mouseup .igv",null,null,mouseUp),event.stopPropagation()}),$(this.innerScrollDiv).click(function(event){event.stopPropagation()}),$(this.outerScrollDiv).click(function(event){moveScrollerTo(event.offsetY-$(innerScrollDiv).height()/2),event.stopPropagation()})},TrackScrollbar.prototype.update=function(){var viewportHeight=$(this.viewportDiv).height(),contentHeight=$(this.contentDiv).height(),newInnerHeight=Math.round(viewportHeight/contentHeight*viewportHeight);contentHeight>viewportHeight?($(this.outerScrollDiv).show(),$(this.innerScrollDiv).height(newInnerHeight)):$(this.outerScrollDiv).hide()},igv.TrackView.prototype.redrawTile=function(features){if(this.tile){var self=this,chr=self.tile.chr,bpStart=self.tile.startBP,bpEnd=self.tile.endBP,buffer=document.createElement("canvas"),bpPerPixel=self.tile.scale;buffer.width=self.tile.image.width,buffer.height=self.tile.image.height;var ctx=buffer.getContext("2d");self.track.draw({features:features,context:ctx,bpStart:bpStart,bpPerPixel:bpPerPixel,pixelWidth:buffer.width,pixelHeight:buffer.height}),self.tile=new Tile(chr,bpStart,bpEnd,bpPerPixel,buffer),self.paintImage()}},igv}(igv||{}),igv=function(igv){return igv.AlertDialog=function($parent,id){var $header,$headerBlurb,self=this;this.$container=$("<div>",{id:id,class:"igv-grid-container-alert-dialog"}),$parent.append(this.$container),$header=$('<div class="igv-grid-header">'),$headerBlurb=$('<div class="igv-grid-header-blurb">'),$header.append($headerBlurb),igv.attachDialogCloseHandlerWithParent($header,function(){self.hide()}),this.$container.append($header),this.$container.append(this.alertTextContainer()),this.$container.append(this.rowOfOk())},igv.AlertDialog.prototype.alertTextContainer=function(){var $rowContainer;return $rowContainer=$('<div class="igv-grid-rect">'),this.$dialogLabel=$("<div>",{class:"igv-col igv-col-4-4 igv-alert-dialog-text"}),$rowContainer.append(this.$dialogLabel),$rowContainer},igv.AlertDialog.prototype.rowOfOk=function(){var $rowContainer,$col,self=this;return $rowContainer=$('<div class="igv-grid-rect">'),$col=$('<div class="igv-col igv-col-1-4">'),$rowContainer.append($col),$col=$('<div class="igv-col igv-col-2-4">'),this.$ok=$('<div class="igv-col-filler-ok-button">'),this.$ok.text("OK"),this.$ok.unbind(),this.$ok.click(function(){self.hide()}),$col.append(this.$ok),$rowContainer.append($col),$rowContainer},igv.AlertDialog.prototype.hide=function(){this.$container.hasClass("igv-grid-container-dialog")&&this.$container.offset({left:0,top:0}),this.$container.hide()},igv.AlertDialog.prototype.show=function($host){var body_scrolltop,offset,_top,_left;body_scrolltop=$("body").scrollTop(),this.$container.hasClass("igv-grid-container-dialog")&&(offset=$host.offset(),_top=offset.top+body_scrolltop,_left=$host.outerWidth()-300,this.$container.offset({left:_left,top:_top})),this.$container.show()},igv}(igv||{}),igv=function(igv){return igv.CenterGuide=function($parent,config){var cssDisplay,self=this;this.$container=$('<div class="igv-center-guide igv-center-guide-thin">'),$parent.append(this.$container),this.$container.css("display",config.showCenterGuide&&1==config.showCenterGuide?"block":"none"),cssDisplay=this.$container.css("display"),this.$centerGuideToggle=$('<div class="igv-toggle-track-labels">'),this.$centerGuideToggle.text("none"===cssDisplay?"show center guide":"hide center guide"),this.$centerGuideToggle.click(function(){cssDisplay=self.$container.css("display"),"none"===cssDisplay?(self.$container.css("display","block"),self.$centerGuideToggle.text("hide center guide")):(self.$container.css("display","none"),self.$centerGuideToggle.text("show center guide"))}),void 0!==config.showCenterGuide&&0!=config.showCenterGuide||this.$centerGuideToggle.css("display","none")},igv.CenterGuide.prototype.repaint=function(){var left,ls,ws,center,ppb=Math.floor(1/igv.browser.referenceFrame.bpPerPixel);center=this.$container.position.x+this.$container.outerWidth()/2,ppb>1?(left=center-ppb/2,ls=left.toString()+"px",ws=ppb.toString()+"px",this.$container.css({left:ls,width:ws}),this.$container.removeClass("igv-center-guide-thin"),this.$container.addClass("igv-center-guide-wide")):(ls="50%",ws="1px",this.$container.css({left:ls,width:ws}),this.$container.removeClass("igv-center-guide-wide"),this.$container.addClass("igv-center-guide-thin"))},igv}(igv||{}),igv=function(igv){var columnCount=8;return igv.ColorPicker=function($parent,userPalette,id){function rowOfUserColors(){function parseColor(value){var rgb,hex;return rgb=self.rgb_re.exec(value),null!==rgb?"rgb("+rgb[0]+")":null!==(hex=self.hex_re.exec(value))?igv.hex2Color(hex[0]):void 0}function addUserColor(color){void 0===self.userColorsIndex?(self.userColorsIndex=0,self.userColorsRowIndex=0):columnCount===self.userColorsRowIndex&&(self.userColorsRowIndex=0,self.userColorsIndex=(1+self.userColorsIndex)%self.userColors.length),presentUserColor(color,self.userColorsIndex,self.userColorsRowIndex),++self.userColorsRowIndex}function presentUserColor(color,c,r){var $rowContainer,$filler;$rowContainer=self.userColors[c],$rowContainer.removeClass("igv-grid-rect-hidden"),$rowContainer.addClass("igv-grid-rect"),$filler=$rowContainer.find(".igv-grid-colorpicker").find(".igv-col").find("div").eq(r),$filler.removeClass("igv-col-filler-no-color"),$filler.removeClass("igv-grid-rect-hidden"),$filler.addClass("igv-col-filler"),$filler.css("background-color",color),$filler.click(function(){igv.setTrackColor(self.trackView.track,$(this).css("background-color")),self.trackView.update()})}var $rowContainer,$row,$column,$userColorInput,digit;for(self.userColors=[],digit=0;digit<5;digit++)$row=rowHidden(digit),self.userColors.push($row),self.$container.append($row[0]),$row.find(".igv-col-filler-no-color").addClass("igv-grid-rect-hidden");return self.userColorsIndex=void 0,self.userColorsRowIndex=0,$row=$('<div class="igv-grid-colorpicker">'),$column=$('<div class="igv-col igv-col-7-8">'),$userColorInput=$('<input class="igv-user-input-colorpicker" type="text" placeholder="Ex: #ff0000 or 255,0,0">'),$userColorInput.change(function(){var parsed=parseColor($(this).val());parsed?(igv.setTrackColor(self.trackView.track,parsed),self.trackView.update(),addUserColor(parsed),$(this).val(""),$(this).attr("placeholder","Ex: #ff0000 or 255,0,0"),self.$userColorFeeback.css("background-color","white"),self.$userColorFeeback.hide()):self.$userError.show()}),$userColorInput.mousedown(function(){$(this).attr("placeholder","")}),$userColorInput.keyup(function(){var parsed;""===$(this).val()&&(self.$userError.hide(),$(this).attr("placeholder","Ex: #ff0000 or 255,0,0")),parsed=parseColor($(this).val()),void 0!==parsed?(self.$userColorFeeback.css("background-color",parsed),self.$userColorFeeback.show()):(self.$userColorFeeback.css("background-color","white"),self.$userColorFeeback.hide())}),$column.append($userColorInput),$row.append($column),$column=makeColumn(null),self.$userColorFeeback=$column.find("div").first(),$row.append($column),self.$userColorFeeback.hide(),$rowContainer=$('<div class="igv-grid-rect">'),$rowContainer.append($row),self.$userError=$("<span>"),self.$userError.text("ERROR.    Ex: #ff0000 or 255,0,0"),self.$userError.hide(),$row=$('<div class="igv-grid-colorpicker-user-error">'),$row.append(self.$userError),$rowContainer.append($row),$rowContainer}function rowOfDefaultColor(){var $rowContainer,$row,$column;return $row=$('<div class="igv-grid-colorpicker">'),self.$defaultColor=$('<div class="igv-col-filler">'),self.$defaultColor.css("background-color","#eee"),$column=$('<div class="igv-col igv-col-1-8">'),$column.append(self.$defaultColor),$column.click(function(){igv.setTrackColor(self.trackView.track,$(this).find(".igv-col-filler").css("background-color")),self.trackView.update()}),$row.append($column),$column=$('<div class="igv-col igv-col-7-8 igv-col-label">'),$column.text("Default Color"),$row.append($column),$rowContainer=$('<div class="igv-grid-rect">'),$rowContainer.append($row),$rowContainer}function rowOfPreviousColor(){var $rowContainer,$row,$column;return $row=$('<div class="igv-grid-colorpicker">'),self.$previousColor=$('<div class="igv-col-filler">'),self.$previousColor.css("background-color","#eee"),$column=$('<div class="igv-col igv-col-1-8">'),$column.append(self.$previousColor),$column.click(function(){igv.setTrackColor(self.trackView.track,$(this).find(".igv-col-filler").css("background-color")),self.trackView.update()}),$row.append($column),$column=$('<div class="igv-col igv-col-7-8 igv-col-label">'),$column.text("Previous Color"),$row.append($column),$rowContainer=$('<div class="igv-grid-rect">'),$rowContainer.append($row),$rowContainer}function rowHidden(rowIndex){var columnIndex,$rowContainer=$('<div class="igv-grid-rect-hidden">'),$row=$('<div class="igv-grid-colorpicker">');for(columnIndex=0;columnIndex<columnCount;columnIndex++)$row.append(makeColumn(null));return $rowContainer.append($row),$rowContainer}function makeRow(colors){var i,$rowContainer=$('<div class="igv-grid-rect">'),$row=$('<div class="igv-grid-colorpicker">');for(i=0;i<Math.min(columnCount,colors.length);i++)$row.append(makeColumn(colors[i]));return $rowContainer.append($row),$rowContainer}function makeColumn(colorOrNull){var $column=$('<div class="igv-col igv-col-1-8">'),$filler=$("<div>");return $column.append($filler),null!==colorOrNull?($filler.addClass("igv-col-filler"),$filler.css("background-color",colorOrNull),$filler.click(function(){igv.setTrackColor(self.trackView.track,$(this).css("background-color")),self.trackView.update()})):($filler.addClass("igv-col-filler-no-color"),$filler.css("background-color","white")),$column}var rowIndex,self=this,palette=userPalette||["#666666","#0000cc","#009900","#cc0000","#ffcc00","#9900cc","#00ccff","#ff6600","#ff6600"],rowCount=Math.ceil(palette.length/columnCount);for(this.rgb_re=/^\s*(0|[1-9]\d?|1\d\d?|2[0-4]\d|25[0-5])\s*,\s*(0|[1-9]\d?|1\d\d?|2[0-4]\d|25[0-5])\s*,\s*(0|[1-9]\d?|1\d\d?|2[0-4]\d|25[0-5])\s*$/,this.hex_re=new RegExp("^#([0-9A-Fa-f]{2})([0-9A-Fa-f]{2})([0-9A-Fa-f]{2})$"),this.$container=$('<div class="igv-grid-container-colorpicker">'),id&&this.$container.attr("id",id),$parent.append(this.$container),this.$container.draggable(),this.$header=$('<div class="igv-grid-header">'),this.$headerBlurb=$('<div class="igv-grid-header-blurb">'),this.$header.append(this.$headerBlurb),igv.attachDialogCloseHandlerWithParent(this.$header,function(){self.hide()}),this.$container.append(this.$header),rowIndex=0;rowIndex<rowCount;rowIndex++)self.$container.append(makeRow(palette.slice(rowIndex*columnCount)));self.$container.append($('<hr class="igv-grid-dividing-line">')),self.$container.append(rowOfUserColors()),self.$container.append(rowOfPreviousColor()),self.$container.append(rowOfDefaultColor())},igv.ColorPicker.prototype.configure=function(trackView){this.trackView=trackView,this.$defaultColor.css("background-color",trackView.track.config.color||igv.browser.constants.defaultColor),this.$previousColor.css("background-color",trackView.track.color)},igv.ColorPicker.prototype.hide=function(){$(this.$container).offset({left:0,top:0}),this.$container.hide()},igv.ColorPicker.prototype.show=function(){var obj,body_scrolltop=$("body").scrollTop(),track_origin=$(this.trackView.trackDiv).offset(),track_size={width:$(this.trackView.trackDiv).outerWidth(),height:$(this.trackView.trackDiv).outerHeight()};$(this.$container).outerWidth(),$(this.$container).outerHeight();$(this.$container).offset({left:track_size.width-300,top:track_origin.top+body_scrolltop}),obj=$(".igv-user-input-color"),obj.val(""),obj.attr("placeholder","Ex: #ff0000 or 255,0,0"),this.$container.show(),this.$userError.hide(),$(this.$container).offset(igv.constrainBBox($(this.$container),$(igv.browser.trackContainerDiv)))},igv}(igv||{}),igv=function(igv){return igv.DataRangeDialog=function($parent,id){function doOKCancel(){var rowContainer,row,column,columnFiller;return row=$('<div class="igv-grid-dialog">'),column=$('<div class="igv-col igv-col-1-8">'),row.append(column[0]),column=$('<div class="igv-col igv-col-3-8">'),self.ok=$('<div class="igv-col-filler-ok-button">'),self.ok.text("OK"),column.append(self.ok[0]),row.append(column[0]),column=$('<div class="igv-col igv-col-3-8">'),columnFiller=$('<div class="igv-col-filler-cancel-button">'),columnFiller.text("Cancel"),columnFiller.click(function(){self.hide()}),column.append(columnFiller[0]),row.append(column[0]),column=$('<div class="igv-col igv-col-1-8">'),row.append(column[0]),rowContainer=$('<div class="igv-grid-rect">'),rowContainer.append(row[0]),rowContainer}function doLayout(){var row,column,rowContainer=$('<div class="igv-grid-rect">');return row=$('<div class="igv-grid-dialog">'),column=$('<div class="spacer10">'),row.append(column[0]),column=$('<div class="igv-col igv-col-3-8">'),self.minLabel=$('<div class="igv-data-range-input-label">'),self.minLabel.text("Minimum"),column.append(self.minLabel[0]),row.append(column[0]),column=$('<div class="igv-col igv-col-3-8">'),self.minInput=$('<input class="igv-data-range-input" type="text" value="125">'),column.append(self.minInput[0]),row.append(column[0]),rowContainer.append(row[0]),row=$('<div class="igv-grid-dialog">'),column=$('<div class="igv-col igv-col-3-8">'),self.maxLabel=$('<div class="igv-data-range-input-label">'),self.maxLabel.text("Maximum"),column.append(self.maxLabel[0]),row.append(column[0]),column=$('<div class="igv-col igv-col-3-8">'),self.maxInput=$('<input class="igv-data-range-input" type="text" value="250">'),column.append(self.maxInput[0]),row.append(column[0]),rowContainer.append(row[0]),rowContainer}var self=this;this.container=$('<div class="igv-grid-container-dialog">'),id&&this.container.attr("id",id),$parent.append(this.container[0]),this.container.draggable(),this.header=$('<div class="igv-grid-header">'),this.headerBlurb=$('<div class="igv-grid-header-blurb">'),this.header.append(this.headerBlurb[0]),igv.attachDialogCloseHandlerWithParent(this.header,function(){self.hide()}),this.container.append(this.header[0]),self.container.append(doLayout()[0]),self.container.append(doOKCancel()[0])},igv.DataRangeDialog.prototype.configureWithTrackView=function(trackView){var min,max,self=this;this.trackView=trackView,trackView.track.dataRange?(min=trackView.track.dataRange.min,max=trackView.track.dataRange.max):(min=0,max=100),this.minInput.val(min),this.maxInput.val(max),this.ok.unbind(),this.ok.click(function(){min=parseFloat(self.minInput.val()),max=parseFloat(self.maxInput.val()),isNaN(min)||isNaN(max)?igv.presentAlert("Must input numeric values"):(trackView.track.dataRange.min=min,trackView.track.dataRange.max=max,trackView.track.autoScale=!1,self.hide(),trackView.update())})},igv.DataRangeDialog.prototype.hide=function(){this.container.offset({left:0,top:0}),this.container.hide()},igv.DataRangeDialog.prototype.show=function(){var body_scrolltop=$("body").scrollTop(),track_origin=($(this.trackView.trackDiv).scrollTop(),$(this.trackView.trackDiv).offset()),track_size={width:$(this.trackView.trackDiv).outerWidth(),height:$(this.trackView.trackDiv).outerHeight()};this.container.outerWidth(),this.container.outerHeight();this.container.show(),this.container.offset({left:track_size.width-300,top:track_origin.top+body_scrolltop}),this.container.offset(igv.constrainBBox(this.container,$(igv.browser.trackContainerDiv)))},igv}(igv||{}),igv=function(igv){return igv.Dialog=function($parent,constructorHelper,id){var $header,$headerBlurb,self=this;this.$container=$('<div class="igv-grid-container-dialog">'),id&&this.$container.attr("id",id),$parent.append(this.$container[0]),$header=$('<div class="igv-grid-header">'),$headerBlurb=$('<div class="igv-grid-header-blurb">'),$header.append($headerBlurb[0]),this.$container.append($header[0]),constructorHelper(this),igv.attachDialogCloseHandlerWithParent($header,function(){self.hide()})},igv.Dialog.dialogConstructor=function(dialog){dialog.$container.append(dialog.rowOfLabel()[0]),dialog.$container.append(dialog.rowOfInput()[0]),dialog.$container.append(dialog.rowOfOkCancel()[0]),dialog.$container.draggable()},igv.Dialog.prototype.rowOfOk=function(){var $rowContainer,$row,$column,$columnFiller;return $row=$('<div class="igv-grid-dialog">'),$column=$('<div class="igv-col igv-col-1-4">'),$row.append($column[0]),$column=$('<div class="igv-col igv-col-2-4">'),$columnFiller=$('<div class="igv-col-filler-ok-button">'),$columnFiller.text("OK"),this.$ok=$columnFiller,$column.append($columnFiller[0]),$row.append($column[0]),$rowContainer=$('<div class="igv-grid-rect">'),$rowContainer.append($row[0]),$rowContainer},igv.Dialog.prototype.rowOfOkCancel=function(){var $rowContainer,$row,$column,$columnFiller,self=this;return $row=$('<div class="igv-grid-dialog">'),$column=$('<div class="igv-col igv-col-1-8">'),$row.append($column[0]),$column=$('<div class="igv-col igv-col-3-8">'),$columnFiller=$('<div class="igv-col-filler-ok-button">'),$columnFiller.text("OK"),this.$ok=$columnFiller,$column.append($columnFiller[0]),$row.append($column[0]),$column=$('<div class="igv-col igv-col-3-8">'),$columnFiller=$('<div class="igv-col-filler-cancel-button">'),$columnFiller.text("Cancel"),$columnFiller.click(function(){self.$dialogInput.val(void 0),self.hide()}),$column.append($columnFiller[0]),$row.append($column[0]),$column=$('<div class="igv-col igv-col-1-8">'),$row.append($column[0]),$rowContainer=$('<div class="igv-grid-rect">'),$rowContainer.append($row[0]),$rowContainer},igv.Dialog.prototype.rowOfLabel=function(){var rowContainer,row,column;return row=$('<div class="igv-grid-dialog">'),column=$('<div class="igv-col igv-col-4-4">'),this.$dialogLabel=$('<div class="igv-user-input-label">'),column.append(this.$dialogLabel[0]),row.append(column[0]),rowContainer=$('<div class="igv-grid-rect">'),rowContainer.append(row[0]),rowContainer},igv.Dialog.prototype.rowOfInput=function(){var rowContainer,row,column;return row=$('<div class="igv-grid-dialog">'),column=$('<div class="igv-col igv-col-4-4">'),this.$dialogInput=$('<input class="igv-user-input-dialog" type="text" value="#000000">'),column.append(this.$dialogInput[0]),row.append(column[0]),rowContainer=$('<div class="igv-grid-rect">'),rowContainer.append(row[0]),rowContainer},igv.Dialog.prototype.configure=function(labelHTMLFunction,inputValue,clickFunction){var self=this;labelHTMLFunction?(self.$dialogLabel.html(labelHTMLFunction()),self.$dialogLabel.show()):self.$dialogLabel.hide(),void 0!==inputValue?(self.$dialogInput.val(inputValue),self.$dialogInput.unbind(),self.$dialogInput.change(function(){clickFunction&&clickFunction(),self.hide()}),self.$dialogInput.show()):self.$dialogInput.hide(),self.$ok.unbind(),self.$ok.click(function(){clickFunction&&clickFunction(),self.hide()})},igv.Dialog.prototype.hide=function(){this.$container.hasClass("igv-grid-container-dialog")&&this.$container.offset({left:0,top:0}),this.$container.hide()},igv.Dialog.prototype.show=function($host){var body_scrolltop,offset,_top,_left;body_scrolltop=$("body").scrollTop(),this.$container.hasClass("igv-grid-container-dialog")&&(offset=$host.offset(),_top=offset.top+body_scrolltop,_left=$host.outerWidth()-300,this.$container.offset({left:_left,top:_top})),this.$container.show()},igv}(igv||{}),igv=function(igv){function popoverPosition(pageX,pageY,popoverWidget){var left,popupRect,containerCoordinates={x:pageX,y:pageY},containerRect={x:0,y:0,width:$(window).width(),height:$(window).height()},popupX=pageX,popupY=pageY;return popupX-=popoverWidget.$parent.offset().left,popupY-=popoverWidget.$parent.offset().top,popupRect={x:popupX,y:popupY,width:popoverWidget.popover.outerWidth(),height:popoverWidget.popover.outerHeight()},left=popupX,containerCoordinates.x+popupRect.width>containerRect.width&&(left=popupX-popupRect.width),{left:left+"px",top:popupY+"px"}}return igv.Popover=function($parent,id){this.markupWith$Parent($parent,id),this.$popoverContent.kinetic({})},igv.Popover.prototype.markupWith$Parent=function($parent,id){var popoverHeader,self=this;this.$parent||(this.$parent=$parent,this.popover=$('<div class="igv-popover">'),id&&this.popover.attr("id",id),this.$parent.append(this.popover[0]),popoverHeader=$('<div class="igv-popoverHeader">'),this.popover.append(popoverHeader[0]),igv.attachDialogCloseHandlerWithParent(popoverHeader,function(){self.hide()}),this.$popoverContent=$("<div>"),this.popover.append(this.$popoverContent[0]),this.popover.draggable())},igv.Popover.prototype.testData=function(rows){var i,name,nameValues=[];for(i=0;i<rows;i++)name="name "+i,nameValues.push({name:name,value:"verbsgohuman"});return nameValues},igv.Popover.prototype.hide=function(){this.popover.hide()},igv.Popover.prototype.presentTrackMenu=function(pageX,pageY,trackView){var $container=$('<div class="igv-track-menu-container">'),trackMenuItems=igv.trackMenuItems(this,trackView);trackMenuItems.forEach(function(item){$container.append(item.object||item)}),this.$popoverContent.empty(),this.$popoverContent.removeClass("igv-popoverTrackPopupContent"),this.$popoverContent.append($container),trackMenuItems.forEach(function(item){item.object&&item.click&&item.object.click(item.click),item.init&&item.init()}),this.popover.css(popoverPosition(pageX,pageY,this)),this.popover.show(),this.popover.offset(igv.constrainBBox(this.popover,$(igv.browser.trackContainerDiv)))},igv.Popover.prototype.presentTrackPopup=function(pageX,pageY,content,showOKButton){var ok_button,markup,self=this;content&&(markup=content,!0===showOKButton&&(ok_button='<button name="button" class="igv-popover-ok-button">OK</button>',markup=content+ok_button),this.$popoverContent.addClass("igv-popoverTrackPopupContent"),this.$popoverContent.html(markup),this.popover.css(popoverPosition(pageX,pageY,this)).show(),!0===showOKButton?($(".igv-dialog-close-container").hide(),$(".igv-popover-ok-button").click(function(){self.hide()})):$(".igv-dialog-close-container").show())},igv}(igv||{}),igv=function(igv){return igv.TrackMenuPopupDialog=function(trackMenu,dialogLabel,inputValue,ok,width,height){var dialogLabelRE,inputValueRE,htmlString,myself=this;htmlString='<div id="dialog-form" title="DIALOG_LABEL"><p class="validateTips"></p><form><fieldset><input type="text" name="name" id="name" value="INPUT_VALUE"></fieldset></form></div>',dialogLabelRE=new RegExp("DIALOG_LABEL","g"),htmlString=htmlString.replace(dialogLabelRE,dialogLabel),inputValueRE=new RegExp("INPUT_VALUE","g"),htmlString=htmlString.replace(inputValueRE,inputValue),$("body").append($.parseHTML(htmlString)),this.dialogForm=$("#dialog-form"),this.form=this.dialogForm.find("form"),this.name=$("#name"),this.tips=$(".validateTips"),this.dialogForm.dialog({autoOpen:!1,width:width||320,height:height||256,modal:!0,buttons:{ok:ok,cancel:function(){myself.dialogForm.dialog("close")}},close:function(){myself.form[0].reset(),myself.dialogForm.remove(),myself.dialogForm=void 0,trackMenu&&trackMenu.hide()}}),this.form.on("submit",function(event){event.preventDefault(),$("#users").find(" tbody").append("<tr><td>"+myself.name.val()+"</td></tr>"),myself.dialogForm.dialog("close")})},igv.TrackMenuPopupDialog.prototype.updateTips=function(t){var myself=this;this.tips.text(t).addClass("ui-state-highlight"),setTimeout(function(){myself.tips.removeClass("ui-state-highlight",1500)},500)},igv}(igv||{}),igv=function(igv){return igv.UserFeedback=function(parentObject){var myself=this;this.userFeedback=$('<div class="igvUserFeedback">'),parentObject.append(this.userFeedback[0]),this.userFeedbackHeader=$('<div class="igvUserFeedbackHeader">'),this.userFeedback.append(this.userFeedbackHeader[0]),this.userFeedbackAlert=$('<i class="fa fa-exclamation-triangle fa-20px igvUserFeedbackAlert">'),this.userFeedbackHeader.append(this.userFeedbackAlert[0]),this.userFeedbackDismiss=$('<i class="fa fa-times-circle fa-20px igvUserFeedbackDismiss">'),this.userFeedbackHeader.append(this.userFeedbackDismiss[0]),this.userFeedbackDismiss.click(function(){myself.userFeedbackBodyCopy.html(""),myself.userFeedback.hide()}),this.userFeedbackBodyCopy=$('<div class="igvUserFeedbackBodyCopy">'),this.userFeedback.append(this.userFeedbackBodyCopy[0])},igv.UserFeedback.prototype.show=function(){this.userFeedback.show()},igv.UserFeedback.prototype.hide=function(){this.userFeedback.hide()},igv.UserFeedback.prototype.bodyCopy=function(htmlString){this.userFeedbackBodyCopy.html(htmlString)},igv}(igv||{}),igv=function(igv){function computeStart(variant){altTokens=variant.alternateBases.split(","),altTokens.length>0?(variant.alleles=[],variant.alleles.push(variant.referenceBases),variant.start=Number.MAX_VALUE,variant.end=0,altTokens.forEach(function(alt){var s,e,diff;variant.alleles.push(alt),alt.length>0&&(diff=variant.referenceBases.length-alt.length,diff>0?(s=variant.pos+alt.length,e=s+diff):diff<0?(s=variant.pos+variant.referenceBases.length,e=s+1):(s=variant.pos,e=s+alt.length),variant.start=Math.min(variant.start,s),variant.end=Math.max(variant.end,e))})):(variant.start=variant.pos-1,variant.end=variant.pos)}function arrayToCommaString(array){if(array){var i,str="";for(array.length>0&&(str=array[0]),i=1;i<array.length;i++)str+=", "+array[1];return str}}return igv.createVCFVariant=function(tokens){var variant=new igv.Variant;return variant.chr=tokens[0],variant.pos=parseInt(tokens[1])-1,variant.names=tokens[2],variant.referenceBases=tokens[3],variant.alternateBases=tokens[4],variant.quality=parseInt(tokens[5]),variant.filter=tokens[6],variant.info=tokens[7],computeStart(variant),variant},igv.createGAVariant=function(json){var variant=new igv.Variant;variant.chr=json.referenceName,variant.pos=parseInt(json.start),variant.names=arrayToCommaString(json.names),variant.referenceBases=json.referenceBases+"",variant.alternateBases=json.alternateBases+"",variant.quality=json.quality,variant.filter=arrayToCommaString(json.filter),variant.info=json.info,variant.calls={};var id,order=0;return json.calls&&json.calls.forEach(function(call){id=call.callSetId,variant.calls[id]=call,order++}),computeStart(variant),variant},igv.Variant=function(){},igv.Variant.prototype.popupData=function(genomicLocation){var fields,gt,self=this;return fields=[{name:"Chr",value:this.chr},{name:"Pos",value:this.pos+1},{name:"Names",value:this.names?this.names:""},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter}],this.calls&&1===this.calls.length&&(gt=this.alleles[this.calls[0].genotype[0]]+this.alleles[this.calls[0].genotype[1]],fields.push({name:"Genotype",value:gt})),this.info&&(fields.push("<HR>"),Object.keys(this.info).forEach(function(key){fields.push({name:key,value:arrayToCommaString(self.info[key])})})),fields},igv}(igv||{}),igv=function(igv){function computeVisibilityWindow(){this.callSets?this.callSets.length<10?this.visibilityWindow=DEFAULT_VISIBILITY_WINDOW:this.visibilityWindow=1e3+2500/this.callSets.length*40:this.visibilityWindow=DEFAULT_VISIBILITY_WINDOW,this.featureSource.visibilityWindow=this.visibilityWindow}function extractPopupData(call,variant){var popupData,gt="";return call.genotype.forEach(function(i){gt+=0===i?variant.referenceBases:variant.alternateBases[i-1]}),popupData=[],void 0!==call.callSetName&&popupData.push({name:"Name",value:call.callSetName}),popupData.push({name:"Genotype",value:gt}),void 0!==call.phaseset&&popupData.push({name:"Phase set",value:call.phaseset}),void 0!==call.genotypeLikelihood&&popupData.push({name:"genotypeLikelihood",value:call.genotypeLikelihood.toString()}),Object.keys(call.info).forEach(function(key){popupData.push({name:key,value:call.info[key]})}),popupData}var vGap=2,DEFAULT_VISIBILITY_WINDOW=1e5;return igv.VariantTrack=function(config){this.visibilityWindow=void 0===config.visibilityWindow?"compute":config.visibilityWindow,igv.configTrack(this,config),this.displayMode=config.displayMode||"EXPANDED",this.labelDisplayMode=config.labelDisplayMode,this.variantHeight=config.variantHeight||10,this.squishedCallHeight=config.squishedCallHeight||1,this.expandedCallHeight=config.expandedCallHeight||10,this.featureHeight=config.featureHeight||14,this.featureSource=new igv.FeatureSource(config),this.homrefColor=config.homrefColor||"rgb(200, 200, 200)",this.homvarColor=config.homvarColor||"rgb(17,248,254)",this.hetvarColor=config.hetvarColor||"rgb(34,12,253)",this.nRows=1},igv.VariantTrack.prototype.getFileHeader=function(){var self=this;return new Promise(function(fulfill,reject){"function"==typeof self.featureSource.getFileHeader?self.featureSource.getFileHeader().then(function(header){header&&(header.name&&!self.config.name&&(self.name=header.name),header.color&&!self.config.color&&(self.color="rgb("+header.color+")"),self.callSets=header.callSets,"compute"===self.visibilityWindow&&computeVisibilityWindow.call(self)),fulfill(header)}).catch(reject):fulfill(null)})},igv.VariantTrack.prototype.getFeatures=function(chr,bpStart,bpEnd){var self=this;return new Promise(function(fulfill,reject){self.featureSource.getFeatures(chr,bpStart,bpEnd).then(function(features){fulfill(features)}).catch(reject)})},igv.VariantTrack.prototype.computePixelHeight=function(features){var nRows,h,callSets=this.callSets,nCalls=callSets?callSets.length:0;if("COLLAPSED"===this.displayMode)return this.nRows=1,10+this.variantHeight;var maxRow=0;return features&&"function"==typeof features.forEach&&features.forEach(function(feature){feature.row&&feature.row>maxRow&&(maxRow=feature.row)}),nRows=maxRow+1,h=10+nRows*(this.variantHeight+vGap),this.nRows=nRows,nCalls*nRows*this.expandedCallHeight>2e3&&(this.expandedCallHeight=Math.max(1,2e3/(nCalls*nRows))),h+vGap+nCalls*nRows*("EXPANDED"===this.displayMode?this.expandedCallHeight:this.squishedCallHeight)},igv.VariantTrack.prototype.draw=function(options){var px,px1,pw,py,h,i,variant,call,callSet,j,allRef,allVar,callSets,featureList=options.features,ctx=options.context,bpPerPixel=options.bpPerPixel,bpStart=options.bpStart,pixelWidth=options.pixelWidth,pixelHeight=options.pixelHeight,bpEnd=bpStart+pixelWidth*bpPerPixel+1,callHeight="EXPANDED"===this.displayMode?this.expandedCallHeight:this.squishedCallHeight;if(this.variantBandHeight=10+this.nRows*(this.variantHeight+vGap),callSets=this.callSets,igv.graphics.fillRect(ctx,0,0,pixelWidth,pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),callSets&&callSets.length>0&&"COLLAPSED"!==this.displayMode&&igv.graphics.strokeLine(ctx,0,this.variantBandHeight,pixelWidth,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),featureList){for(i=0,len=featureList.length;i<len;i++)if(variant=featureList[i],!(variant.end<bpStart)){if(variant.start>bpEnd)break;if(py=10+("COLLAPSED"===this.displayMode?0:variant.row*(this.variantHeight+vGap)),h=this.variantHeight,px=Math.round((variant.start-bpStart)/bpPerPixel),px1=Math.round((variant.end-bpStart)/bpPerPixel),pw=Math.max(1,px1-px),pw<3?(pw=3,px-=1):pw>5&&(px+=1,pw-=2),ctx.fillStyle=this.color,ctx.fillRect(px,py,pw,h),callSets&&variant.calls&&"COLLAPSED"!==this.displayMode)for(h=callHeight,j=0;j<callSets.length;j++)callSet=callSets[j],(call=variant.calls[callSet.id])&&(allVar=allRef=!0,call.genotype.forEach(function(g){0!=g&&(allRef=!1),0==g&&(allVar=!1)}),ctx.fillStyle=allRef?this.homrefColor:allVar?this.homvarColor:this.hetvarColor,py=this.variantBandHeight+vGap+(j+variant.row)*callHeight,ctx.fillRect(px,py,pw,h))}}else console.log("No feature list")},igv.VariantTrack.prototype.popupData=function(genomicLocation,xOffset,yOffset){if(this.featureSource.featureCache){var chr=igv.browser.referenceFrame.chr,tolerance=Math.floor(2*igv.browser.referenceFrame.bpPerPixel),featureList=this.featureSource.featureCache.queryFeatures(chr,genomicLocation-tolerance,genomicLocation+tolerance),popupData=[],self=this;return featureList&&featureList.length>0&&featureList.forEach(function(variant){var row,callHeight,callSets,cs,call;variant.start<=genomicLocation+tolerance&&variant.end>genomicLocation-tolerance&&(popupData.length>0&&popupData.push("<HR>"),"COLLAPSED"==self.displayMode?Array.prototype.push.apply(popupData,variant.popupData(genomicLocation)):yOffset<=self.variantBandHeight?(row=Math.floor((yOffset-10)/(self.variantHeight+vGap)),variant.row===row&&Array.prototype.push.apply(popupData,variant.popupData(genomicLocation))):(callSets=self.callSets)&&variant.calls&&(callHeight=self.nRows*("SQUISHED"===self.displayMode?self.squishedCallHeight:self.expandedCallHeight),row=Math.floor((yOffset-self.variantBandHeight-vGap)/callHeight),cs=callSets[row],call=variant.calls[cs.id],Array.prototype.push.apply(popupData,extractPopupData(call,variant))))}),popupData}},igv.VariantTrack.prototype.popupMenuItems=function(popover){var myself=this,menuItems=[],lut={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};return menuItems.push(igv.colorPickerMenuItem(popover,this.trackView)),["COLLAPSED","SQUISHED","EXPANDED"].forEach(function(displayMode,index){var chosen,str;chosen=0===index?'<div class="igv-track-menu-item igv-track-menu-border-top">':'<div class="igv-track-menu-item">',str=displayMode===myself.displayMode?chosen+'<i class="fa fa-check fa-check-shim"></i>'+lut[displayMode]+"</div>":chosen+'<i class="fa fa-check fa-check-shim fa-check-hidden"></i>'+lut[displayMode]+"</div>",menuItems.push({object:$(str),click:function(){popover.hide(),myself.displayMode=displayMode,myself.trackView.update()}})}),menuItems},igv}(igv||{}),igv=function(igv){function extractCallFields(tokens){var i,callFields={genotypeIndex:-1,genotypeLikelihoodIndex:-1,phasesetIndex:-1,fields:tokens};for(i=0;i<tokens.length;i++)"GT"===tokens[i]?callFields.genotypeIndex=i:"GL"===tokens[i]?callFields.genotypeLikelihoodIndex=i:"PS"===tokens[i]&&(callFields.phasesetIndex=i);return callFields}function Variant(tokens){var altTokens,self=this;this.chr=tokens[0],this.pos=parseInt(tokens[1]),this.names=tokens[2],this.referenceBases=tokens[3],this.alternateBases=tokens[4],this.quality=parseInt(tokens[5]),this.filter=tokens[6],this.info=tokens[7],altTokens=this.alternateBases.split(","),altTokens.length>0?(this.alleles=[],this.start=Number.MAX_VALUE,this.end=0,altTokens.forEach(function(alt){var s,e,diff;alt.length>0&&(diff=self.referenceBases.length-alt.length,diff>0?(s=self.pos-1+alt.length,e=s+diff):diff<0?(s=self.pos-1+self.referenceBases.length,e=s+1):(s=self.pos-1,e=s+alt.length),self.alleles.push({allele:alt,start:s,end:e}),self.start=Math.min(self.start,s),self.end=Math.max(self.end,e))})):(this.start=this.pos-1,this.end=this.pos)}return igv.VcfParser=function(){},igv.VcfParser.prototype.parseHeader=function(data){var line,i,j,tokens,id,values,ltIdx,gtIdx,type,lines=data.splitLines(),len=lines.length,header={};if(!lines[0].startsWith("##fileformat"))throw new Error("Invalid VCF file: missing fileformat line");for(header.version=lines[0].substr(13),i=1;i<len&&(line=lines[i].trim(),line.startsWith("#"));i++)if(id=null,values={},line.startsWith("##")){if(line.startsWith("##INFO")||line.startsWith("##FILTER")||line.startsWith("##FORMAT")){if(ltIdx=line.indexOf("<"),gtIdx=line.lastIndexOf(">"),!(ltIdx>2&&gtIdx>0)){console.log("Malformed VCF header line: "+line);continue}type=line.substring(2,ltIdx-1),header[type]||(header[type]={}),tokens=igv.splitStringRespectingQuotes(line.substring(ltIdx+1,gtIdx-1),","),tokens.forEach(function(token){var kv=token.split("=");kv.length>1&&("ID"===kv[0]?id=kv[1]:values[kv[0]]=kv[1])}),id&&(header[type][id]=values)}}else if(line.startsWith("#CHROM")&&(tokens=line.split("\t"),tokens.length>8))for(header.callSets=[],j=9;j<tokens.length;j++)header.callSets.push({id:j,name:tokens[j]});return this.header=header,header},igv.VcfParser.prototype.parseFeatures=function(data){var lines=data.split("\n"),allFeatures=[],callSets=this.header.callSets;return lines.forEach(function(line){var variant,tokens,callFields,index,token;if(!line.startsWith("#")&&(tokens=line.split("\t"),tokens.length>=8&&(variant=new Variant(tokens),variant.header=this.header,allFeatures.push(variant),tokens.length>9)))for(callFields=extractCallFields(tokens[8].split(":")),variant.calls={},index=9;index<tokens.length;index++){token=tokens[index];var callSet=callSets[index-9],call={callSetName:callSet.name,info:{}};variant.calls[callSet.id]=call,token.split(":").forEach(function(callToken,index){switch(index){case callFields.genotypeIndex:call.genotype=[],callToken.split(/[\|\/]/).forEach(function(s){call.genotype.push(parseInt(s))});break;case callFields.genotypeLikelihoodIndex:call.genotypeLikelihood=[],callToken.split(",").forEach(function(s){call.genotype.push(parseFloat(s))});break;case callFields.phasesetIndex:call.phaseset=callToken;break;default:call.info[callFields.fields[index]]=callToken}})}}),allFeatures},Variant.prototype.popupData=function(genomicLocation){var fields,infoFields;return fields=[{name:"Names",value:this.names},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter},"<hr>"],infoFields=this.info.split(";"),infoFields.forEach(function(f){var tokens=f.split("=");tokens.length>1&&fields.push({name:tokens[0],value:tokens[1]})}),fields},igv}(igv||{}),igv=function(igv){return igv.WindowSizePanel=function($parent){this.contentDiv=$('<div class="igv-windowsizepanel-content-div"></div>'),$parent.append(this.contentDiv[0])},igv.WindowSizePanel.prototype.update=function(size){function prettyNumber(size){return size>1e7?(denom=1e6,units=" mb",value=size/denom,floored=Math.floor(value),floored.toString()+units):size>1e4?(denom=1e3,units=" kb",value=size/denom,floored=Math.floor(value),igv.numberFormatter(floored)+units):igv.numberFormatter(size)+" bp"}var value,floored,denom,units;this.contentDiv.text(prettyNumber(size))},igv}(igv||{}),MAX_WBITS=15,DEF_WBITS=MAX_WBITS,MAX_MEM_LEVEL=9,MANY=1440,BMAX=15,PRESET_DICT=32,Z_NO_FLUSH=0,Z_PARTIAL_FLUSH=1,Z_SYNC_FLUSH=2,Z_FULL_FLUSH=3,Z_FINISH=4,Z_DEFLATED=8,Z_OK=0,Z_STREAM_END=1,Z_NEED_DICT=2,Z_ERRNO=-1,Z_STREAM_ERROR=-2,Z_DATA_ERROR=-3,Z_MEM_ERROR=-4,Z_BUF_ERROR=-5,Z_VERSION_ERROR=-6,METHOD=0,FLAG=1,DICT4=2,DICT3=3,DICT2=4,DICT1=5,DICT0=6,BLOCKS=7,CHECK4=8,CHECK3=9,CHECK2=10,CHECK1=11,DONE=12,BAD=13,inflate_mask=[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535],IB_TYPE=0,IB_LENS=1,IB_STORED=2,IB_TABLE=3,IB_BTREE=4,IB_DTREE=5,IB_CODES=6,IB_DRY=7,IB_DONE=8,IB_BAD=9,fixed_bl=9,fixed_bd=5,fixed_tl=[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255],fixed_td=[80,5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577],cplens=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],cplext=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112],cpdist=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],cpdext=[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];ZStream.prototype.inflateInit=function(w,nowrap){return w||(w=DEF_WBITS),nowrap&&(nowrap=!1),this.istate=new Inflate,this.istate.inflateInit(this,nowrap?-w:w)},ZStream.prototype.inflate=function(f){return null==this.istate?Z_STREAM_ERROR:this.istate.inflate(this,f)},ZStream.prototype.inflateEnd=function(){if(null==this.istate)return Z_STREAM_ERROR;var ret=istate.inflateEnd(this);return this.istate=null,ret},ZStream.prototype.inflateSync=function(){return istate.inflateSync(this)},ZStream.prototype.inflateSetDictionary=function(dictionary,dictLength){return istate.inflateSetDictionary(this,dictionary,dictLength)},Inflate.prototype.inflateReset=function(z){return null==z||null==z.istate?Z_STREAM_ERROR:(z.total_in=z.total_out=0,z.msg=null,z.istate.mode=0!=z.istate.nowrap?BLOCKS:METHOD,z.istate.blocks.reset(z,null),Z_OK)},Inflate.prototype.inflateEnd=function(z){return null!=this.blocks&&this.blocks.free(z),this.blocks=null,Z_OK},Inflate.prototype.inflateInit=function(z,w){return z.msg=null,this.blocks=null,nowrap=0,w<0&&(w=-w,nowrap=1),w<8||w>15?(this.inflateEnd(z),Z_STREAM_ERROR):(this.wbits=w,z.istate.blocks=new InfBlocks(z,0!=z.istate.nowrap?null:this,1<<w),this.inflateReset(z),Z_OK)},Inflate.prototype.inflate=function(z,f){var r,b;if(null==z||null==z.istate||null==z.next_in)return Z_STREAM_ERROR;for(f=f==Z_FINISH?Z_BUF_ERROR:Z_OK,r=Z_BUF_ERROR;;)switch(z.istate.mode){case METHOD:if(0==z.avail_in)return r;if(r=f,z.avail_in--,z.total_in++,(15&(z.istate.method=z.next_in[z.next_in_index++]))!=Z_DEFLATED){z.istate.mode=BAD,z.msg="unknown compression method",z.istate.marker=5;break}if(8+(z.istate.method>>4)>z.istate.wbits){z.istate.mode=BAD,z.msg="invalid window size",z.istate.marker=5;break}z.istate.mode=FLAG;case FLAG:if(0==z.avail_in)return r;if(r=f,z.avail_in--,z.total_in++,b=255&z.next_in[z.next_in_index++],((z.istate.method<<8)+b)%31!=0){z.istate.mode=BAD,z.msg="incorrect header check",z.istate.marker=5;break}if(0==(b&PRESET_DICT)){z.istate.mode=BLOCKS;break}z.istate.mode=DICT4;case DICT4:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need=(255&z.next_in[z.next_in_index++])<<24&4278190080,z.istate.mode=DICT3;case DICT3:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need+=(255&z.next_in[z.next_in_index++])<<16&16711680,z.istate.mode=DICT2;case DICT2:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need+=(255&z.next_in[z.next_in_index++])<<8&65280,z.istate.mode=DICT1;case DICT1:return 0==z.avail_in?r:(r=f,z.avail_in--,z.total_in++,z.istate.need+=255&z.next_in[z.next_in_index++],z.adler=z.istate.need,z.istate.mode=DICT0,Z_NEED_DICT);case DICT0:return z.istate.mode=BAD,z.msg="need dictionary",z.istate.marker=0,Z_STREAM_ERROR;case BLOCKS:if((r=z.istate.blocks.proc(z,r))==Z_DATA_ERROR){z.istate.mode=BAD,z.istate.marker=0;break}if(r==Z_OK&&(r=f),r!=Z_STREAM_END)return r;if(r=f,z.istate.blocks.reset(z,z.istate.was),0!=z.istate.nowrap){z.istate.mode=DONE;break}z.istate.mode=CHECK4;case CHECK4:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need=(255&z.next_in[z.next_in_index++])<<24&4278190080,z.istate.mode=CHECK3;case CHECK3:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need+=(255&z.next_in[z.next_in_index++])<<16&16711680,z.istate.mode=CHECK2;case CHECK2:if(0==z.avail_in)return r;r=f,z.avail_in--,z.total_in++,z.istate.need+=(255&z.next_in[z.next_in_index++])<<8&65280,z.istate.mode=CHECK1;case CHECK1:if(0==z.avail_in)return r;if(r=f,z.avail_in--,z.total_in++,z.istate.need+=255&z.next_in[z.next_in_index++],z.istate.was[0]!=z.istate.need){z.istate.mode=BAD,z.msg="incorrect data check",z.istate.marker=5;break}z.istate.mode=DONE;case DONE:return Z_STREAM_END;case BAD:return Z_DATA_ERROR;default:return Z_STREAM_ERROR}},Inflate.prototype.inflateSetDictionary=function(z,dictionary,dictLength){var index=0,length=dictLength;return null==z||null==z.istate||z.istate.mode!=DICT0?Z_STREAM_ERROR:z._adler.adler32(1,dictionary,0,dictLength)!=z.adler?Z_DATA_ERROR:(z.adler=z._adler.adler32(0,null,0,0),length>=1<<z.istate.wbits&&(length=(1<<z.istate.wbits)-1,index=dictLength-length),z.istate.blocks.set_dictionary(dictionary,index,length),z.istate.mode=BLOCKS,Z_OK)};var mark=[0,0,255,255];Inflate.prototype.inflateSync=function(z){var n,p,m,r,w;if(null==z||null==z.istate)return Z_STREAM_ERROR;if(z.istate.mode!=BAD&&(z.istate.mode=BAD,z.istate.marker=0),0==(n=z.avail_in))return Z_BUF_ERROR;for(p=z.next_in_index,m=z.istate.marker;0!=n&&m<4;)z.next_in[p]==mark[m]?m++:m=0!=z.next_in[p]?0:4-m,p++,n--;return z.total_in+=p-z.next_in_index,z.next_in_index=p,z.avail_in=n,z.istate.marker=m,4!=m?Z_DATA_ERROR:(r=z.total_in,w=z.total_out,this.inflateReset(z),z.total_in=r,z.total_out=w,z.istate.mode=BLOCKS,Z_OK)},Inflate.prototype.inflateSyncPoint=function(z){return null==z||null==z.istate||null==z.istate.blocks?Z_STREAM_ERROR:z.istate.blocks.sync_point()};var INFBLOCKS_BORDER=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];InfBlocks.prototype.reset=function(z,c){c&&(c[0]=this.check),this.mode==IB_CODES&&this.codes.free(z),this.mode=IB_TYPE,this.bitk=0,this.bitb=0,this.read=this.write=0,this.checkfn&&(z.adler=this.check=z._adler.adler32(0,null,0,0))},InfBlocks.prototype.proc=function(z,r){var t,b,k,p,n,q,m;for(p=z.next_in_index,n=z.avail_in,b=this.bitb,k=this.bitk,q=this.write,m=q<this.read?this.read-q-1:this.end-q;;)switch(this.mode){case IB_TYPE:for(;k<3;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}switch(t=7&b,this.last=1&t,t>>>1){case 0:b>>>=3,k-=3,t=7&k,b>>>=t,k-=t,this.mode=IB_LENS;break;case 1:var bl=new Int32Array(1),bd=new Int32Array(1),tl=[],td=[];inflate_trees_fixed(bl,bd,tl,td,z),this.codes.init(bl[0],bd[0],tl[0],0,td[0],0,z),b>>>=3,k-=3,this.mode=IB_CODES;break;case 2:b>>>=3,k-=3,this.mode=IB_TABLE;break;case 3:return b>>>=3,k-=3,this.mode=BAD,z.msg="invalid block type",r=Z_DATA_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r)}break;case IB_LENS:for(;k<32;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if((~b>>>16&65535)!=(65535&b))return this.mode=BAD,z.msg="invalid stored block lengths",r=Z_DATA_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);this.left=65535&b,b=k=0,this.mode=0!=left?IB_STORED:0!=this.last?IB_DRY:IB_TYPE;break;case IB_STORED:if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,write=q,this.inflate_flush(z,r);if(0==m&&(q==end&&0!=read&&(q=0,m=q<this.read?this.read-q-1:this.end-q),0==m&&(this.write=q,r=this.inflate_flush(z,r),q=this.write,m=q<this.read?this.read-q-1:this.end-q,q==this.end&&0!=this.read&&(q=0,m=q<this.read?this.read-q-1:this.end-q),0==m)))return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);if(r=Z_OK,t=this.left,t>n&&(t=n),t>m&&(t=m),arrayCopy(z.next_in,p,window,q,t),p+=t,n-=t,q+=t,m-=t,0!=(this.left-=t))break;this.mode=0!=this.last?IB_DRY:IB_TYPE;break;case IB_TABLE:for(;k<14;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if(this.table=t=16383&b,(31&t)>29||(t>>5&31)>29)return this.mode=IB_BAD,z.msg="too many length or distance symbols",r=Z_DATA_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);if(t=258+(31&t)+(t>>5&31),null==this.blens||this.blens.length<t)this.blens=new Int32Array(t);else for(var i=0;i<t;i++)this.blens[i]=0;b>>>=14,k-=14,this.index=0,mode=IB_BTREE;case IB_BTREE:for(;this.index<4+(this.table>>>10);){for(;k<3;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}this.blens[INFBLOCKS_BORDER[this.index++]]=7&b,b>>>=3,k-=3}for(;this.index<19;)this.blens[INFBLOCKS_BORDER[this.index++]]=0;if(this.bb[0]=7,(t=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,z))!=Z_OK)return r=t,r==Z_DATA_ERROR&&(this.blens=null,this.mode=IB_BAD),this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,write=q,this.inflate_flush(z,r);this.index=0,this.mode=IB_DTREE;case IB_DTREE:for(;;){if(t=this.table,!(this.index<258+(31&t)+(t>>5&31)))break;var i,j,c;for(t=this.bb[0];k<t;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if(t=this.hufts[3*(this.tb[0]+(b&inflate_mask[t]))+1],(c=this.hufts[3*(this.tb[0]+(b&inflate_mask[t]))+2])<16)b>>>=t,k-=t,this.blens[this.index++]=c;else{for(i=18==c?7:c-14,j=18==c?11:3;k<t+i;){if(0==n)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if(b>>>=t,k-=t,j+=b&inflate_mask[i],b>>>=i,k-=i,i=this.index,t=this.table,i+j>258+(31&t)+(t>>5&31)||16==c&&i<1)return this.blens=null,this.mode=IB_BAD,z.msg="invalid bit length repeat",r=Z_DATA_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);c=16==c?this.blens[i-1]:0;do{this.blens[i++]=c}while(0!=--j);this.index=i}}this.tb[0]=-1;var bl=new Int32Array(1),bd=new Int32Array(1),tl=new Int32Array(1),td=new Int32Array(1);if(bl[0]=9,bd[0]=6,t=this.table,(t=this.inftree.inflate_trees_dynamic(257+(31&t),1+(t>>5&31),this.blens,bl,bd,tl,td,this.hufts,z))!=Z_OK)return t==Z_DATA_ERROR&&(this.blens=null,this.mode=BAD),r=t,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);this.codes.init(bl[0],bd[0],this.hufts,tl[0],this.hufts,td[0],z),this.mode=IB_CODES;case IB_CODES:if(this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,(r=this.codes.proc(this,z,r))!=Z_STREAM_END)return this.inflate_flush(z,r);if(r=Z_OK,this.codes.free(z),p=z.next_in_index,n=z.avail_in,b=this.bitb,k=this.bitk,q=this.write,m=q<this.read?this.read-q-1:this.end-q,0==this.last){this.mode=IB_TYPE;break}this.mode=IB_DRY;case IB_DRY:if(this.write=q,r=this.inflate_flush(z,r),q=this.write,m=q<this.read?this.read-q-1:this.end-q,this.read!=this.write)return this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);mode=DONE;case IB_DONE:return r=Z_STREAM_END,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);case IB_BAD:return r=Z_DATA_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r);default:return r=Z_STREAM_ERROR,this.bitb=b,this.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,this.write=q,this.inflate_flush(z,r)}},InfBlocks.prototype.free=function(z){this.reset(z,null),this.window=null,this.hufts=null},InfBlocks.prototype.set_dictionary=function(d,start,n){arrayCopy(d,start,window,0,n),this.read=this.write=n},InfBlocks.prototype.sync_point=function(){return this.mode==IB_LENS},InfBlocks.prototype.inflate_flush=function(z,r){var n,p,q;return p=z.next_out_index,q=this.read,n=(q<=this.write?this.write:this.end)-q,n>z.avail_out&&(n=z.avail_out),0!=n&&r==Z_BUF_ERROR&&(r=Z_OK),z.avail_out-=n,z.total_out+=n,null!=this.checkfn&&(z.adler=this.check=z._adler.adler32(this.check,this.window,q,n)),arrayCopy(this.window,q,z.next_out,p,n),p+=n,q+=n,q==this.end&&(q=0,this.write==this.end&&(this.write=0),n=this.write-q,n>z.avail_out&&(n=z.avail_out),0!=n&&r==Z_BUF_ERROR&&(r=Z_OK),z.avail_out-=n,z.total_out+=n,null!=this.checkfn&&(z.adler=this.check=z._adler.adler32(this.check,this.window,q,n)),arrayCopy(this.window,q,z.next_out,p,n),p+=n,q+=n),z.next_out_index=p,this.read=q,r};var IC_START=0,IC_LEN=1,IC_LENEXT=2,IC_DIST=3,IC_DISTEXT=4,IC_COPY=5,IC_LIT=6,IC_WASH=7,IC_END=8,IC_BADCODE=9;InfCodes.prototype.init=function(bl,bd,tl,tl_index,td,td_index,z){this.mode=IC_START,this.lbits=bl,this.dbits=bd,this.ltree=tl,this.ltree_index=tl_index,this.dtree=td,this.dtree_index=td_index,this.tree=null},InfCodes.prototype.proc=function(s,z,r){var j,tindex,e,n,q,m,f,b=0,k=0,p=0;for(p=z.next_in_index,n=z.avail_in,b=s.bitb,k=s.bitk,q=s.write,m=q<s.read?s.read-q-1:s.end-q;;)switch(this.mode){case IC_START:if(m>=258&&n>=10&&(s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,r=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,s,z),p=z.next_in_index,n=z.avail_in,b=s.bitb,k=s.bitk,q=s.write,m=q<s.read?s.read-q-1:s.end-q,r!=Z_OK)){this.mode=r==Z_STREAM_END?IC_WASH:IC_BADCODE;break}this.need=this.lbits,this.tree=this.ltree,this.tree_index=this.ltree_index,this.mode=IC_LEN;case IC_LEN:for(j=this.need;k<j;){if(0==n)return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if(tindex=3*(this.tree_index+(b&inflate_mask[j])),b>>>=this.tree[tindex+1],k-=this.tree[tindex+1],0==(e=this.tree[tindex])){this.lit=this.tree[tindex+2],this.mode=IC_LIT;break}if(0!=(16&e)){this.get=15&e,this.len=this.tree[tindex+2],this.mode=IC_LENEXT;break}if(0==(64&e)){this.need=e,this.tree_index=tindex/3+this.tree[tindex+2];break}if(0!=(32&e)){this.mode=IC_WASH;break}return this.mode=IC_BADCODE,z.msg="invalid literal/length code",r=Z_DATA_ERROR,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);case IC_LENEXT:for(j=this.get;k<j;){if(0==n)return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}this.len+=b&inflate_mask[j],b>>=j,k-=j,this.need=this.dbits,this.tree=this.dtree,this.tree_index=this.dtree_index,this.mode=IC_DIST;case IC_DIST:for(j=this.need;k<j;){if(0==n)return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}if(tindex=3*(this.tree_index+(b&inflate_mask[j])),b>>=this.tree[tindex+1],k-=this.tree[tindex+1],0!=(16&(e=this.tree[tindex]))){this.get=15&e,this.dist=this.tree[tindex+2],this.mode=IC_DISTEXT;break}if(0==(64&e)){this.need=e,this.tree_index=tindex/3+this.tree[tindex+2];break}return this.mode=IC_BADCODE,z.msg="invalid distance code",r=Z_DATA_ERROR,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);case IC_DISTEXT:for(j=this.get;k<j;){if(0==n)return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);r=Z_OK,n--,b|=(255&z.next_in[p++])<<k,k+=8}this.dist+=b&inflate_mask[j],b>>=j,k-=j,this.mode=IC_COPY;case IC_COPY:for(f=q-this.dist;f<0;)f+=s.end;for(;0!=this.len;){if(0==m&&(q==s.end&&0!=s.read&&(q=0,m=q<s.read?s.read-q-1:s.end-q),0==m&&(s.write=q,r=s.inflate_flush(z,r),q=s.write,m=q<s.read?s.read-q-1:s.end-q,q==s.end&&0!=s.read&&(q=0,m=q<s.read?s.read-q-1:s.end-q),0==m)))return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);s.window[q++]=s.window[f++],m--,f==s.end&&(f=0),this.len--}this.mode=IC_START;break;case IC_LIT:if(0==m&&(q==s.end&&0!=s.read&&(q=0,m=q<s.read?s.read-q-1:s.end-q),0==m&&(s.write=q,r=s.inflate_flush(z,r),q=s.write,m=q<s.read?s.read-q-1:s.end-q,q==s.end&&0!=s.read&&(q=0,m=q<s.read?s.read-q-1:s.end-q),0==m)))return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);r=Z_OK,s.window[q++]=this.lit,m--,this.mode=IC_START;break;case IC_WASH:if(k>7&&(k-=8,n++,p--),s.write=q,r=s.inflate_flush(z,r),q=s.write,m=q<s.read?s.read-q-1:s.end-q,s.read!=s.write)return s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);this.mode=IC_END;case IC_END:return r=Z_STREAM_END,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);case IC_BADCODE:return r=Z_DATA_ERROR,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r);default:return r=Z_STREAM_ERROR,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,s.inflate_flush(z,r)}},InfCodes.prototype.free=function(z){},InfCodes.prototype.inflate_fast=function(bl,bd,tl,tl_index,td,td_index,s,z){var t,tp,tp_index,e,b,k,p,n,q,m,ml,md,c,d,r,tp_index_t_3;p=z.next_in_index,n=z.avail_in,b=s.bitb,k=s.bitk,q=s.write,m=q<s.read?s.read-q-1:s.end-q,ml=inflate_mask[bl],md=inflate_mask[bd];do{for(;k<20;)n--,b|=(255&z.next_in[p++])<<k,k+=8;if(t=b&ml,tp=tl,tp_index=tl_index,tp_index_t_3=3*(tp_index+t),0!=(e=tp[tp_index_t_3]))for(;;){if(b>>=tp[tp_index_t_3+1],k-=tp[tp_index_t_3+1],0!=(16&e)){for(e&=15,c=tp[tp_index_t_3+2]+(b&inflate_mask[e]),b>>=e,k-=e;k<15;)n--,b|=(255&z.next_in[p++])<<k,k+=8;for(t=b&md,tp=td,tp_index=td_index,tp_index_t_3=3*(tp_index+t),e=tp[tp_index_t_3];;){if(b>>=tp[tp_index_t_3+1],k-=tp[tp_index_t_3+1],0!=(16&e)){for(e&=15;k<e;)n--,b|=(255&z.next_in[p++])<<k,k+=8;if(d=tp[tp_index_t_3+2]+(b&inflate_mask[e]),b>>=e,k-=e,m-=c,q>=d)r=q-d,s.window[q++]=s.window[r++],s.window[q++]=s.window[r++],c-=2;else{r=q-d;do{r+=s.end}while(r<0);if(e=s.end-r,c>e){if(c-=e,q-r>0&&e>q-r)do{s.window[q++]=s.window[r++]}while(0!=--e);else arrayCopy(s.window,r,s.window,q,e),q+=e,r+=e,e=0;r=0}}do{s.window[q++]=s.window[r++]}while(0!=--c);break}if(0!=(64&e))return z.msg="invalid distance code",c=z.avail_in-n,c=k>>3<c?k>>3:c,n+=c,p-=c,k-=c<<3,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,Z_DATA_ERROR;t+=tp[tp_index_t_3+2],t+=b&inflate_mask[e],tp_index_t_3=3*(tp_index+t),e=tp[tp_index_t_3]}break}if(0!=(64&e))return 0!=(32&e)?(c=z.avail_in-n,c=k>>3<c?k>>3:c,n+=c,p-=c,k-=c<<3,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,Z_STREAM_END):(z.msg="invalid literal/length code",c=z.avail_in-n,c=k>>3<c?k>>3:c,n+=c,p-=c,k-=c<<3,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,Z_DATA_ERROR);if(t+=tp[tp_index_t_3+2],t+=b&inflate_mask[e],tp_index_t_3=3*(tp_index+t),0==(e=tp[tp_index_t_3])){b>>=tp[tp_index_t_3+1],k-=tp[tp_index_t_3+1],s.window[q++]=tp[tp_index_t_3+2],m--;break}}else b>>=tp[tp_index_t_3+1],k-=tp[tp_index_t_3+1],s.window[q++]=tp[tp_index_t_3+2],m--}while(m>=258&&n>=10);return c=z.avail_in-n,c=k>>3<c?k>>3:c,n+=c,p-=c,k-=c<<3,s.bitb=b,s.bitk=k,z.avail_in=n,z.total_in+=p-z.next_in_index,z.next_in_index=p,s.write=q,Z_OK},InfTree.prototype.huft_build=function(b,bindex,n,s,d,e,t,m,hp,hn,v){var a,f,g,h,i,j,k,l,mask,p,q,w,xp,y,z;p=0,i=n;do{this.c[b[bindex+p]]++,p++,i--}while(0!=i);if(this.c[0]==n)return t[0]=-1,m[0]=0,Z_OK;for(l=m[0],j=1;j<=BMAX&&0==this.c[j];j++);for(k=j,l<j&&(l=j),i=BMAX;0!=i&&0==this.c[i];i--);for(g=i,l>i&&(l=i),m[0]=l,y=1<<j;j<i;j++,y<<=1)if((y-=this.c[j])<0)return Z_DATA_ERROR;if((y-=this.c[i])<0)return Z_DATA_ERROR;for(this.c[i]+=y,this.x[1]=j=0,p=1,xp=2;0!=--i;)this.x[xp]=j+=this.c[p],xp++,p++;i=0,p=0;do{0!=(j=b[bindex+p])&&(this.v[this.x[j]++]=i),p++}while(++i<n);for(n=this.x[g],this.x[0]=i=0,p=0,h=-1,w=-l,this.u[0]=0,q=0,z=0;k<=g;k++)for(a=this.c[k];0!=a--;){for(;k>w+l;){if(h++,w+=l,z=g-w,z=z>l?l:z,(f=1<<(j=k-w))>a+1&&(f-=a+1,xp=k,j<z))for(;++j<z&&!((f<<=1)<=this.c[++xp]);)f-=this.c[xp];if(z=1<<j,this.hn[0]+z>MANY)return Z_DATA_ERROR;this.u[h]=q=this.hn[0],this.hn[0]+=z,0!=h?(this.x[h]=i,this.r[0]=j,this.r[1]=l,j=i>>>w-l,this.r[2]=q-this.u[h-1]-j,arrayCopy(this.r,0,hp,3*(this.u[h-1]+j),3)):t[0]=q}for(this.r[1]=k-w,p>=n?this.r[0]=192:v[p]<s?(this.r[0]=this.v[p]<256?0:96,this.r[2]=this.v[p++]):(this.r[0]=e[this.v[p]-s]+16+64,this.r[2]=d[this.v[p++]-s]),f=1<<k-w,j=i>>>w;j<z;j+=f)arrayCopy(this.r,0,hp,3*(q+j),3);for(j=1<<k-1;0!=(i&j);j>>>=1)i^=j;for(i^=j,mask=(1<<w)-1;(i&mask)!=this.x[h];)h--,w-=l,mask=(1<<w)-1}return 0!=y&&1!=g?Z_BUF_ERROR:Z_OK},InfTree.prototype.inflate_trees_bits=function(c,bb,tb,hp,z){var result;return this.initWorkArea(19),this.hn[0]=0,result=this.huft_build(c,0,19,19,null,null,tb,bb,hp,this.hn,this.v),result==Z_DATA_ERROR?z.msg="oversubscribed dynamic bit lengths tree":result!=Z_BUF_ERROR&&0!=bb[0]||(z.msg="incomplete dynamic bit lengths tree",result=Z_DATA_ERROR),result},InfTree.prototype.inflate_trees_dynamic=function(nl,nd,c,bl,bd,tl,td,hp,z){var result;return this.initWorkArea(288),this.hn[0]=0,(result=this.huft_build(c,0,nl,257,cplens,cplext,tl,bl,hp,this.hn,this.v))!=Z_OK||0==bl[0]?(result==Z_DATA_ERROR?z.msg="oversubscribed literal/length tree":result!=Z_MEM_ERROR&&(z.msg="incomplete literal/length tree",result=Z_DATA_ERROR),result):(this.initWorkArea(288),result=this.huft_build(c,nl,nd,0,cpdist,cpdext,td,bd,hp,this.hn,this.v),result!=Z_OK||0==bd[0]&&nl>257?(result==Z_DATA_ERROR?z.msg="oversubscribed distance tree":result==Z_BUF_ERROR?(z.msg="incomplete distance tree",result=Z_DATA_ERROR):result!=Z_MEM_ERROR&&(z.msg="empty distance tree with lengths",result=Z_DATA_ERROR),result):Z_OK)},InfTree.prototype.initWorkArea=function(vsize){null==this.hn&&(this.hn=new Int32Array(1),this.v=new Int32Array(vsize),this.c=new Int32Array(BMAX+1),this.r=new Int32Array(3),this.u=new Int32Array(BMAX),this.x=new Int32Array(BMAX+1)),this.v.length<vsize&&(this.v=new Int32Array(vsize));for(var i=0;i<vsize;i++)this.v[i]=0;for(var i=0;i<BMAX+1;i++)this.c[i]=0;for(var i=0;i<3;i++)this.r[i]=0;arrayCopy(this.c,0,this.u,0,BMAX),arrayCopy(this.c,0,this.x,0,BMAX+1)};var testArray=new Uint8Array(1),hasSubarray="function"==typeof testArray.subarray,hasSlice=!1,ADLER_BASE=65521,ADLER_NMAX=5552;(function(){"use strict";function q(b){throw b}function A(b,a){var c=b.split("."),d=aa;!(c[0]in d)&&d.execScript&&d.execScript("var "+c[0]);for(var f;c.length&&(f=c.shift());)c.length||a===t?d=d[f]?d[f]:d[f]={}:d[f]=a}function F(b,a){this.index="number"==typeof a?a:0,this.m=0,this.buffer=b instanceof(B?Uint8Array:Array)?b:new(B?Uint8Array:Array)(32768),2*this.buffer.length<=this.index&&q(Error("invalid index")),this.buffer.length<=this.index&&this.f()}function ja(b,a,c){var d,f="number"==typeof a?a:a=0,e="number"==typeof c?c:b.length;for(d=-1,f=7&e;f--;++a)d=d>>>8^O[255&(d^b[a])];for(f=e>>3;f--;a+=8)d=d>>>8^O[255&(d^b[a])],d=d>>>8^O[255&(d^b[a+1])],d=d>>>8^O[255&(d^b[a+2])],d=d>>>8^O[255&(d^b[a+3])],d=d>>>8^O[255&(d^b[a+4])],d=d>>>8^O[255&(d^b[a+5])],d=d>>>8^O[255&(d^b[a+6])],d=d>>>8^O[255&(d^b[a+7])];return(4294967295^d)>>>0}function P(){}function la(b){this.buffer=new(B?Uint16Array:Array)(2*b),this.length=0}function ma(b){var f,e,g,k,h,l,s,n,m,a=b.length,c=0,d=Number.POSITIVE_INFINITY;for(n=0;n<a;++n)b[n]>c&&(c=b[n]),b[n]<d&&(d=b[n]);for(f=1<<c,e=new(B?Uint32Array:Array)(f),g=1,k=0,h=2;g<=c;){for(n=0;n<a;++n)if(b[n]===g){for(l=0,s=k,m=0;m<g;++m)l=l<<1|1&s,s>>=1;for(m=l;m<f;m+=h)e[m]=g<<16|n;++k}++g,k<<=1,h<<=1}return[e,c,d]}function na(b,a){this.k=qa,this.I=0,this.input=B&&b instanceof Array?new Uint8Array(b):b,this.b=0,a&&(a.lazy&&(this.I=a.lazy),"number"==typeof a.compressionType&&(this.k=a.compressionType),a.outputBuffer&&(this.a=B&&a.outputBuffer instanceof Array?new Uint8Array(a.outputBuffer):a.outputBuffer),"number"==typeof a.outputIndex&&(this.b=a.outputIndex)),this.a||(this.a=new(B?Uint8Array:Array)(32768))}function xa(b,a){this.length=b,this.P=a}function ta(b,a){function c(a,c){var f,b=a.P,d=[],e=0;f=Aa[a.length],d[e++]=65535&f,d[e++]=f>>16&255,d[e++]=f>>24;var g;switch(u){case 1===b:g=[0,b-1,0];break;case 2===b:g=[1,b-2,0];break;case 3===b:g=[2,b-3,0];break;case 4===b:g=[3,b-4,0];break;case 6>=b:g=[4,b-5,1];break;case 8>=b:g=[5,b-7,1];break;case 12>=b:g=[6,b-9,2];break;case 16>=b:g=[7,b-13,2];break;case 24>=b:g=[8,b-17,3];break;case 32>=b:g=[9,b-25,3];break;case 48>=b:g=[10,b-33,4];break;case 64>=b:g=[11,b-49,4];break;case 96>=b:g=[12,b-65,5];break;case 128>=b:g=[13,b-97,5];break;case 192>=b:g=[14,b-129,6];break;case 256>=b:g=[15,b-193,6];break;case 384>=b:g=[16,b-257,7];break;case 512>=b:g=[17,b-385,7];break;case 768>=b:g=[18,b-513,8];break;case 1024>=b:g=[19,b-769,8];break;case 1536>=b:g=[20,b-1025,9];break;case 2048>=b:g=[21,b-1537,9];break;case 3072>=b:g=[22,b-2049,10];break;case 4096>=b:g=[23,b-3073,10];break;case 6144>=b:g=[24,b-4097,11];break;case 8192>=b:g=[25,b-6145,11];break;case 12288>=b:g=[26,b-8193,12];break;case 16384>=b:g=[27,b-12289,12];break;case 24576>=b:g=[28,b-16385,13];break;case 32768>=b:g=[29,b-24577,13];break;default:q("invalid distance")}f=g,d[e++]=f[0],d[e++]=f[1],d[e++]=f[2];var h,k;for(h=0,k=d.length;h<k;++h)m[p++]=d[h];v[d[0]]++,x[d[3]]++,r=a.length+c-1,n=null}var d,f,e,g,k,l,s,n,y,h={},m=B?new Uint16Array(2*a.length):[],p=0,r=0,v=new(B?Uint32Array:Array)(286),x=new(B?Uint32Array:Array)(30),Q=b.I;if(!B){for(e=0;285>=e;)v[e++]=0;for(e=0;29>=e;)x[e++]=0}for(v[256]=1,d=0,f=a.length;d<f;++d){for(e=k=0,g=3;e<g&&d+e!==f;++e)k=k<<8|a[d+e];if(h[k]===t&&(h[k]=[]),l=h[k],!(0<r--)){for(;0<l.length&&32768<d-l[0];)l.shift();if(d+3>=f){for(n&&c(n,-1),e=0,g=f-d;e<g;++e)y=a[d+e],m[p++]=y,++v[y];break}0<l.length?(s=Ba(a,d,l),n?n.length<s.length?(y=a[d-1],m[p++]=y,++v[y],c(s,0)):c(n,-1):s.length<Q?n=s:c(s,0)):n?c(n,-1):(y=a[d],m[p++]=y,++v[y])}l.push(d)}return m[p++]=256,v[256]++,b.V=v,b.U=x,B?m.subarray(0,p):m}function Ba(b,a,c){var d,f,g,k,h,l,e=0,s=b.length;k=0,l=c.length;a:for(;k<l;k++){if(d=c[l-k-1],g=3,3<e){for(h=e;3<h;h--)if(b[d+h-1]!==b[a+h-1])continue a;g=e}for(;258>g&&a+g<s&&b[d+g]===b[a+g];)++g;if(g>e&&(f=d,e=g),258===g)break}return new xa(e,a-f)}function ua(b,a){var e,g,k,h,l,c=b.length,d=new la(572),f=new(B?Uint8Array:Array)(c);if(!B)for(h=0;h<c;h++)f[h]=0;for(h=0;h<c;++h)0<b[h]&&d.push(h,b[h]);if(e=Array(d.length/2),g=new(B?Uint32Array:Array)(d.length/2),1===e.length)return f[d.pop().index]=1,f;for(h=0,l=d.length/2;h<l;++h)e[h]=d.pop(),g[h]=e[h].value;for(k=Ca(g,g.length,a),h=0,l=e.length;h<l;++h)f[e[h].index]=k[h];return f}function Ca(b,a,c){function d(b){var c=h[b][l[b]];c===a?(d(b+1),d(b+1)):--g[c],++l[b]}var m,p,r,v,x,f=new(B?Uint16Array:Array)(c),e=new(B?Uint8Array:Array)(c),g=new(B?Uint8Array:Array)(a),k=Array(c),h=Array(c),l=Array(c),s=(1<<c)-a,n=1<<c-1;for(f[c-1]=a,p=0;p<c;++p)s<n?e[p]=0:(e[p]=1,s-=n),s<<=1,f[c-2-p]=(f[c-1-p]/2|0)+a;for(f[0]=e[0],k[0]=Array(f[0]),h[0]=Array(f[0]),p=1;p<c;++p)f[p]>2*f[p-1]+e[p]&&(f[p]=2*f[p-1]+e[p]),k[p]=Array(f[p]),h[p]=Array(f[p]);for(m=0;m<a;++m)g[m]=c;for(r=0;r<f[c-1];++r)k[c-1][r]=b[r],h[c-1][r]=r;for(m=0;m<c;++m)l[m]=0;for(1===e[c-1]&&(--g[0],++l[c-1]),p=c-2;0<=p;--p){for(v=m=0,x=l[p+1],r=0;r<f[p];r++)v=k[p+1][x]+k[p+1][x+1],v>b[m]?(k[p][r]=v,h[p][r]=a,x+=2):(k[p][r]=b[m],h[p][r]=m,++m);l[p]=0,1===e[p]&&d(p)}return g}function va(b){var e,g,k,h,a=new(B?Uint16Array:Array)(b.length),c=[],d=[],f=0;for(e=0,g=b.length;e<g;e++)c[b[e]]=1+(0|c[b[e]]);for(e=1,g=16;e<=g;e++)d[e]=f,f+=0|c[e],f<<=1;for(e=0,g=b.length;e<g;e++)for(f=d[b[e]],d[b[e]]+=1,k=a[e]=0,h=b[e];k<h;k++)a[e]=a[e]<<1|1&f,f>>>=1;return a}function Da(b,a){this.input=b,this.b=this.c=0,this.i={},a&&(a.flags&&(this.i=a.flags),"string"==typeof a.filename&&(this.filename=a.filename),"string"==typeof a.comment&&(this.A=a.comment),a.deflateOptions&&(this.l=a.deflateOptions)),this.l||(this.l={})}function T(b,a){switch(this.p=[],this.q=32768,this.e=this.j=this.c=this.u=0,this.input=B?new Uint8Array(b):b,this.w=!1,this.r=Ia,this.L=!1,!a&&(a={})||(a.index&&(this.c=a.index),a.bufferSize&&(this.q=a.bufferSize),a.bufferType&&(this.r=a.bufferType),a.resize&&(this.L=a.resize)),this.r){case Xa:this.b=32768,this.a=new(B?Uint8Array:Array)(32768+this.q+258);break;case Ia:this.b=0,this.a=new(B?Uint8Array:Array)(this.q),this.f=this.T,this.B=this.Q,this.s=this.S;break;default:q(Error("invalid inflate mode"))}}function U(b,a){for(var g,c=b.j,d=b.e,f=b.input,e=b.c;d<a;)g=f[e++],g===t&&q(Error("input buffer is broken")),c|=g<<d,d+=8;return g=c&(1<<a)-1,b.j=c>>>a,b.e=d-a,b.c=e,g}function rb(b,a){for(var h,l,s,c=b.j,d=b.e,f=b.input,e=b.c,g=a[0],k=a[1];d<k&&(h=f[e++])!==t;)c|=h<<d,d+=8;return l=g[c&(1<<k)-1],s=l>>>16,b.j=c>>s,b.e=d-s,b.c=e,65535&l}function ab(b){function a(a,b,c){var d,e,f,g;for(g=0;g<a;)switch(d=rb(this,b)){case 16:for(f=3+U(this,2);f--;)c[g++]=e;break;case 17:for(f=3+U(this,3);f--;)c[g++]=0;e=0;break;case 18:for(f=11+U(this,7);f--;)c[g++]=0;e=0;break;default:e=c[g++]=d}return c}var g,k,h,l,c=U(b,5)+257,d=U(b,5)+1,f=U(b,4)+4,e=new(B?Uint8Array:Array)(cb.length);for(l=0;l<f;++l)e[cb[l]]=U(b,3);g=ma(e),k=new(B?Uint8Array:Array)(c),h=new(B?Uint8Array:Array)(d),b.s(ma(a.call(b,c,g,k)),ma(a.call(b,d,g,h)))}function sb(b){this.input=b,this.c=0,this.t=[],this.D=!1}function tb(b){if("string"==typeof b){var c,d,a=b.split("");for(c=0,d=a.length;c<d;c++)a[c]=(255&a[c].charCodeAt(0))>>>0;b=a}for(var k,f=1,e=0,g=b.length,h=0;0<g;){k=1024<g?1024:g,g-=k;do{f+=b[h++],e+=f}while(--k);f%=65521,e%=65521}return(e<<16|f)>>>0}function ub(b,a){var c,d;switch(this.input=b,this.c=0,!a&&(a={})||(a.index&&(this.c=a.index),a.verify&&(this.Z=a.verify)),c=b[this.c++],d=b[this.c++],15&c){case vb:this.method=vb;break;default:q(Error("unsupported compression method"))}0!=((c<<8)+d)%31&&q(Error("invalid fcheck flag:"+((c<<8)+d)%31)),32&d&&q(Error("fdict flag is not supported")),this.K=new T(b,{index:this.c,bufferSize:a.bufferSize,bufferType:a.bufferType,resize:a.resize})}function wb(b,a){this.input=b,this.a=new(B?Uint8Array:Array)(32768),this.k=W.o;var d,c={};!a&&(a={})||"number"!=typeof a.compressionType||(this.k=a.compressionType);for(d in a)c[d]=a[d];c.outputBuffer=this.a,this.J=new na(this.input,c)}function xb(b,a){var c,d,f,e;if(Object.keys)c=Object.keys(a);else for(d in c=[],f=0,a)c[f++]=d;for(f=0,e=c.length;f<e;++f)d=c[f],A(b+"."+d,a[d])}var t=void 0,u=!0,aa=this,B="undefined"!=typeof Uint8Array&&"undefined"!=typeof Uint16Array&&"undefined"!=typeof Uint32Array;F.prototype.f=function(){var a,b=this.buffer,c=b.length,d=new(B?Uint8Array:Array)(c<<1);if(B)d.set(b);else for(a=0;a<c;++a)d[a]=b[a];return this.buffer=d},F.prototype.d=function(b,a,c){var k,d=this.buffer,f=this.index,e=this.m,g=d[f];if(c&&1<a&&(b=8<a?(H[255&b]<<24|H[b>>>8&255]<<16|H[b>>>16&255]<<8|H[b>>>24&255])>>32-a:H[b]>>8-a),8>a+e)g=g<<a|b,e+=a;else for(k=0;k<a;++k)g=g<<1|b>>a-k-1&1,8==++e&&(e=0,d[f++]=H[g],g=0,f===d.length&&(d=this.f()));d[f]=g,this.buffer=d,this.m=e,this.index=f},F.prototype.finish=function(){var c,b=this.buffer,a=this.index;return 0<this.m&&(b[a]<<=8-this.m,b[a]=H[b[a]],a++),B?c=b.subarray(0,a):(b.length=a,c=b),c};var ca,ba=new(B?Uint8Array:Array)(256);for(ca=0;256>ca;++ca){for(var K=ca,da=K,ea=7,K=K>>>1;K;K>>>=1)da<<=1,da|=1&K,--ea;ba[ca]=(da<<ea&255)>>>0}var H=ba,ka=[0,1996959894,3993919788,2567524794,124634137,1886057615,3915621685,2657392035,249268274,2044508324,3772115230,2547177864,162941995,2125561021,3887607047,2428444049,498536548,1789927666,4089016648,2227061214,450548861,1843258603,4107580753,2211677639,325883990,1684777152,4251122042,2321926636,335633487,1661365465,4195302755,2366115317,997073096,1281953886,3579855332,2724688242,1006888145,1258607687,3524101629,2768942443,901097722,1119000684,3686517206,2898065728,853044451,1172266101,3705015759,2882616665,651767980,1373503546,3369554304,3218104598,565507253,1454621731,3485111705,3099436303,671266974,1594198024,3322730930,2970347812,795835527,1483230225,3244367275,3060149565,1994146192,31158534,2563907772,4023717930,1907459465,112637215,2680153253,3904427059,2013776290,251722036,2517215374,3775830040,2137656763,141376813,2439277719,3865271297,1802195444,476864866,2238001368,4066508878,1812370925,453092731,2181625025,4111451223,1706088902,314042704,2344532202,4240017532,1658658271,366619977,2362670323,4224994405,1303535960,984961486,2747007092,3569037538,1256170817,1037604311,2765210733,3554079995,1131014506,879679996,2909243462,3663771856,1141124467,855842277,2852801631,3708648649,1342533948,654459306,3188396048,3373015174,1466479909,544179635,3110523913,3462522015,1591671054,702138776,2966460450,3352799412,1504918807,783551873,3082640443,3233442989,3988292384,2596254646,62317068,1957810842,3939845945,2647816111,81470997,1943803523,3814918930,2489596804,225274430,2053790376,3826175755,2466906013,167816743,2097651377,4027552580,2265490386,503444072,1762050814,4150417245,2154129355,426522225,1852507879,4275313526,2312317920,282753626,1742555852,4189708143,2394877945,397917763,1622183637,3604390888,2714866558,953729732,1340076626,3518719985,2797360999,1068828381,1219638859,3624741850,2936675148,906185462,1090812512,3747672003,2825379669,829329135,1181335161,3412177804,3160834842,628085408,1382605366,3423369109,3138078467,570562233,1426400815,3317316542,2998733608,733239954,1555261956,3268935591,3050360625,752459403,1541320221,2607071920,3965973030,1969922972,40735498,2617837225,3943577151,1913087877,83908371,2512341634,3803740692,2075208622,213261112,2463272603,3855990285,2094854071,198958881,2262029012,4057260610,1759359992,534414190,2176718541,4139329115,1873836001,414664567,2282248934,4279200368,1711684554,285281116,2405801727,4167216745,1634467795,376229701,2685067896,3608007406,1308918612,956543938,2808555105,3495958263,1231636301,1047427035,2932959818,3654703836,1088359270,936918e3,2847714899,3736837829,1202900863,817233897,3183342108,3401237130,1404277552,615818150,3134207493,3453421203,1423857449,601450431,3009837614,3294710456,1567103746,711928724,3020668471,3272380065,1510334235,755167117],O=B?new Uint32Array(ka):ka;P.prototype.getName=function(){return this.name},P.prototype.getData=function(){return this.data},P.prototype.X=function(){return this.Y},A("Zlib.GunzipMember",P),A("Zlib.GunzipMember.prototype.getName",P.prototype.getName),A("Zlib.GunzipMember.prototype.getData",P.prototype.getData),A("Zlib.GunzipMember.prototype.getMtime",P.prototype.X),la.prototype.getParent=function(b){return 2*((b-2)/4|0)},la.prototype.push=function(b,a){var c,d,e,f=this.buffer;for(c=this.length,f[this.length++]=a,f[this.length++]=b;0<c&&(d=this.getParent(c),f[c]>f[d]);)e=f[c],f[c]=f[d],f[d]=e,e=f[c+1],f[c+1]=f[d+1],f[d+1]=e,c=d;return this.length},la.prototype.pop=function(){var b,a,d,f,e,c=this.buffer;for(a=c[0],b=c[1],this.length-=2,c[0]=c[this.length],c[1]=c[this.length+1],e=0;!((f=2*e+2)>=this.length)&&(f+2<this.length&&c[f+2]>c[f]&&(f+=2),c[f]>c[e]);)d=c[e],c[e]=c[f],c[f]=d,d=c[e+1],c[e+1]=c[f+1],c[f+1]=d,e=f;return{index:b,value:a,length:this.length}};var S,qa=2,ra={NONE:0,v:1,o:qa,aa:3},sa=[];for(S=0;288>S;S++)switch(u){case 143>=S:sa.push([S+48,8]);break;case 255>=S:sa.push([S-144+400,9]);break;case 279>=S:sa.push([S-256+0,7]);break;case 287>=S:sa.push([S-280+192,8]);break;default:q("invalid literal: "+S)}na.prototype.g=function(){var b,a,c,d,f=this.input;switch(this.k){case 0:for(c=0,d=f.length;c<d;){a=B?f.subarray(c,c+65535):f.slice(c,c+65535),c+=a.length;var e=a,g=c===d,k=t,h=t,l=t,s=t,n=t,m=this.a,p=this.b;if(B){for(m=new Uint8Array(this.a.buffer);m.length<=p+e.length+5;)m=new Uint8Array(m.length<<1);m.set(this.a)}if(k=g?1:0,m[p++]=0|k,h=e.length,l=65536+~h&65535,m[p++]=255&h,m[p++]=h>>>8&255,m[p++]=255&l,m[p++]=l>>>8&255,B)m.set(e,p),p+=e.length,m=m.subarray(0,p);else{for(s=0,n=e.length;s<n;++s)m[p++]=e[s];m.length=p}this.b=p,this.a=m}break;case 1:var r=new F(B?new Uint8Array(this.a.buffer):this.a,this.b);r.d(1,1,u),r.d(1,2,u);var x,Q,y,v=ta(this,f);for(x=0,Q=v.length;x<Q;x++)if(y=v[x],F.prototype.d.apply(r,sa[y]),256<y)r.d(v[++x],v[++x],u),r.d(v[++x],5),r.d(v[++x],v[++x],u);else if(256===y)break;this.a=r.finish(),this.b=this.a.length;break;case qa:var Ja,R,X,Y,Z,fa,Ka,ga,La,oa,Ma,$,pa,C,Na,E=new F(B?new Uint8Array(this.a.buffer):this.a,this.b),pb=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],wa=Array(19);for(Ja=qa,E.d(1,1,u),E.d(Ja,2,u),R=ta(this,f),fa=ua(this.V,15),Ka=va(fa),ga=ua(this.U,7),La=va(ga),X=286;257<X&&0===fa[X-1];X--);for(Y=30;1<Y&&0===ga[Y-1];Y--);var w,L,z,ha,G,D,Oa=X,Pa=Y,J=new(B?Uint32Array:Array)(Oa+Pa),I=new(B?Uint32Array:Array)(316),M=new(B?Uint8Array:Array)(19);for(w=L=0;w<Oa;w++)J[L++]=fa[w];for(w=0;w<Pa;w++)J[L++]=ga[w];if(!B)for(w=0,ha=M.length;w<ha;++w)M[w]=0;for(w=G=0,ha=J.length;w<ha;w+=L){for(L=1;w+L<ha&&J[w+L]===J[w];++L);if(z=L,0===J[w])if(3>z)for(;0<z--;)I[G++]=0,M[0]++;else for(;0<z;)D=138>z?z:138,D>z-3&&D<z&&(D=z-3),10>=D?(I[G++]=17,I[G++]=D-3,M[17]++):(I[G++]=18,I[G++]=D-11,M[18]++),z-=D;else if(I[G++]=J[w],M[J[w]]++,3>--z)for(;0<z--;)I[G++]=J[w],M[J[w]]++;else for(;0<z;)D=6>z?z:6,D>z-3&&D<z&&(D=z-3),I[G++]=16,I[G++]=D-3,M[16]++,z-=D}for(b=B?I.subarray(0,G):I.slice(0,G),oa=ua(M,7),C=0;19>C;C++)wa[C]=oa[pb[C]];for(Z=19;4<Z&&0===wa[Z-1];Z--);for(Ma=va(oa),E.d(X-257,5,u),E.d(Y-1,5,u),E.d(Z-4,4,u),C=0;C<Z;C++)E.d(wa[C],3,u);for(C=0,Na=b.length;C<Na;C++)if($=b[C],E.d(Ma[$],oa[$],u),16<=$){switch(C++,$){case 16:pa=2;break;case 17:pa=3;break;case 18:pa=7;break;default:q("invalid code: "+$)}E.d(b[C],pa,u)}var N,Sa,ia,za,Ta,Ua,Va,Wa,Qa=[Ka,fa],Ra=[La,ga];for(Ta=Qa[0],Ua=Qa[1],Va=Ra[0],Wa=Ra[1],N=0,Sa=R.length;N<Sa;++N)if(ia=R[N],E.d(Ta[ia],Ua[ia],u),256<ia)E.d(R[++N],R[++N],u),za=R[++N],E.d(Va[za],Wa[za],u),E.d(R[++N],R[++N],u);else if(256===ia)break;this.a=E.finish(),this.b=this.a.length;break;default:q("invalid compression type")}return this.a};var ya=function(){function b(a){switch(u){case 3===a:return[257,a-3,0];case 4===a:return[258,a-4,0];case 5===a:return[259,a-5,0];case 6===a:return[260,a-6,0];case 7===a:return[261,a-7,0];case 8===a:return[262,a-8,0];case 9===a:return[263,a-9,0];case 10===a:return[264,a-10,0];case 12>=a:return[265,a-11,1];case 14>=a:return[266,a-13,1];case 16>=a:return[267,a-15,1];case 18>=a:return[268,a-17,1];case 22>=a:return[269,a-19,2];case 26>=a:return[270,a-23,2];case 30>=a:return[271,a-27,2];case 34>=a:return[272,a-31,2];case 42>=a:return[273,a-35,3];case 50>=a:return[274,a-43,3];case 58>=a:return[275,a-51,3];case 66>=a:return[276,a-59,3];case 82>=a:return[277,a-67,4];case 98>=a:return[278,a-83,4];case 114>=a:return[279,a-99,4];case 130>=a:return[280,a-115,4];case 162>=a:return[281,a-131,5];case 194>=a:return[282,a-163,5];case 226>=a:return[283,a-195,5];case 257>=a:return[284,a-227,5];case 258===a:return[285,a-258,0];default:q("invalid length: "+a)}}var c,d,a=[];for(c=3;258>=c;c++)d=b(c),a[c]=d[2]<<24|d[1]<<16|d[0];return a}(),Aa=B?new Uint32Array(ya):ya;Da.prototype.g=function(){var b,a,c,d,f,e,g,k,h=new(B?Uint8Array:Array)(32768),l=0,s=this.input,n=this.c,m=this.filename,p=this.A;if(h[l++]=31,h[l++]=139,h[l++]=8,b=0,this.i.fname&&(b|=Ea),this.i.fcomment&&(b|=Fa),this.i.fhcrc&&(b|=Ga),h[l++]=b,a=(Date.now?Date.now():+new Date)/1e3|0,h[l++]=255&a,h[l++]=a>>>8&255,h[l++]=a>>>16&255,h[l++]=a>>>24&255,h[l++]=0,h[l++]=Ha,this.i.fname!==t){for(g=0,k=m.length;g<k;++g)e=m.charCodeAt(g),255<e&&(h[l++]=e>>>8&255),h[l++]=255&e;h[l++]=0}if(this.i.comment){for(g=0,k=p.length;g<k;++g)e=p.charCodeAt(g),255<e&&(h[l++]=e>>>8&255),h[l++]=255&e;h[l++]=0}return this.i.fhcrc&&(c=65535&ja(h,0,l),h[l++]=255&c,h[l++]=c>>>8&255),this.l.outputBuffer=h,this.l.outputIndex=l,f=new na(s,this.l),h=f.g(),l=f.b,B&&(l+8>h.buffer.byteLength?(this.a=new Uint8Array(l+8),this.a.set(new Uint8Array(h.buffer)),h=this.a):h=new Uint8Array(h.buffer)),d=ja(s,t,t),h[l++]=255&d,h[l++]=d>>>8&255,h[l++]=d>>>16&255,h[l++]=d>>>24&255,k=s.length,h[l++]=255&k,h[l++]=k>>>8&255,h[l++]=k>>>16&255,h[l++]=k>>>24&255,this.c=n,B&&l<h.length&&(this.a=h=h.subarray(0,l)),h};var Ha=255,Ga=2,Ea=8,Fa=16;A("Zlib.Gzip",Da),A("Zlib.Gzip.prototype.compress",Da.prototype.g);var Xa=0,Ia=1,Ya={N:Xa,M:Ia};T.prototype.h=function(){for(;!this.w;){var b=U(this,3);switch(1&b&&(this.w=u),b>>>=1){case 0:var a=this.input,c=this.c,d=this.a,f=this.b,e=t,g=t,k=t,h=d.length,l=t;switch(this.e=this.j=0,e=a[c++],e===t&&q(Error("invalid uncompressed block header: LEN (first byte)")),g=e,e=a[c++],e===t&&q(Error("invalid uncompressed block header: LEN (second byte)")),g|=e<<8,e=a[c++],e===t&&q(Error("invalid uncompressed block header: NLEN (first byte)")),k=e,e=a[c++],e===t&&q(Error("invalid uncompressed block header: NLEN (second byte)")),k|=e<<8,g===~k&&q(Error("invalid uncompressed block header: length verify")),c+g>a.length&&q(Error("input buffer is broken")),this.r){case Xa:for(;f+g>d.length;){if(l=h-f,g-=l,B)d.set(a.subarray(c,c+l),f),f+=l,c+=l;else for(;l--;)d[f++]=a[c++];this.b=f,d=this.f(),f=this.b}break;case Ia:for(;f+g>d.length;)d=this.f({F:2});break;default:q(Error("invalid inflate mode"))}if(B)d.set(a.subarray(c,c+g),f),f+=g,c+=g;else for(;g--;)d[f++]=a[c++];this.c=c,this.b=f,this.a=d;break;case 1:this.s(Za,$a);break;case 2:ab(this);break;default:q(Error("unknown BTYPE: "+b))}}return this.B()};var V,mb,bb=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],cb=B?new Uint16Array(bb):bb,db=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,258,258],eb=B?new Uint16Array(db):db,fb=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,0,0],gb=B?new Uint8Array(fb):fb,hb=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577],ib=B?new Uint16Array(hb):hb,jb=[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],kb=B?new Uint8Array(jb):jb,lb=new(B?Uint8Array:Array)(288);for(V=0,mb=lb.length;V<mb;++V)lb[V]=143>=V?8:255>=V?9:279>=V?7:8;var ob,qb,Za=ma(lb),nb=new(B?Uint8Array:Array)(30);for(ob=0,qb=nb.length;ob<qb;++ob)nb[ob]=5;var $a=ma(nb);T.prototype.s=function(b,a){var c=this.a,d=this.b;this.C=b;for(var e,g,k,h,f=c.length-258;256!==(e=rb(this,b));)if(256>e)d>=f&&(this.b=d,c=this.f(),d=this.b),c[d++]=e;else for(g=e-257,h=eb[g],0<gb[g]&&(h+=U(this,gb[g])),e=rb(this,a),k=ib[e],0<kb[e]&&(k+=U(this,kb[e])),d>=f&&(this.b=d,c=this.f(),d=this.b);h--;)c[d]=c[d++-k];for(;8<=this.e;)this.e-=8,this.c--;this.b=d},T.prototype.S=function(b,a){var c=this.a,d=this.b;this.C=b;for(var e,g,k,h,f=c.length;256!==(e=rb(this,b));)if(256>e)d>=f&&(c=this.f(),f=c.length),c[d++]=e;else for(g=e-257,h=eb[g],0<gb[g]&&(h+=U(this,gb[g])),e=rb(this,a),k=ib[e],0<kb[e]&&(k+=U(this,kb[e])),d+h>f&&(c=this.f(),f=c.length);h--;)c[d]=c[d++-k];for(;8<=this.e;)this.e-=8,this.c--;this.b=d},T.prototype.f=function(){var c,d,b=new(B?Uint8Array:Array)(this.b-32768),a=this.b-32768,f=this.a;if(B)b.set(f.subarray(32768,b.length));else for(c=0,d=b.length;c<d;++c)b[c]=f[c+32768];if(this.p.push(b),this.u+=b.length,B)f.set(f.subarray(a,a+32768));else for(c=0;32768>c;++c)f[c]=f[a+c];return this.b=32768,f},T.prototype.T=function(b){var a,d,f,e,c=this.input.length/this.c+1|0,g=this.input,k=this.a;return b&&("number"==typeof b.F&&(c=b.F),"number"==typeof b.O&&(c+=b.O)),2>c?(d=(g.length-this.c)/this.C[2],e=d/2*258|0,f=e<k.length?k.length+e:k.length<<1):f=k.length*c,B?(a=new Uint8Array(f),a.set(k)):a=k,this.a=a},T.prototype.B=function(){var d,e,g,k,h,b=0,a=this.a,c=this.p,f=new(B?Uint8Array:Array)(this.u+(this.b-32768));if(0===c.length)return B?this.a.subarray(32768,this.b):this.a.slice(32768,this.b);for(e=0,g=c.length;e<g;++e)for(d=c[e],k=0,h=d.length;k<h;++k)f[b++]=d[k];for(e=32768,g=this.b;e<g;++e)f[b++]=a[e];return this.p=[],this.buffer=f},T.prototype.Q=function(){var b,a=this.b;return B?this.L?(b=new Uint8Array(a),b.set(this.a.subarray(0,a))):b=this.a.subarray(0,a):(this.a.length>a&&(this.a.length=a),b=this.a),this.buffer=b},sb.prototype.W=function(){return this.D||this.h(),this.t.slice()},sb.prototype.h=function(){for(var b=this.input.length;this.c<b;){var a=new P,c=t,d=t,f=t,e=t,g=t,k=t,h=t,l=t,s=t,n=this.input,m=this.c;switch(a.G=n[m++],a.H=n[m++],(31!==a.G||139!==a.H)&&q(Error("invalid file signature:"+a.G+","+a.H)),a.z=n[m++],a.z){case 8:break;default:q(Error("unknown compression method: "+a.z))}if(a.n=n[m++],l=n[m++]|n[m++]<<8|n[m++]<<16|n[m++]<<24,a.Y=new Date(1e3*l),a.ea=n[m++],a.da=n[m++],0<(4&a.n)&&(a.$=n[m++]|n[m++]<<8,m+=a.$),0<(a.n&Ea)){for(h=[],k=0;0<(g=n[m++]);)h[k++]=String.fromCharCode(g);a.name=h.join("")}if(0<(a.n&Fa)){for(h=[],k=0;0<(g=n[m++]);)h[k++]=String.fromCharCode(g);a.A=h.join("")}0<(a.n&Ga)&&(a.R=65535&ja(n,0,m),a.R!==(n[m++]|n[m++]<<8)&&q(Error("invalid header crc16"))),c=n[n.length-4]|n[n.length-3]<<8|n[n.length-2]<<16|n[n.length-1]<<24,n.length-m-4-4<512*c&&(e=c),d=new T(n,{index:m,bufferSize:e}),a.data=f=d.h(),m=d.c,a.ba=s=(n[m++]|n[m++]<<8|n[m++]<<16|n[m++]<<24)>>>0,ja(f,t,t)!==s&&q(Error("invalid CRC-32 checksum: 0x"+ja(f,t,t).toString(16)+" / 0x"+s.toString(16))),a.ca=c=(n[m++]|n[m++]<<8|n[m++]<<16|n[m++]<<24)>>>0,(4294967295&f.length)!==c&&q(Error("invalid input size: "+(4294967295&f.length)+" / "+c)),this.t.push(a),this.c=m}this.D=u;var r,v,y,p=this.t,x=0,Q=0;for(r=0,v=p.length;r<v;++r)Q+=p[r].data.length;if(B)for(y=new Uint8Array(Q),r=0;r<v;++r)y.set(p[r].data,x),x+=p[r].data.length;else{for(y=[],r=0;r<v;++r)y[r]=p[r].data;y=Array.prototype.concat.apply([],y)}return y},A("Zlib.Gunzip",sb),A("Zlib.Gunzip.prototype.decompress",sb.prototype.h),A("Zlib.Gunzip.prototype.getMembers",sb.prototype.W),ub.prototype.h=function(){var a,b=this.input;return a=this.K.h(),this.c=this.K.c,this.Z&&(b[this.c++]<<24|b[this.c++]<<16|b[this.c++]<<8|b[this.c++])>>>0!==tb(a)&&q(Error("invalid adler-32 checksum")),a};var vb=8,W=ra;wb.prototype.g=function(){var b,a,c,d,f,e,g,k=0;switch(g=this.a,b=vb){case vb:a=Math.LOG2E*Math.log(32768)-8;break;default:q(Error("invalid compression method"))}switch(c=a<<4|b,g[k++]=c,b){case vb:switch(this.k){case W.NONE:f=0;break;case W.v:f=1;break;case W.o:f=2;break;default:q(Error("unsupported compression type"))}break;default:q(Error("invalid compression method"))}return d=f<<6|0,g[k++]=d|31-(256*c+d)%31,e=tb(this.input),this.J.b=k,g=this.J.g(),k=g.length,B&&(g=new Uint8Array(g.buffer),g.length<=k+4&&(this.a=new Uint8Array(g.length+4),this.a.set(g),g=this.a),g=g.subarray(0,k+4)),g[k++]=e>>24&255,g[k++]=e>>16&255,g[k++]=e>>8&255,g[k++]=255&e,g},A("Zlib.Inflate",ub),A("Zlib.Inflate.prototype.decompress",ub.prototype.h),xb("Zlib.Inflate.BufferType",{ADAPTIVE:Ya.M,BLOCK:Ya.N}),A("Zlib.Deflate",wb),A("Zlib.Deflate.compress",function(b,a){return new wb(b,a).g()}),A("Zlib.Deflate.prototype.compress",wb.prototype.g),xb("Zlib.Deflate.CompressionType",{NONE:W.NONE,FIXED:W.v,DYNAMIC:W.o})}).call(this),function(factory){factory(jQuery)}(function($){function handler(event){var orgEvent=event||window.event,args=slice.call(arguments,1),delta=0,deltaX=0,deltaY=0,absDelta=0,offsetX=0,offsetY=0;if(event=$.event.fix(orgEvent),event.type="mousewheel","detail"in orgEvent&&(deltaY=-1*orgEvent.detail),"wheelDelta"in orgEvent&&(deltaY=orgEvent.wheelDelta),"wheelDeltaY"in orgEvent&&(deltaY=orgEvent.wheelDeltaY),"wheelDeltaX"in orgEvent&&(deltaX=-1*orgEvent.wheelDeltaX),"axis"in orgEvent&&orgEvent.axis===orgEvent.HORIZONTAL_AXIS&&(deltaX=-1*deltaY,deltaY=0),delta=0===deltaY?deltaX:deltaY,"deltaY"in orgEvent&&(deltaY=-1*orgEvent.deltaY,delta=deltaY),"deltaX"in orgEvent&&(deltaX=orgEvent.deltaX,0===deltaY&&(delta=-1*deltaX)),0!==deltaY||0!==deltaX){if(1===orgEvent.deltaMode){var lineHeight=$.data(this,"mousewheel-line-height");delta*=lineHeight,deltaY*=lineHeight,deltaX*=lineHeight}else if(2===orgEvent.deltaMode){var pageHeight=$.data(this,"mousewheel-page-height");delta*=pageHeight,deltaY*=pageHeight,deltaX*=pageHeight}if(absDelta=Math.max(Math.abs(deltaY),Math.abs(deltaX)),(!lowestDelta||absDelta<lowestDelta)&&(lowestDelta=absDelta,shouldAdjustOldDeltas(orgEvent,absDelta)&&(lowestDelta/=40)),shouldAdjustOldDeltas(orgEvent,absDelta)&&(delta/=40,deltaX/=40,deltaY/=40),delta=Math[delta>=1?"floor":"ceil"](delta/lowestDelta),deltaX=Math[deltaX>=1?"floor":"ceil"](deltaX/lowestDelta),deltaY=Math[deltaY>=1?"floor":"ceil"](deltaY/lowestDelta),special.settings.normalizeOffset&&this.getBoundingClientRect){var boundingRect=this.getBoundingClientRect();offsetX=event.clientX-boundingRect.left,offsetY=event.clientY-boundingRect.top}return event.deltaX=deltaX,event.deltaY=deltaY,event.deltaFactor=lowestDelta,event.offsetX=offsetX,event.offsetY=offsetY,event.deltaMode=0,args.unshift(event,delta,deltaX,deltaY),nullLowestDeltaTimeout&&clearTimeout(nullLowestDeltaTimeout),nullLowestDeltaTimeout=setTimeout(nullLowestDelta,200),($.event.dispatch||$.event.handle).apply(this,args)}}function nullLowestDelta(){lowestDelta=null}function shouldAdjustOldDeltas(orgEvent,absDelta){return special.settings.adjustOldDeltas&&"mousewheel"===orgEvent.type&&absDelta%120==0}var nullLowestDeltaTimeout,lowestDelta,toFix=["wheel","mousewheel","DOMMouseScroll","MozMousePixelScroll"],toBind="onwheel"in document||document.documentMode>=9?["wheel"]:["mousewheel","DomMouseScroll","MozMousePixelScroll"],slice=Array.prototype.slice;if($.event.fixHooks)for(var i=toFix.length;i;)$.event.fixHooks[toFix[--i]]=$.event.mouseHooks;var special=$.event.special.mousewheel={version:"3.1.12",setup:function(){if(this.addEventListener)for(var i=toBind.length;i;)this.addEventListener(toBind[--i],handler,!1);else this.onmousewheel=handler;$.data(this,"mousewheel-line-height",special.getLineHeight(this)),$.data(this,"mousewheel-page-height",special.getPageHeight(this))},teardown:function(){if(this.removeEventListener)for(var i=toBind.length;i;)this.removeEventListener(toBind[--i],handler,!1);else this.onmousewheel=null;$.removeData(this,"mousewheel-line-height"),$.removeData(this,"mousewheel-page-height")},getLineHeight:function(elem){var $elem=$(elem),$parent=$elem["offsetParent"in $.fn?"offsetParent":"parent"]();return $parent.length||($parent=$("body")),parseInt($parent.css("fontSize"),10)||parseInt($elem.css("fontSize"),10)||16},getPageHeight:function(elem){return $(elem).height()},settings:{adjustOldDeltas:!0,normalizeOffset:!0}};$.fn.extend({mousewheel:function(fn){return fn?this.bind("mousewheel",fn):this.trigger("mousewheel")},unmousewheel:function(fn){return this.unbind("mousewheel",fn)}})}),function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a="function"==typeof require&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n||e)},l,l.exports,e,t,n,r)}return n[o].exports}for(var i="function"==typeof require&&require,o=0;o<r.length;o++)s(r[o]);return s}({1:[function(require,module,exports){"use strict";function noop(){}function getThen(obj){try{return obj.then}catch(ex){return LAST_ERROR=ex,IS_ERROR}}function tryCallOne(fn,a){try{return fn(a)}catch(ex){return LAST_ERROR=ex,IS_ERROR}}function tryCallTwo(fn,a,b){try{fn(a,b)}catch(ex){return LAST_ERROR=ex,IS_ERROR}}function Promise(fn){if("object"!=typeof this)throw new TypeError("Promises must be constructed via new");if("function"!=typeof fn)throw new TypeError("not a function");this._37=0,this._12=null,this._59=[],fn!==noop&&doResolve(fn,this)}function safeThen(self,onFulfilled,onRejected){return new self.constructor(function(resolve,reject){var res=new Promise(noop);res.then(resolve,reject),handle(self,new Handler(onFulfilled,onRejected,res))})}function handle(self,deferred){for(;3===self._37;)self=self._12;if(0===self._37)return void self._59.push(deferred);asap(function(){var cb=1===self._37?deferred.onFulfilled:deferred.onRejected;if(null===cb)return void(1===self._37?resolve(deferred.promise,self._12):reject(deferred.promise,self._12));var ret=tryCallOne(cb,self._12);ret===IS_ERROR?reject(deferred.promise,LAST_ERROR):resolve(deferred.promise,ret)})}function resolve(self,newValue){if(newValue===self)return reject(self,new TypeError("A promise cannot be resolved with itself."));if(newValue&&("object"==typeof newValue||"function"==typeof newValue)){var then=getThen(newValue);if(then===IS_ERROR)return reject(self,LAST_ERROR);if(then===self.then&&newValue instanceof Promise)return self._37=3,self._12=newValue,void finale(self);if("function"==typeof then)return void doResolve(then.bind(newValue),self)}self._37=1,self._12=newValue,finale(self)}function reject(self,newValue){self._37=2,self._12=newValue,finale(self)}function finale(self){for(var i=0;i<self._59.length;i++)handle(self,self._59[i]);self._59=null}function Handler(onFulfilled,onRejected,promise){this.onFulfilled="function"==typeof onFulfilled?onFulfilled:null,this.onRejected="function"==typeof onRejected?onRejected:null,this.promise=promise}function doResolve(fn,promise){var done=!1,res=tryCallTwo(fn,function(value){done||(done=!0,resolve(promise,value))},function(reason){done||(done=!0,reject(promise,reason))});done||res!==IS_ERROR||(done=!0,reject(promise,LAST_ERROR))}var asap=require("asap/raw"),LAST_ERROR=null,IS_ERROR={};module.exports=Promise,Promise._99=noop,Promise.prototype.then=function(onFulfilled,onRejected){if(this.constructor!==Promise)return safeThen(this,onFulfilled,onRejected);var res=new Promise(noop);return handle(this,new Handler(onFulfilled,onRejected,res)),res}},{"asap/raw":4}],2:[function(require,module,exports){"use strict";function valuePromise(value){var p=new Promise(Promise._99);return p._37=1,p._12=value,p}var Promise=require("./core.js");module.exports=Promise;var TRUE=valuePromise(!0),FALSE=valuePromise(!1),NULL=valuePromise(null),UNDEFINED=valuePromise(void 0),ZERO=valuePromise(0),EMPTYSTRING=valuePromise("");Promise.resolve=function(value){if(value instanceof Promise)return value;if(null===value)return NULL;if(void 0===value)return UNDEFINED;if(!0===value)return TRUE;if(!1===value)return FALSE;if(0===value)return ZERO;if(""===value)return EMPTYSTRING;if("object"==typeof value||"function"==typeof value)try{var then=value.then;if("function"==typeof then)return new Promise(then.bind(value))}catch(ex){return new Promise(function(resolve,reject){reject(ex)})}return valuePromise(value)},Promise.all=function(arr){var args=Array.prototype.slice.call(arr);return new Promise(function(resolve,reject){function res(i,val){if(val&&("object"==typeof val||"function"==typeof val)){if(val instanceof Promise&&val.then===Promise.prototype.then){for(;3===val._37;)val=val._12;return 1===val._37?res(i,val._12):(2===val._37&&reject(val._12),void val.then(function(val){res(i,val)},reject))}var then=val.then;if("function"==typeof then){return void new Promise(then.bind(val)).then(function(val){res(i,val)},reject)}}args[i]=val,0==--remaining&&resolve(args)}if(0===args.length)return resolve([]);for(var remaining=args.length,i=0;i<args.length;i++)res(i,args[i])})},Promise.reject=function(value){return new Promise(function(resolve,reject){reject(value)})},Promise.race=function(values){return new Promise(function(resolve,reject){values.forEach(function(value){Promise.resolve(value).then(resolve,reject)})})},Promise.prototype.catch=function(onRejected){return this.then(null,onRejected)}},{"./core.js":1}],3:[function(require,module,exports){"use strict";function throwFirstError(){if(pendingErrors.length)throw pendingErrors.shift()}function asap(task){var rawTask;rawTask=freeTasks.length?freeTasks.pop():new RawTask,rawTask.task=task,rawAsap(rawTask)}function RawTask(){this.task=null}var rawAsap=require("./raw"),freeTasks=[],pendingErrors=[],requestErrorThrow=rawAsap.makeRequestCallFromTimer(throwFirstError);module.exports=asap,RawTask.prototype.call=function(){try{this.task.call()}catch(error){asap.onerror?asap.onerror(error):(pendingErrors.push(error),requestErrorThrow())}finally{this.task=null,freeTasks[freeTasks.length]=this}}},{"./raw":4}],4:[function(require,module,exports){(function(global){"use strict";function rawAsap(task){queue.length||(requestFlush(),flushing=!0),queue[queue.length]=task}function flush(){for(;index<queue.length;){var currentIndex=index;if(index+=1,queue[currentIndex].call(),index>capacity){for(var scan=0,newLength=queue.length-index;scan<newLength;scan++)queue[scan]=queue[scan+index];queue.length-=index,index=0}}queue.length=0,index=0,flushing=!1}function makeRequestCallFromMutationObserver(callback){var toggle=1,observer=new BrowserMutationObserver(callback),node=document.createTextNode("");return observer.observe(node,{characterData:!0}),function(){toggle=-toggle,node.data=toggle}}function makeRequestCallFromTimer(callback){return function(){function handleTimer(){clearTimeout(timeoutHandle),clearInterval(intervalHandle),callback()}var timeoutHandle=setTimeout(handleTimer,0),intervalHandle=setInterval(handleTimer,50)}}module.exports=rawAsap;var requestFlush,queue=[],flushing=!1,index=0,capacity=1024,BrowserMutationObserver=global.MutationObserver||global.WebKitMutationObserver;requestFlush="function"==typeof BrowserMutationObserver?makeRequestCallFromMutationObserver(flush):makeRequestCallFromTimer(flush),rawAsap.requestFlush=requestFlush,rawAsap.makeRequestCallFromTimer=makeRequestCallFromTimer}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],5:[function(require,module,exports){"function"!=typeof Promise.prototype.done&&(Promise.prototype.done=function(onFulfilled,onRejected){(arguments.length?this.then.apply(this,arguments):this).then(null,function(err){setTimeout(function(){throw err},0)})})},{}],6:[function(require,module,exports){require("asap");"undefined"==typeof Promise&&(Promise=require("./lib/core.js"),require("./lib/es6-extensions.js")),require("./polyfill-done.js")},{"./lib/core.js":1,"./lib/es6-extensions.js":2,"./polyfill-done.js":5,asap:3}]},{},[6]),function(factory){"function"==typeof define&&define.amd?define(["jquery"],factory):"object"==typeof exports&&(module.exports=factory)}(function(ignored){return void 0===igv&&(igv={}),igv}),function(a){"use strict";var b="kinetic-active";window.requestAnimationFrame||(window.requestAnimationFrame=function(){return window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(a){window.setTimeout(a,1e3/60)}}()),a.support=a.support||{},a.extend(a.support,{touch:"ontouchend"in document});var c=function(b,c){return this.settings=c,this.el=b,this.$el=a(b),this._initElements(),this};c.DATA_KEY="kinetic",c.DEFAULTS={cursor:"move",decelerate:!0,triggerHardware:!1,threshold:0,y:!0,x:!0,slowdown:.9,maxvelocity:40,throttleFPS:60,invert:!1,movingClass:{up:"kinetic-moving-up",down:"kinetic-moving-down",left:"kinetic-moving-left",right:"kinetic-moving-right"},deceleratingClass:{up:"kinetic-decelerating-up",down:"kinetic-decelerating-down",left:"kinetic-decelerating-left",right:"kinetic-decelerating-right"}},c.prototype.start=function(b){this.settings=a.extend(this.settings,b),this.velocity=b.velocity||this.velocity,this.velocityY=b.velocityY||this.velocityY,this.settings.decelerate=!1,this._move()},c.prototype.end=function(){this.settings.decelerate=!0},c.prototype.stop=function(){this.velocity=0,this.velocityY=0,this.settings.decelerate=!0,a.isFunction(this.settings.stopped)&&this.settings.stopped.call(this)},c.prototype.detach=function(){this._detachListeners(),this.$el.removeClass(b).css("cursor","")},c.prototype.attach=function(){this.$el.hasClass(b)||(this._attachListeners(this.$el),this.$el.addClass(b).css("cursor",this.settings.cursor))},c.prototype._initElements=function(){this.$el.addClass(b),a.extend(this,{xpos:null,prevXPos:!1,ypos:null,prevYPos:!1,mouseDown:!1,throttleTimeout:1e3/this.settings.throttleFPS,lastMove:null,elementFocused:null}),this.velocity=0,this.velocityY=0,a(document).mouseup(a.proxy(this._resetMouse,this)).click(a.proxy(this._resetMouse,this)),this._initEvents(),this.$el.css("cursor",this.settings.cursor),this.settings.triggerHardware&&this.$el.css({"-webkit-transform":"translate3d(0,0,0)","-webkit-perspective":"1000","-webkit-backface-visibility":"hidden"})},c.prototype._initEvents=function(){var b=this;this.settings.events={touchStart:function(a){var c;b._useTarget(a.target,a)&&(c=a.originalEvent.touches[0],b.threshold=b._threshold(a.target,a),b._start(c.clientX,c.clientY),a.stopPropagation())},touchMove:function(a){var c;b.mouseDown&&(c=a.originalEvent.touches[0],b._inputmove(c.clientX,c.clientY),a.preventDefault&&a.preventDefault())},inputDown:function(a){b._useTarget(a.target,a)&&(b.threshold=b._threshold(a.target,a),b._start(a.clientX,a.clientY),b.elementFocused=a.target,"IMG"===a.target.nodeName&&a.preventDefault(),a.stopPropagation())},inputEnd:function(a){b._useTarget(a.target,a)&&(b._end(),b.elementFocused=null,a.preventDefault&&a.preventDefault())},inputMove:function(a){b.mouseDown&&(b._inputmove(a.clientX,a.clientY),a.preventDefault&&a.preventDefault())},scroll:function(c){a.isFunction(b.settings.moved)&&b.settings.moved.call(b,b.settings),c.preventDefault&&c.preventDefault()},inputClick:function(a){return Math.abs(b.velocity)>0?(a.preventDefault(),!1):void 0},dragStart:function(a){return(!b._useTarget(a.target,a)||!b.elementFocused)&&void 0},selectStart:function(c){return a.isFunction(b.settings.selectStart)?b.settings.selectStart.apply(b,arguments):!b._useTarget(c.target,c)&&void 0}},this._attachListeners(this.$el,this.settings)},c.prototype._inputmove=function(b,c){var d=this.$el;if(this.el,(!this.lastMove||new Date>new Date(this.lastMove.getTime()+this.throttleTimeout))&&(this.lastMove=new Date,this.mouseDown&&(this.xpos||this.ypos))){var e=b-this.xpos,f=c-this.ypos;if(this.settings.invert&&(e*=-1,f*=-1),this.threshold>0){var g=Math.sqrt(e*e+f*f);if(this.threshold>g)return;this.threshold=0}this.elementFocused&&(a(this.elementFocused).blur(),this.elementFocused=null,d.focus()),this.settings.decelerate=!1,this.velocity=this.velocityY=0;var h=this.scrollLeft(),i=this.scrollTop();this.scrollLeft(this.settings.x?h-e:h),this.scrollTop(this.settings.y?i-f:i),this.prevXPos=this.xpos,this.prevYPos=this.ypos,this.xpos=b,this.ypos=c,this._calculateVelocities(),this._setMoveClasses(this.settings.movingClass),a.isFunction(this.settings.moved)&&this.settings.moved.call(this,this.settings)}},c.prototype._calculateVelocities=function(){this.velocity=this._capVelocity(this.prevXPos-this.xpos,this.settings.maxvelocity),this.velocityY=this._capVelocity(this.prevYPos-this.ypos,this.settings.maxvelocity),this.settings.invert&&(this.velocity*=-1,this.velocityY*=-1)},c.prototype._end=function(){this.xpos&&this.prevXPos&&!1===this.settings.decelerate&&(this.settings.decelerate=!0,this._calculateVelocities(),this.xpos=this.prevXPos=this.mouseDown=!1,this._move())},c.prototype._useTarget=function(b,c){return!a.isFunction(this.settings.filterTarget)||!1!==this.settings.filterTarget.call(this,b,c)},c.prototype._threshold=function(b,c){return a.isFunction(this.settings.threshold)?this.settings.threshold.call(this,b,c):this.settings.threshold},c.prototype._start=function(a,b){this.mouseDown=!0,this.velocity=this.prevXPos=0,this.velocityY=this.prevYPos=0,this.xpos=a,this.ypos=b},c.prototype._resetMouse=function(){this.xpos=!1,this.ypos=!1,this.mouseDown=!1},c.prototype._decelerateVelocity=function(a,b){return 0===Math.floor(Math.abs(a))?0:a*b},c.prototype._capVelocity=function(a,b){var c=a;return a>0?a>b&&(c=b):0-b>a&&(c=0-b),c},c.prototype._setMoveClasses=function(a){var b=this.settings,c=this.$el;c.removeClass(b.movingClass.up).removeClass(b.movingClass.down).removeClass(b.movingClass.left).removeClass(b.movingClass.right).removeClass(b.deceleratingClass.up).removeClass(b.deceleratingClass.down).removeClass(b.deceleratingClass.left).removeClass(b.deceleratingClass.right),this.velocity>0&&c.addClass(a.right),this.velocity<0&&c.addClass(a.left),this.velocityY>0&&c.addClass(a.down),this.velocityY<0&&c.addClass(a.up)},c.prototype._move=function(){var b=this._getScroller(),c=b[0],d=this,e=d.settings;e.x&&c.scrollWidth>0?(this.scrollLeft(this.scrollLeft()+this.velocity),Math.abs(this.velocity)>0&&(this.velocity=e.decelerate?d._decelerateVelocity(this.velocity,e.slowdown):this.velocity)):this.velocity=0,e.y&&c.scrollHeight>0?(this.scrollTop(this.scrollTop()+this.velocityY),Math.abs(this.velocityY)>0&&(this.velocityY=e.decelerate?d._decelerateVelocity(this.velocityY,e.slowdown):this.velocityY)):this.velocityY=0,d._setMoveClasses(e.deceleratingClass),a.isFunction(e.moved)&&e.moved.call(this,e),Math.abs(this.velocity)>0||Math.abs(this.velocityY)>0?this.moving||(this.moving=!0,window.requestAnimationFrame(function(){d.moving=!1,d._move()})):d.stop()},c.prototype._getScroller=function(){var b=this.$el;return(this.$el.is("body")||this.$el.is("html"))&&(b=a(window)),b},c.prototype.scrollLeft=function(a){var b=this._getScroller();return"number"!=typeof a?b.scrollLeft():(b.scrollLeft(a),void(this.settings.scrollLeft=a))},c.prototype.scrollTop=function(a){var b=this._getScroller();return"number"!=typeof a?b.scrollTop():(b.scrollTop(a),void(this.settings.scrollTop=a))},c.prototype._attachListeners=function(){var b=this.$el,c=this.settings;a.support.touch&&b.bind("touchstart",c.events.touchStart).bind("touchend",c.events.inputEnd).bind("touchmove",c.events.touchMove),b.mousedown(c.events.inputDown).mouseup(c.events.inputEnd).mousemove(c.events.inputMove),b.click(c.events.inputClick).scroll(c.events.scroll).bind("selectstart",c.events.selectStart).bind("dragstart",c.events.dragStart)},c.prototype._detachListeners=function(){var b=this.$el,c=this.settings;a.support.touch&&b.unbind("touchstart",c.events.touchStart).unbind("touchend",c.events.inputEnd).unbind("touchmove",c.events.touchMove),b.unbind("mousedown",c.events.inputDown).unbind("mouseup",c.events.inputEnd).unbind("mousemove",c.events.inputMove),b.unbind("click",c.events.inputClick).unbind("scroll",c.events.scroll).unbind("selectstart",c.events.selectStart).unbind("dragstart",c.events.dragStart)},a.Kinetic=c,a.fn.kinetic=function(b,d){return this.each(function(){var e=a(this),f=e.data(c.DATA_KEY),g=a.extend({},c.DEFAULTS,e.data(),"object"==typeof b&&b);f||e.data(c.DATA_KEY,f=new c(this,g)),"string"==typeof b&&f[b](d)})}}(window.jQuery||window.Zepto);
//# sourceMappingURL=igv.min.map
    window.jQuery = windowBak;
	// Just return a value to define the module export.
    // This example returns an object, but the module
    // can return a function as the exported value.
    return igv;
}));